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>
36 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
38 ;;; This file is part of GNU Guix.
40 ;;; GNU Guix is free software; you can redistribute it and/or modify it
41 ;;; under the terms of the GNU General Public License as published by
42 ;;; the Free Software Foundation; either version 3 of the License, or (at
43 ;;; your option) any later version.
45 ;;; GNU Guix is distributed in the hope that it will be useful, but
46 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
47 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
48 ;;; GNU General Public License for more details.
50 ;;; You should have received a copy of the GNU General Public License
51 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
53 (define-module (gnu packages cran)
54 #:use-module ((guix licenses) #:prefix license:)
55 #:use-module (guix packages)
56 #:use-module (guix download)
57 #:use-module (guix git-download)
58 #:use-module (guix utils)
59 #:use-module (guix build-system gnu)
60 #:use-module (guix build-system r)
61 #:use-module (gnu packages)
62 #:use-module (gnu packages algebra)
63 #:use-module (gnu packages autotools)
64 #:use-module (gnu packages base)
65 #:use-module (gnu packages bioinformatics)
66 #:use-module (gnu packages c)
67 #:use-module (gnu packages compression)
68 #:use-module (gnu packages crypto)
69 #:use-module (gnu packages curl)
70 #:use-module (gnu packages databases)
71 #:use-module (gnu packages fontutils)
72 #:use-module (gnu packages fribidi)
73 #:use-module (gnu packages gcc)
74 #:use-module (gnu packages geo)
75 #:use-module (gnu packages ghostscript)
76 #:use-module (gnu packages gl)
77 #:use-module (gnu packages gnome)
78 #:use-module (gnu packages graph)
79 #:use-module (gnu packages gtk)
80 #:use-module (gnu packages haskell-xyz)
81 #:use-module (gnu packages icu4c)
82 #:use-module (gnu packages image)
83 #:use-module (gnu packages imagemagick)
84 #:use-module (gnu packages java)
85 #:use-module (gnu packages javascript)
86 #:use-module (gnu packages libevent)
87 #:use-module (gnu packages lisp-xyz)
88 #:use-module (gnu packages machine-learning)
89 #:use-module (gnu packages maths)
90 #:use-module (gnu packages mpi)
91 #:use-module (gnu packages multiprecision)
92 #:use-module (gnu packages networking)
93 #:use-module (gnu packages node)
94 #:use-module (gnu packages pcre)
95 #:use-module (gnu packages pdf)
96 #:use-module (gnu packages perl)
97 #:use-module (gnu packages pkg-config)
98 #:use-module (gnu packages pulseaudio) ;libsndfile
99 #:use-module (gnu packages python)
100 #:use-module (gnu packages python-xyz)
101 #:use-module (gnu packages sqlite)
102 #:use-module (gnu packages statistics)
103 #:use-module (gnu packages tcl)
104 #:use-module (gnu packages textutils)
105 #:use-module (gnu packages tls)
106 #:use-module (gnu packages version-control)
107 #:use-module (gnu packages web)
108 #:use-module (gnu packages xml)
109 #:use-module (gnu packages xorg))
111 (define-public r-brio
118 (uri (cran-uri "brio" version))
121 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
122 (properties `((upstream-name . "brio")))
123 (build-system r-build-system)
124 (home-page "https://github.com/r-lib/brio")
125 (synopsis "Basic R input output")
127 "This package provides functions to handle basic input output. These
128 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
129 files and provide more explicit control over line endings.")
130 (license license:expat)))
132 (define-public r-cachem
139 (uri (cran-uri "cachem" version))
142 "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh"))))
143 (properties `((upstream-name . "cachem")))
144 (build-system r-build-system)
146 `(("r-fastmap" ,r-fastmap)
147 ("r-rlang" ,r-rlang)))
148 (home-page "https://cachem.r-lib.org/")
149 (synopsis "Cache R objects with automatic pruning")
151 "This package provides key-value stores with automatic pruning. Caches
152 can limit either their total size or the age of the oldest object (or both),
153 automatically pruning objects to maintain the constraints.")
154 (license license:expat)))
156 (define-public r-diffobj
163 (uri (cran-uri "diffobj" version))
166 "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q"))))
167 (properties `((upstream-name . "diffobj")))
168 (build-system r-build-system)
169 (propagated-inputs `(("r-crayon" ,r-crayon)))
170 (native-inputs `(("r-knitr" ,r-knitr)))
171 (home-page "https://github.com/brodieG/diffobj")
172 (synopsis "Diffs for R objects")
174 "Generate a colorized diff of two R objects for an intuitive
175 visualization of their differences.")
176 (license license:gpl2+)))
178 (define-public r-waldo
185 (uri (cran-uri "waldo" version))
188 "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr"))))
189 (properties `((upstream-name . "waldo")))
190 (build-system r-build-system)
193 ("r-diffobj" ,r-diffobj)
196 ("r-rematch2" ,r-rematch2)
198 ("r-tibble" ,r-tibble)))
199 (home-page "https://github.com/r-lib/waldo")
200 (synopsis "Find differences between R objects")
202 "Compare complex R objects and reveal the key differences. This package
203 was designed particularly for use in testing packages where being able to
204 quickly isolate key differences makes understanding test failures much
206 (license license:expat)))
208 (define-public r-rticles
215 (uri (cran-uri "rticles" version))
218 "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818"))))
219 (properties `((upstream-name . "rticles")))
220 (build-system r-build-system)
222 `(("r-knitr" ,r-knitr)
223 ("r-rmarkdown" ,r-rmarkdown)
224 ("r-tinytex" ,r-tinytex)
227 (home-page "https://github.com/rstudio/rticles")
228 (synopsis "Article formats for R Markdown")
230 "This package provides a suite of custom R Markdown formats and templates
231 for authoring journal articles and conference submissions.")
232 (license license:gpl3)))
234 (define-public r-bezier
240 (uri (cran-uri "bezier" version))
243 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
244 (build-system r-build-system)
245 (home-page "https://cran.r-project.org/web/packages/bezier/")
246 (synopsis "Bezier curve and spline toolkit")
248 "This package is a toolkit for working with Bezier curves and splines.
249 The package provides functions for point generation, arc length estimation,
250 degree elevation and curve fitting.")
251 (license license:gpl2+)))
260 (uri (cran-uri "V8" version))
263 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
264 (properties `((upstream-name . "V8")))
265 (build-system r-build-system)
268 (modify-phases %standard-phases
269 (add-after 'unpack 'find-v8
270 (lambda* (#:key inputs #:allow-other-keys)
271 (substitute* "configure"
273 (string-append "PKG_LIBS="
274 (assoc-ref inputs "node")
275 "/lib/libnode.so.64\n")))
276 (setenv "INCLUDE_DIR"
278 (assoc-ref inputs "node")
282 (assoc-ref inputs "node") "/lib"))
285 `(("node" ,libnode)))
288 ("r-jsonlite" ,r-jsonlite)
291 `(("r-knitr" ,r-knitr)))
292 (home-page "https://jeroen.cran.dev/V8")
293 (synopsis "Embedded JavaScript and WebAssembly engine for R")
295 "This package provides an R interface to V8: Google's JavaScript and
296 WebAssembly engine.")
297 (license license:expat)))
306 (uri (cran-uri "DOT" version))
309 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
310 (properties `((upstream-name . "DOT")))
311 (build-system r-build-system)
314 (home-page "http://haghish.com/dot")
315 (synopsis "Render and Export DOT Graphs in R")
317 "This package provides tools to render DOT diagram markup language in R
318 and also provides the possibility to export the graphs in PostScript and
319 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
320 programming packages such as @code{knitr} and @code{rmarkdown}.")
321 (license license:expat)))
323 (define-public r-clipr
330 (uri (cran-uri "clipr" version))
333 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
334 (build-system r-build-system)
336 `(("r-knitr" ,r-knitr)))
337 (home-page "https://github.com/mdlincoln/clipr")
338 (synopsis "Read and write from the system clipboard")
340 "This package provides simple utility functions to read from and write to
341 the system clipboards.")
342 (license license:gpl3)))
350 (uri (cran-uri "zoo" version))
353 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
354 (build-system r-build-system)
356 `(("r-lattice" ,r-lattice)))
357 (home-page "http://zoo.R-Forge.R-project.org/")
358 (synopsis "S3 infrastructure for regular and irregular time series")
359 (description "This package contains an S3 class with methods for totally
360 ordered indexed observations. It is particularly aimed at irregular time
361 series of numeric vectors/matrices and factors.")
362 (license license:gpl2+)))
364 (define-public r-ggalluvial
366 (name "r-ggalluvial")
370 (uri (cran-uri "ggalluvial" version))
373 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
374 (properties `((upstream-name . "ggalluvial")))
375 (build-system r-build-system)
377 `(("r-dplyr" ,r-dplyr)
378 ("r-ggplot2" ,r-ggplot2)
379 ("r-lazyeval" ,r-lazyeval)
382 ("r-tidyselect" ,r-tidyselect)))
384 `(("r-knitr" ,r-knitr)))
385 (home-page "http://corybrunson.github.io/ggalluvial/")
386 (synopsis "Alluvial plots for ggplot2")
387 (description "This package provides alluvial plots for @code{ggplot2}.
388 Alluvial plots use variable-width ribbons and stacked bar plots to represent
389 multi-dimensional or repeated-measures data with categorical or ordinal
391 (license license:gpl3)))
393 (define-public r-ggpmisc
399 (uri (cran-uri "ggpmisc" version))
402 "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
403 (build-system r-build-system)
405 `(("r-dplyr" ,r-dplyr)
406 ("r-generics" ,r-generics)
408 ("r-ggplot2" ,r-ggplot2)
409 ("r-gridextra" ,r-gridextra)
410 ("r-lubridate" ,r-lubridate)
411 ("r-magrittr" ,r-magrittr)
414 ("r-polynom" ,r-polynom)
416 ("r-scales" ,r-scales)
417 ("r-splus2r" ,r-splus2r)
418 ("r-stringr" ,r-stringr)
419 ("r-tibble" ,r-tibble)
423 `(("r-knitr" ,r-knitr)))
424 (home-page "https://www.r4photobiology.info/")
425 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
426 (description "This package provides extensions to @code{ggplot2},
427 respecting the grammar of its graphics paradigm.")
428 (license license:gpl2+)))
430 (define-public r-gprofiler
437 (uri (cran-uri "gProfileR" version))
440 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
441 (properties `((upstream-name . "gProfileR")))
442 (build-system r-build-system)
445 ("r-rcurl" ,r-rcurl)))
446 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
447 (synopsis "Interface to the g:Profiler toolkit")
449 "This package provides tools for functional enrichment analysis,
450 gene identifier conversion and mapping homologous genes across related
451 organisms via the @code{g:Profiler} toolkit.")
452 (license license:gpl2+)))
454 (define-public r-gprofiler2
456 (name "r-gprofiler2")
461 (uri (cran-uri "gprofiler2" version))
464 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
465 (properties `((upstream-name . "gprofiler2")))
466 (build-system r-build-system)
468 `(("r-crosstalk" ,r-crosstalk)
470 ("r-ggplot2" ,r-ggplot2)
471 ("r-gridextra" ,r-gridextra)
472 ("r-jsonlite" ,r-jsonlite)
473 ("r-plotly" ,r-plotly)
476 ("r-viridislite" ,r-viridislite)))
477 (native-inputs `(("r-knitr" ,r-knitr)))
478 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
479 (synopsis "Interface to the g:Profiler toolset")
481 "This package provides a toolset for functional enrichment analysis and
482 visualization, gene/protein/SNP identifier conversion and mapping orthologous
483 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
487 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
489 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
491 @item @code{g:Orth}, orthology search across species;
492 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
493 genes and variant effects.
496 This package is an R interface corresponding to the 2019 update of
497 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
499 (license license:gpl2+)))
501 (define-public r-oenb
508 (uri (cran-uri "oenb" version))
511 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
512 (properties `((upstream-name . "oenb")))
513 (build-system r-build-system)
515 `(("r-dplyr" ,r-dplyr)
517 (native-inputs `(("r-knitr" ,r-knitr)))
518 (home-page "https://github.com/franzmohr/oenb")
519 (synopsis "Tools for the OeNB Data Web Service")
521 "Tools to access data from the data web service of the
522 @acronym{OeNB, Oesterreichische Nationalbank},
523 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
524 (license license:gpl2+)))
526 (define-public r-scales
533 (uri (cran-uri "scales" version))
535 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
536 (build-system r-build-system)
538 `(("r-farver" ,r-farver)
539 ("r-labeling" ,r-labeling)
540 ("r-lifecycle" ,r-lifecycle)
541 ("r-munsell" ,r-munsell)
542 ("r-rcolorbrewer" ,r-rcolorbrewer)
544 ("r-viridislite" ,r-viridislite)))
545 (home-page "https://github.com/hadley/scales")
546 (synopsis "Scale functions for visualization")
548 "This package provides graphical scales that map data to aesthetics, and
549 provides methods for automatically determining breaks and labels for axes and
551 (license license:expat)))
553 (define-public r-pheatmap
560 (uri (cran-uri "pheatmap" version))
563 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
564 (build-system r-build-system)
566 `(("r-gtable" ,r-gtable)
567 ("r-rcolorbrewer" ,r-rcolorbrewer)
568 ("r-scales" ,r-scales)))
569 (home-page "https://cran.r-project.org/web/packages/pheatmap")
570 (synopsis "Pretty heatmaps")
572 "This package provides an implementation of heatmaps that offers more
573 control over dimensions and appearance.")
574 (license license:gpl2+)))
582 (uri (cran-uri "ecp" version))
585 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
586 (build-system r-build-system)
588 `(("r-rcpp" ,r-rcpp)))
589 (home-page "https://cran.r-project.org/web/packages/ecp/")
590 (synopsis "Multiple change-point analysis of multivariate data")
592 "This package implements various procedures for finding multiple
593 change-points. Two methods make use of dynamic programming and pruning, with
594 no distributional assumptions other than the existence of certain absolute
595 moments in one method. Hierarchical and exact search methods are included.
596 All methods return the set of estimated change-points as well as other summary
598 (license license:gpl2+)))
600 (define-public r-ellipsis
607 (uri (cran-uri "ellipsis" version))
610 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
611 (build-system r-build-system)
613 `(("r-rlang" ,r-rlang)))
614 (home-page "https://github.com/hadley/ellipsis")
615 (synopsis "Tools for working with additional arguments")
617 "In S3 generics, it's useful to take @code{...} so that methods can have
618 additional arguments. But this flexibility comes at a cost: misspelled
619 arguments will be silently ignored. The @code{ellipsis} package is an
620 experiment that allows a generic to warn if any arguments passed in @code{...}
622 (license license:gpl3)))
631 (uri (cran-uri "grr" version))
634 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
635 (build-system r-build-system)
636 (home-page "https://cran.r-project.org/web/packages/grr")
637 (synopsis "Alternative implementations of base R functions")
639 "This package provides alternative implementations of some base R
640 functions, including @code{sort}, @code{order}, and @code{match}. The
641 functions are simplified but can be faster or have other advantages.")
642 (license license:gpl3)))
644 (define-public r-matrix-utils
646 (name "r-matrix-utils")
651 (uri (cran-uri "Matrix.utils" version))
654 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
655 (properties `((upstream-name . "Matrix.utils")))
656 (build-system r-build-system)
659 ("r-matrix" ,r-matrix)))
660 (home-page "https://github.com/cvarrichio/Matrix.utils")
662 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
664 "This package implements data manipulation methods such as @code{cast},
665 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
667 (license license:gpl3)))
669 (define-public r-mboost
675 (uri (cran-uri "mboost" version))
678 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
679 (build-system r-build-system)
681 `(("r-lattice" ,r-lattice)
682 ("r-matrix" ,r-matrix)
684 ("r-partykit" ,r-partykit)
685 ("r-quadprog" ,r-quadprog)
687 ("r-survival" ,r-survival)))
688 (home-page "https://github.com/boost-R/mboost")
689 (synopsis "Model-based boosting")
691 "This package provides a functional gradient descent algorithm (boosting)
692 for optimizing general risk functions utilizing component-wise (penalised)
693 least squares estimates or regression trees as base-learners for fitting
694 generalized linear, additive and interaction models to potentially
695 high-dimensional data.")
696 (license license:gpl2)))
698 (define-public r-shadowtext
700 (name "r-shadowtext")
704 (uri (cran-uri "shadowtext" version))
707 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
708 (properties `((upstream-name . "shadowtext")))
709 (build-system r-build-system)
711 `(("r-ggplot2" ,r-ggplot2)
712 ("r-scales" ,r-scales)))
714 `(("r-knitr" ,r-knitr)))
715 (home-page "https://github.com/GuangchuangYu/shadowtext/")
716 (synopsis "Shadow text grob and layer")
717 (description "This package implements @code{shadowtextGrob()} for
718 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
719 These functions draw text grob with background shadow.")
720 (license license:artistic2.0)))
729 (uri (cran-uri "sys" version))
732 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
733 (build-system r-build-system)
734 (home-page "https://github.com/jeroen/sys")
735 (synopsis "Powerful and reliable tools for running system commands in R")
737 "This package provides drop-in replacements for the base @code{system2()}
738 function with fine control and consistent behavior across platforms. It
739 supports clean interruption, timeout, background tasks, and streaming STDIN /
740 STDOUT / STDERR over binary or text connections. The package also provides
741 functions for evaluating expressions inside a temporary fork. Such
742 evaluations have no side effects on the main R process, and support reliable
743 interrupts and timeouts. This provides the basis for a sandboxing
745 (license license:expat)))
747 (define-public r-ashr
753 (uri (cran-uri "ashr" version))
756 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
757 (properties `((upstream-name . "ashr")))
758 (build-system r-build-system)
760 `(("r-etrunct" ,r-etrunct)
761 ("r-invgamma" ,r-invgamma)
762 ("r-matrix" ,r-matrix)
763 ("r-mixsqp" ,r-mixsqp)
765 ("r-squarem" ,r-squarem)
766 ("r-truncnorm" ,r-truncnorm)))
768 `(("r-knitr" ,r-knitr)))
769 (home-page "https://github.com/stephens999/ashr")
770 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
771 (description "This package implements an empirical Bayes approach for
772 large-scale hypothesis testing and false discovery rate estimation.")
773 (license license:gpl3+)))
775 (define-public r-askpass
782 (uri (cran-uri "askpass" version))
785 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
786 (build-system r-build-system)
787 (propagated-inputs `(("r-sys" ,r-sys)))
788 (home-page "https://github.com/jeroen/askpass")
789 (synopsis "Safe password entry for R")
791 "This package provides cross-platform utilities for prompting the user
792 for credentials or a passphrase, for example to authenticate with a server or
793 read a protected key.")
794 (license license:expat)))
796 (define-public r-vegan
803 (uri (cran-uri "vegan" version))
806 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
807 (build-system r-build-system)
809 `(("r-knitr" ,r-knitr) ; needed for vignettes
810 ("gfortran" ,gfortran)))
812 `(("r-cluster" ,r-cluster)
813 ("r-lattice" ,r-lattice)
816 ("r-permute" ,r-permute)))
817 (home-page "https://cran.r-project.org/web/packages/vegan")
818 (synopsis "Functions for community ecology")
820 "The vegan package provides tools for descriptive community ecology. It
821 has most basic functions of diversity analysis, community ordination and
822 dissimilarity analysis. Most of its multivariate tools can be used for other
823 data types as well.")
824 (license license:gpl2+)))
826 (define-public r-tidyverse
833 (uri (cran-uri "tidyverse" version))
836 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
837 (build-system r-build-system)
839 `(("r-broom" ,r-broom)
841 ("r-crayon" ,r-crayon)
842 ("r-dbplyr" ,r-dbplyr)
844 ("r-forcats" ,r-forcats)
845 ("r-ggplot2" ,r-ggplot2)
849 ("r-jsonlite" ,r-jsonlite)
850 ("r-lubridate" ,r-lubridate)
851 ("r-magrittr" ,r-magrittr)
852 ("r-modelr" ,r-modelr)
853 ("r-pillar" ,r-pillar)
856 ("r-readxl" ,r-readxl)
857 ("r-reprex" ,r-reprex)
859 ("r-rstudioapi" ,r-rstudioapi)
861 ("r-stringr" ,r-stringr)
862 ("r-tibble" ,r-tibble)
865 (home-page "https://tidyverse.tidyverse.org")
866 (synopsis "Install and load packages from the \"Tidyverse\"")
868 "The @code{tidyverse} is a set of packages that work in harmony because
869 they share common data representations and API design. This package is
870 designed to make it easy to install and load multiple tidyverse packages in a
872 (license license:gpl3)))
874 (define-public r-rvest
881 (uri (cran-uri "rvest" version))
883 (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53"))))
884 (build-system r-build-system)
887 ("r-lifecycle" ,r-lifecycle)
888 ("r-magrittr" ,r-magrittr)
890 ("r-selectr" ,r-selectr)
891 ("r-tibble" ,r-tibble)
894 `(("r-knitr" ,r-knitr)))
895 (home-page "https://github.com/hadley/rvest")
896 (synopsis "Simple web scraping for R")
898 "@code{r-rvest} helps you scrape information from web pages. It is
899 designed to work with @code{magrittr} to make it easy to express common web
900 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
901 (license license:gpl3)))
903 (define-public r-selectr
910 (uri (cran-uri "selectr" version))
912 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
913 (build-system r-build-system)
915 `(("r-stringr" ,r-stringr)
917 (home-page "https://sjp.co.nz/projects/selectr/")
918 (synopsis "Translate CSS selectors to XPath expressions")
920 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
921 expression. This allows you to use CSS selectors when working with the XML
922 package as it can only evaluate XPath expressions. Also provided are
923 convenience functions useful for using CSS selectors on XML nodes. This
924 package is a port of the Python package @code{cssselect}.")
925 (license license:bsd-3)))
927 (define-public r-reprex
934 (uri (cran-uri "reprex" version))
937 "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
938 (build-system r-build-system)
940 `(("r-callr" ,r-callr)
947 ("r-rmarkdown" ,r-rmarkdown)
948 ("r-withr" ,r-withr)))
950 `(("r-knitr" ,r-knitr)))
951 (home-page "https://github.com/tidyverse/reprex")
952 (synopsis "Prepare reproducible R code examples for sharing")
954 "This package provides a convenience wrapper that uses the
955 @code{rmarkdown} package to render small snippets of code to target formats
956 that include both code and output. The goal is to encourage the sharing of
957 small, reproducible, and runnable examples on code-oriented websites or email.
958 @code{reprex} also extracts clean, runnable R code from various common formats,
959 such as copy/paste from an R session.")
960 (license license:expat)))
962 (define-public r-reordercluster
964 (name "r-reordercluster")
968 (uri (cran-uri "ReorderCluster" version))
971 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
972 (build-system r-build-system)
974 `(("r-gplots" ,r-gplots)
976 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
977 (synopsis "Reordering the dendrogram according to the class labels")
978 (description "This package provides tools for performing the leaf reordering
979 for the dendrogram that preserves the hierarchical clustering result and at the
980 same time tries to group instances from the same class together.")
981 (license license:gpl3+)))
983 (define-public r-callr
990 (uri (cran-uri "callr" version))
993 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
994 (build-system r-build-system)
997 ("r-processx" ,r-processx)))
998 (home-page "https://github.com/r-lib/callr#readme")
999 (synopsis "Call R from R")
1001 "It is sometimes useful to perform a computation in a separate R process,
1002 without affecting the current R process at all. This package does exactly
1004 (license license:expat)))
1006 (define-public r-readxl
1013 (uri (cran-uri "readxl" version))
1016 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1017 (build-system r-build-system)
1019 `(("r-cellranger" ,r-cellranger)
1020 ("r-progress" ,r-progress)
1022 ("r-tibble" ,r-tibble)))
1023 (home-page "https://readxl.tidyverse.org")
1024 (synopsis "Read Excel files")
1026 "This package lets you import Excel files into R. It supports
1027 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1028 the embedded @code{RapidXML} C++ library.")
1029 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1030 ;; 'rapidxml' which is Boost.
1031 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1033 (define-public r-modelr
1040 (uri (cran-uri "modelr" version))
1043 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1044 (build-system r-build-system)
1046 `(("r-broom" ,r-broom)
1047 ("r-magrittr" ,r-magrittr)
1048 ("r-purrr" ,r-purrr)
1049 ("r-rlang" ,r-rlang)
1050 ("r-tibble" ,r-tibble)
1051 ("r-tidyr" ,r-tidyr)
1052 ("r-tidyselect" ,r-tidyselect)
1053 ("r-vctrs" ,r-vctrs)))
1054 (home-page "https://github.com/tidyverse/modelr")
1055 (synopsis "Helper functions for modelling in pipelines")
1057 "Functions for modelling that help you seamlessly integrate modelling
1058 into a pipeline of data manipulation and visualisation.")
1059 (license license:gpl3)))
1061 (define-public r-httpuv
1067 (uri (cran-uri "httpuv" version))
1070 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1071 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1072 ;; only contains fixes for building on Solaris.
1073 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1074 (modules '((guix build utils)))
1077 (delete-file-recursively "src/libuv")
1078 ;; Cannot unbundle http-parser, because it contains local
1081 (build-system r-build-system)
1084 (modify-phases %standard-phases
1085 (add-after 'unpack 'unbundle-libuv
1086 (lambda* (#:key outputs #:allow-other-keys)
1087 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1088 (("\"libuv/include/uv\\.h\"")
1090 ;; Fix https://github.com/rstudio/httpuv/issues/282
1091 (substitute* "src/http.cpp"
1092 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1093 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1096 `(("libuv" ,libuv)))
1099 ("r-later" ,r-later)
1100 ("r-promises" ,r-promises)
1102 ("r-rcpp" ,r-rcpp)))
1103 (home-page "https://github.com/rstudio/httpuv")
1104 (synopsis "HTTP and WebSocket server library for R")
1106 "The httpuv package provides low-level socket and protocol support for
1107 handling HTTP and WebSocket requests directly from within R. It is primarily
1108 intended as a building block for other packages, rather than making it
1109 particularly easy to create complete web applications using httpuv alone.")
1110 ;; This package includes third-party code that was originally released
1111 ;; under various non-copyleft licenses. Full licensing information can be
1112 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1113 (license license:gpl3+)))
1115 (define-public r-jsonlite
1121 (uri (cran-uri "jsonlite" version))
1124 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1125 (build-system r-build-system)
1127 `(("r-knitr" ,r-knitr)))
1128 (home-page "https://arxiv.org/abs/1403.2805")
1129 (synopsis "Robust, high performance JSON parser and generator for R")
1131 "The jsonlite package provides a fast JSON parser and generator optimized
1132 for statistical data and the web. It offers flexible, robust, high
1133 performance tools for working with JSON in R and is particularly powerful for
1134 building pipelines and interacting with a web API. In addition to converting
1135 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1136 and prettify JSON data. The unit tests included with the package verify that
1137 all edge cases are encoded and decoded consistently for use with dynamic data
1138 in systems and applications.")
1139 (license license:expat)))
1141 (define-public r-servr
1147 (uri (cran-uri "servr" version))
1150 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1151 (build-system r-build-system)
1153 `(("r-httpuv" ,r-httpuv)
1154 ("r-jsonlite" ,r-jsonlite)
1156 ("r-xfun" ,r-xfun)))
1157 (home-page "https://github.com/yihui/servr")
1158 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1160 "Servr provides an HTTP server in R to serve static files, or dynamic
1161 documents that can be converted to HTML files (e.g., R Markdown) under a given
1163 (license license:expat)))
1165 (define-public r-htmltools
1167 (name "r-htmltools")
1171 (uri (cran-uri "htmltools" version))
1174 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1175 (build-system r-build-system)
1177 `(("r-base64enc" ,r-base64enc)
1178 ("r-digest" ,r-digest)
1179 ("r-rlang" ,r-rlang)))
1180 (home-page "https://cran.r-project.org/web/packages/htmltools")
1181 (synopsis "R tools for HTML")
1183 "This package provides tools for HTML generation and output in R.")
1184 (license license:expat)))
1186 (define-public r-htmlwidgets
1188 (name "r-htmlwidgets")
1192 (uri (cran-uri "htmlwidgets" version))
1195 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1196 (build-system r-build-system)
1198 `(("r-htmltools" ,r-htmltools)
1199 ("r-jsonlite" ,r-jsonlite)
1200 ("r-yaml" ,r-yaml)))
1202 `(("r-knitr" ,r-knitr)))
1203 (home-page "https://github.com/ramnathv/htmlwidgets")
1204 (synopsis "HTML Widgets for R")
1206 "HTML widgets is a framework for creating HTML widgets that render in
1207 various contexts including the R console, R Markdown documents, and Shiny web
1209 (license license:expat)))
1211 (define-public r-htmltable
1213 (name "r-htmltable")
1218 (uri (cran-uri "htmlTable" version))
1220 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1221 (properties `((upstream-name . "htmlTable")))
1222 (build-system r-build-system)
1224 `(("r-checkmate" ,r-checkmate)
1225 ("r-htmltools" ,r-htmltools)
1226 ("r-htmlwidgets" ,r-htmlwidgets)
1227 ("r-knitr" ,r-knitr)
1228 ("r-magrittr" ,r-magrittr)
1229 ("r-rstudioapi" ,r-rstudioapi)
1230 ("r-stringr" ,r-stringr)))
1232 `(("r-knitr" ,r-knitr)))
1233 (home-page "http://gforge.se/packages/")
1234 (synopsis "Advanced tables for Markdown/HTML")
1236 "This package provides functions to build tables with advanced layout
1237 elements such as row spanners, column spanners, table spanners, zebra
1238 striping, and more. While allowing advanced layout, the underlying
1239 CSS-structure is simple in order to maximize compatibility with word
1240 processors such as LibreOffice. The package also contains a few text
1241 formatting functions that help outputting text compatible with HTML or
1243 (license license:gpl3+)))
1245 (define-public r-curl
1251 (uri (cran-uri "curl" version))
1254 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1255 (build-system r-build-system)
1258 (modify-phases %standard-phases
1259 ;; The environment variable CURL_CA_BUNDLE is only respected when
1260 ;; running Windows, so we disable the platform checks.
1261 ;; This can be removed once the libcurl has been patched.
1262 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1264 (substitute* "R/onload.R"
1265 (("if \\(!grepl\\(\"mingw\".*")
1267 (substitute* "src/handle.c"
1268 (("/\\* Only set" m)
1270 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1271 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1278 `(("pkg-config" ,pkg-config)))
1279 (home-page "https://github.com/jeroenooms/curl")
1280 (synopsis "HTTP client for R")
1282 "The @code{curl()} and @code{curl_download()} functions provide highly
1283 configurable drop-in replacements for base @code{url()} and
1284 @code{download.file()} with better performance, support for encryption, gzip
1285 compression, authentication, and other @code{libcurl} goodies. The core of
1286 the package implements a framework for performing fully customized requests
1287 where data can be processed either in memory, on disk, or streaming via the
1288 callback or connection interfaces.")
1289 (license license:expat)))
1291 (define-public r-hwriter
1298 (uri (cran-uri "hwriter" version))
1301 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1302 (build-system r-build-system)
1303 (home-page "https://cran.r-project.org/web/packages/hwriter")
1304 (synopsis "Output R objects in HTML format")
1306 "This package provides easy-to-use and versatile functions to output R
1307 objects in HTML format.")
1308 (license license:lgpl2.1+)))
1310 (define-public r-rjson
1317 (uri (cran-uri "rjson" version))
1320 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1321 (build-system r-build-system)
1322 (home-page "https://cran.r-project.org/web/packages/rjson")
1323 (synopsis "JSON library for R")
1325 "This package provides functions to convert R objects into JSON objects
1327 (license license:gpl2+)))
1329 (define-public r-fastmap
1336 (uri (cran-uri "fastmap" version))
1339 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1340 (properties `((upstream-name . "fastmap")))
1341 (build-system r-build-system)
1342 (home-page "https://r-lib.github.io/fastmap/")
1343 (synopsis "Fast implementation of a key-value store")
1345 "This package provides a fast implementation of a key-value store.
1346 Environments are commonly used as key-value stores, but every time a new key
1347 is used, it is added to R's global symbol table, causing a small amount of
1348 memory leakage. This can be problematic in cases where many different keys
1349 are used. Fastmap avoids this memory leak issue by implementing the map using
1350 data structures in C++.")
1351 (license license:expat)))
1353 (define-public r-fastghquad
1355 (name "r-fastghquad")
1360 (uri (cran-uri "fastGHQuad" version))
1363 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1364 (properties `((upstream-name . "fastGHQuad")))
1365 (build-system r-build-system)
1367 `(("r-rcpp" ,r-rcpp)))
1368 (home-page "https://github.com/awblocker/fastGHQuad")
1369 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1371 "This package implements numerically-stable Gauss-Hermite quadrature
1372 rules and utility functions for adaptive GH quadrature.")
1373 (license license:expat)))
1375 (define-public r-rstpm2
1382 (uri (cran-uri "rstpm2" version))
1385 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1386 (properties `((upstream-name . "rstpm2")))
1387 (build-system r-build-system)
1389 `(("r-bbmle" ,r-bbmle)
1391 ("r-desolve" ,r-desolve)
1392 ("r-fastghquad" ,r-fastghquad)
1395 ("r-rcpparmadillo" ,r-rcpparmadillo)
1396 ("r-survival" ,r-survival)))
1398 `(("gfortran" ,gfortran)))
1399 (home-page "https://github.com/mclements/rstpm2")
1400 (synopsis "Link-based survival models")
1402 "This package provides R implementations of @dfn{generalized survival
1403 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1404 multi-state models.")
1405 ;; One of these licenses
1406 (license (list license:gpl2 license:gpl3))))
1408 ;; This package includes minified JavaScript files. When upgrading please
1409 ;; check that there are no new minified JavaScript files.
1410 (define-public r-jquerylib
1412 (name "r-jquerylib")
1417 (uri (cran-uri "jquerylib" version))
1420 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1422 '(for-each delete-file
1423 '("inst/lib/jquery-1.12.4.min.js"
1424 "inst/lib/jquery-2.2.4.min.js"
1425 "inst/lib/jquery-3.5.1.min.js")))))
1426 (properties `((upstream-name . "jquerylib")))
1427 (build-system r-build-system)
1429 `(#:modules ((guix build utils)
1430 (guix build r-build-system)
1433 (modify-phases %standard-phases
1434 (add-after 'unpack 'process-javascript
1435 (lambda* (#:key inputs #:allow-other-keys)
1436 (with-directory-excursion "inst/lib/"
1440 `(("jquery-1.12.4.js"
1441 "jquery-1.12.4.min.js")
1443 "jquery-2.2.4.min.js")
1445 "jquery-3.5.1.min.js"))))
1446 (lambda (sources targets)
1447 (for-each (lambda (source target)
1448 (format #t "Processing ~a --> ~a~%"
1450 (invoke "esbuild" source "--minify"
1451 (string-append "--outfile=" target)))
1452 sources targets)))))))))
1454 `(("r-htmltools" ,r-htmltools)))
1456 `(("esbuild" ,esbuild)))
1457 (home-page "https://cran.r-project.org/package=jquerylib")
1458 (synopsis "Obtain jQuery as an HTML dependency object")
1460 "Obtain any major version of jQuery and use it in any webpage generated
1461 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1462 need to use this package directly, but other R packages (e.g. shiny,
1463 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1465 (license license:expat)))
1467 (define-public r-sass
1474 (uri (cran-uri "sass" version))
1477 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1478 (properties `((upstream-name . "sass")))
1479 (build-system r-build-system)
1481 `(("r-digest" ,r-digest)
1483 ("r-htmltools" ,r-htmltools)
1485 ("r-rappdirs" ,r-rappdirs)
1486 ("r-rlang" ,r-rlang)))
1487 (native-inputs `(("r-knitr" ,r-knitr)))
1488 (home-page "https://github.com/rstudio/sass")
1489 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1491 "This package provides an SCSS compiler, powered by the libsass library.
1492 With this, R developers can use variables, inheritance, and functions to
1493 generate dynamic style sheets. The package uses the Sass CSS extension
1494 language, which is stable, powerful, and CSS compatible.")
1495 (license license:expat)))
1497 ;; This package includes minified JavaScript files. When upgrading please
1498 ;; check that there are no new minified JavaScript files.
1499 (define-public r-bslib
1506 (uri (cran-uri "bslib" version))
1509 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1511 '(for-each delete-file
1512 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1513 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1514 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1515 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1516 (properties `((upstream-name . "bslib")))
1517 (build-system r-build-system)
1519 `(#:modules ((guix build utils)
1520 (guix build r-build-system)
1523 (modify-phases %standard-phases
1524 (add-after 'unpack 'process-javascript
1525 (lambda* (#:key inputs #:allow-other-keys)
1526 (with-directory-excursion "inst/lib/"
1530 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1531 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1532 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1533 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1534 ("bs-sass/assets/javascripts/bootstrap.js"
1535 "bs-sass/assets/javascripts/bootstrap.min.js")
1536 (,(assoc-ref inputs "js-bootstrap-bundle")
1537 "bs/dist/js/bootstrap.bundle.min.js"))))
1538 (lambda (sources targets)
1539 (for-each (lambda (source target)
1540 (format #t "Processing ~a --> ~a~%"
1542 (invoke "esbuild" source "--minify"
1543 (string-append "--outfile=" target)))
1544 sources targets)))))))))
1546 `(("r-digest" ,r-digest)
1547 ("r-htmltools" ,r-htmltools)
1548 ("r-jquerylib" ,r-jquerylib)
1549 ("r-jsonlite" ,r-jsonlite)
1550 ("r-magrittr" ,r-magrittr)
1551 ("r-rlang" ,r-rlang)
1552 ("r-sass" ,r-sass)))
1554 `(("esbuild" ,esbuild)
1555 ("js-bootstrap-bundle"
1558 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1561 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1562 (home-page "https://rstudio.github.io/bslib/")
1563 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1565 "This package simplifies custom CSS styling of both shiny and rmarkdown
1566 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1567 various Bootswatch themes. An interactive widget is also provided for
1568 previewing themes in real time.")
1569 (license license:expat)))
1571 ;; This package includes minified JavaScript files. When upgrading please
1572 ;; check that there are no new minified JavaScript files.
1573 (define-public r-shiny
1581 (url "https://github.com/rstudio/shiny")
1582 (commit (string-append "v" version))))
1583 (file-name (git-file-name name version))
1586 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1588 '(for-each delete-file
1589 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1590 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1591 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1592 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1593 "inst/www/shared/highlight/highlight.pack.js"
1594 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1595 "inst/www/shared/jquery.min.js"
1596 "inst/www/shared/jqueryui/jquery-ui.min.js"
1597 "inst/www/shared/legacy/jquery.min.js"
1598 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1599 "inst/www/shared/selectize/js/selectize.min.js"
1600 "inst/www/shared/shiny.min.js"
1601 "inst/www/shared/showdown/compressed/showdown.js"
1602 "inst/www/shared/strftime/strftime-min.js")))))
1603 (build-system r-build-system)
1605 `(#:modules ((guix build r-build-system)
1606 (guix build minify-build-system)
1609 #:imported-modules (,@%r-build-system-modules
1610 (guix build minify-build-system))
1612 (modify-phases (@ (guix build r-build-system) %standard-phases)
1613 (add-after 'unpack 'replace-bundled-minified-JavaScript
1614 (lambda* (#:key inputs #:allow-other-keys)
1615 (let ((replace-file (lambda (old new)
1616 (format #t "replacing ~a with ~a\n" old new)
1617 (symlink new old))))
1618 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1619 ;; contain just data. They are not minified code, so we don't
1621 (with-directory-excursion "inst/www/shared"
1622 (replace-file "strftime/strftime-min.js"
1623 (string-append (assoc-ref inputs "js-strftime")
1624 "/share/javascript/strftime.min.js"))
1625 (replace-file "highlight/highlight.pack.js"
1626 (string-append (assoc-ref inputs "js-highlight")
1627 "/share/javascript/highlight.min.js"))
1628 (replace-file "datatables/js/jquery.dataTables.min.js"
1629 (string-append (assoc-ref inputs "js-datatables")
1630 "/share/javascript/jquery.dataTables.min.js"))
1631 (replace-file "selectize/js/selectize.min.js"
1632 (string-append (assoc-ref inputs "js-selectize")
1633 "/share/javascript/selectize.min.js"))
1634 (for-each (match-lambda
1636 (minify source #:target target)))
1637 `(("jqueryui/jquery-ui.js" .
1638 "jqueryui/jquery-ui.min.js")
1639 ("datepicker/js/bootstrap-datepicker.js" .
1640 "datepicker/js/bootstrap-datepicker.min.js")
1641 ("ionrangeslider/js/ion.rangeSlider.js" .
1642 "ionrangeslider/js/ion.rangeSlider.min.js")
1643 ("bootstrap/js/bootstrap.js" .
1644 "bootstrap/js/bootstrap.min.js")
1645 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1646 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1651 ("legacy/jquery.js" .
1652 "legacy/jquery.min.js")
1653 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1654 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1655 ("showdown/src/showdown.js" .
1656 "showdown/compressed/showdown.js"))))))))))
1658 `(("r-bslib" ,r-bslib)
1659 ("r-cachem" ,r-cachem)
1660 ("r-commonmark" ,r-commonmark)
1661 ("r-crayon" ,r-crayon)
1662 ("r-digest" ,r-digest)
1663 ("r-ellipsis" ,r-ellipsis)
1664 ("r-fastmap" ,r-fastmap)
1666 ("r-htmltools" ,r-htmltools)
1667 ("r-httpuv" ,r-httpuv)
1668 ("r-jsonlite" ,r-jsonlite)
1669 ("r-later" ,r-later)
1670 ("r-lifecycle" ,r-lifecycle)
1672 ("r-promises" ,r-promises)
1674 ("r-rlang" ,r-rlang)
1675 ("r-sourcetools" ,r-sourcetools)
1676 ("r-withr" ,r-withr)
1677 ("r-xtable" ,r-xtable)))
1679 `(("js-datatables" ,js-datatables)
1680 ("js-selectize" ,js-selectize)
1681 ("js-strftime" ,js-strftime)
1682 ("js-highlight" ,js-highlight)))
1684 `(("uglify-js" ,uglify-js)
1685 ("gfortran" ,gfortran)
1686 ("js-bootstrap-accessibility"
1689 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1690 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1693 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1694 (home-page "https://shiny.rstudio.com")
1695 (synopsis "Easy interactive web applications with R")
1697 "Makes it incredibly easy to build interactive web applications
1698 with R. Automatic \"reactive\" binding between inputs and outputs and
1699 extensive prebuilt widgets make it possible to build beautiful,
1700 responsive, and powerful applications with minimal effort.")
1701 (license license:artistic2.0)))
1703 ;; This package includes minified JavaScript files. When upgrading please
1704 ;; check that there are no new minified JavaScript files.
1705 (define-public r-shinytree
1707 (name "r-shinytree")
1712 (uri (cran-uri "shinyTree" version))
1715 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1716 (modules '((guix build utils)))
1719 ;; Delete minified JavaScript
1720 (for-each delete-file
1721 '("inst/www/jsTree-3.3.7/libs/require.js"
1722 "inst/www/jsTree-3.3.7/libs/jquery.js"
1723 "inst/www/jsTree-3.3.7/jstree.min.js"))
1725 (properties `((upstream-name . "shinyTree")))
1726 (build-system r-build-system)
1728 `(#:modules ((guix build utils)
1729 (guix build r-build-system)
1733 (modify-phases %standard-phases
1734 (add-after 'unpack 'replace-minified-javascript
1735 (lambda* (#:key inputs #:allow-other-keys)
1736 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1737 (symlink (string-append (assoc-ref inputs "js-requirejs")
1738 "/share/javascript/require.min.js")
1743 `((,(assoc-ref inputs "js-jquery")
1747 (lambda (sources targets)
1748 (for-each (lambda (source target)
1749 (format #t "Processing ~a --> ~a~%"
1751 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1752 (call-with-output-file target
1754 (dump-port minified port)))))
1758 `(("r-htmlwidgets" ,r-htmlwidgets)
1759 ("r-jsonlite" ,r-jsonlite)
1760 ("r-promises" ,r-promises)
1761 ("r-shiny" ,r-shiny)
1762 ("r-stringr" ,r-stringr)))
1764 `(("js-requirejs" ,js-requirejs)))
1766 `(("uglify-js" ,uglify-js)
1770 (uri "https://code.jquery.com/jquery-3.3.1.js")
1773 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1774 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1775 (synopsis "jsTree bindings for Shiny")
1777 "This package exposes R bindings to jsTree, a JavaScript library that
1778 supports interactive trees, to enable rich, editable trees in Shiny.")
1779 (license license:expat)))
1781 (define-public r-shinydashboard
1783 (name "r-shinydashboard")
1787 (uri (cran-uri "shinydashboard" version))
1790 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1791 (build-system r-build-system)
1792 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1793 ;; Regenerate it from the included sources.
1795 `(#:modules ((guix build utils)
1796 (guix build r-build-system)
1799 (modify-phases %standard-phases
1800 (add-after 'unpack 'generate-minified-javascript
1802 (with-directory-excursion "inst/AdminLTE"
1803 (delete-file "app.min.js")
1804 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1805 (call-with-output-file "app.min.js"
1807 (dump-port minified port))))))))))
1809 `(("r-htmltools" ,r-htmltools)
1810 ("r-promises" ,r-promises)
1811 ("r-shiny" ,r-shiny)))
1813 `(("uglify-js" ,uglify-js)))
1814 (home-page "https://rstudio.github.io/shinydashboard/")
1815 (synopsis "Create dashboards with shiny")
1816 (description "This package provides an extension to the Shiny web
1817 application framework for R, making it easy to create attractive dashboards.")
1818 ;; This package includes software that was released under the Expat
1819 ;; license, but the whole package is released under GPL version 2 or
1821 (license license:gpl2+)))
1823 (define-public r-shinyfiles
1825 (name "r-shinyfiles")
1830 (uri (cran-uri "shinyFiles" version))
1832 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1833 (properties `((upstream-name . "shinyFiles")))
1834 (build-system r-build-system)
1837 ("r-htmltools" ,r-htmltools)
1838 ("r-jsonlite" ,r-jsonlite)
1839 ("r-shiny" ,r-shiny)
1840 ("r-tibble" ,r-tibble)))
1841 (home-page "https://github.com/thomasp85/shinyFiles")
1842 (synopsis "Server-side file system viewer for Shiny")
1844 "This package provides functionality for client-side navigation of the
1845 server side file system in shiny apps. In case the app is running locally
1846 this gives the user direct access to the file system without the need to
1847 \"download\" files to a temporary location. Both file and folder selection as
1848 well as file saving is available.")
1849 (license license:gpl2+)))
1851 (define-public r-shinythemes
1853 (name "r-shinythemes")
1858 (uri (cran-uri "shinythemes" version))
1861 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1862 (properties `((upstream-name . "shinythemes")))
1863 (build-system r-build-system)
1864 (propagated-inputs `(("r-shiny" ,r-shiny)))
1865 (home-page "https://rstudio.github.io/shinythemes/")
1866 (synopsis "Themes for Shiny")
1868 "This package provides themes for use with Shiny. It includes several
1869 Bootstrap themes, which are packaged for use with Shiny applications.")
1870 ;; The package is released under version 3 of the GPL, but it includes
1871 ;; source files that are covered by the Expat license. It also includes
1872 ;; fonts under SIL or the ASL.
1873 (license (list license:gpl3 license:expat
1874 license:silofl1.1 license:asl2.0))))
1876 ;; The package sources include minified variants of d3.js and non-minified
1877 ;; source code of d3-jetpack.
1878 (define-public r-d3r
1885 (uri (cran-uri "d3r" version))
1888 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1889 (build-system r-build-system)
1891 `(#:modules ((guix build utils)
1892 (guix build r-build-system)
1895 (modify-phases %standard-phases
1896 (add-after 'unpack 'process-javascript
1897 (lambda* (#:key inputs #:allow-other-keys)
1898 (with-directory-excursion "inst/www/d3/"
1902 `((,(assoc-ref inputs "d3.v3.js")
1903 "v3/dist/d3.min.js")
1904 (,(assoc-ref inputs "d3.v4.js")
1905 "v4/dist/d3.min.js")
1906 (,(assoc-ref inputs "d3.v5.js")
1907 "v5/dist/d3.min.js")
1908 (,(assoc-ref inputs "d3.v6.js")
1909 "v6/dist/d3.min.js"))))
1910 (lambda (sources targets)
1911 (for-each (lambda (source target)
1912 (format #t "Processing ~a --> ~a~%"
1914 (delete-file target)
1915 (invoke "esbuild" source "--minify"
1916 (string-append "--outfile=" target)))
1920 `(("r-dplyr" ,r-dplyr)
1921 ("r-htmltools" ,r-htmltools)
1922 ("r-rlang" ,r-rlang)
1923 ("r-tidyr" ,r-tidyr)))
1925 `(("esbuild" ,esbuild)
1929 (uri "https://d3js.org/d3.v3.js")
1932 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1936 (uri "https://d3js.org/d3.v4.js")
1939 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1943 (uri "https://d3js.org/d3.v5.js")
1946 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1950 (uri "https://d3js.org/d3.v6.js")
1953 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1954 (home-page "https://github.com/timelyportfolio/d3r")
1955 (synopsis "d3.js utilities for R")
1957 "This package provides a suite of functions to help ease the use of the
1958 d3.js visualization library in R. These helpers include
1959 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1960 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1961 R objects into the JSON format that the d3.js library expects.")
1962 (license license:bsd-3)))
1964 ;; We use the latest commit here because the last release was in 2016 while
1965 ;; the latest commit was in 2018.
1966 (define-public r-sankeyd3
1967 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1971 (version (git-version "0.3.2" revision commit))
1976 (url "https://github.com/fbreitwieser/sankeyD3")
1978 (file-name (git-file-name name version))
1981 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1982 (build-system r-build-system)
1985 ("r-htmlwidgets" ,r-htmlwidgets)
1986 ("r-shiny" ,r-shiny)
1987 ("r-magrittr" ,r-magrittr)))
1988 (home-page "https://github.com/fbreitwieser/sankeyD3")
1989 (synopsis "Sankey network graphs from R")
1991 "This package provides an R library to generate Sankey network graphs
1992 in R and Shiny via the D3 visualization library.")
1993 ;; The R code is licensed under GPLv3+. It includes the non-minified
1994 ;; JavaScript source code of d3-sankey, which is released under the
1995 ;; 3-clause BSD license.
1996 (license (list license:gpl3+ license:bsd-3)))))
1998 (define-public r-wesanderson
2000 (name "r-wesanderson")
2005 (uri (cran-uri "wesanderson" version))
2008 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2009 (properties `((upstream-name . "wesanderson")))
2010 (build-system r-build-system)
2011 (home-page "https://github.com/karthik/wesanderson")
2012 (synopsis "Wes Anderson color palette generator")
2014 "This package provides color palettes that have been generated mostly
2015 from Wes Anderson movies.")
2016 (license license:expat)))
2018 (define-public r-gg-gap
2025 (uri (cran-uri "gg.gap" version))
2028 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2029 (properties `((upstream-name . "gg.gap")))
2030 (build-system r-build-system)
2032 `(("r-cowplot" ,r-cowplot)
2033 ("r-ggplot2" ,r-ggplot2)))
2034 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2035 (synopsis "Define segments on the y-axis for ggplot2")
2037 "The @code{gg.gap} function enables you to define segments for the y-axis
2038 in a ggplot2 plot.")
2039 (license license:gpl3)))
2041 (define-public r-tablerdash
2043 (name "r-tablerdash")
2048 (uri (cran-uri "tablerDash" version))
2051 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2054 ;; Delete minified JavaScript
2055 (for-each delete-file
2056 '("inst/tablerDash-0.1.0/require.min.js"
2057 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2059 (properties `((upstream-name . "tablerDash")))
2060 (build-system r-build-system)
2062 `(#:modules ((guix build utils)
2063 (guix build r-build-system)
2066 (modify-phases %standard-phases
2067 (add-after 'unpack 'process-javascript
2068 (lambda* (#:key inputs #:allow-other-keys)
2069 (with-directory-excursion "inst"
2073 `((,(assoc-ref inputs "js-requirejs")
2074 "tablerDash-0.1.0/require.min.js")
2075 (,(assoc-ref inputs "js-bootstrap")
2076 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2077 (lambda (sources targets)
2078 (for-each (lambda (source target)
2079 (format #t "Processing ~a --> ~a~%"
2081 (invoke "esbuild" source "--minify"
2082 (string-append "--outfile=" target)))
2086 `(("r-htmltools" ,r-htmltools)
2087 ("r-knitr" ,r-knitr)
2088 ("r-shiny" ,r-shiny)))
2090 `(("esbuild" ,esbuild)
2094 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2097 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2101 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2102 v4.0.0/dist/js/bootstrap.bundle.js")
2105 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2106 (home-page "https://rinterface.github.io/tablerDash/")
2107 (synopsis "Tabler API for Shiny")
2109 "This package provides an R interface to the
2110 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2111 4 dashboard template. There are different layouts available such as a one
2112 page dashboard or a multi-page template, where the navigation menu is
2113 contained in the navigation bar.")
2114 (license license:gpl2+)))
2116 (define-public r-spelling
2123 (uri (cran-uri "spelling" version))
2126 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2127 (properties `((upstream-name . "spelling")))
2128 (build-system r-build-system)
2130 `(("r-commonmark" ,r-commonmark)
2131 ("r-hunspell" ,r-hunspell)
2132 ("r-knitr" ,r-knitr)
2133 ("r-xml2" ,r-xml2)))
2134 (home-page "https://docs.ropensci.org/spelling/")
2135 (synopsis "Tools for spell checking in R")
2137 "This is an R package for spell checking common document formats
2138 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2139 utilities to automate checking of documentation and vignettes as a unit test
2140 during @code{R CMD check}. Both British and American English are supported
2141 out of the box and other languages can be added. In addition, packages may
2142 define a wordlist to allow custom terminology without having to abuse
2144 (license license:expat)))
2146 (define-public r-crosstalk
2148 (name "r-crosstalk")
2153 (uri (cran-uri "crosstalk" version))
2156 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2157 (build-system r-build-system)
2159 `(("r-htmltools" ,r-htmltools)
2160 ("r-jsonlite" ,r-jsonlite)
2161 ("r-lazyeval" ,r-lazyeval)
2163 (home-page "https://rstudio.github.io/crosstalk/")
2164 (synopsis "Inter-widget interactivity for HTML widgets")
2166 "This package provides building blocks for allowing HTML widgets to
2167 communicate with each other, with Shiny or without (i.e. static @code{.html}
2168 files). It currently supports linked brushing and filtering.")
2169 (license license:expat)))
2171 (define-public r-rook
2178 (uri (cran-uri "Rook" version))
2181 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2182 (properties `((upstream-name . "Rook")))
2183 (build-system r-build-system)
2184 (propagated-inputs `(("r-brew" ,r-brew)))
2185 (home-page "https://cran.r-project.org/web/packages/Rook")
2186 (synopsis "Web server interface for R")
2188 "This package contains the Rook specification and convenience software
2189 for building and running Rook applications. A Rook application is an R
2190 reference class object that implements a @code{call} method or an R closure
2191 that takes exactly one argument, an environment, and returns a list with three
2192 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2193 (license license:gpl2)))
2195 (define-public r-miniui
2202 (uri (cran-uri "miniUI" version))
2205 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2206 (properties `((upstream-name . "miniUI")))
2207 (build-system r-build-system)
2209 `(("r-htmltools" ,r-htmltools)
2210 ("r-shiny" ,r-shiny)))
2211 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2212 (synopsis "Shiny UI widgets for small screens")
2214 "This package provides UI widget and layout functions for writing Shiny apps that
2215 work well on small screens.")
2216 (license license:gpl3)))
2218 (define-public r-feather
2225 (uri (cran-uri "feather" version))
2228 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2229 (build-system r-build-system)
2233 ("r-tibble" ,r-tibble)))
2234 (home-page "https://github.com/wesm/feather")
2235 (synopsis "R Bindings to the Feather API")
2236 (description "Read and write feather files, a lightweight binary columnar
2237 data store designed for maximum speed.")
2238 (license license:asl2.0)))
2240 (define-public r-maps
2247 (uri (cran-uri "maps" version))
2250 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2251 (build-system r-build-system)
2252 (home-page "https://cran.r-project.org/web/packages/maps")
2253 (synopsis "Draw geographical maps")
2254 (description "This package provides an R module for display of maps.
2255 Projection code and larger maps are in separate packages (@code{mapproj} and
2257 (license license:gpl2)))
2259 (define-public r-mapproj
2266 (uri (cran-uri "mapproj" version))
2269 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2270 (build-system r-build-system)
2271 (propagated-inputs `(("r-maps" ,r-maps)))
2272 (home-page "https://cran.r-project.org/web/packages/mapproj")
2273 (synopsis "Map projection in R")
2274 (description "This package converts latitude/longitude into projected
2276 (license (list license:gpl2 ; The R interface
2277 (license:non-copyleft ; The C code
2278 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2279 "Lucent Public License Version 1.02")))))
2281 (define-public r-rgooglemaps
2283 (name "r-rgooglemaps")
2288 (uri (cran-uri "RgoogleMaps" version))
2291 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2292 (properties `((upstream-name . "RgoogleMaps")))
2293 (build-system r-build-system)
2297 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2298 (synopsis "Use Google Maps in R")
2299 (description "This package serves two purposes:
2301 @item Provide a comfortable R interface to query the Google server for static
2303 @item Use the map as a background image to overlay plots within R. This
2304 requires proper coordinate scaling.
2306 (license license:gpl2+)))
2308 (define-public r-geosphere
2310 (name "r-geosphere")
2315 (uri (cran-uri "geosphere" version))
2318 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2319 (build-system r-build-system)
2320 (propagated-inputs `(("r-sp" ,r-sp)))
2321 (home-page "https://cran.r-project.org/web/packages/geosphere")
2322 (synopsis "Spherical trigonometry")
2323 (description "This package computes spherical trigonometry for geographic
2324 applications. That is, compute distances and related measures for angular
2325 (longitude/latitude) locations.")
2326 (license license:gpl3+)))
2328 (define-public r-jpeg
2335 (uri (cran-uri "jpeg" version))
2338 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2339 (build-system r-build-system)
2340 (inputs `(("libjpeg" ,libjpeg-turbo)))
2341 (home-page "https://www.rforge.net/jpeg/")
2342 (synopsis "Read and write JPEG images with R")
2343 (description "This package provides a way to read, write and display
2344 bitmap images stored in the JPEG format with R. It can read and write both
2345 files and in-memory raw vectors.")
2346 (license license:gpl2+)))
2348 (define-public r-ggmap
2355 (uri (cran-uri "ggmap" version))
2358 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2359 (build-system r-build-system)
2361 `(("r-bitops" ,r-bitops)
2362 ("r-digest" ,r-digest)
2363 ("r-dplyr" ,r-dplyr)
2364 ("r-ggplot2" ,r-ggplot2)
2368 ("r-magrittr" ,r-magrittr)
2371 ("r-purrr" ,r-purrr)
2372 ("r-rgooglemaps" ,r-rgooglemaps)
2373 ("r-rjson" ,r-rjson)
2374 ("r-scales" ,r-scales)
2375 ("r-stringr" ,r-stringr)
2376 ("r-tibble" ,r-tibble)
2377 ("r-tidyr" ,r-tidyr)))
2378 (home-page "https://github.com/dkahle/ggmap")
2379 (synopsis "Spatial visualization with ggplot2")
2380 (description "This package provides a collection of functions to visualize
2381 spatial data and models on top of static maps from various online sources (e.g
2382 Google Maps and Stamen Maps). It includes tools common to those tasks,
2383 including functions for geolocation and routing.")
2384 (license license:gpl2)))
2386 (define-public r-haven
2393 (uri (cran-uri "haven" version))
2396 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2397 (modules '((guix build utils)))
2400 ;; unvendor readstat
2401 (delete-file-recursively "src/readstat")
2403 (build-system r-build-system)
2406 (modify-phases %standard-phases
2407 (add-after 'unpack 'unbundle-readstat
2409 ;; Not required, since we’re not building readstat.
2410 (substitute* "src/Makevars"
2411 (("-lz") "-lreadstat"))
2414 `(("readstat" ,readstat)))
2416 `(("r-knitr" ,r-knitr)))
2418 `(("r-forcats" ,r-forcats)
2421 ("r-rlang" ,r-rlang)
2422 ("r-readr" ,r-readr)
2423 ("r-tibble" ,r-tibble)
2424 ("r-tidyselect" ,r-tidyselect)
2425 ("r-vctrs" ,r-vctrs)))
2426 (home-page "https://haven.tidyverse.org")
2427 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2429 "This package lets you mport foreign statistical formats into R via the
2430 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2431 (license license:expat)))
2433 (define-public r-amap
2439 (uri (cran-uri "amap" version))
2442 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2443 (build-system r-build-system)
2445 `(("gfortran" ,gfortran)))
2446 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2447 (synopsis "Another multidimensional analysis package")
2448 (description "This package provides tools for clustering and principal
2449 component analysis (with robust methods, and parallelized functions).")
2450 (license license:gpl2+)))
2452 (define-public r-ape
2459 (uri (cran-uri "ape" version))
2462 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2463 (build-system r-build-system)
2465 `(("r-lattice" ,r-lattice)
2467 ("r-rcpp" ,r-rcpp)))
2468 (home-page "http://ape-package.ird.fr/")
2469 (synopsis "Analyses of phylogenetics and evolution")
2471 "This package provides functions for reading, writing, plotting, and
2472 manipulating phylogenetic trees, analyses of comparative data in a
2473 phylogenetic framework, ancestral character analyses, analyses of
2474 diversification and macroevolution, computing distances from DNA sequences,
2475 and several other tools.")
2476 (license license:gpl2+)))
2478 (define-public r-abbyyr
2485 (uri (cran-uri "abbyyR" version))
2488 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2489 (properties `((upstream-name . "abbyyR")))
2490 (build-system r-build-system)
2492 `(("r-curl" ,r-curl)
2495 ("r-progress" ,r-progress)
2496 ("r-readr" ,r-readr)
2498 (home-page "https://github.com/soodoku/abbyyR")
2499 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2501 "This package provides tools to get text from images of text using Abbyy
2502 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2503 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2504 passports and get the results in a variety of formats including plain text and
2505 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2506 (license license:expat)))
2508 (define-public r-colorspace
2510 (name "r-colorspace")
2515 (uri (cran-uri "colorspace" version))
2517 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2518 (build-system r-build-system)
2520 `(("r-knitr" ,r-knitr)))
2521 (home-page "https://cran.r-project.org/web/packages/colorspace")
2522 (synopsis "Color space manipulation")
2524 "This package carries out a mapping between assorted color spaces
2525 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2526 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2527 colors are provided.")
2528 (license license:bsd-3)))
2530 (define-public r-glue
2537 (uri (cran-uri "glue" version))
2540 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2541 (build-system r-build-system)
2542 ;; knitr depends on glue, so we can't add knitr here to build the
2546 `(("r-knitr" ,r-knitr)))
2547 (home-page "https://github.com/tidyverse/glue")
2548 (synopsis "Interpreted string literals")
2550 "This package provides an implementation of interpreted string literals,
2551 inspired by Python's Literal String Interpolation (PEP-0498) and
2552 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2553 (license license:expat)))
2555 (define-public r-palmerpenguins
2557 (name "r-palmerpenguins")
2562 (uri (cran-uri "palmerpenguins" version))
2565 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2567 `((upstream-name . "palmerpenguins")))
2568 (build-system r-build-system)
2569 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2570 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2572 "This package includes size measurements, clutch observations, and blood
2573 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2574 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2575 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2576 Station Long Term Ecological Research (LTER) Program.")
2577 (license license:cc0)))
2579 (define-public r-pastecs
2585 (uri (cran-uri "pastecs" version))
2588 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2589 (build-system r-build-system)
2591 `(("r-boot" ,r-boot)))
2592 (home-page "https://github.com/phgrosjean/pastecs")
2593 (synopsis "Analysis of space-time ecological series")
2595 "This package provides functions for regulation, decomposition and analysis
2596 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2597 initiative to bring PASSTEC 2000 functionalities to R.")
2598 (license license:gpl2+)))
2600 (define-public r-partykit
2606 (uri (cran-uri "partykit" version))
2609 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2610 (build-system r-build-system)
2612 `(("r-formula" ,r-formula)
2614 ("r-libcoin" ,r-libcoin)
2615 ("r-mvtnorm" ,r-mvtnorm)
2616 ("r-rpart" ,r-rpart)
2617 ("r-survival" ,r-survival)))
2618 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2619 (synopsis "Toolkit for recursive partytioning")
2621 "This package provides a toolkit with infrastructure for representing,
2622 summarizing, and visualizing tree-structured regression and classification
2624 (license license:gpl2+)))
2626 (define-public r-plogr
2633 (uri (cran-uri "plogr" version))
2636 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2637 (build-system r-build-system)
2638 (home-page "https://github.com/krlmlr/plogr")
2639 (synopsis "R bindings for the plog C++ logging library")
2641 "This package provides the header files for a stripped-down version of
2642 the plog header-only C++ logging library, and a method to log to R's standard
2644 (license license:expat)))
2646 (define-public r-pls
2653 (uri (cran-uri "pls" version))
2655 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2656 (build-system r-build-system)
2657 (home-page "https://mevik.net/work/software/pls.html")
2658 (synopsis "Partial Least Squares and Principal Component Regression")
2660 "The pls package implements multivariate regression methods: Partial Least
2661 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2662 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2665 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2666 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2667 @item multi-response models (or @dfn{PLS2})
2668 @item flexible cross-validation
2669 @item Jackknife variance estimates of regression coefficients
2670 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2671 (R)MSEP, R², and correlation loadings
2672 @item formula interface, modelled after @code{lm()}, with methods for predict,
2673 print, summary, plot, update, etc.
2674 @item extraction functions for coefficients, scores, and loadings
2675 @item MSEP, RMSEP, and R² estimates
2676 @item multiplicative scatter correction (@dfn{MSC})
2678 (license license:gpl2)))
2687 (uri (cran-uri "ps" version))
2689 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2690 (build-system r-build-system)
2691 (home-page "https://ps.r-lib.org")
2692 (synopsis "List, query, and manipulate system processes")
2694 "The ps package implements an API to list, query, and manipulate system
2695 processes. Most of its code is based on the @code{psutil} Python package.")
2696 (license license:bsd-3)))
2698 (define-public r-pkgbuild
2705 (uri (cran-uri "pkgbuild" version))
2707 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2708 (build-system r-build-system)
2710 `(("r-callr" ,r-callr)
2712 ("r-crayon" ,r-crayon)
2714 ("r-prettyunits" ,r-prettyunits)
2716 ("r-rprojroot" ,r-rprojroot)
2717 ("r-withr" ,r-withr)))
2718 (home-page "https://github.com/r-pkgs/pkgbuild")
2719 (synopsis "Find tools needed to build R packages")
2721 "This package provides functions used to build R packages. It locates
2722 compilers needed to build R packages on various platforms and ensures the PATH
2723 is configured appropriately so R can use them.")
2724 (license license:gpl3)))
2726 (define-public r-pkgload
2733 (uri (cran-uri "pkgload" version))
2736 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2737 (build-system r-build-system)
2740 ("r-crayon" ,r-crayon)
2742 ("r-pkgbuild" ,r-pkgbuild)
2743 ("r-rlang" ,r-rlang)
2744 ("r-rprojroot" ,r-rprojroot)
2745 ("r-rstudioapi" ,r-rstudioapi)
2746 ("r-withr" ,r-withr)))
2747 (home-page "https://github.com/r-lib/pkgload")
2748 (synopsis "Simulate package installation and attach")
2750 "This package simulates the process of installing a package and then
2751 attaching it. This is a key part of the @code{devtools} package as it allows
2752 you to rapidly iterate while developing a package.")
2753 (license license:gpl3)))
2755 (define-public r-rcpp
2762 (uri (cran-uri "Rcpp" version))
2764 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2765 (build-system r-build-system)
2766 (home-page "http://www.rcpp.org")
2767 (synopsis "Seamless R and C++ integration")
2769 "The Rcpp package provides R functions as well as C++ classes which offer
2770 a seamless integration of R and C++. Many R data types and objects can be
2771 mapped back and forth to C++ equivalents which facilitates both writing of new
2772 code as well as easier integration of third-party libraries. Documentation
2773 about Rcpp is provided by several vignettes included in this package, via the
2774 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2775 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2776 @code{citation(\"Rcpp\")} for details on these last two.")
2777 (license license:gpl2+)))
2779 (define-public r-rcppthread
2781 (name "r-rcppthread")
2786 (uri (cran-uri "RcppThread" version))
2789 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2790 (properties `((upstream-name . "RcppThread")))
2791 (build-system r-build-system)
2793 "https://github.com/tnagler/RcppThread")
2794 (synopsis "R threading in C++")
2796 "This package provides a C++11-style thread class and thread pool that can
2797 safely be interrupted from R.")
2798 (license license:expat)))
2800 (define-public r-bindr
2807 (uri (cran-uri "bindr" version))
2810 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2811 (build-system r-build-system)
2812 (home-page "https://github.com/krlmlr/bindr")
2813 (synopsis "Parametrized active bindings")
2815 "This package provides a simple interface for creating active bindings
2816 where the bound function accepts additional arguments.")
2817 (license license:expat)))
2819 (define-public r-bindrcpp
2826 (uri (cran-uri "bindrcpp" version))
2829 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2830 (build-system r-build-system)
2832 `(("r-bindr" ,r-bindr)
2833 ("r-plogr" ,r-plogr)
2834 ("r-rcpp" ,r-rcpp)))
2835 (home-page "https://github.com/krlmlr/bindrcpp")
2836 (synopsis "Rcpp interface to active bindings")
2838 "This package provides an easy way to fill an environment with active
2839 bindings that call a C++ function.")
2840 (license license:expat)))
2842 (define-public r-auc
2849 (uri (cran-uri "AUC" version))
2852 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2853 (properties `((upstream-name . "AUC")))
2854 (build-system r-build-system)
2855 (home-page "https://cran.r-project.org/web/packages/AUC")
2856 (synopsis "Compute the area under the curve of selected measures")
2858 "This package includes functions to compute the area under the curve of
2859 selected measures: the area under the sensitivity curve (AUSEC), the area
2860 under the specificity curve (AUSPC), the area under the accuracy
2861 curve (AUACC), and the area under the receiver operating characteristic
2862 curve (AUROC). The curves can also be visualized. Support for partial areas
2864 (license license:gpl2+)))
2866 (define-public r-calibrate
2868 (name "r-calibrate")
2873 (uri (cran-uri "calibrate" version))
2875 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2876 (build-system r-build-system)
2878 `(("r-mass" ,r-mass)))
2879 (home-page "https://cran.r-project.org/web/packages/calibrate")
2880 (synopsis "Calibration of scatterplot and biplot axes")
2882 "This is a package for drawing calibrated scales with tick marks
2883 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2884 (license license:gpl2)))
2886 (define-public r-shape
2893 (uri (cran-uri "shape" version))
2896 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2897 (build-system r-build-system)
2898 (home-page "https://cran.r-project.org/web/packages/shape")
2899 (synopsis "Functions for plotting graphical shapes")
2901 "This package provides functions for plotting graphical shapes such as
2902 ellipses, circles, cylinders, arrows, ...")
2903 (license license:gpl3+)))
2905 (define-public r-globaloptions
2907 (name "r-globaloptions")
2912 (uri (cran-uri "GlobalOptions" version))
2914 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2915 (properties `((upstream-name . "GlobalOptions")))
2916 (build-system r-build-system)
2918 `(("r-knitr" ,r-knitr)))
2919 (home-page "https://github.com/jokergoo/GlobalOptions")
2920 (synopsis "Generate functions to get or set global options")
2922 "This package provides more controls on the option values such as
2923 validation and filtering on the values, making options invisible or private.")
2924 (license license:gpl2+)))
2926 (define-public r-circlize
2933 (uri (cran-uri "circlize" version))
2936 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2937 (build-system r-build-system)
2939 `(("r-colorspace" ,r-colorspace)
2940 ("r-globaloptions" ,r-globaloptions)
2941 ("r-shape" ,r-shape)))
2943 `(("r-knitr" ,r-knitr)))
2944 (home-page "https://github.com/jokergoo/circlize")
2945 (synopsis "Circular visualization")
2947 "Circular layout is an efficient way to visualise huge amounts of
2948 information. This package provides an implementation of circular layout
2949 generation in R as well as an enhancement of available software. Its
2950 flexibility is based on the usage of low-level graphics functions such that
2951 self-defined high-level graphics can be easily implemented by users for
2952 specific purposes. Together with the seamless connection between the powerful
2953 computational and visual environment in R, it gives users more convenience and
2954 freedom to design figures for better understanding complex patterns behind
2955 multi-dimensional data.")
2956 (license license:gpl2+)))
2958 (define-public r-powerlaw
2965 (uri (cran-uri "poweRlaw" version))
2967 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2968 (properties `((upstream-name . "poweRlaw")))
2969 (build-system r-build-system)
2971 `(("r-pracma" ,r-pracma)))
2973 `(("r-knitr" ,r-knitr)))
2974 (home-page "https://github.com/csgillespie/poweRlaw")
2975 (synopsis "Tools for the analysis of heavy tailed distributions")
2977 "This package provides an implementation of maximum likelihood estimators
2978 for a variety of heavy tailed distributions, including both the discrete and
2979 continuous power law distributions. Additionally, a goodness-of-fit based
2980 approach is used to estimate the lower cut-off for the scaling region.")
2981 ;; Any of these GPL versions.
2982 (license (list license:gpl2 license:gpl3))))
2984 (define-public r-compare
2991 (uri (cran-uri "compare" version))
2994 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2995 (build-system r-build-system)
2996 (home-page "https://cran.r-project.org/web/packages/compare")
2997 (synopsis "Comparing objects for differences")
2999 "This package provides functions to compare a model object to a
3000 comparison object. If the objects are not identical, the functions can be
3001 instructed to explore various modifications of the objects (e.g., sorting
3002 rows, dropping names) to see if the modified versions are identical.")
3003 (license license:gpl2+)))
3005 (define-public r-dendextend
3007 (name "r-dendextend")
3012 (uri (cran-uri "dendextend" version))
3015 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3016 (build-system r-build-system)
3018 `(("r-ggplot2" ,r-ggplot2)
3019 ("r-magrittr" ,r-magrittr)
3020 ("r-viridis" ,r-viridis)))
3022 `(("r-knitr" ,r-knitr)))
3023 (home-page "https://cran.r-project.org/web/packages/dendextend")
3024 (synopsis "Extending 'dendrogram' functionality in R")
3026 "This package offers a set of functions for extending @code{dendrogram}
3027 objects in R, letting you visualize and compare trees of hierarchical
3028 clusterings. You can adjust a tree's graphical parameters (the color, size,
3029 type, etc of its branches, nodes and labels) and visually and statistically
3030 compare different dendrograms to one another.")
3031 ;; Any of these versions
3032 (license (list license:gpl2 license:gpl3))))
3034 (define-public r-getoptlong
3036 (name "r-getoptlong")
3041 (uri (cran-uri "GetoptLong" version))
3044 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3045 (properties `((upstream-name . "GetoptLong")))
3046 (build-system r-build-system)
3050 `(("r-crayon" ,r-crayon)
3051 ("r-globaloptions" ,r-globaloptions)
3052 ("r-rjson" ,r-rjson)))
3054 `(("r-knitr" ,r-knitr)))
3055 (home-page "https://github.com/jokergoo/GetoptLong")
3056 (synopsis "Parsing command-line arguments and variable interpolation")
3058 "This is yet another command-line argument parser which wraps the
3059 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3060 use in R. It also provides a simple way for variable interpolation in R.")
3061 (license license:gpl2+)))
3063 (define-public r-fastmatch
3065 (name "r-fastmatch")
3070 (uri (cran-uri "fastmatch" version))
3073 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3074 (build-system r-build-system)
3075 (home-page "https://www.rforge.net/fastmatch")
3076 (synopsis "Fast match function")
3078 "This package provides a fast @code{match} replacement for cases that
3079 require repeated look-ups. It is slightly faster that R's built-in
3080 @code{match} function on first match against a table, but extremely fast on
3081 any subsequent lookup as it keeps the hash table in memory.")
3082 (license license:gpl2)))
3091 (uri (cran-uri "ff" version))
3094 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3095 (build-system r-build-system)
3096 (propagated-inputs `(("r-bit" ,r-bit)))
3097 (home-page "http://ff.r-forge.r-project.org/")
3098 (synopsis "Memory-efficient storage of large data on disk and access functions")
3100 "This package provides data structures that are stored on disk but
3101 behave (almost) as if they were in RAM by transparently mapping only a section
3103 ;; error Architecture not supported.
3104 (supported-systems (delete "aarch64-linux" %supported-systems))
3105 (license license:gpl2)))
3107 (define-public r-ffbase
3114 (uri (cran-uri "ffbase" version))
3117 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3118 (build-system r-build-system)
3121 ("r-fastmatch" ,r-fastmatch)
3123 (home-page "https://github.com/edwindj/ffbase")
3124 (synopsis "Basic statistical functions for package 'ff'")
3126 "This package extends the out of memory vectors of @code{ff} with
3127 statistical functions and other utilities to ease their usage.")
3128 (license license:gpl3)))
3130 (define-public r-prettyunits
3132 (name "r-prettyunits")
3137 (uri (cran-uri "prettyunits" version))
3140 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3141 (build-system r-build-system)
3142 (home-page "https://github.com/gaborcsardi/prettyunits")
3143 (synopsis "Pretty, human readable formatting of quantities")
3145 "This package provides tools for pretty, human readable formatting of
3147 (license license:expat)))
3149 (define-public r-reshape
3156 (uri (cran-uri "reshape" version))
3159 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3160 (build-system r-build-system)
3162 `(("r-plyr" ,r-plyr)
3163 ("r-rcpp" ,r-rcpp)))
3164 (home-page "http://had.co.nz/reshape")
3165 (synopsis "Flexibly reshape data")
3167 "Flexibly restructure and aggregate data using just two functions:
3168 @code{melt} and @code{cast}. This package provides them.")
3169 (license license:expat)))
3171 (define-public r-restrserve
3173 (name "r-restrserve")
3178 (uri (cran-uri "RestRserve" version))
3180 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3181 (build-system r-build-system)
3183 `(("r-checkmate" ,r-checkmate)
3184 ("r-jsonlite" ,r-jsonlite)
3188 ("r-rserve" ,r-rserve)
3189 ("r-uuid" ,r-uuid)))
3191 `(("r-knitr" ,r-knitr)))
3192 (home-page "https://restrserve.org")
3193 (synopsis "R web API framework")
3195 "RestRserve is an R web API framework for building high-performance AND
3196 robust microservices and app backends. With Rserve backend on UNIX-like
3197 systems it is parallel by design. It will handle incoming requests in
3198 parallel - each request in a separate fork.")
3199 (license license:gpl2+)))
3201 (define-public r-progress
3208 (uri (cran-uri "progress" version))
3211 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3212 (build-system r-build-system)
3214 `(("r-crayon" ,r-crayon)
3216 ("r-prettyunits" ,r-prettyunits)
3218 (home-page "https://github.com/gaborcsardi/progress")
3219 (synopsis "Terminal progress bars")
3221 "This package provides configurable progress bars. They may include
3222 percentage, elapsed time, and/or the estimated completion time. They work in
3223 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3224 package also provides a C++ API, that works with or without Rcpp.")
3225 (license license:expat)))
3227 (define-public r-ggally
3234 (uri (cran-uri "GGally" version))
3237 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3238 (properties `((upstream-name . "GGally")))
3239 (build-system r-build-system)
3241 `(("openssl" ,openssl)))
3243 `(("r-dplyr" ,r-dplyr)
3244 ("r-forcats" ,r-forcats)
3245 ("r-ggplot2" ,r-ggplot2)
3246 ("r-gtable" ,r-gtable)
3247 ("r-lifecycle" ,r-lifecycle)
3249 ("r-progress" ,r-progress)
3250 ("r-rcolorbrewer" ,r-rcolorbrewer)
3251 ("r-reshape" ,r-reshape)
3252 ("r-rlang" ,r-rlang)
3253 ("r-scales" ,r-scales)
3254 ("r-tidyr" ,r-tidyr)))
3255 (home-page "https://ggobi.github.io/ggally")
3256 (synopsis "Extension to ggplot2")
3258 "The R package ggplot2 is a plotting system based on the grammar of
3259 graphics. GGally extends ggplot2 by adding several functions to reduce the
3260 complexity of combining geometric objects with transformed data. Some of
3261 these functions include a pairwise plot matrix, a two group pairwise plot
3262 matrix, a parallel coordinates plot, a survival plot, and several functions to
3264 (license license:gpl2+)))
3266 (define-public r-proxy
3273 (uri (cran-uri "proxy" version))
3276 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3277 (build-system r-build-system)
3278 (home-page "https://cran.r-project.org/web/packages/proxy")
3279 (synopsis "Distance and similarity measures")
3281 "This package provides an extensible framework for the efficient
3282 calculation of auto- and cross-proximities, along with implementations of the
3283 most popular ones.")
3284 (license license:gpl2)))
3293 (uri (cran-uri "sp" version))
3295 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3296 (build-system r-build-system)
3298 `(("r-lattice" ,r-lattice)))
3299 (home-page "https://cran.r-project.org/web/packages/sp")
3300 (synopsis "Classes and methods for spatial data")
3302 "This package provides classes and methods for spatial data; the classes
3303 document where the spatial location information resides, for 2D or 3D data.
3304 Utility functions are provided, e.g. for plotting data as maps, spatial
3305 selection, as well as methods for retrieving coordinates, for subsetting,
3306 print, summary, etc.")
3307 (license license:gpl2+)))
3309 (define-public r-laplacesdemon
3311 (name "r-laplacesdemon")
3316 (uri (cran-uri "LaplacesDemon" version))
3318 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3319 (properties `((upstream-name . "LaplacesDemon")))
3320 (build-system r-build-system)
3321 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3322 (synopsis "Complete environment for Bayesian inference")
3324 "This package provides a complete environment for Bayesian inference using
3325 a variety of different samplers.")
3326 (license license:expat)))
3328 (define-public r-rmtstat
3335 (uri (cran-uri "RMTstat" version))
3338 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3339 (properties `((upstream-name . "RMTstat")))
3340 (build-system r-build-system)
3341 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3342 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3344 "This package provides functions for working with the Tracy-Widom laws
3345 and other distributions related to the eigenvalues of large Wishart
3347 (license license:bsd-3)))
3349 (define-public r-rmpi
3355 (uri (cran-uri "Rmpi" version))
3358 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3359 (properties `((upstream-name . "Rmpi")))
3360 (build-system r-build-system)
3362 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3363 #:phases (modify-phases %standard-phases
3364 (add-before 'install 'mpi-setup
3367 `(("openmpi" ,openmpi)))
3369 `(("pkg-config" ,pkg-config)))
3370 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3371 (synopsis "R interface to message-passing interface (MPI)")
3373 "This package provides an interface (wrapper) to MPI APIs. It also
3374 provides an interactive R manager and worker environment.")
3375 (license license:gpl2+)))
3377 (define-public r-lmoments
3384 (uri (cran-uri "Lmoments" version))
3387 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3388 (properties `((upstream-name . "Lmoments")))
3389 (build-system r-build-system)
3391 `(("r-rcpp" ,r-rcpp)
3392 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3393 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3394 (synopsis "L-moments and quantile mixtures")
3396 "This package contains functions to estimate L-moments and trimmed
3397 L-moments from the data. It also contains functions to estimate the
3398 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3399 quantile mixture from L-moments and trimmed L-moments.")
3400 (license license:gpl2)))
3402 (define-public r-distillery
3404 (name "r-distillery")
3409 (uri (cran-uri "distillery" version))
3412 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3413 (build-system r-build-system)
3414 (home-page "https://ral.ucar.edu/staff/ericg/")
3415 (synopsis "Functions for confidence intervals and object information")
3417 "This package provides some very simple method functions for confidence
3418 interval calculation and to distill pertinent information from a potentially
3419 complex object; primarily used in common with the packages extRemes and
3421 (license license:gpl2+)))
3423 (define-public r-etrunct
3429 (uri (cran-uri "etrunct" version))
3432 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3433 (properties `((upstream-name . "etrunct")))
3434 (build-system r-build-system)
3435 (home-page "https://cran.r-project.org/web/packages/etrunct")
3436 (synopsis "Computes moments of univariate truncated T distribution")
3437 (description "This package computes moments of univariate truncated
3438 T distribution. There is only one exported function, @code{e_trunct},
3439 which should be seen for details.")
3440 (license license:expat)))
3442 (define-public r-extremes
3449 (uri (cran-uri "extRemes" version))
3452 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3453 (properties `((upstream-name . "extRemes")))
3454 (build-system r-build-system)
3456 `(("r-distillery" ,r-distillery)
3457 ("r-lmoments" ,r-lmoments)))
3458 (home-page "https://www.assessment.ucar.edu/toolkit/")
3459 (synopsis "Extreme value analysis")
3461 "ExtRemes is a suite of functions for carrying out analyses on the
3462 extreme values of a process of interest; be they block maxima over long blocks
3463 or excesses over a high threshold.")
3464 (license license:gpl2+)))
3466 (define-public r-lmtest
3473 (uri (cran-uri "lmtest" version))
3476 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3477 (build-system r-build-system)
3479 `(("r-zoo" ,r-zoo)))
3481 `(("gfortran" ,gfortran)))
3482 (home-page "https://cran.r-project.org/web/packages/lmtest")
3483 (synopsis "Testing linear regression models")
3485 "This package provides a collection of tests, data sets, and examples for
3486 diagnostic checking in linear regression models. Furthermore, some generic
3487 tools for inference in parametric models are provided.")
3488 ;; Either version is okay
3489 (license (list license:gpl2 license:gpl3))))
3491 (define-public r-idr
3497 (uri (cran-uri "idr" version))
3500 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3501 (build-system r-build-system)
3502 (home-page "https://cran.r-project.org/web/packages/idr/")
3503 (synopsis "Irreproducible discovery rate")
3505 "This is a package for estimating the copula mixture model and plotting
3506 correspondence curves in \"Measuring reproducibility of high-throughput
3507 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3508 by Li, Brown, Huang, and Bickel")
3509 (license license:gpl2+)))
3511 (define-public r-inline
3517 (uri (cran-uri "inline" version))
3520 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3521 (build-system r-build-system)
3522 (home-page "https://cran.r-project.org/web/packages/inline")
3523 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3525 "This package provides functionality to dynamically define R functions
3526 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3527 @code{.Call} calling conventions.")
3528 ;; Any version of the LGPL.
3529 (license license:lgpl3+)))
3531 (define-public r-inum
3537 (uri (cran-uri "inum" version))
3540 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3541 (build-system r-build-system)
3543 `(("r-libcoin" ,r-libcoin)))
3544 (home-page "https://cran.r-project.org/web/packages/inum/")
3545 (synopsis "Interval and enum-type representation of vectors")
3547 "This package provides an enum-type representation of vectors and
3548 representation of intervals, including a method of coercing variables
3550 (license license:gpl2)))
3551 (define-public r-invgamma
3557 (uri (cran-uri "invgamma" version))
3560 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3561 (properties `((upstream-name . "invgamma")))
3562 (build-system r-build-system)
3563 (home-page "https://github.com/dkahle/invgamma")
3564 (synopsis "Inverse gamma distribution")
3565 (description "This package provides a light weight implementation of the
3566 standard distribution functions for the inverse gamma distribution, wrapping
3567 those for the gamma distribution in the @code{stats} package.")
3568 (license license:gpl2)))
3570 (define-public r-bdsmatrix
3572 (name "r-bdsmatrix")
3577 (uri (cran-uri "bdsmatrix" version))
3580 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3581 (properties `((upstream-name . "bdsmatrix")))
3582 (build-system r-build-system)
3583 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3584 (synopsis "Routines for block diagonal symmetric matrices")
3586 "This package provides procedures to work with block diagonal symmetric
3587 matrices, a special case of sparse matrices.")
3588 (license license:lgpl2.0)))
3590 (define-public r-bbmle
3593 (version "1.0.23.1")
3597 (uri (cran-uri "bbmle" version))
3600 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3601 (build-system r-build-system)
3603 `(("r-bdsmatrix" ,r-bdsmatrix)
3604 ("r-lattice" ,r-lattice)
3606 ("r-matrix" ,r-matrix)
3607 ("r-mvtnorm" ,r-mvtnorm)
3608 ("r-numderiv" ,r-numderiv)))
3609 (home-page "https://cran.r-project.org/web/packages/bbmle")
3610 (synopsis "Tools for General Maximum Likelihood Estimation")
3612 "This package provides methods and functions for fitting maximum
3613 likelihood models in R. This package modifies and extends the @code{mle}
3614 classes in the @code{stats4} package.")
3615 ;; Any version of the GPL
3616 (license license:gpl2+)))
3618 (define-public r-emdbook
3625 (uri (cran-uri "emdbook" version))
3628 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3629 (build-system r-build-system)
3631 `(("r-bbmle" ,r-bbmle)
3633 ("r-lattice" ,r-lattice)
3635 ("r-plyr" ,r-plyr)))
3636 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3637 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3639 "This package provides auxiliary functions and data sets for \"Ecological
3640 Models and Data\", a book presenting maximum likelihood estimation and related
3641 topics for ecologists (ISBN 978-0-691-12522-0).")
3643 (license (list license:gpl2 license:gpl3))))
3645 (define-public r-lpsolve
3652 (uri (cran-uri "lpSolve" version))
3655 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3656 (properties `((upstream-name . "lpSolve")))
3657 (build-system r-build-system)
3658 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3659 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3661 "Lp_solve is software for solving linear, integer and mixed integer
3662 programs. This implementation supplies a \"wrapper\" function in C and some R
3663 functions that solve general linear/integer problems, assignment problems, and
3664 transportation problems.")
3665 (license license:lgpl2.0)))
3667 (define-public r-limsolve
3674 (uri (cran-uri "limSolve" version))
3677 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3678 (properties `((upstream-name . "limSolve")))
3679 (build-system r-build-system)
3681 `(("r-lpsolve" ,r-lpsolve)
3683 ("r-quadprog" ,r-quadprog)))
3684 (native-inputs `(("gfortran" ,gfortran)))
3685 (home-page "https://cran.r-project.org/web/packages/limSolve")
3686 (synopsis "Solving linear inverse models")
3688 "This package provides functions that:
3691 @item find the minimum/maximum of a linear or quadratic function,
3692 @item sample an underdetermined or overdetermined system,
3693 @item solve a linear system Ax=B for the unknown x.
