1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 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 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 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 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 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
37 ;;; This file is part of GNU Guix.
39 ;;; GNU Guix is free software; you can redistribute it and/or modify it
40 ;;; under the terms of the GNU General Public License as published by
41 ;;; the Free Software Foundation; either version 3 of the License, or (at
42 ;;; your option) any later version.
44 ;;; GNU Guix is distributed in the hope that it will be useful, but
45 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47 ;;; GNU General Public License for more details.
49 ;;; You should have received a copy of the GNU General Public License
50 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
52 (define-module (gnu packages cran)
53 #:use-module ((guix licenses) #:prefix license:)
54 #:use-module (guix packages)
55 #:use-module (guix download)
56 #:use-module (guix git-download)
57 #:use-module (guix utils)
58 #:use-module (guix build-system gnu)
59 #:use-module (guix build-system r)
60 #:use-module (gnu packages)
61 #:use-module (gnu packages algebra)
62 #:use-module (gnu packages autotools)
63 #:use-module (gnu packages base)
64 #:use-module (gnu packages bioinformatics)
65 #:use-module (gnu packages c)
66 #:use-module (gnu packages compression)
67 #:use-module (gnu packages crypto)
68 #:use-module (gnu packages curl)
69 #:use-module (gnu packages databases)
70 #:use-module (gnu packages fontutils)
71 #:use-module (gnu packages fribidi)
72 #:use-module (gnu packages gcc)
73 #:use-module (gnu packages geo)
74 #:use-module (gnu packages ghostscript)
75 #:use-module (gnu packages gl)
76 #:use-module (gnu packages gnome)
77 #:use-module (gnu packages graph)
78 #:use-module (gnu packages gtk)
79 #:use-module (gnu packages haskell-xyz)
80 #:use-module (gnu packages icu4c)
81 #:use-module (gnu packages image)
82 #:use-module (gnu packages imagemagick)
83 #:use-module (gnu packages java)
84 #:use-module (gnu packages javascript)
85 #:use-module (gnu packages libevent)
86 #:use-module (gnu packages lisp-xyz)
87 #:use-module (gnu packages machine-learning)
88 #:use-module (gnu packages maths)
89 #:use-module (gnu packages mpi)
90 #:use-module (gnu packages multiprecision)
91 #:use-module (gnu packages networking)
92 #:use-module (gnu packages node)
93 #:use-module (gnu packages pcre)
94 #:use-module (gnu packages pdf)
95 #:use-module (gnu packages perl)
96 #:use-module (gnu packages pkg-config)
97 #:use-module (gnu packages pulseaudio) ;libsndfile
98 #:use-module (gnu packages python)
99 #:use-module (gnu packages python-xyz)
100 #:use-module (gnu packages sqlite)
101 #:use-module (gnu packages statistics)
102 #:use-module (gnu packages tcl)
103 #:use-module (gnu packages textutils)
104 #:use-module (gnu packages tls)
105 #:use-module (gnu packages version-control)
106 #:use-module (gnu packages web)
107 #:use-module (gnu packages xml)
108 #:use-module (gnu packages xorg))
110 (define-public r-brio
117 (uri (cran-uri "brio" version))
120 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
121 (properties `((upstream-name . "brio")))
122 (build-system r-build-system)
123 (home-page "https://github.com/r-lib/brio")
124 (synopsis "Basic R input output")
126 "This package provides functions to handle basic input output. These
127 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
128 files and provide more explicit control over line endings.")
129 (license license:expat)))
131 (define-public r-cachem
138 (uri (cran-uri "cachem" version))
141 "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh"))))
142 (properties `((upstream-name . "cachem")))
143 (build-system r-build-system)
145 `(("r-fastmap" ,r-fastmap)
146 ("r-rlang" ,r-rlang)))
147 (home-page "https://cachem.r-lib.org/")
148 (synopsis "Cache R objects with automatic pruning")
150 "This package provides key-value stores with automatic pruning. Caches
151 can limit either their total size or the age of the oldest object (or both),
152 automatically pruning objects to maintain the constraints.")
153 (license license:expat)))
155 (define-public r-diffobj
162 (uri (cran-uri "diffobj" version))
165 "1x3d5sk8mk0s2d7dq8wxi1zv6krlx33n22ls2jwnb58b8xrmakj1"))))
166 (properties `((upstream-name . "diffobj")))
167 (build-system r-build-system)
168 (propagated-inputs `(("r-crayon" ,r-crayon)))
169 (native-inputs `(("r-knitr" ,r-knitr)))
170 (home-page "https://github.com/brodieG/diffobj")
171 (synopsis "Diffs for R objects")
173 "Generate a colorized diff of two R objects for an intuitive
174 visualization of their differences.")
175 (license license:gpl2+)))
177 (define-public r-waldo
184 (uri (cran-uri "waldo" version))
187 "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr"))))
188 (properties `((upstream-name . "waldo")))
189 (build-system r-build-system)
192 ("r-diffobj" ,r-diffobj)
195 ("r-rematch2" ,r-rematch2)
197 ("r-tibble" ,r-tibble)))
198 (home-page "https://github.com/r-lib/waldo")
199 (synopsis "Find differences between R objects")
201 "Compare complex R objects and reveal the key differences. This package
202 was designed particularly for use in testing packages where being able to
203 quickly isolate key differences makes understanding test failures much
205 (license license:expat)))
207 (define-public r-rticles
214 (uri (cran-uri "rticles" version))
217 "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818"))))
218 (properties `((upstream-name . "rticles")))
219 (build-system r-build-system)
221 `(("r-knitr" ,r-knitr)
222 ("r-rmarkdown" ,r-rmarkdown)
223 ("r-tinytex" ,r-tinytex)
226 (home-page "https://github.com/rstudio/rticles")
227 (synopsis "Article formats for R Markdown")
229 "This package provides a suite of custom R Markdown formats and templates
230 for authoring journal articles and conference submissions.")
231 (license license:gpl3)))
233 (define-public r-bezier
239 (uri (cran-uri "bezier" version))
242 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
243 (build-system r-build-system)
244 (home-page "https://cran.r-project.org/web/packages/bezier/")
245 (synopsis "Bezier curve and spline toolkit")
247 "This package is a toolkit for working with Bezier curves and splines.
248 The package provides functions for point generation, arc length estimation,
249 degree elevation and curve fitting.")
250 (license license:gpl2+)))
259 (uri (cran-uri "V8" version))
262 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
263 (properties `((upstream-name . "V8")))
264 (build-system r-build-system)
267 (modify-phases %standard-phases
268 (add-after 'unpack 'find-v8
269 (lambda* (#:key inputs #:allow-other-keys)
270 (substitute* "configure"
272 (string-append "PKG_LIBS="
273 (assoc-ref inputs "node")
274 "/lib/libnode.so.64\n")))
275 (setenv "INCLUDE_DIR"
277 (assoc-ref inputs "node")
281 (assoc-ref inputs "node") "/lib"))
284 `(("node" ,libnode)))
287 ("r-jsonlite" ,r-jsonlite)
290 `(("r-knitr" ,r-knitr)))
291 (home-page "https://jeroen.cran.dev/V8")
292 (synopsis "Embedded JavaScript and WebAssembly engine for R")
294 "This package provides an R interface to V8: Google's JavaScript and
295 WebAssembly engine.")
296 (license license:expat)))
305 (uri (cran-uri "DOT" version))
308 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
309 (properties `((upstream-name . "DOT")))
310 (build-system r-build-system)
313 (home-page "http://haghish.com/dot")
314 (synopsis "Render and Export DOT Graphs in R")
316 "This package provides tools to render DOT diagram markup language in R
317 and also provides the possibility to export the graphs in PostScript and
318 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
319 programming packages such as @code{knitr} and @code{rmarkdown}.")
320 (license license:expat)))
322 (define-public r-clipr
329 (uri (cran-uri "clipr" version))
332 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
333 (build-system r-build-system)
335 `(("r-knitr" ,r-knitr)))
336 (home-page "https://github.com/mdlincoln/clipr")
337 (synopsis "Read and write from the system clipboard")
339 "This package provides simple utility functions to read from and write to
340 the system clipboards.")
341 (license license:gpl3)))
349 (uri (cran-uri "zoo" version))
352 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
353 (build-system r-build-system)
355 `(("r-lattice" ,r-lattice)))
356 (home-page "http://zoo.R-Forge.R-project.org/")
357 (synopsis "S3 infrastructure for regular and irregular time series")
358 (description "This package contains an S3 class with methods for totally
359 ordered indexed observations. It is particularly aimed at irregular time
360 series of numeric vectors/matrices and factors.")
361 (license license:gpl2+)))
363 (define-public r-ggalluvial
365 (name "r-ggalluvial")
369 (uri (cran-uri "ggalluvial" version))
372 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
373 (properties `((upstream-name . "ggalluvial")))
374 (build-system r-build-system)
376 `(("r-dplyr" ,r-dplyr)
377 ("r-ggplot2" ,r-ggplot2)
378 ("r-lazyeval" ,r-lazyeval)
381 ("r-tidyselect" ,r-tidyselect)))
383 `(("r-knitr" ,r-knitr)))
384 (home-page "http://corybrunson.github.io/ggalluvial/")
385 (synopsis "Alluvial plots for ggplot2")
386 (description "This package provides alluvial plots for @code{ggplot2}.
387 Alluvial plots use variable-width ribbons and stacked bar plots to represent
388 multi-dimensional or repeated-measures data with categorical or ordinal
390 (license license:gpl3)))
392 (define-public r-ggpmisc
398 (uri (cran-uri "ggpmisc" version))
401 "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
402 (build-system r-build-system)
404 `(("r-dplyr" ,r-dplyr)
405 ("r-generics" ,r-generics)
407 ("r-ggplot2" ,r-ggplot2)
408 ("r-gridextra" ,r-gridextra)
409 ("r-lubridate" ,r-lubridate)
410 ("r-magrittr" ,r-magrittr)
413 ("r-polynom" ,r-polynom)
415 ("r-scales" ,r-scales)
416 ("r-splus2r" ,r-splus2r)
417 ("r-stringr" ,r-stringr)
418 ("r-tibble" ,r-tibble)
422 `(("r-knitr" ,r-knitr)))
423 (home-page "https://www.r4photobiology.info/")
424 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
425 (description "This package provides extensions to @code{ggplot2},
426 respecting the grammar of its graphics paradigm.")
427 (license license:gpl2+)))
429 (define-public r-gprofiler
436 (uri (cran-uri "gProfileR" version))
439 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
440 (properties `((upstream-name . "gProfileR")))
441 (build-system r-build-system)
444 ("r-rcurl" ,r-rcurl)))
445 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
446 (synopsis "Interface to the g:Profiler toolkit")
448 "This package provides tools for functional enrichment analysis,
449 gene identifier conversion and mapping homologous genes across related
450 organisms via the @code{g:Profiler} toolkit.")
451 (license license:gpl2+)))
453 (define-public r-gprofiler2
455 (name "r-gprofiler2")
460 (uri (cran-uri "gprofiler2" version))
463 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
464 (properties `((upstream-name . "gprofiler2")))
465 (build-system r-build-system)
467 `(("r-crosstalk" ,r-crosstalk)
469 ("r-ggplot2" ,r-ggplot2)
470 ("r-gridextra" ,r-gridextra)
471 ("r-jsonlite" ,r-jsonlite)
472 ("r-plotly" ,r-plotly)
475 ("r-viridislite" ,r-viridislite)))
476 (native-inputs `(("r-knitr" ,r-knitr)))
477 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
478 (synopsis "Interface to the g:Profiler toolset")
480 "This package provides a toolset for functional enrichment analysis and
481 visualization, gene/protein/SNP identifier conversion and mapping orthologous
482 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
486 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
488 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
490 @item @code{g:Orth}, orthology search across species;
491 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
492 genes and variant effects.
495 This package is an R interface corresponding to the 2019 update of
496 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
498 (license license:gpl2+)))
500 (define-public r-oenb
507 (uri (cran-uri "oenb" version))
510 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
511 (properties `((upstream-name . "oenb")))
512 (build-system r-build-system)
514 `(("r-dplyr" ,r-dplyr)
516 (native-inputs `(("r-knitr" ,r-knitr)))
517 (home-page "https://github.com/franzmohr/oenb")
518 (synopsis "Tools for the OeNB Data Web Service")
520 "Tools to access data from the data web service of the
521 @acronym{OeNB, Oesterreichische Nationalbank},
522 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
523 (license license:gpl2+)))
525 (define-public r-scales
532 (uri (cran-uri "scales" version))
534 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
535 (build-system r-build-system)
537 `(("r-farver" ,r-farver)
538 ("r-labeling" ,r-labeling)
539 ("r-lifecycle" ,r-lifecycle)
540 ("r-munsell" ,r-munsell)
541 ("r-rcolorbrewer" ,r-rcolorbrewer)
543 ("r-viridislite" ,r-viridislite)))
544 (home-page "https://github.com/hadley/scales")
545 (synopsis "Scale functions for visualization")
547 "This package provides graphical scales that map data to aesthetics, and
548 provides methods for automatically determining breaks and labels for axes and
550 (license license:expat)))
552 (define-public r-pheatmap
559 (uri (cran-uri "pheatmap" version))
562 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
563 (build-system r-build-system)
565 `(("r-gtable" ,r-gtable)
566 ("r-rcolorbrewer" ,r-rcolorbrewer)
567 ("r-scales" ,r-scales)))
568 (home-page "https://cran.r-project.org/web/packages/pheatmap")
569 (synopsis "Pretty heatmaps")
571 "This package provides an implementation of heatmaps that offers more
572 control over dimensions and appearance.")
573 (license license:gpl2+)))
581 (uri (cran-uri "ecp" version))
584 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
585 (build-system r-build-system)
587 `(("r-rcpp" ,r-rcpp)))
588 (home-page "https://cran.r-project.org/web/packages/ecp/")
589 (synopsis "Multiple change-point analysis of multivariate data")
591 "This package implements various procedures for finding multiple
592 change-points. Two methods make use of dynamic programming and pruning, with
593 no distributional assumptions other than the existence of certain absolute
594 moments in one method. Hierarchical and exact search methods are included.
595 All methods return the set of estimated change-points as well as other summary
597 (license license:gpl2+)))
599 (define-public r-ellipsis
606 (uri (cran-uri "ellipsis" version))
609 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
610 (build-system r-build-system)
612 `(("r-rlang" ,r-rlang)))
613 (home-page "https://github.com/hadley/ellipsis")
614 (synopsis "Tools for working with additional arguments")
616 "In S3 generics, it's useful to take @code{...} so that methods can have
617 additional arguments. But this flexibility comes at a cost: misspelled
618 arguments will be silently ignored. The @code{ellipsis} package is an
619 experiment that allows a generic to warn if any arguments passed in @code{...}
621 (license license:gpl3)))
630 (uri (cran-uri "grr" version))
633 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
634 (build-system r-build-system)
635 (home-page "https://cran.r-project.org/web/packages/grr")
636 (synopsis "Alternative implementations of base R functions")
638 "This package provides alternative implementations of some base R
639 functions, including @code{sort}, @code{order}, and @code{match}. The
640 functions are simplified but can be faster or have other advantages.")
641 (license license:gpl3)))
643 (define-public r-matrix-utils
645 (name "r-matrix-utils")
650 (uri (cran-uri "Matrix.utils" version))
653 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
654 (properties `((upstream-name . "Matrix.utils")))
655 (build-system r-build-system)
658 ("r-matrix" ,r-matrix)))
659 (home-page "https://github.com/cvarrichio/Matrix.utils")
661 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
663 "This package implements data manipulation methods such as @code{cast},
664 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
666 (license license:gpl3)))
668 (define-public r-mboost
674 (uri (cran-uri "mboost" version))
677 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
678 (build-system r-build-system)
680 `(("r-lattice" ,r-lattice)
681 ("r-matrix" ,r-matrix)
683 ("r-partykit" ,r-partykit)
684 ("r-quadprog" ,r-quadprog)
686 ("r-survival" ,r-survival)))
687 (home-page "https://github.com/boost-R/mboost")
688 (synopsis "Model-based boosting")
690 "This package provides a functional gradient descent algorithm (boosting)
691 for optimizing general risk functions utilizing component-wise (penalised)
692 least squares estimates or regression trees as base-learners for fitting
693 generalized linear, additive and interaction models to potentially
694 high-dimensional data.")
695 (license license:gpl2)))
697 (define-public r-shadowtext
699 (name "r-shadowtext")
703 (uri (cran-uri "shadowtext" version))
706 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
707 (properties `((upstream-name . "shadowtext")))
708 (build-system r-build-system)
710 `(("r-ggplot2" ,r-ggplot2)
711 ("r-scales" ,r-scales)))
713 `(("r-knitr" ,r-knitr)))
714 (home-page "https://github.com/GuangchuangYu/shadowtext/")
715 (synopsis "Shadow text grob and layer")
716 (description "This package implements @code{shadowtextGrob()} for
717 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
718 These functions draw text grob with background shadow.")
719 (license license:artistic2.0)))
728 (uri (cran-uri "sys" version))
731 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
732 (build-system r-build-system)
733 (home-page "https://github.com/jeroen/sys")
734 (synopsis "Powerful and reliable tools for running system commands in R")
736 "This package provides drop-in replacements for the base @code{system2()}
737 function with fine control and consistent behavior across platforms. It
738 supports clean interruption, timeout, background tasks, and streaming STDIN /
739 STDOUT / STDERR over binary or text connections. The package also provides
740 functions for evaluating expressions inside a temporary fork. Such
741 evaluations have no side effects on the main R process, and support reliable
742 interrupts and timeouts. This provides the basis for a sandboxing
744 (license license:expat)))
746 (define-public r-ashr
752 (uri (cran-uri "ashr" version))
755 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
756 (properties `((upstream-name . "ashr")))
757 (build-system r-build-system)
759 `(("r-etrunct" ,r-etrunct)
760 ("r-invgamma" ,r-invgamma)
761 ("r-matrix" ,r-matrix)
762 ("r-mixsqp" ,r-mixsqp)
764 ("r-squarem" ,r-squarem)
765 ("r-truncnorm" ,r-truncnorm)))
767 `(("r-knitr" ,r-knitr)))
768 (home-page "https://github.com/stephens999/ashr")
769 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
770 (description "This package implements an empirical Bayes approach for
771 large-scale hypothesis testing and false discovery rate estimation.")
772 (license license:gpl3+)))
774 (define-public r-askpass
781 (uri (cran-uri "askpass" version))
784 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
785 (build-system r-build-system)
786 (propagated-inputs `(("r-sys" ,r-sys)))
787 (home-page "https://github.com/jeroen/askpass")
788 (synopsis "Safe password entry for R")
790 "This package provides cross-platform utilities for prompting the user
791 for credentials or a passphrase, for example to authenticate with a server or
792 read a protected key.")
793 (license license:expat)))
795 (define-public r-vegan
802 (uri (cran-uri "vegan" version))
805 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
806 (build-system r-build-system)
808 `(("r-knitr" ,r-knitr) ; needed for vignettes
809 ("gfortran" ,gfortran)))
811 `(("r-cluster" ,r-cluster)
812 ("r-lattice" ,r-lattice)
815 ("r-permute" ,r-permute)))
816 (home-page "https://cran.r-project.org/web/packages/vegan")
817 (synopsis "Functions for community ecology")
819 "The vegan package provides tools for descriptive community ecology. It
820 has most basic functions of diversity analysis, community ordination and
821 dissimilarity analysis. Most of its multivariate tools can be used for other
822 data types as well.")
823 (license license:gpl2+)))
825 (define-public r-tidyverse
832 (uri (cran-uri "tidyverse" version))
835 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
836 (build-system r-build-system)
838 `(("r-broom" ,r-broom)
840 ("r-crayon" ,r-crayon)
841 ("r-dbplyr" ,r-dbplyr)
843 ("r-forcats" ,r-forcats)
844 ("r-ggplot2" ,r-ggplot2)
848 ("r-jsonlite" ,r-jsonlite)
849 ("r-lubridate" ,r-lubridate)
850 ("r-magrittr" ,r-magrittr)
851 ("r-modelr" ,r-modelr)
852 ("r-pillar" ,r-pillar)
855 ("r-readxl" ,r-readxl)
856 ("r-reprex" ,r-reprex)
858 ("r-rstudioapi" ,r-rstudioapi)
860 ("r-stringr" ,r-stringr)
861 ("r-tibble" ,r-tibble)
864 (home-page "https://tidyverse.tidyverse.org")
865 (synopsis "Install and load packages from the \"Tidyverse\"")
867 "The @code{tidyverse} is a set of packages that work in harmony because
868 they share common data representations and API design. This package is
869 designed to make it easy to install and load multiple tidyverse packages in a
871 (license license:gpl3)))
873 (define-public r-rvest
880 (uri (cran-uri "rvest" version))
882 (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53"))))
883 (build-system r-build-system)
886 ("r-lifecycle" ,r-lifecycle)
887 ("r-magrittr" ,r-magrittr)
889 ("r-selectr" ,r-selectr)
890 ("r-tibble" ,r-tibble)
893 `(("r-knitr" ,r-knitr)))
894 (home-page "https://github.com/hadley/rvest")
895 (synopsis "Simple web scraping for R")
897 "@code{r-rvest} helps you scrape information from web pages. It is
898 designed to work with @code{magrittr} to make it easy to express common web
899 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
900 (license license:gpl3)))
902 (define-public r-selectr
909 (uri (cran-uri "selectr" version))
911 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
912 (build-system r-build-system)
914 `(("r-stringr" ,r-stringr)
916 (home-page "https://sjp.co.nz/projects/selectr/")
917 (synopsis "Translate CSS selectors to XPath expressions")
919 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
920 expression. This allows you to use CSS selectors when working with the XML
921 package as it can only evaluate XPath expressions. Also provided are
922 convenience functions useful for using CSS selectors on XML nodes. This
923 package is a port of the Python package @code{cssselect}.")
924 (license license:bsd-3)))
926 (define-public r-reprex
933 (uri (cran-uri "reprex" version))
936 "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
937 (build-system r-build-system)
939 `(("r-callr" ,r-callr)
946 ("r-rmarkdown" ,r-rmarkdown)
947 ("r-withr" ,r-withr)))
949 `(("r-knitr" ,r-knitr)))
950 (home-page "https://github.com/tidyverse/reprex")
951 (synopsis "Prepare reproducible R code examples for sharing")
953 "This package provides a convenience wrapper that uses the
954 @code{rmarkdown} package to render small snippets of code to target formats
955 that include both code and output. The goal is to encourage the sharing of
956 small, reproducible, and runnable examples on code-oriented websites or email.
957 @code{reprex} also extracts clean, runnable R code from various common formats,
958 such as copy/paste from an R session.")
959 (license license:expat)))
961 (define-public r-reordercluster
963 (name "r-reordercluster")
967 (uri (cran-uri "ReorderCluster" version))
970 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
971 (build-system r-build-system)
973 `(("r-gplots" ,r-gplots)
975 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
976 (synopsis "Reordering the dendrogram according to the class labels")
977 (description "This package provides tools for performing the leaf reordering
978 for the dendrogram that preserves the hierarchical clustering result and at the
979 same time tries to group instances from the same class together.")
980 (license license:gpl3+)))
982 (define-public r-callr
989 (uri (cran-uri "callr" version))
992 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
993 (build-system r-build-system)
996 ("r-processx" ,r-processx)))
997 (home-page "https://github.com/r-lib/callr#readme")
998 (synopsis "Call R from R")
1000 "It is sometimes useful to perform a computation in a separate R process,
1001 without affecting the current R process at all. This package does exactly
1003 (license license:expat)))
1005 (define-public r-readxl
1012 (uri (cran-uri "readxl" version))
1015 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1016 (build-system r-build-system)
1018 `(("r-cellranger" ,r-cellranger)
1019 ("r-progress" ,r-progress)
1021 ("r-tibble" ,r-tibble)))
1022 (home-page "https://readxl.tidyverse.org")
1023 (synopsis "Read Excel files")
1025 "This package lets you import Excel files into R. It supports
1026 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1027 the embedded @code{RapidXML} C++ library.")
1028 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1029 ;; 'rapidxml' which is Boost.
1030 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1032 (define-public r-modelr
1039 (uri (cran-uri "modelr" version))
1042 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1043 (build-system r-build-system)
1045 `(("r-broom" ,r-broom)
1046 ("r-magrittr" ,r-magrittr)
1047 ("r-purrr" ,r-purrr)
1048 ("r-rlang" ,r-rlang)
1049 ("r-tibble" ,r-tibble)
1050 ("r-tidyr" ,r-tidyr)
1051 ("r-tidyselect" ,r-tidyselect)
1052 ("r-vctrs" ,r-vctrs)))
1053 (home-page "https://github.com/tidyverse/modelr")
1054 (synopsis "Helper functions for modelling in pipelines")
1056 "Functions for modelling that help you seamlessly integrate modelling
1057 into a pipeline of data manipulation and visualisation.")
1058 (license license:gpl3)))
1060 (define-public r-httpuv
1066 (uri (cran-uri "httpuv" version))
1069 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1070 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1071 ;; only contains fixes for building on Solaris.
1072 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1073 (modules '((guix build utils)))
1076 (delete-file-recursively "src/libuv")
1077 ;; Cannot unbundle http-parser, because it contains local
1080 (build-system r-build-system)
1083 (modify-phases %standard-phases
1084 (add-after 'unpack 'unbundle-libuv
1085 (lambda* (#:key outputs #:allow-other-keys)
1086 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1087 (("\"libuv/include/uv\\.h\"")
1089 ;; Fix https://github.com/rstudio/httpuv/issues/282
1090 (substitute* "src/http.cpp"
1091 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1092 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1095 `(("libuv" ,libuv)))
1098 ("r-later" ,r-later)
1099 ("r-promises" ,r-promises)
1101 ("r-rcpp" ,r-rcpp)))
1102 (home-page "https://github.com/rstudio/httpuv")
1103 (synopsis "HTTP and WebSocket server library for R")
1105 "The httpuv package provides low-level socket and protocol support for
1106 handling HTTP and WebSocket requests directly from within R. It is primarily
1107 intended as a building block for other packages, rather than making it
1108 particularly easy to create complete web applications using httpuv alone.")
1109 ;; This package includes third-party code that was originally released
1110 ;; under various non-copyleft licenses. Full licensing information can be
1111 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1112 (license license:gpl3+)))
1114 (define-public r-jsonlite
1120 (uri (cran-uri "jsonlite" version))
1123 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1124 (build-system r-build-system)
1126 `(("r-knitr" ,r-knitr)))
1127 (home-page "https://arxiv.org/abs/1403.2805")
1128 (synopsis "Robust, high performance JSON parser and generator for R")
1130 "The jsonlite package provides a fast JSON parser and generator optimized
1131 for statistical data and the web. It offers flexible, robust, high
1132 performance tools for working with JSON in R and is particularly powerful for
1133 building pipelines and interacting with a web API. In addition to converting
1134 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1135 and prettify JSON data. The unit tests included with the package verify that
1136 all edge cases are encoded and decoded consistently for use with dynamic data
1137 in systems and applications.")
1138 (license license:expat)))
1140 (define-public r-servr
1146 (uri (cran-uri "servr" version))
1149 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1150 (build-system r-build-system)
1152 `(("r-httpuv" ,r-httpuv)
1153 ("r-jsonlite" ,r-jsonlite)
1155 ("r-xfun" ,r-xfun)))
1156 (home-page "https://github.com/yihui/servr")
1157 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1159 "Servr provides an HTTP server in R to serve static files, or dynamic
1160 documents that can be converted to HTML files (e.g., R Markdown) under a given
1162 (license license:expat)))
1164 (define-public r-htmltools
1166 (name "r-htmltools")
1170 (uri (cran-uri "htmltools" version))
1173 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1174 (build-system r-build-system)
1176 `(("r-base64enc" ,r-base64enc)
1177 ("r-digest" ,r-digest)
1178 ("r-rlang" ,r-rlang)))
1179 (home-page "https://cran.r-project.org/web/packages/htmltools")
1180 (synopsis "R tools for HTML")
1182 "This package provides tools for HTML generation and output in R.")
1183 (license license:expat)))
1185 (define-public r-htmlwidgets
1187 (name "r-htmlwidgets")
1191 (uri (cran-uri "htmlwidgets" version))
1194 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1195 (build-system r-build-system)
1197 `(("r-htmltools" ,r-htmltools)
1198 ("r-jsonlite" ,r-jsonlite)
1199 ("r-yaml" ,r-yaml)))
1201 `(("r-knitr" ,r-knitr)))
1202 (home-page "https://github.com/ramnathv/htmlwidgets")
1203 (synopsis "HTML Widgets for R")
1205 "HTML widgets is a framework for creating HTML widgets that render in
1206 various contexts including the R console, R Markdown documents, and Shiny web
1208 (license license:expat)))
1210 (define-public r-htmltable
1212 (name "r-htmltable")
1217 (uri (cran-uri "htmlTable" version))
1219 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1220 (properties `((upstream-name . "htmlTable")))
1221 (build-system r-build-system)
1223 `(("r-checkmate" ,r-checkmate)
1224 ("r-htmltools" ,r-htmltools)
1225 ("r-htmlwidgets" ,r-htmlwidgets)
1226 ("r-knitr" ,r-knitr)
1227 ("r-magrittr" ,r-magrittr)
1228 ("r-rstudioapi" ,r-rstudioapi)
1229 ("r-stringr" ,r-stringr)))
1231 `(("r-knitr" ,r-knitr)))
1232 (home-page "http://gforge.se/packages/")
1233 (synopsis "Advanced tables for Markdown/HTML")
1235 "This package provides functions to build tables with advanced layout
1236 elements such as row spanners, column spanners, table spanners, zebra
1237 striping, and more. While allowing advanced layout, the underlying
1238 CSS-structure is simple in order to maximize compatibility with word
1239 processors such as LibreOffice. The package also contains a few text
1240 formatting functions that help outputting text compatible with HTML or
1242 (license license:gpl3+)))
1244 (define-public r-curl
1250 (uri (cran-uri "curl" version))
1253 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1254 (build-system r-build-system)
1257 (modify-phases %standard-phases
1258 ;; The environment variable CURL_CA_BUNDLE is only respected when
1259 ;; running Windows, so we disable the platform checks.
1260 ;; This can be removed once the libcurl has been patched.
1261 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1263 (substitute* "R/onload.R"
1264 (("if \\(!grepl\\(\"mingw\".*")
1266 (substitute* "src/handle.c"
1267 (("/\\* Only set" m)
1269 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1270 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1277 `(("pkg-config" ,pkg-config)))
1278 (home-page "https://github.com/jeroenooms/curl")
1279 (synopsis "HTTP client for R")
1281 "The @code{curl()} and @code{curl_download()} functions provide highly
1282 configurable drop-in replacements for base @code{url()} and
1283 @code{download.file()} with better performance, support for encryption, gzip
1284 compression, authentication, and other @code{libcurl} goodies. The core of
1285 the package implements a framework for performing fully customized requests
1286 where data can be processed either in memory, on disk, or streaming via the
1287 callback or connection interfaces.")
1288 (license license:expat)))
1290 (define-public r-hwriter
1297 (uri (cran-uri "hwriter" version))
1300 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1301 (build-system r-build-system)
1302 (home-page "https://cran.r-project.org/web/packages/hwriter")
1303 (synopsis "Output R objects in HTML format")
1305 "This package provides easy-to-use and versatile functions to output R
1306 objects in HTML format.")
1307 (license license:lgpl2.1+)))
1309 (define-public r-rjson
1316 (uri (cran-uri "rjson" version))
1319 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1320 (build-system r-build-system)
1321 (home-page "https://cran.r-project.org/web/packages/rjson")
1322 (synopsis "JSON library for R")
1324 "This package provides functions to convert R objects into JSON objects
1326 (license license:gpl2+)))
1328 (define-public r-fastmap
1335 (uri (cran-uri "fastmap" version))
1338 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1339 (properties `((upstream-name . "fastmap")))
1340 (build-system r-build-system)
1341 (home-page "https://r-lib.github.io/fastmap/")
1342 (synopsis "Fast implementation of a key-value store")
1344 "This package provides a fast implementation of a key-value store.
1345 Environments are commonly used as key-value stores, but every time a new key
1346 is used, it is added to R's global symbol table, causing a small amount of
1347 memory leakage. This can be problematic in cases where many different keys
1348 are used. Fastmap avoids this memory leak issue by implementing the map using
1349 data structures in C++.")
1350 (license license:expat)))
1352 (define-public r-fastghquad
1354 (name "r-fastghquad")
1359 (uri (cran-uri "fastGHQuad" version))
1362 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1363 (properties `((upstream-name . "fastGHQuad")))
1364 (build-system r-build-system)
1366 `(("r-rcpp" ,r-rcpp)))
1367 (home-page "https://github.com/awblocker/fastGHQuad")
1368 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1370 "This package implements numerically-stable Gauss-Hermite quadrature
1371 rules and utility functions for adaptive GH quadrature.")
1372 (license license:expat)))
1374 (define-public r-rstpm2
1381 (uri (cran-uri "rstpm2" version))
1384 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1385 (properties `((upstream-name . "rstpm2")))
1386 (build-system r-build-system)
1388 `(("r-bbmle" ,r-bbmle)
1390 ("r-desolve" ,r-desolve)
1391 ("r-fastghquad" ,r-fastghquad)
1394 ("r-rcpparmadillo" ,r-rcpparmadillo)
1395 ("r-survival" ,r-survival)))
1397 `(("gfortran" ,gfortran)))
1398 (home-page "https://github.com/mclements/rstpm2")
1399 (synopsis "Link-based survival models")
1401 "This package provides R implementations of @dfn{generalized survival
1402 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1403 multi-state models.")
1404 ;; One of these licenses
1405 (license (list license:gpl2 license:gpl3))))
1407 ;; This package includes minified JavaScript files. When upgrading please
1408 ;; check that there are no new minified JavaScript files.
1409 (define-public r-jquerylib
1411 (name "r-jquerylib")
1416 (uri (cran-uri "jquerylib" version))
1419 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1421 '(for-each delete-file
1422 '("inst/lib/jquery-1.12.4.min.js"
1423 "inst/lib/jquery-2.2.4.min.js"
1424 "inst/lib/jquery-3.5.1.min.js")))))
1425 (properties `((upstream-name . "jquerylib")))
1426 (build-system r-build-system)
1428 `(#:modules ((guix build utils)
1429 (guix build r-build-system)
1432 (modify-phases %standard-phases
1433 (add-after 'unpack 'process-javascript
1434 (lambda* (#:key inputs #:allow-other-keys)
1435 (with-directory-excursion "inst/lib/"
1439 `(("jquery-1.12.4.js"
1440 "jquery-1.12.4.min.js")
1442 "jquery-2.2.4.min.js")
1444 "jquery-3.5.1.min.js"))))
1445 (lambda (sources targets)
1446 (for-each (lambda (source target)
1447 (format #t "Processing ~a --> ~a~%"
1449 (invoke "esbuild" source "--minify"
1450 (string-append "--outfile=" target)))
1451 sources targets)))))))))
1453 `(("r-htmltools" ,r-htmltools)))
1455 `(("esbuild" ,esbuild)))
1456 (home-page "https://cran.r-project.org/package=jquerylib")
1457 (synopsis "Obtain jQuery as an HTML dependency object")
1459 "Obtain any major version of jQuery and use it in any webpage generated
1460 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1461 need to use this package directly, but other R packages (e.g. shiny,
1462 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1464 (license license:expat)))
1466 (define-public r-sass
1473 (uri (cran-uri "sass" version))
1476 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1477 (properties `((upstream-name . "sass")))
1478 (build-system r-build-system)
1480 `(("r-digest" ,r-digest)
1482 ("r-htmltools" ,r-htmltools)
1484 ("r-rappdirs" ,r-rappdirs)
1485 ("r-rlang" ,r-rlang)))
1486 (native-inputs `(("r-knitr" ,r-knitr)))
1487 (home-page "https://github.com/rstudio/sass")
1488 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1490 "This package provides an SCSS compiler, powered by the libsass library.
1491 With this, R developers can use variables, inheritance, and functions to
1492 generate dynamic style sheets. The package uses the Sass CSS extension
1493 language, which is stable, powerful, and CSS compatible.")
1494 (license license:expat)))
1496 ;; This package includes minified JavaScript files. When upgrading please
1497 ;; check that there are no new minified JavaScript files.
1498 (define-public r-bslib
1505 (uri (cran-uri "bslib" version))
1508 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1510 '(for-each delete-file
1511 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1512 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1513 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1514 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1515 (properties `((upstream-name . "bslib")))
1516 (build-system r-build-system)
1518 `(#:modules ((guix build utils)
1519 (guix build r-build-system)
1522 (modify-phases %standard-phases
1523 (add-after 'unpack 'process-javascript
1524 (lambda* (#:key inputs #:allow-other-keys)
1525 (with-directory-excursion "inst/lib/"
1529 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1530 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1531 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1532 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1533 ("bs-sass/assets/javascripts/bootstrap.js"
1534 "bs-sass/assets/javascripts/bootstrap.min.js")
1535 (,(assoc-ref inputs "js-bootstrap-bundle")
1536 "bs/dist/js/bootstrap.bundle.min.js"))))
1537 (lambda (sources targets)
1538 (for-each (lambda (source target)
1539 (format #t "Processing ~a --> ~a~%"
1541 (invoke "esbuild" source "--minify"
1542 (string-append "--outfile=" target)))
1543 sources targets)))))))))
1545 `(("r-digest" ,r-digest)
1546 ("r-htmltools" ,r-htmltools)
1547 ("r-jquerylib" ,r-jquerylib)
1548 ("r-jsonlite" ,r-jsonlite)
1549 ("r-magrittr" ,r-magrittr)
1550 ("r-rlang" ,r-rlang)
1551 ("r-sass" ,r-sass)))
1553 `(("esbuild" ,esbuild)
1554 ("js-bootstrap-bundle"
1557 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1560 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1561 (home-page "https://rstudio.github.io/bslib/")
1562 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1564 "This package simplifies custom CSS styling of both shiny and rmarkdown
1565 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1566 various Bootswatch themes. An interactive widget is also provided for
1567 previewing themes in real time.")
1568 (license license:expat)))
1570 ;; This package includes minified JavaScript files. When upgrading please
1571 ;; check that there are no new minified JavaScript files.
1572 (define-public r-shiny
1580 (url "https://github.com/rstudio/shiny")
1581 (commit (string-append "v" version))))
1582 (file-name (git-file-name name version))
1585 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1587 '(for-each delete-file
1588 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1589 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1590 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1591 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1592 "inst/www/shared/highlight/highlight.pack.js"
1593 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1594 "inst/www/shared/jquery.min.js"
1595 "inst/www/shared/jqueryui/jquery-ui.min.js"
1596 "inst/www/shared/legacy/jquery.min.js"
1597 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1598 "inst/www/shared/selectize/js/selectize.min.js"
1599 "inst/www/shared/shiny.min.js"
1600 "inst/www/shared/showdown/compressed/showdown.js"
1601 "inst/www/shared/strftime/strftime-min.js")))))
1602 (build-system r-build-system)
1604 `(#:modules ((guix build r-build-system)
1605 (guix build minify-build-system)
1608 #:imported-modules (,@%r-build-system-modules
1609 (guix build minify-build-system))
1611 (modify-phases (@ (guix build r-build-system) %standard-phases)
1612 (add-after 'unpack 'replace-bundled-minified-JavaScript
1613 (lambda* (#:key inputs #:allow-other-keys)
1614 (let ((replace-file (lambda (old new)
1615 (format #t "replacing ~a with ~a\n" old new)
1616 (symlink new old))))
1617 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1618 ;; contain just data. They are not minified code, so we don't
1620 (with-directory-excursion "inst/www/shared"
1621 (replace-file "strftime/strftime-min.js"
1622 (string-append (assoc-ref inputs "js-strftime")
1623 "/share/javascript/strftime.min.js"))
1624 (replace-file "highlight/highlight.pack.js"
1625 (string-append (assoc-ref inputs "js-highlight")
1626 "/share/javascript/highlight.min.js"))
1627 (replace-file "datatables/js/jquery.dataTables.min.js"
1628 (string-append (assoc-ref inputs "js-datatables")
1629 "/share/javascript/jquery.dataTables.min.js"))
1630 (replace-file "selectize/js/selectize.min.js"
1631 (string-append (assoc-ref inputs "js-selectize")
1632 "/share/javascript/selectize.min.js"))
1633 (for-each (match-lambda
1635 (minify source #:target target)))
1636 `(("jqueryui/jquery-ui.js" .
1637 "jqueryui/jquery-ui.min.js")
1638 ("datepicker/js/bootstrap-datepicker.js" .
1639 "datepicker/js/bootstrap-datepicker.min.js")
1640 ("ionrangeslider/js/ion.rangeSlider.js" .
1641 "ionrangeslider/js/ion.rangeSlider.min.js")
1642 ("bootstrap/js/bootstrap.js" .
1643 "bootstrap/js/bootstrap.min.js")
1644 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1645 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1650 ("legacy/jquery.js" .
1651 "legacy/jquery.min.js")
1652 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1653 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1654 ("showdown/src/showdown.js" .
1655 "showdown/compressed/showdown.js"))))))))))
1657 `(("r-bslib" ,r-bslib)
1658 ("r-cachem" ,r-cachem)
1659 ("r-commonmark" ,r-commonmark)
1660 ("r-crayon" ,r-crayon)
1661 ("r-digest" ,r-digest)
1662 ("r-ellipsis" ,r-ellipsis)
1663 ("r-fastmap" ,r-fastmap)
1665 ("r-htmltools" ,r-htmltools)
1666 ("r-httpuv" ,r-httpuv)
1667 ("r-jsonlite" ,r-jsonlite)
1668 ("r-later" ,r-later)
1669 ("r-lifecycle" ,r-lifecycle)
1671 ("r-promises" ,r-promises)
1673 ("r-rlang" ,r-rlang)
1674 ("r-sourcetools" ,r-sourcetools)
1675 ("r-withr" ,r-withr)
1676 ("r-xtable" ,r-xtable)))
1678 `(("js-datatables" ,js-datatables)
1679 ("js-selectize" ,js-selectize)
1680 ("js-strftime" ,js-strftime)
1681 ("js-highlight" ,js-highlight)))
1683 `(("uglify-js" ,uglify-js)
1684 ("gfortran" ,gfortran)
1685 ("js-bootstrap-accessibility"
1688 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1689 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1692 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1693 (home-page "https://shiny.rstudio.com")
1694 (synopsis "Easy interactive web applications with R")
1696 "Makes it incredibly easy to build interactive web applications
1697 with R. Automatic \"reactive\" binding between inputs and outputs and
1698 extensive prebuilt widgets make it possible to build beautiful,
1699 responsive, and powerful applications with minimal effort.")
1700 (license license:artistic2.0)))
1702 ;; This package includes minified JavaScript files. When upgrading please
1703 ;; check that there are no new minified JavaScript files.
1704 (define-public r-shinytree
1706 (name "r-shinytree")
1711 (uri (cran-uri "shinyTree" version))
1714 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1715 (modules '((guix build utils)))
1718 ;; Delete minified JavaScript
1719 (for-each delete-file
1720 '("inst/www/jsTree-3.3.7/libs/require.js"
1721 "inst/www/jsTree-3.3.7/libs/jquery.js"
1722 "inst/www/jsTree-3.3.7/jstree.min.js"))
1724 (properties `((upstream-name . "shinyTree")))
1725 (build-system r-build-system)
1727 `(#:modules ((guix build utils)
1728 (guix build r-build-system)
1732 (modify-phases %standard-phases
1733 (add-after 'unpack 'replace-minified-javascript
1734 (lambda* (#:key inputs #:allow-other-keys)
1735 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1736 (symlink (string-append (assoc-ref inputs "js-requirejs")
1737 "/share/javascript/require.min.js")
1742 `((,(assoc-ref inputs "js-jquery")
1746 (lambda (sources targets)
1747 (for-each (lambda (source target)
1748 (format #t "Processing ~a --> ~a~%"
1750 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1751 (call-with-output-file target
1753 (dump-port minified port)))))
1757 `(("r-htmlwidgets" ,r-htmlwidgets)
1758 ("r-jsonlite" ,r-jsonlite)
1759 ("r-promises" ,r-promises)
1760 ("r-shiny" ,r-shiny)
1761 ("r-stringr" ,r-stringr)))
1763 `(("js-requirejs" ,js-requirejs)))
1765 `(("uglify-js" ,uglify-js)
1769 (uri "https://code.jquery.com/jquery-3.3.1.js")
1772 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1773 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1774 (synopsis "jsTree bindings for Shiny")
1776 "This package exposes R bindings to jsTree, a JavaScript library that
1777 supports interactive trees, to enable rich, editable trees in Shiny.")
1778 (license license:expat)))
1780 (define-public r-shinydashboard
1782 (name "r-shinydashboard")
1786 (uri (cran-uri "shinydashboard" version))
1789 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1790 (build-system r-build-system)
1791 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1792 ;; Regenerate it from the included sources.
1794 `(#:modules ((guix build utils)
1795 (guix build r-build-system)
1798 (modify-phases %standard-phases
1799 (add-after 'unpack 'generate-minified-javascript
1801 (with-directory-excursion "inst/AdminLTE"
1802 (delete-file "app.min.js")
1803 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1804 (call-with-output-file "app.min.js"
1806 (dump-port minified port))))))))))
1808 `(("r-htmltools" ,r-htmltools)
1809 ("r-promises" ,r-promises)
1810 ("r-shiny" ,r-shiny)))
1812 `(("uglify-js" ,uglify-js)))
1813 (home-page "https://rstudio.github.io/shinydashboard/")
1814 (synopsis "Create dashboards with shiny")
1815 (description "This package provides an extension to the Shiny web
1816 application framework for R, making it easy to create attractive dashboards.")
1817 ;; This package includes software that was released under the Expat
1818 ;; license, but the whole package is released under GPL version 2 or
1820 (license license:gpl2+)))
1822 (define-public r-shinyfiles
1824 (name "r-shinyfiles")
1829 (uri (cran-uri "shinyFiles" version))
1831 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1832 (properties `((upstream-name . "shinyFiles")))
1833 (build-system r-build-system)
1836 ("r-htmltools" ,r-htmltools)
1837 ("r-jsonlite" ,r-jsonlite)
1838 ("r-shiny" ,r-shiny)
1839 ("r-tibble" ,r-tibble)))
1840 (home-page "https://github.com/thomasp85/shinyFiles")
1841 (synopsis "Server-side file system viewer for Shiny")
1843 "This package provides functionality for client-side navigation of the
1844 server side file system in shiny apps. In case the app is running locally
1845 this gives the user direct access to the file system without the need to
1846 \"download\" files to a temporary location. Both file and folder selection as
1847 well as file saving is available.")
1848 (license license:gpl2+)))
1850 (define-public r-shinythemes
1852 (name "r-shinythemes")
1857 (uri (cran-uri "shinythemes" version))
1860 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1861 (properties `((upstream-name . "shinythemes")))
1862 (build-system r-build-system)
1863 (propagated-inputs `(("r-shiny" ,r-shiny)))
1864 (home-page "https://rstudio.github.io/shinythemes/")
1865 (synopsis "Themes for Shiny")
1867 "This package provides themes for use with Shiny. It includes several
1868 Bootstrap themes, which are packaged for use with Shiny applications.")
1869 ;; The package is released under version 3 of the GPL, but it includes
1870 ;; source files that are covered by the Expat license. It also includes
1871 ;; fonts under SIL or the ASL.
1872 (license (list license:gpl3 license:expat
1873 license:silofl1.1 license:asl2.0))))
1875 ;; The package sources include minified variants of d3.js and non-minified
1876 ;; source code of d3-jetpack.
1877 (define-public r-d3r
1884 (uri (cran-uri "d3r" version))
1887 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1888 (build-system r-build-system)
1890 `(#:modules ((guix build utils)
1891 (guix build r-build-system)
1894 (modify-phases %standard-phases
1895 (add-after 'unpack 'process-javascript
1896 (lambda* (#:key inputs #:allow-other-keys)
1897 (with-directory-excursion "inst/www/d3/"
1901 `((,(assoc-ref inputs "d3.v3.js")
1902 "v3/dist/d3.min.js")
1903 (,(assoc-ref inputs "d3.v4.js")
1904 "v4/dist/d3.min.js")
1905 (,(assoc-ref inputs "d3.v5.js")
1906 "v5/dist/d3.min.js")
1907 (,(assoc-ref inputs "d3.v6.js")
1908 "v6/dist/d3.min.js"))))
1909 (lambda (sources targets)
1910 (for-each (lambda (source target)
1911 (format #t "Processing ~a --> ~a~%"
1913 (delete-file target)
1914 (invoke "esbuild" source "--minify"
1915 (string-append "--outfile=" target)))
1919 `(("r-dplyr" ,r-dplyr)
1920 ("r-htmltools" ,r-htmltools)
1921 ("r-rlang" ,r-rlang)
1922 ("r-tidyr" ,r-tidyr)))
1924 `(("esbuild" ,esbuild)
1928 (uri "https://d3js.org/d3.v3.js")
1931 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1935 (uri "https://d3js.org/d3.v4.js")
1938 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1942 (uri "https://d3js.org/d3.v5.js")
1945 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1949 (uri "https://d3js.org/d3.v6.js")
1952 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1953 (home-page "https://github.com/timelyportfolio/d3r")
1954 (synopsis "d3.js utilities for R")
1956 "This package provides a suite of functions to help ease the use of the
1957 d3.js visualization library in R. These helpers include
1958 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1959 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1960 R objects into the JSON format that the d3.js library expects.")
1961 (license license:bsd-3)))
1963 ;; We use the latest commit here because the last release was in 2016 while
1964 ;; the latest commit was in 2018.
1965 (define-public r-sankeyd3
1966 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1970 (version (git-version "0.3.2" revision commit))
1975 (url "https://github.com/fbreitwieser/sankeyD3")
1977 (file-name (git-file-name name version))
1980 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1981 (build-system r-build-system)
1984 ("r-htmlwidgets" ,r-htmlwidgets)
1985 ("r-shiny" ,r-shiny)
1986 ("r-magrittr" ,r-magrittr)))
1987 (home-page "https://github.com/fbreitwieser/sankeyD3")
1988 (synopsis "Sankey network graphs from R")
1990 "This package provides an R library to generate Sankey network graphs
1991 in R and Shiny via the D3 visualization library.")
1992 ;; The R code is licensed under GPLv3+. It includes the non-minified
1993 ;; JavaScript source code of d3-sankey, which is released under the
1994 ;; 3-clause BSD license.
1995 (license (list license:gpl3+ license:bsd-3)))))
1997 (define-public r-wesanderson
1999 (name "r-wesanderson")
2004 (uri (cran-uri "wesanderson" version))
2007 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2008 (properties `((upstream-name . "wesanderson")))
2009 (build-system r-build-system)
2010 (home-page "https://github.com/karthik/wesanderson")
2011 (synopsis "Wes Anderson color palette generator")
2013 "This package provides color palettes that have been generated mostly
2014 from Wes Anderson movies.")
2015 (license license:expat)))
2017 (define-public r-gg-gap
2024 (uri (cran-uri "gg.gap" version))
2027 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2028 (properties `((upstream-name . "gg.gap")))
2029 (build-system r-build-system)
2031 `(("r-cowplot" ,r-cowplot)
2032 ("r-ggplot2" ,r-ggplot2)))
2033 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2034 (synopsis "Define segments on the y-axis for ggplot2")
2036 "The @code{gg.gap} function enables you to define segments for the y-axis
2037 in a ggplot2 plot.")
2038 (license license:gpl3)))
2040 (define-public r-tablerdash
2042 (name "r-tablerdash")
2047 (uri (cran-uri "tablerDash" version))
2050 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2053 ;; Delete minified JavaScript
2054 (for-each delete-file
2055 '("inst/tablerDash-0.1.0/require.min.js"
2056 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2058 (properties `((upstream-name . "tablerDash")))
2059 (build-system r-build-system)
2061 `(#:modules ((guix build utils)
2062 (guix build r-build-system)
2065 (modify-phases %standard-phases
2066 (add-after 'unpack 'process-javascript
2067 (lambda* (#:key inputs #:allow-other-keys)
2068 (with-directory-excursion "inst"
2072 `((,(assoc-ref inputs "js-requirejs")
2073 "tablerDash-0.1.0/require.min.js")
2074 (,(assoc-ref inputs "js-bootstrap")
2075 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2076 (lambda (sources targets)
2077 (for-each (lambda (source target)
2078 (format #t "Processing ~a --> ~a~%"
2080 (invoke "esbuild" source "--minify"
2081 (string-append "--outfile=" target)))
2085 `(("r-htmltools" ,r-htmltools)
2086 ("r-knitr" ,r-knitr)
2087 ("r-shiny" ,r-shiny)))
2089 `(("esbuild" ,esbuild)
2093 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2096 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2100 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2101 v4.0.0/dist/js/bootstrap.bundle.js")
2104 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2105 (home-page "https://rinterface.github.io/tablerDash/")
2106 (synopsis "Tabler API for Shiny")
2108 "This package provides an R interface to the
2109 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2110 4 dashboard template. There are different layouts available such as a one
2111 page dashboard or a multi-page template, where the navigation menu is
2112 contained in the navigation bar.")
2113 (license license:gpl2+)))
2115 (define-public r-spelling
2122 (uri (cran-uri "spelling" version))
2125 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2126 (properties `((upstream-name . "spelling")))
2127 (build-system r-build-system)
2129 `(("r-commonmark" ,r-commonmark)
2130 ("r-hunspell" ,r-hunspell)
2131 ("r-knitr" ,r-knitr)
2132 ("r-xml2" ,r-xml2)))
2133 (home-page "https://docs.ropensci.org/spelling/")
2134 (synopsis "Tools for spell checking in R")
2136 "This is an R package for spell checking common document formats
2137 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2138 utilities to automate checking of documentation and vignettes as a unit test
2139 during @code{R CMD check}. Both British and American English are supported
2140 out of the box and other languages can be added. In addition, packages may
2141 define a wordlist to allow custom terminology without having to abuse
2143 (license license:expat)))
2145 (define-public r-crosstalk
2147 (name "r-crosstalk")
2152 (uri (cran-uri "crosstalk" version))
2155 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2156 (build-system r-build-system)
2158 `(("r-htmltools" ,r-htmltools)
2159 ("r-jsonlite" ,r-jsonlite)
2160 ("r-lazyeval" ,r-lazyeval)
2162 (home-page "https://rstudio.github.io/crosstalk/")
2163 (synopsis "Inter-widget interactivity for HTML widgets")
2165 "This package provides building blocks for allowing HTML widgets to
2166 communicate with each other, with Shiny or without (i.e. static @code{.html}
2167 files). It currently supports linked brushing and filtering.")
2168 (license license:expat)))
2170 (define-public r-rook
2177 (uri (cran-uri "Rook" version))
2180 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2181 (properties `((upstream-name . "Rook")))
2182 (build-system r-build-system)
2183 (propagated-inputs `(("r-brew" ,r-brew)))
2184 (home-page "https://cran.r-project.org/web/packages/Rook")
2185 (synopsis "Web server interface for R")
2187 "This package contains the Rook specification and convenience software
2188 for building and running Rook applications. A Rook application is an R
2189 reference class object that implements a @code{call} method or an R closure
2190 that takes exactly one argument, an environment, and returns a list with three
2191 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2192 (license license:gpl2)))
2194 (define-public r-miniui
2201 (uri (cran-uri "miniUI" version))
2204 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2205 (properties `((upstream-name . "miniUI")))
2206 (build-system r-build-system)
2208 `(("r-htmltools" ,r-htmltools)
2209 ("r-shiny" ,r-shiny)))
2210 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2211 (synopsis "Shiny UI widgets for small screens")
2213 "This package provides UI widget and layout functions for writing Shiny apps that
2214 work well on small screens.")
2215 (license license:gpl3)))
2217 (define-public r-feather
2224 (uri (cran-uri "feather" version))
2227 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2228 (build-system r-build-system)
2232 ("r-tibble" ,r-tibble)))
2233 (home-page "https://github.com/wesm/feather")
2234 (synopsis "R Bindings to the Feather API")
2235 (description "Read and write feather files, a lightweight binary columnar
2236 data store designed for maximum speed.")
2237 (license license:asl2.0)))
2239 (define-public r-maps
2246 (uri (cran-uri "maps" version))
2249 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2250 (build-system r-build-system)
2251 (home-page "https://cran.r-project.org/web/packages/maps")
2252 (synopsis "Draw geographical maps")
2253 (description "This package provides an R module for display of maps.
2254 Projection code and larger maps are in separate packages (@code{mapproj} and
2256 (license license:gpl2)))
2258 (define-public r-mapproj
2265 (uri (cran-uri "mapproj" version))
2268 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2269 (build-system r-build-system)
2270 (propagated-inputs `(("r-maps" ,r-maps)))
2271 (home-page "https://cran.r-project.org/web/packages/mapproj")
2272 (synopsis "Map projection in R")
2273 (description "This package converts latitude/longitude into projected
2275 (license (list license:gpl2 ; The R interface
2276 (license:non-copyleft ; The C code
2277 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2278 "Lucent Public License Version 1.02")))))
2280 (define-public r-rgooglemaps
2282 (name "r-rgooglemaps")
2287 (uri (cran-uri "RgoogleMaps" version))
2290 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2291 (properties `((upstream-name . "RgoogleMaps")))
2292 (build-system r-build-system)
2296 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2297 (synopsis "Use Google Maps in R")
2298 (description "This package serves two purposes:
2300 @item Provide a comfortable R interface to query the Google server for static
2302 @item Use the map as a background image to overlay plots within R. This
2303 requires proper coordinate scaling.
2305 (license license:gpl2+)))
2307 (define-public r-geosphere
2309 (name "r-geosphere")
2314 (uri (cran-uri "geosphere" version))
2317 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2318 (build-system r-build-system)
2319 (propagated-inputs `(("r-sp" ,r-sp)))
2320 (home-page "https://cran.r-project.org/web/packages/geosphere")
2321 (synopsis "Spherical trigonometry")
2322 (description "This package computes spherical trigonometry for geographic
2323 applications. That is, compute distances and related measures for angular
2324 (longitude/latitude) locations.")
2325 (license license:gpl3+)))
2327 (define-public r-jpeg
2334 (uri (cran-uri "jpeg" version))
2337 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2338 (build-system r-build-system)
2339 (inputs `(("libjpeg" ,libjpeg-turbo)))
2340 (home-page "https://www.rforge.net/jpeg/")
2341 (synopsis "Read and write JPEG images with R")
2342 (description "This package provides a way to read, write and display
2343 bitmap images stored in the JPEG format with R. It can read and write both
2344 files and in-memory raw vectors.")
2345 (license license:gpl2+)))
2347 (define-public r-ggmap
2354 (uri (cran-uri "ggmap" version))
2357 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2358 (build-system r-build-system)
2360 `(("r-bitops" ,r-bitops)
2361 ("r-digest" ,r-digest)
2362 ("r-dplyr" ,r-dplyr)
2363 ("r-ggplot2" ,r-ggplot2)
2367 ("r-magrittr" ,r-magrittr)
2370 ("r-purrr" ,r-purrr)
2371 ("r-rgooglemaps" ,r-rgooglemaps)
2372 ("r-rjson" ,r-rjson)
2373 ("r-scales" ,r-scales)
2374 ("r-stringr" ,r-stringr)
2375 ("r-tibble" ,r-tibble)
2376 ("r-tidyr" ,r-tidyr)))
2377 (home-page "https://github.com/dkahle/ggmap")
2378 (synopsis "Spatial visualization with ggplot2")
2379 (description "This package provides a collection of functions to visualize
2380 spatial data and models on top of static maps from various online sources (e.g
2381 Google Maps and Stamen Maps). It includes tools common to those tasks,
2382 including functions for geolocation and routing.")
2383 (license license:gpl2)))
2385 (define-public r-haven
2392 (uri (cran-uri "haven" version))
2395 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2396 (modules '((guix build utils)))
2399 ;; unvendor readstat
2400 (delete-file-recursively "src/readstat")
2402 (build-system r-build-system)
2405 (modify-phases %standard-phases
2406 (add-after 'unpack 'unbundle-readstat
2408 ;; Not required, since we’re not building readstat.
2409 (substitute* "src/Makevars"
2410 (("-lz") "-lreadstat"))
2413 `(("readstat" ,readstat)))
2415 `(("r-knitr" ,r-knitr)))
2417 `(("r-forcats" ,r-forcats)
2420 ("r-rlang" ,r-rlang)
2421 ("r-readr" ,r-readr)
2422 ("r-tibble" ,r-tibble)
2423 ("r-tidyselect" ,r-tidyselect)
2424 ("r-vctrs" ,r-vctrs)))
2425 (home-page "https://haven.tidyverse.org")
2426 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2428 "This package lets you mport foreign statistical formats into R via the
2429 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2430 (license license:expat)))
2432 (define-public r-amap
2438 (uri (cran-uri "amap" version))
2441 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2442 (build-system r-build-system)
2444 `(("gfortran" ,gfortran)))
2445 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2446 (synopsis "Another multidimensional analysis package")
2447 (description "This package provides tools for clustering and principal
2448 component analysis (with robust methods, and parallelized functions).")
2449 (license license:gpl2+)))
2451 (define-public r-ape
2458 (uri (cran-uri "ape" version))
2461 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2462 (build-system r-build-system)
2464 `(("r-lattice" ,r-lattice)
2466 ("r-rcpp" ,r-rcpp)))
2467 (home-page "http://ape-package.ird.fr/")
2468 (synopsis "Analyses of phylogenetics and evolution")
2470 "This package provides functions for reading, writing, plotting, and
2471 manipulating phylogenetic trees, analyses of comparative data in a
2472 phylogenetic framework, ancestral character analyses, analyses of
2473 diversification and macroevolution, computing distances from DNA sequences,
2474 and several other tools.")
2475 (license license:gpl2+)))
2477 (define-public r-abbyyr
2484 (uri (cran-uri "abbyyR" version))
2487 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2488 (properties `((upstream-name . "abbyyR")))
2489 (build-system r-build-system)
2491 `(("r-curl" ,r-curl)
2494 ("r-progress" ,r-progress)
2495 ("r-readr" ,r-readr)
2497 (home-page "https://github.com/soodoku/abbyyR")
2498 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2500 "This package provides tools to get text from images of text using Abbyy
2501 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2502 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2503 passports and get the results in a variety of formats including plain text and
2504 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2505 (license license:expat)))
2507 (define-public r-colorspace
2509 (name "r-colorspace")
2514 (uri (cran-uri "colorspace" version))
2516 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2517 (build-system r-build-system)
2519 `(("r-knitr" ,r-knitr)))
2520 (home-page "https://cran.r-project.org/web/packages/colorspace")
2521 (synopsis "Color space manipulation")
2523 "This package carries out a mapping between assorted color spaces
2524 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2525 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2526 colors are provided.")
2527 (license license:bsd-3)))
2529 (define-public r-glue
2536 (uri (cran-uri "glue" version))
2539 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2540 (build-system r-build-system)
2541 ;; knitr depends on glue, so we can't add knitr here to build the
2545 `(("r-knitr" ,r-knitr)))
2546 (home-page "https://github.com/tidyverse/glue")
2547 (synopsis "Interpreted string literals")
2549 "This package provides an implementation of interpreted string literals,
2550 inspired by Python's Literal String Interpolation (PEP-0498) and
2551 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2552 (license license:expat)))
2554 (define-public r-palmerpenguins
2556 (name "r-palmerpenguins")
2561 (uri (cran-uri "palmerpenguins" version))
2564 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2566 `((upstream-name . "palmerpenguins")))
2567 (build-system r-build-system)
2568 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2569 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2571 "This package includes size measurements, clutch observations, and blood
2572 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2573 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2574 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2575 Station Long Term Ecological Research (LTER) Program.")
2576 (license license:cc0)))
2578 (define-public r-pastecs
2584 (uri (cran-uri "pastecs" version))
2587 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2588 (build-system r-build-system)
2590 `(("r-boot" ,r-boot)))
2591 (home-page "https://github.com/phgrosjean/pastecs")
2592 (synopsis "Analysis of space-time ecological series")
2594 "This package provides functions for regulation, decomposition and analysis
2595 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2596 initiative to bring PASSTEC 2000 functionalities to R.")
2597 (license license:gpl2+)))
2599 (define-public r-partykit
2605 (uri (cran-uri "partykit" version))
2608 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2609 (build-system r-build-system)
2611 `(("r-formula" ,r-formula)
2613 ("r-libcoin" ,r-libcoin)
2614 ("r-mvtnorm" ,r-mvtnorm)
2615 ("r-rpart" ,r-rpart)
2616 ("r-survival" ,r-survival)))
2617 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2618 (synopsis "Toolkit for recursive partytioning")
2620 "This package provides a toolkit with infrastructure for representing,
2621 summarizing, and visualizing tree-structured regression and classification
2623 (license license:gpl2+)))
2625 (define-public r-plogr
2632 (uri (cran-uri "plogr" version))
2635 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2636 (build-system r-build-system)
2637 (home-page "https://github.com/krlmlr/plogr")
2638 (synopsis "R bindings for the plog C++ logging library")
2640 "This package provides the header files for a stripped-down version of
2641 the plog header-only C++ logging library, and a method to log to R's standard
2643 (license license:expat)))
2645 (define-public r-pls
2652 (uri (cran-uri "pls" version))
2654 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2655 (build-system r-build-system)
2656 (home-page "https://mevik.net/work/software/pls.html")
2657 (synopsis "Partial Least Squares and Principal Component Regression")
2659 "The pls package implements multivariate regression methods: Partial Least
2660 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2661 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2664 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2665 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2666 @item multi-response models (or @dfn{PLS2})
2667 @item flexible cross-validation
2668 @item Jackknife variance estimates of regression coefficients
2669 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2670 (R)MSEP, R², and correlation loadings
2671 @item formula interface, modelled after @code{lm()}, with methods for predict,
2672 print, summary, plot, update, etc.
2673 @item extraction functions for coefficients, scores, and loadings
2674 @item MSEP, RMSEP, and R² estimates
2675 @item multiplicative scatter correction (@dfn{MSC})
2677 (license license:gpl2)))
2686 (uri (cran-uri "ps" version))
2688 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2689 (build-system r-build-system)
2690 (home-page "https://ps.r-lib.org")
2691 (synopsis "List, query, and manipulate system processes")
2693 "The ps package implements an API to list, query, and manipulate system
2694 processes. Most of its code is based on the @code{psutil} Python package.")
2695 (license license:bsd-3)))
2697 (define-public r-pkgbuild
2704 (uri (cran-uri "pkgbuild" version))
2706 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2707 (build-system r-build-system)
2709 `(("r-callr" ,r-callr)
2711 ("r-crayon" ,r-crayon)
2713 ("r-prettyunits" ,r-prettyunits)
2715 ("r-rprojroot" ,r-rprojroot)
2716 ("r-withr" ,r-withr)))
2717 (home-page "https://github.com/r-pkgs/pkgbuild")
2718 (synopsis "Find tools needed to build R packages")
2720 "This package provides functions used to build R packages. It locates
2721 compilers needed to build R packages on various platforms and ensures the PATH
2722 is configured appropriately so R can use them.")
2723 (license license:gpl3)))
2725 (define-public r-pkgload
2732 (uri (cran-uri "pkgload" version))
2735 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2736 (build-system r-build-system)
2739 ("r-crayon" ,r-crayon)
2741 ("r-pkgbuild" ,r-pkgbuild)
2742 ("r-rlang" ,r-rlang)
2743 ("r-rprojroot" ,r-rprojroot)
2744 ("r-rstudioapi" ,r-rstudioapi)
2745 ("r-withr" ,r-withr)))
2746 (home-page "https://github.com/r-lib/pkgload")
2747 (synopsis "Simulate package installation and attach")
2749 "This package simulates the process of installing a package and then
2750 attaching it. This is a key part of the @code{devtools} package as it allows
2751 you to rapidly iterate while developing a package.")
2752 (license license:gpl3)))
2754 (define-public r-rcpp
2761 (uri (cran-uri "Rcpp" version))
2763 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2764 (build-system r-build-system)
2765 (home-page "http://www.rcpp.org")
2766 (synopsis "Seamless R and C++ integration")
2768 "The Rcpp package provides R functions as well as C++ classes which offer
2769 a seamless integration of R and C++. Many R data types and objects can be
2770 mapped back and forth to C++ equivalents which facilitates both writing of new
2771 code as well as easier integration of third-party libraries. Documentation
2772 about Rcpp is provided by several vignettes included in this package, via the
2773 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2774 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2775 @code{citation(\"Rcpp\")} for details on these last two.")
2776 (license license:gpl2+)))
2778 (define-public r-rcppthread
2780 (name "r-rcppthread")
2785 (uri (cran-uri "RcppThread" version))
2788 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2789 (properties `((upstream-name . "RcppThread")))
2790 (build-system r-build-system)
2792 "https://github.com/tnagler/RcppThread")
2793 (synopsis "R threading in C++")
2795 "This package provides a C++11-style thread class and thread pool that can
2796 safely be interrupted from R.")
2797 (license license:expat)))
2799 (define-public r-bindr
2806 (uri (cran-uri "bindr" version))
2809 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2810 (build-system r-build-system)
2811 (home-page "https://github.com/krlmlr/bindr")
2812 (synopsis "Parametrized active bindings")
2814 "This package provides a simple interface for creating active bindings
2815 where the bound function accepts additional arguments.")
2816 (license license:expat)))
2818 (define-public r-bindrcpp
2825 (uri (cran-uri "bindrcpp" version))
2828 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2829 (build-system r-build-system)
2831 `(("r-bindr" ,r-bindr)
2832 ("r-plogr" ,r-plogr)
2833 ("r-rcpp" ,r-rcpp)))
2834 (home-page "https://github.com/krlmlr/bindrcpp")
2835 (synopsis "Rcpp interface to active bindings")
2837 "This package provides an easy way to fill an environment with active
2838 bindings that call a C++ function.")
2839 (license license:expat)))
2841 (define-public r-bisquerna
2843 (name "r-bisquerna")
2847 (uri (cran-uri "BisqueRNA" version))
2850 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2851 (properties `((upstream-name . "BisqueRNA")))
2852 (build-system r-build-system)
2854 `(("r-biobase" ,r-biobase)
2855 ("r-limsolve" ,r-limsolve)))
2856 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2857 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2858 (description "This package provides tools to accurately estimate cell type
2859 abundances from heterogeneous bulk expression. A reference-based method
2860 utilizes single-cell information to generate a signature matrix and
2861 transformation of bulk expression for accurate regression based estimates.
2862 A marker-based method utilizes known cell-specific marker genes to measure
2863 relative abundances across samples.")
2864 (license license:gpl3)))
2866 (define-public r-auc
2873 (uri (cran-uri "AUC" version))
2876 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2877 (properties `((upstream-name . "AUC")))
2878 (build-system r-build-system)
2879 (home-page "https://cran.r-project.org/web/packages/AUC")
2880 (synopsis "Compute the area under the curve of selected measures")
2882 "This package includes functions to compute the area under the curve of
2883 selected measures: the area under the sensitivity curve (AUSEC), the area
2884 under the specificity curve (AUSPC), the area under the accuracy
2885 curve (AUACC), and the area under the receiver operating characteristic
2886 curve (AUROC). The curves can also be visualized. Support for partial areas
2888 (license license:gpl2+)))
2890 (define-public r-calibrate
2892 (name "r-calibrate")
2897 (uri (cran-uri "calibrate" version))
2899 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2900 (build-system r-build-system)
2902 `(("r-mass" ,r-mass)))
2903 (home-page "https://cran.r-project.org/web/packages/calibrate")
2904 (synopsis "Calibration of scatterplot and biplot axes")
2906 "This is a package for drawing calibrated scales with tick marks
2907 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2908 (license license:gpl2)))
2910 (define-public r-shape
2917 (uri (cran-uri "shape" version))
2920 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2921 (build-system r-build-system)
2922 (home-page "https://cran.r-project.org/web/packages/shape")
2923 (synopsis "Functions for plotting graphical shapes")
2925 "This package provides functions for plotting graphical shapes such as
2926 ellipses, circles, cylinders, arrows, ...")
2927 (license license:gpl3+)))
2929 (define-public r-globaloptions
2931 (name "r-globaloptions")
2936 (uri (cran-uri "GlobalOptions" version))
2938 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2939 (properties `((upstream-name . "GlobalOptions")))
2940 (build-system r-build-system)
2942 `(("r-knitr" ,r-knitr)))
2943 (home-page "https://github.com/jokergoo/GlobalOptions")
2944 (synopsis "Generate functions to get or set global options")
2946 "This package provides more controls on the option values such as
2947 validation and filtering on the values, making options invisible or private.")
2948 (license license:gpl2+)))
2950 (define-public r-circlize
2957 (uri (cran-uri "circlize" version))
2960 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2961 (build-system r-build-system)
2963 `(("r-colorspace" ,r-colorspace)
2964 ("r-globaloptions" ,r-globaloptions)
2965 ("r-shape" ,r-shape)))
2967 `(("r-knitr" ,r-knitr)))
2968 (home-page "https://github.com/jokergoo/circlize")
2969 (synopsis "Circular visualization")
2971 "Circular layout is an efficient way to visualise huge amounts of
2972 information. This package provides an implementation of circular layout
2973 generation in R as well as an enhancement of available software. Its
2974 flexibility is based on the usage of low-level graphics functions such that
2975 self-defined high-level graphics can be easily implemented by users for
2976 specific purposes. Together with the seamless connection between the powerful
2977 computational and visual environment in R, it gives users more convenience and
2978 freedom to design figures for better understanding complex patterns behind
2979 multi-dimensional data.")
2980 (license license:gpl2+)))
2982 (define-public r-powerlaw
2989 (uri (cran-uri "poweRlaw" version))
2991 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2992 (properties `((upstream-name . "poweRlaw")))
2993 (build-system r-build-system)
2995 `(("r-pracma" ,r-pracma)))
2997 `(("r-knitr" ,r-knitr)))
2998 (home-page "https://github.com/csgillespie/poweRlaw")
2999 (synopsis "Tools for the analysis of heavy tailed distributions")
3001 "This package provides an implementation of maximum likelihood estimators
3002 for a variety of heavy tailed distributions, including both the discrete and
3003 continuous power law distributions. Additionally, a goodness-of-fit based
3004 approach is used to estimate the lower cut-off for the scaling region.")
3005 ;; Any of these GPL versions.
3006 (license (list license:gpl2 license:gpl3))))
3008 (define-public r-compare
3015 (uri (cran-uri "compare" version))
3018 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3019 (build-system r-build-system)
3020 (home-page "https://cran.r-project.org/web/packages/compare")
3021 (synopsis "Comparing objects for differences")
3023 "This package provides functions to compare a model object to a
3024 comparison object. If the objects are not identical, the functions can be
3025 instructed to explore various modifications of the objects (e.g., sorting
3026 rows, dropping names) to see if the modified versions are identical.")
3027 (license license:gpl2+)))
3029 (define-public r-dendextend
3031 (name "r-dendextend")
3036 (uri (cran-uri "dendextend" version))
3039 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3040 (build-system r-build-system)
3042 `(("r-ggplot2" ,r-ggplot2)
3043 ("r-magrittr" ,r-magrittr)
3044 ("r-viridis" ,r-viridis)))
3046 `(("r-knitr" ,r-knitr)))
3047 (home-page "https://cran.r-project.org/web/packages/dendextend")
3048 (synopsis "Extending 'dendrogram' functionality in R")
3050 "This package offers a set of functions for extending @code{dendrogram}
3051 objects in R, letting you visualize and compare trees of hierarchical
3052 clusterings. You can adjust a tree's graphical parameters (the color, size,
3053 type, etc of its branches, nodes and labels) and visually and statistically
3054 compare different dendrograms to one another.")
3055 ;; Any of these versions
3056 (license (list license:gpl2 license:gpl3))))
3058 (define-public r-getoptlong
3060 (name "r-getoptlong")
3065 (uri (cran-uri "GetoptLong" version))
3068 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3069 (properties `((upstream-name . "GetoptLong")))
3070 (build-system r-build-system)
3074 `(("r-crayon" ,r-crayon)
3075 ("r-globaloptions" ,r-globaloptions)
3076 ("r-rjson" ,r-rjson)))
3078 `(("r-knitr" ,r-knitr)))
3079 (home-page "https://github.com/jokergoo/GetoptLong")
3080 (synopsis "Parsing command-line arguments and variable interpolation")
3082 "This is yet another command-line argument parser which wraps the
3083 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3084 use in R. It also provides a simple way for variable interpolation in R.")
3085 (license license:gpl2+)))
3087 (define-public r-fastmatch
3089 (name "r-fastmatch")
3094 (uri (cran-uri "fastmatch" version))
3097 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3098 (build-system r-build-system)
3099 (home-page "https://www.rforge.net/fastmatch")
3100 (synopsis "Fast match function")
3102 "This package provides a fast @code{match} replacement for cases that
3103 require repeated look-ups. It is slightly faster that R's built-in
3104 @code{match} function on first match against a table, but extremely fast on
3105 any subsequent lookup as it keeps the hash table in memory.")
3106 (license license:gpl2)))
3115 (uri (cran-uri "ff" version))
3118 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3119 (build-system r-build-system)
3120 (propagated-inputs `(("r-bit" ,r-bit)))
3121 (home-page "http://ff.r-forge.r-project.org/")
3122 (synopsis "Memory-efficient storage of large data on disk and access functions")
3124 "This package provides data structures that are stored on disk but
3125 behave (almost) as if they were in RAM by transparently mapping only a section
3127 ;; error Architecture not supported.
3128 (supported-systems (delete "aarch64-linux" %supported-systems))
3129 (license license:gpl2)))
3131 (define-public r-ffbase
3138 (uri (cran-uri "ffbase" version))
3141 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3142 (build-system r-build-system)
3145 ("r-fastmatch" ,r-fastmatch)
3147 (home-page "https://github.com/edwindj/ffbase")
3148 (synopsis "Basic statistical functions for package 'ff'")
3150 "This package extends the out of memory vectors of @code{ff} with
3151 statistical functions and other utilities to ease their usage.")
3152 (license license:gpl3)))
3154 (define-public r-prettyunits
3156 (name "r-prettyunits")
3161 (uri (cran-uri "prettyunits" version))
3164 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3165 (build-system r-build-system)
3166 (home-page "https://github.com/gaborcsardi/prettyunits")
3167 (synopsis "Pretty, human readable formatting of quantities")
3169 "This package provides tools for pretty, human readable formatting of
3171 (license license:expat)))
3173 (define-public r-reshape
3180 (uri (cran-uri "reshape" version))
3183 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3184 (build-system r-build-system)
3186 `(("r-plyr" ,r-plyr)
3187 ("r-rcpp" ,r-rcpp)))
3188 (home-page "http://had.co.nz/reshape")
3189 (synopsis "Flexibly reshape data")
3191 "Flexibly restructure and aggregate data using just two functions:
3192 @code{melt} and @code{cast}. This package provides them.")
3193 (license license:expat)))
3195 (define-public r-restrserve
3197 (name "r-restrserve")
3202 (uri (cran-uri "RestRserve" version))
3204 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3205 (build-system r-build-system)
3207 `(("r-checkmate" ,r-checkmate)
3208 ("r-jsonlite" ,r-jsonlite)
3212 ("r-rserve" ,r-rserve)
3213 ("r-uuid" ,r-uuid)))
3215 `(("r-knitr" ,r-knitr)))
3216 (home-page "https://restrserve.org")
3217 (synopsis "R web API framework")
3219 "RestRserve is an R web API framework for building high-performance AND
3220 robust microservices and app backends. With Rserve backend on UNIX-like
3221 systems it is parallel by design. It will handle incoming requests in
3222 parallel - each request in a separate fork.")
3223 (license license:gpl2+)))
3225 (define-public r-progress
3232 (uri (cran-uri "progress" version))
3235 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3236 (build-system r-build-system)
3238 `(("r-crayon" ,r-crayon)
3240 ("r-prettyunits" ,r-prettyunits)
3242 (home-page "https://github.com/gaborcsardi/progress")
3243 (synopsis "Terminal progress bars")
3245 "This package provides configurable progress bars. They may include
3246 percentage, elapsed time, and/or the estimated completion time. They work in
3247 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3248 package also provides a C++ API, that works with or without Rcpp.")
3249 (license license:expat)))
3251 (define-public r-ggally
3258 (uri (cran-uri "GGally" version))
3261 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3262 (properties `((upstream-name . "GGally")))
3263 (build-system r-build-system)
3265 `(("openssl" ,openssl)))
3267 `(("r-dplyr" ,r-dplyr)
3268 ("r-forcats" ,r-forcats)
3269 ("r-ggplot2" ,r-ggplot2)
3270 ("r-gtable" ,r-gtable)
3271 ("r-lifecycle" ,r-lifecycle)
3273 ("r-progress" ,r-progress)
3274 ("r-rcolorbrewer" ,r-rcolorbrewer)
3275 ("r-reshape" ,r-reshape)
3276 ("r-rlang" ,r-rlang)
3277 ("r-scales" ,r-scales)
3278 ("r-tidyr" ,r-tidyr)))
3279 (home-page "https://ggobi.github.io/ggally")
3280 (synopsis "Extension to ggplot2")
3282 "The R package ggplot2 is a plotting system based on the grammar of
3283 graphics. GGally extends ggplot2 by adding several functions to reduce the
3284 complexity of combining geometric objects with transformed data. Some of
3285 these functions include a pairwise plot matrix, a two group pairwise plot
3286 matrix, a parallel coordinates plot, a survival plot, and several functions to
3288 (license license:gpl2+)))
3290 (define-public r-proxy
3297 (uri (cran-uri "proxy" version))
3300 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3301 (build-system r-build-system)
3302 (home-page "https://cran.r-project.org/web/packages/proxy")
3303 (synopsis "Distance and similarity measures")
3305 "This package provides an extensible framework for the efficient
3306 calculation of auto- and cross-proximities, along with implementations of the
3307 most popular ones.")
3308 (license license:gpl2)))
3317 (uri (cran-uri "sp" version))
3319 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3320 (build-system r-build-system)
3322 `(("r-lattice" ,r-lattice)))
3323 (home-page "https://cran.r-project.org/web/packages/sp")
3324 (synopsis "Classes and methods for spatial data")
3326 "This package provides classes and methods for spatial data; the classes
3327 document where the spatial location information resides, for 2D or 3D data.
3328 Utility functions are provided, e.g. for plotting data as maps, spatial
3329 selection, as well as methods for retrieving coordinates, for subsetting,
3330 print, summary, etc.")
3331 (license license:gpl2+)))
3333 (define-public r-laplacesdemon
3335 (name "r-laplacesdemon")
3340 (uri (cran-uri "LaplacesDemon" version))
3342 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3343 (properties `((upstream-name . "LaplacesDemon")))
3344 (build-system r-build-system)
3345 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3346 (synopsis "Complete environment for Bayesian inference")
3348 "This package provides a complete environment for Bayesian inference using
3349 a variety of different samplers.")
3350 (license license:expat)))
3352 (define-public r-rmtstat
3359 (uri (cran-uri "RMTstat" version))
3362 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3363 (properties `((upstream-name . "RMTstat")))
3364 (build-system r-build-system)
3365 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3366 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3368 "This package provides functions for working with the Tracy-Widom laws
3369 and other distributions related to the eigenvalues of large Wishart
3371 (license license:bsd-3)))
3373 (define-public r-rmpi
3379 (uri (cran-uri "Rmpi" version))
3382 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3383 (properties `((upstream-name . "Rmpi")))
3384 (build-system r-build-system)
3386 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3387 #:phases (modify-phases %standard-phases
3388 (add-before 'install 'mpi-setup
3391 `(("openmpi" ,openmpi)))
3393 `(("pkg-config" ,pkg-config)))
3394 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3395 (synopsis "R interface to message-passing interface (MPI)")
3397 "This package provides an interface (wrapper) to MPI APIs. It also
3398 provides an interactive R manager and worker environment.")
3399 (license license:gpl2+)))
3401 (define-public r-lmoments
3408 (uri (cran-uri "Lmoments" version))
3411 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3412 (properties `((upstream-name . "Lmoments")))
3413 (build-system r-build-system)
3415 `(("r-rcpp" ,r-rcpp)
3416 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3417 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3418 (synopsis "L-moments and quantile mixtures")
3420 "This package contains functions to estimate L-moments and trimmed
3421 L-moments from the data. It also contains functions to estimate the
3422 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3423 quantile mixture from L-moments and trimmed L-moments.")
3424 (license license:gpl2)))
3426 (define-public r-distillery
3428 (name "r-distillery")
3433 (uri (cran-uri "distillery" version))
3436 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3437 (build-system r-build-system)
3438 (home-page "https://ral.ucar.edu/staff/ericg/")
3439 (synopsis "Functions for confidence intervals and object information")
3441 "This package provides some very simple method functions for confidence
3442 interval calculation and to distill pertinent information from a potentially
3443 complex object; primarily used in common with the packages extRemes and
3445 (license license:gpl2+)))
3447 (define-public r-etrunct
3453 (uri (cran-uri "etrunct" version))
3456 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3457 (properties `((upstream-name . "etrunct")))
3458 (build-system r-build-system)
3459 (home-page "https://cran.r-project.org/web/packages/etrunct")
3460 (synopsis "Computes moments of univariate truncated T distribution")
3461 (description "This package computes moments of univariate truncated
3462 T distribution. There is only one exported function, @code{e_trunct},
3463 which should be seen for details.")
3464 (license license:expat)))
3466 (define-public r-extremes
3473 (uri (cran-uri "extRemes" version))
3476 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3477 (properties `((upstream-name . "extRemes")))
3478 (build-system r-build-system)
3480 `(("r-distillery" ,r-distillery)
3481 ("r-lmoments" ,r-lmoments)))
3482 (home-page "https://www.assessment.ucar.edu/toolkit/")
3483 (synopsis "Extreme value analysis")
3485 "ExtRemes is a suite of functions for carrying out analyses on the
3486 extreme values of a process of interest; be they block maxima over long blocks
3487 or excesses over a high threshold.")
3488 (license license:gpl2+)))
3490 (define-public r-lmtest
3497 (uri (cran-uri "lmtest" version))
3500 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3501 (build-system r-build-system)
3503 `(("r-zoo" ,r-zoo)))
3505 `(("gfortran" ,gfortran)))
3506 (home-page "https://cran.r-project.org/web/packages/lmtest")
3507 (synopsis "Testing linear regression models")
3509 "This package provides a collection of tests, data sets, and examples for
3510 diagnostic checking in linear regression models. Furthermore, some generic
3511 tools for inference in parametric models are provided.")
3512 ;; Either version is okay
3513 (license (list license:gpl2 license:gpl3))))
3515 (define-public r-idr
3521 (uri (cran-uri "idr" version))
3524 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3525 (build-system r-build-system)
3526 (home-page "https://cran.r-project.org/web/packages/idr/")
3527 (synopsis "Irreproducible discovery rate")
3529 "This is a package for estimating the copula mixture model and plotting
3530 correspondence curves in \"Measuring reproducibility of high-throughput
3531 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3532 by Li, Brown, Huang, and Bickel")
3533 (license license:gpl2+)))
3535 (define-public r-inline
3541 (uri (cran-uri "inline" version))
3544 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3545 (build-system r-build-system)
3546 (home-page "https://cran.r-project.org/web/packages/inline")
3547 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3549 "This package provides functionality to dynamically define R functions
3550 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3551 @code{.Call} calling conventions.")
3552 ;; Any version of the LGPL.
3553 (license license:lgpl3+)))
3555 (define-public r-inum
3561 (uri (cran-uri "inum" version))
3564 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3565 (build-system r-build-system)
3567 `(("r-libcoin" ,r-libcoin)))
3568 (home-page "https://cran.r-project.org/web/packages/inum/")
3569 (synopsis "Interval and enum-type representation of vectors")
3571 "This package provides an enum-type representation of vectors and
3572 representation of intervals, including a method of coercing variables
3574 (license license:gpl2)))
3575 (define-public r-invgamma
3581 (uri (cran-uri "invgamma" version))
3584 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3585 (properties `((upstream-name . "invgamma")))
3586 (build-system r-build-system)
3587 (home-page "https://github.com/dkahle/invgamma")
3588 (synopsis "Inverse gamma distribution")
3589 (description "This package provides a light weight implementation of the
3590 standard distribution functions for the inverse gamma distribution, wrapping
3591 those for the gamma distribution in the @code{stats} package.")
3592 (license license:gpl2)))
3594 (define-public r-bdsmatrix
3596 (name "r-bdsmatrix")
3601 (uri (cran-uri "bdsmatrix" version))
3604 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3605 (properties `((upstream-name . "bdsmatrix")))
3606 (build-system r-build-system)
3607 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3608 (synopsis "Routines for block diagonal symmetric matrices")
3610 "This package provides procedures to work with block diagonal symmetric
3611 matrices, a special case of sparse matrices.")
3612 (license license:lgpl2.0)))
3614 (define-public r-bbmle
3617 (version "1.0.23.1")
3621 (uri (cran-uri "bbmle" version))
3624 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3625 (build-system r-build-system)
3627 `(("r-bdsmatrix" ,r-bdsmatrix)
3628 ("r-lattice" ,r-lattice)
3630 ("r-matrix" ,r-matrix)
3631 ("r-mvtnorm" ,r-mvtnorm)
3632 ("r-numderiv" ,r-numderiv)))
3633 (home-page "https://cran.r-project.org/web/packages/bbmle")
3634 (synopsis "Tools for General Maximum Likelihood Estimation")
3636 "This package provides methods and functions for fitting maximum
3637 likelihood models in R. This package modifies and extends the @code{mle}
3638 classes in the @code{stats4} package.")
3639 ;; Any version of the GPL
3640 (license license:gpl2+)))
3642 (define-public r-emdbook
3649 (uri (cran-uri "emdbook" version))
3652 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3653 (build-system r-build-system)
3655 `(("r-bbmle" ,r-bbmle)
3657 ("r-lattice" ,r-lattice)
3659 ("r-plyr" ,r-plyr)))
3660 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3661 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3663 "This package provides auxiliary functions and data sets for \"Ecological
3664 Models and Data\", a book presenting maximum likelihood estimation and related
3665 topics for ecologists (ISBN 978-0-691-12522-0).")
