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, 2021 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021 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 "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v"))))
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 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
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 "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh"))))
938 (build-system r-build-system)
940 `(("r-callr" ,r-callr)
947 ("r-rmarkdown" ,r-rmarkdown)
948 ("r-rstudioapi" ,r-rstudioapi)
949 ("r-withr" ,r-withr)))
951 `(("r-knitr" ,r-knitr)))
952 (home-page "https://github.com/tidyverse/reprex")
953 (synopsis "Prepare reproducible R code examples for sharing")
955 "This package provides a convenience wrapper that uses the
956 @code{rmarkdown} package to render small snippets of code to target formats
957 that include both code and output. The goal is to encourage the sharing of
958 small, reproducible, and runnable examples on code-oriented websites or email.
959 @code{reprex} also extracts clean, runnable R code from various common formats,
960 such as copy/paste from an R session.")
961 (license license:expat)))
963 (define-public r-reordercluster
965 (name "r-reordercluster")
969 (uri (cran-uri "ReorderCluster" version))
972 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
973 (build-system r-build-system)
975 `(("r-gplots" ,r-gplots)
977 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
978 (synopsis "Reordering the dendrogram according to the class labels")
979 (description "This package provides tools for performing the leaf reordering
980 for the dendrogram that preserves the hierarchical clustering result and at the
981 same time tries to group instances from the same class together.")
982 (license license:gpl3+)))
984 (define-public r-callr
991 (uri (cran-uri "callr" version))
994 "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6"))))
995 (build-system r-build-system)
998 ("r-processx" ,r-processx)))
999 (home-page "https://github.com/r-lib/callr#readme")
1000 (synopsis "Call R from R")
1002 "It is sometimes useful to perform a computation in a separate R process,
1003 without affecting the current R process at all. This package does exactly
1005 (license license:expat)))
1007 (define-public r-readxl
1014 (uri (cran-uri "readxl" version))
1017 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1018 (build-system r-build-system)
1020 `(("r-cellranger" ,r-cellranger)
1021 ("r-progress" ,r-progress)
1023 ("r-tibble" ,r-tibble)))
1024 (home-page "https://readxl.tidyverse.org")
1025 (synopsis "Read Excel files")
1027 "This package lets you import Excel files into R. It supports
1028 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1029 the embedded @code{RapidXML} C++ library.")
1030 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1031 ;; 'rapidxml' which is Boost.
1032 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1034 (define-public r-modelr
1041 (uri (cran-uri "modelr" version))
1044 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1045 (build-system r-build-system)
1047 `(("r-broom" ,r-broom)
1048 ("r-magrittr" ,r-magrittr)
1049 ("r-purrr" ,r-purrr)
1050 ("r-rlang" ,r-rlang)
1051 ("r-tibble" ,r-tibble)
1052 ("r-tidyr" ,r-tidyr)
1053 ("r-tidyselect" ,r-tidyselect)
1054 ("r-vctrs" ,r-vctrs)))
1055 (home-page "https://github.com/tidyverse/modelr")
1056 (synopsis "Helper functions for modelling in pipelines")
1058 "Functions for modelling that help you seamlessly integrate modelling
1059 into a pipeline of data manipulation and visualisation.")
1060 (license license:gpl3)))
1062 (define-public r-hmm
1068 (uri (cran-uri "HMM" version))
1071 "0z0hcqfixx1l2a6d3lpy5hmh0n4gjgs0jnck441akpp3vh37glzw"))))
1072 (properties `((upstream-name . "HMM")))
1073 (build-system r-build-system)
1074 (home-page "https://cran.r-project.org/web/packages/HMM/")
1075 (synopsis "Hidden Markov Models")
1076 (description "This package provides an easy to use library to setup, apply
1077 and make inference with discrete time and discrete space hidden Markov
1079 (license license:gpl2+)))
1081 (define-public r-httpuv
1087 (uri (cran-uri "httpuv" version))
1090 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1091 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1092 ;; only contains fixes for building on Solaris.
1093 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1094 (modules '((guix build utils)))
1097 (delete-file-recursively "src/libuv")
1098 ;; Cannot unbundle http-parser, because it contains local
1101 (build-system r-build-system)
1104 (modify-phases %standard-phases
1105 (add-after 'unpack 'unbundle-libuv
1106 (lambda* (#:key outputs #:allow-other-keys)
1107 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1108 (("\"libuv/include/uv\\.h\"")
1110 ;; Fix https://github.com/rstudio/httpuv/issues/282
1111 (substitute* "src/http.cpp"
1112 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1113 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1116 `(("libuv" ,libuv)))
1119 ("r-later" ,r-later)
1120 ("r-promises" ,r-promises)
1122 ("r-rcpp" ,r-rcpp)))
1123 (home-page "https://github.com/rstudio/httpuv")
1124 (synopsis "HTTP and WebSocket server library for R")
1126 "The httpuv package provides low-level socket and protocol support for
1127 handling HTTP and WebSocket requests directly from within R. It is primarily
1128 intended as a building block for other packages, rather than making it
1129 particularly easy to create complete web applications using httpuv alone.")
1130 ;; This package includes third-party code that was originally released
1131 ;; under various non-copyleft licenses. Full licensing information can be
1132 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1133 (license license:gpl3+)))
1135 (define-public r-jsonlite
1141 (uri (cran-uri "jsonlite" version))
1144 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1145 (build-system r-build-system)
1147 `(("r-knitr" ,r-knitr)))
1148 (home-page "https://arxiv.org/abs/1403.2805")
1149 (synopsis "Robust, high performance JSON parser and generator for R")
1151 "The jsonlite package provides a fast JSON parser and generator optimized
1152 for statistical data and the web. It offers flexible, robust, high
1153 performance tools for working with JSON in R and is particularly powerful for
1154 building pipelines and interacting with a web API. In addition to converting
1155 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1156 and prettify JSON data. The unit tests included with the package verify that
1157 all edge cases are encoded and decoded consistently for use with dynamic data
1158 in systems and applications.")
1159 (license license:expat)))
1161 (define-public r-servr
1167 (uri (cran-uri "servr" version))
1170 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1171 (build-system r-build-system)
1173 `(("r-httpuv" ,r-httpuv)
1174 ("r-jsonlite" ,r-jsonlite)
1176 ("r-xfun" ,r-xfun)))
1177 (home-page "https://github.com/yihui/servr")
1178 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1180 "Servr provides an HTTP server in R to serve static files, or dynamic
1181 documents that can be converted to HTML files (e.g., R Markdown) under a given
1183 (license license:expat)))
1185 (define-public r-htmltools
1187 (name "r-htmltools")
1191 (uri (cran-uri "htmltools" version))
1194 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1195 (build-system r-build-system)
1197 `(("r-base64enc" ,r-base64enc)
1198 ("r-digest" ,r-digest)
1199 ("r-rlang" ,r-rlang)))
1200 (home-page "https://cran.r-project.org/web/packages/htmltools")
1201 (synopsis "R tools for HTML")
1203 "This package provides tools for HTML generation and output in R.")
1204 (license license:expat)))
1206 (define-public r-htmlwidgets
1208 (name "r-htmlwidgets")
1212 (uri (cran-uri "htmlwidgets" version))
1215 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1216 (build-system r-build-system)
1218 `(("r-htmltools" ,r-htmltools)
1219 ("r-jsonlite" ,r-jsonlite)
1220 ("r-yaml" ,r-yaml)))
1222 `(("r-knitr" ,r-knitr)))
1223 (home-page "https://github.com/ramnathv/htmlwidgets")
1224 (synopsis "HTML Widgets for R")
1226 "HTML widgets is a framework for creating HTML widgets that render in
1227 various contexts including the R console, R Markdown documents, and Shiny web
1229 (license license:expat)))
1231 (define-public r-htmltable
1233 (name "r-htmltable")
1238 (uri (cran-uri "htmlTable" version))
1240 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1241 (properties `((upstream-name . "htmlTable")))
1242 (build-system r-build-system)
1244 `(("r-checkmate" ,r-checkmate)
1245 ("r-htmltools" ,r-htmltools)
1246 ("r-htmlwidgets" ,r-htmlwidgets)
1247 ("r-knitr" ,r-knitr)
1248 ("r-magrittr" ,r-magrittr)
1249 ("r-rstudioapi" ,r-rstudioapi)
1250 ("r-stringr" ,r-stringr)))
1252 `(("r-knitr" ,r-knitr)))
1253 (home-page "http://gforge.se/packages/")
1254 (synopsis "Advanced tables for Markdown/HTML")
1256 "This package provides functions to build tables with advanced layout
1257 elements such as row spanners, column spanners, table spanners, zebra
1258 striping, and more. While allowing advanced layout, the underlying
1259 CSS-structure is simple in order to maximize compatibility with word
1260 processors such as LibreOffice. The package also contains a few text
1261 formatting functions that help outputting text compatible with HTML or
1263 (license license:gpl3+)))
1265 (define-public r-curl
1271 (uri (cran-uri "curl" version))
1274 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1275 (build-system r-build-system)
1278 (modify-phases %standard-phases
1279 ;; The environment variable CURL_CA_BUNDLE is only respected when
1280 ;; running Windows, so we disable the platform checks.