3696 It includes banded and tridiagonal linear systems. The package calls Fortran
3697 functions from LINPACK.")
3699 (license (list license:gpl2+ license:gpl3+))))
3701 (define-public r-fitdistrplus
3703 (name "r-fitdistrplus")
3708 (uri (cran-uri "fitdistrplus" version))
3711 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3712 (build-system r-build-system)
3714 `(("r-mass" ,r-mass)
3715 ("r-survival" ,r-survival)))
3717 `(("r-knitr" ,r-knitr)))
3718 (home-page "http://riskassessment.r-forge.r-project.org")
3719 (synopsis "Fitting a parametric distribution from data")
3721 "This package extends the @code{fitdistr} function of the MASS package
3722 with several functions to help the fit of a parametric distribution to
3723 non-censored or censored data. Censored data may contain left-censored,
3724 right-censored and interval-censored values, with several lower and upper
3725 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3726 provides moment matching (MME), quantile matching (QME) and maximum
3727 goodness-of-fit estimation (MGE) methods (available only for non-censored
3728 data). Weighted versions of MLE, MME and QME are available.")
3729 (license license:gpl2+)))
3731 (define-public r-energy
3738 (uri (cran-uri "energy" version))
3741 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3742 (build-system r-build-system)
3744 `(("r-boot" ,r-boot)
3746 ("r-rcpp" ,r-rcpp)))
3747 (home-page "https://cran.r-project.org/web/packages/energy")
3748 (synopsis "Multivariate inference via the energy of data")
3750 "This package provides e-statistics (energy) tests and statistics for
3751 multivariate and univariate inference, including distance correlation,
3752 one-sample, two-sample, and multi-sample tests for comparing multivariate
3753 distributions, are implemented. Measuring and testing multivariate
3754 independence based on distance correlation, partial distance correlation,
3755 multivariate goodness-of-fit tests, clustering based on energy distance,
3756 testing for multivariate normality, distance components (disco) for
3757 non-parametric analysis of structured data, and other energy
3758 statistics/methods are implemented.")
3759 (license license:gpl2+)))
3761 (define-public r-suppdists
3763 (name "r-suppdists")
3768 (uri (cran-uri "SuppDists" version))
3771 "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8"))))
3772 (properties `((upstream-name . "SuppDists")))
3773 (build-system r-build-system)
3774 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3775 (synopsis "Supplementary distributions")
3777 "This package provides ten distributions supplementing those built into
3778 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3779 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3780 coefficient, Johnson distributions, normal scores and generalized
3781 hypergeometric distributions. In addition two random number generators of
3782 George Marsaglia are included.")
3783 (license license:gpl2+)))
3785 (define-public r-ksamples
3792 (uri (cran-uri "kSamples" version))
3795 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3796 (properties `((upstream-name . "kSamples")))
3797 (build-system r-build-system)
3799 `(("r-suppdists" ,r-suppdists)))
3800 (home-page "https://cran.r-project.org/web/packages/kSamples")
3801 (synopsis "K-Sample rank tests and their combinations")
3803 "This package provides tools to compares k samples using the
3804 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3805 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3806 test. It computes asymptotic, simulated or (limited) exact P-values, all
3807 valid under randomization, with or without ties, or conditionally under random
3808 sampling from populations, given the observed tie pattern. Except for Steel's
3809 test and the JT test it also combines these tests across several blocks of
3811 (license license:gpl2+)))
3813 (define-public r-cvst
3820 (uri (cran-uri "CVST" version))
3823 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3824 (properties `((upstream-name . "CVST")))
3825 (build-system r-build-system)
3827 `(("r-kernlab" ,r-kernlab)
3828 ("r-matrix" ,r-matrix)))
3829 (home-page "https://cran.r-project.org/web/packages/CVST")
3830 (synopsis "Fast cross-validation via sequential testing")
3832 "This package implements the fast cross-validation via sequential
3833 testing (CVST) procedure. CVST is an improved cross-validation procedure
3834 which uses non-parametric testing coupled with sequential analysis to
3835 determine the best parameter set on linearly increasing subsets of the data.
3836 Additionally to the CVST the package contains an implementation of the
3837 ordinary k-fold cross-validation with a flexible and powerful set of helper
3838 objects and methods to handle the overall model selection process. The
3839 implementations of the Cochran's Q test with permutations and the sequential
3840 testing framework of Wald are generic and can therefore also be used in other
3842 (license license:gpl2+)))
3844 (define-public r-squarem
3851 (uri (cran-uri "SQUAREM" version))
3854 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3855 (properties `((upstream-name . "SQUAREM")))
3856 (build-system r-build-system)
3857 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3858 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3860 "This package provides algorithms for accelerating the convergence of
3861 slow, monotone sequences from smooth, contraction mapping such as the EM
3862 algorithm. It can be used to accelerate any smooth, linearly convergent
3863 acceleration scheme. A tutorial style introduction to this package is
3864 available in a vignette.")
3865 (license license:gpl2+)))
3867 (define-public r-lava
3874 (uri (cran-uri "lava" version))
3877 "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83"))))
3878 (build-system r-build-system)
3880 `(("r-numderiv" ,r-numderiv)
3881 ("r-squarem" ,r-squarem)
3882 ("r-survival" ,r-survival)))
3884 `(("r-knitr" ,r-knitr)))
3885 (home-page "https://github.com/kkholst/lava")
3886 (synopsis "Latent variable models")
3888 "This package provides tools for the estimation and simulation of latent
3890 (license license:gpl3)))
3892 (define-public r-drr
3899 (uri (cran-uri "DRR" version))
3902 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3903 (properties `((upstream-name . "DRR")))
3904 (build-system r-build-system)
3906 `(("r-cvst" ,r-cvst)
3907 ("r-kernlab" ,r-kernlab)
3908 ("r-matrix" ,r-matrix)))
3909 (home-page "https://cran.r-project.org/web/packages/DRR")
3910 (synopsis "Dimensionality reduction via regression")
3912 "This package provides an implementation of dimensionality reduction via
3913 regression using Kernel Ridge Regression.")
3914 (license license:gpl3)))
3916 (define-public r-prodlim
3919 (version "2019.11.13")
3923 (uri (cran-uri "prodlim" version))
3926 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3927 (build-system r-build-system)
3929 `(("r-kernsmooth" ,r-kernsmooth)
3932 ("r-survival" ,r-survival)))
3933 (home-page "https://cran.r-project.org/web/packages/prodlim")
3934 (synopsis "Product-limit estimation for censored event history analysis")
3936 "This package provides a fast and user-friendly implementation of
3937 nonparametric estimators for censored event history (survival) analysis with
3938 the Kaplan-Meier and Aalen-Johansen methods.")
3939 (license license:gpl2+)))
3941 (define-public r-dimred
3948 (uri (cran-uri "dimRed" version))
3951 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3952 (properties `((upstream-name . "dimRed")))
3953 (build-system r-build-system)
3956 ("r-magrittr" ,r-magrittr)))
3957 (home-page "https://github.com/gdkrmr/dimRed")
3958 (synopsis "Framework for dimensionality reduction")
3960 "This package provides a collection of dimensionality reduction
3961 techniques from R packages and provides a common interface for calling the
3963 (license license:gpl3)))
3965 (define-public r-timedate
3968 (version "3043.102")
3972 (uri (cran-uri "timeDate" version))
3975 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3976 (properties `((upstream-name . "timeDate")))
3977 (build-system r-build-system)
3978 (home-page "https://www.rmetrics.org")
3979 (synopsis "Chronological and calendar objects")
3981 "This package provides an environment for teaching \"Financial
3982 Engineering and Computational Finance\" and for managing chronological and
3984 (license license:gpl2+)))
3986 (define-public r-magic
3993 (uri (cran-uri "magic" version))
3996 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3997 (build-system r-build-system)
3999 `(("r-abind" ,r-abind)))
4000 (home-page "https://github.com/RobinHankin/magic.git")
4001 (synopsis "Create and investigate magic squares")
4003 "This package provides a collection of efficient, vectorized algorithms
4004 for the creation and investigation of magic squares and hypercubes, including
4005 a variety of functions for the manipulation and analysis of arbitrarily
4006 dimensioned arrays.")
4007 (license license:gpl2)))
4009 (define-public r-rmysql
4016 (uri (cran-uri "RMySQL" version))
4019 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4020 (properties `((upstream-name . "RMySQL")))
4021 (build-system r-build-system)
4023 `(("mariadb-dev" ,mariadb "dev")
4026 `(("r-dbi" ,r-dbi)))
4027 (home-page "https://github.com/r-dbi/RMySQL")
4028 (synopsis "Database interface and MySQL driver for R")
4030 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4031 package contains an old implementation based on legacy code from S-PLUS which
4032 is being phased out. A modern MySQL client based on Rcpp is available from
4033 the RMariaDB package.")
4034 (license license:gpl2)))
4036 (define-public r-rpostgresql
4038 (name "r-rpostgresql")
4043 (uri (cran-uri "RPostgreSQL" version))
4046 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4047 (properties `((upstream-name . "RPostgreSQL")))
4048 (build-system r-build-system)
4050 `(("postgresql" ,postgresql)))
4052 `(("r-dbi" ,r-dbi)))
4053 (home-page "https://github.com/tomoakin/RPostgreSQL")
4054 (synopsis "R interface to the PostgreSQL database system")
4056 "This package provides a Database Interface (DBI) compliant driver for R
4057 to access PostgreSQL database systems.")
4058 ;; The whole package is released under GPL version 2. It includes code
4059 ;; under the PostgreSQL license.
4060 (license license:gpl2)))
4062 (define-public r-linprog
4069 (uri (cran-uri "linprog" version))
4072 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4073 (build-system r-build-system)
4074 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4075 (home-page "http://linprog.r-forge.r-project.org/")
4076 (synopsis "Linear programming and optimization")
4078 "This package can be used to solve Linear Programming / Linear
4079 Optimization problems by using the simplex algorithm.")
4080 (license license:gpl2+)))
4082 (define-public r-geometry
4089 (uri (cran-uri "geometry" version))
4092 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4093 (build-system r-build-system)
4095 `(("r-magic" ,r-magic)
4096 ("r-linprog" ,r-linprog)
4097 ("r-lpsolve" ,r-lpsolve)
4099 ("r-rcppprogress" ,r-rcppprogress)))
4100 (home-page "http://geometry.r-forge.r-project.org/")
4101 (synopsis "Mesh generator and surface tessellator")
4103 "This package makes the qhull library available in R, in a similar manner
4104 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4105 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4106 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4107 and higher dimensions. It implements the Quickhull algorithm for computing
4108 the convex hull. Qhull does not support constrained Delaunay triangulations,
4109 or mesh generation of non-convex objects, but the package does include some R
4110 functions that allow for this. Currently the package only gives access to
4111 Delaunay triangulation and convex hull computation.")
4112 ;; The Qhull sources are included and are distributed under a custom
4113 ;; non-copyleft license. The R sources are released under GPL version 2.
4114 (license (list license:gpl2
4115 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4117 (define-public r-ddalpha
4124 (uri (cran-uri "ddalpha" version))
4127 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4128 (build-system r-build-system)
4131 ("r-class" ,r-class)
4132 ("r-geometry" ,r-geometry)
4135 ("r-robustbase" ,r-robustbase)
4136 ("r-sfsmisc" ,r-sfsmisc)))
4138 `(("gfortran" ,gfortran)))
4139 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4140 (synopsis "Depth-Based classification and calculation of data depth")
4142 "This package contains procedures for depth-based supervised learning,
4143 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4144 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4145 statistical depth function to a compact low-dimensional space, where the final
4146 classification is done. It also offers an extension to functional data and
4147 routines for calculating certain notions of statistical depth functions. 50
4148 multivariate and 5 functional classification problems are included.")
4149 (license license:gpl2)))
4151 (define-public r-gower
4158 (uri (cran-uri "gower" version))
4161 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4162 (build-system r-build-system)
4163 (home-page "https://github.com/markvanderloo/gower")
4164 (synopsis "Gower's distance")
4166 "This package provides tools to compute Gower's distance (or similarity)
4167 coefficient between records, and to compute the top-n matches between records.
4168 Core algorithms are executed in parallel on systems supporting OpenMP.")
4169 (license license:gpl3)))
4171 (define-public r-rcpproll
4178 (uri (cran-uri "RcppRoll" version))
4181 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4182 (properties `((upstream-name . "RcppRoll")))
4183 (build-system r-build-system)
4185 `(("r-rcpp" ,r-rcpp)))
4186 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4187 (synopsis "Efficient rolling and windowed operations")
4189 "This package provides fast and efficient routines for common rolling /
4190 windowed operations. Routines for the efficient computation of windowed mean,
4191 median, sum, product, minimum, maximum, standard deviation and variance are
4193 (license license:gpl2+)))
4195 (define-public r-ipred
4202 (uri (cran-uri "ipred" version))
4205 "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp"))))
4206 (build-system r-build-system)
4208 `(("r-class" ,r-class)
4211 ("r-prodlim" ,r-prodlim)
4212 ("r-rpart" ,r-rpart)
4213 ("r-survival" ,r-survival)))
4214 (home-page "https://cran.r-project.org/web/packages/ipred")
4215 (synopsis "Improved predictors")
4217 "This package provides improved predictive models by indirect
4218 classification and bagging for classification, regression and survival
4219 problems as well as resampling based estimators of prediction error.")
4220 (license license:gpl2+)))
4222 (define-public r-psych
4229 (uri (cran-uri "psych" version))
4232 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
4233 (build-system r-build-system)
4235 `(("r-lattice" ,r-lattice)
4236 ("r-mnormt" ,r-mnormt)
4237 ("r-nlme" ,r-nlme)))
4238 (home-page "https://cran.r-project.org/web/packages/psych/")
4239 (synopsis "Procedures for psychological, psychometric, and personality research")
4241 "This package provides a general purpose toolbox for personality,
4242 psychometric theory and experimental psychology. Functions are primarily for
4243 multivariate analysis and scale construction using factor analysis, principal
4244 component analysis, cluster analysis and reliability analysis, although others
4245 provide basic descriptive statistics. Item Response Theory is done using
4246 factor analysis of tetrachoric and polychoric correlations. Functions for
4247 analyzing data at multiple levels include within and between group statistics,
4248 including correlations and factor analysis. Functions for simulating and
4249 testing particular item and test structures are included. Several functions
4250 serve as a useful front end for structural equation modeling. Graphical
4251 displays of path diagrams, factor analysis and structural equation models are
4252 created using basic graphics.")
4253 (license license:gpl2+)))
4255 (define-public r-generics
4262 (uri (cran-uri "generics" version))
4265 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4266 (build-system r-build-system)
4267 (home-page "https://github.com/r-lib/generics")
4268 (synopsis "Common S3 generics not provided by base R methods")
4270 "In order to reduce potential package dependencies and conflicts,
4271 generics provides a number of commonly used S3 generics that are not provided
4272 by base R methods related to model fitting.")
4273 (license license:gpl2)))
4275 (define-public r-broom
4282 (uri (cran-uri "broom" version))
4285 "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw"))))
4286 (build-system r-build-system)
4288 `(("r-backports" ,r-backports)
4289 ("r-dplyr" ,r-dplyr)
4290 ("r-ellipsis" ,r-ellipsis)
4291 ("r-generics" ,r-generics)
4293 ("r-purrr" ,r-purrr)
4294 ("r-rlang" ,r-rlang)
4295 ("r-stringr" ,r-stringr)
4296 ("r-tibble" ,r-tibble)
4297 ("r-tidyr" ,r-tidyr)))
4299 `(("r-knitr" ,r-knitr)))
4300 (home-page "https://github.com/tidyverse/broom")
4301 (synopsis "Convert statistical analysis objects into tidy data frames")
4303 "This package provides tools to convert statistical analysis objects from
4304 R into tidy data frames, so that they can more easily be combined, reshaped
4305 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4306 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4307 summarizes a model's statistical findings such as coefficients of a
4308 regression; @code{augment}, which adds columns to the original data such as
4309 predictions, residuals and cluster assignments; and @code{glance}, which
4310 provides a one-row summary of model-level statistics.")
4311 (license license:expat)))
4313 (define-public r-recipes
4320 (uri (cran-uri "recipes" version))
4323 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4324 (build-system r-build-system)
4326 `(("r-dplyr" ,r-dplyr)
4327 ("r-generics" ,r-generics)
4329 ("r-gower" ,r-gower)
4330 ("r-ipred" ,r-ipred)
4331 ("r-lifecycle" ,r-lifecycle)
4332 ("r-lubridate" ,r-lubridate)
4333 ("r-magrittr" ,r-magrittr)
4334 ("r-matrix" ,r-matrix)
4335 ("r-purrr" ,r-purrr)
4336 ("r-rlang" ,r-rlang)
4337 ("r-tibble" ,r-tibble)
4338 ("r-tidyr" ,r-tidyr)
4339 ("r-tidyselect" ,r-tidyselect)
4340 ("r-timedate" ,r-timedate)
4341 ("r-withr" ,r-withr)))
4343 `(("r-knitr" ,r-knitr)))
4344 (home-page "https://github.com/topepo/recipes")
4345 (synopsis "Preprocessing tools to create design matrices")
4347 "Recipes is an extensible framework to create and preprocess design
4348 matrices. Recipes consist of one or more data manipulation and analysis
4349 \"steps\". Statistical parameters for the steps can be estimated from an
4350 initial data set and then applied to other data sets. The resulting design
4351 matrices can then be used as inputs into statistical or machine learning
4353 (license license:gpl2)))
4355 (define-public r-pdist
4362 (uri (cran-uri "pdist" version))
4365 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4366 (build-system r-build-system)
4367 (home-page "https://github.com/jeffwong/pdist")
4368 (synopsis "Partitioned distance function")
4370 "Pdist computes the euclidean distance between rows of a matrix X and
4371 rows of another matrix Y. Previously, this could be done by binding the two
4372 matrices together and calling @code{dist}, but this creates unnecessary
4373 computation by computing the distances between a row of X and another row of
4374 X, and likewise for Y. Pdist strictly computes distances across the two
4375 matrices, not within the same matrix, making computations significantly faster
4376 for certain use cases.")
4377 (license license:gpl3+)))
4379 (define-public r-ggrepel
4386 (uri (cran-uri "ggrepel" version))
4389 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4390 (build-system r-build-system)
4392 `(("r-ggplot2" ,r-ggplot2)
4394 ("r-rlang" ,r-rlang)
4395 ("r-scales" ,r-scales)))
4397 `(("r-knitr" ,r-knitr))) ; for vignettes
4398 (home-page "https://github.com/slowkow/ggrepel")
4399 (synopsis "Repulsive text and label geometries for ggplot2")
4401 "This package provides text and label geometries for ggplot2 that help to
4402 avoid overlapping text labels. Labels repel away from each other and away
4403 from the data points.")
4404 (license license:gpl3)))
4406 (define-public r-corrplot
4413 (uri (cran-uri "corrplot" version))
4416 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4417 (build-system r-build-system)
4418 (home-page "https://github.com/taiyun/corrplot")
4419 (synopsis "Visualization of a correlation matrix")
4421 "This package provides a graphical display of a correlation matrix or
4422 general matrix. It also contains some algorithms to do matrix reordering. In
4423 addition, corrplot is good at details, including choosing color, text labels,
4424 color labels, layout, etc.")
4425 ;; Any version of the GPL
4426 (license license:gpl2+)))
4428 (define-public r-stringdist
4430 (name "r-stringdist")
4435 (uri (cran-uri "stringdist" version))
4437 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4438 (build-system r-build-system)
4439 (home-page "https://github.com/markvanderloo/stringdist")
4440 (synopsis "Approximate string matching and string distance functions")
4442 "This package implements an approximate string matching version of R's
4443 native @code{match} function. It can calculate various string distances based
4444 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4445 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4446 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4447 can be computed between character vectors while taking proper care of encoding
4448 or between integer vectors representing generic sequences.")
4449 (license license:gpl3+)))
4451 (define-public r-ucminf
4458 (uri (cran-uri "ucminf" version))
4461 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4462 (build-system r-build-system)
4463 (native-inputs `(("gfortran" ,gfortran)))
4464 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4465 (synopsis "General-purpose unconstrained non-linear optimization")
4467 "This package provides an implementation of an algorithm for
4468 general-purpose unconstrained non-linear optimization. The algorithm is of
4469 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4470 search with a trust region type monitoring of the input to the line search
4471 algorithm. The interface of @code{ucminf} is designed for easy interchange
4472 with the package @code{optim}.")
4473 (license license:gpl2+)))
4475 (define-public r-useful
4481 (uri (cran-uri "useful" version))
4484 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4485 (properties `((upstream-name . "useful")))
4486 (build-system r-build-system)
4488 `(("r-assertthat" ,r-assertthat)
4489 ("r-dplyr" ,r-dplyr)
4490 ("r-ggplot2" ,r-ggplot2)
4491 ("r-magrittr" ,r-magrittr)
4492 ("r-matrix" ,r-matrix)
4494 ("r-purrr" ,r-purrr)
4495 ("r-scales" ,r-scales)))
4496 (home-page "https://github.com/jaredlander/useful")
4497 (synopsis "Collection of handy, useful functions")
4498 (description "This package provides a set of little functions that have been
4499 found useful to do little odds and ends such as plotting the results of K-means
4500 clustering, substituting special text characters, viewing parts of a
4501 @code{data.frame}, constructing formulas from text and building design and
4502 response matrices.")
4503 (license license:bsd-3)))
4505 (define-public r-ordinal
4508 (version "2019.12-10")
4512 (uri (cran-uri "ordinal" version))
4515 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4516 (build-system r-build-system)
4518 `(("r-mass" ,r-mass)
4519 ("r-matrix" ,r-matrix)
4520 ("r-numderiv" ,r-numderiv)
4521 ("r-ucminf" ,r-ucminf)))
4522 (home-page "https://github.com/runehaubo/ordinal")
4523 (synopsis "Regression models for ordinal data")
4525 "This package provides an implementation of cumulative link (mixed)
4526 models also known as ordered regression models, proportional odds models,
4527 proportional hazards models for grouped survival times and ordered models.
4528 Estimation is via maximum likelihood and mixed models are fitted with the
4529 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4530 (license license:gpl2+)))
4532 (define-public r-jomo
4539 (uri (cran-uri "jomo" version))
4542 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4543 (build-system r-build-system)
4545 `(("r-lme4" ,r-lme4)
4547 ("r-ordinal" ,r-ordinal)
4548 ("r-survival" ,r-survival)))
4549 (home-page "https://cran.r-project.org/web/packages/jomo/")
4550 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4552 "Similarly to Schafer's package pan, jomo is a package for multilevel
4553 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4554 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4555 possibility of handling binary and categorical data through latent normal
4556 variables, the option to use cluster-specific covariance matrices and to
4557 impute compatibly with the substantive model.")
4558 (license license:gpl2)))
4560 (define-public r-pan
4567 (uri (cran-uri "pan" version))
4570 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4571 (build-system r-build-system)
4572 (native-inputs `(("gfortran" ,gfortran)))
4573 (home-page "https://cran.r-project.org/web/packages/pan/")
4574 (synopsis "Multiple imputation for multivariate panel or clustered data")
4576 "This package implements multiple imputation for multivariate panel or
4578 (license license:gpl3)))
4580 (define-public r-mitml
4587 (uri (cran-uri "mitml" version))
4590 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4591 (build-system r-build-system)
4593 `(("r-haven" ,r-haven)
4597 `(("r-knitr" ,r-knitr)))
4598 (home-page "https://cran.r-project.org/web/packages/mitml/")
4599 (synopsis "Tools for multiple imputation in multilevel modeling")
4601 "This package provides tools for multiple imputation of missing data in
4602 multilevel modeling. It includes a user-friendly interface to the packages
4603 pan and jomo, and several functions for visualization, data management and the
4604 analysis of multiply imputed data sets.")
4605 (license license:gpl2+)))
4607 (define-public r-mice
4614 (uri (cran-uri "mice" version))
4617 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4618 (build-system r-build-system)
4620 `(("r-broom" ,r-broom)
4621 ("r-cpp11" ,r-cpp11)
4622 ("r-dplyr" ,r-dplyr)
4623 ("r-generics" ,r-generics)
4624 ("r-lattice" ,r-lattice)
4626 ("r-rlang" ,r-rlang)
4627 ("r-tidyr" ,r-tidyr)))
4628 (home-page "https://cran.r-project.org/web/packages/mice/")
4629 (synopsis "Multivariate imputation by chained equations")
4631 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4632 implemented by the MICE algorithm as described in @url{Van Buuren and
4633 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4634 variable has its own imputation model. Built-in imputation models are
4635 provided for continuous data (predictive mean matching, normal), binary
4636 data (logistic regression), unordered categorical data (polytomous logistic
4637 regression) and ordered categorical data (proportional odds). MICE can also
4638 impute continuous two-level data (normal model, pan, second-level variables).
4639 Passive imputation can be used to maintain consistency between variables.
4640 Various diagnostic plots are available to inspect the quality of the
4642 ;; Any of these two versions.
4643 (license (list license:gpl2 license:gpl3))))
4645 (define-public r-truncnorm
4647 (name "r-truncnorm")
4652 (uri (cran-uri "truncnorm" version))
4655 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4656 (build-system r-build-system)
4657 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4658 (synopsis "Truncated normal distribution")
4659 (description "This package provides functions for the truncated normal
4660 distribution with mean equal to @code{mean} and standard deviation equal to
4661 @code{sd}. It includes density, distribution, quantile, and expected value
4662 functions, as well as a random generation function.")
4663 (license license:gpl2)))
4665 (define-public r-rsolnp
4672 (uri (cran-uri "Rsolnp" version))
4675 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4676 (properties `((upstream-name . "Rsolnp")))
4677 (build-system r-build-system)
4679 `(("r-truncnorm" ,r-truncnorm)))
4680 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4681 (synopsis "General non-linear optimization")
4682 (description "The Rsolnp package implements a general non-linear augmented
4683 Lagrange multiplier method solver, a @dfn{sequential quadratic
4684 programming} (SQP) based solver).")
4685 ;; Any version of the GPL.
4686 (license license:gpl2+)))
4688 (define-public r-hardyweinberg
4690 (name "r-hardyweinberg")
4695 (uri (cran-uri "HardyWeinberg" version))
4698 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4699 (properties `((upstream-name . "HardyWeinberg")))
4700 (build-system r-build-system)
4702 `(("r-mice" ,r-mice)
4704 ("r-rsolnp" ,r-rsolnp)))
4705 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4706 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4708 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4709 diallelic genetic marker data. All classical tests (chi-square, exact,
4710 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4711 included in the package, as well as functions for power computation and for
4712 the simulation of marker data under equilibrium and disequilibrium. Routines
4713 for dealing with markers on the X-chromosome are included. Functions for
4714 testing equilibrium in the presence of missing data by using multiple
4715 imputation are also provided. Implements several graphics for exploring the
4716 equilibrium status of a large set of diallelic markers: ternary plots with
4717 acceptance regions, log-ratio plots and Q-Q plots.")
4718 (license license:gpl2+)))
4727 (uri (cran-uri "sm" version))
4730 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4731 (build-system r-build-system)
4732 (native-inputs `(("gfortran" ,gfortran)))
4733 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4734 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4736 "This is software accompanying the book 'Applied Smoothing Techniques for
4737 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4738 University Press. It provides smoothing methods for nonparametric regression
4739 and density estimation")
4740 (license license:gpl2+)))
4742 (define-public r-venndiagram
4744 (name "r-venndiagram")
4748 (uri (cran-uri "VennDiagram" version))
4751 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4752 (properties `((upstream-name . "VennDiagram")))
4753 (build-system r-build-system)
4755 `(("r-futile-logger" ,r-futile-logger)))
4756 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4757 (synopsis "Generate High-Resolution Venn and Euler Plots")
4759 "This package provides a set of functions to generate high-resolution
4760 Venn and Euler plots. It includes handling for several special cases,
4761 including two-case scaling, and extensive customization of plot shape and
4763 (license license:gpl2+)))
4765 (define-public r-vioplot
4772 (uri (cran-uri "vioplot" version))
4775 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4776 (build-system r-build-system)
4781 `(("r-knitr" ,r-knitr)))
4782 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4783 (synopsis "Violin plot")
4785 "This package provides a violin plot, which is a combination of a box
4786 plot and a kernel density plot.")
4787 (license license:bsd-3)))
4789 (define-public r-rsofia
4795 ;; This package has been removed from CRAN, so we can
4796 ;; only fetch it from the archives.
4797 (uri (string-append "https://cran.r-project.org/src/"
4798 "contrib/Archive/RSofia/RSofia_"
4802 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4803 (properties `((upstream-name . "RSofia")))
4804 (build-system r-build-system)
4806 `(("r-rcpp" ,r-rcpp)))
4807 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4808 (synopsis "Port of sofia-ml to R")
4809 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4810 suite of fast incremental algorithms for machine learning that can be used for
4811 training models for classification or ranking.")
4812 (license license:asl2.0)))
4814 (define-public r-xts
4821 (uri (cran-uri "xts" version))
4824 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4825 (build-system r-build-system)
4826 (propagated-inputs `(("r-zoo" ,r-zoo)))
4827 (home-page "https://github.com/joshuaulrich/xts")
4828 (synopsis "Extensible time series")
4830 "This package provides for uniform handling of R's different time-based
4831 data classes by extending @code{zoo}, maximizing native format information
4832 preservation and allowing for user-level customization and extension, while
4833 simplifying cross-class interoperability.")
4834 (license license:gpl2+)))
4836 (define-public r-performanceanalytics
4838 (name "r-performanceanalytics")
4843 (uri (cran-uri "PerformanceAnalytics" version))
4846 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4848 `((upstream-name . "PerformanceAnalytics")))
4849 (build-system r-build-system)
4851 `(("r-quadprog" ,r-quadprog)
4854 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4855 (synopsis "Econometric tools for performance and risk analysis")
4856 (description "This is a collection of econometric functions for
4857 performance and risk analysis. This package aims to aid practitioners and
4858 researchers in utilizing the latest research in analysis of non-normal return
4859 streams. In general, it is most tested on return (rather than price) data on
4860 a regular scale, but most functions will work with irregular return data as
4861 well, and increasing numbers of functions will work with P&L or price data
4863 ;; Either version may be picked.
4864 (license (list license:gpl2 license:gpl3))))
4866 (define-public r-laeken
4873 (uri (cran-uri "laeken" version))
4876 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4877 (build-system r-build-system)
4879 `(("r-boot" ,r-boot)
4880 ("r-mass" ,r-mass)))
4881 (home-page "https://cran.r-project.org/web/packages/laeken/")
4882 (synopsis "Estimation of indicators on social exclusion and poverty")
4883 (description "This package provides tools for the estimation of indicators
4884 on social exclusion and poverty, as well as an implementation of Pareto tail
4885 modeling for empirical income distributions.")
4886 (license license:gpl2+)))
4888 (define-public r-vcd
4895 (uri (cran-uri "vcd" version))
4898 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4899 (build-system r-build-system)
4901 `(("r-colorspace" ,r-colorspace)
4902 ("r-lmtest" ,r-lmtest)
4903 ("r-mass" ,r-mass)))
4904 (home-page "https://cran.r-project.org/web/packages/vcd/")
4905 (synopsis "Visualizing categorical data")
4906 (description "This package provides visualization techniques, data sets,
4907 summary and inference procedures aimed particularly at categorical data.
4908 Special emphasis is given to highly extensible grid graphics. The package was
4909 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4910 Friendly and is now the main support package for a new book, \"Discrete Data
4911 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4912 (license license:gpl2)))
4914 (define-public r-ica
4921 (uri (cran-uri "ica" version))
4924 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4925 (build-system r-build-system)
4926 (home-page "https://cran.r-project.org/web/packages/ica/")
4927 (synopsis "Independent component analysis")
4928 (description "This package provides tools for @dfn{Independent Component
4929 Analysis} (ICA) using various algorithms: FastICA,
4930 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4931 of Eigenmatrices} (JADE).")
4932 (license license:gpl2+)))
4934 (define-public r-dtw
4941 (uri (cran-uri "dtw" version))
4944 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4945 (build-system r-build-system)
4946 (propagated-inputs `(("r-proxy" ,r-proxy)))
4947 (home-page "http://dtw.r-forge.r-project.org/")
4948 (synopsis "Dynamic Time Warping Algorithms")
4949 (description "This package provides a comprehensive implementation of
4950 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4951 optimal (least cumulative distance) alignment between points of two time
4952 series. Common DTW variants covered include local (slope) and global (window)
4953 constraints, subsequence matches, arbitrary distance definitions,
4954 normalizations, minimum variance matching, and so on.")
4955 (license license:gpl2+)))
4957 (define-public r-sdmtools
4960 (version "1.1-221.2")
4964 (uri (cran-uri "SDMTools" version))
4967 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4968 (properties `((upstream-name . "SDMTools")))
4969 (build-system r-build-system)
4970 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4971 (home-page "https://www.rforge.net/SDMTools/")
4972 (synopsis "Species distribution modelling tools")
4973 (description "This package provides a set of tools for post processing
4974 the outcomes of species distribution modeling exercises. It includes novel
4975 methods for comparing models and tracking changes in distributions through
4976 time. It further includes methods for visualizing outcomes, selecting
4977 thresholds, calculating measures of accuracy and landscape fragmentation
4979 (license license:gpl3+)))
4981 (define-public r-scatterplot3d
4983 (name "r-scatterplot3d")
4988 (uri (cran-uri "scatterplot3d" version))
4991 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4992 (build-system r-build-system)
4993 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4994 (synopsis "3D scatter plot")
4995 (description "This package provides an implementation of scatter plots for
4996 plotting. a three dimensional point cloud.")
4997 (license license:gpl2)))
4999 (define-public r-ggridges
5006 (uri (cran-uri "ggridges" version))
5009 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5010 (build-system r-build-system)
5012 `(("r-ggplot2" ,r-ggplot2)
5014 ("r-scales" ,r-scales)
5015 ("r-withr" ,r-withr)))
5017 `(("r-knitr" ,r-knitr)))
5018 (home-page "https://github.com/clauswilke/ggridges")
5019 (synopsis "Ridgeline plots in ggplot2")
5021 "Ridgeline plots provide a convenient way of visualizing changes in
5022 distributions over time or space. This package enables the creation of such
5023 plots in @code{ggplot2}.")
5024 (license license:gpl2)))
5026 (define-public r-ggjoy
5033 (uri (cran-uri "ggjoy" version))
5036 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5037 (build-system r-build-system)
5039 `(("r-ggplot2" ,r-ggplot2)
5040 ("r-ggridges" ,r-ggridges)))
5041 (home-page "https://github.com/clauswilke/ggjoy")
5042 (synopsis "Joyplots in ggplot2")
5043 (description "Joyplots provide a convenient way of visualizing changes in
5044 distributions over time or space. This package enables the creation of such
5045 plots in @code{ggplot2}.")
5046 (license license:gpl2)))
5048 (define-public r-cli
5055 (uri (cran-uri "cli" version))
5058 "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i"))))
5059 (build-system r-build-system)
5061 `(("r-assertthat" ,r-assertthat)
5062 ("r-glue" ,r-glue)))
5063 (home-page "https://github.com/r-lib/cli#readme")
5064 (synopsis "Helpers for developing command line interfaces")
5065 (description "This package provides a suite of tools designed to build
5066 attractive command line interfaces (CLIs). It includes tools for drawing
5067 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5068 (license license:expat)))
5070 (define-public r-argparser
5072 (name "r-argparser")
5077 (uri (cran-uri "argparser" version))
5080 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5081 (build-system r-build-system)
5082 (home-page "https://bitbucket.org/djhshih/argparser")
5083 (synopsis "Command-line argument parser")
5085 "This package provides a cross-platform command-line argument parser
5086 written purely in R with no external dependencies. It is useful with the
5087 Rscript front-end and facilitates turning an R script into an executable
5089 (license license:gpl3+)))
5091 (define-public r-debugme
5098 (uri (cran-uri "debugme" version))
5101 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5102 (build-system r-build-system)
5103 (propagated-inputs `(("r-crayon" ,r-crayon)))
5104 (home-page "https://github.com/r-lib/debugme#readme")
5105 (synopsis "Debug R packages")
5107 "This package allows the user to specify debug messages as special string
5108 constants, and control debugging of packages via environment variables.")
5109 (license license:expat)))
5111 (define-public r-processx
5118 (uri (cran-uri "processx" version))
5120 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
5121 (build-system r-build-system)
5125 (home-page "https://github.com/r-lib/processx3")
5126 (synopsis "Execute and control system processes")
5128 "This package provides portable tools to run system processes in the
5129 background. It can check if a background process is running; wait on a
5130 background process to finish; get the exit status of finished processes; kill
5131 background processes and their children; restart processes. It can read the
5132 standard output and error of the processes, using non-blocking connections.
5133 @code{processx} can poll a process for standard output or error, with a
5134 timeout. It can also poll several processes at once.")
5135 (license license:expat)))
5137 (define-public r-tsp
5144 (uri (cran-uri "TSP" version))
5147 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5148 (properties `((upstream-name . "TSP")))
5149 (build-system r-build-system)
5150 (propagated-inputs `(("r-foreach" ,r-foreach)))
5151 (home-page "https://cran.r-project.org/web/packages/TSP/")
5152 (synopsis "Traveling salesperson problem (TSP)")
5153 (description "This package provides basic infrastructure and some
5154 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5155 traveling salesman problem).")
5156 (license license:gpl3)))
5158 (define-public r-qap
5165 (uri (cran-uri "qap" version))
5168 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5169 (build-system r-build-system)
5170 (native-inputs `(("gfortran" ,gfortran)))
5171 (home-page "https://cran.r-project.org/web/packages/qap/")
5172 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5173 (description "This package implements heuristics for the @dfn{quadratic
5174 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5176 (license license:gpl3)))
5178 (define-public r-gclus
5185 (uri (cran-uri "gclus" version))
5188 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5189 (build-system r-build-system)
5190 (propagated-inputs `(("r-cluster" ,r-cluster)))
5191 (home-page "https://cran.r-project.org/web/packages/gclus/")
5192 (synopsis "Clustering graphics")
5193 (description "This package orders panels in scatterplot matrices and
5194 parallel coordinate displays by some merit index. It contains various indices
5195 of merit, ordering functions, and enhanced versions of @code{pairs} and
5196 @code{parcoord} which color panels according to their merit level.")
5197 (license license:gpl2+)))
5199 (define-public r-webshot
5206 (uri (cran-uri "webshot" version))
5209 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5210 (build-system r-build-system)
5212 `(("r-callr" ,r-callr)
5213 ("r-jsonlite" ,r-jsonlite)
5214 ("r-magrittr" ,r-magrittr)))
5215 (home-page "https://github.com/wch/webshot/")
5216 (synopsis "Take screenshots of web pages")
5218 "Webshot makes it easy to take screenshots of web pages from within R.
5219 It can also run Shiny applications locally and take screenshots of the
5220 application; and it can render and screenshot static as well as interactive R
5221 Markdown documents.")
5222 (license license:gpl2)))
5224 (define-public r-seriation
5226 (name "r-seriation")
5231 (uri (cran-uri "seriation" version))
5234 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5235 (build-system r-build-system)
5237 `(("r-cluster" ,r-cluster)
5238 ("r-colorspace" ,r-colorspace)
5239 ("r-dendextend" ,r-dendextend)
5240 ("r-gclus" ,r-gclus)
5241 ("r-gplots" ,r-gplots)
5244 ("r-registry" ,r-registry)
5246 (native-inputs `(("gfortran" ,gfortran)))
5247 (home-page "https://s2.smu.edu/IDA/seriation/")
5248 (synopsis "Infrastructure for ordering objects using seriation")
5250 "This package provides infrastructure for seriation with an
5251 implementation of several seriation/sequencing techniques to reorder matrices,
5252 dissimilarity matrices, and dendrograms. It also provides (optimally)
5253 reordered heatmaps, color images and clustering visualizations like
5254 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5256 (license license:gpl3)))
5258 (define-public r-xfun
5265 (uri (cran-uri "xfun" version))
5267 (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y"))))
5268 (build-system r-build-system)
5269 ;; knitr itself depends on xfun
5272 `(("r-knitr" ,r-knitr)))
5273 (home-page "https://github.com/yihui/xfun")
5274 (synopsis "Miscellaneous functions")
5276 "This package provides miscellaneous functions commonly used in other
5277 packages maintained by Yihui Xie.")
5278 (license license:expat)))
5280 (define-public r-utf8
5287 (uri (cran-uri "utf8" version))
5290 "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk"))))
5291 (build-system r-build-system)
5293 `(("r-knitr" ,r-knitr)))
5294 (home-page "https://github.com/patperry/r-utf8")
5295 (synopsis "Unicode text processing")
5297 "This package provides tools to process and print UTF-8 encoded
5298 international text (Unicode). Input, validate, normalize, encode, format, and
5300 (license license:asl2.0)))
5302 (define-public r-zeallot
5309 (uri (cran-uri "zeallot" version))
5312 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5313 (build-system r-build-system)
5314 (home-page "https://github.com/nteetor/zeallot")
5315 (synopsis "Multiple, unpacking, and destructuring assignment")
5317 "This package provides a @code{%<-%} operator to perform multiple,
5318 unpacking, and destructuring assignment in R. The operator unpacks the
5319 right-hand side of an assignment into multiple values and assigns these values
5320 to variables on the left-hand side of the assignment.")
5321 (license license:expat)))
5323 (define-public r-vctrs
5330 (uri (cran-uri "vctrs" version))
5333 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5334 (build-system r-build-system)
5336 `(("r-digest" ,r-digest)
5337 ("r-ellipsis" ,r-ellipsis)
5339 ("r-rlang" ,r-rlang)))
5341 `(("r-knitr" ,r-knitr)))
5342 (home-page "https://github.com/r-lib/vctrs")
5343 (synopsis "Vector helpers")
5345 "There are three main goals to the @code{vctrs} package:
5348 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5349 @code{length()} and @code{class()}. These definitions are paired with a
5350 framework for type-coercion and size-recycling.
5351 @item To define type- and size-stability as desirable function properties, use
5352 them to analyse existing base function, and to propose better alternatives.
5353 This work has been particularly motivated by thinking about the ideal
5354 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5355 @item To provide a new @code{vctr} base class that makes it easy to create new
5356 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5357 a few new @code{vctrs} generics, making implementation considerably simpler
5360 (license license:gpl3)))
5362 (define-public r-pillar
5369 (uri (cran-uri "pillar" version))
5372 "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c"))))
5373 (build-system r-build-system)
5376 ("r-crayon" ,r-crayon)
5377 ("r-ellipsis" ,r-ellipsis)
5378 ("r-fansi" ,r-fansi)
5379 ("r-lifecycle" ,r-lifecycle)
5380 ("r-rlang" ,r-rlang)
5382 ("r-vctrs" ,r-vctrs)))
5384 `(("r-knitr" ,r-knitr)))
5385 (home-page "https://github.com/r-lib/pillar")
5386 (synopsis "Coloured formatting for columns")
5388 "This package provides a @code{pillar} generic designed for formatting
5389 columns of data using the full range of colours provided by modern
5391 (license license:gpl3)))
5393 (define-public r-uuid
5400 (uri (cran-uri "uuid" version))
5403 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5404 (build-system r-build-system)
5405 (home-page "https://www.rforge.net/uuid")
5406 (synopsis "Tools for generating and handling of UUIDs")
5408 "This package provides tools for generating and handling of
5409 @dfn{Universally Unique Identifiers} (UUIDs).")
5410 (license license:expat)))
5412 (define-public r-tinytex
5419 (uri (cran-uri "tinytex" version))
5422 "0dk6mpszwh1m65b0wfwjlcvpzywmasf6p31niqiq53wnd92my0gw"))))
5423 (build-system r-build-system)
5425 `(("r-xfun" ,r-xfun)))
5426 (home-page "https://github.com/yihui/tinytex")
5427 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5429 "This package provides helper functions to install and maintain the LaTeX
5430 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5431 easy-to-maintain version of TeX Live. This package also contains helper
5432 functions to compile LaTeX documents, and install missing LaTeX packages
5434 (license license:expat)))
5436 (define-public r-tinytest
5443 (uri (cran-uri "tinytest" version))
5446 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5447 (properties `((upstream-name . "tinytest")))
5448 (build-system r-build-system)
5449 (home-page "https://github.com/markvanderloo/tinytest")
5450 (synopsis "Lightweight unit testing framework")
5452 "This package provides a lightweight unit testing framework. Main
5456 @item install tests with the package;
5457 @item test results are treated as data that can be stored and manipulated;
5458 @item test files are R scripts interspersed with test commands, that can be
5460 @item fully automated build-install-test sequence for packages;
5461 @item skip tests when not run locally (e.g. on CRAN);
5462 @item flexible and configurable output printing;
5463 @item compare computed output with output stored with the package;
5464 @item run tests in parallel;
5465 @item extensible by other packages;
5466 @item report side effects.
5469 (license license:gpl3)))
5471 (define-public r-network
5478 (uri (cran-uri "network" version))
5481 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5482 (build-system r-build-system)
5484 `(("r-magrittr" ,r-magrittr)
5485 ("r-tibble" ,r-tibble)))
5486 (home-page "https://statnet.org/")
5487 (synopsis "Classes for relational data")
5489 "This package provides tools to create and modify network objects. The
5490 @code{network} class can represent a range of relational data types, and
5491 supports arbitrary vertex/edge/graph attributes.")
5492 (license license:gpl2+)))
5494 (define-public r-stabs
5501 (uri (cran-uri "stabs" version))
5504 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5505 (build-system r-build-system)
5507 `(("r-knitr" ,r-knitr)))
5508 (home-page "https://github.com/hofnerb/stabs")
5509 (synopsis "Stability selection with error control")
5511 "This package provides resampling procedures to assess the stability of
5512 selected variables with additional finite sample error control for
5513 high-dimensional variable selection procedures such as Lasso or boosting.
5514 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5515 complementary pairs stability selection with improved error bounds
5516 (Shah & Samworth, 2013) are implemented. The package can be combined with
5517 arbitrary user specified variable selection approaches.")
5518 (license license:gpl2)))
5520 (define-public r-rle
5527 (uri (cran-uri "rle" version))
5530 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5531 (properties `((upstream-name . "rle")))
5532 (build-system r-build-system)
5533 (home-page "https://cran.r-project.org/web/packages/rle/")
5534 (synopsis "Common functions for run-length encoded vectors")
5536 "This package provides common @code{base} and @code{stats} methods for
5537 @code{rle} objects, aiming to make it possible to treat them transparently as
5539 (license license:gpl3)))
5541 (define-public r-statnet-common
5543 (name "r-statnet-common")
5548 (uri (cran-uri "statnet.common" version))
5551 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5553 `((upstream-name . "statnet.common")))
5554 (build-system r-build-system)
5556 `(("r-coda" ,r-coda)
5558 (home-page "https://statnet.org")
5559 (synopsis "R scripts and utilities used by the Statnet software")
5560 (description "This package provides non-statistical utilities used by the
5561 software developed by the Statnet Project.")
5562 (license license:gpl3)))
5564 (define-public r-statcheck
5566 (name "r-statcheck")
5571 (uri (cran-uri "statcheck" version))
5574 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5575 (build-system r-build-system)
5577 `(("r-ggplot2" ,r-ggplot2)
5579 ("r-rmarkdown" ,r-rmarkdown)))
5580 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5581 (synopsis "Extract statistics from articles and recompute p-values")
5582 (description "This package can automatically extract statistical
5583 null-hypothesis significant testing (NHST) results from articles and recompute
5584 the p-values based on the reported test statistic and degrees of freedom to
5585 detect possible inconsistencies.")
5586 (license license:gpl2)))
5588 (define-public r-sna
5595 (uri (cran-uri "sna" version))
5598 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5599 (build-system r-build-system)
5601 `(("r-network" ,r-network)
5602 ("r-statnet-common" ,r-statnet-common)))
5603 (home-page "https://statnet.org")
5604 (synopsis "Tools for social network analysis")
5606 "This package provides a range of tools for social network analysis,
5607 including node and graph-level indices, structural distance and covariance
5608 methods, structural equivalence detection, network regression, random graph
5609 generation, and 2D/3D network visualization.")
5610 (license license:gpl2+)))
5612 (define-public r-tfisher
5619 (uri (cran-uri "TFisher" version))
5622 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5623 (properties `((upstream-name . "TFisher")))
5624 (build-system r-build-system)
5626 `(("r-matrix" ,r-matrix)
5627 ("r-mvtnorm" ,r-mvtnorm)
5629 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5630 (synopsis "Optimal thresholding Fisher's p-value combination method")
5632 "This package provides the @dfn{cumulative distribution function} (CDF),
5633 quantile, and statistical power calculator for a collection of thresholding
5634 Fisher's p-value combination methods, including Fisher's p-value combination
5635 method, truncated product method and, in particular, soft-thresholding
5636 Fisher's p-value combination method which is proven to be optimal in some
5637 context of signal detection. The p-value calculator for the omnibus version
5638 of these tests are also included.")
5639 (license license:gpl2)))
5641 (define-public r-ttr
5648 (uri (cran-uri "TTR" version))
5651 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5652 (properties `((upstream-name . "TTR")))
5653 (build-system r-build-system)
5655 `(("r-curl" ,r-curl)
5658 (home-page "https://github.com/joshuaulrich/TTR")
5659 (synopsis "Technical trading rules")
5661 "This package provides functions and data to construct technical trading
5663 (license license:gpl2)))
5665 (define-public r-leaps
5672 (uri (cran-uri "leaps" version))
5675 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5676 (build-system r-build-system)
5677 (native-inputs `(("gfortran" ,gfortran)))
5678 (home-page "https://cran.r-project.org/web/packages/leaps/")
5679 (synopsis "Regression subset selection")
5681 "This package provides tools for regression subset selection, including
5682 exhaustive search.")
5683 (license license:gpl2+)))
5685 (define-public r-splus2r
5692 (uri (cran-uri "splus2R" version))
5695 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5696 (properties `((upstream-name . "splus2R")))
5697 (build-system r-build-system)
5698 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5699 (synopsis "Supplemental S-PLUS functionality in R")
5701 "Currently there are many functions in S-PLUS that are missing in R. To
5702 facilitate the conversion of S-PLUS packages to R packages, this package
5703 provides some missing S-PLUS functionality in R.")
5704 (license license:gpl2)))
5706 (define-public r-ifultools
5708 (name "r-ifultools")
5713 (uri (cran-uri "ifultools" version))
5716 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5717 (build-system r-build-system)
5719 `(("r-mass" ,r-mass)
5720 ("r-splus2r" ,r-splus2r)))
5721 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5722 (synopsis "Insightful research tools")
5723 (description "This package provides C code used by the wmtsa, fractal, and
5725 (license license:gpl2)))
5727 (define-public r-sapa
5734 (uri (cran-uri "sapa" version))
5737 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5738 (build-system r-build-system)
5740 `(("r-ifultools" ,r-ifultools)
5741 ("r-splus2r" ,r-splus2r)))
5742 (home-page "https://cran.r-project.org/web/packages/sapa/")
5743 (synopsis "Spectral analysis for physical applications")
5744 (description "This package provides software for the book Spectral
5745 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5746 Cambridge University Press, 1993.")
5747 (license license:gpl2)))
5749 (define-public r-aggregation
5751 (name "r-aggregation")
5756 (uri (cran-uri "aggregation" version))
5759 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5760 (build-system r-build-system)
5761 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5762 (synopsis "Methods for p-value aggregation")
5764 "This package contains functionality for performing the following methods
5765 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5766 Fisher's method), and Sidak correction.")
5767 (license license:gpl3)))
5769 (define-public r-quantmod
5776 (uri (cran-uri "quantmod" version))
5779 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5780 (build-system r-build-system)
5782 `(("r-curl" ,r-curl)
5786 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5787 (synopsis "Quantitative financial modelling framework")
5788 (description "This package provides a quantitative financial modelling
5789 framework to allow users to specify, build, trade, and analyse quantitative
5790 financial trading strategies.")
5791 (license license:gpl3)))
5793 (define-public r-tseries
5800 (uri (cran-uri "tseries" version))
5803 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5804 (build-system r-build-system)
5806 `(("r-quadprog" ,r-quadprog)
5807 ("r-quantmod" ,r-quantmod)
5810 `(("gfortran" ,gfortran)))
5811 (home-page "https://cran.r-project.org/web/packages/tseries/")
5812 (synopsis "Time series analysis and computational finance")
5814 "This package provides functions relating to time series analysis and
5815 computational finance.")
5816 (license license:gpl2)))
5818 (define-public r-wmtsa
5825 (uri (cran-uri "wmtsa" version))
5828 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5829 (build-system r-build-system)
5831 `(("r-ifultools" ,r-ifultools)
5833 ("r-splus2r" ,r-splus2r)))
5834 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5835 (synopsis "Wavelet methods for time series analysis")
5837 "This package provides software to accompany the book \"Wavelet Methods
5838 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5839 University Press, 2000.")
5840 (license license:gpl2)))
5842 (define-public r-tsa
5849 (uri (cran-uri "TSA" version))
5852 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5853 (properties `((upstream-name . "TSA")))
5854 (build-system r-build-system)
5856 `(("r-leaps" ,r-leaps)
5857 ("r-locfit" ,r-locfit)
5859 ("r-tseries" ,r-tseries)))
5860 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5861 (synopsis "Time series analysis")
5863 "This package contains R functions and datasets detailed in the book
5864 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5865 Cryer and Kung-Sik Chan.")
5866 (license license:gpl2+)))
5868 (define-public r-extradistr
5870 (name "r-extradistr")
5875 (uri (cran-uri "extraDistr" version))
5878 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5879 (properties `((upstream-name . "extraDistr")))
5880 (build-system r-build-system)
5882 `(("r-rcpp" ,r-rcpp)))
5883 (home-page "https://github.com/twolodzko/extraDistr")
5884 (synopsis "Additional univariate and multivariate distributions")
5886 "This package implements density, distribution functions, quantile
5887 functions and random generation functions for a large number of univariate and
5888 multivariate distributions.")
5889 (license license:gpl2)))
5891 (define-public r-fractal
5898 (uri (cran-uri "fractal" version))
5901 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5902 (build-system r-build-system)
5904 `(("r-ifultools" ,r-ifultools)
5907 ("r-scatterplot3d" ,r-scatterplot3d)
5908 ("r-splus2r" ,r-splus2r)
5909 ("r-wmtsa" ,r-wmtsa)))
5910 (home-page "https://cran.r-project.org/web/packages/fractal/")
5911 (synopsis "Fractal time series modeling and analysis")
5913 "This package provides tools for stochastic fractal and deterministic
5914 chaotic time series analysis.")
5915 (license license:gpl2)))
5917 (define-public r-urca
5924 (uri (cran-uri "urca" version))
5927 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5928 (build-system r-build-system)
5929 (propagated-inputs `(("r-nlme" ,r-nlme)))
5930 (native-inputs `(("gfortran" ,gfortran)))
5931 (home-page "https://cran.r-project.org/web/packages/urca/")
5932 (synopsis "Unit root and cointegration tests for time series data")
5934 "This package provides unit root and cointegration tests encountered in
5935 applied econometric analysis.")
5936 (license license:gpl2+)))
5938 (define-public r-cubature
5945 (uri (cran-uri "cubature" version))
5948 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5949 (build-system r-build-system)
5951 `(("r-rcpp" ,r-rcpp)))
5953 `(("r-knitr" ,r-knitr)))
5954 (home-page "https://github.com/bnaras/cubature")
5955 (synopsis "Adaptive multivariate integration over hypercubes")
5957 "This package is an R wrapper around the cubature C library for adaptive
5958 multivariate integration over hypercubes. This version provides both
5959 @code{hcubature} and @code{pcubature} routines in addition to a vector
5961 ;; The included cubature C library is released under GPLv2+, but the
5962 ;; wrapper declares the license to be GPLv3+.
5963 (license (list license:gpl2+ license:gpl3+))))
5965 (define-public r-trend
5972 (uri (cran-uri "trend" version))
5975 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5976 (build-system r-build-system)
5978 `(("r-extradistr" ,r-extradistr)))
5980 `(("gfortran" ,gfortran)))
5981 (home-page "https://cran.r-project.org/web/packages/trend/")
5982 (synopsis "Non-parametric trend tests and change-point detection")
5984 "The analysis of environmental data often requires the detection of
5985 trends and change-points. This package includes tests for trend
5986 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5987 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5988 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5989 correlation trend test), change-point detection (Lanzante's test procedures,
5990 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5991 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5992 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5993 sample Robust Rank-Order Distributional Test.")
5994 (license license:gpl3)))
5996 (define-public r-expm
6003 (uri (cran-uri "expm" version))
6006 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6007 (build-system r-build-system)
6008 (propagated-inputs `(("r-matrix" ,r-matrix)))
6009 (native-inputs `(("gfortran" ,gfortran)))
6010 (home-page "https://r-forge.r-project.org/projects/expm/")
6011 (synopsis "Tools for matrix exponentials and related quantities")
6013 "This package provides tools for the computation of the matrix
6014 exponential, logarithm, square root, and related quantities.")
6015 (license license:gpl2+)))
6017 (define-public r-complexplus
6019 (name "r-complexplus")
6024 (uri (cran-uri "complexplus" version))
6027 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6028 (build-system r-build-system)
6030 `(("r-expm" ,r-expm)
6031 ("r-matrix" ,r-matrix)))
6032 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6033 (synopsis "Functions of complex or real variables")
6035 "This package extends several functions to the complex domain, including
6036 the matrix exponential and logarithm, and the determinant.")
6037 (license license:gpl2)))
6039 (define-public r-phontools
6041 (name "r-phontools")
6046 (uri (cran-uri "phonTools" version))
6049 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6050 (properties `((upstream-name . "phonTools")))
6051 (build-system r-build-system)
6052 (home-page "http://www.santiagobarreda.com/rscripts.html")
6053 (synopsis "Tools for phonetic and acoustic analyses")
6055 "This package contains tools for the organization, display, and analysis
6056 of the sorts of data frequently encountered in phonetics research and
6057 experimentation, including the easy creation of IPA vowel plots, and the
6058 creation and manipulation of WAVE audio files.")
6059 (license license:bsd-2)))
6068 (uri (cran-uri "np" version))
6071 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6072 (build-system r-build-system)
6074 `(("r-boot" ,r-boot)
6075 ("r-cubature" ,r-cubature)
6076 ("r-quadprog" ,r-quadprog)
6077 ("r-quantreg" ,r-quantreg)))
6078 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6079 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6080 (description "This package provides non-parametric (and semi-parametric)
6081 kernel methods that seamlessly handle a mix of continuous, unordered, and
6082 ordered factor data types.")
6083 ;; Any version of the GPL.
6084 (license license:gpl3+)))
6086 (define-public r-powerplus
6088 (name "r-powerplus")
6093 (uri (cran-uri "powerplus" version))
6096 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6097 (build-system r-build-system)
6099 `(("r-complexplus" ,r-complexplus)
6102 ("r-matrix" ,r-matrix)
6103 ("r-phontools" ,r-phontools)))
6104 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6105 (synopsis "Exponentiation operations")
6107 "This package provides tools for the computation of matrix and scalar
6109 (license license:gpl2)))
6111 (define-public r-egg
6118 (uri (cran-uri "egg" version))
6121 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6122 (properties `((upstream-name . "egg")))
6123 (build-system r-build-system)
6125 `(("r-ggplot2" ,r-ggplot2)
6126 ("r-gridextra" ,r-gridextra)
6127 ("r-gtable" ,r-gtable)))
6128 (home-page "https://cran.r-project.org/web/packages/egg")
6129 (synopsis "Extensions for ggplot2")
6131 "This package provides miscellaneous functions to help customize ggplot2
6132 objects. High-level functions are provided to post-process ggplot2 layouts
6133 and allow alignment between plot panels, as well as setting panel sizes to
6134 fixed values. Other functions include a custom @code{geom}, and helper
6135 functions to enforce symmetric scales or add tags to facetted plots.")
6136 (license license:gpl3)))
6138 (define-public r-heatmaply
6140 (name "r-heatmaply")
6145 (uri (cran-uri "heatmaply" version))
6148 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6149 (build-system r-build-system)
6151 `(("r-assertthat" ,r-assertthat)
6152 ("r-colorspace" ,r-colorspace)
6153 ("r-dendextend" ,r-dendextend)
6155 ("r-ggplot2" ,r-ggplot2)
6156 ("r-htmlwidgets" ,r-htmlwidgets)
6157 ("r-magrittr" ,r-magrittr)
6158 ("r-plotly" ,r-plotly)
6159 ("r-rcolorbrewer" ,r-rcolorbrewer)
6160 ("r-reshape2" ,r-reshape2)
6161 ("r-scales" ,r-scales)
6162 ("r-seriation" ,r-seriation)
6163 ("r-viridis" ,r-viridis)
6164 ("r-webshot" ,r-webshot)))
6166 `(("r-knitr" ,r-knitr)))
6167 (home-page "https://cran.r-project.org/package=heatmaply")
6168 (synopsis "Interactive cluster heat maps using plotly")
6170 "This package enables you to create interactive cluster heatmaps that can
6171 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6172 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6173 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6174 a popular graphical method for visualizing high-dimensional data, in which a
6175 table of numbers is encoded as a grid of colored cells. The rows and columns
6176 of the matrix are ordered to highlight patterns and are often accompanied by
6178 ;; Either version of the license.
6179 (license (list license:gpl2 license:gpl3))))
6188 (uri (cran-uri "h5" version))
6191 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6192 (build-system r-build-system)
6197 `(("which" ,which)))
6199 `(("r-rcpp" ,r-rcpp)))
6200 (home-page "https://github.com/mannau/h5")
6201 (synopsis "Interface to the HDF5 Library")
6203 "This package provides an S4 interface to the HDF5 library supporting
6204 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6205 binary files in a language independent format. The HDF5 format can therefore
6206 be used as an alternative to R's save/load mechanism. Since h5 is able to
6207 access only subsets of stored data it can also handle data sets which do not
6209 (license license:bsd-2)))
6211 (define-public r-cgdsr
6218 (uri (cran-uri "cgdsr" version))
6221 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6222 (build-system r-build-system)
6224 `(("r-httr" ,r-httr)
6225 ("r-r-methodss3" ,r-r-methodss3)
6226 ("r-r-oo" ,r-r-oo)))
6227 (home-page "https://github.com/cBioPortal/cgdsr")
6228 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6230 "This package provides a basic set of R functions for querying the Cancer
6231 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6232 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6233 (license license:lgpl3)))
6235 (define-public r-import
6242 (uri (cran-uri "import" version))
6245 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6246 (build-system r-build-system)
6248 `(("r-knitr" ,r-knitr)))
6249 (home-page "https://github.com/smbache/import")
6250 (synopsis "Import mechanism for R")
6252 "This is an alternative mechanism for importing objects from packages.
6253 The syntax allows for importing multiple objects from a package with a single
6254 command in an expressive way. The import package bridges some of the gap
6255 between using @code{library} (or @code{require}) and direct (single-object)
6256 imports. Furthermore the imported objects are not placed in the current
6257 environment. It is also possible to import objects from stand-alone @code{.R}
6259 (license license:expat)))
6261 (define-public r-shinyace
6268 (uri (cran-uri "shinyAce" version))
6271 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6272 (properties `((upstream-name . "shinyAce")))
6273 (build-system r-build-system)
6275 `(("r-shiny" ,r-shiny)
6276 ("r-jsonlite" ,r-jsonlite)))
6277 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6278 (synopsis "Ace editor bindings for Shiny")
6280 "This package provides Ace editor bindings to enable a rich text editing
6281 environment within Shiny.")
6282 (license license:expat)))
6284 (define-public r-randomizr
6286 (name "r-randomizr")
6291 (uri (cran-uri "randomizr" version))
6294 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6295 (properties `((upstream-name . "randomizr")))
6296 (build-system r-build-system)
6298 `(("r-knitr" ,r-knitr)))
6299 (home-page "https://declaredesign.org/r/randomizr/")
6300 (synopsis "Tools for common forms of random assignment and sampling")
6302 "This package provides tools for generating random assignments for common
6303 experimental designs and random samples for common sampling designs.")
6304 (license license:expat)))
6306 (define-public r-base64url
6308 (name "r-base64url")
6313 (uri (cran-uri "base64url" version))
6316 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6317 (build-system r-build-system)
6319 `(("r-backports" ,r-backports)))
6320 (home-page "https://github.com/mllg/base64url")
6321 (synopsis "Fast and URL-safe base64 encoder and decoder")
6323 "This package provides a URL-safe base64 encoder and decoder. In
6324 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6325 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6326 encoder does not fill the string with trailing @code{=}. The resulting
6327 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6328 and thus are safe to use in URLs or for file names. The package also comes
6329 with a simple base32 encoder/decoder suited for case insensitive file
6331 (license license:gpl3)))
6333 (define-public r-radiant-data
6335 (name "r-radiant-data")
6340 (uri (cran-uri "radiant.data" version))
6343 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6344 (modules '((guix build utils)))
6347 ;; Delete files that are under CC-NC-SA.
6348 (delete-file-recursively "inst/app/tools/help")
6350 (properties `((upstream-name . "radiant.data")))
6351 (build-system r-build-system)
6353 `(("r-base64enc" ,r-base64enc)
6354 ("r-broom" ,r-broom)
6357 ("r-dplyr" ,r-dplyr)
6360 ("r-ggplot2" ,r-ggplot2)
6361 ("r-import" ,r-import)
6362 ("r-jsonlite" ,r-jsonlite)
6363 ("r-knitr" ,r-knitr)
6364 ("r-lubridate" ,r-lubridate)
6365 ("r-magrittr" ,r-magrittr)
6366 ("r-markdown" ,r-markdown)
6368 ("r-patchwork" ,r-patchwork)
6369 ("r-plotly" ,r-plotly)
6370 ("r-psych" ,r-psych)
6371 ("r-randomizr" ,r-randomizr)
6372 ("r-readr" ,r-readr)
6373 ("r-readxl" ,r-readxl)
6374 ("r-rlang" ,r-rlang)
6375 ("r-rmarkdown" ,r-rmarkdown)
6376 ("r-rstudioapi" ,r-rstudioapi)
6377 ("r-scales" ,r-scales)
6378 ("r-shiny" ,r-shiny)
6379 ("r-shinyfiles" ,r-shinyfiles)
6380 ("r-shinyace" ,r-shinyace)
6381 ("r-stringi" ,r-stringi)
6382 ("r-tibble" ,r-tibble)
6383 ("r-tidyr" ,r-tidyr)
6384 ("r-writexl" ,r-writexl)))
6385 (home-page "https://github.com/radiant-rstats/radiant.data")
6386 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6388 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6389 visualizing, summarizing, transforming, and combining data. It also contains
6390 functionality to generate reproducible reports of the analyses conducted in
6392 (license license:agpl3)))
6394 (define-public r-algdesign
6396 (name "r-algdesign")
6401 (uri (cran-uri "AlgDesign" version))
6403 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6404 (properties `((upstream-name . "AlgDesign")))
6405 (build-system r-build-system)
6406 (home-page "https://github.com/jvbraun/AlgDesign")
6407 (synopsis "Algorithmic experimental design")
6409 "This package provides tools to calculate exact and approximate theory
6410 experimental designs for D, A, and I criteria. Very large designs may be
6411 created. Experimental designs may be blocked or blocked designs created from
6412 a candidate list, using several criteria. The blocking can be done when whole
6413 and within plot factors interact.")
6414 (license license:gpl2+)))
6416 (define-public r-signal
6423 (uri (cran-uri "signal" version))
6426 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6427 (build-system r-build-system)
6428 (propagated-inputs `(("r-mass" ,r-mass)))
6429 (native-inputs `(("gfortran" ,gfortran)))
6430 (home-page "https://cran.r-project.org/web/packages/signal/")
6431 (synopsis "Signal processing")
6433 "This package provides a set of signal processing functions originally
6434 written for Matlab and GNU Octave. It includes filter generation utilities,
6435 filtering functions, resampling routines, and visualization of filter models.
6436 It also includes interpolation functions.")
6437 (license license:gpl2)))
6439 (define-public r-gsubfn
6446 (uri (cran-uri "gsubfn" version))
6449 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6450 (build-system r-build-system)
6451 (propagated-inputs `(("r-proto" ,r-proto)))
6452 (home-page "https://code.google.com/archive/p/gsubfn/")
6453 (synopsis "Utilities for strings and function arguments.")
6455 "This package provides @code{gsubfn} which is like @code{gsub} but can
6456 take a replacement function or certain other objects instead of the
6457 replacement string. Matches and back references are input to the replacement
6458 function and replaced by the function output. @code{gsubfn} can be used to
6459 split strings based on content rather than delimiters and for quasi-perl-style
6460 string interpolation. The package also has facilities for translating
6461 formulas to functions and allowing such formulas in function calls instead of
6463 (license license:gpl2+)))
6465 (define-public r-sqldf
6472 (uri (cran-uri "sqldf" version))
6475 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6476 (build-system r-build-system)
6478 `(("r-chron" ,r-chron)
6480 ("r-gsubfn" ,r-gsubfn)
6481 ("r-proto" ,r-proto)
6482 ("r-rsqlite" ,r-rsqlite)))
6483 (home-page "https://github.com/ggrothendieck/sqldf")
6484 (synopsis "Manipulate R data frames using SQL")
6486 "The @code{sqldf} function is typically passed a single argument which is
6487 an SQL select statement where the table names are ordinary R data frame names.
6488 @code{sqldf} transparently sets up a database, imports the data frames into
6489 that database, performs the SQL statement and returns the result using a
6490 heuristic to determine which class to assign to each column of the returned
6491 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6492 used to read filtered files into R even if the original files are larger than
6493 R itself can handle.")
6494 (license license:gpl2)))
6496 (define-public r-abind
6503 (uri (cran-uri "abind" version))
6506 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6507 (build-system r-build-system)
6508 (home-page "https://cran.r-project.org/web/packages/abind/")
6509 (synopsis "Combine multidimensional arrays")
6511 "This package provides tools to combine multidimensional arrays into a
6512 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6513 works with vectors, matrices, and higher-dimensional arrays. It also provides
6514 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6515 extracting and replacing data in arrays.")
6516 (license license:lgpl2.0+)))
6518 (define-public r-prroc
6525 (uri (cran-uri "PRROC" version))
6528 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6529 (properties `((upstream-name . "PRROC")))
6530 (build-system r-build-system)
6531 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6532 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6534 "This package computes the areas under the @dfn{precision-recall} (PR)
6535 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6536 contrast to other implementations, the interpolation between points of the PR
6537 curve is done by a non-linear piecewise function. In addition to the areas
6538 under the curves, the curves themselves can also be computed and plotted by a
6539 specific S3-method.")
6540 (license license:gpl3)))
6542 (define-public r-vim
6549 (uri (cran-uri "VIM" version))
6552 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6553 (properties `((upstream-name . "VIM")))
6554 (build-system r-build-system)
6557 ("r-colorspace" ,r-colorspace)
6558 ("r-data-table" ,r-data-table)
6559 ("r-e1071" ,r-e1071)
6560 ("r-laeken" ,r-laeken)
6561 ("r-magrittr" ,r-magrittr)
6564 ("r-ranger" ,r-ranger)
6566 ("r-robustbase" ,r-robustbase)
6570 `(("r-knitr" ,r-knitr)))
6571 (home-page "https://github.com/alexkowa/VIM")
6572 (synopsis "Visualization and imputation of missing values")
6574 "This package provides tools for the visualization of missing and/or
6575 imputed values are introduced, which can be used for exploring the data and
6576 the structure of the missing and/or imputed values. Depending on this
6577 structure of the missing values, the corresponding methods may help to
6578 identify the mechanism generating the missing values and explore the
6579 data including missing values. In addition, the quality of imputation can be
6580 visually explored using various univariate, bivariate, multiple and
6581 multivariate plot methods.")
6582 (license license:gpl2+)))
6584 (define-public r-fnn
6591 (uri (cran-uri "FNN" version))
6594 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6595 (properties `((upstream-name . "FNN")))
6596 (build-system r-build-system)
6597 (home-page "https://cran.r-project.org/web/packages/FNN")
6598 (synopsis "Fast nearest neighbor search algorithms and applications")
6600 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6601 search algorithms. Related applications including KNN classification,
6602 regression and information measures are implemented.")
6603 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6604 ;; later can be used.
6605 (license license:gpl2+)))
6607 (define-public r-smoother
6614 (uri (cran-uri "smoother" version))
6617 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6618 (build-system r-build-system)
6620 `(("r-ttr" ,r-ttr)))
6621 (home-page "https://cran.r-project.org/web/packages/smoother")
6622 (synopsis "Functions relating to the smoothing of numerical data")
6624 "This package provides a collection of methods for smoothing numerical
6625 data, commencing with a port of the Matlab gaussian window smoothing function.
6626 In addition, several functions typically used in smoothing of financial data
6628 (license license:gpl2)))
6630 (define-public r-riverplot
6632 (name "r-riverplot")
6637 (uri (cran-uri "riverplot" version))
6640 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6641 (build-system r-build-system)
6643 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6645 `(("r-knitr" ,r-knitr)))
6646 (home-page "https://logfc.wordpress.com")
6647 (synopsis "Sankey or ribbon plots")
6649 "Sankey plots are a type of diagram that is convenient to illustrate how
6650 flow of information, resources etc. separates and joins, much like observing
6651 how rivers split and merge. For example, they can be used to compare
6652 different clusterings. This package provides an implementation of Sankey
6654 (license license:gpl2+)))
6656 (define-public r-dyn
6663 (uri (cran-uri "dyn" version))
6666 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6667 (build-system r-build-system)
6669 `(("r-zoo" ,r-zoo)))
6670 (home-page "https://cran.r-project.org/web/packages/dyn")
6671 (synopsis "Time series regression")
6673 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6674 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6675 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6676 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6677 @code{randomForest::randomForest()} and other regression functions, allowing
6678 those functions to be used with time series including specifications that may
6679 contain lags, diffs and missing values.")
6681 (license license:gpl2+)))
6683 (define-public r-catdap
6690 (uri (cran-uri "catdap" version))
6693 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6694 (build-system r-build-system)
6696 `(("gfortran" ,gfortran)))
6697 (home-page "https://cran.r-project.org/web/packages/catdap/")
6698 (synopsis "Tools for categorical data analysis")
6700 "This package provides functions for analyzing multivariate data.
6701 Dependencies of the distribution of the specified variable (response
6702 variable) to other variables (explanatory variables) are derived and
6703 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6704 (license license:gpl2+)))
6706 (define-public r-arules
6713 (uri (cran-uri "arules" version))
6716 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6717 (build-system r-build-system)
6719 `(("r-matrix" ,r-matrix)))
6720 (home-page "https://github.com/mhahsler/arules")
6721 (synopsis "Mining association rules and frequent itemsets")
6723 "This package provides an infrastructure for representing, manipulating
6724 and analyzing transaction data and patterns (frequent itemsets and association rules).
6725 It also provides C implementations of the association mining algorithms Apriori
6727 (license license:gpl3)))
6729 (define-public r-parsedate
6731 (name "r-parsedate")
6736 (uri (cran-uri "parsedate" version))
6739 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6740 (build-system r-build-system)
6742 `(("r-rematch2" ,r-rematch2)))
6743 (home-page "https://github.com/gaborcsardi/parsedate")
6745 "Recognize and parse dates in various formats")
6747 "This package provides three functions for dealing with dates:
6748 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6749 time formats, @code{parse_date} parses dates in unspecified formats,
6750 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6751 (license license:gpl2)))
6753 (define-public r-abc-data
6760 (uri (cran-uri "abc.data" version))
6763 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6764 (properties `((upstream-name . "abc.data")))
6765 (build-system r-build-system)
6766 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6767 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6769 "This package contains data which are used by functions of the abc
6770 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6771 algorithms for performing parameter estimation, model selection, and
6773 (license license:gpl3+)))
6775 (define-public r-abc
6782 (uri (cran-uri "abc" version))
6785 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6786 (build-system r-build-system)
6788 `(("r-abc-data" ,r-abc-data)
6789 ("r-locfit" ,r-locfit)
6792 ("r-quantreg" ,r-quantreg)))
6793 (home-page "https://cran.r-project.org/web/packages/abc/")
6794 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6796 "This package implements several @dfn{Approximate Bayesian
6797 Computation} (ABC) algorithms for performing parameter estimation, model
6798 selection, and goodness-of-fit. Cross-validation tools are also available for
6799 measuring the accuracy of ABC estimates, and to calculate the
6800 misclassification probabilities of different models.")
6801 (license license:gpl3+)))
6803 (define-public r-zip
6810 (uri (cran-uri "zip" version))
6813 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6814 (build-system r-build-system)
6815 (home-page "https://github.com/gaborcsardi/zip")
6816 (synopsis "Cross-platform Zip compression")
6818 "This package provides a cross-platform Zip compression library for R.
6819 It is a replacement for the @code{zip} function, that does not require any
6820 additional external tools on any platform.")
6821 (license license:cc0)))
6823 (define-public r-openxlsx
6830 (uri (cran-uri "openxlsx" version))
6833 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6834 (build-system r-build-system)
6836 `(("r-rcpp" ,r-rcpp)
6837 ("r-stringi" ,r-stringi)
6840 `(("r-knitr" ,r-knitr)))
6841 (home-page "https://github.com/awalker89/openxlsx")
6842 (synopsis "Read, write and edit XLSX files")
6844 "This package simplifies the creation of Excel @code{.xlsx} files by
6845 providing a high level interface to writing, styling and editing worksheets.
6846 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6847 and @code{XLConnect} packages with the added benefit of removing the
6848 dependency on Java.")
6849 (license license:gpl3)))
6851 (define-public r-rio
6858 (uri (cran-uri "rio" version))
6861 "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d"))))
6862 (build-system r-build-system)
6864 `(("r-curl" ,r-curl)
6865 ("r-data-table" ,r-data-table)
6866 ("r-foreign" ,r-foreign)
6867 ("r-haven" ,r-haven)
6868 ("r-openxlsx" ,r-openxlsx)
6869 ("r-readxl" ,r-readxl)
6870 ("r-tibble" ,r-tibble)))
6872 `(("r-knitr" ,r-knitr)))
6873 (home-page "https://github.com/leeper/rio")
6874 (synopsis "Swiss-army knife for data I/O")
6876 "This package provides streamlined data import and export infrastructure
6877 by making assumptions that the user is probably willing to make: @code{import}
6878 and @code{export} determine the data structure from the file extension,
6879 reasonable defaults are used for data import and export (e.g.,
6880 @code{stringsAsFactors=FALSE}), web-based import is natively
6881 supported (including from SSL/HTTPS), compressed files can be read directly
6882 without explicit decompression, and fast import packages are used where
6883 appropriate. An additional convenience function, @code{convert}, provides a
6884 simple method for converting between file types.")
6885 (license license:gpl2)))
6887 (define-public r-maptools
6894 (uri (cran-uri "maptools" version))
6897 "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l"))))
6898 (build-system r-build-system)
6900 `(("r-foreign" ,r-foreign)
6901 ("r-lattice" ,r-lattice)
6903 (home-page "https://r-forge.r-project.org/projects/maptools/")
6904 (synopsis "Tools for reading and handling spatial objects")
6906 "This package provides a set of tools for manipulating and reading
6907 geographic data, in particular ESRI Shapefiles. It includes binary access to
6908 GSHHG shoreline files. The package also provides interface wrappers for
6909 exchanging spatial objects with other R packages.")
6910 ;; The C source files from shapelib are released under the Expat license.
6911 ;; The R code is released under GPL version 2 or later.
6912 (license (list license:gpl2+
6915 (define-public r-later
6922 (uri (cran-uri "later" version))
6925 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6926 (build-system r-build-system)
6930 ("r-rlang" ,r-rlang)))
6932 `(("r-knitr" ,r-knitr)))
6933 (home-page "https://github.com/r-lib/later")
6934 (synopsis "Utilities for delaying function execution")
6936 "This package provides tools to execute arbitrary R or C functions some
6937 time after the current time, after the R execution stack has emptied.")
6938 (license license:gpl2+)))
6940 (define-public r-promises
6947 (uri (cran-uri "promises" version))
6950 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
6951 (build-system r-build-system)
6953 `(("r-later" ,r-later)
6954 ("r-magrittr" ,r-magrittr)
6957 ("r-rlang" ,r-rlang)))
6959 `(("r-knitr" ,r-knitr)))
6960 (home-page "https://rstudio.github.io/promises")
6961 (synopsis "Abstractions for promise-based asynchronous programming")
6963 "This package provides fundamental abstractions for doing asynchronous
6964 programming in R using promises. Asynchronous programming is useful for
6965 allowing a single R process to orchestrate multiple tasks in the background
6966 while also attending to something else. Semantics are similar to JavaScript
6967 promises, but with a syntax that is idiomatic R.")
6968 (license license:expat)))
6970 (define-public r-dosnow
6977 (uri (cran-uri "doSNOW" version))
6980 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6981 (properties `((upstream-name . "doSNOW")))
6982 (build-system r-build-system)
6984 `(("r-foreach" ,r-foreach)
6985 ("r-iterators" ,r-iterators)
6986 ("r-snow" ,r-snow)))
6987 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6988 (synopsis "Foreach parallel adaptor for the snow package")
6990 "This package provides a parallel backend for the @code{%dopar%} function
6991 using the @code{snow} package.")
6992 (license license:gpl2)))
6994 (define-public r-fst
7001 (uri (cran-uri "fst" version))
7004 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7005 (properties `((upstream-name . "fst")))
7006 (build-system r-build-system)
7007 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7008 (home-page "http://www.fstpackage.org")
7009 (synopsis "Fast serialization of data frames")
7011 "The fst package for R provides a fast, easy and flexible way to
7012 serialize data frames. With access speeds of multiple GB/s, fst is
7013 specifically designed to unlock the potential of high speed solid state disks.
7014 Data frames stored in the fst format have full random access, both in column
7015 and rows. The fst format allows for random access of stored data and
7016 compression with the LZ4 and ZSTD compressors.")
7017 (license license:agpl3)))
7019 (define-public r-snowfall
7022 (version "1.84-6.1")
7025 (uri (cran-uri "snowfall" version))
7027 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7028 (build-system r-build-system)
7030 `(("r-snow" ,r-snow)))
7031 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7032 (synopsis "Easier cluster computing")
7033 (description "This package is a usability wrapper around snow for easier
7034 development of parallel R programs. This package offers e.g. extended error
7035 checks, and additional functions. All functions work in sequential mode, too,
7036 if no cluster is present or wished. The package is also designed as connector
7037 to the cluster management tool @code{sfCluster}, but can also used without
7039 (license license:gpl2+)))
7041 (define-public r-rgexf
7048 (uri (cran-uri "rgexf" version))
7051 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7054 ;; Delete minified JavaScript files
7055 (for-each delete-file
7056 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7057 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7058 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7060 (properties `((upstream-name . "rgexf")))
7061 (build-system r-build-system)
7063 `(#:modules ((guix build utils)
7064 (guix build r-build-system)
7068 (modify-phases %standard-phases
7069 (add-after 'unpack 'process-javascript
7070 (lambda* (#:key inputs #:allow-other-keys)
7071 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7072 (with-directory-excursion "inst/gexf-js/js/"
7076 `((,(assoc-ref inputs "js-jquery")
7077 "jquery-2.0.2.min.js")
7078 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7079 "jquery-ui-1.10.3.custom.min.js")
7080 (,(assoc-ref inputs "js-jquery-mousewheel")
7081 "jquery.mousewheel.min.js"))))
7082 (lambda (sources targets)
7083 (for-each (lambda (source target)
7084 (format #true "Processing ~a --> ~a~%"
7086 (invoke "esbuild" source "--minify"
7087 (string-append "--outfile=" target)))
7091 `(("r-igraph" ,r-igraph)
7092 ("r-servr" ,r-servr)
7095 `(("r-knitr" ,r-knitr)
7096 ("esbuild" ,esbuild)
7101 (uri "https://code.jquery.com/jquery-2.0.2.js")
7104 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7108 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7111 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7112 ("js-jquery-mousewheel"
7115 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7116 3.0.6/jquery.mousewheel.js")
7119 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7120 (home-page "https://gvegayon.github.io/rgexf")
7121 (synopsis "Build, import and export GEXF graph files")
7123 "Create, read and write GEXF (Graph Exchange XML Format) graph
7124 files (used in Gephi and others). It allows the user to easily build/read
7125 graph files including attributes, GEXF visual attributes (such as color, size,
7126 and position), network dynamics (for both edges and nodes) and edge weighting.
7127 Users can build/handle graphs element-by-element or massively through
7128 data-frames, visualize the graph on a web browser through gexf-js (a
7129 JavaScript library) and interact with the igraph package.")
7130 (license license:expat)))
7132 (define-public r-data-tree
7134 (name "r-data-tree")
7139 (uri (cran-uri "data.tree" version))
7142 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7143 (properties `((upstream-name . "data.tree")))
7144 (build-system r-build-system)
7147 ("r-stringi" ,r-stringi)))
7149 `(("r-knitr" ,r-knitr)))
7150 (home-page "https://github.com/gluc/data.tree")
7151 (synopsis "General purpose hierarchical data structure")
7153 "Create tree structures from hierarchical data, and traverse the tree in
7154 various orders. Aggregate, cumulate, print, plot, convert to and from
7155 data.frame and more. This is useful for decision trees, machine learning,
7156 finance, conversion from and to JSON, and many other applications.")
7157 (license license:gpl2+)))
7159 (define-public r-collapsibletree
7161 (name "r-collapsibletree")
7166 (uri (cran-uri "collapsibleTree" version))
7169 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7172 ;; Delete minified JavaScript file
7173 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7176 `((upstream-name . "collapsibleTree")))
7177 (build-system r-build-system)
7180 (modify-phases %standard-phases
7181 (add-after 'unpack 'process-javascript
7182 (lambda* (#:key inputs #:allow-other-keys)
7183 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7184 (let ((source (assoc-ref inputs "d3.v4.js"))
7185 (target "d3.min.js"))
7186 (format #t "Processing ~a --> ~a~%"
7188 (invoke "esbuild" source "--minify"
7189 (string-append "--outfile=" target)))))))))
7191 `(("r-data-tree" ,r-data-tree)
7192 ("r-htmlwidgets" ,r-htmlwidgets)))
7194 `(("esbuild" ,esbuild)
7198 (uri "https://d3js.org/d3.v4.js")
7201 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7202 (home-page "https://github.com/AdeelK93/collapsibleTree")
7203 (synopsis "Interactive collapsible tree diagrams using D3.js")
7205 "This is a package for interactive Reingold-Tilford tree diagrams created
7206 using D3.js, where every node can be expanded and collapsed by clicking on it.
7207 Tooltips and color gradients can be mapped to nodes using a numeric column in
7208 the source data frame.")
7209 (license license:gpl3+)))
7211 (define-public r-rappdirs
7218 (uri (cran-uri "rappdirs" version))
7221 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7222 (build-system r-build-system)
7223 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7224 (synopsis "Determine where to save data, caches, and logs")
7226 "This package provides an easy way to determine which directories on the
7227 user's computer should be used to save data, caches and logs. It is a port of
7228 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7229 (license license:expat)))
7231 (define-public r-rastervis
7233 (name "r-rastervis")
7238 (uri (cran-uri "rasterVis" version))
7241 "0m7fjd53apxim0d0rjnyzc28vmfcg4spcrn0zbnk8llillxji1hi"))))
7242 (properties `((upstream-name . "rasterVis")))
7243 (build-system r-build-system)
7245 `(("r-hexbin" ,r-hexbin)
7246 ("r-lattice" ,r-lattice)
7247 ("r-latticeextra" ,r-latticeextra)
7248 ("r-raster" ,r-raster)
7249 ("r-rcolorbrewer" ,r-rcolorbrewer)
7251 ("r-terra" ,r-terra)
7252 ("r-viridislite" ,r-viridislite)
7254 (home-page "https://oscarperpinan.github.io/rastervis/")
7255 (synopsis "Visualization methods for raster data")
7257 "This package provides methods for enhanced visualization and interaction
7258 with raster data. It implements visualization methods for quantitative data
7259 and categorical data, both for univariate and multivariate rasters. It also
7260 provides methods to display spatiotemporal rasters, and vector fields.")
7261 (license license:gpl3)))
7263 (define-public r-rentrez
7270 (uri (cran-uri "rentrez" version))
7273 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7274 (properties `((upstream-name . "rentrez")))
7275 (build-system r-build-system)
7277 `(("r-httr" ,r-httr)
7278 ("r-jsonlite" ,r-jsonlite)
7281 `(("r-knitr" ,r-knitr)))
7282 (home-page "https://docs.ropensci.org/rentrez/")
7283 (synopsis "Entrez in R")
7285 "This package provides an R interface to the NCBI's EUtils API,
7286 allowing users to search databases like GenBank PubMed, process the results of
7287 those searches and pull data into their R sessions.")
7288 (license license:expat)))
7290 (define-public r-renv
7297 (uri (cran-uri "renv" version))
7300 "16n2dz9jibc03f7q1wrzxss6l5jmaks7m2lnli9dz9anvcmxbdia"))))
7301 (properties `((upstream-name . "renv")))
7302 (build-system r-build-system)
7304 `(("r-knitr" ,r-knitr)))
7305 (home-page "https://rstudio.github.io/renv")
7306 (synopsis "Project environments")
7308 "This package provides a dependency management toolkit for R. Using
7309 renv, you can create and manage project-local R libraries, save the state of
7310 these libraries to a lockfile, and later restore your library as required.
7311 Together, these tools can help make your projects more isolated, portable, and
7313 (license license:expat)))
7315 (define-public r-learnr
7322 (uri (cran-uri "learnr" version))
7325 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7326 (build-system r-build-system)
7328 `(("r-checkmate" ,r-checkmate)
7329 ("r-ellipsis" ,r-ellipsis)
7330 ("r-evaluate" ,r-evaluate)
7331 ("r-htmltools" ,r-htmltools)
7332 ("r-htmlwidgets" ,r-htmlwidgets)
7333 ("r-jsonlite" ,r-jsonlite)
7334 ("r-knitr" ,r-knitr)
7335 ("r-markdown" ,r-markdown)
7336 ("r-rappdirs" ,r-rappdirs)
7338 ("r-rmarkdown" ,r-rmarkdown)
7339 ("r-rprojroot" ,r-rprojroot)
7340 ("r-shiny" ,r-shiny)
7341 ("r-withr" ,r-withr)))
7342 (home-page "https://rstudio.github.io/learnr/")
7343 (synopsis "Interactive tutorials for R")
7345 "This package provides tools to create interactive tutorials using R
7346 Markdown. Use a combination of narrative, figures, videos, exercises, and
7347 quizzes to create self-paced tutorials for learning about R and R packages.")