3667 (license (list license:gpl2 license:gpl3))))
3669 (define-public r-lpsolve
3676 (uri (cran-uri "lpSolve" version))
3679 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3680 (properties `((upstream-name . "lpSolve")))
3681 (build-system r-build-system)
3682 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3683 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3685 "Lp_solve is software for solving linear, integer and mixed integer
3686 programs. This implementation supplies a \"wrapper\" function in C and some R
3687 functions that solve general linear/integer problems, assignment problems, and
3688 transportation problems.")
3689 (license license:lgpl2.0)))
3691 (define-public r-limsolve
3698 (uri (cran-uri "limSolve" version))
3701 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3702 (properties `((upstream-name . "limSolve")))
3703 (build-system r-build-system)
3705 `(("r-lpsolve" ,r-lpsolve)
3707 ("r-quadprog" ,r-quadprog)))
3708 (native-inputs `(("gfortran" ,gfortran)))
3709 (home-page "https://cran.r-project.org/web/packages/limSolve")
3710 (synopsis "Solving linear inverse models")
3712 "This package provides functions that:
3715 @item find the minimum/maximum of a linear or quadratic function,
3716 @item sample an underdetermined or overdetermined system,
3717 @item solve a linear system Ax=B for the unknown x.
3720 It includes banded and tridiagonal linear systems. The package calls Fortran
3721 functions from LINPACK.")
3723 (license (list license:gpl2+ license:gpl3+))))
3725 (define-public r-fitdistrplus
3727 (name "r-fitdistrplus")
3732 (uri (cran-uri "fitdistrplus" version))
3735 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3736 (build-system r-build-system)
3738 `(("r-mass" ,r-mass)
3739 ("r-survival" ,r-survival)))
3741 `(("r-knitr" ,r-knitr)))
3742 (home-page "http://riskassessment.r-forge.r-project.org")
3743 (synopsis "Fitting a parametric distribution from data")
3745 "This package extends the @code{fitdistr} function of the MASS package
3746 with several functions to help the fit of a parametric distribution to
3747 non-censored or censored data. Censored data may contain left-censored,
3748 right-censored and interval-censored values, with several lower and upper
3749 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3750 provides moment matching (MME), quantile matching (QME) and maximum
3751 goodness-of-fit estimation (MGE) methods (available only for non-censored
3752 data). Weighted versions of MLE, MME and QME are available.")
3753 (license license:gpl2+)))
3755 (define-public r-energy
3762 (uri (cran-uri "energy" version))
3765 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3766 (build-system r-build-system)
3768 `(("r-boot" ,r-boot)
3770 ("r-rcpp" ,r-rcpp)))
3771 (home-page "https://cran.r-project.org/web/packages/energy")
3772 (synopsis "Multivariate inference via the energy of data")
3774 "This package provides e-statistics (energy) tests and statistics for
3775 multivariate and univariate inference, including distance correlation,
3776 one-sample, two-sample, and multi-sample tests for comparing multivariate
3777 distributions, are implemented. Measuring and testing multivariate
3778 independence based on distance correlation, partial distance correlation,
3779 multivariate goodness-of-fit tests, clustering based on energy distance,
3780 testing for multivariate normality, distance components (disco) for
3781 non-parametric analysis of structured data, and other energy
3782 statistics/methods are implemented.")
3783 (license license:gpl2+)))
3785 (define-public r-suppdists
3787 (name "r-suppdists")
3792 (uri (cran-uri "SuppDists" version))
3795 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3796 (properties `((upstream-name . "SuppDists")))
3797 (build-system r-build-system)
3798 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3799 (synopsis "Supplementary distributions")
3801 "This package provides ten distributions supplementing those built into
3802 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3803 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3804 coefficient, Johnson distributions, normal scores and generalized
3805 hypergeometric distributions. In addition two random number generators of
3806 George Marsaglia are included.")
3807 (license license:gpl2+)))
3809 (define-public r-ksamples
3816 (uri (cran-uri "kSamples" version))
3819 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3820 (properties `((upstream-name . "kSamples")))
3821 (build-system r-build-system)
3823 `(("r-suppdists" ,r-suppdists)))
3824 (home-page "https://cran.r-project.org/web/packages/kSamples")
3825 (synopsis "K-Sample rank tests and their combinations")
3827 "This package provides tools to compares k samples using the
3828 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3829 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3830 test. It computes asymptotic, simulated or (limited) exact P-values, all
3831 valid under randomization, with or without ties, or conditionally under random
3832 sampling from populations, given the observed tie pattern. Except for Steel's
3833 test and the JT test it also combines these tests across several blocks of
3835 (license license:gpl2+)))
3837 (define-public r-cvst
3844 (uri (cran-uri "CVST" version))
3847 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3848 (properties `((upstream-name . "CVST")))
3849 (build-system r-build-system)
3851 `(("r-kernlab" ,r-kernlab)
3852 ("r-matrix" ,r-matrix)))
3853 (home-page "https://cran.r-project.org/web/packages/CVST")
3854 (synopsis "Fast cross-validation via sequential testing")
3856 "This package implements the fast cross-validation via sequential
3857 testing (CVST) procedure. CVST is an improved cross-validation procedure
3858 which uses non-parametric testing coupled with sequential analysis to
3859 determine the best parameter set on linearly increasing subsets of the data.
3860 Additionally to the CVST the package contains an implementation of the
3861 ordinary k-fold cross-validation with a flexible and powerful set of helper
3862 objects and methods to handle the overall model selection process. The
3863 implementations of the Cochran's Q test with permutations and the sequential
3864 testing framework of Wald are generic and can therefore also be used in other
3866 (license license:gpl2+)))
3868 (define-public r-squarem
3875 (uri (cran-uri "SQUAREM" version))
3878 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3879 (properties `((upstream-name . "SQUAREM")))
3880 (build-system r-build-system)
3881 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3882 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3884 "This package provides algorithms for accelerating the convergence of
3885 slow, monotone sequences from smooth, contraction mapping such as the EM
3886 algorithm. It can be used to accelerate any smooth, linearly convergent
3887 acceleration scheme. A tutorial style introduction to this package is
3888 available in a vignette.")
3889 (license license:gpl2+)))
3891 (define-public r-lava
3898 (uri (cran-uri "lava" version))
3901 "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83"))))
3902 (build-system r-build-system)
3904 `(("r-numderiv" ,r-numderiv)
3905 ("r-squarem" ,r-squarem)
3906 ("r-survival" ,r-survival)))
3908 `(("r-knitr" ,r-knitr)))
3909 (home-page "https://github.com/kkholst/lava")
3910 (synopsis "Latent variable models")
3912 "This package provides tools for the estimation and simulation of latent
3914 (license license:gpl3)))
3916 (define-public r-drr
3923 (uri (cran-uri "DRR" version))
3926 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3927 (properties `((upstream-name . "DRR")))
3928 (build-system r-build-system)
3930 `(("r-cvst" ,r-cvst)
3931 ("r-kernlab" ,r-kernlab)
3932 ("r-matrix" ,r-matrix)))
3933 (home-page "https://cran.r-project.org/web/packages/DRR")
3934 (synopsis "Dimensionality reduction via regression")
3936 "This package provides an implementation of dimensionality reduction via
3937 regression using Kernel Ridge Regression.")
3938 (license license:gpl3)))
3940 (define-public r-prodlim
3943 (version "2019.11.13")
3947 (uri (cran-uri "prodlim" version))
3950 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3951 (build-system r-build-system)
3953 `(("r-kernsmooth" ,r-kernsmooth)
3956 ("r-survival" ,r-survival)))
3957 (home-page "https://cran.r-project.org/web/packages/prodlim")
3958 (synopsis "Product-limit estimation for censored event history analysis")
3960 "This package provides a fast and user-friendly implementation of
3961 nonparametric estimators for censored event history (survival) analysis with
3962 the Kaplan-Meier and Aalen-Johansen methods.")
3963 (license license:gpl2+)))
3965 (define-public r-dimred
3972 (uri (cran-uri "dimRed" version))
3975 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3976 (properties `((upstream-name . "dimRed")))
3977 (build-system r-build-system)
3980 ("r-magrittr" ,r-magrittr)))
3981 (home-page "https://github.com/gdkrmr/dimRed")
3982 (synopsis "Framework for dimensionality reduction")
3984 "This package provides a collection of dimensionality reduction
3985 techniques from R packages and provides a common interface for calling the
3987 (license license:gpl3)))
3989 (define-public r-timedate
3992 (version "3043.102")
3996 (uri (cran-uri "timeDate" version))
3999 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
4000 (properties `((upstream-name . "timeDate")))
4001 (build-system r-build-system)
4002 (home-page "https://www.rmetrics.org")
4003 (synopsis "Chronological and calendar objects")
4005 "This package provides an environment for teaching \"Financial
4006 Engineering and Computational Finance\" and for managing chronological and
4008 (license license:gpl2+)))
4010 (define-public r-magic
4017 (uri (cran-uri "magic" version))
4020 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4021 (build-system r-build-system)
4023 `(("r-abind" ,r-abind)))
4024 (home-page "https://github.com/RobinHankin/magic.git")
4025 (synopsis "Create and investigate magic squares")
4027 "This package provides a collection of efficient, vectorized algorithms
4028 for the creation and investigation of magic squares and hypercubes, including
4029 a variety of functions for the manipulation and analysis of arbitrarily
4030 dimensioned arrays.")
4031 (license license:gpl2)))
4033 (define-public r-rmysql
4040 (uri (cran-uri "RMySQL" version))
4043 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4044 (properties `((upstream-name . "RMySQL")))
4045 (build-system r-build-system)
4047 `(("mariadb-dev" ,mariadb "dev")
4050 `(("r-dbi" ,r-dbi)))
4051 (home-page "https://github.com/r-dbi/RMySQL")
4052 (synopsis "Database interface and MySQL driver for R")
4054 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4055 package contains an old implementation based on legacy code from S-PLUS which
4056 is being phased out. A modern MySQL client based on Rcpp is available from
4057 the RMariaDB package.")
4058 (license license:gpl2)))
4060 (define-public r-rpostgresql
4062 (name "r-rpostgresql")
4067 (uri (cran-uri "RPostgreSQL" version))
4070 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4071 (properties `((upstream-name . "RPostgreSQL")))
4072 (build-system r-build-system)
4074 `(("postgresql" ,postgresql)))
4076 `(("r-dbi" ,r-dbi)))
4077 (home-page "https://github.com/tomoakin/RPostgreSQL")
4078 (synopsis "R interface to the PostgreSQL database system")
4080 "This package provides a Database Interface (DBI) compliant driver for R
4081 to access PostgreSQL database systems.")
4082 ;; The whole package is released under GPL version 2. It includes code
4083 ;; under the PostgreSQL license.
4084 (license license:gpl2)))
4086 (define-public r-linprog
4093 (uri (cran-uri "linprog" version))
4096 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4097 (build-system r-build-system)
4098 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4099 (home-page "http://linprog.r-forge.r-project.org/")
4100 (synopsis "Linear programming and optimization")
4102 "This package can be used to solve Linear Programming / Linear
4103 Optimization problems by using the simplex algorithm.")
4104 (license license:gpl2+)))
4106 (define-public r-geometry
4113 (uri (cran-uri "geometry" version))
4116 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4117 (build-system r-build-system)
4119 `(("r-magic" ,r-magic)
4120 ("r-linprog" ,r-linprog)
4121 ("r-lpsolve" ,r-lpsolve)
4123 ("r-rcppprogress" ,r-rcppprogress)))
4124 (home-page "http://geometry.r-forge.r-project.org/")
4125 (synopsis "Mesh generator and surface tessellator")
4127 "This package makes the qhull library available in R, in a similar manner
4128 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4129 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4130 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4131 and higher dimensions. It implements the Quickhull algorithm for computing
4132 the convex hull. Qhull does not support constrained Delaunay triangulations,
4133 or mesh generation of non-convex objects, but the package does include some R
4134 functions that allow for this. Currently the package only gives access to
4135 Delaunay triangulation and convex hull computation.")
4136 ;; The Qhull sources are included and are distributed under a custom
4137 ;; non-copyleft license. The R sources are released under GPL version 2.
4138 (license (list license:gpl2
4139 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4141 (define-public r-ddalpha
4148 (uri (cran-uri "ddalpha" version))
4151 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4152 (build-system r-build-system)
4155 ("r-class" ,r-class)
4156 ("r-geometry" ,r-geometry)
4159 ("r-robustbase" ,r-robustbase)
4160 ("r-sfsmisc" ,r-sfsmisc)))
4162 `(("gfortran" ,gfortran)))
4163 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4164 (synopsis "Depth-Based classification and calculation of data depth")
4166 "This package contains procedures for depth-based supervised learning,
4167 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4168 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4169 statistical depth function to a compact low-dimensional space, where the final
4170 classification is done. It also offers an extension to functional data and
4171 routines for calculating certain notions of statistical depth functions. 50
4172 multivariate and 5 functional classification problems are included.")
4173 (license license:gpl2)))
4175 (define-public r-gower
4182 (uri (cran-uri "gower" version))
4185 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4186 (build-system r-build-system)
4187 (home-page "https://github.com/markvanderloo/gower")
4188 (synopsis "Gower's distance")
4190 "This package provides tools to compute Gower's distance (or similarity)
4191 coefficient between records, and to compute the top-n matches between records.
4192 Core algorithms are executed in parallel on systems supporting OpenMP.")
4193 (license license:gpl3)))
4195 (define-public r-rcpproll
4202 (uri (cran-uri "RcppRoll" version))
4205 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4206 (properties `((upstream-name . "RcppRoll")))
4207 (build-system r-build-system)
4209 `(("r-rcpp" ,r-rcpp)))
4210 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4211 (synopsis "Efficient rolling and windowed operations")
4213 "This package provides fast and efficient routines for common rolling /
4214 windowed operations. Routines for the efficient computation of windowed mean,
4215 median, sum, product, minimum, maximum, standard deviation and variance are
4217 (license license:gpl2+)))
4219 (define-public r-ipred
4226 (uri (cran-uri "ipred" version))
4229 "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp"))))
4230 (build-system r-build-system)
4232 `(("r-class" ,r-class)
4235 ("r-prodlim" ,r-prodlim)
4236 ("r-rpart" ,r-rpart)
4237 ("r-survival" ,r-survival)))
4238 (home-page "https://cran.r-project.org/web/packages/ipred")
4239 (synopsis "Improved predictors")
4241 "This package provides improved predictive models by indirect
4242 classification and bagging for classification, regression and survival
4243 problems as well as resampling based estimators of prediction error.")
4244 (license license:gpl2+)))
4246 (define-public r-psych
4253 (uri (cran-uri "psych" version))
4256 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
4257 (build-system r-build-system)
4259 `(("r-lattice" ,r-lattice)
4260 ("r-mnormt" ,r-mnormt)
4261 ("r-nlme" ,r-nlme)))
4262 (home-page "https://cran.r-project.org/web/packages/psych/")
4263 (synopsis "Procedures for psychological, psychometric, and personality research")
4265 "This package provides a general purpose toolbox for personality,
4266 psychometric theory and experimental psychology. Functions are primarily for
4267 multivariate analysis and scale construction using factor analysis, principal
4268 component analysis, cluster analysis and reliability analysis, although others
4269 provide basic descriptive statistics. Item Response Theory is done using
4270 factor analysis of tetrachoric and polychoric correlations. Functions for
4271 analyzing data at multiple levels include within and between group statistics,
4272 including correlations and factor analysis. Functions for simulating and
4273 testing particular item and test structures are included. Several functions
4274 serve as a useful front end for structural equation modeling. Graphical
4275 displays of path diagrams, factor analysis and structural equation models are
4276 created using basic graphics.")
4277 (license license:gpl2+)))
4279 (define-public r-generics
4286 (uri (cran-uri "generics" version))
4289 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4290 (build-system r-build-system)
4291 (home-page "https://github.com/r-lib/generics")
4292 (synopsis "Common S3 generics not provided by base R methods")
4294 "In order to reduce potential package dependencies and conflicts,
4295 generics provides a number of commonly used S3 generics that are not provided
4296 by base R methods related to model fitting.")
4297 (license license:gpl2)))
4299 (define-public r-broom
4306 (uri (cran-uri "broom" version))
4309 "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw"))))
4310 (build-system r-build-system)
4312 `(("r-backports" ,r-backports)
4313 ("r-dplyr" ,r-dplyr)
4314 ("r-ellipsis" ,r-ellipsis)
4315 ("r-generics" ,r-generics)
4317 ("r-purrr" ,r-purrr)
4318 ("r-rlang" ,r-rlang)
4319 ("r-stringr" ,r-stringr)
4320 ("r-tibble" ,r-tibble)
4321 ("r-tidyr" ,r-tidyr)))
4323 `(("r-knitr" ,r-knitr)))
4324 (home-page "https://github.com/tidyverse/broom")
4325 (synopsis "Convert statistical analysis objects into tidy data frames")
4327 "This package provides tools to convert statistical analysis objects from
4328 R into tidy data frames, so that they can more easily be combined, reshaped
4329 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4330 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4331 summarizes a model's statistical findings such as coefficients of a
4332 regression; @code{augment}, which adds columns to the original data such as
4333 predictions, residuals and cluster assignments; and @code{glance}, which
4334 provides a one-row summary of model-level statistics.")
4335 (license license:expat)))
4337 (define-public r-recipes
4344 (uri (cran-uri "recipes" version))
4347 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4348 (build-system r-build-system)
4350 `(("r-dplyr" ,r-dplyr)
4351 ("r-generics" ,r-generics)
4353 ("r-gower" ,r-gower)
4354 ("r-ipred" ,r-ipred)
4355 ("r-lifecycle" ,r-lifecycle)
4356 ("r-lubridate" ,r-lubridate)
4357 ("r-magrittr" ,r-magrittr)
4358 ("r-matrix" ,r-matrix)
4359 ("r-purrr" ,r-purrr)
4360 ("r-rlang" ,r-rlang)
4361 ("r-tibble" ,r-tibble)
4362 ("r-tidyr" ,r-tidyr)
4363 ("r-tidyselect" ,r-tidyselect)
4364 ("r-timedate" ,r-timedate)
4365 ("r-withr" ,r-withr)))
4367 `(("r-knitr" ,r-knitr)))
4368 (home-page "https://github.com/topepo/recipes")
4369 (synopsis "Preprocessing tools to create design matrices")
4371 "Recipes is an extensible framework to create and preprocess design
4372 matrices. Recipes consist of one or more data manipulation and analysis
4373 \"steps\". Statistical parameters for the steps can be estimated from an
4374 initial data set and then applied to other data sets. The resulting design
4375 matrices can then be used as inputs into statistical or machine learning
4377 (license license:gpl2)))
4379 (define-public r-pdist
4386 (uri (cran-uri "pdist" version))
4389 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4390 (build-system r-build-system)
4391 (home-page "https://github.com/jeffwong/pdist")
4392 (synopsis "Partitioned distance function")
4394 "Pdist computes the euclidean distance between rows of a matrix X and
4395 rows of another matrix Y. Previously, this could be done by binding the two
4396 matrices together and calling @code{dist}, but this creates unnecessary
4397 computation by computing the distances between a row of X and another row of
4398 X, and likewise for Y. Pdist strictly computes distances across the two
4399 matrices, not within the same matrix, making computations significantly faster
4400 for certain use cases.")
4401 (license license:gpl3+)))
4403 (define-public r-ggrepel
4410 (uri (cran-uri "ggrepel" version))
4413 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4414 (build-system r-build-system)
4416 `(("r-ggplot2" ,r-ggplot2)
4418 ("r-rlang" ,r-rlang)
4419 ("r-scales" ,r-scales)))
4421 `(("r-knitr" ,r-knitr))) ; for vignettes
4422 (home-page "https://github.com/slowkow/ggrepel")
4423 (synopsis "Repulsive text and label geometries for ggplot2")
4425 "This package provides text and label geometries for ggplot2 that help to
4426 avoid overlapping text labels. Labels repel away from each other and away
4427 from the data points.")
4428 (license license:gpl3)))
4430 (define-public r-corrplot
4437 (uri (cran-uri "corrplot" version))
4440 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4441 (build-system r-build-system)
4442 (home-page "https://github.com/taiyun/corrplot")
4443 (synopsis "Visualization of a correlation matrix")
4445 "This package provides a graphical display of a correlation matrix or
4446 general matrix. It also contains some algorithms to do matrix reordering. In
4447 addition, corrplot is good at details, including choosing color, text labels,
4448 color labels, layout, etc.")
4449 ;; Any version of the GPL
4450 (license license:gpl2+)))
4452 (define-public r-stringdist
4454 (name "r-stringdist")
4459 (uri (cran-uri "stringdist" version))
4461 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4462 (build-system r-build-system)
4463 (home-page "https://github.com/markvanderloo/stringdist")
4464 (synopsis "Approximate string matching and string distance functions")
4466 "This package implements an approximate string matching version of R's
4467 native @code{match} function. It can calculate various string distances based
4468 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4469 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4470 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4471 can be computed between character vectors while taking proper care of encoding
4472 or between integer vectors representing generic sequences.")
4473 (license license:gpl3+)))
4475 (define-public r-ucminf
4482 (uri (cran-uri "ucminf" version))
4485 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4486 (build-system r-build-system)
4487 (native-inputs `(("gfortran" ,gfortran)))
4488 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4489 (synopsis "General-purpose unconstrained non-linear optimization")
4491 "This package provides an implementation of an algorithm for
4492 general-purpose unconstrained non-linear optimization. The algorithm is of
4493 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4494 search with a trust region type monitoring of the input to the line search
4495 algorithm. The interface of @code{ucminf} is designed for easy interchange
4496 with the package @code{optim}.")
4497 (license license:gpl2+)))
4499 (define-public r-useful
4505 (uri (cran-uri "useful" version))
4508 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4509 (properties `((upstream-name . "useful")))
4510 (build-system r-build-system)
4512 `(("r-assertthat" ,r-assertthat)
4513 ("r-dplyr" ,r-dplyr)
4514 ("r-ggplot2" ,r-ggplot2)
4515 ("r-magrittr" ,r-magrittr)
4516 ("r-matrix" ,r-matrix)
4518 ("r-purrr" ,r-purrr)
4519 ("r-scales" ,r-scales)))
4520 (home-page "https://github.com/jaredlander/useful")
4521 (synopsis "Collection of handy, useful functions")
4522 (description "This package provides a set of little functions that have been
4523 found useful to do little odds and ends such as plotting the results of K-means
4524 clustering, substituting special text characters, viewing parts of a
4525 @code{data.frame}, constructing formulas from text and building design and
4526 response matrices.")
4527 (license license:bsd-3)))
4529 (define-public r-ordinal
4532 (version "2019.12-10")
4536 (uri (cran-uri "ordinal" version))
4539 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4540 (build-system r-build-system)
4542 `(("r-mass" ,r-mass)
4543 ("r-matrix" ,r-matrix)
4544 ("r-numderiv" ,r-numderiv)
4545 ("r-ucminf" ,r-ucminf)))
4546 (home-page "https://github.com/runehaubo/ordinal")
4547 (synopsis "Regression models for ordinal data")
4549 "This package provides an implementation of cumulative link (mixed)
4550 models also known as ordered regression models, proportional odds models,
4551 proportional hazards models for grouped survival times and ordered models.
4552 Estimation is via maximum likelihood and mixed models are fitted with the
4553 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4554 (license license:gpl2+)))
4556 (define-public r-jomo
4563 (uri (cran-uri "jomo" version))
4566 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4567 (build-system r-build-system)
4569 `(("r-lme4" ,r-lme4)
4571 ("r-ordinal" ,r-ordinal)
4572 ("r-survival" ,r-survival)))
4573 (home-page "https://cran.r-project.org/web/packages/jomo/")
4574 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4576 "Similarly to Schafer's package pan, jomo is a package for multilevel
4577 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4578 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4579 possibility of handling binary and categorical data through latent normal
4580 variables, the option to use cluster-specific covariance matrices and to
4581 impute compatibly with the substantive model.")
4582 (license license:gpl2)))
4584 (define-public r-pan
4591 (uri (cran-uri "pan" version))
4594 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4595 (build-system r-build-system)
4596 (native-inputs `(("gfortran" ,gfortran)))
4597 (home-page "https://cran.r-project.org/web/packages/pan/")
4598 (synopsis "Multiple imputation for multivariate panel or clustered data")
4600 "This package implements multiple imputation for multivariate panel or
4602 (license license:gpl3)))
4604 (define-public r-mitml
4611 (uri (cran-uri "mitml" version))
4614 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4615 (build-system r-build-system)
4617 `(("r-haven" ,r-haven)
4621 `(("r-knitr" ,r-knitr)))
4622 (home-page "https://cran.r-project.org/web/packages/mitml/")
4623 (synopsis "Tools for multiple imputation in multilevel modeling")
4625 "This package provides tools for multiple imputation of missing data in
4626 multilevel modeling. It includes a user-friendly interface to the packages
4627 pan and jomo, and several functions for visualization, data management and the
4628 analysis of multiply imputed data sets.")
4629 (license license:gpl2+)))
4631 (define-public r-mice
4638 (uri (cran-uri "mice" version))
4641 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4642 (build-system r-build-system)
4644 `(("r-broom" ,r-broom)
4645 ("r-cpp11" ,r-cpp11)
4646 ("r-dplyr" ,r-dplyr)
4647 ("r-generics" ,r-generics)
4648 ("r-lattice" ,r-lattice)
4650 ("r-rlang" ,r-rlang)
4651 ("r-tidyr" ,r-tidyr)))
4652 (home-page "https://cran.r-project.org/web/packages/mice/")
4653 (synopsis "Multivariate imputation by chained equations")
4655 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4656 implemented by the MICE algorithm as described in @url{Van Buuren and
4657 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4658 variable has its own imputation model. Built-in imputation models are
4659 provided for continuous data (predictive mean matching, normal), binary
4660 data (logistic regression), unordered categorical data (polytomous logistic
4661 regression) and ordered categorical data (proportional odds). MICE can also
4662 impute continuous two-level data (normal model, pan, second-level variables).
4663 Passive imputation can be used to maintain consistency between variables.
4664 Various diagnostic plots are available to inspect the quality of the
4666 ;; Any of these two versions.
4667 (license (list license:gpl2 license:gpl3))))
4669 (define-public r-truncnorm
4671 (name "r-truncnorm")
4676 (uri (cran-uri "truncnorm" version))
4679 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4680 (build-system r-build-system)
4681 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4682 (synopsis "Truncated normal distribution")
4683 (description "This package provides functions for the truncated normal
4684 distribution with mean equal to @code{mean} and standard deviation equal to
4685 @code{sd}. It includes density, distribution, quantile, and expected value
4686 functions, as well as a random generation function.")
4687 (license license:gpl2)))
4689 (define-public r-rsolnp
4696 (uri (cran-uri "Rsolnp" version))
4699 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4700 (properties `((upstream-name . "Rsolnp")))
4701 (build-system r-build-system)
4703 `(("r-truncnorm" ,r-truncnorm)))
4704 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4705 (synopsis "General non-linear optimization")
4706 (description "The Rsolnp package implements a general non-linear augmented
4707 Lagrange multiplier method solver, a @dfn{sequential quadratic
4708 programming} (SQP) based solver).")
4709 ;; Any version of the GPL.
4710 (license license:gpl2+)))
4712 (define-public r-hardyweinberg
4714 (name "r-hardyweinberg")
4719 (uri (cran-uri "HardyWeinberg" version))
4722 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4723 (properties `((upstream-name . "HardyWeinberg")))
4724 (build-system r-build-system)
4726 `(("r-mice" ,r-mice)
4728 ("r-rsolnp" ,r-rsolnp)))
4729 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4730 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4732 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4733 diallelic genetic marker data. All classical tests (chi-square, exact,
4734 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4735 included in the package, as well as functions for power computation and for
4736 the simulation of marker data under equilibrium and disequilibrium. Routines
4737 for dealing with markers on the X-chromosome are included. Functions for
4738 testing equilibrium in the presence of missing data by using multiple
4739 imputation are also provided. Implements several graphics for exploring the
4740 equilibrium status of a large set of diallelic markers: ternary plots with
4741 acceptance regions, log-ratio plots and Q-Q plots.")
4742 (license license:gpl2+)))
4751 (uri (cran-uri "sm" version))
4754 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4755 (build-system r-build-system)
4756 (native-inputs `(("gfortran" ,gfortran)))
4757 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4758 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4760 "This is software accompanying the book 'Applied Smoothing Techniques for
4761 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4762 University Press. It provides smoothing methods for nonparametric regression
4763 and density estimation")
4764 (license license:gpl2+)))
4766 (define-public r-venndiagram
4768 (name "r-venndiagram")
4772 (uri (cran-uri "VennDiagram" version))
4775 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4776 (properties `((upstream-name . "VennDiagram")))
4777 (build-system r-build-system)
4779 `(("r-futile-logger" ,r-futile-logger)))
4780 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4781 (synopsis "Generate High-Resolution Venn and Euler Plots")
4783 "This package provides a set of functions to generate high-resolution
4784 Venn and Euler plots. It includes handling for several special cases,
4785 including two-case scaling, and extensive customization of plot shape and
4787 (license license:gpl2+)))
4789 (define-public r-vioplot
4796 (uri (cran-uri "vioplot" version))
4799 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4800 (build-system r-build-system)
4805 `(("r-knitr" ,r-knitr)))
4806 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4807 (synopsis "Violin plot")
4809 "This package provides a violin plot, which is a combination of a box
4810 plot and a kernel density plot.")
4811 (license license:bsd-3)))
4813 (define-public r-rsofia
4819 ;; This package has been removed from CRAN, so we can
4820 ;; only fetch it from the archives.
4821 (uri (string-append "https://cran.r-project.org/src/"
4822 "contrib/Archive/RSofia/RSofia_"
4826 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4827 (properties `((upstream-name . "RSofia")))
4828 (build-system r-build-system)
4830 `(("r-rcpp" ,r-rcpp)))
4831 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4832 (synopsis "Port of sofia-ml to R")
4833 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4834 suite of fast incremental algorithms for machine learning that can be used for
4835 training models for classification or ranking.")
4836 (license license:asl2.0)))
4838 (define-public r-xts
4845 (uri (cran-uri "xts" version))
4848 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4849 (build-system r-build-system)
4850 (propagated-inputs `(("r-zoo" ,r-zoo)))
4851 (home-page "https://github.com/joshuaulrich/xts")
4852 (synopsis "Extensible time series")
4854 "This package provides for uniform handling of R's different time-based
4855 data classes by extending @code{zoo}, maximizing native format information
4856 preservation and allowing for user-level customization and extension, while
4857 simplifying cross-class interoperability.")
4858 (license license:gpl2+)))
4860 (define-public r-performanceanalytics
4862 (name "r-performanceanalytics")
4867 (uri (cran-uri "PerformanceAnalytics" version))
4870 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4872 `((upstream-name . "PerformanceAnalytics")))
4873 (build-system r-build-system)
4875 `(("r-quadprog" ,r-quadprog)
4878 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4879 (synopsis "Econometric tools for performance and risk analysis")
4880 (description "This is a collection of econometric functions for
4881 performance and risk analysis. This package aims to aid practitioners and
4882 researchers in utilizing the latest research in analysis of non-normal return
4883 streams. In general, it is most tested on return (rather than price) data on
4884 a regular scale, but most functions will work with irregular return data as
4885 well, and increasing numbers of functions will work with P&L or price data
4887 ;; Either version may be picked.
4888 (license (list license:gpl2 license:gpl3))))
4890 (define-public r-laeken
4897 (uri (cran-uri "laeken" version))
4900 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4901 (build-system r-build-system)
4903 `(("r-boot" ,r-boot)
4904 ("r-mass" ,r-mass)))
4905 (home-page "https://cran.r-project.org/web/packages/laeken/")
4906 (synopsis "Estimation of indicators on social exclusion and poverty")
4907 (description "This package provides tools for the estimation of indicators
4908 on social exclusion and poverty, as well as an implementation of Pareto tail
4909 modeling for empirical income distributions.")
4910 (license license:gpl2+)))
4912 (define-public r-vcd
4919 (uri (cran-uri "vcd" version))
4922 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4923 (build-system r-build-system)
4925 `(("r-colorspace" ,r-colorspace)
4926 ("r-lmtest" ,r-lmtest)
4927 ("r-mass" ,r-mass)))
4928 (home-page "https://cran.r-project.org/web/packages/vcd/")
4929 (synopsis "Visualizing categorical data")
4930 (description "This package provides visualization techniques, data sets,
4931 summary and inference procedures aimed particularly at categorical data.
4932 Special emphasis is given to highly extensible grid graphics. The package was
4933 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4934 Friendly and is now the main support package for a new book, \"Discrete Data
4935 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4936 (license license:gpl2)))
4938 (define-public r-ica
4945 (uri (cran-uri "ica" version))
4948 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4949 (build-system r-build-system)
4950 (home-page "https://cran.r-project.org/web/packages/ica/")
4951 (synopsis "Independent component analysis")
4952 (description "This package provides tools for @dfn{Independent Component
4953 Analysis} (ICA) using various algorithms: FastICA,
4954 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4955 of Eigenmatrices} (JADE).")
4956 (license license:gpl2+)))
4958 (define-public r-dtw
4965 (uri (cran-uri "dtw" version))
4968 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4969 (build-system r-build-system)
4970 (propagated-inputs `(("r-proxy" ,r-proxy)))
4971 (home-page "http://dtw.r-forge.r-project.org/")
4972 (synopsis "Dynamic Time Warping Algorithms")
4973 (description "This package provides a comprehensive implementation of
4974 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4975 optimal (least cumulative distance) alignment between points of two time
4976 series. Common DTW variants covered include local (slope) and global (window)
4977 constraints, subsequence matches, arbitrary distance definitions,
4978 normalizations, minimum variance matching, and so on.")
4979 (license license:gpl2+)))
4981 (define-public r-sdmtools
4984 (version "1.1-221.2")
4988 (uri (cran-uri "SDMTools" version))
4991 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4992 (properties `((upstream-name . "SDMTools")))
4993 (build-system r-build-system)
4994 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4995 (home-page "https://www.rforge.net/SDMTools/")
4996 (synopsis "Species distribution modelling tools")
4997 (description "This package provides a set of tools for post processing
4998 the outcomes of species distribution modeling exercises. It includes novel
4999 methods for comparing models and tracking changes in distributions through
5000 time. It further includes methods for visualizing outcomes, selecting
5001 thresholds, calculating measures of accuracy and landscape fragmentation
5003 (license license:gpl3+)))
5005 (define-public r-scatterplot3d
5007 (name "r-scatterplot3d")
5012 (uri (cran-uri "scatterplot3d" version))
5015 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5016 (build-system r-build-system)
5017 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5018 (synopsis "3D scatter plot")
5019 (description "This package provides an implementation of scatter plots for
5020 plotting. a three dimensional point cloud.")
5021 (license license:gpl2)))
5023 (define-public r-ggridges
5030 (uri (cran-uri "ggridges" version))
5033 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5034 (build-system r-build-system)
5036 `(("r-ggplot2" ,r-ggplot2)
5038 ("r-scales" ,r-scales)
5039 ("r-withr" ,r-withr)))
5041 `(("r-knitr" ,r-knitr)))
5042 (home-page "https://github.com/clauswilke/ggridges")
5043 (synopsis "Ridgeline plots in ggplot2")
5045 "Ridgeline plots provide a convenient way of visualizing changes in
5046 distributions over time or space. This package enables the creation of such
5047 plots in @code{ggplot2}.")
5048 (license license:gpl2)))
5050 (define-public r-ggjoy
5057 (uri (cran-uri "ggjoy" version))
5060 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5061 (build-system r-build-system)
5063 `(("r-ggplot2" ,r-ggplot2)
5064 ("r-ggridges" ,r-ggridges)))
5065 (home-page "https://github.com/clauswilke/ggjoy")
5066 (synopsis "Joyplots in ggplot2")
5067 (description "Joyplots provide a convenient way of visualizing changes in
5068 distributions over time or space. This package enables the creation of such
5069 plots in @code{ggplot2}.")
5070 (license license:gpl2)))
5072 (define-public r-cli
5079 (uri (cran-uri "cli" version))
5082 "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i"))))
5083 (build-system r-build-system)
5085 `(("r-assertthat" ,r-assertthat)
5086 ("r-glue" ,r-glue)))
5087 (home-page "https://github.com/r-lib/cli#readme")
5088 (synopsis "Helpers for developing command line interfaces")
5089 (description "This package provides a suite of tools designed to build
5090 attractive command line interfaces (CLIs). It includes tools for drawing
5091 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5092 (license license:expat)))
5094 (define-public r-argparser
5096 (name "r-argparser")
5101 (uri (cran-uri "argparser" version))
5104 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5105 (build-system r-build-system)
5106 (home-page "https://bitbucket.org/djhshih/argparser")
5107 (synopsis "Command-line argument parser")
5109 "This package provides a cross-platform command-line argument parser
5110 written purely in R with no external dependencies. It is useful with the
5111 Rscript front-end and facilitates turning an R script into an executable
5113 (license license:gpl3+)))
5115 (define-public r-debugme
5122 (uri (cran-uri "debugme" version))
5125 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5126 (build-system r-build-system)
5127 (propagated-inputs `(("r-crayon" ,r-crayon)))
5128 (home-page "https://github.com/r-lib/debugme#readme")
5129 (synopsis "Debug R packages")
5131 "This package allows the user to specify debug messages as special string
5132 constants, and control debugging of packages via environment variables.")
5133 (license license:expat)))
5135 (define-public r-processx
5142 (uri (cran-uri "processx" version))
5144 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
5145 (build-system r-build-system)
5149 (home-page "https://github.com/r-lib/processx3")
5150 (synopsis "Execute and control system processes")
5152 "This package provides portable tools to run system processes in the
5153 background. It can check if a background process is running; wait on a
5154 background process to finish; get the exit status of finished processes; kill
5155 background processes and their children; restart processes. It can read the
5156 standard output and error of the processes, using non-blocking connections.
5157 @code{processx} can poll a process for standard output or error, with a
5158 timeout. It can also poll several processes at once.")
5159 (license license:expat)))
5161 (define-public r-tsp
5168 (uri (cran-uri "TSP" version))
5171 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5172 (properties `((upstream-name . "TSP")))
5173 (build-system r-build-system)
5174 (propagated-inputs `(("r-foreach" ,r-foreach)))
5175 (home-page "https://cran.r-project.org/web/packages/TSP/")
5176 (synopsis "Traveling salesperson problem (TSP)")
5177 (description "This package provides basic infrastructure and some
5178 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5179 traveling salesman problem).")
5180 (license license:gpl3)))
5182 (define-public r-qap
5189 (uri (cran-uri "qap" version))
5192 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5193 (build-system r-build-system)
5194 (native-inputs `(("gfortran" ,gfortran)))
5195 (home-page "https://cran.r-project.org/web/packages/qap/")
5196 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5197 (description "This package implements heuristics for the @dfn{quadratic
5198 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5200 (license license:gpl3)))
5202 (define-public r-gclus
5209 (uri (cran-uri "gclus" version))
5212 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5213 (build-system r-build-system)
5214 (propagated-inputs `(("r-cluster" ,r-cluster)))
5215 (home-page "https://cran.r-project.org/web/packages/gclus/")
5216 (synopsis "Clustering graphics")
5217 (description "This package orders panels in scatterplot matrices and
5218 parallel coordinate displays by some merit index. It contains various indices
5219 of merit, ordering functions, and enhanced versions of @code{pairs} and
5220 @code{parcoord} which color panels according to their merit level.")
5221 (license license:gpl2+)))
5223 (define-public r-webshot
5230 (uri (cran-uri "webshot" version))
5233 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5234 (build-system r-build-system)
5236 `(("r-callr" ,r-callr)
5237 ("r-jsonlite" ,r-jsonlite)
5238 ("r-magrittr" ,r-magrittr)))
5239 (home-page "https://github.com/wch/webshot/")
5240 (synopsis "Take screenshots of web pages")
5242 "Webshot makes it easy to take screenshots of web pages from within R.
5243 It can also run Shiny applications locally and take screenshots of the
5244 application; and it can render and screenshot static as well as interactive R
5245 Markdown documents.")
5246 (license license:gpl2)))
5248 (define-public r-seriation
5250 (name "r-seriation")
5255 (uri (cran-uri "seriation" version))
5258 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5259 (build-system r-build-system)
5261 `(("r-cluster" ,r-cluster)
5262 ("r-colorspace" ,r-colorspace)
5263 ("r-dendextend" ,r-dendextend)
5264 ("r-gclus" ,r-gclus)
5265 ("r-gplots" ,r-gplots)
5268 ("r-registry" ,r-registry)
5270 (native-inputs `(("gfortran" ,gfortran)))
5271 (home-page "https://s2.smu.edu/IDA/seriation/")
5272 (synopsis "Infrastructure for ordering objects using seriation")
5274 "This package provides infrastructure for seriation with an
5275 implementation of several seriation/sequencing techniques to reorder matrices,
5276 dissimilarity matrices, and dendrograms. It also provides (optimally)
5277 reordered heatmaps, color images and clustering visualizations like
5278 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5280 (license license:gpl3)))
5282 (define-public r-xfun
5289 (uri (cran-uri "xfun" version))
5291 (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y"))))
5292 (build-system r-build-system)
5293 ;; knitr itself depends on xfun
5296 `(("r-knitr" ,r-knitr)))
5297 (home-page "https://github.com/yihui/xfun")
5298 (synopsis "Miscellaneous functions")
5300 "This package provides miscellaneous functions commonly used in other
5301 packages maintained by Yihui Xie.")
5302 (license license:expat)))
5304 (define-public r-utf8
5311 (uri (cran-uri "utf8" version))
5314 "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk"))))
5315 (build-system r-build-system)
5317 `(("r-knitr" ,r-knitr)))
5318 (home-page "https://github.com/patperry/r-utf8")
5319 (synopsis "Unicode text processing")
5321 "This package provides tools to process and print UTF-8 encoded
5322 international text (Unicode). Input, validate, normalize, encode, format, and
5324 (license license:asl2.0)))
5326 (define-public r-zeallot
5333 (uri (cran-uri "zeallot" version))
5336 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5337 (build-system r-build-system)
5338 (home-page "https://github.com/nteetor/zeallot")
5339 (synopsis "Multiple, unpacking, and destructuring assignment")
5341 "This package provides a @code{%<-%} operator to perform multiple,
5342 unpacking, and destructuring assignment in R. The operator unpacks the
5343 right-hand side of an assignment into multiple values and assigns these values
5344 to variables on the left-hand side of the assignment.")
5345 (license license:expat)))
5347 (define-public r-vctrs
5354 (uri (cran-uri "vctrs" version))
5357 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5358 (build-system r-build-system)
5360 `(("r-digest" ,r-digest)
5361 ("r-ellipsis" ,r-ellipsis)
5363 ("r-rlang" ,r-rlang)))
5365 `(("r-knitr" ,r-knitr)))
5366 (home-page "https://github.com/r-lib/vctrs")
5367 (synopsis "Vector helpers")
5369 "There are three main goals to the @code{vctrs} package:
5372 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5373 @code{length()} and @code{class()}. These definitions are paired with a
5374 framework for type-coercion and size-recycling.
5375 @item To define type- and size-stability as desirable function properties, use
5376 them to analyse existing base function, and to propose better alternatives.
5377 This work has been particularly motivated by thinking about the ideal
5378 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5379 @item To provide a new @code{vctr} base class that makes it easy to create new
5380 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5381 a few new @code{vctrs} generics, making implementation considerably simpler
5384 (license license:gpl3)))
5386 (define-public r-pillar
5393 (uri (cran-uri "pillar" version))
5396 "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c"))))
5397 (build-system r-build-system)
5400 ("r-crayon" ,r-crayon)
5401 ("r-ellipsis" ,r-ellipsis)
5402 ("r-fansi" ,r-fansi)
5403 ("r-lifecycle" ,r-lifecycle)
5404 ("r-rlang" ,r-rlang)
5406 ("r-vctrs" ,r-vctrs)))
5408 `(("r-knitr" ,r-knitr)))
5409 (home-page "https://github.com/r-lib/pillar")
5410 (synopsis "Coloured formatting for columns")
5412 "This package provides a @code{pillar} generic designed for formatting
5413 columns of data using the full range of colours provided by modern
5415 (license license:gpl3)))
5417 (define-public r-uuid
5424 (uri (cran-uri "uuid" version))
5427 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5428 (build-system r-build-system)
5429 (home-page "https://www.rforge.net/uuid")
5430 (synopsis "Tools for generating and handling of UUIDs")
5432 "This package provides tools for generating and handling of
5433 @dfn{Universally Unique Identifiers} (UUIDs).")
5434 (license license:expat)))
5436 (define-public r-tinytex
5443 (uri (cran-uri "tinytex" version))
5446 "0dk6mpszwh1m65b0wfwjlcvpzywmasf6p31niqiq53wnd92my0gw"))))
5447 (build-system r-build-system)
5449 `(("r-xfun" ,r-xfun)))
5450 (home-page "https://github.com/yihui/tinytex")
5451 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5453 "This package provides helper functions to install and maintain the LaTeX
5454 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5455 easy-to-maintain version of TeX Live. This package also contains helper
5456 functions to compile LaTeX documents, and install missing LaTeX packages
5458 (license license:expat)))
5460 (define-public r-tinytest
5467 (uri (cran-uri "tinytest" version))
5470 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5471 (properties `((upstream-name . "tinytest")))
5472 (build-system r-build-system)
5473 (home-page "https://github.com/markvanderloo/tinytest")
5474 (synopsis "Lightweight unit testing framework")
5476 "This package provides a lightweight unit testing framework. Main
5480 @item install tests with the package;
5481 @item test results are treated as data that can be stored and manipulated;
5482 @item test files are R scripts interspersed with test commands, that can be
5484 @item fully automated build-install-test sequence for packages;
5485 @item skip tests when not run locally (e.g. on CRAN);
5486 @item flexible and configurable output printing;
5487 @item compare computed output with output stored with the package;
5488 @item run tests in parallel;
5489 @item extensible by other packages;
5490 @item report side effects.
5493 (license license:gpl3)))
5495 (define-public r-network
5502 (uri (cran-uri "network" version))
5505 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5506 (build-system r-build-system)
5508 `(("r-magrittr" ,r-magrittr)
5509 ("r-tibble" ,r-tibble)))
5510 (home-page "https://statnet.org/")
5511 (synopsis "Classes for relational data")
5513 "This package provides tools to create and modify network objects. The
5514 @code{network} class can represent a range of relational data types, and
5515 supports arbitrary vertex/edge/graph attributes.")
5516 (license license:gpl2+)))
5518 (define-public r-stabs
5525 (uri (cran-uri "stabs" version))
5528 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5529 (build-system r-build-system)
5531 `(("r-knitr" ,r-knitr)))
5532 (home-page "https://github.com/hofnerb/stabs")
5533 (synopsis "Stability selection with error control")
5535 "This package provides resampling procedures to assess the stability of
5536 selected variables with additional finite sample error control for
5537 high-dimensional variable selection procedures such as Lasso or boosting.
5538 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5539 complementary pairs stability selection with improved error bounds
5540 (Shah & Samworth, 2013) are implemented. The package can be combined with
5541 arbitrary user specified variable selection approaches.")
5542 (license license:gpl2)))
5544 (define-public r-rle
5551 (uri (cran-uri "rle" version))
5554 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5555 (properties `((upstream-name . "rle")))
5556 (build-system r-build-system)
5557 (home-page "https://cran.r-project.org/web/packages/rle/")
5558 (synopsis "Common functions for run-length encoded vectors")
5560 "This package provides common @code{base} and @code{stats} methods for
5561 @code{rle} objects, aiming to make it possible to treat them transparently as
5563 (license license:gpl3)))
5565 (define-public r-statnet-common
5567 (name "r-statnet-common")
5572 (uri (cran-uri "statnet.common" version))
5575 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5577 `((upstream-name . "statnet.common")))
5578 (build-system r-build-system)
5580 `(("r-coda" ,r-coda)
5582 (home-page "https://statnet.org")
5583 (synopsis "R scripts and utilities used by the Statnet software")
5584 (description "This package provides non-statistical utilities used by the
5585 software developed by the Statnet Project.")
5586 (license license:gpl3)))
5588 (define-public r-statcheck
5590 (name "r-statcheck")
5595 (uri (cran-uri "statcheck" version))
5598 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5599 (build-system r-build-system)
5601 `(("r-ggplot2" ,r-ggplot2)
5603 ("r-rmarkdown" ,r-rmarkdown)))
5604 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5605 (synopsis "Extract statistics from articles and recompute p-values")
5606 (description "This package can automatically extract statistical
5607 null-hypothesis significant testing (NHST) results from articles and recompute
5608 the p-values based on the reported test statistic and degrees of freedom to
5609 detect possible inconsistencies.")
5610 (license license:gpl2)))
5612 (define-public r-sna
5619 (uri (cran-uri "sna" version))
5622 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5623 (build-system r-build-system)
5625 `(("r-network" ,r-network)
5626 ("r-statnet-common" ,r-statnet-common)))
5627 (home-page "https://statnet.org")
5628 (synopsis "Tools for social network analysis")
5630 "This package provides a range of tools for social network analysis,
5631 including node and graph-level indices, structural distance and covariance
5632 methods, structural equivalence detection, network regression, random graph
5633 generation, and 2D/3D network visualization.")
5634 (license license:gpl2+)))
5636 (define-public r-tfisher
5643 (uri (cran-uri "TFisher" version))
5646 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5647 (properties `((upstream-name . "TFisher")))
5648 (build-system r-build-system)
5650 `(("r-matrix" ,r-matrix)
5651 ("r-mvtnorm" ,r-mvtnorm)
5653 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5654 (synopsis "Optimal thresholding Fisher's p-value combination method")
5656 "This package provides the @dfn{cumulative distribution function} (CDF),
5657 quantile, and statistical power calculator for a collection of thresholding
5658 Fisher's p-value combination methods, including Fisher's p-value combination
5659 method, truncated product method and, in particular, soft-thresholding
5660 Fisher's p-value combination method which is proven to be optimal in some
5661 context of signal detection. The p-value calculator for the omnibus version
5662 of these tests are also included.")
5663 (license license:gpl2)))
5665 (define-public r-ttr
5672 (uri (cran-uri "TTR" version))
5675 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5676 (properties `((upstream-name . "TTR")))
5677 (build-system r-build-system)
5679 `(("r-curl" ,r-curl)
5682 (home-page "https://github.com/joshuaulrich/TTR")
5683 (synopsis "Technical trading rules")
5685 "This package provides functions and data to construct technical trading
5687 (license license:gpl2)))
5689 (define-public r-leaps
5696 (uri (cran-uri "leaps" version))
5699 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5700 (build-system r-build-system)
5701 (native-inputs `(("gfortran" ,gfortran)))
5702 (home-page "https://cran.r-project.org/web/packages/leaps/")
5703 (synopsis "Regression subset selection")
5705 "This package provides tools for regression subset selection, including
5706 exhaustive search.")
5707 (license license:gpl2+)))
5709 (define-public r-splus2r
5716 (uri (cran-uri "splus2R" version))
5719 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5720 (properties `((upstream-name . "splus2R")))
5721 (build-system r-build-system)
5722 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5723 (synopsis "Supplemental S-PLUS functionality in R")
5725 "Currently there are many functions in S-PLUS that are missing in R. To
5726 facilitate the conversion of S-PLUS packages to R packages, this package
5727 provides some missing S-PLUS functionality in R.")
5728 (license license:gpl2)))
5730 (define-public r-ifultools
5732 (name "r-ifultools")
5737 (uri (cran-uri "ifultools" version))
5740 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5741 (build-system r-build-system)
5743 `(("r-mass" ,r-mass)
5744 ("r-splus2r" ,r-splus2r)))
5745 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5746 (synopsis "Insightful research tools")
5747 (description "This package provides C code used by the wmtsa, fractal, and
5749 (license license:gpl2)))
5751 (define-public r-sapa
5758 (uri (cran-uri "sapa" version))
5761 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5762 (build-system r-build-system)
5764 `(("r-ifultools" ,r-ifultools)
5765 ("r-splus2r" ,r-splus2r)))
5766 (home-page "https://cran.r-project.org/web/packages/sapa/")
5767 (synopsis "Spectral analysis for physical applications")
5768 (description "This package provides software for the book Spectral
5769 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5770 Cambridge University Press, 1993.")
5771 (license license:gpl2)))
5773 (define-public r-aggregation
5775 (name "r-aggregation")
5780 (uri (cran-uri "aggregation" version))
5783 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5784 (build-system r-build-system)
5785 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5786 (synopsis "Methods for p-value aggregation")
5788 "This package contains functionality for performing the following methods
5789 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5790 Fisher's method), and Sidak correction.")
5791 (license license:gpl3)))
5793 (define-public r-quantmod
5800 (uri (cran-uri "quantmod" version))
5803 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5804 (build-system r-build-system)
5806 `(("r-curl" ,r-curl)
5810 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5811 (synopsis "Quantitative financial modelling framework")
5812 (description "This package provides a quantitative financial modelling
5813 framework to allow users to specify, build, trade, and analyse quantitative
5814 financial trading strategies.")
5815 (license license:gpl3)))
5817 (define-public r-tseries
5824 (uri (cran-uri "tseries" version))
5827 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5828 (build-system r-build-system)
5830 `(("r-quadprog" ,r-quadprog)
5831 ("r-quantmod" ,r-quantmod)
5834 `(("gfortran" ,gfortran)))
5835 (home-page "https://cran.r-project.org/web/packages/tseries/")
5836 (synopsis "Time series analysis and computational finance")
5838 "This package provides functions relating to time series analysis and
5839 computational finance.")
5840 (license license:gpl2)))
5842 (define-public r-wmtsa
5849 (uri (cran-uri "wmtsa" version))
5852 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5853 (build-system r-build-system)
5855 `(("r-ifultools" ,r-ifultools)
5857 ("r-splus2r" ,r-splus2r)))
5858 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5859 (synopsis "Wavelet methods for time series analysis")
5861 "This package provides software to accompany the book \"Wavelet Methods
5862 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5863 University Press, 2000.")
5864 (license license:gpl2)))
5866 (define-public r-tsa
5873 (uri (cran-uri "TSA" version))
5876 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5877 (properties `((upstream-name . "TSA")))
5878 (build-system r-build-system)
5880 `(("r-leaps" ,r-leaps)
5881 ("r-locfit" ,r-locfit)
5883 ("r-tseries" ,r-tseries)))
5884 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5885 (synopsis "Time series analysis")
5887 "This package contains R functions and datasets detailed in the book
5888 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5889 Cryer and Kung-Sik Chan.")
5890 (license license:gpl2+)))
5892 (define-public r-extradistr
5894 (name "r-extradistr")
5899 (uri (cran-uri "extraDistr" version))
5902 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5903 (properties `((upstream-name . "extraDistr")))
5904 (build-system r-build-system)
5906 `(("r-rcpp" ,r-rcpp)))
5907 (home-page "https://github.com/twolodzko/extraDistr")
5908 (synopsis "Additional univariate and multivariate distributions")
5910 "This package implements density, distribution functions, quantile
5911 functions and random generation functions for a large number of univariate and
5912 multivariate distributions.")
5913 (license license:gpl2)))
5915 (define-public r-fractal
5922 (uri (cran-uri "fractal" version))
5925 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5926 (build-system r-build-system)
5928 `(("r-ifultools" ,r-ifultools)
5931 ("r-scatterplot3d" ,r-scatterplot3d)
5932 ("r-splus2r" ,r-splus2r)
5933 ("r-wmtsa" ,r-wmtsa)))
5934 (home-page "https://cran.r-project.org/web/packages/fractal/")
5935 (synopsis "Fractal time series modeling and analysis")
5937 "This package provides tools for stochastic fractal and deterministic
5938 chaotic time series analysis.")
5939 (license license:gpl2)))
5941 (define-public r-urca
5948 (uri (cran-uri "urca" version))
5951 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5952 (build-system r-build-system)
5953 (propagated-inputs `(("r-nlme" ,r-nlme)))
5954 (native-inputs `(("gfortran" ,gfortran)))
5955 (home-page "https://cran.r-project.org/web/packages/urca/")
5956 (synopsis "Unit root and cointegration tests for time series data")
5958 "This package provides unit root and cointegration tests encountered in
5959 applied econometric analysis.")
5960 (license license:gpl2+)))
5962 (define-public r-cubature
5969 (uri (cran-uri "cubature" version))
5972 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5973 (build-system r-build-system)
5975 `(("r-rcpp" ,r-rcpp)))
5977 `(("r-knitr" ,r-knitr)))
5978 (home-page "https://github.com/bnaras/cubature")
5979 (synopsis "Adaptive multivariate integration over hypercubes")
5981 "This package is an R wrapper around the cubature C library for adaptive
5982 multivariate integration over hypercubes. This version provides both
5983 @code{hcubature} and @code{pcubature} routines in addition to a vector
5985 ;; The included cubature C library is released under GPLv2+, but the
5986 ;; wrapper declares the license to be GPLv3+.
5987 (license (list license:gpl2+ license:gpl3+))))
5989 (define-public r-trend
5996 (uri (cran-uri "trend" version))
5999 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
6000 (build-system r-build-system)
6002 `(("r-extradistr" ,r-extradistr)))
6004 `(("gfortran" ,gfortran)))
6005 (home-page "https://cran.r-project.org/web/packages/trend/")
6006 (synopsis "Non-parametric trend tests and change-point detection")
6008 "The analysis of environmental data often requires the detection of
6009 trends and change-points. This package includes tests for trend
6010 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6011 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6012 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6013 correlation trend test), change-point detection (Lanzante's test procedures,
6014 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6015 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6016 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6017 sample Robust Rank-Order Distributional Test.")
6018 (license license:gpl3)))
6020 (define-public r-expm
6027 (uri (cran-uri "expm" version))
6030 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6031 (build-system r-build-system)
6032 (propagated-inputs `(("r-matrix" ,r-matrix)))
6033 (native-inputs `(("gfortran" ,gfortran)))
6034 (home-page "https://r-forge.r-project.org/projects/expm/")
6035 (synopsis "Tools for matrix exponentials and related quantities")
6037 "This package provides tools for the computation of the matrix
6038 exponential, logarithm, square root, and related quantities.")
6039 (license license:gpl2+)))
6041 (define-public r-complexplus
6043 (name "r-complexplus")
6048 (uri (cran-uri "complexplus" version))
6051 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6052 (build-system r-build-system)
6054 `(("r-expm" ,r-expm)
6055 ("r-matrix" ,r-matrix)))
6056 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6057 (synopsis "Functions of complex or real variables")
6059 "This package extends several functions to the complex domain, including
6060 the matrix exponential and logarithm, and the determinant.")
6061 (license license:gpl2)))
6063 (define-public r-phontools
6065 (name "r-phontools")
6070 (uri (cran-uri "phonTools" version))
6073 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6074 (properties `((upstream-name . "phonTools")))
6075 (build-system r-build-system)
6076 (home-page "http://www.santiagobarreda.com/rscripts.html")
6077 (synopsis "Tools for phonetic and acoustic analyses")
6079 "This package contains tools for the organization, display, and analysis
6080 of the sorts of data frequently encountered in phonetics research and
6081 experimentation, including the easy creation of IPA vowel plots, and the
6082 creation and manipulation of WAVE audio files.")
6083 (license license:bsd-2)))
6092 (uri (cran-uri "np" version))
6095 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6096 (build-system r-build-system)
6098 `(("r-boot" ,r-boot)
6099 ("r-cubature" ,r-cubature)
6100 ("r-quadprog" ,r-quadprog)
6101 ("r-quantreg" ,r-quantreg)))
6102 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6103 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6104 (description "This package provides non-parametric (and semi-parametric)
6105 kernel methods that seamlessly handle a mix of continuous, unordered, and
6106 ordered factor data types.")
6107 ;; Any version of the GPL.
6108 (license license:gpl3+)))
6110 (define-public r-powerplus
6112 (name "r-powerplus")
6117 (uri (cran-uri "powerplus" version))
6120 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6121 (build-system r-build-system)
6123 `(("r-complexplus" ,r-complexplus)
6126 ("r-matrix" ,r-matrix)
6127 ("r-phontools" ,r-phontools)))
6128 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6129 (synopsis "Exponentiation operations")
6131 "This package provides tools for the computation of matrix and scalar
6133 (license license:gpl2)))
6135 (define-public r-egg
6142 (uri (cran-uri "egg" version))
6145 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6146 (properties `((upstream-name . "egg")))
6147 (build-system r-build-system)
6149 `(("r-ggplot2" ,r-ggplot2)
6150 ("r-gridextra" ,r-gridextra)
6151 ("r-gtable" ,r-gtable)))
6152 (home-page "https://cran.r-project.org/web/packages/egg")
6153 (synopsis "Extensions for ggplot2")
6155 "This package provides miscellaneous functions to help customize ggplot2
6156 objects. High-level functions are provided to post-process ggplot2 layouts
6157 and allow alignment between plot panels, as well as setting panel sizes to
6158 fixed values. Other functions include a custom @code{geom}, and helper
6159 functions to enforce symmetric scales or add tags to facetted plots.")
6160 (license license:gpl3)))
6162 (define-public r-heatmaply
6164 (name "r-heatmaply")
6169 (uri (cran-uri "heatmaply" version))
6172 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6173 (build-system r-build-system)
6175 `(("r-assertthat" ,r-assertthat)
6176 ("r-colorspace" ,r-colorspace)
6177 ("r-dendextend" ,r-dendextend)
6179 ("r-ggplot2" ,r-ggplot2)
6180 ("r-htmlwidgets" ,r-htmlwidgets)
6181 ("r-magrittr" ,r-magrittr)
6182 ("r-plotly" ,r-plotly)
6183 ("r-rcolorbrewer" ,r-rcolorbrewer)
6184 ("r-reshape2" ,r-reshape2)
6185 ("r-scales" ,r-scales)
6186 ("r-seriation" ,r-seriation)
6187 ("r-viridis" ,r-viridis)
6188 ("r-webshot" ,r-webshot)))
6190 `(("r-knitr" ,r-knitr)))
6191 (home-page "https://cran.r-project.org/package=heatmaply")
6192 (synopsis "Interactive cluster heat maps using plotly")
6194 "This package enables you to create interactive cluster heatmaps that can
6195 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6196 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6197 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6198 a popular graphical method for visualizing high-dimensional data, in which a
6199 table of numbers is encoded as a grid of colored cells. The rows and columns
6200 of the matrix are ordered to highlight patterns and are often accompanied by
6202 ;; Either version of the license.
6203 (license (list license:gpl2 license:gpl3))))
6212 (uri (cran-uri "h5" version))
6215 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6216 (build-system r-build-system)
6221 `(("which" ,which)))
6223 `(("r-rcpp" ,r-rcpp)))
6224 (home-page "https://github.com/mannau/h5")
6225 (synopsis "Interface to the HDF5 Library")
6227 "This package provides an S4 interface to the HDF5 library supporting
6228 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6229 binary files in a language independent format. The HDF5 format can therefore
6230 be used as an alternative to R's save/load mechanism. Since h5 is able to
6231 access only subsets of stored data it can also handle data sets which do not
6233 (license license:bsd-2)))
6235 (define-public r-cgdsr
6242 (uri (cran-uri "cgdsr" version))
6245 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6246 (build-system r-build-system)
6248 `(("r-httr" ,r-httr)
6249 ("r-r-methodss3" ,r-r-methodss3)
6250 ("r-r-oo" ,r-r-oo)))
6251 (home-page "https://github.com/cBioPortal/cgdsr")
6252 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6254 "This package provides a basic set of R functions for querying the Cancer
6255 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6256 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6257 (license license:lgpl3)))
6259 (define-public r-import
6266 (uri (cran-uri "import" version))
6269 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6270 (build-system r-build-system)
6272 `(("r-knitr" ,r-knitr)))
6273 (home-page "https://github.com/smbache/import")
6274 (synopsis "Import mechanism for R")
6276 "This is an alternative mechanism for importing objects from packages.
6277 The syntax allows for importing multiple objects from a package with a single
6278 command in an expressive way. The import package bridges some of the gap
6279 between using @code{library} (or @code{require}) and direct (single-object)
6280 imports. Furthermore the imported objects are not placed in the current
6281 environment. It is also possible to import objects from stand-alone @code{.R}
6283 (license license:expat)))
6285 (define-public r-shinyace
6292 (uri (cran-uri "shinyAce" version))
6295 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6296 (properties `((upstream-name . "shinyAce")))
6297 (build-system r-build-system)
6299 `(("r-shiny" ,r-shiny)
6300 ("r-jsonlite" ,r-jsonlite)))
6301 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6302 (synopsis "Ace editor bindings for Shiny")
6304 "This package provides Ace editor bindings to enable a rich text editing
6305 environment within Shiny.")
6306 (license license:expat)))
6308 (define-public r-randomizr
6310 (name "r-randomizr")
6315 (uri (cran-uri "randomizr" version))
6318 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6319 (properties `((upstream-name . "randomizr")))
6320 (build-system r-build-system)
6322 `(("r-knitr" ,r-knitr)))
6323 (home-page "https://declaredesign.org/r/randomizr/")
6324 (synopsis "Tools for common forms of random assignment and sampling")
6326 "This package provides tools for generating random assignments for common
6327 experimental designs and random samples for common sampling designs.")
6328 (license license:expat)))
6330 (define-public r-base64url
6332 (name "r-base64url")
6337 (uri (cran-uri "base64url" version))
6340 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6341 (build-system r-build-system)
6343 `(("r-backports" ,r-backports)))
6344 (home-page "https://github.com/mllg/base64url")
6345 (synopsis "Fast and URL-safe base64 encoder and decoder")
6347 "This package provides a URL-safe base64 encoder and decoder. In
6348 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6349 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6350 encoder does not fill the string with trailing @code{=}. The resulting
6351 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6352 and thus are safe to use in URLs or for file names. The package also comes
6353 with a simple base32 encoder/decoder suited for case insensitive file
6355 (license license:gpl3)))
6357 (define-public r-radiant-data
6359 (name "r-radiant-data")
6364 (uri (cran-uri "radiant.data" version))
6367 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6368 (modules '((guix build utils)))
6371 ;; Delete files that are under CC-NC-SA.
6372 (delete-file-recursively "inst/app/tools/help")
6374 (properties `((upstream-name . "radiant.data")))
6375 (build-system r-build-system)
6377 `(("r-base64enc" ,r-base64enc)
6378 ("r-broom" ,r-broom)
6381 ("r-dplyr" ,r-dplyr)
6384 ("r-ggplot2" ,r-ggplot2)
6385 ("r-import" ,r-import)
6386 ("r-jsonlite" ,r-jsonlite)
6387 ("r-knitr" ,r-knitr)
6388 ("r-lubridate" ,r-lubridate)
6389 ("r-magrittr" ,r-magrittr)
6390 ("r-markdown" ,r-markdown)
6392 ("r-patchwork" ,r-patchwork)
6393 ("r-plotly" ,r-plotly)
6394 ("r-psych" ,r-psych)
6395 ("r-randomizr" ,r-randomizr)
6396 ("r-readr" ,r-readr)
6397 ("r-readxl" ,r-readxl)
6398 ("r-rlang" ,r-rlang)
6399 ("r-rmarkdown" ,r-rmarkdown)
6400 ("r-rstudioapi" ,r-rstudioapi)
6401 ("r-scales" ,r-scales)
6402 ("r-shiny" ,r-shiny)
6403 ("r-shinyfiles" ,r-shinyfiles)
6404 ("r-shinyace" ,r-shinyace)
6405 ("r-stringi" ,r-stringi)
6406 ("r-tibble" ,r-tibble)
6407 ("r-tidyr" ,r-tidyr)
6408 ("r-writexl" ,r-writexl)))
6409 (home-page "https://github.com/radiant-rstats/radiant.data")
6410 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6412 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6413 visualizing, summarizing, transforming, and combining data. It also contains
6414 functionality to generate reproducible reports of the analyses conducted in
6416 (license license:agpl3)))
6418 (define-public r-algdesign
6420 (name "r-algdesign")
6425 (uri (cran-uri "AlgDesign" version))
6427 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6428 (properties `((upstream-name . "AlgDesign")))
6429 (build-system r-build-system)
6430 (home-page "https://github.com/jvbraun/AlgDesign")
6431 (synopsis "Algorithmic experimental design")
6433 "This package provides tools to calculate exact and approximate theory
6434 experimental designs for D, A, and I criteria. Very large designs may be
6435 created. Experimental designs may be blocked or blocked designs created from
6436 a candidate list, using several criteria. The blocking can be done when whole
6437 and within plot factors interact.")
6438 (license license:gpl2+)))
6440 (define-public r-signal
6447 (uri (cran-uri "signal" version))
6450 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6451 (build-system r-build-system)
6452 (propagated-inputs `(("r-mass" ,r-mass)))
6453 (native-inputs `(("gfortran" ,gfortran)))
6454 (home-page "https://cran.r-project.org/web/packages/signal/")
6455 (synopsis "Signal processing")
6457 "This package provides a set of signal processing functions originally
6458 written for Matlab and GNU Octave. It includes filter generation utilities,
6459 filtering functions, resampling routines, and visualization of filter models.
6460 It also includes interpolation functions.")
6461 (license license:gpl2)))
6463 (define-public r-gsubfn
6470 (uri (cran-uri "gsubfn" version))
6473 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6474 (build-system r-build-system)
6475 (propagated-inputs `(("r-proto" ,r-proto)))
6476 (home-page "https://code.google.com/archive/p/gsubfn/")
6477 (synopsis "Utilities for strings and function arguments.")
6479 "This package provides @code{gsubfn} which is like @code{gsub} but can
6480 take a replacement function or certain other objects instead of the
6481 replacement string. Matches and back references are input to the replacement
6482 function and replaced by the function output. @code{gsubfn} can be used to
6483 split strings based on content rather than delimiters and for quasi-perl-style
6484 string interpolation. The package also has facilities for translating
6485 formulas to functions and allowing such formulas in function calls instead of
6487 (license license:gpl2+)))
6489 (define-public r-sqldf
6496 (uri (cran-uri "sqldf" version))
6499 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6500 (build-system r-build-system)
6502 `(("r-chron" ,r-chron)
6504 ("r-gsubfn" ,r-gsubfn)
6505 ("r-proto" ,r-proto)
6506 ("r-rsqlite" ,r-rsqlite)))
6507 (home-page "https://github.com/ggrothendieck/sqldf")
6508 (synopsis "Manipulate R data frames using SQL")
6510 "The @code{sqldf} function is typically passed a single argument which is
6511 an SQL select statement where the table names are ordinary R data frame names.
6512 @code{sqldf} transparently sets up a database, imports the data frames into
6513 that database, performs the SQL statement and returns the result using a
6514 heuristic to determine which class to assign to each column of the returned
6515 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6516 used to read filtered files into R even if the original files are larger than
6517 R itself can handle.")
6518 (license license:gpl2)))
6520 (define-public r-abind
6527 (uri (cran-uri "abind" version))
6530 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6531 (build-system r-build-system)
6532 (home-page "https://cran.r-project.org/web/packages/abind/")
6533 (synopsis "Combine multidimensional arrays")
6535 "This package provides tools to combine multidimensional arrays into a
6536 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6537 works with vectors, matrices, and higher-dimensional arrays. It also provides
6538 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6539 extracting and replacing data in arrays.")
6540 (license license:lgpl2.0+)))
6542 (define-public r-prroc
6549 (uri (cran-uri "PRROC" version))
6552 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6553 (properties `((upstream-name . "PRROC")))
6554 (build-system r-build-system)
6555 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6556 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6558 "This package computes the areas under the @dfn{precision-recall} (PR)
6559 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6560 contrast to other implementations, the interpolation between points of the PR
6561 curve is done by a non-linear piecewise function. In addition to the areas
6562 under the curves, the curves themselves can also be computed and plotted by a
6563 specific S3-method.")
6564 (license license:gpl3)))
6566 (define-public r-vim
6573 (uri (cran-uri "VIM" version))
6576 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6577 (properties `((upstream-name . "VIM")))
6578 (build-system r-build-system)
6581 ("r-colorspace" ,r-colorspace)
6582 ("r-data-table" ,r-data-table)
6583 ("r-e1071" ,r-e1071)
6584 ("r-laeken" ,r-laeken)
6585 ("r-magrittr" ,r-magrittr)
6588 ("r-ranger" ,r-ranger)
6590 ("r-robustbase" ,r-robustbase)
6594 `(("r-knitr" ,r-knitr)))
6595 (home-page "https://github.com/alexkowa/VIM")
6596 (synopsis "Visualization and imputation of missing values")
6598 "This package provides tools for the visualization of missing and/or
6599 imputed values are introduced, which can be used for exploring the data and
6600 the structure of the missing and/or imputed values. Depending on this
6601 structure of the missing values, the corresponding methods may help to
6602 identify the mechanism generating the missing values and explore the
6603 data including missing values. In addition, the quality of imputation can be
6604 visually explored using various univariate, bivariate, multiple and
6605 multivariate plot methods.")
6606 (license license:gpl2+)))
6608 (define-public r-fnn
6615 (uri (cran-uri "FNN" version))
6618 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6619 (properties `((upstream-name . "FNN")))
6620 (build-system r-build-system)
6621 (home-page "https://cran.r-project.org/web/packages/FNN")
6622 (synopsis "Fast nearest neighbor search algorithms and applications")
6624 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6625 search algorithms. Related applications including KNN classification,
6626 regression and information measures are implemented.")
6627 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6628 ;; later can be used.
6629 (license license:gpl2+)))
6631 (define-public r-smoother
6638 (uri (cran-uri "smoother" version))
6641 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6642 (build-system r-build-system)
6644 `(("r-ttr" ,r-ttr)))
6645 (home-page "https://cran.r-project.org/web/packages/smoother")
6646 (synopsis "Functions relating to the smoothing of numerical data")
6648 "This package provides a collection of methods for smoothing numerical
6649 data, commencing with a port of the Matlab gaussian window smoothing function.
6650 In addition, several functions typically used in smoothing of financial data
6652 (license license:gpl2)))
6654 (define-public r-riverplot
6656 (name "r-riverplot")
6661 (uri (cran-uri "riverplot" version))
6664 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6665 (build-system r-build-system)
6667 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6669 `(("r-knitr" ,r-knitr)))
6670 (home-page "https://logfc.wordpress.com")
6671 (synopsis "Sankey or ribbon plots")
6673 "Sankey plots are a type of diagram that is convenient to illustrate how
6674 flow of information, resources etc. separates and joins, much like observing
6675 how rivers split and merge. For example, they can be used to compare
6676 different clusterings. This package provides an implementation of Sankey
6678 (license license:gpl2+)))
6680 (define-public r-dyn
6687 (uri (cran-uri "dyn" version))
6690 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6691 (build-system r-build-system)
6693 `(("r-zoo" ,r-zoo)))
6694 (home-page "https://cran.r-project.org/web/packages/dyn")
6695 (synopsis "Time series regression")
6697 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6698 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6699 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6700 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6701 @code{randomForest::randomForest()} and other regression functions, allowing
6702 those functions to be used with time series including specifications that may
6703 contain lags, diffs and missing values.")
6705 (license license:gpl2+)))
6707 (define-public r-catdap
6714 (uri (cran-uri "catdap" version))
6717 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6718 (build-system r-build-system)
6720 `(("gfortran" ,gfortran)))
6721 (home-page "https://cran.r-project.org/web/packages/catdap/")
6722 (synopsis "Tools for categorical data analysis")
6724 "This package provides functions for analyzing multivariate data.
6725 Dependencies of the distribution of the specified variable (response
6726 variable) to other variables (explanatory variables) are derived and
6727 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6728 (license license:gpl2+)))
6730 (define-public r-arules
6737 (uri (cran-uri "arules" version))
6740 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6741 (build-system r-build-system)
6743 `(("r-matrix" ,r-matrix)))
6744 (home-page "https://github.com/mhahsler/arules")
6745 (synopsis "Mining association rules and frequent itemsets")
6747 "This package provides an infrastructure for representing, manipulating
6748 and analyzing transaction data and patterns (frequent itemsets and association rules).
6749 It also provides C implementations of the association mining algorithms Apriori
6751 (license license:gpl3)))
6753 (define-public r-parsedate
6755 (name "r-parsedate")
6760 (uri (cran-uri "parsedate" version))
6763 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6764 (build-system r-build-system)
6766 `(("r-rematch2" ,r-rematch2)))
6767 (home-page "https://github.com/gaborcsardi/parsedate")
6769 "Recognize and parse dates in various formats")
6771 "This package provides three functions for dealing with dates:
6772 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6773 time formats, @code{parse_date} parses dates in unspecified formats,
6774 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6775 (license license:gpl2)))
6777 (define-public r-abc-data
6784 (uri (cran-uri "abc.data" version))
6787 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6788 (properties `((upstream-name . "abc.data")))
6789 (build-system r-build-system)
6790 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6791 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6793 "This package contains data which are used by functions of the abc
6794 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6795 algorithms for performing parameter estimation, model selection, and
6797 (license license:gpl3+)))
6799 (define-public r-abc
6806 (uri (cran-uri "abc" version))
6809 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6810 (build-system r-build-system)
6812 `(("r-abc-data" ,r-abc-data)
6813 ("r-locfit" ,r-locfit)
6816 ("r-quantreg" ,r-quantreg)))
6817 (home-page "https://cran.r-project.org/web/packages/abc/")
6818 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6820 "This package implements several @dfn{Approximate Bayesian
6821 Computation} (ABC) algorithms for performing parameter estimation, model
6822 selection, and goodness-of-fit. Cross-validation tools are also available for
6823 measuring the accuracy of ABC estimates, and to calculate the
6824 misclassification probabilities of different models.")
6825 (license license:gpl3+)))
6827 (define-public r-zip
6834 (uri (cran-uri "zip" version))
6837 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6838 (build-system r-build-system)
6839 (home-page "https://github.com/gaborcsardi/zip")
6840 (synopsis "Cross-platform Zip compression")
6842 "This package provides a cross-platform Zip compression library for R.
6843 It is a replacement for the @code{zip} function, that does not require any
6844 additional external tools on any platform.")
6845 (license license:cc0)))
6847 (define-public r-openxlsx
6854 (uri (cran-uri "openxlsx" version))
6857 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6858 (build-system r-build-system)
6860 `(("r-rcpp" ,r-rcpp)
6861 ("r-stringi" ,r-stringi)
6864 `(("r-knitr" ,r-knitr)))
6865 (home-page "https://github.com/awalker89/openxlsx")
6866 (synopsis "Read, write and edit XLSX files")
6868 "This package simplifies the creation of Excel @code{.xlsx} files by
6869 providing a high level interface to writing, styling and editing worksheets.
6870 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6871 and @code{XLConnect} packages with the added benefit of removing the
6872 dependency on Java.")
6873 (license license:gpl3)))
6875 (define-public r-rio
6882 (uri (cran-uri "rio" version))
6885 "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d"))))
6886 (build-system r-build-system)
6888 `(("r-curl" ,r-curl)
6889 ("r-data-table" ,r-data-table)
6890 ("r-foreign" ,r-foreign)
6891 ("r-haven" ,r-haven)
6892 ("r-openxlsx" ,r-openxlsx)
6893 ("r-readxl" ,r-readxl)
6894 ("r-tibble" ,r-tibble)))
6896 `(("r-knitr" ,r-knitr)))
6897 (home-page "https://github.com/leeper/rio")
6898 (synopsis "Swiss-army knife for data I/O")
6900 "This package provides streamlined data import and export infrastructure
6901 by making assumptions that the user is probably willing to make: @code{import}
6902 and @code{export} determine the data structure from the file extension,
6903 reasonable defaults are used for data import and export (e.g.,
6904 @code{stringsAsFactors=FALSE}), web-based import is natively
6905 supported (including from SSL/HTTPS), compressed files can be read directly
6906 without explicit decompression, and fast import packages are used where
6907 appropriate. An additional convenience function, @code{convert}, provides a
6908 simple method for converting between file types.")
6909 (license license:gpl2)))
6911 (define-public r-maptools
6918 (uri (cran-uri "maptools" version))
6921 "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l"))))
6922 (build-system r-build-system)
6924 `(("r-foreign" ,r-foreign)
6925 ("r-lattice" ,r-lattice)
6927 (home-page "https://r-forge.r-project.org/projects/maptools/")
6928 (synopsis "Tools for reading and handling spatial objects")
6930 "This package provides a set of tools for manipulating and reading
6931 geographic data, in particular ESRI Shapefiles. It includes binary access to
6932 GSHHG shoreline files. The package also provides interface wrappers for
6933 exchanging spatial objects with other R packages.")
6934 ;; The C source files from shapelib are released under the Expat license.
6935 ;; The R code is released under GPL version 2 or later.
6936 (license (list license:gpl2+
6939 (define-public r-later
6946 (uri (cran-uri "later" version))
6949 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6950 (build-system r-build-system)
6954 ("r-rlang" ,r-rlang)))
6956 `(("r-knitr" ,r-knitr)))
6957 (home-page "https://github.com/r-lib/later")
6958 (synopsis "Utilities for delaying function execution")
6960 "This package provides tools to execute arbitrary R or C functions some
6961 time after the current time, after the R execution stack has emptied.")
6962 (license license:gpl2+)))
6964 (define-public r-promises
6971 (uri (cran-uri "promises" version))
6974 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
6975 (build-system r-build-system)
6977 `(("r-later" ,r-later)
6978 ("r-magrittr" ,r-magrittr)
6981 ("r-rlang" ,r-rlang)))
6983 `(("r-knitr" ,r-knitr)))
6984 (home-page "https://rstudio.github.io/promises")
6985 (synopsis "Abstractions for promise-based asynchronous programming")
6987 "This package provides fundamental abstractions for doing asynchronous
6988 programming in R using promises. Asynchronous programming is useful for
6989 allowing a single R process to orchestrate multiple tasks in the background
6990 while also attending to something else. Semantics are similar to JavaScript
6991 promises, but with a syntax that is idiomatic R.")
6992 (license license:expat)))
6994 (define-public r-dosnow
7001 (uri (cran-uri "doSNOW" version))
7004 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
7005 (properties `((upstream-name . "doSNOW")))
7006 (build-system r-build-system)
7008 `(("r-foreach" ,r-foreach)
7009 ("r-iterators" ,r-iterators)
7010 ("r-snow" ,r-snow)))
7011 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7012 (synopsis "Foreach parallel adaptor for the snow package")
7014 "This package provides a parallel backend for the @code{%dopar%} function
7015 using the @code{snow} package.")
7016 (license license:gpl2)))
7018 (define-public r-fst
7025 (uri (cran-uri "fst" version))
7028 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7029 (properties `((upstream-name . "fst")))
7030 (build-system r-build-system)
7031 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7032 (home-page "http://www.fstpackage.org")
7033 (synopsis "Fast serialization of data frames")
7035 "The fst package for R provides a fast, easy and flexible way to
7036 serialize data frames. With access speeds of multiple GB/s, fst is
7037 specifically designed to unlock the potential of high speed solid state disks.
7038 Data frames stored in the fst format have full random access, both in column
7039 and rows. The fst format allows for random access of stored data and
7040 compression with the LZ4 and ZSTD compressors.")
7041 (license license:agpl3)))
7043 (define-public r-snowfall
7046 (version "1.84-6.1")
7049 (uri (cran-uri "snowfall" version))
7051 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7052 (build-system r-build-system)
7054 `(("r-snow" ,r-snow)))
7055 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7056 (synopsis "Easier cluster computing")
7057 (description "This package is a usability wrapper around snow for easier
7058 development of parallel R programs. This package offers e.g. extended error
7059 checks, and additional functions. All functions work in sequential mode, too,
7060 if no cluster is present or wished. The package is also designed as connector
7061 to the cluster management tool @code{sfCluster}, but can also used without
7063 (license license:gpl2+)))
7065 (define-public r-rgexf
7072 (uri (cran-uri "rgexf" version))
7075 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7078 ;; Delete minified JavaScript files
7079 (for-each delete-file
7080 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7081 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7082 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7084 (properties `((upstream-name . "rgexf")))
7085 (build-system r-build-system)
7087 `(#:modules ((guix build utils)
7088 (guix build r-build-system)
7092 (modify-phases %standard-phases
7093 (add-after 'unpack 'process-javascript
7094 (lambda* (#:key inputs #:allow-other-keys)
7095 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7096 (with-directory-excursion "inst/gexf-js/js/"
7100 `((,(assoc-ref inputs "js-jquery")
7101 "jquery-2.0.2.min.js")
7102 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7103 "jquery-ui-1.10.3.custom.min.js")
7104 (,(assoc-ref inputs "js-jquery-mousewheel")
7105 "jquery.mousewheel.min.js"))))
7106 (lambda (sources targets)
7107 (for-each (lambda (source target)
7108 (format #true "Processing ~a --> ~a~%"
7110 (invoke "esbuild" source "--minify"
7111 (string-append "--outfile=" target)))
7115 `(("r-igraph" ,r-igraph)
7116 ("r-servr" ,r-servr)
7119 `(("r-knitr" ,r-knitr)
7120 ("esbuild" ,esbuild)
7125 (uri "https://code.jquery.com/jquery-2.0.2.js")
7128 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7132 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7135 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7136 ("js-jquery-mousewheel"
7139 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7140 3.0.6/jquery.mousewheel.js")
7143 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7144 (home-page "https://gvegayon.github.io/rgexf")
7145 (synopsis "Build, import and export GEXF graph files")
7147 "Create, read and write GEXF (Graph Exchange XML Format) graph
7148 files (used in Gephi and others). It allows the user to easily build/read
7149 graph files including attributes, GEXF visual attributes (such as color, size,
7150 and position), network dynamics (for both edges and nodes) and edge weighting.
7151 Users can build/handle graphs element-by-element or massively through
7152 data-frames, visualize the graph on a web browser through gexf-js (a
7153 JavaScript library) and interact with the igraph package.")
7154 (license license:expat)))
7156 (define-public r-data-tree
7158 (name "r-data-tree")
7163 (uri (cran-uri "data.tree" version))
7166 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7167 (properties `((upstream-name . "data.tree")))
7168 (build-system r-build-system)
7171 ("r-stringi" ,r-stringi)))
7173 `(("r-knitr" ,r-knitr)))
7174 (home-page "https://github.com/gluc/data.tree")
7175 (synopsis "General purpose hierarchical data structure")
7177 "Create tree structures from hierarchical data, and traverse the tree in
7178 various orders. Aggregate, cumulate, print, plot, convert to and from
7179 data.frame and more. This is useful for decision trees, machine learning,
7180 finance, conversion from and to JSON, and many other applications.")
7181 (license license:gpl2+)))
7183 (define-public r-collapsibletree
7185 (name "r-collapsibletree")
7190 (uri (cran-uri "collapsibleTree" version))
7193 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7196 ;; Delete minified JavaScript file
7197 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7200 `((upstream-name . "collapsibleTree")))
7201 (build-system r-build-system)
7204 (modify-phases %standard-phases
7205 (add-after 'unpack 'process-javascript
7206 (lambda* (#:key inputs #:allow-other-keys)
7207 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7208 (let ((source (assoc-ref inputs "d3.v4.js"))
7209 (target "d3.min.js"))
7210 (format #t "Processing ~a --> ~a~%"
7212 (invoke "esbuild" source "--minify"
7213 (string-append "--outfile=" target)))))))))
7215 `(("r-data-tree" ,r-data-tree)
7216 ("r-htmlwidgets" ,r-htmlwidgets)))
7218 `(("esbuild" ,esbuild)
7222 (uri "https://d3js.org/d3.v4.js")
7225 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7226 (home-page "https://github.com/AdeelK93/collapsibleTree")
7227 (synopsis "Interactive collapsible tree diagrams using D3.js")
7229 "This is a package for interactive Reingold-Tilford tree diagrams created
7230 using D3.js, where every node can be expanded and collapsed by clicking on it.
7231 Tooltips and color gradients can be mapped to nodes using a numeric column in
7232 the source data frame.")
7233 (license license:gpl3+)))
7235 (define-public r-rappdirs
7242 (uri (cran-uri "rappdirs" version))
7245 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7246 (build-system r-build-system)
7247 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7248 (synopsis "Determine where to save data, caches, and logs")
7250 "This package provides an easy way to determine which directories on the
7251 user's computer should be used to save data, caches and logs. It is a port of
7252 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7253 (license license:expat)))
7255 (define-public r-rastervis
7257 (name "r-rastervis")
7262 (uri (cran-uri "rasterVis" version))
7265 "0m7fjd53apxim0d0rjnyzc28vmfcg4spcrn0zbnk8llillxji1hi"))))
7266 (properties `((upstream-name . "rasterVis")))
7267 (build-system r-build-system)
7269 `(("r-hexbin" ,r-hexbin)
7270 ("r-lattice" ,r-lattice)
7271 ("r-latticeextra" ,r-latticeextra)
7272 ("r-raster" ,r-raster)
7273 ("r-rcolorbrewer" ,r-rcolorbrewer)
7275 ("r-terra" ,r-terra)
7276 ("r-viridislite" ,r-viridislite)
7278 (home-page "https://oscarperpinan.github.io/rastervis/")
7279 (synopsis "Visualization methods for raster data")
7281 "This package provides methods for enhanced visualization and interaction
7282 with raster data. It implements visualization methods for quantitative data
7283 and categorical data, both for univariate and multivariate rasters. It also
7284 provides methods to display spatiotemporal rasters, and vector fields.")
7285 (license license:gpl3)))
7287 (define-public r-rentrez
7294 (uri (cran-uri "rentrez" version))
7297 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7298 (properties `((upstream-name . "rentrez")))
7299 (build-system r-build-system)
7301 `(("r-httr" ,r-httr)
7302 ("r-jsonlite" ,r-jsonlite)
7305 `(("r-knitr" ,r-knitr)))
7306 (home-page "https://docs.ropensci.org/rentrez/")
7307 (synopsis "Entrez in R")
7309 "This package provides an R interface to the NCBI's EUtils API,
7310 allowing users to search databases like GenBank PubMed, process the results of
7311 those searches and pull data into their R sessions.")