1281 ;; This can be removed once the libcurl has been patched.
1282 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1284 (substitute* "R/onload.R"
1285 (("if \\(!grepl\\(\"mingw\".*")
1287 (substitute* "src/handle.c"
1288 (("/\\* Only set" m)
1290 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1291 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1298 `(("pkg-config" ,pkg-config)))
1299 (home-page "https://github.com/jeroenooms/curl")
1300 (synopsis "HTTP client for R")
1302 "The @code{curl()} and @code{curl_download()} functions provide highly
1303 configurable drop-in replacements for base @code{url()} and
1304 @code{download.file()} with better performance, support for encryption, gzip
1305 compression, authentication, and other @code{libcurl} goodies. The core of
1306 the package implements a framework for performing fully customized requests
1307 where data can be processed either in memory, on disk, or streaming via the
1308 callback or connection interfaces.")
1309 (license license:expat)))
1311 (define-public r-hwriter
1318 (uri (cran-uri "hwriter" version))
1321 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1322 (build-system r-build-system)
1323 (home-page "https://cran.r-project.org/web/packages/hwriter")
1324 (synopsis "Output R objects in HTML format")
1326 "This package provides easy-to-use and versatile functions to output R
1327 objects in HTML format.")
1328 (license license:lgpl2.1+)))
1330 (define-public r-rjson
1337 (uri (cran-uri "rjson" version))
1340 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1341 (build-system r-build-system)
1342 (home-page "https://cran.r-project.org/web/packages/rjson")
1343 (synopsis "JSON library for R")
1345 "This package provides functions to convert R objects into JSON objects
1347 (license license:gpl2+)))
1349 (define-public r-fastmap
1356 (uri (cran-uri "fastmap" version))
1359 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1360 (properties `((upstream-name . "fastmap")))
1361 (build-system r-build-system)
1362 (home-page "https://r-lib.github.io/fastmap/")
1363 (synopsis "Fast implementation of a key-value store")
1365 "This package provides a fast implementation of a key-value store.
1366 Environments are commonly used as key-value stores, but every time a new key
1367 is used, it is added to R's global symbol table, causing a small amount of
1368 memory leakage. This can be problematic in cases where many different keys
1369 are used. Fastmap avoids this memory leak issue by implementing the map using
1370 data structures in C++.")
1371 (license license:expat)))
1373 (define-public r-fastghquad
1375 (name "r-fastghquad")
1380 (uri (cran-uri "fastGHQuad" version))
1383 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1384 (properties `((upstream-name . "fastGHQuad")))
1385 (build-system r-build-system)
1387 `(("r-rcpp" ,r-rcpp)))
1388 (home-page "https://github.com/awblocker/fastGHQuad")
1389 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1391 "This package implements numerically-stable Gauss-Hermite quadrature
1392 rules and utility functions for adaptive GH quadrature.")
1393 (license license:expat)))
1395 (define-public r-rstpm2
1402 (uri (cran-uri "rstpm2" version))
1405 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1406 (properties `((upstream-name . "rstpm2")))
1407 (build-system r-build-system)
1409 `(("r-bbmle" ,r-bbmle)
1411 ("r-desolve" ,r-desolve)
1412 ("r-fastghquad" ,r-fastghquad)
1415 ("r-rcpparmadillo" ,r-rcpparmadillo)
1416 ("r-survival" ,r-survival)))
1418 `(("gfortran" ,gfortran)))
1419 (home-page "https://github.com/mclements/rstpm2")
1420 (synopsis "Link-based survival models")
1422 "This package provides R implementations of @dfn{generalized survival
1423 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1424 multi-state models.")
1425 ;; One of these licenses
1426 (license (list license:gpl2 license:gpl3))))
1428 ;; This package includes minified JavaScript files. When upgrading please
1429 ;; check that there are no new minified JavaScript files.
1430 (define-public r-jquerylib
1432 (name "r-jquerylib")
1437 (uri (cran-uri "jquerylib" version))
1440 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1442 '(for-each delete-file
1443 '("inst/lib/jquery-1.12.4.min.js"
1444 "inst/lib/jquery-2.2.4.min.js"
1445 "inst/lib/jquery-3.5.1.min.js")))))
1446 (properties `((upstream-name . "jquerylib")))
1447 (build-system r-build-system)
1449 `(#:modules ((guix build utils)
1450 (guix build r-build-system)
1453 (modify-phases %standard-phases
1454 (add-after 'unpack 'process-javascript
1455 (lambda* (#:key inputs #:allow-other-keys)
1456 (with-directory-excursion "inst/lib/"
1460 `(("jquery-1.12.4.js"
1461 "jquery-1.12.4.min.js")
1463 "jquery-2.2.4.min.js")
1465 "jquery-3.5.1.min.js"))))
1466 (lambda (sources targets)
1467 (for-each (lambda (source target)
1468 (format #t "Processing ~a --> ~a~%"
1470 (invoke "esbuild" source "--minify"
1471 (string-append "--outfile=" target)))
1472 sources targets)))))))))
1474 `(("r-htmltools" ,r-htmltools)))
1476 `(("esbuild" ,esbuild)))
1477 (home-page "https://cran.r-project.org/package=jquerylib")
1478 (synopsis "Obtain jQuery as an HTML dependency object")
1480 "Obtain any major version of jQuery and use it in any webpage generated
1481 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1482 need to use this package directly, but other R packages (e.g. shiny,
1483 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1485 (license license:expat)))
1487 (define-public r-sass
1494 (uri (cran-uri "sass" version))
1497 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1498 (properties `((upstream-name . "sass")))
1499 (build-system r-build-system)
1501 `(("r-digest" ,r-digest)
1503 ("r-htmltools" ,r-htmltools)
1505 ("r-rappdirs" ,r-rappdirs)
1506 ("r-rlang" ,r-rlang)))
1507 (native-inputs `(("r-knitr" ,r-knitr)))
1508 (home-page "https://github.com/rstudio/sass")
1509 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1511 "This package provides an SCSS compiler, powered by the libsass library.
1512 With this, R developers can use variables, inheritance, and functions to
1513 generate dynamic style sheets. The package uses the Sass CSS extension
1514 language, which is stable, powerful, and CSS compatible.")
1515 (license license:expat)))
1517 ;; This package includes minified JavaScript files. When upgrading please
1518 ;; check that there are no new minified JavaScript files.