7348 (license license:asl2.0)))
7350 (define-public r-analytics
7352 (name "r-analytics")
7357 (uri (cran-uri "analytics" version))
7360 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7361 (build-system r-build-system)
7364 ("r-cluster" ,r-cluster)
7365 ("r-fractal" ,r-fractal)
7366 ("r-lmtest" ,r-lmtest)
7369 ("r-powerplus" ,r-powerplus)
7370 ("r-robust" ,r-robust)
7371 ("r-trend" ,r-trend)
7375 (home-page "https://cran.r-project.org/web/packages/analytics/")
7376 (synopsis "Collection of data analysis tools")
7378 "This package is a collection of data analysis tools. It includes tools
7379 for regression outlier detection in a fitted linear model, stationary
7380 bootstrap using a truncated geometric distribution, a comprehensive test for
7381 weak stationarity, column means by group, weighted biplots, and a heuristic to
7382 obtain a better initial configuration in non-metric MDS.")
7383 (license license:gpl2)))
7385 (define-public r-reticulate
7387 (name "r-reticulate")
7392 (uri (cran-uri "reticulate" version))
7395 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7396 (build-system r-build-system)
7397 (inputs `(("python" ,python)))
7399 `(("r-rappdirs" ,r-rappdirs)
7400 ("r-jsonlite" ,r-jsonlite)
7401 ("r-matrix" ,r-matrix)
7402 ("r-rcpp" ,r-rcpp)))
7404 `(("r-knitr" ,r-knitr)))
7405 (home-page "https://github.com/rstudio/reticulate")
7406 (synopsis "R interface to Python")
7408 "This package provides an interface from R to Python modules, classes,
7409 and functions. When calling into Python, R data types are automatically
7410 converted to their equivalent Python types. When values are returned from
7411 Python to R they are converted back to R types.")
7412 (license license:asl2.0)))
7414 (define-public r-bibtex
7421 (uri (cran-uri "bibtex" version))
7424 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7425 (build-system r-build-system)
7426 (propagated-inputs `(("r-stringr" ,r-stringr)))
7427 (home-page "https://github.com/romainfrancois/bibtex")
7428 (synopsis "Bibtex parser")
7429 (description "This package provides a utility for R to parse a bibtex
7431 (license license:gpl2+)))
7433 (define-public r-ggseqlogo
7435 (name "r-ggseqlogo")
7440 (uri (cran-uri "ggseqlogo" version))
7443 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7444 (build-system r-build-system)
7445 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7446 (home-page "https://github.com/omarwagih/ggseqlogo")
7447 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7449 "The range of functions provided by this package makes it possible to
7450 draw highly versatile genomic sequence logos. Features include, but are not
7451 limited to, modifying colour schemes and fonts used to draw the logo,
7452 generating multiple logo plots, and aiding the visualisation with annotations.
7453 Sequence logos can easily be combined with other ggplot2 plots.")
7454 ;; Unspecified version of the LGPL.
7455 (license license:lgpl3+)))
7457 (define-public r-ggsci
7464 (uri (cran-uri "ggsci" version))
7467 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7468 (build-system r-build-system)
7470 `(("r-ggplot2" ,r-ggplot2)
7471 ("r-scales" ,r-scales)))
7472 (home-page "https://nanx.me/ggsci/")
7473 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7475 "This package provides a collection of ggplot2 color palettes inspired by
7476 plots in scientific journals, data visualization libraries, science fiction
7477 movies, and TV shows.")
7478 (license license:gpl3)))
7480 (define-public r-ggsignif
7487 (uri (cran-uri "ggsignif" version))
7490 "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh"))))
7491 (build-system r-build-system)
7493 `(("r-knitr" ,r-knitr)))
7495 `(("r-ggplot2" ,r-ggplot2)))
7496 (home-page "https://github.com/const-ae/ggsignif")
7497 (synopsis "Significance brackets for ggplot2")
7499 "Enrich your ggplots with group-wise comparisons. This package provides
7500 an easy way to indicate if two groups are significantly different. Commonly
7501 this is shown by a bracket on top connecting the groups of interest which
7502 itself is annotated with the level of significance. The package provides a
7503 single layer that takes the groups for comparison and the test as arguments
7504 and adds the annotation to the plot.")
7505 (license license:gpl3)))
7507 (define-public r-rstatix
7514 (uri (cran-uri "rstatix" version))
7517 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
7518 (properties `((upstream-name . "rstatix")))
7519 (build-system r-build-system)
7521 `(("r-broom" ,r-broom)
7523 ("r-corrplot" ,r-corrplot)
7524 ("r-dplyr" ,r-dplyr)
7525 ("r-generics" ,r-generics)
7526 ("r-magrittr" ,r-magrittr)
7527 ("r-purrr" ,r-purrr)
7528 ("r-rlang" ,r-rlang)
7529 ("r-tibble" ,r-tibble)
7530 ("r-tidyr" ,r-tidyr)
7531 ("r-tidyselect" ,r-tidyselect)))
7532 (home-page "https://rpkgs.datanovia.com/rstatix/")
7533 (synopsis "Pipe-friendly framework for basic statistical tests")
7535 "This package provides a simple and intuitive pipe-friendly framework,
7536 coherent with the @code{tidyverse} design philosophy, for performing basic
7537 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7538 correlation analyses. The output of each test is automatically transformed
7539 into a tidy data frame to facilitate visualization. Additional functions are
7540 available for reshaping, reordering, manipulating and visualizing correlation
7542 (license license:gpl2)))
7544 (define-public r-ggpubr
7551 (uri (cran-uri "ggpubr" version))
7554 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7555 (build-system r-build-system)
7557 `(("r-cowplot" ,r-cowplot)
7558 ("r-dplyr" ,r-dplyr)
7559 ("r-ggplot2" ,r-ggplot2)
7560 ("r-ggrepel" ,r-ggrepel)
7561 ("r-ggsci" ,r-ggsci)
7562 ("r-ggsignif" ,r-ggsignif)
7564 ("r-gridextra" ,r-gridextra)
7565 ("r-magrittr" ,r-magrittr)
7566 ("r-polynom" ,r-polynom)
7567 ("r-purrr" ,r-purrr)
7568 ("r-rlang" ,r-rlang)
7569 ("r-scales" ,r-scales)
7570 ("r-rstatix" ,r-rstatix)
7571 ("r-tibble" ,r-tibble)
7572 ("r-tidyr" ,r-tidyr)))
7573 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7574 (synopsis "ggplot2-based publication-ready plots")
7576 "The ggplot2 package is an excellent and flexible package for elegant
7577 data visualization in R. However the default generated plots require some
7578 formatting before we can send them for publication. The ggpubr package
7579 provides some easy-to-use functions for creating and customizing ggplot2-based
7580 publication-ready plots.")
7581 (license license:gpl2)))
7583 (define-public r-ellipse
7590 (uri (cran-uri "ellipse" version))
7593 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7594 (build-system r-build-system)
7595 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7596 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7598 "This package contains various routines for drawing ellipses and
7599 ellipse-like confidence regions, implementing the plots described in Murdoch
7600 and Chow (1996), A graphical display of large correlation matrices, The
7601 American Statistician 50, 178-180. There are also routines implementing the
7602 profile plots described in Bates and Watts (1988), Nonlinear Regression
7603 Analysis and its Applications.")
7604 (license license:gpl2+)))
7606 (define-public r-flashclust
7608 (name "r-flashclust")
7613 (uri (cran-uri "flashClust" version))
7616 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7617 (properties `((upstream-name . "flashClust")))
7618 (build-system r-build-system)
7619 (native-inputs `(("gfortran" ,gfortran)))
7620 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7621 (synopsis "Implementation of optimal hierarchical clustering")
7623 "This package provides a fast implementation of hierarchical
7625 (license license:gpl2+)))
7627 (define-public r-factominer
7629 (name "r-factominer")
7634 (uri (cran-uri "FactoMineR" version))
7637 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7638 (properties `((upstream-name . "FactoMineR")))
7639 (build-system r-build-system)
7642 ("r-cluster" ,r-cluster)
7644 ("r-ellipse" ,r-ellipse)
7645 ("r-flashclust" ,r-flashclust)
7646 ("r-ggplot2" ,r-ggplot2)
7647 ("r-ggrepel" ,r-ggrepel)
7648 ("r-lattice" ,r-lattice)
7649 ("r-leaps" ,r-leaps)
7651 ("r-scatterplot3d" ,r-scatterplot3d)))
7653 `(("r-knitr" ,r-knitr)))
7654 (home-page "http://factominer.free.fr")
7655 (synopsis "Multivariate exploratory data analysis and data mining")
7657 "This package provides exploratory data analysis methods to summarize,
7658 visualize and describe datasets. The main principal component methods are
7659 available, those with the largest potential in terms of applications:
7660 principal component analysis (PCA) when variables are quantitative,
7661 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7662 variables are categorical, Multiple Factor Analysis when variables are
7663 structured in groups, etc. and hierarchical cluster analysis.")
7664 (license license:gpl2+)))
7666 (define-public r-factoextra
7668 (name "r-factoextra")
7673 (uri (cran-uri "factoextra" version))
7676 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7677 (build-system r-build-system)
7679 `(("r-abind" ,r-abind)
7680 ("r-cluster" ,r-cluster)
7681 ("r-dendextend" ,r-dendextend)
7682 ("r-factominer" ,r-factominer)
7683 ("r-ggplot2" ,r-ggplot2)
7684 ("r-ggpubr" ,r-ggpubr)
7685 ("r-ggrepel" ,r-ggrepel)
7686 ("r-reshape2" ,r-reshape2)
7687 ("r-tidyr" ,r-tidyr)))
7688 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7689 (synopsis "Extract and visualize the results of multivariate data analyses")
7691 "This package provides some easy-to-use functions to extract and
7692 visualize the output of multivariate data analyses, including
7693 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7694 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7695 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7696 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7697 packages. It contains also functions for simplifying some clustering analysis
7698 steps and provides ggplot2-based elegant data visualization.")
7699 (license license:gpl2)))
7701 (define-public r-fansi
7708 (uri (cran-uri "fansi" version))
7711 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7712 (build-system r-build-system)
7714 `(("r-knitr" ,r-knitr))) ; for vignettes
7715 (home-page "https://github.com/brodieG/fansi")
7716 (synopsis "ANSI control sequence aware string functions")
7718 "This package provides counterparts to R string manipulation functions
7719 that account for the effects of ANSI text formatting control sequences.")
7720 (license license:gpl2+)))
7722 (define-public r-nbclust
7729 (uri (cran-uri "NbClust" version))
7732 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7733 (properties `((upstream-name . "NbClust")))
7734 (build-system r-build-system)
7735 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7736 (synopsis "Determine the best number of clusters in a data set")
7738 "NbClust provides 30 indexes for determining the optimal number of
7739 clusters in a data set and offers the best clustering scheme from different
7740 results to the user.")
7741 (license license:gpl2)))
7743 (define-public r-hdf5r
7750 (uri (cran-uri "hdf5r" version))
7753 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7754 (build-system r-build-system)
7759 `(("r-bit64" ,r-bit64)
7762 `(("r-knitr" ,r-knitr)))
7763 (home-page "https://hhoeflin.github.io/hdf5r")
7764 (synopsis "Interface to the HDF5 binary data format")
7766 "HDF5 is a data model, library and file format for storing and managing
7767 large amounts of data. This package provides a nearly feature complete,
7768 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7769 functionality is added so that HDF5 objects behave very similar to their
7770 corresponding R counterparts.")
7771 (license license:asl2.0)))
7773 (define-public r-itertools
7775 (name "r-itertools")
7780 (uri (cran-uri "itertools" version))
7783 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7784 (build-system r-build-system)
7786 `(("r-iterators" ,r-iterators)))
7787 (home-page "https://cran.r-project.org/web/packages/itertools/")
7788 (synopsis "Iterator tools")
7790 "This package provides various tools for creating iterators, many
7791 patterned after functions in the Python @code{itertools} module, and others
7792 patterned after functions in the snow package.")
7793 (license license:gpl2)))
7795 (define-public r-polynom
7802 (uri (cran-uri "polynom" version))
7805 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7806 (build-system r-build-system)
7807 (home-page "https://cran.r-project.org/web/packages/polynom/")
7808 (synopsis "Functions for univariate polynomial manipulations")
7810 "This package provides a collection of functions to implement a class for
7811 univariate polynomial manipulations.")
7812 (license license:gpl2)))
7814 (define-public r-gbrd
7821 (uri (cran-uri "gbRd" version))
7824 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7825 (properties `((upstream-name . "gbRd")))
7826 (build-system r-build-system)
7827 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7828 (synopsis "Utilities for processing Rd objects and files")
7830 "This package provides utilities for processing Rd objects and files.
7831 Extract argument descriptions and other parts of the help pages of
7833 (license license:gpl2+)))
7835 (define-public r-rjags
7842 (uri (cran-uri "rjags" version))
7845 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7846 (build-system r-build-system)
7848 `(("r-coda" ,r-coda)))
7852 `(("pkg-config" ,pkg-config)))
7853 (home-page "http://mcmc-jags.sourceforge.net")
7854 (synopsis "Bayesian graphical models using MCMC")
7856 "This package provides an R interface to the JAGS MCMC library. JAGS is
7857 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7858 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7859 (license license:gpl2)))
7861 (define-public r-rbibutils
7863 (name "r-rbibutils")
7868 (uri (cran-uri "rbibutils" version))
7871 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7872 (properties `((upstream-name . "rbibutils")))
7873 (build-system r-build-system)
7874 (home-page "https://geobosh.github.io/rbibutils/")
7875 (synopsis "Convert between bibliography formats")
7877 "This package converts between a number of bibliography formats,
7878 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7879 utilities and supports all bibliography formats and character encodings
7880 implemented in bibutils.")
7881 (license license:gpl2)))
7883 (define-public r-rdpack
7890 (uri (cran-uri "Rdpack" version))
7893 "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
7894 (properties `((upstream-name . "Rdpack")))
7895 (build-system r-build-system)
7897 `(("r-rbibutils" ,r-rbibutils)))
7898 (home-page "https://github.com/GeoBosh/Rdpack")
7899 (synopsis "Update and manipulate Rd documentation objects")
7901 "This package provides functions for manipulation of R documentation
7902 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7903 updating Rd documentation for functions, methods and classes; it also includes
7904 Rd macros for citations and import of references from bibtex files for use in
7905 Rd files and roxygen2 comments, as well as many functions for manipulation of
7906 references and Rd files.")
7907 (license license:gpl2+)))
7909 (define-public r-officer
7916 (uri (cran-uri "officer" version))
7919 "1apg0dh1zfhrqcbbmm8318l40gyjbqc2l9sdvwxx7qi8mzc1mqvw"))))
7920 (build-system r-build-system)
7927 `(("r-knitr" ,r-knitr)))
7928 (home-page "https://davidgohel.github.io/officer")
7929 (synopsis "Manipulation of Word and PowerPoint documents")
7931 "This package provides tools to access and manipulate Word and PowerPoint
7932 documents from R. The package focuses on tabular and graphical reporting from
7933 R; it also provides two functions that let users get document content into
7934 data objects. A set of functions lets add and remove images, tables and
7935 paragraphs of text in new or existing documents. When working with PowerPoint
7936 presentations, slides can be added or removed; shapes inside slides can also
7937 be added or removed. When working with Word documents, a cursor can be used
7938 to help insert or delete content at a specific location in the document.")
7939 (license license:gpl3)))
7941 (define-public r-profilemodel
7943 (name "r-profilemodel")
7948 (uri (cran-uri "profileModel" version))
7951 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7952 (properties `((upstream-name . "profileModel")))
7953 (build-system r-build-system)
7954 (home-page "https://github.com/ikosmidis/profileModel")
7955 (synopsis "Profiling inference functions for various model classes")
7957 "This package provides tools that can be used to calculate, evaluate,
7958 plot and use for inference the profiles of *arbitrary* inference functions for
7959 arbitrary @code{glm}-like fitted models with linear predictors. More information
7960 on the methods that are implemented can be found in Kosmidis (2008)
7961 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7962 (license license:gpl2+)))
7964 (define-public r-brglm
7971 (uri (cran-uri "brglm" version))
7974 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7975 (properties `((upstream-name . "brglm")))
7976 (build-system r-build-system)
7978 `(("r-profilemodel" ,r-profilemodel)))
7979 (home-page "https://github.com/ikosmidis/brglm")
7980 (synopsis "Bias reduction in binomial-response generalized linear models")
7982 "Fit generalized linear models with binomial responses using either an
7983 adjusted-score approach to bias reduction or maximum penalized likelihood
7984 where penalization is by Jeffreys invariant prior. These procedures return
7985 estimates with improved frequentist properties (bias, mean squared error) that
7986 are always finite even in cases where the maximum likelihood estimates are
7987 infinite (data separation). Fitting takes place by fitting generalized linear
7988 models on iteratively updated pseudo-data. The interface is essentially the
7989 same as @code{glm}. More flexibility is provided by the fact that custom
7990 pseudo-data representations can be specified and used for model fitting.
7991 Functions are provided for the construction of confidence intervals for the
7992 reduced-bias estimates.")
7993 (license license:gpl2+)))
7995 (define-public r-entropy
8002 (uri (cran-uri "entropy" version))
8005 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8006 (properties `((upstream-name . "entropy")))
8007 (build-system r-build-system)
8008 (home-page "https://www.strimmerlab.org/software/entropy/")
8009 (synopsis "Estimation of entropy, mutual information and related quantities")
8011 "This package implements various estimators of entropy, such as the
8012 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8013 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8014 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8015 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8016 mutual information, and chi-squared statistic of independence. In addition
8017 there are functions for discretizing continuous random variables.")
8018 (license license:gpl3+)))
8020 (define-public r-abn
8027 (uri (cran-uri "abn" version))
8030 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8031 (build-system r-build-system)
8035 `(("r-lme4" ,r-lme4)
8038 ("r-rcpparmadillo" ,r-rcpparmadillo)
8039 ("r-rjags" ,r-rjags)))
8040 (home-page "https://r-bayesian-networks.org/")
8041 (synopsis "Modelling multivariate data with additive bayesian networks")
8043 "Bayesian network analysis is a form of probabilistic graphical models
8044 which derives from empirical data a directed acyclic graph, DAG, describing
8045 the dependency structure between random variables. An additive Bayesian
8046 network model consists of a form of a DAG where each node comprises a
8047 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8048 equivalent to Bayesian multivariate regression using graphical modelling, they
8049 generalises the usual multivariable regression, GLM, to multiple dependent
8050 variables. This package provides routines to help determine optimal Bayesian
8051 network models for a given data set, where these models are used to identify
8052 statistical dependencies in messy, complex data.")
8053 (license license:gpl2+)))
8055 (define-public r-acd
8062 (uri (cran-uri "ACD" version))
8065 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8066 (properties `((upstream-name . "ACD")))
8067 (build-system r-build-system)
8068 (home-page "https://cran.r-project.org/web/packages/ACD/")
8069 (synopsis "Categorical data analysis with complete or missing responses")
8071 "This package provides tools for categorical data analysis with complete
8072 or missing responses.")
8073 (license license:gpl2+)))
8075 (define-public r-acdm
8082 (uri (cran-uri "ACDm" version))
8085 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8086 (properties `((upstream-name . "ACDm")))
8087 (build-system r-build-system)
8089 `(("r-dplyr" ,r-dplyr)
8090 ("r-ggplot2" ,r-ggplot2)
8092 ("r-rsolnp" ,r-rsolnp)
8094 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8095 (synopsis "Tools for Autoregressive Conditional Duration Models")
8097 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8098 and Russell, 1998) models. It creates trade, price or volume durations from
8099 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8101 (license license:gpl2+)))
8103 (define-public r-overlap
8110 (uri (cran-uri "overlap" version))
8113 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8114 (build-system r-build-system)
8115 (home-page "https://cran.r-project.org/web/packages/overlap/")
8116 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8118 "This package provides functions to fit kernel density functions to data
8119 on temporal activity patterns of animals; estimate coefficients of overlapping
8120 of densities for two species; and calculate bootstrap estimates of confidence
8122 (license license:gpl3+)))
8124 (define-public r-snakecase
8126 (name "r-snakecase")
8131 (uri (cran-uri "snakecase" version))
8134 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8135 (build-system r-build-system)
8137 `(("r-stringi" ,r-stringi)
8138 ("r-stringr" ,r-stringr)))
8139 (home-page "https://github.com/Tazinho/snakecase")
8140 (synopsis "Convert strings into any case")
8142 "This package provides a consistent, flexible and easy to use tool to
8143 parse and convert strings into cases like snake or camel among others.")
8144 (license license:gpl3)))
8146 (define-public r-prediction
8148 (name "r-prediction")
8153 (uri (cran-uri "prediction" version))
8156 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8157 (build-system r-build-system)
8159 `(("r-data-table" ,r-data-table)))
8160 (home-page "https://github.com/leeper/prediction")
8161 (synopsis "Tidy, type-safe prediction methods")
8163 "This package provides the @code{prediction()} function, a type-safe
8164 alternative to @code{predict()} that always returns a data frame. The package
8165 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8166 from the @code{stats} package, as well as numerous other model classes from
8167 other add-on packages.")
8168 (license license:expat)))
8170 (define-public r-insight
8177 (uri (cran-uri "insight" version))
8180 "1la4yxzfl9fnknamnaziil6gvpdzl78z16lfzis9jgzg8r9q0y5l"))))
8181 (build-system r-build-system)
8183 `(("r-knitr" ,r-knitr)))
8184 (home-page "https://easystats.github.io/insight/")
8185 (synopsis "Easy access to model information for various model objects")
8187 "This package provides a tool to provide an easy, intuitive and
8188 consistent access to information contained in various R models, like model
8189 formulas, model terms, information about random effects, data that was used to
8190 fit the model or data from response variables. The package mainly revolves
8191 around two types of functions: Functions that find (the names of) information,
8192 starting with @code{find_}, and functions that get the underlying data,
8193 starting with @code{get_}. The package has a consistent syntax and works with
8194 many different model objects, where otherwise functions to access these
8195 information are missing.")
8196 (license license:gpl3)))
8198 (define-public r-sjlabelled
8200 (name "r-sjlabelled")
8205 (uri (cran-uri "sjlabelled" version))
8208 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8209 (build-system r-build-system)
8211 `(("r-insight" ,r-insight)))
8213 `(("r-knitr" ,r-knitr)))
8214 (home-page "https://github.com/strengejacke/sjlabelled")
8215 (synopsis "Labelled data utility functions")
8217 "This package provides a collection of functions dealing with labelled
8218 data, like reading and writing data between R and other statistical software
8219 packages. This includes easy ways to get, set or change value and variable
8220 label attributes, to convert labelled vectors into factors or numeric (and
8221 vice versa), or to deal with multiple declared missing values.")
8222 (license license:gpl3)))
8224 (define-public r-sjmisc
8231 (uri (cran-uri "sjmisc" version))
8234 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8235 (build-system r-build-system)
8237 `(("r-dplyr" ,r-dplyr)
8238 ("r-insight" ,r-insight)
8239 ("r-magrittr" ,r-magrittr)
8240 ("r-purrr" ,r-purrr)
8241 ("r-rlang" ,r-rlang)
8242 ("r-sjlabelled" ,r-sjlabelled)
8243 ("r-tidyselect" ,r-tidyselect)))
8245 `(("r-knitr" ,r-knitr)))
8246 (home-page "https://github.com/strengejacke/sjmisc")
8247 (synopsis "Data and variable transformation functions")
8249 "This package is a collection of miscellaneous utility functions,
8250 supporting data transformation tasks like recoding, dichotomizing or grouping
8251 variables, setting and replacing missing values. The data transformation
8252 functions also support labelled data, and all integrate seamlessly into a
8253 tidyverse workflow.")
8254 (license license:gpl3)))
8256 (define-public r-nortest
8263 (uri (cran-uri "nortest" version))
8266 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8267 (build-system r-build-system)
8268 (home-page "https://cran.r-project.org/web/packages/nortest/")
8269 (synopsis "Tests for normality")
8271 "This package provides five omnibus tests for testing the composite
8272 hypothesis of normality.")
8273 (license license:gpl2+)))
8275 (define-public r-moonbook
8282 (uri (cran-uri "moonBook" version))
8285 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8286 (properties `((upstream-name . "moonBook")))
8287 (build-system r-build-system)
8289 `(("r-magrittr" ,r-magrittr)
8290 ("r-nortest" ,r-nortest)
8291 ("r-sjmisc" ,r-sjmisc)
8292 ("r-stringr" ,r-stringr)
8293 ("r-survival" ,r-survival)
8294 ("r-ztable" ,r-ztable)))
8296 `(("r-knitr" ,r-knitr)))
8297 (home-page "https://github.com/cardiomoon/moonBook")
8298 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8300 "This package provides several analysis-related functions for the book
8301 entitled \"R statistics and graph for medical articles\" (written in Korean),
8302 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8304 (license license:gpl2)))
8306 (define-public r-flextable
8308 (name "r-flextable")
8313 (uri (cran-uri "flextable" version))
8316 "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma"))))
8317 (build-system r-build-system)
8319 `(("r-base64enc" ,r-base64enc)
8320 ("r-data-table" ,r-data-table)
8321 ("r-gdtools" ,r-gdtools)
8322 ("r-htmltools" ,r-htmltools)
8323 ("r-knitr" ,r-knitr)
8324 ("r-officer" ,r-officer)
8325 ("r-rlang" ,r-rlang)
8326 ("r-rmarkdown" ,r-rmarkdown)
8328 ("r-xml2" ,r-xml2)))
8330 `(("r-knitr" ,r-knitr)))
8331 (home-page "https://davidgohel.github.io/flextable")
8332 (synopsis "Functions for tabular reporting")
8334 "This package provides tools to create pretty tables for HTML documents
8335 and other formats. Functions are provided to let users create tables, modify
8336 and format their content. It extends the @code{officer} package and can be
8337 used within R markdown documents when rendering to HTML and to Word
8339 (license license:gpl3)))
8341 (define-public r-writexl
8348 (uri (cran-uri "writexl" version))
8351 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8352 (build-system r-build-system)
8353 (inputs `(("zlib" ,zlib)))
8354 (home-page "https://github.com/ropensci/writexl")
8355 (synopsis "Export data frames to xlsx format")
8357 "This package provides a data frame to xlsx exporter based on
8359 (license license:bsd-2)))
8361 (define-public r-biasedurn
8363 (name "r-biasedurn")
8368 (uri (cran-uri "BiasedUrn" version))
8371 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8372 (properties `((upstream-name . "BiasedUrn")))
8373 (build-system r-build-system)
8374 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8375 (synopsis "Biased Urn model distributions")
8377 "This package provides statistical models of biased sampling in the form
8378 of univariate and multivariate noncentral hypergeometric distributions,
8379 including Wallenius' noncentral hypergeometric distribution and Fisher's
8380 noncentral hypergeometric distribution (also called extended hypergeometric
8382 (license license:gpl3)))
8384 (define-public r-goplot
8391 (uri (cran-uri "GOplot" version))
8394 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8395 (properties `((upstream-name . "GOplot")))
8396 (build-system r-build-system)
8398 `(("r-ggdendro" ,r-ggdendro)
8399 ("r-ggplot2" ,r-ggplot2)
8400 ("r-gridextra" ,r-gridextra)
8401 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8402 (home-page "https://github.com/wencke/wencke.github.io")
8403 (synopsis "Visualization of functional analysis data")
8405 "This package provides an implementation of multilayered visualizations
8406 for enhanced graphical representation of functional analysis data. It
8407 combines and integrates omics data derived from expression and functional
8408 annotation enrichment analyses. Its plotting functions have been developed
8409 with an hierarchical structure in mind: starting from a general overview to
8410 identify the most enriched categories (modified bar plot, bubble plot) to a
8411 more detailed one displaying different types of relevant information for the
8412 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8413 Venn diagram, heatmap).")
8414 (license license:gpl2)))
8416 (define-public r-getopt
8423 (uri (cran-uri "getopt" version))
8426 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8427 (build-system r-build-system)
8428 (home-page "https://github.com/trevorld/getopt")
8429 (synopsis "Command-line option processor for R")
8431 "This package is designed to be used with Rscript to write shebang
8432 scripts that accept short and long options. Many users will prefer to
8433 use the packages @code{optparse} or @code{argparse} which add extra
8434 features like automatically generated help options and usage texts,
8435 support for default values, positional argument support, etc.")
8436 (license license:gpl2+)))
8438 (define-public r-findpython
8440 (name "r-findpython")
8445 (uri (cran-uri "findpython" version))
8448 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8449 (build-system r-build-system)
8450 (home-page "https://github.com/trevorld/findpython")
8451 (synopsis "Functions to find an acceptable Python binary")
8453 "This package was designed to find an acceptable Python binary that
8454 matches version and feature constraints.")
8455 (license license:expat)))
8457 ;; This in not the same as "r-argparser"
8458 (define-public r-argparse
8465 (uri (cran-uri "argparse" version))
8468 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8469 (build-system r-build-system)
8470 (inputs `(("python" ,python)))
8472 `(("r-findpython" ,r-findpython)
8473 ("r-jsonlite" ,r-jsonlite)
8476 `(("r-knitr" ,r-knitr)))
8477 (home-page "https://github.com/trevorld/argparse")
8478 (synopsis "Command line optional and positional argument parser")
8480 "This package provides a command line parser to be used with Rscript to
8481 write shebang scripts that gracefully accept positional and optional arguments
8482 and automatically generate usage notices.")
8483 (license license:gpl2+)))
8485 (define-public r-hash
8492 (uri (cran-uri "hash" version))
8495 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8496 (build-system r-build-system)
8497 (home-page "https://cran.r-project.org/web/packages/hash/")
8498 (synopsis "Implementation of hash/associated arrays/dictionaries")
8500 "This package implements a data structure similar to hashes in Perl and
8501 dictionaries in Python but with a purposefully R flavor. For objects of
8502 appreciable size, access using hashes outperforms native named lists and
8504 (license license:gpl2+)))
8506 (define-public r-orddom
8513 (uri (cran-uri "orddom" version))
8516 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8517 (build-system r-build-system)
8518 (propagated-inputs `(("r-psych" ,r-psych)))
8519 (home-page "https://cran.r-project.org/web/packages/orddom/")
8520 (synopsis "Ordinal dominance statistics")
8522 "This package provides tools to compute ordinal, statistics and effect
8523 sizes as an alternative to mean comparison: Cliff's delta or success rate
8524 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8525 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8526 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8527 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8528 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8529 Group (Non-)Overlap considerations.")
8530 (license license:gpl2)))
8532 (define-public r-deriv
8539 (uri (cran-uri "Deriv" version))
8542 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
8543 (properties `((upstream-name . "Deriv")))
8544 (build-system r-build-system)
8545 (home-page "https://cran.r-project.org/web/packages/Deriv")
8546 (synopsis "Symbolic differentiation")
8548 "This package provides an R-based solution for symbolic differentiation.
8549 It admits user-defined functions as well as function substitution in arguments
8550 of functions to be differentiated. Some symbolic simplification is part of
8552 (license license:gpl3+)))
8554 (define-public r-doby
8561 (uri (cran-uri "doBy" version))
8564 "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00"))))
8565 (properties `((upstream-name . "doBy")))
8566 (build-system r-build-system)
8568 `(("r-broom" ,r-broom)
8569 ("r-deriv" ,r-deriv)
8570 ("r-dplyr" ,r-dplyr)
8571 ("r-ggplot2" ,r-ggplot2)
8572 ("r-magrittr" ,r-magrittr)
8574 ("r-matrix" ,r-matrix)
8575 ("r-pbkrtest" ,r-pbkrtest)
8576 ("r-tibble" ,r-tibble)))
8578 `(("r-knitr" ,r-knitr)))
8579 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8580 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8582 "This package contains:
8585 @item facilities for working with grouped data: @code{do}
8586 something to data stratified @code{by} some variables.
8587 @item implementations of least-squares means, general linear contrasts, and
8588 @item miscellaneous other utilities.
8590 (license license:gpl2+)))
8592 (define-public r-refgenome
8594 (name "r-refgenome")
8599 (uri (cran-uri "refGenome" version))
8602 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8603 (properties `((upstream-name . "refGenome")))
8604 (build-system r-build-system)
8608 ("r-rsqlite" ,r-rsqlite)))
8609 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8611 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8613 "This package contains functionality for importing and managing of
8614 downloaded genome annotation data from the Ensembl genome browser (European
8615 Bioinformatics Institute) and from the UCSC genome browser (University of
8616 California, Santa Cruz) and annotation routines for genomic positions and
8617 splice site positions.")
8618 (license license:gpl2)))
8620 (define-public r-basix
8627 (uri (cran-uri "BASIX" version))
8630 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8631 (properties `((upstream-name . "BASIX")))
8632 (build-system r-build-system)
8633 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8634 (synopsis "Efficient C/C++ toolset for R")
8636 "BASIX provides some efficient C/C++ implementations of native R
8637 procedures to speed up calculations in R.")
8638 (license license:gpl2)))
8640 (define-public r-blockfest
8642 (name "r-blockfest")
8647 (uri (cran-uri "BlockFeST" version))
8650 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
8651 (properties `((upstream-name . "BlockFeST")))
8652 (build-system r-build-system)
8653 (propagated-inputs `(("r-basix" ,r-basix)))
8654 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8655 (synopsis "Bayesian calculation of region-specific fixation index")
8657 "This package provides an R implementation of an extension of the
8658 BayeScan software for codominant markers, adding the option to group
8659 individual SNPs into pre-defined blocks. A typical application of this new
8660 approach is the identification of genomic regions, genes, or gene sets
8661 containing one or more SNPs that evolved under directional selection.")
8662 (license license:gpl2)))
8664 (define-public r-proc
8667 (version "1.17.0.1")
8671 (uri (cran-uri "pROC" version))
8674 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8675 (properties `((upstream-name . "pROC")))
8676 (build-system r-build-system)
8678 `(("r-plyr" ,r-plyr)
8679 ("r-rcpp" ,r-rcpp)))
8680 (home-page "https://web.expasy.org/pROC/")
8681 (synopsis "Display and analyze ROC curves")
8683 "This package provides tools for visualizing, smoothing and comparing
8684 receiver operating characteristic (ROC curves). The area under the
8685 curve (AUC) can be compared with statistical tests based on U-statistics or
8686 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8687 (license license:gpl3+)))
8689 (define-public r-rootsolve
8691 (name "r-rootsolve")
8696 (uri (cran-uri "rootSolve" version))
8699 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8700 (properties `((upstream-name . "rootSolve")))
8701 (build-system r-build-system)
8702 (native-inputs `(("gfortran" ,gfortran)))
8703 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8704 (synopsis "Tools for the analysis of ordinary differential equations")
8706 "This package provides routines to find the root of nonlinear functions,
8707 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8708 differential equations} (ODE). It includes routines that:
8711 @item generate gradient and jacobian matrices (full and banded),
8712 @item find roots of non-linear equations by the Newton-Raphson method,
8713 @item estimate steady-state conditions of a system of (differential) equations
8714 in full, banded or sparse form, using the Newton-Raphson method, or by
8715 dynamically running,
8716 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8717 and 3-D partial differential equations, that have been converted to ordinary
8718 differential equations by numerical differencing (using the method-of-lines
8721 (license license:gpl2+)))
8723 (define-public r-abcanalysis
8725 (name "r-abcanalysis")
8730 (uri (cran-uri "ABCanalysis" version))
8732 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8733 (properties `((upstream-name . "ABCanalysis")))
8734 (build-system r-build-system)
8735 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8736 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8737 (synopsis "Computed ABC Analysis")
8739 "Multivariate data sets often differ in several factors or derived statistical
8740 parameters, which have to be selected for a valid interpretation. Basing this
8741 selection on traditional statistical limits leads occasionally to the perception
8742 of losing information from a data set. This package provides tools to calculate
8743 these limits on the basis of the mathematical properties of the distribution of
8744 the analyzed items.")
8745 (license license:gpl3)))
8747 (define-public r-slam
8754 (uri (cran-uri "slam" version))
8756 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8757 (build-system r-build-system)
8758 (home-page "https://cran.r-project.org/web/packages/slam/")
8759 (synopsis "Sparse lightweight arrays and matrices")
8761 "This package contains data structures and algorithms for sparse arrays and matrices,
8762 based on index arrays and simple triplet representations, respectively.")
8763 (license license:gpl2)))
8765 (define-public r-manipulatewidget
8767 (name "r-manipulatewidget")
8772 (uri (cran-uri "manipulateWidget" version))
8774 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8776 `((upstream-name . "manipulateWidget")))
8777 (build-system r-build-system)
8779 `(("r-base64enc" ,r-base64enc)
8780 ("r-codetools" ,r-codetools)
8781 ("r-htmltools" ,r-htmltools)
8782 ("r-htmlwidgets" ,r-htmlwidgets)
8783 ("r-knitr" ,r-knitr)
8784 ("r-miniui" ,r-miniui)
8785 ("r-shiny" ,r-shiny)
8786 ("r-webshot" ,r-webshot)))
8787 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8788 (synopsis "Add even more interactivity to interactive charts")
8790 "This package lets you create in just a few lines of R code a nice user interface to
8791 modify the data or the graphical parameters of one or multiple interactive
8792 charts. It is useful to quickly explore visually some data or for package
8793 developers to generate user interfaces easy to maintain.")
8794 (license license:gpl2+)))
8803 (uri (cran-uri "A3" version))
8805 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8806 (properties `((upstream-name . "A3")))
8807 (build-system r-build-system)
8809 `(("r-pbapply" ,r-pbapply)
8810 ("r-xtable" ,r-xtable)))
8811 (home-page "https://cran.r-project.org/web/packages/A3/")
8812 (synopsis "Error metrics for predictive models")
8814 "This package supplies tools for tabulating and analyzing the results of predictive
8815 models. The methods employed are applicable to virtually any predictive model
8816 and make comparisons between different methodologies straightforward.")
8817 (license license:gpl2+)))
8819 (define-public r-infotheo
8826 (uri (cran-uri "infotheo" version))
8829 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8830 (build-system r-build-system)
8831 (home-page "http://homepage.meyerp.com/software")
8832 (synopsis "Information-theoretic measures")
8834 "This package implements various measures of information theory based on
8835 several entropy estimators.")
8836 (license license:gpl3+)))
8838 (define-public r-abcoptim
8845 (uri (cran-uri "ABCoptim" version))
8847 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8848 (properties `((upstream-name . "ABCoptim")))
8849 (build-system r-build-system)
8850 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8851 (home-page "https://github.com/gvegayon/ABCoptim/")
8852 (synopsis "Optimization of Artificial Bee Colony algorithm")
8854 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8855 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8856 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8857 algorithms, and uses only common control parameters such as colony size and
8858 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8859 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8860 This version is a work-in-progress and is written in R code.")
8861 (license license:expat)))
8863 (define-public r-abcp2
8870 (uri (cran-uri "ABCp2" version))
8872 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8873 (properties `((upstream-name . "ABCp2")))
8874 (build-system r-build-system)
8875 (propagated-inputs `(("r-mass" ,r-mass)))
8876 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8877 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8879 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8880 Poisson, and Gamma distribution and estimates the proportional paternity of the
8881 second male (P2) based on the best fit distribution.")
8882 (license license:gpl2)))
8884 (define-public r-abcrf
8891 (uri (cran-uri "abcrf" version))
8893 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8894 (build-system r-build-system)
8896 `(("r-doparallel" ,r-doparallel)
8897 ("r-foreach" ,r-foreach)
8899 ("r-matrixstats" ,r-matrixstats)
8900 ("r-ranger" ,r-ranger)
8902 ("r-rcpparmadillo" ,r-rcpparmadillo)
8903 ("r-readr" ,r-readr)
8904 ("r-stringr" ,r-stringr)))
8905 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8906 (synopsis "Approximate bayesian computation via random forests")
8908 "This package performs approximate bayesian computation (ABC) model choice and
8909 parameter inference via random forests. This machine learning tool named random
8910 forests (RF) can conduct selection among the highly complex models covered by
8912 (license license:gpl2+)))
8914 (define-public r-abctools
8921 (uri (cran-uri "abctools" version))
8923 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8924 (build-system r-build-system)
8927 ("r-abind" ,r-abind)
8928 ("r-hmisc" ,r-hmisc)
8929 ("r-plyr" ,r-plyr)))
8930 (home-page "https://github.com/dennisprangle/abctools/")
8931 (synopsis "Tools for ABC analyses")
8933 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8934 including summary statistic selection and assessing coverage. This includes
8935 recent dimension reduction algorithms to tune the choice of summary statistics,
8936 and coverage methods to tune the choice of threshold.")
8937 (license license:gpl2+)))
8939 (define-public r-ggstance
8946 (uri (cran-uri "ggstance" version))
8948 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8949 (build-system r-build-system)
8951 `(("r-ggplot2" ,r-ggplot2)
8953 ("r-rlang" ,r-rlang)
8954 ("r-withr" ,r-withr)))
8955 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8956 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8958 "This package is a @code{r-ggplot2} extension that provides flipped components:
8960 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8961 @item vertical versions of @code{r-ggplot2} positions.
8963 (license license:gpl3)))
8965 (define-public r-mosaiccore
8967 (name "r-mosaiccore")
8972 (uri (cran-uri "mosaicCore" version))
8974 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8975 (properties `((upstream-name . "mosaicCore")))
8976 (build-system r-build-system)
8978 `(("r-dplyr" ,r-dplyr)
8980 ("r-rlang" ,r-rlang)
8981 ("r-tidyr" ,r-tidyr)))
8982 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8983 (synopsis "Common utilities for mosaic family packages")
8985 "Common utilities used in other Mosaic family packages are collected here.")
8986 (license license:gpl2+)))
8988 (define-public r-labelled
8995 (uri (cran-uri "labelled" version))
8998 "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg"))))
8999 (properties `((upstream-name . "labelled")))
9000 (build-system r-build-system)
9002 `(("r-dplyr" ,r-dplyr)
9003 ("r-haven" ,r-haven)
9004 ("r-lifecycle" ,r-lifecycle)
9005 ("r-rlang" ,r-rlang)
9006 ("r-stringr" ,r-stringr)
9007 ("r-tidyr" ,r-tidyr)
9008 ("r-vctrs" ,r-vctrs)))
9010 `(("r-knitr" ,r-knitr)))
9011 (home-page "http://larmarange.github.io/labelled/")
9012 (synopsis "Manipulating labelled data")
9014 "This package provides useful functions to deal with the
9015 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9017 (license license:gpl3)))
9019 (define-public r-ggformula
9021 (name "r-ggformula")
9026 (uri (cran-uri "ggformula" version))
9028 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9029 (build-system r-build-system)
9031 `(("r-ggforce" ,r-ggforce)
9032 ("r-ggplot2" ,r-ggplot2)
9033 ("r-ggridges" ,r-ggridges)
9034 ("r-ggstance" ,r-ggstance)
9035 ("r-labelled" ,r-labelled)
9036 ("r-magrittr" ,r-magrittr)
9037 ("r-mosaiccore" ,r-mosaiccore)
9038 ("r-rlang" ,r-rlang)
9039 ("r-scales" ,r-scales)
9040 ("r-stringr" ,r-stringr)
9041 ("r-tibble" ,r-tibble)))
9043 `(("r-knitr" ,r-knitr)))
9044 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9045 (synopsis "Formula interface for the @code{r-ggplot2}")
9047 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9048 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9049 and extends the excellent simplicity of the lattice-graphics formula interface,
9050 while providing the intuitive capabilities of @code{r-ggplot2}.")
9051 (license license:expat)))
9053 (define-public r-mosaicdata
9055 (name "r-mosaicdata")
9060 (uri (cran-uri "mosaicData" version))
9062 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9063 (properties `((upstream-name . "mosaicData")))
9064 (build-system r-build-system)
9065 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9066 (synopsis "Data sets for project Mosaic")
9068 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9069 used to teach mathematics, statistics, computation and modeling.")
9070 (license license:gpl2+)))
9072 (define-public r-raster
9079 (uri (cran-uri "raster" version))
9082 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9083 (build-system r-build-system)
9085 `(("r-rcpp" ,r-rcpp)
9087 (home-page "https://www.rspatial.org/")
9088 (synopsis "Geographic data analysis and modeling")
9090 "The package implements basic and high-level functions for reading,
9091 writing, manipulating, analyzing and modeling of gridded spatial data.
9092 Processing of very large files is supported.")
9093 (license license:gpl3+)))
9095 (define-public r-mosaic
9102 (uri (cran-uri "mosaic" version))
9104 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9105 (build-system r-build-system)
9107 `(("r-broom" ,r-broom)
9108 ("r-dplyr" ,r-dplyr)
9109 ("r-ggdendro" ,r-ggdendro)
9110 ("r-ggformula" ,r-ggformula)
9111 ("r-ggplot2" ,r-ggplot2)
9112 ("r-ggrepel" ,r-ggrepel)
9114 ("r-gridextra" ,r-gridextra)
9115 ("r-lattice" ,r-lattice)
9116 ("r-latticeextra" ,r-latticeextra)
9117 ("r-lazyeval" ,r-lazyeval)
9119 ("r-matrix" ,r-matrix)
9120 ("r-mosaiccore" ,r-mosaiccore)
9121 ("r-mosaicdata" ,r-mosaicdata)
9122 ("r-readr" ,r-readr)
9123 ("r-tidyr" ,r-tidyr)))
9125 `(("r-knitr" ,r-knitr)))
9126 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9127 (synopsis "Mathematics, statistics, and computation teaching utilities")
9129 "This package contain data sets and utilities from
9130 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9131 statistics, computation and modeling. Project MOSAIC is a community of
9132 educators working to tie together aspects of quantitative work that students
9133 in science, technology, engineering and mathematics will need in their
9134 professional lives, but which are usually taught in isolation, if at all.")
9135 (license license:gpl2+)))
9137 (define-public r-abd
9144 (uri (cran-uri "abd" version))
9146 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9147 (build-system r-build-system)
9149 `(("r-lattice" ,r-lattice)
9150 ("r-mosaic" ,r-mosaic)
9151 ("r-nlme" ,r-nlme)))
9152 (home-page "https://cran.r-project.org/web/packages/abd/")
9153 (synopsis "Analysis of biological data")
9155 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9156 biological data by Michael Whitlock and Dolph Schluter.")
9157 (license license:gpl2)))
9159 (define-public r-svgui
9166 (uri (cran-uri "svGUI" version))
9168 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9169 (properties `((upstream-name . "svGUI")))
9170 (build-system r-build-system)
9171 (home-page "https://github.com/SciViews/svGUI/")
9172 (synopsis "Functions for managing GUI clients in R")
9174 "The SciViews @code{svGUI} package eases the management of Graphical User
9175 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9176 centralizes info about GUI elements currently used, and it dispatches GUI
9177 calls to the particular toolkits in use in function of the context.")
9178 (license license:gpl2)))
9180 (define-public r-svdialogs
9182 (name "r-svdialogs")
9187 (uri (cran-uri "svDialogs" version))
9189 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9190 (properties `((upstream-name . "svDialogs")))
9191 (build-system r-build-system)
9194 ("zenity" ,zenity)))
9196 `(("r-rstudioapi" ,r-rstudioapi)
9197 ("r-svgui" ,r-svgui)))
9198 (home-page "https://github.com/SciViews/svDialogs/")
9199 (synopsis "Portable dialog boxes")
9201 "This package helps to construct standard dialog boxes for your GUI, including
9202 message boxes, input boxes, list, file or directory selection, and others. In
9203 case R cannot display GUI dialog boxes, a simpler command line version of these
9204 interactive elements is also provided as a fallback solution.")
9205 (license license:gpl2)))
9207 (define-public r-abe
9214 (uri (cran-uri "abe" version))
9217 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9218 (build-system r-build-system)
9219 (home-page "https://cran.r-project.org/web/packages/abe/")
9220 (synopsis "Augmented backward elimination")
9222 "This package performs augmented backward elimination and checks the
9223 stability of the obtained model. Augmented backward elimination combines
9224 significance or information based criteria with the change in estimate to
9225 either select the optimal model for prediction purposes or to serve as a tool
9226 to obtain a practically sound, highly interpretable model.")
9227 (license license:gpl2+)))
9229 (define-public r-abf2
9236 (uri (cran-uri "abf2" version))
9238 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9239 (build-system r-build-system)
9240 (home-page "https://cran.r-project.org/web/packages/abf2/")
9241 (synopsis "Load gap-free axon @code{r-abf2} files")
9243 "This package loads electrophysiology data from ABF2 files, as created by
9244 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9245 mode are currently supported.")
9246 (license license:artistic2.0)))
9248 (define-public r-abhgenotyper
9250 (name "r-abhgenotyper")
9255 (uri (cran-uri "ABHgenotypeR" version))
9257 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9258 (properties `((upstream-name . "ABHgenotypeR")))
9259 (build-system r-build-system)
9261 `(("r-ggplot2" ,r-ggplot2)
9262 ("r-reshape2" ,r-reshape2)))
9263 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9264 (synopsis "Visualize and manipulate ABH genotypes")
9266 "The @code{r-abhgenotyper} package provides simple imputation,
9267 error-correction and plotting capacities for genotype data. The package is
9268 supposed to serve as an intermediate but independent analysis tool between the
9269 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9270 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9271 genotypes as \"graphical genotypes\".")
9272 (license license:gpl3)))
9274 (define-public r-furrr
9281 (uri (cran-uri "furrr" version))
9284 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9285 (build-system r-build-system)
9287 `(("r-ellipsis" ,r-ellipsis)
9288 ("r-future" ,r-future)
9289 ("r-globals" ,r-globals)
9290 ("r-lifecycle" ,r-lifecycle)
9291 ("r-purrr" ,r-purrr)
9292 ("r-rlang" ,r-rlang)
9293 ("r-vctrs" ,r-vctrs)))
9294 (home-page "https://github.com/DavisVaughan/furrr")
9295 (synopsis "Apply mapping functions in parallel using futures")
9297 "This package provides implementations of the family of @code{map()}
9298 functions from the @code{purrr} package that can be resolved using any
9299 @code{future}-supported backend, e.g. parallel on the local machine or
9300 distributed on a compute cluster.")
9301 (license license:lgpl2.1+)))
9303 (define-public r-abjutils
9310 (uri (cran-uri "abjutils" version))
9312 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9313 (build-system r-build-system)
9315 `(("r-dplyr" ,r-dplyr)
9316 ("r-magrittr" ,r-magrittr)
9317 ("r-purrr" ,r-purrr)
9318 ("r-rlang" ,r-rlang)
9319 ("r-rstudioapi" ,r-rstudioapi)
9320 ("r-stringi" ,r-stringi)
9321 ("r-stringr" ,r-stringr)
9322 ("r-tidyr" ,r-tidyr)))
9323 (home-page "https://github.com/abjur/abjutils/")
9324 (synopsis "Collection of tools for jurimetrical analysis")
9326 "This package implements general purpose tools, such as functions for
9327 sampling and basic manipulation of Brazilian lawsuits identification number.
9328 It also implements functions for text cleaning, such as accentuation
9330 (license license:expat)))
9332 (define-public r-abnormality
9334 (name "r-abnormality")
9339 (uri (cran-uri "abnormality" version))
9341 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9342 (build-system r-build-system)
9344 `(("r-mass" ,r-mass)
9345 ("r-matrix" ,r-matrix)))
9346 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9347 (synopsis "Measure a subject's abnormality with respect to a reference population")
9349 "This package contains functions to implement the methodology and
9350 considerations laid out by Marks et al. in the article \"Measuring abnormality
9351 in high dimensional spaces: applications in biomechanical gait analysis\".
9352 Using high-dimensional datasets to measure a subject's overall level of
9353 abnormality as compared to a reference population is often needed in outcomes
9355 (license license:expat)))
9357 (define-public r-abodoutlier
9359 (name "r-abodoutlier")
9364 (uri (cran-uri "abodOutlier" version))
9366 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9367 (properties `((upstream-name . "abodOutlier")))
9368 (build-system r-build-system)
9370 `(("r-cluster" ,r-cluster)))
9371 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9372 (synopsis "Angle-based outlier detection")
9374 "This package performs angle-based outlier detection on a given data
9375 frame. It offers three methods to process data:
9377 @item full but slow implementation using all the data that has cubic
9379 @item a fully randomized method;
9380 @item a method using k-nearest neighbours.
9382 These algorithms are well suited for high dimensional data outlier
9384 (license license:expat)))
9386 (define-public r-abps
9393 (uri (cran-uri "ABPS" version))
9395 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9396 (properties `((upstream-name . "ABPS")))
9397 (build-system r-build-system)
9398 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9399 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9400 (synopsis "Abnormal blood profile score to detect blood doping")
9402 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9403 The ABPS is a part of the Athlete biological passport program of the World
9404 anti-doping agency, which combines several blood parameters into a single
9405 score in order to detect blood doping. The package also contains functions to
9406 calculate other scores used in anti-doping programs, such as the ratio of
9407 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9408 (license license:gpl2+)))
9410 (define-public r-parmigene
9412 (name "r-parmigene")
9417 (uri (cran-uri "parmigene" version))
9420 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9421 (build-system r-build-system)
9422 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9423 (synopsis "Mutual information estimation for gene network reconstruction")
9425 "This package provides a parallel estimation of the mutual information
9426 based on entropy estimates from k-nearest neighbors distances and algorithms
9427 for the reconstruction of gene regulatory networks.")
9428 (license license:agpl3+)))
9430 (define-public r-pscl
9437 (uri (cran-uri "pscl" version))
9439 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9440 (build-system r-build-system)
9442 `(("r-mass" ,r-mass)))
9443 (home-page "https://github.com/atahk/pscl/")
9444 (synopsis "Political science computational laboratory")
9446 "The @code{pscl} is an R package providing classes and methods for:
9448 @item Bayesian analysis of roll call data (item-response models);
9449 @item elementary Bayesian statistics;
9450 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9452 @item utility functions.
9454 (license license:gpl2)))
9456 (define-public r-accelmissing
9458 (name "r-accelmissing")
9463 (uri (cran-uri "accelmissing" version))
9465 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9466 (build-system r-build-system)
9468 `(("r-mice" ,r-mice)
9469 ("r-pscl" ,r-pscl)))
9470 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9471 (synopsis "Missing value imputation for accelerometer data")
9473 "This package provides a statistical method to impute the missing values in
9474 accelerometer data. The methodology includes both parametric and
9475 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9476 model. It also provides multiple functions to preprocess the accelerometer data
9477 previous to the missing data imputation. These include detecting the wearing
9478 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9479 (license license:gpl2+)))
9481 (define-public r-mhsmm
9488 (uri (cran-uri "mhsmm" version))
9490 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9491 (build-system r-build-system)
9492 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9493 (home-page "https://github.com/jaredo/mhsmm/")
9494 (synopsis "Inference for hidden Markov and semi-Markov models")
9496 "The @code{r-mhsmm} package implements estimation and prediction methods for
9497 hidden Markov and semi-Markov models for multiple observation sequences. Such
9498 techniques are of interest when observed data is thought to be dependent on some
9499 unobserved (or hidden) state. Also, this package is suitable for equidistant
9500 time series data, with multivariate and/or missing data. Allows user defined
9501 emission distributions.")
9502 (license license:gpl2+)))
9504 (define-public r-nleqslv
9511 (uri (cran-uri "nleqslv" version))
9513 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9514 (build-system r-build-system)
9515 (native-inputs `(("gfortran" ,gfortran)))
9516 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9517 (synopsis "Solve systems of nonlinear equations")
9519 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9520 Broyden or a Newton method with a choice of global strategies such as line
9521 search and trust region. There are options for using a numerical or user
9522 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9523 singular or ill-conditioned Jacobian.")
9524 (license license:gpl2+)))
9526 (define-public r-physicalactivity
9528 (name "r-physicalactivity")
9533 (uri (cran-uri "PhysicalActivity" version))
9535 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9537 `((upstream-name . "PhysicalActivity")))
9538 (build-system r-build-system)
9539 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9540 (synopsis "Procesing accelerometer data for physical activity measurement")
9542 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9543 for classification of monitor wear and nonwear time intervals in accelerometer
9544 data collected to assess physical activity. The package also contains functions
9545 for making plots of accelerometer data and obtaining the summary of various
9546 information including daily monitor wear time and the mean monitor wear time
9547 during valid days. The revised package version 0.2-1 improved the functions
9548 regarding speed, robustness and add better support for time zones and daylight
9549 saving. In addition, several functions were added:
9551 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9552 @item the @code{markPAI} can categorize physical activity intensity level based
9553 on user-defined cut-points of accelerometer counts.
9555 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9556 @code{queryActigraph} functions.")
9557 (license license:gpl3+)))
9559 (define-public r-acc
9566 (uri (cran-uri "acc" version))
9568 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9569 (build-system r-build-system)
9571 `(("r-circlize" ,r-circlize)
9573 ("r-ggplot2" ,r-ggplot2)
9574 ("r-iterators" ,r-iterators)
9575 ("r-mhsmm" ,r-mhsmm)
9576 ("r-nleqslv" ,r-nleqslv)
9577 ("r-physicalactivity" ,r-physicalactivity)
9579 ("r-r-utils" ,r-r-utils)
9581 ("r-rcpparmadillo" ,r-rcpparmadillo)
9582 ("r-rsqlite" ,r-rsqlite)
9584 (home-page "https://cran.r-project.org/web/packages/acc/")
9585 (synopsis "Exploring accelerometer data")
9587 "This package processes accelerometer data from uni-axial and tri-axial devices
9588 and generates data summaries. Also, includes functions to plot, analyze, and
9589 simulate accelerometer data.")
9590 (license license:gpl2+)))
9592 (define-public r-rbenchmark
9594 (name "r-rbenchmark")
9599 (uri (cran-uri "rbenchmark" version))
9601 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9602 (build-system r-build-system)
9603 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9604 (synopsis "Benchmarking routine for R")
9606 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9607 and is intended to facilitate benchmarking of arbitrary R code. The library
9608 consists of just one function, benchmark, which is a simple wrapper around
9609 system.time. Given a specification of the benchmarking process (counts of
9610 replications, evaluation environment) and an arbitrary number of expressions,
9611 benchmark evaluates each of the expressions in the specified environment,
9612 replicating the evaluation as many times as specified, and returning the results
9613 conveniently wrapped into a data frame.")
9614 (license license:gpl2+)))
9616 (define-public r-mitools
9623 (uri (cran-uri "mitools" version))
9626 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9627 (build-system r-build-system)
9628 (propagated-inputs `(("r-dbi" ,r-dbi)))
9629 (home-page "https://cran.r-project.org/web/packages/mitools/")
9630 (synopsis "Tools for multiple imputation of missing data")
9632 "This package provides tools to perform analyses and combine results from
9633 multiple-imputation datasets.")
9634 (license license:gpl2)))
9636 (define-public r-mixsqp
9642 (uri (cran-uri "mixsqp" version))
9645 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9646 (properties `((upstream-name . "mixsqp")))
9647 (build-system r-build-system)
9649 `(("r-irlba" ,r-irlba)
9651 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9653 `(("r-knitr" ,r-knitr)))
9654 (home-page "https://github.com/stephenslab/mixsqp")
9656 "Sequential quadratic programming for maximum-likelihood estimation")
9658 "This package provides an optimization method based on sequential
9659 quadratic programming for maximum likelihood estimation of the mixture
9660 proportions in a finite mixture model where the component densities are
9661 known. The algorithm is expected to obtain solutions that are at least
9662 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9663 are expected to arrive at solutions more quickly when the number of
9664 samples is large and the number of mixture components is not too large.")
9665 (license license:expat)))
9667 (define-public r-magick
9674 (uri (cran-uri "magick" version))
9677 "0m1kij6pp7dmsrhl80h60iyccjqmbbb3zdnqdc9sgy1kj1x3pscp"))))
9678 (build-system r-build-system)
9680 `(("imagemagick" ,imagemagick)
9683 `(("r-curl" ,r-curl)
9684 ("r-magrittr" ,r-magrittr)
9685 ("r-rcpp" ,r-rcpp)))
9687 `(("pkg-config" ,pkg-config)
9688 ("r-knitr" ,r-knitr)))
9689 (home-page "https://github.com/ropensci/magick")
9690 (synopsis "Advanced graphics and image-processing in R")
9692 "This package provides bindings to ImageMagick, a comprehensive image
9693 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9694 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9695 operations are vectorized via the Magick++ STL meaning they operate either on
9696 a single frame or a series of frames for working with layers, collages, or
9697 animation. In RStudio, images are automatically previewed when printed to the
9698 console, resulting in an interactive editing environment.")
9699 (license license:expat)))
9701 (define-public r-survey
9708 (uri (cran-uri "survey" version))
9711 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9712 (build-system r-build-system)
9714 `(("r-lattice" ,r-lattice)
9715 ("r-matrix" ,r-matrix)
9716 ("r-minqa" ,r-minqa)
9717 ("r-mitools" ,r-mitools)
9718 ("r-numderiv" ,r-numderiv)
9719 ("r-survival" ,r-survival)))
9720 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9721 (synopsis "Analysis of complex survey samples")
9723 "This package provides tools for the analysis of complex survey samples.
9724 The provided features include: summary statistics, two-sample tests, rank
9725 tests, generalised linear models, cumulative link models, Cox models,
9726 loglinear models, and general maximum pseudolikelihood estimation for
9727 multistage stratified, cluster-sampled, unequally weighted survey samples;
9728 variances by Taylor series linearisation or replicate weights;
9729 post-stratification, calibration, and raking; two-phase subsampling designs;
9730 graphics; PPS sampling without replacement; principal components, and factor
9732 ;; Either version of the GPL.
9733 (license (list license:gpl2 license:gpl3))))
9735 (define-public r-gee
9742 (uri (cran-uri "gee" version))
9745 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9746 (properties `((upstream-name . "gee")))
9747 (build-system r-build-system)
9749 `(("gfortran" ,gfortran)))
9750 (home-page "https://cran.r-project.org/web/packages/gee/")
9751 (synopsis "Generalized estimation equation solver")
9753 "This package provides a solver for generalized estimation equations.")
9754 (license license:gpl2)))
9756 (define-public r-tab
9763 (uri (cran-uri "tab" version))
9766 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9767 (properties `((upstream-name . "tab")))
9768 (build-system r-build-system)
9770 `(("r-dplyr" ,r-dplyr)
9772 ("r-knitr" ,r-knitr)
9774 ("r-survey" ,r-survey)
9775 ("r-survival" ,r-survival)
9776 ("r-xtable" ,r-xtable)))
9777 (home-page "https://cran.r-project.org/web/packages/tab/")
9778 (synopsis "Create summary tables for statistical reports")
9780 "This package contains functions for creating various types of summary
9781 tables, e.g. comparing characteristics across levels of a categorical variable
9782 and summarizing fitted generalized linear models, generalized estimating
9783 equations, and Cox proportional hazards models. Functions are available to
9784 handle data from simple random samples as well as complex surveys.")
9785 (license license:gpl3+)))
9787 (define-public r-dvmisc
9794 (uri (cran-uri "dvmisc" version))
9796 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9797 (build-system r-build-system)
9799 `(("r-cubature" ,r-cubature)
9800 ("r-data-table" ,r-data-table)
9801 ("r-dplyr" ,r-dplyr)
9802 ("r-ggplot2" ,r-ggplot2)
9804 ("r-mvtnorm" ,r-mvtnorm)
9805 ("r-pracma" ,r-pracma)
9806 ("r-rbenchmark" ,r-rbenchmark)
9808 ("r-survey" ,r-survey)
9810 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9811 (synopsis "Faster computation of common statistics and miscellaneous functions")
9813 "This package implements faster versions of base R functions (e.g. mean, standard
9814 deviation, covariance, weighted mean), mostly written in C++, along with
9815 miscellaneous functions for various purposes (e.g. create the histogram with
9816 fitted probability density function or probability mass function curve, create
9817 the body mass index groups, assess the linearity assumption in logistic
9819 (license license:gpl2)))
9821 (define-public r-accelerometry
9823 (name "r-accelerometry")
9828 (uri (cran-uri "accelerometry" version))
9830 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9831 (build-system r-build-system)
9833 `(("r-dvmisc" ,r-dvmisc)
9834 ("r-rcpp" ,r-rcpp)))
9835 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9836 (synopsis "Functions for processing accelerometer data")
9838 "This package provides a collection of functions that perform operations on
9839 time-series accelerometer data, such as identify the non-wear time, flag minutes
9840 that are part of an activity bout, and find the maximum 10-minute average count
9841 value. The functions are generally very flexible, allowing for a variety of
9842 algorithms to be implemented.")
9843 (license license:gpl3)))
9845 (define-public r-absim
9852 (uri (cran-uri "AbSim" version))
9854 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9855 (properties `((upstream-name . "AbSim")))
9856 (build-system r-build-system)
9859 ("r-powerlaw" ,r-powerlaw)))
9860 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9861 (synopsis "Time resolved simulations of antibody repertoires")
9863 "This package provides simulation methods for the evolution of antibody repertoires.
9864 The heavy and light chain variable region of both human and C57BL/6 mice can
9865 be simulated in a time-dependent fashion. Both single lineages using one set of
9866 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9867 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9868 Upon completion, the main loop of the algorithm begins, with each iteration
9869 representing one simulated time step. Various mutation events are possible at
9870 each time step, contributing to a diverse final repertoire.")
9871 (license license:gpl2)))
9873 (define-public r-quic
9880 (uri (cran-uri "QUIC" version))
9882 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9883 (properties `((upstream-name . "QUIC")))
9884 (build-system r-build-system)
9885 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9886 (synopsis "Regularized sparse inverse covariance matrix estimation")
9888 "This package implements the regularized Gaussian maximum likelihood
9889 estimation of the inverse of a covariance matrix. It uses Newton's method and
9890 coordinate descent to solve the regularized inverse covariance matrix
9891 estimation problem.")
9892 ;; The project home page states that the release is under GPLv3 or later.
9893 ;; The CRAN page only says GPL-3.
9894 (license license:gpl3+)))
9896 (define-public r-abundant
9903 (uri (cran-uri "abundant" version))
9905 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9906 (build-system r-build-system)
9908 `(("r-quic" ,r-quic)))
9909 (home-page "https://cran.r-project.org/web/packages/abundant/")
9910 (synopsis "Abundant regression and high-dimensional principal fitted components")
9912 "This package provides tools to fit and predict with the high-dimensional
9913 principal fitted components model. This model is described by Cook, Forzani,
9914 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9915 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9916 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9917 (license license:gpl2+)))
9919 (define-public r-ac3net
9926 (uri (cran-uri "Ac3net" version))
9928 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9929 (properties `((upstream-name . "Ac3net")))
9930 (build-system r-build-system)
9932 `(("r-data-table" ,r-data-table)))
9933 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9934 (synopsis "Inferring directional conservative causal core gene networks")
9935 (description "This package infers directional Conservative causal core
9936 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9937 directional network.")
9938 (license license:gpl3+)))
9940 (define-public r-aca
9947 (uri (cran-uri "ACA" version))
9949 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9950 (properties `((upstream-name . "ACA")))
9951 (build-system r-build-system)
9952 (home-page "https://cran.r-project.org/web/packages/ACA/")
9953 (synopsis "Abrupt change-point or aberration detection in point series")
9955 "This package offers an interactive function for the detection of breakpoints in
9957 ;; Any version of the GPL
9958 (license (list license:gpl2+ license:gpl3+))))
9960 (define-public r-acceptancesampling
9962 (name "r-acceptancesampling")
9967 (uri (cran-uri "AcceptanceSampling" version))
9969 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9971 `((upstream-name . "AcceptanceSampling")))
9972 (build-system r-build-system)
9973 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9974 (synopsis "Creation and evaluation of acceptance sampling plans")
9976 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9977 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9978 in quality control and improvement. International standards of acceptance
9979 sampling provide sampling plans for specific circumstances. The aim of this
9980 package is to provide an easy-to-use interface to visualize single, double or
9981 multiple sampling plans. In addition, methods have been provided to enable the
9982 user to assess sampling plans against pre-specified levels of performance, as
9983 measured by the probability of acceptance for a given level of quality in the
9985 (license license:gpl3+)))
9987 (define-public r-acclma
9994 (uri (cran-uri "ACCLMA" version))
9996 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
9997 (properties `((upstream-name . "ACCLMA")))
9998 (build-system r-build-system)
9999 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10000 (synopsis "ACC & LMA graph plotting")
10002 "This package contains a function that imports data from a @acronym{CSV,
10003 Comma-Separated Values} file, or uses manually entered data from the format (x,
10004 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10005 Curve} vs @acronym{LOI, Line of Independence} graph and
10006 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10007 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10008 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10009 string) was passed, a manual data entry window is opened. The header parameter
10010 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10011 a header row or not. The dataset should contain only one independent variable
10012 (x) and one dependent variable (y) and can contain a weight for each
10014 (license license:gpl2)))
10016 (define-public r-aspi
10023 (uri (cran-uri "aspi" version))
10025 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10026 (build-system r-build-system)
10028 "https://cran.r-project.org/web/packages/aspi/")
10030 "Analysis of symmetry of parasitic infections")
10032 "This package provides tools for the analysis and visualization of bilateral
10033 asymmetry in parasitic infections.")
10034 (license license:gpl3+)))
10036 (define-public r-sandwich
10038 (name "r-sandwich")
10043 (uri (cran-uri "sandwich" version))
10046 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10047 (build-system r-build-system)
10049 `(("r-zoo" ,r-zoo)))
10050 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10051 (synopsis "Robust Covariance Matrix Estimators")
10053 "This package provides model-robust standard error estimators for
10054 cross-sectional, time series, clustered, panel, and longitudinal data.")
10055 ;; Either version of the license.
10056 (license (list license:gpl2 license:gpl3))))
10058 (define-public r-th-data
10065 (uri (cran-uri "TH.data" version))
10068 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10069 (properties `((upstream-name . "TH.data")))
10070 (build-system r-build-system)
10072 `(("r-mass" ,r-mass)
10073 ("r-survival" ,r-survival)))
10074 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10075 (synopsis "Shared data sets")
10077 "This package contains supporting data sets that are used in other
10078 packages maintained by Torsten Hothorn.")
10079 (license license:gpl3)))
10081 (define-public r-multcomp
10083 (name "r-multcomp")
10088 (uri (cran-uri "multcomp" version))
10091 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10092 (build-system r-build-system)
10094 `(("r-codetools" ,r-codetools)
10095 ("r-mvtnorm" ,r-mvtnorm)
10096 ("r-sandwich" ,r-sandwich)
10097 ("r-survival" ,r-survival)
10098 ("r-th-data" ,r-th-data)))
10099 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10100 (synopsis "Simultaneous inference in general parametric models")
10102 "Simultaneous tests and confidence intervals for general linear
10103 hypotheses in parametric models, including linear, generalized linear, linear
10104 mixed effects, and survival models. The package includes demos reproducing
10105 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10106 Hothorn, Westfall, 2010, CRC Press).")
10107 (license license:gpl2)))
10109 (define-public r-emmeans
10116 (uri (cran-uri "emmeans" version))
10119 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
10120 (build-system r-build-system)
10122 `(("r-estimability" ,r-estimability)
10123 ("r-mvtnorm" ,r-mvtnorm)
10124 ("r-numderiv" ,r-numderiv)
10126 ("r-xtable" ,r-xtable)))
10128 `(("r-knitr" ,r-knitr)))
10129 (home-page "https://github.com/rvlenth/emmeans")
10130 (synopsis "Estimated marginal means, aka least-squares means")
10132 "This package provides tools to obtain @dfn{estimated marginal
10133 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10134 be used to compute contrasts or linear functions of EMMs, trends, and
10135 comparisons of slopes.")
10136 ;; Either version of the license.
10137 (license (list license:gpl2 license:gpl3))))
10139 (define-public r-pwr
10146 (uri (cran-uri "pwr" version))
10149 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10150 (build-system r-build-system)
10152 `(("r-knitr" ,r-knitr)))
10153 (home-page "https://github.com/heliosdrm/pwr")
10154 (synopsis "Basic functions for power analysis")
10156 "This package provides power analysis functions along the lines of
10158 (license license:gpl3+)))
10160 (define-public r-libcoin
10167 (uri (cran-uri "libcoin" version))
10169 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10170 (build-system r-build-system)
10171 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10172 (home-page "https://cran.r-project.org/web/packages/libcoin")
10173 (synopsis "Linear test statistics for permutation inference")
10175 "This package provides basic infrastructure for linear test statistics
10176 and permutation inference in the framework of Strasser and Weber (1999).")
10177 (license license:gpl2)))
10179 (define-public r-coin
10186 (uri (cran-uri "coin" version))
10189 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10190 (build-system r-build-system)
10192 `(("r-libcoin" ,r-libcoin)
10193 ("r-matrixstats" ,r-matrixstats)
10194 ("r-modeltools" ,r-modeltools)
10195 ("r-multcomp" ,r-multcomp)
10196 ("r-mvtnorm" ,r-mvtnorm)
10197 ("r-survival" ,r-survival)))
10198 (home-page "http://coin.r-forge.r-project.org")
10199 (synopsis "Conditional inference procedures in a permutation test framework")
10201 "This package provides conditional inference procedures for the general
10202 independence problem including two-sample, K-sample (non-parametric ANOVA),
10203 correlation, censored, ordered and multivariate problems.")
10204 (license license:gpl2)))
10206 (define-public r-bayesplot
10208 (name "r-bayesplot")
10213 (uri (cran-uri "bayesplot" version))
10216 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10217 (build-system r-build-system)
10219 `(("pandoc" ,pandoc)
10220 ("pandoc-citeproc" ,pandoc-citeproc)))
10222 `(("r-knitr" ,r-knitr)))
10224 `(("r-dplyr" ,r-dplyr)
10225 ("r-ggplot2" ,r-ggplot2)
10226 ("r-ggridges" ,r-ggridges)
10228 ("r-reshape2" ,r-reshape2)
10229 ("r-rlang" ,r-rlang)
10230 ("r-tibble" ,r-tibble)
10231 ("r-tidyselect" ,r-tidyselect)))
10232 (home-page "https://mc-stan.org/bayesplot")
10233 (synopsis "Plotting for Bayesian models")
10235 "This package provides plotting functions for posterior analysis, model
10236 checking, and MCMC diagnostics. The package is designed not only to provide
10237 convenient functionality for users, but also a common set of functions that
10238 can be easily used by developers working on a variety of R packages for
10239 Bayesian modeling.")
10240 (license license:gpl3+)))
10242 (define-public r-tmb
10249 (uri (cran-uri "TMB" version))
10252 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10253 (properties `((upstream-name . "TMB")))
10254 (build-system r-build-system)
10256 `(("r-matrix" ,r-matrix)
10257 ("r-rcppeigen" ,r-rcppeigen)))
10258 (home-page "http://tmb-project.org")
10259 (synopsis "Template model builder: a general random effect tool")
10261 "With this tool, a user should be able to quickly implement complex
10262 random effect models through simple C++ templates. The package combines
10263 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10264 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10265 from R) to obtain an efficient implementation of the applied Laplace
10266 approximation with exact derivatives. Key features are: Automatic sparseness
10267 detection, parallelism through BLAS and parallel user templates.")
10268 (license license:gpl2)))
10270 (define-public r-sjstats
10277 (uri (cran-uri "sjstats" version))
10279 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10280 (build-system r-build-system)
10282 `(("r-bayestestr" ,r-bayestestr)
10283 ("r-broom" ,r-broom)
10284 ("r-dplyr" ,r-dplyr)
10285 ("r-effectsize" ,r-effectsize)
10286 ("r-emmeans" ,r-emmeans)
10287 ("r-insight" ,r-insight)
10289 ("r-magrittr" ,r-magrittr)
10291 ("r-modelr" ,r-modelr)
10292 ("r-parameters" ,r-parameters)
10293 ("r-performance" ,r-performance)
10294 ("r-purrr" ,r-purrr)
10295 ("r-rlang" ,r-rlang)
10296 ("r-sjlabelled" ,r-sjlabelled)
10297 ("r-sjmisc" ,r-sjmisc)
10298 ("r-tidyr" ,r-tidyr)))
10299 (home-page "https://github.com/strengejacke/sjstats")
10300 (synopsis "Functions for common statistical computations")
10302 "This package provides a collection of convenient functions for common
10303 statistical computations, which are not directly provided by R's @code{base}
10304 or @code{stats} packages. This package aims at providing, first, shortcuts
10305 for statistical measures, which otherwise could only be calculated with
10306 additional effort. Second, these shortcut functions are generic, and can be
10307 applied not only to vectors, but also to other objects as well. The focus of
10308 most functions lies on summary statistics or fit measures for regression
10309 models, including generalized linear models, mixed effects models and Bayesian
10311 (license license:gpl3)))
10313 (define-public r-glmmtmb
10316 (version "1.0.2.1")
10320 (uri (cran-uri "glmmTMB" version))
10323 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10324 (properties `((upstream-name . "glmmTMB")))
10325 (build-system r-build-system)
10327 `(("r-lme4" ,r-lme4)
10328 ("r-matrix" ,r-matrix)
10330 ("r-rcppeigen" ,r-rcppeigen)
10333 `(("r-knitr" ,r-knitr))) ; for vignettes
10334 (home-page "https://github.com/glmmTMB")
10335 (synopsis "Generalized linear mixed models")
10337 "Fit linear and generalized linear mixed models with various extensions,
10338 including zero-inflation. The models are fitted using maximum likelihood
10339 estimation via the Template Model Builder. Random effects are assumed to be
10340 Gaussian on the scale of the linear predictor and are integrated out using the
10341 Laplace approximation. Gradients are calculated using automatic
10343 (license license:agpl3+)))
10345 (define-public r-bayestestr
10347 (name "r-bayestestr")
10352 (uri (cran-uri "bayestestR" version))
10355 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10356 (properties `((upstream-name . "bayestestR")))
10357 (build-system r-build-system)
10359 `(("r-insight" ,r-insight)))
10361 `(("r-knitr" ,r-knitr)))
10362 (home-page "https://github.com/easystats/bayestestR")
10363 (synopsis "Describe Bayesian models and posterior distributions")
10365 "This package provides utilities to understand and describe posterior
10366 distributions and Bayesian models. It includes point-estimates such as
10367 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10368 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10369 ROPE percentage and pd).")
10370 (license license:gpl3)))
10372 (define-public r-performance
10374 (name "r-performance")
10379 (uri (cran-uri "performance" version))
10382 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10383 (build-system r-build-system)
10385 `(("r-bayestestr" ,r-bayestestr)
10386 ("r-insight" ,r-insight)))
10387 (home-page "https://easystats.github.io/performance/")
10388 (synopsis "Assessment of regression models performance")
10390 "This package provides utilities for computing measures to assess model
10391 quality, which are not directly provided by R's @code{base} or @code{stats}
10392 packages. These include e.g. measures like r-squared, intraclass correlation
10393 coefficient, root mean squared error or functions to check models for
10394 overdispersion, singularity or zero-inflation and more. Functions apply to a
10395 large variety of regression models, including generalized linear models, mixed
10396 effects models and Bayesian models.")
10397 (license license:gpl3)))
10399 (define-public r-ggeffects
10401 (name "r-ggeffects")
10406 (uri (cran-uri "ggeffects" version))
10409 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10410 (build-system r-build-system)
10412 `(("r-insight" ,r-insight)
10414 ("r-sjlabelled" ,r-sjlabelled)))
10416 `(("r-knitr" ,r-knitr)))
10417 (home-page "https://github.com/strengejacke/ggeffects")
10418 (synopsis "Create tidy data frames of marginal effects for ggplot")
10420 "This package provides tools to compute marginal effects from statistical
10421 models and return the result as tidy data frames. These data frames are ready
10422 to use with the @code{ggplot2} package. Marginal effects can be calculated
10423 for many different models. Interaction terms, splines and polynomial terms
10424 are also supported. The two main functions are @code{ggpredict()} and
10425 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10426 results using @code{ggplot2}.")
10427 (license license:gpl3)))
10429 (define-public r-effectsize
10431 (name "r-effectsize")
10436 (uri (cran-uri "effectsize" version))
10439 "0mgkq12ym72ncakkjpkzkjglhksyhj3iw8v4a8fjgpf7prvn191g"))))
10440 (properties `((upstream-name . "effectsize")))
10441 (build-system r-build-system)
10443 `(("r-bayestestr" ,r-bayestestr)
10444 ("r-insight" ,r-insight)
10445 ("r-parameters" ,r-parameters)))
10447 `(("r-knitr" ,r-knitr)))
10448 (home-page "https://github.com/easystats/effectsize")
10449 (synopsis "Indices of effect size and standardized parameters")
10451 "This package provides utilities to work with indices of effect size and
10452 standardized parameters for a wide variety of models, allowing computation and
10453 conversion of indices such as Cohen's d, r, odds, etc.")
10454 (license license:gpl3)))
10456 (define-public r-sjplot
10463 (uri (cran-uri "sjPlot" version))
10465 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10466 (properties `((upstream-name . "sjPlot")))
10467 (build-system r-build-system)
10469 `(("r-bayestestr" ,r-bayestestr)
10470 ("r-dplyr" ,r-dplyr)
10471 ("r-effectsize" ,r-effectsize)
10472 ("r-ggeffects" ,r-ggeffects)
10473 ("r-ggplot2" ,r-ggplot2)
10474 ("r-insight" ,r-insight)
10475 ("r-knitr" ,r-knitr)
10477 ("r-parameters" ,r-parameters)
10478 ("r-performance" ,r-performance)
10479 ("r-purrr" ,r-purrr)
10480 ("r-rlang" ,r-rlang)
10481 ("r-scales" ,r-scales)
10482 ("r-sjlabelled" ,r-sjlabelled)
10483 ("r-sjmisc" ,r-sjmisc)
10484 ("r-sjstats" ,r-sjstats)
10485 ("r-tidyr" ,r-tidyr)))
10487 `(("r-knitr" ,r-knitr)))
10488 (home-page "https://strengejacke.github.io/sjPlot/")
10489 (synopsis "Data visualization for statistics in social science")
10491 "This package represents a collection of plotting and table output
10492 functions for data visualization. Results of various statistical
10493 analyses (that are commonly used in social sciences) can be visualized using
10494 this package, including simple and cross tabulated frequencies, histograms,
10495 box plots, (generalized) linear models, mixed effects models, principal
10496 component analysis and correlation matrices, cluster analyses, scatter plots,
10497 stacked scales, effects plots of regression models (including interaction
10498 terms) and much more. This package supports labelled data.")
10499 (license license:gpl3)))
10501 (define-public r-ini
10508 (uri (cran-uri "ini" version))
10511 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10512 (build-system r-build-system)
10513 (home-page "https://github.com/dvdscripter/ini")
10514 (synopsis "Read and write configuration files")
10516 "This package provides tools to parse simple @code{.ini} configuration
10517 files to an structured list. Users can manipulate this resulting list with
10518 @code{lapply()} functions. This same structured list can be used to write
10519 back to file after modifications.")
10520 (license license:gpl3)))
10522 (define-public r-gitcreds
10524 (name "r-gitcreds")
10529 (uri (cran-uri "gitcreds" version))
10532 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10533 (properties `((upstream-name . "gitcreds")))
10534 (build-system r-build-system)
10535 (inputs `(("git" ,git-minimal)))
10536 (native-inputs `(("r-knitr" ,r-knitr)))
10537 (home-page "https://github.com/r-lib/gitcreds")
10538 (synopsis "Query git credentials from R")
10540 "Query, set, and delete credentials from the git credential store.
10541 Manage GitHub tokens and other git credentials. This package is to be used by
10542 other packages that need to authenticate to GitHub and/or other git
10544 (license license:expat)))
10546 (define-public r-gh
10553 (uri (cran-uri "gh" version))
10556 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10557 (build-system r-build-system)
10560 ("r-gitcreds" ,r-gitcreds)
10563 ("r-jsonlite" ,r-jsonlite)))
10565 `(("r-knitr" ,r-knitr)))
10566 (home-page "https://github.com/r-lib/gh#readme")
10567 (synopsis "Access the GitHub API via R")
10569 "This package provides a minimal R client to access the GitHub API.")
10570 (license license:expat)))
10572 (define-public r-fs
10579 (uri (cran-uri "fs" version))
10582 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10583 (build-system r-build-system)
10585 `(("r-knitr" ,r-knitr)))
10586 (home-page "https://fs.r-lib.org")
10587 (synopsis "Cross-platform file system operations based on libuv")
10589 "This package provides a cross-platform interface to file system
10590 operations, built on top of the libuv C library.")
10591 (license license:gpl3)))
10593 (define-public r-clisymbols
10595 (name "r-clisymbols")
10600 (uri (cran-uri "clisymbols" version))
10603 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10604 (build-system r-build-system)
10605 (home-page "https://github.com/gaborcsardi/clisymbols")
10606 (synopsis "Unicode symbols at the R prompt")
10608 "This package provides a small subset of Unicode symbols, that are useful
10609 when building command line applications. They fall back to alternatives on
10610 terminals that do not support Unicode.")
10611 (license license:expat)))
10613 (define-public r-credentials
10615 (name "r-credentials")
10620 (uri (cran-uri "credentials" version))
10623 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10624 (properties `((upstream-name . "credentials")))
10625 (build-system r-build-system)
10628 (modify-phases %standard-phases
10629 (add-after 'unpack 'setenv-HOME
10631 ;; This is necessary because git looks for $HOME/.gitconfig
10632 (setenv "HOME" "/tmp")
10635 `(("git" ,git-minimal)))
10637 `(("r-askpass" ,r-askpass)
10639 ("r-jsonlite" ,r-jsonlite)
10640 ("r-openssl" ,r-openssl)
10643 `(("r-knitr" ,r-knitr)))
10644 (home-page "https://docs.ropensci.org/credentials/")
10645 (synopsis "Tools for managing SSH and Git credentials")
10647 "This package assists you in setting up and retrieving of HTTPS and SSH
10648 credentials for use with git and other services. For HTTPS remotes the
10649 package interfaces the @command{git-credential} utility which @command{git}
10650 uses to store HTTP usernames and passwords. For SSH remotes this package
10651 provides convenient functions to find or generate appropriate SSH keys. The
10652 package both helps the user to setup a local git installation, and also
10653 provides a back-end for git/ssh client libraries to authenticate with existing
10654 user credentials.")
10655 (license license:expat)))
10657 (define-public r-gert
10664 (uri (cran-uri "gert" version))
10667 "0ag2ia6cfb5drf3517lg5nhik1w0nv09a75wdy5jdciws1qra3d6"))))
10668 (properties `((upstream-name . "gert")))
10669 (build-system r-build-system)
10671 `(("libgit2" ,libgit2)
10674 `(("r-askpass" ,r-askpass)
10675 ("r-credentials" ,r-credentials)
10676 ("r-openssl" ,r-openssl)
10677 ("r-rstudioapi" ,r-rstudioapi)
10681 `(("pkg-config" ,pkg-config)
10682 ("r-knitr" ,r-knitr)))
10683 (home-page "https://docs.ropensci.org/gert/")
10684 (synopsis "Simple Git client for R")
10686 "This package provides a simple git client for R based on libgit2 with
10687 support for SSH and HTTPS remotes. All functions in gert use basic R data
10688 types (such as vectors and data-frames) for their arguments and return values.
10689 User credentials are shared with command line git through the
10690 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10691 (license license:expat)))
10693 (define-public r-usethis
10700 (uri (cran-uri "usethis" version))
10703 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10704 (build-system r-build-system)
10707 ("r-clipr" ,r-clipr)
10708 ("r-crayon" ,r-crayon)
10715 ("r-jsonlite" ,r-jsonlite)
10716 ("r-lifecycle" ,r-lifecycle)
10717 ("r-purrr" ,r-purrr)
10718 ("r-rappdirs" ,r-rappdirs)
10719 ("r-rlang" ,r-rlang)
10720 ("r-rprojroot" ,r-rprojroot)
10721 ("r-rstudioapi" ,r-rstudioapi)
10722 ("r-whisker" ,r-whisker)
10723 ("r-withr" ,r-withr)
10724 ("r-yaml" ,r-yaml)))
10725 (home-page "https://github.com/r-lib/usethis")
10726 (synopsis "Automate R package and project setup")
10728 "This package helps you to automate R package and project setup tasks
10729 that are otherwise performed manually. This includes setting up unit testing,
10730 test coverage, continuous integration, Git, GitHub integration, licenses,
10731 Rcpp, RStudio projects, and more.")
10732 (license license:gpl3)))
10734 (define-public r-sessioninfo
10736 (name "r-sessioninfo")
10741 (uri (cran-uri "sessioninfo" version))
10744 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10745 (build-system r-build-system)
10748 ("r-withr" ,r-withr)))
10749 (home-page "https://github.com/r-lib/sessioninfo#readme")
10750 (synopsis "R session information")
10752 "This package provides tools to query and print information about the
10753 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10754 more information about packages, and where they were installed from.")
10755 (license license:gpl2)))
10757 (define-public r-remotes
10764 (uri (cran-uri "remotes" version))
10767 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10768 (build-system r-build-system)
10770 `(("r-knitr" ,r-knitr)))
10771 (home-page "https://github.com/r-lib/remotes#readme")
10772 (synopsis "R package installation from remote repositories")
10774 "Download and install R packages stored in GitHub, BitBucket, or plain
10775 subversion or git repositories. This package is a lightweight replacement of
10776 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10777 the code was copied over from @code{devtools}.")
10778 (license license:gpl2+)))
10780 (define-public r-xopen
10787 (uri (cran-uri "xopen" version))
10790 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10791 (build-system r-build-system)
10793 `(("r-processx" ,r-processx)))
10794 (home-page "https://github.com/r-lib/xopen#readme")
10795 (synopsis "Open system files, URLs, anything")
10797 "This package provides a cross-platform solution to open files,
10798 directories or URLs with their associated programs.")