7312 (license license:expat)))
7314 (define-public r-renv
7321 (uri (cran-uri "renv" version))
7324 "16n2dz9jibc03f7q1wrzxss6l5jmaks7m2lnli9dz9anvcmxbdia"))))
7325 (properties `((upstream-name . "renv")))
7326 (build-system r-build-system)
7328 `(("r-knitr" ,r-knitr)))
7329 (home-page "https://rstudio.github.io/renv")
7330 (synopsis "Project environments")
7332 "This package provides a dependency management toolkit for R. Using
7333 renv, you can create and manage project-local R libraries, save the state of
7334 these libraries to a lockfile, and later restore your library as required.
7335 Together, these tools can help make your projects more isolated, portable, and
7337 (license license:expat)))
7339 (define-public r-learnr
7346 (uri (cran-uri "learnr" version))
7349 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7350 (build-system r-build-system)
7352 `(("r-checkmate" ,r-checkmate)
7353 ("r-ellipsis" ,r-ellipsis)
7354 ("r-evaluate" ,r-evaluate)
7355 ("r-htmltools" ,r-htmltools)
7356 ("r-htmlwidgets" ,r-htmlwidgets)
7357 ("r-jsonlite" ,r-jsonlite)
7358 ("r-knitr" ,r-knitr)
7359 ("r-markdown" ,r-markdown)
7360 ("r-rappdirs" ,r-rappdirs)
7362 ("r-rmarkdown" ,r-rmarkdown)
7363 ("r-rprojroot" ,r-rprojroot)
7364 ("r-shiny" ,r-shiny)
7365 ("r-withr" ,r-withr)))
7366 (home-page "https://rstudio.github.io/learnr/")
7367 (synopsis "Interactive tutorials for R")
7369 "This package provides tools to create interactive tutorials using R
7370 Markdown. Use a combination of narrative, figures, videos, exercises, and
7371 quizzes to create self-paced tutorials for learning about R and R packages.")
7372 (license license:asl2.0)))
7374 (define-public r-analytics
7376 (name "r-analytics")
7381 (uri (cran-uri "analytics" version))
7384 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7385 (build-system r-build-system)
7388 ("r-cluster" ,r-cluster)
7389 ("r-fractal" ,r-fractal)
7390 ("r-lmtest" ,r-lmtest)
7393 ("r-powerplus" ,r-powerplus)
7394 ("r-robust" ,r-robust)
7395 ("r-trend" ,r-trend)
7399 (home-page "https://cran.r-project.org/web/packages/analytics/")
7400 (synopsis "Collection of data analysis tools")
7402 "This package is a collection of data analysis tools. It includes tools
7403 for regression outlier detection in a fitted linear model, stationary
7404 bootstrap using a truncated geometric distribution, a comprehensive test for
7405 weak stationarity, column means by group, weighted biplots, and a heuristic to
7406 obtain a better initial configuration in non-metric MDS.")
7407 (license license:gpl2)))
7409 (define-public r-reticulate
7411 (name "r-reticulate")
7416 (uri (cran-uri "reticulate" version))
7419 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7420 (build-system r-build-system)
7421 (inputs `(("python" ,python)))
7423 `(("r-rappdirs" ,r-rappdirs)
7424 ("r-jsonlite" ,r-jsonlite)
7425 ("r-matrix" ,r-matrix)
7426 ("r-rcpp" ,r-rcpp)))
7428 `(("r-knitr" ,r-knitr)))
7429 (home-page "https://github.com/rstudio/reticulate")
7430 (synopsis "R interface to Python")
7432 "This package provides an interface from R to Python modules, classes,
7433 and functions. When calling into Python, R data types are automatically
7434 converted to their equivalent Python types. When values are returned from
7435 Python to R they are converted back to R types.")
7436 (license license:asl2.0)))
7438 (define-public r-bibtex
7445 (uri (cran-uri "bibtex" version))
7448 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7449 (build-system r-build-system)
7450 (propagated-inputs `(("r-stringr" ,r-stringr)))
7451 (home-page "https://github.com/romainfrancois/bibtex")
7452 (synopsis "Bibtex parser")
7453 (description "This package provides a utility for R to parse a bibtex
7455 (license license:gpl2+)))
7457 (define-public r-ggseqlogo
7459 (name "r-ggseqlogo")
7464 (uri (cran-uri "ggseqlogo" version))
7467 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7468 (build-system r-build-system)
7469 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7470 (home-page "https://github.com/omarwagih/ggseqlogo")
7471 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7473 "The range of functions provided by this package makes it possible to
7474 draw highly versatile genomic sequence logos. Features include, but are not
7475 limited to, modifying colour schemes and fonts used to draw the logo,
7476 generating multiple logo plots, and aiding the visualisation with annotations.
7477 Sequence logos can easily be combined with other ggplot2 plots.")
7478 ;; Unspecified version of the LGPL.
7479 (license license:lgpl3+)))
7481 (define-public r-ggsci
7488 (uri (cran-uri "ggsci" version))
7491 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7492 (build-system r-build-system)
7494 `(("r-ggplot2" ,r-ggplot2)
7495 ("r-scales" ,r-scales)))
7496 (home-page "https://nanx.me/ggsci/")
7497 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7499 "This package provides a collection of ggplot2 color palettes inspired by
7500 plots in scientific journals, data visualization libraries, science fiction
7501 movies, and TV shows.")
7502 (license license:gpl3)))
7504 (define-public r-ggsignif
7511 (uri (cran-uri "ggsignif" version))
7514 "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh"))))
7515 (build-system r-build-system)
7517 `(("r-knitr" ,r-knitr)))
7519 `(("r-ggplot2" ,r-ggplot2)))
7520 (home-page "https://github.com/const-ae/ggsignif")
7521 (synopsis "Significance brackets for ggplot2")
7523 "Enrich your ggplots with group-wise comparisons. This package provides
7524 an easy way to indicate if two groups are significantly different. Commonly
7525 this is shown by a bracket on top connecting the groups of interest which
7526 itself is annotated with the level of significance. The package provides a
7527 single layer that takes the groups for comparison and the test as arguments
7528 and adds the annotation to the plot.")
7529 (license license:gpl3)))
7531 (define-public r-rstatix
7538 (uri (cran-uri "rstatix" version))
7541 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
7542 (properties `((upstream-name . "rstatix")))
7543 (build-system r-build-system)
7545 `(("r-broom" ,r-broom)
7547 ("r-corrplot" ,r-corrplot)
7548 ("r-dplyr" ,r-dplyr)
7549 ("r-generics" ,r-generics)
7550 ("r-magrittr" ,r-magrittr)
7551 ("r-purrr" ,r-purrr)
7552 ("r-rlang" ,r-rlang)
7553 ("r-tibble" ,r-tibble)
7554 ("r-tidyr" ,r-tidyr)
7555 ("r-tidyselect" ,r-tidyselect)))
7556 (home-page "https://rpkgs.datanovia.com/rstatix/")
7557 (synopsis "Pipe-friendly framework for basic statistical tests")
7559 "This package provides a simple and intuitive pipe-friendly framework,
7560 coherent with the @code{tidyverse} design philosophy, for performing basic
7561 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7562 correlation analyses. The output of each test is automatically transformed
7563 into a tidy data frame to facilitate visualization. Additional functions are
7564 available for reshaping, reordering, manipulating and visualizing correlation
7566 (license license:gpl2)))
7568 (define-public r-ggpubr
7575 (uri (cran-uri "ggpubr" version))
7578 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7579 (build-system r-build-system)
7581 `(("r-cowplot" ,r-cowplot)
7582 ("r-dplyr" ,r-dplyr)
7583 ("r-ggplot2" ,r-ggplot2)
7584 ("r-ggrepel" ,r-ggrepel)
7585 ("r-ggsci" ,r-ggsci)
7586 ("r-ggsignif" ,r-ggsignif)
7588 ("r-gridextra" ,r-gridextra)
7589 ("r-magrittr" ,r-magrittr)
7590 ("r-polynom" ,r-polynom)
7591 ("r-purrr" ,r-purrr)
7592 ("r-rlang" ,r-rlang)
7593 ("r-scales" ,r-scales)
7594 ("r-rstatix" ,r-rstatix)
7595 ("r-tibble" ,r-tibble)
7596 ("r-tidyr" ,r-tidyr)))
7597 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7598 (synopsis "ggplot2-based publication-ready plots")
7600 "The ggplot2 package is an excellent and flexible package for elegant
7601 data visualization in R. However the default generated plots require some
7602 formatting before we can send them for publication. The ggpubr package
7603 provides some easy-to-use functions for creating and customizing ggplot2-based
7604 publication-ready plots.")
7605 (license license:gpl2)))
7607 (define-public r-ellipse
7614 (uri (cran-uri "ellipse" version))
7617 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7618 (build-system r-build-system)
7619 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7620 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7622 "This package contains various routines for drawing ellipses and
7623 ellipse-like confidence regions, implementing the plots described in Murdoch
7624 and Chow (1996), A graphical display of large correlation matrices, The
7625 American Statistician 50, 178-180. There are also routines implementing the
7626 profile plots described in Bates and Watts (1988), Nonlinear Regression
7627 Analysis and its Applications.")
7628 (license license:gpl2+)))
7630 (define-public r-flashclust
7632 (name "r-flashclust")
7637 (uri (cran-uri "flashClust" version))
7640 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7641 (properties `((upstream-name . "flashClust")))
7642 (build-system r-build-system)
7643 (native-inputs `(("gfortran" ,gfortran)))
7644 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7645 (synopsis "Implementation of optimal hierarchical clustering")
7647 "This package provides a fast implementation of hierarchical
7649 (license license:gpl2+)))
7651 (define-public r-factominer
7653 (name "r-factominer")
7658 (uri (cran-uri "FactoMineR" version))
7661 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7662 (properties `((upstream-name . "FactoMineR")))
7663 (build-system r-build-system)
7666 ("r-cluster" ,r-cluster)
7668 ("r-ellipse" ,r-ellipse)
7669 ("r-flashclust" ,r-flashclust)
7670 ("r-ggplot2" ,r-ggplot2)
7671 ("r-ggrepel" ,r-ggrepel)
7672 ("r-lattice" ,r-lattice)
7673 ("r-leaps" ,r-leaps)
7675 ("r-scatterplot3d" ,r-scatterplot3d)))
7677 `(("r-knitr" ,r-knitr)))
7678 (home-page "http://factominer.free.fr")
7679 (synopsis "Multivariate exploratory data analysis and data mining")
7681 "This package provides exploratory data analysis methods to summarize,
7682 visualize and describe datasets. The main principal component methods are
7683 available, those with the largest potential in terms of applications:
7684 principal component analysis (PCA) when variables are quantitative,
7685 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7686 variables are categorical, Multiple Factor Analysis when variables are
7687 structured in groups, etc. and hierarchical cluster analysis.")
7688 (license license:gpl2+)))
7690 (define-public r-factoextra
7692 (name "r-factoextra")
7697 (uri (cran-uri "factoextra" version))
7700 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7701 (build-system r-build-system)
7703 `(("r-abind" ,r-abind)
7704 ("r-cluster" ,r-cluster)
7705 ("r-dendextend" ,r-dendextend)
7706 ("r-factominer" ,r-factominer)
7707 ("r-ggplot2" ,r-ggplot2)
7708 ("r-ggpubr" ,r-ggpubr)
7709 ("r-ggrepel" ,r-ggrepel)
7710 ("r-reshape2" ,r-reshape2)
7711 ("r-tidyr" ,r-tidyr)))
7712 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7713 (synopsis "Extract and visualize the results of multivariate data analyses")
7715 "This package provides some easy-to-use functions to extract and
7716 visualize the output of multivariate data analyses, including
7717 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7718 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7719 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7720 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7721 packages. It contains also functions for simplifying some clustering analysis
7722 steps and provides ggplot2-based elegant data visualization.")
7723 (license license:gpl2)))
7725 (define-public r-fansi
7732 (uri (cran-uri "fansi" version))
7735 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7736 (build-system r-build-system)
7738 `(("r-knitr" ,r-knitr))) ; for vignettes
7739 (home-page "https://github.com/brodieG/fansi")
7740 (synopsis "ANSI control sequence aware string functions")
7742 "This package provides counterparts to R string manipulation functions
7743 that account for the effects of ANSI text formatting control sequences.")
7744 (license license:gpl2+)))
7746 (define-public r-nbclust
7753 (uri (cran-uri "NbClust" version))
7756 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7757 (properties `((upstream-name . "NbClust")))
7758 (build-system r-build-system)
7759 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7760 (synopsis "Determine the best number of clusters in a data set")
7762 "NbClust provides 30 indexes for determining the optimal number of
7763 clusters in a data set and offers the best clustering scheme from different
7764 results to the user.")
7765 (license license:gpl2)))
7767 (define-public r-hdf5r
7774 (uri (cran-uri "hdf5r" version))
7777 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7778 (build-system r-build-system)
7783 `(("r-bit64" ,r-bit64)
7786 `(("r-knitr" ,r-knitr)))
7787 (home-page "https://hhoeflin.github.io/hdf5r")
7788 (synopsis "Interface to the HDF5 binary data format")
7790 "HDF5 is a data model, library and file format for storing and managing
7791 large amounts of data. This package provides a nearly feature complete,
7792 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7793 functionality is added so that HDF5 objects behave very similar to their
7794 corresponding R counterparts.")
7795 (license license:asl2.0)))
7797 (define-public r-itertools
7799 (name "r-itertools")
7804 (uri (cran-uri "itertools" version))
7807 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7808 (build-system r-build-system)
7810 `(("r-iterators" ,r-iterators)))
7811 (home-page "https://cran.r-project.org/web/packages/itertools/")
7812 (synopsis "Iterator tools")
7814 "This package provides various tools for creating iterators, many
7815 patterned after functions in the Python @code{itertools} module, and others
7816 patterned after functions in the snow package.")
7817 (license license:gpl2)))
7819 (define-public r-polynom
7826 (uri (cran-uri "polynom" version))
7829 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7830 (build-system r-build-system)
7831 (home-page "https://cran.r-project.org/web/packages/polynom/")
7832 (synopsis "Functions for univariate polynomial manipulations")
7834 "This package provides a collection of functions to implement a class for
7835 univariate polynomial manipulations.")
7836 (license license:gpl2)))
7838 (define-public r-gbrd
7845 (uri (cran-uri "gbRd" version))
7848 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7849 (properties `((upstream-name . "gbRd")))
7850 (build-system r-build-system)
7851 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7852 (synopsis "Utilities for processing Rd objects and files")
7854 "This package provides utilities for processing Rd objects and files.
7855 Extract argument descriptions and other parts of the help pages of
7857 (license license:gpl2+)))
7859 (define-public r-rjags
7866 (uri (cran-uri "rjags" version))
7869 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7870 (build-system r-build-system)
7872 `(("r-coda" ,r-coda)))
7876 `(("pkg-config" ,pkg-config)))
7877 (home-page "http://mcmc-jags.sourceforge.net")
7878 (synopsis "Bayesian graphical models using MCMC")
7880 "This package provides an R interface to the JAGS MCMC library. JAGS is
7881 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7882 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7883 (license license:gpl2)))
7885 (define-public r-rbibutils
7887 (name "r-rbibutils")
7892 (uri (cran-uri "rbibutils" version))
7895 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7896 (properties `((upstream-name . "rbibutils")))
7897 (build-system r-build-system)
7898 (home-page "https://geobosh.github.io/rbibutils/")
7899 (synopsis "Convert between bibliography formats")
7901 "This package converts between a number of bibliography formats,
7902 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7903 utilities and supports all bibliography formats and character encodings
7904 implemented in bibutils.")
7905 (license license:gpl2)))
7907 (define-public r-rdpack
7914 (uri (cran-uri "Rdpack" version))
7917 "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
7918 (properties `((upstream-name . "Rdpack")))
7919 (build-system r-build-system)
7921 `(("r-rbibutils" ,r-rbibutils)))
7922 (home-page "https://github.com/GeoBosh/Rdpack")
7923 (synopsis "Update and manipulate Rd documentation objects")
7925 "This package provides functions for manipulation of R documentation
7926 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7927 updating Rd documentation for functions, methods and classes; it also includes
7928 Rd macros for citations and import of references from bibtex files for use in
7929 Rd files and roxygen2 comments, as well as many functions for manipulation of
7930 references and Rd files.")
7931 (license license:gpl2+)))
7933 (define-public r-officer
7940 (uri (cran-uri "officer" version))
7943 "1apg0dh1zfhrqcbbmm8318l40gyjbqc2l9sdvwxx7qi8mzc1mqvw"))))
7944 (build-system r-build-system)
7951 `(("r-knitr" ,r-knitr)))
7952 (home-page "https://davidgohel.github.io/officer")
7953 (synopsis "Manipulation of Word and PowerPoint documents")
7955 "This package provides tools to access and manipulate Word and PowerPoint
7956 documents from R. The package focuses on tabular and graphical reporting from
7957 R; it also provides two functions that let users get document content into
7958 data objects. A set of functions lets add and remove images, tables and
7959 paragraphs of text in new or existing documents. When working with PowerPoint
7960 presentations, slides can be added or removed; shapes inside slides can also
7961 be added or removed. When working with Word documents, a cursor can be used
7962 to help insert or delete content at a specific location in the document.")
7963 (license license:gpl3)))
7965 (define-public r-profilemodel
7967 (name "r-profilemodel")
7972 (uri (cran-uri "profileModel" version))
7975 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7976 (properties `((upstream-name . "profileModel")))
7977 (build-system r-build-system)
7978 (home-page "https://github.com/ikosmidis/profileModel")
7979 (synopsis "Profiling inference functions for various model classes")
7981 "This package provides tools that can be used to calculate, evaluate,
7982 plot and use for inference the profiles of *arbitrary* inference functions for
7983 arbitrary @code{glm}-like fitted models with linear predictors. More information
7984 on the methods that are implemented can be found in Kosmidis (2008)
7985 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7986 (license license:gpl2+)))
7988 (define-public r-brglm
7995 (uri (cran-uri "brglm" version))
7998 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7999 (properties `((upstream-name . "brglm")))
8000 (build-system r-build-system)
8002 `(("r-profilemodel" ,r-profilemodel)))
8003 (home-page "https://github.com/ikosmidis/brglm")
8004 (synopsis "Bias reduction in binomial-response generalized linear models")
8006 "Fit generalized linear models with binomial responses using either an
8007 adjusted-score approach to bias reduction or maximum penalized likelihood
8008 where penalization is by Jeffreys invariant prior. These procedures return
8009 estimates with improved frequentist properties (bias, mean squared error) that
8010 are always finite even in cases where the maximum likelihood estimates are
8011 infinite (data separation). Fitting takes place by fitting generalized linear
8012 models on iteratively updated pseudo-data. The interface is essentially the
8013 same as @code{glm}. More flexibility is provided by the fact that custom
8014 pseudo-data representations can be specified and used for model fitting.
8015 Functions are provided for the construction of confidence intervals for the
8016 reduced-bias estimates.")
8017 (license license:gpl2+)))
8019 (define-public r-entropy
8026 (uri (cran-uri "entropy" version))
8029 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8030 (properties `((upstream-name . "entropy")))
8031 (build-system r-build-system)
8032 (home-page "https://www.strimmerlab.org/software/entropy/")
8033 (synopsis "Estimation of entropy, mutual information and related quantities")
8035 "This package implements various estimators of entropy, such as the
8036 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8037 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8038 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8039 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8040 mutual information, and chi-squared statistic of independence. In addition
8041 there are functions for discretizing continuous random variables.")
8042 (license license:gpl3+)))
8044 (define-public r-abn
8051 (uri (cran-uri "abn" version))
8054 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8055 (build-system r-build-system)
8059 `(("r-lme4" ,r-lme4)
8062 ("r-rcpparmadillo" ,r-rcpparmadillo)
8063 ("r-rjags" ,r-rjags)))
8064 (home-page "https://r-bayesian-networks.org/")
8065 (synopsis "Modelling multivariate data with additive bayesian networks")
8067 "Bayesian network analysis is a form of probabilistic graphical models
8068 which derives from empirical data a directed acyclic graph, DAG, describing
8069 the dependency structure between random variables. An additive Bayesian
8070 network model consists of a form of a DAG where each node comprises a
8071 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8072 equivalent to Bayesian multivariate regression using graphical modelling, they
8073 generalises the usual multivariable regression, GLM, to multiple dependent
8074 variables. This package provides routines to help determine optimal Bayesian
8075 network models for a given data set, where these models are used to identify
8076 statistical dependencies in messy, complex data.")
8077 (license license:gpl2+)))
8079 (define-public r-acd
8086 (uri (cran-uri "ACD" version))
8089 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8090 (properties `((upstream-name . "ACD")))
8091 (build-system r-build-system)
8092 (home-page "https://cran.r-project.org/web/packages/ACD/")
8093 (synopsis "Categorical data analysis with complete or missing responses")
8095 "This package provides tools for categorical data analysis with complete
8096 or missing responses.")
8097 (license license:gpl2+)))
8099 (define-public r-acdm
8106 (uri (cran-uri "ACDm" version))
8109 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8110 (properties `((upstream-name . "ACDm")))
8111 (build-system r-build-system)
8113 `(("r-dplyr" ,r-dplyr)
8114 ("r-ggplot2" ,r-ggplot2)
8116 ("r-rsolnp" ,r-rsolnp)
8118 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8119 (synopsis "Tools for Autoregressive Conditional Duration Models")
8121 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8122 and Russell, 1998) models. It creates trade, price or volume durations from
8123 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8125 (license license:gpl2+)))
8127 (define-public r-overlap
8134 (uri (cran-uri "overlap" version))
8137 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8138 (build-system r-build-system)
8139 (home-page "https://cran.r-project.org/web/packages/overlap/")
8140 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8142 "This package provides functions to fit kernel density functions to data
8143 on temporal activity patterns of animals; estimate coefficients of overlapping
8144 of densities for two species; and calculate bootstrap estimates of confidence
8146 (license license:gpl3+)))
8148 (define-public r-snakecase
8150 (name "r-snakecase")
8155 (uri (cran-uri "snakecase" version))
8158 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8159 (build-system r-build-system)
8161 `(("r-stringi" ,r-stringi)
8162 ("r-stringr" ,r-stringr)))
8163 (home-page "https://github.com/Tazinho/snakecase")
8164 (synopsis "Convert strings into any case")
8166 "This package provides a consistent, flexible and easy to use tool to
8167 parse and convert strings into cases like snake or camel among others.")
8168 (license license:gpl3)))
8170 (define-public r-prediction
8172 (name "r-prediction")
8177 (uri (cran-uri "prediction" version))
8180 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8181 (build-system r-build-system)
8183 `(("r-data-table" ,r-data-table)))
8184 (home-page "https://github.com/leeper/prediction")
8185 (synopsis "Tidy, type-safe prediction methods")
8187 "This package provides the @code{prediction()} function, a type-safe
8188 alternative to @code{predict()} that always returns a data frame. The package
8189 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8190 from the @code{stats} package, as well as numerous other model classes from
8191 other add-on packages.")
8192 (license license:expat)))
8194 (define-public r-insight
8201 (uri (cran-uri "insight" version))
8204 "1la4yxzfl9fnknamnaziil6gvpdzl78z16lfzis9jgzg8r9q0y5l"))))
8205 (build-system r-build-system)
8207 `(("r-knitr" ,r-knitr)))
8208 (home-page "https://easystats.github.io/insight/")
8209 (synopsis "Easy access to model information for various model objects")
8211 "This package provides a tool to provide an easy, intuitive and
8212 consistent access to information contained in various R models, like model
8213 formulas, model terms, information about random effects, data that was used to
8214 fit the model or data from response variables. The package mainly revolves
8215 around two types of functions: Functions that find (the names of) information,
8216 starting with @code{find_}, and functions that get the underlying data,
8217 starting with @code{get_}. The package has a consistent syntax and works with
8218 many different model objects, where otherwise functions to access these
8219 information are missing.")
8220 (license license:gpl3)))
8222 (define-public r-sjlabelled
8224 (name "r-sjlabelled")
8229 (uri (cran-uri "sjlabelled" version))
8232 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8233 (build-system r-build-system)
8235 `(("r-insight" ,r-insight)))
8237 `(("r-knitr" ,r-knitr)))
8238 (home-page "https://github.com/strengejacke/sjlabelled")
8239 (synopsis "Labelled data utility functions")
8241 "This package provides a collection of functions dealing with labelled
8242 data, like reading and writing data between R and other statistical software
8243 packages. This includes easy ways to get, set or change value and variable
8244 label attributes, to convert labelled vectors into factors or numeric (and
8245 vice versa), or to deal with multiple declared missing values.")
8246 (license license:gpl3)))
8248 (define-public r-sjmisc
8255 (uri (cran-uri "sjmisc" version))
8258 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8259 (build-system r-build-system)
8261 `(("r-dplyr" ,r-dplyr)
8262 ("r-insight" ,r-insight)
8263 ("r-magrittr" ,r-magrittr)
8264 ("r-purrr" ,r-purrr)
8265 ("r-rlang" ,r-rlang)
8266 ("r-sjlabelled" ,r-sjlabelled)
8267 ("r-tidyselect" ,r-tidyselect)))
8269 `(("r-knitr" ,r-knitr)))
8270 (home-page "https://github.com/strengejacke/sjmisc")
8271 (synopsis "Data and variable transformation functions")
8273 "This package is a collection of miscellaneous utility functions,
8274 supporting data transformation tasks like recoding, dichotomizing or grouping
8275 variables, setting and replacing missing values. The data transformation
8276 functions also support labelled data, and all integrate seamlessly into a
8277 tidyverse workflow.")
8278 (license license:gpl3)))
8280 (define-public r-nortest
8287 (uri (cran-uri "nortest" version))
8290 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8291 (build-system r-build-system)
8292 (home-page "https://cran.r-project.org/web/packages/nortest/")
8293 (synopsis "Tests for normality")
8295 "This package provides five omnibus tests for testing the composite
8296 hypothesis of normality.")
8297 (license license:gpl2+)))
8299 (define-public r-moonbook
8306 (uri (cran-uri "moonBook" version))
8309 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8310 (properties `((upstream-name . "moonBook")))
8311 (build-system r-build-system)
8313 `(("r-magrittr" ,r-magrittr)
8314 ("r-nortest" ,r-nortest)
8315 ("r-sjmisc" ,r-sjmisc)
8316 ("r-stringr" ,r-stringr)
8317 ("r-survival" ,r-survival)
8318 ("r-ztable" ,r-ztable)))
8320 `(("r-knitr" ,r-knitr)))
8321 (home-page "https://github.com/cardiomoon/moonBook")
8322 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8324 "This package provides several analysis-related functions for the book
8325 entitled \"R statistics and graph for medical articles\" (written in Korean),
8326 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8328 (license license:gpl2)))
8330 (define-public r-flextable
8332 (name "r-flextable")
8337 (uri (cran-uri "flextable" version))
8340 "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma"))))
8341 (build-system r-build-system)
8343 `(("r-base64enc" ,r-base64enc)
8344 ("r-data-table" ,r-data-table)
8345 ("r-gdtools" ,r-gdtools)
8346 ("r-htmltools" ,r-htmltools)
8347 ("r-knitr" ,r-knitr)
8348 ("r-officer" ,r-officer)
8349 ("r-rlang" ,r-rlang)
8350 ("r-rmarkdown" ,r-rmarkdown)
8352 ("r-xml2" ,r-xml2)))
8354 `(("r-knitr" ,r-knitr)))
8355 (home-page "https://davidgohel.github.io/flextable")
8356 (synopsis "Functions for tabular reporting")
8358 "This package provides tools to create pretty tables for HTML documents
8359 and other formats. Functions are provided to let users create tables, modify
8360 and format their content. It extends the @code{officer} package and can be
8361 used within R markdown documents when rendering to HTML and to Word
8363 (license license:gpl3)))
8365 (define-public r-writexl
8372 (uri (cran-uri "writexl" version))
8375 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8376 (build-system r-build-system)
8377 (inputs `(("zlib" ,zlib)))
8378 (home-page "https://github.com/ropensci/writexl")
8379 (synopsis "Export data frames to xlsx format")
8381 "This package provides a data frame to xlsx exporter based on
8383 (license license:bsd-2)))
8385 (define-public r-biasedurn
8387 (name "r-biasedurn")
8392 (uri (cran-uri "BiasedUrn" version))
8395 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8396 (properties `((upstream-name . "BiasedUrn")))
8397 (build-system r-build-system)
8398 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8399 (synopsis "Biased Urn model distributions")
8401 "This package provides statistical models of biased sampling in the form
8402 of univariate and multivariate noncentral hypergeometric distributions,
8403 including Wallenius' noncentral hypergeometric distribution and Fisher's
8404 noncentral hypergeometric distribution (also called extended hypergeometric
8406 (license license:gpl3)))
8408 (define-public r-goplot
8415 (uri (cran-uri "GOplot" version))
8418 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8419 (properties `((upstream-name . "GOplot")))
8420 (build-system r-build-system)
8422 `(("r-ggdendro" ,r-ggdendro)
8423 ("r-ggplot2" ,r-ggplot2)
8424 ("r-gridextra" ,r-gridextra)
8425 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8426 (home-page "https://github.com/wencke/wencke.github.io")
8427 (synopsis "Visualization of functional analysis data")
8429 "This package provides an implementation of multilayered visualizations
8430 for enhanced graphical representation of functional analysis data. It
8431 combines and integrates omics data derived from expression and functional
8432 annotation enrichment analyses. Its plotting functions have been developed
8433 with an hierarchical structure in mind: starting from a general overview to
8434 identify the most enriched categories (modified bar plot, bubble plot) to a
8435 more detailed one displaying different types of relevant information for the
8436 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8437 Venn diagram, heatmap).")
8438 (license license:gpl2)))
8440 (define-public r-getopt
8447 (uri (cran-uri "getopt" version))
8450 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8451 (build-system r-build-system)
8452 (home-page "https://github.com/trevorld/getopt")
8453 (synopsis "Command-line option processor for R")
8455 "This package is designed to be used with Rscript to write shebang
8456 scripts that accept short and long options. Many users will prefer to
8457 use the packages @code{optparse} or @code{argparse} which add extra
8458 features like automatically generated help options and usage texts,
8459 support for default values, positional argument support, etc.")
8460 (license license:gpl2+)))
8462 (define-public r-findpython
8464 (name "r-findpython")
8469 (uri (cran-uri "findpython" version))
8472 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8473 (build-system r-build-system)
8474 (home-page "https://github.com/trevorld/findpython")
8475 (synopsis "Functions to find an acceptable Python binary")
8477 "This package was designed to find an acceptable Python binary that
8478 matches version and feature constraints.")
8479 (license license:expat)))
8481 ;; This in not the same as "r-argparser"
8482 (define-public r-argparse
8489 (uri (cran-uri "argparse" version))
8492 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8493 (build-system r-build-system)
8494 (inputs `(("python" ,python)))
8496 `(("r-findpython" ,r-findpython)
8497 ("r-jsonlite" ,r-jsonlite)
8500 `(("r-knitr" ,r-knitr)))
8501 (home-page "https://github.com/trevorld/argparse")
8502 (synopsis "Command line optional and positional argument parser")
8504 "This package provides a command line parser to be used with Rscript to
8505 write shebang scripts that gracefully accept positional and optional arguments
8506 and automatically generate usage notices.")
8507 (license license:gpl2+)))
8509 (define-public r-hash
8516 (uri (cran-uri "hash" version))
8519 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8520 (build-system r-build-system)
8521 (home-page "https://cran.r-project.org/web/packages/hash/")
8522 (synopsis "Implementation of hash/associated arrays/dictionaries")
8524 "This package implements a data structure similar to hashes in Perl and
8525 dictionaries in Python but with a purposefully R flavor. For objects of
8526 appreciable size, access using hashes outperforms native named lists and
8528 (license license:gpl2+)))
8530 (define-public r-orddom
8537 (uri (cran-uri "orddom" version))
8540 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8541 (build-system r-build-system)
8542 (propagated-inputs `(("r-psych" ,r-psych)))
8543 (home-page "https://cran.r-project.org/web/packages/orddom/")
8544 (synopsis "Ordinal dominance statistics")
8546 "This package provides tools to compute ordinal, statistics and effect
8547 sizes as an alternative to mean comparison: Cliff's delta or success rate
8548 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8549 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8550 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8551 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8552 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8553 Group (Non-)Overlap considerations.")
8554 (license license:gpl2)))
8556 (define-public r-deriv
8563 (uri (cran-uri "Deriv" version))
8566 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
8567 (properties `((upstream-name . "Deriv")))
8568 (build-system r-build-system)
8569 (home-page "https://cran.r-project.org/web/packages/Deriv")
8570 (synopsis "Symbolic differentiation")
8572 "This package provides an R-based solution for symbolic differentiation.
8573 It admits user-defined functions as well as function substitution in arguments
8574 of functions to be differentiated. Some symbolic simplification is part of
8576 (license license:gpl3+)))
8578 (define-public r-doby
8585 (uri (cran-uri "doBy" version))
8588 "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00"))))
8589 (properties `((upstream-name . "doBy")))
8590 (build-system r-build-system)
8592 `(("r-broom" ,r-broom)
8593 ("r-deriv" ,r-deriv)
8594 ("r-dplyr" ,r-dplyr)
8595 ("r-ggplot2" ,r-ggplot2)
8596 ("r-magrittr" ,r-magrittr)
8598 ("r-matrix" ,r-matrix)
8599 ("r-pbkrtest" ,r-pbkrtest)
8600 ("r-tibble" ,r-tibble)))
8602 `(("r-knitr" ,r-knitr)))
8603 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8604 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8606 "This package contains:
8609 @item facilities for working with grouped data: @code{do}
8610 something to data stratified @code{by} some variables.
8611 @item implementations of least-squares means, general linear contrasts, and
8612 @item miscellaneous other utilities.
8614 (license license:gpl2+)))
8616 (define-public r-refgenome
8618 (name "r-refgenome")
8623 (uri (cran-uri "refGenome" version))
8626 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8627 (properties `((upstream-name . "refGenome")))
8628 (build-system r-build-system)
8632 ("r-rsqlite" ,r-rsqlite)))
8633 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8635 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8637 "This package contains functionality for importing and managing of
8638 downloaded genome annotation data from the Ensembl genome browser (European
8639 Bioinformatics Institute) and from the UCSC genome browser (University of
8640 California, Santa Cruz) and annotation routines for genomic positions and
8641 splice site positions.")
8642 (license license:gpl2)))
8644 (define-public r-basix
8651 (uri (cran-uri "BASIX" version))
8654 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8655 (properties `((upstream-name . "BASIX")))
8656 (build-system r-build-system)
8657 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8658 (synopsis "Efficient C/C++ toolset for R")
8660 "BASIX provides some efficient C/C++ implementations of native R
8661 procedures to speed up calculations in R.")
8662 (license license:gpl2)))
8664 (define-public r-blockfest
8666 (name "r-blockfest")
8671 (uri (cran-uri "BlockFeST" version))
8674 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
8675 (properties `((upstream-name . "BlockFeST")))
8676 (build-system r-build-system)
8677 (propagated-inputs `(("r-basix" ,r-basix)))
8678 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8679 (synopsis "Bayesian calculation of region-specific fixation index")
8681 "This package provides an R implementation of an extension of the
8682 BayeScan software for codominant markers, adding the option to group
8683 individual SNPs into pre-defined blocks. A typical application of this new
8684 approach is the identification of genomic regions, genes, or gene sets
8685 containing one or more SNPs that evolved under directional selection.")
8686 (license license:gpl2)))
8688 (define-public r-proc
8691 (version "1.17.0.1")
8695 (uri (cran-uri "pROC" version))
8698 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8699 (properties `((upstream-name . "pROC")))
8700 (build-system r-build-system)
8702 `(("r-plyr" ,r-plyr)
8703 ("r-rcpp" ,r-rcpp)))
8704 (home-page "https://web.expasy.org/pROC/")
8705 (synopsis "Display and analyze ROC curves")
8707 "This package provides tools for visualizing, smoothing and comparing
8708 receiver operating characteristic (ROC curves). The area under the
8709 curve (AUC) can be compared with statistical tests based on U-statistics or
8710 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8711 (license license:gpl3+)))
8713 (define-public r-rootsolve
8715 (name "r-rootsolve")
8720 (uri (cran-uri "rootSolve" version))
8723 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8724 (properties `((upstream-name . "rootSolve")))
8725 (build-system r-build-system)
8726 (native-inputs `(("gfortran" ,gfortran)))
8727 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8728 (synopsis "Tools for the analysis of ordinary differential equations")
8730 "This package provides routines to find the root of nonlinear functions,
8731 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8732 differential equations} (ODE). It includes routines that:
8735 @item generate gradient and jacobian matrices (full and banded),
8736 @item find roots of non-linear equations by the Newton-Raphson method,
8737 @item estimate steady-state conditions of a system of (differential) equations
8738 in full, banded or sparse form, using the Newton-Raphson method, or by
8739 dynamically running,
8740 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8741 and 3-D partial differential equations, that have been converted to ordinary
8742 differential equations by numerical differencing (using the method-of-lines
8745 (license license:gpl2+)))
8747 (define-public r-abcanalysis
8749 (name "r-abcanalysis")
8754 (uri (cran-uri "ABCanalysis" version))
8756 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8757 (properties `((upstream-name . "ABCanalysis")))
8758 (build-system r-build-system)
8759 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8760 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8761 (synopsis "Computed ABC Analysis")
8763 "Multivariate data sets often differ in several factors or derived statistical
8764 parameters, which have to be selected for a valid interpretation. Basing this
8765 selection on traditional statistical limits leads occasionally to the perception
8766 of losing information from a data set. This package provides tools to calculate
8767 these limits on the basis of the mathematical properties of the distribution of
8768 the analyzed items.")
8769 (license license:gpl3)))
8771 (define-public r-slam
8778 (uri (cran-uri "slam" version))
8780 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8781 (build-system r-build-system)
8782 (home-page "https://cran.r-project.org/web/packages/slam/")
8783 (synopsis "Sparse lightweight arrays and matrices")
8785 "This package contains data structures and algorithms for sparse arrays and matrices,
8786 based on index arrays and simple triplet representations, respectively.")
8787 (license license:gpl2)))
8789 (define-public r-manipulatewidget
8791 (name "r-manipulatewidget")
8796 (uri (cran-uri "manipulateWidget" version))
8798 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8800 `((upstream-name . "manipulateWidget")))
8801 (build-system r-build-system)
8803 `(("r-base64enc" ,r-base64enc)
8804 ("r-codetools" ,r-codetools)
8805 ("r-htmltools" ,r-htmltools)
8806 ("r-htmlwidgets" ,r-htmlwidgets)
8807 ("r-knitr" ,r-knitr)
8808 ("r-miniui" ,r-miniui)
8809 ("r-shiny" ,r-shiny)
8810 ("r-webshot" ,r-webshot)))
8811 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8812 (synopsis "Add even more interactivity to interactive charts")
8814 "This package lets you create in just a few lines of R code a nice user interface to
8815 modify the data or the graphical parameters of one or multiple interactive
8816 charts. It is useful to quickly explore visually some data or for package
8817 developers to generate user interfaces easy to maintain.")
8818 (license license:gpl2+)))
8827 (uri (cran-uri "A3" version))
8829 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8830 (properties `((upstream-name . "A3")))
8831 (build-system r-build-system)
8833 `(("r-pbapply" ,r-pbapply)
8834 ("r-xtable" ,r-xtable)))
8835 (home-page "https://cran.r-project.org/web/packages/A3/")
8836 (synopsis "Error metrics for predictive models")
8838 "This package supplies tools for tabulating and analyzing the results of predictive
8839 models. The methods employed are applicable to virtually any predictive model
8840 and make comparisons between different methodologies straightforward.")
8841 (license license:gpl2+)))
8843 (define-public r-infotheo
8850 (uri (cran-uri "infotheo" version))
8853 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8854 (build-system r-build-system)
8855 (home-page "http://homepage.meyerp.com/software")
8856 (synopsis "Information-theoretic measures")
8858 "This package implements various measures of information theory based on
8859 several entropy estimators.")
8860 (license license:gpl3+)))
8862 (define-public r-abcoptim
8869 (uri (cran-uri "ABCoptim" version))
8871 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8872 (properties `((upstream-name . "ABCoptim")))
8873 (build-system r-build-system)
8874 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8875 (home-page "https://github.com/gvegayon/ABCoptim/")
8876 (synopsis "Optimization of Artificial Bee Colony algorithm")
8878 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8879 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8880 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8881 algorithms, and uses only common control parameters such as colony size and
8882 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8883 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8884 This version is a work-in-progress and is written in R code.")
8885 (license license:expat)))
8887 (define-public r-abcp2
8894 (uri (cran-uri "ABCp2" version))
8896 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8897 (properties `((upstream-name . "ABCp2")))
8898 (build-system r-build-system)
8899 (propagated-inputs `(("r-mass" ,r-mass)))
8900 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8901 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8903 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8904 Poisson, and Gamma distribution and estimates the proportional paternity of the
8905 second male (P2) based on the best fit distribution.")
8906 (license license:gpl2)))
8908 (define-public r-abcrf
8915 (uri (cran-uri "abcrf" version))
8917 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8918 (build-system r-build-system)
8920 `(("r-doparallel" ,r-doparallel)
8921 ("r-foreach" ,r-foreach)
8923 ("r-matrixstats" ,r-matrixstats)
8924 ("r-ranger" ,r-ranger)
8926 ("r-rcpparmadillo" ,r-rcpparmadillo)
8927 ("r-readr" ,r-readr)
8928 ("r-stringr" ,r-stringr)))
8929 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8930 (synopsis "Approximate bayesian computation via random forests")
8932 "This package performs approximate bayesian computation (ABC) model choice and
8933 parameter inference via random forests. This machine learning tool named random
8934 forests (RF) can conduct selection among the highly complex models covered by
8936 (license license:gpl2+)))
8938 (define-public r-abctools
8945 (uri (cran-uri "abctools" version))
8947 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8948 (build-system r-build-system)
8951 ("r-abind" ,r-abind)
8952 ("r-hmisc" ,r-hmisc)
8953 ("r-plyr" ,r-plyr)))
8954 (home-page "https://github.com/dennisprangle/abctools/")
8955 (synopsis "Tools for ABC analyses")
8957 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8958 including summary statistic selection and assessing coverage. This includes
8959 recent dimension reduction algorithms to tune the choice of summary statistics,
8960 and coverage methods to tune the choice of threshold.")
8961 (license license:gpl2+)))
8963 (define-public r-ggstance
8970 (uri (cran-uri "ggstance" version))
8972 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8973 (build-system r-build-system)
8975 `(("r-ggplot2" ,r-ggplot2)
8977 ("r-rlang" ,r-rlang)
8978 ("r-withr" ,r-withr)))
8979 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8980 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8982 "This package is a @code{r-ggplot2} extension that provides flipped components:
8984 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8985 @item vertical versions of @code{r-ggplot2} positions.
8987 (license license:gpl3)))
8989 (define-public r-mosaiccore
8991 (name "r-mosaiccore")
8996 (uri (cran-uri "mosaicCore" version))
8998 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8999 (properties `((upstream-name . "mosaicCore")))
9000 (build-system r-build-system)
9002 `(("r-dplyr" ,r-dplyr)
9004 ("r-rlang" ,r-rlang)
9005 ("r-tidyr" ,r-tidyr)))
9006 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
9007 (synopsis "Common utilities for mosaic family packages")
9009 "Common utilities used in other Mosaic family packages are collected here.")
9010 (license license:gpl2+)))
9012 (define-public r-labelled
9019 (uri (cran-uri "labelled" version))
9022 "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg"))))
9023 (properties `((upstream-name . "labelled")))
9024 (build-system r-build-system)
9026 `(("r-dplyr" ,r-dplyr)
9027 ("r-haven" ,r-haven)
9028 ("r-lifecycle" ,r-lifecycle)
9029 ("r-rlang" ,r-rlang)
9030 ("r-stringr" ,r-stringr)
9031 ("r-tidyr" ,r-tidyr)
9032 ("r-vctrs" ,r-vctrs)))
9034 `(("r-knitr" ,r-knitr)))
9035 (home-page "http://larmarange.github.io/labelled/")
9036 (synopsis "Manipulating labelled data")
9038 "This package provides useful functions to deal with the
9039 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9041 (license license:gpl3)))
9043 (define-public r-ggformula
9045 (name "r-ggformula")
9050 (uri (cran-uri "ggformula" version))
9052 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9053 (build-system r-build-system)
9055 `(("r-ggforce" ,r-ggforce)
9056 ("r-ggplot2" ,r-ggplot2)
9057 ("r-ggridges" ,r-ggridges)
9058 ("r-ggstance" ,r-ggstance)
9059 ("r-labelled" ,r-labelled)
9060 ("r-magrittr" ,r-magrittr)
9061 ("r-mosaiccore" ,r-mosaiccore)
9062 ("r-rlang" ,r-rlang)
9063 ("r-scales" ,r-scales)
9064 ("r-stringr" ,r-stringr)
9065 ("r-tibble" ,r-tibble)))
9067 `(("r-knitr" ,r-knitr)))
9068 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9069 (synopsis "Formula interface for the @code{r-ggplot2}")
9071 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9072 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9073 and extends the excellent simplicity of the lattice-graphics formula interface,
9074 while providing the intuitive capabilities of @code{r-ggplot2}.")
9075 (license license:expat)))
9077 (define-public r-mosaicdata
9079 (name "r-mosaicdata")
9084 (uri (cran-uri "mosaicData" version))
9086 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9087 (properties `((upstream-name . "mosaicData")))
9088 (build-system r-build-system)
9089 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9090 (synopsis "Data sets for project Mosaic")
9092 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9093 used to teach mathematics, statistics, computation and modeling.")
9094 (license license:gpl2+)))
9096 (define-public r-raster
9103 (uri (cran-uri "raster" version))
9106 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9107 (build-system r-build-system)
9109 `(("r-rcpp" ,r-rcpp)
9111 (home-page "https://www.rspatial.org/")
9112 (synopsis "Geographic data analysis and modeling")
9114 "The package implements basic and high-level functions for reading,
9115 writing, manipulating, analyzing and modeling of gridded spatial data.
9116 Processing of very large files is supported.")
9117 (license license:gpl3+)))
9119 (define-public r-mosaic
9126 (uri (cran-uri "mosaic" version))
9128 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9129 (build-system r-build-system)
9131 `(("r-broom" ,r-broom)
9132 ("r-dplyr" ,r-dplyr)
9133 ("r-ggdendro" ,r-ggdendro)
9134 ("r-ggformula" ,r-ggformula)
9135 ("r-ggplot2" ,r-ggplot2)
9136 ("r-ggrepel" ,r-ggrepel)
9138 ("r-gridextra" ,r-gridextra)
9139 ("r-lattice" ,r-lattice)
9140 ("r-latticeextra" ,r-latticeextra)
9141 ("r-lazyeval" ,r-lazyeval)
9143 ("r-matrix" ,r-matrix)
9144 ("r-mosaiccore" ,r-mosaiccore)
9145 ("r-mosaicdata" ,r-mosaicdata)
9146 ("r-readr" ,r-readr)
9147 ("r-tidyr" ,r-tidyr)))
9149 `(("r-knitr" ,r-knitr)))
9150 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9151 (synopsis "Mathematics, statistics, and computation teaching utilities")
9153 "This package contain data sets and utilities from
9154 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9155 statistics, computation and modeling. Project MOSAIC is a community of
9156 educators working to tie together aspects of quantitative work that students
9157 in science, technology, engineering and mathematics will need in their
9158 professional lives, but which are usually taught in isolation, if at all.")
9159 (license license:gpl2+)))
9161 (define-public r-abd
9168 (uri (cran-uri "abd" version))
9170 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9171 (build-system r-build-system)
9173 `(("r-lattice" ,r-lattice)
9174 ("r-mosaic" ,r-mosaic)
9175 ("r-nlme" ,r-nlme)))
9176 (home-page "https://cran.r-project.org/web/packages/abd/")
9177 (synopsis "Analysis of biological data")
9179 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9180 biological data by Michael Whitlock and Dolph Schluter.")
9181 (license license:gpl2)))
9183 (define-public r-svgui
9190 (uri (cran-uri "svGUI" version))
9192 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9193 (properties `((upstream-name . "svGUI")))
9194 (build-system r-build-system)
9195 (home-page "https://github.com/SciViews/svGUI/")
9196 (synopsis "Functions for managing GUI clients in R")
9198 "The SciViews @code{svGUI} package eases the management of Graphical User
9199 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9200 centralizes info about GUI elements currently used, and it dispatches GUI
9201 calls to the particular toolkits in use in function of the context.")
9202 (license license:gpl2)))
9204 (define-public r-svdialogs
9206 (name "r-svdialogs")
9211 (uri (cran-uri "svDialogs" version))
9213 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9214 (properties `((upstream-name . "svDialogs")))
9215 (build-system r-build-system)
9218 ("zenity" ,zenity)))
9220 `(("r-rstudioapi" ,r-rstudioapi)
9221 ("r-svgui" ,r-svgui)))
9222 (home-page "https://github.com/SciViews/svDialogs/")
9223 (synopsis "Portable dialog boxes")
9225 "This package helps to construct standard dialog boxes for your GUI, including
9226 message boxes, input boxes, list, file or directory selection, and others. In
9227 case R cannot display GUI dialog boxes, a simpler command line version of these
9228 interactive elements is also provided as a fallback solution.")
9229 (license license:gpl2)))
9231 (define-public r-abe
9238 (uri (cran-uri "abe" version))
9241 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9242 (build-system r-build-system)
9243 (home-page "https://cran.r-project.org/web/packages/abe/")
9244 (synopsis "Augmented backward elimination")
9246 "This package performs augmented backward elimination and checks the
9247 stability of the obtained model. Augmented backward elimination combines
9248 significance or information based criteria with the change in estimate to
9249 either select the optimal model for prediction purposes or to serve as a tool
9250 to obtain a practically sound, highly interpretable model.")
9251 (license license:gpl2+)))
9253 (define-public r-abf2
9260 (uri (cran-uri "abf2" version))
9262 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9263 (build-system r-build-system)
9264 (home-page "https://cran.r-project.org/web/packages/abf2/")
9265 (synopsis "Load gap-free axon @code{r-abf2} files")
9267 "This package loads electrophysiology data from ABF2 files, as created by
9268 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9269 mode are currently supported.")
9270 (license license:artistic2.0)))
9272 (define-public r-abhgenotyper
9274 (name "r-abhgenotyper")
9279 (uri (cran-uri "ABHgenotypeR" version))
9281 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9282 (properties `((upstream-name . "ABHgenotypeR")))
9283 (build-system r-build-system)
9285 `(("r-ggplot2" ,r-ggplot2)
9286 ("r-reshape2" ,r-reshape2)))
9287 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9288 (synopsis "Visualize and manipulate ABH genotypes")
9290 "The @code{r-abhgenotyper} package provides simple imputation,
9291 error-correction and plotting capacities for genotype data. The package is
9292 supposed to serve as an intermediate but independent analysis tool between the
9293 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9294 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9295 genotypes as \"graphical genotypes\".")
9296 (license license:gpl3)))
9298 (define-public r-furrr
9305 (uri (cran-uri "furrr" version))
9308 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9309 (build-system r-build-system)
9311 `(("r-ellipsis" ,r-ellipsis)
9312 ("r-future" ,r-future)
9313 ("r-globals" ,r-globals)
9314 ("r-lifecycle" ,r-lifecycle)
9315 ("r-purrr" ,r-purrr)
9316 ("r-rlang" ,r-rlang)
9317 ("r-vctrs" ,r-vctrs)))
9318 (home-page "https://github.com/DavisVaughan/furrr")
9319 (synopsis "Apply mapping functions in parallel using futures")
9321 "This package provides implementations of the family of @code{map()}
9322 functions from the @code{purrr} package that can be resolved using any
9323 @code{future}-supported backend, e.g. parallel on the local machine or
9324 distributed on a compute cluster.")
9325 (license license:lgpl2.1+)))
9327 (define-public r-abjutils
9334 (uri (cran-uri "abjutils" version))
9336 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9337 (build-system r-build-system)
9339 `(("r-dplyr" ,r-dplyr)
9340 ("r-magrittr" ,r-magrittr)
9341 ("r-purrr" ,r-purrr)
9342 ("r-rlang" ,r-rlang)
9343 ("r-rstudioapi" ,r-rstudioapi)
9344 ("r-stringi" ,r-stringi)
9345 ("r-stringr" ,r-stringr)
9346 ("r-tidyr" ,r-tidyr)))
9347 (home-page "https://github.com/abjur/abjutils/")
9348 (synopsis "Collection of tools for jurimetrical analysis")
9350 "This package implements general purpose tools, such as functions for
9351 sampling and basic manipulation of Brazilian lawsuits identification number.
9352 It also implements functions for text cleaning, such as accentuation
9354 (license license:expat)))
9356 (define-public r-abnormality
9358 (name "r-abnormality")
9363 (uri (cran-uri "abnormality" version))
9365 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9366 (build-system r-build-system)
9368 `(("r-mass" ,r-mass)
9369 ("r-matrix" ,r-matrix)))
9370 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9371 (synopsis "Measure a subject's abnormality with respect to a reference population")
9373 "This package contains functions to implement the methodology and
9374 considerations laid out by Marks et al. in the article \"Measuring abnormality
9375 in high dimensional spaces: applications in biomechanical gait analysis\".
9376 Using high-dimensional datasets to measure a subject's overall level of
9377 abnormality as compared to a reference population is often needed in outcomes
9379 (license license:expat)))
9381 (define-public r-abodoutlier
9383 (name "r-abodoutlier")
9388 (uri (cran-uri "abodOutlier" version))
9390 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9391 (properties `((upstream-name . "abodOutlier")))
9392 (build-system r-build-system)
9394 `(("r-cluster" ,r-cluster)))
9395 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9396 (synopsis "Angle-based outlier detection")
9398 "This package performs angle-based outlier detection on a given data
9399 frame. It offers three methods to process data:
9401 @item full but slow implementation using all the data that has cubic
9403 @item a fully randomized method;
9404 @item a method using k-nearest neighbours.
9406 These algorithms are well suited for high dimensional data outlier
9408 (license license:expat)))
9410 (define-public r-abps
9417 (uri (cran-uri "ABPS" version))
9419 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9420 (properties `((upstream-name . "ABPS")))
9421 (build-system r-build-system)
9422 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9423 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9424 (synopsis "Abnormal blood profile score to detect blood doping")
9426 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9427 The ABPS is a part of the Athlete biological passport program of the World
9428 anti-doping agency, which combines several blood parameters into a single
9429 score in order to detect blood doping. The package also contains functions to
9430 calculate other scores used in anti-doping programs, such as the ratio of
9431 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9432 (license license:gpl2+)))
9434 (define-public r-parmigene
9436 (name "r-parmigene")
9441 (uri (cran-uri "parmigene" version))
9444 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9445 (build-system r-build-system)
9446 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9447 (synopsis "Mutual information estimation for gene network reconstruction")
9449 "This package provides a parallel estimation of the mutual information
9450 based on entropy estimates from k-nearest neighbors distances and algorithms
9451 for the reconstruction of gene regulatory networks.")
9452 (license license:agpl3+)))
9454 (define-public r-pscl
9461 (uri (cran-uri "pscl" version))
9463 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9464 (build-system r-build-system)
9466 `(("r-mass" ,r-mass)))
9467 (home-page "https://github.com/atahk/pscl/")
9468 (synopsis "Political science computational laboratory")
9470 "The @code{pscl} is an R package providing classes and methods for:
9472 @item Bayesian analysis of roll call data (item-response models);
9473 @item elementary Bayesian statistics;
9474 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9476 @item utility functions.
9478 (license license:gpl2)))
9480 (define-public r-accelmissing
9482 (name "r-accelmissing")
9487 (uri (cran-uri "accelmissing" version))
9489 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9490 (build-system r-build-system)
9492 `(("r-mice" ,r-mice)
9493 ("r-pscl" ,r-pscl)))
9494 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9495 (synopsis "Missing value imputation for accelerometer data")
9497 "This package provides a statistical method to impute the missing values in
9498 accelerometer data. The methodology includes both parametric and
9499 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9500 model. It also provides multiple functions to preprocess the accelerometer data
9501 previous to the missing data imputation. These include detecting the wearing
9502 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9503 (license license:gpl2+)))
9505 (define-public r-mhsmm
9512 (uri (cran-uri "mhsmm" version))
9514 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9515 (build-system r-build-system)
9516 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9517 (home-page "https://github.com/jaredo/mhsmm/")
9518 (synopsis "Inference for hidden Markov and semi-Markov models")
9520 "The @code{r-mhsmm} package implements estimation and prediction methods for
9521 hidden Markov and semi-Markov models for multiple observation sequences. Such
9522 techniques are of interest when observed data is thought to be dependent on some
9523 unobserved (or hidden) state. Also, this package is suitable for equidistant
9524 time series data, with multivariate and/or missing data. Allows user defined
9525 emission distributions.")
9526 (license license:gpl2+)))
9528 (define-public r-nleqslv
9535 (uri (cran-uri "nleqslv" version))
9537 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9538 (build-system r-build-system)
9539 (native-inputs `(("gfortran" ,gfortran)))
9540 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9541 (synopsis "Solve systems of nonlinear equations")
9543 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9544 Broyden or a Newton method with a choice of global strategies such as line
9545 search and trust region. There are options for using a numerical or user
9546 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9547 singular or ill-conditioned Jacobian.")
9548 (license license:gpl2+)))
9550 (define-public r-physicalactivity
9552 (name "r-physicalactivity")
9557 (uri (cran-uri "PhysicalActivity" version))
9559 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9561 `((upstream-name . "PhysicalActivity")))
9562 (build-system r-build-system)
9563 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9564 (synopsis "Procesing accelerometer data for physical activity measurement")
9566 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9567 for classification of monitor wear and nonwear time intervals in accelerometer
9568 data collected to assess physical activity. The package also contains functions
9569 for making plots of accelerometer data and obtaining the summary of various
9570 information including daily monitor wear time and the mean monitor wear time
9571 during valid days. The revised package version 0.2-1 improved the functions
9572 regarding speed, robustness and add better support for time zones and daylight
9573 saving. In addition, several functions were added:
9575 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9576 @item the @code{markPAI} can categorize physical activity intensity level based
9577 on user-defined cut-points of accelerometer counts.
9579 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9580 @code{queryActigraph} functions.")
9581 (license license:gpl3+)))
9583 (define-public r-acc
9590 (uri (cran-uri "acc" version))
9592 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9593 (build-system r-build-system)
9595 `(("r-circlize" ,r-circlize)
9597 ("r-ggplot2" ,r-ggplot2)
9598 ("r-iterators" ,r-iterators)
9599 ("r-mhsmm" ,r-mhsmm)
9600 ("r-nleqslv" ,r-nleqslv)
9601 ("r-physicalactivity" ,r-physicalactivity)
9603 ("r-r-utils" ,r-r-utils)
9605 ("r-rcpparmadillo" ,r-rcpparmadillo)
9606 ("r-rsqlite" ,r-rsqlite)
9608 (home-page "https://cran.r-project.org/web/packages/acc/")
9609 (synopsis "Exploring accelerometer data")
9611 "This package processes accelerometer data from uni-axial and tri-axial devices
9612 and generates data summaries. Also, includes functions to plot, analyze, and
9613 simulate accelerometer data.")
9614 (license license:gpl2+)))
9616 (define-public r-rbenchmark
9618 (name "r-rbenchmark")
9623 (uri (cran-uri "rbenchmark" version))
9625 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9626 (build-system r-build-system)
9627 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9628 (synopsis "Benchmarking routine for R")
9630 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9631 and is intended to facilitate benchmarking of arbitrary R code. The library
9632 consists of just one function, benchmark, which is a simple wrapper around
9633 system.time. Given a specification of the benchmarking process (counts of
9634 replications, evaluation environment) and an arbitrary number of expressions,
9635 benchmark evaluates each of the expressions in the specified environment,
9636 replicating the evaluation as many times as specified, and returning the results
9637 conveniently wrapped into a data frame.")
9638 (license license:gpl2+)))
9640 (define-public r-mitools
9647 (uri (cran-uri "mitools" version))
9650 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9651 (build-system r-build-system)
9652 (propagated-inputs `(("r-dbi" ,r-dbi)))
9653 (home-page "https://cran.r-project.org/web/packages/mitools/")
9654 (synopsis "Tools for multiple imputation of missing data")
9656 "This package provides tools to perform analyses and combine results from
9657 multiple-imputation datasets.")
9658 (license license:gpl2)))
9660 (define-public r-mixsqp
9666 (uri (cran-uri "mixsqp" version))
9669 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9670 (properties `((upstream-name . "mixsqp")))
9671 (build-system r-build-system)
9673 `(("r-irlba" ,r-irlba)
9675 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9677 `(("r-knitr" ,r-knitr)))
9678 (home-page "https://github.com/stephenslab/mixsqp")
9680 "Sequential quadratic programming for maximum-likelihood estimation")
9682 "This package provides an optimization method based on sequential
9683 quadratic programming for maximum likelihood estimation of the mixture
9684 proportions in a finite mixture model where the component densities are
9685 known. The algorithm is expected to obtain solutions that are at least
9686 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9687 are expected to arrive at solutions more quickly when the number of
9688 samples is large and the number of mixture components is not too large.")
9689 (license license:expat)))
9691 (define-public r-magick
9698 (uri (cran-uri "magick" version))
9701 "0m1kij6pp7dmsrhl80h60iyccjqmbbb3zdnqdc9sgy1kj1x3pscp"))))
9702 (build-system r-build-system)
9704 `(("imagemagick" ,imagemagick)
9707 `(("r-curl" ,r-curl)
9708 ("r-magrittr" ,r-magrittr)
9709 ("r-rcpp" ,r-rcpp)))
9711 `(("pkg-config" ,pkg-config)
9712 ("r-knitr" ,r-knitr)))
9713 (home-page "https://github.com/ropensci/magick")
9714 (synopsis "Advanced graphics and image-processing in R")
9716 "This package provides bindings to ImageMagick, a comprehensive image
9717 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9718 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9719 operations are vectorized via the Magick++ STL meaning they operate either on
9720 a single frame or a series of frames for working with layers, collages, or
9721 animation. In RStudio, images are automatically previewed when printed to the
9722 console, resulting in an interactive editing environment.")
9723 (license license:expat)))
9725 (define-public r-survey
9732 (uri (cran-uri "survey" version))
9735 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9736 (build-system r-build-system)
9738 `(("r-lattice" ,r-lattice)
9739 ("r-matrix" ,r-matrix)
9740 ("r-minqa" ,r-minqa)
9741 ("r-mitools" ,r-mitools)
9742 ("r-numderiv" ,r-numderiv)
9743 ("r-survival" ,r-survival)))
9744 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9745 (synopsis "Analysis of complex survey samples")
9747 "This package provides tools for the analysis of complex survey samples.
9748 The provided features include: summary statistics, two-sample tests, rank
9749 tests, generalised linear models, cumulative link models, Cox models,
9750 loglinear models, and general maximum pseudolikelihood estimation for
9751 multistage stratified, cluster-sampled, unequally weighted survey samples;
9752 variances by Taylor series linearisation or replicate weights;
9753 post-stratification, calibration, and raking; two-phase subsampling designs;
9754 graphics; PPS sampling without replacement; principal components, and factor
9756 ;; Either version of the GPL.
9757 (license (list license:gpl2 license:gpl3))))
9759 (define-public r-gee
9766 (uri (cran-uri "gee" version))
9769 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9770 (properties `((upstream-name . "gee")))
9771 (build-system r-build-system)
9773 `(("gfortran" ,gfortran)))
9774 (home-page "https://cran.r-project.org/web/packages/gee/")
9775 (synopsis "Generalized estimation equation solver")
9777 "This package provides a solver for generalized estimation equations.")
9778 (license license:gpl2)))
9780 (define-public r-tab
9787 (uri (cran-uri "tab" version))
9790 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9791 (properties `((upstream-name . "tab")))
9792 (build-system r-build-system)
9794 `(("r-dplyr" ,r-dplyr)
9796 ("r-knitr" ,r-knitr)
9798 ("r-survey" ,r-survey)
9799 ("r-survival" ,r-survival)
9800 ("r-xtable" ,r-xtable)))
9801 (home-page "https://cran.r-project.org/web/packages/tab/")
9802 (synopsis "Create summary tables for statistical reports")
9804 "This package contains functions for creating various types of summary
9805 tables, e.g. comparing characteristics across levels of a categorical variable
9806 and summarizing fitted generalized linear models, generalized estimating
9807 equations, and Cox proportional hazards models. Functions are available to
9808 handle data from simple random samples as well as complex surveys.")
9809 (license license:gpl3+)))
9811 (define-public r-dvmisc
9818 (uri (cran-uri "dvmisc" version))
9820 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9821 (build-system r-build-system)
9823 `(("r-cubature" ,r-cubature)
9824 ("r-data-table" ,r-data-table)
9825 ("r-dplyr" ,r-dplyr)
9826 ("r-ggplot2" ,r-ggplot2)
9828 ("r-mvtnorm" ,r-mvtnorm)
9829 ("r-pracma" ,r-pracma)
9830 ("r-rbenchmark" ,r-rbenchmark)
9832 ("r-survey" ,r-survey)
9834 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9835 (synopsis "Faster computation of common statistics and miscellaneous functions")
9837 "This package implements faster versions of base R functions (e.g. mean, standard
9838 deviation, covariance, weighted mean), mostly written in C++, along with
9839 miscellaneous functions for various purposes (e.g. create the histogram with
9840 fitted probability density function or probability mass function curve, create
9841 the body mass index groups, assess the linearity assumption in logistic
9843 (license license:gpl2)))
9845 (define-public r-accelerometry
9847 (name "r-accelerometry")
9852 (uri (cran-uri "accelerometry" version))
9854 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9855 (build-system r-build-system)
9857 `(("r-dvmisc" ,r-dvmisc)
9858 ("r-rcpp" ,r-rcpp)))
9859 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9860 (synopsis "Functions for processing accelerometer data")
9862 "This package provides a collection of functions that perform operations on
9863 time-series accelerometer data, such as identify the non-wear time, flag minutes
9864 that are part of an activity bout, and find the maximum 10-minute average count
9865 value. The functions are generally very flexible, allowing for a variety of
9866 algorithms to be implemented.")
9867 (license license:gpl3)))
9869 (define-public r-absim
9876 (uri (cran-uri "AbSim" version))
9878 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9879 (properties `((upstream-name . "AbSim")))
9880 (build-system r-build-system)
9883 ("r-powerlaw" ,r-powerlaw)))
9884 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9885 (synopsis "Time resolved simulations of antibody repertoires")
9887 "This package provides simulation methods for the evolution of antibody repertoires.
9888 The heavy and light chain variable region of both human and C57BL/6 mice can
9889 be simulated in a time-dependent fashion. Both single lineages using one set of
9890 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9891 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9892 Upon completion, the main loop of the algorithm begins, with each iteration
9893 representing one simulated time step. Various mutation events are possible at
9894 each time step, contributing to a diverse final repertoire.")
9895 (license license:gpl2)))
9897 (define-public r-quic
9904 (uri (cran-uri "QUIC" version))
9906 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9907 (properties `((upstream-name . "QUIC")))
9908 (build-system r-build-system)
9909 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9910 (synopsis "Regularized sparse inverse covariance matrix estimation")
9912 "This package implements the regularized Gaussian maximum likelihood
9913 estimation of the inverse of a covariance matrix. It uses Newton's method and
9914 coordinate descent to solve the regularized inverse covariance matrix
9915 estimation problem.")
9916 ;; The project home page states that the release is under GPLv3 or later.
9917 ;; The CRAN page only says GPL-3.
9918 (license license:gpl3+)))
9920 (define-public r-abundant
9927 (uri (cran-uri "abundant" version))
9929 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9930 (build-system r-build-system)
9932 `(("r-quic" ,r-quic)))
9933 (home-page "https://cran.r-project.org/web/packages/abundant/")
9934 (synopsis "Abundant regression and high-dimensional principal fitted components")
9936 "This package provides tools to fit and predict with the high-dimensional
9937 principal fitted components model. This model is described by Cook, Forzani,
9938 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9939 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9940 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9941 (license license:gpl2+)))
9943 (define-public r-ac3net
9950 (uri (cran-uri "Ac3net" version))
9952 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9953 (properties `((upstream-name . "Ac3net")))
9954 (build-system r-build-system)
9956 `(("r-data-table" ,r-data-table)))
9957 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9958 (synopsis "Inferring directional conservative causal core gene networks")
9959 (description "This package infers directional Conservative causal core
9960 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9961 directional network.")
9962 (license license:gpl3+)))
9964 (define-public r-aca
9971 (uri (cran-uri "ACA" version))
9973 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9974 (properties `((upstream-name . "ACA")))
9975 (build-system r-build-system)
9976 (home-page "https://cran.r-project.org/web/packages/ACA/")
9977 (synopsis "Abrupt change-point or aberration detection in point series")
9979 "This package offers an interactive function for the detection of breakpoints in
9981 ;; Any version of the GPL
9982 (license (list license:gpl2+ license:gpl3+))))
9984 (define-public r-acceptancesampling
9986 (name "r-acceptancesampling")
9991 (uri (cran-uri "AcceptanceSampling" version))
9993 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9995 `((upstream-name . "AcceptanceSampling")))
9996 (build-system r-build-system)
9997 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9998 (synopsis "Creation and evaluation of acceptance sampling plans")
10000 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
10001 acceptance sampling plans. Acceptance sampling is a methodology commonly used
10002 in quality control and improvement. International standards of acceptance
10003 sampling provide sampling plans for specific circumstances. The aim of this
10004 package is to provide an easy-to-use interface to visualize single, double or
10005 multiple sampling plans. In addition, methods have been provided to enable the
10006 user to assess sampling plans against pre-specified levels of performance, as
10007 measured by the probability of acceptance for a given level of quality in the
10009 (license license:gpl3+)))
10011 (define-public r-acclma
10018 (uri (cran-uri "ACCLMA" version))
10020 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
10021 (properties `((upstream-name . "ACCLMA")))
10022 (build-system r-build-system)
10023 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10024 (synopsis "ACC & LMA graph plotting")
10026 "This package contains a function that imports data from a @acronym{CSV,
10027 Comma-Separated Values} file, or uses manually entered data from the format (x,
10028 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10029 Curve} vs @acronym{LOI, Line of Independence} graph and
10030 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10031 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10032 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10033 string) was passed, a manual data entry window is opened. The header parameter
10034 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10035 a header row or not. The dataset should contain only one independent variable
10036 (x) and one dependent variable (y) and can contain a weight for each
10038 (license license:gpl2)))
10040 (define-public r-aspi
10047 (uri (cran-uri "aspi" version))
10049 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10050 (build-system r-build-system)
10052 "https://cran.r-project.org/web/packages/aspi/")
10054 "Analysis of symmetry of parasitic infections")
10056 "This package provides tools for the analysis and visualization of bilateral
10057 asymmetry in parasitic infections.")
10058 (license license:gpl3+)))
10060 (define-public r-sandwich
10062 (name "r-sandwich")
10067 (uri (cran-uri "sandwich" version))
10070 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10071 (build-system r-build-system)
10073 `(("r-zoo" ,r-zoo)))
10074 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10075 (synopsis "Robust Covariance Matrix Estimators")
10077 "This package provides model-robust standard error estimators for
10078 cross-sectional, time series, clustered, panel, and longitudinal data.")
10079 ;; Either version of the license.
10080 (license (list license:gpl2 license:gpl3))))
10082 (define-public r-th-data
10089 (uri (cran-uri "TH.data" version))
10092 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10093 (properties `((upstream-name . "TH.data")))
10094 (build-system r-build-system)
10096 `(("r-mass" ,r-mass)
10097 ("r-survival" ,r-survival)))
10098 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10099 (synopsis "Shared data sets")
10101 "This package contains supporting data sets that are used in other
10102 packages maintained by Torsten Hothorn.")
10103 (license license:gpl3)))
10105 (define-public r-multcomp
10107 (name "r-multcomp")
10112 (uri (cran-uri "multcomp" version))
10115 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10116 (build-system r-build-system)
10118 `(("r-codetools" ,r-codetools)
10119 ("r-mvtnorm" ,r-mvtnorm)
10120 ("r-sandwich" ,r-sandwich)
10121 ("r-survival" ,r-survival)
10122 ("r-th-data" ,r-th-data)))
10123 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10124 (synopsis "Simultaneous inference in general parametric models")
10126 "Simultaneous tests and confidence intervals for general linear
10127 hypotheses in parametric models, including linear, generalized linear, linear
10128 mixed effects, and survival models. The package includes demos reproducing
10129 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10130 Hothorn, Westfall, 2010, CRC Press).")
10131 (license license:gpl2)))
10133 (define-public r-emmeans
10140 (uri (cran-uri "emmeans" version))
10143 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
10144 (build-system r-build-system)
10146 `(("r-estimability" ,r-estimability)
10147 ("r-mvtnorm" ,r-mvtnorm)
10148 ("r-numderiv" ,r-numderiv)
10150 ("r-xtable" ,r-xtable)))
10152 `(("r-knitr" ,r-knitr)))
10153 (home-page "https://github.com/rvlenth/emmeans")
10154 (synopsis "Estimated marginal means, aka least-squares means")
10156 "This package provides tools to obtain @dfn{estimated marginal
10157 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10158 be used to compute contrasts or linear functions of EMMs, trends, and
10159 comparisons of slopes.")
10160 ;; Either version of the license.
10161 (license (list license:gpl2 license:gpl3))))
10163 (define-public r-pwr
10170 (uri (cran-uri "pwr" version))
10173 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10174 (build-system r-build-system)
10176 `(("r-knitr" ,r-knitr)))
10177 (home-page "https://github.com/heliosdrm/pwr")
10178 (synopsis "Basic functions for power analysis")
10180 "This package provides power analysis functions along the lines of
10182 (license license:gpl3+)))
10184 (define-public r-libcoin
10191 (uri (cran-uri "libcoin" version))
10193 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10194 (build-system r-build-system)
10195 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10196 (home-page "https://cran.r-project.org/web/packages/libcoin")
10197 (synopsis "Linear test statistics for permutation inference")
10199 "This package provides basic infrastructure for linear test statistics
10200 and permutation inference in the framework of Strasser and Weber (1999).")
10201 (license license:gpl2)))
10203 (define-public r-coin
10210 (uri (cran-uri "coin" version))
10213 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10214 (build-system r-build-system)
10216 `(("r-libcoin" ,r-libcoin)
10217 ("r-matrixstats" ,r-matrixstats)
10218 ("r-modeltools" ,r-modeltools)
10219 ("r-multcomp" ,r-multcomp)
10220 ("r-mvtnorm" ,r-mvtnorm)
10221 ("r-survival" ,r-survival)))
10222 (home-page "http://coin.r-forge.r-project.org")
10223 (synopsis "Conditional inference procedures in a permutation test framework")
10225 "This package provides conditional inference procedures for the general
10226 independence problem including two-sample, K-sample (non-parametric ANOVA),
10227 correlation, censored, ordered and multivariate problems.")
10228 (license license:gpl2)))
10230 (define-public r-bayesplot
10232 (name "r-bayesplot")
10237 (uri (cran-uri "bayesplot" version))
10240 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10241 (build-system r-build-system)
10243 `(("pandoc" ,pandoc)
10244 ("pandoc-citeproc" ,pandoc-citeproc)))
10246 `(("r-knitr" ,r-knitr)))
10248 `(("r-dplyr" ,r-dplyr)
10249 ("r-ggplot2" ,r-ggplot2)
10250 ("r-ggridges" ,r-ggridges)
10252 ("r-reshape2" ,r-reshape2)
10253 ("r-rlang" ,r-rlang)
10254 ("r-tibble" ,r-tibble)
10255 ("r-tidyselect" ,r-tidyselect)))
10256 (home-page "https://mc-stan.org/bayesplot")
10257 (synopsis "Plotting for Bayesian models")
10259 "This package provides plotting functions for posterior analysis, model
10260 checking, and MCMC diagnostics. The package is designed not only to provide
10261 convenient functionality for users, but also a common set of functions that
10262 can be easily used by developers working on a variety of R packages for
10263 Bayesian modeling.")
10264 (license license:gpl3+)))
10266 (define-public r-tmb
10273 (uri (cran-uri "TMB" version))
10276 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10277 (properties `((upstream-name . "TMB")))
10278 (build-system r-build-system)
10280 `(("r-matrix" ,r-matrix)
10281 ("r-rcppeigen" ,r-rcppeigen)))
10282 (home-page "http://tmb-project.org")
10283 (synopsis "Template model builder: a general random effect tool")
10285 "With this tool, a user should be able to quickly implement complex
10286 random effect models through simple C++ templates. The package combines
10287 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10288 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10289 from R) to obtain an efficient implementation of the applied Laplace
10290 approximation with exact derivatives. Key features are: Automatic sparseness
10291 detection, parallelism through BLAS and parallel user templates.")
10292 (license license:gpl2)))
10294 (define-public r-sjstats
10301 (uri (cran-uri "sjstats" version))
10303 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10304 (build-system r-build-system)
10306 `(("r-bayestestr" ,r-bayestestr)
10307 ("r-broom" ,r-broom)
10308 ("r-dplyr" ,r-dplyr)
10309 ("r-effectsize" ,r-effectsize)
10310 ("r-emmeans" ,r-emmeans)
10311 ("r-insight" ,r-insight)
10313 ("r-magrittr" ,r-magrittr)
10315 ("r-modelr" ,r-modelr)
10316 ("r-parameters" ,r-parameters)
10317 ("r-performance" ,r-performance)
10318 ("r-purrr" ,r-purrr)
10319 ("r-rlang" ,r-rlang)
10320 ("r-sjlabelled" ,r-sjlabelled)
10321 ("r-sjmisc" ,r-sjmisc)
10322 ("r-tidyr" ,r-tidyr)))
10323 (home-page "https://github.com/strengejacke/sjstats")
10324 (synopsis "Functions for common statistical computations")
10326 "This package provides a collection of convenient functions for common
10327 statistical computations, which are not directly provided by R's @code{base}
10328 or @code{stats} packages. This package aims at providing, first, shortcuts
10329 for statistical measures, which otherwise could only be calculated with
10330 additional effort. Second, these shortcut functions are generic, and can be
10331 applied not only to vectors, but also to other objects as well. The focus of
10332 most functions lies on summary statistics or fit measures for regression
10333 models, including generalized linear models, mixed effects models and Bayesian
10335 (license license:gpl3)))
10337 (define-public r-glmmtmb
10340 (version "1.0.2.1")
10344 (uri (cran-uri "glmmTMB" version))
10347 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10348 (properties `((upstream-name . "glmmTMB")))
10349 (build-system r-build-system)
10351 `(("r-lme4" ,r-lme4)
10352 ("r-matrix" ,r-matrix)
10354 ("r-rcppeigen" ,r-rcppeigen)
10357 `(("r-knitr" ,r-knitr))) ; for vignettes
10358 (home-page "https://github.com/glmmTMB")
10359 (synopsis "Generalized linear mixed models")
10361 "Fit linear and generalized linear mixed models with various extensions,
10362 including zero-inflation. The models are fitted using maximum likelihood
10363 estimation via the Template Model Builder. Random effects are assumed to be
10364 Gaussian on the scale of the linear predictor and are integrated out using the
10365 Laplace approximation. Gradients are calculated using automatic
10367 (license license:agpl3+)))
10369 (define-public r-bayestestr
10371 (name "r-bayestestr")
10376 (uri (cran-uri "bayestestR" version))
10379 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10380 (properties `((upstream-name . "bayestestR")))
10381 (build-system r-build-system)
10383 `(("r-insight" ,r-insight)))
10385 `(("r-knitr" ,r-knitr)))
10386 (home-page "https://github.com/easystats/bayestestR")
10387 (synopsis "Describe Bayesian models and posterior distributions")
10389 "This package provides utilities to understand and describe posterior
10390 distributions and Bayesian models. It includes point-estimates such as
10391 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10392 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10393 ROPE percentage and pd).")
10394 (license license:gpl3)))
10396 (define-public r-performance
10398 (name "r-performance")
10403 (uri (cran-uri "performance" version))
10406 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10407 (build-system r-build-system)
10409 `(("r-bayestestr" ,r-bayestestr)
10410 ("r-insight" ,r-insight)))
10411 (home-page "https://easystats.github.io/performance/")
10412 (synopsis "Assessment of regression models performance")
10414 "This package provides utilities for computing measures to assess model
10415 quality, which are not directly provided by R's @code{base} or @code{stats}
10416 packages. These include e.g. measures like r-squared, intraclass correlation
10417 coefficient, root mean squared error or functions to check models for
10418 overdispersion, singularity or zero-inflation and more. Functions apply to a
10419 large variety of regression models, including generalized linear models, mixed
10420 effects models and Bayesian models.")
10421 (license license:gpl3)))
10423 (define-public r-ggeffects
10425 (name "r-ggeffects")
10430 (uri (cran-uri "ggeffects" version))
10433 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10434 (build-system r-build-system)
10436 `(("r-insight" ,r-insight)
10438 ("r-sjlabelled" ,r-sjlabelled)))
10440 `(("r-knitr" ,r-knitr)))
10441 (home-page "https://github.com/strengejacke/ggeffects")
10442 (synopsis "Create tidy data frames of marginal effects for ggplot")
10444 "This package provides tools to compute marginal effects from statistical
10445 models and return the result as tidy data frames. These data frames are ready
10446 to use with the @code{ggplot2} package. Marginal effects can be calculated
10447 for many different models. Interaction terms, splines and polynomial terms
10448 are also supported. The two main functions are @code{ggpredict()} and
10449 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10450 results using @code{ggplot2}.")
10451 (license license:gpl3)))
10453 (define-public r-effectsize
10455 (name "r-effectsize")
10460 (uri (cran-uri "effectsize" version))
10463 "0mgkq12ym72ncakkjpkzkjglhksyhj3iw8v4a8fjgpf7prvn191g"))))
10464 (properties `((upstream-name . "effectsize")))
10465 (build-system r-build-system)
10467 `(("r-bayestestr" ,r-bayestestr)
10468 ("r-insight" ,r-insight)
10469 ("r-parameters" ,r-parameters)))
10471 `(("r-knitr" ,r-knitr)))
10472 (home-page "https://github.com/easystats/effectsize")
10473 (synopsis "Indices of effect size and standardized parameters")
10475 "This package provides utilities to work with indices of effect size and
10476 standardized parameters for a wide variety of models, allowing computation and
10477 conversion of indices such as Cohen's d, r, odds, etc.")
10478 (license license:gpl3)))
10480 (define-public r-sjplot
10487 (uri (cran-uri "sjPlot" version))
10489 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10490 (properties `((upstream-name . "sjPlot")))
10491 (build-system r-build-system)
10493 `(("r-bayestestr" ,r-bayestestr)
10494 ("r-dplyr" ,r-dplyr)
10495 ("r-effectsize" ,r-effectsize)
10496 ("r-ggeffects" ,r-ggeffects)
10497 ("r-ggplot2" ,r-ggplot2)
10498 ("r-insight" ,r-insight)
10499 ("r-knitr" ,r-knitr)
10501 ("r-parameters" ,r-parameters)
10502 ("r-performance" ,r-performance)
10503 ("r-purrr" ,r-purrr)
10504 ("r-rlang" ,r-rlang)
10505 ("r-scales" ,r-scales)
10506 ("r-sjlabelled" ,r-sjlabelled)
10507 ("r-sjmisc" ,r-sjmisc)
10508 ("r-sjstats" ,r-sjstats)
10509 ("r-tidyr" ,r-tidyr)))
10511 `(("r-knitr" ,r-knitr)))
10512 (home-page "https://strengejacke.github.io/sjPlot/")
10513 (synopsis "Data visualization for statistics in social science")
10515 "This package represents a collection of plotting and table output
10516 functions for data visualization. Results of various statistical
10517 analyses (that are commonly used in social sciences) can be visualized using
10518 this package, including simple and cross tabulated frequencies, histograms,
10519 box plots, (generalized) linear models, mixed effects models, principal
10520 component analysis and correlation matrices, cluster analyses, scatter plots,
10521 stacked scales, effects plots of regression models (including interaction
10522 terms) and much more. This package supports labelled data.")
10523 (license license:gpl3)))
10525 (define-public r-ini
10532 (uri (cran-uri "ini" version))
10535 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10536 (build-system r-build-system)
10537 (home-page "https://github.com/dvdscripter/ini")
10538 (synopsis "Read and write configuration files")
10540 "This package provides tools to parse simple @code{.ini} configuration
10541 files to an structured list. Users can manipulate this resulting list with
10542 @code{lapply()} functions. This same structured list can be used to write
10543 back to file after modifications.")
10544 (license license:gpl3)))
10546 (define-public r-gitcreds
10548 (name "r-gitcreds")
10553 (uri (cran-uri "gitcreds" version))
10556 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10557 (properties `((upstream-name . "gitcreds")))
10558 (build-system r-build-system)
10559 (inputs `(("git" ,git-minimal)))
10560 (native-inputs `(("r-knitr" ,r-knitr)))
10561 (home-page "https://github.com/r-lib/gitcreds")
10562 (synopsis "Query git credentials from R")
10564 "Query, set, and delete credentials from the git credential store.
10565 Manage GitHub tokens and other git credentials. This package is to be used by
10566 other packages that need to authenticate to GitHub and/or other git
10568 (license license:expat)))
10570 (define-public r-gh
10577 (uri (cran-uri "gh" version))
10580 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10581 (build-system r-build-system)
10584 ("r-gitcreds" ,r-gitcreds)
10587 ("r-jsonlite" ,r-jsonlite)))
10589 `(("r-knitr" ,r-knitr)))
10590 (home-page "https://github.com/r-lib/gh#readme")
10591 (synopsis "Access the GitHub API via R")
10593 "This package provides a minimal R client to access the GitHub API.")
10594 (license license:expat)))
10596 (define-public r-fs
10603 (uri (cran-uri "fs" version))
10606 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10607 (build-system r-build-system)
10609 `(("r-knitr" ,r-knitr)))
10610 (home-page "https://fs.r-lib.org")
10611 (synopsis "Cross-platform file system operations based on libuv")
10613 "This package provides a cross-platform interface to file system
10614 operations, built on top of the libuv C library.")
10615 (license license:gpl3)))
10617 (define-public r-clisymbols
10619 (name "r-clisymbols")
10624 (uri (cran-uri "clisymbols" version))
10627 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10628 (build-system r-build-system)
10629 (home-page "https://github.com/gaborcsardi/clisymbols")
10630 (synopsis "Unicode symbols at the R prompt")
10632 "This package provides a small subset of Unicode symbols, that are useful
10633 when building command line applications. They fall back to alternatives on
10634 terminals that do not support Unicode.")
10635 (license license:expat)))
10637 (define-public r-credentials
10639 (name "r-credentials")
10644 (uri (cran-uri "credentials" version))
10647 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10648 (properties `((upstream-name . "credentials")))
10649 (build-system r-build-system)
10652 (modify-phases %standard-phases
10653 (add-after 'unpack 'setenv-HOME
10655 ;; This is necessary because git looks for $HOME/.gitconfig
10656 (setenv "HOME" "/tmp")
10659 `(("git" ,git-minimal)))
10661 `(("r-askpass" ,r-askpass)
10663 ("r-jsonlite" ,r-jsonlite)
10664 ("r-openssl" ,r-openssl)
10667 `(("r-knitr" ,r-knitr)))
10668 (home-page "https://docs.ropensci.org/credentials/")
10669 (synopsis "Tools for managing SSH and Git credentials")
10671 "This package assists you in setting up and retrieving of HTTPS and SSH
10672 credentials for use with git and other services. For HTTPS remotes the
10673 package interfaces the @command{git-credential} utility which @command{git}
10674 uses to store HTTP usernames and passwords. For SSH remotes this package
10675 provides convenient functions to find or generate appropriate SSH keys. The
10676 package both helps the user to setup a local git installation, and also
10677 provides a back-end for git/ssh client libraries to authenticate with existing
10678 user credentials.")
10679 (license license:expat)))
10681 (define-public r-gert
10688 (uri (cran-uri "gert" version))
10691 "0ag2ia6cfb5drf3517lg5nhik1w0nv09a75wdy5jdciws1qra3d6"))))
10692 (properties `((upstream-name . "gert")))
10693 (build-system r-build-system)
10695 `(("libgit2" ,libgit2)
10698 `(("r-askpass" ,r-askpass)
10699 ("r-credentials" ,r-credentials)
10700 ("r-openssl" ,r-openssl)
10701 ("r-rstudioapi" ,r-rstudioapi)
10705 `(("pkg-config" ,pkg-config)
10706 ("r-knitr" ,r-knitr)))
10707 (home-page "https://docs.ropensci.org/gert/")
10708 (synopsis "Simple Git client for R")
10710 "This package provides a simple git client for R based on libgit2 with
10711 support for SSH and HTTPS remotes. All functions in gert use basic R data
10712 types (such as vectors and data-frames) for their arguments and return values.
10713 User credentials are shared with command line git through the
10714 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10715 (license license:expat)))
10717 (define-public r-usethis
10724 (uri (cran-uri "usethis" version))
10727 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10728 (build-system r-build-system)
10731 ("r-clipr" ,r-clipr)
10732 ("r-crayon" ,r-crayon)
10739 ("r-jsonlite" ,r-jsonlite)
10740 ("r-lifecycle" ,r-lifecycle)
10741 ("r-purrr" ,r-purrr)
10742 ("r-rappdirs" ,r-rappdirs)
10743 ("r-rlang" ,r-rlang)
10744 ("r-rprojroot" ,r-rprojroot)
10745 ("r-rstudioapi" ,r-rstudioapi)
10746 ("r-whisker" ,r-whisker)
10747 ("r-withr" ,r-withr)
10748 ("r-yaml" ,r-yaml)))
10749 (home-page "https://github.com/r-lib/usethis")
10750 (synopsis "Automate R package and project setup")
10752 "This package helps you to automate R package and project setup tasks
10753 that are otherwise performed manually. This includes setting up unit testing,
10754 test coverage, continuous integration, Git, GitHub integration, licenses,
10755 Rcpp, RStudio projects, and more.")
10756 (license license:gpl3)))
10758 (define-public r-sessioninfo
10760 (name "r-sessioninfo")
10765 (uri (cran-uri "sessioninfo" version))
10768 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10769 (build-system r-build-system)
10772 ("r-withr" ,r-withr)))
10773 (home-page "https://github.com/r-lib/sessioninfo#readme")
10774 (synopsis "R session information")
10776 "This package provides tools to query and print information about the
10777 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10778 more information about packages, and where they were installed from.")