1519 (define-public r-bslib
1526 (uri (cran-uri "bslib" version))
1529 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1531 '(for-each delete-file
1532 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1533 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1534 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1535 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1536 (properties `((upstream-name . "bslib")))
1537 (build-system r-build-system)
1539 `(#:modules ((guix build utils)
1540 (guix build r-build-system)
1543 (modify-phases %standard-phases
1544 (add-after 'unpack 'process-javascript
1545 (lambda* (#:key inputs #:allow-other-keys)
1546 (with-directory-excursion "inst/lib/"
1550 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1551 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1552 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1553 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1554 ("bs-sass/assets/javascripts/bootstrap.js"
1555 "bs-sass/assets/javascripts/bootstrap.min.js")
1556 (,(assoc-ref inputs "js-bootstrap-bundle")
1557 "bs/dist/js/bootstrap.bundle.min.js"))))
1558 (lambda (sources targets)
1559 (for-each (lambda (source target)
1560 (format #t "Processing ~a --> ~a~%"
1562 (invoke "esbuild" source "--minify"
1563 (string-append "--outfile=" target)))
1564 sources targets)))))))))
1566 `(("r-digest" ,r-digest)
1567 ("r-htmltools" ,r-htmltools)
1568 ("r-jquerylib" ,r-jquerylib)
1569 ("r-jsonlite" ,r-jsonlite)
1570 ("r-magrittr" ,r-magrittr)
1571 ("r-rlang" ,r-rlang)
1572 ("r-sass" ,r-sass)))
1574 `(("esbuild" ,esbuild)
1575 ("js-bootstrap-bundle"
1578 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1581 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1582 (home-page "https://rstudio.github.io/bslib/")
1583 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1585 "This package simplifies custom CSS styling of both shiny and rmarkdown
1586 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1587 various Bootswatch themes. An interactive widget is also provided for
1588 previewing themes in real time.")
1589 (license license:expat)))
1591 ;; This package includes minified JavaScript files. When upgrading please
1592 ;; check that there are no new minified JavaScript files.
1593 (define-public r-shiny
1601 (url "https://github.com/rstudio/shiny")
1602 (commit (string-append "v" version))))
1603 (file-name (git-file-name name version))
1606 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1608 '(for-each delete-file
1609 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1610 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1611 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1612 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1613 "inst/www/shared/highlight/highlight.pack.js"
1614 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1615 "inst/www/shared/jquery.min.js"
1616 "inst/www/shared/jqueryui/jquery-ui.min.js"
1617 "inst/www/shared/legacy/jquery.min.js"
1618 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1619 "inst/www/shared/selectize/js/selectize.min.js"
1620 "inst/www/shared/shiny.min.js"
1621 "inst/www/shared/showdown/compressed/showdown.js"
1622 "inst/www/shared/strftime/strftime-min.js")))))
1623 (build-system r-build-system)
1625 `(#:modules ((guix build r-build-system)
1626 (guix build minify-build-system)
1629 #:imported-modules (,@%r-build-system-modules
1630 (guix build minify-build-system))
1632 (modify-phases (@ (guix build r-build-system) %standard-phases)
1633 (add-after 'unpack 'replace-bundled-minified-JavaScript
1634 (lambda* (#:key inputs #:allow-other-keys)
1635 (let ((replace-file (lambda (old new)
1636 (format #t "replacing ~a with ~a\n" old new)
1637 (symlink new old))))
1638 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1639 ;; contain just data. They are not minified code, so we don't
1641 (with-directory-excursion "inst/www/shared"
1642 (replace-file "strftime/strftime-min.js"
1643 (string-append (assoc-ref inputs "js-strftime")
1644 "/share/javascript/strftime.min.js"))
1645 (replace-file "highlight/highlight.pack.js"
1646 (string-append (assoc-ref inputs "js-highlight")
1647 "/share/javascript/highlight.min.js"))
1648 (replace-file "datatables/js/jquery.dataTables.min.js"
1649 (string-append (assoc-ref inputs "js-datatables")
1650 "/share/javascript/jquery.dataTables.min.js"))
1651 (replace-file "selectize/js/selectize.min.js"
1652 (string-append (assoc-ref inputs "js-selectize")
1653 "/share/javascript/selectize.min.js"))
1654 (for-each (match-lambda
1656 (minify source #:target target)))
1657 `(("jqueryui/jquery-ui.js" .
1658 "jqueryui/jquery-ui.min.js")
1659 ("datepicker/js/bootstrap-datepicker.js" .
1660 "datepicker/js/bootstrap-datepicker.min.js")
1661 ("ionrangeslider/js/ion.rangeSlider.js" .
1662 "ionrangeslider/js/ion.rangeSlider.min.js")
1663 ("bootstrap/js/bootstrap.js" .
1664 "bootstrap/js/bootstrap.min.js")
1665 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1666 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1671 ("legacy/jquery.js" .
1672 "legacy/jquery.min.js")
1673 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1674 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1675 ("showdown/src/showdown.js" .
1676 "showdown/compressed/showdown.js"))))))))))
1678 `(("r-bslib" ,r-bslib)
1679 ("r-cachem" ,r-cachem)
1680 ("r-commonmark" ,r-commonmark)
1681 ("r-crayon" ,r-crayon)
1682 ("r-digest" ,r-digest)
1683 ("r-ellipsis" ,r-ellipsis)
1684 ("r-fastmap" ,r-fastmap)
1686 ("r-htmltools" ,r-htmltools)
1687 ("r-httpuv" ,r-httpuv)
1688 ("r-jsonlite" ,r-jsonlite)
1689 ("r-later" ,r-later)
1690 ("r-lifecycle" ,r-lifecycle)
1692 ("r-promises" ,r-promises)
1694 ("r-rlang" ,r-rlang)
1695 ("r-sourcetools" ,r-sourcetools)
1696 ("r-withr" ,r-withr)
1697 ("r-xtable" ,r-xtable)))
1699 `(("js-datatables" ,js-datatables)
1700 ("js-selectize" ,js-selectize)
1701 ("js-strftime" ,js-strftime)
1702 ("js-highlight" ,js-highlight)))
1704 `(("uglify-js" ,uglify-js)
1705 ("gfortran" ,gfortran)
1706 ("js-bootstrap-accessibility"
1709 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1710 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1713 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1714 (home-page "https://shiny.rstudio.com")
1715 (synopsis "Easy interactive web applications with R")
1717 "Makes it incredibly easy to build interactive web applications
1718 with R. Automatic \"reactive\" binding between inputs and outputs and
1719 extensive prebuilt widgets make it possible to build beautiful,
1720 responsive, and powerful applications with minimal effort.")
1721 (license license:artistic2.0)))
1723 ;; This package includes minified JavaScript files. When upgrading please
1724 ;; check that there are no new minified JavaScript files.
1725 (define-public r-shinytree
1727 (name "r-shinytree")
1732 (uri (cran-uri "shinyTree" version))
1735 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1736 (modules '((guix build utils)))
1739 ;; Delete minified JavaScript
1740 (for-each delete-file
1741 '("inst/www/jsTree-3.3.7/libs/require.js"
1742 "inst/www/jsTree-3.3.7/libs/jquery.js"
1743 "inst/www/jsTree-3.3.7/jstree.min.js"))
1745 (properties `((upstream-name . "shinyTree")))
1746 (build-system r-build-system)
1748 `(#:modules ((guix build utils)
1749 (guix build r-build-system)
1753 (modify-phases %standard-phases
1754 (add-after 'unpack 'replace-minified-javascript
1755 (lambda* (#:key inputs #:allow-other-keys)
1756 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1757 (symlink (string-append (assoc-ref inputs "js-requirejs")
1758 "/share/javascript/require.min.js")
1763 `((,(assoc-ref inputs "js-jquery")
1767 (lambda (sources targets)
1768 (for-each (lambda (source target)
1769 (format #t "Processing ~a --> ~a~%"
1771 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1772 (call-with-output-file target
1774 (dump-port minified port)))))
1778 `(("r-htmlwidgets" ,r-htmlwidgets)
1779 ("r-jsonlite" ,r-jsonlite)
1780 ("r-promises" ,r-promises)
1781 ("r-shiny" ,r-shiny)
1782 ("r-stringr" ,r-stringr)))
1784 `(("js-requirejs" ,js-requirejs)))
1786 `(("uglify-js" ,uglify-js)
1790 (uri "https://code.jquery.com/jquery-3.3.1.js")
1793 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1794 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1795 (synopsis "jsTree bindings for Shiny")
1797 "This package exposes R bindings to jsTree, a JavaScript library that
1798 supports interactive trees, to enable rich, editable trees in Shiny.")
1799 (license license:expat)))
1801 (define-public r-shinydashboard
1803 (name "r-shinydashboard")
1807 (uri (cran-uri "shinydashboard" version))
1810 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1811 (build-system r-build-system)
1812 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1813 ;; Regenerate it from the included sources.