10799 (license license:expat)))
10801 (define-public r-rcmdcheck
10803 (name "r-rcmdcheck")
10808 (uri (cran-uri "rcmdcheck" version))
10811 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10812 (build-system r-build-system)
10814 `(("r-callr" ,r-callr)
10816 ("r-crayon" ,r-crayon)
10818 ("r-digest" ,r-digest)
10819 ("r-pkgbuild" ,r-pkgbuild)
10820 ("r-prettyunits" ,r-prettyunits)
10822 ("r-rprojroot" ,r-rprojroot)
10823 ("r-sessioninfo" ,r-sessioninfo)
10824 ("r-withr" ,r-withr)
10825 ("r-xopen" ,r-xopen)))
10826 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10827 (synopsis "Run R CMD check from R and capture results")
10829 "Run @code{R CMD check} from R programmatically, and capture the results
10830 of the individual checks.")
10831 (license license:expat)))
10833 (define-public r-rapportools
10835 (name "r-rapportools")
10840 (uri (cran-uri "rapportools" version))
10843 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10844 (build-system r-build-system)
10846 `(("r-pander" ,r-pander)
10848 ("r-reshape" ,r-reshape)))
10849 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10850 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10852 "This package provides helper functions that act as wrappers to more
10853 advanced statistical methods with the advantage of having sane defaults for
10855 (license license:agpl3+)))
10857 (define-public r-pander
10864 (uri (cran-uri "pander" version))
10867 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10868 (build-system r-build-system)
10870 `(("r-digest" ,r-digest)
10871 ("r-rcpp" ,r-rcpp)))
10872 (home-page "https://rapporter.github.io/pander")
10873 (synopsis "Render R objects into Pandoc's markdown")
10875 "The main aim of the pander R package is to provide a minimal and easy
10876 tool for rendering R objects into Pandoc's markdown. The package is also
10877 capable of exporting/converting complex Pandoc documents (reports) in various
10879 ;; This package is licensed under either the AGPLv3+ or the very rarely
10881 (license license:agpl3+)))
10883 (define-public r-summarytools
10885 (name "r-summarytools")
10890 (uri (cran-uri "summarytools" version))
10893 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10894 (build-system r-build-system)
10896 `(("r-base64enc" ,r-base64enc)
10897 ("r-checkmate" ,r-checkmate)
10898 ("r-dplyr" ,r-dplyr)
10899 ("r-htmltools" ,r-htmltools)
10900 ("r-lubridate" ,r-lubridate)
10901 ("r-magick" ,r-magick)
10902 ("r-matrixstats" ,r-matrixstats)
10903 ("r-pander" ,r-pander)
10905 ("r-rapportools" ,r-rapportools)
10906 ("r-tibble" ,r-tibble)
10907 ("r-tidyr" ,r-tidyr)))
10909 `(("r-knitr" ,r-knitr)))
10910 (home-page "https://github.com/dcomtois/summarytools")
10911 (synopsis "Tools to quickly and neatly summarize data")
10913 "This package provides tools for data frame summaries, cross-tabulations,
10914 weight-enabled frequency tables and common univariate statistics in concise
10915 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10916 good point-of-entry for exploring data, both for experienced and new R
10918 (license license:gpl2)))
10920 (define-public r-lsei
10927 (uri (cran-uri "lsei" version))
10930 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10931 (build-system r-build-system)
10933 `(("gfortran" ,gfortran)))
10934 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10935 (synopsis "Solve regression problems under equality/inequality constraints")
10937 "It contains functions that solve least squares linear regression
10938 problems under linear equality/inequality constraints. Functions for solving
10939 quadratic programming problems are also available, which transform such
10940 problems into least squares ones first.")
10941 (license license:gpl2+)))
10943 (define-public r-npsurv
10950 (uri (cran-uri "npsurv" version))
10953 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10954 (build-system r-build-system)
10956 `(("r-lsei" ,r-lsei)))
10957 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10958 (synopsis "Nonparametric survival analysis")
10960 "This package contains functions for non-parametric survival analysis of
10961 exact and interval-censored observations.")
10962 (license license:gpl2+)))
10964 (define-public r-clusteval
10966 (name "r-clusteval")
10971 (uri (cran-uri "clusteval" version))
10974 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10975 (build-system r-build-system)
10977 `(("r-mvtnorm" ,r-mvtnorm)
10978 ("r-rcpp" ,r-rcpp)))
10979 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10980 (synopsis "Evaluation of clustering algorithms")
10982 "This R package provides a suite of tools to evaluate clustering
10983 algorithms, clusterings, and individual clusters.")
10984 (license license:expat)))
10986 (define-public r-tweedie
10993 (uri (cran-uri "tweedie" version))
10996 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
10997 (build-system r-build-system)
10998 (native-inputs `(("gfortran" ,gfortran)))
10999 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11000 (synopsis "Evaluation of Tweedie exponential family models")
11002 "Maximum likelihood computations for Tweedie families, including the
11003 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11004 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11005 and related methods.")
11006 (license license:gpl2+)))
11008 (define-public r-rcppgsl
11015 (uri (cran-uri "RcppGSL" version))
11017 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11018 (properties `((upstream-name . "RcppGSL")))
11019 (build-system r-build-system)
11021 `(("r-rcpp" ,r-rcpp)
11023 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11024 (synopsis "Rcpp integration for GSL vectors and matrices")
11026 "The GNU Scientific Library (or GSL) is a collection of numerical
11027 routines for scientific computing. It is particularly useful for C and C++
11028 programs as it provides a standard C interface to a wide range of mathematical
11029 routines. There are over 1000 functions in total with an extensive test
11030 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11031 structures and R using concepts from Rcpp which is itself a package that eases
11032 the interfaces between R and C++.")
11033 (license license:gpl2+)))
11035 (define-public r-mvabund
11042 (uri (cran-uri "mvabund" version))
11045 "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
11046 (build-system r-build-system)
11048 `(("r-mass" ,r-mass)
11050 ("r-rcppgsl" ,r-rcppgsl)
11051 ("r-statmod" ,r-statmod)
11052 ("r-tweedie" ,r-tweedie)))
11053 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11054 (synopsis "Statistical methods for analysing multivariate abundance data")
11056 "This package provides a set of tools for displaying, modeling and
11057 analysing multivariate abundance data in community ecology.")
11058 (license license:lgpl2.1+)))
11060 (define-public r-afex
11067 (uri (cran-uri "afex" version))
11070 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11071 (build-system r-build-system)
11075 ("r-lmertest" ,r-lmertest)
11076 ("r-pbkrtest" ,r-pbkrtest)
11077 ("r-reshape2" ,r-reshape2)))
11079 `(("r-knitr" ,r-knitr)))
11080 (home-page "https://afex.singmann.science/")
11081 (synopsis "Analysis of factorial experiments")
11083 "This package provides convenience functions for analyzing factorial
11084 experiments using ANOVA or mixed models.")
11085 (license license:gpl2+)))
11087 (define-public r-lmertest
11089 (name "r-lmertest")
11094 (uri (cran-uri "lmerTest" version))
11097 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11098 (properties `((upstream-name . "lmerTest")))
11099 (build-system r-build-system)
11101 `(("r-ggplot2" ,r-ggplot2)
11104 ("r-numderiv" ,r-numderiv)))
11105 (home-page "https://github.com/runehaubo/lmerTestR")
11106 (synopsis "Tests in linear mixed effects models")
11108 "This package provides p-values in type I, II or III anova and summary
11109 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11110 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11111 package. Model selection methods include step, drop1 and anova-like tables
11112 for random effects (ranova). Methods for Least-Square means (LS-means) and
11113 tests of linear contrasts of fixed effects are also available.")
11114 (license license:gpl2+)))
11116 (define-public r-r2glmm
11123 (uri (cran-uri "r2glmm" version))
11126 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11127 (build-system r-build-system)
11129 `(("r-afex" ,r-afex)
11130 ("r-data-table" ,r-data-table)
11131 ("r-dplyr" ,r-dplyr)
11132 ("r-ggplot2" ,r-ggplot2)
11133 ("r-gridextra" ,r-gridextra)
11134 ("r-lmertest" ,r-lmertest)
11136 ("r-matrix" ,r-matrix)
11138 ("r-pbkrtest" ,r-pbkrtest)))
11139 (home-page "https://github.com/bcjaeger/r2glmm")
11140 (synopsis "Compute R squared for mixed (multilevel) models")
11142 "This package computes model and semi partial R squared with confidence
11143 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11144 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11145 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11147 (license license:gpl2)))
11149 (define-public r-weights
11156 (uri (cran-uri "weights" version))
11159 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11160 (build-system r-build-system)
11162 `(("r-gdata" ,r-gdata)
11163 ("r-hmisc" ,r-hmisc)
11164 ("r-mice" ,r-mice)))
11166 "https://cran.r-project.org/web/packages/weights/")
11167 (synopsis "Weighting and weighted statistics")
11168 (description "This package Provides a variety of functions for producing
11169 simple weighted statistics, such as weighted Pearson's correlations, partial
11170 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11171 includes some software for quickly recoding survey data and plotting point
11172 estimates from interaction terms in regressions (and multiply imputed
11173 regressions). NOTE: Weighted partial correlation calculations pulled to
11175 (license license:gpl2+)))
11177 (define-public r-rcppannoy
11179 (name "r-rcppannoy")
11184 (uri (cran-uri "RcppAnnoy" version))
11187 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11188 (properties `((upstream-name . "RcppAnnoy")))
11189 (build-system r-build-system)
11191 `(("r-rcpp" ,r-rcpp)))
11192 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11193 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11195 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11196 for efficient memory usage as well an ability to load from and save to disk.
11197 This package provides an R interface.")
11198 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11200 (license (list license:gpl2+ license:asl2.0))))
11202 (define-public r-rcpphnsw
11204 (name "r-rcpphnsw")
11209 (uri (cran-uri "RcppHNSW" version))
11212 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11213 (properties `((upstream-name . "RcppHNSW")))
11214 (build-system r-build-system)
11215 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11216 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11217 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11219 "Hnswlib is a C++ library for approximate nearest neighbors. This
11220 package provides a minimal R interface by relying on the Rcpp package.")
11221 ;; hnswlib is released under Version 2.0 of the Apache License.
11222 (license (list license:gpl3 license:asl2.0))))
11224 (define-public r-rcppparallel
11226 (name "r-rcppparallel")
11231 (uri (cran-uri "RcppParallel" version))
11234 "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki"))))
11235 (properties `((upstream-name . "RcppParallel")))
11236 (build-system r-build-system)
11237 (home-page "https://rcppcore.github.io/RcppParallel/")
11238 (synopsis "Parallel programming tools for Rcpp")
11240 "This package provides high level functions for parallel programming with
11241 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11242 the work of a standard serial @code{for} loop into a parallel one and the
11243 @code{parallelReduce()} function can be used for accumulating aggregates or
11245 (license license:gpl2)))
11247 (define-public r-ncdf4
11254 (uri (cran-uri "ncdf4" version))
11257 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11258 (build-system r-build-system)
11260 `(("netcdf" ,netcdf)
11262 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11263 (synopsis "R interface to Unidata netCDF format data files")
11265 "This package provides a high-level R interface to data files written
11266 using Unidata's netCDF library (version 4 or earlier), which are binary data
11267 files that are portable across platforms and include metadata information in
11268 addition to the data sets. Using this package, netCDF files can be opened and
11269 data sets read in easily. It is also easy to create new netCDF dimensions,
11270 variables, and files, in either version 3 or 4 format, and manipulate existing
11272 (license license:gpl3+)))
11274 (define-public r-biocmanager
11276 (name "r-biocmanager")
11277 (version "1.30.10")
11281 (uri (cran-uri "BiocManager" version))
11283 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
11284 (properties `((upstream-name . "BiocManager")))
11285 (build-system r-build-system)
11286 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11287 (synopsis "Access the Bioconductor project package repository")
11289 "This package provides a convenient tool to install and update
11290 Bioconductor packages.")
11291 (license license:artistic2.0)))
11293 (define-public r-rgl
11296 (version "0.105.22")
11300 (uri (cran-uri "rgl" version))
11303 "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz"))))
11304 (build-system r-build-system)
11306 `(("pkg-config" ,pkg-config)
11307 ("r-knitr" ,r-knitr)))
11309 `(("freetype" ,freetype)
11316 `(("r-crosstalk" ,r-crosstalk)
11317 ("r-htmltools" ,r-htmltools)
11318 ("r-htmlwidgets" ,r-htmlwidgets)
11319 ("r-jsonlite" ,r-jsonlite)
11320 ("r-knitr" ,r-knitr)
11321 ("r-magrittr" ,r-magrittr)
11322 ("r-manipulatewidget" ,r-manipulatewidget)
11323 ("r-shiny" ,r-shiny)))
11324 (home-page "https://r-forge.r-project.org/projects/rgl/")
11325 (synopsis "3D visualization using OpenGL")
11327 "This package provides medium to high level functions for 3D interactive graphics,
11328 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11329 as functions for constructing representations of geometric
11330 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11331 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11332 image formats, including PNG, Postscript, SVG, PGF.")
11333 ;; Any version of the GPL.
11334 (license (list license:gpl2+ license:gpl3+))))
11336 (define-public r-multicool
11338 (name "r-multicool")
11343 (uri (cran-uri "multicool" version))
11346 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11347 (build-system r-build-system)
11348 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11349 (home-page "https://cran.r-project.org/web/packages/multicool/")
11350 (synopsis "Permutations of multisets in cool-lex order")
11352 "This package provides a set of tools to permute multisets without loops
11353 or hash tables and to generate integer partitions. Cool-lex order is similar
11354 to colexicographical order.")
11355 (license license:gpl2)))
11357 (define-public r-misc3d
11364 (uri (cran-uri "misc3d" version))
11367 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11368 (build-system r-build-system)
11369 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11370 (synopsis "Miscellaneous 3D Plots")
11372 "This package provides a collection of miscellaneous 3d plots, including
11374 ;; Any version of the GPL.
11375 (license (list license:gpl2+ license:gpl3+))))
11377 (define-public r-ks
11384 (uri (cran-uri "ks" version))
11386 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11387 (build-system r-build-system)
11390 ("r-kernlab" ,r-kernlab)
11391 ("r-kernsmooth" ,r-kernsmooth)
11392 ("r-matrix" ,r-matrix)
11393 ("r-mclust" ,r-mclust)
11395 ("r-multicool" ,r-multicool)
11396 ("r-mvtnorm" ,r-mvtnorm)
11397 ("r-plot3d" ,r-plot3d)))
11398 (home-page "https://www.mvstat.net/tduong/")
11399 (synopsis "Kernel smoothing")
11401 "This package provides kernel smoothers for univariate and multivariate
11402 data, including density functions, density derivatives, cumulative
11403 distributions, modal clustering, discriminant analysis, and two-sample
11404 hypothesis testing.")
11405 ;; Either version of the GPL.
11406 (license (list license:gpl2 license:gpl3))))
11408 (define-public r-feature
11415 (uri (cran-uri "feature" version))
11418 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11419 (build-system r-build-system)
11422 ("r-plot3d" ,r-plot3d)))
11424 `(("r-knitr" ,r-knitr)))
11425 (home-page "https://www.mvstat.net/tduong/")
11426 (synopsis "Inferential feature significance for kernel density estimation")
11428 "The feature package contains functions to display and compute kernel
11429 density estimates, significant gradient and significant curvature regions.
11430 Significant gradient and/or curvature regions often correspond to significant
11431 features (e.g. local modes).")
11432 ;; Either version of the GPL.
11433 (license (list license:gpl2 license:gpl3))))
11435 (define-public r-arm
11442 (uri (cran-uri "arm" version))
11445 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11446 (build-system r-build-system)
11448 `(("r-abind" ,r-abind)
11450 ("r-hmisc" ,r-hmisc)
11453 ("r-matrix" ,r-matrix)
11454 ("r-nlme" ,r-nlme)))
11455 (home-page "https://cran.r-project.org/web/packages/arm/")
11456 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11458 "This package provides functions to accompany A. Gelman and J. Hill,
11459 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11460 University Press, 2007.")
11461 (license license:gpl3+)))
11463 (define-public r-circular
11465 (name "r-circular")
11470 (uri (cran-uri "circular" version))
11473 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11474 (build-system r-build-system)
11476 `(("r-boot" ,r-boot)
11477 ("r-mvtnorm" ,r-mvtnorm)))
11479 `(("gfortran" ,gfortran)))
11480 (home-page "https://cran.r-project.org/web/packages/circular/")
11481 (synopsis "Circular statistics")
11483 "This package provides tools for circular statistics, from \"Topics in
11484 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11486 (license license:gpl2+)))
11488 (define-public r-activity
11490 (name "r-activity")
11495 (uri (cran-uri "activity" version))
11498 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
11499 (build-system r-build-system)
11501 `(("r-circular" ,r-circular)
11502 ("r-insol" ,r-insol)
11503 ("r-pbapply" ,r-pbapply)))
11504 (home-page "https://cran.r-project.org/web/packages/activity/")
11505 (synopsis "Animal activity statistics")
11507 "This package provides functions to fit kernel density functions to
11508 animal activity time data; plot activity distributions; quantify overall
11509 levels of activity; statistically compare activity metrics through
11510 bootstrapping; and evaluate variation in linear variables with time (or other
11511 circular variables).")
11512 (license license:gpl3)))
11514 (define-public r-ouch
11521 (uri (cran-uri "ouch" version))
11524 "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q"))))
11525 (build-system r-build-system)
11526 (propagated-inputs `(("r-subplex" ,r-subplex)))
11527 (home-page "https://kingaa.github.io/ouch/")
11528 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11530 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11531 for evolution along a phylogenetic tree.")
11532 (license license:gpl2+)))
11534 (define-public r-fmsb
11541 (uri (cran-uri "fmsb" version))
11544 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11545 (build-system r-build-system)
11546 (home-page "http://minato.sip21c.org/msb/")
11547 (synopsis "Functions for medical statistics book with demographic data")
11549 "This package provides several utility functions for the book entitled
11550 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11551 Japan, 2007) with Japanese demographic data and some demographic analysis
11552 related functions.")
11553 (license license:gpl2+)))
11555 (define-public r-stabledist
11557 (name "r-stabledist")
11562 (uri (cran-uri "stabledist" version))
11565 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11566 (build-system r-build-system)
11567 (home-page "https://www.rmetrics.org")
11568 (synopsis "Stable distribution functions")
11570 "This package provides density, probability and quantile functions, and
11571 random number generation for (skew) stable distributions, using the
11572 parametrizations of Nolan.")
11573 (license license:gpl2+)))
11575 (define-public r-gsl
11582 (uri (cran-uri "gsl" version))
11585 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11586 (build-system r-build-system)
11589 (home-page "https://cran.r-project.org/web/packages/gsl")
11590 (synopsis "Wrapper for the GNU Scientific Library")
11592 "This package provides an R wrapper for the special functions and quasi
11593 random number generators of the GNU Scientific Library.")
11594 (license license:gpl2+)))
11596 (define-public r-adgoftest
11598 (name "r-adgoftest")
11603 (uri (cran-uri "ADGofTest" version))
11606 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11607 (properties `((upstream-name . "ADGofTest")))
11608 (build-system r-build-system)
11609 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11610 (synopsis "Anderson-Darling GoF test")
11612 "This package provides an implementation of the Anderson-Darling GoF test
11613 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11614 Anderson-Darling Distribution\".")
11615 ;; Any version of the GPL.
11616 (license license:gpl3+)))
11618 (define-public r-sodium
11625 (uri (cran-uri "sodium" version))
11628 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11629 (properties `((upstream-name . "sodium")))
11630 (build-system r-build-system)
11632 `(("libsodium" ,libsodium)))
11634 `(("pkg-config" ,pkg-config)
11635 ("r-knitr" ,r-knitr)))
11636 (home-page "https://github.com/jeroen/sodium")
11637 (synopsis "R bindings to the libsodium crypto library")
11639 "This package provides bindings to libsodium: a library for encryption,
11640 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11641 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11642 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11643 (license license:expat)))
11645 (define-public r-softimpute
11647 (name "r-softimpute")
11652 (uri (cran-uri "softImpute" version))
11655 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11656 (properties `((upstream-name . "softImpute")))
11657 (build-system r-build-system)
11659 `(("r-matrix" ,r-matrix)))
11661 `(("gfortran" ,gfortran)))
11662 (home-page "https://cran.r-project.org/web/packages/softImpute")
11663 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11665 "This package provides iterative methods for matrix completion that use
11666 nuclear-norm regularization. The package includes procedures for centering
11667 and scaling rows, columns or both, and for computing low-rank @dfn{single
11668 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11670 (license license:gpl2)))
11672 (define-public r-fftwtools
11674 (name "r-fftwtools")
11679 (uri (cran-uri "fftwtools" version))
11682 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
11683 (build-system r-build-system)
11684 (inputs `(("fftw" ,fftw)))
11686 `(("pkg-config" ,pkg-config)))
11687 (home-page "https://github.com/krahim/fftwtools")
11688 (synopsis "Wrapper for FFTW3")
11690 "This package provides a wrapper for several FFTW functions. It provides
11691 access to the two-dimensional FFT, the multivariate FFT, and the
11692 one-dimensional real to complex FFT using the FFTW3 library. The package
11693 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11694 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11695 The FFT functions have a parameter that allows them to not return the
11696 redundant complex conjugate when the input is real data.")
11697 (license license:gpl2+)))
11699 (define-public r-tiff
11706 (uri (cran-uri "tiff" version))
11709 "101n6x70fr1dhcwx53g3s8q1j4wh93y0388v1s1316f8558rxqxh"))))
11710 (build-system r-build-system)
11712 `(("libtiff" ,libtiff)
11713 ("libjpeg" ,libjpeg-turbo)
11715 (home-page "https://www.rforge.net/tiff/")
11716 (synopsis "Read and write TIFF images")
11718 "This package provides an easy and simple way to read, write and display
11719 bitmap images stored in the TIFF format. It can read and write both files and
11720 in-memory raw vectors.")
11721 ;; Either of these two license versions.
11722 (license (list license:gpl2 license:gpl3))))
11724 (define-public r-nlp
11731 (uri (cran-uri "NLP" version))
11734 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11735 (properties `((upstream-name . "NLP")))
11736 (build-system r-build-system)
11737 (home-page "https://cran.r-project.org/web/packages/NLP/")
11738 (synopsis "Natural language processing infrastructure")
11740 "This package provides basic classes and methods for Natural Language
11742 (license license:gpl3)))
11744 (define-public r-tm
11751 (uri (cran-uri "tm" version))
11754 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11755 (properties `((upstream-name . "tm")))
11756 (build-system r-build-system)
11762 ("r-xml2" ,r-xml2)))
11763 (home-page "http://tm.r-forge.r-project.org/")
11764 (synopsis "Text mining package")
11766 "This package provides a framework for text mining applications within R.")
11767 (license license:gpl3)))
11769 (define-public r-waveslim
11771 (name "r-waveslim")
11776 (uri (cran-uri "waveslim" version))
11779 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11780 (build-system r-build-system)
11782 `(("gfortran" ,gfortran)))
11783 (home-page "http://waveslim.blogspot.com")
11784 (synopsis "Basic wavelet routines for signal processing")
11786 "This package provides basic wavelet routines for time series (1D),
11787 image (2D) and array (3D) analysis. The code provided here is based on
11788 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11789 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11790 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11791 pairs (Selesnick 2001, 2002).")
11792 (license license:bsd-3)))
11794 (define-public r-wordcloud
11796 (name "r-wordcloud")
11801 (uri (cran-uri "wordcloud" version))
11804 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11805 (build-system r-build-system)
11807 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11809 ;; The "tm" package is only "suggested" according to CRAN, but the
11810 ;; wordcloud package cannot be loaded without it.
11812 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11813 (synopsis "Word clouds")
11815 "This package provides functionality to create pretty word clouds,
11816 visualize differences and similarity between documents, and avoid
11817 over-plotting in scatter plots with text.")
11818 (license license:lgpl2.1)))
11820 (define-public r-colorramps
11822 (name "r-colorramps")
11827 (uri (cran-uri "colorRamps" version))
11830 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11831 (properties `((upstream-name . "colorRamps")))
11832 (build-system r-build-system)
11833 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11834 (synopsis "Build color tables")
11835 (description "This package provides features to build gradient color
11837 ;; Any version of the GPL
11838 (license license:gpl3+)))
11840 (define-public r-tidytree
11842 (name "r-tidytree")
11847 (uri (cran-uri "tidytree" version))
11849 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11850 (build-system r-build-system)
11853 ("r-dplyr" ,r-dplyr)
11854 ("r-lazyeval" ,r-lazyeval)
11855 ("r-magrittr" ,r-magrittr)
11856 ("r-rlang" ,r-rlang)
11857 ("r-tibble" ,r-tibble)))
11859 `(("r-knitr" ,r-knitr)))
11860 (home-page "https://github.com/GuangchuangYu/tidytree")
11861 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11863 "Phylogenetic trees generally contain multiple components including nodes,
11864 edges, branches and associated data. This package provides an approach to
11865 convert tree objects to tidy data frames. It also provides tidy interfaces to
11866 manipulate tree data.")
11867 (license license:artistic2.0)))
11869 (define-public r-rvcheck
11876 (uri (cran-uri "rvcheck" version))
11878 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11879 (build-system r-build-system)
11881 `(("r-biocmanager" ,r-biocmanager)
11882 ("r-rlang" ,r-rlang)))
11883 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11884 (synopsis "R package version check")
11886 "This package provides tools to check the latest release version of R and
11887 R packages (on CRAN, Bioconductor or Github).")
11888 (license license:artistic2.0)))
11890 (define-public r-docopt
11897 (uri (cran-uri "docopt" version))
11900 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11901 (build-system r-build-system)
11902 (home-page "https://github.com/docopt/docopt.R")
11903 (synopsis "Command-line interface specification language")
11905 "This package enables you to define a command-line interface by just
11906 giving it a description in the specific format.")
11907 (license license:expat)))
11909 (define-public r-sparsesvd
11911 (name "r-sparsesvd")
11916 (uri (cran-uri "sparsesvd" version))
11919 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11920 (build-system r-build-system)
11921 (propagated-inputs `(("r-matrix" ,r-matrix)))
11922 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11923 (synopsis "Sparse truncated singular value decomposition")
11925 "This package provides a Wrapper around the SVDLIBC library
11926 for (truncated) singular value decomposition of a sparse matrix. Currently,
11927 only sparse real matrices in Matrix package format are supported.")
11928 ;; SVDLIBC is released under BSD-2. The R interface is released under
11930 (license (list license:bsd-3 license:bsd-2))))
11932 (define-public r-speedglm
11934 (name "r-speedglm")
11939 (uri (cran-uri "speedglm" version))
11942 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11943 (build-system r-build-system)
11945 `(("r-mass" ,r-mass)
11946 ("r-matrix" ,r-matrix)))
11947 (home-page "https://cran.r-project.org/web/packages/speedglm")
11948 (synopsis "Fit linear and generalized linear models to large data sets")
11950 "This package provides tools for fitting linear models and generalized
11951 linear models to large data sets by updating algorithms.")
11952 ;; Any version of the GPL
11953 (license license:gpl2+)))
11955 (define-public r-densityclust
11957 (name "r-densityclust")
11962 (uri (cran-uri "densityClust" version))
11965 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11966 (properties `((upstream-name . "densityClust")))
11967 (build-system r-build-system)
11970 ("r-ggplot2" ,r-ggplot2)
11971 ("r-ggrepel" ,r-ggrepel)
11972 ("r-gridextra" ,r-gridextra)
11973 ("r-rcolorbrewer" ,r-rcolorbrewer)
11975 ("r-rtsne" ,r-rtsne)))
11976 (home-page "https://cran.r-project.org/web/packages/densityClust")
11977 (synopsis "Clustering by fast search and find of density peaks")
11979 "This package provides an improved implementation (based on k-nearest
11980 neighbors) of the density peak clustering algorithm, originally described by
11981 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11982 large datasets (> 100,000 samples) very efficiently.")
11983 (license license:gpl2+)))
11985 (define-public r-combinat
11987 (name "r-combinat")
11992 (uri (cran-uri "combinat" version))
11995 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
11996 (build-system r-build-system)
11997 (home-page "https://cran.r-project.org/web/packages/combinat")
11998 (synopsis "Combinatorics utilities")
11999 (description "This package provides assorted routines for combinatorics.")
12000 (license license:gpl2)))
12002 (define-public r-qlcmatrix
12004 (name "r-qlcmatrix")
12009 (uri (cran-uri "qlcMatrix" version))
12012 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12013 (properties `((upstream-name . "qlcMatrix")))
12014 (build-system r-build-system)
12016 `(("r-docopt" ,r-docopt)
12017 ("r-matrix" ,r-matrix)
12019 ("r-sparsesvd" ,r-sparsesvd)))
12020 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12021 (synopsis "Sparse matrix functions for quantitative language comparison")
12023 "This package provides an extension of the functionality of the Matrix
12024 package for using sparse matrices. Some of the functions are very general,
12025 while other are highly specific for the special data format used for
12026 @dfn{quantitative language comparison} (QLC).")
12027 (license license:gpl3)))
12029 (define-public r-ddrtree
12036 (uri (cran-uri "DDRTree" version))
12039 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12040 (properties `((upstream-name . "DDRTree")))
12041 (build-system r-build-system)
12044 ("r-irlba" ,r-irlba)
12046 ("r-rcppeigen" ,r-rcppeigen)))
12047 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12048 (synopsis "Learning principal graphs with DDRTree")
12050 "This package provides an implementation of the framework of
12051 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12052 dimensional space while constructs a principal tree which passes through the
12053 middle of the data simultaneously. DDRTree shows superiority to
12054 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12055 intrinsic structure of single cell genomics data. In general, it could be
12056 used to reconstruct the temporal progression as well as the bifurcation
12057 structure of any data type.")
12058 (license license:asl2.0)))
12060 (define-public r-corpcor
12067 (uri (cran-uri "corpcor" version))
12070 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12071 (build-system r-build-system)
12072 (home-page "http://strimmerlab.org/software/corpcor/")
12073 (synopsis "Efficient estimation of covariance and (partial) correlation")
12075 "This package implements a James-Stein-type shrinkage estimator for the
12076 covariance matrix, with separate shrinkage for variances and correlations.
12077 Furthermore, functions are available for fast singular value decomposition,
12078 for computing the pseudoinverse, and for checking the rank and positive
12079 definiteness of a matrix.")
12080 (license license:gpl3+)))
12082 (define-public r-rspectra
12084 (name "r-rspectra")
12089 (uri (cran-uri "RSpectra" version))
12092 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12093 (properties `((upstream-name . "RSpectra")))
12094 (build-system r-build-system)
12096 `(("r-matrix" ,r-matrix)
12098 ("r-rcppeigen" ,r-rcppeigen)))
12099 (home-page "https://github.com/yixuan/RSpectra")
12100 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12102 "This package provides an R interface to the Spectra library for
12103 large-scale eigenvalue and SVD problems. It is typically used to compute a
12104 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12105 which is usually more efficient than @code{eigen()} if k << n.")
12107 (license license:mpl2.0)))
12109 (define-public r-vbsr
12116 (uri (cran-uri "vbsr" version))
12119 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12120 (build-system r-build-system)
12121 (home-page "https://cran.r-project.org/web/packages/vbsr")
12122 (synopsis "Variational Bayes spike regression regularized linear models")
12124 "This package provides an efficient algorithm for solving ultra-sparse
12125 regularized regression models using a variational Bayes algorithm with a spike
12126 prior. The algorithm is solved on a path, with coordinate updates, and is
12127 capable of generating very sparse models. Very general model
12128 diagnostics for controlling type-1 errors are also provided.")
12129 (license license:gpl2)))
12131 (define-public r-flare
12138 (uri (cran-uri "flare" version))
12141 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12142 (build-system r-build-system)
12144 `(("r-igraph" ,r-igraph)
12145 ("r-lattice" ,r-lattice)
12147 ("r-matrix" ,r-matrix)))
12148 (home-page "https://cran.r-project.org/web/packages/flare")
12149 (synopsis "Family of Lasso regression implementations")
12151 "This package provides implementations of a family of Lasso variants
12152 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12153 high dimensional sparse linear models.")
12154 (license license:gpl2)))
12156 (define-public r-lassopv
12163 (uri (cran-uri "lassopv" version))
12166 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12167 (build-system r-build-system)
12168 (propagated-inputs `(("r-lars" ,r-lars)))
12169 (home-page "https://github.com/lingfeiwang/lassopv")
12170 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12172 "This package enables you to estimate the p-values for predictors x
12173 against target variable y in Lasso regression, using the regularization
12174 strength when each predictor enters the active set of regularization path for
12175 the first time as the statistic.")
12176 (license license:gpl3)))
12178 (define-public r-splitstackshape
12180 (name "r-splitstackshape")
12185 (uri (cran-uri "splitstackshape" version))
12188 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12189 (build-system r-build-system)
12191 `(("r-data-table" ,r-data-table)))
12192 (home-page "https://github.com/mrdwab/splitstackshape")
12193 (synopsis "Stack and reshape datasets after splitting concatenated values")
12195 "Online data collection tools like Google Forms often export
12196 multiple-response questions with data concatenated in cells. The
12197 @code{concat.split} (cSplit) family of functions provided by this package
12198 splits such data into separate cells. This package also includes functions to
12199 stack groups of columns and to reshape wide data, even when the data are
12200 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12201 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12203 (license license:gpl3)))
12205 (define-public r-tfmpvalue
12207 (name "r-tfmpvalue")
12212 (uri (cran-uri "TFMPvalue" version))
12215 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12216 (properties `((upstream-name . "TFMPvalue")))
12217 (build-system r-build-system)
12218 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12219 (home-page "https://github.com/ge11232002/TFMPvalue")
12220 (synopsis "P-value computation for position weight matrices")
12222 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12223 identification from sequence/alignments, we are interested in the significance
12224 of certain match scores. TFMPvalue provides the accurate calculation of a
12225 p-value with a score threshold for position weight matrices, or the score with
12226 a given p-value. It is an interface to code originally made available by
12227 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12228 Touzet and Varre (2007).")
12229 (license license:gpl2)))
12231 (define-public r-rnifti
12238 (uri (cran-uri "RNifti" version))
12241 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12242 (properties `((upstream-name . "RNifti")))
12243 (build-system r-build-system)
12244 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12245 (home-page "https://github.com/jonclayden/RNifti")
12246 (synopsis "Fast R and C++ access to NIfTI images")
12248 "This package provides very fast read and write access to images stored
12249 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12250 compiled C and interpreted R code. It also provides a C/C++ API that can be
12251 used by other packages.")
12252 (license license:gpl2)))
12254 (define-public r-shades
12261 (uri (cran-uri "shades" version))
12264 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12265 (build-system r-build-system)
12266 (home-page "https://github.com/jonclayden/shades")
12267 (synopsis "Simple color manipulation")
12269 "This package provides functions for easily manipulating colors,
12270 creating color scales and calculating color distances.")
12271 (license license:bsd-3)))
12273 (define-public r-ore
12280 (uri (cran-uri "ore" version))
12282 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12283 (build-system r-build-system)
12284 (home-page "https://github.com/jonclayden/ore")
12285 (synopsis "R interface to the Onigmo regular expression library")
12287 "This package provides an alternative to R's built-in functionality for
12288 handling regular expressions, based on the Onigmo library. It offers
12289 first-class compiled regex objects, partial matching and function-based
12290 substitutions, amongst other features.")
12291 (license license:bsd-3)))
12293 (define-public r-reportr
12300 (uri (cran-uri "reportr" version))
12303 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12304 (build-system r-build-system)
12305 (propagated-inputs `(("r-ore" ,r-ore)))
12306 (home-page "https://github.com/jonclayden/reportr")
12307 (synopsis "General message and error reporting system")
12309 "This package provides a system for reporting messages, which offers
12310 certain useful features over the standard R system, such as the incorporation
12311 of output consolidation, message filtering, assertions, expression
12312 substitution, automatic generation of stack traces for debugging, and
12313 conditional reporting based on the current \"output level\".")
12314 (license license:gpl2)))
12316 (define-public r-tractor-base
12318 (name "r-tractor-base")
12319 (version "3.3.3.1")
12323 (uri (cran-uri "tractor.base" version))
12326 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12327 (properties `((upstream-name . "tractor.base")))
12328 (build-system r-build-system)
12331 ("r-reportr" ,r-reportr)
12332 ("r-rnifti" ,r-rnifti)
12333 ("r-shades" ,r-shades)))
12334 (home-page "https://www.tractor-mri.org.uk")
12335 (synopsis "Read, manipulate and visualize magnetic resonance images")
12337 "This package provides functions for working with magnetic resonance
12338 images. It supports reading and writing of popular file formats (DICOM,
12339 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12340 visualization; flexible image manipulation; metadata and sparse image
12342 (license license:gpl2)))
12344 (define-public r-grimport
12346 (name "r-grimport")
12351 (uri (cran-uri "grImport" version))
12354 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12355 (properties `((upstream-name . "grImport")))
12356 (build-system r-build-system)
12358 `(("ghostscript" ,ghostscript)))
12360 `(("r-xml" ,r-xml)))
12361 (home-page "https://cran.r-project.org/web/packages/grImport")
12362 (synopsis "Convert, import, and draw PostScript pictures")
12364 "This package provides functions for converting, importing, and drawing
12365 PostScript pictures in R plots.")
12366 (license license:gpl2+)))
12368 (define-public r-grimport2
12370 (name "r-grimport2")
12375 (uri (cran-uri "grImport2" version))
12378 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12379 (properties `((upstream-name . "grImport2")))
12380 (build-system r-build-system)
12382 `(("r-base64enc" ,r-base64enc)
12386 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12387 (synopsis "Import SVG graphics")
12389 "This package provides functions for importing external vector images and
12390 drawing them as part of R plots. This package is different from the
12391 @code{grImport} package because, where that package imports PostScript format
12392 images, this package imports SVG format images. Furthermore, this package
12393 imports a specific subset of SVG, so external images must be preprocessed
12394 using a package like @code{rsvg} to produce SVG that this package can import.
12395 SVG features that are not supported by R graphics, such as gradient fills, can
12396 be imported and then exported via the @code{gridSVG} package.")
12397 (license license:gpl2+)))
12399 (define-public r-kohonen
12406 (uri (cran-uri "kohonen" version))
12409 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12410 (build-system r-build-system)
12412 `(("r-rcpp" ,r-rcpp)))
12413 (home-page "https://cran.r-project.org/web/packages/kohonen")
12414 (synopsis "Supervised and unsupervised self-organising maps")
12416 "This package provides functions to train @dfn{self-organising
12417 maps} (SOMs). Also interrogation of the maps and prediction using trained
12418 maps are supported. The name of the package refers to Teuvo Kohonen, the
12419 inventor of the SOM.")
12420 (license license:gpl2+)))
12422 (define-public r-nnls
12429 (uri (cran-uri "nnls" version))
12432 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12433 (build-system r-build-system)
12434 (native-inputs `(("gfortran" ,gfortran)))
12435 (home-page "https://cran.r-project.org/web/packages/nnls")
12436 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12438 "This package provides an R interface to the Lawson-Hanson implementation
12439 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12440 the combination of non-negative and non-positive constraints.")
12441 (license license:gpl2+)))
12443 (define-public r-iso
12446 (version "0.0-18.1")
12450 (uri (cran-uri "Iso" version))
12453 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12454 (properties `((upstream-name . "Iso")))
12455 (build-system r-build-system)
12456 (native-inputs `(("gfortran" ,gfortran)))
12457 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12458 (synopsis "Functions to perform isotonic regression")
12460 "This package provides support for linear order and unimodal
12461 order (univariate) isotonic regression and bivariate isotonic regression with
12462 linear order on both variables.")
12463 (license license:gpl2+)))
12465 (define-public r-chemometricswithr
12467 (name "r-chemometricswithr")
12472 (uri (cran-uri "ChemometricsWithR" version))
12475 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12477 `((upstream-name . "ChemometricsWithR")))
12478 (build-system r-build-system)
12480 `(("r-devtools" ,r-devtools)
12481 ("r-kohonen" ,r-kohonen)
12484 (home-page "https://github.com/rwehrens/CWR")
12485 (synopsis "Chemometrics with R")
12487 "This package provides functions and scripts used in the book
12488 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12489 Life Sciences\" by Ron Wehrens, Springer (2011).")
12490 (license license:gpl2+)))
12492 (define-public r-als
12499 (uri (cran-uri "ALS" version))
12502 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12503 (properties `((upstream-name . "ALS")))
12504 (build-system r-build-system)
12507 ("r-nnls" ,r-nnls)))
12508 (home-page "https://cran.r-project.org/web/packages/ALS")
12509 (synopsis "Multivariate curve resolution alternating least squares")
12511 "Alternating least squares is often used to resolve components
12512 contributing to data with a bilinear structure; the basic technique may be
12513 extended to alternating constrained least squares. This package provides an
12514 implementation of @dfn{multivariate curve resolution alternating least
12515 squares} (MCR-ALS).
12517 Commonly applied constraints include unimodality, non-negativity, and
12518 normalization of components. Several data matrices may be decomposed
12519 simultaneously by assuming that one of the two matrices in the bilinear
12520 decomposition is shared between datasets.")
12521 (license license:gpl2+)))
12523 (define-public r-strucchange
12525 (name "r-strucchange")
12530 (uri (cran-uri "strucchange" version))
12533 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12534 (build-system r-build-system)
12536 `(("r-sandwich" ,r-sandwich)
12538 (home-page "https://cran.r-project.org/web/packages/strucchange")
12539 (synopsis "Testing, monitoring, and dating structural changes")
12541 "This package provides tools for testing, monitoring and dating
12542 structural changes in (linear) regression models. It features tests/methods
12543 from the generalized fluctuation test framework as well as from the F
12544 test (Chow test) framework. This includes methods to fit, plot and test
12545 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12546 statistics, respectively. It is possible to monitor incoming data online
12547 using fluctuation processes. Finally, the breakpoints in regression models
12548 with structural changes can be estimated together with confidence intervals.
12549 Emphasis is always given to methods for visualizing the data.")
12550 ;; Either of these two GPL versions
12551 (license (list license:gpl2 license:gpl3))))
12553 (define-public r-pixmap
12560 (uri (cran-uri "pixmap" version))
12563 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12564 (build-system r-build-system)
12565 (home-page "https://cran.r-project.org/web/packages/pixmap")
12566 (synopsis "Tools for bitmap images")
12568 "This package provides functions for importing, exporting, plotting and
12569 other manipulations of bitmapped images.")
12570 (license license:gpl2)))
12572 (define-public r-rapidjsonr
12574 (name "r-rapidjsonr")
12579 (uri (cran-uri "rapidjsonr" version))
12582 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12583 (build-system r-build-system)
12584 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12585 (synopsis "JSON parser")
12587 "This package provides JSON parsing capability through the Rapidjson
12589 (license license:expat)))
12591 (define-public r-ontologyindex
12593 (name "r-ontologyindex")
12598 (uri (cran-uri "ontologyIndex" version))
12601 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12602 (properties `((upstream-name . "ontologyIndex")))
12603 (build-system r-build-system)
12605 `(("r-knitr" ,r-knitr)))
12606 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12607 (synopsis "Functions for processing ontologies in R")
12609 "This package provides functions for reading ontologies into R as lists
12610 and manipulating sets of ontological terms.")
12611 (license license:gpl2+)))
12613 (define-public r-gargle
12620 (uri (cran-uri "gargle" version))
12623 "0hsqn4hf935wn6vk2pwym7la4sdvy271y4cashp38pg4hkpg9zph"))))
12624 (build-system r-build-system)
12629 ("r-jsonlite" ,r-jsonlite)
12630 ("r-rlang" ,r-rlang)
12631 ("r-withr" ,r-withr)))
12633 `(("r-knitr" ,r-knitr)))
12634 (home-page "https://gargle.r-lib.org")
12635 (synopsis "Utilities for working with Google APIs")
12637 "This package provides utilities for working with Google APIs. This
12638 includes functions and classes for handling common credential types and for
12639 preparing, executing, and processing HTTP requests.")
12640 (license license:expat)))
12642 (define-public r-bigrquery
12644 (name "r-bigrquery")
12649 (uri (cran-uri "bigrquery" version))
12652 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12653 (build-system r-build-system)
12655 `(("r-assertthat" ,r-assertthat)
12656 ("r-bit64" ,r-bit64)
12659 ("r-gargle" ,r-gargle)
12662 ("r-jsonlite" ,r-jsonlite)
12663 ("r-prettyunits" ,r-prettyunits)
12664 ("r-progress" ,r-progress)
12665 ("r-rapidjsonr" ,r-rapidjsonr)
12667 ("r-rlang" ,r-rlang)
12668 ("r-tibble" ,r-tibble)))
12669 (home-page "https://github.com/rstats-db/bigrquery")
12670 (synopsis "R interface to Google's BigQuery API")
12672 "This package provides an R interface to Google's BigQuery database.")
12673 (license license:gpl3)))
12675 (define-public r-gmp
12682 (uri (cran-uri "gmp" version))
12685 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12686 (build-system r-build-system)
12689 (modify-phases %standard-phases
12690 (add-after 'unpack 'set-CC
12691 (lambda _ (setenv "CC" "gcc") #t)))))
12692 (inputs `(("gmp" ,gmp)))
12693 (home-page "https://cran.r-project.org/web/packages/gmp")
12694 (synopsis "Multiple precision arithmetic")
12696 "This package supports multiple precision arithmetic (big integers and
12697 rationals, prime number tests, matrix computation), \"arithmetic without
12698 limitations\" using the GNU Multiple Precision library.")
12699 ;; Any version of the GPL.
12700 (license license:gpl3+)))
12702 (define-public r-rmpfr
12709 (uri (cran-uri "Rmpfr" version))
12712 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12713 (properties `((upstream-name . "Rmpfr")))
12714 (build-system r-build-system)
12719 `(("r-gmp" ,r-gmp)))
12721 `(("pkg-config" ,pkg-config)))
12722 (home-page "http://rmpfr.r-forge.r-project.org/")
12723 (synopsis "R bindings to the MPFR library")
12725 "This package supports arithmetic (via S4 classes and methods) for
12726 arbitrary precision floating point numbers, including transcendental
12727 functions. To this end, the package interfaces with the @dfn{Multiple
12728 Precision Floating-Point Reliable} (MPFR) library.")
12729 (license license:gpl2+)))
12731 (define-public r-assertive-base
12733 (name "r-assertive-base")
12738 (uri (cran-uri "assertive.base" version))
12741 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12743 `((upstream-name . "assertive.base")))
12744 (build-system r-build-system)
12745 (home-page "https://bitbucket.org/richierocks/assertive.base")
12746 (synopsis "Core of the assertive package")
12748 "This package provides a minimal set of predicates and assertions used by
12749 the assertive package. This is mainly for use by other package developers who
12750 want to include run-time testing features in their own packages.")
12751 (license license:gpl3+)))
12753 (define-public r-assertive-properties
12755 (name "r-assertive-properties")
12760 (uri (cran-uri "assertive.properties" version))
12763 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12765 `((upstream-name . "assertive.properties")))
12766 (build-system r-build-system)
12768 `(("r-assertive-base" ,r-assertive-base)))
12769 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12770 (synopsis "Assertions to check properties of variables")
12772 "This package provides a set of predicates and assertions for checking
12773 the properties of variables, such as length, names and attributes. This is
12774 mainly for use by other package developers who want to include run-time
12775 testing features in their own packages.")
12776 (license license:gpl3+)))
12778 (define-public r-assertive-numbers
12780 (name "r-assertive-numbers")
12785 (uri (cran-uri "assertive.numbers" version))
12788 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12790 `((upstream-name . "assertive.numbers")))
12791 (build-system r-build-system)
12793 `(("r-assertive-base" ,r-assertive-base)))
12794 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12795 (synopsis "Assertions to check properties of numbers")
12797 "This package provides a set of predicates and assertions for checking
12798 the properties of numbers. This is mainly for use by other package developers
12799 who want to include run-time testing features in their own packages.")
12800 (license license:gpl3+)))
12802 (define-public r-assertive-sets
12804 (name "r-assertive-sets")
12809 (uri (cran-uri "assertive.sets" version))
12812 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12814 `((upstream-name . "assertive.sets")))
12815 (build-system r-build-system)
12817 `(("r-assertive-base" ,r-assertive-base)))
12818 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12819 (synopsis "Assertions to check properties of sets")
12821 "This package provides a set of predicates and assertions for checking
12822 the properties of sets. 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-matrices
12828 (name "r-assertive-matrices")
12833 (uri (cran-uri "assertive.matrices" version))
12836 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12838 `((upstream-name . "assertive.matrices")))
12839 (build-system r-build-system)
12841 `(("r-assertive-base" ,r-assertive-base)))
12842 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12843 (synopsis "Assertions to check properties of matrices")
12845 "This package provides a set of predicates and assertions for checking
12846 the properties of matrices. This is mainly for use by other package
12847 developers who want to include run-time testing features in their own
12849 (license license:gpl3+)))
12851 (define-public r-assertive-models
12853 (name "r-assertive-models")
12858 (uri (cran-uri "assertive.models" version))
12861 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12863 `((upstream-name . "assertive.models")))
12864 (build-system r-build-system)
12866 `(("r-assertive-base" ,r-assertive-base)))
12867 (home-page "https://bitbucket.org/richierocks/assertive.models")
12868 (synopsis "Assertions to check properties of models")
12870 "This package provides a set of predicates and assertions for checking
12871 the properties of models. This is mainly for use by other package developers
12872 who want to include run-time testing features in their own packages.")
12873 (license license:gpl3+)))
12875 (define-public r-assertive-reflection
12877 (name "r-assertive-reflection")
12882 (uri (cran-uri "assertive.reflection" version))
12885 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12887 `((upstream-name . "assertive.reflection")))
12888 (build-system r-build-system)
12890 `(("r-assertive-base" ,r-assertive-base)))
12891 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12892 (synopsis "Assertions for checking the state of R")
12894 "This package provides a set of predicates and assertions for checking
12895 the state and capabilities of R, the operating system it is running on, and
12896 the IDE being used. This is mainly for use by other package developers who
12897 want to include run-time testing features in their own packages.")
12898 (license license:gpl3+)))
12900 (define-public r-assertive-types
12902 (name "r-assertive-types")
12907 (uri (cran-uri "assertive.types" version))
12910 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12912 `((upstream-name . "assertive.types")))
12913 (build-system r-build-system)
12915 `(("r-assertive-base" ,r-assertive-base)
12916 ("r-assertive-properties" ,r-assertive-properties)
12917 ("r-codetools" ,r-codetools)))
12918 (home-page "https://bitbucket.org/richierocks/assertive.types")
12919 (synopsis "Assertions to check types of variables")
12921 "This package provides a set of predicates and assertions for checking
12922 the types of variables. This is mainly for use by other package developers
12923 who want to include run-time testing features in their own packages.")
12924 (license license:gpl3+)))
12926 (define-public r-assertive-files
12928 (name "r-assertive-files")
12933 (uri (cran-uri "assertive.files" version))
12936 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12938 `((upstream-name . "assertive.files")))
12939 (build-system r-build-system)
12941 `(("r-assertive-base" ,r-assertive-base)
12942 ("r-assertive-numbers" ,r-assertive-numbers)))
12943 (home-page "https://bitbucket.org/richierocks/assertive.files")
12944 (synopsis "Assertions to check properties of files")
12946 "This package provides a set of predicates and assertions for checking
12947 the properties of files and connections. This is mainly for use by other
12948 package developers who want to include run-time testing features in their own
12950 (license license:gpl3+)))
12952 (define-public r-assertive-code
12954 (name "r-assertive-code")
12959 (uri (cran-uri "assertive.code" version))
12962 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12964 `((upstream-name . "assertive.code")))
12965 (build-system r-build-system)
12967 `(("r-assertive-base" ,r-assertive-base)
12968 ("r-assertive-properties" ,r-assertive-properties)
12969 ("r-assertive-types" ,r-assertive-types)))
12970 (home-page "https://bitbucket.org/richierocks/assertive.code")
12971 (synopsis "Assertions to check properties of code")
12973 "This package provides a set of predicates and assertions for checking
12974 the properties of code. This is mainly for use by other package developers
12975 who want to include run-time testing features in their own packages.")
12976 (license license:gpl3+)))
12978 (define-public r-assertive-datetimes
12980 (name "r-assertive-datetimes")
12985 (uri (cran-uri "assertive.datetimes" version))
12988 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
12990 `((upstream-name . "assertive.datetimes")))
12991 (build-system r-build-system)
12993 `(("r-assertive-base" ,r-assertive-base)
12994 ("r-assertive-types" ,r-assertive-types)))
12995 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
12996 (synopsis "Assertions to check properties of dates and times")
12998 "This package provides a set of predicates and assertions for checking
12999 the properties of dates and times. This is mainly for use by other package
13000 developers who want to include run-time testing features in their own
13002 (license license:gpl3+)))
13004 (define-public r-assertive-strings
13006 (name "r-assertive-strings")
13011 (uri (cran-uri "assertive.strings" version))
13014 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13016 `((upstream-name . "assertive.strings")))
13017 (build-system r-build-system)
13019 `(("r-assertive-base" ,r-assertive-base)
13020 ("r-assertive-types" ,r-assertive-types)
13021 ("r-stringi" ,r-stringi)))
13022 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13023 (synopsis "Assertions to check properties of strings")
13025 "This package provides a set of predicates and assertions for checking
13026 the properties of strings. This is mainly for use by other package developers
13027 who want to include run-time testing features in their own packages.")
13028 (license license:gpl3+)))
13030 (define-public r-assertive-data-us
13032 (name "r-assertive-data-us")
13037 (uri (cran-uri "assertive.data.us" version))
13040 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13042 `((upstream-name . "assertive.data.us")))
13043 (build-system r-build-system)
13045 `(("r-assertive-base" ,r-assertive-base)
13046 ("r-assertive-strings" ,r-assertive-strings)))
13047 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13048 (synopsis "Assertions to check properties of strings")
13050 "This package provides a set of predicates and assertions for checking
13051 the properties of US-specific complex data types. This is mainly for use by
13052 other package developers who want to include run-time testing features in
13053 their own packages.")
13054 (license license:gpl3+)))
13056 (define-public r-assertive-data-uk
13058 (name "r-assertive-data-uk")
13063 (uri (cran-uri "assertive.data.uk" version))
13066 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13068 `((upstream-name . "assertive.data.uk")))
13069 (build-system r-build-system)
13071 `(("r-assertive-base" ,r-assertive-base)
13072 ("r-assertive-strings" ,r-assertive-strings)))
13073 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13074 (synopsis "Assertions to check properties of strings")
13076 "This package provides a set of predicates and assertions for checking
13077 the properties of UK-specific complex data types. This is mainly for use by
13078 other package developers who want to include run-time testing features in
13079 their own packages.")
13080 (license license:gpl3+)))
13082 (define-public r-assertive-data
13084 (name "r-assertive-data")
13089 (uri (cran-uri "assertive.data" version))
13092 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13094 `((upstream-name . "assertive.data")))
13095 (build-system r-build-system)
13097 `(("r-assertive-base" ,r-assertive-base)
13098 ("r-assertive-strings" ,r-assertive-strings)))
13099 (home-page "https://bitbucket.org/richierocks/assertive.data")
13100 (synopsis "Assertions to check properties of data")
13102 "This package provides a set of predicates and assertions for checking
13103 the properties of (country independent) complex data types. This is mainly
13104 for use by other package developers who want to include run-time testing
13105 features in their own packages.")
13106 (license license:gpl3+)))
13108 (define-public r-assertive
13110 (name "r-assertive")
13115 (uri (cran-uri "assertive" version))
13118 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13119 (build-system r-build-system)
13121 `(("r-assertive-base" ,r-assertive-base)
13122 ("r-assertive-code" ,r-assertive-code)
13123 ("r-assertive-data" ,r-assertive-data)
13124 ("r-assertive-data-uk" ,r-assertive-data-uk)
13125 ("r-assertive-data-us" ,r-assertive-data-us)
13126 ("r-assertive-datetimes" ,r-assertive-datetimes)
13127 ("r-assertive-files" ,r-assertive-files)
13128 ("r-assertive-matrices" ,r-assertive-matrices)
13129 ("r-assertive-models" ,r-assertive-models)
13130 ("r-assertive-numbers" ,r-assertive-numbers)
13131 ("r-assertive-properties" ,r-assertive-properties)
13132 ("r-assertive-reflection" ,r-assertive-reflection)
13133 ("r-assertive-sets" ,r-assertive-sets)
13134 ("r-assertive-strings" ,r-assertive-strings)
13135 ("r-assertive-types" ,r-assertive-types)
13136 ("r-knitr" ,r-knitr)))
13138 `(("r-knitr" ,r-knitr)))
13139 (home-page "https://bitbucket.org/richierocks/assertive")
13140 (synopsis "Readable check functions to ensure code integrity")
13142 "This package provides lots of predicates (@code{is_*} functions) to
13143 check the state of your variables, and assertions (@code{assert_*} functions)
13144 to throw errors if they aren't in the right form.")
13145 (license license:gpl3+)))
13147 (define-public r-dotcall64
13149 (name "r-dotcall64")
13154 (uri (cran-uri "dotCall64" version))
13157 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
13158 (properties `((upstream-name . "dotCall64")))
13159 (build-system r-build-system)
13160 (native-inputs `(("gfortran" ,gfortran)))
13161 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13162 (synopsis "Enhanced foreign function interface supporting long vectors")
13164 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13165 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13166 supports long vectors, arguments of type 64-bit integer, and provides a
13167 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13168 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13169 (license license:gpl2+)))
13171 (define-public r-spam
13178 (uri (cran-uri "spam" version))
13180 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13181 (build-system r-build-system)
13183 `(("r-dotcall64" ,r-dotcall64)))
13185 `(("gfortran" ,gfortran)
13186 ("r-knitr" ,r-knitr)))
13187 (home-page "https://www.math.uzh.ch/pages/spam/")
13188 (synopsis "Sparse matrix algebra")
13190 "This package provides a set of functions for sparse matrix algebra.
13191 Differences with other sparse matrix packages are:
13194 @item it only supports (essentially) one sparse matrix format;
13195 @item it is based on transparent and simple structure(s);
13196 @item it is tailored for MCMC calculations within G(M)RF;
13197 @item and it is fast and scalable (with the extension package @code{spam64}).
13199 ;; Either of these licenses
13200 (license (list license:bsd-3 license:lgpl2.0))))
13202 (define-public r-fields
13209 (uri (cran-uri "fields" version))
13211 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13212 (build-system r-build-system)
13214 `(("r-maps" ,r-maps)
13215 ("r-spam" ,r-spam)))
13217 `(("gfortran" ,gfortran)))
13218 (home-page "https://www.image.ucar.edu/fields")
13219 (synopsis "Tools for spatial data")
13221 "This is a package for curve, surface and function fitting with an
13222 emphasis on splines, spatial data and spatial statistics. The major methods
13223 include cubic, and thin plate splines, Kriging, and compactly supported
13224 covariance functions for large data sets.")
13225 (license license:gpl2+)))
13227 (define-public r-spatialextremes
13229 (name "r-spatialextremes")
13234 (uri (cran-uri "SpatialExtremes" version))
13237 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13239 `((upstream-name . "SpatialExtremes")))
13240 (build-system r-build-system)
13242 `(("r-fields" ,r-fields)
13243 ("r-maps" ,r-maps)))
13244 (home-page "http://spatialextremes.r-forge.r-project.org/")
13245 (synopsis "Modelling spatial extremes")
13247 "This package provides tools for the statistical modelling of spatial
13248 extremes using max-stable processes, copula or Bayesian hierarchical models.
13249 More precisely, this package allows (conditional) simulations from various
13250 parametric max-stable models, analysis of the extremal spatial dependence, the
13251 fitting of such processes using composite likelihoods or least square (simple
13252 max-stable processes only), model checking and selection and prediction.")
13253 (license license:gpl2+)))
13255 (define-public r-drc
13262 (uri (cran-uri "drc" version))
13265 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13266 (build-system r-build-system)
13269 ("r-gtools" ,r-gtools)
13271 ("r-multcomp" ,r-multcomp)
13272 ("r-plotrix" ,r-plotrix)
13273 ("r-scales" ,r-scales)))
13274 (home-page "https://cran.r-project.org/web/packages/drc")
13275 (synopsis "Analysis of dose-response curves")
13277 "This package provides a suite of flexible and versatile model fitting
13278 and after-fitting functions for the analysis of dose-response data.")
13279 (license license:gpl2+)))
13281 (define-public r-rmeta
13288 (uri (cran-uri "rmeta" version))
13291 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13292 (build-system r-build-system)
13293 (home-page "https://cran.r-project.org/web/packages/rmeta")
13294 (synopsis "Tools for meta-analysis")
13296 "This package provides functions for simple fixed and random effects
13297 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13298 draws standard summary plots, funnel plots, and computes summaries and tests
13299 for association and heterogeneity.")
13300 (license license:gpl2)))
13302 (define-public r-bootstrap
13304 (name "r-bootstrap")
13309 (uri (cran-uri "bootstrap" version))
13312 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13313 (build-system r-build-system)
13314 (native-inputs `(("gfortran" ,gfortran)))
13315 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13316 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13318 "This package provides software and data for the book \"An Introduction
13319 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13320 This package is primarily provided for projects already based on it, and for
13321 support of the book. New projects should preferentially use the recommended
13322 package \"boot\".")
13323 (license license:bsd-3)))
13325 (define-public r-survivalroc
13327 (name "r-survivalroc")
13332 (uri (cran-uri "survivalROC" version))
13335 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13336 (properties `((upstream-name . "survivalROC")))
13337 (build-system r-build-system)
13338 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13339 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13341 "Compute time-dependent ROC curve from censored survival data using
13342 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13343 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13344 (license license:gpl2+)))
13346 (define-public r-longitudinal
13348 (name "r-longitudinal")
13353 (uri (cran-uri "longitudinal" version))
13356 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13357 (build-system r-build-system)
13358 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13359 (home-page "http://strimmerlab.org/software/longitudinal/")
13360 (synopsis "Analysis of multiple time course data")
13362 "This package contains general data structures and functions for
13363 longitudinal data with multiple variables, repeated measurements, and
13364 irregularly spaced time points. It also implements a shrinkage estimator of
13365 dynamical correlation and dynamical covariance.")
13366 (license license:gpl3+)))
13368 (define-public r-genenet
13375 (uri (cran-uri "GeneNet" version))
13378 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13379 (properties `((upstream-name . "GeneNet")))
13380 (build-system r-build-system)
13382 `(("r-corpcor" ,r-corpcor)
13383 ("r-fdrtool" ,r-fdrtool)
13384 ("r-longitudinal" ,r-longitudinal)))
13385 (home-page "http://strimmerlab.org/software/genenet/")
13386 (synopsis "Modeling and inferring gene networks")
13388 "This package analyzes gene expression (time series) data with focus on
13389 the inference of gene networks. In particular, GeneNet implements the methods
13390 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13391 for learning large-scale gene association networks (including assignment of
13392 putative directions).")
13393 (license license:gpl3+)))
13395 (define-public r-rbamtools
13397 (name "r-rbamtools")
13398 (version "2.16.17")
13402 (uri (cran-uri "rbamtools" version))
13405 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13406 (build-system r-build-system)
13407 (inputs `(("zlib" ,zlib)))
13409 `(("r-refgenome" ,r-refgenome)))
13410 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13411 (synopsis "Read and write BAM (binary alignment) files")
13413 "This package provides an R interface to functions of the SAMtools
13415 (license license:artistic2.0)))
13417 (define-public r-protviz
13424 (uri (cran-uri "protViz" version))
13427 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13428 (properties `((upstream-name . "protViz")))
13429 (build-system r-build-system)
13430 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13431 (home-page "https://github.com/protViz/protViz/")
13432 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13434 "This package helps with quality checks, visualizations and analysis of
13435 mass spectrometry data, coming from proteomics experiments. The package is
13436 developed, tested and used at the Functional Genomics Center Zurich, where it
13437 is used mainly for prototyping, teaching, and having fun with proteomics data.
13438 But it can also be used to do data analysis for small scale data sets.")
13439 (license license:gpl3)))
13441 (define-public r-cmprsk
13448 (uri (cran-uri "cmprsk" version))
13450 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13451 (build-system r-build-system)
13453 `(("r-survival" ,r-survival)))
13455 `(("gfortran" ,gfortran)))
13456 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13457 (synopsis "Subdistribution analysis of competing risks")
13459 "This package provides tool for estimation, testing and regression
13460 modeling of subdistribution functions in competing risks, as described in
13461 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13462 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13463 A proportional hazards model for the subdistribution of a competing risk,
13464 JASA, 94:496-509.")
13465 (license license:gpl2+)))
13467 (define-public r-etm
13474 (uri (cran-uri "etm" version))
13477 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13478 (build-system r-build-system)
13480 `(("r-data-table" ,r-data-table)
13481 ("r-lattice" ,r-lattice)
13483 ("r-rcpparmadillo" ,r-rcpparmadillo)
13484 ("r-survival" ,r-survival)))
13485 (home-page "https://cran.r-project.org/web/packages/etm")
13486 (synopsis "Empirical transition matrix")
13488 "The @dfn{empirical transition matrix} (etm) package estimates
13489 the matrix of transition probabilities for any time-inhomogeneous multistate
13490 model with finite state space using the Aalen-Johansen estimator.")
13491 (license license:expat)))
13493 (define-public r-epi
13500 (uri (cran-uri "Epi" version))
13503 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
13504 (properties `((upstream-name . "Epi")))
13505 (build-system r-build-system)
13507 `(("r-cmprsk" ,r-cmprsk)
13508 ("r-data-table" ,r-data-table)
13509 ("r-dplyr" ,r-dplyr)
13512 ("r-matrix" ,r-matrix)
13514 ("r-numderiv" ,r-numderiv)
13516 ("r-purrr" ,r-purrr)
13517 ("r-survival" ,r-survival)
13519 (home-page "https://BendixCarstensen.com/Epi/")
13520 (synopsis "Statistical analysis in epidemiology")
13522 "This package provides functions for demographic and epidemiological
13523 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13524 particular representation, manipulation and simulation of multistate data -
13525 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13526 @code{etm} and @code{cmprsk} packages. It also contains functions for
13527 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13528 data and some useful functions for tabulation and plotting, as well as a
13529 number of epidemiological data sets.")
13530 (license license:gpl2)))
13532 (define-public r-ppls
13535 (version "1.6-1.1")
13539 (uri (cran-uri "ppls" version))
13542 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13543 (build-system r-build-system)
13544 (propagated-inputs `(("r-mass" ,r-mass)))
13545 (home-page "https://cran.r-project.org/web/packages/ppls")
13546 (synopsis "Penalized partial least squares")
13548 "This package contains linear and nonlinear regression methods based on
13549 partial least squares and penalization techniques. Model parameters are
13550 selected via cross-validation, and confidence intervals ans tests for the
13551 regression coefficients can be conducted via jackknifing.")
13552 (license license:gpl2+)))
13554 (define-public r-huge
13557 (version "1.3.4.1")
13561 (uri (cran-uri "huge" version))
13563 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13564 (build-system r-build-system)
13566 `(("r-igraph" ,r-igraph)
13568 ("r-matrix" ,r-matrix)
13570 ("r-rcppeigen" ,r-rcppeigen)))
13571 (home-page "https://cran.r-project.org/web/packages/huge")
13572 (synopsis "High-dimensional undirected graph estimation")
13574 "This package provides a general framework for high-dimensional
13575 undirected graph estimation. It integrates data preprocessing, neighborhood
13576 screening, graph estimation, and model selection techniques into a pipeline.")
13577 (license license:gpl2)))
13579 (define-public r-parcor
13586 (uri (cran-uri "parcor" version))
13589 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13590 (build-system r-build-system)
13593 ("r-genenet" ,r-genenet)
13594 ("r-glmnet" ,r-glmnet)
13596 ("r-ppls" ,r-ppls)))
13597 (home-page "https://cran.r-project.org/web/packages/parcor")
13598 (synopsis "Regularized estimation of partial correlation matrices")
13600 "This package estimates the matrix of partial correlations based on
13601 different regularized regression methods: lasso, adaptive lasso, PLS, and
13602 Ridge Regression. In addition, the package provides model selection for
13603 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13604 (license license:gpl2+)))
13606 (define-public r-mcmc
13613 (uri (cran-uri "mcmc" version))
13616 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13617 (build-system r-build-system)
13618 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13619 (synopsis "Markov chain Monte Carlo")
13621 "This package simulates continuous distributions of random vectors using
13622 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13623 function that evaluates the log unnormalized density. Algorithms are random
13624 walk Metropolis algorithm (function @code{metrop}), simulated
13625 tempering (function @code{temper}), and morphometric random walk
13626 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13627 by change of variable.")
13628 (license license:expat)))
13630 (define-public r-listenv
13637 (uri (cran-uri "listenv" version))
13640 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13641 (build-system r-build-system)
13643 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13644 (home-page "https://github.com/HenrikBengtsson/listenv")
13645 (synopsis "Environments behaving (almost) as lists")
13647 "This package implements list environments. List environments are
13648 environments that have list-like properties. For instance, the elements of a
13649 list environment are ordered and can be accessed and iterated over using index
13651 (license license:lgpl2.1+)))
13653 (define-public r-globals
13660 (uri (cran-uri "globals" version))
13663 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13664 (build-system r-build-system)
13666 `(("r-codetools" ,r-codetools)))
13667 (home-page "https://github.com/HenrikBengtsson/globals")
13668 (synopsis "Identify global objects in R expressions")
13670 "This package provides tools to identify global (\"unknown\" or \"free\")
13671 objects in R expressions by code inspection using various strategies, e.g.
13672 conservative or liberal. The objective of this package is to make it as
13673 simple as possible to identify global objects for the purpose of exporting
13674 them in distributed compute environments.")
13675 (license license:lgpl2.1+)))
13677 (define-public r-parallelly
13679 (name "r-parallelly")
13684 (uri (cran-uri "parallelly" version))
13687 "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6"))))
13688 (properties `((upstream-name . "parallelly")))
13689 (build-system r-build-system)
13690 (home-page "https://github.com/HenrikBengtsson/parallelly")
13691 (synopsis "Enhancements of the parallel package")
13693 "This package provides utility functions that enhance the @code{parallel}
13694 package and support the built-in parallel backends of the @code{future}
13695 package. For example, @code{availableCores} gives the number of CPU cores
13696 available to your R process as given by R options and environment variables,
13697 including those set by job schedulers on high-performance compute clusters.
13698 If none is set, it will fall back to @code{parallel::detectCores}. Another
13699 example is @code{makeClusterPSOCK}, which is backward compatible with
13700 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13701 remote cluster workers without the need for configuring the firewall to do
13702 port-forwarding to your local computer.")
13703 (license license:lgpl2.1+)))
13705 (define-public r-future
13712 (uri (cran-uri "future" version))
13715 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13716 (build-system r-build-system)
13718 `(("r-digest" ,r-digest)
13719 ("r-globals" ,r-globals)
13720 ("r-listenv" ,r-listenv)
13721 ("r-parallelly" ,r-parallelly)))
13723 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13724 (home-page "https://github.com/HenrikBengtsson/future")
13725 (synopsis "Unified parallel and distributed processing in R")
13727 "The purpose of this package is to provide a lightweight and unified
13728 Future API for sequential and parallel processing of R expression via futures.
13729 This package implements sequential, multicore, multisession, and cluster
13730 futures. With these, R expressions can be evaluated on the local machine, in
13731 parallel a set of local machines, or distributed on a mix of local and remote
13732 machines. Extensions to this package implement additional backends for
13733 processing futures via compute cluster schedulers etc. Because of its unified
13734 API, there is no need to modify any code in order to switch from sequential on
13735 the local machine to, say, distributed processing on a remote compute cluster.")
13736 (license license:lgpl2.1+)))
13738 (define-public r-future-apply
13740 (name "r-future-apply")
13745 (uri (cran-uri "future.apply" version))
13748 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13749 (properties `((upstream-name . "future.apply")))
13750 (build-system r-build-system)
13752 `(("r-future" ,r-future)
13753 ("r-globals" ,r-globals)))
13755 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13756 (home-page "https://github.com/HenrikBengtsson/future.apply")
13757 (synopsis "Apply function to elements in parallel using futures")
13759 "This package provides implementations of @code{apply()},
13760 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13761 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13762 can be resolved using any future-supported backend, e.g. parallel on the local
13763 machine or distributed on a compute cluster.")
13764 (license license:gpl2+)))
13766 (define-public r-rsvd
13773 (uri (cran-uri "rsvd" version))
13776 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13777 (build-system r-build-system)
13779 `(("r-matrix" ,r-matrix)))
13780 (home-page "https://github.com/erichson/rSVD")
13781 (synopsis "Randomized singular value decomposition")
13783 "Low-rank matrix decompositions are fundamental tools and widely used for
13784 data analysis, dimension reduction, and data compression. Classically, highly
13785 accurate deterministic matrix algorithms are used for this task. However, the
13786 emergence of large-scale data has severely challenged our computational
13787 ability to analyze big data. The concept of randomness has been demonstrated
13788 as an effective strategy to quickly produce approximate answers to familiar
13789 problems such as the @dfn{singular value decomposition} (SVD). This package
13790 provides several randomized matrix algorithms such as the randomized singular
13791 value decomposition (@code{rsvd}), randomized principal component
13792 analysis (@code{rpca}), randomized robust principal component
13793 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13794 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13795 functions are provided.")
13796 (license license:gpl3+)))
13798 (define-public r-sloop
13805 (uri (cran-uri "sloop" version))
13808 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13809 (build-system r-build-system)
13811 `(("r-codetools" ,r-codetools)
13812 ("r-crayon" ,r-crayon)
13813 ("r-purrr" ,r-purrr)
13814 ("r-rlang" ,r-rlang)
13815 ("r-tibble" ,r-tibble)))
13816 (home-page "https://github.com/r-lib/sloop")
13817 (synopsis "Helpers for object-oriented programming in R")
13819 "This package provides a collection of helper functions designed to
13820 help you to better understand object oriented programming in R, particularly
13822 (license license:gpl3)))
13824 (define-public r-capushe
13831 (uri (cran-uri "capushe" version))
13834 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13835 (build-system r-build-system)
13836 (propagated-inputs `(("r-mass" ,r-mass)))
13837 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13838 (synopsis "Calibrating penalties using slope heuristics")
13840 "This package provides tools for the calibration of penalized criteria
13841 for model selection. The calibration methods available are based on the slope
13843 (license license:gpl2+)))
13845 (define-public r-dorng
13852 (uri (cran-uri "doRNG" version))
13855 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13856 (properties `((upstream-name . "doRNG")))
13857 (build-system r-build-system)
13859 `(("r-foreach" ,r-foreach)
13860 ("r-iterators" ,r-iterators)
13861 ("r-rngtools" ,r-rngtools)))
13862 (home-page "https://renozao.github.io/doRNG/")
13863 (synopsis "Generic reproducible parallel backend for foreach loops")
13865 "This package provides functions to perform reproducible parallel
13866 @code{foreach} loops, using independent random streams as generated by
13867 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13868 convert standard @code{%dopar%} loops into fully reproducible loops,
13869 independently of the number of workers, the task scheduling strategy, or the
13870 chosen parallel environment and associated foreach backend.")
13871 (license license:gpl2+)))
13873 (define-public r-blockmodeling
13875 (name "r-blockmodeling")
13880 (uri (cran-uri "blockmodeling" version))
13883 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13884 (build-system r-build-system)
13886 `(("r-matrix" ,r-matrix)))
13887 (native-inputs `(("gfortran" ,gfortran)))
13888 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13889 (synopsis "Generalized and classical blockmodeling of valued networks")
13891 "This package is primarily meant as an implementation of generalized
13892 blockmodeling for valued networks. In addition, measures of similarity or
13893 dissimilarity based on structural equivalence and regular equivalence (REGE
13894 algorithms) can be computed and partitioned matrices can be plotted.")
13895 (license license:gpl2+)))
13897 (define-public r-upsetr
13904 (uri (cran-uri "UpSetR" version))
13907 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13908 (properties `((upstream-name . "UpSetR")))
13909 (build-system r-build-system)
13911 `(("r-ggplot2" ,r-ggplot2)
13912 ("r-gridextra" ,r-gridextra)
13914 ("r-scales" ,r-scales)))
13915 (home-page "https://github.com/hms-dbmi/UpSetR")
13916 (synopsis "Visualize intersecting sets")
13918 "This package provides a more scalable alternative to Venn and Euler
13919 diagrams for visualizing intersecting sets. Create visualizations of
13920 intersecting sets using a novel matrix design, along with visualizations of
13921 several common set, element and attribute related tasks.")
13922 (license license:expat)))
13924 ;; This package includes a JavaScript file, which is not minified. When
13925 ;; upgrading please check that there are no new minified JavaScript files.
13926 (define-public r-shinybs
13933 (uri (cran-uri "shinyBS" version))
13936 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13937 (properties `((upstream-name . "shinyBS")))
13938 (build-system r-build-system)
13939 ;; The tests spawn Shiny browser apps. They cannot be run
13940 ;; non-interactively.
13941 (arguments '(#:tests? #f))
13943 `(("r-htmltools" ,r-htmltools)
13944 ("r-shiny" ,r-shiny)))
13945 (home-page "https://ebailey78.github.io/shinyBS/")
13946 (synopsis "Twitter Bootstrap components for Shiny")
13948 "This package adds additional Twitter Bootstrap components to Shiny.")
13949 (license license:gpl3)))
13951 (define-public r-shinyjqui
13953 (name "r-shinyjqui")
13958 (uri (cran-uri "shinyjqui" version))
13961 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
13964 (delete-file "inst/www/shinyjqui.min.js")))))
13965 (properties `((upstream-name . "shinyjqui")))
13966 (build-system r-build-system)
13969 (modify-phases %standard-phases
13970 (add-after 'unpack 'process-javascript
13971 (lambda* (#:key inputs #:allow-other-keys)
13972 (with-directory-excursion "inst/www/"
13973 (let ((source "shinyjqui.js")
13974 (target "shinyjqui.min.js"))
13975 (format #true "Processing ~a --> ~a~%"
13977 (invoke "esbuild" source "--minify"
13978 (string-append "--outfile=" target)))))))))
13980 `(("r-htmltools" ,r-htmltools)
13981 ("r-htmlwidgets" ,r-htmlwidgets)
13982 ("r-jsonlite" ,r-jsonlite)
13983 ("r-shiny" ,r-shiny)))
13985 `(("r-knitr" ,r-knitr)
13986 ("esbuild" ,esbuild)))
13987 (home-page "https://github.com/yang-tang/shinyjqui")
13988 (synopsis "jQuery UI interactions and effects for Shiny")
13990 "This is an extension to Shiny that brings interactions and animation
13991 effects from the jQuery UI library.")
13992 (license license:expat)))
13994 (define-public r-outliers
13996 (name "r-outliers")
14001 (uri (cran-uri "outliers" version))
14004 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14005 (build-system r-build-system)
14006 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14007 (synopsis "Tests for outliers")
14009 "This package provides a collection of some tests commonly used for
14010 identifying outliers.")
14011 (license license:gpl2+)))
14013 (define-public r-bayesm
14020 (uri (cran-uri "bayesm" version))
14022 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14023 (build-system r-build-system)
14025 `(("r-rcpp" ,r-rcpp)
14026 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14027 (home-page "http://www.perossi.org/home/bsm-1")
14028 (synopsis "Bayesian inference for marketing/micro-econometrics")
14030 "This package covers many important models used in marketing and
14031 micro-econometrics applications, including Bayes Regression (univariate or
14032 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14033 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14034 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14035 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14036 Estimation with normal base, Hierarchical Linear Models with normal prior and
14037 covariates, Hierarchical Linear Models with a mixture of normals prior and
14038 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14039 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14040 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14041 analysis of choice-based conjoint data, Bayesian treatment of linear
14042 instrumental variables models, Analysis of Multivariate Ordinal survey data
14043 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14044 Coefficient Logit Models.")
14045 (license license:gpl2+)))
14047 (define-public r-tensora
14054 (uri (cran-uri "tensorA" version))
14057 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14058 (properties `((upstream-name . "tensorA")))
14059 (build-system r-build-system)
14060 (home-page "http://www.stat.boogaart.de/tensorA")
14061 (synopsis "Advanced tensor arithmetic with named indices")
14063 "This package provides convenience functions for advanced linear algebra
14064 with tensors and computation with datasets of tensors on a higher level
14065 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14066 co- and contravariate indices, and parallel computations on sequences of
14068 (license license:gpl2+)))
14070 (define-public r-rarpack
14077 (uri (cran-uri "rARPACK" version))
14080 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14081 (properties `((upstream-name . "rARPACK")))
14082 (build-system r-build-system)
14083 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14084 (home-page "https://github.com/yixuan/rARPACK")
14085 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14087 "This package was previously an R wrapper of the ARPACK library, and now
14088 a shell of the R package RSpectra, an R interface to the Spectra library for
14089 solving large scale eigenvalue/vector problems. The current version of
14090 rARPACK simply imports and exports the functions provided by RSpectra. New
14091 users of rARPACK are advised to switch to the RSpectra package.")
14092 (license license:bsd-3)))
14094 (define-public r-compositions
14096 (name "r-compositions")
14101 (uri (cran-uri "compositions" version))
14104 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14105 (build-system r-build-system)
14107 `(("r-bayesm" ,r-bayesm)
14109 ("r-robustbase" ,r-robustbase)
14110 ("r-tensora" ,r-tensora)))
14112 `(("r-knitr" ,r-knitr)))
14113 (home-page "http://www.stat.boogaart.de/compositions")
14114 (synopsis "Compositional data analysis")
14116 "This package provides functions for the consistent analysis of
14117 compositional data (e.g. portions of substances) and positive
14118 numbers (e.g. concentrations).")
14119 (license license:gpl2+)))
14121 (define-public r-cobs
14128 (uri (cran-uri "cobs" version))
14131 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14132 (build-system r-build-system)
14134 `(("r-quantreg" ,r-quantreg)
14135 ("r-sparsem" ,r-sparsem)))
14136 (home-page "https://cran.r-project.org/web/packages/cobs")
14137 (synopsis "Constrained B-Splines (sparse matrix based)")
14139 "This package provides qualitatively constrained (regression) smoothing
14140 splines via linear programming and sparse matrices.")
14141 (license license:gpl2+)))
14143 (define-public r-drimpute
14145 (name "r-drimpute")
14150 (uri (cran-uri "DrImpute" version))
14153 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14154 (properties `((upstream-name . "DrImpute")))
14155 (build-system r-build-system)
14157 `(("r-rcpp" ,r-rcpp)
14158 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14159 (home-page "https://github.com/ikwak2/DrImpute")
14160 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14162 "This is an R package for imputing dropout events. Many statistical
14163 methods in cell type identification, visualization and lineage reconstruction
14164 do not account for dropout events. DrImpute can improve the performance of
14165 such software by imputing dropout events.")
14166 (license license:gpl3)))
14168 (define-public r-gamlss-dist
14170 (name "r-gamlss-dist")
14175 (uri (cran-uri "gamlss.dist" version))
14177 (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc"))))
14178 (properties `((upstream-name . "gamlss.dist")))
14179 (build-system r-build-system)
14180 (propagated-inputs `(("r-mass" ,r-mass)))
14181 (home-page "http://www.gamlss.org/")
14182 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14184 "This package provides a set of distributions which can be used for
14185 modelling the response variables in Generalized Additive Models for Location
14186 Scale and Shape. The distributions can be continuous, discrete or mixed
14187 distributions. Extra distributions can be created, by transforming, any
14188 continuous distribution defined on the real line, to a distribution defined on
14189 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14190 transformation, respectively.")
14191 ;; Either version of the GPL.
14192 (license (list license:gpl2 license:gpl3))))
14194 ;; This package includes JavaScript files, which are not minified. When
14195 ;; upgrading please check that there are no new minified JavaScript files.
14196 (define-public r-shinyjs
14203 (uri (cran-uri "shinyjs" version))
14206 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14207 (build-system r-build-system)
14209 `(("r-digest" ,r-digest)
14210 ("r-htmltools" ,r-htmltools)
14211 ("r-jsonlite" ,r-jsonlite)
14212 ("r-shiny" ,r-shiny)))
14214 `(("r-knitr" ,r-knitr)))
14215 (home-page "https://deanattali.com/shinyjs")
14216 (synopsis "Improve the user experience of your Shiny apps")
14218 "Perform common useful JavaScript operations in Shiny apps that will
14219 greatly improve your apps without having to know any JavaScript. Examples
14220 include: hiding an element, disabling an input, resetting an input back to its
14221 original value, delaying code execution by a few seconds, and many more useful
14222 functions for both the end user and the developer. Shinyjs can also be used
14223 to easily call your own custom JavaScript functions from R.")
14224 (license license:agpl3+)))
14226 ;; This package includes minified JavaScript files. When upgrading please
14227 ;; check that there are no new minified JavaScript files.
14228 (define-public r-colourpicker
14230 (name "r-colourpicker")
14235 (uri (cran-uri "colourpicker" version))
14238 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14239 (build-system r-build-system)
14241 `(#:modules ((guix build utils)
14242 (guix build r-build-system)
14246 (modify-phases %standard-phases
14247 (add-after 'unpack 'process-javascript
14248 (lambda* (#:key inputs #:allow-other-keys)
14249 (with-directory-excursion "inst"
14253 `((,(assoc-ref inputs "js-salvattore")
14254 "examples/colourInput/www/salvattore.min.js")
14255 (,(assoc-ref inputs "js-jquery")
14256 "htmlwidgets/lib/jquery/jquery.min.js")
14257 ("www/shared/colourpicker/js/colourpicker.js"
14258 "www/shared/colourpicker/js/colourpicker.min.js"))))
14259 (lambda (sources targets)
14260 (for-each (lambda (source target)
14261 (format #t "Processing ~a --> ~a~%"
14263 (delete-file target)
14264 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14265 (call-with-output-file target
14267 (dump-port minified port)))))
14268 sources targets))))
14271 `(("r-ggplot2" ,r-ggplot2)
14272 ("r-htmltools" ,r-htmltools)
14273 ("r-htmlwidgets" ,r-htmlwidgets)
14274 ("r-jsonlite" ,r-jsonlite)
14275 ("r-miniui" ,r-miniui)
14276 ("r-shiny" ,r-shiny)
14277 ("r-shinyjs" ,r-shinyjs)))
14279 `(("r-knitr" ,r-knitr)
14280 ("uglify-js" ,uglify-js)
14284 (uri "https://code.jquery.com/jquery-3.3.1.js")
14287 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14291 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14294 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14295 (home-page "https://github.com/daattali/colourpicker")
14296 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14298 "This package provides a color picker that can be used as an input in
14299 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14300 custom color palettes, and many more options. A plot color helper tool is
14301 available as an RStudio Addin, which helps you pick colors to use in your
14302 plots. A more generic color picker RStudio Addin is also provided to let you
14303 select colors to use in your R code.")
14304 (license license:expat)))
14306 (define-public r-ggextra
14313 (uri (cran-uri "ggExtra" version))
14316 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14317 (properties `((upstream-name . "ggExtra")))
14318 (build-system r-build-system)
14320 `(("r-colourpicker" ,r-colourpicker)
14321 ("r-ggplot2" ,r-ggplot2)
14322 ("r-gtable" ,r-gtable)
14323 ("r-miniui" ,r-miniui)
14325 ("r-scales" ,r-scales)
14326 ("r-shiny" ,r-shiny)
14327 ("r-shinyjs" ,r-shinyjs)))
14329 `(("r-knitr" ,r-knitr)))
14330 (home-page "https://github.com/daattali/ggExtra")
14331 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14333 "This package is a collection of functions and layers to enhance ggplot2.
14334 The flagship function is @code{ggMarginal()}, which can be used to add
14335 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14336 (license license:expat)))
14338 (define-public r-minpack-lm
14340 (name "r-minpack-lm")
14345 (uri (cran-uri "minpack.lm" version))
14348 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14349 (properties `((upstream-name . "minpack.lm")))
14350 (build-system r-build-system)
14351 (native-inputs `(("gfortran" ,gfortran)))
14352 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14353 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14355 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14356 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14357 problems by a modification of the Levenberg-Marquardt algorithm, with support
14358 for lower and upper parameter bounds. The implementation can be used via
14359 @code{nls}-like calls using the @code{nlsLM} function.")
14360 (license license:gpl3)))
14362 (define-public r-moments
14369 (uri (cran-uri "moments" version))
14372 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14373 (build-system r-build-system)
14374 (home-page "https://cran.r-project.org/web/packages/moments")
14375 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14377 "This package provides functions to calculate: moments, Pearson's
14378 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14379 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14380 (license license:gpl2+)))
14382 (define-public r-msir
14389 (uri (cran-uri "msir" version))
14392 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14393 (build-system r-build-system)
14395 `(("r-mclust" ,r-mclust)))
14397 `(("r-knitr" ,r-knitr)))
14398 (home-page "https://cran.r-project.org/web/packages/msir")
14399 (synopsis "Model-based sliced inverse regression")
14401 "This is an R package for dimension reduction based on finite Gaussian
14402 mixture modeling of inverse regression.")
14403 (license license:gpl2+)))
14405 (define-public r-pbivnorm
14407 (name "r-pbivnorm")
14412 (uri (cran-uri "pbivnorm" version))
14415 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14416 (build-system r-build-system)
14417 (native-inputs `(("gfortran" ,gfortran)))
14418 (home-page "https://github.com/brentonk/pbivnorm")
14419 (synopsis "Vectorized bivariate normal CDF")
14421 "This package provides a vectorized R function for calculating
14422 probabilities from a standard bivariate normal CDF.")
14423 (license license:gpl2+)))
14425 (define-public r-lavaan
14432 (uri (cran-uri "lavaan" version))
14435 "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0"))))
14436 (build-system r-build-system)
14438 `(("r-mass" ,r-mass)
14439 ("r-mnormt" ,r-mnormt)
14440 ("r-numderiv" ,r-numderiv)
14441 ("r-pbivnorm" ,r-pbivnorm)))
14442 (home-page "https://lavaan.ugent.be")
14443 (synopsis "Latent variable analysis")
14445 "This package provides tools to fit a variety of latent variable models,
14446 including confirmatory factor analysis, structural equation modeling and
14447 latent growth curve models.")