10779 (license license:gpl2)))
10781 (define-public r-remotes
10788 (uri (cran-uri "remotes" version))
10791 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10792 (build-system r-build-system)
10794 `(("r-knitr" ,r-knitr)))
10795 (home-page "https://github.com/r-lib/remotes#readme")
10796 (synopsis "R package installation from remote repositories")
10798 "Download and install R packages stored in GitHub, BitBucket, or plain
10799 subversion or git repositories. This package is a lightweight replacement of
10800 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10801 the code was copied over from @code{devtools}.")
10802 (license license:gpl2+)))
10804 (define-public r-xopen
10811 (uri (cran-uri "xopen" version))
10814 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10815 (build-system r-build-system)
10817 `(("r-processx" ,r-processx)))
10818 (home-page "https://github.com/r-lib/xopen#readme")
10819 (synopsis "Open system files, URLs, anything")
10821 "This package provides a cross-platform solution to open files,
10822 directories or URLs with their associated programs.")
10823 (license license:expat)))
10825 (define-public r-rcmdcheck
10827 (name "r-rcmdcheck")
10832 (uri (cran-uri "rcmdcheck" version))
10835 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10836 (build-system r-build-system)
10838 `(("r-callr" ,r-callr)
10840 ("r-crayon" ,r-crayon)
10842 ("r-digest" ,r-digest)
10843 ("r-pkgbuild" ,r-pkgbuild)
10844 ("r-prettyunits" ,r-prettyunits)
10846 ("r-rprojroot" ,r-rprojroot)
10847 ("r-sessioninfo" ,r-sessioninfo)
10848 ("r-withr" ,r-withr)
10849 ("r-xopen" ,r-xopen)))
10850 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10851 (synopsis "Run R CMD check from R and capture results")
10853 "Run @code{R CMD check} from R programmatically, and capture the results
10854 of the individual checks.")
10855 (license license:expat)))
10857 (define-public r-rapportools
10859 (name "r-rapportools")
10864 (uri (cran-uri "rapportools" version))
10867 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10868 (build-system r-build-system)
10870 `(("r-pander" ,r-pander)
10872 ("r-reshape" ,r-reshape)))
10873 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10874 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10876 "This package provides helper functions that act as wrappers to more
10877 advanced statistical methods with the advantage of having sane defaults for
10879 (license license:agpl3+)))
10881 (define-public r-pander
10888 (uri (cran-uri "pander" version))
10891 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10892 (build-system r-build-system)
10894 `(("r-digest" ,r-digest)
10895 ("r-rcpp" ,r-rcpp)))
10896 (home-page "https://rapporter.github.io/pander")
10897 (synopsis "Render R objects into Pandoc's markdown")
10899 "The main aim of the pander R package is to provide a minimal and easy
10900 tool for rendering R objects into Pandoc's markdown. The package is also
10901 capable of exporting/converting complex Pandoc documents (reports) in various
10903 ;; This package is licensed under either the AGPLv3+ or the very rarely
10905 (license license:agpl3+)))
10907 (define-public r-summarytools
10909 (name "r-summarytools")
10914 (uri (cran-uri "summarytools" version))
10917 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10918 (build-system r-build-system)
10920 `(("r-base64enc" ,r-base64enc)
10921 ("r-checkmate" ,r-checkmate)
10922 ("r-dplyr" ,r-dplyr)
10923 ("r-htmltools" ,r-htmltools)
10924 ("r-lubridate" ,r-lubridate)
10925 ("r-magick" ,r-magick)
10926 ("r-matrixstats" ,r-matrixstats)
10927 ("r-pander" ,r-pander)
10929 ("r-rapportools" ,r-rapportools)
10930 ("r-tibble" ,r-tibble)
10931 ("r-tidyr" ,r-tidyr)))
10933 `(("r-knitr" ,r-knitr)))
10934 (home-page "https://github.com/dcomtois/summarytools")
10935 (synopsis "Tools to quickly and neatly summarize data")
10937 "This package provides tools for data frame summaries, cross-tabulations,
10938 weight-enabled frequency tables and common univariate statistics in concise
10939 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10940 good point-of-entry for exploring data, both for experienced and new R
10942 (license license:gpl2)))
10944 (define-public r-lsei
10951 (uri (cran-uri "lsei" version))
10954 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10955 (build-system r-build-system)
10957 `(("gfortran" ,gfortran)))
10958 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10959 (synopsis "Solve regression problems under equality/inequality constraints")
10961 "It contains functions that solve least squares linear regression
10962 problems under linear equality/inequality constraints. Functions for solving
10963 quadratic programming problems are also available, which transform such
10964 problems into least squares ones first.")
10965 (license license:gpl2+)))
10967 (define-public r-npsurv
10974 (uri (cran-uri "npsurv" version))
10977 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10978 (build-system r-build-system)
10980 `(("r-lsei" ,r-lsei)))
10981 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10982 (synopsis "Nonparametric survival analysis")
10984 "This package contains functions for non-parametric survival analysis of
10985 exact and interval-censored observations.")
10986 (license license:gpl2+)))
10988 (define-public r-clusteval
10990 (name "r-clusteval")
10995 (uri (cran-uri "clusteval" version))
10998 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10999 (build-system r-build-system)
11001 `(("r-mvtnorm" ,r-mvtnorm)
11002 ("r-rcpp" ,r-rcpp)))
11003 (home-page "https://cran.r-project.org/web/packages/clusteval/")
11004 (synopsis "Evaluation of clustering algorithms")
11006 "This R package provides a suite of tools to evaluate clustering
11007 algorithms, clusterings, and individual clusters.")
11008 (license license:expat)))
11010 (define-public r-tweedie
11017 (uri (cran-uri "tweedie" version))
11020 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
11021 (build-system r-build-system)
11022 (native-inputs `(("gfortran" ,gfortran)))
11023 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11024 (synopsis "Evaluation of Tweedie exponential family models")
11026 "Maximum likelihood computations for Tweedie families, including the
11027 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11028 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11029 and related methods.")
11030 (license license:gpl2+)))
11032 (define-public r-rcppgsl
11039 (uri (cran-uri "RcppGSL" version))
11041 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11042 (properties `((upstream-name . "RcppGSL")))
11043 (build-system r-build-system)
11045 `(("r-rcpp" ,r-rcpp)
11047 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11048 (synopsis "Rcpp integration for GSL vectors and matrices")
11050 "The GNU Scientific Library (or GSL) is a collection of numerical
11051 routines for scientific computing. It is particularly useful for C and C++
11052 programs as it provides a standard C interface to a wide range of mathematical
11053 routines. There are over 1000 functions in total with an extensive test
11054 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11055 structures and R using concepts from Rcpp which is itself a package that eases
11056 the interfaces between R and C++.")
11057 (license license:gpl2+)))
11059 (define-public r-mvabund
11066 (uri (cran-uri "mvabund" version))
11069 "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
11070 (build-system r-build-system)
11072 `(("r-mass" ,r-mass)
11074 ("r-rcppgsl" ,r-rcppgsl)
11075 ("r-statmod" ,r-statmod)
11076 ("r-tweedie" ,r-tweedie)))
11077 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11078 (synopsis "Statistical methods for analysing multivariate abundance data")
11080 "This package provides a set of tools for displaying, modeling and
11081 analysing multivariate abundance data in community ecology.")
11082 (license license:lgpl2.1+)))
11084 (define-public r-afex
11091 (uri (cran-uri "afex" version))
11094 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11095 (build-system r-build-system)
11099 ("r-lmertest" ,r-lmertest)
11100 ("r-pbkrtest" ,r-pbkrtest)
11101 ("r-reshape2" ,r-reshape2)))
11103 `(("r-knitr" ,r-knitr)))
11104 (home-page "https://afex.singmann.science/")
11105 (synopsis "Analysis of factorial experiments")
11107 "This package provides convenience functions for analyzing factorial
11108 experiments using ANOVA or mixed models.")
11109 (license license:gpl2+)))
11111 (define-public r-lmertest
11113 (name "r-lmertest")
11118 (uri (cran-uri "lmerTest" version))
11121 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11122 (properties `((upstream-name . "lmerTest")))
11123 (build-system r-build-system)
11125 `(("r-ggplot2" ,r-ggplot2)
11128 ("r-numderiv" ,r-numderiv)))
11129 (home-page "https://github.com/runehaubo/lmerTestR")
11130 (synopsis "Tests in linear mixed effects models")
11132 "This package provides p-values in type I, II or III anova and summary
11133 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11134 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11135 package. Model selection methods include step, drop1 and anova-like tables
11136 for random effects (ranova). Methods for Least-Square means (LS-means) and
11137 tests of linear contrasts of fixed effects are also available.")
11138 (license license:gpl2+)))
11140 (define-public r-r2glmm
11147 (uri (cran-uri "r2glmm" version))
11150 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11151 (build-system r-build-system)
11153 `(("r-afex" ,r-afex)
11154 ("r-data-table" ,r-data-table)
11155 ("r-dplyr" ,r-dplyr)
11156 ("r-ggplot2" ,r-ggplot2)
11157 ("r-gridextra" ,r-gridextra)
11158 ("r-lmertest" ,r-lmertest)
11160 ("r-matrix" ,r-matrix)
11162 ("r-pbkrtest" ,r-pbkrtest)))
11163 (home-page "https://github.com/bcjaeger/r2glmm")
11164 (synopsis "Compute R squared for mixed (multilevel) models")
11166 "This package computes model and semi partial R squared with confidence
11167 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11168 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11169 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11171 (license license:gpl2)))
11173 (define-public r-weights
11180 (uri (cran-uri "weights" version))
11183 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11184 (build-system r-build-system)
11186 `(("r-gdata" ,r-gdata)
11187 ("r-hmisc" ,r-hmisc)
11188 ("r-mice" ,r-mice)))
11190 "https://cran.r-project.org/web/packages/weights/")
11191 (synopsis "Weighting and weighted statistics")
11192 (description "This package Provides a variety of functions for producing
11193 simple weighted statistics, such as weighted Pearson's correlations, partial
11194 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11195 includes some software for quickly recoding survey data and plotting point
11196 estimates from interaction terms in regressions (and multiply imputed
11197 regressions). NOTE: Weighted partial correlation calculations pulled to
11199 (license license:gpl2+)))
11201 (define-public r-rcppannoy
11203 (name "r-rcppannoy")
11208 (uri (cran-uri "RcppAnnoy" version))
11211 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11212 (properties `((upstream-name . "RcppAnnoy")))
11213 (build-system r-build-system)
11215 `(("r-rcpp" ,r-rcpp)))
11216 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11217 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11219 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11220 for efficient memory usage as well an ability to load from and save to disk.
11221 This package provides an R interface.")
11222 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11224 (license (list license:gpl2+ license:asl2.0))))
11226 (define-public r-rcpphnsw
11228 (name "r-rcpphnsw")
11233 (uri (cran-uri "RcppHNSW" version))
11236 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11237 (properties `((upstream-name . "RcppHNSW")))
11238 (build-system r-build-system)
11239 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11240 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11241 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11243 "Hnswlib is a C++ library for approximate nearest neighbors. This
11244 package provides a minimal R interface by relying on the Rcpp package.")
11245 ;; hnswlib is released under Version 2.0 of the Apache License.
11246 (license (list license:gpl3 license:asl2.0))))
11248 (define-public r-rcppparallel
11250 (name "r-rcppparallel")
11255 (uri (cran-uri "RcppParallel" version))
11258 "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki"))))
11259 (properties `((upstream-name . "RcppParallel")))
11260 (build-system r-build-system)
11261 (home-page "https://rcppcore.github.io/RcppParallel/")
11262 (synopsis "Parallel programming tools for Rcpp")
11264 "This package provides high level functions for parallel programming with
11265 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11266 the work of a standard serial @code{for} loop into a parallel one and the
11267 @code{parallelReduce()} function can be used for accumulating aggregates or
11269 (license license:gpl2)))
11271 (define-public r-ncdf4
11278 (uri (cran-uri "ncdf4" version))
11281 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11282 (build-system r-build-system)
11284 `(("netcdf" ,netcdf)
11286 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11287 (synopsis "R interface to Unidata netCDF format data files")
11289 "This package provides a high-level R interface to data files written
11290 using Unidata's netCDF library (version 4 or earlier), which are binary data
11291 files that are portable across platforms and include metadata information in
11292 addition to the data sets. Using this package, netCDF files can be opened and
11293 data sets read in easily. It is also easy to create new netCDF dimensions,
11294 variables, and files, in either version 3 or 4 format, and manipulate existing
11296 (license license:gpl3+)))
11298 (define-public r-biocmanager
11300 (name "r-biocmanager")
11301 (version "1.30.10")
11305 (uri (cran-uri "BiocManager" version))
11307 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
11308 (properties `((upstream-name . "BiocManager")))
11309 (build-system r-build-system)
11310 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11311 (synopsis "Access the Bioconductor project package repository")
11313 "This package provides a convenient tool to install and update
11314 Bioconductor packages.")
11315 (license license:artistic2.0)))
11317 (define-public r-rgl
11320 (version "0.105.22")
11324 (uri (cran-uri "rgl" version))
11327 "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz"))))
11328 (build-system r-build-system)
11330 `(("pkg-config" ,pkg-config)
11331 ("r-knitr" ,r-knitr)))
11333 `(("freetype" ,freetype)
11340 `(("r-crosstalk" ,r-crosstalk)
11341 ("r-htmltools" ,r-htmltools)
11342 ("r-htmlwidgets" ,r-htmlwidgets)
11343 ("r-jsonlite" ,r-jsonlite)
11344 ("r-knitr" ,r-knitr)
11345 ("r-magrittr" ,r-magrittr)
11346 ("r-manipulatewidget" ,r-manipulatewidget)
11347 ("r-shiny" ,r-shiny)))
11348 (home-page "https://r-forge.r-project.org/projects/rgl/")
11349 (synopsis "3D visualization using OpenGL")
11351 "This package provides medium to high level functions for 3D interactive graphics,
11352 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11353 as functions for constructing representations of geometric
11354 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11355 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11356 image formats, including PNG, Postscript, SVG, PGF.")
11357 ;; Any version of the GPL.
11358 (license (list license:gpl2+ license:gpl3+))))
11360 (define-public r-multicool
11362 (name "r-multicool")
11367 (uri (cran-uri "multicool" version))
11370 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11371 (build-system r-build-system)
11372 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11373 (home-page "https://cran.r-project.org/web/packages/multicool/")
11374 (synopsis "Permutations of multisets in cool-lex order")
11376 "This package provides a set of tools to permute multisets without loops
11377 or hash tables and to generate integer partitions. Cool-lex order is similar
11378 to colexicographical order.")
11379 (license license:gpl2)))
11381 (define-public r-misc3d
11388 (uri (cran-uri "misc3d" version))
11391 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11392 (build-system r-build-system)
11393 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11394 (synopsis "Miscellaneous 3D Plots")
11396 "This package provides a collection of miscellaneous 3d plots, including
11398 ;; Any version of the GPL.
11399 (license (list license:gpl2+ license:gpl3+))))
11401 (define-public r-ks
11408 (uri (cran-uri "ks" version))
11410 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11411 (build-system r-build-system)
11414 ("r-kernlab" ,r-kernlab)
11415 ("r-kernsmooth" ,r-kernsmooth)
11416 ("r-matrix" ,r-matrix)
11417 ("r-mclust" ,r-mclust)
11419 ("r-multicool" ,r-multicool)
11420 ("r-mvtnorm" ,r-mvtnorm)
11421 ("r-plot3d" ,r-plot3d)))
11422 (home-page "https://www.mvstat.net/tduong/")
11423 (synopsis "Kernel smoothing")
11425 "This package provides kernel smoothers for univariate and multivariate
11426 data, including density functions, density derivatives, cumulative
11427 distributions, modal clustering, discriminant analysis, and two-sample
11428 hypothesis testing.")
11429 ;; Either version of the GPL.
11430 (license (list license:gpl2 license:gpl3))))
11432 (define-public r-feature
11439 (uri (cran-uri "feature" version))
11442 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11443 (build-system r-build-system)
11446 ("r-plot3d" ,r-plot3d)))
11448 `(("r-knitr" ,r-knitr)))
11449 (home-page "https://www.mvstat.net/tduong/")
11450 (synopsis "Inferential feature significance for kernel density estimation")
11452 "The feature package contains functions to display and compute kernel
11453 density estimates, significant gradient and significant curvature regions.
11454 Significant gradient and/or curvature regions often correspond to significant
11455 features (e.g. local modes).")
11456 ;; Either version of the GPL.
11457 (license (list license:gpl2 license:gpl3))))
11459 (define-public r-arm
11466 (uri (cran-uri "arm" version))
11469 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11470 (build-system r-build-system)
11472 `(("r-abind" ,r-abind)
11474 ("r-hmisc" ,r-hmisc)
11477 ("r-matrix" ,r-matrix)
11478 ("r-nlme" ,r-nlme)))
11479 (home-page "https://cran.r-project.org/web/packages/arm/")
11480 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11482 "This package provides functions to accompany A. Gelman and J. Hill,
11483 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11484 University Press, 2007.")
11485 (license license:gpl3+)))
11487 (define-public r-circular
11489 (name "r-circular")
11494 (uri (cran-uri "circular" version))
11497 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11498 (build-system r-build-system)
11500 `(("r-boot" ,r-boot)
11501 ("r-mvtnorm" ,r-mvtnorm)))
11503 `(("gfortran" ,gfortran)))
11504 (home-page "https://cran.r-project.org/web/packages/circular/")
11505 (synopsis "Circular statistics")
11507 "This package provides tools for circular statistics, from \"Topics in
11508 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11510 (license license:gpl2+)))
11512 (define-public r-activity
11514 (name "r-activity")
11519 (uri (cran-uri "activity" version))
11522 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
11523 (build-system r-build-system)
11525 `(("r-circular" ,r-circular)
11526 ("r-insol" ,r-insol)
11527 ("r-pbapply" ,r-pbapply)))
11528 (home-page "https://cran.r-project.org/web/packages/activity/")
11529 (synopsis "Animal activity statistics")
11531 "This package provides functions to fit kernel density functions to
11532 animal activity time data; plot activity distributions; quantify overall
11533 levels of activity; statistically compare activity metrics through
11534 bootstrapping; and evaluate variation in linear variables with time (or other
11535 circular variables).")
11536 (license license:gpl3)))
11538 (define-public r-ouch
11545 (uri (cran-uri "ouch" version))
11548 "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q"))))
11549 (build-system r-build-system)
11550 (propagated-inputs `(("r-subplex" ,r-subplex)))
11551 (home-page "https://kingaa.github.io/ouch/")
11552 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11554 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11555 for evolution along a phylogenetic tree.")
11556 (license license:gpl2+)))
11558 (define-public r-fmsb
11565 (uri (cran-uri "fmsb" version))
11568 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11569 (build-system r-build-system)
11570 (home-page "http://minato.sip21c.org/msb/")
11571 (synopsis "Functions for medical statistics book with demographic data")
11573 "This package provides several utility functions for the book entitled
11574 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11575 Japan, 2007) with Japanese demographic data and some demographic analysis
11576 related functions.")
11577 (license license:gpl2+)))
11579 (define-public r-stabledist
11581 (name "r-stabledist")
11586 (uri (cran-uri "stabledist" version))
11589 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11590 (build-system r-build-system)
11591 (home-page "https://www.rmetrics.org")
11592 (synopsis "Stable distribution functions")
11594 "This package provides density, probability and quantile functions, and
11595 random number generation for (skew) stable distributions, using the
11596 parametrizations of Nolan.")
11597 (license license:gpl2+)))
11599 (define-public r-gsl
11606 (uri (cran-uri "gsl" version))
11609 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11610 (build-system r-build-system)
11613 (home-page "https://cran.r-project.org/web/packages/gsl")
11614 (synopsis "Wrapper for the GNU Scientific Library")
11616 "This package provides an R wrapper for the special functions and quasi
11617 random number generators of the GNU Scientific Library.")
11618 (license license:gpl2+)))
11620 (define-public r-adgoftest
11622 (name "r-adgoftest")
11627 (uri (cran-uri "ADGofTest" version))
11630 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11631 (properties `((upstream-name . "ADGofTest")))
11632 (build-system r-build-system)
11633 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11634 (synopsis "Anderson-Darling GoF test")
11636 "This package provides an implementation of the Anderson-Darling GoF test
11637 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11638 Anderson-Darling Distribution\".")
11639 ;; Any version of the GPL.
11640 (license license:gpl3+)))
11642 (define-public r-sodium
11649 (uri (cran-uri "sodium" version))
11652 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11653 (properties `((upstream-name . "sodium")))
11654 (build-system r-build-system)
11656 `(("libsodium" ,libsodium)))
11658 `(("pkg-config" ,pkg-config)
11659 ("r-knitr" ,r-knitr)))
11660 (home-page "https://github.com/jeroen/sodium")
11661 (synopsis "R bindings to the libsodium crypto library")
11663 "This package provides bindings to libsodium: a library for encryption,
11664 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11665 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11666 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11667 (license license:expat)))
11669 (define-public r-softimpute
11671 (name "r-softimpute")
11676 (uri (cran-uri "softImpute" version))
11679 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11680 (properties `((upstream-name . "softImpute")))
11681 (build-system r-build-system)
11683 `(("r-matrix" ,r-matrix)))
11685 `(("gfortran" ,gfortran)))
11686 (home-page "https://cran.r-project.org/web/packages/softImpute")
11687 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11689 "This package provides iterative methods for matrix completion that use
11690 nuclear-norm regularization. The package includes procedures for centering
11691 and scaling rows, columns or both, and for computing low-rank @dfn{single
11692 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11694 (license license:gpl2)))
11696 (define-public r-fftwtools
11698 (name "r-fftwtools")
11703 (uri (cran-uri "fftwtools" version))
11706 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
11707 (build-system r-build-system)
11708 (inputs `(("fftw" ,fftw)))
11710 `(("pkg-config" ,pkg-config)))
11711 (home-page "https://github.com/krahim/fftwtools")
11712 (synopsis "Wrapper for FFTW3")
11714 "This package provides a wrapper for several FFTW functions. It provides
11715 access to the two-dimensional FFT, the multivariate FFT, and the
11716 one-dimensional real to complex FFT using the FFTW3 library. The package
11717 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11718 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11719 The FFT functions have a parameter that allows them to not return the
11720 redundant complex conjugate when the input is real data.")
11721 (license license:gpl2+)))
11723 (define-public r-tiff
11730 (uri (cran-uri "tiff" version))
11733 "101n6x70fr1dhcwx53g3s8q1j4wh93y0388v1s1316f8558rxqxh"))))
11734 (build-system r-build-system)
11736 `(("libtiff" ,libtiff)
11737 ("libjpeg" ,libjpeg-turbo)
11739 (home-page "https://www.rforge.net/tiff/")
11740 (synopsis "Read and write TIFF images")
11742 "This package provides an easy and simple way to read, write and display
11743 bitmap images stored in the TIFF format. It can read and write both files and
11744 in-memory raw vectors.")
11745 ;; Either of these two license versions.
11746 (license (list license:gpl2 license:gpl3))))
11748 (define-public r-nlp
11755 (uri (cran-uri "NLP" version))
11758 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11759 (properties `((upstream-name . "NLP")))
11760 (build-system r-build-system)
11761 (home-page "https://cran.r-project.org/web/packages/NLP/")
11762 (synopsis "Natural language processing infrastructure")
11764 "This package provides basic classes and methods for Natural Language
11766 (license license:gpl3)))
11768 (define-public r-tm
11775 (uri (cran-uri "tm" version))
11778 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11779 (properties `((upstream-name . "tm")))
11780 (build-system r-build-system)
11786 ("r-xml2" ,r-xml2)))
11787 (home-page "http://tm.r-forge.r-project.org/")
11788 (synopsis "Text mining package")
11790 "This package provides a framework for text mining applications within R.")
11791 (license license:gpl3)))
11793 (define-public r-waveslim
11795 (name "r-waveslim")
11800 (uri (cran-uri "waveslim" version))
11803 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11804 (build-system r-build-system)
11806 `(("gfortran" ,gfortran)))
11807 (home-page "http://waveslim.blogspot.com")
11808 (synopsis "Basic wavelet routines for signal processing")
11810 "This package provides basic wavelet routines for time series (1D),
11811 image (2D) and array (3D) analysis. The code provided here is based on
11812 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11813 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11814 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11815 pairs (Selesnick 2001, 2002).")
11816 (license license:bsd-3)))
11818 (define-public r-wordcloud
11820 (name "r-wordcloud")
11825 (uri (cran-uri "wordcloud" version))
11828 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11829 (build-system r-build-system)
11831 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11833 ;; The "tm" package is only "suggested" according to CRAN, but the
11834 ;; wordcloud package cannot be loaded without it.
11836 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11837 (synopsis "Word clouds")
11839 "This package provides functionality to create pretty word clouds,
11840 visualize differences and similarity between documents, and avoid
11841 over-plotting in scatter plots with text.")
11842 (license license:lgpl2.1)))
11844 (define-public r-colorramps
11846 (name "r-colorramps")
11851 (uri (cran-uri "colorRamps" version))
11854 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11855 (properties `((upstream-name . "colorRamps")))
11856 (build-system r-build-system)
11857 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11858 (synopsis "Build color tables")
11859 (description "This package provides features to build gradient color
11861 ;; Any version of the GPL
11862 (license license:gpl3+)))
11864 (define-public r-tidytree
11866 (name "r-tidytree")
11871 (uri (cran-uri "tidytree" version))
11873 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11874 (build-system r-build-system)
11877 ("r-dplyr" ,r-dplyr)
11878 ("r-lazyeval" ,r-lazyeval)
11879 ("r-magrittr" ,r-magrittr)
11880 ("r-rlang" ,r-rlang)
11881 ("r-tibble" ,r-tibble)))
11883 `(("r-knitr" ,r-knitr)))
11884 (home-page "https://github.com/GuangchuangYu/tidytree")
11885 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11887 "Phylogenetic trees generally contain multiple components including nodes,
11888 edges, branches and associated data. This package provides an approach to
11889 convert tree objects to tidy data frames. It also provides tidy interfaces to
11890 manipulate tree data.")
11891 (license license:artistic2.0)))
11893 (define-public r-rvcheck
11900 (uri (cran-uri "rvcheck" version))
11902 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11903 (build-system r-build-system)
11905 `(("r-biocmanager" ,r-biocmanager)
11906 ("r-rlang" ,r-rlang)))
11907 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11908 (synopsis "R package version check")
11910 "This package provides tools to check the latest release version of R and
11911 R packages (on CRAN, Bioconductor or Github).")
11912 (license license:artistic2.0)))
11914 (define-public r-docopt
11921 (uri (cran-uri "docopt" version))
11924 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11925 (build-system r-build-system)
11926 (home-page "https://github.com/docopt/docopt.R")
11927 (synopsis "Command-line interface specification language")
11929 "This package enables you to define a command-line interface by just
11930 giving it a description in the specific format.")
11931 (license license:expat)))
11933 (define-public r-sparsesvd
11935 (name "r-sparsesvd")
11940 (uri (cran-uri "sparsesvd" version))
11943 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11944 (build-system r-build-system)
11945 (propagated-inputs `(("r-matrix" ,r-matrix)))
11946 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11947 (synopsis "Sparse truncated singular value decomposition")
11949 "This package provides a Wrapper around the SVDLIBC library
11950 for (truncated) singular value decomposition of a sparse matrix. Currently,
11951 only sparse real matrices in Matrix package format are supported.")
11952 ;; SVDLIBC is released under BSD-2. The R interface is released under
11954 (license (list license:bsd-3 license:bsd-2))))
11956 (define-public r-speedglm
11958 (name "r-speedglm")
11963 (uri (cran-uri "speedglm" version))
11966 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11967 (build-system r-build-system)
11969 `(("r-mass" ,r-mass)
11970 ("r-matrix" ,r-matrix)))
11971 (home-page "https://cran.r-project.org/web/packages/speedglm")
11972 (synopsis "Fit linear and generalized linear models to large data sets")
11974 "This package provides tools for fitting linear models and generalized
11975 linear models to large data sets by updating algorithms.")
11976 ;; Any version of the GPL
11977 (license license:gpl2+)))
11979 (define-public r-densityclust
11981 (name "r-densityclust")
11986 (uri (cran-uri "densityClust" version))
11989 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11990 (properties `((upstream-name . "densityClust")))
11991 (build-system r-build-system)
11994 ("r-ggplot2" ,r-ggplot2)
11995 ("r-ggrepel" ,r-ggrepel)
11996 ("r-gridextra" ,r-gridextra)
11997 ("r-rcolorbrewer" ,r-rcolorbrewer)
11999 ("r-rtsne" ,r-rtsne)))
12000 (home-page "https://cran.r-project.org/web/packages/densityClust")
12001 (synopsis "Clustering by fast search and find of density peaks")
12003 "This package provides an improved implementation (based on k-nearest
12004 neighbors) of the density peak clustering algorithm, originally described by
12005 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
12006 large datasets (> 100,000 samples) very efficiently.")
12007 (license license:gpl2+)))
12009 (define-public r-combinat
12011 (name "r-combinat")
12016 (uri (cran-uri "combinat" version))
12019 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12020 (build-system r-build-system)
12021 (home-page "https://cran.r-project.org/web/packages/combinat")
12022 (synopsis "Combinatorics utilities")
12023 (description "This package provides assorted routines for combinatorics.")
12024 (license license:gpl2)))
12026 (define-public r-qlcmatrix
12028 (name "r-qlcmatrix")
12033 (uri (cran-uri "qlcMatrix" version))
12036 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12037 (properties `((upstream-name . "qlcMatrix")))
12038 (build-system r-build-system)
12040 `(("r-docopt" ,r-docopt)
12041 ("r-matrix" ,r-matrix)
12043 ("r-sparsesvd" ,r-sparsesvd)))
12044 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12045 (synopsis "Sparse matrix functions for quantitative language comparison")
12047 "This package provides an extension of the functionality of the Matrix
12048 package for using sparse matrices. Some of the functions are very general,
12049 while other are highly specific for the special data format used for
12050 @dfn{quantitative language comparison} (QLC).")
12051 (license license:gpl3)))
12053 (define-public r-ddrtree
12060 (uri (cran-uri "DDRTree" version))
12063 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12064 (properties `((upstream-name . "DDRTree")))
12065 (build-system r-build-system)
12068 ("r-irlba" ,r-irlba)
12070 ("r-rcppeigen" ,r-rcppeigen)))
12071 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12072 (synopsis "Learning principal graphs with DDRTree")
12074 "This package provides an implementation of the framework of
12075 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12076 dimensional space while constructs a principal tree which passes through the
12077 middle of the data simultaneously. DDRTree shows superiority to
12078 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12079 intrinsic structure of single cell genomics data. In general, it could be
12080 used to reconstruct the temporal progression as well as the bifurcation
12081 structure of any data type.")
12082 (license license:asl2.0)))
12084 (define-public r-corpcor
12091 (uri (cran-uri "corpcor" version))
12094 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12095 (build-system r-build-system)
12096 (home-page "http://strimmerlab.org/software/corpcor/")
12097 (synopsis "Efficient estimation of covariance and (partial) correlation")
12099 "This package implements a James-Stein-type shrinkage estimator for the
12100 covariance matrix, with separate shrinkage for variances and correlations.
12101 Furthermore, functions are available for fast singular value decomposition,
12102 for computing the pseudoinverse, and for checking the rank and positive
12103 definiteness of a matrix.")
12104 (license license:gpl3+)))
12106 (define-public r-rspectra
12108 (name "r-rspectra")
12113 (uri (cran-uri "RSpectra" version))
12116 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12117 (properties `((upstream-name . "RSpectra")))
12118 (build-system r-build-system)
12120 `(("r-matrix" ,r-matrix)
12122 ("r-rcppeigen" ,r-rcppeigen)))
12123 (home-page "https://github.com/yixuan/RSpectra")
12124 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12126 "This package provides an R interface to the Spectra library for
12127 large-scale eigenvalue and SVD problems. It is typically used to compute a
12128 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12129 which is usually more efficient than @code{eigen()} if k << n.")
12131 (license license:mpl2.0)))
12133 (define-public r-vbsr
12140 (uri (cran-uri "vbsr" version))
12143 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12144 (build-system r-build-system)
12145 (home-page "https://cran.r-project.org/web/packages/vbsr")
12146 (synopsis "Variational Bayes spike regression regularized linear models")
12148 "This package provides an efficient algorithm for solving ultra-sparse
12149 regularized regression models using a variational Bayes algorithm with a spike
12150 prior. The algorithm is solved on a path, with coordinate updates, and is
12151 capable of generating very sparse models. Very general model
12152 diagnostics for controlling type-1 errors are also provided.")
12153 (license license:gpl2)))
12155 (define-public r-flare
12162 (uri (cran-uri "flare" version))
12165 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12166 (build-system r-build-system)
12168 `(("r-igraph" ,r-igraph)
12169 ("r-lattice" ,r-lattice)
12171 ("r-matrix" ,r-matrix)))
12172 (home-page "https://cran.r-project.org/web/packages/flare")
12173 (synopsis "Family of Lasso regression implementations")
12175 "This package provides implementations of a family of Lasso variants
12176 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12177 high dimensional sparse linear models.")
12178 (license license:gpl2)))
12180 (define-public r-lassopv
12187 (uri (cran-uri "lassopv" version))
12190 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12191 (build-system r-build-system)
12192 (propagated-inputs `(("r-lars" ,r-lars)))
12193 (home-page "https://github.com/lingfeiwang/lassopv")
12194 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12196 "This package enables you to estimate the p-values for predictors x
12197 against target variable y in Lasso regression, using the regularization
12198 strength when each predictor enters the active set of regularization path for
12199 the first time as the statistic.")
12200 (license license:gpl3)))
12202 (define-public r-splitstackshape
12204 (name "r-splitstackshape")
12209 (uri (cran-uri "splitstackshape" version))
12212 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12213 (build-system r-build-system)
12215 `(("r-data-table" ,r-data-table)))
12216 (home-page "https://github.com/mrdwab/splitstackshape")
12217 (synopsis "Stack and reshape datasets after splitting concatenated values")
12219 "Online data collection tools like Google Forms often export
12220 multiple-response questions with data concatenated in cells. The
12221 @code{concat.split} (cSplit) family of functions provided by this package
12222 splits such data into separate cells. This package also includes functions to
12223 stack groups of columns and to reshape wide data, even when the data are
12224 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12225 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12227 (license license:gpl3)))
12229 (define-public r-tfmpvalue
12231 (name "r-tfmpvalue")
12236 (uri (cran-uri "TFMPvalue" version))
12239 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12240 (properties `((upstream-name . "TFMPvalue")))
12241 (build-system r-build-system)
12242 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12243 (home-page "https://github.com/ge11232002/TFMPvalue")
12244 (synopsis "P-value computation for position weight matrices")
12246 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12247 identification from sequence/alignments, we are interested in the significance
12248 of certain match scores. TFMPvalue provides the accurate calculation of a
12249 p-value with a score threshold for position weight matrices, or the score with
12250 a given p-value. It is an interface to code originally made available by
12251 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12252 Touzet and Varre (2007).")
12253 (license license:gpl2)))
12255 (define-public r-rnifti
12262 (uri (cran-uri "RNifti" version))
12265 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12266 (properties `((upstream-name . "RNifti")))
12267 (build-system r-build-system)
12268 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12269 (home-page "https://github.com/jonclayden/RNifti")
12270 (synopsis "Fast R and C++ access to NIfTI images")
12272 "This package provides very fast read and write access to images stored
12273 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12274 compiled C and interpreted R code. It also provides a C/C++ API that can be
12275 used by other packages.")
12276 (license license:gpl2)))
12278 (define-public r-shades
12285 (uri (cran-uri "shades" version))
12288 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12289 (build-system r-build-system)
12290 (home-page "https://github.com/jonclayden/shades")
12291 (synopsis "Simple color manipulation")
12293 "This package provides functions for easily manipulating colors,
12294 creating color scales and calculating color distances.")
12295 (license license:bsd-3)))
12297 (define-public r-ore
12304 (uri (cran-uri "ore" version))
12306 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12307 (build-system r-build-system)
12308 (home-page "https://github.com/jonclayden/ore")
12309 (synopsis "R interface to the Onigmo regular expression library")
12311 "This package provides an alternative to R's built-in functionality for
12312 handling regular expressions, based on the Onigmo library. It offers
12313 first-class compiled regex objects, partial matching and function-based
12314 substitutions, amongst other features.")
12315 (license license:bsd-3)))
12317 (define-public r-reportr
12324 (uri (cran-uri "reportr" version))
12327 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12328 (build-system r-build-system)
12329 (propagated-inputs `(("r-ore" ,r-ore)))
12330 (home-page "https://github.com/jonclayden/reportr")
12331 (synopsis "General message and error reporting system")
12333 "This package provides a system for reporting messages, which offers
12334 certain useful features over the standard R system, such as the incorporation
12335 of output consolidation, message filtering, assertions, expression
12336 substitution, automatic generation of stack traces for debugging, and
12337 conditional reporting based on the current \"output level\".")
12338 (license license:gpl2)))
12340 (define-public r-tractor-base
12342 (name "r-tractor-base")
12343 (version "3.3.3.1")
12347 (uri (cran-uri "tractor.base" version))
12350 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12351 (properties `((upstream-name . "tractor.base")))
12352 (build-system r-build-system)
12355 ("r-reportr" ,r-reportr)
12356 ("r-rnifti" ,r-rnifti)
12357 ("r-shades" ,r-shades)))
12358 (home-page "https://www.tractor-mri.org.uk")
12359 (synopsis "Read, manipulate and visualize magnetic resonance images")
12361 "This package provides functions for working with magnetic resonance
12362 images. It supports reading and writing of popular file formats (DICOM,
12363 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12364 visualization; flexible image manipulation; metadata and sparse image
12366 (license license:gpl2)))
12368 (define-public r-grimport
12370 (name "r-grimport")
12375 (uri (cran-uri "grImport" version))
12378 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12379 (properties `((upstream-name . "grImport")))
12380 (build-system r-build-system)
12382 `(("ghostscript" ,ghostscript)))
12384 `(("r-xml" ,r-xml)))
12385 (home-page "https://cran.r-project.org/web/packages/grImport")
12386 (synopsis "Convert, import, and draw PostScript pictures")
12388 "This package provides functions for converting, importing, and drawing
12389 PostScript pictures in R plots.")
12390 (license license:gpl2+)))
12392 (define-public r-grimport2
12394 (name "r-grimport2")
12399 (uri (cran-uri "grImport2" version))
12402 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12403 (properties `((upstream-name . "grImport2")))
12404 (build-system r-build-system)
12406 `(("r-base64enc" ,r-base64enc)
12410 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12411 (synopsis "Import SVG graphics")
12413 "This package provides functions for importing external vector images and
12414 drawing them as part of R plots. This package is different from the
12415 @code{grImport} package because, where that package imports PostScript format
12416 images, this package imports SVG format images. Furthermore, this package
12417 imports a specific subset of SVG, so external images must be preprocessed
12418 using a package like @code{rsvg} to produce SVG that this package can import.
12419 SVG features that are not supported by R graphics, such as gradient fills, can
12420 be imported and then exported via the @code{gridSVG} package.")
12421 (license license:gpl2+)))
12423 (define-public r-kohonen
12430 (uri (cran-uri "kohonen" version))
12433 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12434 (build-system r-build-system)
12436 `(("r-rcpp" ,r-rcpp)))
12437 (home-page "https://cran.r-project.org/web/packages/kohonen")
12438 (synopsis "Supervised and unsupervised self-organising maps")
12440 "This package provides functions to train @dfn{self-organising
12441 maps} (SOMs). Also interrogation of the maps and prediction using trained
12442 maps are supported. The name of the package refers to Teuvo Kohonen, the
12443 inventor of the SOM.")
12444 (license license:gpl2+)))
12446 (define-public r-nnls
12453 (uri (cran-uri "nnls" version))
12456 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12457 (build-system r-build-system)
12458 (native-inputs `(("gfortran" ,gfortran)))
12459 (home-page "https://cran.r-project.org/web/packages/nnls")
12460 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12462 "This package provides an R interface to the Lawson-Hanson implementation
12463 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12464 the combination of non-negative and non-positive constraints.")
12465 (license license:gpl2+)))
12467 (define-public r-iso
12470 (version "0.0-18.1")
12474 (uri (cran-uri "Iso" version))
12477 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12478 (properties `((upstream-name . "Iso")))
12479 (build-system r-build-system)
12480 (native-inputs `(("gfortran" ,gfortran)))
12481 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12482 (synopsis "Functions to perform isotonic regression")
12484 "This package provides support for linear order and unimodal
12485 order (univariate) isotonic regression and bivariate isotonic regression with
12486 linear order on both variables.")
12487 (license license:gpl2+)))
12489 (define-public r-chemometricswithr
12491 (name "r-chemometricswithr")
12496 (uri (cran-uri "ChemometricsWithR" version))
12499 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12501 `((upstream-name . "ChemometricsWithR")))
12502 (build-system r-build-system)
12504 `(("r-devtools" ,r-devtools)
12505 ("r-kohonen" ,r-kohonen)
12508 (home-page "https://github.com/rwehrens/CWR")
12509 (synopsis "Chemometrics with R")
12511 "This package provides functions and scripts used in the book
12512 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12513 Life Sciences\" by Ron Wehrens, Springer (2011).")
12514 (license license:gpl2+)))
12516 (define-public r-als
12523 (uri (cran-uri "ALS" version))
12526 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12527 (properties `((upstream-name . "ALS")))
12528 (build-system r-build-system)
12531 ("r-nnls" ,r-nnls)))
12532 (home-page "https://cran.r-project.org/web/packages/ALS")
12533 (synopsis "Multivariate curve resolution alternating least squares")
12535 "Alternating least squares is often used to resolve components
12536 contributing to data with a bilinear structure; the basic technique may be
12537 extended to alternating constrained least squares. This package provides an
12538 implementation of @dfn{multivariate curve resolution alternating least
12539 squares} (MCR-ALS).
12541 Commonly applied constraints include unimodality, non-negativity, and
12542 normalization of components. Several data matrices may be decomposed
12543 simultaneously by assuming that one of the two matrices in the bilinear
12544 decomposition is shared between datasets.")
12545 (license license:gpl2+)))
12547 (define-public r-strucchange
12549 (name "r-strucchange")
12554 (uri (cran-uri "strucchange" version))
12557 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12558 (build-system r-build-system)
12560 `(("r-sandwich" ,r-sandwich)
12562 (home-page "https://cran.r-project.org/web/packages/strucchange")
12563 (synopsis "Testing, monitoring, and dating structural changes")
12565 "This package provides tools for testing, monitoring and dating
12566 structural changes in (linear) regression models. It features tests/methods
12567 from the generalized fluctuation test framework as well as from the F
12568 test (Chow test) framework. This includes methods to fit, plot and test
12569 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12570 statistics, respectively. It is possible to monitor incoming data online
12571 using fluctuation processes. Finally, the breakpoints in regression models
12572 with structural changes can be estimated together with confidence intervals.
12573 Emphasis is always given to methods for visualizing the data.")
12574 ;; Either of these two GPL versions
12575 (license (list license:gpl2 license:gpl3))))
12577 (define-public r-pixmap
12584 (uri (cran-uri "pixmap" version))
12587 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12588 (build-system r-build-system)
12589 (home-page "https://cran.r-project.org/web/packages/pixmap")
12590 (synopsis "Tools for bitmap images")
12592 "This package provides functions for importing, exporting, plotting and
12593 other manipulations of bitmapped images.")
12594 (license license:gpl2)))
12596 (define-public r-rapidjsonr
12598 (name "r-rapidjsonr")
12603 (uri (cran-uri "rapidjsonr" version))
12606 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12607 (build-system r-build-system)
12608 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12609 (synopsis "JSON parser")
12611 "This package provides JSON parsing capability through the Rapidjson
12613 (license license:expat)))
12615 (define-public r-ontologyindex
12617 (name "r-ontologyindex")
12622 (uri (cran-uri "ontologyIndex" version))
12625 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12626 (properties `((upstream-name . "ontologyIndex")))
12627 (build-system r-build-system)
12629 `(("r-knitr" ,r-knitr)))
12630 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12631 (synopsis "Functions for processing ontologies in R")
12633 "This package provides functions for reading ontologies into R as lists
12634 and manipulating sets of ontological terms.")
12635 (license license:gpl2+)))
12637 (define-public r-gargle
12644 (uri (cran-uri "gargle" version))
12647 "0hsqn4hf935wn6vk2pwym7la4sdvy271y4cashp38pg4hkpg9zph"))))
12648 (build-system r-build-system)
12653 ("r-jsonlite" ,r-jsonlite)
12654 ("r-rlang" ,r-rlang)
12655 ("r-withr" ,r-withr)))
12657 `(("r-knitr" ,r-knitr)))
12658 (home-page "https://gargle.r-lib.org")
12659 (synopsis "Utilities for working with Google APIs")
12661 "This package provides utilities for working with Google APIs. This
12662 includes functions and classes for handling common credential types and for
12663 preparing, executing, and processing HTTP requests.")
12664 (license license:expat)))
12666 (define-public r-bigrquery
12668 (name "r-bigrquery")
12673 (uri (cran-uri "bigrquery" version))
12676 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12677 (build-system r-build-system)
12679 `(("r-assertthat" ,r-assertthat)
12680 ("r-bit64" ,r-bit64)
12683 ("r-gargle" ,r-gargle)
12686 ("r-jsonlite" ,r-jsonlite)
12687 ("r-prettyunits" ,r-prettyunits)
12688 ("r-progress" ,r-progress)
12689 ("r-rapidjsonr" ,r-rapidjsonr)
12691 ("r-rlang" ,r-rlang)
12692 ("r-tibble" ,r-tibble)))
12693 (home-page "https://github.com/rstats-db/bigrquery")
12694 (synopsis "R interface to Google's BigQuery API")
12696 "This package provides an R interface to Google's BigQuery database.")
12697 (license license:gpl3)))
12699 (define-public r-gmp
12706 (uri (cran-uri "gmp" version))
12709 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12710 (build-system r-build-system)
12713 (modify-phases %standard-phases
12714 (add-after 'unpack 'set-CC
12715 (lambda _ (setenv "CC" "gcc") #t)))))
12716 (inputs `(("gmp" ,gmp)))
12717 (home-page "https://cran.r-project.org/web/packages/gmp")
12718 (synopsis "Multiple precision arithmetic")
12720 "This package supports multiple precision arithmetic (big integers and
12721 rationals, prime number tests, matrix computation), \"arithmetic without
12722 limitations\" using the GNU Multiple Precision library.")
12723 ;; Any version of the GPL.
12724 (license license:gpl3+)))
12726 (define-public r-rmpfr
12733 (uri (cran-uri "Rmpfr" version))
12736 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12737 (properties `((upstream-name . "Rmpfr")))
12738 (build-system r-build-system)
12743 `(("r-gmp" ,r-gmp)))
12745 `(("pkg-config" ,pkg-config)))
12746 (home-page "http://rmpfr.r-forge.r-project.org/")
12747 (synopsis "R bindings to the MPFR library")
12749 "This package supports arithmetic (via S4 classes and methods) for
12750 arbitrary precision floating point numbers, including transcendental
12751 functions. To this end, the package interfaces with the @dfn{Multiple
12752 Precision Floating-Point Reliable} (MPFR) library.")
12753 (license license:gpl2+)))
12755 (define-public r-assertive-base
12757 (name "r-assertive-base")
12762 (uri (cran-uri "assertive.base" version))
12765 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12767 `((upstream-name . "assertive.base")))
12768 (build-system r-build-system)
12769 (home-page "https://bitbucket.org/richierocks/assertive.base")
12770 (synopsis "Core of the assertive package")
12772 "This package provides a minimal set of predicates and assertions used by
12773 the assertive package. This is mainly for use by other package developers who
12774 want to include run-time testing features in their own packages.")
12775 (license license:gpl3+)))
12777 (define-public r-assertive-properties
12779 (name "r-assertive-properties")
12784 (uri (cran-uri "assertive.properties" version))
12787 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12789 `((upstream-name . "assertive.properties")))
12790 (build-system r-build-system)
12792 `(("r-assertive-base" ,r-assertive-base)))
12793 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12794 (synopsis "Assertions to check properties of variables")
12796 "This package provides a set of predicates and assertions for checking
12797 the properties of variables, such as length, names and attributes. This is
12798 mainly for use by other package developers who want to include run-time
12799 testing features in their own packages.")
12800 (license license:gpl3+)))
12802 (define-public r-assertive-numbers
12804 (name "r-assertive-numbers")
12809 (uri (cran-uri "assertive.numbers" version))
12812 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12814 `((upstream-name . "assertive.numbers")))
12815 (build-system r-build-system)
12817 `(("r-assertive-base" ,r-assertive-base)))
12818 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12819 (synopsis "Assertions to check properties of numbers")
12821 "This package provides a set of predicates and assertions for checking
12822 the properties of numbers. This is mainly for use by other package developers
12823 who want to include run-time testing features in their own packages.")
12824 (license license:gpl3+)))
12826 (define-public r-assertive-sets
12828 (name "r-assertive-sets")
12833 (uri (cran-uri "assertive.sets" version))
12836 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12838 `((upstream-name . "assertive.sets")))
12839 (build-system r-build-system)
12841 `(("r-assertive-base" ,r-assertive-base)))
12842 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12843 (synopsis "Assertions to check properties of sets")
12845 "This package provides a set of predicates and assertions for checking
12846 the properties of sets. This is mainly for use by other package developers
12847 who want to include run-time testing features in their own packages.")
12848 (license license:gpl3+)))
12850 (define-public r-assertive-matrices
12852 (name "r-assertive-matrices")
12857 (uri (cran-uri "assertive.matrices" version))
12860 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12862 `((upstream-name . "assertive.matrices")))
12863 (build-system r-build-system)
12865 `(("r-assertive-base" ,r-assertive-base)))
12866 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12867 (synopsis "Assertions to check properties of matrices")
12869 "This package provides a set of predicates and assertions for checking
12870 the properties of matrices. This is mainly for use by other package
12871 developers who want to include run-time testing features in their own
12873 (license license:gpl3+)))
12875 (define-public r-assertive-models
12877 (name "r-assertive-models")
12882 (uri (cran-uri "assertive.models" version))
12885 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12887 `((upstream-name . "assertive.models")))
12888 (build-system r-build-system)
12890 `(("r-assertive-base" ,r-assertive-base)))
12891 (home-page "https://bitbucket.org/richierocks/assertive.models")
12892 (synopsis "Assertions to check properties of models")
12894 "This package provides a set of predicates and assertions for checking
12895 the properties of models. This is mainly for use by other package developers
12896 who want to include run-time testing features in their own packages.")
12897 (license license:gpl3+)))
12899 (define-public r-assertive-reflection
12901 (name "r-assertive-reflection")
12906 (uri (cran-uri "assertive.reflection" version))
12909 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12911 `((upstream-name . "assertive.reflection")))
12912 (build-system r-build-system)
12914 `(("r-assertive-base" ,r-assertive-base)))
12915 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12916 (synopsis "Assertions for checking the state of R")
12918 "This package provides a set of predicates and assertions for checking
12919 the state and capabilities of R, the operating system it is running on, and
12920 the IDE being used. This is mainly for use by other package developers who
12921 want to include run-time testing features in their own packages.")
12922 (license license:gpl3+)))
12924 (define-public r-assertive-types
12926 (name "r-assertive-types")
12931 (uri (cran-uri "assertive.types" version))
12934 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12936 `((upstream-name . "assertive.types")))
12937 (build-system r-build-system)
12939 `(("r-assertive-base" ,r-assertive-base)
12940 ("r-assertive-properties" ,r-assertive-properties)
12941 ("r-codetools" ,r-codetools)))
12942 (home-page "https://bitbucket.org/richierocks/assertive.types")
12943 (synopsis "Assertions to check types of variables")
12945 "This package provides a set of predicates and assertions for checking
12946 the types of variables. This is mainly for use by other package developers
12947 who want to include run-time testing features in their own packages.")
12948 (license license:gpl3+)))
12950 (define-public r-assertive-files
12952 (name "r-assertive-files")
12957 (uri (cran-uri "assertive.files" version))
12960 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12962 `((upstream-name . "assertive.files")))
12963 (build-system r-build-system)
12965 `(("r-assertive-base" ,r-assertive-base)
12966 ("r-assertive-numbers" ,r-assertive-numbers)))
12967 (home-page "https://bitbucket.org/richierocks/assertive.files")
12968 (synopsis "Assertions to check properties of files")
12970 "This package provides a set of predicates and assertions for checking
12971 the properties of files and connections. This is mainly for use by other
12972 package developers who want to include run-time testing features in their own
12974 (license license:gpl3+)))
12976 (define-public r-assertive-code
12978 (name "r-assertive-code")
12983 (uri (cran-uri "assertive.code" version))
12986 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12988 `((upstream-name . "assertive.code")))
12989 (build-system r-build-system)
12991 `(("r-assertive-base" ,r-assertive-base)
12992 ("r-assertive-properties" ,r-assertive-properties)
12993 ("r-assertive-types" ,r-assertive-types)))
12994 (home-page "https://bitbucket.org/richierocks/assertive.code")
12995 (synopsis "Assertions to check properties of code")
12997 "This package provides a set of predicates and assertions for checking
12998 the properties of code. This is mainly for use by other package developers
12999 who want to include run-time testing features in their own packages.")
13000 (license license:gpl3+)))
13002 (define-public r-assertive-datetimes
13004 (name "r-assertive-datetimes")
13009 (uri (cran-uri "assertive.datetimes" version))
13012 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
13014 `((upstream-name . "assertive.datetimes")))
13015 (build-system r-build-system)
13017 `(("r-assertive-base" ,r-assertive-base)
13018 ("r-assertive-types" ,r-assertive-types)))
13019 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13020 (synopsis "Assertions to check properties of dates and times")
13022 "This package provides a set of predicates and assertions for checking
13023 the properties of dates and times. This is mainly for use by other package
13024 developers who want to include run-time testing features in their own
13026 (license license:gpl3+)))
13028 (define-public r-assertive-strings
13030 (name "r-assertive-strings")
13035 (uri (cran-uri "assertive.strings" version))
13038 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13040 `((upstream-name . "assertive.strings")))
13041 (build-system r-build-system)
13043 `(("r-assertive-base" ,r-assertive-base)
13044 ("r-assertive-types" ,r-assertive-types)
13045 ("r-stringi" ,r-stringi)))
13046 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13047 (synopsis "Assertions to check properties of strings")
13049 "This package provides a set of predicates and assertions for checking
13050 the properties of strings. This is mainly for use by other package developers
13051 who want to include run-time testing features in their own packages.")
13052 (license license:gpl3+)))
13054 (define-public r-assertive-data-us
13056 (name "r-assertive-data-us")
13061 (uri (cran-uri "assertive.data.us" version))
13064 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13066 `((upstream-name . "assertive.data.us")))
13067 (build-system r-build-system)
13069 `(("r-assertive-base" ,r-assertive-base)
13070 ("r-assertive-strings" ,r-assertive-strings)))
13071 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13072 (synopsis "Assertions to check properties of strings")
13074 "This package provides a set of predicates and assertions for checking
13075 the properties of US-specific complex data types. This is mainly for use by
13076 other package developers who want to include run-time testing features in
13077 their own packages.")
13078 (license license:gpl3+)))
13080 (define-public r-assertive-data-uk
13082 (name "r-assertive-data-uk")
13087 (uri (cran-uri "assertive.data.uk" version))
13090 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13092 `((upstream-name . "assertive.data.uk")))
13093 (build-system r-build-system)
13095 `(("r-assertive-base" ,r-assertive-base)
13096 ("r-assertive-strings" ,r-assertive-strings)))
13097 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13098 (synopsis "Assertions to check properties of strings")
13100 "This package provides a set of predicates and assertions for checking
13101 the properties of UK-specific complex data types. This is mainly for use by
13102 other package developers who want to include run-time testing features in
13103 their own packages.")
13104 (license license:gpl3+)))
13106 (define-public r-assertive-data
13108 (name "r-assertive-data")
13113 (uri (cran-uri "assertive.data" version))
13116 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13118 `((upstream-name . "assertive.data")))
13119 (build-system r-build-system)
13121 `(("r-assertive-base" ,r-assertive-base)
13122 ("r-assertive-strings" ,r-assertive-strings)))
13123 (home-page "https://bitbucket.org/richierocks/assertive.data")
13124 (synopsis "Assertions to check properties of data")
13126 "This package provides a set of predicates and assertions for checking
13127 the properties of (country independent) complex data types. This is mainly
13128 for use by other package developers who want to include run-time testing
13129 features in their own packages.")
13130 (license license:gpl3+)))
13132 (define-public r-assertive
13134 (name "r-assertive")
13139 (uri (cran-uri "assertive" version))
13142 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13143 (build-system r-build-system)
13145 `(("r-assertive-base" ,r-assertive-base)
13146 ("r-assertive-code" ,r-assertive-code)
13147 ("r-assertive-data" ,r-assertive-data)
13148 ("r-assertive-data-uk" ,r-assertive-data-uk)
13149 ("r-assertive-data-us" ,r-assertive-data-us)
13150 ("r-assertive-datetimes" ,r-assertive-datetimes)
13151 ("r-assertive-files" ,r-assertive-files)
13152 ("r-assertive-matrices" ,r-assertive-matrices)
13153 ("r-assertive-models" ,r-assertive-models)
13154 ("r-assertive-numbers" ,r-assertive-numbers)
13155 ("r-assertive-properties" ,r-assertive-properties)
13156 ("r-assertive-reflection" ,r-assertive-reflection)
13157 ("r-assertive-sets" ,r-assertive-sets)
13158 ("r-assertive-strings" ,r-assertive-strings)
13159 ("r-assertive-types" ,r-assertive-types)
13160 ("r-knitr" ,r-knitr)))
13162 `(("r-knitr" ,r-knitr)))
13163 (home-page "https://bitbucket.org/richierocks/assertive")
13164 (synopsis "Readable check functions to ensure code integrity")
13166 "This package provides lots of predicates (@code{is_*} functions) to
13167 check the state of your variables, and assertions (@code{assert_*} functions)
13168 to throw errors if they aren't in the right form.")
13169 (license license:gpl3+)))
13171 (define-public r-dotcall64
13173 (name "r-dotcall64")
13178 (uri (cran-uri "dotCall64" version))
13181 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
13182 (properties `((upstream-name . "dotCall64")))
13183 (build-system r-build-system)
13184 (native-inputs `(("gfortran" ,gfortran)))
13185 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13186 (synopsis "Enhanced foreign function interface supporting long vectors")
13188 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13189 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13190 supports long vectors, arguments of type 64-bit integer, and provides a
13191 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13192 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13193 (license license:gpl2+)))
13195 (define-public r-spam
13202 (uri (cran-uri "spam" version))
13204 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13205 (build-system r-build-system)
13207 `(("r-dotcall64" ,r-dotcall64)))
13209 `(("gfortran" ,gfortran)
13210 ("r-knitr" ,r-knitr)))
13211 (home-page "https://www.math.uzh.ch/pages/spam/")
13212 (synopsis "Sparse matrix algebra")
13214 "This package provides a set of functions for sparse matrix algebra.
13215 Differences with other sparse matrix packages are:
13218 @item it only supports (essentially) one sparse matrix format;
13219 @item it is based on transparent and simple structure(s);
13220 @item it is tailored for MCMC calculations within G(M)RF;
13221 @item and it is fast and scalable (with the extension package @code{spam64}).
13223 ;; Either of these licenses
13224 (license (list license:bsd-3 license:lgpl2.0))))
13226 (define-public r-fields
13233 (uri (cran-uri "fields" version))
13235 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13236 (build-system r-build-system)
13238 `(("r-maps" ,r-maps)
13239 ("r-spam" ,r-spam)))
13241 `(("gfortran" ,gfortran)))
13242 (home-page "https://www.image.ucar.edu/fields")
13243 (synopsis "Tools for spatial data")
13245 "This is a package for curve, surface and function fitting with an
13246 emphasis on splines, spatial data and spatial statistics. The major methods
13247 include cubic, and thin plate splines, Kriging, and compactly supported
13248 covariance functions for large data sets.")
13249 (license license:gpl2+)))
13251 (define-public r-spatialextremes
13253 (name "r-spatialextremes")
13258 (uri (cran-uri "SpatialExtremes" version))
13261 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13263 `((upstream-name . "SpatialExtremes")))
13264 (build-system r-build-system)
13266 `(("r-fields" ,r-fields)
13267 ("r-maps" ,r-maps)))
13268 (home-page "http://spatialextremes.r-forge.r-project.org/")
13269 (synopsis "Modelling spatial extremes")
13271 "This package provides tools for the statistical modelling of spatial
13272 extremes using max-stable processes, copula or Bayesian hierarchical models.
13273 More precisely, this package allows (conditional) simulations from various
13274 parametric max-stable models, analysis of the extremal spatial dependence, the
13275 fitting of such processes using composite likelihoods or least square (simple
13276 max-stable processes only), model checking and selection and prediction.")
13277 (license license:gpl2+)))
13279 (define-public r-drc
13286 (uri (cran-uri "drc" version))
13289 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13290 (build-system r-build-system)
13293 ("r-gtools" ,r-gtools)
13295 ("r-multcomp" ,r-multcomp)
13296 ("r-plotrix" ,r-plotrix)
13297 ("r-scales" ,r-scales)))
13298 (home-page "https://cran.r-project.org/web/packages/drc")
13299 (synopsis "Analysis of dose-response curves")
13301 "This package provides a suite of flexible and versatile model fitting
13302 and after-fitting functions for the analysis of dose-response data.")
13303 (license license:gpl2+)))
13305 (define-public r-rmeta
13312 (uri (cran-uri "rmeta" version))
13315 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13316 (build-system r-build-system)
13317 (home-page "https://cran.r-project.org/web/packages/rmeta")
13318 (synopsis "Tools for meta-analysis")
13320 "This package provides functions for simple fixed and random effects
13321 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13322 draws standard summary plots, funnel plots, and computes summaries and tests
13323 for association and heterogeneity.")
13324 (license license:gpl2)))
13326 (define-public r-bootstrap
13328 (name "r-bootstrap")
13333 (uri (cran-uri "bootstrap" version))
13336 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13337 (build-system r-build-system)
13338 (native-inputs `(("gfortran" ,gfortran)))
13339 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13340 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13342 "This package provides software and data for the book \"An Introduction
13343 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13344 This package is primarily provided for projects already based on it, and for
13345 support of the book. New projects should preferentially use the recommended
13346 package \"boot\".")
13347 (license license:bsd-3)))
13349 (define-public r-survivalroc
13351 (name "r-survivalroc")
13356 (uri (cran-uri "survivalROC" version))
13359 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13360 (properties `((upstream-name . "survivalROC")))
13361 (build-system r-build-system)
13362 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13363 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13365 "Compute time-dependent ROC curve from censored survival data using
13366 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13367 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13368 (license license:gpl2+)))
13370 (define-public r-longitudinal
13372 (name "r-longitudinal")
13377 (uri (cran-uri "longitudinal" version))
13380 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13381 (build-system r-build-system)
13382 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13383 (home-page "http://strimmerlab.org/software/longitudinal/")
13384 (synopsis "Analysis of multiple time course data")
13386 "This package contains general data structures and functions for
13387 longitudinal data with multiple variables, repeated measurements, and
13388 irregularly spaced time points. It also implements a shrinkage estimator of
13389 dynamical correlation and dynamical covariance.")
13390 (license license:gpl3+)))
13392 (define-public r-genenet
13399 (uri (cran-uri "GeneNet" version))
13402 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13403 (properties `((upstream-name . "GeneNet")))
13404 (build-system r-build-system)
13406 `(("r-corpcor" ,r-corpcor)
13407 ("r-fdrtool" ,r-fdrtool)
13408 ("r-longitudinal" ,r-longitudinal)))
13409 (home-page "http://strimmerlab.org/software/genenet/")
13410 (synopsis "Modeling and inferring gene networks")
13412 "This package analyzes gene expression (time series) data with focus on
13413 the inference of gene networks. In particular, GeneNet implements the methods
13414 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13415 for learning large-scale gene association networks (including assignment of
13416 putative directions).")
13417 (license license:gpl3+)))
13419 (define-public r-rbamtools
13421 (name "r-rbamtools")
13422 (version "2.16.17")
13426 (uri (cran-uri "rbamtools" version))
13429 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13430 (build-system r-build-system)
13431 (inputs `(("zlib" ,zlib)))
13433 `(("r-refgenome" ,r-refgenome)))
13434 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13435 (synopsis "Read and write BAM (binary alignment) files")
13437 "This package provides an R interface to functions of the SAMtools
13439 (license license:artistic2.0)))
13441 (define-public r-protviz
13448 (uri (cran-uri "protViz" version))
13451 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13452 (properties `((upstream-name . "protViz")))
13453 (build-system r-build-system)
13454 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13455 (home-page "https://github.com/protViz/protViz/")
13456 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13458 "This package helps with quality checks, visualizations and analysis of
13459 mass spectrometry data, coming from proteomics experiments. The package is
13460 developed, tested and used at the Functional Genomics Center Zurich, where it
13461 is used mainly for prototyping, teaching, and having fun with proteomics data.
13462 But it can also be used to do data analysis for small scale data sets.")
13463 (license license:gpl3)))
13465 (define-public r-cmprsk
13472 (uri (cran-uri "cmprsk" version))
13474 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13475 (build-system r-build-system)
13477 `(("r-survival" ,r-survival)))
13479 `(("gfortran" ,gfortran)))
13480 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13481 (synopsis "Subdistribution analysis of competing risks")
13483 "This package provides tool for estimation, testing and regression
13484 modeling of subdistribution functions in competing risks, as described in
13485 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13486 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13487 A proportional hazards model for the subdistribution of a competing risk,
13488 JASA, 94:496-509.")
13489 (license license:gpl2+)))
13491 (define-public r-etm
13498 (uri (cran-uri "etm" version))
13501 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13502 (build-system r-build-system)
13504 `(("r-data-table" ,r-data-table)
13505 ("r-lattice" ,r-lattice)
13507 ("r-rcpparmadillo" ,r-rcpparmadillo)
13508 ("r-survival" ,r-survival)))
13509 (home-page "https://cran.r-project.org/web/packages/etm")
13510 (synopsis "Empirical transition matrix")
13512 "The @dfn{empirical transition matrix} (etm) package estimates
13513 the matrix of transition probabilities for any time-inhomogeneous multistate
13514 model with finite state space using the Aalen-Johansen estimator.")
13515 (license license:expat)))
13517 (define-public r-epi
13524 (uri (cran-uri "Epi" version))
13527 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
13528 (properties `((upstream-name . "Epi")))
13529 (build-system r-build-system)
13531 `(("r-cmprsk" ,r-cmprsk)
13532 ("r-data-table" ,r-data-table)
13533 ("r-dplyr" ,r-dplyr)
13536 ("r-matrix" ,r-matrix)
13538 ("r-numderiv" ,r-numderiv)
13540 ("r-purrr" ,r-purrr)
13541 ("r-survival" ,r-survival)
13543 (home-page "https://BendixCarstensen.com/Epi/")
13544 (synopsis "Statistical analysis in epidemiology")
13546 "This package provides functions for demographic and epidemiological
13547 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13548 particular representation, manipulation and simulation of multistate data -
13549 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13550 @code{etm} and @code{cmprsk} packages. It also contains functions for
13551 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13552 data and some useful functions for tabulation and plotting, as well as a
13553 number of epidemiological data sets.")
13554 (license license:gpl2)))
13556 (define-public r-ppls
13559 (version "1.6-1.1")
13563 (uri (cran-uri "ppls" version))
13566 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13567 (build-system r-build-system)
13568 (propagated-inputs `(("r-mass" ,r-mass)))
13569 (home-page "https://cran.r-project.org/web/packages/ppls")
13570 (synopsis "Penalized partial least squares")
13572 "This package contains linear and nonlinear regression methods based on
13573 partial least squares and penalization techniques. Model parameters are
13574 selected via cross-validation, and confidence intervals ans tests for the
13575 regression coefficients can be conducted via jackknifing.")
13576 (license license:gpl2+)))
13578 (define-public r-huge
13581 (version "1.3.4.1")
13585 (uri (cran-uri "huge" version))
13587 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13588 (build-system r-build-system)
13590 `(("r-igraph" ,r-igraph)
13592 ("r-matrix" ,r-matrix)
13594 ("r-rcppeigen" ,r-rcppeigen)))
13595 (home-page "https://cran.r-project.org/web/packages/huge")
13596 (synopsis "High-dimensional undirected graph estimation")
13598 "This package provides a general framework for high-dimensional
13599 undirected graph estimation. It integrates data preprocessing, neighborhood
13600 screening, graph estimation, and model selection techniques into a pipeline.")
13601 (license license:gpl2)))
13603 (define-public r-parcor
13610 (uri (cran-uri "parcor" version))
13613 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13614 (build-system r-build-system)
13617 ("r-genenet" ,r-genenet)
13618 ("r-glmnet" ,r-glmnet)
13620 ("r-ppls" ,r-ppls)))
13621 (home-page "https://cran.r-project.org/web/packages/parcor")
13622 (synopsis "Regularized estimation of partial correlation matrices")
13624 "This package estimates the matrix of partial correlations based on
13625 different regularized regression methods: lasso, adaptive lasso, PLS, and
13626 Ridge Regression. In addition, the package provides model selection for
13627 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13628 (license license:gpl2+)))
13630 (define-public r-mcmc
13637 (uri (cran-uri "mcmc" version))
13640 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13641 (build-system r-build-system)
13642 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13643 (synopsis "Markov chain Monte Carlo")
13645 "This package simulates continuous distributions of random vectors using
13646 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13647 function that evaluates the log unnormalized density. Algorithms are random
13648 walk Metropolis algorithm (function @code{metrop}), simulated
13649 tempering (function @code{temper}), and morphometric random walk
13650 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13651 by change of variable.")
13652 (license license:expat)))
13654 (define-public r-listenv
13661 (uri (cran-uri "listenv" version))
13664 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13665 (build-system r-build-system)
13667 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13668 (home-page "https://github.com/HenrikBengtsson/listenv")
13669 (synopsis "Environments behaving (almost) as lists")
13671 "This package implements list environments. List environments are
13672 environments that have list-like properties. For instance, the elements of a
13673 list environment are ordered and can be accessed and iterated over using index
13675 (license license:lgpl2.1+)))
13677 (define-public r-globals
13684 (uri (cran-uri "globals" version))
13687 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13688 (build-system r-build-system)
13690 `(("r-codetools" ,r-codetools)))
13691 (home-page "https://github.com/HenrikBengtsson/globals")
13692 (synopsis "Identify global objects in R expressions")
13694 "This package provides tools to identify global (\"unknown\" or \"free\")
13695 objects in R expressions by code inspection using various strategies, e.g.
13696 conservative or liberal. The objective of this package is to make it as
13697 simple as possible to identify global objects for the purpose of exporting
13698 them in distributed compute environments.")
13699 (license license:lgpl2.1+)))
13701 (define-public r-parallelly
13703 (name "r-parallelly")
13708 (uri (cran-uri "parallelly" version))
13711 "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6"))))
13712 (properties `((upstream-name . "parallelly")))
13713 (build-system r-build-system)
13714 (home-page "https://github.com/HenrikBengtsson/parallelly")
13715 (synopsis "Enhancements of the parallel package")
13717 "This package provides utility functions that enhance the @code{parallel}
13718 package and support the built-in parallel backends of the @code{future}
13719 package. For example, @code{availableCores} gives the number of CPU cores
13720 available to your R process as given by R options and environment variables,
13721 including those set by job schedulers on high-performance compute clusters.
13722 If none is set, it will fall back to @code{parallel::detectCores}. Another
13723 example is @code{makeClusterPSOCK}, which is backward compatible with
13724 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13725 remote cluster workers without the need for configuring the firewall to do
13726 port-forwarding to your local computer.")
13727 (license license:lgpl2.1+)))
13729 (define-public r-future
13736 (uri (cran-uri "future" version))
13739 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13740 (build-system r-build-system)
13742 `(("r-digest" ,r-digest)
13743 ("r-globals" ,r-globals)
13744 ("r-listenv" ,r-listenv)
13745 ("r-parallelly" ,r-parallelly)))
13747 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13748 (home-page "https://github.com/HenrikBengtsson/future")
13749 (synopsis "Unified parallel and distributed processing in R")
13751 "The purpose of this package is to provide a lightweight and unified
13752 Future API for sequential and parallel processing of R expression via futures.
13753 This package implements sequential, multicore, multisession, and cluster
13754 futures. With these, R expressions can be evaluated on the local machine, in
13755 parallel a set of local machines, or distributed on a mix of local and remote
13756 machines. Extensions to this package implement additional backends for
13757 processing futures via compute cluster schedulers etc. Because of its unified
13758 API, there is no need to modify any code in order to switch from sequential on
13759 the local machine to, say, distributed processing on a remote compute cluster.")
13760 (license license:lgpl2.1+)))
13762 (define-public r-future-apply
13764 (name "r-future-apply")
13769 (uri (cran-uri "future.apply" version))
13772 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13773 (properties `((upstream-name . "future.apply")))
13774 (build-system r-build-system)
13776 `(("r-future" ,r-future)
13777 ("r-globals" ,r-globals)))
13779 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13780 (home-page "https://github.com/HenrikBengtsson/future.apply")
13781 (synopsis "Apply function to elements in parallel using futures")
13783 "This package provides implementations of @code{apply()},
13784 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13785 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13786 can be resolved using any future-supported backend, e.g. parallel on the local
13787 machine or distributed on a compute cluster.")
13788 (license license:gpl2+)))
13790 (define-public r-rsvd
13797 (uri (cran-uri "rsvd" version))
13800 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13801 (build-system r-build-system)
13803 `(("r-matrix" ,r-matrix)))
13804 (home-page "https://github.com/erichson/rSVD")
13805 (synopsis "Randomized singular value decomposition")
13807 "Low-rank matrix decompositions are fundamental tools and widely used for
13808 data analysis, dimension reduction, and data compression. Classically, highly
13809 accurate deterministic matrix algorithms are used for this task. However, the
13810 emergence of large-scale data has severely challenged our computational
13811 ability to analyze big data. The concept of randomness has been demonstrated
13812 as an effective strategy to quickly produce approximate answers to familiar
13813 problems such as the @dfn{singular value decomposition} (SVD). This package
13814 provides several randomized matrix algorithms such as the randomized singular
13815 value decomposition (@code{rsvd}), randomized principal component
13816 analysis (@code{rpca}), randomized robust principal component
13817 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13818 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13819 functions are provided.")
13820 (license license:gpl3+)))
13822 (define-public r-sloop
13829 (uri (cran-uri "sloop" version))
13832 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13833 (build-system r-build-system)
13835 `(("r-codetools" ,r-codetools)
13836 ("r-crayon" ,r-crayon)
13837 ("r-purrr" ,r-purrr)
13838 ("r-rlang" ,r-rlang)
13839 ("r-tibble" ,r-tibble)))
13840 (home-page "https://github.com/r-lib/sloop")
13841 (synopsis "Helpers for object-oriented programming in R")
13843 "This package provides a collection of helper functions designed to
13844 help you to better understand object oriented programming in R, particularly
13846 (license license:gpl3)))
13848 (define-public r-capushe
13855 (uri (cran-uri "capushe" version))
13858 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13859 (build-system r-build-system)
13860 (propagated-inputs `(("r-mass" ,r-mass)))
13861 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13862 (synopsis "Calibrating penalties using slope heuristics")
13864 "This package provides tools for the calibration of penalized criteria
13865 for model selection. The calibration methods available are based on the slope
13867 (license license:gpl2+)))
13869 (define-public r-dorng
13876 (uri (cran-uri "doRNG" version))
13879 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13880 (properties `((upstream-name . "doRNG")))
13881 (build-system r-build-system)
13883 `(("r-foreach" ,r-foreach)
13884 ("r-iterators" ,r-iterators)
13885 ("r-rngtools" ,r-rngtools)))
13886 (home-page "https://renozao.github.io/doRNG/")
13887 (synopsis "Generic reproducible parallel backend for foreach loops")
13889 "This package provides functions to perform reproducible parallel
13890 @code{foreach} loops, using independent random streams as generated by
13891 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13892 convert standard @code{%dopar%} loops into fully reproducible loops,
13893 independently of the number of workers, the task scheduling strategy, or the
13894 chosen parallel environment and associated foreach backend.")
13895 (license license:gpl2+)))
13897 (define-public r-blockmodeling
13899 (name "r-blockmodeling")
13904 (uri (cran-uri "blockmodeling" version))
13907 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13908 (build-system r-build-system)
13910 `(("r-matrix" ,r-matrix)))
13911 (native-inputs `(("gfortran" ,gfortran)))
13912 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13913 (synopsis "Generalized and classical blockmodeling of valued networks")
13915 "This package is primarily meant as an implementation of generalized
13916 blockmodeling for valued networks. In addition, measures of similarity or
13917 dissimilarity based on structural equivalence and regular equivalence (REGE
13918 algorithms) can be computed and partitioned matrices can be plotted.")
13919 (license license:gpl2+)))
13921 (define-public r-upsetr
13928 (uri (cran-uri "UpSetR" version))
13931 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13932 (properties `((upstream-name . "UpSetR")))
13933 (build-system r-build-system)
13935 `(("r-ggplot2" ,r-ggplot2)
13936 ("r-gridextra" ,r-gridextra)
13938 ("r-scales" ,r-scales)))
13939 (home-page "https://github.com/hms-dbmi/UpSetR")
13940 (synopsis "Visualize intersecting sets")
13942 "This package provides a more scalable alternative to Venn and Euler
13943 diagrams for visualizing intersecting sets. Create visualizations of
13944 intersecting sets using a novel matrix design, along with visualizations of
13945 several common set, element and attribute related tasks.")
13946 (license license:expat)))
13948 ;; This package includes a JavaScript file, which is not minified. When
13949 ;; upgrading please check that there are no new minified JavaScript files.
13950 (define-public r-shinybs
13957 (uri (cran-uri "shinyBS" version))
13960 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13961 (properties `((upstream-name . "shinyBS")))
13962 (build-system r-build-system)
13963 ;; The tests spawn Shiny browser apps. They cannot be run
13964 ;; non-interactively.
13965 (arguments '(#:tests? #f))
13967 `(("r-htmltools" ,r-htmltools)
13968 ("r-shiny" ,r-shiny)))
13969 (home-page "https://ebailey78.github.io/shinyBS/")
13970 (synopsis "Twitter Bootstrap components for Shiny")
13972 "This package adds additional Twitter Bootstrap components to Shiny.")
13973 (license license:gpl3)))
13975 (define-public r-shinyjqui
13977 (name "r-shinyjqui")
13982 (uri (cran-uri "shinyjqui" version))
13985 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
13988 (delete-file "inst/www/shinyjqui.min.js")))))
13989 (properties `((upstream-name . "shinyjqui")))
13990 (build-system r-build-system)
13993 (modify-phases %standard-phases
13994 (add-after 'unpack 'process-javascript
13995 (lambda* (#:key inputs #:allow-other-keys)
13996 (with-directory-excursion "inst/www/"
13997 (let ((source "shinyjqui.js")
13998 (target "shinyjqui.min.js"))
13999 (format #true "Processing ~a --> ~a~%"
14001 (invoke "esbuild" source "--minify"
14002 (string-append "--outfile=" target)))))))))
14004 `(("r-htmltools" ,r-htmltools)
14005 ("r-htmlwidgets" ,r-htmlwidgets)
14006 ("r-jsonlite" ,r-jsonlite)
14007 ("r-shiny" ,r-shiny)))
14009 `(("r-knitr" ,r-knitr)
14010 ("esbuild" ,esbuild)))
14011 (home-page "https://github.com/yang-tang/shinyjqui")
14012 (synopsis "jQuery UI interactions and effects for Shiny")
14014 "This is an extension to Shiny that brings interactions and animation
14015 effects from the jQuery UI library.")
14016 (license license:expat)))
14018 (define-public r-outliers
14020 (name "r-outliers")
14025 (uri (cran-uri "outliers" version))
14028 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14029 (build-system r-build-system)
14030 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14031 (synopsis "Tests for outliers")
14033 "This package provides a collection of some tests commonly used for
14034 identifying outliers.")
14035 (license license:gpl2+)))
14037 (define-public r-bayesm
14044 (uri (cran-uri "bayesm" version))
14046 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14047 (build-system r-build-system)
14049 `(("r-rcpp" ,r-rcpp)
14050 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14051 (home-page "http://www.perossi.org/home/bsm-1")
14052 (synopsis "Bayesian inference for marketing/micro-econometrics")
14054 "This package covers many important models used in marketing and
14055 micro-econometrics applications, including Bayes Regression (univariate or
14056 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14057 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14058 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14059 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14060 Estimation with normal base, Hierarchical Linear Models with normal prior and
14061 covariates, Hierarchical Linear Models with a mixture of normals prior and
14062 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14063 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14064 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14065 analysis of choice-based conjoint data, Bayesian treatment of linear
14066 instrumental variables models, Analysis of Multivariate Ordinal survey data
14067 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14068 Coefficient Logit Models.")
14069 (license license:gpl2+)))
14071 (define-public r-tensora
14078 (uri (cran-uri "tensorA" version))
14081 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14082 (properties `((upstream-name . "tensorA")))
14083 (build-system r-build-system)
14084 (home-page "http://www.stat.boogaart.de/tensorA")
14085 (synopsis "Advanced tensor arithmetic with named indices")
14087 "This package provides convenience functions for advanced linear algebra
14088 with tensors and computation with datasets of tensors on a higher level
14089 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14090 co- and contravariate indices, and parallel computations on sequences of
14092 (license license:gpl2+)))
14094 (define-public r-rarpack
14101 (uri (cran-uri "rARPACK" version))
14104 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14105 (properties `((upstream-name . "rARPACK")))
14106 (build-system r-build-system)
14107 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14108 (home-page "https://github.com/yixuan/rARPACK")
14109 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14111 "This package was previously an R wrapper of the ARPACK library, and now
14112 a shell of the R package RSpectra, an R interface to the Spectra library for
14113 solving large scale eigenvalue/vector problems. The current version of
14114 rARPACK simply imports and exports the functions provided by RSpectra. New
14115 users of rARPACK are advised to switch to the RSpectra package.")
14116 (license license:bsd-3)))
14118 (define-public r-compositions
14120 (name "r-compositions")
14125 (uri (cran-uri "compositions" version))
14128 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14129 (build-system r-build-system)
14131 `(("r-bayesm" ,r-bayesm)
14133 ("r-robustbase" ,r-robustbase)
14134 ("r-tensora" ,r-tensora)))
14136 `(("r-knitr" ,r-knitr)))
14137 (home-page "http://www.stat.boogaart.de/compositions")
14138 (synopsis "Compositional data analysis")
14140 "This package provides functions for the consistent analysis of
14141 compositional data (e.g. portions of substances) and positive
14142 numbers (e.g. concentrations).")
14143 (license license:gpl2+)))
14145 (define-public r-cobs
14152 (uri (cran-uri "cobs" version))
14155 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14156 (build-system r-build-system)
14158 `(("r-quantreg" ,r-quantreg)
14159 ("r-sparsem" ,r-sparsem)))
14160 (home-page "https://cran.r-project.org/web/packages/cobs")
14161 (synopsis "Constrained B-Splines (sparse matrix based)")
14163 "This package provides qualitatively constrained (regression) smoothing
14164 splines via linear programming and sparse matrices.")
14165 (license license:gpl2+)))
14167 (define-public r-drimpute
14169 (name "r-drimpute")
14174 (uri (cran-uri "DrImpute" version))
14177 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14178 (properties `((upstream-name . "DrImpute")))
14179 (build-system r-build-system)
14181 `(("r-rcpp" ,r-rcpp)
14182 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14183 (home-page "https://github.com/ikwak2/DrImpute")
14184 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14186 "This is an R package for imputing dropout events. Many statistical
14187 methods in cell type identification, visualization and lineage reconstruction
14188 do not account for dropout events. DrImpute can improve the performance of
14189 such software by imputing dropout events.")
14190 (license license:gpl3)))
14192 (define-public r-gamlss-dist
14194 (name "r-gamlss-dist")
14199 (uri (cran-uri "gamlss.dist" version))
14201 (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc"))))
14202 (properties `((upstream-name . "gamlss.dist")))
14203 (build-system r-build-system)
14204 (propagated-inputs `(("r-mass" ,r-mass)))
14205 (home-page "http://www.gamlss.org/")
14206 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14208 "This package provides a set of distributions which can be used for
14209 modelling the response variables in Generalized Additive Models for Location
14210 Scale and Shape. The distributions can be continuous, discrete or mixed
14211 distributions. Extra distributions can be created, by transforming, any
14212 continuous distribution defined on the real line, to a distribution defined on
14213 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14214 transformation, respectively.")
14215 ;; Either version of the GPL.
14216 (license (list license:gpl2 license:gpl3))))
14218 ;; This package includes JavaScript files, which are not minified. When
14219 ;; upgrading please check that there are no new minified JavaScript files.
14220 (define-public r-shinyjs
14227 (uri (cran-uri "shinyjs" version))
14230 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14231 (build-system r-build-system)
14233 `(("r-digest" ,r-digest)
14234 ("r-htmltools" ,r-htmltools)
14235 ("r-jsonlite" ,r-jsonlite)
14236 ("r-shiny" ,r-shiny)))
14238 `(("r-knitr" ,r-knitr)))
14239 (home-page "https://deanattali.com/shinyjs")
14240 (synopsis "Improve the user experience of your Shiny apps")
14242 "Perform common useful JavaScript operations in Shiny apps that will
14243 greatly improve your apps without having to know any JavaScript. Examples
14244 include: hiding an element, disabling an input, resetting an input back to its
14245 original value, delaying code execution by a few seconds, and many more useful
14246 functions for both the end user and the developer. Shinyjs can also be used
14247 to easily call your own custom JavaScript functions from R.")
14248 (license license:agpl3+)))
14250 ;; This package includes minified JavaScript files. When upgrading please
14251 ;; check that there are no new minified JavaScript files.
14252 (define-public r-colourpicker
14254 (name "r-colourpicker")
14259 (uri (cran-uri "colourpicker" version))
14262 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14263 (build-system r-build-system)
14265 `(#:modules ((guix build utils)
14266 (guix build r-build-system)
14270 (modify-phases %standard-phases
14271 (add-after 'unpack 'process-javascript
14272 (lambda* (#:key inputs #:allow-other-keys)
14273 (with-directory-excursion "inst"
14277 `((,(assoc-ref inputs "js-salvattore")
14278 "examples/colourInput/www/salvattore.min.js")
14279 (,(assoc-ref inputs "js-jquery")
14280 "htmlwidgets/lib/jquery/jquery.min.js")
14281 ("www/shared/colourpicker/js/colourpicker.js"
14282 "www/shared/colourpicker/js/colourpicker.min.js"))))
14283 (lambda (sources targets)
14284 (for-each (lambda (source target)
14285 (format #t "Processing ~a --> ~a~%"
14287 (delete-file target)
14288 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14289 (call-with-output-file target
14291 (dump-port minified port)))))
14292 sources targets))))
14295 `(("r-ggplot2" ,r-ggplot2)
14296 ("r-htmltools" ,r-htmltools)
14297 ("r-htmlwidgets" ,r-htmlwidgets)
14298 ("r-jsonlite" ,r-jsonlite)
14299 ("r-miniui" ,r-miniui)
14300 ("r-shiny" ,r-shiny)
14301 ("r-shinyjs" ,r-shinyjs)))
14303 `(("r-knitr" ,r-knitr)
14304 ("uglify-js" ,uglify-js)
14308 (uri "https://code.jquery.com/jquery-3.3.1.js")
14311 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14315 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14318 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14319 (home-page "https://github.com/daattali/colourpicker")
14320 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14322 "This package provides a color picker that can be used as an input in
14323 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14324 custom color palettes, and many more options. A plot color helper tool is
14325 available as an RStudio Addin, which helps you pick colors to use in your
14326 plots. A more generic color picker RStudio Addin is also provided to let you
14327 select colors to use in your R code.")
14328 (license license:expat)))
14330 (define-public r-ggextra
14337 (uri (cran-uri "ggExtra" version))
14340 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14341 (properties `((upstream-name . "ggExtra")))
14342 (build-system r-build-system)
14344 `(("r-colourpicker" ,r-colourpicker)
14345 ("r-ggplot2" ,r-ggplot2)
14346 ("r-gtable" ,r-gtable)
14347 ("r-miniui" ,r-miniui)
14349 ("r-scales" ,r-scales)
14350 ("r-shiny" ,r-shiny)
14351 ("r-shinyjs" ,r-shinyjs)))
14353 `(("r-knitr" ,r-knitr)))
14354 (home-page "https://github.com/daattali/ggExtra")
14355 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14357 "This package is a collection of functions and layers to enhance ggplot2.
14358 The flagship function is @code{ggMarginal()}, which can be used to add
14359 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14360 (license license:expat)))
14362 (define-public r-minpack-lm
14364 (name "r-minpack-lm")
14369 (uri (cran-uri "minpack.lm" version))
14372 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14373 (properties `((upstream-name . "minpack.lm")))
14374 (build-system r-build-system)
14375 (native-inputs `(("gfortran" ,gfortran)))
14376 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14377 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14379 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14380 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14381 problems by a modification of the Levenberg-Marquardt algorithm, with support
14382 for lower and upper parameter bounds. The implementation can be used via
14383 @code{nls}-like calls using the @code{nlsLM} function.")