1815 `(#:modules ((guix build utils)
1816 (guix build r-build-system)
1819 (modify-phases %standard-phases
1820 (add-after 'unpack 'generate-minified-javascript
1822 (with-directory-excursion "inst/AdminLTE"
1823 (delete-file "app.min.js")
1824 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1825 (call-with-output-file "app.min.js"
1827 (dump-port minified port))))))))))
1829 `(("r-htmltools" ,r-htmltools)
1830 ("r-promises" ,r-promises)
1831 ("r-shiny" ,r-shiny)))
1833 `(("uglify-js" ,uglify-js)))
1834 (home-page "https://rstudio.github.io/shinydashboard/")
1835 (synopsis "Create dashboards with shiny")
1836 (description "This package provides an extension to the Shiny web
1837 application framework for R, making it easy to create attractive dashboards.")
1838 ;; This package includes software that was released under the Expat
1839 ;; license, but the whole package is released under GPL version 2 or
1841 (license license:gpl2+)))
1843 (define-public r-shinyfiles
1845 (name "r-shinyfiles")
1850 (uri (cran-uri "shinyFiles" version))
1852 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1853 (properties `((upstream-name . "shinyFiles")))
1854 (build-system r-build-system)
1857 ("r-htmltools" ,r-htmltools)
1858 ("r-jsonlite" ,r-jsonlite)
1859 ("r-shiny" ,r-shiny)
1860 ("r-tibble" ,r-tibble)))
1861 (home-page "https://github.com/thomasp85/shinyFiles")
1862 (synopsis "Server-side file system viewer for Shiny")
1864 "This package provides functionality for client-side navigation of the
1865 server side file system in shiny apps. In case the app is running locally
1866 this gives the user direct access to the file system without the need to
1867 \"download\" files to a temporary location. Both file and folder selection as
1868 well as file saving is available.")
1869 (license license:gpl2+)))
1871 (define-public r-shinythemes
1873 (name "r-shinythemes")
1878 (uri (cran-uri "shinythemes" version))
1881 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1882 (properties `((upstream-name . "shinythemes")))
1883 (build-system r-build-system)
1884 (propagated-inputs `(("r-shiny" ,r-shiny)))
1885 (home-page "https://rstudio.github.io/shinythemes/")
1886 (synopsis "Themes for Shiny")
1888 "This package provides themes for use with Shiny. It includes several
1889 Bootstrap themes, which are packaged for use with Shiny applications.")
1890 ;; The package is released under version 3 of the GPL, but it includes
1891 ;; source files that are covered by the Expat license. It also includes
1892 ;; fonts under SIL or the ASL.
1893 (license (list license:gpl3 license:expat
1894 license:silofl1.1 license:asl2.0))))
1896 ;; The package sources include minified variants of d3.js and non-minified
1897 ;; source code of d3-jetpack.
1898 (define-public r-d3r
1905 (uri (cran-uri "d3r" version))
1908 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1909 (build-system r-build-system)
1911 `(#:modules ((guix build utils)
1912 (guix build r-build-system)
1915 (modify-phases %standard-phases
1916 (add-after 'unpack 'process-javascript
1917 (lambda* (#:key inputs #:allow-other-keys)
1918 (with-directory-excursion "inst/www/d3/"
1922 `((,(assoc-ref inputs "d3.v3.js")
1923 "v3/dist/d3.min.js")
1924 (,(assoc-ref inputs "d3.v4.js")
1925 "v4/dist/d3.min.js")
1926 (,(assoc-ref inputs "d3.v5.js")
1927 "v5/dist/d3.min.js")
1928 (,(assoc-ref inputs "d3.v6.js")
1929 "v6/dist/d3.min.js"))))
1930 (lambda (sources targets)
1931 (for-each (lambda (source target)
1932 (format #t "Processing ~a --> ~a~%"
1934 (delete-file target)
1935 (invoke "esbuild" source "--minify"
1936 (string-append "--outfile=" target)))
1940 `(("r-dplyr" ,r-dplyr)
1941 ("r-htmltools" ,r-htmltools)
1942 ("r-rlang" ,r-rlang)
1943 ("r-tidyr" ,r-tidyr)))
1945 `(("esbuild" ,esbuild)
1949 (uri "https://d3js.org/d3.v3.js")
1952 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1956 (uri "https://d3js.org/d3.v4.js")
1959 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1963 (uri "https://d3js.org/d3.v5.js")
1966 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1970 (uri "https://d3js.org/d3.v6.js")
1973 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1974 (home-page "https://github.com/timelyportfolio/d3r")
1975 (synopsis "d3.js utilities for R")
1977 "This package provides a suite of functions to help ease the use of the
1978 d3.js visualization library in R. These helpers include
1979 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1980 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1981 R objects into the JSON format that the d3.js library expects.")
1982 (license license:bsd-3)))
1984 ;; We use the latest commit here because the last release was in 2016 while
1985 ;; the latest commit was in 2018.
1986 (define-public r-sankeyd3
1987 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1991 (version (git-version "0.3.2" revision commit))
1996 (url "https://github.com/fbreitwieser/sankeyD3")
1998 (file-name (git-file-name name version))
2001 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2002 (build-system r-build-system)
2005 ("r-htmlwidgets" ,r-htmlwidgets)
2006 ("r-shiny" ,r-shiny)
2007 ("r-magrittr" ,r-magrittr)))
2008 (home-page "https://github.com/fbreitwieser/sankeyD3")
2009 (synopsis "Sankey network graphs from R")
2011 "This package provides an R library to generate Sankey network graphs
2012 in R and Shiny via the D3 visualization library.")
2013 ;; The R code is licensed under GPLv3+. It includes the non-minified
2014 ;; JavaScript source code of d3-sankey, which is released under the
2015 ;; 3-clause BSD license.
2016 (license (list license:gpl3+ license:bsd-3)))))
2018 (define-public r-wesanderson
2020 (name "r-wesanderson")
2025 (uri (cran-uri "wesanderson" version))
2028 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2029 (properties `((upstream-name . "wesanderson")))
2030 (build-system r-build-system)
2031 (home-page "https://github.com/karthik/wesanderson")
2032 (synopsis "Wes Anderson color palette generator")
2034 "This package provides color palettes that have been generated mostly
2035 from Wes Anderson movies.")
2036 (license license:expat)))
2038 (define-public r-gg-gap
2045 (uri (cran-uri "gg.gap" version))
2048 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2049 (properties `((upstream-name . "gg.gap")))
2050 (build-system r-build-system)
2052 `(("r-cowplot" ,r-cowplot)
2053 ("r-ggplot2" ,r-ggplot2)))
2054 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2055 (synopsis "Define segments on the y-axis for ggplot2")
2057 "The @code{gg.gap} function enables you to define segments for the y-axis
2058 in a ggplot2 plot.")
2059 (license license:gpl3)))
2061 (define-public r-tablerdash
2063 (name "r-tablerdash")
2068 (uri (cran-uri "tablerDash" version))
2071 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2074 ;; Delete minified JavaScript
2075 (for-each delete-file
2076 '("inst/tablerDash-0.1.0/require.min.js"
2077 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2079 (properties `((upstream-name . "tablerDash")))
2080 (build-system r-build-system)
2082 `(#:modules ((guix build utils)
2083 (guix build r-build-system)
2086 (modify-phases %standard-phases
2087 (add-after 'unpack 'process-javascript
2088 (lambda* (#:key inputs #:allow-other-keys)
2089 (with-directory-excursion "inst"
2093 `((,(assoc-ref inputs "js-requirejs")
2094 "tablerDash-0.1.0/require.min.js")
2095 (,(assoc-ref inputs "js-bootstrap")
2096 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2097 (lambda (sources targets)
2098 (for-each (lambda (source target)
2099 (format #t "Processing ~a --> ~a~%"
2101 (invoke "esbuild" source "--minify"
2102 (string-append "--outfile=" target)))
2106 `(("r-htmltools" ,r-htmltools)
2107 ("r-knitr" ,r-knitr)
2108 ("r-shiny" ,r-shiny)))
2110 `(("esbuild" ,esbuild)
2114 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2117 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2121 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2122 v4.0.0/dist/js/bootstrap.bundle.js")
2125 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2126 (home-page "https://rinterface.github.io/tablerDash/")
2127 (synopsis "Tabler API for Shiny")
2129 "This package provides an R interface to the
2130 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2131 4 dashboard template. There are different layouts available such as a one
2132 page dashboard or a multi-page template, where the navigation menu is
2133 contained in the navigation bar.")