14448 (license license:gpl2+)))
14450 (define-public r-nonnest2
14452 (name "r-nonnest2")
14457 (uri (cran-uri "nonnest2" version))
14460 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14461 (build-system r-build-system)
14463 `(("r-compquadform" ,r-compquadform)
14464 ("r-lavaan" ,r-lavaan)
14465 ("r-mvtnorm" ,r-mvtnorm)
14466 ("r-sandwich" ,r-sandwich)))
14468 `(("r-knitr" ,r-knitr)))
14469 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14470 (synopsis "Tests of non-nested models")
14472 "This package allows for testing of non-nested models. It includes tests
14473 of model distinguishability and of model fit that can be applied to both
14474 nested and non-nested models. The package also includes functionality to
14475 obtain confidence intervals associated with AIC and BIC.")
14476 ;; Either version of the GPL.
14477 (license (list license:gpl2 license:gpl3))))
14479 (define-public r-penalized
14481 (name "r-penalized")
14486 (uri (cran-uri "penalized" version))
14489 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14490 (build-system r-build-system)
14492 `(("r-rcpp" ,r-rcpp)
14493 ("r-rcpparmadillo" ,r-rcpparmadillo)
14494 ("r-survival" ,r-survival)))
14495 (home-page "https://cran.r-project.org/web/packages/penalized/")
14496 (synopsis "Penalized estimation in GLMs and in the Cox model")
14498 "This package provides tools for fitting possibly high dimensional
14499 penalized regression models. The penalty structure can be any combination of
14500 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14501 constraint on the regression coefficients. The supported regression models
14502 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14503 model. Cross-validation routines allow optimization of the tuning
14505 (license license:gpl2+)))
14507 (define-public r-zim
14514 (uri (cran-uri "ZIM" version))
14517 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14518 (properties `((upstream-name . "ZIM")))
14519 (build-system r-build-system)
14520 (propagated-inputs `(("r-mass" ,r-mass)))
14521 (home-page "https://github.com/biostatstudio/ZIM")
14522 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14524 "Analyze count time series with excess zeros. Two types of statistical
14525 models are supported: Markov regression and state-space models. They are also
14526 known as observation-driven and parameter-driven models respectively in the
14527 time series literature. The functions used for Markov regression or
14528 observation-driven models can also be used to fit ordinary regression models
14529 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14530 negative binomial (ZINB) assumption. The package also contains miscellaneous
14531 functions to compute density, distribution, quantile, and generate random
14532 numbers from ZIP and ZINB distributions.")
14533 (license license:gpl3)))
14535 (define-public r-nor1mix
14542 (uri (cran-uri "nor1mix" version))
14545 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14546 (build-system r-build-system)
14547 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14548 (synopsis "Normal (1-d) mixture models")
14550 "This package provides S3 classes and methods for one-dimensional normal
14551 mixture models, for, e.g., density estimation or clustering algorithms
14552 research and teaching; it provides the widely used Marron-Wand densities. It
14553 also provides tools for efficient random number generation and graphics.")
14554 (license license:gpl2+)))
14556 (define-public r-beanplot
14558 (name "r-beanplot")
14563 (uri (cran-uri "beanplot" version))
14566 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14567 (build-system r-build-system)
14568 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14569 (synopsis "Visualization via beanplots")
14571 "This package provides beanplots, an alternative to
14572 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14574 (license license:gpl2)))
14576 (define-public r-pbdzmq
14583 (uri (cran-uri "pbdZMQ" version))
14586 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14587 (properties `((upstream-name . "pbdZMQ")))
14588 (build-system r-build-system)
14590 `(("zeromq" ,zeromq)
14593 `(("pkg-config" ,pkg-config)))
14594 (home-page "https://pbdr.org/")
14595 (synopsis "R interface to ZeroMQ")
14597 "ZeroMQ is a well-known library for high-performance asynchronous
14598 messaging in scalable, distributed applications. This package provides high
14599 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14600 interactive client/server programming frameworks. A few wrapper functions
14601 compatible with @code{rzmq} are also provided.")
14602 (license license:gpl3)))
14604 (define-public r-repr
14611 (uri (cran-uri "repr" version))
14614 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14615 (build-system r-build-system)
14617 `(("r-base64enc" ,r-base64enc)
14618 ("r-htmltools" ,r-htmltools)
14619 ("r-jsonlite" ,r-jsonlite)
14620 ("r-pillar" ,r-pillar)))
14621 (home-page "https://cran.r-project.org/web/packages/repr/")
14622 (synopsis "Serializable representations")
14624 "This package provides string and binary representations of objects for
14625 several formats and MIME types.")
14626 (license license:gpl3)))
14628 (define-public r-irdisplay
14630 (name "r-irdisplay")
14635 (uri (cran-uri "IRdisplay" version))
14638 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14639 (properties `((upstream-name . "IRdisplay")))
14640 (build-system r-build-system)
14642 `(("r-repr" ,r-repr)))
14643 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14644 (synopsis "Jupyter display machinery")
14646 "This package provides an interface to the rich display capabilities of
14647 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14648 running IRkernel session.")
14649 (license license:expat)))
14651 (define-public r-irkernel
14653 (name "r-irkernel")
14658 (uri (cran-uri "IRkernel" version))
14661 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14662 (properties `((upstream-name . "IRkernel")))
14663 (build-system r-build-system)
14666 (modify-phases %standard-phases
14667 (add-after 'install 'install-kernelspec
14668 (lambda* (#:key outputs #:allow-other-keys)
14669 (let ((out (assoc-ref outputs "out")))
14670 (setenv "HOME" "/tmp")
14671 (invoke "jupyter" "kernelspec" "install"
14674 (string-append out "/site-library/IRkernel/kernelspec"))
14675 ;; Record the absolute file name of the 'R' executable in
14677 (substitute* (string-append out "/share/jupyter"
14678 "/kernels/ir/kernel.json")
14680 (string-append "[\"" (which "R") "\",")))
14683 `(("jupyter" ,jupyter)))
14685 `(("r-crayon" ,r-crayon)
14686 ("r-digest" ,r-digest)
14687 ("r-evaluate" ,r-evaluate)
14688 ("r-irdisplay" ,r-irdisplay)
14689 ("r-jsonlite" ,r-jsonlite)
14690 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14691 ("r-minimal" ,r-minimal)
14692 ("r-pbdzmq" ,r-pbdzmq)
14694 ("r-uuid" ,r-uuid)))
14695 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14696 (synopsis "Native R kernel for Jupyter")
14698 "The R kernel for the Jupyter environment executes R code which the
14699 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14701 (license license:expat)))
14703 (define-public r-gmodels
14710 (uri (cran-uri "gmodels" version))
14713 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14714 (build-system r-build-system)
14716 `(("r-gdata" ,r-gdata)
14717 ("r-mass" ,r-mass)))
14718 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14719 (synopsis "Various R programming tools for model fitting")
14721 "This package provides various R programming tools for model fitting.")
14722 (license license:gpl2)))
14724 (define-public r-apcluster
14726 (name "r-apcluster")
14731 (uri (cran-uri "apcluster" version))
14734 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14735 (build-system r-build-system)
14737 `(("r-matrix" ,r-matrix)
14738 ("r-rcpp" ,r-rcpp)))
14739 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14740 (synopsis "Affinity propagation clustering")
14742 "This package implements affinity propagation clustering introduced by
14743 Frey and Dueck (2007). The package further provides leveraged affinity
14744 propagation and an algorithm for exemplar-based agglomerative clustering that
14745 can also be used to join clusters obtained from affinity propagation. Various
14746 plotting functions are available for analyzing clustering results.")
14747 (license license:gpl2+)))
14749 (define-public r-valr
14756 (uri (cran-uri "valr" version))
14759 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14760 (build-system r-build-system)
14762 `(("r-broom" ,r-broom)
14763 ("r-dplyr" ,r-dplyr)
14764 ("r-ggplot2" ,r-ggplot2)
14766 ("r-readr" ,r-readr)
14767 ("r-rlang" ,r-rlang)
14768 ("r-stringr" ,r-stringr)
14769 ("r-tibble" ,r-tibble)))
14771 `(("r-knitr" ,r-knitr)))
14772 (home-page "https://github.com/rnabioco/valr")
14773 (synopsis "Genome interval arithmetic in R")
14775 "This package enables you to read and manipulate genome intervals and
14776 signals. It provides functionality similar to command-line tool suites within
14777 R, enabling interactive analysis and visualization of genome-scale data.")
14778 (license license:expat)))
14780 (define-public r-rematch2
14782 (name "r-rematch2")
14787 (uri (cran-uri "rematch2" version))
14790 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14791 (build-system r-build-system)
14793 `(("r-tibble" ,r-tibble)))
14794 (home-page "https://github.com/r-lib/rematch2")
14795 (synopsis "Tidy output from regular expression matching")
14797 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14798 return the match results in tidy data frames.")
14799 (license license:expat)))
14801 (define-public r-picante
14808 (uri (cran-uri "picante" version))
14811 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14812 (build-system r-build-system)
14816 ("r-vegan" ,r-vegan)))
14817 (home-page "https://cran.r-project.org/web/packages/picante/")
14818 (synopsis "Integrating phylogenies and ecology")
14820 "This package provides functions for phylocom integration, community
14821 analyses, null-models, traits and evolution. It implements numerous
14822 ecophylogenetic approaches including measures of community phylogenetic and
14823 trait diversity, phylogenetic signal, estimation of trait values for
14824 unobserved taxa, null models for community and phylogeny randomizations, and
14825 utility functions for data input/output and phylogeny plotting. A full
14826 description of package functionality and methods are provided by Kembel et
14828 (license license:gpl2)))
14830 (define-public r-reinforcelearn
14832 (name "r-reinforcelearn")
14837 (uri (cran-uri "reinforcelearn" version))
14840 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14841 (build-system r-build-system)
14843 `(("r-checkmate" ,r-checkmate)
14845 ("r-purrr" ,r-purrr)
14847 (home-page "https://markusdumke.github.io/reinforcelearn")
14848 (synopsis "Reinforcement learning")
14850 "This package implements reinforcement learning environments and
14851 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14852 can be used with function approximation, eligibility traces (Singh & Sutton,
14853 1996) and experience replay (Mnih et al., 2013).")
14854 (license license:expat)))
14856 (define-public r-lemon
14863 (uri (cran-uri "lemon" version))
14866 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14867 (build-system r-build-system)
14869 `(("r-ggplot2" ,r-ggplot2)
14870 ("r-gridextra" ,r-gridextra)
14871 ("r-gtable" ,r-gtable)
14872 ("r-knitr" ,r-knitr)
14873 ("r-lattice" ,r-lattice)
14875 ("r-rlang" ,r-rlang)
14876 ("r-scales" ,r-scales)))
14878 `(("r-knitr" ,r-knitr)))
14879 (home-page "https://github.com/stefanedwards/lemon")
14880 (synopsis "Freshen up your ggplot2 plots")
14882 "This package provides functions for working with legends and axis lines
14883 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14885 (license license:gpl3)))
14887 (define-public r-wgaim
14894 (uri (cran-uri "wgaim" version))
14896 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14897 (build-system r-build-system)
14899 `(("r-ggplot2" ,r-ggplot2)
14901 (home-page "https://cran.r-project.org/web/packages/wgaim")
14902 (synopsis "Whole genome average interval mapping for QTL detection")
14904 "This package integrates sophisticated mixed modelling methods with a
14905 whole genome approach to detecting significant QTL in linkage maps.")
14906 (license license:gpl2+)))
14908 (define-public r-bedr
14915 (uri (cran-uri "bedr" version))
14918 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14919 (build-system r-build-system)
14921 `(("r-data-table" ,r-data-table)
14922 ("r-r-utils" ,r-r-utils)
14923 ("r-testthat" ,r-testthat)
14924 ("r-venndiagram" ,r-venndiagram)
14927 ("bedtools" ,bedtools)
14928 ("htslib" ,htslib))) ; for tabix
14930 `(("r-knitr" ,r-knitr))) ; for vignettes
14931 (home-page "https://cran.r-project.org/web/packages/bedr")
14932 (synopsis "Genomic region processing")
14934 "This package is for genomic regions processing using command line tools
14935 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14936 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14937 The bedr package's API enhances access to these tools as well as offers
14938 additional utilities for genomic regions processing.")
14939 (license license:gpl2)))
14941 (define-public r-sets
14948 (uri (cran-uri "sets" version))
14951 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14952 (properties `((upstream-name . "sets")))
14953 (build-system r-build-system)
14954 (home-page "https://cran.r-project.org/web/packages/sets")
14955 (synopsis "Sets, generalized sets, customizable sets and intervals")
14957 "This package provides data structures and basic operations for ordinary
14958 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14959 customizable sets, and intervals.")
14960 (license license:gpl2)))
14962 (define-public r-partitions
14964 (name "r-partitions")
14969 (uri (cran-uri "partitions" version))
14972 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14973 (build-system r-build-system)
14976 ("r-polynom" ,r-polynom)
14977 ("r-sets" ,r-sets)))
14978 (home-page "https://cran.r-project.org/web/packages/partitions")
14979 (synopsis "Additive partitions of integers")
14981 "This package provides tools to enumerates the partitions, unequal
14982 partitions, and restricted partitions of an integer; the three corresponding
14983 partition functions are also given.")
14984 ;; Any version of the GPL
14985 (license license:gpl2+)))
14987 (define-public r-brobdingnag
14989 (name "r-brobdingnag")
14994 (uri (cran-uri "Brobdingnag" version))
14997 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
14998 (properties `((upstream-name . "Brobdingnag")))
14999 (build-system r-build-system)
15000 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15001 (synopsis "Very large numbers in R")
15003 "This package handles very large numbers in R. Real numbers are held
15004 using their natural logarithms, plus a logical flag indicating sign. The
15005 package includes a vignette that gives a step-by-step introduction to using S4
15007 ;; Any version of the GPL
15008 (license license:gpl2+)))
15010 (define-public r-untb
15017 (uri (cran-uri "untb" version))
15020 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15021 (build-system r-build-system)
15023 `(("r-brobdingnag" ,r-brobdingnag)
15024 ("r-partitions" ,r-partitions)
15025 ("r-polynom" ,r-polynom)))
15026 (home-page "https://github.com/RobinHankin/untb.git")
15027 (synopsis "Ecological drift under the UNTB")
15029 "This package provides numerical simulations, and visualizations, of
15030 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15031 (license license:gpl2+)))
15033 (define-public r-stepwise
15035 (name "r-stepwise")
15040 (uri (cran-uri "stepwise" version))
15043 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15044 (build-system r-build-system)
15045 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15046 (synopsis "Stepwise detection of recombination breakpoints")
15048 "This package provides a stepwise approach to identifying recombination
15049 breakpoints in a genomic sequence alignment.")
15050 (license license:gpl2+)))
15052 (define-public r-snpmaxsel
15054 (name "r-snpmaxsel")
15059 (uri (cran-uri "SNPmaxsel" version))
15062 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15063 (properties `((upstream-name . "SNPmaxsel")))
15064 (build-system r-build-system)
15066 `(("r-combinat" ,r-combinat)
15067 ("r-mvtnorm" ,r-mvtnorm)))
15068 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15069 (synopsis "Maximally selected statistics for SNP data")
15071 "This package implements asymptotic methods related to maximally selected
15072 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15074 (license license:gpl2+)))
15076 (define-public r-acsnminer
15078 (name "r-acsnminer")
15079 (version "0.16.8.25")
15082 (uri (cran-uri "ACSNMineR" version))
15085 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15086 (properties `((upstream-name . "ACSNMineR")))
15087 (build-system r-build-system)
15089 `(("r-ggplot2" ,r-ggplot2)
15090 ("r-gridextra" ,r-gridextra)))
15091 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15092 (synopsis "Gene enrichment analysis")
15094 "This package provides tools to compute and represent gene set enrichment
15095 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15096 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15097 enrichment can be run with hypergeometric test or Fisher exact test, and can
15098 use multiple corrections. Visualization of data can be done either by
15099 barplots or heatmaps.")
15100 (license license:gpl2+)))
15102 (define-public r-seqinr
15109 (uri (cran-uri "seqinr" version))
15112 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15113 (build-system r-build-system)
15115 `(("r-ade4" ,r-ade4)
15116 ("r-segmented" ,r-segmented)))
15119 (home-page "http://seqinr.r-forge.r-project.org/")
15120 (synopsis "Biological sequences retrieval and analysis")
15122 "This package provides tools for exploratory data analysis and data
15123 visualization of biological sequence (DNA and protein) data. It also includes
15124 utilities for sequence data management under the ACNUC system.")
15125 (license license:gpl2+)))
15127 (define-public r-units
15134 (uri (cran-uri "units" version))
15137 "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js"))))
15138 (build-system r-build-system)
15140 `(("udunits" ,udunits)))
15142 `(("r-rcpp" ,r-rcpp)))
15144 `(("r-knitr" ,r-knitr)))
15145 (home-page "https://github.com/r-quantities/units/")
15146 (synopsis "Measurement Units for R Vectors")
15148 "This package provides support for measurement units in R vectors,
15149 matrices and arrays: automatic propagation, conversion, derivation and
15150 simplification of units; raising errors in case of unit incompatibility. It
15151 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15153 (license license:gpl2)))
15155 (define-public r-udunits2
15157 (name "r-udunits2")
15162 (uri (cran-uri "udunits2" version))
15165 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15166 (properties `((upstream-name . "udunits2")))
15167 (build-system r-build-system)
15169 `(("udunits" ,udunits)))
15170 (home-page "https://cran.r-project.org/package=udunits2")
15171 (synopsis "Udunits-2 bindings for R")
15173 "This package provides simple bindings to Unidata's udunits library.")
15174 (license license:gpl2)))
15176 (define-public r-classint
15178 (name "r-classint")
15183 (uri (cran-uri "classInt" version))
15186 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15187 (properties `((upstream-name . "classInt")))
15188 (build-system r-build-system)
15190 `(("r-class" ,r-class)
15191 ("r-e1071" ,r-e1071)
15192 ("r-kernsmooth" ,r-kernsmooth)))
15194 `(("gfortran" ,gfortran)
15195 ("r-knitr" ,r-knitr)))
15196 (home-page "https://github.com/r-spatial/classInt/")
15197 (synopsis "Choose univariate class intervals")
15199 "This package provides selected commonly used methods for choosing
15200 univariate class intervals for mapping or other graphics purposes.")
15201 (license license:gpl2+)))
15203 (define-public r-spdata
15210 (uri (cran-uri "spData" version))
15213 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15214 (properties `((upstream-name . "spData")))
15215 (build-system r-build-system)
15217 `(("r-raster" ,r-raster)
15219 (home-page "https://github.com/Nowosad/spData")
15220 (synopsis "Datasets for spatial analysis")
15222 "This a package containing diverse spatial datasets for demonstrating,
15223 benchmarking and teaching spatial data analysis. It includes R data of class
15224 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15225 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15226 of the datasets are designed to illustrate specific analysis techniques.
15227 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15228 illustrate point pattern analysis techniques.")
15229 (license license:cc0)))
15231 (define-public r-learnbayes
15233 (name "r-learnbayes")
15238 (uri (cran-uri "LearnBayes" version))
15241 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15242 (properties `((upstream-name . "LearnBayes")))
15243 (build-system r-build-system)
15244 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15245 (synopsis "Functions for learning Bayesian inference")
15247 "This package provides a collection of functions helpful in learning the
15248 basic tenets of Bayesian statistical inference. It contains functions for
15249 summarizing basic one and two parameter posterior distributions and predictive
15250 distributions. It contains MCMC algorithms for summarizing posterior
15251 distributions defined by the user. It also contains functions for regression
15252 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15254 (license license:gpl2+)))
15256 (define-public r-deldir
15263 (uri (cran-uri "deldir" version))
15266 "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
15267 (build-system r-build-system)
15268 (native-inputs `(("gfortran" ,gfortran)))
15269 (home-page "https://cran.r-project.org/web/packages/deldir")
15270 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15272 "This package provides tools for calculating the Delaunay triangulation
15273 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15274 of a planar point set. It plots triangulations and tessellations in various
15275 ways, clips tessellations to sub-windows, calculates perimeters of
15276 tessellations, and summarizes information about the tiles of the
15278 (license license:gpl2+)))
15280 (define-public r-sf
15287 (uri (cran-uri "sf" version))
15290 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15291 (build-system r-build-system)
15299 `(("r-classint" ,r-classint)
15301 ("r-magrittr" ,r-magrittr)
15303 ("r-units" ,r-units)))
15305 `(("pkg-config" ,pkg-config)
15306 ("r-knitr" ,r-knitr)))
15307 (home-page "https://github.com/r-spatial/sf/")
15308 (synopsis "Simple features for R")
15310 "This package provides support for simple features, a standardized way to
15311 encode spatial vector data. It binds to GDAL for reading and writing data, to
15312 GEOS for geometrical operations, and to PROJ for projection conversions and
15313 datum transformations.")
15314 ;; Either of these licenses
15315 (license (list license:gpl2 license:expat))))
15317 (define-public r-spdep
15324 (uri (cran-uri "spdep" version))
15327 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15328 (build-system r-build-system)
15330 `(("r-boot" ,r-boot)
15332 ("r-deldir" ,r-deldir)
15334 ("r-gmodels" ,r-gmodels)
15335 ("r-learnbayes" ,r-learnbayes)
15337 ("r-matrix" ,r-matrix)
15341 ("r-spdata" ,r-spdata)))
15343 `(("r-knitr" ,r-knitr)))
15344 (home-page "https://github.com/r-spatial/spdep/")
15345 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15347 "This package provides a collection of functions to create spatial
15348 weights matrix objects from polygon contiguities, from point patterns by
15349 distance and tessellations, for summarizing these objects, and for permitting
15350 their use in spatial data analysis, including regional aggregation by minimum
15352 (license license:gpl2+)))
15354 (define-public r-adegenet
15356 (name "r-adegenet")
15361 (uri (cran-uri "adegenet" version))
15364 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15365 (build-system r-build-system)
15367 `(("r-ade4" ,r-ade4)
15370 ("r-dplyr" ,r-dplyr)
15371 ("r-ggplot2" ,r-ggplot2)
15372 ("r-igraph" ,r-igraph)
15374 ("r-reshape2" ,r-reshape2)
15375 ("r-seqinr" ,r-seqinr)
15376 ("r-shiny" ,r-shiny)
15377 ("r-spdep" ,r-spdep)
15378 ("r-vegan" ,r-vegan)))
15379 (home-page "https://github.com/thibautjombart/adegenet")
15380 (synopsis "Exploratory analysis of genetic and genomic data")
15382 "This package provides a toolset for the exploration of genetic and
15383 genomic data. Adegenet provides formal (S4) classes for storing and handling
15384 various genetic data, including genetic markers with varying ploidy and
15385 hierarchical population structure (@code{genind} class), alleles counts by
15386 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15387 also implements original multivariate methods (DAPC, sPCA), graphics,
15388 statistical tests, simulation tools, distance and similarity measures, and
15389 several spatial methods. A range of both empirical and simulated datasets is
15390 also provided to illustrate various methods.")
15391 (license license:gpl2+)))
15393 (define-public r-pegas
15400 (uri (cran-uri "pegas" version))
15402 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15403 (build-system r-build-system)
15405 `(("r-adegenet" ,r-adegenet)
15407 (home-page "http://ape-package.ird.fr/pegas.html")
15408 (synopsis "Population and evolutionary genetics analysis system")
15410 "This package provides functions for reading, writing, plotting,
15411 analysing, and manipulating allelic and haplotypic data, including from VCF
15412 files, and for the analysis of population nucleotide sequences and
15413 micro-satellites including coalescent analyses, linkage disequilibrium,
15414 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15415 minimum spanning tree and network, and median-joining networks.")
15416 (license license:gpl2+)))
15418 (define-public r-rmetasim
15420 (name "r-rmetasim")
15425 (uri (cran-uri "rmetasim" version))
15428 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15429 (build-system r-build-system)
15431 `(("r-ade4" ,r-ade4)
15432 ("r-adegenet" ,r-adegenet)
15433 ("r-gtools" ,r-gtools)
15434 ("r-pegas" ,r-pegas)))
15435 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15436 (synopsis "Individual-based population genetic simulation environment")
15438 "This package provides an interface between R and the metasim simulation
15439 engine. The simulation environment is documented in: Strand, A.(2002),
15440 Metasim 1.0: an individual-based environment for simulating population
15441 genetics of complex population dynamics.")
15443 (license license:gpl2+)))
15445 (define-public r-genetics
15447 (name "r-genetics")
15448 (version "1.3.8.1.3")
15452 (uri (cran-uri "genetics" version))
15455 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
15456 (build-system r-build-system)
15458 `(("r-combinat" ,r-combinat)
15459 ("r-gdata" ,r-gdata)
15460 ("r-gtools" ,r-gtools)
15462 ("r-mvtnorm" ,r-mvtnorm)))
15463 (home-page "https://cran.r-project.org/web/packages/genetics/")
15464 (synopsis "Population genetics")
15466 "This package provides classes and methods for handling genetic data.
15467 It includes classes to represent genotypes and haplotypes at single markers up
15468 to multiple markers on multiple chromosomes. Function include allele
15469 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15470 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15471 and testing for linkage disequilibrium, ...")
15472 ;; Any GPL version.
15473 (license license:gpl2+)))
15475 (define-public r-snp-plotter
15477 (name "r-snp-plotter")
15482 (uri (cran-uri "snp.plotter" version))
15485 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15486 (properties `((upstream-name . "snp.plotter")))
15487 (build-system r-build-system)
15488 (propagated-inputs `(("r-genetics" ,r-genetics)))
15489 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15490 (synopsis "Plot p-values using single SNP and/or haplotype data")
15492 "This package helps you create plots of p-values using single SNP and/or
15493 haplotype data. Main features of the package include options to display a
15494 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15495 datasets simultaneously. Plots can be created using global and/or individual
15496 haplotype p-values along with single SNP p-values. Images are created as
15497 either PDF/EPS files.")
15498 (license license:gpl2+)))
15500 (define-public r-polspline
15502 (name "r-polspline")
15507 (uri (cran-uri "polspline" version))
15509 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15510 (build-system r-build-system)
15511 (native-inputs `(("gfortran" ,gfortran)))
15512 (home-page "https://cran.r-project.org/web/packages/polspline/")
15513 (synopsis "Polynomial spline routines")
15515 "This package provides routines for the polynomial spline fitting
15516 routines hazard regression, hazard estimation with flexible tails, logspline,
15517 lspec, polyclass, and polymars.")
15518 (license license:gpl2+)))
15520 (define-public r-rms
15527 (uri (cran-uri "rms" version))
15529 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15530 (build-system r-build-system)
15532 `(("r-cluster" ,r-cluster)
15533 ("r-digest" ,r-digest)
15534 ("r-ggplot2" ,r-ggplot2)
15535 ("r-hmisc" ,r-hmisc)
15536 ("r-htmltable" ,r-htmltable)
15537 ("r-htmltools" ,r-htmltools)
15538 ("r-lattice" ,r-lattice)
15540 ("r-multcomp" ,r-multcomp)
15542 ("r-polspline" ,r-polspline)
15543 ("r-quantreg" ,r-quantreg)
15544 ("r-rpart" ,r-rpart)
15545 ("r-sparsem" ,r-sparsem)
15546 ("r-survival" ,r-survival)))
15547 (native-inputs `(("gfortran" ,gfortran)))
15548 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15549 (synopsis "Regression modeling strategies")
15551 "This is a package for regression modeling, testing, estimation,
15552 validation, graphics, prediction, and typesetting by storing enhanced model
15553 design attributes in the fit. The rms package is a collection of functions
15554 that assist with and streamline modeling. It also contains functions for
15555 binary and ordinal logistic regression models, ordinal models for continuous Y
15556 with a variety of distribution families, and the Buckley-James multiple
15557 regression model for right-censored responses, and implements penalized
15558 maximum likelihood estimation for logistic and ordinary linear models. The
15559 package works with almost any regression model, but it was especially written
15560 to work with binary or ordinal regression models, Cox regression, accelerated
15561 failure time models, ordinary linear models, the Buckley-James model,
15562 generalized least squares for serially or spatially correlated observations,
15563 generalized linear models, and quantile regression.")
15564 (license license:gpl2+)))
15566 (define-public r-arsenal
15573 (uri (cran-uri "arsenal" version))
15576 "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn"))))
15577 (properties `((upstream-name . "arsenal")))
15578 (build-system r-build-system)
15579 (propagated-inputs `(("r-knitr" ,r-knitr)))
15580 (native-inputs `(("r-knitr" ,r-knitr)))
15581 (home-page "https://github.com/mayoverse/arsenal")
15582 (synopsis "Functions for large-scale statistical summaries")
15584 "This package provides an arsenal of R functions for large-scale
15585 statistical summaries, which are streamlined to work within the latest
15586 reporting tools in R and RStudio and which use formulas and versatile
15587 summary statistics for summary tables and models. The primary functions
15591 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15592 levels of one or more categorical variables;
15593 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15594 across two time points;
15595 @item @code{modelsum}, which performs simple model fits on one or more
15596 endpoints for many variables (univariate or adjusted for covariates);
15597 @item @code{freqlist}, a powerful frequency table across many categorical
15599 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15600 @item @code{write2}, a function to output tables to a document.
15603 (license license:gpl2+)))
15605 (define-public r-haplo-stats
15607 (name "r-haplo-stats")
15612 (uri (cran-uri "haplo.stats" version))
15615 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15616 (properties `((upstream-name . "haplo.stats")))
15617 (build-system r-build-system)
15619 `(("r-arsenal" ,r-arsenal)
15622 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15623 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15624 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15626 "This package provides routines for the analysis of indirectly measured
15627 haplotypes. The statistical methods assume that all subjects are unrelated
15628 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15629 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15630 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15631 examples in the vignette.")
15632 (license license:gpl2+)))
15634 (define-public r-bqtl
15641 (uri (cran-uri "bqtl" version))
15644 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15645 (build-system r-build-system)
15646 (native-inputs `(("gfortran" ,gfortran)))
15647 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15648 (synopsis "Bayesian QTL mapping toolkit")
15650 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15651 lines. It includes maximum likelihood and Bayesian tools.")
15652 (license license:gpl2+)))
15654 (define-public r-ibdreg
15661 (uri (cran-uri "ibdreg" version))
15664 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15665 (build-system r-build-system)
15666 (home-page "https://www.mayo.edu/research/labs/\
15667 statistical-genetics-genetic-epidemiology/software")
15668 (synopsis "Regression methods for IBD linkage with covariates")
15670 "This package provides a method to test genetic linkage with covariates
15671 by regression methods with response IBD sharing for relative pairs. Account
15672 for correlations of IBD statistics and covariates for relative pairs within
15673 the same pedigree.")
15674 (license license:gpl2+)))
15676 (define-public r-dlmap
15683 (uri (cran-uri "dlmap" version))
15686 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15687 (build-system r-build-system)
15689 `(("r-ibdreg" ,r-ibdreg)
15693 ("r-wgaim" ,r-wgaim)))
15694 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15695 (synopsis "Detection localization mapping for QTL")
15697 "This is package for QTL mapping in a mixed model framework with separate
15698 detection and localization stages. The first stage detects the number of QTL
15699 on each chromosome based on the genetic variation due to grouped markers on
15700 the chromosome; the second stage uses this information to determine the most
15701 likely QTL positions. The mixed model can accommodate general fixed and
15702 random effects, including spatial effects in field trials and pedigree
15703 effects. It is applicable to backcrosses, doubled haploids, recombinant
15704 inbred lines, F2 intercrosses, and association mapping populations.")
15705 (license license:gpl2)))
15707 (define-public r-hwde
15714 (uri (cran-uri "hwde" version))
15717 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15718 (build-system r-build-system)
15719 (home-page "https://cran.r-project.org/web/packages/hwde/")
15720 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15722 "This package fits models for genotypic disequilibria, as described in
15723 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15724 terms are available that account for first order interactions between loci.
15725 It also implements, for a single locus in a single population, a conditional
15726 exact test for Hardy-Weinberg equilibrium.")
15727 (license license:gpl2+)))
15729 (define-public r-tdthap
15736 (uri (cran-uri "tdthap" version))
15739 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15740 (build-system r-build-system)
15741 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15742 (synopsis "TDT tests for extended haplotypes")
15744 "Functions and examples are provided for transmission/disequilibrium
15745 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15746 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15747 (license license:artistic2.0)))
15749 (define-public r-sparql
15755 (uri (cran-uri "SPARQL" version))
15758 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15759 (properties `((upstream-name . "SPARQL")))
15760 (build-system r-build-system)
15762 `(("r-rcurl" ,r-rcurl)
15764 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15765 (synopsis "SPARQL client for R")
15766 (description "This package provides an interface to use SPARQL to pose
15767 SELECT or UPDATE queries to an end-point.")
15768 ;; The only license indication is found in the DESCRIPTION file,
15769 ;; which states GPL-3. So we cannot assume GPLv3+.
15770 (license license:gpl3)))
15772 (define-public r-bookdown
15774 (name "r-bookdown")
15778 (uri (cran-uri "bookdown" version))
15781 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15782 (build-system r-build-system)
15784 `(("r-htmltools" ,r-htmltools)
15785 ("r-knitr" ,r-knitr)
15786 ("r-rmarkdown" ,r-rmarkdown)
15787 ("r-tinytex" ,r-tinytex)
15790 ("pandoc" ,pandoc)))
15791 (home-page "https://github.com/rstudio/bookdown")
15792 (synopsis "Authoring books and technical documents with R markdown")
15793 (description "This package provides output formats and utilities for
15794 authoring books and technical documents with R Markdown.")
15795 (license license:gpl3)))
15797 (define-public r-optparse
15799 (name "r-optparse")
15804 (uri (cran-uri "optparse" version))
15807 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15808 (build-system r-build-system)
15810 `(("r-getopt" ,r-getopt)))
15812 `(("r-knitr" ,r-knitr)))
15813 (home-page "https://github.com/trevorld/optparse")
15814 (synopsis "Command line option parser")
15816 "This package provides a command line parser inspired by Python's
15817 @code{optparse} library to be used with Rscript to write shebang scripts
15818 that accept short and long options.")
15819 (license license:gpl2+)))
15821 (define-public r-kernlab
15828 (uri (cran-uri "kernlab" version))
15830 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15831 (build-system r-build-system)
15832 (home-page "https://cran.r-project.org/web/packages/kernlab")
15833 (synopsis "Kernel-based machine learning tools")
15835 "This package provides kernel-based machine learning methods for
15836 classification, regression, clustering, novelty detection, quantile regression
15837 and dimensionality reduction. Among other methods @code{kernlab} includes
15838 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15840 (license license:gpl2)))
15842 (define-public r-hierfstat
15844 (name "r-hierfstat")
15849 (uri (cran-uri "hierfstat" version))
15852 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15853 (build-system r-build-system)
15855 `(("r-ade4" ,r-ade4)
15856 ("r-adegenet" ,r-adegenet)
15857 ("r-gaston" ,r-gaston)
15858 ("r-gtools" ,r-gtools)))
15860 `(("r-knitr" ,r-knitr)))
15861 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15862 (synopsis "Estimation and tests of hierarchical F-statistics")
15864 "This package allows the estimation of hierarchical F-statistics from
15865 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15866 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15867 are also given to test via randomisations the significance of each F and
15868 variance components, using the likelihood-ratio statistics G.")
15869 (license license:gpl2+)))
15871 (define-public r-hapassoc
15873 (name "r-hapassoc")
15878 (uri (cran-uri "hapassoc" version))
15881 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15882 (build-system r-build-system)
15883 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15884 (synopsis "Inference of trait associations with SNP haplotypes")
15886 "Hapassoc performs likelihood inference of trait associations with
15887 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15888 functions are developed primarily for data collected in cohort or
15889 cross-sectional studies. They can accommodate uncertain haplotype phase and
15890 handle missing genotypes at some SNPs.")
15891 (license license:gpl2)))
15893 (define-public r-sampling
15895 (name "r-sampling")
15900 (uri (cran-uri "sampling" version))
15903 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15904 (build-system r-build-system)
15906 `(("r-lpsolve" ,r-lpsolve)
15907 ("r-mass" ,r-mass)))
15908 (home-page "https://cran.r-project.org/web/packages/sampling/")
15909 (synopsis "Survey sampling")
15911 "This package provides functions for drawing and calibrating samples.")
15912 (license license:gpl2+)))
15914 (define-public r-r2html
15921 (uri (cran-uri "R2HTML" version))
15924 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15925 (properties `((upstream-name . "R2HTML")))
15926 (build-system r-build-system)
15927 (home-page "https://github.com/nalimilan/R2HTML")
15928 (synopsis "HTML export for R objects")
15930 "This package includes HTML functions and methods to write in an HTML
15931 file. Thus, making HTML reports is easy. It includes a function that allows
15932 redirection on the fly, which appears to be very useful for teaching purposes,
15933 as the student can keep a copy of the produced output to keep all that they
15934 did during the course. The package comes with a vignette describing how to
15935 write HTML reports for statistical analysis. Finally, a driver for Sweave
15936 parses HTML flat files containing R code and to automatically write
15937 the corresponding outputs (tables and graphs).")
15938 (license license:gpl2+)))
15940 (define-public r-rjava
15947 (uri (cran-uri "rJava" version))
15950 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15951 (properties `((upstream-name . "rJava")))
15952 (build-system r-build-system)
15954 `(#:modules ((guix build utils)
15955 (guix build r-build-system)
15958 (modify-phases %standard-phases
15959 (add-after 'unpack 'set-JAVA_HOME
15960 (lambda* (#:key inputs #:allow-other-keys)
15961 (let ((jdk (assoc-ref inputs "jdk")))
15962 (setenv "JAVA_HOME" jdk)
15963 (setenv "JAVA" (which "java"))
15964 (setenv "JAR" (which "jar"))
15965 (setenv "JAVAC" (which "javac"))
15966 (setenv "JAVAH" (which "javah"))
15967 (setenv "JAVA_CPPFLAGS"
15968 (string-append "-I" jdk "/include "
15969 "-I" jdk "/include/linux"))
15970 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15971 ((lib) (setenv "JAVA_LIBS" lib))
15972 (_ (error "Could not find libjvm.so"))))
15976 ("jdk" ,icedtea-8 "jdk")
15979 (home-page "https://www.rforge.net/rJava/")
15980 (synopsis "Low-Level R to Java interface")
15982 "This package provides a low-level interface to the Java VM very much
15983 like .C/.Call and friends. It allows the creation of objects, calling methods
15984 and accessing fields.")
15985 (license license:gpl2)))
15987 (define-public r-svmisc
15994 (uri (cran-uri "svMisc" version))
15997 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
15998 (properties `((upstream-name . "svMisc")))
15999 (build-system r-build-system)
16000 (home-page "https://github.com/SciViews/svMisc")
16001 (synopsis "Miscellaneous functions for SciViews")
16003 "This package provides miscellaneous functions for SciViews or general
16004 use, including tools to manage a temporary environment attached to the search
16005 path for temporary variables you do not want to @code{save()} or
16006 @code{load()}; test the current platform; showing progress bars, etc.")
16007 (license license:gpl2)))
16009 (define-public r-xyz
16016 (uri (cran-uri "xyz" version))
16019 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16020 (build-system r-build-system)
16022 `(("r-rcpp" ,r-rcpp)))
16023 (home-page "https://cran.r-project.org/web/packages/xyz/")
16024 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16026 "High dimensional interaction search by brute force requires a quadratic
16027 computational cost in the number of variables. The xyz algorithm provably
16028 finds strong interactions in almost linear time. For details of the algorithm
16029 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16030 interaction search in high-dimensional data.")
16031 ;; Any version of the GPL.
16032 (license license:gpl2+)))
16034 (define-public r-rttf2pt1
16036 (name "r-rttf2pt1")
16041 (uri (cran-uri "Rttf2pt1" version))
16044 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16045 (properties `((upstream-name . "Rttf2pt1")))
16046 (build-system r-build-system)
16047 (home-page "https://github.com/wch/Rttf2pt1")
16048 (synopsis "Font conversion utility")
16050 "This package contains the program @code{ttf2pt1}, for use with the
16051 @code{extrafont} package.")
16052 ;; Most of the files are covered under the Expat license. Some files are
16053 ;; covered under BSD-3. Deviations for individual files are recorded in
16054 ;; the LICENSE file.
16055 (license (list license:bsd-3 license:expat
16056 (license:non-copyleft "file://LICENSE")))))
16058 (define-public r-extrafontdb
16060 (name "r-extrafontdb")
16065 (uri (cran-uri "extrafontdb" version))
16068 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16069 (build-system r-build-system)
16070 (home-page "https://github.com/wch/extrafontdb")
16071 (synopsis "Database for the extrafont package")
16073 "This package holds the database for the @code{extrafont} package.")
16074 (license license:gpl2)))
16076 (define-public r-extrafont
16078 (name "r-extrafont")
16083 (uri (cran-uri "extrafont" version))
16086 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16087 (build-system r-build-system)
16089 `(("r-extrafontdb" ,r-extrafontdb)
16090 ("r-rttf2pt1" ,r-rttf2pt1)))
16091 (home-page "https://github.com/wch/extrafont")
16092 (synopsis "Tools for using fonts in R")
16094 "The extrafont package makes it easier to use fonts other than the basic
16095 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16096 used with PDF or PostScript output files. There are two hurdles for using
16097 fonts in PDF (or Postscript) output files:
16100 @item Making R aware of the font and the dimensions of the characters.
16101 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16102 properly on a device that doesn't have the font. This is usually needed if
16103 you want to print the PDF file or share it with others.
16106 The extrafont package makes both of these things easier.")
16107 (license license:gpl2)))
16109 (define-public r-xkcd
16116 (uri (cran-uri "xkcd" version))
16119 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16120 (build-system r-build-system)
16122 `(("r-extrafont" ,r-extrafont)
16123 ("r-ggplot2" ,r-ggplot2)
16124 ("r-hmisc" ,r-hmisc)))
16125 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16126 (synopsis "Plot ggplot2 graphics in the XKCD style")
16128 "This package provides the means to plot ggplot2 graphs in the style of
16129 the XKCD web comic.")
16130 (license license:gpl3)))
16132 (define-public r-msigdbr
16139 (uri (cran-uri "msigdbr" version))
16142 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16143 (build-system r-build-system)
16145 `(("r-dplyr" ,r-dplyr)
16146 ("r-magrittr" ,r-magrittr)
16147 ("r-rlang" ,r-rlang)
16148 ("r-tibble" ,r-tibble)
16149 ("r-tidyselect" ,r-tidyselect)))
16151 `(("r-knitr" ,r-knitr)))
16152 (home-page "https://github.com/igordot/msigdbr")
16153 (synopsis "MSigDB gene sets for multiple organisms")
16155 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16156 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16157 software in a standard R data frame with key-value pairs. Included are the
16158 original human gene symbols and Entrez IDs as well as the equivalents for
16159 various frequently studied model organisms such as mouse, rat, pig, fly, and
16161 ;; The package is covered under the Expat license, but the upstream MSigDB
16162 ;; files are made available under the Creative Commons Attribution 4.0
16163 ;; International license.
16164 (license (list license:expat license:cc-by4.0))))
16166 (define-public r-gridgraphics
16168 (name "r-gridgraphics")
16173 (uri (cran-uri "gridGraphics" version))
16176 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16177 (properties `((upstream-name . "gridGraphics")))
16178 (build-system r-build-system)
16179 (home-page "https://github.com/pmur002/gridgraphics")
16180 (synopsis "Redraw base graphics using @code{grid} graphics")
16182 "This package provides functions to convert a page of plots drawn with
16183 the @code{graphics} package into identical output drawn with the @code{grid}
16184 package. The result looks like the original @code{graphics}-based plot, but
16185 consists of @code{grid} grobs and viewports that can then be manipulated with
16186 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16187 (license license:gpl2+)))
16189 (define-public r-farver
16196 (uri (cran-uri "farver" version))
16199 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
16200 (build-system r-build-system)
16201 (home-page "https://github.com/thomasp85/farver")
16202 (synopsis "Vectorized color conversion and comparison")
16204 "The encoding of color can be handled in many different ways, using
16205 different color spaces. As different color spaces have different uses,
16206 efficient conversion between these representations are important. This
16207 package provides a set of functions that gives access to very fast color space
16208 conversion and comparisons implemented in C++, and offers 100-fold speed
16209 improvements over the @code{convertColor} function in the @code{grDevices}
16211 (license license:expat)))
16213 (define-public r-ggplotify
16215 (name "r-ggplotify")
16220 (uri (cran-uri "ggplotify" version))
16223 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16224 (build-system r-build-system)
16226 `(("r-ggplot2" ,r-ggplot2)
16227 ("r-gridgraphics" ,r-gridgraphics)
16228 ("r-rvcheck" ,r-rvcheck)))
16230 `(("r-knitr" ,r-knitr)))
16231 (home-page "https://github.com/GuangchuangYu/ggplotify")
16232 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16234 "This package provides tools to convert plot function calls (using
16235 expression or formula) to @code{grob} or @code{ggplot} objects that are
16236 compatible with the @code{grid} and @code{ggplot2} environment. With this
16237 package, we are able to e.g. use @code{cowplot} to align plots produced by
16238 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16239 converting them to @code{ggplot} objects.")
16240 (license license:artistic2.0)))
16242 (define-public r-triebeard
16244 (name "r-triebeard")
16249 (uri (cran-uri "triebeard" version))
16252 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16253 (build-system r-build-system)
16254 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16255 (home-page "https://github.com/Ironholds/triebeard/")
16256 (synopsis "Radix trees in Rcpp")
16258 "Radix trees, or tries, are key-value data structures optimized for
16259 efficient lookups, similar in purpose to hash tables. This package provides
16260 an implementation of radix trees for use in R programming and in developing
16261 packages with Rcpp.")
16262 (license license:expat)))
16264 (define-public r-tweenr
16271 (uri (cran-uri "tweenr" version))
16274 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16275 (build-system r-build-system)
16277 `(("r-farver" ,r-farver)
16278 ("r-magrittr" ,r-magrittr)
16280 ("r-rlang" ,r-rlang)))
16281 (home-page "https://github.com/thomasp85/tweenr")
16282 (synopsis "Interpolate data for smooth animations")
16284 "In order to create smooth animation between states of data, tweening is
16285 necessary. This package provides a range of functions for creating tweened
16286 data that can be used as basis for animation. Furthermore it adds a number of
16287 vectorized interpolaters for common R data types such as numeric, date and
16289 (license license:expat)))
16291 (define-public r-polyclip
16293 (name "r-polyclip")
16298 (uri (cran-uri "polyclip" version))
16301 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16302 (build-system r-build-system)
16303 (native-inputs `(("pkg-config" ,pkg-config)))
16304 (home-page "http://www.angusj.com/delphi/clipper.php")
16305 (synopsis "Polygon clipping")
16307 "This package provides an R port of the library Clipper. It performs
16308 polygon clipping operations (intersection, union, set minus, set difference)
16309 for polygonal regions of arbitrary complexity, including holes. It computes
16310 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16311 dilations) for polygonal regions and polygonal lines. It computes the
16312 Minkowski Sum of general polygons. There is a function for removing
16313 self-intersections from polygon data.")
16314 (license license:boost1.0)))
16316 (define-public r-urltools
16318 (name "r-urltools")
16323 (uri (cran-uri "urltools" version))
16326 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16327 (build-system r-build-system)
16329 `(("r-rcpp" ,r-rcpp)
16330 ("r-triebeard" ,r-triebeard)))
16331 (home-page "https://github.com/Ironholds/urltools/")
16332 (synopsis "Vectorized tools for URL handling and parsing")
16334 "This package provides a toolkit for all URL-handling needs, including
16335 encoding and decoding, parsing, parameter extraction and modification. All
16336 functions are designed to be both fast and entirely vectorized. It is
16337 intended to be useful for people dealing with web-related datasets, such as
16338 server-side logs, although may be useful for other situations involving large
16340 (license license:expat)))
16342 (define-public r-ggforce
16349 (uri (cran-uri "ggforce" version))
16352 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
16353 (build-system r-build-system)
16355 `(("r-ggplot2" ,r-ggplot2)
16356 ("r-gtable" ,r-gtable)
16358 ("r-polyclip" ,r-polyclip)
16360 ("r-rcppeigen" ,r-rcppeigen)
16361 ("r-rlang" ,r-rlang)
16362 ("r-scales" ,r-scales)
16363 ("r-tidyselect" ,r-tidyselect)
16364 ("r-tweenr" ,r-tweenr)
16365 ("r-withr" ,r-withr)))
16366 (home-page "https://ggforce.data-imaginist.com")
16367 (synopsis "Accelerating ggplot2")
16369 "The aim of the ggplot2 package is to aid in visual data investigations.
16370 This focus has led to a lack of facilities for composing specialized plots.
16371 Thi package aims to be a collection of mainly new statistics and geometries
16372 that fills this gap.")
16373 (license license:expat)))
16375 (define-public r-europepmc
16377 (name "r-europepmc")
16382 (uri (cran-uri "europepmc" version))
16385 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16386 (build-system r-build-system)
16388 `(("r-dplyr" ,r-dplyr)
16390 ("r-jsonlite" ,r-jsonlite)
16392 ("r-progress" ,r-progress)
16393 ("r-purrr" ,r-purrr)
16394 ("r-rlang" ,r-rlang)
16395 ("r-tibble" ,r-tibble)
16396 ("r-tidyr" ,r-tidyr)
16397 ("r-urltools" ,r-urltools)
16398 ("r-xml2" ,r-xml2)))
16400 `(("r-knitr" ,r-knitr)))
16401 (home-page "https://github.com/ropensci/europepmc/")
16402 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16404 "This package provides an R Client for the
16405 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16406 Service}. It gives access to both metadata on life science literature and
16407 open access full texts. Europe PMC indexes all PubMed content and other
16408 literature sources including Agricola, a bibliographic database of citations
16409 to the agricultural literature, or Biological Patents. In addition to
16410 bibliographic metadata, the client allows users to fetch citations and
16411 reference lists. Links between life-science literature and other EBI
16412 databases, including ENA, PDB or ChEMBL are also accessible.")
16413 (license license:gpl3)))
16415 (define-public r-ggraph
16422 (uri (cran-uri "ggraph" version))
16425 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
16426 (build-system r-build-system)
16428 `(("r-digest" ,r-digest)
16429 ("r-dplyr" ,r-dplyr)
16430 ("r-ggforce" ,r-ggforce)
16431 ("r-ggplot2" ,r-ggplot2)
16432 ("r-ggrepel" ,r-ggrepel)
16433 ("r-graphlayouts" ,r-graphlayouts)
16434 ("r-gtable" ,r-gtable)
16435 ("r-igraph" ,r-igraph)
16438 ("r-rlang" ,r-rlang)
16439 ("r-scales" ,r-scales)
16440 ("r-tidygraph" ,r-tidygraph)
16441 ("r-viridis" ,r-viridis)
16442 ("r-withr" ,r-withr)))
16444 `(("r-knitr" ,r-knitr)))
16445 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16446 (synopsis "Implementation of grammar of graphics for graphs and networks")
16448 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16449 graph and network visualizations due to its reliance on tabular data input.
16450 The ggraph package is an extension of the ggplot2 API tailored to graph
16451 visualizations and provides the same flexible approach to building up plots
16453 (license license:gpl3)))
16455 (define-public r-gkmsvm
16462 (uri (cran-uri "gkmSVM" version))
16465 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
16466 (properties `((upstream-name . "gkmSVM")))
16467 (build-system r-build-system)
16469 `(("r-kernlab" ,r-kernlab)
16472 ("r-seqinr" ,r-seqinr)))
16473 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
16474 (synopsis "Gapped-kmer support vector machine")
16476 "This R package provides tools for training gapped-kmer SVM classifiers
16477 for DNA and protein sequences. This package supports several sequence
16478 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
16479 (license license:gpl2+)))
16481 (define-public r-varselrf
16483 (name "r-varselrf")
16488 (uri (cran-uri "varSelRF" version))
16491 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16492 (properties `((upstream-name . "varSelRF")))
16493 (build-system r-build-system)
16495 `(("r-randomforest" ,r-randomforest)))
16496 (home-page "https://www.ligarto.org/rdiaz/software/software")
16497 (synopsis "Variable selection using random forests")
16499 "This package provides tools for the variable selection from random
16500 forests using both backwards variable elimination (for the selection of small
16501 sets of non-redundant variables) and selection based on the importance
16502 spectrum (somewhat similar to scree plots; for the selection of large,
16503 potentially highly-correlated variables). The main applications are in
16504 high-dimensional data (e.g., microarray data, and other genomics and
16505 proteomics applications).")
16506 (license license:gpl2+)))
16508 (define-public r-pamr
16515 (uri (cran-uri "pamr" version))
16518 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16519 (build-system r-build-system)
16521 `(("r-cluster" ,r-cluster)
16522 ("r-survival" ,r-survival)))
16523 (native-inputs `(("gfortran" ,gfortran)))
16524 (home-page "https://cran.r-project.org/web/packages/pamr/")
16525 (synopsis "Prediction Analysis for Microarrays")
16527 "This package provides some functions for sample classification in
16529 (license license:gpl2)))
16531 (define-public r-rda
16534 (version "1.0.2-2.1")
16538 (uri (cran-uri "rda" version))
16541 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16542 (build-system r-build-system)
16543 (home-page "https://cran.r-project.org/web/packages/rda/")
16544 (synopsis "Shrunken centroids regularized discriminant analysis")
16546 "This package provides tools for shrunken centroids regularized
16547 discriminant analysis for the purpose of classifying high dimensional data.")
16548 (license license:gpl2+)))
16550 (define-public r-ggvis
16557 (uri (cran-uri "ggvis" version))
16560 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16561 (build-system r-build-system)
16563 `(("r-assertthat" ,r-assertthat)
16564 ("r-dplyr" ,r-dplyr)
16565 ("r-htmltools" ,r-htmltools)
16566 ("r-jsonlite" ,r-jsonlite)
16567 ("r-magrittr" ,r-magrittr)
16568 ("r-rlang" ,r-rlang)
16569 ("r-shiny" ,r-shiny)))
16570 (home-page "https://ggvis.rstudio.com/")
16571 (synopsis "Interactive grammar of graphics")
16573 "This package is a data visualization package for R providing an
16574 implementation of an interactive grammar of graphics, taking the best parts of
16575 ggplot2, combining them with the reactive framework of Shiny and drawing web
16576 graphics using Vega.")
16577 (license license:gpl2)))
16579 (define-public r-gbm
16586 (uri (cran-uri "gbm" version))
16589 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16590 (build-system r-build-system)
16592 `(("r-lattice" ,r-lattice)
16593 ("r-survival" ,r-survival)))
16595 `(("r-knitr" ,r-knitr)))
16596 (home-page "https://github.com/gbm-developers/gbm")
16597 (synopsis "Generalized boosted regression models")
16599 "This package is an implementation of extensions to Freund and Schapire's
16600 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16601 regression methods for least squares, absolute loss, t-distribution loss,
16602 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16603 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16604 and Learning to Rank measures (LambdaMart).")
16605 (license license:gpl2+)))
16607 (define-public r-threejs
16614 (uri (cran-uri "threejs" version))
16617 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16618 (build-system r-build-system)
16620 `(#:modules ((guix build utils)
16621 (guix build r-build-system)
16625 (modify-phases %standard-phases
16626 (add-after 'unpack 'process-javascript
16627 (lambda* (#:key inputs #:allow-other-keys)
16628 (with-directory-excursion "inst"
16632 `((,(assoc-ref inputs "js-jquery")
16633 "htmlwidgets/lib/jquery/jquery.min.js")
16634 (,(assoc-ref inputs "js-threejs-111")
16635 "htmlwidgets/lib/threejs-111/three.min.js"))))
16636 (lambda (sources targets)
16637 (for-each (lambda (source target)
16638 (format #t "Processing ~a --> ~a~%"
16640 (delete-file target)
16641 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16642 (call-with-output-file target
16644 (dump-port minified port)))))
16645 sources targets))))
16648 `(("r-base64enc" ,r-base64enc)
16649 ("r-crosstalk" ,r-crosstalk)
16650 ("r-htmlwidgets" ,r-htmlwidgets)
16651 ("r-igraph" ,r-igraph)))
16653 `(("uglify-js" ,uglify-js)
16657 (uri "https://code.jquery.com/jquery-1.12.4.js")
16660 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16664 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16667 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16668 (home-page "https://bwlewis.github.io/rthreejs")
16669 (synopsis "Interactive 3D scatter plots, networks and globes")
16671 "Create interactive 3D scatter plots, network plots, and globes in R
16672 using the three.js visualization library.")
16673 (license license:expat)))
16675 (define-public r-mlbench
16682 (uri (cran-uri "mlbench" version))
16685 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16686 (build-system r-build-system)
16687 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16688 (synopsis "Machine learning benchmark problems")
16690 "This package provides a collection of artificial and real-world machine
16691 learning benchmark problems, including, e.g., several data sets from the UCI
16693 (license license:gpl2)))
16695 (define-public r-mpm
16702 (uri (cran-uri "mpm" version))
16705 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16706 (build-system r-build-system)
16708 `(("r-kernsmooth" ,r-kernsmooth)
16709 ("r-mass" ,r-mass)))
16710 (home-page "http://mpm.r-forge.r-project.org")
16711 (synopsis "Multivariate projection methods")
16713 "This is a package for exploratory graphical analysis of multivariate
16714 data, specifically gene expression data with different projection methods:
16715 principal component analysis, correspondence analysis, spectral map
16717 (license license:gpl2+)))
16719 (define-public r-png
16725 (uri (cran-uri "png" version))
16728 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16729 (build-system r-build-system)
16731 `(("libpng" ,libpng)
16733 (home-page "https://www.rforge.net/png/")
16734 (synopsis "Read and write PNG images")
16736 "This package provides an easy and simple way to read, write and display
16737 bitmap images stored in the PNG format. It can read and write both files and
16738 in-memory raw vectors.")
16739 ;; Any of these GPL versions.
16740 (license (list license:gpl2 license:gpl3))))
16742 (define-public r-ggcorrplot
16744 (name "r-ggcorrplot")
16749 (uri (cran-uri "ggcorrplot" version))
16752 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16753 (build-system r-build-system)
16755 `(("r-ggplot2" ,r-ggplot2)
16756 ("r-reshape2" ,r-reshape2)))
16757 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16758 (synopsis "Visualization of a correlation matrix using ggplot2")
16760 "The ggcorrplot package can be used to visualize easily a correlation
16761 matrix using ggplot2. It provides a solution for reordering the correlation
16762 matrix and displays the significance level on the plot. It also includes a
16763 function for computing a matrix of correlation p-values.")
16764 (license license:gpl2)))
16766 (define-public r-gridtext
16768 (name "r-gridtext")
16773 (uri (cran-uri "gridtext" version))
16776 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16777 (properties `((upstream-name . "gridtext")))
16778 (build-system r-build-system)
16780 `(("r-jpeg" ,r-jpeg)
16781 ("r-markdown" ,r-markdown)
16784 ("r-rcurl" ,r-rcurl)
16785 ("r-rlang" ,r-rlang)
16786 ("r-stringr" ,r-stringr)
16787 ("r-xml2" ,r-xml2)))
16788 (home-page "https://wilkelab.org/gridtext/")
16789 (synopsis "Improved text rendering support for Grid graphics")
16791 "This package provides support for rendering of formatted text using Grid
16792 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16793 inline CSS directives, and it can be rendered both with and without word
16795 (license license:expat)))
16797 (define-public r-ggtext
16804 (uri (cran-uri "ggtext" version))
16807 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16808 (properties `((upstream-name . "ggtext")))
16809 (build-system r-build-system)
16811 `(("r-ggplot2" ,r-ggplot2)
16812 ("r-gridtext" ,r-gridtext)
16813 ("r-rlang" ,r-rlang)
16814 ("r-scales" ,r-scales)))
16815 (native-inputs `(("r-knitr" ,r-knitr)))
16816 (home-page "https://wilkelab.org/ggtext/")
16817 (synopsis "Improved text rendering support for ggplot2")
16819 "This package provides a ggplot2 extension that enables the rendering of
16820 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16821 etc.). Text boxes with automatic word wrap are also supported.")
16822 (license license:gpl2)))
16824 ;; This package includes minified JavaScript files. When upgrading please
16825 ;; check that there are no new minified JavaScript files.
16826 (define-public r-flexdashboard
16828 (name "r-flexdashboard")
16833 (uri (cran-uri "flexdashboard" version))
16836 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16837 (modules '((guix build utils)))
16840 ;; Delete bundled minified JavaScript files
16841 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16842 (delete-file "inst/www/sly/sly.min.js")
16843 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16844 (delete-file "inst/www/prism/prism.js")
16846 (build-system r-build-system)
16848 `(#:modules ((guix build utils)
16849 (guix build r-build-system)
16853 (ice-9 textual-ports))
16855 (modify-phases %standard-phases
16856 (add-after 'unpack 'process-javascript
16857 (lambda* (#:key inputs #:allow-other-keys)
16858 (with-directory-excursion "inst"
16859 ;; Concatenate all components of prism.js
16860 (let ((contents (string-join
16861 (map (lambda (name)
16862 (call-with-input-file
16863 (assoc-ref inputs name)
16867 "js-prism-line-numbers"))
16869 (call-with-output-file "prism-src.js"
16870 (cut display contents <>)))
16874 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16875 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16877 "www/sly/sly.min.js")
16879 "www/prism/prism.js")
16880 (,(assoc-ref inputs "js-raphael")
16881 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16882 (,(assoc-ref inputs "js-featherlight")
16883 "www/featherlight/featherlight.min.js"))))
16884 (lambda (sources targets)
16885 (for-each (lambda (source target)
16886 (format #t "Processing ~a --> ~a~%"
16888 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16889 (call-with-output-file target
16891 (dump-port minified port)))))
16892 sources targets))))
16895 `(("r-htmltools" ,r-htmltools)
16896 ("r-htmlwidgets" ,r-htmlwidgets)
16897 ("r-jsonlite" ,r-jsonlite)
16898 ("r-knitr" ,r-knitr)
16899 ("r-rmarkdown" ,r-rmarkdown)
16900 ("r-shiny" ,r-shiny)))
16902 `(("uglify-js" ,uglify-js)
16906 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16909 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16913 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16916 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16920 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16923 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16924 ("js-prism-line-numbers"
16927 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16930 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16934 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16937 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16938 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16939 (synopsis "R Markdown format for flexible dashboards")
16941 "This package provides an R Markdown format for converting an R Markdown
16942 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16943 of its components to the containing web page.")
16944 (license license:expat)))
16946 (define-public r-preseqr
16953 (uri (cran-uri "preseqR" version))
16956 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16957 (properties `((upstream-name . "preseqR")))
16958 (build-system r-build-system)
16960 `(("r-polynom" ,r-polynom)))
16961 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16962 (synopsis "Predicting species accumulation curves")
16964 "This package can be used to predict the r-species accumulation
16965 curve (r-SAC), which is the number of species represented at least r times as
16966 a function of the sampling effort. When r = 1, the curve is known as the
16967 species accumulation curve, or the library complexity curve in high-throughput
16968 genomic sequencing. The package includes both parametric and nonparametric
16969 methods, as described by Deng C, et al. (2018).")
16970 (license license:gpl3)))
16972 (define-public r-mapplots
16974 (name "r-mapplots")
16979 (uri (cran-uri "mapplots" version))
16982 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16983 (build-system r-build-system)
16984 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16985 (synopsis "Data visualization on maps")
16987 "This package helps you create simple maps; add sub-plots like pie plots
16988 to a map or any other plot; format, plot and export gridded data. The package
16989 was developed for displaying fisheries data but most functions can be used for
16990 more generic data visualisation.")
16991 (license license:gpl2+)))
16993 (define-public r-pmcmr
17000 (uri (cran-uri "PMCMR" version))
17003 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
17004 (properties `((upstream-name . "PMCMR")))
17005 (build-system r-build-system)
17006 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
17007 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
17009 "This is a deprecated package for calculating pairwise multiple
17010 comparisons of mean rank sums. This package is superseded by the novel
17011 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
17012 compatibility of dependent packages for some time.")
17013 (license license:gpl3+)))
17015 (define-public r-downloader
17017 (name "r-downloader")
17022 (uri (cran-uri "downloader" version))
17025 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17026 (build-system r-build-system)
17028 `(("r-digest" ,r-digest)))
17029 (home-page "https://github.com/wch/downloader")
17030 (synopsis "Download files over HTTP and HTTPS")
17032 "This package provides a wrapper for the @code{download.file} function,
17033 making it possible to download files over HTTPS across platforms. The
17034 @code{RCurl} package provides this functionality (and much more) but has
17035 external dependencies. This package has is implemented purely in R.")
17036 (license license:gpl2)))
17038 (define-public r-rex
17045 (uri (cran-uri "rex" version))
17048 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17049 (build-system r-build-system)
17051 `(("r-lazyeval" ,r-lazyeval)))
17053 `(("r-knitr" ,r-knitr)))
17054 (home-page "https://github.com/kevinushey/rex")
17055 (synopsis "Friendly regular expressions")
17057 "This package provides a friendly interface for the construction of
17058 regular expressions. Regular expressions are a very powerful feature, however
17059 they are often difficult to interpret. Rex allows you to build complex
17060 regular expressions from human readable expressions")
17061 (license license:expat)))
17063 (define-public r-xmlparsedata
17065 (name "r-xmlparsedata")
17070 (uri (cran-uri "xmlparsedata" version))
17073 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
17074 (properties `((upstream-name . "xmlparsedata")))
17075 (build-system r-build-system)
17076 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17077 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17079 "This package provides tools to convert the output of
17080 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17081 @code{XPath}, and is easier to manipulate in general.")
17082 (license license:expat)))
17084 (define-public r-cyclocomp
17086 (name "r-cyclocomp")
17091 (uri (cran-uri "cyclocomp" version))
17094 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17095 (properties `((upstream-name . "cyclocomp")))
17096 (build-system r-build-system)
17098 `(("r-callr" ,r-callr)
17099 ("r-crayon" ,r-crayon)
17101 ("r-remotes" ,r-remotes)
17102 ("r-withr" ,r-withr)))
17103 (home-page "https://github.com/MangoTheCat/cyclocomp")
17104 (synopsis "Cyclomatic complexity of R code")
17106 "Cyclomatic complexity is a software metric, used to indicate the
17107 complexity of a program. It is a quantitative measure of the number of
17108 linearly independent paths through a program's source code. This package
17109 provides tools to compute this metric.")
17110 (license license:expat)))
17112 (define-public r-lintr
17119 (uri (cran-uri "lintr" version))
17122 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17123 (properties `((upstream-name . "lintr")))
17124 (build-system r-build-system)
17126 `(("r-codetools" ,r-codetools)
17127 ("r-crayon" ,r-crayon)
17128 ("r-cyclocomp" ,r-cyclocomp)
17129 ("r-digest" ,r-digest)
17131 ("r-jsonlite" ,r-jsonlite)
17132 ("r-knitr" ,r-knitr)
17134 ("r-rstudioapi" ,r-rstudioapi)
17135 ("r-testthat" ,r-testthat)
17137 ("r-xmlparsedata" ,r-xmlparsedata)))
17138 (home-page "https://github.com/jimhester/lintr")
17139 (synopsis "Linter for R code")
17140 (description "This package checks adherence to a given style, syntax
17141 errors and possible semantic issues. It supports on the fly checking of R
17142 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17143 (license license:expat)))
17145 (define-public r-sctransform
17147 (name "r-sctransform")
17152 (uri (cran-uri "sctransform" version))
17155 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17156 (build-system r-build-system)
17158 `(("r-future" ,r-future)
17159 ("r-future-apply" ,r-future-apply)
17160 ("r-ggplot2" ,r-ggplot2)
17161 ("r-gridextra" ,r-gridextra)
17163 ("r-matrix" ,r-matrix)
17164 ("r-matrixstats" ,r-matrixstats)
17166 ("r-rcpparmadillo" ,r-rcpparmadillo)
17167 ("r-reshape2" ,r-reshape2)))
17168 (home-page "https://github.com/ChristophH/sctransform")
17169 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17171 "This package provides a normalization method for single-cell UMI count
17172 data using a variance stabilizing transformation. The transformation is based
17173 on a negative binomial regression model with regularized parameters. As part
17174 of the same regression framework, this package also provides functions for
17175 batch correction, and data correction.")
17176 (license license:gpl3)))
17178 (define-public r-styler
17185 (uri (cran-uri "styler" version))
17188 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17189 (build-system r-build-system)
17191 `(("r-backports" ,r-backports)
17193 ("r-magrittr" ,r-magrittr)
17194 ("r-purrr" ,r-purrr)
17195 ("r-r-cache" ,r-r-cache)
17196 ("r-rematch2" ,r-rematch2)
17197 ("r-rlang" ,r-rlang)
17198 ("r-rprojroot" ,r-rprojroot)
17199 ("r-tibble" ,r-tibble)
17200 ("r-withr" ,r-withr)
17201 ("r-xfun" ,r-xfun)))
17202 (home-page "https://github.com/r-lib/styler")
17203 (synopsis "Non-invasive pretty printing of R code")
17205 "This is a package for pretty-printing R code without changing the user's
17206 formatting intent.")
17207 (license license:gpl3)))
17209 (define-public r-scrime
17216 (uri (cran-uri "scrime" version))
17219 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17220 (build-system r-build-system)
17221 (home-page "https://cran.r-project.org/web/packages/scrime/")
17222 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17224 "This package provides tools for the analysis of high-dimensional data
17225 developed/implemented at the group \"Statistical Complexity Reduction In
17226 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17227 the functions can also be applied to other types of categorical data.")
17228 (license license:gpl2)))
17230 (define-public r-pbmcapply
17232 (name "r-pbmcapply")
17237 (uri (cran-uri "pbmcapply" version))
17240 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17241 (build-system r-build-system)
17242 (home-page "https://github.com/kvnkuang/pbmcapply")
17243 (synopsis "Track the progress of apply procedures with a progress bar")
17245 "This light-weight package helps you track and visualize the progress of
17246 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17247 (license license:expat)))
17249 (define-public r-blme
17256 (uri (cran-uri "blme" version))
17259 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17260 (build-system r-build-system)
17261 (propagated-inputs `(("r-lme4" ,r-lme4)))
17262 (home-page "https://github.com/vdorie/blme")
17263 (synopsis "Bayesian linear mixed-effects models")
17265 "This package provides tools for maximum a posteriori estimation for
17266 linear and generalized linear mixed-effects models in a Bayesian setting. It
17267 extends the lme4 package.")
17268 (license license:gpl2+)))
17270 (define-public r-batchtools
17272 (name "r-batchtools")
17277 (uri (cran-uri "batchtools" version))
17280 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17281 (build-system r-build-system)
17283 `(("r-backports" ,r-backports)
17284 ("r-base64url" ,r-base64url)
17286 ("r-checkmate" ,r-checkmate)
17287 ("r-data-table" ,r-data-table)
17288 ("r-digest" ,r-digest)
17290 ("r-progress" ,r-progress)
17292 ("r-rappdirs" ,r-rappdirs)
17293 ("r-stringi" ,r-stringi)
17294 ("r-withr" ,r-withr)))
17296 `(("r-knitr" ,r-knitr)))
17297 (home-page "https://github.com/mllg/batchtools")
17298 (synopsis "Tools for computation on batch systems")
17300 "As a successor of the packages BatchJobs and BatchExperiments, this
17301 package provides a parallel implementation of the Map function for high
17302 performance computing systems managed by various schedulers. A multicore and
17303 socket mode allow the parallelization on a local machines, and multiple
17304 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17305 the package provides an abstraction mechanism to define large-scale computer
17306 experiments in a well-organized and reproducible way.")
17307 (license license:lgpl3)))
17309 (define-public r-clue
17316 (uri (cran-uri "clue" version))
17319 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17320 (build-system r-build-system)
17321 (propagated-inputs `(("r-cluster" ,r-cluster)))
17322 (home-page "https://cran.r-project.org/web/packages/clue/")
17323 (synopsis "Tools for analyzing cluster ensembles")
17324 (description "Cluster ensembles are collections of individual solutions to
17325 a given clustering problem which are useful or necessary to consider in a wide
17326 range of applications. This R package provides an extensible computational
17327 environment for creating and analyzing cluster ensembles, with basic data
17328 structures for representing partitions and hierarchies, and facilities for
17329 computing on them, including methods for measuring proximity and obtaining
17330 consensus and secondary clusterings.")
17331 (license license:gpl2)))
17333 (define-public r-sitmo
17340 (uri (cran-uri "sitmo" version))
17343 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17344 (build-system r-build-system)
17345 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17346 (home-page "https://github.com/coatless/sitmo/")
17347 (synopsis "Parallel pseudo random number generator header files")
17349 "This package provides two high quality and fast PPRNGs that may be used
17350 in an OpenMP parallel environment. In addition, there is a generator for one
17351 dimensional low-discrepancy sequence.")
17352 (license license:expat)))
17354 (define-public r-dqrng
17361 (uri (cran-uri "dqrng" version))
17364 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17365 (build-system r-build-system)
17369 ("r-sitmo" ,r-sitmo)))
17370 (home-page "https://www.daqana.org/dqrng")
17371 (synopsis "Fast pseudo random number generators")
17373 "Several fast random number generators are provided as C++ header-only
17374 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17375 Additionally, fast functions for generating random numbers according to a
17376 uniform, normal and exponential distribution are included. The latter two use
17377 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17378 functions are exported to R and as a C++ interface and are enabled for use
17379 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17380 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17381 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17382 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17383 ;; whole is distributed under the terms of the AGPL 3.
17384 (license license:agpl3)))
17386 (define-public r-ingredients
17388 (name "r-ingredients")
17393 (uri (cran-uri "ingredients" version))
17396 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17397 (properties `((upstream-name . "ingredients")))
17398 (build-system r-build-system)
17400 `(("r-ggplot2" ,r-ggplot2)
17401 ("r-gridextra" ,r-gridextra)
17402 ("r-scales" ,r-scales)))
17403 (native-inputs `(("r-knitr" ,r-knitr)))
17404 (home-page "https://ModelOriented.github.io/ingredients/")
17405 (synopsis "Effects and importances of model ingredients")
17407 "This is a collection of tools for assessment of feature importance and
17408 feature effects. Key functions are:
17411 @item @code{feature_importance()} for assessment of global level feature
17413 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17414 @item @code{partial_dependence()} for partial dependence plots,
17415 @item @code{conditional_dependence()} for conditional dependence plots,
17416 @item @code{accumulated_dependence()} for accumulated local effects plots,
17417 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17418 aggregation of ceteris paribus profiles,
17419 @item generic @code{print()} and @code{plot()} for better usability of
17420 selected explainers,
17421 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17422 @item generic @code{describe()} for explanations in natural language.
17424 (license license:gpl3)))
17426 (define-public r-ibreakdown
17428 (name "r-ibreakdown")
17433 (uri (cran-uri "iBreakDown" version))
17436 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17437 (properties `((upstream-name . "iBreakDown")))
17438 (build-system r-build-system)
17439 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17440 (native-inputs `(("r-knitr" ,r-knitr)))
17441 (home-page "https://ModelOriented.github.io/iBreakDown/")
17442 (synopsis "Model agnostic instance level variable attributions")
17444 "This package provides a model agnostic tool for decomposition of
17445 predictions from black boxes. It supports additive attributions and
17446 attributions with interactions. The Break Down Table shows contributions of
17447 every variable to a final prediction. The Break Down Plot presents variable
17448 contributions in a concise graphical way. This package works for
17449 classification and regression models.")
17450 (license license:gpl3)))
17452 (define-public r-dae
17459 (uri (cran-uri "dae" version))
17462 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17463 (build-system r-build-system)
17465 `(("r-ggplot2" ,r-ggplot2)
17466 ("r-plyr" ,r-plyr)))
17468 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17469 (home-page "http://chris.brien.name")
17470 (synopsis "Functions useful in the design and ANOVA of experiments")
17472 "This package provides functions useful in the design and ANOVA of
17473 experiments. The content falls into the following groupings:
17477 @item factor manipulation functions,
17478 @item design functions,
17479 @item ANOVA functions,
17480 @item matrix functions,
17481 @item projector and canonical efficiency functions, and
17482 @item miscellaneous functions.
17485 There is a vignette called @code{DesignNotes} describing how to use the design
17486 functions for randomizing and assessing designs. The ANOVA functions
17487 facilitate the extraction of information when the @code{Error} function has
17488 been used in the call to @code{aov}.")
17489 (license license:gpl2)))
17491 (define-public r-dalex
17498 (uri (cran-uri "DALEX" version))
17501 "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz"))))
17502 (properties `((upstream-name . "DALEX")))
17503 (build-system r-build-system)
17505 `(("r-ggplot2" ,r-ggplot2)
17506 ("r-ibreakdown" ,r-ibreakdown)
17507 ("r-ingredients" ,r-ingredients)))
17508 (home-page "https://pbiecek.github.io/DALEX/")
17509 (synopsis "Descriptive machine learning explanations")
17511 "Machine Learning models are widely used and have various applications in
17512 classification or regression. Models created with boosting, bagging, stacking
17513 or similar techniques are often used due to their high performance, but such
17514 black-box models usually lack interpretability. The DALEX package contains
17515 various explainers that help to understand the link between input variables
17516 and model output.")
17517 ;; Any version of the GPL
17518 (license license:gpl3+)))
17520 (define-public r-enrichr
17527 (uri (cran-uri "enrichR" version))
17530 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17531 (properties `((upstream-name . "enrichR")))
17532 (build-system r-build-system)
17534 `(("r-ggplot2" ,r-ggplot2)
17536 ("r-rjson" ,r-rjson)))
17538 `(("r-knitr" ,r-knitr)))
17539 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17540 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17542 "This package provides an R interface to all Enrichr databases, a
17543 web-based tool for analyzing gene sets and returns any enrichment of common
17544 annotated biological functions.")
17545 (license license:gpl2+)))
17547 (define-public r-plot3d
17554 (uri (cran-uri "plot3D" version))
17557 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17558 (properties `((upstream-name . "plot3D")))
17559 (build-system r-build-system)
17560 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17561 (home-page "https://cran.r-project.org/web/packages/plot3D")
17562 (synopsis "Plot multi-dimensional data")
17564 "This package provides functions for viewing 2D and 3D data, including
17565 perspective plots, slice plots, surface plots, scatter plots, etc. It
17566 includes data sets from oceanography.")
17567 (license license:gpl3+)))
17569 (define-public r-ggfortify
17571 (name "r-ggfortify")
17576 (uri (cran-uri "ggfortify" version))
17579 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17580 (build-system r-build-system)
17582 `(("r-dplyr" ,r-dplyr)
17583 ("r-ggplot2" ,r-ggplot2)
17584 ("r-gridextra" ,r-gridextra)
17585 ("r-scales" ,r-scales)
17586 ("r-stringr" ,r-stringr)
17587 ("r-tibble" ,r-tibble)
17588 ("r-tidyr" ,r-tidyr)))
17590 `(("r-knitr" ,r-knitr)))
17591 (home-page "https://github.com/sinhrks/ggfortify")
17592 (synopsis "Data visualization tools for statistical analysis results")
17594 "This package provides unified plotting tools for statistics commonly
17595 used, such as GLM, time series, PCA families, clustering and survival
17596 analysis. The package offers a single plotting interface for these analysis
17597 results and plots in a unified style using the @code{ggplot2} package.")
17598 (license license:gpl2)))
17600 (define-public r-refmanager
17602 (name "r-refmanager")
17607 (uri (cran-uri "RefManageR" version))
17610 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17611 (properties `((upstream-name . "RefManageR")))
17612 (build-system r-build-system)
17614 `(("r-httr" ,r-httr)
17615 ("r-jsonlite" ,r-jsonlite)
17616 ("r-lubridate" ,r-lubridate)
17618 ("r-stringr" ,r-stringr)
17619 ("r-xml2" ,r-xml2)))
17621 `(("r-knitr" ,r-knitr)))
17622 (home-page "https://github.com/ropensci/RefManageR/")
17623 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17625 "This package provides tools for importing and working with bibliographic
17626 references. It greatly enhances the @code{bibentry} class by providing a
17627 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17628 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17629 by various formats for name lists (author by last names, translator by full
17630 names, etc.). Entries can be updated, combined, sorted, printed in a number
17631 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17632 into R and converted to @code{BibEntry} objects.")
17633 ;; Any of these licenses may be picked.
17634 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17636 (define-public r-citr
17643 (uri (cran-uri "citr" version))
17646 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17647 (build-system r-build-system)
17649 `(("r-assertthat" ,r-assertthat)
17652 ("r-miniui" ,r-miniui)
17653 ("r-refmanager" ,r-refmanager)
17654 ("r-rstudioapi" ,r-rstudioapi)
17655 ("r-shiny" ,r-shiny)
17656 ("r-shinyjs" ,r-shinyjs)
17657 ("r-yaml" ,r-yaml)))
17658 (home-page "https://github.com/crsh/citr")
17659 (synopsis "RStudio add-in to insert Markdown citations")
17661 "This package provides functions and an RStudio add-in that search a
17662 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17663 the current document.")
17664 (license license:expat)))
17666 (define-public r-xgboost
17669 (version "1.3.2.1")
17673 (uri (cran-uri "xgboost" version))
17676 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17677 (build-system r-build-system)
17679 `(("r-data-table" ,r-data-table)
17680 ("r-magrittr" ,r-magrittr)
17681 ("r-matrix" ,r-matrix)))
17683 `(("r-knitr" ,r-knitr)))
17684 (home-page "https://github.com/dmlc/xgboost")
17685 (synopsis "Extreme gradient boosting")
17687 "This package provides an R interface to Extreme Gradient Boosting, which
17688 is an efficient implementation of the gradient boosting framework from Chen
17689 and Guestrin (2016). The package includes efficient linear model solver and
17690 tree learning algorithms. The package can automatically do parallel
17691 computation on a single machine. It supports various objective functions,
17692 including regression, classification and ranking. The package is made to be
17693 extensible, so that users are also allowed to define their own objectives
17695 (license license:asl2.0)))
17697 (define-public r-umap
17700 (version "0.2.7.0")
17704 (uri (cran-uri "umap" version))
17707 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17708 (build-system r-build-system)
17710 `(("r-openssl" ,r-openssl)
17712 ("r-reticulate" ,r-reticulate)
17713 ("r-rspectra" ,r-rspectra)))
17715 `(("r-knitr" ,r-knitr)))
17716 (home-page "https://github.com/tkonopka/umap")
17717 (synopsis "Uniform manifold approximation and projection")
17719 "Uniform manifold approximation and projection is a technique for
17720 dimension reduction. This package provides an interface to the UMAP algorithm
17721 in R, including a translation of the original algorithm into R.")
17722 (license license:expat)))
17724 (define-public r-uwot
17731 (uri (cran-uri "uwot" version))
17734 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17735 (build-system r-build-system)
17737 `(("r-dqrng" ,r-dqrng)
17739 ("r-irlba" ,r-irlba)
17740 ("r-matrix" ,r-matrix)
17742 ("r-rcppannoy" ,r-rcppannoy)
17743 ("r-rcppprogress" ,r-rcppprogress)
17744 ("r-rspectra" ,r-rspectra)))
17745 (home-page "https://github.com/jlmelville/uwot")
17746 (synopsis "Uniform manifold approximation and projection")
17748 "This package provides an implementation of the Uniform Manifold
17749 Approximation and Projection dimensionality reduction by McInnes et
17750 al. (2018). It also provides means to transform new data and to carry out
17751 supervised dimensionality reduction. An implementation of the related
17752 LargeVis method of Tang et al. (2016) is also provided.")
17753 (license license:gpl3)))
17755 (define-public r-kableextra
17757 (name "r-kableextra")
17762 (uri (cran-uri "kableExtra" version))
17765 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
17766 (properties `((upstream-name . "kableExtra")))
17767 (build-system r-build-system)
17769 `(("r-digest" ,r-digest)
17771 ("r-htmltools" ,r-htmltools)
17772 ("r-knitr" ,r-knitr)
17773 ("r-magrittr" ,r-magrittr)
17774 ("r-rmarkdown" ,r-rmarkdown)
17775 ("r-rstudioapi" ,r-rstudioapi)
17776 ("r-rvest" ,r-rvest)
17777 ("r-scales" ,r-scales)
17778 ("r-stringr" ,r-stringr)
17779 ("r-svglite" ,r-svglite)
17780 ("r-viridislite" ,r-viridislite)
17781 ("r-webshot" ,r-webshot)
17782 ("r-xml2" ,r-xml2)))
17784 `(("r-knitr" ,r-knitr)))
17785 (home-page "https://haozhu233.github.io/kableExtra/")
17786 (synopsis "Construct complex tables with pipe syntax")
17788 "Build complex HTML or LaTeX tables using @code{kable()} from
17789 @code{knitr} and the piping syntax from @code{magrittr}. The function
17790 @code{kable()} is a light weight table generator coming from @code{knitr}.
17791 This package simplifies the way to manipulate the HTML or LaTeX codes
17792 generated by @code{kable()} and allows users to construct complex tables and
17793 customize styles using a readable syntax.")
17794 (license license:expat)))
17796 (define-public r-glasso
17803 (uri (cran-uri "glasso" version))
17805 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17806 (build-system r-build-system)
17807 (native-inputs `(("gfortran" ,gfortran)))
17808 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17809 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17811 "This is a package for estimation of a sparse inverse covariance matrix
17812 using a lasso (L1) penalty. Facilities are provided for estimates along a
17813 path of values for the regularization parameter.")
17814 (license license:gpl2)))
17816 (define-public r-rhpcblasctl
17818 (name "r-rhpcblasctl")
17819 (version "0.20-137")
17823 (uri (cran-uri "RhpcBLASctl" version))
17826 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17827 (properties `((upstream-name . "RhpcBLASctl")))
17828 (build-system r-build-system)
17829 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17830 (synopsis "Control the number of threads on BLAS")
17832 "This package allows you to control the number of threads the BLAS
17833 library uses. It is also possible to control the number of threads in
17835 (license license:agpl3+)))
17837 (define-public r-lda
17844 (uri (cran-uri "lda" version))
17847 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17848 (build-system r-build-system)
17849 (home-page "https://cran.r-project.org/web/packages/lda/")
17850 (synopsis "Collapsed Gibbs sampling methods for topic models")
17852 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17853 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17854 mixed-membership stochastic blockmodel. Inference for all of these models is
17855 implemented via a fast collapsed Gibbs sampler written in C. Utility
17856 functions for reading/writing data typically used in topic models, as well as
17857 tools for examining posterior distributions are also included.")
17858 ;; Any version of the LGPL
17859 (license license:lgpl3+)))
17861 (define-public r-rann-l1
17868 (uri (cran-uri "RANN.L1" version))
17871 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17872 (properties `((upstream-name . "RANN.L1")))
17873 (build-system r-build-system)
17874 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17875 (synopsis "Fast nearest neighbour search using L1 metric")
17877 "This package provides tools to find the k nearest neighbours for every
17878 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17879 library. There is support for approximate as well as exact searches, fixed
17880 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17881 computed using the L1 (Manhattan, taxicab) metric.")
17882 (license license:gpl3+)))
17884 (define-public r-leiden
17891 (uri (cran-uri "leiden" version))
17894 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17895 (properties `((upstream-name . "leiden")))
17896 (build-system r-build-system)
17898 `(("r-igraph" ,r-igraph)
17899 ("r-matrix" ,r-matrix)
17900 ("r-reticulate" ,r-reticulate)))
17902 `(("r-knitr" ,r-knitr)))
17903 (home-page "https://github.com/TomKellyGenetics/leiden")
17904 (synopsis "R implementation of Leiden clustering algorithm")
17906 "This package implements the Python @code{leidenalg} module to be called
17907 in R. It enables clustering using the Leiden algorithm for partitioning a
17908 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17909 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17910 (license license:gpl3)))
17912 (define-public r-patchwork
17914 (name "r-patchwork")
17919 (uri (cran-uri "patchwork" version))
17922 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17923 (build-system r-build-system)
17925 `(("r-ggplot2" ,r-ggplot2)
17926 ("r-gtable" ,r-gtable)))
17928 `(("r-knitr" ,r-knitr)))
17929 (home-page "https://github.com/thomasp85/patchwork")
17930 (synopsis "Compose ggplot2 plots")
17932 "The @code{ggplot2} package provides a strong API for sequentially
17933 building up a plot, but does not concern itself with composition of multiple
17934 plots. Patchwork is a package that expands the API to allow for arbitrarily
17935 complex composition of plots by providing mathematical operators for combining
17937 (license license:expat)))
17939 (define-public r-liger
17946 (uri (git-reference
17947 (url "https://github.com/MacoskoLab/liger")
17948 (commit (string-append "v" version))))
17949 (file-name (git-file-name name version))
17952 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17953 (modules '((guix build utils)))
17956 (delete-file "inst/java/ModularityOptimizer.jar")
17958 (build-system r-build-system)
17961 (modify-phases %standard-phases
17962 (add-after 'unpack 'build-java-part
17963 (lambda* (#:key inputs #:allow-other-keys)
17964 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17965 (for-each (lambda (file) (invoke "javac" file))
17966 (find-files "." "\\.java$"))
17967 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17968 (find-files "." "\\.class$"))
17971 `(("r-cowplot" ,r-cowplot)
17972 ("r-dosnow" ,r-dosnow)
17973 ("r-dplyr" ,r-dplyr)
17975 ("r-foreach" ,r-foreach)
17976 ("r-ggplot2" ,r-ggplot2)
17977 ("r-ggrepel" ,r-ggrepel)
17978 ("r-hmisc" ,r-hmisc)
17980 ("r-irlba" ,r-irlba)
17981 ("r-matrix" ,r-matrix)
17982 ("r-mclust" ,r-mclust)
17983 ("r-patchwork" ,r-patchwork)
17985 ("r-rann-l1" ,r-rann-l1)
17987 ("r-rcpparmadillo" ,r-rcpparmadillo)
17988 ("r-riverplot" ,r-riverplot)
17989 ("r-rtsne" ,r-rtsne)
17990 ("r-snow" ,r-snow)))
17992 `(("jdk" ,icedtea "jdk")
17993 ;; See https://github.com/MacoskoLab/liger/issues/96
17994 ;; The optimizer is released under the Expat license.
17998 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
18001 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
18003 ("r-knitr" ,r-knitr))) ; for vignettes
18004 (home-page "https://github.com/MacoskoLab/liger")
18005 (synopsis "Integrate and analyze multiple single-cell datasets")
18007 "LIGER is a package for integrating and analyzing multiple single-cell
18008 datasets, developed and maintained by the Macosko lab. It relies on
18009 integrative non-negative matrix factorization to identify shared and
18010 dataset-specific factors.")