14384 (license license:gpl3)))
14386 (define-public r-moments
14393 (uri (cran-uri "moments" version))
14396 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14397 (build-system r-build-system)
14398 (home-page "https://cran.r-project.org/web/packages/moments")
14399 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14401 "This package provides functions to calculate: moments, Pearson's
14402 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14403 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14404 (license license:gpl2+)))
14406 (define-public r-msir
14413 (uri (cran-uri "msir" version))
14416 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14417 (build-system r-build-system)
14419 `(("r-mclust" ,r-mclust)))
14421 `(("r-knitr" ,r-knitr)))
14422 (home-page "https://cran.r-project.org/web/packages/msir")
14423 (synopsis "Model-based sliced inverse regression")
14425 "This is an R package for dimension reduction based on finite Gaussian
14426 mixture modeling of inverse regression.")
14427 (license license:gpl2+)))
14429 (define-public r-pbivnorm
14431 (name "r-pbivnorm")
14436 (uri (cran-uri "pbivnorm" version))
14439 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14440 (build-system r-build-system)
14441 (native-inputs `(("gfortran" ,gfortran)))
14442 (home-page "https://github.com/brentonk/pbivnorm")
14443 (synopsis "Vectorized bivariate normal CDF")
14445 "This package provides a vectorized R function for calculating
14446 probabilities from a standard bivariate normal CDF.")
14447 (license license:gpl2+)))
14449 (define-public r-lavaan
14456 (uri (cran-uri "lavaan" version))
14459 "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0"))))
14460 (build-system r-build-system)
14462 `(("r-mass" ,r-mass)
14463 ("r-mnormt" ,r-mnormt)
14464 ("r-numderiv" ,r-numderiv)
14465 ("r-pbivnorm" ,r-pbivnorm)))
14466 (home-page "https://lavaan.ugent.be")
14467 (synopsis "Latent variable analysis")
14469 "This package provides tools to fit a variety of latent variable models,
14470 including confirmatory factor analysis, structural equation modeling and
14471 latent growth curve models.")
14472 (license license:gpl2+)))
14474 (define-public r-nonnest2
14476 (name "r-nonnest2")
14481 (uri (cran-uri "nonnest2" version))
14484 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14485 (build-system r-build-system)
14487 `(("r-compquadform" ,r-compquadform)
14488 ("r-lavaan" ,r-lavaan)
14489 ("r-mvtnorm" ,r-mvtnorm)
14490 ("r-sandwich" ,r-sandwich)))
14492 `(("r-knitr" ,r-knitr)))
14493 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14494 (synopsis "Tests of non-nested models")
14496 "This package allows for testing of non-nested models. It includes tests
14497 of model distinguishability and of model fit that can be applied to both
14498 nested and non-nested models. The package also includes functionality to
14499 obtain confidence intervals associated with AIC and BIC.")
14500 ;; Either version of the GPL.
14501 (license (list license:gpl2 license:gpl3))))
14503 (define-public r-penalized
14505 (name "r-penalized")
14510 (uri (cran-uri "penalized" version))
14513 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14514 (build-system r-build-system)
14516 `(("r-rcpp" ,r-rcpp)
14517 ("r-rcpparmadillo" ,r-rcpparmadillo)
14518 ("r-survival" ,r-survival)))
14519 (home-page "https://cran.r-project.org/web/packages/penalized/")
14520 (synopsis "Penalized estimation in GLMs and in the Cox model")
14522 "This package provides tools for fitting possibly high dimensional
14523 penalized regression models. The penalty structure can be any combination of
14524 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14525 constraint on the regression coefficients. The supported regression models
14526 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14527 model. Cross-validation routines allow optimization of the tuning
14529 (license license:gpl2+)))
14531 (define-public r-zim
14538 (uri (cran-uri "ZIM" version))
14541 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14542 (properties `((upstream-name . "ZIM")))
14543 (build-system r-build-system)
14544 (propagated-inputs `(("r-mass" ,r-mass)))
14545 (home-page "https://github.com/biostatstudio/ZIM")
14546 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14548 "Analyze count time series with excess zeros. Two types of statistical
14549 models are supported: Markov regression and state-space models. They are also
14550 known as observation-driven and parameter-driven models respectively in the
14551 time series literature. The functions used for Markov regression or
14552 observation-driven models can also be used to fit ordinary regression models
14553 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14554 negative binomial (ZINB) assumption. The package also contains miscellaneous
14555 functions to compute density, distribution, quantile, and generate random
14556 numbers from ZIP and ZINB distributions.")
14557 (license license:gpl3)))
14559 (define-public r-nor1mix
14566 (uri (cran-uri "nor1mix" version))
14569 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14570 (build-system r-build-system)
14571 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14572 (synopsis "Normal (1-d) mixture models")
14574 "This package provides S3 classes and methods for one-dimensional normal
14575 mixture models, for, e.g., density estimation or clustering algorithms
14576 research and teaching; it provides the widely used Marron-Wand densities. It
14577 also provides tools for efficient random number generation and graphics.")
14578 (license license:gpl2+)))
14580 (define-public r-beanplot
14582 (name "r-beanplot")
14587 (uri (cran-uri "beanplot" version))
14590 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14591 (build-system r-build-system)
14592 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14593 (synopsis "Visualization via beanplots")
14595 "This package provides beanplots, an alternative to
14596 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14598 (license license:gpl2)))
14600 (define-public r-pbdzmq
14607 (uri (cran-uri "pbdZMQ" version))
14610 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14611 (properties `((upstream-name . "pbdZMQ")))
14612 (build-system r-build-system)
14614 `(("zeromq" ,zeromq)
14617 `(("pkg-config" ,pkg-config)))
14618 (home-page "https://pbdr.org/")
14619 (synopsis "R interface to ZeroMQ")
14621 "ZeroMQ is a well-known library for high-performance asynchronous
14622 messaging in scalable, distributed applications. This package provides high
14623 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14624 interactive client/server programming frameworks. A few wrapper functions
14625 compatible with @code{rzmq} are also provided.")
14626 (license license:gpl3)))
14628 (define-public r-repr
14635 (uri (cran-uri "repr" version))
14638 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14639 (build-system r-build-system)
14641 `(("r-base64enc" ,r-base64enc)
14642 ("r-htmltools" ,r-htmltools)
14643 ("r-jsonlite" ,r-jsonlite)
14644 ("r-pillar" ,r-pillar)))
14645 (home-page "https://cran.r-project.org/web/packages/repr/")
14646 (synopsis "Serializable representations")
14648 "This package provides string and binary representations of objects for
14649 several formats and MIME types.")
14650 (license license:gpl3)))
14652 (define-public r-irdisplay
14654 (name "r-irdisplay")
14659 (uri (cran-uri "IRdisplay" version))
14662 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14663 (properties `((upstream-name . "IRdisplay")))
14664 (build-system r-build-system)
14666 `(("r-repr" ,r-repr)))
14667 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14668 (synopsis "Jupyter display machinery")
14670 "This package provides an interface to the rich display capabilities of
14671 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14672 running IRkernel session.")
14673 (license license:expat)))
14675 (define-public r-irkernel
14677 (name "r-irkernel")
14682 (uri (cran-uri "IRkernel" version))
14685 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14686 (properties `((upstream-name . "IRkernel")))
14687 (build-system r-build-system)
14690 (modify-phases %standard-phases
14691 (add-after 'install 'install-kernelspec
14692 (lambda* (#:key outputs #:allow-other-keys)
14693 (let ((out (assoc-ref outputs "out")))
14694 (setenv "HOME" "/tmp")
14695 (invoke "jupyter" "kernelspec" "install"
14698 (string-append out "/site-library/IRkernel/kernelspec"))
14699 ;; Record the absolute file name of the 'R' executable in
14701 (substitute* (string-append out "/share/jupyter"
14702 "/kernels/ir/kernel.json")
14704 (string-append "[\"" (which "R") "\",")))
14707 `(("jupyter" ,jupyter)))
14709 `(("r-crayon" ,r-crayon)
14710 ("r-digest" ,r-digest)
14711 ("r-evaluate" ,r-evaluate)
14712 ("r-irdisplay" ,r-irdisplay)
14713 ("r-jsonlite" ,r-jsonlite)
14714 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14715 ("r-minimal" ,r-minimal)
14716 ("r-pbdzmq" ,r-pbdzmq)
14718 ("r-uuid" ,r-uuid)))
14719 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14720 (synopsis "Native R kernel for Jupyter")
14722 "The R kernel for the Jupyter environment executes R code which the
14723 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14725 (license license:expat)))
14727 (define-public r-gmodels
14734 (uri (cran-uri "gmodels" version))
14737 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14738 (build-system r-build-system)
14740 `(("r-gdata" ,r-gdata)
14741 ("r-mass" ,r-mass)))
14742 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14743 (synopsis "Various R programming tools for model fitting")
14745 "This package provides various R programming tools for model fitting.")
14746 (license license:gpl2)))
14748 (define-public r-apcluster
14750 (name "r-apcluster")
14755 (uri (cran-uri "apcluster" version))
14758 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14759 (build-system r-build-system)
14761 `(("r-matrix" ,r-matrix)
14762 ("r-rcpp" ,r-rcpp)))
14763 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14764 (synopsis "Affinity propagation clustering")
14766 "This package implements affinity propagation clustering introduced by
14767 Frey and Dueck (2007). The package further provides leveraged affinity
14768 propagation and an algorithm for exemplar-based agglomerative clustering that
14769 can also be used to join clusters obtained from affinity propagation. Various
14770 plotting functions are available for analyzing clustering results.")
14771 (license license:gpl2+)))
14773 (define-public r-valr
14780 (uri (cran-uri "valr" version))
14783 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14784 (build-system r-build-system)
14786 `(("r-broom" ,r-broom)
14787 ("r-dplyr" ,r-dplyr)
14788 ("r-ggplot2" ,r-ggplot2)
14790 ("r-readr" ,r-readr)
14791 ("r-rlang" ,r-rlang)
14792 ("r-stringr" ,r-stringr)
14793 ("r-tibble" ,r-tibble)))
14795 `(("r-knitr" ,r-knitr)))
14796 (home-page "https://github.com/rnabioco/valr")
14797 (synopsis "Genome interval arithmetic in R")
14799 "This package enables you to read and manipulate genome intervals and
14800 signals. It provides functionality similar to command-line tool suites within
14801 R, enabling interactive analysis and visualization of genome-scale data.")
14802 (license license:expat)))
14804 (define-public r-rematch2
14806 (name "r-rematch2")
14811 (uri (cran-uri "rematch2" version))
14814 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14815 (build-system r-build-system)
14817 `(("r-tibble" ,r-tibble)))
14818 (home-page "https://github.com/r-lib/rematch2")
14819 (synopsis "Tidy output from regular expression matching")
14821 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14822 return the match results in tidy data frames.")
14823 (license license:expat)))
14825 (define-public r-picante
14832 (uri (cran-uri "picante" version))
14835 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14836 (build-system r-build-system)
14840 ("r-vegan" ,r-vegan)))
14841 (home-page "https://cran.r-project.org/web/packages/picante/")
14842 (synopsis "Integrating phylogenies and ecology")
14844 "This package provides functions for phylocom integration, community
14845 analyses, null-models, traits and evolution. It implements numerous
14846 ecophylogenetic approaches including measures of community phylogenetic and
14847 trait diversity, phylogenetic signal, estimation of trait values for
14848 unobserved taxa, null models for community and phylogeny randomizations, and
14849 utility functions for data input/output and phylogeny plotting. A full
14850 description of package functionality and methods are provided by Kembel et
14852 (license license:gpl2)))
14854 (define-public r-reinforcelearn
14856 (name "r-reinforcelearn")
14861 (uri (cran-uri "reinforcelearn" version))
14864 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14865 (build-system r-build-system)
14867 `(("r-checkmate" ,r-checkmate)
14869 ("r-purrr" ,r-purrr)
14871 (home-page "https://markusdumke.github.io/reinforcelearn")
14872 (synopsis "Reinforcement learning")
14874 "This package implements reinforcement learning environments and
14875 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14876 can be used with function approximation, eligibility traces (Singh & Sutton,
14877 1996) and experience replay (Mnih et al., 2013).")
14878 (license license:expat)))
14880 (define-public r-lemon
14887 (uri (cran-uri "lemon" version))
14890 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14891 (build-system r-build-system)
14893 `(("r-ggplot2" ,r-ggplot2)
14894 ("r-gridextra" ,r-gridextra)
14895 ("r-gtable" ,r-gtable)
14896 ("r-knitr" ,r-knitr)
14897 ("r-lattice" ,r-lattice)
14899 ("r-rlang" ,r-rlang)
14900 ("r-scales" ,r-scales)))
14902 `(("r-knitr" ,r-knitr)))
14903 (home-page "https://github.com/stefanedwards/lemon")
14904 (synopsis "Freshen up your ggplot2 plots")
14906 "This package provides functions for working with legends and axis lines
14907 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14909 (license license:gpl3)))
14911 (define-public r-wgaim
14918 (uri (cran-uri "wgaim" version))
14920 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14921 (build-system r-build-system)
14923 `(("r-ggplot2" ,r-ggplot2)
14925 (home-page "https://cran.r-project.org/web/packages/wgaim")
14926 (synopsis "Whole genome average interval mapping for QTL detection")
14928 "This package integrates sophisticated mixed modelling methods with a
14929 whole genome approach to detecting significant QTL in linkage maps.")
14930 (license license:gpl2+)))
14932 (define-public r-bedr
14939 (uri (cran-uri "bedr" version))
14942 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14943 (build-system r-build-system)
14945 `(("r-data-table" ,r-data-table)
14946 ("r-r-utils" ,r-r-utils)
14947 ("r-testthat" ,r-testthat)
14948 ("r-venndiagram" ,r-venndiagram)
14951 ("bedtools" ,bedtools)
14952 ("htslib" ,htslib))) ; for tabix
14954 `(("r-knitr" ,r-knitr))) ; for vignettes
14955 (home-page "https://cran.r-project.org/web/packages/bedr")
14956 (synopsis "Genomic region processing")
14958 "This package is for genomic regions processing using command line tools
14959 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14960 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14961 The bedr package's API enhances access to these tools as well as offers
14962 additional utilities for genomic regions processing.")
14963 (license license:gpl2)))
14965 (define-public r-sets
14972 (uri (cran-uri "sets" version))
14975 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14976 (properties `((upstream-name . "sets")))
14977 (build-system r-build-system)
14978 (home-page "https://cran.r-project.org/web/packages/sets")
14979 (synopsis "Sets, generalized sets, customizable sets and intervals")
14981 "This package provides data structures and basic operations for ordinary
14982 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14983 customizable sets, and intervals.")
14984 (license license:gpl2)))
14986 (define-public r-partitions
14988 (name "r-partitions")
14993 (uri (cran-uri "partitions" version))
14996 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14997 (build-system r-build-system)
15000 ("r-polynom" ,r-polynom)
15001 ("r-sets" ,r-sets)))
15002 (home-page "https://cran.r-project.org/web/packages/partitions")
15003 (synopsis "Additive partitions of integers")
15005 "This package provides tools to enumerates the partitions, unequal
15006 partitions, and restricted partitions of an integer; the three corresponding
15007 partition functions are also given.")
15008 ;; Any version of the GPL
15009 (license license:gpl2+)))
15011 (define-public r-brobdingnag
15013 (name "r-brobdingnag")
15018 (uri (cran-uri "Brobdingnag" version))
15021 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15022 (properties `((upstream-name . "Brobdingnag")))
15023 (build-system r-build-system)
15024 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15025 (synopsis "Very large numbers in R")
15027 "This package handles very large numbers in R. Real numbers are held
15028 using their natural logarithms, plus a logical flag indicating sign. The
15029 package includes a vignette that gives a step-by-step introduction to using S4
15031 ;; Any version of the GPL
15032 (license license:gpl2+)))
15034 (define-public r-untb
15041 (uri (cran-uri "untb" version))
15044 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15045 (build-system r-build-system)
15047 `(("r-brobdingnag" ,r-brobdingnag)
15048 ("r-partitions" ,r-partitions)
15049 ("r-polynom" ,r-polynom)))
15050 (home-page "https://github.com/RobinHankin/untb.git")
15051 (synopsis "Ecological drift under the UNTB")
15053 "This package provides numerical simulations, and visualizations, of
15054 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15055 (license license:gpl2+)))
15057 (define-public r-stepwise
15059 (name "r-stepwise")
15064 (uri (cran-uri "stepwise" version))
15067 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15068 (build-system r-build-system)
15069 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15070 (synopsis "Stepwise detection of recombination breakpoints")
15072 "This package provides a stepwise approach to identifying recombination
15073 breakpoints in a genomic sequence alignment.")
15074 (license license:gpl2+)))
15076 (define-public r-snpmaxsel
15078 (name "r-snpmaxsel")
15083 (uri (cran-uri "SNPmaxsel" version))
15086 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15087 (properties `((upstream-name . "SNPmaxsel")))
15088 (build-system r-build-system)
15090 `(("r-combinat" ,r-combinat)
15091 ("r-mvtnorm" ,r-mvtnorm)))
15092 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15093 (synopsis "Maximally selected statistics for SNP data")
15095 "This package implements asymptotic methods related to maximally selected
15096 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15098 (license license:gpl2+)))
15100 (define-public r-acsnminer
15102 (name "r-acsnminer")
15103 (version "0.16.8.25")
15106 (uri (cran-uri "ACSNMineR" version))
15109 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15110 (properties `((upstream-name . "ACSNMineR")))
15111 (build-system r-build-system)
15113 `(("r-ggplot2" ,r-ggplot2)
15114 ("r-gridextra" ,r-gridextra)))
15115 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15116 (synopsis "Gene enrichment analysis")
15118 "This package provides tools to compute and represent gene set enrichment
15119 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15120 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15121 enrichment can be run with hypergeometric test or Fisher exact test, and can
15122 use multiple corrections. Visualization of data can be done either by
15123 barplots or heatmaps.")
15124 (license license:gpl2+)))
15126 (define-public r-seqinr
15133 (uri (cran-uri "seqinr" version))
15136 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15137 (build-system r-build-system)
15139 `(("r-ade4" ,r-ade4)
15140 ("r-segmented" ,r-segmented)))
15143 (home-page "http://seqinr.r-forge.r-project.org/")
15144 (synopsis "Biological sequences retrieval and analysis")
15146 "This package provides tools for exploratory data analysis and data
15147 visualization of biological sequence (DNA and protein) data. It also includes
15148 utilities for sequence data management under the ACNUC system.")
15149 (license license:gpl2+)))
15151 (define-public r-units
15158 (uri (cran-uri "units" version))
15161 "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js"))))
15162 (build-system r-build-system)
15164 `(("udunits" ,udunits)))
15166 `(("r-rcpp" ,r-rcpp)))
15168 `(("r-knitr" ,r-knitr)))
15169 (home-page "https://github.com/r-quantities/units/")
15170 (synopsis "Measurement Units for R Vectors")
15172 "This package provides support for measurement units in R vectors,
15173 matrices and arrays: automatic propagation, conversion, derivation and
15174 simplification of units; raising errors in case of unit incompatibility. It
15175 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15177 (license license:gpl2)))
15179 (define-public r-udunits2
15181 (name "r-udunits2")
15186 (uri (cran-uri "udunits2" version))
15189 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15190 (properties `((upstream-name . "udunits2")))
15191 (build-system r-build-system)
15193 `(("udunits" ,udunits)))
15194 (home-page "https://cran.r-project.org/package=udunits2")
15195 (synopsis "Udunits-2 bindings for R")
15197 "This package provides simple bindings to Unidata's udunits library.")
15198 (license license:gpl2)))
15200 (define-public r-classint
15202 (name "r-classint")
15207 (uri (cran-uri "classInt" version))
15210 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15211 (properties `((upstream-name . "classInt")))
15212 (build-system r-build-system)
15214 `(("r-class" ,r-class)
15215 ("r-e1071" ,r-e1071)
15216 ("r-kernsmooth" ,r-kernsmooth)))
15218 `(("gfortran" ,gfortran)
15219 ("r-knitr" ,r-knitr)))
15220 (home-page "https://github.com/r-spatial/classInt/")
15221 (synopsis "Choose univariate class intervals")
15223 "This package provides selected commonly used methods for choosing
15224 univariate class intervals for mapping or other graphics purposes.")
15225 (license license:gpl2+)))
15227 (define-public r-spdata
15234 (uri (cran-uri "spData" version))
15237 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15238 (properties `((upstream-name . "spData")))
15239 (build-system r-build-system)
15241 `(("r-raster" ,r-raster)
15243 (home-page "https://github.com/Nowosad/spData")
15244 (synopsis "Datasets for spatial analysis")
15246 "This a package containing diverse spatial datasets for demonstrating,
15247 benchmarking and teaching spatial data analysis. It includes R data of class
15248 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15249 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15250 of the datasets are designed to illustrate specific analysis techniques.
15251 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15252 illustrate point pattern analysis techniques.")
15253 (license license:cc0)))
15255 (define-public r-learnbayes
15257 (name "r-learnbayes")
15262 (uri (cran-uri "LearnBayes" version))
15265 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15266 (properties `((upstream-name . "LearnBayes")))
15267 (build-system r-build-system)
15268 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15269 (synopsis "Functions for learning Bayesian inference")
15271 "This package provides a collection of functions helpful in learning the
15272 basic tenets of Bayesian statistical inference. It contains functions for
15273 summarizing basic one and two parameter posterior distributions and predictive
15274 distributions. It contains MCMC algorithms for summarizing posterior
15275 distributions defined by the user. It also contains functions for regression
15276 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15278 (license license:gpl2+)))
15280 (define-public r-deldir
15287 (uri (cran-uri "deldir" version))
15290 "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
15291 (build-system r-build-system)
15292 (native-inputs `(("gfortran" ,gfortran)))
15293 (home-page "https://cran.r-project.org/web/packages/deldir")
15294 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15296 "This package provides tools for calculating the Delaunay triangulation
15297 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15298 of a planar point set. It plots triangulations and tessellations in various
15299 ways, clips tessellations to sub-windows, calculates perimeters of
15300 tessellations, and summarizes information about the tiles of the
15302 (license license:gpl2+)))
15304 (define-public r-sf
15311 (uri (cran-uri "sf" version))
15314 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15315 (build-system r-build-system)
15323 `(("r-classint" ,r-classint)
15325 ("r-magrittr" ,r-magrittr)
15327 ("r-units" ,r-units)))
15329 `(("pkg-config" ,pkg-config)
15330 ("r-knitr" ,r-knitr)))
15331 (home-page "https://github.com/r-spatial/sf/")
15332 (synopsis "Simple features for R")
15334 "This package provides support for simple features, a standardized way to
15335 encode spatial vector data. It binds to GDAL for reading and writing data, to
15336 GEOS for geometrical operations, and to PROJ for projection conversions and
15337 datum transformations.")
15338 ;; Either of these licenses
15339 (license (list license:gpl2 license:expat))))
15341 (define-public r-spdep
15348 (uri (cran-uri "spdep" version))
15351 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15352 (build-system r-build-system)
15354 `(("r-boot" ,r-boot)
15356 ("r-deldir" ,r-deldir)
15358 ("r-gmodels" ,r-gmodels)
15359 ("r-learnbayes" ,r-learnbayes)
15361 ("r-matrix" ,r-matrix)
15365 ("r-spdata" ,r-spdata)))
15367 `(("r-knitr" ,r-knitr)))
15368 (home-page "https://github.com/r-spatial/spdep/")
15369 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15371 "This package provides a collection of functions to create spatial
15372 weights matrix objects from polygon contiguities, from point patterns by
15373 distance and tessellations, for summarizing these objects, and for permitting
15374 their use in spatial data analysis, including regional aggregation by minimum
15376 (license license:gpl2+)))
15378 (define-public r-adegenet
15380 (name "r-adegenet")
15385 (uri (cran-uri "adegenet" version))
15388 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15389 (build-system r-build-system)
15391 `(("r-ade4" ,r-ade4)
15394 ("r-dplyr" ,r-dplyr)
15395 ("r-ggplot2" ,r-ggplot2)
15396 ("r-igraph" ,r-igraph)
15398 ("r-reshape2" ,r-reshape2)
15399 ("r-seqinr" ,r-seqinr)
15400 ("r-shiny" ,r-shiny)
15401 ("r-spdep" ,r-spdep)
15402 ("r-vegan" ,r-vegan)))
15403 (home-page "https://github.com/thibautjombart/adegenet")
15404 (synopsis "Exploratory analysis of genetic and genomic data")
15406 "This package provides a toolset for the exploration of genetic and
15407 genomic data. Adegenet provides formal (S4) classes for storing and handling
15408 various genetic data, including genetic markers with varying ploidy and
15409 hierarchical population structure (@code{genind} class), alleles counts by
15410 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15411 also implements original multivariate methods (DAPC, sPCA), graphics,
15412 statistical tests, simulation tools, distance and similarity measures, and
15413 several spatial methods. A range of both empirical and simulated datasets is
15414 also provided to illustrate various methods.")
15415 (license license:gpl2+)))
15417 (define-public r-pegas
15424 (uri (cran-uri "pegas" version))
15426 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15427 (build-system r-build-system)
15429 `(("r-adegenet" ,r-adegenet)
15431 (home-page "http://ape-package.ird.fr/pegas.html")
15432 (synopsis "Population and evolutionary genetics analysis system")
15434 "This package provides functions for reading, writing, plotting,
15435 analysing, and manipulating allelic and haplotypic data, including from VCF
15436 files, and for the analysis of population nucleotide sequences and
15437 micro-satellites including coalescent analyses, linkage disequilibrium,
15438 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15439 minimum spanning tree and network, and median-joining networks.")
15440 (license license:gpl2+)))
15442 (define-public r-rmetasim
15444 (name "r-rmetasim")
15449 (uri (cran-uri "rmetasim" version))
15452 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15453 (build-system r-build-system)
15455 `(("r-ade4" ,r-ade4)
15456 ("r-adegenet" ,r-adegenet)
15457 ("r-gtools" ,r-gtools)
15458 ("r-pegas" ,r-pegas)))
15459 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15460 (synopsis "Individual-based population genetic simulation environment")
15462 "This package provides an interface between R and the metasim simulation
15463 engine. The simulation environment is documented in: Strand, A.(2002),
15464 Metasim 1.0: an individual-based environment for simulating population
15465 genetics of complex population dynamics.")
15467 (license license:gpl2+)))
15469 (define-public r-genetics
15471 (name "r-genetics")
15472 (version "1.3.8.1.3")
15476 (uri (cran-uri "genetics" version))
15479 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
15480 (build-system r-build-system)
15482 `(("r-combinat" ,r-combinat)
15483 ("r-gdata" ,r-gdata)
15484 ("r-gtools" ,r-gtools)
15486 ("r-mvtnorm" ,r-mvtnorm)))
15487 (home-page "https://cran.r-project.org/web/packages/genetics/")
15488 (synopsis "Population genetics")
15490 "This package provides classes and methods for handling genetic data.
15491 It includes classes to represent genotypes and haplotypes at single markers up
15492 to multiple markers on multiple chromosomes. Function include allele
15493 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15494 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15495 and testing for linkage disequilibrium, ...")
15496 ;; Any GPL version.
15497 (license license:gpl2+)))
15499 (define-public r-snp-plotter
15501 (name "r-snp-plotter")
15506 (uri (cran-uri "snp.plotter" version))
15509 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15510 (properties `((upstream-name . "snp.plotter")))
15511 (build-system r-build-system)
15512 (propagated-inputs `(("r-genetics" ,r-genetics)))
15513 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15514 (synopsis "Plot p-values using single SNP and/or haplotype data")
15516 "This package helps you create plots of p-values using single SNP and/or
15517 haplotype data. Main features of the package include options to display a
15518 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15519 datasets simultaneously. Plots can be created using global and/or individual
15520 haplotype p-values along with single SNP p-values. Images are created as
15521 either PDF/EPS files.")
15522 (license license:gpl2+)))
15524 (define-public r-polspline
15526 (name "r-polspline")
15531 (uri (cran-uri "polspline" version))
15533 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15534 (build-system r-build-system)
15535 (native-inputs `(("gfortran" ,gfortran)))
15536 (home-page "https://cran.r-project.org/web/packages/polspline/")
15537 (synopsis "Polynomial spline routines")
15539 "This package provides routines for the polynomial spline fitting
15540 routines hazard regression, hazard estimation with flexible tails, logspline,
15541 lspec, polyclass, and polymars.")
15542 (license license:gpl2+)))
15544 (define-public r-rms
15551 (uri (cran-uri "rms" version))
15553 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15554 (build-system r-build-system)
15556 `(("r-cluster" ,r-cluster)
15557 ("r-digest" ,r-digest)
15558 ("r-ggplot2" ,r-ggplot2)
15559 ("r-hmisc" ,r-hmisc)
15560 ("r-htmltable" ,r-htmltable)
15561 ("r-htmltools" ,r-htmltools)
15562 ("r-lattice" ,r-lattice)
15564 ("r-multcomp" ,r-multcomp)
15566 ("r-polspline" ,r-polspline)
15567 ("r-quantreg" ,r-quantreg)
15568 ("r-rpart" ,r-rpart)
15569 ("r-sparsem" ,r-sparsem)
15570 ("r-survival" ,r-survival)))
15571 (native-inputs `(("gfortran" ,gfortran)))
15572 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15573 (synopsis "Regression modeling strategies")
15575 "This is a package for regression modeling, testing, estimation,
15576 validation, graphics, prediction, and typesetting by storing enhanced model
15577 design attributes in the fit. The rms package is a collection of functions
15578 that assist with and streamline modeling. It also contains functions for
15579 binary and ordinal logistic regression models, ordinal models for continuous Y
15580 with a variety of distribution families, and the Buckley-James multiple
15581 regression model for right-censored responses, and implements penalized
15582 maximum likelihood estimation for logistic and ordinary linear models. The
15583 package works with almost any regression model, but it was especially written
15584 to work with binary or ordinal regression models, Cox regression, accelerated
15585 failure time models, ordinary linear models, the Buckley-James model,
15586 generalized least squares for serially or spatially correlated observations,
15587 generalized linear models, and quantile regression.")
15588 (license license:gpl2+)))
15590 (define-public r-arsenal
15597 (uri (cran-uri "arsenal" version))
15600 "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn"))))
15601 (properties `((upstream-name . "arsenal")))
15602 (build-system r-build-system)
15603 (propagated-inputs `(("r-knitr" ,r-knitr)))
15604 (native-inputs `(("r-knitr" ,r-knitr)))
15605 (home-page "https://github.com/mayoverse/arsenal")
15606 (synopsis "Functions for large-scale statistical summaries")
15608 "This package provides an arsenal of R functions for large-scale
15609 statistical summaries, which are streamlined to work within the latest
15610 reporting tools in R and RStudio and which use formulas and versatile
15611 summary statistics for summary tables and models. The primary functions
15615 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15616 levels of one or more categorical variables;
15617 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15618 across two time points;
15619 @item @code{modelsum}, which performs simple model fits on one or more
15620 endpoints for many variables (univariate or adjusted for covariates);
15621 @item @code{freqlist}, a powerful frequency table across many categorical
15623 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15624 @item @code{write2}, a function to output tables to a document.
15627 (license license:gpl2+)))
15629 (define-public r-haplo-stats
15631 (name "r-haplo-stats")
15636 (uri (cran-uri "haplo.stats" version))
15639 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15640 (properties `((upstream-name . "haplo.stats")))
15641 (build-system r-build-system)
15643 `(("r-arsenal" ,r-arsenal)
15646 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15647 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15648 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15650 "This package provides routines for the analysis of indirectly measured
15651 haplotypes. The statistical methods assume that all subjects are unrelated
15652 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15653 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15654 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15655 examples in the vignette.")
15656 (license license:gpl2+)))
15658 (define-public r-bqtl
15665 (uri (cran-uri "bqtl" version))
15668 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15669 (build-system r-build-system)
15670 (native-inputs `(("gfortran" ,gfortran)))
15671 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15672 (synopsis "Bayesian QTL mapping toolkit")
15674 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15675 lines. It includes maximum likelihood and Bayesian tools.")
15676 (license license:gpl2+)))
15678 (define-public r-ibdreg
15685 (uri (cran-uri "ibdreg" version))
15688 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15689 (build-system r-build-system)
15690 (home-page "https://www.mayo.edu/research/labs/\
15691 statistical-genetics-genetic-epidemiology/software")
15692 (synopsis "Regression methods for IBD linkage with covariates")
15694 "This package provides a method to test genetic linkage with covariates
15695 by regression methods with response IBD sharing for relative pairs. Account
15696 for correlations of IBD statistics and covariates for relative pairs within
15697 the same pedigree.")
15698 (license license:gpl2+)))
15700 (define-public r-dlmap
15707 (uri (cran-uri "dlmap" version))
15710 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15711 (build-system r-build-system)
15713 `(("r-ibdreg" ,r-ibdreg)
15717 ("r-wgaim" ,r-wgaim)))
15718 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15719 (synopsis "Detection localization mapping for QTL")
15721 "This is package for QTL mapping in a mixed model framework with separate
15722 detection and localization stages. The first stage detects the number of QTL
15723 on each chromosome based on the genetic variation due to grouped markers on
15724 the chromosome; the second stage uses this information to determine the most
15725 likely QTL positions. The mixed model can accommodate general fixed and
15726 random effects, including spatial effects in field trials and pedigree
15727 effects. It is applicable to backcrosses, doubled haploids, recombinant
15728 inbred lines, F2 intercrosses, and association mapping populations.")
15729 (license license:gpl2)))
15731 (define-public r-hwde
15738 (uri (cran-uri "hwde" version))
15741 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15742 (build-system r-build-system)
15743 (home-page "https://cran.r-project.org/web/packages/hwde/")
15744 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15746 "This package fits models for genotypic disequilibria, as described in
15747 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15748 terms are available that account for first order interactions between loci.
15749 It also implements, for a single locus in a single population, a conditional
15750 exact test for Hardy-Weinberg equilibrium.")
15751 (license license:gpl2+)))
15753 (define-public r-tdthap
15760 (uri (cran-uri "tdthap" version))
15763 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15764 (build-system r-build-system)
15765 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15766 (synopsis "TDT tests for extended haplotypes")
15768 "Functions and examples are provided for transmission/disequilibrium
15769 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15770 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15771 (license license:artistic2.0)))
15773 (define-public r-sparql
15779 (uri (cran-uri "SPARQL" version))
15782 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15783 (properties `((upstream-name . "SPARQL")))
15784 (build-system r-build-system)
15786 `(("r-rcurl" ,r-rcurl)
15788 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15789 (synopsis "SPARQL client for R")
15790 (description "This package provides an interface to use SPARQL to pose
15791 SELECT or UPDATE queries to an end-point.")
15792 ;; The only license indication is found in the DESCRIPTION file,
15793 ;; which states GPL-3. So we cannot assume GPLv3+.
15794 (license license:gpl3)))
15796 (define-public r-bookdown
15798 (name "r-bookdown")
15802 (uri (cran-uri "bookdown" version))
15805 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15806 (build-system r-build-system)
15808 `(("r-htmltools" ,r-htmltools)
15809 ("r-knitr" ,r-knitr)
15810 ("r-rmarkdown" ,r-rmarkdown)
15811 ("r-tinytex" ,r-tinytex)
15814 ("pandoc" ,pandoc)))
15815 (home-page "https://github.com/rstudio/bookdown")
15816 (synopsis "Authoring books and technical documents with R markdown")
15817 (description "This package provides output formats and utilities for
15818 authoring books and technical documents with R Markdown.")
15819 (license license:gpl3)))
15821 (define-public r-optparse
15823 (name "r-optparse")
15828 (uri (cran-uri "optparse" version))
15831 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15832 (build-system r-build-system)
15834 `(("r-getopt" ,r-getopt)))
15836 `(("r-knitr" ,r-knitr)))
15837 (home-page "https://github.com/trevorld/optparse")
15838 (synopsis "Command line option parser")
15840 "This package provides a command line parser inspired by Python's
15841 @code{optparse} library to be used with Rscript to write shebang scripts
15842 that accept short and long options.")
15843 (license license:gpl2+)))
15845 (define-public r-kernlab
15852 (uri (cran-uri "kernlab" version))
15854 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15855 (build-system r-build-system)
15856 (home-page "https://cran.r-project.org/web/packages/kernlab")
15857 (synopsis "Kernel-based machine learning tools")
15859 "This package provides kernel-based machine learning methods for
15860 classification, regression, clustering, novelty detection, quantile regression
15861 and dimensionality reduction. Among other methods @code{kernlab} includes
15862 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15864 (license license:gpl2)))
15866 (define-public r-hierfstat
15868 (name "r-hierfstat")
15873 (uri (cran-uri "hierfstat" version))
15876 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15877 (build-system r-build-system)
15879 `(("r-ade4" ,r-ade4)
15880 ("r-adegenet" ,r-adegenet)
15881 ("r-gaston" ,r-gaston)
15882 ("r-gtools" ,r-gtools)))
15884 `(("r-knitr" ,r-knitr)))
15885 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15886 (synopsis "Estimation and tests of hierarchical F-statistics")
15888 "This package allows the estimation of hierarchical F-statistics from
15889 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15890 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15891 are also given to test via randomisations the significance of each F and
15892 variance components, using the likelihood-ratio statistics G.")
15893 (license license:gpl2+)))
15895 (define-public r-hapassoc
15897 (name "r-hapassoc")
15902 (uri (cran-uri "hapassoc" version))
15905 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15906 (build-system r-build-system)
15907 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15908 (synopsis "Inference of trait associations with SNP haplotypes")
15910 "Hapassoc performs likelihood inference of trait associations with
15911 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15912 functions are developed primarily for data collected in cohort or
15913 cross-sectional studies. They can accommodate uncertain haplotype phase and
15914 handle missing genotypes at some SNPs.")
15915 (license license:gpl2)))
15917 (define-public r-sampling
15919 (name "r-sampling")
15924 (uri (cran-uri "sampling" version))
15927 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15928 (build-system r-build-system)
15930 `(("r-lpsolve" ,r-lpsolve)
15931 ("r-mass" ,r-mass)))
15932 (home-page "https://cran.r-project.org/web/packages/sampling/")
15933 (synopsis "Survey sampling")
15935 "This package provides functions for drawing and calibrating samples.")
15936 (license license:gpl2+)))
15938 (define-public r-r2html
15945 (uri (cran-uri "R2HTML" version))
15948 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15949 (properties `((upstream-name . "R2HTML")))
15950 (build-system r-build-system)
15951 (home-page "https://github.com/nalimilan/R2HTML")
15952 (synopsis "HTML export for R objects")
15954 "This package includes HTML functions and methods to write in an HTML
15955 file. Thus, making HTML reports is easy. It includes a function that allows
15956 redirection on the fly, which appears to be very useful for teaching purposes,
15957 as the student can keep a copy of the produced output to keep all that they
15958 did during the course. The package comes with a vignette describing how to
15959 write HTML reports for statistical analysis. Finally, a driver for Sweave
15960 parses HTML flat files containing R code and to automatically write
15961 the corresponding outputs (tables and graphs).")
15962 (license license:gpl2+)))
15964 (define-public r-rjava
15971 (uri (cran-uri "rJava" version))
15974 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15975 (properties `((upstream-name . "rJava")))
15976 (build-system r-build-system)
15978 `(#:modules ((guix build utils)
15979 (guix build r-build-system)
15982 (modify-phases %standard-phases
15983 (add-after 'unpack 'set-JAVA_HOME
15984 (lambda* (#:key inputs #:allow-other-keys)
15985 (let ((jdk (assoc-ref inputs "jdk")))
15986 (setenv "JAVA_HOME" jdk)
15987 (setenv "JAVA" (which "java"))
15988 (setenv "JAR" (which "jar"))
15989 (setenv "JAVAC" (which "javac"))
15990 (setenv "JAVAH" (which "javah"))
15991 (setenv "JAVA_CPPFLAGS"
15992 (string-append "-I" jdk "/include "
15993 "-I" jdk "/include/linux"))
15994 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15995 ((lib) (setenv "JAVA_LIBS" lib))
15996 (_ (error "Could not find libjvm.so"))))
16000 ("jdk" ,icedtea-8 "jdk")
16003 (home-page "https://www.rforge.net/rJava/")
16004 (synopsis "Low-Level R to Java interface")
16006 "This package provides a low-level interface to the Java VM very much
16007 like .C/.Call and friends. It allows the creation of objects, calling methods
16008 and accessing fields.")
16009 (license license:gpl2)))
16011 (define-public r-svmisc
16018 (uri (cran-uri "svMisc" version))
16021 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
16022 (properties `((upstream-name . "svMisc")))
16023 (build-system r-build-system)
16024 (home-page "https://github.com/SciViews/svMisc")
16025 (synopsis "Miscellaneous functions for SciViews")
16027 "This package provides miscellaneous functions for SciViews or general
16028 use, including tools to manage a temporary environment attached to the search
16029 path for temporary variables you do not want to @code{save()} or
16030 @code{load()}; test the current platform; showing progress bars, etc.")
16031 (license license:gpl2)))
16033 (define-public r-xyz
16040 (uri (cran-uri "xyz" version))
16043 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16044 (build-system r-build-system)
16046 `(("r-rcpp" ,r-rcpp)))
16047 (home-page "https://cran.r-project.org/web/packages/xyz/")
16048 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16050 "High dimensional interaction search by brute force requires a quadratic
16051 computational cost in the number of variables. The xyz algorithm provably
16052 finds strong interactions in almost linear time. For details of the algorithm
16053 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16054 interaction search in high-dimensional data.")
16055 ;; Any version of the GPL.
16056 (license license:gpl2+)))
16058 (define-public r-rttf2pt1
16060 (name "r-rttf2pt1")
16065 (uri (cran-uri "Rttf2pt1" version))
16068 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16069 (properties `((upstream-name . "Rttf2pt1")))
16070 (build-system r-build-system)
16071 (home-page "https://github.com/wch/Rttf2pt1")
16072 (synopsis "Font conversion utility")
16074 "This package contains the program @code{ttf2pt1}, for use with the
16075 @code{extrafont} package.")
16076 ;; Most of the files are covered under the Expat license. Some files are
16077 ;; covered under BSD-3. Deviations for individual files are recorded in
16078 ;; the LICENSE file.
16079 (license (list license:bsd-3 license:expat
16080 (license:non-copyleft "file://LICENSE")))))
16082 (define-public r-extrafontdb
16084 (name "r-extrafontdb")
16089 (uri (cran-uri "extrafontdb" version))
16092 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16093 (build-system r-build-system)
16094 (home-page "https://github.com/wch/extrafontdb")
16095 (synopsis "Database for the extrafont package")
16097 "This package holds the database for the @code{extrafont} package.")
16098 (license license:gpl2)))
16100 (define-public r-extrafont
16102 (name "r-extrafont")
16107 (uri (cran-uri "extrafont" version))
16110 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16111 (build-system r-build-system)
16113 `(("r-extrafontdb" ,r-extrafontdb)
16114 ("r-rttf2pt1" ,r-rttf2pt1)))
16115 (home-page "https://github.com/wch/extrafont")
16116 (synopsis "Tools for using fonts in R")
16118 "The extrafont package makes it easier to use fonts other than the basic
16119 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16120 used with PDF or PostScript output files. There are two hurdles for using
16121 fonts in PDF (or Postscript) output files:
16124 @item Making R aware of the font and the dimensions of the characters.
16125 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16126 properly on a device that doesn't have the font. This is usually needed if
16127 you want to print the PDF file or share it with others.
16130 The extrafont package makes both of these things easier.")
16131 (license license:gpl2)))
16133 (define-public r-xkcd
16140 (uri (cran-uri "xkcd" version))
16143 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16144 (build-system r-build-system)
16146 `(("r-extrafont" ,r-extrafont)
16147 ("r-ggplot2" ,r-ggplot2)
16148 ("r-hmisc" ,r-hmisc)))
16149 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16150 (synopsis "Plot ggplot2 graphics in the XKCD style")
16152 "This package provides the means to plot ggplot2 graphs in the style of
16153 the XKCD web comic.")
16154 (license license:gpl3)))
16156 (define-public r-msigdbr
16163 (uri (cran-uri "msigdbr" version))
16166 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16167 (build-system r-build-system)
16169 `(("r-dplyr" ,r-dplyr)
16170 ("r-magrittr" ,r-magrittr)
16171 ("r-rlang" ,r-rlang)
16172 ("r-tibble" ,r-tibble)
16173 ("r-tidyselect" ,r-tidyselect)))
16175 `(("r-knitr" ,r-knitr)))
16176 (home-page "https://github.com/igordot/msigdbr")
16177 (synopsis "MSigDB gene sets for multiple organisms")
16179 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16180 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16181 software in a standard R data frame with key-value pairs. Included are the
16182 original human gene symbols and Entrez IDs as well as the equivalents for
16183 various frequently studied model organisms such as mouse, rat, pig, fly, and
16185 ;; The package is covered under the Expat license, but the upstream MSigDB
16186 ;; files are made available under the Creative Commons Attribution 4.0
16187 ;; International license.
16188 (license (list license:expat license:cc-by4.0))))
16190 (define-public r-gridgraphics
16192 (name "r-gridgraphics")
16197 (uri (cran-uri "gridGraphics" version))
16200 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16201 (properties `((upstream-name . "gridGraphics")))
16202 (build-system r-build-system)
16203 (home-page "https://github.com/pmur002/gridgraphics")
16204 (synopsis "Redraw base graphics using @code{grid} graphics")
16206 "This package provides functions to convert a page of plots drawn with
16207 the @code{graphics} package into identical output drawn with the @code{grid}
16208 package. The result looks like the original @code{graphics}-based plot, but
16209 consists of @code{grid} grobs and viewports that can then be manipulated with
16210 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16211 (license license:gpl2+)))
16213 (define-public r-farver
16220 (uri (cran-uri "farver" version))
16223 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
16224 (build-system r-build-system)
16225 (home-page "https://github.com/thomasp85/farver")
16226 (synopsis "Vectorized color conversion and comparison")
16228 "The encoding of color can be handled in many different ways, using
16229 different color spaces. As different color spaces have different uses,
16230 efficient conversion between these representations are important. This
16231 package provides a set of functions that gives access to very fast color space
16232 conversion and comparisons implemented in C++, and offers 100-fold speed
16233 improvements over the @code{convertColor} function in the @code{grDevices}
16235 (license license:expat)))
16237 (define-public r-ggplotify
16239 (name "r-ggplotify")
16244 (uri (cran-uri "ggplotify" version))
16247 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16248 (build-system r-build-system)
16250 `(("r-ggplot2" ,r-ggplot2)
16251 ("r-gridgraphics" ,r-gridgraphics)
16252 ("r-rvcheck" ,r-rvcheck)))
16254 `(("r-knitr" ,r-knitr)))
16255 (home-page "https://github.com/GuangchuangYu/ggplotify")
16256 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16258 "This package provides tools to convert plot function calls (using
16259 expression or formula) to @code{grob} or @code{ggplot} objects that are
16260 compatible with the @code{grid} and @code{ggplot2} environment. With this
16261 package, we are able to e.g. use @code{cowplot} to align plots produced by
16262 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16263 converting them to @code{ggplot} objects.")
16264 (license license:artistic2.0)))
16266 (define-public r-triebeard
16268 (name "r-triebeard")
16273 (uri (cran-uri "triebeard" version))
16276 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16277 (build-system r-build-system)
16278 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16279 (home-page "https://github.com/Ironholds/triebeard/")
16280 (synopsis "Radix trees in Rcpp")
16282 "Radix trees, or tries, are key-value data structures optimized for
16283 efficient lookups, similar in purpose to hash tables. This package provides
16284 an implementation of radix trees for use in R programming and in developing
16285 packages with Rcpp.")
16286 (license license:expat)))
16288 (define-public r-tweenr
16295 (uri (cran-uri "tweenr" version))
16298 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16299 (build-system r-build-system)
16301 `(("r-farver" ,r-farver)
16302 ("r-magrittr" ,r-magrittr)
16304 ("r-rlang" ,r-rlang)))
16305 (home-page "https://github.com/thomasp85/tweenr")
16306 (synopsis "Interpolate data for smooth animations")
16308 "In order to create smooth animation between states of data, tweening is
16309 necessary. This package provides a range of functions for creating tweened
16310 data that can be used as basis for animation. Furthermore it adds a number of
16311 vectorized interpolaters for common R data types such as numeric, date and
16313 (license license:expat)))
16315 (define-public r-polyclip
16317 (name "r-polyclip")
16322 (uri (cran-uri "polyclip" version))
16325 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16326 (build-system r-build-system)
16327 (native-inputs `(("pkg-config" ,pkg-config)))
16328 (home-page "http://www.angusj.com/delphi/clipper.php")
16329 (synopsis "Polygon clipping")
16331 "This package provides an R port of the library Clipper. It performs
16332 polygon clipping operations (intersection, union, set minus, set difference)
16333 for polygonal regions of arbitrary complexity, including holes. It computes
16334 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16335 dilations) for polygonal regions and polygonal lines. It computes the
16336 Minkowski Sum of general polygons. There is a function for removing
16337 self-intersections from polygon data.")
16338 (license license:boost1.0)))
16340 (define-public r-urltools
16342 (name "r-urltools")
16347 (uri (cran-uri "urltools" version))
16350 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16351 (build-system r-build-system)
16353 `(("r-rcpp" ,r-rcpp)
16354 ("r-triebeard" ,r-triebeard)))
16355 (home-page "https://github.com/Ironholds/urltools/")
16356 (synopsis "Vectorized tools for URL handling and parsing")
16358 "This package provides a toolkit for all URL-handling needs, including
16359 encoding and decoding, parsing, parameter extraction and modification. All
16360 functions are designed to be both fast and entirely vectorized. It is
16361 intended to be useful for people dealing with web-related datasets, such as
16362 server-side logs, although may be useful for other situations involving large
16364 (license license:expat)))
16366 (define-public r-ggforce
16373 (uri (cran-uri "ggforce" version))
16376 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
16377 (build-system r-build-system)
16379 `(("r-ggplot2" ,r-ggplot2)
16380 ("r-gtable" ,r-gtable)
16382 ("r-polyclip" ,r-polyclip)
16384 ("r-rcppeigen" ,r-rcppeigen)
16385 ("r-rlang" ,r-rlang)
16386 ("r-scales" ,r-scales)
16387 ("r-tidyselect" ,r-tidyselect)
16388 ("r-tweenr" ,r-tweenr)
16389 ("r-withr" ,r-withr)))
16390 (home-page "https://ggforce.data-imaginist.com")
16391 (synopsis "Accelerating ggplot2")
16393 "The aim of the ggplot2 package is to aid in visual data investigations.
16394 This focus has led to a lack of facilities for composing specialized plots.
16395 Thi package aims to be a collection of mainly new statistics and geometries
16396 that fills this gap.")
16397 (license license:expat)))
16399 (define-public r-europepmc
16401 (name "r-europepmc")
16406 (uri (cran-uri "europepmc" version))
16409 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16410 (build-system r-build-system)
16412 `(("r-dplyr" ,r-dplyr)
16414 ("r-jsonlite" ,r-jsonlite)
16416 ("r-progress" ,r-progress)
16417 ("r-purrr" ,r-purrr)
16418 ("r-rlang" ,r-rlang)
16419 ("r-tibble" ,r-tibble)
16420 ("r-tidyr" ,r-tidyr)
16421 ("r-urltools" ,r-urltools)
16422 ("r-xml2" ,r-xml2)))
16424 `(("r-knitr" ,r-knitr)))
16425 (home-page "https://github.com/ropensci/europepmc/")
16426 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16428 "This package provides an R Client for the
16429 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16430 Service}. It gives access to both metadata on life science literature and
16431 open access full texts. Europe PMC indexes all PubMed content and other
16432 literature sources including Agricola, a bibliographic database of citations
16433 to the agricultural literature, or Biological Patents. In addition to
16434 bibliographic metadata, the client allows users to fetch citations and
16435 reference lists. Links between life-science literature and other EBI
16436 databases, including ENA, PDB or ChEMBL are also accessible.")
16437 (license license:gpl3)))
16439 (define-public r-ggraph
16446 (uri (cran-uri "ggraph" version))
16449 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
16450 (build-system r-build-system)
16452 `(("r-digest" ,r-digest)
16453 ("r-dplyr" ,r-dplyr)
16454 ("r-ggforce" ,r-ggforce)
16455 ("r-ggplot2" ,r-ggplot2)
16456 ("r-ggrepel" ,r-ggrepel)
16457 ("r-graphlayouts" ,r-graphlayouts)
16458 ("r-gtable" ,r-gtable)
16459 ("r-igraph" ,r-igraph)
16462 ("r-rlang" ,r-rlang)
16463 ("r-scales" ,r-scales)
16464 ("r-tidygraph" ,r-tidygraph)
16465 ("r-viridis" ,r-viridis)
16466 ("r-withr" ,r-withr)))
16468 `(("r-knitr" ,r-knitr)))
16469 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16470 (synopsis "Implementation of grammar of graphics for graphs and networks")
16472 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16473 graph and network visualizations due to its reliance on tabular data input.
16474 The ggraph package is an extension of the ggplot2 API tailored to graph
16475 visualizations and provides the same flexible approach to building up plots
16477 (license license:gpl3)))
16479 (define-public r-gkmsvm
16486 (uri (cran-uri "gkmSVM" version))
16489 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
16490 (properties `((upstream-name . "gkmSVM")))
16491 (build-system r-build-system)
16493 `(("r-kernlab" ,r-kernlab)
16496 ("r-seqinr" ,r-seqinr)))
16497 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
16498 (synopsis "Gapped-kmer support vector machine")
16500 "This R package provides tools for training gapped-kmer SVM classifiers
16501 for DNA and protein sequences. This package supports several sequence
16502 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
16503 (license license:gpl2+)))
16505 (define-public r-varselrf
16507 (name "r-varselrf")
16512 (uri (cran-uri "varSelRF" version))
16515 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16516 (properties `((upstream-name . "varSelRF")))
16517 (build-system r-build-system)
16519 `(("r-randomforest" ,r-randomforest)))
16520 (home-page "https://www.ligarto.org/rdiaz/software/software")
16521 (synopsis "Variable selection using random forests")
16523 "This package provides tools for the variable selection from random
16524 forests using both backwards variable elimination (for the selection of small
16525 sets of non-redundant variables) and selection based on the importance
16526 spectrum (somewhat similar to scree plots; for the selection of large,
16527 potentially highly-correlated variables). The main applications are in
16528 high-dimensional data (e.g., microarray data, and other genomics and
16529 proteomics applications).")
16530 (license license:gpl2+)))
16532 (define-public r-pamr
16539 (uri (cran-uri "pamr" version))
16542 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16543 (build-system r-build-system)
16545 `(("r-cluster" ,r-cluster)
16546 ("r-survival" ,r-survival)))
16547 (native-inputs `(("gfortran" ,gfortran)))
16548 (home-page "https://cran.r-project.org/web/packages/pamr/")
16549 (synopsis "Prediction Analysis for Microarrays")
16551 "This package provides some functions for sample classification in
16553 (license license:gpl2)))
16555 (define-public r-rda
16558 (version "1.0.2-2.1")
16562 (uri (cran-uri "rda" version))
16565 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16566 (build-system r-build-system)
16567 (home-page "https://cran.r-project.org/web/packages/rda/")
16568 (synopsis "Shrunken centroids regularized discriminant analysis")
16570 "This package provides tools for shrunken centroids regularized
16571 discriminant analysis for the purpose of classifying high dimensional data.")
16572 (license license:gpl2+)))
16574 (define-public r-ggvis
16581 (uri (cran-uri "ggvis" version))
16584 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16585 (build-system r-build-system)
16587 `(("r-assertthat" ,r-assertthat)
16588 ("r-dplyr" ,r-dplyr)
16589 ("r-htmltools" ,r-htmltools)
16590 ("r-jsonlite" ,r-jsonlite)
16591 ("r-magrittr" ,r-magrittr)
16592 ("r-rlang" ,r-rlang)
16593 ("r-shiny" ,r-shiny)))
16594 (home-page "https://ggvis.rstudio.com/")
16595 (synopsis "Interactive grammar of graphics")
16597 "This package is a data visualization package for R providing an
16598 implementation of an interactive grammar of graphics, taking the best parts of
16599 ggplot2, combining them with the reactive framework of Shiny and drawing web
16600 graphics using Vega.")
16601 (license license:gpl2)))
16603 (define-public r-gbm
16610 (uri (cran-uri "gbm" version))
16613 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16614 (build-system r-build-system)
16616 `(("r-lattice" ,r-lattice)
16617 ("r-survival" ,r-survival)))
16619 `(("r-knitr" ,r-knitr)))
16620 (home-page "https://github.com/gbm-developers/gbm")
16621 (synopsis "Generalized boosted regression models")
16623 "This package is an implementation of extensions to Freund and Schapire's
16624 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16625 regression methods for least squares, absolute loss, t-distribution loss,
16626 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16627 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16628 and Learning to Rank measures (LambdaMart).")
16629 (license license:gpl2+)))
16631 (define-public r-threejs
16638 (uri (cran-uri "threejs" version))
16641 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16642 (build-system r-build-system)
16644 `(#:modules ((guix build utils)
16645 (guix build r-build-system)
16649 (modify-phases %standard-phases
16650 (add-after 'unpack 'process-javascript
16651 (lambda* (#:key inputs #:allow-other-keys)
16652 (with-directory-excursion "inst"
16656 `((,(assoc-ref inputs "js-jquery")
16657 "htmlwidgets/lib/jquery/jquery.min.js")
16658 (,(assoc-ref inputs "js-threejs-111")
16659 "htmlwidgets/lib/threejs-111/three.min.js"))))
16660 (lambda (sources targets)
16661 (for-each (lambda (source target)
16662 (format #t "Processing ~a --> ~a~%"
16664 (delete-file target)
16665 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16666 (call-with-output-file target
16668 (dump-port minified port)))))
16669 sources targets))))
16672 `(("r-base64enc" ,r-base64enc)
16673 ("r-crosstalk" ,r-crosstalk)
16674 ("r-htmlwidgets" ,r-htmlwidgets)
16675 ("r-igraph" ,r-igraph)))
16677 `(("uglify-js" ,uglify-js)
16681 (uri "https://code.jquery.com/jquery-1.12.4.js")
16684 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16688 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16691 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16692 (home-page "https://bwlewis.github.io/rthreejs")
16693 (synopsis "Interactive 3D scatter plots, networks and globes")
16695 "Create interactive 3D scatter plots, network plots, and globes in R
16696 using the three.js visualization library.")
16697 (license license:expat)))
16699 (define-public r-mlbench
16706 (uri (cran-uri "mlbench" version))
16709 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16710 (build-system r-build-system)
16711 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16712 (synopsis "Machine learning benchmark problems")
16714 "This package provides a collection of artificial and real-world machine
16715 learning benchmark problems, including, e.g., several data sets from the UCI
16717 (license license:gpl2)))
16719 (define-public r-mpm
16726 (uri (cran-uri "mpm" version))
16729 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16730 (build-system r-build-system)
16732 `(("r-kernsmooth" ,r-kernsmooth)
16733 ("r-mass" ,r-mass)))
16734 (home-page "http://mpm.r-forge.r-project.org")
16735 (synopsis "Multivariate projection methods")
16737 "This is a package for exploratory graphical analysis of multivariate
16738 data, specifically gene expression data with different projection methods:
16739 principal component analysis, correspondence analysis, spectral map
16741 (license license:gpl2+)))
16743 (define-public r-png
16749 (uri (cran-uri "png" version))
16752 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16753 (build-system r-build-system)
16755 `(("libpng" ,libpng)
16757 (home-page "https://www.rforge.net/png/")
16758 (synopsis "Read and write PNG images")
16760 "This package provides an easy and simple way to read, write and display
16761 bitmap images stored in the PNG format. It can read and write both files and
16762 in-memory raw vectors.")
16763 ;; Any of these GPL versions.
16764 (license (list license:gpl2 license:gpl3))))
16766 (define-public r-ggcorrplot
16768 (name "r-ggcorrplot")
16773 (uri (cran-uri "ggcorrplot" version))
16776 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16777 (build-system r-build-system)
16779 `(("r-ggplot2" ,r-ggplot2)
16780 ("r-reshape2" ,r-reshape2)))
16781 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16782 (synopsis "Visualization of a correlation matrix using ggplot2")
16784 "The ggcorrplot package can be used to visualize easily a correlation
16785 matrix using ggplot2. It provides a solution for reordering the correlation
16786 matrix and displays the significance level on the plot. It also includes a
16787 function for computing a matrix of correlation p-values.")
16788 (license license:gpl2)))
16790 (define-public r-gridtext
16792 (name "r-gridtext")
16797 (uri (cran-uri "gridtext" version))
16800 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16801 (properties `((upstream-name . "gridtext")))
16802 (build-system r-build-system)
16804 `(("r-jpeg" ,r-jpeg)
16805 ("r-markdown" ,r-markdown)
16808 ("r-rcurl" ,r-rcurl)
16809 ("r-rlang" ,r-rlang)
16810 ("r-stringr" ,r-stringr)
16811 ("r-xml2" ,r-xml2)))
16812 (home-page "https://wilkelab.org/gridtext/")
16813 (synopsis "Improved text rendering support for Grid graphics")
16815 "This package provides support for rendering of formatted text using Grid
16816 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16817 inline CSS directives, and it can be rendered both with and without word
16819 (license license:expat)))
16821 (define-public r-ggtext
16828 (uri (cran-uri "ggtext" version))
16831 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16832 (properties `((upstream-name . "ggtext")))
16833 (build-system r-build-system)
16835 `(("r-ggplot2" ,r-ggplot2)
16836 ("r-gridtext" ,r-gridtext)
16837 ("r-rlang" ,r-rlang)
16838 ("r-scales" ,r-scales)))
16839 (native-inputs `(("r-knitr" ,r-knitr)))
16840 (home-page "https://wilkelab.org/ggtext/")
16841 (synopsis "Improved text rendering support for ggplot2")
16843 "This package provides a ggplot2 extension that enables the rendering of
16844 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16845 etc.). Text boxes with automatic word wrap are also supported.")
16846 (license license:gpl2)))
16848 ;; This package includes minified JavaScript files. When upgrading please
16849 ;; check that there are no new minified JavaScript files.
16850 (define-public r-flexdashboard
16852 (name "r-flexdashboard")
16857 (uri (cran-uri "flexdashboard" version))
16860 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16861 (modules '((guix build utils)))
16864 ;; Delete bundled minified JavaScript files
16865 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16866 (delete-file "inst/www/sly/sly.min.js")
16867 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16868 (delete-file "inst/www/prism/prism.js")
16870 (build-system r-build-system)
16872 `(#:modules ((guix build utils)
16873 (guix build r-build-system)
16877 (ice-9 textual-ports))
16879 (modify-phases %standard-phases
16880 (add-after 'unpack 'process-javascript
16881 (lambda* (#:key inputs #:allow-other-keys)
16882 (with-directory-excursion "inst"
16883 ;; Concatenate all components of prism.js
16884 (let ((contents (string-join
16885 (map (lambda (name)
16886 (call-with-input-file
16887 (assoc-ref inputs name)
16891 "js-prism-line-numbers"))
16893 (call-with-output-file "prism-src.js"
16894 (cut display contents <>)))
16898 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16899 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16901 "www/sly/sly.min.js")
16903 "www/prism/prism.js")
16904 (,(assoc-ref inputs "js-raphael")
16905 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16906 (,(assoc-ref inputs "js-featherlight")
16907 "www/featherlight/featherlight.min.js"))))
16908 (lambda (sources targets)
16909 (for-each (lambda (source target)
16910 (format #t "Processing ~a --> ~a~%"
16912 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16913 (call-with-output-file target
16915 (dump-port minified port)))))
16916 sources targets))))
16919 `(("r-htmltools" ,r-htmltools)
16920 ("r-htmlwidgets" ,r-htmlwidgets)
16921 ("r-jsonlite" ,r-jsonlite)
16922 ("r-knitr" ,r-knitr)
16923 ("r-rmarkdown" ,r-rmarkdown)
16924 ("r-shiny" ,r-shiny)))
16926 `(("uglify-js" ,uglify-js)
16930 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16933 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16937 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16940 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16944 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16947 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16948 ("js-prism-line-numbers"
16951 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16954 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16958 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16961 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16962 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16963 (synopsis "R Markdown format for flexible dashboards")
16965 "This package provides an R Markdown format for converting an R Markdown
16966 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16967 of its components to the containing web page.")
16968 (license license:expat)))
16970 (define-public r-preseqr
16977 (uri (cran-uri "preseqR" version))
16980 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16981 (properties `((upstream-name . "preseqR")))
16982 (build-system r-build-system)
16984 `(("r-polynom" ,r-polynom)))
16985 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16986 (synopsis "Predicting species accumulation curves")
16988 "This package can be used to predict the r-species accumulation
16989 curve (r-SAC), which is the number of species represented at least r times as
16990 a function of the sampling effort. When r = 1, the curve is known as the
16991 species accumulation curve, or the library complexity curve in high-throughput
16992 genomic sequencing. The package includes both parametric and nonparametric
16993 methods, as described by Deng C, et al. (2018).")
16994 (license license:gpl3)))
16996 (define-public r-mapplots
16998 (name "r-mapplots")
17003 (uri (cran-uri "mapplots" version))
17006 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
17007 (build-system r-build-system)
17008 (home-page "https://cran.r-project.org/web/packages/mapplots/")
17009 (synopsis "Data visualization on maps")
17011 "This package helps you create simple maps; add sub-plots like pie plots
17012 to a map or any other plot; format, plot and export gridded data. The package
17013 was developed for displaying fisheries data but most functions can be used for
17014 more generic data visualisation.")
17015 (license license:gpl2+)))
17017 (define-public r-pmcmr
17024 (uri (cran-uri "PMCMR" version))
17027 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
17028 (properties `((upstream-name . "PMCMR")))
17029 (build-system r-build-system)
17030 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
17031 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
17033 "This is a deprecated package for calculating pairwise multiple
17034 comparisons of mean rank sums. This package is superseded by the novel
17035 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
17036 compatibility of dependent packages for some time.")
17037 (license license:gpl3+)))
17039 (define-public r-downloader
17041 (name "r-downloader")
17046 (uri (cran-uri "downloader" version))
17049 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17050 (build-system r-build-system)
17052 `(("r-digest" ,r-digest)))
17053 (home-page "https://github.com/wch/downloader")
17054 (synopsis "Download files over HTTP and HTTPS")
17056 "This package provides a wrapper for the @code{download.file} function,
17057 making it possible to download files over HTTPS across platforms. The
17058 @code{RCurl} package provides this functionality (and much more) but has
17059 external dependencies. This package has is implemented purely in R.")
17060 (license license:gpl2)))
17062 (define-public r-rex
17069 (uri (cran-uri "rex" version))
17072 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17073 (build-system r-build-system)
17075 `(("r-lazyeval" ,r-lazyeval)))
17077 `(("r-knitr" ,r-knitr)))
17078 (home-page "https://github.com/kevinushey/rex")
17079 (synopsis "Friendly regular expressions")
17081 "This package provides a friendly interface for the construction of
17082 regular expressions. Regular expressions are a very powerful feature, however
17083 they are often difficult to interpret. Rex allows you to build complex
17084 regular expressions from human readable expressions")
17085 (license license:expat)))
17087 (define-public r-xmlparsedata
17089 (name "r-xmlparsedata")
17094 (uri (cran-uri "xmlparsedata" version))
17097 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
17098 (properties `((upstream-name . "xmlparsedata")))
17099 (build-system r-build-system)
17100 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17101 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17103 "This package provides tools to convert the output of
17104 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17105 @code{XPath}, and is easier to manipulate in general.")
17106 (license license:expat)))
17108 (define-public r-cyclocomp
17110 (name "r-cyclocomp")
17115 (uri (cran-uri "cyclocomp" version))
17118 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17119 (properties `((upstream-name . "cyclocomp")))
17120 (build-system r-build-system)
17122 `(("r-callr" ,r-callr)
17123 ("r-crayon" ,r-crayon)
17125 ("r-remotes" ,r-remotes)
17126 ("r-withr" ,r-withr)))
17127 (home-page "https://github.com/MangoTheCat/cyclocomp")
17128 (synopsis "Cyclomatic complexity of R code")
17130 "Cyclomatic complexity is a software metric, used to indicate the
17131 complexity of a program. It is a quantitative measure of the number of
17132 linearly independent paths through a program's source code. This package
17133 provides tools to compute this metric.")
17134 (license license:expat)))
17136 (define-public r-lintr
17143 (uri (cran-uri "lintr" version))
17146 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17147 (properties `((upstream-name . "lintr")))
17148 (build-system r-build-system)
17150 `(("r-codetools" ,r-codetools)
17151 ("r-crayon" ,r-crayon)
17152 ("r-cyclocomp" ,r-cyclocomp)
17153 ("r-digest" ,r-digest)
17155 ("r-jsonlite" ,r-jsonlite)
17156 ("r-knitr" ,r-knitr)
17158 ("r-rstudioapi" ,r-rstudioapi)
17159 ("r-testthat" ,r-testthat)
17161 ("r-xmlparsedata" ,r-xmlparsedata)))
17162 (home-page "https://github.com/jimhester/lintr")
17163 (synopsis "Linter for R code")
17164 (description "This package checks adherence to a given style, syntax
17165 errors and possible semantic issues. It supports on the fly checking of R
17166 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17167 (license license:expat)))
17169 (define-public r-sctransform
17171 (name "r-sctransform")
17176 (uri (cran-uri "sctransform" version))
17179 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17180 (build-system r-build-system)
17182 `(("r-future" ,r-future)
17183 ("r-future-apply" ,r-future-apply)
17184 ("r-ggplot2" ,r-ggplot2)
17185 ("r-gridextra" ,r-gridextra)
17187 ("r-matrix" ,r-matrix)
17188 ("r-matrixstats" ,r-matrixstats)
17190 ("r-rcpparmadillo" ,r-rcpparmadillo)
17191 ("r-reshape2" ,r-reshape2)))
17192 (home-page "https://github.com/ChristophH/sctransform")
17193 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17195 "This package provides a normalization method for single-cell UMI count
17196 data using a variance stabilizing transformation. The transformation is based
17197 on a negative binomial regression model with regularized parameters. As part
17198 of the same regression framework, this package also provides functions for
17199 batch correction, and data correction.")
17200 (license license:gpl3)))
17202 (define-public r-styler
17209 (uri (cran-uri "styler" version))
17212 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17213 (build-system r-build-system)
17215 `(("r-backports" ,r-backports)
17217 ("r-magrittr" ,r-magrittr)
17218 ("r-purrr" ,r-purrr)
17219 ("r-r-cache" ,r-r-cache)
17220 ("r-rematch2" ,r-rematch2)
17221 ("r-rlang" ,r-rlang)
17222 ("r-rprojroot" ,r-rprojroot)
17223 ("r-tibble" ,r-tibble)
17224 ("r-withr" ,r-withr)
17225 ("r-xfun" ,r-xfun)))
17226 (home-page "https://github.com/r-lib/styler")
17227 (synopsis "Non-invasive pretty printing of R code")
17229 "This is a package for pretty-printing R code without changing the user's
17230 formatting intent.")
17231 (license license:gpl3)))
17233 (define-public r-scrime
17240 (uri (cran-uri "scrime" version))
17243 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17244 (build-system r-build-system)
17245 (home-page "https://cran.r-project.org/web/packages/scrime/")
17246 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17248 "This package provides tools for the analysis of high-dimensional data
17249 developed/implemented at the group \"Statistical Complexity Reduction In
17250 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17251 the functions can also be applied to other types of categorical data.")
17252 (license license:gpl2)))
17254 (define-public r-pbmcapply
17256 (name "r-pbmcapply")
17261 (uri (cran-uri "pbmcapply" version))
17264 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17265 (build-system r-build-system)
17266 (home-page "https://github.com/kvnkuang/pbmcapply")
17267 (synopsis "Track the progress of apply procedures with a progress bar")
17269 "This light-weight package helps you track and visualize the progress of
17270 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17271 (license license:expat)))
17273 (define-public r-blme
17280 (uri (cran-uri "blme" version))
17283 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17284 (build-system r-build-system)
17285 (propagated-inputs `(("r-lme4" ,r-lme4)))
17286 (home-page "https://github.com/vdorie/blme")
17287 (synopsis "Bayesian linear mixed-effects models")
17289 "This package provides tools for maximum a posteriori estimation for
17290 linear and generalized linear mixed-effects models in a Bayesian setting. It
17291 extends the lme4 package.")
17292 (license license:gpl2+)))
17294 (define-public r-batchtools
17296 (name "r-batchtools")
17301 (uri (cran-uri "batchtools" version))
17304 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17305 (build-system r-build-system)
17307 `(("r-backports" ,r-backports)
17308 ("r-base64url" ,r-base64url)
17310 ("r-checkmate" ,r-checkmate)
17311 ("r-data-table" ,r-data-table)
17312 ("r-digest" ,r-digest)
17314 ("r-progress" ,r-progress)
17316 ("r-rappdirs" ,r-rappdirs)
17317 ("r-stringi" ,r-stringi)
17318 ("r-withr" ,r-withr)))
17320 `(("r-knitr" ,r-knitr)))
17321 (home-page "https://github.com/mllg/batchtools")
17322 (synopsis "Tools for computation on batch systems")
17324 "As a successor of the packages BatchJobs and BatchExperiments, this
17325 package provides a parallel implementation of the Map function for high
17326 performance computing systems managed by various schedulers. A multicore and
17327 socket mode allow the parallelization on a local machines, and multiple
17328 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17329 the package provides an abstraction mechanism to define large-scale computer
17330 experiments in a well-organized and reproducible way.")
17331 (license license:lgpl3)))
17333 (define-public r-clue
17340 (uri (cran-uri "clue" version))
17343 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17344 (build-system r-build-system)
17345 (propagated-inputs `(("r-cluster" ,r-cluster)))
17346 (home-page "https://cran.r-project.org/web/packages/clue/")
17347 (synopsis "Tools for analyzing cluster ensembles")
17348 (description "Cluster ensembles are collections of individual solutions to
17349 a given clustering problem which are useful or necessary to consider in a wide
17350 range of applications. This R package provides an extensible computational
17351 environment for creating and analyzing cluster ensembles, with basic data
17352 structures for representing partitions and hierarchies, and facilities for
17353 computing on them, including methods for measuring proximity and obtaining
17354 consensus and secondary clusterings.")
17355 (license license:gpl2)))
17357 (define-public r-sitmo
17364 (uri (cran-uri "sitmo" version))
17367 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17368 (build-system r-build-system)
17369 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17370 (home-page "https://github.com/coatless/sitmo/")
17371 (synopsis "Parallel pseudo random number generator header files")
17373 "This package provides two high quality and fast PPRNGs that may be used
17374 in an OpenMP parallel environment. In addition, there is a generator for one
17375 dimensional low-discrepancy sequence.")
17376 (license license:expat)))
17378 (define-public r-dqrng
17385 (uri (cran-uri "dqrng" version))
17388 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17389 (build-system r-build-system)
17393 ("r-sitmo" ,r-sitmo)))
17394 (home-page "https://www.daqana.org/dqrng")
17395 (synopsis "Fast pseudo random number generators")
17397 "Several fast random number generators are provided as C++ header-only
17398 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17399 Additionally, fast functions for generating random numbers according to a
17400 uniform, normal and exponential distribution are included. The latter two use
17401 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17402 functions are exported to R and as a C++ interface and are enabled for use
17403 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17404 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17405 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17406 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17407 ;; whole is distributed under the terms of the AGPL 3.
17408 (license license:agpl3)))
17410 (define-public r-ingredients
17412 (name "r-ingredients")
17417 (uri (cran-uri "ingredients" version))
17420 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17421 (properties `((upstream-name . "ingredients")))
17422 (build-system r-build-system)
17424 `(("r-ggplot2" ,r-ggplot2)
17425 ("r-gridextra" ,r-gridextra)
17426 ("r-scales" ,r-scales)))
17427 (native-inputs `(("r-knitr" ,r-knitr)))
17428 (home-page "https://ModelOriented.github.io/ingredients/")
17429 (synopsis "Effects and importances of model ingredients")
17431 "This is a collection of tools for assessment of feature importance and
17432 feature effects. Key functions are:
17435 @item @code{feature_importance()} for assessment of global level feature
17437 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17438 @item @code{partial_dependence()} for partial dependence plots,
17439 @item @code{conditional_dependence()} for conditional dependence plots,
17440 @item @code{accumulated_dependence()} for accumulated local effects plots,
17441 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17442 aggregation of ceteris paribus profiles,
17443 @item generic @code{print()} and @code{plot()} for better usability of
17444 selected explainers,
17445 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17446 @item generic @code{describe()} for explanations in natural language.
17448 (license license:gpl3)))
17450 (define-public r-ibreakdown
17452 (name "r-ibreakdown")
17457 (uri (cran-uri "iBreakDown" version))
17460 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17461 (properties `((upstream-name . "iBreakDown")))
17462 (build-system r-build-system)
17463 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17464 (native-inputs `(("r-knitr" ,r-knitr)))
17465 (home-page "https://ModelOriented.github.io/iBreakDown/")
17466 (synopsis "Model agnostic instance level variable attributions")
17468 "This package provides a model agnostic tool for decomposition of
17469 predictions from black boxes. It supports additive attributions and
17470 attributions with interactions. The Break Down Table shows contributions of
17471 every variable to a final prediction. The Break Down Plot presents variable
17472 contributions in a concise graphical way. This package works for
17473 classification and regression models.")
17474 (license license:gpl3)))
17476 (define-public r-dae
17483 (uri (cran-uri "dae" version))
17486 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17487 (build-system r-build-system)
17489 `(("r-ggplot2" ,r-ggplot2)
17490 ("r-plyr" ,r-plyr)))
17492 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17493 (home-page "http://chris.brien.name")
17494 (synopsis "Functions useful in the design and ANOVA of experiments")
17496 "This package provides functions useful in the design and ANOVA of
17497 experiments. The content falls into the following groupings:
17501 @item factor manipulation functions,
17502 @item design functions,
17503 @item ANOVA functions,
17504 @item matrix functions,
17505 @item projector and canonical efficiency functions, and
17506 @item miscellaneous functions.
17509 There is a vignette called @code{DesignNotes} describing how to use the design
17510 functions for randomizing and assessing designs. The ANOVA functions
17511 facilitate the extraction of information when the @code{Error} function has
17512 been used in the call to @code{aov}.")
17513 (license license:gpl2)))
17515 (define-public r-dalex
17522 (uri (cran-uri "DALEX" version))
17525 "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz"))))
17526 (properties `((upstream-name . "DALEX")))
17527 (build-system r-build-system)
17529 `(("r-ggplot2" ,r-ggplot2)
17530 ("r-ibreakdown" ,r-ibreakdown)
17531 ("r-ingredients" ,r-ingredients)))
17532 (home-page "https://pbiecek.github.io/DALEX/")
17533 (synopsis "Descriptive machine learning explanations")
17535 "Machine Learning models are widely used and have various applications in
17536 classification or regression. Models created with boosting, bagging, stacking
17537 or similar techniques are often used due to their high performance, but such
17538 black-box models usually lack interpretability. The DALEX package contains
17539 various explainers that help to understand the link between input variables
17540 and model output.")
17541 ;; Any version of the GPL
17542 (license license:gpl3+)))
17544 (define-public r-enrichr
17551 (uri (cran-uri "enrichR" version))
17554 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17555 (properties `((upstream-name . "enrichR")))
17556 (build-system r-build-system)
17558 `(("r-ggplot2" ,r-ggplot2)
17560 ("r-rjson" ,r-rjson)))
17562 `(("r-knitr" ,r-knitr)))
17563 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17564 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17566 "This package provides an R interface to all Enrichr databases, a
17567 web-based tool for analyzing gene sets and returns any enrichment of common
17568 annotated biological functions.")
17569 (license license:gpl2+)))
17571 (define-public r-plot3d
17578 (uri (cran-uri "plot3D" version))
17581 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17582 (properties `((upstream-name . "plot3D")))
17583 (build-system r-build-system)
17584 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17585 (home-page "https://cran.r-project.org/web/packages/plot3D")
17586 (synopsis "Plot multi-dimensional data")
17588 "This package provides functions for viewing 2D and 3D data, including
17589 perspective plots, slice plots, surface plots, scatter plots, etc. It
17590 includes data sets from oceanography.")
17591 (license license:gpl3+)))
17593 (define-public r-ggfortify
17595 (name "r-ggfortify")
17600 (uri (cran-uri "ggfortify" version))
17603 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17604 (build-system r-build-system)
17606 `(("r-dplyr" ,r-dplyr)
17607 ("r-ggplot2" ,r-ggplot2)
17608 ("r-gridextra" ,r-gridextra)
17609 ("r-scales" ,r-scales)
17610 ("r-stringr" ,r-stringr)
17611 ("r-tibble" ,r-tibble)
17612 ("r-tidyr" ,r-tidyr)))
17614 `(("r-knitr" ,r-knitr)))
17615 (home-page "https://github.com/sinhrks/ggfortify")
17616 (synopsis "Data visualization tools for statistical analysis results")
17618 "This package provides unified plotting tools for statistics commonly
17619 used, such as GLM, time series, PCA families, clustering and survival
17620 analysis. The package offers a single plotting interface for these analysis
17621 results and plots in a unified style using the @code{ggplot2} package.")
17622 (license license:gpl2)))
17624 (define-public r-refmanager
17626 (name "r-refmanager")
17631 (uri (cran-uri "RefManageR" version))
17634 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17635 (properties `((upstream-name . "RefManageR")))
17636 (build-system r-build-system)
17638 `(("r-httr" ,r-httr)
17639 ("r-jsonlite" ,r-jsonlite)
17640 ("r-lubridate" ,r-lubridate)
17642 ("r-stringr" ,r-stringr)
17643 ("r-xml2" ,r-xml2)))
17645 `(("r-knitr" ,r-knitr)))
17646 (home-page "https://github.com/ropensci/RefManageR/")
17647 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17649 "This package provides tools for importing and working with bibliographic
17650 references. It greatly enhances the @code{bibentry} class by providing a
17651 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17652 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17653 by various formats for name lists (author by last names, translator by full
17654 names, etc.). Entries can be updated, combined, sorted, printed in a number
17655 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17656 into R and converted to @code{BibEntry} objects.")
17657 ;; Any of these licenses may be picked.
17658 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17660 (define-public r-citr
17667 (uri (cran-uri "citr" version))
17670 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17671 (build-system r-build-system)
17673 `(("r-assertthat" ,r-assertthat)
17676 ("r-miniui" ,r-miniui)
17677 ("r-refmanager" ,r-refmanager)
17678 ("r-rstudioapi" ,r-rstudioapi)
17679 ("r-shiny" ,r-shiny)
17680 ("r-shinyjs" ,r-shinyjs)
17681 ("r-yaml" ,r-yaml)))
17682 (home-page "https://github.com/crsh/citr")
17683 (synopsis "RStudio add-in to insert Markdown citations")
17685 "This package provides functions and an RStudio add-in that search a
17686 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17687 the current document.")
17688 (license license:expat)))
17690 (define-public r-xgboost
17693 (version "1.3.2.1")
17697 (uri (cran-uri "xgboost" version))
17700 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17701 (build-system r-build-system)
17703 `(("r-data-table" ,r-data-table)
17704 ("r-magrittr" ,r-magrittr)
17705 ("r-matrix" ,r-matrix)))
17707 `(("r-knitr" ,r-knitr)))
17708 (home-page "https://github.com/dmlc/xgboost")
17709 (synopsis "Extreme gradient boosting")
17711 "This package provides an R interface to Extreme Gradient Boosting, which
17712 is an efficient implementation of the gradient boosting framework from Chen
17713 and Guestrin (2016). The package includes efficient linear model solver and
17714 tree learning algorithms. The package can automatically do parallel
17715 computation on a single machine. It supports various objective functions,
17716 including regression, classification and ranking. The package is made to be
17717 extensible, so that users are also allowed to define their own objectives
17719 (license license:asl2.0)))
17721 (define-public r-umap
17724 (version "0.2.7.0")
17728 (uri (cran-uri "umap" version))
17731 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17732 (build-system r-build-system)
17734 `(("r-openssl" ,r-openssl)
17736 ("r-reticulate" ,r-reticulate)
17737 ("r-rspectra" ,r-rspectra)))
17739 `(("r-knitr" ,r-knitr)))
17740 (home-page "https://github.com/tkonopka/umap")
17741 (synopsis "Uniform manifold approximation and projection")
17743 "Uniform manifold approximation and projection is a technique for
17744 dimension reduction. This package provides an interface to the UMAP algorithm
17745 in R, including a translation of the original algorithm into R.")
17746 (license license:expat)))
17748 (define-public r-uwot
17755 (uri (cran-uri "uwot" version))
17758 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17759 (build-system r-build-system)
17761 `(("r-dqrng" ,r-dqrng)
17763 ("r-irlba" ,r-irlba)
17764 ("r-matrix" ,r-matrix)
17766 ("r-rcppannoy" ,r-rcppannoy)
17767 ("r-rcppprogress" ,r-rcppprogress)
17768 ("r-rspectra" ,r-rspectra)))
17769 (home-page "https://github.com/jlmelville/uwot")
17770 (synopsis "Uniform manifold approximation and projection")
17772 "This package provides an implementation of the Uniform Manifold
17773 Approximation and Projection dimensionality reduction by McInnes et
17774 al. (2018). It also provides means to transform new data and to carry out
17775 supervised dimensionality reduction. An implementation of the related
17776 LargeVis method of Tang et al. (2016) is also provided.")
17777 (license license:gpl3)))
17779 (define-public r-kableextra
17781 (name "r-kableextra")
17786 (uri (cran-uri "kableExtra" version))
17789 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
17790 (properties `((upstream-name . "kableExtra")))
17791 (build-system r-build-system)
17793 `(("r-digest" ,r-digest)
17795 ("r-htmltools" ,r-htmltools)
17796 ("r-knitr" ,r-knitr)
17797 ("r-magrittr" ,r-magrittr)
17798 ("r-rmarkdown" ,r-rmarkdown)
17799 ("r-rstudioapi" ,r-rstudioapi)
17800 ("r-rvest" ,r-rvest)
17801 ("r-scales" ,r-scales)
17802 ("r-stringr" ,r-stringr)
17803 ("r-svglite" ,r-svglite)
17804 ("r-viridislite" ,r-viridislite)
17805 ("r-webshot" ,r-webshot)
17806 ("r-xml2" ,r-xml2)))
17808 `(("r-knitr" ,r-knitr)))
17809 (home-page "https://haozhu233.github.io/kableExtra/")
17810 (synopsis "Construct complex tables with pipe syntax")
17812 "Build complex HTML or LaTeX tables using @code{kable()} from
17813 @code{knitr} and the piping syntax from @code{magrittr}. The function
17814 @code{kable()} is a light weight table generator coming from @code{knitr}.
17815 This package simplifies the way to manipulate the HTML or LaTeX codes
17816 generated by @code{kable()} and allows users to construct complex tables and
17817 customize styles using a readable syntax.")
17818 (license license:expat)))
17820 (define-public r-glasso
17827 (uri (cran-uri "glasso" version))
17829 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17830 (build-system r-build-system)
17831 (native-inputs `(("gfortran" ,gfortran)))
17832 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17833 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17835 "This is a package for estimation of a sparse inverse covariance matrix
17836 using a lasso (L1) penalty. Facilities are provided for estimates along a
17837 path of values for the regularization parameter.")
17838 (license license:gpl2)))
17840 (define-public r-rhpcblasctl
17842 (name "r-rhpcblasctl")
17843 (version "0.20-137")
17847 (uri (cran-uri "RhpcBLASctl" version))
17850 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17851 (properties `((upstream-name . "RhpcBLASctl")))
17852 (build-system r-build-system)
17853 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17854 (synopsis "Control the number of threads on BLAS")
17856 "This package allows you to control the number of threads the BLAS
17857 library uses. It is also possible to control the number of threads in
17859 (license license:agpl3+)))
17861 (define-public r-lda
17868 (uri (cran-uri "lda" version))
17871 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17872 (build-system r-build-system)
17873 (home-page "https://cran.r-project.org/web/packages/lda/")
17874 (synopsis "Collapsed Gibbs sampling methods for topic models")
17876 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17877 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17878 mixed-membership stochastic blockmodel. Inference for all of these models is
17879 implemented via a fast collapsed Gibbs sampler written in C. Utility
17880 functions for reading/writing data typically used in topic models, as well as
17881 tools for examining posterior distributions are also included.")
17882 ;; Any version of the LGPL
17883 (license license:lgpl3+)))
17885 (define-public r-rann-l1
17892 (uri (cran-uri "RANN.L1" version))
17895 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17896 (properties `((upstream-name . "RANN.L1")))
17897 (build-system r-build-system)
17898 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17899 (synopsis "Fast nearest neighbour search using L1 metric")
17901 "This package provides tools to find the k nearest neighbours for every
17902 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17903 library. There is support for approximate as well as exact searches, fixed
17904 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17905 computed using the L1 (Manhattan, taxicab) metric.")