2134 (license license:gpl2+)))
2136 (define-public r-spelling
2143 (uri (cran-uri "spelling" version))
2146 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2147 (properties `((upstream-name . "spelling")))
2148 (build-system r-build-system)
2150 `(("r-commonmark" ,r-commonmark)
2151 ("r-hunspell" ,r-hunspell)
2152 ("r-knitr" ,r-knitr)
2153 ("r-xml2" ,r-xml2)))
2154 (home-page "https://docs.ropensci.org/spelling/")
2155 (synopsis "Tools for spell checking in R")
2157 "This is an R package for spell checking common document formats
2158 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2159 utilities to automate checking of documentation and vignettes as a unit test
2160 during @code{R CMD check}. Both British and American English are supported
2161 out of the box and other languages can be added. In addition, packages may
2162 define a wordlist to allow custom terminology without having to abuse
2164 (license license:expat)))
2166 (define-public r-crosstalk
2168 (name "r-crosstalk")
2173 (uri (cran-uri "crosstalk" version))
2176 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2177 (build-system r-build-system)
2179 `(("r-htmltools" ,r-htmltools)
2180 ("r-jsonlite" ,r-jsonlite)
2181 ("r-lazyeval" ,r-lazyeval)
2183 (home-page "https://rstudio.github.io/crosstalk/")
2184 (synopsis "Inter-widget interactivity for HTML widgets")
2186 "This package provides building blocks for allowing HTML widgets to
2187 communicate with each other, with Shiny or without (i.e. static @code{.html}
2188 files). It currently supports linked brushing and filtering.")
2189 (license license:expat)))
2191 (define-public r-rook
2198 (uri (cran-uri "Rook" version))
2201 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2202 (properties `((upstream-name . "Rook")))
2203 (build-system r-build-system)
2204 (propagated-inputs `(("r-brew" ,r-brew)))
2205 (home-page "https://cran.r-project.org/web/packages/Rook")
2206 (synopsis "Web server interface for R")
2208 "This package contains the Rook specification and convenience software
2209 for building and running Rook applications. A Rook application is an R
2210 reference class object that implements a @code{call} method or an R closure
2211 that takes exactly one argument, an environment, and returns a list with three
2212 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2213 (license license:gpl2)))
2215 (define-public r-miniui
2222 (uri (cran-uri "miniUI" version))
2225 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2226 (properties `((upstream-name . "miniUI")))
2227 (build-system r-build-system)
2229 `(("r-htmltools" ,r-htmltools)
2230 ("r-shiny" ,r-shiny)))
2231 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2232 (synopsis "Shiny UI widgets for small screens")
2234 "This package provides UI widget and layout functions for writing Shiny apps that
2235 work well on small screens.")
2236 (license license:gpl3)))
2238 (define-public r-feather
2245 (uri (cran-uri "feather" version))
2248 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2249 (build-system r-build-system)
2253 ("r-tibble" ,r-tibble)))
2254 (home-page "https://github.com/wesm/feather")
2255 (synopsis "R Bindings to the Feather API")
2256 (description "Read and write feather files, a lightweight binary columnar
2257 data store designed for maximum speed.")
2258 (license license:asl2.0)))
2260 (define-public r-maps
2267 (uri (cran-uri "maps" version))
2270 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2271 (build-system r-build-system)
2272 (home-page "https://cran.r-project.org/web/packages/maps")
2273 (synopsis "Draw geographical maps")
2274 (description "This package provides an R module for display of maps.
2275 Projection code and larger maps are in separate packages (@code{mapproj} and
2277 (license license:gpl2)))
2279 (define-public r-mapproj
2286 (uri (cran-uri "mapproj" version))
2289 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2290 (build-system r-build-system)
2291 (propagated-inputs `(("r-maps" ,r-maps)))
2292 (home-page "https://cran.r-project.org/web/packages/mapproj")
2293 (synopsis "Map projection in R")
2294 (description "This package converts latitude/longitude into projected
2296 (license (list license:gpl2 ; The R interface
2297 (license:non-copyleft ; The C code
2298 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2299 "Lucent Public License Version 1.02")))))
2301 (define-public r-rgooglemaps
2303 (name "r-rgooglemaps")
2308 (uri (cran-uri "RgoogleMaps" version))
2311 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2312 (properties `((upstream-name . "RgoogleMaps")))
2313 (build-system r-build-system)
2317 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2318 (synopsis "Use Google Maps in R")
2319 (description "This package serves two purposes:
2321 @item Provide a comfortable R interface to query the Google server for static
2323 @item Use the map as a background image to overlay plots within R. This
2324 requires proper coordinate scaling.
2326 (license license:gpl2+)))
2328 (define-public r-geosphere
2330 (name "r-geosphere")
2335 (uri (cran-uri "geosphere" version))
2338 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2339 (build-system r-build-system)
2340 (propagated-inputs `(("r-sp" ,r-sp)))
2341 (home-page "https://cran.r-project.org/web/packages/geosphere")
2342 (synopsis "Spherical trigonometry")
2343 (description "This package computes spherical trigonometry for geographic
2344 applications. That is, compute distances and related measures for angular
2345 (longitude/latitude) locations.")
2346 (license license:gpl3+)))
2348 (define-public r-jpeg
2355 (uri (cran-uri "jpeg" version))
2358 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2359 (build-system r-build-system)
2360 (inputs `(("libjpeg" ,libjpeg-turbo)))
2361 (home-page "https://www.rforge.net/jpeg/")
2362 (synopsis "Read and write JPEG images with R")
2363 (description "This package provides a way to read, write and display
2364 bitmap images stored in the JPEG format with R. It can read and write both
2365 files and in-memory raw vectors.")
2366 (license license:gpl2+)))
2368 (define-public r-ggmap
2375 (uri (cran-uri "ggmap" version))
2378 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2379 (build-system r-build-system)
2381 `(("r-bitops" ,r-bitops)
2382 ("r-digest" ,r-digest)
2383 ("r-dplyr" ,r-dplyr)
2384 ("r-ggplot2" ,r-ggplot2)
2388 ("r-magrittr" ,r-magrittr)
2391 ("r-purrr" ,r-purrr)
2392 ("r-rgooglemaps" ,r-rgooglemaps)
2393 ("r-rjson" ,r-rjson)
2394 ("r-scales" ,r-scales)
2395 ("r-stringr" ,r-stringr)
2396 ("r-tibble" ,r-tibble)
2397 ("r-tidyr" ,r-tidyr)))
2398 (home-page "https://github.com/dkahle/ggmap")
2399 (synopsis "Spatial visualization with ggplot2")
2400 (description "This package provides a collection of functions to visualize
2401 spatial data and models on top of static maps from various online sources (e.g
2402 Google Maps and Stamen Maps). It includes tools common to those tasks,
2403 including functions for geolocation and routing.")
2404 (license license:gpl2)))
2406 (define-public r-haven
2413 (uri (cran-uri "haven" version))
2416 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2417 (modules '((guix build utils)))
2420 ;; unvendor readstat
2421 (delete-file-recursively "src/readstat")
2423 (build-system r-build-system)
2426 (modify-phases %standard-phases
2427 (add-after 'unpack 'unbundle-readstat
2429 ;; Not required, since we’re not building readstat.
2430 (substitute* "src/Makevars"
2431 (("-lz") "-lreadstat"))
2434 `(("readstat" ,readstat)))
2436 `(("r-knitr" ,r-knitr)))
2438 `(("r-forcats" ,r-forcats)
2441 ("r-rlang" ,r-rlang)
2442 ("r-readr" ,r-readr)
2443 ("r-tibble" ,r-tibble)
2444 ("r-tidyselect" ,r-tidyselect)
2445 ("r-vctrs" ,r-vctrs)))
2446 (home-page "https://haven.tidyverse.org")
2447 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2449 "This package lets you mport foreign statistical formats into R via the
2450 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2451 (license license:expat)))
2453 (define-public r-amap
2459 (uri (cran-uri "amap" version))
2462 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2463 (build-system r-build-system)
2465 `(("gfortran" ,gfortran)))
2466 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2467 (synopsis "Another multidimensional analysis package")
2468 (description "This package provides tools for clustering and principal
2469 component analysis (with robust methods, and parallelized functions).")