18011 (license license:gpl3)))
18013 (define-public r-harmony
18020 (uri (git-reference
18021 (url "https://github.com/immunogenomics/harmony")
18023 (file-name (git-file-name name version))
18026 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18027 (modules '((guix build utils)))
18030 (for-each delete-file '("config.status" "configure"))
18032 (build-system r-build-system)
18034 `(("r-cowplot" ,r-cowplot)
18035 ("r-dplyr" ,r-dplyr)
18036 ("r-ggplot2" ,r-ggplot2)
18037 ("r-irlba" ,r-irlba)
18038 ("r-matrix" ,r-matrix)
18040 ("r-rcpparmadillo" ,r-rcpparmadillo)
18041 ("r-rcppprogress" ,r-rcppprogress)
18042 ("r-rlang" ,r-rlang)
18043 ("r-tibble" ,r-tibble)
18044 ("r-tidyr" ,r-tidyr)))
18046 `(("autoconf" ,autoconf)))
18047 (home-page "https://github.com/immunogenomics/harmony")
18048 (synopsis "Integration of single cell sequencing data")
18050 "This package provides an implementation of the Harmony algorithm for
18051 single cell integration, described in Korsunsky et al
18052 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18053 function and interfaces to external frameworks.")
18054 (license license:gpl3)))
18056 (define-public r-covr
18063 (uri (cran-uri "covr" version))
18065 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18066 (properties `((upstream-name . "covr")))
18067 (build-system r-build-system)
18069 `(("r-crayon" ,r-crayon)
18070 ("r-digest" ,r-digest)
18072 ("r-jsonlite" ,r-jsonlite)
18074 ("r-withr" ,r-withr)
18075 ("r-yaml" ,r-yaml)))
18077 `(("r-knitr" ,r-knitr))) ; for vignettes
18078 (home-page "https://github.com/r-lib/covr")
18079 (synopsis "Test coverage for R packages")
18081 "Thisp package enables you to track and report code coverage for your
18082 package and (optionally) upload the results to a coverage service. Code
18083 coverage is a measure of the amount of code being exercised by a set of tests.
18084 It is an indirect measure of test quality and completeness. This package is
18085 compatible with any testing methodology or framework and tracks coverage of
18086 both R code and compiled C/C++/FORTRAN code.")
18087 (license license:gpl3)))
18089 (define-public r-systemfonts
18091 (name "r-systemfonts")
18096 (uri (cran-uri "systemfonts" version))
18099 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18100 (properties `((upstream-name . "systemfonts")))
18101 (build-system r-build-system)
18103 `(("r-cpp11" ,r-cpp11)))
18105 `(("fontconfig" ,fontconfig)
18108 `(("pkg-config" ,pkg-config)
18109 ("r-knitr" ,r-knitr)))
18110 (home-page "https://github.com/r-lib/systemfonts")
18111 (synopsis "System native font finding")
18113 "This package provides system native access to the font catalogue. As
18114 font handling varies between systems it is difficult to correctly locate
18115 installed fonts across different operating systems. The 'systemfonts' package
18116 provides bindings to the native libraries for finding font files that can then
18117 be used further by e.g. graphic devices.")
18118 (license license:expat)))
18120 (define-public r-graphlayouts
18122 (name "r-graphlayouts")
18127 (uri (cran-uri "graphlayouts" version))
18130 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18131 (properties `((upstream-name . "graphlayouts")))
18132 (build-system r-build-system)
18134 `(("r-igraph" ,r-igraph)
18136 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18137 (home-page "https://github.com/schochastics/graphlayouts")
18138 (synopsis "Additional layout algorithms for network visualizations")
18140 "This package provides several layout algorithms to visualize networks
18141 which are not part of the igraph library. Most are based on the concept of
18142 stress majorization by Gansner et al. (2004)
18143 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18144 emphasize hidden group structures in networks or focus on specific nodes.")
18145 (license license:expat)))
18147 (define-public r-terra
18154 (uri (cran-uri "terra" version))
18157 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18158 (properties `((upstream-name . "terra")))
18159 (build-system r-build-system)
18164 ("sqlite" ,sqlite) ; needed for proj
18167 `(("r-raster" ,r-raster)
18168 ("r-rcpp" ,r-rcpp)))
18170 `(("pkg-config" ,pkg-config)))
18171 (home-page "https://rspatial.org/terra")
18172 (synopsis "Spatial data analysis")
18174 "This package provides methods for spatial data analysis, especially
18175 raster data. The included methods allow for low-level data manipulation as
18176 well as high-level global, local, zonal, and focal computation. The predict
18177 and interpolate methods facilitate the use of regression type (interpolation,
18178 machine learning) models for spatial prediction. Processing of very large
18179 files is supported.")
18180 (license license:gpl3+)))
18182 (define-public r-tidygraph
18184 (name "r-tidygraph")
18189 (uri (cran-uri "tidygraph" version))
18192 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18193 (properties `((upstream-name . "tidygraph")))
18194 (build-system r-build-system)
18196 `(("r-dplyr" ,r-dplyr)
18197 ("r-igraph" ,r-igraph)
18198 ("r-magrittr" ,r-magrittr)
18199 ("r-pillar" ,r-pillar)
18202 ("r-rlang" ,r-rlang)
18203 ("r-tibble" ,r-tibble)
18204 ("r-tidyr" ,r-tidyr)))
18205 (home-page "https://github.com/thomasp85/tidygraph")
18206 (synopsis "Tidy API for graph manipulation")
18208 "This package provides a graph implementation that can be thought of as
18209 two tidy data frames describing node and edge data respectively. It provides
18210 an approach to manipulate these two virtual data frames using the API defined
18211 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18212 common graph algorithms.")
18213 (license license:expat)))
18215 (define-public r-soupx
18216 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18220 (version (git-version "0.3.1" revision commit))
18224 (uri (git-reference
18225 (url "https://github.com/constantAmateur/SoupX")
18227 (file-name (git-file-name name version))
18230 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18231 (properties `((upstream-name . "SoupX")))
18232 (build-system r-build-system)
18234 `(("r-ggplot2" ,r-ggplot2)
18235 ("r-matrix" ,r-matrix)
18236 ("r-seurat" ,r-seurat)))
18237 (home-page "https://github.com/constantAmateur/SoupX")
18238 (synopsis "Single cell mRNA Soup eXterminator")
18240 "This package provides a package for quantifying, profiling and
18241 removing cell free mRNA contamination (the \"soup\") from droplet based single
18242 cell RNA-seq experiments.")
18243 (license license:gpl2))))
18245 (define-public r-assertr
18252 (uri (cran-uri "assertr" version))
18255 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18256 (build-system r-build-system)
18258 `(("r-dplyr" ,r-dplyr)
18260 ("r-rlang" ,r-rlang)))
18262 `(("r-knitr" ,r-knitr))) ; needed for vignette
18263 (home-page "https://github.com/ropensci/assertr")
18264 (synopsis "Assertive programming for R analysis pipelines")
18266 "This package provides functionality to assert conditions that have to be
18267 met so that errors in data used in analysis pipelines can fail quickly. It is
18268 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18270 (license license:expat)))
18272 (define-public r-parameters
18274 (name "r-parameters")
18279 (uri (cran-uri "parameters" version))
18282 "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm"))))
18283 (properties `((upstream-name . "parameters")))
18284 (build-system r-build-system)
18286 `(("r-bayestestr" ,r-bayestestr)
18287 ("r-insight" ,r-insight)))
18289 `(("r-knitr" ,r-knitr)))
18290 (home-page "https://cran.r-project.org/web/packages/parameters")
18291 (synopsis "Processing of model parameters")
18293 "This package provides utilities for processing the parameters of various
18294 statistical models. Beyond computing p values, CIs, and other indices for a
18295 wide variety of models, this package implements features like standardization
18296 or bootstrapping of parameters and models, feature reduction (feature
18297 extraction and variable selection) as well as conversion between indices of
18299 (license license:gpl3)))
18301 (define-public r-rgdal
18308 (uri (cran-uri "rgdal" version))
18310 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18311 (properties `((upstream-name . "rgdal")))
18312 (build-system r-build-system)
18320 `(("pkg-config" ,pkg-config)
18321 ("r-knitr" ,r-knitr)))
18322 (home-page "http://rgdal.r-forge.r-project.org")
18323 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18325 "This package provides bindings to the Geospatial Data Abstraction
18326 Library (GDAL) and access to projection/transformation operations from the
18328 (license license:gpl2+)))
18330 (define-public r-insol
18337 (uri (cran-uri "insol" version))
18340 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18341 (properties `((upstream-name . "insol")))
18342 (build-system r-build-system)
18344 `(("r-raster" ,r-raster)))
18346 `(("gfortran" ,gfortran)))
18347 (home-page "https://meteoexploration.com/R/insol/index.html")
18348 (synopsis "Tools for calculating solar radiation")
18350 "This package provides functions to compute insolation on tilted
18351 surfaces, computes atmospheric transmittance and related parameters such as:
18352 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18353 time, vector in the direction of the sun, vector normal to surface, and some
18354 atmospheric physics.")
18355 (license license:gpl2+)))
18357 (define-public r-lifecycle
18359 (name "r-lifecycle")
18364 (uri (cran-uri "lifecycle" version))
18367 "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3"))))
18368 (properties `((upstream-name . "lifecycle")))
18369 (build-system r-build-system)
18371 `(("r-glue" ,r-glue)
18372 ("r-rlang" ,r-rlang)))
18374 `(("r-knitr" ,r-knitr))) ; for vignettes
18375 (home-page "https://github.com/r-lib/lifecycle")
18376 (synopsis "Manage the life cycle of your package functions")
18378 "Manage the life cycle of your exported functions with shared
18379 conventions, documentation badges, and non-invasive deprecation warnings. The
18380 lifecycle package defines four development stages (experimental, maturing,
18381 stable, and questioning) and three deprecation stages (soft-deprecated,
18382 deprecated, and defunct). It makes it easy to insert badges corresponding to
18383 these stages in your documentation. Usage of deprecated functions are
18384 signalled with increasing levels of non-invasive verbosity.")
18385 (license license:gpl3)))
18387 (define-public r-assertable
18389 (name "r-assertable")
18394 (uri (cran-uri "assertable" version))
18397 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18398 (build-system r-build-system)
18400 `(("r-data-table" ,r-data-table)))
18402 `(("r-knitr" ,r-knitr)))
18403 (home-page "https://cran.r-project.org/web/packages/assertable/")
18404 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18405 (description "This package provides simple, flexible assertions on
18406 data.frame or data.table objects with verbose output for vetting. While other
18407 assertion packages apply towards more general use-cases, @code{assertable} is
18408 tailored towards tabular data. It includes functions to check variable names
18409 and values, whether the dataset contains all combinations of a given set of
18410 unique identifiers, and whether it is a certain length. In addition,
18411 @code{assertable} includes utility functions to check the existence of target
18412 files and to efficiently import multiple tabular data files into one
18414 (license license:gpl3)))
18416 (define-public r-quadprog
18418 (name "r-quadprog")
18423 (uri (cran-uri "quadprog" version))
18425 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18426 (build-system r-build-system)
18428 `(("gfortran" ,gfortran)))
18429 (home-page "https://cran.r-project.org/web/packages/quadprog")
18430 (synopsis "Functions to solve quadratic programming problems")
18432 "This package contains routines and documentation for solving quadratic
18433 programming problems.")
18434 (license license:gpl3+)))
18436 (define-public r-desolve
18443 (uri (cran-uri "deSolve" version))
18445 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18446 (properties `((upstream-name . "deSolve")))
18447 (build-system r-build-system)
18449 `(("gfortran" ,gfortran)))
18450 (home-page "https://desolve.r-forge.r-project.org/")
18451 (synopsis "Solvers for initial value problems of differential equations")
18452 (description "This package provides functions that solve initial value
18453 problems of a system of first-order @dfn{ordinary differential
18454 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18455 @dfn{differential algebraic equations} (DAE), and of delay differential
18456 equations. The functions provide an interface to the FORTRAN functions
18457 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18458 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18459 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18460 time steps. The package contains routines designed for solving ODEs resulting
18461 from 1-D, 2-D and 3-D partial differential equations that have been converted
18462 to ODEs by numerical differencing.")
18463 (license license:gpl2+)))
18465 (define-public r-pracma
18471 (uri (cran-uri "pracma" version))
18473 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18474 (build-system r-build-system)
18475 (home-page "https://cran.r-project.org/web/packages/pracma/")
18476 (synopsis "Practical numerical math functions")
18477 (description "This package provides functions for numerical analysis and
18478 linear algebra, numerical optimization, differential equations, plus some
18479 special functions. It uses Matlab function names where appropriate to simplify
18481 (license license:gpl3+)))
18483 (define-public r-subplex
18490 (uri (cran-uri "subplex" version))
18493 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18494 (build-system r-build-system)
18496 `(("gfortran" ,gfortran)))
18497 (home-page "https://cran.r-project.org/web/packages/subplex")
18498 (synopsis "Unconstrained optimization using the subplex algorithm")
18500 "This package implements the Subplex optimization algorithm.
18501 It solves unconstrained optimization problems using a simplex method on
18502 subspaces. The method is well suited for optimizing objective functions that
18503 are noisy or are discontinuous at the solution.")
18504 (license license:gpl3+)))
18506 (define-public r-txtplot
18513 (uri (cran-uri "txtplot" version))
18516 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18517 (build-system r-build-system)
18518 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18519 (synopsis "Text-based plotting")
18520 (description "This package provides functions to produce rudimentary ASCII
18521 graphics directly in the terminal window. This package provides a basic
18522 plotting function (and equivalents of curve, density, acf and barplot) as well
18523 as a boxplot function.")
18524 (license license:lgpl3+)))
18526 (define-public r-bio3d
18533 (uri (cran-uri "bio3d" version))
18536 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18537 (properties `((upstream-name . "bio3d")))
18538 (build-system r-build-system)
18539 (inputs `(("zlib" ,zlib)))
18540 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18541 (home-page "http://thegrantlab.org/bio3d/")
18542 (synopsis "Biological structure analysis")
18544 "This package provides utilities to process, organize and explore protein
18545 structure, sequence and dynamics data. Features include the ability to read
18546 and write structure, sequence and dynamic trajectory data, perform sequence
18547 and structure database searches, data summaries, atom selection, alignment,
18548 superposition, rigid core identification, clustering, torsion analysis,
18549 distance matrix analysis, structure and sequence conservation analysis, normal
18550 mode analysis, principal component analysis of heterogeneous structure data,
18551 and correlation network analysis from normal mode and molecular dynamics data.
18552 In addition, various utility functions are provided to enable the statistical
18553 and graphical power of the R environment to work with biological sequence and
18555 (license license:gpl2+)))
18557 (define-public r-bios2cor
18559 (name "r-bios2cor")
18564 (uri (cran-uri "Bios2cor" version))
18567 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18568 (properties `((upstream-name . "Bios2cor")))
18569 (build-system r-build-system)
18571 `(("r-bigmemory" ,r-bigmemory)
18572 ("r-bio3d" ,r-bio3d)
18573 ("r-circular" ,r-circular)
18574 ("r-igraph" ,r-igraph)))
18575 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18576 (synopsis "From biological sequences and simulations to correlation analysis")
18578 "This package provides utilities for computation and analysis of
18579 correlation/covariation in multiple sequence alignments and in side chain
18580 motions during molecular dynamics simulations. Features include the
18581 computation of correlation/covariation scores using a variety of scoring
18582 functions between either sequence positions in alignments or side chain
18583 dihedral angles in molecular dynamics simulations and utilities to analyze the
18584 correlation/covariation matrix through a variety of tools including network
18585 representation and principal components analysis. In addition, several
18586 utility functions are based on the R graphical environment to provide friendly
18587 tools for help in data interpretation.")
18588 (license license:gpl2+)))
18590 ;; This package includes minified JavaScript files. When upgrading please
18591 ;; check that there are no new minified JavaScript files.
18592 (define-public r-networkd3
18594 (name "r-networkd3")
18599 (uri (cran-uri "networkD3" version))
18602 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18605 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18607 (properties `((upstream-name . "networkD3")))
18608 (build-system r-build-system)
18610 `(#:modules ((guix build utils)
18611 (guix build r-build-system)
18615 (modify-phases %standard-phases
18616 (add-after 'unpack 'process-javascript
18617 (lambda* (#:key inputs #:allow-other-keys)
18618 (with-directory-excursion "inst/htmlwidgets/lib/"
18622 `((,(assoc-ref inputs "d3.v4.js")
18623 "d3-4.5.0/d3.min.js"))))
18624 (lambda (sources targets)
18625 (for-each (lambda (source target)
18626 (format #t "Processing ~a --> ~a~%"
18628 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18629 (call-with-output-file target
18631 (dump-port minified port)))))
18632 sources targets))))
18635 `(("uglify-js" ,uglify-js)
18636 ;; NOTE: Make sure that this version of d3 is still valid when
18637 ;; upgrading the package.
18641 (uri "https://d3js.org/d3.v4.js")
18644 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18646 `(("r-htmlwidgets" ,r-htmlwidgets)
18647 ("r-igraph" ,r-igraph)
18648 ("r-magrittr" ,r-magrittr)))
18649 (home-page "https://cran.r-project.org/package=networkD3")
18650 (synopsis "D3 JavaScript network graphs from R")
18652 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18654 (license license:gpl3+)))
18656 (define-public r-aasea
18663 (uri (cran-uri "aaSEA" version))
18666 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18667 (properties `((upstream-name . "aaSEA")))
18668 (build-system r-build-system)
18670 `(("r-bios2cor" ,r-bios2cor)
18672 ("r-hmisc" ,r-hmisc)
18673 ("r-magrittr" ,r-magrittr)
18674 ("r-networkd3" ,r-networkd3)
18675 ("r-plotly" ,r-plotly)
18676 ("r-seqinr" ,r-seqinr)
18677 ("r-shiny" ,r-shiny)
18678 ("r-shinydashboard" ,r-shinydashboard)))
18679 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18680 (synopsis "Amino acid substitution effect analyzer")
18682 "Given a protein multiple sequence alignment, it is a daunting task to
18683 assess the effects of substitutions along sequence length. The aaSEA package
18684 is intended to help researchers to rapidly analyze property changes caused by
18685 single, multiple and correlated amino acid substitutions in proteins.")
18686 (license license:gpl3)))
18688 (define-public r-abacus
18695 (uri (cran-uri "ABACUS" version))
18698 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18699 (properties `((upstream-name . "ABACUS")))
18700 (build-system r-build-system)
18702 `(("r-ggplot2" ,r-ggplot2)
18703 ("r-shiny" ,r-shiny)))
18704 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18705 (synopsis "Apps-based activities for communicating and understanding statistics")
18707 "This package provides a set of Shiny apps for effective communication
18708 and understanding in statistics. The current version includes properties of
18709 normal distribution, properties of sampling distribution, one-sample z and t
18710 tests, two samples independent (unpaired) t test and analysis of variance.")
18711 (license license:gpl3)))
18713 (define-public r-abc-rap
18720 (uri (cran-uri "ABC.RAP" version))
18723 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18724 (properties `((upstream-name . "ABC.RAP")))
18725 (build-system r-build-system)
18726 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18727 (synopsis "Array-based CpG region analysis pipeline")
18729 "This package aims to identify candidate genes that are differentially
18730 methylated between cases and controls. It applies Student's t-test and delta
18731 beta analysis to identify candidate genes containing multiple CpG sites.")
18732 (license license:gpl3)))
18734 (define-public r-abcadm
18741 (uri (cran-uri "abcADM" version))
18744 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18745 (properties `((upstream-name . "abcADM")))
18746 (build-system r-build-system)
18749 ("r-rcpp" ,r-rcpp)))
18750 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18751 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18753 "This package provides tools to estimate parameters of accumulated
18754 damage (load duration) models based on failure time data under a Bayesian
18755 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18756 long-term reliability under stochastic load profiles.")
18757 (license license:gpl3)))
18759 (define-public r-rglpk
18766 (uri (cran-uri "Rglpk" version))
18769 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18770 (properties `((upstream-name . "Rglpk")))
18771 (build-system r-build-system)
18773 `(("r-slam" ,r-slam)))
18776 (home-page "https://r-forge.r-project.org/projects/rglp/")
18777 (synopsis "R interface to the GNU Linear Programming Kit")
18779 "This package provides an R interface to the GNU Linear Programming Kit,
18780 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18781 integer linear programming} (MILP) and other related problems.")
18783 (license (list license:gpl2 license:gpl3))))
18785 (define-public r-abcdefba
18787 (name "r-abcdefba")
18792 (uri (cran-uri "abcdeFBA" version))
18795 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18796 (properties `((upstream-name . "abcdeFBA")))
18797 (build-system r-build-system)
18799 `(("r-corrplot" ,r-corrplot)
18800 ("r-lattice" ,r-lattice)
18802 ("r-rglpk" ,r-rglpk)))
18803 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18804 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18806 "This package provides functions for Constraint Based Simulation using
18807 Flux Balance Analysis and informative analysis of the data generated during
18809 (license license:gpl2)))
18811 (define-public r-abcrlda
18818 (uri (cran-uri "abcrlda" version))
18821 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18822 (properties `((upstream-name . "abcrlda")))
18823 (build-system r-build-system)
18824 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18825 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18827 "This package offers methods to perform @dfn{asymptotically
18828 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18829 cost-sensitive binary classification. The bias-correction is an estimate of
18830 the bias term added to regularized discriminant analysis that minimizes the
18832 (license license:gpl3)))
18834 (define-public r-abemus
18841 (uri (cran-uri "abemus" version))
18844 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18845 (properties `((upstream-name . "abemus")))
18846 (build-system r-build-system)
18848 `(("r-data-table" ,r-data-table)))
18849 (home-page "https://cran.r-project.org/web/packages/abemus/")
18850 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18852 "This package provides an implementation of @dfn{Adaptive Base Error
18853 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18854 platform-specific genetic knowledge and empirical signal to readily detect and
18855 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18856 cell free DNA} (cfDNA).")
18857 (license license:gpl3)))
18859 ;; This package includes minified JavaScript files. When upgrading please
18860 ;; check that there are no new minified JavaScript files.
18861 (define-public r-rintrojs
18863 (name "r-rintrojs")
18868 (uri (cran-uri "rintrojs" version))
18871 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18872 (properties `((upstream-name . "rintrojs")))
18873 (build-system r-build-system)
18875 `(#:modules ((guix build utils)
18876 (guix build r-build-system)
18880 (modify-phases %standard-phases
18881 (add-after 'unpack 'process-javascript
18882 (lambda* (#:key inputs #:allow-other-keys)
18883 (with-directory-excursion "inst/javascript/introjs/"
18887 `((,(assoc-ref inputs "intro.js")
18889 (lambda (sources targets)
18890 (for-each (lambda (source target)
18891 (format #t "Processing ~a --> ~a~%"
18893 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18894 (call-with-output-file target
18896 (dump-port minified port)))))
18897 sources targets))))
18900 `(("uglify-js" ,uglify-js)
18904 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18907 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18909 `(("r-jsonlite" ,r-jsonlite)
18910 ("r-shiny" ,r-shiny)))
18911 (home-page "https://github.com/carlganz/rintrojs")
18912 (synopsis "Wrapper for the Intro.js library")
18914 "This package provides a wrapper for the @url{http://www.introjs.com,
18915 Intro.js} library. This package makes it easy to include step-by-step
18916 introductions, and clickable hints in a Shiny application. It supports both
18917 static introductions in the UI, and programmatic introductions from the
18919 (license license:agpl3+)))
18921 (define-public r-sysfonts
18923 (name "r-sysfonts")
18928 (uri (cran-uri "sysfonts" version))
18931 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18932 (properties `((upstream-name . "sysfonts")))
18933 (build-system r-build-system)
18935 `(("freetype" ,freetype)
18939 `(("pkg-config" ,pkg-config)))
18940 (home-page "https://github.com/yixuan/sysfonts")
18941 (synopsis "Loading fonts into R")
18943 "This is a package to simplify loading of system fonts and Google Fonts
18944 into R, in order to support other packages.")
18945 (license license:gpl2)))
18947 (define-public r-showtextdb
18949 (name "r-showtextdb")
18954 (uri (cran-uri "showtextdb" version))
18957 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18958 (properties `((upstream-name . "showtextdb")))
18959 (build-system r-build-system)
18961 `(("r-sysfonts" ,r-sysfonts)))
18962 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18963 (synopsis "Font files for the 'showtext' package")
18965 "This package provides font files that can be used by the @code{showtext}
18967 (license license:asl2.0)))
18969 (define-public r-showtext
18971 (name "r-showtext")
18976 (uri (cran-uri "showtext" version))
18979 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18980 (properties `((upstream-name . "showtext")))
18981 (build-system r-build-system)
18983 `(("freetype" ,freetype)
18987 `(("r-showtextdb" ,r-showtextdb)
18988 ("r-sysfonts" ,r-sysfonts)))
18990 `(("pkg-config" ,pkg-config)
18991 ("r-knitr" ,r-knitr)))
18992 (home-page "https://github.com/yixuan/showtext")
18993 (synopsis "Using fonts more easily in R graphs")
18995 "This package aims to make it easy to use various types of
18996 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
18997 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
18998 will be converted into polygons or raster images, hence after the plot has
18999 been created, it no longer relies on the font files. No external software
19000 such as Ghostscript is needed to use this package.")
19001 (license license:asl2.0)))
19003 (define-public r-emojifont
19005 (name "r-emojifont")
19010 (uri (cran-uri "emojifont" version))
19013 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
19014 (properties `((upstream-name . "emojifont")))
19015 (build-system r-build-system)
19017 `(("r-ggplot2" ,r-ggplot2)
19018 ("r-proto" ,r-proto)
19019 ("r-showtext" ,r-showtext)
19020 ("r-sysfonts" ,r-sysfonts)))
19021 (home-page "https://guangchuangyu.github.io/emojifont")
19022 (synopsis "Emoji and Font Awesome in R graphics")
19024 "This package enables the use of emoji and the Font Awesome glyphs in
19025 both base and ggplot2 graphics.")
19026 (license license:artistic2.0)))
19028 (define-public r-abstractr
19030 (name "r-abstractr")
19035 (uri (cran-uri "abstractr" version))
19038 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19039 (properties `((upstream-name . "abstractr")))
19040 (build-system r-build-system)
19042 `(("r-colourpicker" ,r-colourpicker)
19043 ("r-emojifont" ,r-emojifont)
19044 ("r-ggplot2" ,r-ggplot2)
19045 ("r-gridextra" ,r-gridextra)
19046 ("r-rintrojs" ,r-rintrojs)
19047 ("r-shiny" ,r-shiny)
19048 ("r-shinythemes" ,r-shinythemes)))
19049 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19050 (synopsis "R-Shiny application for creating visual abstracts")
19052 "This package provides an R Shiny application to create visual abstracts
19053 for original research. A variety of user defined options and formatting are
19055 (license license:gpl3)))
19057 (define-public r-qgam
19064 (uri (cran-uri "qgam" version))
19067 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19068 (properties `((upstream-name . "qgam")))
19069 (build-system r-build-system)
19071 `(("r-doparallel" ,r-doparallel)
19074 ("r-shiny" ,r-shiny)))
19075 (native-inputs `(("r-knitr" ,r-knitr)))
19076 (home-page "https://cran.r-project.org/web/packages/qgam/")
19077 (synopsis "Smooth additive quantile regression models")
19079 "This package provides smooth additive quantile regression models, fitted
19080 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19081 the smoothing parameters are estimated automatically by marginal loss
19082 minimization, while the regression coefficients are estimated using either
19083 PIRLS or Newton algorithm. The learning rate is determined so that the
19084 Bayesian credible intervals of the estimated effects have approximately the
19085 correct coverage. The main function is @code{qgam()} which is similar to
19086 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19087 regression models.")
19088 (license license:gpl2+)))
19090 (define-public r-abtest
19097 (uri (cran-uri "abtest" version))
19100 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19101 (properties `((upstream-name . "abtest")))
19102 (build-system r-build-system)
19104 `(("r-matrix" ,r-matrix)
19105 ("r-mvtnorm" ,r-mvtnorm)
19106 ("r-plotrix" ,r-plotrix)
19108 ("r-rcolorbrewer" ,r-rcolorbrewer)
19111 ("r-truncnorm" ,r-truncnorm)))
19112 (home-page "https://cran.r-project.org/web/packages/abtest/")
19113 (synopsis "Bayesian A/B testing")
19115 "This package provides functions for Bayesian A/B testing including prior
19116 elicitation options based on Kass and Vaidyanathan (1992)
19117 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19118 (license license:gpl2+)))
19120 (define-public r-accept
19127 (uri (cran-uri "accept" version))
19130 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19131 (properties `((upstream-name . "accept")))
19132 (build-system r-build-system)
19134 `(("r-dplyr" ,r-dplyr)
19135 ("r-extrafont" ,r-extrafont)
19137 ("r-plotly" ,r-plotly)
19138 ("r-stringr" ,r-stringr)
19139 ("r-viridis" ,r-viridis)))
19140 (home-page "https://cran.r-project.org/web/packages/accept/")
19141 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19143 "This package allows clinicians to predict the rate and severity of
19144 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19145 Disease} (COPD) patients, based on the clinical prediction model published in
19146 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19147 (license license:gpl3)))
19149 (define-public r-smpracticals
19151 (name "r-smpracticals")
19156 (uri (cran-uri "SMPracticals" version))
19159 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19160 (properties `((upstream-name . "SMPracticals")))
19161 (build-system r-build-system)
19163 `(("r-ellipse" ,r-ellipse)
19166 ("r-survival" ,r-survival)))
19167 (home-page "http://statwww.epfl.ch/davison/SM/")
19168 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19170 "This package contains the datasets and a few functions for use with the
19171 practicals outlined in Appendix A of the book Statistical Models (Davison,
19172 2003, Cambridge University Press). The practicals themselves can be found at
19173 @url{http://statwww.epfl.ch/davison/SM/}.")
19174 (license license:gpl2+)))
19176 (define-public r-fgui
19183 (uri (cran-uri "fgui" version))
19186 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19187 (properties `((upstream-name . "fgui")))
19188 (build-system r-build-system)
19190 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19191 (synopsis "Create GUI for R functions")
19193 "Rapidly create a GUI for a function you created by automatically
19194 creating widgets for arguments of the function. This package automatically
19195 parses help routines for context-sensitive help to these arguments. The
19196 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19197 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19198 incorporated into the interface for greater customization for the more
19200 ;; Any version of the GPL.
19201 (license (list license:gpl2+ license:gpl3+))))
19203 (define-public r-tcltk2
19210 (uri (cran-uri "tcltk2" version))
19213 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19214 (properties `((upstream-name . "tcltk2")))
19215 (build-system r-build-system)
19219 (home-page "https://www.sciviews.org/SciViews-R")
19220 (synopsis "Tcl/Tk additions")
19222 "This package provides a series of additional Tcl commands and Tk widgets
19223 with style and various functions to supplement the tcltk package")
19224 (license license:lgpl3)))
19226 (define-public r-accrual
19233 (uri (cran-uri "accrual" version))
19236 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19237 (properties `((upstream-name . "accrual")))
19238 (build-system r-build-system)
19240 `(("r-fgui" ,r-fgui)
19241 ("r-smpracticals" ,r-smpracticals)
19242 ("r-tcltk2" ,r-tcltk2)))
19243 (home-page "https://cran.r-project.org/web/packages/accrual/")
19244 (synopsis "Bayesian accrual prediction")
19246 "Subject recruitment for medical research is challenging. Slow patient
19247 accrual leads to delay in research. Accrual monitoring during the process of
19248 recruitment is critical. Researchers need reliable tools to manage the
19249 accrual rate. This package provides an implementation of a Bayesian method
19250 that integrates researcher's experience on previous trials and data from the
19251 current study, providing reliable prediction on accrual rate for clinical
19252 studies. It provides functions for Bayesian accrual prediction which can be
19253 easily used by statisticians and clinical researchers.")
19254 (license license:gpl2)))
19256 (define-public r-accrued
19263 (uri (cran-uri "accrued" version))
19266 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19267 (properties `((upstream-name . "accrued")))
19268 (build-system r-build-system)
19269 (home-page "https://cran.r-project.org/web/packages/accrued/")
19270 (synopsis "Data quality visualization tools for partially accruing data")
19272 "This is a package for visualizing data quality of partially accruing
19274 (license license:gpl3)))
19276 (define-public r-mda
19283 (uri (cran-uri "mda" version))
19286 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19287 (properties `((upstream-name . "mda")))
19288 (build-system r-build-system)
19289 (propagated-inputs `(("r-class" ,r-class)))
19290 (native-inputs `(("gfortran" ,gfortran)))
19291 (home-page "https://cran.r-project.org/web/packages/mda/")
19292 (synopsis "Mixture and flexible discriminant analysis")
19294 "This is a package for mixture and flexible discriminant analysis,
19295 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19296 (license license:gpl2)))
19298 (define-public r-elasticnet
19300 (name "r-elasticnet")
19305 (uri (cran-uri "elasticnet" version))
19308 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19309 (properties `((upstream-name . "elasticnet")))
19310 (build-system r-build-system)
19312 `(("r-lars" ,r-lars)))
19313 (home-page "http://users.stat.umn.edu/~zouxx019/")
19314 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19316 "This package provides functions for fitting the entire solution path of
19317 the Elastic-Net and also provides functions for estimating sparse Principal
19318 Components. The Lasso solution paths can be computed by the same function.")
19319 (license license:gpl2+)))
19321 (define-public r-sparselda
19323 (name "r-sparselda")
19328 (uri (cran-uri "sparseLDA" version))
19331 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19332 (properties `((upstream-name . "sparseLDA")))
19333 (build-system r-build-system)
19335 `(("r-elasticnet" ,r-elasticnet)
19338 (home-page "https://www.imm.dtu.dk/~lkhc/")
19339 (synopsis "Sparse discriminant analysis")
19341 "This package performs sparse linear discriminant analysis for Gaussians
19342 and mixture of Gaussian models.")
19343 (license license:gpl2+)))
19345 (define-public r-accsda
19352 (uri (cran-uri "accSDA" version))
19355 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19356 (properties `((upstream-name . "accSDA")))
19357 (build-system r-build-system)
19359 `(("r-ggplot2" ,r-ggplot2)
19360 ("r-ggthemes" ,r-ggthemes)
19361 ("r-gridextra" ,r-gridextra)
19363 ("r-rarpack" ,r-rarpack)
19364 ("r-sparselda" ,r-sparselda)))
19365 (home-page "https://github.com/gumeo/accSDA/wiki")
19366 (synopsis "Accelerated sparse discriminant analysis")
19368 "This package provides an implementation of sparse linear discriminant
19369 analysis, which is a supervised classification method for multiple classes.
19370 Various novel optimization approaches to this problem are implemented
19371 including @dfn{alternating direction method of multipliers} (ADMM),
19372 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19373 Functions for performing cross validation are also supplied along with basic
19374 prediction and plotting functions. @dfn{Sparse zero variance
19375 discriminant} (SZVD) analysis is also included in the package.")
19376 (license license:gpl2+)))
19378 (define-public r-ace2fastq
19380 (name "r-ace2fastq")
19385 (uri (cran-uri "ace2fastq" version))
19388 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19389 (properties `((upstream-name . "ace2fastq")))
19390 (build-system r-build-system)
19392 `(("r-stringr" ,r-stringr)))
19393 (home-page "https://github.com/c5sire/ace2fastq")
19394 (synopsis "ACE file to FASTQ converter")
19396 "The ACE file format is used in genomics to store contigs from sequencing
19397 machines. This tools converts it into FASTQ format. Both formats contain the
19398 sequence characters and their corresponding quality information. Unlike the
19399 FASTQ file, the ACE file stores the quality values numerically. The
19400 conversion algorithm uses the standard Sanger formula. The package
19401 facilitates insertion into pipelines, and content inspection.")
19402 (license license:gpl3)))
19404 (define-public r-rngwell
19411 (uri (cran-uri "rngWELL" version))
19414 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19415 (properties `((upstream-name . "rngWELL")))
19416 (build-system r-build-system)
19417 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19418 (synopsis "Toolbox for WELL random number generators")
19420 "This is a dedicated package to WELL pseudo random generators, which were
19421 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19422 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19423 (license license:bsd-3)))
19425 (define-public r-randtoolbox
19427 (name "r-randtoolbox")
19432 (uri (cran-uri "randtoolbox" version))
19435 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19436 (properties `((upstream-name . "randtoolbox")))
19437 (build-system r-build-system)
19439 `(("r-rngwell" ,r-rngwell)))
19441 `(("gfortran" ,gfortran)))
19442 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19443 (synopsis "Toolbox for pseudo and quasi random number generation")
19445 "This package provides
19448 @item pseudo random generators, such as general linear
19449 congruential generators, multiple recursive generators and generalized
19450 feedback shift register (SF-Mersenne Twister algorithm and WELL
19453 @item quasi random generators, such as the Torus algorithm, the Sobol
19454 sequence, the Halton sequence (including the Van der Corput sequence), and
19456 @item some generator tests: the gap test, the serial test, the poker test.
19459 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19460 (license license:bsd-3)))
19462 (define-public r-lhs
19469 (uri (cran-uri "lhs" version))
19472 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19473 (properties `((upstream-name . "lhs")))
19474 (build-system r-build-system)
19475 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19477 `(("r-knitr" ,r-knitr)))
19478 (home-page "https://github.com/bertcarnell/lhs")
19479 (synopsis "Latin Hypercube Samples")
19481 "This package provides a number of methods for creating and augmenting
19482 Latin Hypercube Samples.")
19483 (license license:gpl3)))
19485 (define-public r-acebayes
19487 (name "r-acebayes")
19492 (uri (cran-uri "acebayes" version))
19495 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19496 (properties `((upstream-name . "acebayes")))
19497 (build-system r-build-system)
19499 `(("r-compare" ,r-compare)
19501 ("r-randtoolbox" ,r-randtoolbox)
19503 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19504 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19505 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19507 "Finding an optimal Bayesian experimental design involves maximizing an
19508 objective function given by the expectation of some appropriately chosen
19509 utility function with respect to the joint distribution of unknown
19510 quantities (including responses). This objective function is usually not
19511 available in closed form and the design space can be continuous and of high
19512 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19513 to maximise an approximation to the expectation of the utility function.")
19514 (license license:gpl2)))
19516 (define-public r-acet
19523 (uri (cran-uri "ACEt" version))
19526 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19527 (properties `((upstream-name . "ACEt")))
19528 (build-system r-build-system)
19533 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19534 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19535 (synopsis "Estimating dynamic heritability and twin model comparison")
19537 "This package supports twin models that are able to estimate the dynamic
19538 behaviour of the variance components in the classical twin models with respect
19539 to age using B-splines and P-splines.")
19540 (license license:gpl2+)))
19542 (define-public r-acfmperiod
19544 (name "r-acfmperiod")
19549 (uri (cran-uri "acfMPeriod" version))
19552 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19553 (properties `((upstream-name . "acfMPeriod")))
19554 (build-system r-build-system)
19556 `(("r-mass" ,r-mass)))
19557 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19558 (synopsis "Estimation of the ACF from the M-periodogram")
19560 "This package support non-robust and robust computations of the sample
19561 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19562 univariate and multivariate processes. The methodology consists in reversing
19563 the diagonalization procedure involving the periodogram or the
19564 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19565 ACOVF or the ACF as discussed in Fuller (1995)
19566 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19567 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19568 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19569 (license license:gpl2+)))
19571 (define-public r-gamlss-data
19573 (name "r-gamlss-data")
19578 (uri (cran-uri "gamlss.data" version))
19581 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19582 (properties `((upstream-name . "gamlss.data")))
19583 (build-system r-build-system)
19584 (home-page "http://www.gamlss.org/")
19585 (synopsis "GAMLSS data")
19587 "This package provides data used as examples to demonstrate GAMLSS
19589 ;; Either version of the license
19590 (license (list license:gpl2 license:gpl3))))
19592 (define-public r-gamlss
19599 (uri (cran-uri "gamlss" version))
19602 "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr"))))
19603 (properties `((upstream-name . "gamlss")))
19604 (build-system r-build-system)
19606 `(("r-gamlss-data" ,r-gamlss-data)
19607 ("r-gamlss-dist" ,r-gamlss-dist)
19610 ("r-survival" ,r-survival)))
19611 (home-page "http://www.gamlss.org/")
19612 (synopsis "Generalized additive models for location scale and shape")
19614 "This package provides functions for fitting the generalized additive
19615 models for location scale and shape introduced by Rigby and
19616 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19617 use a distributional regression approach where all the parameters of the
19618 conditional distribution of the response variable are modelled using
19619 explanatory variables.")
19620 ;; Either version of the license
19621 (license (list license:gpl2 license:gpl3))))
19623 (define-public r-acid
19630 (uri (cran-uri "acid" version))
19633 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19634 (properties `((upstream-name . "acid")))
19635 (build-system r-build-system)
19637 `(("r-gamlss" ,r-gamlss)
19638 ("r-gamlss-dist" ,r-gamlss-dist)
19639 ("r-hmisc" ,r-hmisc)))
19640 (home-page "https://cran.r-project.org/web/packages/acid/")
19641 (synopsis "Analysing conditional income distributions")
19643 "This package provides functions for the analysis of income distributions
19644 for subgroups of the population as defined by a set of variables like age,
19645 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19646 distribution as well as functions for moments, inequality measures, entropy
19647 measures and polarisation measures of income distributions. This package thus
19648 aides the analysis of income inequality by offering tools for the exploratory
19649 analysis of income distributions at the disaggregated level.")
19650 (license license:gpl3)))
19652 (define-public r-acm4r
19659 (uri (cran-uri "acm4r" version))
19662 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19663 (properties `((upstream-name . "acm4r")))
19664 (build-system r-build-system)
19665 (propagated-inputs `(("r-mass" ,r-mass)))
19666 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19667 (synopsis "Align-and-count method comparisons of RFLP data")
19669 "This is a package to compare sequence fragment lengths or molecular
19670 weights from pairs of lanes. The number of matching bands in the
19671 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19672 the align-and-count method.")
19673 ;; Any version of the GPL
19674 (license (list license:gpl2+ license:gpl3+))))
19676 (define-public r-filelock
19678 (name "r-filelock")
19683 (uri (cran-uri "filelock" version))
19686 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19687 (properties `((upstream-name . "filelock")))
19688 (build-system r-build-system)
19689 (home-page "https://github.com/r-lib/filelock")
19690 (synopsis "Portable file locking")
19692 "This library lets you place an exclusive or shared lock on a file using
19693 the appropriate system call provided by the underlying operating system.")
19694 (license license:expat)))
19696 (define-public r-filematrix
19698 (name "r-filematrix")
19703 (uri (cran-uri "filematrix" version))
19706 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19707 (properties `((upstream-name . "filematrix")))
19708 (build-system r-build-system)
19709 ;; These inputs are needed for vignettes
19711 `(("r-knitr" ,r-knitr)
19712 ("r-rmarkdown" ,r-rmarkdown)
19713 ("pandoc-citeproc" ,pandoc-citeproc)))
19714 (home-page "https://github.com/andreyshabalin/filematrix")
19715 (synopsis "File-backed matrix class with convenient read and write access")
19717 "This package provides an interface for working with large matrices
19718 stored in files, not in computer memory. It supports multiple non-character
19719 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19720 byte real values). Access to parts of the matrix is done by indexing, exactly
19721 as with usual R matrices. It supports very large matrices; the package has
19722 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19723 columns, ad allows for quick addition of extra columns to a filematrix.")
19724 (license license:lgpl3)))
19726 (define-public r-acmeeqtl
19728 (name "r-acmeeqtl")
19733 (uri (cran-uri "ACMEeqtl" version))
19736 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19737 (properties `((upstream-name . "ACMEeqtl")))
19738 (build-system r-build-system)
19740 `(("r-filematrix" ,r-filematrix)))
19741 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19742 (synopsis "Estimation of interpretable eQTL effect sizes")
19744 "This package provides a non-linear model, termed ACME, that reflects a
19745 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19746 With non-linear least-squares algorithm the maximum likelihood parameters can
19747 be estimated. The ACME model provides interpretable effect size estimates and
19748 p-values with well controlled Type-I error.")
19749 (license license:lgpl3)))
19751 (define-public r-acmer
19758 (uri (cran-uri "acmeR" version))
19761 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19762 (properties `((upstream-name . "acmeR")))
19763 (build-system r-build-system)
19764 (propagated-inputs `(("r-foreign" ,r-foreign)))
19765 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19766 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19768 "This package provides an implementation of the ACME estimator, described
19769 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19770 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19771 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19772 as carcasses age; variable bleed-through at successive searches; and interval
19773 mortality estimates. The package provides, based on search data, functions
19774 for estimating the mortality inflation factor in Frequentist and Bayesian
19776 (license license:expat)))
19778 (define-public r-r-huge
19785 (uri (cran-uri "R.huge" version))
19788 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19789 (properties `((upstream-name . "R.huge")))
19790 (build-system r-build-system)
19792 `(("r-r-methodss3" ,r-r-methodss3)
19794 ("r-r-utils" ,r-r-utils)))
19795 (home-page "https://github.com/HenrikBengtsson/R.huge")
19796 (synopsis "Methods for accessing huge amounts of data")
19798 "This is a deprecated package for accessing huge amounts of data.
19799 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19800 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19801 the @code{aroma.affymetrix} package.")
19802 (license license:lgpl2.1+)))
19804 (define-public r-r-filesets
19806 (name "r-r-filesets")
19811 (uri (cran-uri "R.filesets" version))
19814 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19815 (properties `((upstream-name . "R.filesets")))
19816 (build-system r-build-system)
19818 `(("r-digest" ,r-digest)
19819 ("r-r-cache" ,r-r-cache)
19820 ("r-r-methodss3" ,r-r-methodss3)
19822 ("r-r-utils" ,r-r-utils)))
19823 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19824 (synopsis "Easy handling of and access to files")
19826 "This package provides classes and methods to locate, setup, subset,
19827 navigate and iterate file sets, i.e. sets of files located in one or more
19828 directories on the file system. The API is designed such that these classes
19829 can be extended via inheritance to provide a richer API for special file
19830 formats. Moreover, a specific name format is defined such that filenames and
19831 directories can be considered to have full names which consists of a name
19832 followed by comma-separated tags. This adds additional flexibility to
19833 identify file sets and individual files.")
19834 (license license:lgpl2.1+)))
19836 (define-public r-r-devices
19838 (name "r-r-devices")
19843 (uri (cran-uri "R.devices" version))
19846 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19847 (properties `((upstream-name . "R.devices")))
19848 (build-system r-build-system)
19850 `(("r-base64enc" ,r-base64enc)
19851 ("r-r-methodss3" ,r-r-methodss3)
19853 ("r-r-utils" ,r-r-utils)))
19854 (home-page "https://github.com/HenrikBengtsson/R.devices")
19855 (synopsis "Unified handling of graphics devices")
19857 "This package provides functions for creating plots and image files in a
19858 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19859 Default device options as well as scales and aspect ratios are controlled in a
19860 uniform way across all device types. Switching output format requires minimal
19861 changes in code. This package is ideal for large-scale batch processing,
19862 because it will never leave open graphics devices or incomplete image files
19863 behind, even on errors or user interrupts.")
19864 (license license:lgpl2.1+)))
19866 (define-public r-acnr
19873 (uri (cran-uri "acnr" version))
19876 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19877 (properties `((upstream-name . "acnr")))
19878 (build-system r-build-system)
19879 (home-page "https://github.com/mpierrejean/acnr")
19880 (synopsis "Annotated copy-number regions")
19882 "This package provides SNP array data from different types of copy-number
19883 regions. These regions were identified manually by the authors of the package
19884 and may be used to generate realistic data sets with known truth.")
19885 (license license:lgpl2.1+)))
19887 (define-public r-acopula
19894 (uri (cran-uri "acopula" version))
19897 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19898 (properties `((upstream-name . "acopula")))
19899 (build-system r-build-system)
19900 (home-page "https://cran.r-project.org/web/packages/acopula/")
19901 (synopsis "Modelling dependence with multivariate Archimax copulas")
19903 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19904 package provides definitions of several parametric families of generator and
19905 dependence function, computes CDF and PDF, estimates parameters, tests for
19906 goodness of fit, generates random sample and checks copula properties for
19907 custom constructs. In the 2-dimensional case explicit formulas for density
19908 are used, contrary to higher dimensions when all derivatives are linearly
19909 approximated. Several non-archimax families (normal, FGM, Plackett) are
19910 provided as well.")
19911 (license license:gpl2)))
19913 (define-public r-tuner
19920 (uri (cran-uri "tuneR" version))
19923 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19924 (properties `((upstream-name . "tuneR")))
19925 (build-system r-build-system)
19926 (propagated-inputs `(("r-signal" ,r-signal)))
19927 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19928 (synopsis "Analysis of music and speech")
19930 "This is a package for the analysis of music and speech. Analyze music
19931 and speech, extract features like MFCCs, handle wave files and their
19932 representation in various ways, read MP3, read MIDI, perform steps of a
19933 transcription, ...")
19934 ;; Either of these versions.
19935 (license (list license:gpl2 license:gpl3))))
19937 (define-public r-seewave
19944 (uri (cran-uri "seewave" version))
19947 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19948 (properties `((upstream-name . "seewave")))
19949 (build-system r-build-system)
19951 `(("libsndfile" ,libsndfile)))
19953 `(("r-tuner" ,r-tuner)))
19954 (home-page "http://rug.mnhn.fr/seewave")
19955 (synopsis "Sound analysis and synthesis")
19957 "This package provides functions for analysing, manipulating, displaying,
19958 editing and synthesizing time waves (particularly sound). This package
19959 processes time analysis (oscillograms and envelopes), spectral content,
19960 resonance quality factor, entropy, cross correlation and autocorrelation,
19961 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19962 and 3D spectrograms and many other analyses.")
19963 (license license:gpl2+)))
19965 (define-public r-acousticndlcoder
19967 (name "r-acousticndlcoder")
19972 (uri (cran-uri "AcousticNDLCodeR" version))
19975 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19977 `((upstream-name . "AcousticNDLCodeR")))
19978 (build-system r-build-system)
19980 `(("r-seewave" ,r-seewave)
19981 ("r-tuner" ,r-tuner)
19983 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19984 (synopsis "Coding sound files for use with NDL")
19986 "Make acoustic cues to use with the R package @code{ndl}.
19987 The package implements functions used in the PLoS ONE paper \"Words from
19988 spontaneous conversational speech can be recognized with human-like accuracy
19989 by an error-driven learning algorithm that discriminates between meanings
19990 straight from smart acoustic features, bypassing the phoneme as recognition
19991 unit.\" @url{doi:10.1371/journal.pone.0174623}")
19992 (license license:gpl2+)))
19994 (define-public r-acp
20001 (uri (cran-uri "acp" version))
20004 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
20005 (properties `((upstream-name . "acp")))
20006 (build-system r-build-system)
20008 `(("r-quantmod" ,r-quantmod)
20009 ("r-tseries" ,r-tseries)))
20010 (home-page "https://cran.r-project.org/web/packages/acp/")
20011 (synopsis "Autoregressive conditional Poisson")
20013 "This package supports the analysis of count data exhibiting
20014 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
20015 model (ACP(p,q)) proposed by Heinen (2003).")
20016 (license license:gpl2)))
20018 (define-public r-ada
20025 (uri (cran-uri "ada" version))
20028 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20029 (properties `((upstream-name . "ada")))
20030 (build-system r-build-system)
20031 (propagated-inputs `(("r-rpart" ,r-rpart)))
20032 (home-page "https://cran.r-project.org/web/packages/ada/")
20033 (synopsis "Stochastic boosting")
20035 "This package provides a straightforward, well-documented, and broad
20036 boosting routine for classification, ideally suited for small to
20037 moderate-sized data sets. It performs discrete, real, and gentle boost under
20038 both exponential and logistic loss on a given data set.")
20039 ;; Any version of the GPL.
20040 (license (list license:gpl2+ license:gpl3+))))
20042 (define-public r-genalg
20049 (uri (cran-uri "genalg" version))
20052 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20053 (properties `((upstream-name . "genalg")))
20054 (build-system r-build-system)
20055 (home-page "https://github.com/egonw/genalg")
20056 (synopsis "R based genetic algorithm")
20058 "This package provides an R based genetic algorithm for binary and
20059 floating point chromosomes.")
20060 (license license:gpl2)))
20062 (define-public r-kernelfactory
20064 (name "r-kernelfactory")
20069 (uri (cran-uri "kernelFactory" version))
20072 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20073 (properties `((upstream-name . "kernelFactory")))
20074 (build-system r-build-system)
20077 ("r-genalg" ,r-genalg)
20078 ("r-kernlab" ,r-kernlab)
20079 ("r-randomforest" ,r-randomforest)))
20080 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20081 (synopsis "Ensemble of kernel machines")
20083 "Kernel factory is an ensemble method where each base classifier (random
20084 forest) is fit on the kernel matrix of a subset of the training data.")
20085 (license license:gpl2+)))
20087 (define-public r-dummies
20094 (uri (cran-uri "dummies" version))
20097 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20098 (properties `((upstream-name . "dummies")))
20099 (build-system r-build-system)
20100 (home-page "https://decisionpatterns.com")
20101 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20103 "This package lets you expand factors, characters and other eligible
20104 classes into dummy/indicator variables.")
20105 (license license:gpl2+)))
20107 (define-public r-acrm
20114 (uri (cran-uri "aCRM" version))
20117 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20118 (properties `((upstream-name . "aCRM")))
20119 (build-system r-build-system)
20122 ("r-dummies" ,r-dummies)
20123 ("r-kernelfactory" ,r-kernelfactory)
20124 ("r-randomforest" ,r-randomforest)))
20125 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20126 (synopsis "Convenience functions for analytical customer relationship management")
20128 "This package provides convenience functions for data preparation and
20129 modeling often used in @dfn{analytical customer relationship
20130 management} (aCRM).")
20131 (license license:gpl2+)))
20133 (define-public r-treeclust
20135 (name "r-treeclust")
20140 (uri (cran-uri "treeClust" version))
20143 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20144 (properties `((upstream-name . "treeClust")))
20145 (build-system r-build-system)
20147 `(("r-cluster" ,r-cluster)
20148 ("r-rpart" ,r-rpart)))
20149 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20150 (synopsis "Cluster distances through trees")
20152 "This package provides tools to create a measure of inter-point
20153 dissimilarity useful for clustering mixed data, and, optionally, perform the
20155 (license license:gpl2+)))
20157 (define-public r-acrosstic
20159 (name "r-acrosstic")
20164 (uri (cran-uri "AcrossTic" version))
20167 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20168 (properties `((upstream-name . "AcrossTic")))
20169 (build-system r-build-system)
20171 `(("r-lpsolve" ,r-lpsolve)
20172 ("r-treeclust" ,r-treeclust)))
20173 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20174 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20176 "This is a package for constructing minimum-cost regular spanning
20177 subgraph as part of a non-parametric two-sample test for equality of
20179 (license license:gpl2+)))
20181 (define-public r-acrt
20188 (uri (cran-uri "acrt" version))
20191 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20192 (properties `((upstream-name . "acrt")))
20193 (build-system r-build-system)
20195 `(("r-rcpp" ,r-rcpp)
20196 ("r-rcppeigen" ,r-rcppeigen)
20197 ("r-sandwich" ,r-sandwich)))
20198 (home-page "https://cran.r-project.org/web/packages/acrt/")
20199 (synopsis "Autocorrelation robust testing")
20201 "This package provides functions for testing affine hypotheses on the
20202 regression coefficient vector in regression models with autocorrelated
20204 (license license:gpl2)))
20206 (define-public r-acs
20213 (uri (cran-uri "acs" version))
20216 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20217 (properties `((upstream-name . "acs")))
20218 (build-system r-build-system)
20220 `(("r-httr" ,r-httr)
20223 ("r-stringr" ,r-stringr)
20225 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20226 (synopsis "Work with data from the US Census")
20228 "This package provides a general toolkit for downloading, managing,
20229 analyzing, and presenting data from the
20230 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20231 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20232 American Community Survey (ACS). Confidence intervals provided with ACS data
20233 are converted to standard errors to be bundled with estimates in complex
20234 @code{acs} objects. The package provides new methods to conduct standard
20235 operations on @code{acs} objects and present/plot data in statistically
20236 appropriate ways.")
20237 (license license:gpl3)))
20239 (define-public r-acss-data
20241 (name "r-acss-data")
20246 (uri (cran-uri "acss.data" version))
20249 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20250 (properties `((upstream-name . "acss.data")))
20251 (build-system r-build-system)
20252 (home-page "http://complexitycalculator.com/methodology.html")
20253 (synopsis "Data for algorithmic complexity of short strings")
20255 "This is a data only package providing the algorithmic complexity of
20256 short strings, computed using the coding theorem method. For a given set of
20257 symbols in a string, all possible or a large number of random samples of
20258 Turing machines with a given number of states (e.g., 5) and number of symbols
20259 corresponding to the number of symbols in the strings were simulated until
20260 they reached a halting state or failed to end. This package contains data on
20261 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20262 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20263 distribution of the halting states.")
20264 (license license:gpl2+)))
20266 (define-public r-acss
20273 (uri (cran-uri "acss" version))
20276 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20277 (properties `((upstream-name . "acss")))
20278 (build-system r-build-system)
20280 `(("r-acss-data" ,r-acss-data)
20282 (home-page "http://complexitycalculator.com/methodology.html")
20283 (synopsis "Algorithmic complexity for short strings")
20285 "The main purpose of this package is to provide the algorithmic
20286 complexity for short strings, an approximation of the Kolmogorov Complexity of
20287 a short string using the coding theorem method. While the database containing
20288 the complexity is provided in the data only package @code{acss.data}, this
20289 package provides functions accessing the data such as @code{prob_random}
20290 returning the posterior probability that a given string was produced by a
20291 random process. In addition, two traditional (but problematic) measures of
20292 complexity are also provided: entropy and change complexity.")
20293 (license license:gpl2+)))
20295 (define-public r-acswr
20302 (uri (cran-uri "ACSWR" version))
20305 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20306 (properties `((upstream-name . "ACSWR")))
20307 (build-system r-build-system)
20309 `(("r-mass" ,r-mass)))
20310 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20311 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20313 "This is a companion package for the book \"A Course in Statistics with
20314 R\" (ISBN 978-1-119-15272-9.)")
20315 (license license:gpl2)))
20317 (define-public r-alabama
20320 (version "2015.3-1")
20324 (uri (cran-uri "alabama" version))
20327 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20328 (properties `((upstream-name . "alabama")))
20329 (build-system r-build-system)
20330 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20331 (home-page "https://cran.r-project.org/web/packages/alabama/")
20332 (synopsis "Constrained nonlinear optimization")
20334 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20335 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20336 constraints. Linear or nonlinear equality and inequality constraints are
20338 (license license:gpl2+)))
20340 (define-public r-gdina
20347 (uri (cran-uri "GDINA" version))
20350 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20351 (properties `((upstream-name . "GDINA")))
20352 (build-system r-build-system)
20354 `(("r-alabama" ,r-alabama)
20355 ("r-ggplot2" ,r-ggplot2)
20357 ("r-nloptr" ,r-nloptr)
20358 ("r-numderiv" ,r-numderiv)
20360 ("r-rcpparmadillo" ,r-rcpparmadillo)
20361 ("r-rsolnp" ,r-rsolnp)
20362 ("r-shiny" ,r-shiny)
20363 ("r-shinydashboard" ,r-shinydashboard)))
20365 `(("r-knitr" ,r-knitr)))
20366 (home-page "https://github.com/Wenchao-Ma/GDINA")
20367 (synopsis "Generalized DINA model framework")
20369 "This package provides a set of psychometric tools for cognitive
20370 diagnosis modeling based on the generalized deterministic inputs, noisy and
20371 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20372 and its extensions, including the sequential G-DINA model by Ma and de la
20373 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20374 polytomous G-DINA model by Chen and de la Torre
20375 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20376 distribution can be independent, saturated, higher-order, loglinear smoothed
20377 or structured. Q-matrix validation, item and model fit statistics, model
20378 comparison at test and item level and differential item functioning can also
20379 be conducted. A graphical user interface is also provided.")
20380 (license license:gpl3)))
20382 (define-public r-actcd
20389 (uri (cran-uri "ACTCD" version))
20392 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20393 (properties `((upstream-name . "ACTCD")))
20394 (build-system r-build-system)
20396 `(("r-gdina" ,r-gdina)
20397 ("r-r-methodss3" ,r-r-methodss3)))
20399 `(("gfortran" ,gfortran)))
20400 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20401 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20403 "This is a package supporting cluster analysis for cognitive diagnosis
20404 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20405 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20406 sum-scores, cluster analysis techniques can be used to classify examinees into
20407 latent classes based on their attribute patterns. In addition to the
20408 algorithms used to classify data, three labeling approaches are proposed to
20409 label clusters so that examinees' attribute profiles can be obtained.")
20410 (license license:gpl2+)))
20412 (define-public r-ineq
20419 (uri (cran-uri "ineq" version))
20422 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20423 (properties `((upstream-name . "ineq")))
20424 (build-system r-build-system)
20425 (home-page "https://cran.r-project.org/web/packages/ineq/")
20426 (synopsis "Measuring inequality, concentration, and poverty")
20428 "This package provides tools for measuring inequality, concentration, and
20429 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20430 ;; Either of these two versions.
20431 (license (list license:gpl2 license:gpl3))))
20433 (define-public r-actfrag
20440 (uri (cran-uri "ActFrag" version))
20443 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20444 (properties `((upstream-name . "ActFrag")))
20445 (build-system r-build-system)
20447 `(("r-accelerometry" ,r-accelerometry)
20448 ("r-dplyr" ,r-dplyr)
20450 ("r-survival" ,r-survival)
20451 ("r-tidyr" ,r-tidyr)))
20452 (home-page "https://github.com/junruidi/ActFrag")
20453 (synopsis "Activity fragmentation metrics extraction")
20455 "This package provides functions to extract commonly used fragmentation
20456 metrics to quantify time accumulation strategies based on minute level
20457 actigraphy-measured activity counts data.")
20458 (license license:gpl3)))
20460 (define-public r-ash
20467 (uri (cran-uri "ash" version))
20470 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20471 (properties `((upstream-name . "ash")))
20472 (build-system r-build-system)
20473 (native-inputs `(("gfortran" ,gfortran)))
20474 (home-page "https://cran.r-project.org/web/packages/ash/")
20475 (synopsis "David Scott's ASH routines")
20477 "This package provides David Scott's ASH routines ported from S-PLUS to
20479 (license license:gpl2+)))
20481 (define-public r-hdrcde
20488 (uri (cran-uri "hdrcde" version))
20491 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20492 (properties `((upstream-name . "hdrcde")))
20493 (build-system r-build-system)
20496 ("r-ggplot2" ,r-ggplot2)
20497 ("r-kernsmooth" ,r-kernsmooth)
20499 ("r-locfit" ,r-locfit)
20500 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20501 (native-inputs `(("gfortran" ,gfortran)))
20502 (home-page "http://pkg.robjhyndman.com/hdrcde")
20503 (synopsis "Highest density regions and conditional density estimation")
20505 "This is a package for the computation of highest density regions in one
20506 and two dimensions, kernel estimation of univariate density functions
20507 conditional on one covariate, and multimodal regression.")
20508 (license license:gpl3)))
20510 (define-public r-rainbow
20517 (uri (cran-uri "rainbow" version))
20520 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20521 (properties `((upstream-name . "rainbow")))
20522 (build-system r-build-system)
20524 `(("r-cluster" ,r-cluster)
20525 ("r-colorspace" ,r-colorspace)
20526 ("r-hdrcde" ,r-hdrcde)
20529 ("r-pcapp" ,r-pcapp)))
20530 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20531 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20533 "This is a package for visualizing functional data and identifying
20534 functional outliers with bagplots, boxplots and rainbow plots.")
20535 (license license:gpl3)))
20537 (define-public r-fds
20544 (uri (cran-uri "fds" version))
20547 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20548 (properties `((upstream-name . "fds")))
20549 (build-system r-build-system)
20551 `(("r-rainbow" ,r-rainbow)
20552 ("r-rcurl" ,r-rcurl)))
20553 (home-page "https://cran.r-project.org/web/packages/fds/")
20554 (synopsis "Functional data sets")
20555 (description "This package contains a list of functional time series,
20556 sliced functional time series, and functional data sets. Functional time
20557 series is a special type of functional data observed over time. Sliced
20558 functional time series is a special type of functional time series with a time
20559 variable observed over time.")
20560 (license license:gpl2+)))
20562 (define-public r-fda
20569 (uri (cran-uri "fda" version))
20572 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20573 (properties `((upstream-name . "fda")))
20574 (build-system r-build-system)
20577 ("r-matrix" ,r-matrix)))
20578 (home-page "https://www.functionaldata.org")
20579 (synopsis "Functional data analysis")
20581 "These functions were developed to support functional data analysis as
20582 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20583 Analysis. The package includes data sets and script files working many
20585 (license license:gpl2+)))
20587 (define-public r-actigraphy
20589 (name "r-actigraphy")
20594 (uri (cran-uri "Actigraphy" version))
20597 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20598 (properties `((upstream-name . "Actigraphy")))
20599 (build-system r-build-system)
20601 `(("r-fda" ,r-fda)))
20602 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20603 (synopsis "Actigraphy data analysis")
20605 "This package provides tools for functional linear modeling and analysis
20606 of actigraphy data.")
20607 (license license:asl2.0)))
20609 (define-public r-activedriver
20611 (name "r-activedriver")
20616 (uri (cran-uri "ActiveDriver" version))
20619 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20620 (properties `((upstream-name . "ActiveDriver")))
20621 (build-system r-build-system)
20623 `(("r-mass" ,r-mass)))
20624 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20625 (synopsis "Tools for finding cancer driver proteins")
20627 "This package provides a mutation analysis tool that discovers cancer
20628 driver genes with frequent mutations in protein signalling sites such as
20629 post-translational modifications (phosphorylation, ubiquitination, etc). The
20630 Poisson generalized linear regression model identifies genes where cancer
20631 mutations in signalling sites are more frequent than expected from the
20632 sequence of the entire gene. Integration of mutations with signalling
20633 information helps find new driver genes and propose candidate mechanisms to
20635 (license license:gpl2+)))
20637 (define-public r-activitycounts
20639 (name "r-activitycounts")
20644 (uri (cran-uri "activityCounts" version))
20647 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20649 `((upstream-name . "activityCounts")))
20650 (build-system r-build-system)
20652 `(("r-lubridate" ,r-lubridate)
20653 ("r-magrittr" ,r-magrittr)
20654 ("r-seewave" ,r-seewave)
20655 ("r-signal" ,r-signal)
20656 ("r-tibble" ,r-tibble)))
20657 (home-page "https://github.com/walkabillylab/activityCounts")
20658 (synopsis "Generate ActiLife counts")
20660 "ActiLife generates activity counts from data collected by Actigraph
20661 accelerometers. Actigraph is one of the most common research-grade
20662 accelerometers. There is considerable research validating and developing
20663 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20664 counts are proprietary and difficult to implement if researchers use different
20665 accelerometer brands. The code creates ActiLife counts from raw acceleration
20666 data for different accelerometer brands.")
20667 (license license:gpl3)))
20669 (define-public r-activityindex
20671 (name "r-activityindex")
20676 (uri (cran-uri "ActivityIndex" version))
20679 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20680 (properties `((upstream-name . "ActivityIndex")))
20681 (build-system r-build-system)
20683 `(("r-data-table" ,r-data-table)
20684 ("r-matrixstats" ,r-matrixstats)
20685 ("r-r-utils" ,r-r-utils)))
20687 `(("r-knitr" ,r-knitr)))
20688 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20689 (synopsis "Activity Index calculation using raw accelerometry data")
20691 "This is a package to read raw accelerometry from GT3X+ accelerometry
20692 data and plain table data to calculate the Activity Index from Bai et
20693 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20694 (license license:gpl3)))
20696 (define-public r-activpal
20698 (name "r-activpal")
20703 (uri (cran-uri "activPAL" version))
20706 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20707 (properties `((upstream-name . "activPAL")))
20708 (build-system r-build-system)
20710 `(("r-devtools" ,r-devtools)
20711 ("r-dplyr" ,r-dplyr)
20712 ("r-ggplot2" ,r-ggplot2)
20713 ("r-lubridate" ,r-lubridate)
20714 ("r-magrittr" ,r-magrittr)
20715 ("r-tidyr" ,r-tidyr)))
20716 (home-page "https://cran.r-project.org/web/packages/activPAL")
20717 (synopsis "Processing and chart generation from activPAL events files")
20719 "This package contains functions to generate pre-defined summary
20720 statistics from activPAL events files. The package also contains functions to
20721 produce informative graphics that visualize physical activity behaviour and
20722 trends. This includes generating graphs that align physical activity
20723 behaviour with additional time based observations described by other data
20724 sets, such as sleep diaries and continuous glucose monitoring data.")
20725 (license license:gpl3)))
20727 (define-public r-activpalprocessing
20729 (name "r-activpalprocessing")
20734 (uri (cran-uri "activpalProcessing" version))
20737 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20739 `((upstream-name . "activpalProcessing")))
20740 (build-system r-build-system)
20742 `(("r-chron" ,r-chron)))
20743 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20744 (synopsis "Process activPAL events files")
20746 "This package performs estimation of physical activity and sedentary
20747 behavior variables from activPAL events files.")
20748 ;; Either version of the GPL.
20749 (license (list license:gpl2 license:gpl3))))
20751 (define-public r-actogrammr
20753 (name "r-actogrammr")
20758 (uri (cran-uri "actogrammr" version))
20761 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20762 (properties `((upstream-name . "actogrammr")))
20763 (build-system r-build-system)
20765 `(("r-dplyr" ,r-dplyr)
20766 ("r-ggplot2" ,r-ggplot2)
20767 ("r-lubridate" ,r-lubridate)
20768 ("r-readr" ,r-readr)
20769 ("r-tidyr" ,r-tidyr)))
20770 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20771 (synopsis "Read in activity data and plot actograms")
20773 "Read in activity measurements from standard file formats used by
20774 circadian rhythm researchers, currently only ClockLab format, and process and
20775 plot the data. The central type of plot is the actogram, as first described
20776 in \"Activity and distribution of certain wild mice in relation to biotic
20777 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20778 (license license:gpl3)))
20780 (define-public r-expint
20787 (uri (cran-uri "expint" version))
20790 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20791 (properties `((upstream-name . "expint")))
20792 (build-system r-build-system)
20793 (home-page "https://gitlab.com/vigou3/expint")
20794 (synopsis "Exponential integral and incomplete Gamma function")
20796 "This package provides the exponential integrals @code{E_1(x)},
20797 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20798 function @code{G(a, x)} defined for negative values of its first argument.
20799 The package also gives easy access to the underlying C routines through an
20800 API; see the package vignette for details.")
20801 (license license:gpl2+)))
20803 (define-public r-actuar
20810 (uri (cran-uri "actuar" version))
20813 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20814 (properties `((upstream-name . "actuar")))
20815 (build-system r-build-system)
20816 (propagated-inputs `(("r-expint" ,r-expint)))
20817 (home-page "https://gitlab.com/vigou3/actuar")
20818 (synopsis "Actuarial functions and heavy tailed distributions")
20820 "This package provides functions and data sets for actuarial science:
20821 modeling of loss distributions; risk theory and ruin theory; simulation of
20822 compound models, discrete mixtures and compound hierarchical models;
20823 credibility theory. It boasts support for many additional probability
20824 distributions to model insurance loss amounts and loss frequency: 19
20825 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20826 distribution; zero-truncated and zero-modified extensions of the standard
20827 discrete distributions. It also supports phase-type distributions commonly
20828 used to compute ruin probabilities.")
20829 (license license:gpl2+)))
20831 (define-public r-bmp
20838 (uri (cran-uri "bmp" version))
20841 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20842 (properties `((upstream-name . "bmp")))
20843 (build-system r-build-system)
20844 (home-page "https://cran.r-project.org/web/packages/bmp/")
20845 (synopsis "Read Bitmap (BMP) images")
20847 "This package provides pure R tools to read BMP format images. It is
20848 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20849 (license license:gpl2+)))
20851 (define-public r-readbitmap
20853 (name "r-readbitmap")
20858 (uri (cran-uri "readbitmap" version))
20861 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20862 (properties `((upstream-name . "readbitmap")))
20863 (build-system r-build-system)
20865 `(("libjpeg" ,libjpeg-turbo)
20866 ("libpng" ,libpng)))
20871 ("r-tiff" ,r-tiff)))
20872 (home-page "https://github.com/jefferis/readbitmap")
20873 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20875 "This package provides tools to identify and read BMP, JPEG, PNG, and
20876 TIFF format bitmap images. Identification defaults to the use of the magic
20877 number embedded in the file rather than the file extension.")
20878 (license license:gpl2+)))
20880 (define-public r-imager
20887 (uri (cran-uri "imager" version))
20890 "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd"))))
20891 (properties `((upstream-name . "imager")))
20892 (build-system r-build-system)
20895 ("libtiff" ,libtiff)
20899 `(("r-downloader" ,r-downloader)
20900 ("r-igraph" ,r-igraph)
20902 ("r-magrittr" ,r-magrittr)
20904 ("r-purrr" ,r-purrr)
20906 ("r-readbitmap" ,r-readbitmap)
20907 ("r-stringr" ,r-stringr)))
20909 `(("pkg-config" ,pkg-config)
20910 ("r-knitr" ,r-knitr)))
20911 (home-page "https://dahtah.github.io/imager/")
20912 (synopsis "Image processing library")
20914 "This is a package for fast image processing for images in up to 4
20915 dimensions (two spatial dimensions, one time/depth dimension, one color
20916 dimension). It provides most traditional image processing tools (filtering,
20917 morphology, transformations, etc.) as well as various functions for easily
20918 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20919 simple, modern C++ library for image processing.")
20920 (license license:lgpl3)))
20922 (define-public r-acuityview
20924 (name "r-acuityview")
20929 (uri (cran-uri "AcuityView" version))
20932 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20933 (properties `((upstream-name . "AcuityView")))
20934 (build-system r-build-system)
20936 `(("r-fftwtools" ,r-fftwtools)
20937 ("r-imager" ,r-imager)
20938 ("r-plotrix" ,r-plotrix)))
20939 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20940 (synopsis "Display scenes as seen by an animal with less acute vision")
20942 "This package provides a simple method for representing a visual scene as
20943 it may be seen by an animal with less acute vision.")
20944 (license license:gpl2+)))
20946 (define-public r-caret
20953 (uri (cran-uri "caret" version))
20956 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20957 (build-system r-build-system)
20959 `(("r-foreach" ,r-foreach)
20960 ("r-ggplot2" ,r-ggplot2)
20961 ("r-lattice" ,r-lattice)
20962 ("r-modelmetrics" ,r-modelmetrics)
20966 ("r-recipes" ,r-recipes)
20967 ("r-reshape2" ,r-reshape2)
20968 ("r-withr" ,r-withr)))
20970 `(("r-knitr" ,r-knitr)))
20971 (home-page "https://github.com/topepo/caret")
20972 (synopsis "Classification and regression training")
20974 "This package provides miscellaneous functions for training and plotting
20975 classification and regression models.")
20976 (license license:gpl2+)))
20978 (define-public r-adabag
20985 (uri (cran-uri "adabag" version))
20988 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20989 (properties `((upstream-name . "adabag")))
20990 (build-system r-build-system)
20992 `(("r-caret" ,r-caret)
20993 ("r-doparallel" ,r-doparallel)
20994 ("r-foreach" ,r-foreach)
20995 ("r-rpart" ,r-rpart)))
20996 (home-page "https://cran.r-project.org/web/packages/adabag/")
20997 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
20999 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
21000 Breiman's Bagging algorithm using classification trees as individual
21001 classifiers. Once these classifiers have been trained, they can be used to
21002 predict on new data. Also, cross validation estimation of the error can be
21004 (license license:gpl2+)))
21006 (define-public r-adagio
21013 (uri (cran-uri "adagio" version))
21016 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21017 (properties `((upstream-name . "adagio")))
21018 (build-system r-build-system)
21019 (native-inputs `(("gfortran" ,gfortran)))
21020 (home-page "https://cran.r-project.org/web/packages/adagio/")
21021 (synopsis "Discrete and global optimization routines")
21023 "This package provides methods and algorithms for discrete optimization,
21024 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21025 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21027 (license license:gpl3+)))
21029 (define-public r-univoutl
21031 (name "r-univoutl")
21036 (uri (cran-uri "univOutl" version))
21039 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21040 (properties `((upstream-name . "univOutl")))
21041 (build-system r-build-system)
21043 `(("r-hmisc" ,r-hmisc)
21044 ("r-robustbase" ,r-robustbase)))
21045 (home-page "https://github.com/marcellodo/univOutl")
21046 (synopsis "Detection of univariate outliers")
21048 "This package provides well-known outlier detection techniques in the
21049 univariate case. Methods to deal with skewed distribution are included too.
21050 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21051 historical data is implemented as well. When available, survey weights can be
21052 used in outliers detection.")
21053 (license license:gpl2+)))
21055 (define-public r-tolerance
21057 (name "r-tolerance")
21062 (uri (cran-uri "tolerance" version))
21065 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21066 (properties `((upstream-name . "tolerance")))
21067 (build-system r-build-system)
21069 `(("r-mass" ,r-mass)
21071 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21072 (synopsis "Statistical tolerance intervals and regions")
21074 "This package provides functions for estimating tolerance
21075 limits (intervals) for various univariate distributions (binomial, Cauchy,
21076 discrete Pareto, exponential, two-parameter exponential, extreme value,
21077 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21078 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21079 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21080 nonparametric tolerance intervals, tolerance bands for regression
21081 settings (linear regression, nonlinear regression, nonparametric regression,
21082 and multivariate regression), and analysis of variance tolerance intervals.
21083 Visualizations are also available for most of these settings.")
21084 (license license:gpl2+)))
21086 (define-public r-additivitytests
21088 (name "r-additivitytests")
21093 (uri (cran-uri "additivityTests" version))
21096 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21098 `((upstream-name . "additivityTests")))
21099 (build-system r-build-system)
21100 (home-page "https://github.com/simecek/additivityTests")
21101 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21103 "This package provides an implementation of the Tukey, Mandel,
21104 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21105 (license license:gpl3)))
21107 (define-public r-flexclust
21109 (name "r-flexclust")
21114 (uri (cran-uri "flexclust" version))
21117 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21118 (properties `((upstream-name . "flexclust")))
21119 (build-system r-build-system)
21121 `(("r-class" ,r-class)
21122 ("r-lattice" ,r-lattice)
21123 ("r-modeltools" ,r-modeltools)))
21124 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21125 (synopsis "Flexible cluster algorithms")
21127 "The main function @code{kcca} implements a general framework for
21128 k-centroids cluster analysis supporting arbitrary distance measures and
21129 centroid computation. Further cluster methods include hard competitive
21130 learning, neural gas, and QT clustering. There are numerous visualization
21131 methods for cluster results (neighborhood graphs, convex cluster hulls,
21132 barcharts of centroids, ...), and bootstrap methods for the analysis of
21133 cluster stability.")
21134 (license license:gpl2)))
21136 (define-public r-biclust
21143 (uri (cran-uri "biclust" version))
21146 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21147 (properties `((upstream-name . "biclust")))
21148 (build-system r-build-system)
21150 `(("r-additivitytests" ,r-additivitytests)
21151 ("r-colorspace" ,r-colorspace)
21152 ("r-flexclust" ,r-flexclust)
21153 ("r-ggplot2" ,r-ggplot2)
21154 ("r-lattice" ,r-lattice)
21156 ("r-tidyr" ,r-tidyr)))
21157 (home-page "https://cran.r-project.org/web/packages/biclust/")
21158 (synopsis "BiCluster algorithms")
21160 "The main function @code{biclust()} provides several algorithms to find
21161 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21162 In addition, the package provides methods for data
21163 preprocessing (normalization and discretization), visualization, and
21164 validation of bicluster solutions.")
21165 (license license:gpl3)))
21167 (define-public r-icge
21174 (uri (cran-uri "ICGE" version))
21177 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21178 (properties `((upstream-name . "ICGE")))
21179 (build-system r-build-system)
21181 `(("r-cluster" ,r-cluster)
21182 ("r-mass" ,r-mass)))
21183 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21184 (synopsis "Cluster estimation and identification of atypical units")
21186 "ICGE is a package that helps to estimate the number of real clusters in
21187 data as well as to identify atypical units. The underlying methods are based
21188 on distances rather than on unit x variables.")
21189 (license license:gpl2+)))
21191 (define-public r-depth
21194 (version "2.1-1.1")
21198 (uri (cran-uri "depth" version))
21201 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21202 (properties `((upstream-name . "depth")))
21203 (build-system r-build-system)
21205 `(("r-abind" ,r-abind)
21206 ("r-circular" ,r-circular)
21209 `(("gfortran" ,gfortran)))
21210 (home-page "https://cran.r-project.org/web/packages/depth/")
21211 (synopsis "Nonparametric depth functions for multivariate analysis")
21213 "This package provides tools for depth functions methodology applied to
21214 multivariate analysis. Besides allowing calculation of depth values and
21215 depth-based location estimators, the package includes functions or drawing
21216 contour plots and perspective plots of depth functions. Euclidean and
21217 spherical depths are supported.")
21218 (license license:gpl2)))
21220 (define-public r-archetypes
21222 (name "r-archetypes")
21223 (version "2.2-0.1")
21227 (uri (cran-uri "archetypes" version))
21230 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21231 (properties `((upstream-name . "archetypes")))
21232 (build-system r-build-system)
21234 `(("r-modeltools" ,r-modeltools)
21235 ("r-nnls" ,r-nnls)))
21236 (home-page "https://cran.r-project.org/web/packages/archetypes")
21237 (synopsis "Archetypal analysis")
21239 "The main function @code{archetypes} implements a framework for
21240 archetypal analysis supporting arbitrary problem solving mechanisms for the
21241 different conceptual parts of the algorithm.")
21242 (license license:gpl2+)))
21244 (define-public r-shapes
21251 (uri (cran-uri "shapes" version))
21254 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21255 (properties `((upstream-name . "shapes")))
21256 (build-system r-build-system)
21258 `(("r-mass" ,r-mass)
21259 ("r-minpack-lm" ,r-minpack-lm)
21261 ("r-scatterplot3d" ,r-scatterplot3d)))
21262 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21263 (synopsis "Statistical shape analysis")
21265 "This package provides routines for the statistical analysis of landmark
21266 shapes, including Procrustes analysis, graphical displays, principal
21267 components analysis, permutation and bootstrap tests, thin-plate spline
21268 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21269 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21270 Edition), John Wiley and Sons.")
21271 (license license:gpl2)))
21273 (define-public r-anthropometry
21275 (name "r-anthropometry")
21280 (uri (cran-uri "Anthropometry" version))
21283 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21284 (properties `((upstream-name . "Anthropometry")))
21285 (build-system r-build-system)
21287 `(("r-archetypes" ,r-archetypes)
21288 ("r-biclust" ,r-biclust)
21289 ("r-cluster" ,r-cluster)
21290 ("r-depth" ,r-depth)
21295 ("r-shapes" ,r-shapes)))
21297 `(("r-knitr" ,r-knitr)))
21298 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21299 (synopsis "Statistical methods for anthropometric data")
21301 "This package provides statistical methods especially developed to
21302 analyze anthropometric data. These methods are aimed at providing effective
21303 solutions to some commons problems related to Ergonomics and Anthropometry.
21304 They are based on clustering, the statistical concept of data depth,
21305 statistical shape analysis and archetypal analysis.")
21306 (license license:gpl2+)))
21308 (define-public r-adamethods
21310 (name "r-adamethods")
21315 (uri (cran-uri "adamethods" version))
21318 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21319 (properties `((upstream-name . "adamethods")))
21320 (build-system r-build-system)
21322 `(("r-anthropometry" ,r-anthropometry)
21323 ("r-archetypes" ,r-archetypes)
21325 ("r-foreach" ,r-foreach)
21327 ("r-tolerance" ,r-tolerance)
21328 ("r-univoutl" ,r-univoutl)))
21329 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21330 (synopsis "Archetypoid algorithms and anomaly detection")
21332 "This package is a collection of several algorithms to obtain
21333 archetypoids with small and large databases and with both classical
21334 multivariate data and functional data (univariate and multivariate). Some of
21335 these algorithms also detect anomalies (outliers).")
21336 (license license:gpl2+)))
21338 (define-public r-idpmisc
21345 (uri (cran-uri "IDPmisc" version))
21348 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21349 (properties `((upstream-name . "IDPmisc")))
21350 (build-system r-build-system)
21352 `(("r-lattice" ,r-lattice)))
21353 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21354 (synopsis "Functions for data analyses and visualization")
21356 "This package provides different high-level graphics functions for
21357 displaying large datasets, displaying circular data in a very flexible way,
21358 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21359 2D-plots, creating figures with differently colored margin and plot region.
21360 In addition, the package contains auxiliary functions for data manipulation
21361 like omitting observations with irregular values or selecting data by logical
21362 vectors, which include NAs. Other functions are especially useful in
21363 spectroscopy and analyses of environmental data: robust baseline fitting,
21364 finding peaks in spectra, converting humidity measures.")
21365 (license license:gpl3+)))
21367 (define-public r-qqman
21374 (uri (cran-uri "qqman" version))
21377 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21378 (properties `((upstream-name . "qqman")))
21379 (build-system r-build-system)
21381 `(("r-calibrate" ,r-calibrate)))
21382 (home-page "https://cran.r-project.org/web/packages/qqman/")
21383 (synopsis "Q-Q and Manhattan plots for GWAS data")
21385 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21386 from PLINK results.")
21387 (license license:gpl3)))
21389 (define-public r-ggplot-multistats
21391 (name "r-ggplot-multistats")
21396 (uri (cran-uri "ggplot.multistats" version))
21399 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21401 `((upstream-name . "ggplot.multistats")))
21402 (build-system r-build-system)
21404 `(("r-ggplot2" ,r-ggplot2)
21405 ("r-hexbin" ,r-hexbin)
21406 ("r-rlang" ,r-rlang)
21407 ("r-scales" ,r-scales)))
21408 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21409 (synopsis "Multiple summary statistics for binned stats/geometries")
21411 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21412 which functions similar to its singular form, but allows the use of multiple
21413 statistics per bin. Those statistics can be mapped to multiple bin
21415 (license license:gpl3)))
21417 (define-public r-knn-covertree
21419 (name "r-knn-covertree")
21424 (uri (cran-uri "knn.covertree" version))
21427 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21428 (properties `((upstream-name . "knn.covertree")))
21429 (build-system r-build-system)
21431 `(("r-matrix" ,r-matrix)
21433 ("r-rcppeigen" ,r-rcppeigen)))
21434 (home-page "https://github.com/flying-sheep/knn.covertree")
21435 (synopsis "Accurate kNN Implementation with multiple distance measures")
21437 "Similarly to the FNN package, this package allows calculation of the k
21438 nearest neighbors (kNN) of a data matrix. The implementation is based on
21439 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21440 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21441 (license license:agpl3+)))
21443 (define-public r-poibin
21450 (uri (cran-uri "poibin" version))
21453 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21454 (properties `((upstream-name . "poibin")))
21455 (build-system r-build-system)
21456 (home-page "https://cran.r-project.org/web/packages/poibin/")
21457 (synopsis "Poisson binomial distribution")
21459 "This package provides an implementation of both the exact and
21460 approximation methods for computing the @dfn{cumulative distribution
21461 function} (CDF) of the Poisson binomial distribution. It also provides the
21462 @dfn{probability mass function} (PMF), quantile function, and random number
21463 generation for the Poisson binomial distribution.")
21464 (license license:gpl2)))
21466 (define-public r-diagram
21473 (uri (cran-uri "diagram" version))
21476 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21477 (properties `((upstream-name . "diagram")))
21478 (build-system r-build-system)
21480 `(("r-shape" ,r-shape)))
21481 (home-page "https://cran.r-project.org/web/packages/diagram/")
21482 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21484 "This package provides tools to visualize simple graphs (networks) based
21485 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21486 electrical networks, etc. It also includes supporting material for the book
21487 \"A practical guide to ecological modelling - using R as a simulation
21488 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21489 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21490 Francesca Mazzia (2012).")
21491 (license license:gpl2+)))
21493 (define-public r-lim
21500 (uri (cran-uri "LIM" version))
21503 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21504 (properties `((upstream-name . "LIM")))
21505 (build-system r-build-system)
21507 `(("r-diagram" ,r-diagram)
21508 ("r-limsolve" ,r-limsolve)))
21509 (home-page "https://cran.r-project.org/web/packages/LIM/")
21510 (synopsis "Linear inverse model examples and solution methods")
21512 "This package provides functions that read and solve linear inverse
21513 problems (food web problems, linear programming problems).")
21514 (license license:gpl2+)))
21516 (define-public r-shinycssloaders
21518 (name "r-shinycssloaders")
21523 (uri (cran-uri "shinycssloaders" version))
21526 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21528 `((upstream-name . "shinycssloaders")))
21529 (build-system r-build-system)
21531 `(("r-digest" ,r-digest)
21533 ("r-shiny" ,r-shiny)))
21534 (home-page "https://github.com/andrewsali/shinycssloaders")
21535 (synopsis "Add CSS loading animations to Shiny outputs")
21537 "This package provides tools to create a lightweight Shiny wrapper for
21538 the css-loaders created by Luke Hass
21539 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21540 automatically show a loader when the output is (re)calculating.")