17906 (license license:gpl3+)))
17908 (define-public r-leiden
17915 (uri (cran-uri "leiden" version))
17918 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17919 (properties `((upstream-name . "leiden")))
17920 (build-system r-build-system)
17922 `(("r-igraph" ,r-igraph)
17923 ("r-matrix" ,r-matrix)
17924 ("r-reticulate" ,r-reticulate)))
17926 `(("r-knitr" ,r-knitr)))
17927 (home-page "https://github.com/TomKellyGenetics/leiden")
17928 (synopsis "R implementation of Leiden clustering algorithm")
17930 "This package implements the Python @code{leidenalg} module to be called
17931 in R. It enables clustering using the Leiden algorithm for partitioning a
17932 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17933 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17934 (license license:gpl3)))
17936 (define-public r-patchwork
17938 (name "r-patchwork")
17943 (uri (cran-uri "patchwork" version))
17946 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17947 (build-system r-build-system)
17949 `(("r-ggplot2" ,r-ggplot2)
17950 ("r-gtable" ,r-gtable)))
17952 `(("r-knitr" ,r-knitr)))
17953 (home-page "https://github.com/thomasp85/patchwork")
17954 (synopsis "Compose ggplot2 plots")
17956 "The @code{ggplot2} package provides a strong API for sequentially
17957 building up a plot, but does not concern itself with composition of multiple
17958 plots. Patchwork is a package that expands the API to allow for arbitrarily
17959 complex composition of plots by providing mathematical operators for combining
17961 (license license:expat)))
17963 (define-public r-liger
17970 (uri (git-reference
17971 (url "https://github.com/MacoskoLab/liger")
17972 (commit (string-append "v" version))))
17973 (file-name (git-file-name name version))
17976 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17977 (modules '((guix build utils)))
17980 (delete-file "inst/java/ModularityOptimizer.jar")
17982 (build-system r-build-system)
17985 (modify-phases %standard-phases
17986 (add-after 'unpack 'build-java-part
17987 (lambda* (#:key inputs #:allow-other-keys)
17988 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17989 (for-each (lambda (file) (invoke "javac" file))
17990 (find-files "." "\\.java$"))
17991 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17992 (find-files "." "\\.class$"))
17995 `(("r-cowplot" ,r-cowplot)
17996 ("r-dosnow" ,r-dosnow)
17997 ("r-dplyr" ,r-dplyr)
17999 ("r-foreach" ,r-foreach)
18000 ("r-ggplot2" ,r-ggplot2)
18001 ("r-ggrepel" ,r-ggrepel)
18002 ("r-hmisc" ,r-hmisc)
18004 ("r-irlba" ,r-irlba)
18005 ("r-matrix" ,r-matrix)
18006 ("r-mclust" ,r-mclust)
18007 ("r-patchwork" ,r-patchwork)
18009 ("r-rann-l1" ,r-rann-l1)
18011 ("r-rcpparmadillo" ,r-rcpparmadillo)
18012 ("r-riverplot" ,r-riverplot)
18013 ("r-rtsne" ,r-rtsne)
18014 ("r-snow" ,r-snow)))
18016 `(("jdk" ,icedtea "jdk")
18017 ;; See https://github.com/MacoskoLab/liger/issues/96
18018 ;; The optimizer is released under the Expat license.
18022 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
18025 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
18027 ("r-knitr" ,r-knitr))) ; for vignettes
18028 (home-page "https://github.com/MacoskoLab/liger")
18029 (synopsis "Integrate and analyze multiple single-cell datasets")
18031 "LIGER is a package for integrating and analyzing multiple single-cell
18032 datasets, developed and maintained by the Macosko lab. It relies on
18033 integrative non-negative matrix factorization to identify shared and
18034 dataset-specific factors.")
18035 (license license:gpl3)))
18037 (define-public r-harmony
18044 (uri (git-reference
18045 (url "https://github.com/immunogenomics/harmony")
18047 (file-name (git-file-name name version))
18050 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18051 (modules '((guix build utils)))
18054 (for-each delete-file '("config.status" "configure"))
18056 (build-system r-build-system)
18058 `(("r-cowplot" ,r-cowplot)
18059 ("r-dplyr" ,r-dplyr)
18060 ("r-ggplot2" ,r-ggplot2)
18061 ("r-irlba" ,r-irlba)
18062 ("r-matrix" ,r-matrix)
18064 ("r-rcpparmadillo" ,r-rcpparmadillo)
18065 ("r-rcppprogress" ,r-rcppprogress)
18066 ("r-rlang" ,r-rlang)
18067 ("r-tibble" ,r-tibble)
18068 ("r-tidyr" ,r-tidyr)))
18070 `(("autoconf" ,autoconf)))
18071 (home-page "https://github.com/immunogenomics/harmony")
18072 (synopsis "Integration of single cell sequencing data")
18074 "This package provides an implementation of the Harmony algorithm for
18075 single cell integration, described in Korsunsky et al
18076 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18077 function and interfaces to external frameworks.")
18078 (license license:gpl3)))
18080 (define-public r-covr
18087 (uri (cran-uri "covr" version))
18089 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18090 (properties `((upstream-name . "covr")))
18091 (build-system r-build-system)
18093 `(("r-crayon" ,r-crayon)
18094 ("r-digest" ,r-digest)
18096 ("r-jsonlite" ,r-jsonlite)
18098 ("r-withr" ,r-withr)
18099 ("r-yaml" ,r-yaml)))
18101 `(("r-knitr" ,r-knitr))) ; for vignettes
18102 (home-page "https://github.com/r-lib/covr")
18103 (synopsis "Test coverage for R packages")
18105 "Thisp package enables you to track and report code coverage for your
18106 package and (optionally) upload the results to a coverage service. Code
18107 coverage is a measure of the amount of code being exercised by a set of tests.
18108 It is an indirect measure of test quality and completeness. This package is
18109 compatible with any testing methodology or framework and tracks coverage of
18110 both R code and compiled C/C++/FORTRAN code.")
18111 (license license:gpl3)))
18113 (define-public r-systemfonts
18115 (name "r-systemfonts")
18120 (uri (cran-uri "systemfonts" version))
18123 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18124 (properties `((upstream-name . "systemfonts")))
18125 (build-system r-build-system)
18127 `(("r-cpp11" ,r-cpp11)))
18129 `(("fontconfig" ,fontconfig)
18132 `(("pkg-config" ,pkg-config)
18133 ("r-knitr" ,r-knitr)))
18134 (home-page "https://github.com/r-lib/systemfonts")
18135 (synopsis "System native font finding")
18137 "This package provides system native access to the font catalogue. As
18138 font handling varies between systems it is difficult to correctly locate
18139 installed fonts across different operating systems. The 'systemfonts' package
18140 provides bindings to the native libraries for finding font files that can then
18141 be used further by e.g. graphic devices.")
18142 (license license:expat)))
18144 (define-public r-graphlayouts
18146 (name "r-graphlayouts")
18151 (uri (cran-uri "graphlayouts" version))
18154 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18155 (properties `((upstream-name . "graphlayouts")))
18156 (build-system r-build-system)
18158 `(("r-igraph" ,r-igraph)
18160 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18161 (home-page "https://github.com/schochastics/graphlayouts")
18162 (synopsis "Additional layout algorithms for network visualizations")
18164 "This package provides several layout algorithms to visualize networks
18165 which are not part of the igraph library. Most are based on the concept of
18166 stress majorization by Gansner et al. (2004)
18167 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18168 emphasize hidden group structures in networks or focus on specific nodes.")
18169 (license license:expat)))
18171 (define-public r-terra
18178 (uri (cran-uri "terra" version))
18181 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18182 (properties `((upstream-name . "terra")))
18183 (build-system r-build-system)
18188 ("sqlite" ,sqlite) ; needed for proj
18191 `(("r-raster" ,r-raster)
18192 ("r-rcpp" ,r-rcpp)))
18194 `(("pkg-config" ,pkg-config)))
18195 (home-page "https://rspatial.org/terra")
18196 (synopsis "Spatial data analysis")
18198 "This package provides methods for spatial data analysis, especially
18199 raster data. The included methods allow for low-level data manipulation as
18200 well as high-level global, local, zonal, and focal computation. The predict
18201 and interpolate methods facilitate the use of regression type (interpolation,
18202 machine learning) models for spatial prediction. Processing of very large
18203 files is supported.")
18204 (license license:gpl3+)))
18206 (define-public r-tidygraph
18208 (name "r-tidygraph")
18213 (uri (cran-uri "tidygraph" version))
18216 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18217 (properties `((upstream-name . "tidygraph")))
18218 (build-system r-build-system)
18220 `(("r-dplyr" ,r-dplyr)
18221 ("r-igraph" ,r-igraph)
18222 ("r-magrittr" ,r-magrittr)
18223 ("r-pillar" ,r-pillar)
18226 ("r-rlang" ,r-rlang)
18227 ("r-tibble" ,r-tibble)
18228 ("r-tidyr" ,r-tidyr)))
18229 (home-page "https://github.com/thomasp85/tidygraph")
18230 (synopsis "Tidy API for graph manipulation")
18232 "This package provides a graph implementation that can be thought of as
18233 two tidy data frames describing node and edge data respectively. It provides
18234 an approach to manipulate these two virtual data frames using the API defined
18235 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18236 common graph algorithms.")
18237 (license license:expat)))
18239 (define-public r-soupx
18240 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18244 (version (git-version "0.3.1" revision commit))
18248 (uri (git-reference
18249 (url "https://github.com/constantAmateur/SoupX")
18251 (file-name (git-file-name name version))
18254 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18255 (properties `((upstream-name . "SoupX")))
18256 (build-system r-build-system)
18258 `(("r-ggplot2" ,r-ggplot2)
18259 ("r-matrix" ,r-matrix)
18260 ("r-seurat" ,r-seurat)))
18261 (home-page "https://github.com/constantAmateur/SoupX")
18262 (synopsis "Single cell mRNA Soup eXterminator")
18264 "This package provides a package for quantifying, profiling and
18265 removing cell free mRNA contamination (the \"soup\") from droplet based single
18266 cell RNA-seq experiments.")
18267 (license license:gpl2))))
18269 (define-public r-assertr
18276 (uri (cran-uri "assertr" version))
18279 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18280 (build-system r-build-system)
18282 `(("r-dplyr" ,r-dplyr)
18284 ("r-rlang" ,r-rlang)))
18286 `(("r-knitr" ,r-knitr))) ; needed for vignette
18287 (home-page "https://github.com/ropensci/assertr")
18288 (synopsis "Assertive programming for R analysis pipelines")
18290 "This package provides functionality to assert conditions that have to be
18291 met so that errors in data used in analysis pipelines can fail quickly. It is
18292 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18294 (license license:expat)))
18296 (define-public r-parameters
18298 (name "r-parameters")
18303 (uri (cran-uri "parameters" version))
18306 "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm"))))
18307 (properties `((upstream-name . "parameters")))
18308 (build-system r-build-system)
18310 `(("r-bayestestr" ,r-bayestestr)
18311 ("r-insight" ,r-insight)))
18313 `(("r-knitr" ,r-knitr)))
18314 (home-page "https://cran.r-project.org/web/packages/parameters")
18315 (synopsis "Processing of model parameters")
18317 "This package provides utilities for processing the parameters of various
18318 statistical models. Beyond computing p values, CIs, and other indices for a
18319 wide variety of models, this package implements features like standardization
18320 or bootstrapping of parameters and models, feature reduction (feature
18321 extraction and variable selection) as well as conversion between indices of
18323 (license license:gpl3)))
18325 (define-public r-rgdal
18332 (uri (cran-uri "rgdal" version))
18334 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18335 (properties `((upstream-name . "rgdal")))
18336 (build-system r-build-system)
18344 `(("pkg-config" ,pkg-config)
18345 ("r-knitr" ,r-knitr)))
18346 (home-page "http://rgdal.r-forge.r-project.org")
18347 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18349 "This package provides bindings to the Geospatial Data Abstraction
18350 Library (GDAL) and access to projection/transformation operations from the
18352 (license license:gpl2+)))
18354 (define-public r-insol
18361 (uri (cran-uri "insol" version))
18364 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18365 (properties `((upstream-name . "insol")))
18366 (build-system r-build-system)
18368 `(("r-raster" ,r-raster)))
18370 `(("gfortran" ,gfortran)))
18371 (home-page "https://meteoexploration.com/R/insol/index.html")
18372 (synopsis "Tools for calculating solar radiation")
18374 "This package provides functions to compute insolation on tilted
18375 surfaces, computes atmospheric transmittance and related parameters such as:
18376 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18377 time, vector in the direction of the sun, vector normal to surface, and some
18378 atmospheric physics.")
18379 (license license:gpl2+)))
18381 (define-public r-lifecycle
18383 (name "r-lifecycle")
18388 (uri (cran-uri "lifecycle" version))
18391 "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3"))))
18392 (properties `((upstream-name . "lifecycle")))
18393 (build-system r-build-system)
18395 `(("r-glue" ,r-glue)
18396 ("r-rlang" ,r-rlang)))
18398 `(("r-knitr" ,r-knitr))) ; for vignettes
18399 (home-page "https://github.com/r-lib/lifecycle")
18400 (synopsis "Manage the life cycle of your package functions")
18402 "Manage the life cycle of your exported functions with shared
18403 conventions, documentation badges, and non-invasive deprecation warnings. The
18404 lifecycle package defines four development stages (experimental, maturing,
18405 stable, and questioning) and three deprecation stages (soft-deprecated,
18406 deprecated, and defunct). It makes it easy to insert badges corresponding to
18407 these stages in your documentation. Usage of deprecated functions are
18408 signalled with increasing levels of non-invasive verbosity.")
18409 (license license:gpl3)))
18411 (define-public r-assertable
18413 (name "r-assertable")
18418 (uri (cran-uri "assertable" version))
18421 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18422 (build-system r-build-system)
18424 `(("r-data-table" ,r-data-table)))
18426 `(("r-knitr" ,r-knitr)))
18427 (home-page "https://cran.r-project.org/web/packages/assertable/")
18428 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18429 (description "This package provides simple, flexible assertions on
18430 data.frame or data.table objects with verbose output for vetting. While other
18431 assertion packages apply towards more general use-cases, @code{assertable} is
18432 tailored towards tabular data. It includes functions to check variable names
18433 and values, whether the dataset contains all combinations of a given set of
18434 unique identifiers, and whether it is a certain length. In addition,
18435 @code{assertable} includes utility functions to check the existence of target
18436 files and to efficiently import multiple tabular data files into one
18438 (license license:gpl3)))
18440 (define-public r-quadprog
18442 (name "r-quadprog")
18447 (uri (cran-uri "quadprog" version))
18449 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18450 (build-system r-build-system)
18452 `(("gfortran" ,gfortran)))
18453 (home-page "https://cran.r-project.org/web/packages/quadprog")
18454 (synopsis "Functions to solve quadratic programming problems")
18456 "This package contains routines and documentation for solving quadratic
18457 programming problems.")
18458 (license license:gpl3+)))
18460 (define-public r-desolve
18467 (uri (cran-uri "deSolve" version))
18469 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18470 (properties `((upstream-name . "deSolve")))
18471 (build-system r-build-system)
18473 `(("gfortran" ,gfortran)))
18474 (home-page "https://desolve.r-forge.r-project.org/")
18475 (synopsis "Solvers for initial value problems of differential equations")
18476 (description "This package provides functions that solve initial value
18477 problems of a system of first-order @dfn{ordinary differential
18478 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18479 @dfn{differential algebraic equations} (DAE), and of delay differential
18480 equations. The functions provide an interface to the FORTRAN functions
18481 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18482 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18483 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18484 time steps. The package contains routines designed for solving ODEs resulting
18485 from 1-D, 2-D and 3-D partial differential equations that have been converted
18486 to ODEs by numerical differencing.")
18487 (license license:gpl2+)))
18489 (define-public r-pracma
18495 (uri (cran-uri "pracma" version))
18497 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18498 (build-system r-build-system)
18499 (home-page "https://cran.r-project.org/web/packages/pracma/")
18500 (synopsis "Practical numerical math functions")
18501 (description "This package provides functions for numerical analysis and
18502 linear algebra, numerical optimization, differential equations, plus some
18503 special functions. It uses Matlab function names where appropriate to simplify
18505 (license license:gpl3+)))
18507 (define-public r-subplex
18514 (uri (cran-uri "subplex" version))
18517 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18518 (build-system r-build-system)
18520 `(("gfortran" ,gfortran)))
18521 (home-page "https://cran.r-project.org/web/packages/subplex")
18522 (synopsis "Unconstrained optimization using the subplex algorithm")
18524 "This package implements the Subplex optimization algorithm.
18525 It solves unconstrained optimization problems using a simplex method on
18526 subspaces. The method is well suited for optimizing objective functions that
18527 are noisy or are discontinuous at the solution.")
18528 (license license:gpl3+)))
18530 (define-public r-txtplot
18537 (uri (cran-uri "txtplot" version))
18540 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18541 (build-system r-build-system)
18542 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18543 (synopsis "Text-based plotting")
18544 (description "This package provides functions to produce rudimentary ASCII
18545 graphics directly in the terminal window. This package provides a basic
18546 plotting function (and equivalents of curve, density, acf and barplot) as well
18547 as a boxplot function.")
18548 (license license:lgpl3+)))
18550 (define-public r-bio3d
18557 (uri (cran-uri "bio3d" version))
18560 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18561 (properties `((upstream-name . "bio3d")))
18562 (build-system r-build-system)
18563 (inputs `(("zlib" ,zlib)))
18564 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18565 (home-page "http://thegrantlab.org/bio3d/")
18566 (synopsis "Biological structure analysis")
18568 "This package provides utilities to process, organize and explore protein
18569 structure, sequence and dynamics data. Features include the ability to read
18570 and write structure, sequence and dynamic trajectory data, perform sequence
18571 and structure database searches, data summaries, atom selection, alignment,
18572 superposition, rigid core identification, clustering, torsion analysis,
18573 distance matrix analysis, structure and sequence conservation analysis, normal
18574 mode analysis, principal component analysis of heterogeneous structure data,
18575 and correlation network analysis from normal mode and molecular dynamics data.
18576 In addition, various utility functions are provided to enable the statistical
18577 and graphical power of the R environment to work with biological sequence and
18579 (license license:gpl2+)))
18581 (define-public r-bios2cor
18583 (name "r-bios2cor")
18588 (uri (cran-uri "Bios2cor" version))
18591 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18592 (properties `((upstream-name . "Bios2cor")))
18593 (build-system r-build-system)
18595 `(("r-bigmemory" ,r-bigmemory)
18596 ("r-bio3d" ,r-bio3d)
18597 ("r-circular" ,r-circular)
18598 ("r-igraph" ,r-igraph)))
18599 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18600 (synopsis "From biological sequences and simulations to correlation analysis")
18602 "This package provides utilities for computation and analysis of
18603 correlation/covariation in multiple sequence alignments and in side chain
18604 motions during molecular dynamics simulations. Features include the
18605 computation of correlation/covariation scores using a variety of scoring
18606 functions between either sequence positions in alignments or side chain
18607 dihedral angles in molecular dynamics simulations and utilities to analyze the
18608 correlation/covariation matrix through a variety of tools including network
18609 representation and principal components analysis. In addition, several
18610 utility functions are based on the R graphical environment to provide friendly
18611 tools for help in data interpretation.")
18612 (license license:gpl2+)))
18614 ;; This package includes minified JavaScript files. When upgrading please
18615 ;; check that there are no new minified JavaScript files.
18616 (define-public r-networkd3
18618 (name "r-networkd3")
18623 (uri (cran-uri "networkD3" version))
18626 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18629 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18631 (properties `((upstream-name . "networkD3")))
18632 (build-system r-build-system)
18634 `(#:modules ((guix build utils)
18635 (guix build r-build-system)
18639 (modify-phases %standard-phases
18640 (add-after 'unpack 'process-javascript
18641 (lambda* (#:key inputs #:allow-other-keys)
18642 (with-directory-excursion "inst/htmlwidgets/lib/"
18646 `((,(assoc-ref inputs "d3.v4.js")
18647 "d3-4.5.0/d3.min.js"))))
18648 (lambda (sources targets)
18649 (for-each (lambda (source target)
18650 (format #t "Processing ~a --> ~a~%"
18652 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18653 (call-with-output-file target
18655 (dump-port minified port)))))
18656 sources targets))))
18659 `(("uglify-js" ,uglify-js)
18660 ;; NOTE: Make sure that this version of d3 is still valid when
18661 ;; upgrading the package.
18665 (uri "https://d3js.org/d3.v4.js")
18668 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18670 `(("r-htmlwidgets" ,r-htmlwidgets)
18671 ("r-igraph" ,r-igraph)
18672 ("r-magrittr" ,r-magrittr)))
18673 (home-page "https://cran.r-project.org/package=networkD3")
18674 (synopsis "D3 JavaScript network graphs from R")
18676 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18678 (license license:gpl3+)))
18680 (define-public r-aasea
18687 (uri (cran-uri "aaSEA" version))
18690 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18691 (properties `((upstream-name . "aaSEA")))
18692 (build-system r-build-system)
18694 `(("r-bios2cor" ,r-bios2cor)
18696 ("r-hmisc" ,r-hmisc)
18697 ("r-magrittr" ,r-magrittr)
18698 ("r-networkd3" ,r-networkd3)
18699 ("r-plotly" ,r-plotly)
18700 ("r-seqinr" ,r-seqinr)
18701 ("r-shiny" ,r-shiny)
18702 ("r-shinydashboard" ,r-shinydashboard)))
18703 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18704 (synopsis "Amino acid substitution effect analyzer")
18706 "Given a protein multiple sequence alignment, it is a daunting task to
18707 assess the effects of substitutions along sequence length. The aaSEA package
18708 is intended to help researchers to rapidly analyze property changes caused by
18709 single, multiple and correlated amino acid substitutions in proteins.")
18710 (license license:gpl3)))
18712 (define-public r-abacus
18719 (uri (cran-uri "ABACUS" version))
18722 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18723 (properties `((upstream-name . "ABACUS")))
18724 (build-system r-build-system)
18726 `(("r-ggplot2" ,r-ggplot2)
18727 ("r-shiny" ,r-shiny)))
18728 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18729 (synopsis "Apps-based activities for communicating and understanding statistics")
18731 "This package provides a set of Shiny apps for effective communication
18732 and understanding in statistics. The current version includes properties of
18733 normal distribution, properties of sampling distribution, one-sample z and t
18734 tests, two samples independent (unpaired) t test and analysis of variance.")
18735 (license license:gpl3)))
18737 (define-public r-abc-rap
18744 (uri (cran-uri "ABC.RAP" version))
18747 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18748 (properties `((upstream-name . "ABC.RAP")))
18749 (build-system r-build-system)
18750 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18751 (synopsis "Array-based CpG region analysis pipeline")
18753 "This package aims to identify candidate genes that are differentially
18754 methylated between cases and controls. It applies Student's t-test and delta
18755 beta analysis to identify candidate genes containing multiple CpG sites.")
18756 (license license:gpl3)))
18758 (define-public r-abcadm
18765 (uri (cran-uri "abcADM" version))
18768 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18769 (properties `((upstream-name . "abcADM")))
18770 (build-system r-build-system)
18773 ("r-rcpp" ,r-rcpp)))
18774 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18775 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18777 "This package provides tools to estimate parameters of accumulated
18778 damage (load duration) models based on failure time data under a Bayesian
18779 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18780 long-term reliability under stochastic load profiles.")
18781 (license license:gpl3)))
18783 (define-public r-rglpk
18790 (uri (cran-uri "Rglpk" version))
18793 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18794 (properties `((upstream-name . "Rglpk")))
18795 (build-system r-build-system)
18797 `(("r-slam" ,r-slam)))
18800 (home-page "https://r-forge.r-project.org/projects/rglp/")
18801 (synopsis "R interface to the GNU Linear Programming Kit")
18803 "This package provides an R interface to the GNU Linear Programming Kit,
18804 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18805 integer linear programming} (MILP) and other related problems.")
18807 (license (list license:gpl2 license:gpl3))))
18809 (define-public r-abcdefba
18811 (name "r-abcdefba")
18816 (uri (cran-uri "abcdeFBA" version))
18819 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18820 (properties `((upstream-name . "abcdeFBA")))
18821 (build-system r-build-system)
18823 `(("r-corrplot" ,r-corrplot)
18824 ("r-lattice" ,r-lattice)
18826 ("r-rglpk" ,r-rglpk)))
18827 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18828 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18830 "This package provides functions for Constraint Based Simulation using
18831 Flux Balance Analysis and informative analysis of the data generated during
18833 (license license:gpl2)))
18835 (define-public r-abcrlda
18842 (uri (cran-uri "abcrlda" version))
18845 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18846 (properties `((upstream-name . "abcrlda")))
18847 (build-system r-build-system)
18848 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18849 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18851 "This package offers methods to perform @dfn{asymptotically
18852 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18853 cost-sensitive binary classification. The bias-correction is an estimate of
18854 the bias term added to regularized discriminant analysis that minimizes the
18856 (license license:gpl3)))
18858 (define-public r-abemus
18865 (uri (cran-uri "abemus" version))
18868 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18869 (properties `((upstream-name . "abemus")))
18870 (build-system r-build-system)
18872 `(("r-data-table" ,r-data-table)))
18873 (home-page "https://cran.r-project.org/web/packages/abemus/")
18874 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18876 "This package provides an implementation of @dfn{Adaptive Base Error
18877 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18878 platform-specific genetic knowledge and empirical signal to readily detect and
18879 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18880 cell free DNA} (cfDNA).")
18881 (license license:gpl3)))
18883 ;; This package includes minified JavaScript files. When upgrading please
18884 ;; check that there are no new minified JavaScript files.
18885 (define-public r-rintrojs
18887 (name "r-rintrojs")
18892 (uri (cran-uri "rintrojs" version))
18895 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18896 (properties `((upstream-name . "rintrojs")))
18897 (build-system r-build-system)
18899 `(#:modules ((guix build utils)
18900 (guix build r-build-system)
18904 (modify-phases %standard-phases
18905 (add-after 'unpack 'process-javascript
18906 (lambda* (#:key inputs #:allow-other-keys)
18907 (with-directory-excursion "inst/javascript/introjs/"
18911 `((,(assoc-ref inputs "intro.js")
18913 (lambda (sources targets)
18914 (for-each (lambda (source target)
18915 (format #t "Processing ~a --> ~a~%"
18917 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18918 (call-with-output-file target
18920 (dump-port minified port)))))
18921 sources targets))))
18924 `(("uglify-js" ,uglify-js)
18928 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18931 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18933 `(("r-jsonlite" ,r-jsonlite)
18934 ("r-shiny" ,r-shiny)))
18935 (home-page "https://github.com/carlganz/rintrojs")
18936 (synopsis "Wrapper for the Intro.js library")
18938 "This package provides a wrapper for the @url{http://www.introjs.com,
18939 Intro.js} library. This package makes it easy to include step-by-step
18940 introductions, and clickable hints in a Shiny application. It supports both
18941 static introductions in the UI, and programmatic introductions from the
18943 (license license:agpl3+)))
18945 (define-public r-sysfonts
18947 (name "r-sysfonts")
18952 (uri (cran-uri "sysfonts" version))
18955 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18956 (properties `((upstream-name . "sysfonts")))
18957 (build-system r-build-system)
18959 `(("freetype" ,freetype)
18963 `(("pkg-config" ,pkg-config)))
18964 (home-page "https://github.com/yixuan/sysfonts")
18965 (synopsis "Loading fonts into R")
18967 "This is a package to simplify loading of system fonts and Google Fonts
18968 into R, in order to support other packages.")
18969 (license license:gpl2)))
18971 (define-public r-showtextdb
18973 (name "r-showtextdb")
18978 (uri (cran-uri "showtextdb" version))
18981 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18982 (properties `((upstream-name . "showtextdb")))
18983 (build-system r-build-system)
18985 `(("r-sysfonts" ,r-sysfonts)))
18986 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18987 (synopsis "Font files for the 'showtext' package")
18989 "This package provides font files that can be used by the @code{showtext}
18991 (license license:asl2.0)))
18993 (define-public r-showtext
18995 (name "r-showtext")
19000 (uri (cran-uri "showtext" version))
19003 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
19004 (properties `((upstream-name . "showtext")))
19005 (build-system r-build-system)
19007 `(("freetype" ,freetype)
19011 `(("r-showtextdb" ,r-showtextdb)
19012 ("r-sysfonts" ,r-sysfonts)))
19014 `(("pkg-config" ,pkg-config)
19015 ("r-knitr" ,r-knitr)))
19016 (home-page "https://github.com/yixuan/showtext")
19017 (synopsis "Using fonts more easily in R graphs")
19019 "This package aims to make it easy to use various types of
19020 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
19021 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
19022 will be converted into polygons or raster images, hence after the plot has
19023 been created, it no longer relies on the font files. No external software
19024 such as Ghostscript is needed to use this package.")
19025 (license license:asl2.0)))
19027 (define-public r-emojifont
19029 (name "r-emojifont")
19034 (uri (cran-uri "emojifont" version))
19037 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
19038 (properties `((upstream-name . "emojifont")))
19039 (build-system r-build-system)
19041 `(("r-ggplot2" ,r-ggplot2)
19042 ("r-proto" ,r-proto)
19043 ("r-showtext" ,r-showtext)
19044 ("r-sysfonts" ,r-sysfonts)))
19045 (home-page "https://guangchuangyu.github.io/emojifont")
19046 (synopsis "Emoji and Font Awesome in R graphics")
19048 "This package enables the use of emoji and the Font Awesome glyphs in
19049 both base and ggplot2 graphics.")
19050 (license license:artistic2.0)))
19052 (define-public r-abstractr
19054 (name "r-abstractr")
19059 (uri (cran-uri "abstractr" version))
19062 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19063 (properties `((upstream-name . "abstractr")))
19064 (build-system r-build-system)
19066 `(("r-colourpicker" ,r-colourpicker)
19067 ("r-emojifont" ,r-emojifont)
19068 ("r-ggplot2" ,r-ggplot2)
19069 ("r-gridextra" ,r-gridextra)
19070 ("r-rintrojs" ,r-rintrojs)
19071 ("r-shiny" ,r-shiny)
19072 ("r-shinythemes" ,r-shinythemes)))
19073 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19074 (synopsis "R-Shiny application for creating visual abstracts")
19076 "This package provides an R Shiny application to create visual abstracts
19077 for original research. A variety of user defined options and formatting are
19079 (license license:gpl3)))
19081 (define-public r-qgam
19088 (uri (cran-uri "qgam" version))
19091 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19092 (properties `((upstream-name . "qgam")))
19093 (build-system r-build-system)
19095 `(("r-doparallel" ,r-doparallel)
19098 ("r-shiny" ,r-shiny)))
19099 (native-inputs `(("r-knitr" ,r-knitr)))
19100 (home-page "https://cran.r-project.org/web/packages/qgam/")
19101 (synopsis "Smooth additive quantile regression models")
19103 "This package provides smooth additive quantile regression models, fitted
19104 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19105 the smoothing parameters are estimated automatically by marginal loss
19106 minimization, while the regression coefficients are estimated using either
19107 PIRLS or Newton algorithm. The learning rate is determined so that the
19108 Bayesian credible intervals of the estimated effects have approximately the
19109 correct coverage. The main function is @code{qgam()} which is similar to
19110 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19111 regression models.")
19112 (license license:gpl2+)))
19114 (define-public r-abtest
19121 (uri (cran-uri "abtest" version))
19124 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19125 (properties `((upstream-name . "abtest")))
19126 (build-system r-build-system)
19128 `(("r-matrix" ,r-matrix)
19129 ("r-mvtnorm" ,r-mvtnorm)
19130 ("r-plotrix" ,r-plotrix)
19132 ("r-rcolorbrewer" ,r-rcolorbrewer)
19135 ("r-truncnorm" ,r-truncnorm)))
19136 (home-page "https://cran.r-project.org/web/packages/abtest/")
19137 (synopsis "Bayesian A/B testing")
19139 "This package provides functions for Bayesian A/B testing including prior
19140 elicitation options based on Kass and Vaidyanathan (1992)
19141 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19142 (license license:gpl2+)))
19144 (define-public r-accept
19151 (uri (cran-uri "accept" version))
19154 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19155 (properties `((upstream-name . "accept")))
19156 (build-system r-build-system)
19158 `(("r-dplyr" ,r-dplyr)
19159 ("r-extrafont" ,r-extrafont)
19161 ("r-plotly" ,r-plotly)
19162 ("r-stringr" ,r-stringr)
19163 ("r-viridis" ,r-viridis)))
19164 (home-page "https://cran.r-project.org/web/packages/accept/")
19165 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19167 "This package allows clinicians to predict the rate and severity of
19168 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19169 Disease} (COPD) patients, based on the clinical prediction model published in
19170 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19171 (license license:gpl3)))
19173 (define-public r-smpracticals
19175 (name "r-smpracticals")
19180 (uri (cran-uri "SMPracticals" version))
19183 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19184 (properties `((upstream-name . "SMPracticals")))
19185 (build-system r-build-system)
19187 `(("r-ellipse" ,r-ellipse)
19190 ("r-survival" ,r-survival)))
19191 (home-page "http://statwww.epfl.ch/davison/SM/")
19192 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19194 "This package contains the datasets and a few functions for use with the
19195 practicals outlined in Appendix A of the book Statistical Models (Davison,
19196 2003, Cambridge University Press). The practicals themselves can be found at
19197 @url{http://statwww.epfl.ch/davison/SM/}.")
19198 (license license:gpl2+)))
19200 (define-public r-fgui
19207 (uri (cran-uri "fgui" version))
19210 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19211 (properties `((upstream-name . "fgui")))
19212 (build-system r-build-system)
19214 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19215 (synopsis "Create GUI for R functions")
19217 "Rapidly create a GUI for a function you created by automatically
19218 creating widgets for arguments of the function. This package automatically
19219 parses help routines for context-sensitive help to these arguments. The
19220 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19221 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19222 incorporated into the interface for greater customization for the more
19224 ;; Any version of the GPL.
19225 (license (list license:gpl2+ license:gpl3+))))
19227 (define-public r-tcltk2
19234 (uri (cran-uri "tcltk2" version))
19237 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19238 (properties `((upstream-name . "tcltk2")))
19239 (build-system r-build-system)
19243 (home-page "https://www.sciviews.org/SciViews-R")
19244 (synopsis "Tcl/Tk additions")
19246 "This package provides a series of additional Tcl commands and Tk widgets
19247 with style and various functions to supplement the tcltk package")
19248 (license license:lgpl3)))
19250 (define-public r-accrual
19257 (uri (cran-uri "accrual" version))
19260 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19261 (properties `((upstream-name . "accrual")))
19262 (build-system r-build-system)
19264 `(("r-fgui" ,r-fgui)
19265 ("r-smpracticals" ,r-smpracticals)
19266 ("r-tcltk2" ,r-tcltk2)))
19267 (home-page "https://cran.r-project.org/web/packages/accrual/")
19268 (synopsis "Bayesian accrual prediction")
19270 "Subject recruitment for medical research is challenging. Slow patient
19271 accrual leads to delay in research. Accrual monitoring during the process of
19272 recruitment is critical. Researchers need reliable tools to manage the
19273 accrual rate. This package provides an implementation of a Bayesian method
19274 that integrates researcher's experience on previous trials and data from the
19275 current study, providing reliable prediction on accrual rate for clinical
19276 studies. It provides functions for Bayesian accrual prediction which can be
19277 easily used by statisticians and clinical researchers.")
19278 (license license:gpl2)))
19280 (define-public r-accrued
19287 (uri (cran-uri "accrued" version))
19290 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19291 (properties `((upstream-name . "accrued")))
19292 (build-system r-build-system)
19293 (home-page "https://cran.r-project.org/web/packages/accrued/")
19294 (synopsis "Data quality visualization tools for partially accruing data")
19296 "This is a package for visualizing data quality of partially accruing
19298 (license license:gpl3)))
19300 (define-public r-mda
19307 (uri (cran-uri "mda" version))
19310 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19311 (properties `((upstream-name . "mda")))
19312 (build-system r-build-system)
19313 (propagated-inputs `(("r-class" ,r-class)))
19314 (native-inputs `(("gfortran" ,gfortran)))
19315 (home-page "https://cran.r-project.org/web/packages/mda/")
19316 (synopsis "Mixture and flexible discriminant analysis")
19318 "This is a package for mixture and flexible discriminant analysis,
19319 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19320 (license license:gpl2)))
19322 (define-public r-elasticnet
19324 (name "r-elasticnet")
19329 (uri (cran-uri "elasticnet" version))
19332 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19333 (properties `((upstream-name . "elasticnet")))
19334 (build-system r-build-system)
19336 `(("r-lars" ,r-lars)))
19337 (home-page "http://users.stat.umn.edu/~zouxx019/")
19338 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19340 "This package provides functions for fitting the entire solution path of
19341 the Elastic-Net and also provides functions for estimating sparse Principal
19342 Components. The Lasso solution paths can be computed by the same function.")
19343 (license license:gpl2+)))
19345 (define-public r-sparselda
19347 (name "r-sparselda")
19352 (uri (cran-uri "sparseLDA" version))
19355 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19356 (properties `((upstream-name . "sparseLDA")))
19357 (build-system r-build-system)
19359 `(("r-elasticnet" ,r-elasticnet)
19362 (home-page "https://www.imm.dtu.dk/~lkhc/")
19363 (synopsis "Sparse discriminant analysis")
19365 "This package performs sparse linear discriminant analysis for Gaussians
19366 and mixture of Gaussian models.")
19367 (license license:gpl2+)))
19369 (define-public r-accsda
19376 (uri (cran-uri "accSDA" version))
19379 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19380 (properties `((upstream-name . "accSDA")))
19381 (build-system r-build-system)
19383 `(("r-ggplot2" ,r-ggplot2)
19384 ("r-ggthemes" ,r-ggthemes)
19385 ("r-gridextra" ,r-gridextra)
19387 ("r-rarpack" ,r-rarpack)
19388 ("r-sparselda" ,r-sparselda)))
19389 (home-page "https://github.com/gumeo/accSDA/wiki")
19390 (synopsis "Accelerated sparse discriminant analysis")
19392 "This package provides an implementation of sparse linear discriminant
19393 analysis, which is a supervised classification method for multiple classes.
19394 Various novel optimization approaches to this problem are implemented
19395 including @dfn{alternating direction method of multipliers} (ADMM),
19396 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19397 Functions for performing cross validation are also supplied along with basic
19398 prediction and plotting functions. @dfn{Sparse zero variance
19399 discriminant} (SZVD) analysis is also included in the package.")
19400 (license license:gpl2+)))
19402 (define-public r-ace2fastq
19404 (name "r-ace2fastq")
19409 (uri (cran-uri "ace2fastq" version))
19412 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19413 (properties `((upstream-name . "ace2fastq")))
19414 (build-system r-build-system)
19416 `(("r-stringr" ,r-stringr)))
19417 (home-page "https://github.com/c5sire/ace2fastq")
19418 (synopsis "ACE file to FASTQ converter")
19420 "The ACE file format is used in genomics to store contigs from sequencing
19421 machines. This tools converts it into FASTQ format. Both formats contain the
19422 sequence characters and their corresponding quality information. Unlike the
19423 FASTQ file, the ACE file stores the quality values numerically. The
19424 conversion algorithm uses the standard Sanger formula. The package
19425 facilitates insertion into pipelines, and content inspection.")
19426 (license license:gpl3)))
19428 (define-public r-rngwell
19435 (uri (cran-uri "rngWELL" version))
19438 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19439 (properties `((upstream-name . "rngWELL")))
19440 (build-system r-build-system)
19441 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19442 (synopsis "Toolbox for WELL random number generators")
19444 "This is a dedicated package to WELL pseudo random generators, which were
19445 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19446 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19447 (license license:bsd-3)))
19449 (define-public r-randtoolbox
19451 (name "r-randtoolbox")
19456 (uri (cran-uri "randtoolbox" version))
19459 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19460 (properties `((upstream-name . "randtoolbox")))
19461 (build-system r-build-system)
19463 `(("r-rngwell" ,r-rngwell)))
19465 `(("gfortran" ,gfortran)))
19466 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19467 (synopsis "Toolbox for pseudo and quasi random number generation")
19469 "This package provides
19472 @item pseudo random generators, such as general linear
19473 congruential generators, multiple recursive generators and generalized
19474 feedback shift register (SF-Mersenne Twister algorithm and WELL
19477 @item quasi random generators, such as the Torus algorithm, the Sobol
19478 sequence, the Halton sequence (including the Van der Corput sequence), and
19480 @item some generator tests: the gap test, the serial test, the poker test.
19483 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19484 (license license:bsd-3)))
19486 (define-public r-lhs
19493 (uri (cran-uri "lhs" version))
19496 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19497 (properties `((upstream-name . "lhs")))
19498 (build-system r-build-system)
19499 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19501 `(("r-knitr" ,r-knitr)))
19502 (home-page "https://github.com/bertcarnell/lhs")
19503 (synopsis "Latin Hypercube Samples")
19505 "This package provides a number of methods for creating and augmenting
19506 Latin Hypercube Samples.")
19507 (license license:gpl3)))
19509 (define-public r-acebayes
19511 (name "r-acebayes")
19516 (uri (cran-uri "acebayes" version))
19519 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19520 (properties `((upstream-name . "acebayes")))
19521 (build-system r-build-system)
19523 `(("r-compare" ,r-compare)
19525 ("r-randtoolbox" ,r-randtoolbox)
19527 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19528 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19529 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19531 "Finding an optimal Bayesian experimental design involves maximizing an
19532 objective function given by the expectation of some appropriately chosen
19533 utility function with respect to the joint distribution of unknown
19534 quantities (including responses). This objective function is usually not
19535 available in closed form and the design space can be continuous and of high
19536 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19537 to maximise an approximation to the expectation of the utility function.")
19538 (license license:gpl2)))
19540 (define-public r-acet
19547 (uri (cran-uri "ACEt" version))
19550 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19551 (properties `((upstream-name . "ACEt")))
19552 (build-system r-build-system)
19557 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19558 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19559 (synopsis "Estimating dynamic heritability and twin model comparison")
19561 "This package supports twin models that are able to estimate the dynamic
19562 behaviour of the variance components in the classical twin models with respect
19563 to age using B-splines and P-splines.")
19564 (license license:gpl2+)))
19566 (define-public r-acfmperiod
19568 (name "r-acfmperiod")
19573 (uri (cran-uri "acfMPeriod" version))
19576 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19577 (properties `((upstream-name . "acfMPeriod")))
19578 (build-system r-build-system)
19580 `(("r-mass" ,r-mass)))
19581 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19582 (synopsis "Estimation of the ACF from the M-periodogram")
19584 "This package support non-robust and robust computations of the sample
19585 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19586 univariate and multivariate processes. The methodology consists in reversing
19587 the diagonalization procedure involving the periodogram or the
19588 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19589 ACOVF or the ACF as discussed in Fuller (1995)
19590 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19591 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19592 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19593 (license license:gpl2+)))
19595 (define-public r-gamlss-data
19597 (name "r-gamlss-data")
19602 (uri (cran-uri "gamlss.data" version))
19605 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19606 (properties `((upstream-name . "gamlss.data")))
19607 (build-system r-build-system)
19608 (home-page "http://www.gamlss.org/")
19609 (synopsis "GAMLSS data")
19611 "This package provides data used as examples to demonstrate GAMLSS
19613 ;; Either version of the license
19614 (license (list license:gpl2 license:gpl3))))
19616 (define-public r-gamlss
19623 (uri (cran-uri "gamlss" version))
19626 "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr"))))
19627 (properties `((upstream-name . "gamlss")))
19628 (build-system r-build-system)
19630 `(("r-gamlss-data" ,r-gamlss-data)
19631 ("r-gamlss-dist" ,r-gamlss-dist)
19634 ("r-survival" ,r-survival)))
19635 (home-page "http://www.gamlss.org/")
19636 (synopsis "Generalized additive models for location scale and shape")
19638 "This package provides functions for fitting the generalized additive
19639 models for location scale and shape introduced by Rigby and
19640 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19641 use a distributional regression approach where all the parameters of the
19642 conditional distribution of the response variable are modelled using
19643 explanatory variables.")
19644 ;; Either version of the license
19645 (license (list license:gpl2 license:gpl3))))
19647 (define-public r-acid
19654 (uri (cran-uri "acid" version))
19657 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19658 (properties `((upstream-name . "acid")))
19659 (build-system r-build-system)
19661 `(("r-gamlss" ,r-gamlss)
19662 ("r-gamlss-dist" ,r-gamlss-dist)
19663 ("r-hmisc" ,r-hmisc)))
19664 (home-page "https://cran.r-project.org/web/packages/acid/")
19665 (synopsis "Analysing conditional income distributions")
19667 "This package provides functions for the analysis of income distributions
19668 for subgroups of the population as defined by a set of variables like age,
19669 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19670 distribution as well as functions for moments, inequality measures, entropy
19671 measures and polarisation measures of income distributions. This package thus
19672 aides the analysis of income inequality by offering tools for the exploratory
19673 analysis of income distributions at the disaggregated level.")
19674 (license license:gpl3)))
19676 (define-public r-acm4r
19683 (uri (cran-uri "acm4r" version))
19686 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19687 (properties `((upstream-name . "acm4r")))
19688 (build-system r-build-system)
19689 (propagated-inputs `(("r-mass" ,r-mass)))
19690 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19691 (synopsis "Align-and-count method comparisons of RFLP data")
19693 "This is a package to compare sequence fragment lengths or molecular
19694 weights from pairs of lanes. The number of matching bands in the
19695 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19696 the align-and-count method.")
19697 ;; Any version of the GPL
19698 (license (list license:gpl2+ license:gpl3+))))
19700 (define-public r-filelock
19702 (name "r-filelock")
19707 (uri (cran-uri "filelock" version))
19710 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19711 (properties `((upstream-name . "filelock")))
19712 (build-system r-build-system)
19713 (home-page "https://github.com/r-lib/filelock")
19714 (synopsis "Portable file locking")
19716 "This library lets you place an exclusive or shared lock on a file using
19717 the appropriate system call provided by the underlying operating system.")
19718 (license license:expat)))
19720 (define-public r-filematrix
19722 (name "r-filematrix")
19727 (uri (cran-uri "filematrix" version))
19730 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19731 (properties `((upstream-name . "filematrix")))
19732 (build-system r-build-system)
19733 ;; These inputs are needed for vignettes
19735 `(("r-knitr" ,r-knitr)
19736 ("r-rmarkdown" ,r-rmarkdown)
19737 ("pandoc-citeproc" ,pandoc-citeproc)))
19738 (home-page "https://github.com/andreyshabalin/filematrix")
19739 (synopsis "File-backed matrix class with convenient read and write access")
19741 "This package provides an interface for working with large matrices
19742 stored in files, not in computer memory. It supports multiple non-character
19743 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19744 byte real values). Access to parts of the matrix is done by indexing, exactly
19745 as with usual R matrices. It supports very large matrices; the package has
19746 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19747 columns, ad allows for quick addition of extra columns to a filematrix.")
19748 (license license:lgpl3)))
19750 (define-public r-acmeeqtl
19752 (name "r-acmeeqtl")
19757 (uri (cran-uri "ACMEeqtl" version))
19760 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19761 (properties `((upstream-name . "ACMEeqtl")))
19762 (build-system r-build-system)
19764 `(("r-filematrix" ,r-filematrix)))
19765 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19766 (synopsis "Estimation of interpretable eQTL effect sizes")
19768 "This package provides a non-linear model, termed ACME, that reflects a
19769 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19770 With non-linear least-squares algorithm the maximum likelihood parameters can
19771 be estimated. The ACME model provides interpretable effect size estimates and
19772 p-values with well controlled Type-I error.")
19773 (license license:lgpl3)))
19775 (define-public r-acmer
19782 (uri (cran-uri "acmeR" version))
19785 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19786 (properties `((upstream-name . "acmeR")))
19787 (build-system r-build-system)
19788 (propagated-inputs `(("r-foreign" ,r-foreign)))
19789 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19790 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19792 "This package provides an implementation of the ACME estimator, described
19793 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19794 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19795 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19796 as carcasses age; variable bleed-through at successive searches; and interval
19797 mortality estimates. The package provides, based on search data, functions
19798 for estimating the mortality inflation factor in Frequentist and Bayesian
19800 (license license:expat)))
19802 (define-public r-r-huge
19809 (uri (cran-uri "R.huge" version))
19812 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19813 (properties `((upstream-name . "R.huge")))
19814 (build-system r-build-system)
19816 `(("r-r-methodss3" ,r-r-methodss3)
19818 ("r-r-utils" ,r-r-utils)))
19819 (home-page "https://github.com/HenrikBengtsson/R.huge")
19820 (synopsis "Methods for accessing huge amounts of data")
19822 "This is a deprecated package for accessing huge amounts of data.
19823 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19824 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19825 the @code{aroma.affymetrix} package.")
19826 (license license:lgpl2.1+)))
19828 (define-public r-r-filesets
19830 (name "r-r-filesets")
19835 (uri (cran-uri "R.filesets" version))
19838 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19839 (properties `((upstream-name . "R.filesets")))
19840 (build-system r-build-system)
19842 `(("r-digest" ,r-digest)
19843 ("r-r-cache" ,r-r-cache)
19844 ("r-r-methodss3" ,r-r-methodss3)
19846 ("r-r-utils" ,r-r-utils)))
19847 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19848 (synopsis "Easy handling of and access to files")
19850 "This package provides classes and methods to locate, setup, subset,
19851 navigate and iterate file sets, i.e. sets of files located in one or more
19852 directories on the file system. The API is designed such that these classes
19853 can be extended via inheritance to provide a richer API for special file
19854 formats. Moreover, a specific name format is defined such that filenames and
19855 directories can be considered to have full names which consists of a name
19856 followed by comma-separated tags. This adds additional flexibility to
19857 identify file sets and individual files.")
19858 (license license:lgpl2.1+)))
19860 (define-public r-r-devices
19862 (name "r-r-devices")
19867 (uri (cran-uri "R.devices" version))
19870 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19871 (properties `((upstream-name . "R.devices")))
19872 (build-system r-build-system)
19874 `(("r-base64enc" ,r-base64enc)
19875 ("r-r-methodss3" ,r-r-methodss3)
19877 ("r-r-utils" ,r-r-utils)))
19878 (home-page "https://github.com/HenrikBengtsson/R.devices")
19879 (synopsis "Unified handling of graphics devices")
19881 "This package provides functions for creating plots and image files in a
19882 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19883 Default device options as well as scales and aspect ratios are controlled in a
19884 uniform way across all device types. Switching output format requires minimal
19885 changes in code. This package is ideal for large-scale batch processing,
19886 because it will never leave open graphics devices or incomplete image files
19887 behind, even on errors or user interrupts.")
19888 (license license:lgpl2.1+)))
19890 (define-public r-acnr
19897 (uri (cran-uri "acnr" version))
19900 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19901 (properties `((upstream-name . "acnr")))
19902 (build-system r-build-system)
19903 (home-page "https://github.com/mpierrejean/acnr")
19904 (synopsis "Annotated copy-number regions")
19906 "This package provides SNP array data from different types of copy-number
19907 regions. These regions were identified manually by the authors of the package
19908 and may be used to generate realistic data sets with known truth.")
19909 (license license:lgpl2.1+)))
19911 (define-public r-acopula
19918 (uri (cran-uri "acopula" version))
19921 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19922 (properties `((upstream-name . "acopula")))
19923 (build-system r-build-system)
19924 (home-page "https://cran.r-project.org/web/packages/acopula/")
19925 (synopsis "Modelling dependence with multivariate Archimax copulas")
19927 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19928 package provides definitions of several parametric families of generator and
19929 dependence function, computes CDF and PDF, estimates parameters, tests for
19930 goodness of fit, generates random sample and checks copula properties for
19931 custom constructs. In the 2-dimensional case explicit formulas for density
19932 are used, contrary to higher dimensions when all derivatives are linearly
19933 approximated. Several non-archimax families (normal, FGM, Plackett) are
19934 provided as well.")
19935 (license license:gpl2)))
19937 (define-public r-tuner
19944 (uri (cran-uri "tuneR" version))
19947 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19948 (properties `((upstream-name . "tuneR")))
19949 (build-system r-build-system)
19950 (propagated-inputs `(("r-signal" ,r-signal)))
19951 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19952 (synopsis "Analysis of music and speech")
19954 "This is a package for the analysis of music and speech. Analyze music
19955 and speech, extract features like MFCCs, handle wave files and their
19956 representation in various ways, read MP3, read MIDI, perform steps of a
19957 transcription, ...")
19958 ;; Either of these versions.
19959 (license (list license:gpl2 license:gpl3))))
19961 (define-public r-seewave
19968 (uri (cran-uri "seewave" version))
19971 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19972 (properties `((upstream-name . "seewave")))
19973 (build-system r-build-system)
19975 `(("libsndfile" ,libsndfile)))
19977 `(("r-tuner" ,r-tuner)))
19978 (home-page "http://rug.mnhn.fr/seewave")
19979 (synopsis "Sound analysis and synthesis")
19981 "This package provides functions for analysing, manipulating, displaying,
19982 editing and synthesizing time waves (particularly sound). This package
19983 processes time analysis (oscillograms and envelopes), spectral content,
19984 resonance quality factor, entropy, cross correlation and autocorrelation,
19985 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19986 and 3D spectrograms and many other analyses.")
19987 (license license:gpl2+)))
19989 (define-public r-acousticndlcoder
19991 (name "r-acousticndlcoder")
19996 (uri (cran-uri "AcousticNDLCodeR" version))
19999 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
20001 `((upstream-name . "AcousticNDLCodeR")))
20002 (build-system r-build-system)
20004 `(("r-seewave" ,r-seewave)
20005 ("r-tuner" ,r-tuner)
20007 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
20008 (synopsis "Coding sound files for use with NDL")
20010 "Make acoustic cues to use with the R package @code{ndl}.
20011 The package implements functions used in the PLoS ONE paper \"Words from
20012 spontaneous conversational speech can be recognized with human-like accuracy
20013 by an error-driven learning algorithm that discriminates between meanings
20014 straight from smart acoustic features, bypassing the phoneme as recognition
20015 unit.\" @url{doi:10.1371/journal.pone.0174623}")
20016 (license license:gpl2+)))
20018 (define-public r-acp
20025 (uri (cran-uri "acp" version))
20028 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
20029 (properties `((upstream-name . "acp")))
20030 (build-system r-build-system)
20032 `(("r-quantmod" ,r-quantmod)
20033 ("r-tseries" ,r-tseries)))
20034 (home-page "https://cran.r-project.org/web/packages/acp/")
20035 (synopsis "Autoregressive conditional Poisson")
20037 "This package supports the analysis of count data exhibiting
20038 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
20039 model (ACP(p,q)) proposed by Heinen (2003).")
20040 (license license:gpl2)))
20042 (define-public r-ada
20049 (uri (cran-uri "ada" version))
20052 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20053 (properties `((upstream-name . "ada")))
20054 (build-system r-build-system)
20055 (propagated-inputs `(("r-rpart" ,r-rpart)))
20056 (home-page "https://cran.r-project.org/web/packages/ada/")
20057 (synopsis "Stochastic boosting")
20059 "This package provides a straightforward, well-documented, and broad
20060 boosting routine for classification, ideally suited for small to
20061 moderate-sized data sets. It performs discrete, real, and gentle boost under
20062 both exponential and logistic loss on a given data set.")
20063 ;; Any version of the GPL.
20064 (license (list license:gpl2+ license:gpl3+))))
20066 (define-public r-genalg
20073 (uri (cran-uri "genalg" version))
20076 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20077 (properties `((upstream-name . "genalg")))
20078 (build-system r-build-system)
20079 (home-page "https://github.com/egonw/genalg")
20080 (synopsis "R based genetic algorithm")
20082 "This package provides an R based genetic algorithm for binary and
20083 floating point chromosomes.")
20084 (license license:gpl2)))
20086 (define-public r-kernelfactory
20088 (name "r-kernelfactory")
20093 (uri (cran-uri "kernelFactory" version))
20096 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20097 (properties `((upstream-name . "kernelFactory")))
20098 (build-system r-build-system)
20101 ("r-genalg" ,r-genalg)
20102 ("r-kernlab" ,r-kernlab)
20103 ("r-randomforest" ,r-randomforest)))
20104 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20105 (synopsis "Ensemble of kernel machines")
20107 "Kernel factory is an ensemble method where each base classifier (random
20108 forest) is fit on the kernel matrix of a subset of the training data.")
20109 (license license:gpl2+)))
20111 (define-public r-dummies
20118 (uri (cran-uri "dummies" version))
20121 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20122 (properties `((upstream-name . "dummies")))
20123 (build-system r-build-system)
20124 (home-page "https://decisionpatterns.com")
20125 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20127 "This package lets you expand factors, characters and other eligible
20128 classes into dummy/indicator variables.")
20129 (license license:gpl2+)))
20131 (define-public r-acrm
20138 (uri (cran-uri "aCRM" version))
20141 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20142 (properties `((upstream-name . "aCRM")))
20143 (build-system r-build-system)
20146 ("r-dummies" ,r-dummies)
20147 ("r-kernelfactory" ,r-kernelfactory)
20148 ("r-randomforest" ,r-randomforest)))
20149 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20150 (synopsis "Convenience functions for analytical customer relationship management")
20152 "This package provides convenience functions for data preparation and
20153 modeling often used in @dfn{analytical customer relationship
20154 management} (aCRM).")
20155 (license license:gpl2+)))
20157 (define-public r-treeclust
20159 (name "r-treeclust")
20164 (uri (cran-uri "treeClust" version))
20167 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20168 (properties `((upstream-name . "treeClust")))
20169 (build-system r-build-system)
20171 `(("r-cluster" ,r-cluster)
20172 ("r-rpart" ,r-rpart)))
20173 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20174 (synopsis "Cluster distances through trees")
20176 "This package provides tools to create a measure of inter-point
20177 dissimilarity useful for clustering mixed data, and, optionally, perform the
20179 (license license:gpl2+)))
20181 (define-public r-acrosstic
20183 (name "r-acrosstic")
20188 (uri (cran-uri "AcrossTic" version))
20191 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20192 (properties `((upstream-name . "AcrossTic")))
20193 (build-system r-build-system)
20195 `(("r-lpsolve" ,r-lpsolve)
20196 ("r-treeclust" ,r-treeclust)))
20197 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20198 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20200 "This is a package for constructing minimum-cost regular spanning
20201 subgraph as part of a non-parametric two-sample test for equality of
20203 (license license:gpl2+)))
20205 (define-public r-acrt
20212 (uri (cran-uri "acrt" version))
20215 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20216 (properties `((upstream-name . "acrt")))
20217 (build-system r-build-system)
20219 `(("r-rcpp" ,r-rcpp)
20220 ("r-rcppeigen" ,r-rcppeigen)
20221 ("r-sandwich" ,r-sandwich)))
20222 (home-page "https://cran.r-project.org/web/packages/acrt/")
20223 (synopsis "Autocorrelation robust testing")
20225 "This package provides functions for testing affine hypotheses on the
20226 regression coefficient vector in regression models with autocorrelated
20228 (license license:gpl2)))
20230 (define-public r-acs
20237 (uri (cran-uri "acs" version))
20240 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20241 (properties `((upstream-name . "acs")))
20242 (build-system r-build-system)
20244 `(("r-httr" ,r-httr)
20247 ("r-stringr" ,r-stringr)
20249 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20250 (synopsis "Work with data from the US Census")
20252 "This package provides a general toolkit for downloading, managing,
20253 analyzing, and presenting data from the
20254 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20255 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20256 American Community Survey (ACS). Confidence intervals provided with ACS data
20257 are converted to standard errors to be bundled with estimates in complex
20258 @code{acs} objects. The package provides new methods to conduct standard
20259 operations on @code{acs} objects and present/plot data in statistically
20260 appropriate ways.")
20261 (license license:gpl3)))
20263 (define-public r-acss-data
20265 (name "r-acss-data")
20270 (uri (cran-uri "acss.data" version))
20273 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20274 (properties `((upstream-name . "acss.data")))
20275 (build-system r-build-system)
20276 (home-page "http://complexitycalculator.com/methodology.html")
20277 (synopsis "Data for algorithmic complexity of short strings")
20279 "This is a data only package providing the algorithmic complexity of
20280 short strings, computed using the coding theorem method. For a given set of
20281 symbols in a string, all possible or a large number of random samples of
20282 Turing machines with a given number of states (e.g., 5) and number of symbols
20283 corresponding to the number of symbols in the strings were simulated until
20284 they reached a halting state or failed to end. This package contains data on
20285 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20286 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20287 distribution of the halting states.")
20288 (license license:gpl2+)))
20290 (define-public r-acss
20297 (uri (cran-uri "acss" version))
20300 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20301 (properties `((upstream-name . "acss")))
20302 (build-system r-build-system)
20304 `(("r-acss-data" ,r-acss-data)
20306 (home-page "http://complexitycalculator.com/methodology.html")
20307 (synopsis "Algorithmic complexity for short strings")
20309 "The main purpose of this package is to provide the algorithmic
20310 complexity for short strings, an approximation of the Kolmogorov Complexity of
20311 a short string using the coding theorem method. While the database containing
20312 the complexity is provided in the data only package @code{acss.data}, this
20313 package provides functions accessing the data such as @code{prob_random}
20314 returning the posterior probability that a given string was produced by a
20315 random process. In addition, two traditional (but problematic) measures of
20316 complexity are also provided: entropy and change complexity.")
20317 (license license:gpl2+)))
20319 (define-public r-acswr
20326 (uri (cran-uri "ACSWR" version))
20329 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20330 (properties `((upstream-name . "ACSWR")))
20331 (build-system r-build-system)
20333 `(("r-mass" ,r-mass)))
20334 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20335 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20337 "This is a companion package for the book \"A Course in Statistics with
20338 R\" (ISBN 978-1-119-15272-9.)")
20339 (license license:gpl2)))
20341 (define-public r-alabama
20344 (version "2015.3-1")
20348 (uri (cran-uri "alabama" version))
20351 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20352 (properties `((upstream-name . "alabama")))
20353 (build-system r-build-system)
20354 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20355 (home-page "https://cran.r-project.org/web/packages/alabama/")
20356 (synopsis "Constrained nonlinear optimization")
20358 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20359 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20360 constraints. Linear or nonlinear equality and inequality constraints are
20362 (license license:gpl2+)))
20364 (define-public r-gdina
20371 (uri (cran-uri "GDINA" version))
20374 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20375 (properties `((upstream-name . "GDINA")))
20376 (build-system r-build-system)
20378 `(("r-alabama" ,r-alabama)
20379 ("r-ggplot2" ,r-ggplot2)
20381 ("r-nloptr" ,r-nloptr)
20382 ("r-numderiv" ,r-numderiv)
20384 ("r-rcpparmadillo" ,r-rcpparmadillo)
20385 ("r-rsolnp" ,r-rsolnp)
20386 ("r-shiny" ,r-shiny)
20387 ("r-shinydashboard" ,r-shinydashboard)))
20389 `(("r-knitr" ,r-knitr)))
20390 (home-page "https://github.com/Wenchao-Ma/GDINA")
20391 (synopsis "Generalized DINA model framework")
20393 "This package provides a set of psychometric tools for cognitive
20394 diagnosis modeling based on the generalized deterministic inputs, noisy and
20395 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20396 and its extensions, including the sequential G-DINA model by Ma and de la
20397 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20398 polytomous G-DINA model by Chen and de la Torre
20399 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20400 distribution can be independent, saturated, higher-order, loglinear smoothed
20401 or structured. Q-matrix validation, item and model fit statistics, model
20402 comparison at test and item level and differential item functioning can also
20403 be conducted. A graphical user interface is also provided.")
20404 (license license:gpl3)))
20406 (define-public r-actcd
20413 (uri (cran-uri "ACTCD" version))
20416 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20417 (properties `((upstream-name . "ACTCD")))
20418 (build-system r-build-system)
20420 `(("r-gdina" ,r-gdina)
20421 ("r-r-methodss3" ,r-r-methodss3)))
20423 `(("gfortran" ,gfortran)))
20424 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20425 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20427 "This is a package supporting cluster analysis for cognitive diagnosis
20428 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20429 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20430 sum-scores, cluster analysis techniques can be used to classify examinees into
20431 latent classes based on their attribute patterns. In addition to the
20432 algorithms used to classify data, three labeling approaches are proposed to
20433 label clusters so that examinees' attribute profiles can be obtained.")
20434 (license license:gpl2+)))
20436 (define-public r-ineq
20443 (uri (cran-uri "ineq" version))
20446 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20447 (properties `((upstream-name . "ineq")))
20448 (build-system r-build-system)
20449 (home-page "https://cran.r-project.org/web/packages/ineq/")
20450 (synopsis "Measuring inequality, concentration, and poverty")
20452 "This package provides tools for measuring inequality, concentration, and
20453 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20454 ;; Either of these two versions.
20455 (license (list license:gpl2 license:gpl3))))
20457 (define-public r-actfrag
20464 (uri (cran-uri "ActFrag" version))
20467 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20468 (properties `((upstream-name . "ActFrag")))
20469 (build-system r-build-system)
20471 `(("r-accelerometry" ,r-accelerometry)
20472 ("r-dplyr" ,r-dplyr)
20474 ("r-survival" ,r-survival)
20475 ("r-tidyr" ,r-tidyr)))
20476 (home-page "https://github.com/junruidi/ActFrag")
20477 (synopsis "Activity fragmentation metrics extraction")
20479 "This package provides functions to extract commonly used fragmentation
20480 metrics to quantify time accumulation strategies based on minute level
20481 actigraphy-measured activity counts data.")
20482 (license license:gpl3)))
20484 (define-public r-ash
20491 (uri (cran-uri "ash" version))
20494 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20495 (properties `((upstream-name . "ash")))
20496 (build-system r-build-system)
20497 (native-inputs `(("gfortran" ,gfortran)))
20498 (home-page "https://cran.r-project.org/web/packages/ash/")
20499 (synopsis "David Scott's ASH routines")
20501 "This package provides David Scott's ASH routines ported from S-PLUS to
20503 (license license:gpl2+)))
20505 (define-public r-hdrcde
20512 (uri (cran-uri "hdrcde" version))
20515 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20516 (properties `((upstream-name . "hdrcde")))
20517 (build-system r-build-system)
20520 ("r-ggplot2" ,r-ggplot2)
20521 ("r-kernsmooth" ,r-kernsmooth)
20523 ("r-locfit" ,r-locfit)
20524 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20525 (native-inputs `(("gfortran" ,gfortran)))
20526 (home-page "http://pkg.robjhyndman.com/hdrcde")
20527 (synopsis "Highest density regions and conditional density estimation")
20529 "This is a package for the computation of highest density regions in one
20530 and two dimensions, kernel estimation of univariate density functions
20531 conditional on one covariate, and multimodal regression.")
20532 (license license:gpl3)))
20534 (define-public r-rainbow
20541 (uri (cran-uri "rainbow" version))
20544 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20545 (properties `((upstream-name . "rainbow")))
20546 (build-system r-build-system)
20548 `(("r-cluster" ,r-cluster)
20549 ("r-colorspace" ,r-colorspace)
20550 ("r-hdrcde" ,r-hdrcde)
20553 ("r-pcapp" ,r-pcapp)))
20554 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20555 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20557 "This is a package for visualizing functional data and identifying
20558 functional outliers with bagplots, boxplots and rainbow plots.")
20559 (license license:gpl3)))
20561 (define-public r-fds
20568 (uri (cran-uri "fds" version))
20571 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20572 (properties `((upstream-name . "fds")))
20573 (build-system r-build-system)
20575 `(("r-rainbow" ,r-rainbow)
20576 ("r-rcurl" ,r-rcurl)))
20577 (home-page "https://cran.r-project.org/web/packages/fds/")
20578 (synopsis "Functional data sets")
20579 (description "This package contains a list of functional time series,
20580 sliced functional time series, and functional data sets. Functional time
20581 series is a special type of functional data observed over time. Sliced
20582 functional time series is a special type of functional time series with a time
20583 variable observed over time.")
20584 (license license:gpl2+)))
20586 (define-public r-fda
20593 (uri (cran-uri "fda" version))
20596 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20597 (properties `((upstream-name . "fda")))
20598 (build-system r-build-system)
20601 ("r-matrix" ,r-matrix)))
20602 (home-page "https://www.functionaldata.org")
20603 (synopsis "Functional data analysis")
20605 "These functions were developed to support functional data analysis as
20606 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20607 Analysis. The package includes data sets and script files working many
20609 (license license:gpl2+)))
20611 (define-public r-actigraphy
20613 (name "r-actigraphy")
20618 (uri (cran-uri "Actigraphy" version))
20621 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20622 (properties `((upstream-name . "Actigraphy")))
20623 (build-system r-build-system)
20625 `(("r-fda" ,r-fda)))
20626 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20627 (synopsis "Actigraphy data analysis")
20629 "This package provides tools for functional linear modeling and analysis
20630 of actigraphy data.")
20631 (license license:asl2.0)))
20633 (define-public r-activedriver
20635 (name "r-activedriver")
20640 (uri (cran-uri "ActiveDriver" version))
20643 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20644 (properties `((upstream-name . "ActiveDriver")))
20645 (build-system r-build-system)
20647 `(("r-mass" ,r-mass)))
20648 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20649 (synopsis "Tools for finding cancer driver proteins")
20651 "This package provides a mutation analysis tool that discovers cancer
20652 driver genes with frequent mutations in protein signalling sites such as
20653 post-translational modifications (phosphorylation, ubiquitination, etc). The
20654 Poisson generalized linear regression model identifies genes where cancer
20655 mutations in signalling sites are more frequent than expected from the
20656 sequence of the entire gene. Integration of mutations with signalling
20657 information helps find new driver genes and propose candidate mechanisms to
20659 (license license:gpl2+)))
20661 (define-public r-activitycounts
20663 (name "r-activitycounts")
20668 (uri (cran-uri "activityCounts" version))
20671 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20673 `((upstream-name . "activityCounts")))
20674 (build-system r-build-system)
20676 `(("r-lubridate" ,r-lubridate)
20677 ("r-magrittr" ,r-magrittr)
20678 ("r-seewave" ,r-seewave)
20679 ("r-signal" ,r-signal)
20680 ("r-tibble" ,r-tibble)))
20681 (home-page "https://github.com/walkabillylab/activityCounts")
20682 (synopsis "Generate ActiLife counts")
20684 "ActiLife generates activity counts from data collected by Actigraph
20685 accelerometers. Actigraph is one of the most common research-grade
20686 accelerometers. There is considerable research validating and developing
20687 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20688 counts are proprietary and difficult to implement if researchers use different
20689 accelerometer brands. The code creates ActiLife counts from raw acceleration
20690 data for different accelerometer brands.")
20691 (license license:gpl3)))
20693 (define-public r-activityindex
20695 (name "r-activityindex")
20700 (uri (cran-uri "ActivityIndex" version))
20703 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20704 (properties `((upstream-name . "ActivityIndex")))
20705 (build-system r-build-system)
20707 `(("r-data-table" ,r-data-table)
20708 ("r-matrixstats" ,r-matrixstats)
20709 ("r-r-utils" ,r-r-utils)))
20711 `(("r-knitr" ,r-knitr)))
20712 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20713 (synopsis "Activity Index calculation using raw accelerometry data")
20715 "This is a package to read raw accelerometry from GT3X+ accelerometry
20716 data and plain table data to calculate the Activity Index from Bai et
20717 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20718 (license license:gpl3)))
20720 (define-public r-activpal
20722 (name "r-activpal")
20727 (uri (cran-uri "activPAL" version))
20730 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20731 (properties `((upstream-name . "activPAL")))
20732 (build-system r-build-system)
20734 `(("r-devtools" ,r-devtools)
20735 ("r-dplyr" ,r-dplyr)
20736 ("r-ggplot2" ,r-ggplot2)
20737 ("r-lubridate" ,r-lubridate)
20738 ("r-magrittr" ,r-magrittr)
20739 ("r-tidyr" ,r-tidyr)))
20740 (home-page "https://cran.r-project.org/web/packages/activPAL")
20741 (synopsis "Processing and chart generation from activPAL events files")
20743 "This package contains functions to generate pre-defined summary
20744 statistics from activPAL events files. The package also contains functions to
20745 produce informative graphics that visualize physical activity behaviour and
20746 trends. This includes generating graphs that align physical activity
20747 behaviour with additional time based observations described by other data
20748 sets, such as sleep diaries and continuous glucose monitoring data.")
20749 (license license:gpl3)))
20751 (define-public r-activpalprocessing
20753 (name "r-activpalprocessing")
20758 (uri (cran-uri "activpalProcessing" version))
20761 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20763 `((upstream-name . "activpalProcessing")))
20764 (build-system r-build-system)
20766 `(("r-chron" ,r-chron)))
20767 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20768 (synopsis "Process activPAL events files")
20770 "This package performs estimation of physical activity and sedentary
20771 behavior variables from activPAL events files.")
20772 ;; Either version of the GPL.
20773 (license (list license:gpl2 license:gpl3))))
20775 (define-public r-actogrammr
20777 (name "r-actogrammr")
20782 (uri (cran-uri "actogrammr" version))
20785 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20786 (properties `((upstream-name . "actogrammr")))
20787 (build-system r-build-system)
20789 `(("r-dplyr" ,r-dplyr)
20790 ("r-ggplot2" ,r-ggplot2)
20791 ("r-lubridate" ,r-lubridate)
20792 ("r-readr" ,r-readr)
20793 ("r-tidyr" ,r-tidyr)))
20794 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20795 (synopsis "Read in activity data and plot actograms")
20797 "Read in activity measurements from standard file formats used by
20798 circadian rhythm researchers, currently only ClockLab format, and process and
20799 plot the data. The central type of plot is the actogram, as first described
20800 in \"Activity and distribution of certain wild mice in relation to biotic
20801 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20802 (license license:gpl3)))
20804 (define-public r-expint
20811 (uri (cran-uri "expint" version))
20814 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20815 (properties `((upstream-name . "expint")))
20816 (build-system r-build-system)
20817 (home-page "https://gitlab.com/vigou3/expint")
20818 (synopsis "Exponential integral and incomplete Gamma function")
20820 "This package provides the exponential integrals @code{E_1(x)},
20821 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20822 function @code{G(a, x)} defined for negative values of its first argument.
20823 The package also gives easy access to the underlying C routines through an
20824 API; see the package vignette for details.")
20825 (license license:gpl2+)))
20827 (define-public r-actuar
20834 (uri (cran-uri "actuar" version))
20837 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20838 (properties `((upstream-name . "actuar")))
20839 (build-system r-build-system)
20840 (propagated-inputs `(("r-expint" ,r-expint)))
20841 (home-page "https://gitlab.com/vigou3/actuar")
20842 (synopsis "Actuarial functions and heavy tailed distributions")
20844 "This package provides functions and data sets for actuarial science:
20845 modeling of loss distributions; risk theory and ruin theory; simulation of
20846 compound models, discrete mixtures and compound hierarchical models;
20847 credibility theory. It boasts support for many additional probability
20848 distributions to model insurance loss amounts and loss frequency: 19
20849 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20850 distribution; zero-truncated and zero-modified extensions of the standard
20851 discrete distributions. It also supports phase-type distributions commonly
20852 used to compute ruin probabilities.")
20853 (license license:gpl2+)))
20855 (define-public r-bmp
20862 (uri (cran-uri "bmp" version))
20865 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20866 (properties `((upstream-name . "bmp")))
20867 (build-system r-build-system)
20868 (home-page "https://cran.r-project.org/web/packages/bmp/")
20869 (synopsis "Read Bitmap (BMP) images")
20871 "This package provides pure R tools to read BMP format images. It is
20872 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20873 (license license:gpl2+)))
20875 (define-public r-readbitmap
20877 (name "r-readbitmap")
20882 (uri (cran-uri "readbitmap" version))
20885 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20886 (properties `((upstream-name . "readbitmap")))
20887 (build-system r-build-system)
20889 `(("libjpeg" ,libjpeg-turbo)
20890 ("libpng" ,libpng)))
20895 ("r-tiff" ,r-tiff)))
20896 (home-page "https://github.com/jefferis/readbitmap")
20897 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20899 "This package provides tools to identify and read BMP, JPEG, PNG, and
20900 TIFF format bitmap images. Identification defaults to the use of the magic
20901 number embedded in the file rather than the file extension.")
20902 (license license:gpl2+)))
20904 (define-public r-imager
20911 (uri (cran-uri "imager" version))
20914 "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd"))))
20915 (properties `((upstream-name . "imager")))
20916 (build-system r-build-system)
20919 ("libtiff" ,libtiff)
20923 `(("r-downloader" ,r-downloader)
20924 ("r-igraph" ,r-igraph)
20926 ("r-magrittr" ,r-magrittr)
20928 ("r-purrr" ,r-purrr)
20930 ("r-readbitmap" ,r-readbitmap)
20931 ("r-stringr" ,r-stringr)))
20933 `(("pkg-config" ,pkg-config)
20934 ("r-knitr" ,r-knitr)))
20935 (home-page "https://dahtah.github.io/imager/")
20936 (synopsis "Image processing library")
20938 "This is a package for fast image processing for images in up to 4
20939 dimensions (two spatial dimensions, one time/depth dimension, one color
20940 dimension). It provides most traditional image processing tools (filtering,
20941 morphology, transformations, etc.) as well as various functions for easily
20942 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20943 simple, modern C++ library for image processing.")
20944 (license license:lgpl3)))
20946 (define-public r-acuityview
20948 (name "r-acuityview")
20953 (uri (cran-uri "AcuityView" version))
20956 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20957 (properties `((upstream-name . "AcuityView")))
20958 (build-system r-build-system)
20960 `(("r-fftwtools" ,r-fftwtools)
20961 ("r-imager" ,r-imager)
20962 ("r-plotrix" ,r-plotrix)))
20963 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20964 (synopsis "Display scenes as seen by an animal with less acute vision")
20966 "This package provides a simple method for representing a visual scene as
20967 it may be seen by an animal with less acute vision.")
20968 (license license:gpl2+)))
20970 (define-public r-caret
20977 (uri (cran-uri "caret" version))
20980 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20981 (build-system r-build-system)
20983 `(("r-foreach" ,r-foreach)
20984 ("r-ggplot2" ,r-ggplot2)
20985 ("r-lattice" ,r-lattice)
20986 ("r-modelmetrics" ,r-modelmetrics)
20990 ("r-recipes" ,r-recipes)
20991 ("r-reshape2" ,r-reshape2)
20992 ("r-withr" ,r-withr)))
20994 `(("r-knitr" ,r-knitr)))
20995 (home-page "https://github.com/topepo/caret")
20996 (synopsis "Classification and regression training")
20998 "This package provides miscellaneous functions for training and plotting
20999 classification and regression models.")
21000 (license license:gpl2+)))
21002 (define-public r-adabag
21009 (uri (cran-uri "adabag" version))
21012 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
21013 (properties `((upstream-name . "adabag")))
21014 (build-system r-build-system)
21016 `(("r-caret" ,r-caret)
21017 ("r-doparallel" ,r-doparallel)
21018 ("r-foreach" ,r-foreach)
21019 ("r-rpart" ,r-rpart)))
21020 (home-page "https://cran.r-project.org/web/packages/adabag/")
21021 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
21023 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
21024 Breiman's Bagging algorithm using classification trees as individual
21025 classifiers. Once these classifiers have been trained, they can be used to
21026 predict on new data. Also, cross validation estimation of the error can be
21028 (license license:gpl2+)))
21030 (define-public r-adagio
21037 (uri (cran-uri "adagio" version))
21040 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21041 (properties `((upstream-name . "adagio")))
21042 (build-system r-build-system)
21043 (native-inputs `(("gfortran" ,gfortran)))
21044 (home-page "https://cran.r-project.org/web/packages/adagio/")
21045 (synopsis "Discrete and global optimization routines")
21047 "This package provides methods and algorithms for discrete optimization,
21048 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21049 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21051 (license license:gpl3+)))
21053 (define-public r-univoutl
21055 (name "r-univoutl")
21060 (uri (cran-uri "univOutl" version))
21063 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21064 (properties `((upstream-name . "univOutl")))
21065 (build-system r-build-system)
21067 `(("r-hmisc" ,r-hmisc)
21068 ("r-robustbase" ,r-robustbase)))
21069 (home-page "https://github.com/marcellodo/univOutl")
21070 (synopsis "Detection of univariate outliers")
21072 "This package provides well-known outlier detection techniques in the
21073 univariate case. Methods to deal with skewed distribution are included too.
21074 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21075 historical data is implemented as well. When available, survey weights can be
21076 used in outliers detection.")
21077 (license license:gpl2+)))
21079 (define-public r-tolerance
21081 (name "r-tolerance")
21086 (uri (cran-uri "tolerance" version))
21089 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21090 (properties `((upstream-name . "tolerance")))
21091 (build-system r-build-system)
21093 `(("r-mass" ,r-mass)
21095 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21096 (synopsis "Statistical tolerance intervals and regions")
21098 "This package provides functions for estimating tolerance
21099 limits (intervals) for various univariate distributions (binomial, Cauchy,
21100 discrete Pareto, exponential, two-parameter exponential, extreme value,
21101 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21102 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21103 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21104 nonparametric tolerance intervals, tolerance bands for regression
21105 settings (linear regression, nonlinear regression, nonparametric regression,
21106 and multivariate regression), and analysis of variance tolerance intervals.
21107 Visualizations are also available for most of these settings.")
21108 (license license:gpl2+)))
21110 (define-public r-additivitytests
21112 (name "r-additivitytests")
21117 (uri (cran-uri "additivityTests" version))
21120 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21122 `((upstream-name . "additivityTests")))
21123 (build-system r-build-system)
21124 (home-page "https://github.com/simecek/additivityTests")
21125 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21127 "This package provides an implementation of the Tukey, Mandel,
21128 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21129 (license license:gpl3)))
21131 (define-public r-flexclust
21133 (name "r-flexclust")
21138 (uri (cran-uri "flexclust" version))
21141 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21142 (properties `((upstream-name . "flexclust")))
21143 (build-system r-build-system)
21145 `(("r-class" ,r-class)
21146 ("r-lattice" ,r-lattice)
21147 ("r-modeltools" ,r-modeltools)))
21148 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21149 (synopsis "Flexible cluster algorithms")
21151 "The main function @code{kcca} implements a general framework for
21152 k-centroids cluster analysis supporting arbitrary distance measures and
21153 centroid computation. Further cluster methods include hard competitive
21154 learning, neural gas, and QT clustering. There are numerous visualization
21155 methods for cluster results (neighborhood graphs, convex cluster hulls,
21156 barcharts of centroids, ...), and bootstrap methods for the analysis of
21157 cluster stability.")
21158 (license license:gpl2)))
21160 (define-public r-biclust
21167 (uri (cran-uri "biclust" version))
21170 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21171 (properties `((upstream-name . "biclust")))
21172 (build-system r-build-system)
21174 `(("r-additivitytests" ,r-additivitytests)
21175 ("r-colorspace" ,r-colorspace)
21176 ("r-flexclust" ,r-flexclust)
21177 ("r-ggplot2" ,r-ggplot2)
21178 ("r-lattice" ,r-lattice)
21180 ("r-tidyr" ,r-tidyr)))
21181 (home-page "https://cran.r-project.org/web/packages/biclust/")
21182 (synopsis "BiCluster algorithms")
21184 "The main function @code{biclust()} provides several algorithms to find
21185 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21186 In addition, the package provides methods for data
21187 preprocessing (normalization and discretization), visualization, and
21188 validation of bicluster solutions.")
21189 (license license:gpl3)))
21191 (define-public r-icge
21198 (uri (cran-uri "ICGE" version))
21201 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21202 (properties `((upstream-name . "ICGE")))
21203 (build-system r-build-system)
21205 `(("r-cluster" ,r-cluster)
21206 ("r-mass" ,r-mass)))
21207 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21208 (synopsis "Cluster estimation and identification of atypical units")
21210 "ICGE is a package that helps to estimate the number of real clusters in
21211 data as well as to identify atypical units. The underlying methods are based
21212 on distances rather than on unit x variables.")
21213 (license license:gpl2+)))
21215 (define-public r-depth
21218 (version "2.1-1.1")
21222 (uri (cran-uri "depth" version))
21225 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21226 (properties `((upstream-name . "depth")))
21227 (build-system r-build-system)
21229 `(("r-abind" ,r-abind)
21230 ("r-circular" ,r-circular)
21233 `(("gfortran" ,gfortran)))
21234 (home-page "https://cran.r-project.org/web/packages/depth/")
21235 (synopsis "Nonparametric depth functions for multivariate analysis")
21237 "This package provides tools for depth functions methodology applied to
21238 multivariate analysis. Besides allowing calculation of depth values and
21239 depth-based location estimators, the package includes functions or drawing
21240 contour plots and perspective plots of depth functions. Euclidean and
21241 spherical depths are supported.")
21242 (license license:gpl2)))
21244 (define-public r-archetypes
21246 (name "r-archetypes")
21247 (version "2.2-0.1")
21251 (uri (cran-uri "archetypes" version))
21254 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21255 (properties `((upstream-name . "archetypes")))
21256 (build-system r-build-system)
21258 `(("r-modeltools" ,r-modeltools)
21259 ("r-nnls" ,r-nnls)))
21260 (home-page "https://cran.r-project.org/web/packages/archetypes")
21261 (synopsis "Archetypal analysis")
21263 "The main function @code{archetypes} implements a framework for
21264 archetypal analysis supporting arbitrary problem solving mechanisms for the
21265 different conceptual parts of the algorithm.")
21266 (license license:gpl2+)))
21268 (define-public r-shapes
21275 (uri (cran-uri "shapes" version))
21278 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21279 (properties `((upstream-name . "shapes")))
21280 (build-system r-build-system)
21282 `(("r-mass" ,r-mass)
21283 ("r-minpack-lm" ,r-minpack-lm)
21285 ("r-scatterplot3d" ,r-scatterplot3d)))
21286 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21287 (synopsis "Statistical shape analysis")
21289 "This package provides routines for the statistical analysis of landmark
21290 shapes, including Procrustes analysis, graphical displays, principal
21291 components analysis, permutation and bootstrap tests, thin-plate spline
21292 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21293 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21294 Edition), John Wiley and Sons.")
21295 (license license:gpl2)))
21297 (define-public r-anthropometry
21299 (name "r-anthropometry")
21304 (uri (cran-uri "Anthropometry" version))
21307 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21308 (properties `((upstream-name . "Anthropometry")))
21309 (build-system r-build-system)
21311 `(("r-archetypes" ,r-archetypes)
21312 ("r-biclust" ,r-biclust)
21313 ("r-cluster" ,r-cluster)
21314 ("r-depth" ,r-depth)
21319 ("r-shapes" ,r-shapes)))
21321 `(("r-knitr" ,r-knitr)))
21322 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21323 (synopsis "Statistical methods for anthropometric data")
21325 "This package provides statistical methods especially developed to
21326 analyze anthropometric data. These methods are aimed at providing effective
21327 solutions to some commons problems related to Ergonomics and Anthropometry.
21328 They are based on clustering, the statistical concept of data depth,
21329 statistical shape analysis and archetypal analysis.")
21330 (license license:gpl2+)))
21332 (define-public r-adamethods
21334 (name "r-adamethods")
21339 (uri (cran-uri "adamethods" version))
21342 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21343 (properties `((upstream-name . "adamethods")))
21344 (build-system r-build-system)
21346 `(("r-anthropometry" ,r-anthropometry)
21347 ("r-archetypes" ,r-archetypes)
21349 ("r-foreach" ,r-foreach)
21351 ("r-tolerance" ,r-tolerance)
21352 ("r-univoutl" ,r-univoutl)))
21353 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21354 (synopsis "Archetypoid algorithms and anomaly detection")
21356 "This package is a collection of several algorithms to obtain
21357 archetypoids with small and large databases and with both classical
21358 multivariate data and functional data (univariate and multivariate). Some of
21359 these algorithms also detect anomalies (outliers).")
21360 (license license:gpl2+)))
21362 (define-public r-idpmisc
21369 (uri (cran-uri "IDPmisc" version))
21372 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21373 (properties `((upstream-name . "IDPmisc")))
21374 (build-system r-build-system)
21376 `(("r-lattice" ,r-lattice)))
21377 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21378 (synopsis "Functions for data analyses and visualization")
21380 "This package provides different high-level graphics functions for
21381 displaying large datasets, displaying circular data in a very flexible way,
21382 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21383 2D-plots, creating figures with differently colored margin and plot region.
21384 In addition, the package contains auxiliary functions for data manipulation
21385 like omitting observations with irregular values or selecting data by logical
21386 vectors, which include NAs. Other functions are especially useful in
21387 spectroscopy and analyses of environmental data: robust baseline fitting,
21388 finding peaks in spectra, converting humidity measures.")
21389 (license license:gpl3+)))
21391 (define-public r-qqman
21398 (uri (cran-uri "qqman" version))
21401 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21402 (properties `((upstream-name . "qqman")))
21403 (build-system r-build-system)
21405 `(("r-calibrate" ,r-calibrate)))
21406 (home-page "https://cran.r-project.org/web/packages/qqman/")
21407 (synopsis "Q-Q and Manhattan plots for GWAS data")
21409 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21410 from PLINK results.")
21411 (license license:gpl3)))
21413 (define-public r-ggplot-multistats
21415 (name "r-ggplot-multistats")
21420 (uri (cran-uri "ggplot.multistats" version))
21423 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21425 `((upstream-name . "ggplot.multistats")))
21426 (build-system r-build-system)
21428 `(("r-ggplot2" ,r-ggplot2)
21429 ("r-hexbin" ,r-hexbin)
21430 ("r-rlang" ,r-rlang)
21431 ("r-scales" ,r-scales)))
21432 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21433 (synopsis "Multiple summary statistics for binned stats/geometries")
21435 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21436 which functions similar to its singular form, but allows the use of multiple
21437 statistics per bin. Those statistics can be mapped to multiple bin
21439 (license license:gpl3)))
21441 (define-public r-knn-covertree
21443 (name "r-knn-covertree")
21448 (uri (cran-uri "knn.covertree" version))
21451 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21452 (properties `((upstream-name . "knn.covertree")))
21453 (build-system r-build-system)
21455 `(("r-matrix" ,r-matrix)
21457 ("r-rcppeigen" ,r-rcppeigen)))
21458 (home-page "https://github.com/flying-sheep/knn.covertree")
21459 (synopsis "Accurate kNN Implementation with multiple distance measures")
21461 "Similarly to the FNN package, this package allows calculation of the k
21462 nearest neighbors (kNN) of a data matrix. The implementation is based on
21463 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21464 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21465 (license license:agpl3+)))
21467 (define-public r-poibin
21474 (uri (cran-uri "poibin" version))
21477 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21478 (properties `((upstream-name . "poibin")))
21479 (build-system r-build-system)
21480 (home-page "https://cran.r-project.org/web/packages/poibin/")
21481 (synopsis "Poisson binomial distribution")
21483 "This package provides an implementation of both the exact and
21484 approximation methods for computing the @dfn{cumulative distribution
21485 function} (CDF) of the Poisson binomial distribution. It also provides the
21486 @dfn{probability mass function} (PMF), quantile function, and random number
21487 generation for the Poisson binomial distribution.")
21488 (license license:gpl2)))
21490 (define-public r-diagram
21497 (uri (cran-uri "diagram" version))
21500 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21501 (properties `((upstream-name . "diagram")))
21502 (build-system r-build-system)
21504 `(("r-shape" ,r-shape)))
21505 (home-page "https://cran.r-project.org/web/packages/diagram/")
21506 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21508 "This package provides tools to visualize simple graphs (networks) based
21509 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21510 electrical networks, etc. It also includes supporting material for the book
21511 \"A practical guide to ecological modelling - using R as a simulation
21512 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21513 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21514 Francesca Mazzia (2012).")