2470 (license license:gpl2+)))
2472 (define-public r-ape
2479 (uri (cran-uri "ape" version))
2482 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2483 (build-system r-build-system)
2485 `(("r-lattice" ,r-lattice)
2487 ("r-rcpp" ,r-rcpp)))
2488 (home-page "http://ape-package.ird.fr/")
2489 (synopsis "Analyses of phylogenetics and evolution")
2491 "This package provides functions for reading, writing, plotting, and
2492 manipulating phylogenetic trees, analyses of comparative data in a
2493 phylogenetic framework, ancestral character analyses, analyses of
2494 diversification and macroevolution, computing distances from DNA sequences,
2495 and several other tools.")
2496 (license license:gpl2+)))
2498 (define-public r-abbyyr
2505 (uri (cran-uri "abbyyR" version))
2508 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2509 (properties `((upstream-name . "abbyyR")))
2510 (build-system r-build-system)
2512 `(("r-curl" ,r-curl)
2515 ("r-progress" ,r-progress)
2516 ("r-readr" ,r-readr)
2518 (home-page "https://github.com/soodoku/abbyyR")
2519 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2521 "This package provides tools to get text from images of text using Abbyy
2522 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2523 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2524 passports and get the results in a variety of formats including plain text and
2525 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2526 (license license:expat)))
2528 (define-public r-colorspace
2530 (name "r-colorspace")
2535 (uri (cran-uri "colorspace" version))
2537 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2538 (build-system r-build-system)
2540 `(("r-knitr" ,r-knitr)))
2541 (home-page "https://cran.r-project.org/web/packages/colorspace")
2542 (synopsis "Color space manipulation")
2544 "This package carries out a mapping between assorted color spaces
2545 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2546 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2547 colors are provided.")
2548 (license license:bsd-3)))
2550 (define-public r-glue
2557 (uri (cran-uri "glue" version))
2560 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2561 (build-system r-build-system)
2562 ;; knitr depends on glue, so we can't add knitr here to build the
2566 `(("r-knitr" ,r-knitr)))
2567 (home-page "https://github.com/tidyverse/glue")
2568 (synopsis "Interpreted string literals")
2570 "This package provides an implementation of interpreted string literals,
2571 inspired by Python's Literal String Interpolation (PEP-0498) and
2572 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2573 (license license:expat)))
2575 (define-public r-palmerpenguins
2577 (name "r-palmerpenguins")
2582 (uri (cran-uri "palmerpenguins" version))
2585 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2587 `((upstream-name . "palmerpenguins")))
2588 (build-system r-build-system)
2589 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2590 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2592 "This package includes size measurements, clutch observations, and blood
2593 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2594 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2595 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2596 Station Long Term Ecological Research (LTER) Program.")
2597 (license license:cc0)))
2599 (define-public r-pastecs
2605 (uri (cran-uri "pastecs" version))
2608 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2609 (build-system r-build-system)
2611 `(("r-boot" ,r-boot)))
2612 (home-page "https://github.com/phgrosjean/pastecs")
2613 (synopsis "Analysis of space-time ecological series")
2615 "This package provides functions for regulation, decomposition and analysis
2616 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2617 initiative to bring PASSTEC 2000 functionalities to R.")
2618 (license license:gpl2+)))
2620 (define-public r-partykit
2626 (uri (cran-uri "partykit" version))
2629 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2630 (build-system r-build-system)
2632 `(("r-formula" ,r-formula)
2634 ("r-libcoin" ,r-libcoin)
2635 ("r-mvtnorm" ,r-mvtnorm)
2636 ("r-rpart" ,r-rpart)
2637 ("r-survival" ,r-survival)))
2638 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2639 (synopsis "Toolkit for recursive partytioning")
2641 "This package provides a toolkit with infrastructure for representing,
2642 summarizing, and visualizing tree-structured regression and classification
2644 (license license:gpl2+)))
2646 (define-public r-plogr
2653 (uri (cran-uri "plogr" version))
2656 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2657 (build-system r-build-system)
2658 (home-page "https://github.com/krlmlr/plogr")
2659 (synopsis "R bindings for the plog C++ logging library")
2661 "This package provides the header files for a stripped-down version of
2662 the plog header-only C++ logging library, and a method to log to R's standard
2664 (license license:expat)))
2666 (define-public r-pls
2673 (uri (cran-uri "pls" version))
2675 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2676 (build-system r-build-system)
2677 (home-page "https://mevik.net/work/software/pls.html")
2678 (synopsis "Partial Least Squares and Principal Component Regression")
2680 "The pls package implements multivariate regression methods: Partial Least
2681 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2682 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2685 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2686 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2687 @item multi-response models (or @dfn{PLS2})
2688 @item flexible cross-validation
2689 @item Jackknife variance estimates of regression coefficients
2690 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2691 (R)MSEP, R², and correlation loadings
2692 @item formula interface, modelled after @code{lm()}, with methods for predict,
2693 print, summary, plot, update, etc.
2694 @item extraction functions for coefficients, scores, and loadings
2695 @item MSEP, RMSEP, and R² estimates
2696 @item multiplicative scatter correction (@dfn{MSC})
2698 (license license:gpl2)))
2707 (uri (cran-uri "ps" version))
2709 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2710 (build-system r-build-system)
2711 (home-page "https://ps.r-lib.org")
2712 (synopsis "List, query, and manipulate system processes")
2714 "The ps package implements an API to list, query, and manipulate system
2715 processes. Most of its code is based on the @code{psutil} Python package.")
2716 (license license:bsd-3)))
2718 (define-public r-pkgbuild
2725 (uri (cran-uri "pkgbuild" version))
2727 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2728 (build-system r-build-system)
2730 `(("r-callr" ,r-callr)
2732 ("r-crayon" ,r-crayon)
2734 ("r-prettyunits" ,r-prettyunits)
2736 ("r-rprojroot" ,r-rprojroot)
2737 ("r-withr" ,r-withr)))
2738 (home-page "https://github.com/r-pkgs/pkgbuild")
2739 (synopsis "Find tools needed to build R packages")
2741 "This package provides functions used to build R packages. It locates
2742 compilers needed to build R packages on various platforms and ensures the PATH
2743 is configured appropriately so R can use them.")
2744 (license license:gpl3)))
2746 (define-public r-pkgload
2753 (uri (cran-uri "pkgload" version))
2756 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2757 (build-system r-build-system)
2760 ("r-crayon" ,r-crayon)
2762 ("r-pkgbuild" ,r-pkgbuild)
2763 ("r-rlang" ,r-rlang)
2764 ("r-rprojroot" ,r-rprojroot)
2765 ("r-rstudioapi" ,r-rstudioapi)
2766 ("r-withr" ,r-withr)))
2767 (home-page "https://github.com/r-lib/pkgload")
2768 (synopsis "Simulate package installation and attach")
2770 "This package simulates the process of installing a package and then
2771 attaching it. This is a key part of the @code{devtools} package as it allows
2772 you to rapidly iterate while developing a package.")
2773 (license license:gpl3)))
2775 (define-public r-rcpp
2782 (uri (cran-uri "Rcpp" version))
2784 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2785 (build-system r-build-system)
2786 (home-page "http://www.rcpp.org")
2787 (synopsis "Seamless R and C++ integration")
2789 "The Rcpp package provides R functions as well as C++ classes which offer
2790 a seamless integration of R and C++. Many R data types and objects can be
2791 mapped back and forth to C++ equivalents which facilitates both writing of new
2792 code as well as easier integration of third-party libraries. Documentation
2793 about Rcpp is provided by several vignettes included in this package, via the
2794 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2795 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2796 @code{citation(\"Rcpp\")} for details on these last two.")