21541 (license license:gpl3)))
21543 (define-public r-rsvg
21550 (uri (cran-uri "rsvg" version))
21553 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21554 (properties `((upstream-name . "rsvg")))
21555 (build-system r-build-system)
21557 `(("librsvg" ,librsvg)
21560 `(("pkg-config" ,pkg-config)
21561 ("r-knitr" ,r-knitr)))
21562 (home-page "https://github.com/jeroen/rsvg#readme")
21563 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21565 "This package allows you to render vector-based SVG images into
21566 high-quality custom-size bitmap arrays using the librsvg2 library. The
21567 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21568 addition, the package can convert images directly to various formats such as
21569 PDF or PostScript.")
21570 (license license:expat)))
21572 (define-public r-influencer
21574 (name "r-influencer")
21579 (uri (cran-uri "influenceR" version))
21582 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21583 (properties `((upstream-name . "influenceR")))
21584 (build-system r-build-system)
21586 `(("r-igraph" ,r-igraph)
21587 ("r-matrix" ,r-matrix)))
21588 (home-page "https://github.com/rcc-uchicago/influenceR")
21589 (synopsis "Tools to quantify structural importance of nodes in a network")
21591 "This package provides functionality to compute various node centrality
21592 measures on networks. Included are functions to compute betweenness
21593 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21594 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21595 algorithm to identify key players, and Valente's bridging metric. The
21596 betweenness, Key Players, and bridging implementations are parallelized with
21598 (license license:gpl2)))
21600 (define-public r-emplik
21607 (uri (cran-uri "emplik" version))
21610 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21611 (properties `((upstream-name . "emplik")))
21612 (build-system r-build-system)
21614 `(("r-quantreg" ,r-quantreg)))
21615 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21616 (synopsis "Empirical likelihood ratio for censored/truncated data")
21618 "This package provides empirical likelihood ratio tests for
21619 means/quantiles/hazards from possibly censored and/or truncated data. It also
21621 (license license:gpl2+)))
21623 (define-public r-imputeyn
21625 (name "r-imputeyn")
21630 (uri (cran-uri "imputeYn" version))
21633 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21634 (properties `((upstream-name . "imputeYn")))
21635 (build-system r-build-system)
21637 `(("r-boot" ,r-boot)
21638 ("r-emplik" ,r-emplik)
21639 ("r-mvtnorm" ,r-mvtnorm)
21640 ("r-quadprog" ,r-quadprog)
21641 ("r-survival" ,r-survival)))
21642 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21643 (synopsis "Impute last largest censored observation under weighted least squares")
21645 "This package allows for the imputation of the last largest censored
21646 observantions. This method brings less bias and more efficient estimates for
21648 (license license:gpl2)))
21650 (define-public r-adapenetclass
21652 (name "r-adapenetclass")
21657 (uri (cran-uri "AdapEnetClass" version))
21660 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21661 (properties `((upstream-name . "AdapEnetClass")))
21662 (build-system r-build-system)
21664 `(("r-glmnet" ,r-glmnet)
21665 ("r-imputeyn" ,r-imputeyn)
21667 ("r-quadprog" ,r-quadprog)))
21668 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21669 (synopsis "Class of adaptive elastic net methods for censored data")
21671 "This package provides methods for variable selection for AFT models.")
21672 (license license:gpl2)))
21674 (define-public r-flock
21681 (uri (cran-uri "flock" version))
21684 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21685 (properties `((upstream-name . "flock")))
21686 (build-system r-build-system)
21687 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21688 (home-page "https://cran.r-project.org/web/packages/flock/")
21689 (synopsis "Process synchronization using file locks")
21691 "This package implements synchronization between R processes (spawned by
21692 using the @code{parallel} package for instance) using file locks. It supports
21693 both exclusive and shared locking.")
21694 (license license:asl2.0)))
21696 (define-public r-archivist
21698 (name "r-archivist")
21703 (uri (cran-uri "archivist" version))
21706 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21707 (properties `((upstream-name . "archivist")))
21708 (build-system r-build-system)
21711 ("r-digest" ,r-digest)
21712 ("r-flock" ,r-flock)
21714 ("r-lubridate" ,r-lubridate)
21715 ("r-magrittr" ,r-magrittr)
21716 ("r-rcurl" ,r-rcurl)
21717 ("r-rsqlite" ,r-rsqlite)))
21719 `(("r-knitr" ,r-knitr)))
21720 (home-page "https://pbiecek.github.io/archivist/")
21721 (synopsis "Tools for storing, restoring and searching for R objects")
21723 "Data exploration and modelling is a process in which a lot of data
21724 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21725 statistical models, different versions of data sets and different versions of
21726 results. Archivist helps to store and manage artifacts created in R. It
21727 allows you to store selected artifacts as binary files together with their
21728 metadata and relations. Archivist allows sharing artifacts with others. It
21729 can look for already created artifacts by using its class, name, date of the
21730 creation or other properties. It also makes it easy to restore such
21732 (license license:gpl2)))
21734 (define-public r-versions
21736 (name "r-versions")
21741 (uri (cran-uri "versions" version))
21744 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21745 (properties `((upstream-name . "versions")))
21746 (build-system r-build-system)
21747 (home-page "https://cran.r-project.org/web/packages/versions/")
21748 (synopsis "Query and install specific versions of CRAN packages")
21750 "This package allows you to install specified versions of R packages
21751 hosted on CRAN and provides functions to list available versions and the
21752 versions of currently installed packages.")
21753 (license license:bsd-3)))
21755 (define-public r-adapr
21762 (uri (cran-uri "adapr" version))
21765 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21766 (properties `((upstream-name . "adapr")))
21767 (build-system r-build-system)
21769 `(("r-archivist" ,r-archivist)
21770 ("r-devtools" ,r-devtools)
21771 ("r-digest" ,r-digest)
21772 ("r-doparallel" ,r-doparallel)
21773 ("r-gdata" ,r-gdata)
21774 ("r-ggplot2" ,r-ggplot2)
21775 ("r-git2r" ,r-git2r)
21776 ("r-igraph" ,r-igraph)
21777 ("r-knitr" ,r-knitr)
21778 ("r-plotly" ,r-plotly)
21780 ("r-rmarkdown" ,r-rmarkdown)
21781 ("r-shiny" ,r-shiny)
21782 ("r-shinydashboard" ,r-shinydashboard)
21783 ("r-versions" ,r-versions)))
21784 (home-page "https://cran.r-project.org/web/packages/adapr/")
21785 (synopsis "Implementation of an accountable data analysis process")
21787 "This package tracks reading and writing within R scripts that are
21788 organized into a directed acyclic graph. It contains an interactive Shiny
21789 application @code{adaprApp()}. It uses Git and file hashes to track version
21790 histories of inputs and outputs.")
21791 (license license:lgpl2.0)))
21793 (define-public r-adapsamp
21795 (name "r-adapsamp")
21800 (uri (cran-uri "AdapSamp" version))
21803 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21804 (properties `((upstream-name . "AdapSamp")))
21805 (build-system r-build-system)
21806 (propagated-inputs `(("r-pracma" ,r-pracma)))
21807 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21808 (synopsis "Adaptive sampling algorithms")
21810 "For distributions whose probability density functions are log-concave,
21811 the adaptive rejection sampling algorithm can be used to build envelope
21812 functions for sampling. For others, the modified adaptive rejection sampling
21813 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21814 adaptive slice sampling algorithm can be used. This R package mainly includes
21815 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21816 @code{rASS()}. These functions can realize sampling based on the algorithms
21818 (license license:gpl2)))
21820 (define-public r-adaptalint
21822 (name "r-adaptalint")
21827 (uri (cran-uri "adaptalint" version))
21830 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21831 (properties `((upstream-name . "adaptalint")))
21832 (build-system r-build-system)
21834 `(("r-dplyr" ,r-dplyr)
21835 ("r-lintr" ,r-lintr)
21836 ("r-purrr" ,r-purrr)))
21837 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21838 (synopsis "Check R code style")
21840 "This package provides tools to infer the code style (which style rules
21841 are followed and which ones are not) from one package and use it to check
21842 another. This makes it easier to find and correct the most important problems
21844 (license license:gpl3)))
21846 (define-public r-fracdiff
21848 (name "r-fracdiff")
21853 (uri (cran-uri "fracdiff" version))
21856 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21857 (properties `((upstream-name . "fracdiff")))
21858 (build-system r-build-system)
21859 (home-page "https://github.com/mmaechler/fracdiff")
21861 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21863 "This package provides tools for the maximum likelihood estimation of the
21864 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21865 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21866 (license license:gpl2+)))
21868 (define-public r-forecast
21870 (name "r-forecast")
21875 (uri (cran-uri "forecast" version))
21878 "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
21879 (properties `((upstream-name . "forecast")))
21880 (build-system r-build-system)
21882 `(("r-colorspace" ,r-colorspace)
21883 ("r-fracdiff" ,r-fracdiff)
21884 ("r-ggplot2" ,r-ggplot2)
21885 ("r-lmtest" ,r-lmtest)
21886 ("r-magrittr" ,r-magrittr)
21889 ("r-rcpparmadillo" ,r-rcpparmadillo)
21890 ("r-timedate" ,r-timedate)
21891 ("r-tseries" ,r-tseries)
21895 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21896 (home-page "https://pkg.robjhyndman.com/forecast/")
21897 (synopsis "Forecasting functions for time series and linear models")
21899 "This package provides methods and tools for displaying and analysing
21900 univariate time series forecasts including exponential smoothing via state
21901 space models and automatic ARIMA modelling.")
21902 (license license:gpl3)))
21904 (define-public r-xmisc
21911 (uri (cran-uri "Xmisc" version))
21914 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21915 (properties `((upstream-name . "Xmisc")))
21916 (build-system r-build-system)
21917 (home-page "https://cran.r-project.org/package=Xmisc")
21919 "Xiaobei's miscellaneous classes and functions")
21921 "This package provides Xiaobei's miscellaneous classes and functions,
21922 which are useful when developing R packages for @dfn{object oriented
21923 programming} (OOP) using R Reference Class.")
21924 (license license:gpl2+)))
21926 (define-public r-proxyc
21933 (uri (cran-uri "proxyC" version))
21936 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21937 (properties `((upstream-name . "proxyC")))
21938 (build-system r-build-system)
21940 `(("r-matrix" ,r-matrix)
21942 ("r-rcpparmadillo" ,r-rcpparmadillo)
21943 ("r-rcppparallel" ,r-rcppparallel)))
21944 (home-page "https://cran.r-project.org/package=proxyC")
21945 (synopsis "Compute proximity in large sparse matrices")
21947 "This package provides efficient tools to compute the proximity between
21948 rows or columns of large matrices. Functions are optimised for large sparse
21949 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21950 similarity/distance measures, computation of correlation, cosine similarity
21951 and Euclidean distance is particularly fast.")
21952 (license license:gpl3)))
21954 (define-public r-isocodes
21956 (name "r-isocodes")
21957 (version "2021.02.24")
21961 (uri (cran-uri "ISOcodes" version))
21964 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
21965 (properties `((upstream-name . "ISOcodes")))
21966 (build-system r-build-system)
21967 (home-page "https://cran.r-project.org/package=ISOcodes")
21968 (synopsis "Selected ISO codes")
21970 "This package provides ISO language, territory, currency, script and
21971 character codes. It provides ISO 639 language codes, ISO 3166 territory
21972 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21973 character codes as well as the UN M.49 area codes.")
21974 (license license:gpl2)))
21976 (define-public r-stopwords
21978 (name "r-stopwords")
21983 (uri (cran-uri "stopwords" version))
21986 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
21987 (properties `((upstream-name . "stopwords")))
21988 (build-system r-build-system)
21990 `(("r-isocodes" ,r-isocodes)))
21991 (home-page "https://github.com/quanteda/stopwords")
21992 (synopsis "Multilingual stopword lists")
21994 "This package provides multiple sources of stopwords, for use in text
21995 analysis and natural language processing.")
21996 (license license:expat)))
21998 (define-public r-spacyr
22005 (uri (cran-uri "spacyr" version))
22008 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
22009 (properties `((upstream-name . "spacyr")))
22010 (build-system r-build-system)
22012 `(("r-data-table" ,r-data-table)
22013 ("r-reticulate" ,r-reticulate)))
22014 (home-page "https://spacyr.quanteda.io")
22015 (synopsis "R wrapper for the spaCy NLP library")
22017 "This package provides an R wrapper to the Python @dfn{natural language
22018 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22019 (license license:gpl3)))
22021 (define-public r-snowballc
22023 (name "r-snowballc")
22028 (uri (cran-uri "SnowballC" version))
22031 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22032 (properties `((upstream-name . "SnowballC")))
22033 (build-system r-build-system)
22034 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22035 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22037 "This package provides an R interface to the C @code{libstemmer} library
22038 that implements Porter's word stemming algorithm for collapsing words to a
22039 common root to aid comparison of vocabulary. Currently supported languages
22040 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22041 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22042 (license license:bsd-3)))
22044 (define-public r-quanteda
22046 (name "r-quanteda")
22051 (uri (cran-uri "quanteda" version))
22054 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22055 (properties `((upstream-name . "quanteda")))
22056 (build-system r-build-system)
22058 `(("r-data-table" ,r-data-table)
22059 ("r-digest" ,r-digest)
22060 ("r-extrafont" ,r-extrafont)
22061 ("r-fastmatch" ,r-fastmatch)
22062 ("r-ggplot2" ,r-ggplot2)
22063 ("r-ggrepel" ,r-ggrepel)
22064 ("r-jsonlite" ,r-jsonlite)
22065 ("r-magrittr" ,r-magrittr)
22066 ("r-matrix" ,r-matrix)
22067 ("r-network" ,r-network)
22068 ("r-proxyc" ,r-proxyc)
22070 ("r-rcpparmadillo" ,r-rcpparmadillo)
22071 ("r-rcppparallel" ,r-rcppparallel)
22073 ("r-snowballc" ,r-snowballc)
22074 ("r-stopwords" ,r-stopwords)
22075 ("r-stringi" ,r-stringi)
22077 ("r-yaml" ,r-yaml)))
22079 `(("r-knitr" ,r-knitr)))
22080 (home-page "https://quanteda.io")
22081 (synopsis "Quantitative analysis of textual data")
22083 "This package provides a fast, flexible, and comprehensive framework for
22084 quantitative text analysis in R. It provides functionality for corpus
22085 management, creating and manipulating tokens and ngrams, exploring keywords in
22086 context, forming and manipulating sparse matrices of documents by features and
22087 feature co-occurrences, analyzing keywords, computing feature similarities and
22088 distances, applying content dictionaries, applying supervised and unsupervised
22089 machine learning, visually representing text and text analyses, and more.")
22090 (license license:gpl3)))
22092 (define-public r-topicmodels
22094 (name "r-topicmodels")
22099 (uri (cran-uri "topicmodels" version))
22102 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22103 (properties `((upstream-name . "topicmodels")))
22104 (build-system r-build-system)
22108 `(("r-modeltools" ,r-modeltools)
22111 (home-page "https://cran.r-project.org/package=topicmodels")
22112 (synopsis "Topic models")
22114 "This package provides an interface to the C code for @dfn{Latent
22115 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22116 David M. Blei and co-authors and the C++ code for fitting LDA models using
22117 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22118 (license license:gpl2)))
22120 (define-public r-stm
22127 (uri (cran-uri "stm" version))
22130 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22131 (properties `((upstream-name . "stm")))
22132 (build-system r-build-system)
22134 `(("r-data-table" ,r-data-table)
22135 ("r-glmnet" ,r-glmnet)
22137 ("r-matrix" ,r-matrix)
22138 ("r-matrixstats" ,r-matrixstats)
22139 ("r-quadprog" ,r-quadprog)
22140 ("r-quanteda" ,r-quanteda)
22142 ("r-rcpparmadillo" ,r-rcpparmadillo)
22144 ("r-stringr" ,r-stringr)))
22145 (home-page "http://www.structuraltopicmodel.com/")
22146 (synopsis "Estimation of the Structural Topic Model")
22148 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22149 topic models with document-level covariates. The package also includes tools
22150 for model selection, visualization, and estimation of topic-covariate
22152 (license license:expat)))
22154 (define-public r-polycor
22161 (uri (cran-uri "polycor" version))
22164 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22165 (properties `((upstream-name . "polycor")))
22166 (build-system r-build-system)
22168 `(("r-matrix" ,r-matrix)
22169 ("r-mvtnorm" ,r-mvtnorm)))
22170 (home-page "https://r-forge.r-project.org/projects/polycor/")
22171 (synopsis "Polychoric and polyserial correlations")
22173 "This package provides tools to compute polychoric and polyserial
22174 correlations by quick \"two-step\" methods or ML, optionally with standard
22175 errors; tetrachoric and biserial correlations are special cases.")
22176 (license license:gpl2+)))
22178 (define-public r-msm
22185 (uri (cran-uri "msm" version))
22188 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22189 (properties `((upstream-name . "msm")))
22190 (build-system r-build-system)
22192 `(("r-expm" ,r-expm)
22193 ("r-mvtnorm" ,r-mvtnorm)
22194 ("r-survival" ,r-survival)))
22195 (home-page "https://github.com/chjackson/msm")
22196 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22198 "This package provides functions for fitting continuous-time Markov and
22199 hidden Markov multi-state models to longitudinal data. It was designed for
22200 processes observed at arbitrary times in continuous time (panel data) but some
22201 other observation schemes are supported. Both Markov transition rates and the
22202 hidden Markov output process can be modelled in terms of covariates, which may
22203 be constant or piecewise-constant in time.")
22204 (license license:gpl2+)))
22206 (define-public r-ltm
22213 (uri (cran-uri "ltm" version))
22216 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22217 (properties `((upstream-name . "ltm")))
22218 (build-system r-build-system)
22220 `(("r-mass" ,r-mass)
22222 ("r-polycor" ,r-polycor)))
22223 (home-page "https://github.com/drizopoulos/ltm")
22224 (synopsis "Latent trait models under IRT")
22226 "This is a package supporting the analysis of multivariate dichotomous
22227 and polytomous data using latent trait models under the Item Response Theory
22228 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22229 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22231 (license license:gpl2+)))
22233 (define-public r-mi
22240 (uri (cran-uri "mi" version))
22243 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22244 (properties `((upstream-name . "mi")))
22245 (build-system r-build-system)
22248 ("r-matrix" ,r-matrix)))
22249 (home-page "http://www.stat.columbia.edu/~gelman/")
22250 (synopsis "Missing data imputation and model checking")
22252 "This package provides functions for data manipulation, imputing missing
22253 values in an approximate Bayesian framework, diagnostics of the models used to
22254 generate the imputations, confidence-building mechanisms to validate some of
22255 the assumptions of the imputation algorithm, and functions to analyze multiply
22256 imputed data sets with the appropriate degree of sampling uncertainty.")
22257 (license license:gpl2+)))
22259 (define-public r-matrixcalc
22261 (name "r-matrixcalc")
22266 (uri (cran-uri "matrixcalc" version))
22269 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22270 (properties `((upstream-name . "matrixcalc")))
22271 (build-system r-build-system)
22272 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22273 (synopsis "Collection of functions for matrix calculations")
22275 "This package provides a collection of functions to support matrix
22276 calculations for probability, econometric and numerical analysis. There are
22277 additional functions that are comparable to APL functions which are useful for
22278 actuarial models such as pension mathematics.")
22279 (license license:gpl2+)))
22281 (define-public r-sem
22288 (uri (cran-uri "sem" version))
22291 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22292 (properties `((upstream-name . "sem")))
22293 (build-system r-build-system)
22295 `(("r-boot" ,r-boot)
22297 ("r-matrixcalc" ,r-matrixcalc)
22299 (home-page "https://cran.r-project.org/package=sem")
22300 (synopsis "Structural equation models")
22302 "This package provides functions for fitting general linear structural
22303 equation models (with observed and latent variables) using the RAM approach,
22304 and for fitting structural equations in observed-variable models by two-stage
22306 (license license:gpl2+)))
22308 (define-public r-semtools
22310 (name "r-semtools")
22315 (uri (cran-uri "semTools" version))
22318 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22319 (properties `((upstream-name . "semTools")))
22320 (build-system r-build-system)
22322 `(("r-lavaan" ,r-lavaan)))
22323 (home-page "https://github.com/simsem/semTools/wiki")
22324 (synopsis "Useful tools for structural equation modeling")
22326 "This package provides useful tools for structural equation modeling.")
22327 (license license:gpl2+)))
22329 (define-public r-regsem
22336 (uri (cran-uri "regsem" version))
22339 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22340 (properties `((upstream-name . "regsem")))
22341 (build-system r-build-system)
22343 `(("r-lavaan" ,r-lavaan)
22345 ("r-rcpparmadillo" ,r-rcpparmadillo)
22346 ("r-rsolnp" ,r-rsolnp)))
22348 `(("r-knitr" ,r-knitr)))
22349 (home-page "https://cran.r-project.org/package=regsem")
22350 (synopsis "Regularized structural equation modeling")
22352 "This package uses both ridge and lasso penalties (and extensions) to
22353 penalize specific parameters in structural equation models. The package
22354 offers additional cost functions, cross validation, and other extensions
22355 beyond traditional structural equation models. It also contains a function to
22356 perform @dfn{exploratory mediation} (XMed).")
22357 (license license:gpl2+)))
22359 (define-public r-stanheaders
22361 (name "r-stanheaders")
22362 (version "2.21.0-7")
22366 (uri (cran-uri "StanHeaders" version))
22369 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22370 (properties `((upstream-name . "StanHeaders")))
22371 (build-system r-build-system)
22372 (inputs `(("pandoc" ,pandoc)))
22374 `(("r-rcppeigen" ,r-rcppeigen)
22375 ("r-rcppparallel" ,r-rcppparallel)))
22377 `(("gfortran" ,gfortran)
22378 ("r-knitr" ,r-knitr))) ; for vignettes
22379 (home-page "https://mc-stan.org/")
22380 (synopsis "C++ header files for Stan")
22382 "The C++ header files of the Stan project are provided by this package.
22383 There is a shared object containing part of the @code{CVODES} library, but it
22384 is not accessible from R. @code{r-stanheaders} is only useful for developers
22385 who want to utilize the @code{LinkingTo} directive of their package's
22386 DESCRIPTION file to build on the Stan library without incurring unnecessary
22389 The Stan project develops a probabilistic programming language that implements
22390 full or approximate Bayesian statistical inference via Markov Chain Monte
22391 Carlo or variational methods and implements (optionally penalized) maximum
22392 likelihood estimation via optimization. The Stan library includes an advanced
22393 automatic differentiation scheme, templated statistical and linear algebra
22394 functions that can handle the automatically differentiable scalar types (and
22395 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22396 package provides user-facing R functions to parse, compile, test, estimate,
22397 and analyze Stan models.")
22398 (license license:bsd-3)))
22400 (define-public r-rpf
22407 (uri (cran-uri "rpf" version))
22410 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22411 (properties `((upstream-name . "rpf")))
22412 (build-system r-build-system)
22414 `(("r-lifecycle" ,r-lifecycle)
22415 ("r-mvtnorm" ,r-mvtnorm)
22417 ("r-rcppeigen" ,r-rcppeigen)))
22419 `(("r-knitr" ,r-knitr)))
22420 (home-page "https://github.com/jpritikin/rpf")
22421 (synopsis "Response probability functions")
22423 "The purpose of this package is to factor out logic and math common to
22424 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22425 core support code suitable for more specialized IRT packages to build upon.
22426 Complete access to optimized C functions is made available with
22427 @code{R_RegisterCCallable()}.")
22428 (license license:gpl3+)))
22430 (define-public r-openmx
22437 (uri (cran-uri "OpenMx" version))
22440 "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj"))))
22441 (properties `((upstream-name . "OpenMx")))
22442 (build-system r-build-system)
22445 ("r-digest" ,r-digest)
22446 ("r-lifecycle" ,r-lifecycle)
22448 ("r-matrix" ,r-matrix)
22450 ("r-rcppeigen" ,r-rcppeigen)
22452 ("r-stanheaders" ,r-stanheaders)))
22453 (native-inputs `(("gfortran" ,gfortran)))
22454 (home-page "http://openmx.ssri.psu.edu")
22455 (synopsis "Extended structural equation modelling")
22457 "This package allows for the estimation of a wide variety of advanced
22458 multivariate statistical models. It consists of a library of functions and
22459 optimizers that allow you to quickly and flexibly define an SEM model and
22460 estimate parameters given observed data.")
22461 (license license:asl2.0)))
22463 (define-public r-kutils
22470 (uri (cran-uri "kutils" version))
22473 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22474 (properties `((upstream-name . "kutils")))
22475 (build-system r-build-system)
22477 `(("r-foreign" ,r-foreign)
22478 ("r-openxlsx" ,r-openxlsx)
22480 ("r-runit" ,r-runit)
22481 ("r-xtable" ,r-xtable)))
22482 (home-page "https://cran.r-project.org/package=kutils")
22483 (synopsis "Project management tools")
22485 "This package provides tools for data importation, recoding, and
22486 inspection. There are functions to create new project folders, R code
22487 templates, create uniquely named output directories, and to quickly obtain a
22488 visual summary for each variable in a data frame. The main feature here is
22489 the systematic implementation of the \"variable key\" framework for data
22490 importation and recoding.")
22491 (license license:gpl2)))
22493 (define-public r-rockchalk
22495 (name "r-rockchalk")
22496 (version "1.8.144")
22500 (uri (cran-uri "rockchalk" version))
22503 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22504 (properties `((upstream-name . "rockchalk")))
22505 (build-system r-build-system)
22507 `(("r-cardata" ,r-cardata)
22508 ("r-kutils" ,r-kutils)
22510 ("r-mass" ,r-mass)))
22511 (home-page "https://cran.r-project.org/package=rockchalk")
22512 (synopsis "Regression estimation and presentation")
22514 "This package provides a collection of functions for interpretation and
22515 presentation of regression analysis. These functions are used to produce the
22516 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22517 includes regression diagnostics, regression tables, and plots of interactions
22518 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22519 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22520 fairly comprehensive overview.")
22521 (license license:gpl3+)))
22523 (define-public r-lisreltor
22525 (name "r-lisreltor")
22530 (uri (cran-uri "lisrelToR" version))
22533 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22534 (properties `((upstream-name . "lisrelToR")))
22535 (build-system r-build-system)
22536 (home-page "https://cran.r-project.org/package=lisrelToR")
22537 (synopsis "Import output from LISREL into R")
22539 "This is an unofficial package aimed at automating the import of LISREL
22541 (license license:gpl2)))
22543 (define-public r-bdgraph
22550 (uri (cran-uri "BDgraph" version))
22553 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22554 (properties `((upstream-name . "BDgraph")))
22555 (build-system r-build-system)
22557 `(("r-igraph" ,r-igraph)))
22558 (home-page "https://www.uva.nl/profile/a.mohammadi")
22559 (synopsis "Bayesian structure learning in graphical models")
22561 "This package provides statistical tools for Bayesian structure learning
22562 in undirected graphical models for continuous, discrete, and mixed data. It
22563 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22564 on a continuous-time birth-death process.")
22565 (license license:gpl2+)))
22567 (define-public r-d3network
22569 (name "r-d3network")
22570 (version "0.5.2.1")
22574 (uri (cran-uri "d3Network" version))
22577 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22578 (properties `((upstream-name . "d3Network")))
22579 (build-system r-build-system)
22581 `(("r-plyr" ,r-plyr)
22582 ("r-rjson" ,r-rjson)
22583 ("r-whisker" ,r-whisker)))
22584 (home-page "http://christophergandrud.github.io/d3Network/")
22585 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22587 "This package is intended to make it easy to create D3 JavaScript
22588 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22589 (license license:gpl3+)))
22591 (define-public r-qgraph
22598 (uri (cran-uri "qgraph" version))
22601 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22602 (properties `((upstream-name . "qgraph")))
22603 (build-system r-build-system)
22605 `(("r-abind" ,r-abind)
22606 ("r-colorspace" ,r-colorspace)
22607 ("r-corpcor" ,r-corpcor)
22608 ("r-dplyr" ,r-dplyr)
22609 ("r-fdrtool" ,r-fdrtool)
22610 ("r-ggplot2" ,r-ggplot2)
22611 ("r-glasso" ,r-glasso)
22612 ("r-gtools" ,r-gtools)
22613 ("r-hmisc" ,r-hmisc)
22614 ("r-igraph" ,r-igraph)
22616 ("r-lavaan" ,r-lavaan)
22617 ("r-matrix" ,r-matrix)
22618 ("r-pbapply" ,r-pbapply)
22621 ("r-psych" ,r-psych)
22623 ("r-reshape2" ,r-reshape2)))
22624 (home-page "http://sachaepskamp.com/qgraph/")
22625 (synopsis "Weighted network visualization and analysis")
22627 "This package implements tools for weighted network visualization and
22628 analysis, as well as Gaussian graphical model computation. It contains graph
22629 plotting methods, and tools for psychometric data visualization and graphical
22630 model estimation. See Epskamp et al. (2012)
22631 @url{doi:10.18637/jss.v048.i04}.")
22632 (license license:gpl2)))
22634 (define-public r-semplot
22641 (uri (cran-uri "semPlot" version))
22644 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22645 (properties `((upstream-name . "semPlot")))
22646 (build-system r-build-system)
22648 `(("r-colorspace" ,r-colorspace)
22649 ("r-corpcor" ,r-corpcor)
22650 ("r-igraph" ,r-igraph)
22651 ("r-lavaan" ,r-lavaan)
22652 ("r-lisreltor" ,r-lisreltor)
22653 ("r-openmx" ,r-openmx)
22655 ("r-qgraph" ,r-qgraph)
22656 ("r-regsem" ,r-regsem)
22657 ("r-rockchalk" ,r-rockchalk)
22660 (home-page "https://github.com/SachaEpskamp/semPlot")
22661 (synopsis "Unified visualizations of structural equation models")
22663 "Structural equation modeling (SEM) has a long history of representing
22664 models graphically as path diagrams. The semPlot package for R fills the gap
22665 between advanced, but time-consuming, graphical software and the limited
22666 graphics produced automatically by SEM software. In addition, semPlot offers
22667 more functionality than drawing path diagrams: it can act as a common ground
22668 for importing SEM results into R. Any result usable as input to semPlot can
22669 also be represented in any of the three popular SEM frame-works, as well as
22670 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22671 (license license:gpl2)))
22673 (define-public r-cdm
22680 (uri (cran-uri "CDM" version))
22683 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22684 (properties `((upstream-name . "CDM")))
22685 (build-system r-build-system)
22687 `(("r-mvtnorm" ,r-mvtnorm)
22688 ("r-polycor" ,r-polycor)
22690 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22692 "https://github.com/alexanderrobitzsch/CDM")
22693 (synopsis "Cognitive diagnosis modeling")
22695 "This package provides functions for cognitive diagnosis modeling and
22696 multidimensional item response modeling for dichotomous and polytomous item
22697 responses. It enables the estimation of the DINA and DINO model, the multiple
22698 group (polytomous) GDINA model, the multiple choice DINA model, the general
22699 diagnostic model (GDM), the structured latent class model (SLCA), and
22700 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22701 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22702 estimation and the package structure. For tutorials on how to use the CDM
22703 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22704 well as Ravand and Robitzsch (2015).")
22705 (license license:gpl2+)))
22707 (define-public r-tam
22714 (uri (cran-uri "TAM" version))
22717 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22718 (properties `((upstream-name . "TAM")))
22719 (build-system r-build-system)
22723 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22724 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22725 (synopsis "Test analysis modules")
22727 "This package includes tools for marginal maximum likelihood estimation
22728 and joint maximum likelihood estimation for unidimensional and
22729 multidimensional item response models. The package functionality covers the
22730 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22731 multi-faceted Rasch model, nominal item response model, structured latent
22732 class model, mixture distribution IRT models, and located latent class models.
22733 Latent regression models and plausible value imputation are also supported.")
22734 (license license:gpl2+)))
22736 (define-public r-erm
22743 (uri (cran-uri "eRm" version))
22746 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
22747 (properties `((upstream-name . "eRm")))
22748 (build-system r-build-system)
22750 `(("r-colorspace" ,r-colorspace)
22751 ("r-lattice" ,r-lattice)
22753 ("r-matrix" ,r-matrix)
22754 ("r-psych" ,r-psych)))
22755 (native-inputs `(("gfortran" ,gfortran)))
22756 (home-page "https://cran.r-project.org/package=eRm")
22757 (synopsis "Extended Rasch modeling")
22759 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22760 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22761 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22762 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22763 data matrix. Additional features are the ML estimation of the person
22764 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22765 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22766 infit and outfit measures, ICC and other plots, automated stepwise item
22767 elimination, and a simulation module for various binary data matrices.")
22768 (license license:gpl3)))
22770 (define-public r-irtoys
22777 (uri (cran-uri "irtoys" version))
22780 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22781 (properties `((upstream-name . "irtoys")))
22782 (build-system r-build-system)
22786 (home-page "https://cran.r-project.org/package=irtoys")
22787 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22789 "This package provides a collection of functions useful in learning and
22790 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22791 programs. It provides basic CTT analysis, a simple common interface to the
22792 estimation of item parameters in IRT models for binary responses with three
22793 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22794 EAP, WLE, plausible values), item and person fit statistics, scaling
22795 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22796 array of parametric and non-parametric (kernel) plots. It estimates and plots
22797 Haberman's interaction model when all items are dichotomously scored.")
22798 (license license:gpl2+)))
22800 (define-public r-iheatmapr
22802 (name "r-iheatmapr")
22807 (uri (cran-uri "iheatmapr" version))
22810 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22811 (properties `((upstream-name . "iheatmapr")))
22812 (build-system r-build-system)
22814 `(("r-fastcluster" ,r-fastcluster)
22815 ("r-ggdendro" ,r-ggdendro)
22816 ("r-htmlwidgets" ,r-htmlwidgets)
22817 ("r-jsonlite" ,r-jsonlite)
22818 ("r-knitr" ,r-knitr)
22819 ("r-magrittr" ,r-magrittr)
22820 ("r-rcolorbrewer" ,r-rcolorbrewer)
22821 ("r-scales" ,r-scales)))
22823 `(("r-knitr" ,r-knitr)))
22824 (home-page "https://docs.ropensci.org/iheatmapr")
22825 (synopsis "Interactive, Complex Heatmaps")
22827 "iheatmapr is an R package for building complex, interactive heatmaps
22828 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22829 subplots along the rows or columns of the main heatmap add more information
22830 about each row or column. For example, a one column additional heatmap may
22831 indicate what group a particular row or column belongs to. Complex heatmaps
22832 may also include multiple side by side heatmaps which show different types of
22833 data for the same conditions. Interactivity can improve complex heatmaps by
22834 providing tooltips with information about each cell and enabling zooming into
22835 interesting features. iheatmapr uses the plotly library for interactivity.")
22836 (license license:expat)))
22838 (define-public r-packrat
22845 (uri (cran-uri "packrat" version))
22848 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22849 (properties `((upstream-name . "packrat")))
22850 (build-system r-build-system)
22851 (home-page "https://github.com/rstudio/packrat/")
22852 (synopsis "Dependency management R projects")
22854 "This package provides a dependency manager for R projects that allows
22855 you to manage the R packages your project depends on in an isolated, portable,
22856 and reproducible way.")
22857 (license license:gpl2)))
22859 (define-public r-rsconnect
22861 (name "r-rsconnect")
22866 (uri (cran-uri "rsconnect" version))
22869 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22870 (properties `((upstream-name . "rsconnect")))
22871 (build-system r-build-system)
22873 `(("r-curl" ,r-curl)
22874 ("r-digest" ,r-digest)
22875 ("r-jsonlite" ,r-jsonlite)
22876 ("r-openssl" ,r-openssl)
22877 ("r-packrat" ,r-packrat)
22878 ("r-rstudioapi" ,r-rstudioapi)
22879 ("r-yaml" ,r-yaml)))
22880 (home-page "https://github.com/rstudio/rsconnect")
22881 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22883 "This package provides a programmatic deployment interface for RPubs,
22884 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22885 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22886 (license license:gpl2)))
22888 ;; This package includes minified JavaScript files. When upgrading please
22889 ;; check that there are no new minified JavaScript files.
22890 (define-public r-dygraphs
22892 (name "r-dygraphs")
22893 (version "1.1.1.6")
22897 (uri (cran-uri "dygraphs" version))
22900 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22901 (properties `((upstream-name . "dygraphs")))
22902 (build-system r-build-system)
22904 `(#:modules ((guix build utils)
22905 (guix build r-build-system)
22909 (modify-phases %standard-phases
22910 (add-after 'unpack 'process-javascript
22911 (lambda* (#:key inputs #:allow-other-keys)
22912 (with-directory-excursion "inst/htmlwidgets/lib/"
22916 `(("dygraphs/dygraph-combined-dev.js"
22917 "dygraph-combined.js")
22918 (,(assoc-ref inputs "js-jquery")
22919 "jquery/jquery.min.js")
22920 (,(assoc-ref inputs "js-fquarter")
22921 "fquarter/moment-fquarter.min.js"))))
22922 (lambda (sources targets)
22923 (for-each (lambda (source target)
22924 (format #t "Processing ~a --> ~a~%"
22926 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22927 (call-with-output-file target
22929 (dump-port minified port)))))
22930 sources targets))))
22933 `(("uglify-js" ,uglify-js)
22934 ;; They actually use version 1.11.1, but this more recent version
22935 ;; should be just fine.
22939 (uri "https://code.jquery.com/jquery-1.12.4.js")
22942 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22946 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22947 "moment-fquarter/1.0.1/moment-fquarter.js"))
22950 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22952 `(("r-htmltools" ,r-htmltools)
22953 ("r-htmlwidgets" ,r-htmlwidgets)
22954 ("r-magrittr" ,r-magrittr)
22957 (home-page "https://github.com/rstudio/dygraphs")
22958 (synopsis "Interface to Dygraphs interactive time series charting library")
22960 "This package provides an R interface to the dygraphs JavaScript charting
22961 library (a copy of which is included in the package). It provides rich
22962 facilities for charting time-series data in R, including highly configurable
22963 series- and axis-display and interactive features like zoom/pan and
22964 series/point highlighting.")
22965 (license license:expat)))
22967 (define-public r-shinystan
22969 (name "r-shinystan")
22974 (uri (cran-uri "shinystan" version))
22977 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22978 (properties `((upstream-name . "shinystan")))
22979 (build-system r-build-system)
22981 `(("r-bayesplot" ,r-bayesplot)
22982 ("r-colourpicker" ,r-colourpicker)
22984 ("r-dygraphs" ,r-dygraphs)
22985 ("r-ggplot2" ,r-ggplot2)
22986 ("r-gridextra" ,r-gridextra)
22987 ("r-gtools" ,r-gtools)
22988 ("r-markdown" ,r-markdown)
22989 ("r-reshape2" ,r-reshape2)
22990 ("r-rsconnect" ,r-rsconnect)
22991 ("r-rstan" ,r-rstan)
22992 ("r-shiny" ,r-shiny)
22993 ("r-shinyjs" ,r-shinyjs)
22994 ("r-shinythemes" ,r-shinythemes)
22995 ("r-threejs" ,r-threejs)
22996 ("r-xtable" ,r-xtable)
22998 (home-page "https://mc-stan.org/")
22999 (synopsis "Interactive visual and numerical analysis for Bayesian models")
23001 "This package provides a graphical user interface for interactive
23002 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
23003 for analyzing a posterior sample. The interface is powered by the Shiny web
23004 application framework and works with the output of MCMC programs written in
23005 any programming language (and has extended functionality for Stan models fit
23006 using the @code{rstan} and @code{rstanarm} packages).")
23007 (license license:gpl3+)))
23009 (define-public r-rstantools
23011 (name "r-rstantools")
23016 (uri (cran-uri "rstantools" version))
23019 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23020 (properties `((upstream-name . "rstantools")))
23021 (build-system r-build-system)
23022 (inputs `(("pandoc" ,pandoc)))
23024 `(("r-desc" ,r-desc)
23026 ("r-rcppparallel" ,r-rcppparallel)))
23028 `(("r-knitr" ,r-knitr)))
23029 (home-page "https://mc-stan.org/rstantools/")
23030 (synopsis "Tools for developing R packages interfacing with Stan")
23032 "This package provides various tools for developers of R packages
23033 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23034 up the required package structure, S3 generics and default methods to unify
23035 function naming across Stan-based R packages, and vignettes with
23036 recommendations for developers.")
23037 (license license:gpl3+)))
23039 (define-public r-loo
23046 (uri (cran-uri "loo" version))
23048 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23049 (properties `((upstream-name . "loo")))
23050 (build-system r-build-system)
23052 `(("pandoc" ,pandoc)
23053 ("pandoc-citeproc" ,pandoc-citeproc)))
23055 `(("r-checkmate" ,r-checkmate)
23056 ("r-matrixstats" ,r-matrixstats)))
23058 `(("r-knitr" ,r-knitr)))
23059 (home-page "https://mc-stan.org/loo/")
23060 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23062 "This package provides an implementation of efficient approximate
23063 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23064 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23065 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23066 procedure for regularizing importance weights. As a byproduct of the
23067 calculations, we also obtain approximate standard errors for estimated
23068 predictive errors and for the comparison of predictive errors between models.
23069 The package also provides methods for using stacking and other model weighting
23070 techniques to average Bayesian predictive distributions.")
23071 (license license:gpl3+)))
23073 (define-public r-rstan
23080 (uri (cran-uri "rstan" version))
23083 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23084 (properties `((upstream-name . "rstan")))
23085 (build-system r-build-system)
23088 (modify-phases %standard-phases
23089 (add-before 'install 'set-timezone
23090 ;; This package is picky about timezones.
23091 (lambda* (#:key inputs #:allow-other-keys)
23092 (setenv "TZ" "UTC+1")
23094 (string-append (assoc-ref inputs "tzdata")
23095 "/share/zoneinfo"))
23098 `(("tzdata" ,tzdata-for-tests)
23100 ("r-knitr" ,r-knitr)))
23103 ("r-ggplot2" ,r-ggplot2)
23104 ("r-gridextra" ,r-gridextra)
23105 ("r-inline" ,r-inline)
23107 ("r-pkgbuild" ,r-pkgbuild)
23109 ("r-rcppeigen" ,r-rcppeigen)
23110 ("r-rcppparallel" ,r-rcppparallel)
23111 ("r-stanheaders" ,r-stanheaders)
23113 ("r-withr" ,r-withr)))
23114 (home-page "https://discourse.mc-stan.org/")
23115 (synopsis "R interface to Stan")
23117 "User-facing R functions are provided to parse, compile, test, estimate,
23118 and analyze Stan models by accessing the header-only Stan library provided by
23119 the StanHeaders package. The Stan project develops a probabilistic
23120 programming language that implements full Bayesian statistical inference via
23121 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23122 approximation, and (optionally penalized) maximum likelihood estimation via
23123 optimization. In all three cases, automatic differentiation is used to
23124 quickly and accurately evaluate gradients without burdening the user with the
23125 need to derive the partial derivatives.")
23126 (license license:gpl3+)))
23128 (define-public r-rstanarm
23130 (name "r-rstanarm")
23135 (uri (cran-uri "rstanarm" version))
23138 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23139 (properties `((upstream-name . "rstanarm")))
23140 (build-system r-build-system)
23142 `(("pandoc" ,pandoc)
23143 ("pandoc-citeproc" ,pandoc-citeproc)))
23145 `(("r-bayesplot" ,r-bayesplot)
23147 ("r-ggplot2" ,r-ggplot2)
23150 ("r-matrix" ,r-matrix)
23153 ("r-rcppeigen" ,r-rcppeigen)
23154 ("r-rcppparallel" ,r-rcppparallel)
23155 ("r-rstan" ,r-rstan)
23156 ("r-rstantools" ,r-rstantools)
23157 ("r-shinystan" ,r-shinystan)
23158 ("r-stanheaders" ,r-stanheaders)
23159 ("r-survival" ,r-survival)))
23161 `(("r-knitr" ,r-knitr)))
23162 (home-page "https://mc-stan.org/rstanarm/")
23163 (synopsis "Bayesian applied regression modeling via Stan")
23165 "This package estimates previously compiled regression models using the
23166 @code{rstan} package, which provides the R interface to the Stan C++ library
23167 for Bayesian estimation. Users specify models via the customary R syntax with
23168 a formula and @code{data.frame} plus some additional arguments for priors.")
23169 (license license:gpl3+)))
23171 (define-public r-kendall
23178 (uri (cran-uri "Kendall" version))
23181 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23182 (properties `((upstream-name . "Kendall")))
23183 (build-system r-build-system)
23185 `(("r-boot" ,r-boot)))
23187 `(("gfortran" ,gfortran)))
23188 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23189 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23191 "This package computes the Kendall rank correlation and Mann-Kendall
23193 (license license:gpl2+)))
23195 (define-public r-keyring
23202 (uri (cran-uri "keyring" version))
23205 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23206 (properties `((upstream-name . "keyring")))
23207 (build-system r-build-system)
23209 `(("r-assertthat" ,r-assertthat)
23210 ("r-filelock" ,r-filelock)
23211 ("r-getpass" ,r-getpass)
23212 ("r-openssl" ,r-openssl)
23214 ("r-rappdirs" ,r-rappdirs)
23215 ("r-sodium" ,r-sodium)
23216 ("r-yaml" ,r-yaml)))
23217 (native-inputs `(("pkg-config" ,pkg-config)))
23218 (home-page "https://github.com/r-lib/keyring")
23219 (synopsis "Access the system credential store from R")
23221 "This package provides a platform-independent API to access the operating
23222 system's credential store. It currently supports Keychain on macOS,
23223 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23224 simple, platform independent store implemented with environment variables.
23225 Additional storage back-ends can be added easily.")
23226 (license license:expat)))
23228 (define-public r-zyp
23231 (version "0.10-1.1")
23235 (uri (cran-uri "zyp" version))
23238 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23239 (properties `((upstream-name . "zyp")))
23240 (build-system r-build-system)
23242 `(("r-kendall" ,r-kendall)))
23243 (home-page "https://cran.r-project.org/web/packages/zyp/")
23244 (synopsis "Zhang + Yue-Pilon Trends Package")
23246 "This package contains an efficient implementation of Sen's slope
23247 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23248 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23250 (license license:lgpl2.1)))
23252 (define-public r-rlinsolve
23254 (name "r-rlinsolve")
23259 (uri (cran-uri "Rlinsolve" version))
23262 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23263 (properties `((upstream-name . "Rlinsolve")))
23264 (build-system r-build-system)
23266 `(("r-matrix" ,r-matrix)
23268 ("r-rcpparmadillo" ,r-rcpparmadillo)
23269 ("r-rdpack" ,r-rdpack)))
23270 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23271 (synopsis "Iterative solvers for (sparse) linear system of equations")
23273 "Solving a system of linear equations is one of the most fundamental
23274 computational problems for many fields of mathematical studies, such as
23275 regression problems from statistics or numerical partial differential
23276 equations. This package provides basic stationary iterative solvers such as
23277 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23278 Nonstationary, also known as Krylov subspace methods are also provided.
23279 Sparse matrix computation is also supported in that solving large and sparse
23280 linear systems can be manageable using the @code{Matrix} package along with
23281 @code{RcppArmadillo}.")
23282 (license license:gpl3+)))
23284 (define-public r-zvcv
23291 (uri (cran-uri "ZVCV" version))
23294 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23295 (properties `((upstream-name . "ZVCV")))
23296 (build-system r-build-system)
23298 `(("r-abind" ,r-abind)
23300 ("r-dplyr" ,r-dplyr)
23301 ("r-glmnet" ,r-glmnet)
23302 ("r-magrittr" ,r-magrittr)
23303 ("r-mvtnorm" ,r-mvtnorm)
23305 ("r-rcpparmadillo" ,r-rcpparmadillo)
23306 ("r-rlinsolve" ,r-rlinsolve)))
23307 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23308 (synopsis "Zero-Variance Control Variates")
23310 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23311 to reduce the variance of Monte Carlo estimators of expectations using the
23312 derivatives of the log target. Once the derivatives are available, the only
23313 additional computational effort is in solving a linear regression problem.
23314 This method has been extended to higher dimensions using regularisation. This
23315 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23316 samples, derivatives and function evaluations are available. Additional
23317 functions for applying ZV-CV to two estimators for the normalising constant of
23318 the posterior distribution in Bayesian statistics are also supplied.")
23319 (license license:gpl2+)))
23321 (define-public r-ztype
23328 (uri (cran-uri "ztype" version))
23331 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23332 (properties `((upstream-name . "ztype")))
23333 (build-system r-build-system)
23335 `(("r-assertthat" ,r-assertthat)
23336 ("r-dplyr" ,r-dplyr)
23337 ("r-ggplot2" ,r-ggplot2)
23338 ("r-lubridate" ,r-lubridate)
23339 ("r-magrittr" ,r-magrittr)
23340 ("r-rvest" ,r-rvest)
23341 ("r-stringr" ,r-stringr)))
23342 (home-page "https://cran.r-project.org/web/packages/ztype/")
23343 (synopsis "Run a Ztype game loaded with R functions")
23345 "How fast can you type R functions on your keyboard? Find out by running
23346 a @code{zty.pe} game: export R functions as instructions to type to destroy
23347 opponents' vessels.")
23348 (license license:gpl3)))
23350 (define-public r-zseq
23357 (uri (cran-uri "Zseq" version))
23360 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23361 (properties `((upstream-name . "Zseq")))
23362 (build-system r-build-system)
23364 `(("r-gmp" ,r-gmp)))
23365 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23366 (synopsis "Integer sequence generator")
23368 "This package generates well-known integer sequences. The @code{gmp}
23369 package is adopted for computing with arbitrarily large numbers. Every
23370 function has a hyperlink to its corresponding item in the @dfn{On-Line
23371 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23372 (license license:gpl3+)))
23374 (define-public r-isoband
23381 (uri (cran-uri "isoband" version))
23384 "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn"))))
23385 (properties `((upstream-name . "isoband")))
23386 (build-system r-build-system)
23388 `(("r-knitr" ,r-knitr)))
23389 (home-page "https://github.com/wilkelab/isoband")
23390 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23392 "This package provides a fast C++ implementation to generate contour
23393 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23394 containing elevation data.")
23395 (license license:expat)))
23397 (define-public r-ppcor
23404 (uri (cran-uri "ppcor" version))
23407 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23408 (properties `((upstream-name . "ppcor")))
23409 (build-system r-build-system)
23411 `(("r-mass" ,r-mass)))
23412 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23413 (synopsis "Partial and semi-partial correlation")
23415 "This package provides users not only with a function to readily
23416 calculate the higher-order partial and semi-partial correlations but also with
23417 statistics and p-values of the correlation coefficients.")
23418 (license license:gpl2)))
23420 (define-public r-hrbrthemes
23422 (name "r-hrbrthemes")
23427 (uri (cran-uri "hrbrthemes" version))
23429 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23430 (properties `((upstream-name . "hrbrthemes")))
23431 (build-system r-build-system)
23433 `(("r-extrafont" ,r-extrafont)
23434 ("r-gdtools" ,r-gdtools)
23435 ("r-ggplot2" ,r-ggplot2)
23436 ("r-htmltools" ,r-htmltools)
23437 ("r-knitr" ,r-knitr)
23438 ("r-magrittr" ,r-magrittr)
23439 ("r-rmarkdown" ,r-rmarkdown)
23440 ("r-scales" ,r-scales)))
23442 `(("r-knitr" ,r-knitr)))
23443 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23444 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23446 "This package provides a compilation of extra @code{ggplot2} themes,
23447 scales and utilities, including a spell check function for plot label fields
23448 and an overall emphasis on typography.")
23449 (license license:expat)))
23451 (define-public r-crochet
23458 (uri (cran-uri "crochet" version))
23461 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23462 (build-system r-build-system)
23464 `(("r-knitr" ,r-knitr)))
23465 (home-page "https://github.com/agrueneberg/crochet")
23466 (synopsis "Implementation Helper for Matrix-Like Types")
23468 "Functions to help implement the extraction / subsetting / indexing
23469 function @code{[} and replacement function @code{[<-} of custom matrix-like
23470 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23471 as possible (with tests to prove it).")
23472 (license license:expat)))
23474 (define-public r-boa
23477 (version "1.1.8-2")
23481 (uri (cran-uri "boa" version))
23484 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23485 (properties `((upstream-name . "boa")))
23486 (build-system r-build-system)
23487 (home-page "https://www.jstatsoft.org/v21/i11")
23488 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23490 "This package provides a menu-driven program and library of functions for
23491 carrying out convergence diagnostics and statistical and graphical analysis of
23492 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23493 (license license:gpl2+)))
23495 (define-public r-httpcode
23497 (name "r-httpcode")
23501 (uri (cran-uri "httpcode" version))
23504 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23505 (build-system r-build-system)
23506 (home-page "https://github.com/sckott/httpcode")
23507 (synopsis "HTTP status code helper")
23508 (description "@code{httpcode} provides functionality for finding and
23509 explaining the meaning of @code{HTTP} status codes. Functions are included for
23510 searching for codes by full or partial number, by message, and to get
23511 appropriate dog and cat images for many status codes.")
23512 (license license:expat)))
23514 (define-public r-latex2exp
23516 (name "r-latex2exp")
23520 (uri (cran-uri "latex2exp" version))
23523 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23524 (build-system r-build-system)
23526 `(("r-stringr" ,r-stringr)
23527 ("r-magrittr" ,r-magrittr)))
23528 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23529 (synopsis "Use LaTeX expressions in plots")
23530 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23531 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23532 rendered as text, axis labels, etc. throughout R's plotting system.")
23533 (license license:expat)))
23535 (define-public r-oai
23541 (uri (cran-uri "oai" version))
23544 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23545 (build-system r-build-system)
23547 `(("r-xml2" ,r-xml2)
23550 ("r-stringr" ,r-stringr)
23551 ("r-tibble" ,r-tibble)))
23552 (home-page "https://github.com/ropensci/oai/")
23553 (synopsis "General purpose OAI-PMH services client")
23554 (description "@code{oai} provides a general purpose client to work with
23555 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23556 service. Functions are provided to work with the OAI-PMH verbs:
23557 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23558 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23559 (license license:expat)))
23561 (define-public r-argon2
23568 (uri (cran-uri "argon2" version))
23571 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23572 (properties `((upstream-name . "argon2")))
23573 (build-system r-build-system)
23574 (home-page "https://github.com/wrathematics/argon2")
23575 (synopsis "Secure password hashing based on the argon2 algorithm")
23577 "This package provides utilities for secure password hashing via the
23578 argon2 algorithm.")
23579 (license license:bsd-2)))
23581 (define-public r-getpass
23588 (uri (cran-uri "getPass" version))
23591 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23592 (properties `((upstream-name . "getPass")))
23593 (build-system r-build-system)
23595 `(("r-rstudioapi" ,r-rstudioapi)))
23596 (home-page "https://github.com/wrathematics/getPass")
23597 (synopsis "Masked user input")
23599 "This package provides a micro-package for reading \"passwords\", i.e.
23600 reading user input with masking, so that the input is not displayed as it is
23601 typed. Currently, RStudio, the command line (every OS), and any platform
23602 where tcltk is present are supported.")
23603 (license license:bsd-2)))
23605 (define-public r-remoter
23612 (uri (cran-uri "remoter" version))
23615 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23616 (properties `((upstream-name . "remoter")))
23617 (build-system r-build-system)
23619 `(("r-argon2" ,r-argon2)
23620 ("r-getpass" ,r-getpass)
23621 ("r-pbdzmq" ,r-pbdzmq)
23623 (home-page "https://github.com/RBigData/remoter")
23624 (synopsis "Control a remote R session from a local one")
23626 "This package provides a set of utilities for client/server computing
23627 with R, controlling a remote R session (the server) from a local one (the
23629 (license license:bsd-2)))
23631 (define-public r-asd
23638 (uri (cran-uri "asd" version))
23641 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23642 (properties `((upstream-name . "asd")))
23643 (build-system r-build-system)
23645 `(("r-mvtnorm" ,r-mvtnorm)))
23646 (home-page "https://cran.r-project.org/web/packages/asd")
23647 (synopsis "Simulations for Adaptive Seamless Designs")
23649 "This package provdes means to run simulations for adaptive seamless
23650 designs with and without early outcomes for treatment selection and
23651 subpopulation type designs.")
23652 (license license:gpl3)))
23654 (define-public r-nbconvertr
23656 (name "r-nbconvertr")
23661 (uri (cran-uri "nbconvertR" version))
23664 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23665 (properties `((upstream-name . "nbconvertR")))
23666 (build-system r-build-system)
23668 `(("jupyter" ,python-nbconvert)
23669 ("pandoc" ,pandoc)))
23670 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23671 (synopsis "Vignette engine wrapping Jupyter notebooks")
23673 "This package calls the Jupyter script @code{nbconvert} to create
23674 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23675 containing rich text, code, and its output. Code cells can be edited and
23676 evaluated interactively.")
23677 (license license:gpl3)))
23679 (define-public r-bridgesampling
23681 (name "r-bridgesampling")
23686 (uri (cran-uri "bridgesampling" version))
23689 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23691 `((upstream-name . "bridgesampling")))
23692 (build-system r-build-system)
23694 `(("r-brobdingnag" ,r-brobdingnag)
23696 ("r-matrix" ,r-matrix)
23697 ("r-mvtnorm" ,r-mvtnorm)
23698 ("r-scales" ,r-scales)
23699 ("r-stringr" ,r-stringr)))
23701 `(("r-knitr" ,r-knitr)))
23702 (home-page "https://github.com/quentingronau/bridgesampling")
23703 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23705 "This package provides functions for estimating marginal likelihoods,
23706 Bayes factors, posterior model probabilities, and normalizing constants in
23707 general, via different versions of bridge sampling.")
23708 (license license:gpl2+)))
23710 (define-public r-tea
23717 (uri (cran-uri "tea" version))
23720 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23722 `((upstream-name . "tea")))
23723 (build-system r-build-system)
23725 `(("r-matrix" ,r-matrix)))
23726 (home-page "https://cran.r-project.org/web/packages/tea/")
23727 (synopsis "Threshold estimation approaches")
23729 "This package provides different approaches for selecting the threshold
23730 in generalized Pareto distributions. Most of them are based on minimizing the
23731 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23732 Others are heuristically motivated by searching for stable sample paths, i.e.
23733 a nearly constant region of the tail index estimator with respect to k, which
23734 is the number of data in the tail. The third class is motivated by graphical
23735 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23736 is also implemented here.")
23737 (license license:gpl3)))
23739 (define-public r-awsmethods
23741 (name "r-awsmethods")
23746 (uri (cran-uri "awsMethods" version))
23749 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23751 `((upstream-name . "awsMethods")))
23752 (build-system r-build-system)
23753 (home-page "http://www.wias-berlin.de/software/imaging/")
23754 (synopsis "Class and methods definitions")
23756 "This package defines the generic method @code{extract} and provides
23757 @code{openMP} support as needed in several packages like
23758 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23759 (license license:gpl2+)))
23761 (define-public r-aws
23768 (uri (cran-uri "aws" version))
23771 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23773 `((upstream-name . "aws")))
23774 (build-system r-build-system)
23776 `(("r-awsmethods" ,r-awsmethods)
23779 `(("gfortran" ,gfortran)))
23780 (home-page "https://cran.r-project.org/web/packages/aws/")
23781 (synopsis "Adaptive weights smoothing")
23783 "This package provides a collection of R-functions implementing adaptive
23784 smoothing procedures in 1D, 2D and 3D. This includes the
23785 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23786 Confidence Intervals} (ICI), variational approaches, and a non-local means
23788 (license license:gpl2+)))
23790 (define-public r-sgloptim
23792 (name "r-sgloptim")
23797 (uri (cran-uri "sglOptim" version))
23800 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23802 `((upstream-name . "sglOptim")))
23803 (build-system r-build-system)
23806 ("r-doparallel" ,r-doparallel)
23807 ("r-foreach" ,r-foreach)
23808 ("r-matrix" ,r-matrix)
23810 ("r-rcpparmadillo" ,r-rcpparmadillo)
23811 ("r-rcppprogress" ,r-rcppprogress)))
23813 `(("r-knitr" ,r-knitr)))
23814 (home-page "https://github.com/nielsrhansen/sglOptim")
23815 (synopsis "Generic sparse group Lasso solver")
23817 "This package provides a fast generic solver for sparse group lasso
23818 optimization problems. The loss (objective) function must be defined in a C++
23819 module. The optimization problem is solved using a coordinate gradient
23820 descent algorithm. Convergence of the algorithm is established and the
23821 algorithm is applicable to a broad class of loss functions. Use of parallel
23822 computing for cross validation and subsampling is supported through the
23823 @code{foreach} and @code{doParallel} packages.")
23824 (license license:gpl2+)))
23826 (define-public r-grouped
23833 (uri (cran-uri "grouped" version))
23836 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23838 `((upstream-name . "grouped")))
23839 (build-system r-build-system)
23841 `(("r-mass" ,r-mass)))
23842 (home-page "https://cran.r-project.org/web/packages/grouped/")
23843 (synopsis "Regression analysis of grouped and coarse data")
23845 "This package provides regression models for grouped and coarse data,
23846 under the coarsened at random assumption.")
23847 (license license:gpl2+)))
23849 (define-public r-stam
23856 (uri (cran-uri "stam" version))
23859 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23861 `((upstream-name . "stam")))
23862 (build-system r-build-system)
23866 (home-page "https://cran.r-project.org/web/packages/stam")
23867 (synopsis "Spatio-temporal analysis and modelling")
23869 "This package provides various methods to conduct Spatio-Temporal
23870 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23871 Inferred Spatio-Temporal Modelling.")
23872 (license license:gpl2+)))
23874 (define-public r-dcv
23881 (uri (cran-uri "dcv" version))
23884 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23886 `((upstream-name . "dcv")))
23887 (build-system r-build-system)
23889 `(("r-lmtest" ,r-lmtest)))
23890 (home-page "https://cran.r-project.org/web/packages/dcv/")
23891 (synopsis "Conventional cross-validation statistics for climate-growth model")
23893 "This package performs several conventional cross-validation statistical
23894 methods for climate-growth model in the climate reconstruction from tree
23895 rings, including Sign Test statistic, Reduction of Error statistic, Product
23896 Mean Test, Durbin-Watson statistic etc.")
23897 (license license:gpl2)))
23899 (define-public r-rcdd
23906 (uri (cran-uri "rcdd" version))
23909 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23911 `((upstream-name . "rcdd")))
23912 (build-system r-build-system)
23915 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23916 (synopsis "Computational geometry")
23918 "This package converts back and forth between two representations of a
23919 convex polytope: as solution of a set of linear equalities and inequalities
23920 and as convex hull of set of points and rays. Also does linear programming
23921 and redundant generator elimination. All functions can use exact
23922 infinite-precision rational arithmetic.")
23923 (license license:gpl2)))
23925 (define-public r-rxnat
23932 (uri (cran-uri "Rxnat" version))
23935 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23937 `((upstream-name . "Rxnat")))
23938 (build-system r-build-system)
23940 `(("r-dplyr" ,r-dplyr)
23942 ("r-rcurl" ,r-rcurl)
23943 ("r-tibble" ,r-tibble)))
23945 `(("r-knitr" ,r-knitr)))
23946 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23947 (synopsis "Queries and extracts images from neuroimaging datasets")
23949 "This package allows communication with the Extensible Neuroimaging
23950 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23952 (license license:gpl2)))
23954 (define-public r-rserve
23961 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23962 version ".tar.gz"))
23965 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23966 (build-system r-build-system)
23969 (modify-phases %standard-phases
23970 (add-before 'install 'install-server-binary
23971 ;; Makevars tries to install to R's store directory.
23972 (lambda* (#:key outputs #:allow-other-keys)
23973 (let* ((out (assoc-ref outputs "out"))
23974 (bin (string-append out "/bin")))
23975 (substitute* "src/Makevars.in"
23976 (("\\$\\(R_HOME\\)") out))
23977 (mkdir-p bin)))))))
23979 `(("r-checkmate" ,r-checkmate)
23981 ("r-jsonlite" ,r-jsonlite)
23982 ("r-knitr" ,r-knitr)
23985 ("r-uuid" ,r-uuid)))
23987 `(("openssl" ,openssl)
23989 (home-page "https://github.com/s-u/Rserve")
23991 "Server providing access to R from many languages and systems")
23993 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
23994 binary requests to be sent to R. Every connection has a separate workspace
23995 and working directory. Client-side implementations are available for popular
23996 languages such as C/C++ and Java, allowing any application to use facilities
23997 of R without the need of linking to R code. Rserve supports remote
23998 connection, user authentication and file transfer. A simple R client is
23999 included in this package as well.")
24000 (license license:gpl2)))
24002 (define-public r-gamm4
24009 (uri (cran-uri "gamm4" version))
24012 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
24013 (properties `((upstream-name . "gamm4")))
24014 (build-system r-build-system)
24016 `(("r-lme4" ,r-lme4)
24017 ("r-matrix" ,r-matrix)
24018 ("r-mgcv" ,r-mgcv)))
24019 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24020 (synopsis "Generalized additive mixed models using mgcv and lme4")
24022 "Estimate generalized additive mixed models via a version of function
24023 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24025 (license license:gpl2+)))
24027 (define-public r-optimx
24030 (version "2020-4.2")
24034 (uri (cran-uri "optimx" version))
24037 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24038 (properties `((upstream-name . "optimx")))
24039 (build-system r-build-system)
24040 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24041 (native-inputs `(("r-knitr" ,r-knitr)))
24042 (home-page "https://cran.r-project.org/web/packages/optimx/")
24043 (synopsis "Expanded replacement and extension of the optim function")
24045 "This package provides a replacement and extension of the @code{optim}
24046 function to call to several function minimization codes in R in a single
24047 statement. These methods handle smooth, possibly box constrained functions of
24048 several or many parameters. Note that the function @code{optimr} was prepared
24049 to simplify the incorporation of minimization codes going forward. This
24050 package also implements some utility codes and some extra solvers, including
24051 safeguarded Newton methods. Many methods previously separate are now included
24053 (license license:gpl2)))
24055 (define-public r-projpred
24057 (name "r-projpred")
24062 (uri (cran-uri "projpred" version))
24065 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24066 (properties `((upstream-name . "projpred")))
24067 (build-system r-build-system)
24069 `(("r-dplyr" ,r-dplyr)
24070 ("r-gamm4" ,r-gamm4)
24071 ("r-ggplot2" ,r-ggplot2)
24074 ("r-magrittr" ,r-magrittr)
24077 ("r-optimx" ,r-optimx)
24079 ("r-rcpparmadillo" ,r-rcpparmadillo)
24080 ("r-rngtools" ,r-rngtools)
24081 ("r-rstantools" ,r-rstantools)
24082 ("r-tidyverse" ,r-tidyverse)))
24083 (native-inputs `(("r-knitr" ,r-knitr)))
24084 (home-page "https://mc-stan.org/projpred/")
24085 (synopsis "Projection predictive feature selection")
24087 "This package performs projection predictive feature selection for
24088 generalized linear models and generalized linear and additive multilevel
24089 models. The package is compatible with the @code{rstanarm} and @code{brms}
24090 packages, but other reference models can also be used. See the package
24091 vignette for more information and examples.")
24092 (license license:gpl3)))
24094 (define-public r-brms
24101 (uri (cran-uri "brms" version))
24104 "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1"))))
24105 (properties `((upstream-name . "brms")))
24106 (build-system r-build-system)
24108 `(("r-abind" ,r-abind)
24109 ("r-backports" ,r-backports)
24110 ("r-bayesplot" ,r-bayesplot)
24111 ("r-bridgesampling" ,r-bridgesampling)
24113 ("r-future" ,r-future)
24114 ("r-ggplot2" ,r-ggplot2)
24117 ("r-matrix" ,r-matrix)
24118 ("r-matrixstats" ,r-matrixstats)
24120 ("r-nleqslv" ,r-nleqslv)
24122 ("r-projpred" ,r-projpred)
24124 ("r-rstan" ,r-rstan)
24125 ("r-rstantools" ,r-rstantools)
24126 ("r-shinystan" ,r-shinystan)))
24127 (native-inputs `(("r-knitr" ,r-knitr)))
24129 "https://github.com/paul-buerkner/brms")
24131 "Bayesian Regression Models using 'Stan'")
24133 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24134 using 'Stan' for full Bayesian inference. A wide range of distributions and
24135 link functions are supported, allowing users to fit -- among others -- linear,
24136 robust linear, count data, survival, response times, ordinal, zero-inflated,
24137 hurdle, and even self-defined mixture models all in a multilevel context.
24138 Further modeling options include non-linear and smooth terms, auto-correlation
24139 structures, censored data, meta-analytic standard errors, and quite a few
24140 more. In addition, all parameters of the response distribution can be
24141 predicted in order to perform distributional regression. Prior specifications
24142 are flexible and explicitly encourage users to apply prior distributions that
24143 actually reflect their beliefs. Model fit can easily be assessed and compared
24144 with posterior predictive checks and leave-one-out cross-validation.")
24145 (license license:gpl2)))
24147 (define-public r-mstate
24154 (uri (cran-uri "mstate" version))
24157 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24158 (properties `((upstream-name . "mstate")))
24159 (build-system r-build-system)
24161 `(("r-data-table" ,r-data-table)
24162 ("r-lattice" ,r-lattice)
24163 ("r-magrittr" ,r-magrittr)
24164 ("r-rcolorbrewer" ,r-rcolorbrewer)
24165 ("r-rlang" ,r-rlang)
24166 ("r-survival" ,r-survival)
24167 ("r-viridis" ,r-viridis)))
24169 `(("r-knitr" ,r-knitr)))
24171 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24173 "Data Preparation, Estimation and Prediction in Multi-State Models")
24175 "Contains functions for data preparation, descriptives, hazard estimation
24176 and prediction with Aalen-Johansen or simulation in competing risks and
24177 multi-state models.")
24178 (license license:gpl2+)))
24180 (define-public r-scatterpie
24182 (name "r-scatterpie")
24187 (uri (cran-uri "scatterpie" version))
24190 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24191 (properties `((upstream-name . "scatterpie")))
24192 (build-system r-build-system)
24194 `(("r-ggforce" ,r-ggforce)
24195 ("r-ggplot2" ,r-ggplot2)
24196 ("r-rlang" ,r-rlang)
24197 ("r-rvcheck" ,r-rvcheck)
24198 ("r-tidyr" ,r-tidyr)))
24200 `(("r-knitr" ,r-knitr)))
24201 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24202 (synopsis "Scatter pie plot")
24204 "This package creates scatterpie plots, especially useful for plotting
24206 (license license:artistic2.0)))
24208 (define-public r-scrypt
24215 (uri (cran-uri "scrypt" version))
24218 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24219 (properties `((upstream-name . "scrypt")))
24220 (build-system r-build-system)
24222 `(("r-rcpp" ,r-rcpp)))
24223 (home-page "https://github.com/rstudio/rscrypt")
24224 (synopsis "Key derivation functions for R based on Scrypt")
24226 "This package provides functions for working with the scrypt key
24227 derivation functions. Scrypt is a password-based key derivation function
24228 created by Colin Percival. The algorithm was specifically designed to make it
24229 costly to perform large-scale custom hardware attacks by requiring large
24230 amounts of memory.")
24231 (license license:bsd-2)))
24233 (define-public r-boruta
24240 (uri (cran-uri "Boruta" version))
24243 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24244 (properties `((upstream-name . "Boruta")))
24245 (build-system r-build-system)
24246 (propagated-inputs `(("r-ranger" ,r-ranger)))
24247 (home-page "https://gitlab.com/mbq/Boruta/")
24248 (synopsis "Wrapper algorithm for all relevant feature selection")
24250 "This package provides an all relevant feature selection wrapper
24251 algorithm. It finds relevant features by comparing original attributes'
24252 importance with importance achievable at random, estimated using their
24253 permuted copies (shadows).")
24254 (license license:gpl2+)))
24256 (define-public r-directlabels
24258 (name "r-directlabels")
24259 (version "2021.1.13")
24263 (uri (cran-uri "directlabels" version))
24266 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24267 (build-system r-build-system)
24269 `(("r-quadprog" ,r-quadprog)))
24271 `(("r-knitr" ,r-knitr)))
24272 (home-page "http://directlabels.r-forge.r-project.org/")
24273 (synopsis "Direct labels for multicolor plots")
24275 "This package provides an extensible framework for automatically placing
24276 direct labels onto multicolor plots. Label positions are described using
24277 positioning methods that can be re-used across several different plots. There
24278 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24279 inferring an appropriate positioning method.")
24280 (license license:gpl3)))
24282 (define-public r-lsd
24289 (uri (cran-uri "LSD" version))
24291 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24292 (properties `((upstream-name . "LSD")))
24293 (build-system r-build-system)
24294 (home-page "https://cran.r-project.org/web/packages/LSD/")
24295 (synopsis "Lots of superior depictions tool creates colorful plots")
24297 "This package creates lots of colorful plots in a multitude of variations.
24298 Try a demo of the LSD by running @code{demotour()}.")
24300 (license (list license:gpl2 license:gpl3))))
24302 (define-public r-phylogram
24304 (name "r-phylogram")
24309 (uri (cran-uri "phylogram" version))
24311 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24312 (properties `((upstream-name . "phylogram")))
24313 (build-system r-build-system)
24314 (propagated-inputs `(("r-ape" ,r-ape)))
24315 (home-page "https://github.com/ropensci/phylogram/")
24316 (synopsis "Dendrograms for evolutionary analysis")
24318 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24319 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24320 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24321 as well as several tools for command-line tree manipulation and import/export
24322 via Newick parenthetic text. This improves accessibility to the comprehensive
24323 range of object-specific analytical and tree-visualization functions found
24324 across a wide array of bioinformatic R packages.")
24325 (license license:gpl3)))
24327 (define-public r-kmer
24334 (uri (cran-uri "kmer" version))
24336 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24337 (properties `((upstream-name . "kmer")))
24338 (build-system r-build-system)
24340 `(("r-openssl" ,r-openssl)
24341 ("r-phylogram" ,r-phylogram)
24342 ("r-rcpp" ,r-rcpp)))
24343 (home-page "https://github.com/shaunpwilkinson/kmer/")
24344 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24346 "@code{r-kmer} is an R package for rapidly computing distance matrices
24347 and clustering large sequence datasets using fast alignment-free k-mer
24348 counting and recursive k-means partitioning.")
24349 (license license:gpl3)))
24351 (define-public r-hardhat
24358 (uri (cran-uri "hardhat" version))
24361 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24362 (properties `((upstream-name . "hardhat")))
24363 (build-system r-build-system)
24365 `(("r-glue" ,r-glue)
24366 ("r-rlang" ,r-rlang)
24367 ("r-tibble" ,r-tibble)
24368 ("r-vctrs" ,r-vctrs)))
24370 `(("r-knitr" ,r-knitr)))
24371 (home-page "https://github.com/tidymodels/hardhat")
24372 (synopsis "Construct modeling packages")
24374 "Building modeling packages is hard. A large amount of effort generally
24375 goes into providing an implementation for a new method that is efficient,
24376 fast, and correct, but often less emphasis is put on the user interface. A
24377 good interface requires specialized knowledge about S3 methods and formulas,
24378 which the average package developer might not have. The goal of
24379 @code{hardhat} is to reduce the burden around building new modeling packages
24380 by providing functionality for preprocessing, predicting, and validating
24382 (license license:expat)))
24384 (define-public r-lightgbm
24386 (name "r-lightgbm")
24391 (uri (cran-uri "lightgbm" version))
24394 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24395 (properties `((upstream-name . "lightgbm")))
24396 (build-system r-build-system)
24398 `(("r-data-table" ,r-data-table)
24399 ("r-jsonlite" ,r-jsonlite)
24400 ("r-matrix" ,r-matrix)
24402 (home-page "https://github.com/Microsoft/LightGBM")
24403 (synopsis "Light gradient boosting machine")
24405 "Tree based algorithms can be improved by introducing boosting
24406 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24407 al. (2017). This package offers an R interface to work with it. It is
24408 designed to be distributed and efficient with the following goals:
24411 @item Faster training speed and higher efficiency;
24412 @item lower memory usage;
24413 @item better accuracy;
24414 @item parallel learning supported; and
24415 @item capable of handling large-scale data.
24418 (license license:expat)))
24420 (define-public r-shapforxgboost
24422 (name "r-shapforxgboost")
24427 (uri (cran-uri "SHAPforxgboost" version))
24430 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24432 `((upstream-name . "SHAPforxgboost")))
24433 (build-system r-build-system)
24435 `(("r-bbmisc" ,r-bbmisc)
24436 ("r-data-table" ,r-data-table)
24437 ("r-ggextra" ,r-ggextra)
24438 ("r-ggforce" ,r-ggforce)
24439 ("r-ggplot2" ,r-ggplot2)
24440 ("r-ggpubr" ,r-ggpubr)
24441 ("r-lightgbm" ,r-lightgbm)
24442 ("r-rcolorbrewer" ,r-rcolorbrewer)
24443 ("r-xgboost" ,r-xgboost)))
24444 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24445 (synopsis "SHAP Plots for XGBoost")
24447 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24448 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24449 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24450 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24452 (license license:expat)))
24454 (define-public r-rismed
24461 (uri (cran-uri "RISmed" version))
24464 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24465 (properties `((upstream-name . "RISmed")))
24466 (build-system r-build-system)
24467 (home-page "https://cran.r-project.org/web/packages/RISmed")
24468 (synopsis "Download content from NCBI databases")
24470 "This package provides a set of tools to extract bibliographic
24471 content from the National Center for Biotechnology Information (NCBI)
24472 databases, including PubMed. The name RISmed is a portmanteau of
24473 RIS (for Research Information Systems, a common tag format for
24474 bibliographic data) and PubMed.")
24475 (license license:gpl2+)))
24477 (define-public r-semver
24484 (uri (cran-uri "semver" version))
24487 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24488 (properties `((upstream-name . "semver")))
24489 (build-system r-build-system)
24491 `(("r-assertthat" ,r-assertthat)
24492 ("r-rcpp" ,r-rcpp)))
24493 (native-inputs `(("r-knitr" ,r-knitr)))
24494 (home-page "https://github.com/johndharrison/semver")
24495 (synopsis "Parser for Semantic Versioning 2.0.0")
24497 "This package provides tools and functions for parsing, rendering and
24498 operating on semantic version strings. Semantic versioning is a simple set of
24499 rules and requirements that dictate how version numbers are assigned and
24500 incremented as outlined at @url{http://semver.org}.")
24501 (license license:expat)))
24503 (define-public r-binman
24510 (uri (cran-uri "binman" version))
24513 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24514 (properties `((upstream-name . "binman")))
24515 (build-system r-build-system)
24517 `(("r-assertthat" ,r-assertthat)
24519 ("r-jsonlite" ,r-jsonlite)
24520 ("r-rappdirs" ,r-rappdirs)
24521 ("r-semver" ,r-semver)
24523 ("r-yaml" ,r-yaml)))
24524 (native-inputs `(("r-knitr" ,r-knitr)))
24525 (home-page "https://github.com/ropensci/binman")
24526 (synopsis "Binary download manager")
24528 "This package provides tools and functions for managing the download of
24529 binary files. Binary repositories are defined in the YAML format. Defining
24530 new pre-download, download and post-download templates allow additional
24531 repositories to be added.")
24532 (license license:expat)))
24534 (define-public r-wdman
24541 (uri (cran-uri "wdman" version))
24544 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24545 (properties `((upstream-name . "wdman")))
24546 (build-system r-build-system)
24548 `(("r-assertthat" ,r-assertthat)
24549 ("r-binman" ,r-binman)
24550 ("r-processx" ,r-processx)
24551 ("r-semver" ,r-semver)
24552 ("r-yaml" ,r-yaml)))
24553 (native-inputs `(("r-knitr" ,r-knitr)))
24554 (home-page "https://docs.ropensci.org/wdman/")
24555 (synopsis "Webdriver/Selenium binary manager")
24557 "There are a number of binary files associated with the
24558 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24559 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24560 @url{https://github.com/mozilla/geckodriver},
24561 @url{http://phantomjs.org/download.html}, and
24562 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24563 more information). This package provides functions to download these binaries
24564 and to manage processes involving them.")
24565 (license license:expat)))
24567 (define-public r-rselenium
24569 (name "r-rselenium")
24574 (uri (cran-uri "RSelenium" version))
24577 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24578 (properties `((upstream-name . "RSelenium")))
24579 (build-system r-build-system)
24581 `(("r-binman" ,r-binman)
24582 ("r-catools" ,r-catools)
24584 ("r-openssl" ,r-openssl)
24585 ("r-wdman" ,r-wdman)
24587 (native-inputs `(("r-knitr" ,r-knitr)))
24588 (home-page "https://docs.ropensci.org/RSelenium/")
24589 (synopsis "R bindings for Selenium WebDriver")
24591 "This package provides a set of R bindings for the Selenium 2.0
24592 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24593 information) using the @code{JsonWireProtocol} (see
24594 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24595 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24596 a user would either locally or on a remote machine using the Selenium server
24597 it marks a leap forward in terms of web browser automation. Selenium
24598 automates web browsers (commonly referred to as browsers). Using RSelenium
24599 you can automate browsers locally or remotely.")
24600 (license license:agpl3+)))
24602 (define-public r-conquer
24609 (uri (cran-uri "conquer" version))
24612 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24613 (properties `((upstream-name . "conquer")))
24614 (build-system r-build-system)
24616 `(("r-matrix" ,r-matrix)
24617 ("r-matrixstats" ,r-matrixstats)
24619 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24620 (home-page "https://github.com/XiaoouPan/conquer")
24621 (synopsis "Convolution-type smoothed quantile regression")
24623 "This package provides fast and accurate convolution-type smoothed
24624 quantile regression, implemented using Barzilai-Borwein gradient descent with
24625 a Huber regression warm start. Confidence intervals for regression
24626 coefficients are constructed using multiplier bootstrap.")
24627 (license license:gpl3)))
24629 (define-public r-fastshap
24631 (name "r-fastshap")
24636 (uri (cran-uri "fastshap" version))
24639 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24640 (properties `((upstream-name . "fastshap")))
24641 (build-system r-build-system)
24643 `(("r-abind" ,r-abind)
24644 ("r-ggplot2" ,r-ggplot2)
24645 ("r-gridextra" ,r-gridextra)
24646 ("r-matrixstats" ,r-matrixstats)
24649 ("r-rcpparmadillo" ,r-rcpparmadillo)
24650 ("r-tibble" ,r-tibble)))
24651 (home-page "https://github.com/bgreenwell/fastshap")
24652 (synopsis "Fast approximate Shapley values")
24654 "This package computes fast (relative to other implementations)
24655 approximate Shapley values for any supervised learning model. Shapley values
24656 help to explain the predictions from any black box model using ideas from game
24657 theory; see @url{Strumbel and Kononenko (2014),
24658 doi.org/10.1007/s10115-013-0679-x} for details.")
24659 (license license:gpl2+)))
24661 (define-public r-metrics
24668 (uri (cran-uri "Metrics" version))
24671 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24672 (properties `((upstream-name . "Metrics")))
24673 (build-system r-build-system)
24674 (home-page "https://github.com/mfrasco/Metrics")
24675 (synopsis "Evaluation metrics for machine learning")
24677 "This package provides an implementation of evaluation metrics in R that
24678 are commonly used in supervised machine learning. It implements metrics for
24679 regression, time series, binary classification, classification, and
24680 information retrieval problems. It has zero dependencies and a consistent,
24681 simple interface for all functions.")
24682 (license license:bsd-3)))
24684 (define-public r-iml
24691 (uri (cran-uri "iml" version))
24694 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24695 (properties `((upstream-name . "iml")))
24696 (build-system r-build-system)
24698 `(("r-checkmate" ,r-checkmate)
24699 ("r-data-table" ,r-data-table)
24700 ("r-formula" ,r-formula)
24701 ("r-future" ,r-future)
24702 ("r-future-apply" ,r-future-apply)
24703 ("r-ggplot2" ,r-ggplot2)
24704 ("r-gridextra" ,r-gridextra)
24705 ("r-metrics" ,r-metrics)
24706 ("r-prediction" ,r-prediction)
24708 (native-inputs `(("r-knitr" ,r-knitr)))
24709 (home-page "https://github.com/christophM/iml")
24710 (synopsis "Interpretable machine learning")
24712 "This package provides interpretability methods to analyze the behavior
24713 and predictions of any machine learning model. Implemented methods are:
24716 @item Feature importance described by Fisher et al. (2018),
24717 @item accumulated local effects plots described by Apley (2018),
24718 @item partial dependence plots described by Friedman (2001),
24719 @item individual conditional expectation ('ice') plots described by Goldstein
24720 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24721 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24722 @item the Shapley Value described by Strumbelj et. al (2014)
24723 @url{https://doi.org/10.1007/s10115-013-0679-x},
24724 @item feature interactions described by Friedman et. al
24725 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24728 (license license:expat)))
24730 (define-public r-goftest
24737 (uri (cran-uri "goftest" version))
24740 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24741 (properties `((upstream-name . "goftest")))
24742 (build-system r-build-system)
24743 (home-page "https://github.com/baddstats/goftest")
24744 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24746 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24747 goodness-of-fit for continuous univariate distributions, using efficient
24749 (license license:gpl2+)))
24751 (define-public r-tensor
24758 (uri (cran-uri "tensor" version))
24761 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24762 (properties `((upstream-name . "tensor")))
24763 (build-system r-build-system)
24764 (home-page "https://cran.r-project.org/web/packages/tensor/")
24765 (synopsis "Tensor product of arrays")
24767 "The tensor product of two arrays is notionally an outer product of the
24768 arrays collapsed in specific extents by summing along the appropriate
24769 diagonals. This package allows you to compute the tensor product of arrays.")
24770 (license license:gpl2+)))
24772 (define-public r-spatstat-utils
24774 (name "r-spatstat-utils")
24779 (uri (cran-uri "spatstat.utils" version))
24782 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24784 `((upstream-name . "spatstat.utils")))
24785 (build-system r-build-system)
24786 (home-page "http://www.spatstat.org")
24787 (synopsis "Utility functions for spatstat")
24789 "This package contains utility functions for the @code{spatstat} package
24790 which may also be useful for other purposes.")
24791 (license license:gpl2+)))
24793 (define-public r-spatstat-sparse
24795 (name "r-spatstat-sparse")
24800 (uri (cran-uri "spatstat.sparse" version))
24803 "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2"))))
24805 `((upstream-name . "spatstat.sparse")))
24806 (build-system r-build-system)
24808 `(("r-abind" ,r-abind)
24809 ("r-matrix" ,r-matrix)
24810 ("r-spatstat-utils" ,r-spatstat-utils)
24811 ("r-tensor" ,r-tensor)))
24812 (home-page "http://spatstat.org/")
24813 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
24815 "This package defines sparse three-dimensional arrays and supports
24816 standard operations on them. The package also includes utility functions for
24817 matrix calculations that are common in statistics, such as quadratic forms.")
24818 (license license:gpl2+)))
24820 (define-public r-spatstat-data
24822 (name "r-spatstat-data")
24827 (uri (cran-uri "spatstat.data" version))
24830 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24831 (properties `((upstream-name . "spatstat.data")))
24832 (build-system r-build-system)
24834 `(("r-matrix" ,r-matrix)
24835 ("r-spatstat-utils" ,r-spatstat-utils)))
24836 (home-page "http://www.spatstat.org")
24837 (synopsis "Datasets for spatstat")
24839 "This package contains all the datasets for the @code{spatstat}
24841 (license license:gpl2+)))
24843 (define-public r-spatstat-geom
24845 (name "r-spatstat-geom")
24850 (uri (cran-uri "spatstat.geom" version))
24853 "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk"))))
24854 (properties `((upstream-name . "spatstat.geom")))
24855 (build-system r-build-system)
24857 `(("r-deldir" ,r-deldir)
24858 ("r-polyclip" ,r-polyclip)
24859 ("r-spatstat-data" ,r-spatstat-data)
24860 ("r-spatstat-sparse" ,r-spatstat-sparse)
24861 ("r-spatstat-utils" ,r-spatstat-utils)))
24862 (home-page "http://spatstat.org/")
24863 (synopsis "Geometrical functionality of the spatstat package")
24865 "This is a subset of the original spatstat package, containing the
24866 user-level code from spatstat which performs geometrical operations, except
24867 for the geometry of linear networks.")
24868 (license license:gpl2+)))
24870 (define-public r-spatstat-core
24872 (name "r-spatstat-core")
24877 (uri (cran-uri "spatstat.core" version))
24880 "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3"))))
24881 (properties `((upstream-name . "spatstat.core")))
24882 (build-system r-build-system)
24884 `(("r-abind" ,r-abind)
24885 ("r-goftest" ,r-goftest)
24886 ("r-matrix" ,r-matrix)
24889 ("r-rpart" ,r-rpart)
24890 ("r-spatstat-data" ,r-spatstat-data)
24891 ("r-spatstat-geom" ,r-spatstat-geom)
24892 ("r-spatstat-sparse" ,r-spatstat-sparse)
24893 ("r-spatstat-utils" ,r-spatstat-utils)
24894 ("r-tensor" ,r-tensor)))
24895 (home-page "http://spatstat.org/")
24896 (synopsis "Core functionality of the spatstat package")
24898 "This is a subset of the original spatstat package, containing all of the
24899 user-level code from spatstat, except for the code for linear networks.")
24900 (license license:gpl2+)))
24902 (define-public r-spatstat-linnet
24904 (name "r-spatstat-linnet")
24909 (uri (cran-uri "spatstat.linnet" version))
24912 "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv"))))
24914 `((upstream-name . "spatstat.linnet")))
24915 (build-system r-build-system)
24917 `(("r-matrix" ,r-matrix)
24918 ("r-spatstat-core" ,r-spatstat-core)
24919 ("r-spatstat-data" ,r-spatstat-data)
24920 ("r-spatstat-geom" ,r-spatstat-geom)
24921 ("r-spatstat-utils" ,r-spatstat-utils)))
24922 (home-page "http://spatstat.org/")
24923 (synopsis "Linear networks functionality of the spatstat package")
24925 "This is a subset of the spatstat package, containing its functionality
24926 for spatial data on a linear network.")
24927 (license license:gpl2+)))
24929 (define-public r-spatstat
24931 (name "r-spatstat")
24936 (uri (cran-uri "spatstat" version))
24939 "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw"))))
24940 (properties `((upstream-name . "spatstat")))
24941 (build-system r-build-system)
24943 `(("r-spatstat-core" ,r-spatstat-core)
24944 ("r-spatstat-data" ,r-spatstat-data)
24945 ("r-spatstat-geom" ,r-spatstat-geom)
24946 ("r-spatstat-linnet" ,r-spatstat-linnet)
24947 ("r-spatstat-utils" ,r-spatstat-utils)))
24948 (home-page "http://www.spatstat.org")
24949 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24951 "This package provides a comprehensive toolbox for analysing Spatial
24952 Point Patterns. It is focused mainly on two-dimensional point patterns,
24953 including multitype/marked points, in any spatial region. It also supports
24954 three-dimensional point patterns, space-time point patterns in any number of
24955 dimensions, point patterns on a linear network, and patterns of other
24956 geometrical objects. It supports spatial covariate data such as pixel images
24957 and contains over 2000 functions for plotting spatial data, exploratory data
24958 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24959 formal inference.")