21515 (license license:gpl2+)))
21517 (define-public r-lim
21524 (uri (cran-uri "LIM" version))
21527 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21528 (properties `((upstream-name . "LIM")))
21529 (build-system r-build-system)
21531 `(("r-diagram" ,r-diagram)
21532 ("r-limsolve" ,r-limsolve)))
21533 (home-page "https://cran.r-project.org/web/packages/LIM/")
21534 (synopsis "Linear inverse model examples and solution methods")
21536 "This package provides functions that read and solve linear inverse
21537 problems (food web problems, linear programming problems).")
21538 (license license:gpl2+)))
21540 (define-public r-shinycssloaders
21542 (name "r-shinycssloaders")
21547 (uri (cran-uri "shinycssloaders" version))
21550 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21552 `((upstream-name . "shinycssloaders")))
21553 (build-system r-build-system)
21555 `(("r-digest" ,r-digest)
21557 ("r-shiny" ,r-shiny)))
21558 (home-page "https://github.com/andrewsali/shinycssloaders")
21559 (synopsis "Add CSS loading animations to Shiny outputs")
21561 "This package provides tools to create a lightweight Shiny wrapper for
21562 the css-loaders created by Luke Hass
21563 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21564 automatically show a loader when the output is (re)calculating.")
21565 (license license:gpl3)))
21567 (define-public r-rsvg
21574 (uri (cran-uri "rsvg" version))
21577 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21578 (properties `((upstream-name . "rsvg")))
21579 (build-system r-build-system)
21581 `(("librsvg" ,librsvg)
21584 `(("pkg-config" ,pkg-config)
21585 ("r-knitr" ,r-knitr)))
21586 (home-page "https://github.com/jeroen/rsvg#readme")
21587 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21589 "This package allows you to render vector-based SVG images into
21590 high-quality custom-size bitmap arrays using the librsvg2 library. The
21591 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21592 addition, the package can convert images directly to various formats such as
21593 PDF or PostScript.")
21594 (license license:expat)))
21596 (define-public r-influencer
21598 (name "r-influencer")
21603 (uri (cran-uri "influenceR" version))
21606 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21607 (properties `((upstream-name . "influenceR")))
21608 (build-system r-build-system)
21610 `(("r-igraph" ,r-igraph)
21611 ("r-matrix" ,r-matrix)))
21612 (home-page "https://github.com/rcc-uchicago/influenceR")
21613 (synopsis "Tools to quantify structural importance of nodes in a network")
21615 "This package provides functionality to compute various node centrality
21616 measures on networks. Included are functions to compute betweenness
21617 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21618 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21619 algorithm to identify key players, and Valente's bridging metric. The
21620 betweenness, Key Players, and bridging implementations are parallelized with
21622 (license license:gpl2)))
21624 (define-public r-emplik
21631 (uri (cran-uri "emplik" version))
21634 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21635 (properties `((upstream-name . "emplik")))
21636 (build-system r-build-system)
21638 `(("r-quantreg" ,r-quantreg)))
21639 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21640 (synopsis "Empirical likelihood ratio for censored/truncated data")
21642 "This package provides empirical likelihood ratio tests for
21643 means/quantiles/hazards from possibly censored and/or truncated data. It also
21645 (license license:gpl2+)))
21647 (define-public r-imputeyn
21649 (name "r-imputeyn")
21654 (uri (cran-uri "imputeYn" version))
21657 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21658 (properties `((upstream-name . "imputeYn")))
21659 (build-system r-build-system)
21661 `(("r-boot" ,r-boot)
21662 ("r-emplik" ,r-emplik)
21663 ("r-mvtnorm" ,r-mvtnorm)
21664 ("r-quadprog" ,r-quadprog)
21665 ("r-survival" ,r-survival)))
21666 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21667 (synopsis "Impute last largest censored observation under weighted least squares")
21669 "This package allows for the imputation of the last largest censored
21670 observantions. This method brings less bias and more efficient estimates for
21672 (license license:gpl2)))
21674 (define-public r-adapenetclass
21676 (name "r-adapenetclass")
21681 (uri (cran-uri "AdapEnetClass" version))
21684 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21685 (properties `((upstream-name . "AdapEnetClass")))
21686 (build-system r-build-system)
21688 `(("r-glmnet" ,r-glmnet)
21689 ("r-imputeyn" ,r-imputeyn)
21691 ("r-quadprog" ,r-quadprog)))
21692 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21693 (synopsis "Class of adaptive elastic net methods for censored data")
21695 "This package provides methods for variable selection for AFT models.")
21696 (license license:gpl2)))
21698 (define-public r-flock
21705 (uri (cran-uri "flock" version))
21708 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21709 (properties `((upstream-name . "flock")))
21710 (build-system r-build-system)
21711 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21712 (home-page "https://cran.r-project.org/web/packages/flock/")
21713 (synopsis "Process synchronization using file locks")
21715 "This package implements synchronization between R processes (spawned by
21716 using the @code{parallel} package for instance) using file locks. It supports
21717 both exclusive and shared locking.")
21718 (license license:asl2.0)))
21720 (define-public r-archivist
21722 (name "r-archivist")
21727 (uri (cran-uri "archivist" version))
21730 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21731 (properties `((upstream-name . "archivist")))
21732 (build-system r-build-system)
21735 ("r-digest" ,r-digest)
21736 ("r-flock" ,r-flock)
21738 ("r-lubridate" ,r-lubridate)
21739 ("r-magrittr" ,r-magrittr)
21740 ("r-rcurl" ,r-rcurl)
21741 ("r-rsqlite" ,r-rsqlite)))
21743 `(("r-knitr" ,r-knitr)))
21744 (home-page "https://pbiecek.github.io/archivist/")
21745 (synopsis "Tools for storing, restoring and searching for R objects")
21747 "Data exploration and modelling is a process in which a lot of data
21748 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21749 statistical models, different versions of data sets and different versions of
21750 results. Archivist helps to store and manage artifacts created in R. It
21751 allows you to store selected artifacts as binary files together with their
21752 metadata and relations. Archivist allows sharing artifacts with others. It
21753 can look for already created artifacts by using its class, name, date of the
21754 creation or other properties. It also makes it easy to restore such
21756 (license license:gpl2)))
21758 (define-public r-versions
21760 (name "r-versions")
21765 (uri (cran-uri "versions" version))
21768 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21769 (properties `((upstream-name . "versions")))
21770 (build-system r-build-system)
21771 (home-page "https://cran.r-project.org/web/packages/versions/")
21772 (synopsis "Query and install specific versions of CRAN packages")
21774 "This package allows you to install specified versions of R packages
21775 hosted on CRAN and provides functions to list available versions and the
21776 versions of currently installed packages.")
21777 (license license:bsd-3)))
21779 (define-public r-adapr
21786 (uri (cran-uri "adapr" version))
21789 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21790 (properties `((upstream-name . "adapr")))
21791 (build-system r-build-system)
21793 `(("r-archivist" ,r-archivist)
21794 ("r-devtools" ,r-devtools)
21795 ("r-digest" ,r-digest)
21796 ("r-doparallel" ,r-doparallel)
21797 ("r-gdata" ,r-gdata)
21798 ("r-ggplot2" ,r-ggplot2)
21799 ("r-git2r" ,r-git2r)
21800 ("r-igraph" ,r-igraph)
21801 ("r-knitr" ,r-knitr)
21802 ("r-plotly" ,r-plotly)
21804 ("r-rmarkdown" ,r-rmarkdown)
21805 ("r-shiny" ,r-shiny)
21806 ("r-shinydashboard" ,r-shinydashboard)
21807 ("r-versions" ,r-versions)))
21808 (home-page "https://cran.r-project.org/web/packages/adapr/")
21809 (synopsis "Implementation of an accountable data analysis process")
21811 "This package tracks reading and writing within R scripts that are
21812 organized into a directed acyclic graph. It contains an interactive Shiny
21813 application @code{adaprApp()}. It uses Git and file hashes to track version
21814 histories of inputs and outputs.")
21815 (license license:lgpl2.0)))
21817 (define-public r-adapsamp
21819 (name "r-adapsamp")
21824 (uri (cran-uri "AdapSamp" version))
21827 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21828 (properties `((upstream-name . "AdapSamp")))
21829 (build-system r-build-system)
21830 (propagated-inputs `(("r-pracma" ,r-pracma)))
21831 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21832 (synopsis "Adaptive sampling algorithms")
21834 "For distributions whose probability density functions are log-concave,
21835 the adaptive rejection sampling algorithm can be used to build envelope
21836 functions for sampling. For others, the modified adaptive rejection sampling
21837 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21838 adaptive slice sampling algorithm can be used. This R package mainly includes
21839 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21840 @code{rASS()}. These functions can realize sampling based on the algorithms
21842 (license license:gpl2)))
21844 (define-public r-adaptalint
21846 (name "r-adaptalint")
21851 (uri (cran-uri "adaptalint" version))
21854 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21855 (properties `((upstream-name . "adaptalint")))
21856 (build-system r-build-system)
21858 `(("r-dplyr" ,r-dplyr)
21859 ("r-lintr" ,r-lintr)
21860 ("r-purrr" ,r-purrr)))
21861 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21862 (synopsis "Check R code style")
21864 "This package provides tools to infer the code style (which style rules
21865 are followed and which ones are not) from one package and use it to check
21866 another. This makes it easier to find and correct the most important problems
21868 (license license:gpl3)))
21870 (define-public r-fracdiff
21872 (name "r-fracdiff")
21877 (uri (cran-uri "fracdiff" version))
21880 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21881 (properties `((upstream-name . "fracdiff")))
21882 (build-system r-build-system)
21883 (home-page "https://github.com/mmaechler/fracdiff")
21885 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21887 "This package provides tools for the maximum likelihood estimation of the
21888 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21889 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21890 (license license:gpl2+)))
21892 (define-public r-forecast
21894 (name "r-forecast")
21899 (uri (cran-uri "forecast" version))
21902 "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
21903 (properties `((upstream-name . "forecast")))
21904 (build-system r-build-system)
21906 `(("r-colorspace" ,r-colorspace)
21907 ("r-fracdiff" ,r-fracdiff)
21908 ("r-ggplot2" ,r-ggplot2)
21909 ("r-lmtest" ,r-lmtest)
21910 ("r-magrittr" ,r-magrittr)
21913 ("r-rcpparmadillo" ,r-rcpparmadillo)
21914 ("r-timedate" ,r-timedate)
21915 ("r-tseries" ,r-tseries)
21919 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21920 (home-page "https://pkg.robjhyndman.com/forecast/")
21921 (synopsis "Forecasting functions for time series and linear models")
21923 "This package provides methods and tools for displaying and analysing
21924 univariate time series forecasts including exponential smoothing via state
21925 space models and automatic ARIMA modelling.")
21926 (license license:gpl3)))
21928 (define-public r-xmisc
21935 (uri (cran-uri "Xmisc" version))
21938 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21939 (properties `((upstream-name . "Xmisc")))
21940 (build-system r-build-system)
21941 (home-page "https://cran.r-project.org/package=Xmisc")
21943 "Xiaobei's miscellaneous classes and functions")
21945 "This package provides Xiaobei's miscellaneous classes and functions,
21946 which are useful when developing R packages for @dfn{object oriented
21947 programming} (OOP) using R Reference Class.")
21948 (license license:gpl2+)))
21950 (define-public r-proxyc
21957 (uri (cran-uri "proxyC" version))
21960 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21961 (properties `((upstream-name . "proxyC")))
21962 (build-system r-build-system)
21964 `(("r-matrix" ,r-matrix)
21966 ("r-rcpparmadillo" ,r-rcpparmadillo)
21967 ("r-rcppparallel" ,r-rcppparallel)))
21968 (home-page "https://cran.r-project.org/package=proxyC")
21969 (synopsis "Compute proximity in large sparse matrices")
21971 "This package provides efficient tools to compute the proximity between
21972 rows or columns of large matrices. Functions are optimised for large sparse
21973 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21974 similarity/distance measures, computation of correlation, cosine similarity
21975 and Euclidean distance is particularly fast.")
21976 (license license:gpl3)))
21978 (define-public r-isocodes
21980 (name "r-isocodes")
21981 (version "2021.02.24")
21985 (uri (cran-uri "ISOcodes" version))
21988 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
21989 (properties `((upstream-name . "ISOcodes")))
21990 (build-system r-build-system)
21991 (home-page "https://cran.r-project.org/package=ISOcodes")
21992 (synopsis "Selected ISO codes")
21994 "This package provides ISO language, territory, currency, script and
21995 character codes. It provides ISO 639 language codes, ISO 3166 territory
21996 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21997 character codes as well as the UN M.49 area codes.")
21998 (license license:gpl2)))
22000 (define-public r-stopwords
22002 (name "r-stopwords")
22007 (uri (cran-uri "stopwords" version))
22010 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
22011 (properties `((upstream-name . "stopwords")))
22012 (build-system r-build-system)
22014 `(("r-isocodes" ,r-isocodes)))
22015 (home-page "https://github.com/quanteda/stopwords")
22016 (synopsis "Multilingual stopword lists")
22018 "This package provides multiple sources of stopwords, for use in text
22019 analysis and natural language processing.")
22020 (license license:expat)))
22022 (define-public r-spacyr
22029 (uri (cran-uri "spacyr" version))
22032 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
22033 (properties `((upstream-name . "spacyr")))
22034 (build-system r-build-system)
22036 `(("r-data-table" ,r-data-table)
22037 ("r-reticulate" ,r-reticulate)))
22038 (home-page "https://spacyr.quanteda.io")
22039 (synopsis "R wrapper for the spaCy NLP library")
22041 "This package provides an R wrapper to the Python @dfn{natural language
22042 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22043 (license license:gpl3)))
22045 (define-public r-snowballc
22047 (name "r-snowballc")
22052 (uri (cran-uri "SnowballC" version))
22055 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22056 (properties `((upstream-name . "SnowballC")))
22057 (build-system r-build-system)
22058 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22059 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22061 "This package provides an R interface to the C @code{libstemmer} library
22062 that implements Porter's word stemming algorithm for collapsing words to a
22063 common root to aid comparison of vocabulary. Currently supported languages
22064 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22065 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22066 (license license:bsd-3)))
22068 (define-public r-quanteda
22070 (name "r-quanteda")
22075 (uri (cran-uri "quanteda" version))
22078 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22079 (properties `((upstream-name . "quanteda")))
22080 (build-system r-build-system)
22082 `(("r-data-table" ,r-data-table)
22083 ("r-digest" ,r-digest)
22084 ("r-extrafont" ,r-extrafont)
22085 ("r-fastmatch" ,r-fastmatch)
22086 ("r-ggplot2" ,r-ggplot2)
22087 ("r-ggrepel" ,r-ggrepel)
22088 ("r-jsonlite" ,r-jsonlite)
22089 ("r-magrittr" ,r-magrittr)
22090 ("r-matrix" ,r-matrix)
22091 ("r-network" ,r-network)
22092 ("r-proxyc" ,r-proxyc)
22094 ("r-rcpparmadillo" ,r-rcpparmadillo)
22095 ("r-rcppparallel" ,r-rcppparallel)
22097 ("r-snowballc" ,r-snowballc)
22098 ("r-stopwords" ,r-stopwords)
22099 ("r-stringi" ,r-stringi)
22101 ("r-yaml" ,r-yaml)))
22103 `(("r-knitr" ,r-knitr)))
22104 (home-page "https://quanteda.io")
22105 (synopsis "Quantitative analysis of textual data")
22107 "This package provides a fast, flexible, and comprehensive framework for
22108 quantitative text analysis in R. It provides functionality for corpus
22109 management, creating and manipulating tokens and ngrams, exploring keywords in
22110 context, forming and manipulating sparse matrices of documents by features and
22111 feature co-occurrences, analyzing keywords, computing feature similarities and
22112 distances, applying content dictionaries, applying supervised and unsupervised
22113 machine learning, visually representing text and text analyses, and more.")
22114 (license license:gpl3)))
22116 (define-public r-topicmodels
22118 (name "r-topicmodels")
22123 (uri (cran-uri "topicmodels" version))
22126 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22127 (properties `((upstream-name . "topicmodels")))
22128 (build-system r-build-system)
22132 `(("r-modeltools" ,r-modeltools)
22135 (home-page "https://cran.r-project.org/package=topicmodels")
22136 (synopsis "Topic models")
22138 "This package provides an interface to the C code for @dfn{Latent
22139 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22140 David M. Blei and co-authors and the C++ code for fitting LDA models using
22141 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22142 (license license:gpl2)))
22144 (define-public r-stm
22151 (uri (cran-uri "stm" version))
22154 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22155 (properties `((upstream-name . "stm")))
22156 (build-system r-build-system)
22158 `(("r-data-table" ,r-data-table)
22159 ("r-glmnet" ,r-glmnet)
22161 ("r-matrix" ,r-matrix)
22162 ("r-matrixstats" ,r-matrixstats)
22163 ("r-quadprog" ,r-quadprog)
22164 ("r-quanteda" ,r-quanteda)
22166 ("r-rcpparmadillo" ,r-rcpparmadillo)
22168 ("r-stringr" ,r-stringr)))
22169 (home-page "http://www.structuraltopicmodel.com/")
22170 (synopsis "Estimation of the Structural Topic Model")
22172 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22173 topic models with document-level covariates. The package also includes tools
22174 for model selection, visualization, and estimation of topic-covariate
22176 (license license:expat)))
22178 (define-public r-polycor
22185 (uri (cran-uri "polycor" version))
22188 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22189 (properties `((upstream-name . "polycor")))
22190 (build-system r-build-system)
22192 `(("r-matrix" ,r-matrix)
22193 ("r-mvtnorm" ,r-mvtnorm)))
22194 (home-page "https://r-forge.r-project.org/projects/polycor/")
22195 (synopsis "Polychoric and polyserial correlations")
22197 "This package provides tools to compute polychoric and polyserial
22198 correlations by quick \"two-step\" methods or ML, optionally with standard
22199 errors; tetrachoric and biserial correlations are special cases.")
22200 (license license:gpl2+)))
22202 (define-public r-msm
22209 (uri (cran-uri "msm" version))
22212 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22213 (properties `((upstream-name . "msm")))
22214 (build-system r-build-system)
22216 `(("r-expm" ,r-expm)
22217 ("r-mvtnorm" ,r-mvtnorm)
22218 ("r-survival" ,r-survival)))
22219 (home-page "https://github.com/chjackson/msm")
22220 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22222 "This package provides functions for fitting continuous-time Markov and
22223 hidden Markov multi-state models to longitudinal data. It was designed for
22224 processes observed at arbitrary times in continuous time (panel data) but some
22225 other observation schemes are supported. Both Markov transition rates and the
22226 hidden Markov output process can be modelled in terms of covariates, which may
22227 be constant or piecewise-constant in time.")
22228 (license license:gpl2+)))
22230 (define-public r-ltm
22237 (uri (cran-uri "ltm" version))
22240 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22241 (properties `((upstream-name . "ltm")))
22242 (build-system r-build-system)
22244 `(("r-mass" ,r-mass)
22246 ("r-polycor" ,r-polycor)))
22247 (home-page "https://github.com/drizopoulos/ltm")
22248 (synopsis "Latent trait models under IRT")
22250 "This is a package supporting the analysis of multivariate dichotomous
22251 and polytomous data using latent trait models under the Item Response Theory
22252 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22253 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22255 (license license:gpl2+)))
22257 (define-public r-mi
22264 (uri (cran-uri "mi" version))
22267 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22268 (properties `((upstream-name . "mi")))
22269 (build-system r-build-system)
22272 ("r-matrix" ,r-matrix)))
22273 (home-page "http://www.stat.columbia.edu/~gelman/")
22274 (synopsis "Missing data imputation and model checking")
22276 "This package provides functions for data manipulation, imputing missing
22277 values in an approximate Bayesian framework, diagnostics of the models used to
22278 generate the imputations, confidence-building mechanisms to validate some of
22279 the assumptions of the imputation algorithm, and functions to analyze multiply
22280 imputed data sets with the appropriate degree of sampling uncertainty.")
22281 (license license:gpl2+)))
22283 (define-public r-matrixcalc
22285 (name "r-matrixcalc")
22290 (uri (cran-uri "matrixcalc" version))
22293 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22294 (properties `((upstream-name . "matrixcalc")))
22295 (build-system r-build-system)
22296 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22297 (synopsis "Collection of functions for matrix calculations")
22299 "This package provides a collection of functions to support matrix
22300 calculations for probability, econometric and numerical analysis. There are
22301 additional functions that are comparable to APL functions which are useful for
22302 actuarial models such as pension mathematics.")
22303 (license license:gpl2+)))
22305 (define-public r-sem
22312 (uri (cran-uri "sem" version))
22315 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22316 (properties `((upstream-name . "sem")))
22317 (build-system r-build-system)
22319 `(("r-boot" ,r-boot)
22321 ("r-matrixcalc" ,r-matrixcalc)
22323 (home-page "https://cran.r-project.org/package=sem")
22324 (synopsis "Structural equation models")
22326 "This package provides functions for fitting general linear structural
22327 equation models (with observed and latent variables) using the RAM approach,
22328 and for fitting structural equations in observed-variable models by two-stage
22330 (license license:gpl2+)))
22332 (define-public r-semtools
22334 (name "r-semtools")
22339 (uri (cran-uri "semTools" version))
22342 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22343 (properties `((upstream-name . "semTools")))
22344 (build-system r-build-system)
22346 `(("r-lavaan" ,r-lavaan)))
22347 (home-page "https://github.com/simsem/semTools/wiki")
22348 (synopsis "Useful tools for structural equation modeling")
22350 "This package provides useful tools for structural equation modeling.")
22351 (license license:gpl2+)))
22353 (define-public r-regsem
22360 (uri (cran-uri "regsem" version))
22363 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22364 (properties `((upstream-name . "regsem")))
22365 (build-system r-build-system)
22367 `(("r-lavaan" ,r-lavaan)
22369 ("r-rcpparmadillo" ,r-rcpparmadillo)
22370 ("r-rsolnp" ,r-rsolnp)))
22372 `(("r-knitr" ,r-knitr)))
22373 (home-page "https://cran.r-project.org/package=regsem")
22374 (synopsis "Regularized structural equation modeling")
22376 "This package uses both ridge and lasso penalties (and extensions) to
22377 penalize specific parameters in structural equation models. The package
22378 offers additional cost functions, cross validation, and other extensions
22379 beyond traditional structural equation models. It also contains a function to
22380 perform @dfn{exploratory mediation} (XMed).")
22381 (license license:gpl2+)))
22383 (define-public r-stanheaders
22385 (name "r-stanheaders")
22386 (version "2.21.0-7")
22390 (uri (cran-uri "StanHeaders" version))
22393 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22394 (properties `((upstream-name . "StanHeaders")))
22395 (build-system r-build-system)
22396 (inputs `(("pandoc" ,pandoc)))
22398 `(("r-rcppeigen" ,r-rcppeigen)
22399 ("r-rcppparallel" ,r-rcppparallel)))
22401 `(("gfortran" ,gfortran)
22402 ("r-knitr" ,r-knitr))) ; for vignettes
22403 (home-page "https://mc-stan.org/")
22404 (synopsis "C++ header files for Stan")
22406 "The C++ header files of the Stan project are provided by this package.
22407 There is a shared object containing part of the @code{CVODES} library, but it
22408 is not accessible from R. @code{r-stanheaders} is only useful for developers
22409 who want to utilize the @code{LinkingTo} directive of their package's
22410 DESCRIPTION file to build on the Stan library without incurring unnecessary
22413 The Stan project develops a probabilistic programming language that implements
22414 full or approximate Bayesian statistical inference via Markov Chain Monte
22415 Carlo or variational methods and implements (optionally penalized) maximum
22416 likelihood estimation via optimization. The Stan library includes an advanced
22417 automatic differentiation scheme, templated statistical and linear algebra
22418 functions that can handle the automatically differentiable scalar types (and
22419 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22420 package provides user-facing R functions to parse, compile, test, estimate,
22421 and analyze Stan models.")
22422 (license license:bsd-3)))
22424 (define-public r-rpf
22431 (uri (cran-uri "rpf" version))
22434 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22435 (properties `((upstream-name . "rpf")))
22436 (build-system r-build-system)
22438 `(("r-lifecycle" ,r-lifecycle)
22439 ("r-mvtnorm" ,r-mvtnorm)
22441 ("r-rcppeigen" ,r-rcppeigen)))
22443 `(("r-knitr" ,r-knitr)))
22444 (home-page "https://github.com/jpritikin/rpf")
22445 (synopsis "Response probability functions")
22447 "The purpose of this package is to factor out logic and math common to
22448 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22449 core support code suitable for more specialized IRT packages to build upon.
22450 Complete access to optimized C functions is made available with
22451 @code{R_RegisterCCallable()}.")
22452 (license license:gpl3+)))
22454 (define-public r-openmx
22461 (uri (cran-uri "OpenMx" version))
22464 "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj"))))
22465 (properties `((upstream-name . "OpenMx")))
22466 (build-system r-build-system)
22469 ("r-digest" ,r-digest)
22470 ("r-lifecycle" ,r-lifecycle)
22472 ("r-matrix" ,r-matrix)
22474 ("r-rcppeigen" ,r-rcppeigen)
22476 ("r-stanheaders" ,r-stanheaders)))
22477 (native-inputs `(("gfortran" ,gfortran)))
22478 (home-page "http://openmx.ssri.psu.edu")
22479 (synopsis "Extended structural equation modelling")
22481 "This package allows for the estimation of a wide variety of advanced
22482 multivariate statistical models. It consists of a library of functions and
22483 optimizers that allow you to quickly and flexibly define an SEM model and
22484 estimate parameters given observed data.")
22485 (license license:asl2.0)))
22487 (define-public r-kutils
22494 (uri (cran-uri "kutils" version))
22497 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22498 (properties `((upstream-name . "kutils")))
22499 (build-system r-build-system)
22501 `(("r-foreign" ,r-foreign)
22502 ("r-openxlsx" ,r-openxlsx)
22504 ("r-runit" ,r-runit)
22505 ("r-xtable" ,r-xtable)))
22506 (home-page "https://cran.r-project.org/package=kutils")
22507 (synopsis "Project management tools")
22509 "This package provides tools for data importation, recoding, and
22510 inspection. There are functions to create new project folders, R code
22511 templates, create uniquely named output directories, and to quickly obtain a
22512 visual summary for each variable in a data frame. The main feature here is
22513 the systematic implementation of the \"variable key\" framework for data
22514 importation and recoding.")
22515 (license license:gpl2)))
22517 (define-public r-rockchalk
22519 (name "r-rockchalk")
22520 (version "1.8.144")
22524 (uri (cran-uri "rockchalk" version))
22527 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22528 (properties `((upstream-name . "rockchalk")))
22529 (build-system r-build-system)
22531 `(("r-cardata" ,r-cardata)
22532 ("r-kutils" ,r-kutils)
22534 ("r-mass" ,r-mass)))
22535 (home-page "https://cran.r-project.org/package=rockchalk")
22536 (synopsis "Regression estimation and presentation")
22538 "This package provides a collection of functions for interpretation and
22539 presentation of regression analysis. These functions are used to produce the
22540 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22541 includes regression diagnostics, regression tables, and plots of interactions
22542 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22543 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22544 fairly comprehensive overview.")
22545 (license license:gpl3+)))
22547 (define-public r-lisreltor
22549 (name "r-lisreltor")
22554 (uri (cran-uri "lisrelToR" version))
22557 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22558 (properties `((upstream-name . "lisrelToR")))
22559 (build-system r-build-system)
22560 (home-page "https://cran.r-project.org/package=lisrelToR")
22561 (synopsis "Import output from LISREL into R")
22563 "This is an unofficial package aimed at automating the import of LISREL
22565 (license license:gpl2)))
22567 (define-public r-bdgraph
22574 (uri (cran-uri "BDgraph" version))
22577 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22578 (properties `((upstream-name . "BDgraph")))
22579 (build-system r-build-system)
22581 `(("r-igraph" ,r-igraph)))
22582 (home-page "https://www.uva.nl/profile/a.mohammadi")
22583 (synopsis "Bayesian structure learning in graphical models")
22585 "This package provides statistical tools for Bayesian structure learning
22586 in undirected graphical models for continuous, discrete, and mixed data. It
22587 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22588 on a continuous-time birth-death process.")
22589 (license license:gpl2+)))
22591 (define-public r-d3network
22593 (name "r-d3network")
22594 (version "0.5.2.1")
22598 (uri (cran-uri "d3Network" version))
22601 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22602 (properties `((upstream-name . "d3Network")))
22603 (build-system r-build-system)
22605 `(("r-plyr" ,r-plyr)
22606 ("r-rjson" ,r-rjson)
22607 ("r-whisker" ,r-whisker)))
22608 (home-page "http://christophergandrud.github.io/d3Network/")
22609 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22611 "This package is intended to make it easy to create D3 JavaScript
22612 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22613 (license license:gpl3+)))
22615 (define-public r-qgraph
22622 (uri (cran-uri "qgraph" version))
22625 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22626 (properties `((upstream-name . "qgraph")))
22627 (build-system r-build-system)
22629 `(("r-abind" ,r-abind)
22630 ("r-colorspace" ,r-colorspace)
22631 ("r-corpcor" ,r-corpcor)
22632 ("r-dplyr" ,r-dplyr)
22633 ("r-fdrtool" ,r-fdrtool)
22634 ("r-ggplot2" ,r-ggplot2)
22635 ("r-glasso" ,r-glasso)
22636 ("r-gtools" ,r-gtools)
22637 ("r-hmisc" ,r-hmisc)
22638 ("r-igraph" ,r-igraph)
22640 ("r-lavaan" ,r-lavaan)
22641 ("r-matrix" ,r-matrix)
22642 ("r-pbapply" ,r-pbapply)
22645 ("r-psych" ,r-psych)
22647 ("r-reshape2" ,r-reshape2)))
22648 (home-page "http://sachaepskamp.com/qgraph/")
22649 (synopsis "Weighted network visualization and analysis")
22651 "This package implements tools for weighted network visualization and
22652 analysis, as well as Gaussian graphical model computation. It contains graph
22653 plotting methods, and tools for psychometric data visualization and graphical
22654 model estimation. See Epskamp et al. (2012)
22655 @url{doi:10.18637/jss.v048.i04}.")
22656 (license license:gpl2)))
22658 (define-public r-semplot
22665 (uri (cran-uri "semPlot" version))
22668 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22669 (properties `((upstream-name . "semPlot")))
22670 (build-system r-build-system)
22672 `(("r-colorspace" ,r-colorspace)
22673 ("r-corpcor" ,r-corpcor)
22674 ("r-igraph" ,r-igraph)
22675 ("r-lavaan" ,r-lavaan)
22676 ("r-lisreltor" ,r-lisreltor)
22677 ("r-openmx" ,r-openmx)
22679 ("r-qgraph" ,r-qgraph)
22680 ("r-regsem" ,r-regsem)
22681 ("r-rockchalk" ,r-rockchalk)
22684 (home-page "https://github.com/SachaEpskamp/semPlot")
22685 (synopsis "Unified visualizations of structural equation models")
22687 "Structural equation modeling (SEM) has a long history of representing
22688 models graphically as path diagrams. The semPlot package for R fills the gap
22689 between advanced, but time-consuming, graphical software and the limited
22690 graphics produced automatically by SEM software. In addition, semPlot offers
22691 more functionality than drawing path diagrams: it can act as a common ground
22692 for importing SEM results into R. Any result usable as input to semPlot can
22693 also be represented in any of the three popular SEM frame-works, as well as
22694 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22695 (license license:gpl2)))
22697 (define-public r-cdm
22704 (uri (cran-uri "CDM" version))
22707 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22708 (properties `((upstream-name . "CDM")))
22709 (build-system r-build-system)
22711 `(("r-mvtnorm" ,r-mvtnorm)
22712 ("r-polycor" ,r-polycor)
22714 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22716 "https://github.com/alexanderrobitzsch/CDM")
22717 (synopsis "Cognitive diagnosis modeling")
22719 "This package provides functions for cognitive diagnosis modeling and
22720 multidimensional item response modeling for dichotomous and polytomous item
22721 responses. It enables the estimation of the DINA and DINO model, the multiple
22722 group (polytomous) GDINA model, the multiple choice DINA model, the general
22723 diagnostic model (GDM), the structured latent class model (SLCA), and
22724 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22725 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22726 estimation and the package structure. For tutorials on how to use the CDM
22727 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22728 well as Ravand and Robitzsch (2015).")
22729 (license license:gpl2+)))
22731 (define-public r-tam
22738 (uri (cran-uri "TAM" version))
22741 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22742 (properties `((upstream-name . "TAM")))
22743 (build-system r-build-system)
22747 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22748 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22749 (synopsis "Test analysis modules")
22751 "This package includes tools for marginal maximum likelihood estimation
22752 and joint maximum likelihood estimation for unidimensional and
22753 multidimensional item response models. The package functionality covers the
22754 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22755 multi-faceted Rasch model, nominal item response model, structured latent
22756 class model, mixture distribution IRT models, and located latent class models.
22757 Latent regression models and plausible value imputation are also supported.")
22758 (license license:gpl2+)))
22760 (define-public r-erm
22767 (uri (cran-uri "eRm" version))
22770 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
22771 (properties `((upstream-name . "eRm")))
22772 (build-system r-build-system)
22774 `(("r-colorspace" ,r-colorspace)
22775 ("r-lattice" ,r-lattice)
22777 ("r-matrix" ,r-matrix)
22778 ("r-psych" ,r-psych)))
22779 (native-inputs `(("gfortran" ,gfortran)))
22780 (home-page "https://cran.r-project.org/package=eRm")
22781 (synopsis "Extended Rasch modeling")
22783 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22784 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22785 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22786 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22787 data matrix. Additional features are the ML estimation of the person
22788 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22789 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22790 infit and outfit measures, ICC and other plots, automated stepwise item
22791 elimination, and a simulation module for various binary data matrices.")
22792 (license license:gpl3)))
22794 (define-public r-irtoys
22801 (uri (cran-uri "irtoys" version))
22804 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22805 (properties `((upstream-name . "irtoys")))
22806 (build-system r-build-system)
22810 (home-page "https://cran.r-project.org/package=irtoys")
22811 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22813 "This package provides a collection of functions useful in learning and
22814 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22815 programs. It provides basic CTT analysis, a simple common interface to the
22816 estimation of item parameters in IRT models for binary responses with three
22817 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22818 EAP, WLE, plausible values), item and person fit statistics, scaling
22819 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22820 array of parametric and non-parametric (kernel) plots. It estimates and plots
22821 Haberman's interaction model when all items are dichotomously scored.")
22822 (license license:gpl2+)))
22824 (define-public r-iheatmapr
22826 (name "r-iheatmapr")
22831 (uri (cran-uri "iheatmapr" version))
22834 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22835 (properties `((upstream-name . "iheatmapr")))
22836 (build-system r-build-system)
22838 `(("r-fastcluster" ,r-fastcluster)
22839 ("r-ggdendro" ,r-ggdendro)
22840 ("r-htmlwidgets" ,r-htmlwidgets)
22841 ("r-jsonlite" ,r-jsonlite)
22842 ("r-knitr" ,r-knitr)
22843 ("r-magrittr" ,r-magrittr)
22844 ("r-rcolorbrewer" ,r-rcolorbrewer)
22845 ("r-scales" ,r-scales)))
22847 `(("r-knitr" ,r-knitr)))
22848 (home-page "https://docs.ropensci.org/iheatmapr")
22849 (synopsis "Interactive, Complex Heatmaps")
22851 "iheatmapr is an R package for building complex, interactive heatmaps
22852 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22853 subplots along the rows or columns of the main heatmap add more information
22854 about each row or column. For example, a one column additional heatmap may
22855 indicate what group a particular row or column belongs to. Complex heatmaps
22856 may also include multiple side by side heatmaps which show different types of
22857 data for the same conditions. Interactivity can improve complex heatmaps by
22858 providing tooltips with information about each cell and enabling zooming into
22859 interesting features. iheatmapr uses the plotly library for interactivity.")
22860 (license license:expat)))
22862 (define-public r-packrat
22869 (uri (cran-uri "packrat" version))
22872 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22873 (properties `((upstream-name . "packrat")))
22874 (build-system r-build-system)
22875 (home-page "https://github.com/rstudio/packrat/")
22876 (synopsis "Dependency management R projects")
22878 "This package provides a dependency manager for R projects that allows
22879 you to manage the R packages your project depends on in an isolated, portable,
22880 and reproducible way.")
22881 (license license:gpl2)))
22883 (define-public r-rsconnect
22885 (name "r-rsconnect")
22890 (uri (cran-uri "rsconnect" version))
22893 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22894 (properties `((upstream-name . "rsconnect")))
22895 (build-system r-build-system)
22897 `(("r-curl" ,r-curl)
22898 ("r-digest" ,r-digest)
22899 ("r-jsonlite" ,r-jsonlite)
22900 ("r-openssl" ,r-openssl)
22901 ("r-packrat" ,r-packrat)
22902 ("r-rstudioapi" ,r-rstudioapi)
22903 ("r-yaml" ,r-yaml)))
22904 (home-page "https://github.com/rstudio/rsconnect")
22905 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22907 "This package provides a programmatic deployment interface for RPubs,
22908 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22909 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22910 (license license:gpl2)))
22912 ;; This package includes minified JavaScript files. When upgrading please
22913 ;; check that there are no new minified JavaScript files.
22914 (define-public r-dygraphs
22916 (name "r-dygraphs")
22917 (version "1.1.1.6")
22921 (uri (cran-uri "dygraphs" version))
22924 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22925 (properties `((upstream-name . "dygraphs")))
22926 (build-system r-build-system)
22928 `(#:modules ((guix build utils)
22929 (guix build r-build-system)
22933 (modify-phases %standard-phases
22934 (add-after 'unpack 'process-javascript
22935 (lambda* (#:key inputs #:allow-other-keys)
22936 (with-directory-excursion "inst/htmlwidgets/lib/"
22940 `(("dygraphs/dygraph-combined-dev.js"
22941 "dygraph-combined.js")
22942 (,(assoc-ref inputs "js-jquery")
22943 "jquery/jquery.min.js")
22944 (,(assoc-ref inputs "js-fquarter")
22945 "fquarter/moment-fquarter.min.js"))))
22946 (lambda (sources targets)
22947 (for-each (lambda (source target)
22948 (format #t "Processing ~a --> ~a~%"
22950 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22951 (call-with-output-file target
22953 (dump-port minified port)))))
22954 sources targets))))
22957 `(("uglify-js" ,uglify-js)
22958 ;; They actually use version 1.11.1, but this more recent version
22959 ;; should be just fine.
22963 (uri "https://code.jquery.com/jquery-1.12.4.js")
22966 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22970 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22971 "moment-fquarter/1.0.1/moment-fquarter.js"))
22974 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22976 `(("r-htmltools" ,r-htmltools)
22977 ("r-htmlwidgets" ,r-htmlwidgets)
22978 ("r-magrittr" ,r-magrittr)
22981 (home-page "https://github.com/rstudio/dygraphs")
22982 (synopsis "Interface to Dygraphs interactive time series charting library")
22984 "This package provides an R interface to the dygraphs JavaScript charting
22985 library (a copy of which is included in the package). It provides rich
22986 facilities for charting time-series data in R, including highly configurable
22987 series- and axis-display and interactive features like zoom/pan and
22988 series/point highlighting.")
22989 (license license:expat)))
22991 (define-public r-shinystan
22993 (name "r-shinystan")
22998 (uri (cran-uri "shinystan" version))
23001 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
23002 (properties `((upstream-name . "shinystan")))
23003 (build-system r-build-system)
23005 `(("r-bayesplot" ,r-bayesplot)
23006 ("r-colourpicker" ,r-colourpicker)
23008 ("r-dygraphs" ,r-dygraphs)
23009 ("r-ggplot2" ,r-ggplot2)
23010 ("r-gridextra" ,r-gridextra)
23011 ("r-gtools" ,r-gtools)
23012 ("r-markdown" ,r-markdown)
23013 ("r-reshape2" ,r-reshape2)
23014 ("r-rsconnect" ,r-rsconnect)
23015 ("r-rstan" ,r-rstan)
23016 ("r-shiny" ,r-shiny)
23017 ("r-shinyjs" ,r-shinyjs)
23018 ("r-shinythemes" ,r-shinythemes)
23019 ("r-threejs" ,r-threejs)
23020 ("r-xtable" ,r-xtable)
23022 (home-page "https://mc-stan.org/")
23023 (synopsis "Interactive visual and numerical analysis for Bayesian models")
23025 "This package provides a graphical user interface for interactive
23026 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
23027 for analyzing a posterior sample. The interface is powered by the Shiny web
23028 application framework and works with the output of MCMC programs written in
23029 any programming language (and has extended functionality for Stan models fit
23030 using the @code{rstan} and @code{rstanarm} packages).")
23031 (license license:gpl3+)))
23033 (define-public r-rstantools
23035 (name "r-rstantools")
23040 (uri (cran-uri "rstantools" version))
23043 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23044 (properties `((upstream-name . "rstantools")))
23045 (build-system r-build-system)
23046 (inputs `(("pandoc" ,pandoc)))
23048 `(("r-desc" ,r-desc)
23050 ("r-rcppparallel" ,r-rcppparallel)))
23052 `(("r-knitr" ,r-knitr)))
23053 (home-page "https://mc-stan.org/rstantools/")
23054 (synopsis "Tools for developing R packages interfacing with Stan")
23056 "This package provides various tools for developers of R packages
23057 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23058 up the required package structure, S3 generics and default methods to unify
23059 function naming across Stan-based R packages, and vignettes with
23060 recommendations for developers.")
23061 (license license:gpl3+)))
23063 (define-public r-loo
23070 (uri (cran-uri "loo" version))
23072 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23073 (properties `((upstream-name . "loo")))
23074 (build-system r-build-system)
23076 `(("pandoc" ,pandoc)
23077 ("pandoc-citeproc" ,pandoc-citeproc)))
23079 `(("r-checkmate" ,r-checkmate)
23080 ("r-matrixstats" ,r-matrixstats)))
23082 `(("r-knitr" ,r-knitr)))
23083 (home-page "https://mc-stan.org/loo/")
23084 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23086 "This package provides an implementation of efficient approximate
23087 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23088 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23089 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23090 procedure for regularizing importance weights. As a byproduct of the
23091 calculations, we also obtain approximate standard errors for estimated
23092 predictive errors and for the comparison of predictive errors between models.
23093 The package also provides methods for using stacking and other model weighting
23094 techniques to average Bayesian predictive distributions.")
23095 (license license:gpl3+)))
23097 (define-public r-rstan
23104 (uri (cran-uri "rstan" version))
23107 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23108 (properties `((upstream-name . "rstan")))
23109 (build-system r-build-system)
23112 (modify-phases %standard-phases
23113 (add-before 'install 'set-timezone
23114 ;; This package is picky about timezones.
23115 (lambda* (#:key inputs #:allow-other-keys)
23116 (setenv "TZ" "UTC+1")
23118 (string-append (assoc-ref inputs "tzdata")
23119 "/share/zoneinfo"))
23122 `(("tzdata" ,tzdata-for-tests)
23124 ("r-knitr" ,r-knitr)))
23127 ("r-ggplot2" ,r-ggplot2)
23128 ("r-gridextra" ,r-gridextra)
23129 ("r-inline" ,r-inline)
23131 ("r-pkgbuild" ,r-pkgbuild)
23133 ("r-rcppeigen" ,r-rcppeigen)
23134 ("r-rcppparallel" ,r-rcppparallel)
23135 ("r-stanheaders" ,r-stanheaders)
23137 ("r-withr" ,r-withr)))
23138 (home-page "https://discourse.mc-stan.org/")
23139 (synopsis "R interface to Stan")
23141 "User-facing R functions are provided to parse, compile, test, estimate,
23142 and analyze Stan models by accessing the header-only Stan library provided by
23143 the StanHeaders package. The Stan project develops a probabilistic
23144 programming language that implements full Bayesian statistical inference via
23145 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23146 approximation, and (optionally penalized) maximum likelihood estimation via
23147 optimization. In all three cases, automatic differentiation is used to
23148 quickly and accurately evaluate gradients without burdening the user with the
23149 need to derive the partial derivatives.")
23150 (license license:gpl3+)))
23152 (define-public r-rstanarm
23154 (name "r-rstanarm")
23159 (uri (cran-uri "rstanarm" version))
23162 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23163 (properties `((upstream-name . "rstanarm")))
23164 (build-system r-build-system)
23166 `(("pandoc" ,pandoc)
23167 ("pandoc-citeproc" ,pandoc-citeproc)))
23169 `(("r-bayesplot" ,r-bayesplot)
23171 ("r-ggplot2" ,r-ggplot2)
23174 ("r-matrix" ,r-matrix)
23177 ("r-rcppeigen" ,r-rcppeigen)
23178 ("r-rcppparallel" ,r-rcppparallel)
23179 ("r-rstan" ,r-rstan)
23180 ("r-rstantools" ,r-rstantools)
23181 ("r-shinystan" ,r-shinystan)
23182 ("r-stanheaders" ,r-stanheaders)
23183 ("r-survival" ,r-survival)))
23185 `(("r-knitr" ,r-knitr)))
23186 (home-page "https://mc-stan.org/rstanarm/")
23187 (synopsis "Bayesian applied regression modeling via Stan")
23189 "This package estimates previously compiled regression models using the
23190 @code{rstan} package, which provides the R interface to the Stan C++ library
23191 for Bayesian estimation. Users specify models via the customary R syntax with
23192 a formula and @code{data.frame} plus some additional arguments for priors.")
23193 (license license:gpl3+)))
23195 (define-public r-kendall
23202 (uri (cran-uri "Kendall" version))
23205 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23206 (properties `((upstream-name . "Kendall")))
23207 (build-system r-build-system)
23209 `(("r-boot" ,r-boot)))
23211 `(("gfortran" ,gfortran)))
23212 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23213 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23215 "This package computes the Kendall rank correlation and Mann-Kendall
23217 (license license:gpl2+)))
23219 (define-public r-keyring
23226 (uri (cran-uri "keyring" version))
23229 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23230 (properties `((upstream-name . "keyring")))
23231 (build-system r-build-system)
23233 `(("r-assertthat" ,r-assertthat)
23234 ("r-filelock" ,r-filelock)
23235 ("r-getpass" ,r-getpass)
23236 ("r-openssl" ,r-openssl)
23238 ("r-rappdirs" ,r-rappdirs)
23239 ("r-sodium" ,r-sodium)
23240 ("r-yaml" ,r-yaml)))
23241 (native-inputs `(("pkg-config" ,pkg-config)))
23242 (home-page "https://github.com/r-lib/keyring")
23243 (synopsis "Access the system credential store from R")
23245 "This package provides a platform-independent API to access the operating
23246 system's credential store. It currently supports Keychain on macOS,
23247 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23248 simple, platform independent store implemented with environment variables.
23249 Additional storage back-ends can be added easily.")
23250 (license license:expat)))
23252 (define-public r-zyp
23255 (version "0.10-1.1")
23259 (uri (cran-uri "zyp" version))
23262 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23263 (properties `((upstream-name . "zyp")))
23264 (build-system r-build-system)
23266 `(("r-kendall" ,r-kendall)))
23267 (home-page "https://cran.r-project.org/web/packages/zyp/")
23268 (synopsis "Zhang + Yue-Pilon Trends Package")
23270 "This package contains an efficient implementation of Sen's slope
23271 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23272 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23274 (license license:lgpl2.1)))
23276 (define-public r-rlinsolve
23278 (name "r-rlinsolve")
23283 (uri (cran-uri "Rlinsolve" version))
23286 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23287 (properties `((upstream-name . "Rlinsolve")))
23288 (build-system r-build-system)
23290 `(("r-matrix" ,r-matrix)
23292 ("r-rcpparmadillo" ,r-rcpparmadillo)
23293 ("r-rdpack" ,r-rdpack)))
23294 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23295 (synopsis "Iterative solvers for (sparse) linear system of equations")
23297 "Solving a system of linear equations is one of the most fundamental
23298 computational problems for many fields of mathematical studies, such as
23299 regression problems from statistics or numerical partial differential
23300 equations. This package provides basic stationary iterative solvers such as
23301 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23302 Nonstationary, also known as Krylov subspace methods are also provided.
23303 Sparse matrix computation is also supported in that solving large and sparse
23304 linear systems can be manageable using the @code{Matrix} package along with
23305 @code{RcppArmadillo}.")
23306 (license license:gpl3+)))
23308 (define-public r-zvcv
23315 (uri (cran-uri "ZVCV" version))
23318 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23319 (properties `((upstream-name . "ZVCV")))
23320 (build-system r-build-system)
23322 `(("r-abind" ,r-abind)
23324 ("r-dplyr" ,r-dplyr)
23325 ("r-glmnet" ,r-glmnet)
23326 ("r-magrittr" ,r-magrittr)
23327 ("r-mvtnorm" ,r-mvtnorm)
23329 ("r-rcpparmadillo" ,r-rcpparmadillo)
23330 ("r-rlinsolve" ,r-rlinsolve)))
23331 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23332 (synopsis "Zero-Variance Control Variates")
23334 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23335 to reduce the variance of Monte Carlo estimators of expectations using the
23336 derivatives of the log target. Once the derivatives are available, the only
23337 additional computational effort is in solving a linear regression problem.
23338 This method has been extended to higher dimensions using regularisation. This
23339 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23340 samples, derivatives and function evaluations are available. Additional
23341 functions for applying ZV-CV to two estimators for the normalising constant of
23342 the posterior distribution in Bayesian statistics are also supplied.")
23343 (license license:gpl2+)))
23345 (define-public r-ztype
23352 (uri (cran-uri "ztype" version))
23355 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23356 (properties `((upstream-name . "ztype")))
23357 (build-system r-build-system)
23359 `(("r-assertthat" ,r-assertthat)
23360 ("r-dplyr" ,r-dplyr)
23361 ("r-ggplot2" ,r-ggplot2)
23362 ("r-lubridate" ,r-lubridate)
23363 ("r-magrittr" ,r-magrittr)
23364 ("r-rvest" ,r-rvest)
23365 ("r-stringr" ,r-stringr)))
23366 (home-page "https://cran.r-project.org/web/packages/ztype/")
23367 (synopsis "Run a Ztype game loaded with R functions")
23369 "How fast can you type R functions on your keyboard? Find out by running
23370 a @code{zty.pe} game: export R functions as instructions to type to destroy
23371 opponents' vessels.")
23372 (license license:gpl3)))
23374 (define-public r-zseq
23381 (uri (cran-uri "Zseq" version))
23384 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23385 (properties `((upstream-name . "Zseq")))
23386 (build-system r-build-system)
23388 `(("r-gmp" ,r-gmp)))
23389 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23390 (synopsis "Integer sequence generator")
23392 "This package generates well-known integer sequences. The @code{gmp}
23393 package is adopted for computing with arbitrarily large numbers. Every
23394 function has a hyperlink to its corresponding item in the @dfn{On-Line
23395 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23396 (license license:gpl3+)))
23398 (define-public r-isoband
23405 (uri (cran-uri "isoband" version))
23408 "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn"))))
23409 (properties `((upstream-name . "isoband")))
23410 (build-system r-build-system)
23412 `(("r-knitr" ,r-knitr)))
23413 (home-page "https://github.com/wilkelab/isoband")
23414 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23416 "This package provides a fast C++ implementation to generate contour
23417 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23418 containing elevation data.")
23419 (license license:expat)))
23421 (define-public r-ppcor
23428 (uri (cran-uri "ppcor" version))
23431 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23432 (properties `((upstream-name . "ppcor")))
23433 (build-system r-build-system)
23435 `(("r-mass" ,r-mass)))
23436 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23437 (synopsis "Partial and semi-partial correlation")
23439 "This package provides users not only with a function to readily
23440 calculate the higher-order partial and semi-partial correlations but also with
23441 statistics and p-values of the correlation coefficients.")
23442 (license license:gpl2)))
23444 (define-public r-hrbrthemes
23446 (name "r-hrbrthemes")
23451 (uri (cran-uri "hrbrthemes" version))
23453 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23454 (properties `((upstream-name . "hrbrthemes")))
23455 (build-system r-build-system)
23457 `(("r-extrafont" ,r-extrafont)
23458 ("r-gdtools" ,r-gdtools)
23459 ("r-ggplot2" ,r-ggplot2)
23460 ("r-htmltools" ,r-htmltools)
23461 ("r-knitr" ,r-knitr)
23462 ("r-magrittr" ,r-magrittr)
23463 ("r-rmarkdown" ,r-rmarkdown)
23464 ("r-scales" ,r-scales)))
23466 `(("r-knitr" ,r-knitr)))
23467 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23468 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23470 "This package provides a compilation of extra @code{ggplot2} themes,
23471 scales and utilities, including a spell check function for plot label fields
23472 and an overall emphasis on typography.")
23473 (license license:expat)))
23475 (define-public r-crochet
23482 (uri (cran-uri "crochet" version))
23485 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23486 (build-system r-build-system)
23488 `(("r-knitr" ,r-knitr)))
23489 (home-page "https://github.com/agrueneberg/crochet")
23490 (synopsis "Implementation Helper for Matrix-Like Types")
23492 "Functions to help implement the extraction / subsetting / indexing
23493 function @code{[} and replacement function @code{[<-} of custom matrix-like
23494 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23495 as possible (with tests to prove it).")
23496 (license license:expat)))
23498 (define-public r-boa
23501 (version "1.1.8-2")
23505 (uri (cran-uri "boa" version))
23508 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23509 (properties `((upstream-name . "boa")))
23510 (build-system r-build-system)
23511 (home-page "https://www.jstatsoft.org/v21/i11")
23512 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23514 "This package provides a menu-driven program and library of functions for
23515 carrying out convergence diagnostics and statistical and graphical analysis of
23516 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23517 (license license:gpl2+)))
23519 (define-public r-httpcode
23521 (name "r-httpcode")
23525 (uri (cran-uri "httpcode" version))
23528 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23529 (build-system r-build-system)
23530 (home-page "https://github.com/sckott/httpcode")
23531 (synopsis "HTTP status code helper")
23532 (description "@code{httpcode} provides functionality for finding and
23533 explaining the meaning of @code{HTTP} status codes. Functions are included for
23534 searching for codes by full or partial number, by message, and to get
23535 appropriate dog and cat images for many status codes.")
23536 (license license:expat)))
23538 (define-public r-latex2exp
23540 (name "r-latex2exp")
23544 (uri (cran-uri "latex2exp" version))
23547 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23548 (build-system r-build-system)
23550 `(("r-stringr" ,r-stringr)
23551 ("r-magrittr" ,r-magrittr)))
23552 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23553 (synopsis "Use LaTeX expressions in plots")
23554 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23555 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23556 rendered as text, axis labels, etc. throughout R's plotting system.")
23557 (license license:expat)))
23559 (define-public r-oai
23565 (uri (cran-uri "oai" version))
23568 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23569 (build-system r-build-system)
23571 `(("r-xml2" ,r-xml2)
23574 ("r-stringr" ,r-stringr)
23575 ("r-tibble" ,r-tibble)))
23576 (home-page "https://github.com/ropensci/oai/")
23577 (synopsis "General purpose OAI-PMH services client")
23578 (description "@code{oai} provides a general purpose client to work with
23579 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23580 service. Functions are provided to work with the OAI-PMH verbs:
23581 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23582 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23583 (license license:expat)))
23585 (define-public r-argon2
23592 (uri (cran-uri "argon2" version))
23595 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23596 (properties `((upstream-name . "argon2")))
23597 (build-system r-build-system)
23598 (home-page "https://github.com/wrathematics/argon2")
23599 (synopsis "Secure password hashing based on the argon2 algorithm")
23601 "This package provides utilities for secure password hashing via the
23602 argon2 algorithm.")
23603 (license license:bsd-2)))
23605 (define-public r-getpass
23612 (uri (cran-uri "getPass" version))
23615 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23616 (properties `((upstream-name . "getPass")))
23617 (build-system r-build-system)
23619 `(("r-rstudioapi" ,r-rstudioapi)))
23620 (home-page "https://github.com/wrathematics/getPass")
23621 (synopsis "Masked user input")
23623 "This package provides a micro-package for reading \"passwords\", i.e.
23624 reading user input with masking, so that the input is not displayed as it is
23625 typed. Currently, RStudio, the command line (every OS), and any platform
23626 where tcltk is present are supported.")
23627 (license license:bsd-2)))
23629 (define-public r-remoter
23636 (uri (cran-uri "remoter" version))
23639 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23640 (properties `((upstream-name . "remoter")))
23641 (build-system r-build-system)
23643 `(("r-argon2" ,r-argon2)
23644 ("r-getpass" ,r-getpass)
23645 ("r-pbdzmq" ,r-pbdzmq)
23647 (home-page "https://github.com/RBigData/remoter")
23648 (synopsis "Control a remote R session from a local one")
23650 "This package provides a set of utilities for client/server computing
23651 with R, controlling a remote R session (the server) from a local one (the
23653 (license license:bsd-2)))
23655 (define-public r-asd
23662 (uri (cran-uri "asd" version))
23665 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23666 (properties `((upstream-name . "asd")))
23667 (build-system r-build-system)
23669 `(("r-mvtnorm" ,r-mvtnorm)))
23670 (home-page "https://cran.r-project.org/web/packages/asd")
23671 (synopsis "Simulations for Adaptive Seamless Designs")
23673 "This package provdes means to run simulations for adaptive seamless
23674 designs with and without early outcomes for treatment selection and
23675 subpopulation type designs.")
23676 (license license:gpl3)))
23678 (define-public r-nbconvertr
23680 (name "r-nbconvertr")
23685 (uri (cran-uri "nbconvertR" version))
23688 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23689 (properties `((upstream-name . "nbconvertR")))
23690 (build-system r-build-system)
23692 `(("jupyter" ,python-nbconvert)
23693 ("pandoc" ,pandoc)))
23694 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23695 (synopsis "Vignette engine wrapping Jupyter notebooks")
23697 "This package calls the Jupyter script @code{nbconvert} to create
23698 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23699 containing rich text, code, and its output. Code cells can be edited and
23700 evaluated interactively.")
23701 (license license:gpl3)))
23703 (define-public r-bridgesampling
23705 (name "r-bridgesampling")
23710 (uri (cran-uri "bridgesampling" version))
23713 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23715 `((upstream-name . "bridgesampling")))
23716 (build-system r-build-system)
23718 `(("r-brobdingnag" ,r-brobdingnag)
23720 ("r-matrix" ,r-matrix)
23721 ("r-mvtnorm" ,r-mvtnorm)
23722 ("r-scales" ,r-scales)
23723 ("r-stringr" ,r-stringr)))
23725 `(("r-knitr" ,r-knitr)))
23726 (home-page "https://github.com/quentingronau/bridgesampling")
23727 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23729 "This package provides functions for estimating marginal likelihoods,
23730 Bayes factors, posterior model probabilities, and normalizing constants in
23731 general, via different versions of bridge sampling.")
23732 (license license:gpl2+)))
23734 (define-public r-tea
23741 (uri (cran-uri "tea" version))
23744 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23746 `((upstream-name . "tea")))
23747 (build-system r-build-system)
23749 `(("r-matrix" ,r-matrix)))
23750 (home-page "https://cran.r-project.org/web/packages/tea/")
23751 (synopsis "Threshold estimation approaches")
23753 "This package provides different approaches for selecting the threshold
23754 in generalized Pareto distributions. Most of them are based on minimizing the
23755 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23756 Others are heuristically motivated by searching for stable sample paths, i.e.
23757 a nearly constant region of the tail index estimator with respect to k, which
23758 is the number of data in the tail. The third class is motivated by graphical
23759 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23760 is also implemented here.")
23761 (license license:gpl3)))
23763 (define-public r-awsmethods
23765 (name "r-awsmethods")
23770 (uri (cran-uri "awsMethods" version))
23773 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23775 `((upstream-name . "awsMethods")))
23776 (build-system r-build-system)
23777 (home-page "http://www.wias-berlin.de/software/imaging/")
23778 (synopsis "Class and methods definitions")
23780 "This package defines the generic method @code{extract} and provides
23781 @code{openMP} support as needed in several packages like
23782 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23783 (license license:gpl2+)))
23785 (define-public r-aws
23792 (uri (cran-uri "aws" version))
23795 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23797 `((upstream-name . "aws")))
23798 (build-system r-build-system)
23800 `(("r-awsmethods" ,r-awsmethods)
23803 `(("gfortran" ,gfortran)))
23804 (home-page "https://cran.r-project.org/web/packages/aws/")
23805 (synopsis "Adaptive weights smoothing")
23807 "This package provides a collection of R-functions implementing adaptive
23808 smoothing procedures in 1D, 2D and 3D. This includes the
23809 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23810 Confidence Intervals} (ICI), variational approaches, and a non-local means
23812 (license license:gpl2+)))
23814 (define-public r-sgloptim
23816 (name "r-sgloptim")
23821 (uri (cran-uri "sglOptim" version))
23824 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23826 `((upstream-name . "sglOptim")))
23827 (build-system r-build-system)
23830 ("r-doparallel" ,r-doparallel)
23831 ("r-foreach" ,r-foreach)
23832 ("r-matrix" ,r-matrix)
23834 ("r-rcpparmadillo" ,r-rcpparmadillo)
23835 ("r-rcppprogress" ,r-rcppprogress)))
23837 `(("r-knitr" ,r-knitr)))
23838 (home-page "https://github.com/nielsrhansen/sglOptim")
23839 (synopsis "Generic sparse group Lasso solver")
23841 "This package provides a fast generic solver for sparse group lasso
23842 optimization problems. The loss (objective) function must be defined in a C++
23843 module. The optimization problem is solved using a coordinate gradient
23844 descent algorithm. Convergence of the algorithm is established and the
23845 algorithm is applicable to a broad class of loss functions. Use of parallel
23846 computing for cross validation and subsampling is supported through the
23847 @code{foreach} and @code{doParallel} packages.")
23848 (license license:gpl2+)))
23850 (define-public r-grouped
23857 (uri (cran-uri "grouped" version))
23860 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23862 `((upstream-name . "grouped")))
23863 (build-system r-build-system)
23865 `(("r-mass" ,r-mass)))
23866 (home-page "https://cran.r-project.org/web/packages/grouped/")
23867 (synopsis "Regression analysis of grouped and coarse data")
23869 "This package provides regression models for grouped and coarse data,
23870 under the coarsened at random assumption.")
23871 (license license:gpl2+)))
23873 (define-public r-stam
23880 (uri (cran-uri "stam" version))
23883 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23885 `((upstream-name . "stam")))
23886 (build-system r-build-system)
23890 (home-page "https://cran.r-project.org/web/packages/stam")
23891 (synopsis "Spatio-temporal analysis and modelling")
23893 "This package provides various methods to conduct Spatio-Temporal
23894 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23895 Inferred Spatio-Temporal Modelling.")
23896 (license license:gpl2+)))
23898 (define-public r-dcv
23905 (uri (cran-uri "dcv" version))
23908 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23910 `((upstream-name . "dcv")))
23911 (build-system r-build-system)
23913 `(("r-lmtest" ,r-lmtest)))
23914 (home-page "https://cran.r-project.org/web/packages/dcv/")
23915 (synopsis "Conventional cross-validation statistics for climate-growth model")
23917 "This package performs several conventional cross-validation statistical
23918 methods for climate-growth model in the climate reconstruction from tree
23919 rings, including Sign Test statistic, Reduction of Error statistic, Product
23920 Mean Test, Durbin-Watson statistic etc.")
23921 (license license:gpl2)))
23923 (define-public r-rcdd
23930 (uri (cran-uri "rcdd" version))
23933 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23935 `((upstream-name . "rcdd")))
23936 (build-system r-build-system)
23939 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23940 (synopsis "Computational geometry")
23942 "This package converts back and forth between two representations of a
23943 convex polytope: as solution of a set of linear equalities and inequalities
23944 and as convex hull of set of points and rays. Also does linear programming
23945 and redundant generator elimination. All functions can use exact
23946 infinite-precision rational arithmetic.")
23947 (license license:gpl2)))
23949 (define-public r-rxnat
23956 (uri (cran-uri "Rxnat" version))
23959 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23961 `((upstream-name . "Rxnat")))
23962 (build-system r-build-system)
23964 `(("r-dplyr" ,r-dplyr)
23966 ("r-rcurl" ,r-rcurl)
23967 ("r-tibble" ,r-tibble)))
23969 `(("r-knitr" ,r-knitr)))
23970 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23971 (synopsis "Queries and extracts images from neuroimaging datasets")
23973 "This package allows communication with the Extensible Neuroimaging
23974 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23976 (license license:gpl2)))
23978 (define-public r-rserve
23985 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23986 version ".tar.gz"))
23989 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23990 (build-system r-build-system)
23993 (modify-phases %standard-phases
23994 (add-before 'install 'install-server-binary
23995 ;; Makevars tries to install to R's store directory.
23996 (lambda* (#:key outputs #:allow-other-keys)
23997 (let* ((out (assoc-ref outputs "out"))
23998 (bin (string-append out "/bin")))
23999 (substitute* "src/Makevars.in"
24000 (("\\$\\(R_HOME\\)") out))
24001 (mkdir-p bin)))))))
24003 `(("r-checkmate" ,r-checkmate)
24005 ("r-jsonlite" ,r-jsonlite)
24006 ("r-knitr" ,r-knitr)
24009 ("r-uuid" ,r-uuid)))
24011 `(("openssl" ,openssl)
24013 (home-page "https://github.com/s-u/Rserve")
24015 "Server providing access to R from many languages and systems")
24017 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
24018 binary requests to be sent to R. Every connection has a separate workspace
24019 and working directory. Client-side implementations are available for popular
24020 languages such as C/C++ and Java, allowing any application to use facilities
24021 of R without the need of linking to R code. Rserve supports remote
24022 connection, user authentication and file transfer. A simple R client is
24023 included in this package as well.")
24024 (license license:gpl2)))
24026 (define-public r-gamm4
24033 (uri (cran-uri "gamm4" version))
24036 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
24037 (properties `((upstream-name . "gamm4")))
24038 (build-system r-build-system)
24040 `(("r-lme4" ,r-lme4)
24041 ("r-matrix" ,r-matrix)
24042 ("r-mgcv" ,r-mgcv)))
24043 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24044 (synopsis "Generalized additive mixed models using mgcv and lme4")
24046 "Estimate generalized additive mixed models via a version of function
24047 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24049 (license license:gpl2+)))
24051 (define-public r-optimx
24054 (version "2020-4.2")
24058 (uri (cran-uri "optimx" version))
24061 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24062 (properties `((upstream-name . "optimx")))
24063 (build-system r-build-system)
24064 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24065 (native-inputs `(("r-knitr" ,r-knitr)))
24066 (home-page "https://cran.r-project.org/web/packages/optimx/")
24067 (synopsis "Expanded replacement and extension of the optim function")
24069 "This package provides a replacement and extension of the @code{optim}
24070 function to call to several function minimization codes in R in a single
24071 statement. These methods handle smooth, possibly box constrained functions of
24072 several or many parameters. Note that the function @code{optimr} was prepared
24073 to simplify the incorporation of minimization codes going forward. This
24074 package also implements some utility codes and some extra solvers, including
24075 safeguarded Newton methods. Many methods previously separate are now included
24077 (license license:gpl2)))
24079 (define-public r-projpred
24081 (name "r-projpred")
24086 (uri (cran-uri "projpred" version))
24089 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24090 (properties `((upstream-name . "projpred")))
24091 (build-system r-build-system)
24093 `(("r-dplyr" ,r-dplyr)
24094 ("r-gamm4" ,r-gamm4)
24095 ("r-ggplot2" ,r-ggplot2)
24098 ("r-magrittr" ,r-magrittr)
24101 ("r-optimx" ,r-optimx)
24103 ("r-rcpparmadillo" ,r-rcpparmadillo)
24104 ("r-rngtools" ,r-rngtools)
24105 ("r-rstantools" ,r-rstantools)
24106 ("r-tidyverse" ,r-tidyverse)))
24107 (native-inputs `(("r-knitr" ,r-knitr)))
24108 (home-page "https://mc-stan.org/projpred/")
24109 (synopsis "Projection predictive feature selection")
24111 "This package performs projection predictive feature selection for
24112 generalized linear models and generalized linear and additive multilevel
24113 models. The package is compatible with the @code{rstanarm} and @code{brms}
24114 packages, but other reference models can also be used. See the package
24115 vignette for more information and examples.")
24116 (license license:gpl3)))
24118 (define-public r-brms
24125 (uri (cran-uri "brms" version))
24128 "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1"))))
24129 (properties `((upstream-name . "brms")))
24130 (build-system r-build-system)
24132 `(("r-abind" ,r-abind)
24133 ("r-backports" ,r-backports)
24134 ("r-bayesplot" ,r-bayesplot)
24135 ("r-bridgesampling" ,r-bridgesampling)
24137 ("r-future" ,r-future)
24138 ("r-ggplot2" ,r-ggplot2)
24141 ("r-matrix" ,r-matrix)
24142 ("r-matrixstats" ,r-matrixstats)
24144 ("r-nleqslv" ,r-nleqslv)
24146 ("r-projpred" ,r-projpred)
24148 ("r-rstan" ,r-rstan)
24149 ("r-rstantools" ,r-rstantools)
24150 ("r-shinystan" ,r-shinystan)))
24151 (native-inputs `(("r-knitr" ,r-knitr)))
24153 "https://github.com/paul-buerkner/brms")
24155 "Bayesian Regression Models using 'Stan'")
24157 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24158 using 'Stan' for full Bayesian inference. A wide range of distributions and
24159 link functions are supported, allowing users to fit -- among others -- linear,
24160 robust linear, count data, survival, response times, ordinal, zero-inflated,
24161 hurdle, and even self-defined mixture models all in a multilevel context.
24162 Further modeling options include non-linear and smooth terms, auto-correlation
24163 structures, censored data, meta-analytic standard errors, and quite a few
24164 more. In addition, all parameters of the response distribution can be
24165 predicted in order to perform distributional regression. Prior specifications
24166 are flexible and explicitly encourage users to apply prior distributions that
24167 actually reflect their beliefs. Model fit can easily be assessed and compared
24168 with posterior predictive checks and leave-one-out cross-validation.")
24169 (license license:gpl2)))
24171 (define-public r-mstate
24178 (uri (cran-uri "mstate" version))
24181 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24182 (properties `((upstream-name . "mstate")))
24183 (build-system r-build-system)
24185 `(("r-data-table" ,r-data-table)
24186 ("r-lattice" ,r-lattice)
24187 ("r-magrittr" ,r-magrittr)
24188 ("r-rcolorbrewer" ,r-rcolorbrewer)
24189 ("r-rlang" ,r-rlang)
24190 ("r-survival" ,r-survival)
24191 ("r-viridis" ,r-viridis)))
24193 `(("r-knitr" ,r-knitr)))
24195 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24197 "Data Preparation, Estimation and Prediction in Multi-State Models")
24199 "Contains functions for data preparation, descriptives, hazard estimation
24200 and prediction with Aalen-Johansen or simulation in competing risks and
24201 multi-state models.")
24202 (license license:gpl2+)))
24204 (define-public r-scatterpie
24206 (name "r-scatterpie")
24211 (uri (cran-uri "scatterpie" version))
24214 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24215 (properties `((upstream-name . "scatterpie")))
24216 (build-system r-build-system)
24218 `(("r-ggforce" ,r-ggforce)
24219 ("r-ggplot2" ,r-ggplot2)
24220 ("r-rlang" ,r-rlang)
24221 ("r-rvcheck" ,r-rvcheck)
24222 ("r-tidyr" ,r-tidyr)))
24224 `(("r-knitr" ,r-knitr)))
24225 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24226 (synopsis "Scatter pie plot")
24228 "This package creates scatterpie plots, especially useful for plotting
24230 (license license:artistic2.0)))
24232 (define-public r-scrypt
24239 (uri (cran-uri "scrypt" version))
24242 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24243 (properties `((upstream-name . "scrypt")))
24244 (build-system r-build-system)
24246 `(("r-rcpp" ,r-rcpp)))
24247 (home-page "https://github.com/rstudio/rscrypt")
24248 (synopsis "Key derivation functions for R based on Scrypt")
24250 "This package provides functions for working with the scrypt key
24251 derivation functions. Scrypt is a password-based key derivation function
24252 created by Colin Percival. The algorithm was specifically designed to make it
24253 costly to perform large-scale custom hardware attacks by requiring large
24254 amounts of memory.")
24255 (license license:bsd-2)))
24257 (define-public r-boruta
24264 (uri (cran-uri "Boruta" version))
24267 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24268 (properties `((upstream-name . "Boruta")))
24269 (build-system r-build-system)
24270 (propagated-inputs `(("r-ranger" ,r-ranger)))
24271 (home-page "https://gitlab.com/mbq/Boruta/")
24272 (synopsis "Wrapper algorithm for all relevant feature selection")
24274 "This package provides an all relevant feature selection wrapper
24275 algorithm. It finds relevant features by comparing original attributes'
24276 importance with importance achievable at random, estimated using their
24277 permuted copies (shadows).")
24278 (license license:gpl2+)))
24280 (define-public r-directlabels
24282 (name "r-directlabels")
24283 (version "2021.1.13")
24287 (uri (cran-uri "directlabels" version))
24290 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24291 (build-system r-build-system)
24293 `(("r-quadprog" ,r-quadprog)))
24295 `(("r-knitr" ,r-knitr)))
24296 (home-page "http://directlabels.r-forge.r-project.org/")
24297 (synopsis "Direct labels for multicolor plots")
24299 "This package provides an extensible framework for automatically placing
24300 direct labels onto multicolor plots. Label positions are described using
24301 positioning methods that can be re-used across several different plots. There
24302 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24303 inferring an appropriate positioning method.")
24304 (license license:gpl3)))
24306 (define-public r-lsd
24313 (uri (cran-uri "LSD" version))
24315 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24316 (properties `((upstream-name . "LSD")))
24317 (build-system r-build-system)
24318 (home-page "https://cran.r-project.org/web/packages/LSD/")
24319 (synopsis "Lots of superior depictions tool creates colorful plots")
24321 "This package creates lots of colorful plots in a multitude of variations.
24322 Try a demo of the LSD by running @code{demotour()}.")
24324 (license (list license:gpl2 license:gpl3))))
24326 (define-public r-phylogram
24328 (name "r-phylogram")
24333 (uri (cran-uri "phylogram" version))
24335 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24336 (properties `((upstream-name . "phylogram")))
24337 (build-system r-build-system)
24338 (propagated-inputs `(("r-ape" ,r-ape)))
24339 (home-page "https://github.com/ropensci/phylogram/")
24340 (synopsis "Dendrograms for evolutionary analysis")
24342 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24343 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24344 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24345 as well as several tools for command-line tree manipulation and import/export
24346 via Newick parenthetic text. This improves accessibility to the comprehensive
24347 range of object-specific analytical and tree-visualization functions found
24348 across a wide array of bioinformatic R packages.")
24349 (license license:gpl3)))
24351 (define-public r-kmer
24358 (uri (cran-uri "kmer" version))
24360 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24361 (properties `((upstream-name . "kmer")))
24362 (build-system r-build-system)
24364 `(("r-openssl" ,r-openssl)
24365 ("r-phylogram" ,r-phylogram)
24366 ("r-rcpp" ,r-rcpp)))
24367 (home-page "https://github.com/shaunpwilkinson/kmer/")
24368 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24370 "@code{r-kmer} is an R package for rapidly computing distance matrices
24371 and clustering large sequence datasets using fast alignment-free k-mer
24372 counting and recursive k-means partitioning.")
24373 (license license:gpl3)))
24375 (define-public r-hardhat
24382 (uri (cran-uri "hardhat" version))
24385 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24386 (properties `((upstream-name . "hardhat")))
24387 (build-system r-build-system)
24389 `(("r-glue" ,r-glue)
24390 ("r-rlang" ,r-rlang)
24391 ("r-tibble" ,r-tibble)
24392 ("r-vctrs" ,r-vctrs)))
24394 `(("r-knitr" ,r-knitr)))
24395 (home-page "https://github.com/tidymodels/hardhat")
24396 (synopsis "Construct modeling packages")
24398 "Building modeling packages is hard. A large amount of effort generally
24399 goes into providing an implementation for a new method that is efficient,
24400 fast, and correct, but often less emphasis is put on the user interface. A
24401 good interface requires specialized knowledge about S3 methods and formulas,
24402 which the average package developer might not have. The goal of
24403 @code{hardhat} is to reduce the burden around building new modeling packages
24404 by providing functionality for preprocessing, predicting, and validating
24406 (license license:expat)))
24408 (define-public r-lightgbm
24410 (name "r-lightgbm")
24415 (uri (cran-uri "lightgbm" version))
24418 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24419 (properties `((upstream-name . "lightgbm")))
24420 (build-system r-build-system)
24422 `(("r-data-table" ,r-data-table)
24423 ("r-jsonlite" ,r-jsonlite)
24424 ("r-matrix" ,r-matrix)
24426 (home-page "https://github.com/Microsoft/LightGBM")
24427 (synopsis "Light gradient boosting machine")
24429 "Tree based algorithms can be improved by introducing boosting
24430 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24431 al. (2017). This package offers an R interface to work with it. It is
24432 designed to be distributed and efficient with the following goals:
24435 @item Faster training speed and higher efficiency;
24436 @item lower memory usage;
24437 @item better accuracy;
24438 @item parallel learning supported; and
24439 @item capable of handling large-scale data.
24442 (license license:expat)))
24444 (define-public r-shapforxgboost
24446 (name "r-shapforxgboost")
24451 (uri (cran-uri "SHAPforxgboost" version))
24454 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24456 `((upstream-name . "SHAPforxgboost")))
24457 (build-system r-build-system)
24459 `(("r-bbmisc" ,r-bbmisc)
24460 ("r-data-table" ,r-data-table)
24461 ("r-ggextra" ,r-ggextra)
24462 ("r-ggforce" ,r-ggforce)
24463 ("r-ggplot2" ,r-ggplot2)
24464 ("r-ggpubr" ,r-ggpubr)
24465 ("r-lightgbm" ,r-lightgbm)
24466 ("r-rcolorbrewer" ,r-rcolorbrewer)
24467 ("r-xgboost" ,r-xgboost)))
24468 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24469 (synopsis "SHAP Plots for XGBoost")
24471 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24472 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24473 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24474 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24476 (license license:expat)))
24478 (define-public r-rismed
24485 (uri (cran-uri "RISmed" version))
24488 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24489 (properties `((upstream-name . "RISmed")))
24490 (build-system r-build-system)
24491 (home-page "https://cran.r-project.org/web/packages/RISmed")
24492 (synopsis "Download content from NCBI databases")
24494 "This package provides a set of tools to extract bibliographic
24495 content from the National Center for Biotechnology Information (NCBI)
24496 databases, including PubMed. The name RISmed is a portmanteau of
24497 RIS (for Research Information Systems, a common tag format for
24498 bibliographic data) and PubMed.")
24499 (license license:gpl2+)))
24501 (define-public r-semver
24508 (uri (cran-uri "semver" version))
24511 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24512 (properties `((upstream-name . "semver")))
24513 (build-system r-build-system)
24515 `(("r-assertthat" ,r-assertthat)
24516 ("r-rcpp" ,r-rcpp)))
24517 (native-inputs `(("r-knitr" ,r-knitr)))
24518 (home-page "https://github.com/johndharrison/semver")
24519 (synopsis "Parser for Semantic Versioning 2.0.0")
24521 "This package provides tools and functions for parsing, rendering and
24522 operating on semantic version strings. Semantic versioning is a simple set of
24523 rules and requirements that dictate how version numbers are assigned and
24524 incremented as outlined at @url{http://semver.org}.")
24525 (license license:expat)))
24527 (define-public r-binman
24534 (uri (cran-uri "binman" version))
24537 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24538 (properties `((upstream-name . "binman")))
24539 (build-system r-build-system)
24541 `(("r-assertthat" ,r-assertthat)
24543 ("r-jsonlite" ,r-jsonlite)
24544 ("r-rappdirs" ,r-rappdirs)
24545 ("r-semver" ,r-semver)
24547 ("r-yaml" ,r-yaml)))
24548 (native-inputs `(("r-knitr" ,r-knitr)))
24549 (home-page "https://github.com/ropensci/binman")
24550 (synopsis "Binary download manager")
24552 "This package provides tools and functions for managing the download of
24553 binary files. Binary repositories are defined in the YAML format. Defining
24554 new pre-download, download and post-download templates allow additional
24555 repositories to be added.")
24556 (license license:expat)))
24558 (define-public r-wdman
24565 (uri (cran-uri "wdman" version))
24568 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24569 (properties `((upstream-name . "wdman")))
24570 (build-system r-build-system)
24572 `(("r-assertthat" ,r-assertthat)
24573 ("r-binman" ,r-binman)
24574 ("r-processx" ,r-processx)
24575 ("r-semver" ,r-semver)
24576 ("r-yaml" ,r-yaml)))
24577 (native-inputs `(("r-knitr" ,r-knitr)))
24578 (home-page "https://docs.ropensci.org/wdman/")
24579 (synopsis "Webdriver/Selenium binary manager")
24581 "There are a number of binary files associated with the
24582 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24583 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24584 @url{https://github.com/mozilla/geckodriver},
24585 @url{http://phantomjs.org/download.html}, and
24586 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24587 more information). This package provides functions to download these binaries
24588 and to manage processes involving them.")
24589 (license license:expat)))
24591 (define-public r-rselenium
24593 (name "r-rselenium")
24598 (uri (cran-uri "RSelenium" version))
24601 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24602 (properties `((upstream-name . "RSelenium")))
24603 (build-system r-build-system)
24605 `(("r-binman" ,r-binman)
24606 ("r-catools" ,r-catools)
24608 ("r-openssl" ,r-openssl)
24609 ("r-wdman" ,r-wdman)
24611 (native-inputs `(("r-knitr" ,r-knitr)))
24612 (home-page "https://docs.ropensci.org/RSelenium/")
24613 (synopsis "R bindings for Selenium WebDriver")
24615 "This package provides a set of R bindings for the Selenium 2.0
24616 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24617 information) using the @code{JsonWireProtocol} (see
24618 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24619 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24620 a user would either locally or on a remote machine using the Selenium server
24621 it marks a leap forward in terms of web browser automation. Selenium
24622 automates web browsers (commonly referred to as browsers). Using RSelenium
24623 you can automate browsers locally or remotely.")
24624 (license license:agpl3+)))
24626 (define-public r-conquer
24633 (uri (cran-uri "conquer" version))
24636 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24637 (properties `((upstream-name . "conquer")))
24638 (build-system r-build-system)
24640 `(("r-matrix" ,r-matrix)
24641 ("r-matrixstats" ,r-matrixstats)
24643 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24644 (home-page "https://github.com/XiaoouPan/conquer")
24645 (synopsis "Convolution-type smoothed quantile regression")
24647 "This package provides fast and accurate convolution-type smoothed
24648 quantile regression, implemented using Barzilai-Borwein gradient descent with
24649 a Huber regression warm start. Confidence intervals for regression
24650 coefficients are constructed using multiplier bootstrap.")
24651 (license license:gpl3)))
24653 (define-public r-fastshap
24655 (name "r-fastshap")
24660 (uri (cran-uri "fastshap" version))
24663 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24664 (properties `((upstream-name . "fastshap")))
24665 (build-system r-build-system)
24667 `(("r-abind" ,r-abind)
24668 ("r-ggplot2" ,r-ggplot2)
24669 ("r-gridextra" ,r-gridextra)
24670 ("r-matrixstats" ,r-matrixstats)
24673 ("r-rcpparmadillo" ,r-rcpparmadillo)
24674 ("r-tibble" ,r-tibble)))
24675 (home-page "https://github.com/bgreenwell/fastshap")
24676 (synopsis "Fast approximate Shapley values")
24678 "This package computes fast (relative to other implementations)
24679 approximate Shapley values for any supervised learning model. Shapley values
24680 help to explain the predictions from any black box model using ideas from game
24681 theory; see @url{Strumbel and Kononenko (2014),
24682 doi.org/10.1007/s10115-013-0679-x} for details.")
24683 (license license:gpl2+)))
24685 (define-public r-metrics
24692 (uri (cran-uri "Metrics" version))
24695 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24696 (properties `((upstream-name . "Metrics")))
24697 (build-system r-build-system)
24698 (home-page "https://github.com/mfrasco/Metrics")
24699 (synopsis "Evaluation metrics for machine learning")
24701 "This package provides an implementation of evaluation metrics in R that
24702 are commonly used in supervised machine learning. It implements metrics for
24703 regression, time series, binary classification, classification, and
24704 information retrieval problems. It has zero dependencies and a consistent,
24705 simple interface for all functions.")
24706 (license license:bsd-3)))
24708 (define-public r-iml
24715 (uri (cran-uri "iml" version))
24718 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24719 (properties `((upstream-name . "iml")))
24720 (build-system r-build-system)
24722 `(("r-checkmate" ,r-checkmate)
24723 ("r-data-table" ,r-data-table)
24724 ("r-formula" ,r-formula)
24725 ("r-future" ,r-future)
24726 ("r-future-apply" ,r-future-apply)
24727 ("r-ggplot2" ,r-ggplot2)
24728 ("r-gridextra" ,r-gridextra)
24729 ("r-metrics" ,r-metrics)
24730 ("r-prediction" ,r-prediction)
24732 (native-inputs `(("r-knitr" ,r-knitr)))
24733 (home-page "https://github.com/christophM/iml")
24734 (synopsis "Interpretable machine learning")
24736 "This package provides interpretability methods to analyze the behavior
24737 and predictions of any machine learning model. Implemented methods are:
24740 @item Feature importance described by Fisher et al. (2018),
24741 @item accumulated local effects plots described by Apley (2018),
24742 @item partial dependence plots described by Friedman (2001),
24743 @item individual conditional expectation ('ice') plots described by Goldstein
24744 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24745 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24746 @item the Shapley Value described by Strumbelj et. al (2014)
24747 @url{https://doi.org/10.1007/s10115-013-0679-x},
24748 @item feature interactions described by Friedman et. al
24749 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24752 (license license:expat)))
24754 (define-public r-goftest
24761 (uri (cran-uri "goftest" version))
24764 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24765 (properties `((upstream-name . "goftest")))
24766 (build-system r-build-system)
24767 (home-page "https://github.com/baddstats/goftest")
24768 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24770 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24771 goodness-of-fit for continuous univariate distributions, using efficient
24773 (license license:gpl2+)))
24775 (define-public r-tensor
24782 (uri (cran-uri "tensor" version))
24785 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24786 (properties `((upstream-name . "tensor")))
24787 (build-system r-build-system)
24788 (home-page "https://cran.r-project.org/web/packages/tensor/")
24789 (synopsis "Tensor product of arrays")
24791 "The tensor product of two arrays is notionally an outer product of the
24792 arrays collapsed in specific extents by summing along the appropriate
24793 diagonals. This package allows you to compute the tensor product of arrays.")
24794 (license license:gpl2+)))
24796 (define-public r-spatstat-utils
24798 (name "r-spatstat-utils")
24803 (uri (cran-uri "spatstat.utils" version))
24806 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24808 `((upstream-name . "spatstat.utils")))
24809 (build-system r-build-system)
24810 (home-page "http://www.spatstat.org")
24811 (synopsis "Utility functions for spatstat")
24813 "This package contains utility functions for the @code{spatstat} package
24814 which may also be useful for other purposes.")
24815 (license license:gpl2+)))
24817 (define-public r-spatstat-sparse
24819 (name "r-spatstat-sparse")
24824 (uri (cran-uri "spatstat.sparse" version))
24827 "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2"))))
24829 `((upstream-name . "spatstat.sparse")))
24830 (build-system r-build-system)
24832 `(("r-abind" ,r-abind)
24833 ("r-matrix" ,r-matrix)
24834 ("r-spatstat-utils" ,r-spatstat-utils)
24835 ("r-tensor" ,r-tensor)))
24836 (home-page "http://spatstat.org/")
24837 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
24839 "This package defines sparse three-dimensional arrays and supports
24840 standard operations on them. The package also includes utility functions for
24841 matrix calculations that are common in statistics, such as quadratic forms.")
24842 (license license:gpl2+)))
24844 (define-public r-spatstat-data
24846 (name "r-spatstat-data")
24851 (uri (cran-uri "spatstat.data" version))
24854 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24855 (properties `((upstream-name . "spatstat.data")))
24856 (build-system r-build-system)
24858 `(("r-matrix" ,r-matrix)
24859 ("r-spatstat-utils" ,r-spatstat-utils)))
24860 (home-page "http://www.spatstat.org")
24861 (synopsis "Datasets for spatstat")
24863 "This package contains all the datasets for the @code{spatstat}
24865 (license license:gpl2+)))
24867 (define-public r-spatstat-geom
24869 (name "r-spatstat-geom")
24874 (uri (cran-uri "spatstat.geom" version))
24877 "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk"))))
24878 (properties `((upstream-name . "spatstat.geom")))
24879 (build-system r-build-system)
24881 `(("r-deldir" ,r-deldir)
24882 ("r-polyclip" ,r-polyclip)
24883 ("r-spatstat-data" ,r-spatstat-data)
24884 ("r-spatstat-sparse" ,r-spatstat-sparse)
24885 ("r-spatstat-utils" ,r-spatstat-utils)))
24886 (home-page "http://spatstat.org/")
24887 (synopsis "Geometrical functionality of the spatstat package")
24889 "This is a subset of the original spatstat package, containing the
24890 user-level code from spatstat which performs geometrical operations, except
24891 for the geometry of linear networks.")