2797 (license license:gpl2+)))
2799 (define-public r-rcppthread
2801 (name "r-rcppthread")
2806 (uri (cran-uri "RcppThread" version))
2809 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2810 (properties `((upstream-name . "RcppThread")))
2811 (build-system r-build-system)
2813 "https://github.com/tnagler/RcppThread")
2814 (synopsis "R threading in C++")
2816 "This package provides a C++11-style thread class and thread pool that can
2817 safely be interrupted from R.")
2818 (license license:expat)))
2820 (define-public r-bindr
2827 (uri (cran-uri "bindr" version))
2830 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2831 (build-system r-build-system)
2832 (home-page "https://github.com/krlmlr/bindr")
2833 (synopsis "Parametrized active bindings")
2835 "This package provides a simple interface for creating active bindings
2836 where the bound function accepts additional arguments.")
2837 (license license:expat)))
2839 (define-public r-bindrcpp
2846 (uri (cran-uri "bindrcpp" version))
2849 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2850 (build-system r-build-system)
2852 `(("r-bindr" ,r-bindr)
2853 ("r-plogr" ,r-plogr)
2854 ("r-rcpp" ,r-rcpp)))
2855 (home-page "https://github.com/krlmlr/bindrcpp")
2856 (synopsis "Rcpp interface to active bindings")
2858 "This package provides an easy way to fill an environment with active
2859 bindings that call a C++ function.")
2860 (license license:expat)))
2862 (define-public r-auc
2869 (uri (cran-uri "AUC" version))
2872 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2873 (properties `((upstream-name . "AUC")))
2874 (build-system r-build-system)
2875 (home-page "https://cran.r-project.org/web/packages/AUC")
2876 (synopsis "Compute the area under the curve of selected measures")
2878 "This package includes functions to compute the area under the curve of
2879 selected measures: the area under the sensitivity curve (AUSEC), the area
2880 under the specificity curve (AUSPC), the area under the accuracy
2881 curve (AUACC), and the area under the receiver operating characteristic
2882 curve (AUROC). The curves can also be visualized. Support for partial areas
2884 (license license:gpl2+)))
2886 (define-public r-calibrate
2888 (name "r-calibrate")
2893 (uri (cran-uri "calibrate" version))
2895 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2896 (build-system r-build-system)
2898 `(("r-mass" ,r-mass)))
2899 (home-page "https://cran.r-project.org/web/packages/calibrate")
2900 (synopsis "Calibration of scatterplot and biplot axes")
2902 "This is a package for drawing calibrated scales with tick marks
2903 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2904 (license license:gpl2)))
2906 (define-public r-shape
2913 (uri (cran-uri "shape" version))
2916 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2917 (build-system r-build-system)
2918 (home-page "https://cran.r-project.org/web/packages/shape")
2919 (synopsis "Functions for plotting graphical shapes")
2921 "This package provides functions for plotting graphical shapes such as
2922 ellipses, circles, cylinders, arrows, ...")
2923 (license license:gpl3+)))
2925 (define-public r-globaloptions
2927 (name "r-globaloptions")
2932 (uri (cran-uri "GlobalOptions" version))
2934 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2935 (properties `((upstream-name . "GlobalOptions")))
2936 (build-system r-build-system)
2938 `(("r-knitr" ,r-knitr)))
2939 (home-page "https://github.com/jokergoo/GlobalOptions")
2940 (synopsis "Generate functions to get or set global options")
2942 "This package provides more controls on the option values such as
2943 validation and filtering on the values, making options invisible or private.")
2944 (license license:gpl2+)))
2946 (define-public r-circlize
2953 (uri (cran-uri "circlize" version))
2956 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2957 (build-system r-build-system)
2959 `(("r-colorspace" ,r-colorspace)
2960 ("r-globaloptions" ,r-globaloptions)
2961 ("r-shape" ,r-shape)))
2963 `(("r-knitr" ,r-knitr)))
2964 (home-page "https://github.com/jokergoo/circlize")
2965 (synopsis "Circular visualization")
2967 "Circular layout is an efficient way to visualise huge amounts of
2968 information. This package provides an implementation of circular layout
2969 generation in R as well as an enhancement of available software. Its
2970 flexibility is based on the usage of low-level graphics functions such that
2971 self-defined high-level graphics can be easily implemented by users for
2972 specific purposes. Together with the seamless connection between the powerful
2973 computational and visual environment in R, it gives users more convenience and
2974 freedom to design figures for better understanding complex patterns behind
2975 multi-dimensional data.")
2976 (license license:gpl2+)))
2978 (define-public r-powerlaw
2985 (uri (cran-uri "poweRlaw" version))
2987 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2988 (properties `((upstream-name . "poweRlaw")))
2989 (build-system r-build-system)
2991 `(("r-pracma" ,r-pracma)))
2993 `(("r-knitr" ,r-knitr)))
2994 (home-page "https://github.com/csgillespie/poweRlaw")
2995 (synopsis "Tools for the analysis of heavy tailed distributions")
2997 "This package provides an implementation of maximum likelihood estimators
2998 for a variety of heavy tailed distributions, including both the discrete and
2999 continuous power law distributions. Additionally, a goodness-of-fit based
3000 approach is used to estimate the lower cut-off for the scaling region.")
3001 ;; Any of these GPL versions.
3002 (license (list license:gpl2 license:gpl3))))
3004 (define-public r-compare
3011 (uri (cran-uri "compare" version))
3014 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3015 (build-system r-build-system)
3016 (home-page "https://cran.r-project.org/web/packages/compare")
3017 (synopsis "Comparing objects for differences")
3019 "This package provides functions to compare a model object to a
3020 comparison object. If the objects are not identical, the functions can be
3021 instructed to explore various modifications of the objects (e.g., sorting
3022 rows, dropping names) to see if the modified versions are identical.")
3023 (license license:gpl2+)))
3025 (define-public r-dendextend
3027 (name "r-dendextend")
3032 (uri (cran-uri "dendextend" version))
3035 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3036 (build-system r-build-system)
3038 `(("r-ggplot2" ,r-ggplot2)
3039 ("r-magrittr" ,r-magrittr)
3040 ("r-viridis" ,r-viridis)))
3042 `(("r-knitr" ,r-knitr)))
3043 (home-page "https://cran.r-project.org/web/packages/dendextend")
3044 (synopsis "Extending 'dendrogram' functionality in R")
3046 "This package offers a set of functions for extending @code{dendrogram}
3047 objects in R, letting you visualize and compare trees of hierarchical
3048 clusterings. You can adjust a tree's graphical parameters (the color, size,
3049 type, etc of its branches, nodes and labels) and visually and statistically
3050 compare different dendrograms to one another.")
3051 ;; Any of these versions
3052 (license (list license:gpl2 license:gpl3))))
3054 (define-public r-getoptlong
3056 (name "r-getoptlong")
3061 (uri (cran-uri "GetoptLong" version))
3064 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3065 (properties `((upstream-name . "GetoptLong")))
3066 (build-system r-build-system)
3070 `(("r-crayon" ,r-crayon)
3071 ("r-globaloptions" ,r-globaloptions)
3072 ("r-rjson" ,r-rjson)))
3074 `(("r-knitr" ,r-knitr)))
3075 (home-page "https://github.com/jokergoo/GetoptLong")
3076 (synopsis "Parsing command-line arguments and variable interpolation")
3078 "This is yet another command-line argument parser which wraps the
3079 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3080 use in R. It also provides a simple way for variable interpolation in R.")
3081 (license license:gpl2+)))
3083 (define-public r-fastmatch
3085 (name "r-fastmatch")
3090 (uri (cran-uri "fastmatch" version))
3093 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3094 (build-system r-build-system)
3095 (home-page "https://www.rforge.net/fastmatch")
3096 (synopsis "Fast match function")
3098 "This package provides a fast @code{match} replacement for cases that
3099 require repeated look-ups. It is slightly faster that R's built-in
3100 @code{match} function on first match against a table, but extremely fast on
3101 any subsequent lookup as it keeps the hash table in memory.")