24960 (license license:gpl2+)))
24962 (define-public r-gaston
24969 (uri (cran-uri "gaston" version))
24972 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24973 (properties `((upstream-name . "gaston")))
24974 (build-system r-build-system)
24975 (inputs `(("zlib" ,zlib)))
24977 `(("r-rcpp" ,r-rcpp)
24978 ("r-rcppeigen" ,r-rcppeigen)
24979 ("r-rcppparallel" ,r-rcppparallel)))
24980 (native-inputs `(("r-knitr" ,r-knitr)))
24981 (home-page "https://cran.r-project.org/web/packages/gaston/")
24982 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24984 "This is a package for the manipulation of genetic data (SNPs).
24985 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24986 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24987 for linear mixed models (AIREML).")
24988 (license license:gpl3)))
24990 (define-public r-cpp11
24997 (uri (cran-uri "cpp11" version))
25000 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
25001 (properties `((upstream-name . "cpp11")))
25002 (build-system r-build-system)
25003 (native-inputs `(("r-knitr" ,r-knitr)))
25004 (home-page "https://github.com/r-lib/cpp11")
25005 (synopsis "C++11 Interface for R's C Interface")
25007 "This package provides a header only, C++11 interface to R's C interface.
25008 Compared to other approaches @code{cpp11} strives to be safe against long
25009 jumps from the C API as well as C++ exceptions, conform to normal R function
25010 semantics and supports interaction with @code{ALTREP} vectors.")
25011 (license license:expat)))
25013 (define-public r-rcppziggurat
25015 (name "r-rcppziggurat")
25020 (uri (cran-uri "RcppZiggurat" version))
25023 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
25024 (properties `((upstream-name . "RcppZiggurat")))
25025 (build-system r-build-system)
25027 `(("r-rcpp" ,r-rcpp)
25028 ("r-rcppgsl" ,r-rcppgsl)))
25029 (native-inputs `(("r-knitr" ,r-knitr)))
25030 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
25031 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
25033 "The Ziggurat generator for normally distributed random numbers,
25034 originally proposed by Marsaglia and Tsang (2000,
25035 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
25036 times starting with Leong et al (2005,
25037 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
25038 aggregation for comparing different implementations in order to provide a
25039 'faster but good enough' alternative for use with R and C++ code.")
25040 (license license:gpl2+)))
25042 (define-public r-rfast
25049 (uri (cran-uri "Rfast" version))
25052 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
25053 (properties `((upstream-name . "Rfast")))
25054 (build-system r-build-system)
25056 `(("r-rcpp" ,r-rcpp)
25057 ("r-rcpparmadillo" ,r-rcpparmadillo)
25058 ("r-rcppziggurat" ,r-rcppziggurat)))
25059 (home-page "https://github.com/RfastOfficial/Rfast")
25060 (synopsis "Collection of efficient and fast R functions")
25062 "This package provides a collection of fast (utility) functions for data
25063 analysis. Column- and row- wise means, medians, variances, minimums,
25064 maximums, many t, F and G-square tests, many regressions (normal, logistic,
25065 Poisson), are some of the many fast functions.")
25066 (license license:gpl2+)))
25068 (define-public r-clusterr
25070 (name "r-clusterr")
25075 (uri (cran-uri "ClusterR" version))
25078 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
25079 (properties `((upstream-name . "ClusterR")))
25080 (build-system r-build-system)
25082 `(("r-ggplot2" ,r-ggplot2)
25084 ("r-gtools" ,r-gtools)
25086 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25087 (native-inputs `(("r-knitr" ,r-knitr)))
25088 (home-page "https://github.com/mlampros/ClusterR")
25089 (synopsis "Clustering")
25091 "This package provides Gaussian mixture models, k-means,
25092 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
25093 option to plot, validate, predict (new data) and estimate the optimal number
25094 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
25095 the computationally intensive parts of the functions. For more information,
25099 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
25100 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
25101 @url{https://doi.org/10.18637/jss.v001.i04};
25102 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
25103 Library, @url{https://doi.org/10.1145/1772690.1772862};
25104 @item \"Armadillo: a template-based C++ library
25105 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
25106 Software, @url{https://doi.org/10.21105/joss.00026};
25107 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
25108 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
25109 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
25112 (license license:gpl3)))
25114 (define-public r-spectrum
25116 (name "r-spectrum")
25121 (uri (cran-uri "Spectrum" version))
25124 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25125 (properties `((upstream-name . "Spectrum")))
25126 (build-system r-build-system)
25128 `(("r-clusterr" ,r-clusterr)
25129 ("r-diptest" ,r-diptest)
25130 ("r-ggplot2" ,r-ggplot2)
25131 ("r-rfast" ,r-rfast)))
25132 (native-inputs `(("r-knitr" ,r-knitr)))
25133 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25134 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25136 "This package provides a self-tuning spectral clustering method for
25137 single or multi-view data. Spectrum uses a new type of adaptive density aware
25138 kernel that strengthens connections in the graph based on common nearest
25139 neighbours. It uses a tensor product graph data integration and diffusion
25140 procedure to integrate different data sources and reduce noise. Spectrum uses
25141 either the eigengap or multimodality gap heuristics to determine the number of
25142 clusters. The method is sufficiently flexible so that a wide range of
25143 Gaussian and non-Gaussian structures can be clustered with automatic selection
25145 (license license:agpl3+)))
25147 (define-public r-nabor
25154 (uri (cran-uri "nabor" version))
25157 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25158 (properties `((upstream-name . "nabor")))
25159 (build-system r-build-system)
25163 ("r-rcppeigen" ,r-rcppeigen)))
25164 (home-page "https://cran.r-project.org/web/packages/nabor/")
25165 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25167 "This package provides an R wrapper for libnabo, an exact or approximate
25168 k nearest neighbour library which is optimised for low dimensional
25169 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25170 designed as a drop-in replacement for the RANN function @code{nn2}. In
25171 addition, objects which include the k-d tree search structure can be returned
25172 to speed up repeated queries of the same set of target points.")
25173 (license license:bsd-3)))
25175 (define-public r-muhaz
25178 (version "1.2.6.1")
25182 (uri (cran-uri "muhaz" version))
25185 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25186 (properties `((upstream-name . "muhaz")))
25187 (build-system r-build-system)
25189 `(("r-survival" ,r-survival)))
25191 `(("gfortran" ,gfortran)))
25192 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25193 (synopsis "Hazard function estimation in survival analysis")
25195 "This package produces a smooth estimate of the hazard function for
25197 ;; Any version of the GPL.
25198 (license license:gpl3+)))
25200 (define-public r-flexsurv
25202 (name "r-flexsurv")
25207 (uri (cran-uri "flexsurv" version))
25210 "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9"))))
25211 (properties `((upstream-name . "flexsurv")))
25212 (build-system r-build-system)
25214 `(("r-assertthat" ,r-assertthat)
25215 ("r-desolve" ,r-desolve)
25216 ("r-dplyr" ,r-dplyr)
25217 ("r-generics" ,r-generics)
25218 ("r-magrittr" ,r-magrittr)
25219 ("r-matrix" ,r-matrix)
25220 ("r-mstate" ,r-mstate)
25221 ("r-muhaz" ,r-muhaz)
25222 ("r-mvtnorm" ,r-mvtnorm)
25223 ("r-numderiv" ,r-numderiv)
25224 ("r-purrr" ,r-purrr)
25225 ("r-quadprog" ,r-quadprog)
25227 ("r-rlang" ,r-rlang)
25228 ("r-rstpm2" ,r-rstpm2)
25229 ("r-survival" ,r-survival)
25230 ("r-tibble" ,r-tibble)
25231 ("r-tidyr" ,r-tidyr)
25232 ("r-tidyselect" ,r-tidyselect)))
25234 `(("r-knitr" ,r-knitr)))
25235 (home-page "https://github.com/chjackson/flexsurv-dev")
25236 (synopsis "Flexible parametric survival and multi-state models")
25238 "This package provides flexible parametric models for time-to-event data,
25239 including the Royston-Parmar spline model, generalized gamma and generalized F
25240 distributions. Any user-defined parametric distribution can be fitted, given
25241 at least an R function defining the probability density or hazard. There are
25242 also tools for fitting and predicting from fully parametric multi-state
25244 (license license:gpl2+)))
25246 (define-public r-transphylo
25248 (name "r-transphylo")
25253 (uri (cran-uri "TransPhylo" version))
25256 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25257 (properties `((upstream-name . "TransPhylo")))
25258 (build-system r-build-system)
25261 ("r-rcpp" ,r-rcpp)))
25263 `(("r-knitr" ,r-knitr)))
25264 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25265 (synopsis "Inference of transmission tree from a dated phylogeny")
25267 "This is a package to infer transmission trees from a dated phylogeny.
25268 It includes methods to simulate and analyze outbreaks. The methodology is
25269 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25270 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25271 (license license:gpl2+)))
25273 (define-public r-km-ci
25280 (uri (cran-uri "km.ci" version))
25283 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25284 (properties `((upstream-name . "km.ci")))
25285 (build-system r-build-system)
25287 `(("r-survival" ,r-survival)))
25288 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25289 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25291 "This package computes various @dfn{confidence intervals} (CI) for the
25292 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25293 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25294 Nair and Hall and Wellner.")
25295 (license license:gpl2+)))
25297 (define-public r-kmsurv
25304 (uri (cran-uri "KMsurv" version))
25307 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25308 (properties `((upstream-name . "KMsurv")))
25309 (build-system r-build-system)
25310 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25311 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25313 "This package provides data sets and functions for Klein and Moeschberger
25314 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25316 (license license:gpl3+)))
25318 (define-public r-survmisc
25320 (name "r-survmisc")
25325 (uri (cran-uri "survMisc" version))
25328 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25329 (properties `((upstream-name . "survMisc")))
25330 (build-system r-build-system)
25332 `(("r-data-table" ,r-data-table)
25333 ("r-ggplot2" ,r-ggplot2)
25334 ("r-gridextra" ,r-gridextra)
25335 ("r-km-ci" ,r-km-ci)
25336 ("r-kmsurv" ,r-kmsurv)
25337 ("r-knitr" ,r-knitr)
25338 ("r-survival" ,r-survival)
25339 ("r-xtable" ,r-xtable)
25342 `(("r-knitr" ,r-knitr)))
25343 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25344 (synopsis "Miscellaneous functions for survival data")
25346 "This package provides a collection of functions to help in the analysis
25347 of right-censored survival data. These extend the methods available in
25348 the @code{survival} package.")
25349 (license license:gpl2)))
25351 (define-public r-exactranktests
25353 (name "r-exactranktests")
25358 (uri (cran-uri "exactRankTests" version))
25361 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25363 `((upstream-name . "exactRankTests")))
25364 (build-system r-build-system)
25365 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25366 (synopsis "Exact distributions for rank and permutation tests")
25368 "This package computes exact conditional p-values and quantiles using an
25369 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25370 (license license:gpl2+)))
25372 (define-public r-maxstat
25379 (uri (cran-uri "maxstat" version))
25382 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25383 (properties `((upstream-name . "maxstat")))
25384 (build-system r-build-system)
25386 `(("r-exactranktests" ,r-exactranktests)
25387 ("r-mvtnorm" ,r-mvtnorm)))
25388 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25389 (synopsis "Maximally selected rank statistics")
25391 "This package provides maximally selected rank statistics with several
25392 p-value approximations.")
25393 (license license:gpl2+)))
25395 (define-public r-survminer
25397 (name "r-survminer")
25402 (uri (cran-uri "survminer" version))
25405 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
25406 (properties `((upstream-name . "survminer")))
25407 (build-system r-build-system)
25409 `(("r-broom" ,r-broom)
25410 ("r-dplyr" ,r-dplyr)
25411 ("r-ggplot2" ,r-ggplot2)
25412 ("r-ggpubr" ,r-ggpubr)
25413 ("r-ggtext" ,r-ggtext)
25414 ("r-gridextra" ,r-gridextra)
25415 ("r-magrittr" ,r-magrittr)
25416 ("r-maxstat" ,r-maxstat)
25417 ("r-purrr" ,r-purrr)
25418 ("r-rlang" ,r-rlang)
25419 ("r-scales" ,r-scales)
25420 ("r-survival" ,r-survival)
25421 ("r-survmisc" ,r-survmisc)
25422 ("r-tibble" ,r-tibble)
25423 ("r-tidyr" ,r-tidyr)))
25425 `(("r-knitr" ,r-knitr)))
25426 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25427 (synopsis "Drawing survival curves using ggplot2")
25429 "This package contains the function @code{ggsurvplot()} for easily
25430 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25431 risk' table and 'censoring count plot'. Other functions are also available to
25432 plot adjusted curves for Cox model and to visually examine Cox model
25434 (license license:gpl2)))
25436 (define-public r-forge
25443 (uri (cran-uri "forge" version))
25446 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25447 (properties `((upstream-name . "forge")))
25448 (build-system r-build-system)
25450 `(("r-magrittr" ,r-magrittr)
25451 ("r-rlang" ,r-rlang)))
25452 (home-page "https://cran.r-project.org/web/packages/forge/")
25453 (synopsis "Cast values into shape")
25455 "This package provides helper functions with a consistent interface to
25456 coerce and verify the types and shapes of values for input checking.")
25457 (license license:asl2.0)))
25459 (define-public r-config
25466 (uri (cran-uri "config" version))
25469 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25470 (properties `((upstream-name . "config")))
25471 (build-system r-build-system)
25473 `(("r-yaml" ,r-yaml)))
25475 `(("r-knitr" ,r-knitr)))
25476 (home-page "https://github.com/rstudio/config")
25477 (synopsis "Manage environment specific configuration values")
25479 "This package lets you manage configuration values across multiple
25480 environments (e.g. development, test, production). It reads values using a
25481 function that determines the current environment and returns the appropriate
25483 (license license:gpl3)))
25485 (define-public r-adaptivesparsity
25487 (name "r-adaptivesparsity")
25491 (uri (cran-uri "AdaptiveSparsity" version))
25494 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25496 `((upstream-name . "AdaptiveSparsity")))
25497 (build-system r-build-system)
25500 (modify-phases %standard-phases
25501 (add-after 'unpack 'link-against-armadillo
25503 (substitute* "src/Makevars"
25504 (("PKG_LIBS=" prefix)
25505 (string-append prefix "-larmadillo")))
25508 `(("r-mass" ,r-mass)
25509 ("r-matrix" ,r-matrix)
25511 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25513 `(("armadillo" ,armadillo)))
25514 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25515 (synopsis "Adaptive sparsity models")
25517 "This package implements the Figueiredo machine learning algorithm for
25518 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25519 geometric models.")
25520 (license license:lgpl3+)))
25522 (define-public r-diffusionmap
25524 (name "r-diffusionmap")
25529 (uri (cran-uri "diffusionMap" version))
25532 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25533 (properties `((upstream-name . "diffusionMap")))
25534 (build-system r-build-system)
25536 `(("r-igraph" ,r-igraph)
25537 ("r-matrix" ,r-matrix)
25538 ("r-scatterplot3d" ,r-scatterplot3d)))
25539 (home-page "https://www.r-project.org")
25540 (synopsis "Diffusion map")
25541 (description "This package implements the diffusion map method of data
25542 parametrization, including creation and visualization of diffusion maps,
25543 clustering with diffusion K-means and regression using the adaptive regression
25545 (license license:gpl2)))
25547 (define-public r-igraph
25554 (uri (cran-uri "igraph" version))
25557 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25558 (build-system r-build-system)
25560 `(("gfortran" ,gfortran)))
25564 ("libxml2" ,libxml2)
25567 `(("r-magrittr" ,r-magrittr)
25568 ("r-matrix" ,r-matrix)
25569 ("r-pkgconfig" ,r-pkgconfig)))
25570 (home-page "https://igraph.org")
25571 (synopsis "Network analysis and visualization")
25573 "This package provides routines for simple graphs and network analysis.
25574 It can handle large graphs very well and provides functions for generating
25575 random and regular graphs, graph visualization, centrality methods and much
25577 (license license:gpl2+)))
25579 (define-public r-workflows
25581 (name "r-workflows")
25586 (uri (cran-uri "workflows" version))
25589 "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz"))))
25590 (properties `((upstream-name . "workflows")))
25591 (build-system r-build-system)
25594 ("r-ellipsis" ,r-ellipsis)
25595 ("r-generics" ,r-generics)
25597 ("r-hardhat" ,r-hardhat)
25598 ("r-parsnip" ,r-parsnip)
25599 ("r-rlang" ,r-rlang)
25600 ("r-tidyselect" ,r-tidyselect)
25601 ("r-vctrs" ,r-vctrs)))
25603 `(("r-knitr" ,r-knitr)))
25604 (home-page "https://github.com/tidymodels/workflows")
25605 (synopsis "Modeling workflows")
25607 "A workflow is an object that can bundle together your pre-processing,
25608 modeling, and post-processing requests. For example, if you have a
25609 @code{recipe} and @code{parsnip} model, these can be combined into a
25610 workflow. The advantages are:
25613 @item You don’t have to keep track of separate objects in your workspace.
25614 @item The recipe prepping and model fitting can be executed using a single
25615 call to @code{fit()}.
25616 @item If you have custom tuning parameter settings, these can be defined using
25617 a simpler interface when combined with @code{tune}.
25618 @item In the future, workflows will be able to add post-processing operations,
25619 such as modifying the probability cutoff for two-class models.
25622 (license license:expat)))
25624 (define-public r-gpfit
25631 (uri (cran-uri "GPfit" version))
25634 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25635 (properties `((upstream-name . "GPfit")))
25636 (build-system r-build-system)
25638 `(("r-lattice" ,r-lattice)
25640 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25641 (synopsis "Gaussian Processes modeling")
25643 "This package provides a computationally stable approach of fitting a
25644 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25645 (license license:gpl2)))
25647 (define-public r-yardstick
25649 (name "r-yardstick")
25654 (uri (cran-uri "yardstick" version))
25657 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25658 (properties `((upstream-name . "yardstick")))
25659 (build-system r-build-system)
25661 `(("r-dplyr" ,r-dplyr)
25662 ("r-generics" ,r-generics)
25664 ("r-rlang" ,r-rlang)
25665 ("r-tidyselect" ,r-tidyselect)))
25667 `(("r-knitr" ,r-knitr)))
25668 (home-page "https://github.com/tidymodels/yardstick")
25669 (synopsis "Tidy characterizations of model performance")
25671 "This package provides tidy tools for quantifying how well a model fits
25672 to a data set such as confusion matrices, class probability curve summaries,
25673 and regression metrics (e.g., RMSE).")
25674 (license license:gpl2)))
25676 (define-public r-warp
25683 (uri (cran-uri "warp" version))
25686 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25687 (properties `((upstream-name . "warp")))
25688 (build-system r-build-system)
25689 (native-inputs `(("r-knitr" ,r-knitr)))
25690 (home-page "https://github.com/DavisVaughan/warp")
25691 (synopsis "Group dates")
25693 "This package provides tooling to group dates by a variety of periods
25694 including: yearly, monthly, by second, by week of the month, and more. The
25695 groups are defined in such a way that they also represent the distance between
25696 dates in terms of the period. This extracts valuable information that can be
25697 used in further calculations that rely on a specific temporal spacing between
25699 (license license:expat)))
25701 (define-public r-slider
25708 (uri (cran-uri "slider" version))
25711 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25712 (properties `((upstream-name . "slider")))
25713 (build-system r-build-system)
25715 `(("r-glue" ,r-glue)
25716 ("r-rlang" ,r-rlang)
25717 ("r-vctrs" ,r-vctrs)
25718 ("r-warp" ,r-warp)))
25719 (native-inputs `(("r-knitr" ,r-knitr)))
25720 (home-page "https://github.com/DavisVaughan/slider")
25721 (synopsis "Sliding window functions")
25723 "This package provides type-stable rolling window functions over any R
25724 data type. Cumulative and expanding windows are also supported. For more
25725 advanced usage, an index can be used as a secondary vector that defines how
25726 sliding windows are to be created.")
25727 (license license:expat)))
25729 (define-public r-rsample
25736 (uri (cran-uri "rsample" version))
25739 "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c"))))
25740 (properties `((upstream-name . "rsample")))
25741 (build-system r-build-system)
25743 `(("r-dplyr" ,r-dplyr)
25744 ("r-ellipsis" ,r-ellipsis)
25745 ("r-furrr" ,r-furrr)
25746 ("r-generics" ,r-generics)
25747 ("r-purrr" ,r-purrr)
25748 ("r-rlang" ,r-rlang)
25749 ("r-slider" ,r-slider)
25750 ("r-tibble" ,r-tibble)
25751 ("r-tidyr" ,r-tidyr)
25752 ("r-tidyselect" ,r-tidyselect)
25753 ("r-vctrs" ,r-vctrs)))
25755 `(("r-knitr" ,r-knitr)))
25756 (home-page "https://rsample.tidymodels.org")
25757 (synopsis "General resampling infrastructure")
25759 "This package provides classes and functions to create and summarize
25760 different types of resampling objects (e.g. bootstrap, cross-validation).")
25761 (license license:gpl2)))
25763 (define-public r-dicedesign
25765 (name "r-dicedesign")
25770 (uri (cran-uri "DiceDesign" version))
25773 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
25774 (properties `((upstream-name . "DiceDesign")))
25775 (build-system r-build-system)
25776 (home-page "http://dice.emse.fr/")
25777 (synopsis "Designs of computer experiments")
25779 "This package provides tools to create some specific @code{Space-Filling
25780 Design} (SFD) and to test their quality.")
25781 (license license:gpl3)))
25783 (define-public r-dials
25790 (uri (cran-uri "dials" version))
25793 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25794 (properties `((upstream-name . "dials")))
25795 (build-system r-build-system)
25797 `(("r-dicedesign" ,r-dicedesign)
25798 ("r-dplyr" ,r-dplyr)
25800 ("r-purrr" ,r-purrr)
25801 ("r-rlang" ,r-rlang)
25802 ("r-scales" ,r-scales)
25803 ("r-tibble" ,r-tibble)
25804 ("r-vctrs" ,r-vctrs)
25805 ("r-withr" ,r-withr)))
25806 (native-inputs `(("r-knitr" ,r-knitr)))
25807 (home-page "https://dials.tidymodels.org/")
25808 (synopsis "Tools for creating tuning parameter values")
25810 "Many models contain tuning parameters (i.e. parameters that cannot be
25811 directly estimated from the data). These tools can be used to define objects
25812 for creating, simulating, or validating values for such parameters.")
25813 (license license:gpl2)))
25815 (define-public r-tune
25822 (uri (cran-uri "tune" version))
25825 "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293"))))
25826 (properties `((upstream-name . "tune")))
25827 (build-system r-build-system)
25830 ("r-dials" ,r-dials)
25831 ("r-dplyr" ,r-dplyr)
25832 ("r-foreach" ,r-foreach)
25833 ("r-generics" ,r-generics)
25834 ("r-ggplot2" ,r-ggplot2)
25836 ("r-gpfit" ,r-gpfit)
25837 ("r-parsnip" ,r-parsnip)
25838 ("r-purrr" ,r-purrr)
25839 ("r-recipes" ,r-recipes)
25840 ("r-rlang" ,r-rlang)
25841 ("r-rsample" ,r-rsample)
25842 ("r-tibble" ,r-tibble)
25843 ("r-tidyr" ,r-tidyr)
25844 ("r-vctrs" ,r-vctrs)
25845 ("r-workflows" ,r-workflows)
25846 ("r-yardstick" ,r-yardstick)))
25847 (home-page "https://github.com/tidymodels/tune")
25848 (synopsis "Tidy tuning tools")
25850 "The ability to tune models is important. @code{tune} contains functions
25851 and classes to be used in conjunction with other @code{tidymodels} packages
25852 for finding reasonable values of hyper-parameters in models, pre-processing
25853 methods, and post-processing steps.")
25854 (license license:expat)))
25856 (define-public r-workflowsets
25858 (name "r-workflowsets")
25863 (uri (cran-uri "workflowsets" version))
25866 "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p"))))
25867 (properties `((upstream-name . "workflowsets")))
25868 (build-system r-build-system)
25871 ("r-dplyr" ,r-dplyr)
25872 ("r-ggplot2" ,r-ggplot2)
25873 ("r-prettyunits" ,r-prettyunits)
25874 ("r-purrr" ,r-purrr)
25875 ("r-rlang" ,r-rlang)
25876 ("r-rsample" ,r-rsample)
25877 ("r-tibble" ,r-tibble)
25878 ("r-tidyr" ,r-tidyr)
25880 ("r-vctrs" ,r-vctrs)
25881 ("r-withr" ,r-withr)
25882 ("r-workflows" ,r-workflows)))
25884 `(("r-knitr" ,r-knitr)))
25885 (home-page "https://github.com/tidymodels/workflowsets")
25886 (synopsis "Create a collection of tidymodels workflows")
25888 "A workflow is a combination of a model and preprocessors (e.g, a
25889 formula, recipe, etc.). In order to try different combinations of these, an
25890 object can be created that contains many workflows. There are functions to
25891 create workflows en masse as well as training them and visualizing the
25893 (license license:expat)))
25895 (define-public r-tidyposterior
25897 (name "r-tidyposterior")
25902 (uri (cran-uri "tidyposterior" version))
25905 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25906 (properties `((upstream-name . "tidyposterior")))
25907 (build-system r-build-system)
25909 `(("r-dplyr" ,r-dplyr)
25910 ("r-generics" ,r-generics)
25911 ("r-ggplot2" ,r-ggplot2)
25912 ("r-lifecycle" ,r-lifecycle)
25913 ("r-purrr" ,r-purrr)
25914 ("r-rlang" ,r-rlang)
25915 ("r-rsample" ,r-rsample)
25916 ("r-rstanarm" ,r-rstanarm)
25917 ("r-tibble" ,r-tibble)
25918 ("r-tidyr" ,r-tidyr)
25919 ("r-vctrs" ,r-vctrs)))
25921 `(("r-knitr" ,r-knitr)))
25922 (home-page "https://tidyposterior.tidymodels.org")
25923 (synopsis "Bayesian analysis to compare models using resampling statistics")
25925 "This package can be used to conduct post hoc analyses of resampling
25926 results generated by models. For example, if two models are evaluated with
25927 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25928 are 10 paired statistics. These can be used to make comparisons between
25929 models without involving a test set.")
25930 (license license:gpl2)))
25932 (define-public r-tidypredict
25934 (name "r-tidypredict")
25939 (uri (cran-uri "tidypredict" version))
25942 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25943 (properties `((upstream-name . "tidypredict")))
25944 (build-system r-build-system)
25946 `(("r-dplyr" ,r-dplyr)
25947 ("r-generics" ,r-generics)
25948 ("r-knitr" ,r-knitr)
25949 ("r-purrr" ,r-purrr)
25950 ("r-rlang" ,r-rlang)
25951 ("r-stringr" ,r-stringr)
25952 ("r-tibble" ,r-tibble)
25953 ("r-tidyr" ,r-tidyr)))
25955 `(("r-knitr" ,r-knitr)))
25956 (home-page "https://tidypredict.tidymodels.org")
25957 (synopsis "Run predictions inside the database")
25959 "This package parses a fitted R model object, and returns a formula in
25960 Tidy Eval code that calculates the predictions. It works with several
25961 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25962 final SQL translation of the algorithm. It currently supports @code{lm()},
25963 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25964 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25965 (license license:gpl3)))
25967 (define-public r-janeaustenr
25969 (name "r-janeaustenr")
25974 (uri (cran-uri "janeaustenr" version))
25977 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25978 (properties `((upstream-name . "janeaustenr")))
25979 (build-system r-build-system)
25980 (home-page "https://github.com/juliasilge/janeaustenr")
25981 (synopsis "Jane Austen's complete novels")
25983 "This package provides the full texts for Jane Austen's six completed
25984 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25985 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25986 and \"Persuasion\".")
25987 (license license:expat)))
25989 (define-public r-tokenizers
25991 (name "r-tokenizers")
25996 (uri (cran-uri "tokenizers" version))
25999 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
26000 (properties `((upstream-name . "tokenizers")))
26001 (build-system r-build-system)
26003 `(("r-rcpp" ,r-rcpp)
26004 ("r-snowballc" ,r-snowballc)
26005 ("r-stringi" ,r-stringi)))
26007 `(("r-knitr" ,r-knitr)))
26008 (home-page "https://lincolnmullen.com/software/tokenizers/")
26009 (synopsis "Fast, consistent tokenization of natural language text")
26011 "This is a package for converting natural language text into tokens.
26012 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
26013 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
26014 Treebank, regular expressions, as well as functions for counting characters,
26015 words, and sentences, and a function for splitting longer texts into separate
26016 documents, each with the same number of words. The tokenizers have a
26017 consistent interface, and the package is built on the @code{stringi} and
26018 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
26019 (license license:expat)))
26021 (define-public r-hunspell
26023 (name "r-hunspell")
26028 (uri (cran-uri "hunspell" version))
26031 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
26032 (properties `((upstream-name . "hunspell")))
26033 (build-system r-build-system)
26035 `(("r-digest" ,r-digest)
26036 ("r-rcpp" ,r-rcpp)))
26038 `(("r-knitr" ,r-knitr)))
26039 (home-page "https://github.com/ropensci/hunspell#readme")
26040 (synopsis "High-performance stemmer, tokenizer, and spell checker")
26042 "This package provides a low-level spell checker and morphological
26043 analyzer based on the famous @code{hunspell} library. The package can analyze
26044 or check individual words as well as parse text, LaTeX, HTML or XML documents.
26045 For a more user-friendly interface use the @code{spelling} package which
26046 builds on this package to automate checking of files, documentation and
26047 vignettes in all common formats.")
26048 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
26049 ;; MPL; in addition to these licenses the rest of the R wrapper is also
26050 ;; available under the Expat license.
26051 (license (list license:gpl2
26056 (define-public r-tidytext
26058 (name "r-tidytext")
26063 (uri (cran-uri "tidytext" version))
26066 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
26067 (properties `((upstream-name . "tidytext")))
26068 (build-system r-build-system)
26070 `(("r-dplyr" ,r-dplyr)
26071 ("r-generics" ,r-generics)
26072 ("r-hunspell" ,r-hunspell)
26073 ("r-janeaustenr" ,r-janeaustenr)
26074 ("r-lifecycle" ,r-lifecycle)
26075 ("r-matrix" ,r-matrix)
26076 ("r-purrr" ,r-purrr)
26077 ("r-rlang" ,r-rlang)
26078 ("r-stringr" ,r-stringr)
26079 ("r-tibble" ,r-tibble)
26080 ("r-tokenizers" ,r-tokenizers)
26081 ("r-vctrs" ,r-vctrs)))
26083 `(("r-knitr" ,r-knitr)))
26084 (home-page "https://github.com/juliasilge/tidytext")
26085 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
26087 "This is a package for text mining for word processing and sentiment
26088 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
26089 (license license:expat)))
26091 (define-public r-parsnip
26098 (uri (cran-uri "parsnip" version))
26101 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
26102 (properties `((upstream-name . "parsnip")))
26103 (build-system r-build-system)
26105 `(("r-dplyr" ,r-dplyr)
26106 ("r-generics" ,r-generics)
26107 ("r-globals" ,r-globals)
26109 ("r-magrittr" ,r-magrittr)
26110 ("r-prettyunits" ,r-prettyunits)
26111 ("r-purrr" ,r-purrr)
26112 ("r-rlang" ,r-rlang)
26113 ("r-tibble" ,r-tibble)
26114 ("r-tidyr" ,r-tidyr)
26115 ("r-vctrs" ,r-vctrs)))
26117 `(("r-knitr" ,r-knitr)))
26118 (home-page "https://parsnip.tidymodels.org")
26119 (synopsis "Common API to modeling and analysis functions")
26121 "This package provides a common interface to allow users to specify a
26122 model without having to remember the different argument names across different
26123 functions or computational engines (e.g. R, Spark, Stan, etc).")
26124 (license license:gpl2)))
26126 (define-public r-infer
26133 (uri (cran-uri "infer" version))
26136 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
26137 (properties `((upstream-name . "infer")))
26138 (build-system r-build-system)
26140 `(("r-dplyr" ,r-dplyr)
26141 ("r-ggplot2" ,r-ggplot2)
26143 ("r-magrittr" ,r-magrittr)
26144 ("r-purrr" ,r-purrr)
26145 ("r-rlang" ,r-rlang)
26146 ("r-tibble" ,r-tibble)))
26148 `(("r-knitr" ,r-knitr)))
26149 (home-page "https://github.com/tidymodels/infer")
26150 (synopsis "Tidy statistical inference")
26152 "The objective of this package is to perform inference using an
26153 expressive statistical grammar that coheres with the Tidy design framework.")
26154 (license license:cc0)))
26156 (define-public r-modeldata
26158 (name "r-modeldata")
26163 (uri (cran-uri "modeldata" version))
26166 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
26167 (properties `((upstream-name . "modeldata")))
26168 (build-system r-build-system)
26169 (home-page "https://modeldata.tidymodels.org")
26170 (synopsis "Data sets useful for modeling packages")
26172 "This package provides data sets used for demonstrating or testing
26173 model-related packages.")
26174 (license license:expat)))
26176 (define-public r-tidymodels
26178 (name "r-tidymodels")
26183 (uri (cran-uri "tidymodels" version))
26186 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26187 (properties `((upstream-name . "tidymodels")))
26188 (build-system r-build-system)
26190 `(("r-broom" ,r-broom)
26192 ("r-dials" ,r-dials)
26193 ("r-dplyr" ,r-dplyr)
26194 ("r-ggplot2" ,r-ggplot2)
26195 ("r-infer" ,r-infer)
26196 ("r-magrittr" ,r-magrittr)
26197 ("r-modeldata" ,r-modeldata)
26198 ("r-parsnip" ,r-parsnip)
26199 ("r-purrr" ,r-purrr)
26200 ("r-recipes" ,r-recipes)
26201 ("r-rlang" ,r-rlang)
26202 ("r-rsample" ,r-rsample)
26203 ("r-rstudioapi" ,r-rstudioapi)
26204 ("r-tibble" ,r-tibble)
26205 ("r-tidyr" ,r-tidyr)
26207 ("r-workflows" ,r-workflows)
26208 ("r-yardstick" ,r-yardstick)))
26210 `(("r-knitr" ,r-knitr)
26211 ("r-rmarkdown" ,r-rmarkdown)
26213 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26214 (home-page "https://github.com/tidymodels/tidymodels")
26215 (synopsis "Tidy collection for modeling and statistical analysis")
26217 "The tidy modeling \"verse\" is a collection of packages for modeling and
26218 statistical analysis that share the underlying design philosophy, grammar, and
26219 data structures of the tidyverse.")
26220 (license license:gpl3)))
26222 (define-public r-lsa
26229 (uri (cran-uri "lsa" version))
26232 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
26233 (properties `((upstream-name . "lsa")))
26234 (build-system r-build-system)
26236 `(("r-snowballc" ,r-snowballc)))
26237 (home-page "https://cran.r-project.org/package=lsa")
26238 (synopsis "Latent semantic analysis")
26240 "The basic idea of latent semantic analysis (LSA) is, that text do have a
26241 higher order (=latent semantic) structure which, however, is obscured by word
26242 usage (e.g. through the use of synonyms or polysemy). By using conceptual
26243 indices that are derived statistically via a truncated singular value
26244 decomposition (a two-mode factor analysis) over a given document-term matrix,
26245 this variability problem can be overcome.")
26246 (license license:gpl2+)))
26248 (define-public r-mlecens
26255 (uri (cran-uri "MLEcens" version))
26258 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26259 (properties `((upstream-name . "MLEcens")))
26260 (build-system r-build-system)
26261 (home-page "http://stat.ethz.ch/~maathuis/")
26262 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26264 "This package contains functions to compute the nonparametric
26265 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26266 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26267 To be more precise, we consider the situation where we observe a set of
26268 rectangles that are known to contain the unobservable realizations of (X,Y).
26269 We compute the MLE based on such a set of rectangles. The methods can also be
26270 used for univariate censored data (see data set @code{cosmesis}), and for
26271 censored data with competing risks (see data set @code{menopause}). The
26272 package also provides functions to visualize the observed data and the MLE.")
26273 (license license:gpl2+)))
26275 (define-public r-metafor
26282 (uri (cran-uri "metafor" version))
26285 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26286 (properties `((upstream-name . "metafor")))
26287 (build-system r-build-system)
26289 `(("r-matrix" ,r-matrix)
26290 ("r-nlme" ,r-nlme)))
26291 (home-page "https://cran.r-project.org/web/packages/metafor/")
26292 (synopsis "Meta-analysis package for R")
26294 "This package provides a comprehensive collection of functions for
26295 conducting meta-analyses in R. The package includes functions to calculate
26296 various effect sizes or outcome measures, fit fixed-, random-, and
26297 mixed-effects models to such data, carry out moderator and meta-regression
26298 analyses, and create various types of meta-analytical plots (e.g., forest,
26299 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26300 and person-time data, the package also provides functions that implement
26301 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26302 a variety of suitable generalized linear (mixed-effects) models (i.e.
26303 mixed-effects logistic and Poisson regression models). Finally, the package
26304 provides functionality for fitting meta-analytic multivariate/multilevel
26305 models that account for non-independent sampling errors and/or true
26306 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26307 endpoints, or other forms of clustering). Network meta-analyses and
26308 meta-analyses accounting for known correlation structures (e.g. due to
26309 phylogenetic relatedness) can also be conducted.")
26310 (license license:gpl2+)))
26312 (define-public r-altmeta
26319 (uri (cran-uri "altmeta" version))
26322 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26323 (properties `((upstream-name . "altmeta")))
26324 (build-system r-build-system)
26326 `(("r-coda" ,r-coda)
26328 ("r-matrix" ,r-matrix)
26329 ("r-metafor" ,r-metafor)
26330 ("r-rjags" ,r-rjags)))
26331 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26332 (synopsis "Alternative meta-analysis methods")
26334 "This package provides alternative statistical methods for meta-analysis,
26338 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26339 relative risks, and risk differences
26340 @item heterogeneity tests and measures that are robust to outliers;
26341 @item measures, tests, and visualization tools for publication bias or
26342 small-study effects;
26343 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26344 specificities, etc.;
26345 @item meta-analysis methods for synthesizing proportions;
26346 @item models for multivariate meta-analysis.
26349 (license license:gpl2+)))
26351 (define-public r-perm
26354 (version "1.0-0.0")
26358 (uri (cran-uri "perm" version))
26361 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26362 (properties `((upstream-name . "perm")))
26363 (build-system r-build-system)
26364 (home-page "https://cran.r-project.org/web/packages/perm/")
26365 (synopsis "Exact or asymptotic permutation tests")
26367 "This package provides several methods for performing permutation tests.
26368 It has three main functions, to perform linear permutation tests. These tests
26369 are tests where the test statistic is the sum of the product of a
26370 covariate (usually group indicator) and the scores.")
26371 ;; Any version of the GPL
26372 (license license:gpl2+)))
26374 (define-public r-qtl
26381 (uri (cran-uri "qtl" version))
26384 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26385 (build-system r-build-system)
26386 (home-page "https://rqtl.org/")
26387 (synopsis "R package for analyzing QTL experiments in genetics")
26388 (description "R/qtl is an extension library for the R statistics system.
26389 It is used to analyze experimental crosses for identifying genes contributing
26390 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26392 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26393 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26395 (license license:gpl3)))
26397 (define-public r-qtl2
26403 (uri (cran-uri "qtl2" version))
26405 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26406 (build-system r-build-system)
26408 `(("r-data-table" ,r-data-table)
26409 ("r-jsonlite" ,r-jsonlite)
26411 ("r-rcppeigen" ,r-rcppeigen)
26412 ("r-rsqlite" ,r-rsqlite)
26413 ("r-yaml" ,r-yaml)))
26414 (home-page "https://kbroman.org/qtl2/")
26415 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26417 "This package provides a set of tools to perform @dfn{Quantitative Trait
26418 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26419 @code{R/qtl} package to better handle high-dimensional data and complex cross
26420 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26421 (license license:gpl3)))
26423 (define-public r-seqminer
26425 (name "r-seqminer")
26430 (uri (cran-uri "seqminer" version))
26433 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26434 (build-system r-build-system)
26437 (home-page "http://seqminer.genomic.codes")
26438 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26440 "This package provides tools to integrate nucleotide sequencing
26441 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26442 ;; Any version of the GPL is acceptable
26443 (license (list license:gpl2+ license:gpl3+))))
26445 (define-public r-maldiquant
26447 (name "r-maldiquant")
26452 (uri (cran-uri "MALDIquant" version))
26455 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26456 (properties `((upstream-name . "MALDIquant")))
26457 (build-system r-build-system)
26458 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26459 (synopsis "Quantitative analysis of mass spectrometry data")
26461 "This package provides a complete analysis pipeline for matrix-assisted
26462 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26463 two-dimensional mass spectrometry data. In addition to commonly used plotting
26464 and processing methods it includes distinctive features, namely baseline
26465 subtraction methods such as morphological filters (TopHat) or the
26466 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26467 alignment using warping functions, handling of replicated measurements as well
26468 as allowing spectra with different resolutions.")
26469 (license license:gpl3+)))
26471 (define-public r-scattermore
26473 (name "r-scattermore")
26478 (uri (cran-uri "scattermore" version))
26481 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26482 (properties `((upstream-name . "scattermore")))
26483 (build-system r-build-system)
26485 `(("r-ggplot2" ,r-ggplot2)
26486 ("r-scales" ,r-scales)))
26487 (home-page "https://github.com/exaexa/scattermore")
26488 (synopsis "Scatterplots with more points")
26490 "This package provides C-based tools for converting large scatterplot
26491 data to rasters. It speeds up plotting of data with millions of points.")
26492 (license license:gpl3+)))
26494 (define-public r-seuratobject
26496 (name "r-seuratobject")
26501 (uri (cran-uri "SeuratObject" version))
26504 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26505 (properties `((upstream-name . "SeuratObject")))
26506 (build-system r-build-system)
26508 `(("r-matrix" ,r-matrix)
26510 ("r-rcppeigen" ,r-rcppeigen)
26511 ("r-rlang" ,r-rlang)
26512 ("r-sctransform" ,r-sctransform)))
26513 (home-page "https://satijalab.org/seurat")
26514 (synopsis "Data structures for single cell data")
26516 "This package defines S4 classes for single-cell genomic data and
26517 associated information, such as dimensionality reduction embeddings,
26518 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26519 access methods and R-native hooks to ensure the Seurat object is familiar to
26521 (license license:gpl3)))
26523 (define-public r-seurat
26529 (uri (cran-uri "Seurat" version))
26532 "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
26533 (properties `((upstream-name . "Seurat")))
26534 (build-system r-build-system)
26536 `(("r-cluster" ,r-cluster)
26537 ("r-cowplot" ,r-cowplot)
26538 ("r-fitdistrplus" ,r-fitdistrplus)
26539 ("r-future" ,r-future)
26540 ("r-future-apply" ,r-future-apply)
26541 ("r-ggplot2" ,r-ggplot2)
26542 ("r-ggrepel" ,r-ggrepel)
26543 ("r-ggridges" ,r-ggridges)
26546 ("r-igraph" ,r-igraph)
26547 ("r-irlba" ,r-irlba)
26548 ("r-jsonlite" ,r-jsonlite)
26549 ("r-kernsmooth" ,r-kernsmooth)
26550 ("r-leiden" ,r-leiden)
26551 ("r-lmtest" ,r-lmtest)
26553 ("r-matrix" ,r-matrix)
26554 ("r-matrixstats" ,r-matrixstats)
26555 ("r-miniui" ,r-miniui)
26556 ("r-patchwork" ,r-patchwork)
26557 ("r-pbapply" ,r-pbapply)
26558 ("r-plotly" ,r-plotly)
26561 ("r-rcolorbrewer" ,r-rcolorbrewer)
26563 ("r-rcppannoy" ,r-rcppannoy)
26564 ("r-rcppeigen" ,r-rcppeigen)
26565 ("r-rcppprogress" ,r-rcppprogress)
26566 ("r-reticulate" ,r-reticulate)
26567 ("r-rlang" ,r-rlang)
26569 ("r-rtsne" ,r-rtsne)
26570 ("r-scales" ,r-scales)
26571 ("r-scattermore" ,r-scattermore)
26572 ("r-sctransform" ,r-sctransform)
26573 ("r-seuratobject" ,r-seuratobject)
26574 ("r-shiny" ,r-shiny)
26575 ("r-spatstat-core" ,r-spatstat-core)
26576 ("r-spatstat-geom" ,r-spatstat-geom)
26577 ("r-tibble" ,r-tibble)
26578 ("r-uwot" ,r-uwot)))
26579 (home-page "http://www.satijalab.org/seurat")
26580 (synopsis "Seurat is an R toolkit for single cell genomics")
26582 "This package is an R package designed for QC, analysis, and
26583 exploration of single cell RNA-seq data. It easily enables widely-used
26584 analytical techniques, including the identification of highly variable genes,
26585 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26586 algorithms; density clustering, hierarchical clustering, k-means, and the
26587 discovery of differentially expressed genes and markers.")
26588 (license license:gpl3)))
26590 (define-public r-phangorn
26592 (name "r-phangorn")
26597 (uri (cran-uri "phangorn" version))
26600 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26601 (build-system r-build-system)
26604 ("r-fastmatch" ,r-fastmatch)
26605 ("r-igraph" ,r-igraph)
26606 ("r-magrittr" ,r-magrittr)
26607 ("r-matrix" ,r-matrix)
26608 ("r-quadprog" ,r-quadprog)
26609 ("r-rcpp" ,r-rcpp)))
26610 (home-page "https://github.com/KlausVigo/phangorn")
26611 (synopsis "Phylogenetic analysis in R")
26613 "Phangorn is a package for phylogenetic analysis in R. It supports
26614 estimation of phylogenetic trees and networks using Maximum Likelihood,
26615 Maximum Parsimony, distance methods and Hadamard conjugation.")
26616 (license license:gpl2+)))
26618 (define-public r-diversitree
26620 (name "r-diversitree")
26625 (uri (cran-uri "diversitree" version))
26628 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26629 (build-system r-build-system)
26631 `(("gfortran" ,gfortran)))
26632 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26635 ("r-desolve" ,r-desolve)
26637 ("r-subplex" ,r-subplex)))
26638 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26639 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26640 (description "This package contains a number of comparative \"phylogenetic\"
26641 methods, mostly focusing on analysing diversification and character evolution.
26642 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26643 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26644 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26645 include Markov models of discrete and continuous trait evolution and constant
26646 rate speciation and extinction.")
26647 (license license:gpl2+)))
26649 (define-public r-calculus
26651 (name "r-calculus")
26656 (uri (cran-uri "calculus" version))
26659 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26660 (properties `((upstream-name . "calculus")))
26661 (build-system r-build-system)
26663 `(("r-rcpp" ,r-rcpp)))
26665 `(("r-knitr" ,r-knitr)))
26666 (home-page "https://github.com/eguidotti/calculus")
26667 (synopsis "High dimensional numerical and symbolic calculus")
26669 "Efficient C++ optimized functions for numerical and symbolic calculus.
26670 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26671 convention, fast computation of the Levi-Civita symbol and generalized
26672 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26673 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26674 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26675 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26676 parabolic or user defined by custom scale factors.")
26677 (license license:gpl3)))
26679 (define-public r-decon
26686 (uri (cran-uri "decon" version))
26689 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26690 (properties `((upstream-name . "decon")))
26691 (build-system r-build-system)
26693 `(("gfortran" ,gfortran)))
26695 "https://cran.r-project.org/web/packages/decon/")
26696 (synopsis "Deconvolution Estimation in Measurement Error Models")
26698 "This package contains a collection of functions to deal with
26699 nonparametric measurement error problems using deconvolution
26700 kernel methods. We focus two measurement error models in the
26701 package: (1) an additive measurement error model, where the
26702 goal is to estimate the density or distribution function from
26703 contaminated data; (2) nonparametric regression model with
26704 errors-in-variables. The R functions allow the measurement errors
26705 to be either homoscedastic or heteroscedastic. To make the
26706 deconvolution estimators computationally more efficient in R,
26707 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26708 density estimation with error-free data to the deconvolution
26709 kernel estimation. Several methods for the selection of the
26710 data-driven smoothing parameter are also provided in the package.
26711 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26712 estimation in measurement error models: The R package decon.
26713 Journal of Statistical Software, 39(10), 1-24.")
26714 (license license:gpl3+)))
26716 (define-public r-locpol
26723 (uri (cran-uri "locpol" version))
26726 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26727 (properties `((upstream-name . "locpol")))
26728 (build-system r-build-system)
26730 "https://cran.r-project.org/web/packages/locpol/")
26731 (synopsis "Kernel Local Polynomial Regression")
26733 "Computes local polynomial estimators for the regression and
26734 also density. It comprises several different utilities to handle
26735 kernel estimators.")
26736 (license license:gpl2+)))
26738 (define-public r-lpme
26745 (uri (cran-uri "lpme" version))
26748 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26749 (properties `((upstream-name . "lpme")))
26750 (build-system r-build-system)
26752 `(("r-decon" ,r-decon)
26753 ("r-flexmix" ,r-flexmix)
26754 ("r-locpol" ,r-locpol)
26756 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26758 "https://cran.r-project.org/web/packages/lpme/")
26759 (synopsis "Nonparametric Estimation of Measurement Error Models")
26761 "Provide nonparametric methods for mean regression model,
26762 modal regression and conditional density estimation in the
26763 presence/absence of measurement error. Bandwidth selection is
26764 also provided for each method.")
26765 (license license:gpl2+)))
26767 (define-public r-aws-signature
26769 (name "r-aws-signature")
26774 (uri (cran-uri "aws.signature" version))
26777 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26778 (properties `((upstream-name . "aws.signature")))
26779 (build-system r-build-system)
26781 `(("r-base64enc" ,r-base64enc)
26782 ("r-digest" ,r-digest)))
26783 (home-page "https://github.com/cloudyr/aws.signature")
26784 (synopsis "Amazon Web Services Request Signatures")
26786 "This package generates version 2 and 4 request signatures for Amazon Web
26787 Services (AWS) and provides a mechanism for retrieving credentials from
26788 environment variables, AWS credentials files, and EC2 instance metadata. For
26789 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26790 (license license:gpl2+)))
26792 (define-public r-aws-s3
26799 (uri (cran-uri "aws.s3" version))
26802 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26803 (properties `((upstream-name . "aws.s3")))
26804 (build-system r-build-system)
26806 `(("r-aws-signature" ,r-aws-signature)
26807 ("r-base64enc" ,r-base64enc)
26809 ("r-digest" ,r-digest)
26811 ("r-xml2" ,r-xml2)))
26812 (home-page "https://github.com/cloudyr/aws.s3")
26813 (synopsis "AWS S3 Client Package")
26815 "This package provides a simple client package for the Amazon Web
26816 Services (AWS) Simple Storage Service (S3) REST API.")
26817 (license license:gpl2+)))
26819 (define-public r-lgr
26825 (uri (cran-uri "lgr" version))
26828 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26829 (build-system r-build-system)
26833 `(("r-knitr" ,r-knitr)))
26834 (home-page "https://s-fleck.github.io/lgr/")
26835 (synopsis "Fully featured logging framework")
26836 (description "This package offers a flexible, feature-rich yet
26837 light-weight logging framework based on @code{R6} classes. It supports
26838 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26839 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26840 well as email and push notifications.")
26841 (license license:expat)))
26843 (define-public r-mlr3measures
26845 (name "r-mlr3measures")
26849 (uri (cran-uri "mlr3measures" version))
26852 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26853 (build-system r-build-system)
26855 `(("r-checkmate" ,r-checkmate)
26856 ("r-prroc" ,r-prroc)))
26857 (home-page "https://mlr3measures.mlr-org.com/")
26858 (synopsis "Performance measures for mlr3")
26859 (description "This package implements multiple performance measures for
26860 supervised learning. It includes over 40 measures for regression and
26861 classification. Additionally, meta information about the performance measures
26862 can be queried, e.g. what the best and worst possible performances scores
26864 (license license:lgpl3)))
26866 (define-public r-mlr3misc
26868 (name "r-mlr3misc")
26872 (uri (cran-uri "mlr3misc" version))
26875 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26876 (build-system r-build-system)
26878 `(("r-backports" ,r-backports)
26879 ("r-checkmate" ,r-checkmate)
26880 ("r-data-table" ,r-data-table)
26882 (home-page "https://mlr3misc.mlr-org.com/")
26883 (synopsis "Helper functions for mlr3")
26884 (description "@code{mlr3misc} provides frequently used helper functions
26885 and assertions used in @code{mlr3} and its companion packages. It comes with
26886 helper functions for functional programming, for printing, to work with
26887 @code{data.table}, as well as some generally useful @code{R6} classes. This
26888 package also supersedes the package @code{BBmisc}.")
26889 (license license:lgpl3)))
26891 (define-public r-paradox
26897 (uri (cran-uri "paradox" version))
26900 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
26901 (build-system r-build-system)
26903 `(("r-backports" ,r-backports)
26904 ("r-checkmate" ,r-checkmate)
26905 ("r-data-table" ,r-data-table)
26906 ("r-mlr3misc" ,r-mlr3misc)
26908 (home-page "https://paradox.mlr-org.com/")
26909 (synopsis "Define and work with parameter spaces for complex algorithms")
26910 (description "With this package it is possible to define parameter spaces,
26911 constraints and dependencies for arbitrary algorithms, and to program on such
26912 spaces. It also includes statistical designs and random samplers. Objects are
26913 implemented as @code{R6} classes.")
26914 (license license:lgpl3)))
26916 (define-public r-mlr3
26922 (uri (cran-uri "mlr3" version))
26925 "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl"))))
26926 (build-system r-build-system)
26929 ("r-backports" ,r-backports)
26930 ("r-checkmate" ,r-checkmate)
26931 ("r-data-table" ,r-data-table)
26932 ("r-digest" ,r-digest)
26933 ("r-future-apply" ,r-future-apply)
26935 ("r-mlbench" ,r-mlbench)
26936 ("r-mlr3measures" ,r-mlr3measures)
26937 ("r-mlr3misc" ,r-mlr3misc)
26938 ("r-palmerpenguins" ,r-palmerpenguins)
26939 ("r-paradox" ,r-paradox)
26940 ("r-parallelly" ,r-parallelly)
26941 ("r-uuid" ,r-uuid)))
26942 (home-page "https://mlr3.mlr-org.com/")
26943 (synopsis "Machine Learning in R - Next Generation")
26944 (description "@code{mlr3} enables efficient, object-oriented programming
26945 on the building blocks of machine learning. It provides @code{R6} objects for
26946 tasks, learners, resamplings, and measures. The package is geared towards
26947 scalability and larger datasets by supporting parallelization and out-of-memory
26948 data-backends like databases. While @code{mlr3} focuses on the core
26949 computational operations, add-on packages provide additional functionality.")
26950 (license license:lgpl3)))
26952 (define-public r-mlr3learners
26954 (name "r-mlr3learners")
26958 (uri (cran-uri "mlr3learners" version))
26961 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26962 (build-system r-build-system)
26964 `(("r-data-table" ,r-data-table)
26966 ("r-mlr3misc" ,r-mlr3misc)
26967 ("r-paradox" ,r-paradox)
26969 (home-page "https://mlr3learners.mlr-org.com/")
26970 (synopsis "Recommended Learners for @code{mlr3}")
26971 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26972 with interfaces to essential machine learning packages on CRAN. This includes,
26973 but is not limited to: (penalized) linear and logistic regression, linear and
26974 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26975 vector machines, and gradient boosting.")
26976 (license license:lgpl3)))
26978 (define-public r-bbotk
26985 (uri (cran-uri "bbotk" version))
26988 "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550"))))
26989 (properties `((upstream-name . "bbotk")))
26990 (build-system r-build-system)
26992 `(("r-checkmate" ,r-checkmate)
26993 ("r-data-table" ,r-data-table)
26995 ("r-mlr3misc" ,r-mlr3misc)
26996 ("r-paradox" ,r-paradox)
26999 `(("r-knitr" ,r-knitr)))
27000 (home-page "https://bbotk.mlr-org.com")
27001 (synopsis "Black-Box Optimization Toolkit")
27002 (description "This package provides a common framework for optimization of
27003 black-box functions for other packages, e.g. @code{mlr3}. It offers various
27004 optimization methods e.g. grid search, random search and generalized simulated
27006 (license license:lgpl3)))
27008 (define-public r-mlr3tuning
27010 (name "r-mlr3tuning")
27014 (uri (cran-uri "mlr3tuning" version))
27017 "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv"))))
27018 (build-system r-build-system)
27020 `(("r-bbotk" ,r-bbotk)
27021 ("r-checkmate" ,r-checkmate)
27022 ("r-data-table" ,r-data-table)
27025 ("r-mlr3misc" ,r-mlr3misc)
27026 ("r-paradox" ,r-paradox)
27028 (home-page "https://mlr3tuning.mlr-org.com/")
27029 (synopsis "Tuning for @code{mlr3}")
27030 (description "@code{mlr3tuning} implements methods for hyperparameter
27031 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
27032 termination criteria can be set and combined. The class @code{AutoTuner} provides a
27033 convenient way to perform nested resampling in combination with @code{mlr3}.")
27034 (license license:lgpl3)))
27036 (define-public r-fontliberation
27038 (name "r-fontliberation")
27043 (uri (cran-uri "fontLiberation" version))
27046 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
27048 `((upstream-name . "fontLiberation")))
27049 (build-system r-build-system)
27050 (home-page "https://cran.r-project.org/package=fontLiberation")
27051 (synopsis "Liberation fonts")
27053 "This package provides a placeholder for the Liberation fontset intended
27054 for the fontquiver package. This fontset covers the 12 combinations of
27055 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
27056 supported in R graphics devices.")
27057 (license license:silofl1.1)))
27059 (define-public r-fontbitstreamvera
27061 (name "r-fontbitstreamvera")
27066 (uri (cran-uri "fontBitstreamVera" version))
27069 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
27071 `((upstream-name . "fontBitstreamVera")))
27072 (build-system r-build-system)
27073 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
27074 (synopsis "Fonts for fontquiver")
27076 "This package is a placeholder for the Bitstream Vera font. It is
27077 intended for the fontquiver package.")
27079 (license:fsdg-compatible
27080 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
27081 "The Font Software may be sold as part of a larger software package but
27082 no copy of one or more of the Font Software typefaces may be sold by
27085 (define-public r-fontquiver
27087 (name "r-fontquiver")
27092 (uri (cran-uri "fontquiver" version))
27095 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
27096 (properties `((upstream-name . "fontquiver")))
27097 (build-system r-build-system)
27099 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
27100 ("r-fontliberation" ,r-fontliberation)))
27101 (home-page "https://cran.r-project.org/package=fontquiver")
27102 (synopsis "Set of installed fonts")
27104 "This package provides a set of fonts. This is useful when you want to
27105 avoid system fonts to make sure your outputs are reproducible.")
27106 (license license:gpl3)))
27108 (define-public r-freetypeharfbuzz
27110 (name "r-freetypeharfbuzz")
27115 (uri (cran-uri "freetypeharfbuzz" version))
27118 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
27120 `((upstream-name . "freetypeharfbuzz")))
27121 (build-system r-build-system)
27124 (modify-phases %standard-phases
27125 (add-after 'unpack 'prepare-static-libraries
27126 (lambda* (#:key inputs #:allow-other-keys)
27127 (mkdir-p "src/target/include")
27128 (let ((freetype (assoc-ref inputs "static-freetype"))
27129 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
27130 (substitute* "src/Makevars.in"
27131 (("include @MK_FILE@") "") ; do not build static libs
27132 (("^HB_STATIC_LIB =.*")
27133 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
27134 (("^FT_STATIC_LIB =.*")
27135 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
27136 (copy-recursively (string-append freetype "/include")
27137 "src/target/include")
27138 (copy-recursively (string-append harfbuzz "/include")
27139 "src/target/include")))))))
27141 `(("r-fontquiver" ,r-fontquiver)))
27142 ;; This may defeat the purpose of this package as our versions of freetype
27143 ;; and harfbuzz obviously differ from the tarballs offered by this
27144 ;; project. On the other hand, Guix arguably does a better job at
27145 ;; "ensur[ing] deterministic computation".
27147 `(("static-freetype"
27149 (inherit (static-package freetype))
27151 `(#:configure-flags
27152 (list "--enable-static=yes"
27157 "--without-harfbuzz")))))
27160 (inherit (static-package harfbuzz))
27162 `(#:tests? #false ; fail because shared library is disabled
27164 (list "--enable-static=yes"
27165 "--enable-shared=no"
27167 "--with-freetype=yes"
27170 "--without-fontconfig"
27171 "--without-glib")))))))
27174 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27175 (synopsis "Deterministic computation of text box metrics")
27177 "Unlike other tools that dynamically link to the Cairo stack,
27178 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27179 harfbuzz libraries. This ensures deterministic computation of text box
27180 extents for situations where reproducible results are crucial (for instance
27181 unit tests of graphics).")
27182 (license license:gpl3)))
27184 (define-public r-vdiffr
27191 (uri (cran-uri "vdiffr" version))
27194 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27197 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27198 (properties `((upstream-name . "vdiffr")))
27199 (build-system r-build-system)
27202 (modify-phases %standard-phases
27203 (add-after 'unpack 'process-javascript
27204 (lambda* (#:key inputs #:allow-other-keys)
27205 (with-directory-excursion "inst/htmlwidgets/lib/"
27206 (let ((source (assoc-ref inputs "js-jquery"))
27207 (target "jquery.min.js"))
27208 (format #true "Processing ~a --> ~a~%"
27210 (invoke "esbuild" source "--minify"
27211 (string-append "--outfile=" target)))))))))
27213 `(("freetype" ,freetype)
27214 ("harfbuzz" ,harfbuzz)))
27217 ("r-devtools" ,r-devtools)
27218 ("r-diffobj" ,r-diffobj)
27219 ("r-fontquiver" ,r-fontquiver)
27220 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27221 ("r-gdtools" ,r-gdtools)
27223 ("r-htmltools" ,r-htmltools)
27224 ("r-htmlwidgets" ,r-htmlwidgets)
27225 ("r-purrr" ,r-purrr)
27228 ("r-rlang" ,r-rlang)
27229 ("r-shiny" ,r-shiny)
27230 ("r-testthat" ,r-testthat)
27231 ("r-usethis" ,r-usethis)
27232 ("r-xml2" ,r-xml2)))
27234 `(("esbuild" ,esbuild)
27238 (uri "https://code.jquery.com/jquery-1.12.4.js")
27241 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27242 (home-page "https://github.com/r-lib/vdiffr")
27243 (synopsis "Visual regression testing and graphical diffing")
27245 "This package is an extension to the testthat package that makes it easy
27246 to add graphical unit tests. It provides a Shiny application to manage the
27248 (license license:gpl3)))
27250 (define-public r-highlight
27252 (name "r-highlight")
27257 (uri (cran-uri "highlight" version))
27260 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27261 (properties `((upstream-name . "highlight")))
27262 (build-system r-build-system)
27263 (home-page "https://github.com/hadley/highlight")
27264 (synopsis "Syntax highlighter for R code")
27266 "This package provides a syntax highlighter for R code based on the
27267 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27268 includes a custom Sweave driver performing syntax highlighting of R code
27270 (license license:gpl3+)))
27272 (define-public r-clustree
27274 (name "r-clustree")
27279 (uri (cran-uri "clustree" version))
27282 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27283 (properties `((upstream-name . "clustree")))
27284 (build-system r-build-system)
27286 `(("r-checkmate" ,r-checkmate)
27287 ("r-dplyr" ,r-dplyr)
27288 ("r-ggplot2" ,r-ggplot2)
27289 ("r-ggraph" ,r-ggraph)
27290 ("r-ggrepel" ,r-ggrepel)
27291 ("r-igraph" ,r-igraph)
27292 ("r-rlang" ,r-rlang)
27293 ("r-tidygraph" ,r-tidygraph)
27294 ("r-viridis" ,r-viridis)))
27296 `(("r-knitr" ,r-knitr)))
27297 (home-page "https://github.com/lazappi/clustree")
27298 (synopsis "Visualize clusterings at different resolutions")
27300 "Deciding what resolution to use can be a difficult question when
27301 approaching a clustering analysis. One way to approach this problem is to
27302 look at how samples move as the number of clusters increases. This package
27303 allows you to produce clustering trees, a visualization for interrogating
27304 clusterings as resolution increases.")
27305 (license license:gpl3)))
27307 (define-public r-textshaping
27309 (name "r-textshaping")
27314 (uri (cran-uri "textshaping" version))
27317 "0fqh4z505b2qriqcj70g2hhdgiawd3w2rs9rqxdwizz5vk8jjygx"))))
27318 (properties `((upstream-name . "textshaping")))
27319 (build-system r-build-system)
27321 `(("freetype" ,freetype)
27322 ("fribidi" ,fribidi)
27323 ("harfbuzz" ,harfbuzz)
27326 `(("r-cpp11" ,r-cpp11)
27327 ("r-systemfonts" ,r-systemfonts)))
27329 `(("pkg-config" ,pkg-config)
27330 ("r-knitr" ,r-knitr)))
27331 (home-page "https://github.com/r-lib/textshaping")
27332 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27334 "This package provides access to the text shaping functionality in the
27335 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27336 is a low-level utility package mainly for graphic devices that expands upon
27337 the font tool-set provided by the @code{systemfonts} package.")
27338 (license license:expat)))
27340 (define-public r-ragg
27347 (uri (cran-uri "ragg" version))
27350 "0nh1xxrxgdbq9anzkc6k3n519czp9hqyiizakm3m2gl4l4w0vp0q"))))
27351 (properties `((upstream-name . "ragg")))
27352 (build-system r-build-system)
27354 `(("freetype" ,freetype)
27355 ("libjpeg" ,libjpeg-turbo)
27357 ("libtiff" ,libtiff)
27360 `(("r-systemfonts" ,r-systemfonts)
27361 ("r-textshaping" ,r-textshaping)))
27363 `(("pkg-config" ,pkg-config)))
27364 (home-page "https://ragg.r-lib.org")
27365 (synopsis "Graphic devices based on AGG")
27367 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27368 drawing library. The ragg package provides a set of graphic devices based on
27369 AGG to use as alternative to the raster devices provided through the
27370 @code{grDevices} package.")
27371 (license license:expat)))
27373 (define-public r-downlit
27380 (uri (cran-uri "downlit" version))
27383 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27384 (properties `((upstream-name . "downlit")))
27385 (build-system r-build-system)
27387 `(("r-brio" ,r-brio)
27388 ("r-digest" ,r-digest)
27389 ("r-evaluate" ,r-evaluate)
27390 ("r-fansi" ,r-fansi)
27391 ("r-rlang" ,r-rlang)
27392 ("r-vctrs" ,r-vctrs)
27393 ("r-yaml" ,r-yaml)))
27394 (home-page "https://downlit.r-lib.org/")
27395 (synopsis "Syntax highlighting and automatic linking")
27397 "This package provides syntax highlighting of R code, specifically
27398 designed for the needs of RMarkdown packages like @code{pkgdown},
27399 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27400 to their documentation on the web, and automatic translation of ANSI escapes
27401 in output to the equivalent HTML.")
27402 (license license:expat)))
27404 (define-public r-pkgdown
27411 (uri (cran-uri "pkgdown" version))
27414 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27415 (properties `((upstream-name . "pkgdown")))
27416 (build-system r-build-system)
27417 (inputs `(("pandoc" ,pandoc)))
27419 `(("r-callr" ,r-callr)
27420 ("r-crayon" ,r-crayon)
27422 ("r-digest" ,r-digest)
27423 ("r-downlit" ,r-downlit)
27426 ("r-magrittr" ,r-magrittr)
27427 ("r-memoise" ,r-memoise)
27428 ("r-openssl" ,r-openssl)
27429 ("r-purrr" ,r-purrr)
27431 ("r-rematch2" ,r-rematch2)
27432 ("r-rlang" ,r-rlang)
27433 ("r-rmarkdown" ,r-rmarkdown)
27434 ("r-tibble" ,r-tibble)
27435 ("r-whisker" ,r-whisker)
27436 ("r-withr" ,r-withr)
27438 ("r-yaml" ,r-yaml)))
27440 `(("r-knitr" ,r-knitr)))
27441 (home-page "https://pkgdown.r-lib.org")
27442 (synopsis "Make static HTML documentation for an R package")
27444 "The goal of this package is to generate an attractive and useful website
27445 from a source package. @code{pkgdown} converts your documentation, vignettes,
27446 README file, and more to HTML making it easy to share information about your
27448 (license license:expat)))
27450 (define-public r-prereg
27457 (uri (cran-uri "prereg" version))
27460 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
27461 (properties `((upstream-name . "prereg")))
27462 (build-system r-build-system)
27464 `(("r-rmarkdown" ,r-rmarkdown)))
27465 (home-page "https://github.com/crsh/prereg")
27467 "R Markdown Templates to preregister Scientific Studies")
27469 "This package provides a collection of templates to author
27470 preregistration documents for scientific studies in PDF format.")
27471 (license license:gpl3)))
27473 (define-public r-ez
27480 (uri (cran-uri "ez" version))
27483 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
27484 (properties `((upstream-name . "ez")))
27485 (build-system r-build-system)
27488 ("r-ggplot2" ,r-ggplot2)
27491 ("r-matrix" ,r-matrix)
27494 ("r-reshape2" ,r-reshape2)
27495 ("r-scales" ,r-scales)
27496 ("r-stringr" ,r-stringr)))
27497 (home-page "https://github.com/mike-lawrence/ez")
27498 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
27500 "Facilitates easy analysis of factorial experiments, including purely
27501 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
27502 and mixed within-and-between-Ss designs. The functions in this package aim to
27503 provide simple, intuitive and consistent specification of data analysis and
27504 visualization. Visualization functions also include design visualization for
27505 pre-analysis data auditing, and correlation matrix visualization. Finally,
27506 this package includes functions for non-parametric analysis, including
27507 permutation tests and bootstrap resampling. The bootstrap function obtains
27508 predictions either by cell means or by more advanced/powerful mixed effects
27509 models, yielding predictions and confidence intervals that may be easily
27510 visualized at any level of the experiment's design.")
27511 (license license:gpl2+)))
27513 (define-public r-qdapregex
27515 (name "r-qdapregex")
27520 (uri (cran-uri "qdapRegex" version))
27523 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
27524 (properties `((upstream-name . "qdapRegex")))
27525 (build-system r-build-system)
27526 (propagated-inputs `(("r-stringi" ,r-stringi)))
27528 "https://trinker.github.com/qdapRegex/")
27530 "Regular Expression Removal, Extraction, and Replacement Tools")
27532 "This package provides a collection of regular expression tools
27533 associated with the @code{qdap} package that may be useful outside of the
27534 context of discourse analysis. Tools include removal/extraction/replacement of
27535 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
27536 percentages, citations, person tags, phone numbers, times, and zip codes.")
27537 (license license:gpl2)))
27539 (define-public r-mgsub
27546 (uri (cran-uri "mgsub" version))
27549 "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr"))))
27550 (properties `((upstream-name . "mgsub")))
27551 (build-system r-build-system)
27552 (native-inputs `(("r-knitr" ,r-knitr)))
27554 "https://cran.r-project.org/package=mgsub")
27556 "Safe, Multiple, Simultaneous String Substitution")
27558 "Designed to enable simultaneous substitution in strings in a safe
27559 fashion. Safe means it does not rely on placeholders (which can cause errors
27560 in same length matches).")
27561 (license license:expat)))
27563 (define-public r-textshape
27565 (name "r-textshape")
27570 (uri (cran-uri "textshape" version))
27573 "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
27574 (properties `((upstream-name . "textshape")))
27575 (build-system r-build-system)
27577 `(("r-data-table" ,r-data-table)
27579 ("r-stringi" ,r-stringi)))
27580 (home-page "https://github.com/trinker/textshape")
27581 (synopsis "Tools for Reshaping Text")
27583 "Tools that can be used to reshape and restructure text data.")
27584 (license license:gpl2)))
27586 (define-public r-syuzhet
27593 (uri (cran-uri "syuzhet" version))
27596 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
27597 (properties `((upstream-name . "syuzhet")))
27598 (build-system r-build-system)
27600 `(("r-dplyr" ,r-dplyr)
27603 ("r-rlang" ,r-rlang)
27604 ("r-textshape" ,r-textshape)
27605 ("r-tidyr" ,r-tidyr)
27607 (native-inputs `(("r-knitr" ,r-knitr)))
27608 (home-page "https://github.com/mjockers/syuzhet")
27610 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
27612 "Extracts sentiment and sentiment-derived plot arcs from text using a
27613 variety of sentiment dictionaries conveniently packaged for consumption by R
27614 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
27615 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
27616 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
27617 M. and Turney, Peter D. Applicable references are available in
27618 @file{README.md} and in the documentation for the @code{get_sentiment}
27619 function. The package also provides a hack for implementing Stanford's coreNLP
27620 sentiment parser. The package provides several methods for plot arc
27622 (license license:gpl3)))
27624 (define-public r-lexicon
27631 (uri (cran-uri "lexicon" version))
27634 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
27635 (properties `((upstream-name . "lexicon")))
27636 (build-system r-build-system)
27638 `(("r-data-table" ,r-data-table)
27639 ("r-syuzhet" ,r-syuzhet)))
27640 (home-page "https://github.com/trinker/lexicon")
27641 (synopsis "Lexicons for Text Analysis")
27643 "This package provides a collection of lexical hash tables, dictionaries,
27645 (license license:gpl3)))
27647 (define-public r-english
27654 (uri (cran-uri "english" version))
27657 "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1"))))
27658 (properties `((upstream-name . "english")))
27659 (build-system r-build-system)
27660 (native-inputs `(("r-knitr" ,r-knitr)))
27662 "https://cran.r-project.org/package=english")
27663 (synopsis "Translate Integers into English")
27665 "Allow numbers to be presented in an English language version, one, two,
27666 three, ... Ordinals are also available, first, second, third, ... and
27667 indefinite article choice, \"a\" or \"an\".")
27668 (license license:gpl2)))
27670 (define-public r-textclean
27672 (name "r-textclean")
27677 (uri (cran-uri "textclean" version))
27680 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
27681 (properties `((upstream-name . "textclean")))
27682 (build-system r-build-system)
27684 `(("r-data-table" ,r-data-table)
27685 ("r-english" ,r-english)
27687 ("r-lexicon" ,r-lexicon)
27688 ("r-mgsub" ,r-mgsub)
27689 ("r-qdapregex" ,r-qdapregex)
27690 ("r-stringi" ,r-stringi)
27691 ("r-textshape" ,r-textshape)))
27693 "https://github.com/trinker/textclean")
27694 (synopsis "Text Cleaning Tools")
27696 "Tools to clean and process text. Tools are geared at checking for
27697 substrings that are not optimal for analysis and replacing or removing them
27698 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
27699 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
27700 extracting them into new variables. For example, emoticons are often used in
27701 text but not always easily handled by analysis algorithms. The
27702 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
27703 (license license:gpl2)))
27705 (define-public r-striprtf
27707 (name "r-striprtf")
27712 (uri (cran-uri "striprtf" version))
27715 "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd"))))
27716 (properties `((upstream-name . "striprtf")))
27717 (build-system r-build-system)
27719 `(("r-magrittr" ,r-magrittr)
27721 ("r-stringr" ,r-stringr)))
27722 (home-page "https://github.com/kota7/striprtf")
27723 (synopsis "Extract Text from RTF File")
27725 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
27726 (license license:expat)))
27728 (define-public r-ndjson
27735 (uri (cran-uri "ndjson" version))
27738 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
27739 (modules '((guix build utils)))
27742 ;; unvendor gzstream
27743 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
27745 (properties `((upstream-name . "ndjson")))
27746 (build-system r-build-system)
27749 (modify-phases %standard-phases
27750 (add-after 'unpack 'use-system-gzstream
27751 (lambda* (#:key inputs #:allow-other-keys)
27752 (substitute* "src/Makevars"
27753 (("PKG_LIBS = " all)
27754 (string-append all "-lgzstream ")))
27756 (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream)))
27758 `(("r-data-table" ,r-data-table)
27760 ("r-tibble" ,r-tibble)))
27761 (home-page "https://gitlab.com/hrbrmstr/ndjson")
27763 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
27765 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
27766 modern ndjson files contain large numbers of records. These constructs may not
27767 be columnar in nature, but it is often useful to read in these files and
27768 \"flatten\" the structure out to enable working with the data in an R
27769 @code{data.frame}-like context. Functions are provided that make it possible
27770 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
27771 validate the format of the records or create \"flat\" @code{data.table}
27772 structures from them.")
27773 (license license:expat)))
27775 (define-public r-streamr
27782 (uri (cran-uri "streamR" version))
27785 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
27786 (properties `((upstream-name . "streamR")))
27787 (build-system r-build-system)
27789 `(("r-ndjson" ,r-ndjson)
27790 ("r-rcurl" ,r-rcurl)
27791 ("r-rjson" ,r-rjson)))
27793 "https://cran.r-project.org/package=streamR")
27795 "Access to Twitter Streaming API via R")
27797 "This package provides functions to access Twitter's filter, sample, and
27798 user streams, and to parse the output into data frames.")
27799 (license license:gpl2)))
27801 (define-public r-readods
27808 (uri (cran-uri "readODS" version))
27811 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
27812 (properties `((upstream-name . "readODS")))
27813 (build-system r-build-system)
27815 `(("r-cellranger" ,r-cellranger)
27816 ("r-readr" ,r-readr)
27817 ("r-stringi" ,r-stringi)
27818 ("r-xml2" ,r-xml2)))
27819 (native-inputs `(("r-knitr" ,r-knitr)))
27821 "https://cran.r-project.org/package=readODS")
27822 (synopsis "Read and Write ODS Files")
27824 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
27825 Also support writing data frame into ODS file.")
27826 (license license:gpl3)))
27828 (define-public r-qpdf
27835 (uri (cran-uri "qpdf" version))
27838 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
27839 (modules '((guix build utils)))
27842 ;; unvendor libqpdf
27843 (delete-file-recursively "src/libqpdf")
27844 (delete-file-recursively "src/include/qpdf")
27846 (properties `((upstream-name . "qpdf")))
27847 (build-system r-build-system)
27850 (modify-phases %standard-phases
27851 (add-after 'unpack 'configure
27853 (setenv "EXTERNAL_QPDF" "1")
27859 `(("r-askpass" ,r-askpass)
27861 ("r-rcpp" ,r-rcpp)))
27862 (native-inputs `(("pkg-config" ,pkg-config)))
27863 (home-page "https://github.com/ropensci/qpdf")
27865 "Split, Combine and Compress PDF Files")
27867 "Content-preserving transformations transformations of PDF files such as
27868 split, combine, and compress. This package interfaces directly to the
27869 @code{qpdf} C++ API and does not require any command line utilities. Note that
27870 @code{qpdf} does not read actual content from PDF files: to extract text and
27871 data you need the @code{pdftools} package.")
27872 (license license:asl2.0)))
27874 (define-public r-pdftools
27876 (name "r-pdftools")
27881 (uri (cran-uri "pdftools" version))
27884 "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx"))))
27885 (properties `((upstream-name . "pdftools")))
27886 (build-system r-build-system)
27889 ("poppler" ,poppler)))
27891 `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp)))
27892 (native-inputs `(("pkg-config" ,pkg-config)))
27894 "https://docs.ropensci.org/pdftools/")
27896 "Text Extraction, Rendering and Converting of PDF Documents")
27898 "Utilities based on @code{libpoppler} for extracting text, fonts,
27899 attachments and metadata from a PDF file. Also supports high quality rendering
27900 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
27901 further processing in R.")
27902 (license license:expat)))
27904 (define-public r-antiword
27906 (name "r-antiword")
27911 (uri (cran-uri "antiword" version))
27914 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
27915 (modules '((guix build utils)))
27918 ;; unvendor libantiword
27919 (delete-file-recursively "src")
27921 (properties `((upstream-name . "antiword")))
27922 (build-system r-build-system)
27925 (modify-phases %standard-phases
27926 (add-after 'unpack 'use-system-antiword
27927 (lambda* (#:key inputs #:allow-other-keys)
27928 (substitute* "R/antiword.R"
27929 (("system.file\\(\"bin\", package = \"antiword\"\\)")
27930 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
27932 (inputs `(("antiword" ,antiword)))
27933 (propagated-inputs `(("r-sys" ,r-sys)))
27935 "https://github.com/ropensci/antiword#readme")
27937 "Extract Text from Microsoft Word Documents")
27939 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
27940 documents. The utility only supports the old @code{doc} format, not the new
27941 xml based @code{docx} format. Use the @code{xml2} package to read the
27943 (license license:gpl2)))
27945 (define-public r-readtext
27947 (name "r-readtext")
27952 (uri (cran-uri "readtext" version))
27955 "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y"))))
27956 (properties `((upstream-name . "readtext")))
27957 (build-system r-build-system)
27959 `(("r-antiword" ,r-antiword)
27960 ("r-data-table" ,r-data-table)
27961 ("r-digest" ,r-digest)
27963 ("r-jsonlite" ,r-jsonlite)
27964 ("r-pdftools" ,r-pdftools)
27965 ("r-readods" ,r-readods)
27966 ("r-readxl" ,r-readxl)
27967 ("r-streamr" ,r-streamr)
27968 ("r-stringi" ,r-stringi)
27969 ("r-striprtf" ,r-striprtf)
27970 ("r-tibble" ,r-tibble)
27971 ("r-xml2" ,r-xml2)))
27972 (native-inputs `(("r-knitr" ,r-knitr)))
27974 "https://github.com/quanteda/readtext")
27976 "Import and Handling for Plain and Formatted Text Files")
27978 "This package provides functions for importing and handling text files
27979 and formatted text files with additional meta-data, such including @code{.csv},
27980 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
27981 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
27982 (license license:gpl3)))
27984 (define-public r-packcircles
27986 (name "r-packcircles")
27991 (uri (cran-uri "packcircles" version))
27994 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
27995 (properties `((upstream-name . "packcircles")))
27996 (build-system r-build-system)
27997 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
27998 (native-inputs `(("r-knitr" ,r-knitr)))
28000 "https://github.com/mbedward/packcircles")
28001 (synopsis "Circle Packing")
28003 "Algorithms to find arrangements of non-overlapping circles.")
28004 (license license:expat)))
28006 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
28008 (define-public r-lwgeom
28015 (uri (cran-uri "lwgeom" version))
28018 "0byhjqa2acns8mznl1ngnfygxxxyszvnq66qfg0smhhhdkwr67aa"))))
28019 (properties `((upstream-name . "lwgeom")))
28020 (build-system r-build-system)
28021 (inputs `(("geos" ,geos) ("proj" ,proj) ("sqlite" ,sqlite)))
28023 `(("r-rcpp" ,r-rcpp)
28025 ("r-units" ,r-units)))
28026 (native-inputs `(("pkg-config" ,pkg-config)))
28028 "https://github.com/r-spatial/lwgeom/")
28030 "Bindings to Selected 'liblwgeom' Functions for Simple Features")
28032 "Access to selected functions found in
28033 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
28034 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
28035 (license license:gpl2)))
28037 (define-public r-stars
28044 (uri (cran-uri "stars" version))
28047 "0ybk899rc0rpf2cv5kwk78fvis5xnr255hfcy5khdxsxdqgl0m9j"))))
28048 (properties `((upstream-name . "stars")))
28049 (build-system r-build-system)
28051 `(("r-abind" ,r-abind)
28052 ("r-classint" ,r-classint)
28053 ("r-lwgeom" ,r-lwgeom)
28054 ("r-rlang" ,r-rlang)
28056 ("r-units" ,r-units)))
28057 (native-inputs `(("r-knitr" ,r-knitr)))
28058 (home-page "https://r-spatial.github.io/stars/")
28060 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
28062 "Reading, manipulating, writing and plotting spatiotemporal arrays
28063 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
28064 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
28065 (license license:asl2.0)))
28067 (define-public r-tmaptools
28069 (name "r-tmaptools")
28074 (uri (cran-uri "tmaptools" version))
28077 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
28078 (properties `((upstream-name . "tmaptools")))
28079 (build-system r-build-system)
28081 `(("r-dichromat" ,r-dichromat)
28082 ("r-lwgeom" ,r-lwgeom)
28083 ("r-magrittr" ,r-magrittr)
28084 ("r-rcolorbrewer" ,r-rcolorbrewer)
28086 ("r-stars" ,r-stars)
28087 ("r-units" ,r-units)
28088 ("r-viridislite" ,r-viridislite)
28091 "https://github.com/mtennekes/tmaptools")
28092 (synopsis "Thematic Map Tools")
28094 "Set of tools for reading and processing spatial data. The aim is to
28095 supply the workflow to create thematic maps. This package also facilitates
28096 @code{tmap}, the package for visualizing thematic maps.")
28097 (license license:gpl3)))
28099 (define-public r-rworldmap
28101 (name "r-rworldmap")
28106 (uri (cran-uri "rworldmap" version))
28109 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
28110 (properties `((upstream-name . "rworldmap")))
28111 (build-system r-build-system)
28113 `(("r-fields" ,r-fields)
28114 ("r-maptools" ,r-maptools)
28117 "https://github.com/AndySouth/rworldmap/")
28118 (synopsis "Mapping Global Data")
28120 "Enables mapping of country level and gridded user datasets.")
28121 (license license:gpl2+)))
28123 (define-public r-rtweet
28130 (uri (cran-uri "rtweet" version))
28133 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
28134 (properties `((upstream-name . "rtweet")))
28135 (build-system r-build-system)
28137 `(("r-httpuv" ,r-httpuv)
28139 ("r-jsonlite" ,r-jsonlite)
28140 ("r-magrittr" ,r-magrittr)
28141 ("r-progress" ,r-progress)
28143 ("r-tibble" ,r-tibble)))
28144 (native-inputs `(("r-knitr" ,r-knitr)))
28146 "https://docs.ropensci.org/rtweet/")
28147 (synopsis "Collecting Twitter Data")
28149 "An implementation of calls designed to collect and organize Twitter data
28150 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
28151 Application Program Interfaces (API)}.")
28152 (license license:expat)))
28154 (define-public r-intervals
28156 (name "r-intervals")
28161 (uri (cran-uri "intervals" version))
28164 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
28165 (properties `((upstream-name . "intervals")))
28166 (build-system r-build-system)
28167 (home-page "https://github.com/edzer/intervals")
28169 "Tools for Working with Points and Intervals")
28171 "Tools for working with and comparing sets of points and intervals.")
28172 (license license:artistic2.0)))
28174 (define-public r-eyelinker
28176 (name "r-eyelinker")
28181 (uri (cran-uri "eyelinker" version))
28184 "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2"))))
28185 (properties `((upstream-name . "eyelinker")))
28186 (build-system r-build-system)
28188 `(("r-intervals" ,r-intervals)
28189 ("r-readr" ,r-readr)
28190 ("r-stringi" ,r-stringi)
28191 ("r-stringr" ,r-stringr)
28192 ("r-tibble" ,r-tibble)))
28193 (native-inputs `(("r-knitr" ,r-knitr)))
28195 "https://github.com/a-hurst/eyelinker")
28197 "Import ASC Files from EyeLink Eye Trackers")
28199 "Imports plain-text ASC data files from EyeLink eye trackers into
28200 (relatively) tidy data frames for analysis and visualization.")
28201 (license license:gpl3)))
28203 (define-public r-btm
28210 (uri (cran-uri "BTM" version))
28213 "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb"))))
28214 (properties `((upstream-name . "BTM")))
28215 (build-system r-build-system)
28216 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28217 (home-page "https://github.com/bnosac/BTM")
28218 (synopsis "Biterm Topic Models for Short Text")
28220 "Biterm Topic Models find topics in collections of short texts. It is a
28221 word co-occurrence based topic model that learns topics by modeling word-word
28222 co-occurrences patterns which are called biterms. This in contrast to
28223 traditional topic models like Latent Dirichlet Allocation and Probabilistic
28224 Latent Semantic Analysis which are word-document co-occurrence topic models. A
28225 biterm consists of two words co-occurring in the same short text window. This
28226 context window can for example be a twitter message, a short answer on a
28227 survey, a sentence of a text or a document identifier. The techniques are
28228 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
28229 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
28230 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
28232 (license license:asl2.0)))
28234 (define-public r-textplot
28236 (name "r-textplot")
28241 (uri (cran-uri "textplot" version))
28244 "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy"))))
28245 (properties `((upstream-name . "textplot")))
28246 (build-system r-build-system)
28248 `(("r-data-table" ,r-data-table)
28249 ("r-lattice" ,r-lattice)
28250 ("r-matrix" ,r-matrix)))
28251 (native-inputs `(("r-knitr" ,r-knitr)))
28252 (home-page "https://github.com/bnosac/textplot")
28253 (synopsis "Text Plots")
28255 "Visualise complex relations in texts. This is done by providing
28256 functionalities for displaying text co-occurrence networks, text correlation
28257 networks, dependency relationships as well as text clustering. Feel free to
28258 join the effort of providing interesting text visualisations.")
28259 (license license:gpl2)))
28261 (define-public r-gsa
28268 (uri (cran-uri "GSA" version))
28271 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
28272 (properties `((upstream-name . "GSA")))
28273 (build-system r-build-system)
28274 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
28275 (synopsis "Gene set analysis")
28276 (description "This package lets you determine the significance of
28277 pre-defined sets of genes with respect to an outcome variable, such as a group
28278 indicator, a quantitative variable or a survival time.")
28279 ;; Any version of the LGPL
28280 (license license:lgpl3+)))
28282 (define-public r-samr
28289 (uri (cran-uri "samr" version))
28292 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
28293 (properties `((upstream-name . "samr")))
28294 (build-system r-build-system)
28297 ("r-impute" ,r-impute)
28298 ("r-matrixstats" ,r-matrixstats)
28299 ("r-openxlsx" ,r-openxlsx)
28300 ("r-shiny" ,r-shiny)
28301 ("r-shinyfiles" ,r-shinyfiles)))
28302 (native-inputs `(("gfortran" ,gfortran)))
28303 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
28304 (synopsis "Significance analysis of Microarrays")
28306 "This is a package for significance analysis of Microarrays for
28307 differential expression analysis, RNAseq data and related problems.")
28308 ;; Any version of the LGPL
28309 (license license:lgpl3+)))