24892 (license license:gpl2+)))
24894 (define-public r-spatstat-core
24896 (name "r-spatstat-core")
24901 (uri (cran-uri "spatstat.core" version))
24904 "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3"))))
24905 (properties `((upstream-name . "spatstat.core")))
24906 (build-system r-build-system)
24908 `(("r-abind" ,r-abind)
24909 ("r-goftest" ,r-goftest)
24910 ("r-matrix" ,r-matrix)
24913 ("r-rpart" ,r-rpart)
24914 ("r-spatstat-data" ,r-spatstat-data)
24915 ("r-spatstat-geom" ,r-spatstat-geom)
24916 ("r-spatstat-sparse" ,r-spatstat-sparse)
24917 ("r-spatstat-utils" ,r-spatstat-utils)
24918 ("r-tensor" ,r-tensor)))
24919 (home-page "http://spatstat.org/")
24920 (synopsis "Core functionality of the spatstat package")
24922 "This is a subset of the original spatstat package, containing all of the
24923 user-level code from spatstat, except for the code for linear networks.")
24924 (license license:gpl2+)))
24926 (define-public r-spatstat-linnet
24928 (name "r-spatstat-linnet")
24933 (uri (cran-uri "spatstat.linnet" version))
24936 "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv"))))
24938 `((upstream-name . "spatstat.linnet")))
24939 (build-system r-build-system)
24941 `(("r-matrix" ,r-matrix)
24942 ("r-spatstat-core" ,r-spatstat-core)
24943 ("r-spatstat-data" ,r-spatstat-data)
24944 ("r-spatstat-geom" ,r-spatstat-geom)
24945 ("r-spatstat-utils" ,r-spatstat-utils)))
24946 (home-page "http://spatstat.org/")
24947 (synopsis "Linear networks functionality of the spatstat package")
24949 "This is a subset of the spatstat package, containing its functionality
24950 for spatial data on a linear network.")
24951 (license license:gpl2+)))
24953 (define-public r-spatstat
24955 (name "r-spatstat")
24960 (uri (cran-uri "spatstat" version))
24963 "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw"))))
24964 (properties `((upstream-name . "spatstat")))
24965 (build-system r-build-system)
24967 `(("r-spatstat-core" ,r-spatstat-core)
24968 ("r-spatstat-data" ,r-spatstat-data)
24969 ("r-spatstat-geom" ,r-spatstat-geom)
24970 ("r-spatstat-linnet" ,r-spatstat-linnet)
24971 ("r-spatstat-utils" ,r-spatstat-utils)))
24972 (home-page "http://www.spatstat.org")
24973 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24975 "This package provides a comprehensive toolbox for analysing Spatial
24976 Point Patterns. It is focused mainly on two-dimensional point patterns,
24977 including multitype/marked points, in any spatial region. It also supports
24978 three-dimensional point patterns, space-time point patterns in any number of
24979 dimensions, point patterns on a linear network, and patterns of other
24980 geometrical objects. It supports spatial covariate data such as pixel images
24981 and contains over 2000 functions for plotting spatial data, exploratory data
24982 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24983 formal inference.")
24984 (license license:gpl2+)))
24986 (define-public r-gaston
24993 (uri (cran-uri "gaston" version))
24996 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24997 (properties `((upstream-name . "gaston")))
24998 (build-system r-build-system)
24999 (inputs `(("zlib" ,zlib)))
25001 `(("r-rcpp" ,r-rcpp)
25002 ("r-rcppeigen" ,r-rcppeigen)
25003 ("r-rcppparallel" ,r-rcppparallel)))
25004 (native-inputs `(("r-knitr" ,r-knitr)))
25005 (home-page "https://cran.r-project.org/web/packages/gaston/")
25006 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
25008 "This is a package for the manipulation of genetic data (SNPs).
25009 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
25010 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
25011 for linear mixed models (AIREML).")
25012 (license license:gpl3)))
25014 (define-public r-cpp11
25021 (uri (cran-uri "cpp11" version))
25024 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
25025 (properties `((upstream-name . "cpp11")))
25026 (build-system r-build-system)
25027 (native-inputs `(("r-knitr" ,r-knitr)))
25028 (home-page "https://github.com/r-lib/cpp11")
25029 (synopsis "C++11 Interface for R's C Interface")
25031 "This package provides a header only, C++11 interface to R's C interface.
25032 Compared to other approaches @code{cpp11} strives to be safe against long
25033 jumps from the C API as well as C++ exceptions, conform to normal R function
25034 semantics and supports interaction with @code{ALTREP} vectors.")
25035 (license license:expat)))
25037 (define-public r-rcppziggurat
25039 (name "r-rcppziggurat")
25044 (uri (cran-uri "RcppZiggurat" version))
25047 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
25048 (properties `((upstream-name . "RcppZiggurat")))
25049 (build-system r-build-system)
25051 `(("r-rcpp" ,r-rcpp)
25052 ("r-rcppgsl" ,r-rcppgsl)))
25053 (native-inputs `(("r-knitr" ,r-knitr)))
25054 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
25055 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
25057 "The Ziggurat generator for normally distributed random numbers,
25058 originally proposed by Marsaglia and Tsang (2000,
25059 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
25060 times starting with Leong et al (2005,
25061 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
25062 aggregation for comparing different implementations in order to provide a
25063 'faster but good enough' alternative for use with R and C++ code.")
25064 (license license:gpl2+)))
25066 (define-public r-rfast
25073 (uri (cran-uri "Rfast" version))
25076 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
25077 (properties `((upstream-name . "Rfast")))
25078 (build-system r-build-system)
25080 `(("r-rcpp" ,r-rcpp)
25081 ("r-rcpparmadillo" ,r-rcpparmadillo)
25082 ("r-rcppziggurat" ,r-rcppziggurat)))
25083 (home-page "https://github.com/RfastOfficial/Rfast")
25084 (synopsis "Collection of efficient and fast R functions")
25086 "This package provides a collection of fast (utility) functions for data
25087 analysis. Column- and row- wise means, medians, variances, minimums,
25088 maximums, many t, F and G-square tests, many regressions (normal, logistic,
25089 Poisson), are some of the many fast functions.")
25090 (license license:gpl2+)))
25092 (define-public r-clusterr
25094 (name "r-clusterr")
25099 (uri (cran-uri "ClusterR" version))
25102 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
25103 (properties `((upstream-name . "ClusterR")))
25104 (build-system r-build-system)
25106 `(("r-ggplot2" ,r-ggplot2)
25108 ("r-gtools" ,r-gtools)
25110 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25111 (native-inputs `(("r-knitr" ,r-knitr)))
25112 (home-page "https://github.com/mlampros/ClusterR")
25113 (synopsis "Clustering")
25115 "This package provides Gaussian mixture models, k-means,
25116 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
25117 option to plot, validate, predict (new data) and estimate the optimal number
25118 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
25119 the computationally intensive parts of the functions. For more information,
25123 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
25124 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
25125 @url{https://doi.org/10.18637/jss.v001.i04};
25126 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
25127 Library, @url{https://doi.org/10.1145/1772690.1772862};
25128 @item \"Armadillo: a template-based C++ library
25129 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
25130 Software, @url{https://doi.org/10.21105/joss.00026};
25131 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
25132 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
25133 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
25136 (license license:gpl3)))
25138 (define-public r-spectrum
25140 (name "r-spectrum")
25145 (uri (cran-uri "Spectrum" version))
25148 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25149 (properties `((upstream-name . "Spectrum")))
25150 (build-system r-build-system)
25152 `(("r-clusterr" ,r-clusterr)
25153 ("r-diptest" ,r-diptest)
25154 ("r-ggplot2" ,r-ggplot2)
25155 ("r-rfast" ,r-rfast)))
25156 (native-inputs `(("r-knitr" ,r-knitr)))
25157 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25158 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25160 "This package provides a self-tuning spectral clustering method for
25161 single or multi-view data. Spectrum uses a new type of adaptive density aware
25162 kernel that strengthens connections in the graph based on common nearest
25163 neighbours. It uses a tensor product graph data integration and diffusion
25164 procedure to integrate different data sources and reduce noise. Spectrum uses
25165 either the eigengap or multimodality gap heuristics to determine the number of
25166 clusters. The method is sufficiently flexible so that a wide range of
25167 Gaussian and non-Gaussian structures can be clustered with automatic selection
25169 (license license:agpl3+)))
25171 (define-public r-nabor
25178 (uri (cran-uri "nabor" version))
25181 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25182 (properties `((upstream-name . "nabor")))
25183 (build-system r-build-system)
25187 ("r-rcppeigen" ,r-rcppeigen)))
25188 (home-page "https://cran.r-project.org/web/packages/nabor/")
25189 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25191 "This package provides an R wrapper for libnabo, an exact or approximate
25192 k nearest neighbour library which is optimised for low dimensional
25193 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25194 designed as a drop-in replacement for the RANN function @code{nn2}. In
25195 addition, objects which include the k-d tree search structure can be returned
25196 to speed up repeated queries of the same set of target points.")
25197 (license license:bsd-3)))
25199 (define-public r-muhaz
25202 (version "1.2.6.1")
25206 (uri (cran-uri "muhaz" version))
25209 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25210 (properties `((upstream-name . "muhaz")))
25211 (build-system r-build-system)
25213 `(("r-survival" ,r-survival)))
25215 `(("gfortran" ,gfortran)))
25216 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25217 (synopsis "Hazard function estimation in survival analysis")
25219 "This package produces a smooth estimate of the hazard function for
25221 ;; Any version of the GPL.
25222 (license license:gpl3+)))
25224 (define-public r-flexsurv
25226 (name "r-flexsurv")
25231 (uri (cran-uri "flexsurv" version))
25234 "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9"))))
25235 (properties `((upstream-name . "flexsurv")))
25236 (build-system r-build-system)
25238 `(("r-assertthat" ,r-assertthat)
25239 ("r-desolve" ,r-desolve)
25240 ("r-dplyr" ,r-dplyr)
25241 ("r-generics" ,r-generics)
25242 ("r-magrittr" ,r-magrittr)
25243 ("r-matrix" ,r-matrix)
25244 ("r-mstate" ,r-mstate)
25245 ("r-muhaz" ,r-muhaz)
25246 ("r-mvtnorm" ,r-mvtnorm)
25247 ("r-numderiv" ,r-numderiv)
25248 ("r-purrr" ,r-purrr)
25249 ("r-quadprog" ,r-quadprog)
25251 ("r-rlang" ,r-rlang)
25252 ("r-rstpm2" ,r-rstpm2)
25253 ("r-survival" ,r-survival)
25254 ("r-tibble" ,r-tibble)
25255 ("r-tidyr" ,r-tidyr)
25256 ("r-tidyselect" ,r-tidyselect)))
25258 `(("r-knitr" ,r-knitr)))
25259 (home-page "https://github.com/chjackson/flexsurv-dev")
25260 (synopsis "Flexible parametric survival and multi-state models")
25262 "This package provides flexible parametric models for time-to-event data,
25263 including the Royston-Parmar spline model, generalized gamma and generalized F
25264 distributions. Any user-defined parametric distribution can be fitted, given
25265 at least an R function defining the probability density or hazard. There are
25266 also tools for fitting and predicting from fully parametric multi-state
25268 (license license:gpl2+)))
25270 (define-public r-transphylo
25272 (name "r-transphylo")
25277 (uri (cran-uri "TransPhylo" version))
25280 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25281 (properties `((upstream-name . "TransPhylo")))
25282 (build-system r-build-system)
25285 ("r-rcpp" ,r-rcpp)))
25287 `(("r-knitr" ,r-knitr)))
25288 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25289 (synopsis "Inference of transmission tree from a dated phylogeny")
25291 "This is a package to infer transmission trees from a dated phylogeny.
25292 It includes methods to simulate and analyze outbreaks. The methodology is
25293 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25294 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25295 (license license:gpl2+)))
25297 (define-public r-km-ci
25304 (uri (cran-uri "km.ci" version))
25307 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25308 (properties `((upstream-name . "km.ci")))
25309 (build-system r-build-system)
25311 `(("r-survival" ,r-survival)))
25312 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25313 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25315 "This package computes various @dfn{confidence intervals} (CI) for the
25316 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25317 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25318 Nair and Hall and Wellner.")
25319 (license license:gpl2+)))
25321 (define-public r-kmsurv
25328 (uri (cran-uri "KMsurv" version))
25331 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25332 (properties `((upstream-name . "KMsurv")))
25333 (build-system r-build-system)
25334 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25335 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25337 "This package provides data sets and functions for Klein and Moeschberger
25338 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25340 (license license:gpl3+)))
25342 (define-public r-survmisc
25344 (name "r-survmisc")
25349 (uri (cran-uri "survMisc" version))
25352 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25353 (properties `((upstream-name . "survMisc")))
25354 (build-system r-build-system)
25356 `(("r-data-table" ,r-data-table)
25357 ("r-ggplot2" ,r-ggplot2)
25358 ("r-gridextra" ,r-gridextra)
25359 ("r-km-ci" ,r-km-ci)
25360 ("r-kmsurv" ,r-kmsurv)
25361 ("r-knitr" ,r-knitr)
25362 ("r-survival" ,r-survival)
25363 ("r-xtable" ,r-xtable)
25366 `(("r-knitr" ,r-knitr)))
25367 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25368 (synopsis "Miscellaneous functions for survival data")
25370 "This package provides a collection of functions to help in the analysis
25371 of right-censored survival data. These extend the methods available in
25372 the @code{survival} package.")
25373 (license license:gpl2)))
25375 (define-public r-exactranktests
25377 (name "r-exactranktests")
25382 (uri (cran-uri "exactRankTests" version))
25385 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25387 `((upstream-name . "exactRankTests")))
25388 (build-system r-build-system)
25389 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25390 (synopsis "Exact distributions for rank and permutation tests")
25392 "This package computes exact conditional p-values and quantiles using an
25393 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25394 (license license:gpl2+)))
25396 (define-public r-maxstat
25403 (uri (cran-uri "maxstat" version))
25406 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25407 (properties `((upstream-name . "maxstat")))
25408 (build-system r-build-system)
25410 `(("r-exactranktests" ,r-exactranktests)
25411 ("r-mvtnorm" ,r-mvtnorm)))
25412 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25413 (synopsis "Maximally selected rank statistics")
25415 "This package provides maximally selected rank statistics with several
25416 p-value approximations.")
25417 (license license:gpl2+)))
25419 (define-public r-survminer
25421 (name "r-survminer")
25426 (uri (cran-uri "survminer" version))
25429 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
25430 (properties `((upstream-name . "survminer")))
25431 (build-system r-build-system)
25433 `(("r-broom" ,r-broom)
25434 ("r-dplyr" ,r-dplyr)
25435 ("r-ggplot2" ,r-ggplot2)
25436 ("r-ggpubr" ,r-ggpubr)
25437 ("r-ggtext" ,r-ggtext)
25438 ("r-gridextra" ,r-gridextra)
25439 ("r-magrittr" ,r-magrittr)
25440 ("r-maxstat" ,r-maxstat)
25441 ("r-purrr" ,r-purrr)
25442 ("r-rlang" ,r-rlang)
25443 ("r-scales" ,r-scales)
25444 ("r-survival" ,r-survival)
25445 ("r-survmisc" ,r-survmisc)
25446 ("r-tibble" ,r-tibble)
25447 ("r-tidyr" ,r-tidyr)))
25449 `(("r-knitr" ,r-knitr)))
25450 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25451 (synopsis "Drawing survival curves using ggplot2")
25453 "This package contains the function @code{ggsurvplot()} for easily
25454 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25455 risk' table and 'censoring count plot'. Other functions are also available to
25456 plot adjusted curves for Cox model and to visually examine Cox model
25458 (license license:gpl2)))
25460 (define-public r-forge
25467 (uri (cran-uri "forge" version))
25470 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25471 (properties `((upstream-name . "forge")))
25472 (build-system r-build-system)
25474 `(("r-magrittr" ,r-magrittr)
25475 ("r-rlang" ,r-rlang)))
25476 (home-page "https://cran.r-project.org/web/packages/forge/")
25477 (synopsis "Cast values into shape")
25479 "This package provides helper functions with a consistent interface to
25480 coerce and verify the types and shapes of values for input checking.")
25481 (license license:asl2.0)))
25483 (define-public r-config
25490 (uri (cran-uri "config" version))
25493 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25494 (properties `((upstream-name . "config")))
25495 (build-system r-build-system)
25497 `(("r-yaml" ,r-yaml)))
25499 `(("r-knitr" ,r-knitr)))
25500 (home-page "https://github.com/rstudio/config")
25501 (synopsis "Manage environment specific configuration values")
25503 "This package lets you manage configuration values across multiple
25504 environments (e.g. development, test, production). It reads values using a
25505 function that determines the current environment and returns the appropriate
25507 (license license:gpl3)))
25509 (define-public r-adaptivesparsity
25511 (name "r-adaptivesparsity")
25515 (uri (cran-uri "AdaptiveSparsity" version))
25518 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25520 `((upstream-name . "AdaptiveSparsity")))
25521 (build-system r-build-system)
25524 (modify-phases %standard-phases
25525 (add-after 'unpack 'link-against-armadillo
25527 (substitute* "src/Makevars"
25528 (("PKG_LIBS=" prefix)
25529 (string-append prefix "-larmadillo")))
25532 `(("r-mass" ,r-mass)
25533 ("r-matrix" ,r-matrix)
25535 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25537 `(("armadillo" ,armadillo)))
25538 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25539 (synopsis "Adaptive sparsity models")
25541 "This package implements the Figueiredo machine learning algorithm for
25542 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25543 geometric models.")
25544 (license license:lgpl3+)))
25546 (define-public r-diffusionmap
25548 (name "r-diffusionmap")
25553 (uri (cran-uri "diffusionMap" version))
25556 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25557 (properties `((upstream-name . "diffusionMap")))
25558 (build-system r-build-system)
25560 `(("r-igraph" ,r-igraph)
25561 ("r-matrix" ,r-matrix)
25562 ("r-scatterplot3d" ,r-scatterplot3d)))
25563 (home-page "https://www.r-project.org")
25564 (synopsis "Diffusion map")
25565 (description "This package implements the diffusion map method of data
25566 parametrization, including creation and visualization of diffusion maps,
25567 clustering with diffusion K-means and regression using the adaptive regression
25569 (license license:gpl2)))
25571 (define-public r-igraph
25578 (uri (cran-uri "igraph" version))
25581 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25582 (build-system r-build-system)
25584 `(("gfortran" ,gfortran)))
25588 ("libxml2" ,libxml2)
25591 `(("r-magrittr" ,r-magrittr)
25592 ("r-matrix" ,r-matrix)
25593 ("r-pkgconfig" ,r-pkgconfig)))
25594 (home-page "https://igraph.org")
25595 (synopsis "Network analysis and visualization")
25597 "This package provides routines for simple graphs and network analysis.
25598 It can handle large graphs very well and provides functions for generating
25599 random and regular graphs, graph visualization, centrality methods and much
25601 (license license:gpl2+)))
25603 (define-public r-workflows
25605 (name "r-workflows")
25610 (uri (cran-uri "workflows" version))
25613 "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz"))))
25614 (properties `((upstream-name . "workflows")))
25615 (build-system r-build-system)
25618 ("r-ellipsis" ,r-ellipsis)
25619 ("r-generics" ,r-generics)
25621 ("r-hardhat" ,r-hardhat)
25622 ("r-parsnip" ,r-parsnip)
25623 ("r-rlang" ,r-rlang)
25624 ("r-tidyselect" ,r-tidyselect)
25625 ("r-vctrs" ,r-vctrs)))
25627 `(("r-knitr" ,r-knitr)))
25628 (home-page "https://github.com/tidymodels/workflows")
25629 (synopsis "Modeling workflows")
25631 "A workflow is an object that can bundle together your pre-processing,
25632 modeling, and post-processing requests. For example, if you have a
25633 @code{recipe} and @code{parsnip} model, these can be combined into a
25634 workflow. The advantages are:
25637 @item You don’t have to keep track of separate objects in your workspace.
25638 @item The recipe prepping and model fitting can be executed using a single
25639 call to @code{fit()}.
25640 @item If you have custom tuning parameter settings, these can be defined using
25641 a simpler interface when combined with @code{tune}.
25642 @item In the future, workflows will be able to add post-processing operations,
25643 such as modifying the probability cutoff for two-class models.
25646 (license license:expat)))
25648 (define-public r-gpfit
25655 (uri (cran-uri "GPfit" version))
25658 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25659 (properties `((upstream-name . "GPfit")))
25660 (build-system r-build-system)
25662 `(("r-lattice" ,r-lattice)
25664 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25665 (synopsis "Gaussian Processes modeling")
25667 "This package provides a computationally stable approach of fitting a
25668 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25669 (license license:gpl2)))
25671 (define-public r-yardstick
25673 (name "r-yardstick")
25678 (uri (cran-uri "yardstick" version))
25681 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25682 (properties `((upstream-name . "yardstick")))
25683 (build-system r-build-system)
25685 `(("r-dplyr" ,r-dplyr)
25686 ("r-generics" ,r-generics)
25688 ("r-rlang" ,r-rlang)
25689 ("r-tidyselect" ,r-tidyselect)))
25691 `(("r-knitr" ,r-knitr)))
25692 (home-page "https://github.com/tidymodels/yardstick")
25693 (synopsis "Tidy characterizations of model performance")
25695 "This package provides tidy tools for quantifying how well a model fits
25696 to a data set such as confusion matrices, class probability curve summaries,
25697 and regression metrics (e.g., RMSE).")
25698 (license license:gpl2)))
25700 (define-public r-warp
25707 (uri (cran-uri "warp" version))
25710 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25711 (properties `((upstream-name . "warp")))
25712 (build-system r-build-system)
25713 (native-inputs `(("r-knitr" ,r-knitr)))
25714 (home-page "https://github.com/DavisVaughan/warp")
25715 (synopsis "Group dates")
25717 "This package provides tooling to group dates by a variety of periods
25718 including: yearly, monthly, by second, by week of the month, and more. The
25719 groups are defined in such a way that they also represent the distance between
25720 dates in terms of the period. This extracts valuable information that can be
25721 used in further calculations that rely on a specific temporal spacing between
25723 (license license:expat)))
25725 (define-public r-slider
25732 (uri (cran-uri "slider" version))
25735 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25736 (properties `((upstream-name . "slider")))
25737 (build-system r-build-system)
25739 `(("r-glue" ,r-glue)
25740 ("r-rlang" ,r-rlang)
25741 ("r-vctrs" ,r-vctrs)
25742 ("r-warp" ,r-warp)))
25743 (native-inputs `(("r-knitr" ,r-knitr)))
25744 (home-page "https://github.com/DavisVaughan/slider")
25745 (synopsis "Sliding window functions")
25747 "This package provides type-stable rolling window functions over any R
25748 data type. Cumulative and expanding windows are also supported. For more
25749 advanced usage, an index can be used as a secondary vector that defines how
25750 sliding windows are to be created.")
25751 (license license:expat)))
25753 (define-public r-rsample
25760 (uri (cran-uri "rsample" version))
25763 "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c"))))
25764 (properties `((upstream-name . "rsample")))
25765 (build-system r-build-system)
25767 `(("r-dplyr" ,r-dplyr)
25768 ("r-ellipsis" ,r-ellipsis)
25769 ("r-furrr" ,r-furrr)
25770 ("r-generics" ,r-generics)
25771 ("r-purrr" ,r-purrr)
25772 ("r-rlang" ,r-rlang)
25773 ("r-slider" ,r-slider)
25774 ("r-tibble" ,r-tibble)
25775 ("r-tidyr" ,r-tidyr)
25776 ("r-tidyselect" ,r-tidyselect)
25777 ("r-vctrs" ,r-vctrs)))
25779 `(("r-knitr" ,r-knitr)))
25780 (home-page "https://rsample.tidymodels.org")
25781 (synopsis "General resampling infrastructure")
25783 "This package provides classes and functions to create and summarize
25784 different types of resampling objects (e.g. bootstrap, cross-validation).")
25785 (license license:gpl2)))
25787 (define-public r-dicedesign
25789 (name "r-dicedesign")
25794 (uri (cran-uri "DiceDesign" version))
25797 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
25798 (properties `((upstream-name . "DiceDesign")))
25799 (build-system r-build-system)
25800 (home-page "http://dice.emse.fr/")
25801 (synopsis "Designs of computer experiments")
25803 "This package provides tools to create some specific @code{Space-Filling
25804 Design} (SFD) and to test their quality.")
25805 (license license:gpl3)))
25807 (define-public r-dials
25814 (uri (cran-uri "dials" version))
25817 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25818 (properties `((upstream-name . "dials")))
25819 (build-system r-build-system)
25821 `(("r-dicedesign" ,r-dicedesign)
25822 ("r-dplyr" ,r-dplyr)
25824 ("r-purrr" ,r-purrr)
25825 ("r-rlang" ,r-rlang)
25826 ("r-scales" ,r-scales)
25827 ("r-tibble" ,r-tibble)
25828 ("r-vctrs" ,r-vctrs)
25829 ("r-withr" ,r-withr)))
25830 (native-inputs `(("r-knitr" ,r-knitr)))
25831 (home-page "https://dials.tidymodels.org/")
25832 (synopsis "Tools for creating tuning parameter values")
25834 "Many models contain tuning parameters (i.e. parameters that cannot be
25835 directly estimated from the data). These tools can be used to define objects
25836 for creating, simulating, or validating values for such parameters.")
25837 (license license:gpl2)))
25839 (define-public r-tune
25846 (uri (cran-uri "tune" version))
25849 "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293"))))
25850 (properties `((upstream-name . "tune")))
25851 (build-system r-build-system)
25854 ("r-dials" ,r-dials)
25855 ("r-dplyr" ,r-dplyr)
25856 ("r-foreach" ,r-foreach)
25857 ("r-generics" ,r-generics)
25858 ("r-ggplot2" ,r-ggplot2)
25860 ("r-gpfit" ,r-gpfit)
25861 ("r-parsnip" ,r-parsnip)
25862 ("r-purrr" ,r-purrr)
25863 ("r-recipes" ,r-recipes)
25864 ("r-rlang" ,r-rlang)
25865 ("r-rsample" ,r-rsample)
25866 ("r-tibble" ,r-tibble)
25867 ("r-tidyr" ,r-tidyr)
25868 ("r-vctrs" ,r-vctrs)
25869 ("r-workflows" ,r-workflows)
25870 ("r-yardstick" ,r-yardstick)))
25871 (home-page "https://github.com/tidymodels/tune")
25872 (synopsis "Tidy tuning tools")
25874 "The ability to tune models is important. @code{tune} contains functions
25875 and classes to be used in conjunction with other @code{tidymodels} packages
25876 for finding reasonable values of hyper-parameters in models, pre-processing
25877 methods, and post-processing steps.")
25878 (license license:expat)))
25880 (define-public r-tidyposterior
25882 (name "r-tidyposterior")
25887 (uri (cran-uri "tidyposterior" version))
25890 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25891 (properties `((upstream-name . "tidyposterior")))
25892 (build-system r-build-system)
25894 `(("r-dplyr" ,r-dplyr)
25895 ("r-generics" ,r-generics)
25896 ("r-ggplot2" ,r-ggplot2)
25897 ("r-lifecycle" ,r-lifecycle)
25898 ("r-purrr" ,r-purrr)
25899 ("r-rlang" ,r-rlang)
25900 ("r-rsample" ,r-rsample)
25901 ("r-rstanarm" ,r-rstanarm)
25902 ("r-tibble" ,r-tibble)
25903 ("r-tidyr" ,r-tidyr)
25904 ("r-vctrs" ,r-vctrs)))
25906 `(("r-knitr" ,r-knitr)))
25907 (home-page "https://tidyposterior.tidymodels.org")
25908 (synopsis "Bayesian analysis to compare models using resampling statistics")
25910 "This package can be used to conduct post hoc analyses of resampling
25911 results generated by models. For example, if two models are evaluated with
25912 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25913 are 10 paired statistics. These can be used to make comparisons between
25914 models without involving a test set.")
25915 (license license:gpl2)))
25917 (define-public r-tidypredict
25919 (name "r-tidypredict")
25924 (uri (cran-uri "tidypredict" version))
25927 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25928 (properties `((upstream-name . "tidypredict")))
25929 (build-system r-build-system)
25931 `(("r-dplyr" ,r-dplyr)
25932 ("r-generics" ,r-generics)
25933 ("r-knitr" ,r-knitr)
25934 ("r-purrr" ,r-purrr)
25935 ("r-rlang" ,r-rlang)
25936 ("r-stringr" ,r-stringr)
25937 ("r-tibble" ,r-tibble)
25938 ("r-tidyr" ,r-tidyr)))
25940 `(("r-knitr" ,r-knitr)))
25941 (home-page "https://tidypredict.tidymodels.org")
25942 (synopsis "Run predictions inside the database")
25944 "This package parses a fitted R model object, and returns a formula in
25945 Tidy Eval code that calculates the predictions. It works with several
25946 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25947 final SQL translation of the algorithm. It currently supports @code{lm()},
25948 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25949 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25950 (license license:gpl3)))
25952 (define-public r-janeaustenr
25954 (name "r-janeaustenr")
25959 (uri (cran-uri "janeaustenr" version))
25962 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25963 (properties `((upstream-name . "janeaustenr")))
25964 (build-system r-build-system)
25965 (home-page "https://github.com/juliasilge/janeaustenr")
25966 (synopsis "Jane Austen's complete novels")
25968 "This package provides the full texts for Jane Austen's six completed
25969 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25970 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25971 and \"Persuasion\".")
25972 (license license:expat)))
25974 (define-public r-tokenizers
25976 (name "r-tokenizers")
25981 (uri (cran-uri "tokenizers" version))
25984 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
25985 (properties `((upstream-name . "tokenizers")))
25986 (build-system r-build-system)
25988 `(("r-rcpp" ,r-rcpp)
25989 ("r-snowballc" ,r-snowballc)
25990 ("r-stringi" ,r-stringi)))
25992 `(("r-knitr" ,r-knitr)))
25993 (home-page "https://lincolnmullen.com/software/tokenizers/")
25994 (synopsis "Fast, consistent tokenization of natural language text")
25996 "This is a package for converting natural language text into tokens.
25997 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
25998 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
25999 Treebank, regular expressions, as well as functions for counting characters,
26000 words, and sentences, and a function for splitting longer texts into separate
26001 documents, each with the same number of words. The tokenizers have a
26002 consistent interface, and the package is built on the @code{stringi} and
26003 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
26004 (license license:expat)))
26006 (define-public r-hunspell
26008 (name "r-hunspell")
26013 (uri (cran-uri "hunspell" version))
26016 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
26017 (properties `((upstream-name . "hunspell")))
26018 (build-system r-build-system)
26020 `(("r-digest" ,r-digest)
26021 ("r-rcpp" ,r-rcpp)))
26023 `(("r-knitr" ,r-knitr)))
26024 (home-page "https://github.com/ropensci/hunspell#readme")
26025 (synopsis "High-performance stemmer, tokenizer, and spell checker")
26027 "This package provides a low-level spell checker and morphological
26028 analyzer based on the famous @code{hunspell} library. The package can analyze
26029 or check individual words as well as parse text, LaTeX, HTML or XML documents.
26030 For a more user-friendly interface use the @code{spelling} package which
26031 builds on this package to automate checking of files, documentation and
26032 vignettes in all common formats.")
26033 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
26034 ;; MPL; in addition to these licenses the rest of the R wrapper is also
26035 ;; available under the Expat license.
26036 (license (list license:gpl2
26041 (define-public r-tidytext
26043 (name "r-tidytext")
26048 (uri (cran-uri "tidytext" version))
26051 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
26052 (properties `((upstream-name . "tidytext")))
26053 (build-system r-build-system)
26055 `(("r-dplyr" ,r-dplyr)
26056 ("r-generics" ,r-generics)
26057 ("r-hunspell" ,r-hunspell)
26058 ("r-janeaustenr" ,r-janeaustenr)
26059 ("r-lifecycle" ,r-lifecycle)
26060 ("r-matrix" ,r-matrix)
26061 ("r-purrr" ,r-purrr)
26062 ("r-rlang" ,r-rlang)
26063 ("r-stringr" ,r-stringr)
26064 ("r-tibble" ,r-tibble)
26065 ("r-tokenizers" ,r-tokenizers)
26066 ("r-vctrs" ,r-vctrs)))
26068 `(("r-knitr" ,r-knitr)))
26069 (home-page "https://github.com/juliasilge/tidytext")
26070 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
26072 "This is a package for text mining for word processing and sentiment
26073 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
26074 (license license:expat)))
26076 (define-public r-parsnip
26083 (uri (cran-uri "parsnip" version))
26086 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
26087 (properties `((upstream-name . "parsnip")))
26088 (build-system r-build-system)
26090 `(("r-dplyr" ,r-dplyr)
26091 ("r-generics" ,r-generics)
26092 ("r-globals" ,r-globals)
26094 ("r-magrittr" ,r-magrittr)
26095 ("r-prettyunits" ,r-prettyunits)
26096 ("r-purrr" ,r-purrr)
26097 ("r-rlang" ,r-rlang)
26098 ("r-tibble" ,r-tibble)
26099 ("r-tidyr" ,r-tidyr)
26100 ("r-vctrs" ,r-vctrs)))
26102 `(("r-knitr" ,r-knitr)))
26103 (home-page "https://parsnip.tidymodels.org")
26104 (synopsis "Common API to modeling and analysis functions")
26106 "This package provides a common interface to allow users to specify a
26107 model without having to remember the different argument names across different
26108 functions or computational engines (e.g. R, Spark, Stan, etc).")
26109 (license license:gpl2)))
26111 (define-public r-infer
26118 (uri (cran-uri "infer" version))
26121 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
26122 (properties `((upstream-name . "infer")))
26123 (build-system r-build-system)
26125 `(("r-dplyr" ,r-dplyr)
26126 ("r-ggplot2" ,r-ggplot2)
26128 ("r-magrittr" ,r-magrittr)
26129 ("r-purrr" ,r-purrr)
26130 ("r-rlang" ,r-rlang)
26131 ("r-tibble" ,r-tibble)))
26133 `(("r-knitr" ,r-knitr)))
26134 (home-page "https://github.com/tidymodels/infer")
26135 (synopsis "Tidy statistical inference")
26137 "The objective of this package is to perform inference using an
26138 expressive statistical grammar that coheres with the Tidy design framework.")
26139 (license license:cc0)))
26141 (define-public r-modeldata
26143 (name "r-modeldata")
26148 (uri (cran-uri "modeldata" version))
26151 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
26152 (properties `((upstream-name . "modeldata")))
26153 (build-system r-build-system)
26154 (home-page "https://modeldata.tidymodels.org")
26155 (synopsis "Data sets useful for modeling packages")
26157 "This package provides data sets used for demonstrating or testing
26158 model-related packages.")
26159 (license license:expat)))
26161 (define-public r-tidymodels
26163 (name "r-tidymodels")
26168 (uri (cran-uri "tidymodels" version))
26171 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26172 (properties `((upstream-name . "tidymodels")))
26173 (build-system r-build-system)
26175 `(("r-broom" ,r-broom)
26177 ("r-dials" ,r-dials)
26178 ("r-dplyr" ,r-dplyr)
26179 ("r-ggplot2" ,r-ggplot2)
26180 ("r-infer" ,r-infer)
26181 ("r-magrittr" ,r-magrittr)
26182 ("r-modeldata" ,r-modeldata)
26183 ("r-parsnip" ,r-parsnip)
26184 ("r-purrr" ,r-purrr)
26185 ("r-recipes" ,r-recipes)
26186 ("r-rlang" ,r-rlang)
26187 ("r-rsample" ,r-rsample)
26188 ("r-rstudioapi" ,r-rstudioapi)
26189 ("r-tibble" ,r-tibble)
26190 ("r-tidyr" ,r-tidyr)
26192 ("r-workflows" ,r-workflows)
26193 ("r-yardstick" ,r-yardstick)))
26195 `(("r-knitr" ,r-knitr)
26196 ("r-rmarkdown" ,r-rmarkdown)
26198 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26199 (home-page "https://github.com/tidymodels/tidymodels")
26200 (synopsis "Tidy collection for modeling and statistical analysis")
26202 "The tidy modeling \"verse\" is a collection of packages for modeling and
26203 statistical analysis that share the underlying design philosophy, grammar, and
26204 data structures of the tidyverse.")
26205 (license license:gpl3)))
26207 (define-public r-mlecens
26214 (uri (cran-uri "MLEcens" version))
26217 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26218 (properties `((upstream-name . "MLEcens")))
26219 (build-system r-build-system)
26220 (home-page "http://stat.ethz.ch/~maathuis/")
26221 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26223 "This package contains functions to compute the nonparametric
26224 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26225 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26226 To be more precise, we consider the situation where we observe a set of
26227 rectangles that are known to contain the unobservable realizations of (X,Y).
26228 We compute the MLE based on such a set of rectangles. The methods can also be
26229 used for univariate censored data (see data set @code{cosmesis}), and for
26230 censored data with competing risks (see data set @code{menopause}). The
26231 package also provides functions to visualize the observed data and the MLE.")
26232 (license license:gpl2+)))
26234 (define-public r-metafor
26241 (uri (cran-uri "metafor" version))
26244 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26245 (properties `((upstream-name . "metafor")))
26246 (build-system r-build-system)
26248 `(("r-matrix" ,r-matrix)
26249 ("r-nlme" ,r-nlme)))
26250 (home-page "https://cran.r-project.org/web/packages/metafor/")
26251 (synopsis "Meta-analysis package for R")
26253 "This package provides a comprehensive collection of functions for
26254 conducting meta-analyses in R. The package includes functions to calculate
26255 various effect sizes or outcome measures, fit fixed-, random-, and
26256 mixed-effects models to such data, carry out moderator and meta-regression
26257 analyses, and create various types of meta-analytical plots (e.g., forest,
26258 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26259 and person-time data, the package also provides functions that implement
26260 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26261 a variety of suitable generalized linear (mixed-effects) models (i.e.
26262 mixed-effects logistic and Poisson regression models). Finally, the package
26263 provides functionality for fitting meta-analytic multivariate/multilevel
26264 models that account for non-independent sampling errors and/or true
26265 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26266 endpoints, or other forms of clustering). Network meta-analyses and
26267 meta-analyses accounting for known correlation structures (e.g. due to
26268 phylogenetic relatedness) can also be conducted.")
26269 (license license:gpl2+)))
26271 (define-public r-altmeta
26278 (uri (cran-uri "altmeta" version))
26281 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26282 (properties `((upstream-name . "altmeta")))
26283 (build-system r-build-system)
26285 `(("r-coda" ,r-coda)
26287 ("r-matrix" ,r-matrix)
26288 ("r-metafor" ,r-metafor)
26289 ("r-rjags" ,r-rjags)))
26290 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26291 (synopsis "Alternative meta-analysis methods")
26293 "This package provides alternative statistical methods for meta-analysis,
26297 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26298 relative risks, and risk differences
26299 @item heterogeneity tests and measures that are robust to outliers;
26300 @item measures, tests, and visualization tools for publication bias or
26301 small-study effects;
26302 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26303 specificities, etc.;
26304 @item meta-analysis methods for synthesizing proportions;
26305 @item models for multivariate meta-analysis.
26308 (license license:gpl2+)))
26310 (define-public r-perm
26313 (version "1.0-0.0")
26317 (uri (cran-uri "perm" version))
26320 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26321 (properties `((upstream-name . "perm")))
26322 (build-system r-build-system)
26323 (home-page "https://cran.r-project.org/web/packages/perm/")
26324 (synopsis "Exact or asymptotic permutation tests")
26326 "This package provides several methods for performing permutation tests.
26327 It has three main functions, to perform linear permutation tests. These tests
26328 are tests where the test statistic is the sum of the product of a
26329 covariate (usually group indicator) and the scores.")
26330 ;; Any version of the GPL
26331 (license license:gpl2+)))
26333 (define-public r-qtl
26340 (uri (cran-uri "qtl" version))
26343 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26344 (build-system r-build-system)
26345 (home-page "https://rqtl.org/")
26346 (synopsis "R package for analyzing QTL experiments in genetics")
26347 (description "R/qtl is an extension library for the R statistics system.
26348 It is used to analyze experimental crosses for identifying genes contributing
26349 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26351 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26352 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26354 (license license:gpl3)))
26356 (define-public r-qtl2
26362 (uri (cran-uri "qtl2" version))
26364 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26365 (build-system r-build-system)
26367 `(("r-data-table" ,r-data-table)
26368 ("r-jsonlite" ,r-jsonlite)
26370 ("r-rcppeigen" ,r-rcppeigen)
26371 ("r-rsqlite" ,r-rsqlite)
26372 ("r-yaml" ,r-yaml)))
26373 (home-page "https://kbroman.org/qtl2/")
26374 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26376 "This package provides a set of tools to perform @dfn{Quantitative Trait
26377 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26378 @code{R/qtl} package to better handle high-dimensional data and complex cross
26379 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26380 (license license:gpl3)))
26382 (define-public r-seqminer
26384 (name "r-seqminer")
26389 (uri (cran-uri "seqminer" version))
26392 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26393 (build-system r-build-system)
26396 (home-page "http://seqminer.genomic.codes")
26397 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26399 "This package provides tools to integrate nucleotide sequencing
26400 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26401 ;; Any version of the GPL is acceptable
26402 (license (list license:gpl2+ license:gpl3+))))
26404 (define-public r-maldiquant
26406 (name "r-maldiquant")
26411 (uri (cran-uri "MALDIquant" version))
26414 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26415 (properties `((upstream-name . "MALDIquant")))
26416 (build-system r-build-system)
26417 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26418 (synopsis "Quantitative analysis of mass spectrometry data")
26420 "This package provides a complete analysis pipeline for matrix-assisted
26421 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26422 two-dimensional mass spectrometry data. In addition to commonly used plotting
26423 and processing methods it includes distinctive features, namely baseline
26424 subtraction methods such as morphological filters (TopHat) or the
26425 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26426 alignment using warping functions, handling of replicated measurements as well
26427 as allowing spectra with different resolutions.")
26428 (license license:gpl3+)))
26430 (define-public r-scattermore
26432 (name "r-scattermore")
26437 (uri (cran-uri "scattermore" version))
26440 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26441 (properties `((upstream-name . "scattermore")))
26442 (build-system r-build-system)
26444 `(("r-ggplot2" ,r-ggplot2)
26445 ("r-scales" ,r-scales)))
26446 (home-page "https://github.com/exaexa/scattermore")
26447 (synopsis "Scatterplots with more points")
26449 "This package provides C-based tools for converting large scatterplot
26450 data to rasters. It speeds up plotting of data with millions of points.")
26451 (license license:gpl3+)))
26453 (define-public r-seuratobject
26455 (name "r-seuratobject")
26460 (uri (cran-uri "SeuratObject" version))
26463 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26464 (properties `((upstream-name . "SeuratObject")))
26465 (build-system r-build-system)
26467 `(("r-matrix" ,r-matrix)
26469 ("r-rcppeigen" ,r-rcppeigen)
26470 ("r-rlang" ,r-rlang)
26471 ("r-sctransform" ,r-sctransform)))
26472 (home-page "https://satijalab.org/seurat")
26473 (synopsis "Data structures for single cell data")
26475 "This package defines S4 classes for single-cell genomic data and
26476 associated information, such as dimensionality reduction embeddings,
26477 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26478 access methods and R-native hooks to ensure the Seurat object is familiar to
26480 (license license:gpl3)))
26482 (define-public r-seurat
26488 (uri (cran-uri "Seurat" version))
26491 "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
26492 (properties `((upstream-name . "Seurat")))
26493 (build-system r-build-system)
26495 `(("r-cluster" ,r-cluster)
26496 ("r-cowplot" ,r-cowplot)
26497 ("r-fitdistrplus" ,r-fitdistrplus)
26498 ("r-future" ,r-future)
26499 ("r-future-apply" ,r-future-apply)
26500 ("r-ggplot2" ,r-ggplot2)
26501 ("r-ggrepel" ,r-ggrepel)
26502 ("r-ggridges" ,r-ggridges)
26505 ("r-igraph" ,r-igraph)
26506 ("r-irlba" ,r-irlba)
26507 ("r-jsonlite" ,r-jsonlite)
26508 ("r-kernsmooth" ,r-kernsmooth)
26509 ("r-leiden" ,r-leiden)
26510 ("r-lmtest" ,r-lmtest)
26512 ("r-matrix" ,r-matrix)
26513 ("r-matrixstats" ,r-matrixstats)
26514 ("r-miniui" ,r-miniui)
26515 ("r-patchwork" ,r-patchwork)
26516 ("r-pbapply" ,r-pbapply)
26517 ("r-plotly" ,r-plotly)
26520 ("r-rcolorbrewer" ,r-rcolorbrewer)
26522 ("r-rcppannoy" ,r-rcppannoy)
26523 ("r-rcppeigen" ,r-rcppeigen)
26524 ("r-rcppprogress" ,r-rcppprogress)
26525 ("r-reticulate" ,r-reticulate)
26526 ("r-rlang" ,r-rlang)
26528 ("r-rtsne" ,r-rtsne)
26529 ("r-scales" ,r-scales)
26530 ("r-scattermore" ,r-scattermore)
26531 ("r-sctransform" ,r-sctransform)
26532 ("r-seuratobject" ,r-seuratobject)
26533 ("r-shiny" ,r-shiny)
26534 ("r-spatstat" ,r-spatstat)
26535 ("r-tibble" ,r-tibble)
26536 ("r-uwot" ,r-uwot)))
26537 (home-page "http://www.satijalab.org/seurat")
26538 (synopsis "Seurat is an R toolkit for single cell genomics")
26540 "This package is an R package designed for QC, analysis, and
26541 exploration of single cell RNA-seq data. It easily enables widely-used
26542 analytical techniques, including the identification of highly variable genes,
26543 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26544 algorithms; density clustering, hierarchical clustering, k-means, and the
26545 discovery of differentially expressed genes and markers.")
26546 (license license:gpl3)))
26548 (define-public r-phangorn
26550 (name "r-phangorn")
26555 (uri (cran-uri "phangorn" version))
26558 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26559 (build-system r-build-system)
26562 ("r-fastmatch" ,r-fastmatch)
26563 ("r-igraph" ,r-igraph)
26564 ("r-magrittr" ,r-magrittr)
26565 ("r-matrix" ,r-matrix)
26566 ("r-quadprog" ,r-quadprog)
26567 ("r-rcpp" ,r-rcpp)))
26568 (home-page "https://github.com/KlausVigo/phangorn")
26569 (synopsis "Phylogenetic analysis in R")
26571 "Phangorn is a package for phylogenetic analysis in R. It supports
26572 estimation of phylogenetic trees and networks using Maximum Likelihood,
26573 Maximum Parsimony, distance methods and Hadamard conjugation.")
26574 (license license:gpl2+)))
26576 (define-public r-diversitree
26578 (name "r-diversitree")
26583 (uri (cran-uri "diversitree" version))
26586 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26587 (build-system r-build-system)
26589 `(("gfortran" ,gfortran)))
26590 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26593 ("r-desolve" ,r-desolve)
26595 ("r-subplex" ,r-subplex)))
26596 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26597 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26598 (description "This package contains a number of comparative \"phylogenetic\"
26599 methods, mostly focusing on analysing diversification and character evolution.
26600 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26601 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26602 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26603 include Markov models of discrete and continuous trait evolution and constant
26604 rate speciation and extinction.")
26605 (license license:gpl2+)))
26607 (define-public r-absfiltergsea
26609 (name "r-absfiltergsea")
26614 (uri (cran-uri "AbsFilterGSEA" version))
26616 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
26617 (properties `((upstream-name . "AbsFilterGSEA")))
26618 (build-system r-build-system)
26620 `(("r-biobase" ,r-biobase)
26621 ("r-deseq" ,r-deseq)
26622 ("r-limma" ,r-limma)
26624 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26625 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
26626 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
26628 "This package provides a function that performs gene-permuting of a gene-set
26629 enrichment analysis (GSEA) calculation with or without the absolute filtering.
26630 Without filtering, users can perform (original) two-tailed or one-tailed
26632 (license license:gpl2)))
26634 (define-public r-calculus
26636 (name "r-calculus")
26641 (uri (cran-uri "calculus" version))
26644 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26645 (properties `((upstream-name . "calculus")))
26646 (build-system r-build-system)
26648 `(("r-rcpp" ,r-rcpp)))
26650 `(("r-knitr" ,r-knitr)))
26651 (home-page "https://github.com/eguidotti/calculus")
26652 (synopsis "High dimensional numerical and symbolic calculus")
26654 "Efficient C++ optimized functions for numerical and symbolic calculus.
26655 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26656 convention, fast computation of the Levi-Civita symbol and generalized
26657 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26658 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26659 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26660 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26661 parabolic or user defined by custom scale factors.")
26662 (license license:gpl3)))
26664 (define-public r-decon
26671 (uri (cran-uri "decon" version))
26674 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26675 (properties `((upstream-name . "decon")))
26676 (build-system r-build-system)
26678 `(("gfortran" ,gfortran)))
26680 "https://cran.r-project.org/web/packages/decon/")
26681 (synopsis "Deconvolution Estimation in Measurement Error Models")
26683 "This package contains a collection of functions to deal with
26684 nonparametric measurement error problems using deconvolution
26685 kernel methods. We focus two measurement error models in the
26686 package: (1) an additive measurement error model, where the
26687 goal is to estimate the density or distribution function from
26688 contaminated data; (2) nonparametric regression model with
26689 errors-in-variables. The R functions allow the measurement errors
26690 to be either homoscedastic or heteroscedastic. To make the
26691 deconvolution estimators computationally more efficient in R,
26692 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26693 density estimation with error-free data to the deconvolution
26694 kernel estimation. Several methods for the selection of the
26695 data-driven smoothing parameter are also provided in the package.
26696 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26697 estimation in measurement error models: The R package decon.
26698 Journal of Statistical Software, 39(10), 1-24.")
26699 (license license:gpl3+)))
26701 (define-public r-locpol
26708 (uri (cran-uri "locpol" version))
26711 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26712 (properties `((upstream-name . "locpol")))
26713 (build-system r-build-system)
26715 "https://cran.r-project.org/web/packages/locpol/")
26716 (synopsis "Kernel Local Polynomial Regression")
26718 "Computes local polynomial estimators for the regression and
26719 also density. It comprises several different utilities to handle
26720 kernel estimators.")
26721 (license license:gpl2+)))
26723 (define-public r-lpme
26730 (uri (cran-uri "lpme" version))
26733 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26734 (properties `((upstream-name . "lpme")))
26735 (build-system r-build-system)
26737 `(("r-decon" ,r-decon)
26738 ("r-flexmix" ,r-flexmix)
26739 ("r-locpol" ,r-locpol)
26741 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26743 "https://cran.r-project.org/web/packages/lpme/")
26744 (synopsis "Nonparametric Estimation of Measurement Error Models")
26746 "Provide nonparametric methods for mean regression model,
26747 modal regression and conditional density estimation in the
26748 presence/absence of measurement error. Bandwidth selection is
26749 also provided for each method.")
26750 (license license:gpl2+)))
26752 (define-public r-aws-signature
26754 (name "r-aws-signature")
26759 (uri (cran-uri "aws.signature" version))
26762 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26763 (properties `((upstream-name . "aws.signature")))
26764 (build-system r-build-system)
26766 `(("r-base64enc" ,r-base64enc)
26767 ("r-digest" ,r-digest)))
26768 (home-page "https://github.com/cloudyr/aws.signature")
26769 (synopsis "Amazon Web Services Request Signatures")
26771 "This package generates version 2 and 4 request signatures for Amazon Web
26772 Services (AWS) and provides a mechanism for retrieving credentials from
26773 environment variables, AWS credentials files, and EC2 instance metadata. For
26774 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26775 (license license:gpl2+)))
26777 (define-public r-aws-s3
26784 (uri (cran-uri "aws.s3" version))
26787 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26788 (properties `((upstream-name . "aws.s3")))
26789 (build-system r-build-system)
26791 `(("r-aws-signature" ,r-aws-signature)
26792 ("r-base64enc" ,r-base64enc)
26794 ("r-digest" ,r-digest)
26796 ("r-xml2" ,r-xml2)))
26797 (home-page "https://github.com/cloudyr/aws.s3")
26798 (synopsis "AWS S3 Client Package")
26800 "This package provides a simple client package for the Amazon Web
26801 Services (AWS) Simple Storage Service (S3) REST API.")
26802 (license license:gpl2+)))
26804 (define-public r-lgr
26810 (uri (cran-uri "lgr" version))
26813 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26814 (build-system r-build-system)
26818 `(("r-knitr" ,r-knitr)))
26819 (home-page "https://s-fleck.github.io/lgr/")
26820 (synopsis "Fully featured logging framework")
26821 (description "This package offers a flexible, feature-rich yet
26822 light-weight logging framework based on @code{R6} classes. It supports
26823 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26824 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26825 well as email and push notifications.")
26826 (license license:expat)))
26828 (define-public r-mlr3measures
26830 (name "r-mlr3measures")
26834 (uri (cran-uri "mlr3measures" version))
26837 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26838 (build-system r-build-system)
26840 `(("r-checkmate" ,r-checkmate)
26841 ("r-prroc" ,r-prroc)))
26842 (home-page "https://mlr3measures.mlr-org.com/")
26843 (synopsis "Performance measures for mlr3")
26844 (description "This package implements multiple performance measures for
26845 supervised learning. It includes over 40 measures for regression and
26846 classification. Additionally, meta information about the performance measures
26847 can be queried, e.g. what the best and worst possible performances scores
26849 (license license:lgpl3)))
26851 (define-public r-mlr3misc
26853 (name "r-mlr3misc")
26857 (uri (cran-uri "mlr3misc" version))
26860 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26861 (build-system r-build-system)
26863 `(("r-backports" ,r-backports)
26864 ("r-checkmate" ,r-checkmate)
26865 ("r-data-table" ,r-data-table)
26867 (home-page "https://mlr3misc.mlr-org.com/")
26868 (synopsis "Helper functions for mlr3")
26869 (description "@code{mlr3misc} provides frequently used helper functions
26870 and assertions used in @code{mlr3} and its companion packages. It comes with
26871 helper functions for functional programming, for printing, to work with
26872 @code{data.table}, as well as some generally useful @code{R6} classes. This
26873 package also supersedes the package @code{BBmisc}.")
26874 (license license:lgpl3)))
26876 (define-public r-paradox
26882 (uri (cran-uri "paradox" version))
26885 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
26886 (build-system r-build-system)
26888 `(("r-backports" ,r-backports)
26889 ("r-checkmate" ,r-checkmate)
26890 ("r-data-table" ,r-data-table)
26891 ("r-mlr3misc" ,r-mlr3misc)
26893 (home-page "https://paradox.mlr-org.com/")
26894 (synopsis "Define and work with parameter spaces for complex algorithms")
26895 (description "With this package it is possible to define parameter spaces,
26896 constraints and dependencies for arbitrary algorithms, and to program on such
26897 spaces. It also includes statistical designs and random samplers. Objects are
26898 implemented as @code{R6} classes.")
26899 (license license:lgpl3)))
26901 (define-public r-mlr3
26907 (uri (cran-uri "mlr3" version))
26910 "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl"))))
26911 (build-system r-build-system)
26914 ("r-backports" ,r-backports)
26915 ("r-checkmate" ,r-checkmate)
26916 ("r-data-table" ,r-data-table)
26917 ("r-digest" ,r-digest)
26918 ("r-future-apply" ,r-future-apply)
26920 ("r-mlbench" ,r-mlbench)
26921 ("r-mlr3measures" ,r-mlr3measures)
26922 ("r-mlr3misc" ,r-mlr3misc)
26923 ("r-palmerpenguins" ,r-palmerpenguins)
26924 ("r-paradox" ,r-paradox)
26925 ("r-parallelly" ,r-parallelly)
26926 ("r-uuid" ,r-uuid)))
26927 (home-page "https://mlr3.mlr-org.com/")
26928 (synopsis "Machine Learning in R - Next Generation")
26929 (description "@code{mlr3} enables efficient, object-oriented programming
26930 on the building blocks of machine learning. It provides @code{R6} objects for
26931 tasks, learners, resamplings, and measures. The package is geared towards
26932 scalability and larger datasets by supporting parallelization and out-of-memory
26933 data-backends like databases. While @code{mlr3} focuses on the core
26934 computational operations, add-on packages provide additional functionality.")
26935 (license license:lgpl3)))
26937 (define-public r-mlr3learners
26939 (name "r-mlr3learners")
26943 (uri (cran-uri "mlr3learners" version))
26946 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26947 (build-system r-build-system)
26949 `(("r-data-table" ,r-data-table)
26951 ("r-mlr3misc" ,r-mlr3misc)
26952 ("r-paradox" ,r-paradox)
26954 (home-page "https://mlr3learners.mlr-org.com/")
26955 (synopsis "Recommended Learners for @code{mlr3}")
26956 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26957 with interfaces to essential machine learning packages on CRAN. This includes,
26958 but is not limited to: (penalized) linear and logistic regression, linear and
26959 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26960 vector machines, and gradient boosting.")
26961 (license license:lgpl3)))
26963 (define-public r-bbotk
26970 (uri (cran-uri "bbotk" version))
26973 "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550"))))
26974 (properties `((upstream-name . "bbotk")))
26975 (build-system r-build-system)
26977 `(("r-checkmate" ,r-checkmate)
26978 ("r-data-table" ,r-data-table)
26980 ("r-mlr3misc" ,r-mlr3misc)
26981 ("r-paradox" ,r-paradox)
26984 `(("r-knitr" ,r-knitr)))
26985 (home-page "https://bbotk.mlr-org.com")
26986 (synopsis "Black-Box Optimization Toolkit")
26987 (description "This package provides a common framework for optimization of
26988 black-box functions for other packages, e.g. @code{mlr3}. It offers various
26989 optimization methods e.g. grid search, random search and generalized simulated
26991 (license license:lgpl3)))
26993 (define-public r-mlr3tuning
26995 (name "r-mlr3tuning")
26999 (uri (cran-uri "mlr3tuning" version))
27002 "0xpq16qij05nsfwg0qnfziqjvgk5wn0dgl0sb5gg3qsp1cs6vfqj"))))
27003 (build-system r-build-system)
27005 `(("r-bbotk" ,r-bbotk)
27006 ("r-checkmate" ,r-checkmate)
27007 ("r-data-table" ,r-data-table)
27010 ("r-mlr3misc" ,r-mlr3misc)
27011 ("r-paradox" ,r-paradox)
27013 (home-page "https://mlr3tuning.mlr-org.com/")
27014 (synopsis "Tuning for @code{mlr3}")
27015 (description "@code{mlr3tuning} implements methods for hyperparameter
27016 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
27017 termination criteria can be set and combined. The class @code{AutoTuner} provides a
27018 convenient way to perform nested resampling in combination with @code{mlr3}.")
27019 (license license:lgpl3)))
27021 (define-public r-fontliberation
27023 (name "r-fontliberation")
27028 (uri (cran-uri "fontLiberation" version))
27031 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
27033 `((upstream-name . "fontLiberation")))
27034 (build-system r-build-system)
27035 (home-page "https://cran.r-project.org/package=fontLiberation")
27036 (synopsis "Liberation fonts")
27038 "This package provides a placeholder for the Liberation fontset intended
27039 for the fontquiver package. This fontset covers the 12 combinations of
27040 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
27041 supported in R graphics devices.")
27042 (license license:silofl1.1)))
27044 (define-public r-fontbitstreamvera
27046 (name "r-fontbitstreamvera")
27051 (uri (cran-uri "fontBitstreamVera" version))
27054 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
27056 `((upstream-name . "fontBitstreamVera")))
27057 (build-system r-build-system)
27058 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
27059 (synopsis "Fonts for fontquiver")
27061 "This package is a placeholder for the Bitstream Vera font. It is
27062 intended for the fontquiver package.")
27064 (license:fsdg-compatible
27065 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
27066 "The Font Software may be sold as part of a larger software package but
27067 no copy of one or more of the Font Software typefaces may be sold by
27070 (define-public r-fontquiver
27072 (name "r-fontquiver")
27077 (uri (cran-uri "fontquiver" version))
27080 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
27081 (properties `((upstream-name . "fontquiver")))
27082 (build-system r-build-system)
27084 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
27085 ("r-fontliberation" ,r-fontliberation)))
27086 (home-page "https://cran.r-project.org/package=fontquiver")
27087 (synopsis "Set of installed fonts")
27089 "This package provides a set of fonts. This is useful when you want to
27090 avoid system fonts to make sure your outputs are reproducible.")
27091 (license license:gpl3)))
27093 (define-public r-freetypeharfbuzz
27095 (name "r-freetypeharfbuzz")
27100 (uri (cran-uri "freetypeharfbuzz" version))
27103 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
27105 `((upstream-name . "freetypeharfbuzz")))
27106 (build-system r-build-system)
27109 (modify-phases %standard-phases
27110 (add-after 'unpack 'prepare-static-libraries
27111 (lambda* (#:key inputs #:allow-other-keys)
27112 (mkdir-p "src/target/include")
27113 (let ((freetype (assoc-ref inputs "static-freetype"))
27114 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
27115 (substitute* "src/Makevars.in"
27116 (("include @MK_FILE@") "") ; do not build static libs
27117 (("^HB_STATIC_LIB =.*")
27118 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
27119 (("^FT_STATIC_LIB =.*")
27120 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
27121 (copy-recursively (string-append freetype "/include")
27122 "src/target/include")
27123 (copy-recursively (string-append harfbuzz "/include")
27124 "src/target/include")))))))
27126 `(("r-fontquiver" ,r-fontquiver)))
27127 ;; This may defeat the purpose of this package as our versions of freetype
27128 ;; and harfbuzz obviously differ from the tarballs offered by this
27129 ;; project. On the other hand, Guix arguably does a better job at
27130 ;; "ensur[ing] deterministic computation".
27132 `(("static-freetype"
27134 (inherit (static-package freetype))
27136 `(#:configure-flags
27137 (list "--enable-static=yes"
27142 "--without-harfbuzz")))))
27145 (inherit (static-package harfbuzz))
27147 `(#:tests? #false ; fail because shared library is disabled
27149 (list "--enable-static=yes"
27150 "--enable-shared=no"
27152 "--with-freetype=yes"
27155 "--without-fontconfig"
27156 "--without-glib")))))))
27159 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27160 (synopsis "Deterministic computation of text box metrics")
27162 "Unlike other tools that dynamically link to the Cairo stack,
27163 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27164 harfbuzz libraries. This ensures deterministic computation of text box
27165 extents for situations where reproducible results are crucial (for instance
27166 unit tests of graphics).")
27167 (license license:gpl3)))
27169 (define-public r-vdiffr
27176 (uri (cran-uri "vdiffr" version))
27179 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27182 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27183 (properties `((upstream-name . "vdiffr")))
27184 (build-system r-build-system)
27187 (modify-phases %standard-phases
27188 (add-after 'unpack 'process-javascript
27189 (lambda* (#:key inputs #:allow-other-keys)
27190 (with-directory-excursion "inst/htmlwidgets/lib/"
27191 (let ((source (assoc-ref inputs "js-jquery"))
27192 (target "jquery.min.js"))
27193 (format #true "Processing ~a --> ~a~%"
27195 (invoke "esbuild" source "--minify"
27196 (string-append "--outfile=" target)))))))))
27198 `(("freetype" ,freetype)
27199 ("harfbuzz" ,harfbuzz)))
27202 ("r-devtools" ,r-devtools)
27203 ("r-diffobj" ,r-diffobj)
27204 ("r-fontquiver" ,r-fontquiver)
27205 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27206 ("r-gdtools" ,r-gdtools)
27208 ("r-htmltools" ,r-htmltools)
27209 ("r-htmlwidgets" ,r-htmlwidgets)
27210 ("r-purrr" ,r-purrr)
27213 ("r-rlang" ,r-rlang)
27214 ("r-shiny" ,r-shiny)
27215 ("r-testthat" ,r-testthat)
27216 ("r-usethis" ,r-usethis)
27217 ("r-xml2" ,r-xml2)))
27219 `(("esbuild" ,esbuild)
27223 (uri "https://code.jquery.com/jquery-1.12.4.js")
27226 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27227 (home-page "https://github.com/r-lib/vdiffr")
27228 (synopsis "Visual regression testing and graphical diffing")
27230 "This package is an extension to the testthat package that makes it easy
27231 to add graphical unit tests. It provides a Shiny application to manage the
27233 (license license:gpl3)))
27235 (define-public r-highlight
27237 (name "r-highlight")
27242 (uri (cran-uri "highlight" version))
27245 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27246 (properties `((upstream-name . "highlight")))
27247 (build-system r-build-system)
27248 (home-page "https://github.com/hadley/highlight")
27249 (synopsis "Syntax highlighter for R code")
27251 "This package provides a syntax highlighter for R code based on the
27252 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27253 includes a custom Sweave driver performing syntax highlighting of R code
27255 (license license:gpl3+)))
27257 (define-public r-clustree
27259 (name "r-clustree")
27264 (uri (cran-uri "clustree" version))
27267 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27268 (properties `((upstream-name . "clustree")))
27269 (build-system r-build-system)
27271 `(("r-checkmate" ,r-checkmate)
27272 ("r-dplyr" ,r-dplyr)
27273 ("r-ggplot2" ,r-ggplot2)
27274 ("r-ggraph" ,r-ggraph)
27275 ("r-ggrepel" ,r-ggrepel)
27276 ("r-igraph" ,r-igraph)
27277 ("r-rlang" ,r-rlang)
27278 ("r-tidygraph" ,r-tidygraph)
27279 ("r-viridis" ,r-viridis)))
27281 `(("r-knitr" ,r-knitr)))
27282 (home-page "https://github.com/lazappi/clustree")
27283 (synopsis "Visualize clusterings at different resolutions")
27285 "Deciding what resolution to use can be a difficult question when
27286 approaching a clustering analysis. One way to approach this problem is to
27287 look at how samples move as the number of clusters increases. This package
27288 allows you to produce clustering trees, a visualization for interrogating
27289 clusterings as resolution increases.")
27290 (license license:gpl3)))
27292 (define-public r-textshaping
27294 (name "r-textshaping")
27299 (uri (cran-uri "textshaping" version))
27302 "16y3amb9cxwq126q1mxssx7kswzalqf9n2437mi5n7q1nqby6wlq"))))
27303 (properties `((upstream-name . "textshaping")))
27304 (build-system r-build-system)
27306 `(("freetype" ,freetype)
27307 ("fribidi" ,fribidi)
27308 ("harfbuzz" ,harfbuzz)
27311 `(("r-cpp11" ,r-cpp11)
27312 ("r-systemfonts" ,r-systemfonts)))
27314 `(("pkg-config" ,pkg-config)
27315 ("r-knitr" ,r-knitr)))
27316 (home-page "https://github.com/r-lib/textshaping")
27317 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27319 "This package provides access to the text shaping functionality in the
27320 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27321 is a low-level utility package mainly for graphic devices that expands upon
27322 the font tool-set provided by the @code{systemfonts} package.")
27323 (license license:expat)))
27325 (define-public r-ragg
27332 (uri (cran-uri "ragg" version))
27335 "0nh1xxrxgdbq9anzkc6k3n519czp9hqyiizakm3m2gl4l4w0vp0q"))))
27336 (properties `((upstream-name . "ragg")))
27337 (build-system r-build-system)
27339 `(("freetype" ,freetype)
27340 ("libjpeg" ,libjpeg-turbo)
27342 ("libtiff" ,libtiff)
27345 `(("r-systemfonts" ,r-systemfonts)
27346 ("r-textshaping" ,r-textshaping)))
27348 `(("pkg-config" ,pkg-config)))
27349 (home-page "https://ragg.r-lib.org")
27350 (synopsis "Graphic devices based on AGG")
27352 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27353 drawing library. The ragg package provides a set of graphic devices based on
27354 AGG to use as alternative to the raster devices provided through the
27355 @code{grDevices} package.")
27356 (license license:expat)))
27358 (define-public r-downlit
27365 (uri (cran-uri "downlit" version))
27368 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27369 (properties `((upstream-name . "downlit")))
27370 (build-system r-build-system)
27372 `(("r-brio" ,r-brio)
27373 ("r-digest" ,r-digest)
27374 ("r-evaluate" ,r-evaluate)
27375 ("r-fansi" ,r-fansi)
27376 ("r-rlang" ,r-rlang)
27377 ("r-vctrs" ,r-vctrs)
27378 ("r-yaml" ,r-yaml)))
27379 (home-page "https://downlit.r-lib.org/")
27380 (synopsis "Syntax highlighting and automatic linking")
27382 "This package provides syntax highlighting of R code, specifically
27383 designed for the needs of RMarkdown packages like @code{pkgdown},
27384 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27385 to their documentation on the web, and automatic translation of ANSI escapes
27386 in output to the equivalent HTML.")
27387 (license license:expat)))
27389 (define-public r-pkgdown
27396 (uri (cran-uri "pkgdown" version))
27399 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27400 (properties `((upstream-name . "pkgdown")))
27401 (build-system r-build-system)
27402 (inputs `(("pandoc" ,pandoc)))
27404 `(("r-callr" ,r-callr)
27405 ("r-crayon" ,r-crayon)
27407 ("r-digest" ,r-digest)
27408 ("r-downlit" ,r-downlit)
27411 ("r-magrittr" ,r-magrittr)
27412 ("r-memoise" ,r-memoise)
27413 ("r-openssl" ,r-openssl)
27414 ("r-purrr" ,r-purrr)
27416 ("r-rematch2" ,r-rematch2)
27417 ("r-rlang" ,r-rlang)
27418 ("r-rmarkdown" ,r-rmarkdown)
27419 ("r-tibble" ,r-tibble)
27420 ("r-whisker" ,r-whisker)
27421 ("r-withr" ,r-withr)
27423 ("r-yaml" ,r-yaml)))
27425 `(("r-knitr" ,r-knitr)))
27426 (home-page "https://pkgdown.r-lib.org")
27427 (synopsis "Make static HTML documentation for an R package")
27429 "The goal of this package is to generate an attractive and useful website
27430 from a source package. @code{pkgdown} converts your documentation, vignettes,
27431 README file, and more to HTML making it easy to share information about your
27433 (license license:expat)))
27435 (define-public r-prereg
27442 (uri (cran-uri "prereg" version))
27445 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
27446 (properties `((upstream-name . "prereg")))
27447 (build-system r-build-system)
27449 `(("r-rmarkdown" ,r-rmarkdown)))
27450 (home-page "https://github.com/crsh/prereg")
27452 "R Markdown Templates to preregister Scientific Studies")
27454 "This package provides a collection of templates to author
27455 preregistration documents for scientific studies in PDF format.")
27456 (license license:gpl3)))
27458 (define-public r-ez
27465 (uri (cran-uri "ez" version))
27468 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
27469 (properties `((upstream-name . "ez")))
27470 (build-system r-build-system)
27473 ("r-ggplot2" ,r-ggplot2)
27476 ("r-matrix" ,r-matrix)
27479 ("r-reshape2" ,r-reshape2)
27480 ("r-scales" ,r-scales)
27481 ("r-stringr" ,r-stringr)))
27482 (home-page "https://github.com/mike-lawrence/ez")
27483 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
27485 "Facilitates easy analysis of factorial experiments, including purely
27486 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
27487 and mixed within-and-between-Ss designs. The functions in this package aim to
27488 provide simple, intuitive and consistent specification of data analysis and
27489 visualization. Visualization functions also include design visualization for
27490 pre-analysis data auditing, and correlation matrix visualization. Finally,
27491 this package includes functions for non-parametric analysis, including
27492 permutation tests and bootstrap resampling. The bootstrap function obtains
27493 predictions either by cell means or by more advanced/powerful mixed effects
27494 models, yielding predictions and confidence intervals that may be easily
27495 visualized at any level of the experiment's design.")
27496 (license license:gpl2+)))
27498 (define-public r-qdapregex
27500 (name "r-qdapregex")
27505 (uri (cran-uri "qdapRegex" version))
27508 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
27509 (properties `((upstream-name . "qdapRegex")))
27510 (build-system r-build-system)
27511 (propagated-inputs `(("r-stringi" ,r-stringi)))
27513 "https://trinker.github.com/qdapRegex/")
27515 "Regular Expression Removal, Extraction, and Replacement Tools")
27517 "This package provides a collection of regular expression tools
27518 associated with the @code{qdap} package that may be useful outside of the
27519 context of discourse analysis. Tools include removal/extraction/replacement of
27520 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
27521 percentages, citations, person tags, phone numbers, times, and zip codes.")
27522 (license license:gpl2)))
27524 (define-public r-mgsub
27531 (uri (cran-uri "mgsub" version))
27534 "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr"))))
27535 (properties `((upstream-name . "mgsub")))
27536 (build-system r-build-system)
27537 (native-inputs `(("r-knitr" ,r-knitr)))
27539 "https://cran.r-project.org/package=mgsub")
27541 "Safe, Multiple, Simultaneous String Substitution")
27543 "Designed to enable simultaneous substitution in strings in a safe
27544 fashion. Safe means it does not rely on placeholders (which can cause errors
27545 in same length matches).")
27546 (license license:expat)))
27548 (define-public r-textshape
27550 (name "r-textshape")
27555 (uri (cran-uri "textshape" version))
27558 "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
27559 (properties `((upstream-name . "textshape")))
27560 (build-system r-build-system)
27562 `(("r-data-table" ,r-data-table)
27564 ("r-stringi" ,r-stringi)))
27565 (home-page "http://github.com/trinker/textshape")
27566 (synopsis "Tools for Reshaping Text")
27568 "Tools that can be used to reshape and restructure text data.")
27569 (license license:gpl2)))
27571 (define-public r-syuzhet
27578 (uri (cran-uri "syuzhet" version))
27581 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
27582 (properties `((upstream-name . "syuzhet")))
27583 (build-system r-build-system)
27585 `(("r-dplyr" ,r-dplyr)
27588 ("r-rlang" ,r-rlang)
27589 ("r-textshape" ,r-textshape)
27590 ("r-tidyr" ,r-tidyr)
27592 (native-inputs `(("r-knitr" ,r-knitr)))
27593 (home-page "https://github.com/mjockers/syuzhet")
27595 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
27597 "Extracts sentiment and sentiment-derived plot arcs from text using a
27598 variety of sentiment dictionaries conveniently packaged for consumption by R
27599 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
27600 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
27601 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
27602 M. and Turney, Peter D. Applicable references are available in
27603 @file{README.md} and in the documentation for the @code{get_sentiment}
27604 function. The package also provides a hack for implementing Stanford's coreNLP
27605 sentiment parser. The package provides several methods for plot arc
27607 (license license:gpl3)))
27609 (define-public r-lexicon
27616 (uri (cran-uri "lexicon" version))
27619 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
27620 (properties `((upstream-name . "lexicon")))
27621 (build-system r-build-system)
27623 `(("r-data-table" ,r-data-table)
27624 ("r-syuzhet" ,r-syuzhet)))
27625 (home-page "https://github.com/trinker/lexicon")
27626 (synopsis "Lexicons for Text Analysis")
27628 "This package provides a collection of lexical hash tables, dictionaries,
27630 (license license:gpl3)))
27632 (define-public r-english
27639 (uri (cran-uri "english" version))
27642 "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1"))))
27643 (properties `((upstream-name . "english")))
27644 (build-system r-build-system)
27645 (native-inputs `(("r-knitr" ,r-knitr)))
27647 "https://cran.r-project.org/package=english")
27648 (synopsis "Translate Integers into English")
27650 "Allow numbers to be presented in an English language version, one, two,
27651 three, ... Ordinals are also available, first, second, third, ... and
27652 indefinite article choice, \"a\" or \"an\".")
27653 (license license:gpl2)))
27655 (define-public r-textclean
27657 (name "r-textclean")
27662 (uri (cran-uri "textclean" version))
27665 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
27666 (properties `((upstream-name . "textclean")))
27667 (build-system r-build-system)
27669 `(("r-data-table" ,r-data-table)
27670 ("r-english" ,r-english)
27672 ("r-lexicon" ,r-lexicon)
27673 ("r-mgsub" ,r-mgsub)
27674 ("r-qdapregex" ,r-qdapregex)
27675 ("r-stringi" ,r-stringi)
27676 ("r-textshape" ,r-textshape)))
27678 "https://github.com/trinker/textclean")
27679 (synopsis "Text Cleaning Tools")
27681 "Tools to clean and process text. Tools are geared at checking for
27682 substrings that are not optimal for analysis and replacing or removing them
27683 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
27684 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
27685 extracting them into new variables. For example, emoticons are often used in
27686 text but not always easily handled by analysis algorithms. The
27687 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
27688 (license license:gpl2)))
27690 (define-public r-striprtf
27692 (name "r-striprtf")
27697 (uri (cran-uri "striprtf" version))
27700 "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd"))))
27701 (properties `((upstream-name . "striprtf")))
27702 (build-system r-build-system)
27704 `(("r-magrittr" ,r-magrittr)
27706 ("r-stringr" ,r-stringr)))
27707 (home-page "https://github.com/kota7/striprtf")
27708 (synopsis "Extract Text from RTF File")
27710 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
27711 (license license:expat)))
27713 (define-public r-ndjson
27720 (uri (cran-uri "ndjson" version))
27723 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
27724 (modules '((guix build utils)))
27727 ;; unvendor gzstream
27728 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
27730 (properties `((upstream-name . "ndjson")))
27731 (build-system r-build-system)
27734 (modify-phases %standard-phases
27735 (add-after 'unpack 'use-system-gzstream
27736 (lambda* (#:key inputs #:allow-other-keys)
27737 (substitute* "src/Makevars"
27738 (("PKG_LIBS = " all)
27739 (string-append all "-lgzstream ")))
27741 (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream)))
27743 `(("r-data-table" ,r-data-table)
27745 ("r-tibble" ,r-tibble)))
27746 (home-page "https://gitlab.com/hrbrmstr/ndjson")
27748 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
27750 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
27751 modern ndjson files contain large numbers of records. These constructs may not
27752 be columnar in nature, but it is often useful to read in these files and
27753 \"flatten\" the structure out to enable working with the data in an R
27754 @code{data.frame}-like context. Functions are provided that make it possible
27755 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
27756 validate the format of the records or create \"flat\" @code{data.table}
27757 structures from them.")
27758 (license license:expat)))
27760 (define-public r-streamr
27767 (uri (cran-uri "streamR" version))
27770 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
27771 (properties `((upstream-name . "streamR")))
27772 (build-system r-build-system)
27774 `(("r-ndjson" ,r-ndjson)
27775 ("r-rcurl" ,r-rcurl)
27776 ("r-rjson" ,r-rjson)))
27778 "https://cran.r-project.org/package=streamR")
27780 "Access to Twitter Streaming API via R")
27782 "This package provides functions to access Twitter's filter, sample, and
27783 user streams, and to parse the output into data frames.")
27784 (license license:gpl2)))
27786 (define-public r-readods
27793 (uri (cran-uri "readODS" version))
27796 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
27797 (properties `((upstream-name . "readODS")))
27798 (build-system r-build-system)
27800 `(("r-cellranger" ,r-cellranger)
27801 ("r-readr" ,r-readr)
27802 ("r-stringi" ,r-stringi)
27803 ("r-xml2" ,r-xml2)))
27804 (native-inputs `(("r-knitr" ,r-knitr)))
27806 "https://cran.r-project.org/package=readODS")
27807 (synopsis "Read and Write ODS Files")
27809 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
27810 Also support writing data frame into ODS file.")
27811 (license license:gpl3)))
27813 (define-public r-qpdf
27820 (uri (cran-uri "qpdf" version))
27823 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
27824 (modules '((guix build utils)))
27827 ;; unvendor libqpdf
27828 (delete-file-recursively "src/libqpdf")
27829 (delete-file-recursively "src/include/qpdf")
27831 (properties `((upstream-name . "qpdf")))
27832 (build-system r-build-system)
27835 (modify-phases %standard-phases
27836 (add-after 'unpack 'configure
27838 (setenv "EXTERNAL_QPDF" "1")
27844 `(("r-askpass" ,r-askpass)
27846 ("r-rcpp" ,r-rcpp)))
27847 (native-inputs `(("pkg-config" ,pkg-config)))
27848 (home-page "https://github.com/ropensci/qpdf")
27850 "Split, Combine and Compress PDF Files")
27852 "Content-preserving transformations transformations of PDF files such as
27853 split, combine, and compress. This package interfaces directly to the
27854 @code{qpdf} C++ API and does not require any command line utilities. Note that
27855 @code{qpdf} does not read actual content from PDF files: to extract text and
27856 data you need the @code{pdftools} package.")
27857 (license license:asl2.0)))
27859 (define-public r-pdftools
27861 (name "r-pdftools")
27866 (uri (cran-uri "pdftools" version))
27869 "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx"))))
27870 (properties `((upstream-name . "pdftools")))
27871 (build-system r-build-system)
27874 ("poppler" ,poppler)))
27876 `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp)))
27877 (native-inputs `(("pkg-config" ,pkg-config)))
27879 "https://docs.ropensci.org/pdftools/")
27881 "Text Extraction, Rendering and Converting of PDF Documents")
27883 "Utilities based on @code{libpoppler} for extracting text, fonts,
27884 attachments and metadata from a PDF file. Also supports high quality rendering
27885 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
27886 further processing in R.")
27887 (license license:expat)))
27889 (define-public r-antiword
27891 (name "r-antiword")
27896 (uri (cran-uri "antiword" version))
27899 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
27900 (modules '((guix build utils)))
27903 ;; unvendor libantiword
27904 (delete-file-recursively "src")
27906 (properties `((upstream-name . "antiword")))
27907 (build-system r-build-system)
27910 (modify-phases %standard-phases
27911 (add-after 'unpack 'use-system-antiword
27912 (lambda* (#:key inputs #:allow-other-keys)
27913 (substitute* "R/antiword.R"
27914 (("system.file\\(\"bin\", package = \"antiword\"\\)")
27915 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
27917 (inputs `(("antiword" ,antiword)))
27918 (propagated-inputs `(("r-sys" ,r-sys)))
27920 "https://github.com/ropensci/antiword#readme")
27922 "Extract Text from Microsoft Word Documents")
27924 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
27925 documents. The utility only supports the old @code{doc} format, not the new
27926 xml based @code{docx} format. Use the @code{xml2} package to read the
27928 (license license:gpl2)))
27930 (define-public r-readtext
27932 (name "r-readtext")
27937 (uri (cran-uri "readtext" version))
27940 "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y"))))
27941 (properties `((upstream-name . "readtext")))
27942 (build-system r-build-system)
27944 `(("r-antiword" ,r-antiword)
27945 ("r-data-table" ,r-data-table)
27946 ("r-digest" ,r-digest)
27948 ("r-jsonlite" ,r-jsonlite)
27949 ("r-pdftools" ,r-pdftools)
27950 ("r-readods" ,r-readods)
27951 ("r-readxl" ,r-readxl)
27952 ("r-streamr" ,r-streamr)
27953 ("r-stringi" ,r-stringi)
27954 ("r-striprtf" ,r-striprtf)
27955 ("r-tibble" ,r-tibble)
27956 ("r-xml2" ,r-xml2)))
27957 (native-inputs `(("r-knitr" ,r-knitr)))
27959 "https://github.com/quanteda/readtext")
27961 "Import and Handling for Plain and Formatted Text Files")
27963 "This package provides functions for importing and handling text files
27964 and formatted text files with additional meta-data, such including @code{.csv},
27965 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
27966 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
27967 (license license:gpl3)))
27969 (define-public r-packcircles
27971 (name "r-packcircles")
27976 (uri (cran-uri "packcircles" version))
27979 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
27980 (properties `((upstream-name . "packcircles")))
27981 (build-system r-build-system)
27982 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
27983 (native-inputs `(("r-knitr" ,r-knitr)))
27985 "https://github.com/mbedward/packcircles")
27986 (synopsis "Circle Packing")
27988 "Algorithms to find arrangements of non-overlapping circles.")
27989 (license license:expat)))
27991 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
27993 (define-public r-lwgeom
28000 (uri (cran-uri "lwgeom" version))
28003 "0byhjqa2acns8mznl1ngnfygxxxyszvnq66qfg0smhhhdkwr67aa"))))
28004 (properties `((upstream-name . "lwgeom")))
28005 (build-system r-build-system)
28006 (inputs `(("geos" ,geos) ("proj" ,proj) ("sqlite" ,sqlite)))
28008 `(("r-rcpp" ,r-rcpp)
28010 ("r-units" ,r-units)))
28011 (native-inputs `(("pkg-config" ,pkg-config)))
28013 "https://github.com/r-spatial/lwgeom/")
28015 "Bindings to Selected 'liblwgeom' Functions for Simple Features")
28017 "Access to selected functions found in
28018 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
28019 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
28020 (license license:gpl2)))
28022 (define-public r-stars
28029 (uri (cran-uri "stars" version))
28032 "0ybk899rc0rpf2cv5kwk78fvis5xnr255hfcy5khdxsxdqgl0m9j"))))
28033 (properties `((upstream-name . "stars")))
28034 (build-system r-build-system)
28036 `(("r-abind" ,r-abind)
28037 ("r-classint" ,r-classint)
28038 ("r-lwgeom" ,r-lwgeom)
28039 ("r-rlang" ,r-rlang)
28041 ("r-units" ,r-units)))
28042 (native-inputs `(("r-knitr" ,r-knitr)))
28043 (home-page "https://r-spatial.github.io/stars/")
28045 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
28047 "Reading, manipulating, writing and plotting spatiotemporal arrays
28048 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
28049 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
28050 (license license:asl2.0)))
28052 (define-public r-tmaptools
28054 (name "r-tmaptools")
28059 (uri (cran-uri "tmaptools" version))
28062 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
28063 (properties `((upstream-name . "tmaptools")))
28064 (build-system r-build-system)
28066 `(("r-dichromat" ,r-dichromat)
28067 ("r-lwgeom" ,r-lwgeom)
28068 ("r-magrittr" ,r-magrittr)
28069 ("r-rcolorbrewer" ,r-rcolorbrewer)
28071 ("r-stars" ,r-stars)
28072 ("r-units" ,r-units)
28073 ("r-viridislite" ,r-viridislite)
28076 "https://github.com/mtennekes/tmaptools")
28077 (synopsis "Thematic Map Tools")
28079 "Set of tools for reading and processing spatial data. The aim is to
28080 supply the workflow to create thematic maps. This package also facilitates
28081 @code{tmap}, the package for visualizing thematic maps.")
28082 (license license:gpl3)))
28084 (define-public r-rworldmap
28086 (name "r-rworldmap")
28091 (uri (cran-uri "rworldmap" version))
28094 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
28095 (properties `((upstream-name . "rworldmap")))
28096 (build-system r-build-system)
28098 `(("r-fields" ,r-fields)
28099 ("r-maptools" ,r-maptools)
28102 "https://github.com/AndySouth/rworldmap/")
28103 (synopsis "Mapping Global Data")
28105 "Enables mapping of country level and gridded user datasets.")
28106 (license license:gpl2+)))
28108 (define-public r-rtweet
28115 (uri (cran-uri "rtweet" version))
28118 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
28119 (properties `((upstream-name . "rtweet")))
28120 (build-system r-build-system)
28122 `(("r-httpuv" ,r-httpuv)
28124 ("r-jsonlite" ,r-jsonlite)
28125 ("r-magrittr" ,r-magrittr)
28126 ("r-progress" ,r-progress)
28128 ("r-tibble" ,r-tibble)))
28129 (native-inputs `(("r-knitr" ,r-knitr)))
28131 "https://docs.ropensci.org/rtweet/")
28132 (synopsis "Collecting Twitter Data")
28134 "An implementation of calls designed to collect and organize Twitter data
28135 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
28136 Application Program Interfaces (API)}.")
28137 (license license:expat)))
28139 (define-public r-intervals
28141 (name "r-intervals")
28146 (uri (cran-uri "intervals" version))
28149 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
28150 (properties `((upstream-name . "intervals")))
28151 (build-system r-build-system)
28152 (home-page "https://github.com/edzer/intervals")
28154 "Tools for Working with Points and Intervals")
28156 "Tools for working with and comparing sets of points and intervals.")
28157 (license license:artistic2.0)))
28159 (define-public r-eyelinker
28161 (name "r-eyelinker")
28166 (uri (cran-uri "eyelinker" version))
28169 "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2"))))
28170 (properties `((upstream-name . "eyelinker")))
28171 (build-system r-build-system)
28173 `(("r-intervals" ,r-intervals)
28174 ("r-readr" ,r-readr)
28175 ("r-stringi" ,r-stringi)
28176 ("r-stringr" ,r-stringr)
28177 ("r-tibble" ,r-tibble)))
28178 (native-inputs `(("r-knitr" ,r-knitr)))
28180 "https://github.com/a-hurst/eyelinker")
28182 "Import ASC Files from EyeLink Eye Trackers")
28184 "Imports plain-text ASC data files from EyeLink eye trackers into
28185 (relatively) tidy data frames for analysis and visualization.")
28186 (license license:gpl3)))
28188 (define-public r-btm
28195 (uri (cran-uri "BTM" version))
28198 "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb"))))
28199 (properties `((upstream-name . "BTM")))
28200 (build-system r-build-system)
28201 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28202 (home-page "https://github.com/bnosac/BTM")
28203 (synopsis "Biterm Topic Models for Short Text")
28205 "Biterm Topic Models find topics in collections of short texts. It is a
28206 word co-occurrence based topic model that learns topics by modeling word-word
28207 co-occurrences patterns which are called biterms. This in contrast to
28208 traditional topic models like Latent Dirichlet Allocation and Probabilistic
28209 Latent Semantic Analysis which are word-document co-occurrence topic models. A
28210 biterm consists of two words co-occurring in the same short text window. This
28211 context window can for example be a twitter message, a short answer on a
28212 survey, a sentence of a text or a document identifier. The techniques are
28213 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
28214 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
28215 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
28217 (license license:asl2.0)))
28219 (define-public r-textplot
28221 (name "r-textplot")
28226 (uri (cran-uri "textplot" version))
28229 "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy"))))
28230 (properties `((upstream-name . "textplot")))
28231 (build-system r-build-system)
28233 `(("r-data-table" ,r-data-table)
28234 ("r-lattice" ,r-lattice)
28235 ("r-matrix" ,r-matrix)))
28236 (native-inputs `(("r-knitr" ,r-knitr)))
28237 (home-page "https://github.com/bnosac/textplot")
28238 (synopsis "Text Plots")
28240 "Visualise complex relations in texts. This is done by providing
28241 functionalities for displaying text co-occurrence networks, text correlation
28242 networks, dependency relationships as well as text clustering. Feel free to
28243 join the effort of providing interesting text visualisations.")
28244 (license license:gpl2)))