3102 (license license:gpl2)))
3111 (uri (cran-uri "ff" version))
3114 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3115 (build-system r-build-system)
3116 (propagated-inputs `(("r-bit" ,r-bit)))
3117 (home-page "http://ff.r-forge.r-project.org/")
3118 (synopsis "Memory-efficient storage of large data on disk and access functions")
3120 "This package provides data structures that are stored on disk but
3121 behave (almost) as if they were in RAM by transparently mapping only a section
3123 ;; error Architecture not supported.
3124 (supported-systems (delete "aarch64-linux" %supported-systems))
3125 (license license:gpl2)))
3127 (define-public r-ffbase
3134 (uri (cran-uri "ffbase" version))
3137 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3138 (build-system r-build-system)
3141 ("r-fastmatch" ,r-fastmatch)
3143 (home-page "https://github.com/edwindj/ffbase")
3144 (synopsis "Basic statistical functions for package 'ff'")
3146 "This package extends the out of memory vectors of @code{ff} with
3147 statistical functions and other utilities to ease their usage.")
3148 (license license:gpl3)))
3150 (define-public r-prettyunits
3152 (name "r-prettyunits")
3157 (uri (cran-uri "prettyunits" version))
3160 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3161 (build-system r-build-system)
3162 (home-page "https://github.com/gaborcsardi/prettyunits")
3163 (synopsis "Pretty, human readable formatting of quantities")
3165 "This package provides tools for pretty, human readable formatting of
3167 (license license:expat)))
3169 (define-public r-reshape
3176 (uri (cran-uri "reshape" version))
3179 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3180 (build-system r-build-system)
3182 `(("r-plyr" ,r-plyr)
3183 ("r-rcpp" ,r-rcpp)))
3184 (home-page "http://had.co.nz/reshape")
3185 (synopsis "Flexibly reshape data")
3187 "Flexibly restructure and aggregate data using just two functions:
3188 @code{melt} and @code{cast}. This package provides them.")
3189 (license license:expat)))
3191 (define-public r-restrserve
3193 (name "r-restrserve")
3198 (uri (cran-uri "RestRserve" version))
3200 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3201 (build-system r-build-system)
3203 `(("r-checkmate" ,r-checkmate)
3204 ("r-jsonlite" ,r-jsonlite)
3208 ("r-rserve" ,r-rserve)
3209 ("r-uuid" ,r-uuid)))
3211 `(("r-knitr" ,r-knitr)))
3212 (home-page "https://restrserve.org")
3213 (synopsis "R web API framework")
3215 "RestRserve is an R web API framework for building high-performance AND
3216 robust microservices and app backends. With Rserve backend on UNIX-like
3217 systems it is parallel by design. It will handle incoming requests in
3218 parallel - each request in a separate fork.")
3219 (license license:gpl2+)))
3221 (define-public r-progress
3228 (uri (cran-uri "progress" version))
3231 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3232 (build-system r-build-system)
3234 `(("r-crayon" ,r-crayon)
3236 ("r-prettyunits" ,r-prettyunits)
3238 (home-page "https://github.com/gaborcsardi/progress")
3239 (synopsis "Terminal progress bars")
3241 "This package provides configurable progress bars. They may include
3242 percentage, elapsed time, and/or the estimated completion time. They work in
3243 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3244 package also provides a C++ API, that works with or without Rcpp.")
3245 (license license:expat)))
3247 (define-public r-ggally
3254 (uri (cran-uri "GGally" version))
3257 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3258 (properties `((upstream-name . "GGally")))
3259 (build-system r-build-system)
3261 `(("openssl" ,openssl)))
3263 `(("r-dplyr" ,r-dplyr)
3264 ("r-forcats" ,r-forcats)
3265 ("r-ggplot2" ,r-ggplot2)
3266 ("r-gtable" ,r-gtable)
3267 ("r-lifecycle" ,r-lifecycle)
3269 ("r-progress" ,r-progress)
3270 ("r-rcolorbrewer" ,r-rcolorbrewer)
3271 ("r-reshape" ,r-reshape)
3272 ("r-rlang" ,r-rlang)
3273 ("r-scales" ,r-scales)
3274 ("r-tidyr" ,r-tidyr)))
3275 (home-page "https://ggobi.github.io/ggally")
3276 (synopsis "Extension to ggplot2")
3278 "The R package ggplot2 is a plotting system based on the grammar of
3279 graphics. GGally extends ggplot2 by adding several functions to reduce the
3280 complexity of combining geometric objects with transformed data. Some of
3281 these functions include a pairwise plot matrix, a two group pairwise plot
3282 matrix, a parallel coordinates plot, a survival plot, and several functions to
3284 (license license:gpl2+)))
3286 (define-public r-proxy
3293 (uri (cran-uri "proxy" version))
3296 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3297 (build-system r-build-system)
3298 (home-page "https://cran.r-project.org/web/packages/proxy")
3299 (synopsis "Distance and similarity measures")
3301 "This package provides an extensible framework for the efficient
3302 calculation of auto- and cross-proximities, along with implementations of the
3303 most popular ones.")
3304 (license license:gpl2)))
3313 (uri (cran-uri "sp" version))
3315 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3316 (build-system r-build-system)
3318 `(("r-lattice" ,r-lattice)))
3319 (home-page "https://cran.r-project.org/web/packages/sp")
3320 (synopsis "Classes and methods for spatial data")
3322 "This package provides classes and methods for spatial data; the classes
3323 document where the spatial location information resides, for 2D or 3D data.
3324 Utility functions are provided, e.g. for plotting data as maps, spatial
3325 selection, as well as methods for retrieving coordinates, for subsetting,
3326 print, summary, etc.")
3327 (license license:gpl2+)))
3329 (define-public r-laplacesdemon
3331 (name "r-laplacesdemon")
3336 (uri (cran-uri "LaplacesDemon" version))
3338 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3339 (properties `((upstream-name . "LaplacesDemon")))
3340 (build-system r-build-system)
3341 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3342 (synopsis "Complete environment for Bayesian inference")
3344 "This package provides a complete environment for Bayesian inference using
3345 a variety of different samplers.")
3346 (license license:expat)))
3348 (define-public r-rmtstat
3355 (uri (cran-uri "RMTstat" version))
3358 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3359 (properties `((upstream-name . "RMTstat")))
3360 (build-system r-build-system)
3361 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3362 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3364 "This package provides functions for working with the Tracy-Widom laws
3365 and other distributions related to the eigenvalues of large Wishart
3367 (license license:bsd-3)))
3369 (define-public r-rmpi
3375 (uri (cran-uri "Rmpi" version))
3378 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3379 (properties `((upstream-name . "Rmpi")))
3380 (build-system r-build-system)
3382 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3383 #:phases (modify-phases %standard-phases
3384 (add-before 'install 'mpi-setup
3387 `(("openmpi" ,openmpi)))
3389 `(("pkg-config" ,pkg-config)))
3390 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3391 (synopsis "R interface to message-passing interface (MPI)")
3393 "This package provides an interface (wrapper) to MPI APIs. It also
3394 provides an interactive R manager and worker environment.")
3395 (license license:gpl2+)))
3397 (define-public r-lmoments
3404 (uri (cran-uri "Lmoments" version))
3407 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3408 (properties `((upstream-name . "Lmoments")))
3409 (build-system r-build-system)
3411 `(("r-rcpp" ,r-rcpp)
3412 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3413 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3414 (synopsis "L-moments and quantile mixtures")
3416 "This package contains functions to estimate L-moments and trimmed
3417 L-moments from the data. It also contains functions to estimate the
3418 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3419 quantile mixture from L-moments and trimmed L-moments.")
3420 (license license:gpl2)))
3422 (define-public r-distillery
3424 (name "r-distillery")
3429 (uri (cran-uri "distillery" version))
3432 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3433 (build-system r-build-system)
3434 (home-page "https://ral.ucar.edu/staff/ericg/")
3435 (synopsis "Functions for confidence intervals and object information")
3437 "This package provides some very simple method functions for confidence
3438 interval calculation and to distill pertinent information from a potentially
3439 complex object; primarily used in common with the packages extRemes and
3441 (license license:gpl2+)))
3443 (define-public r-etrunct
3449 (uri (cran-uri "etrunct" version))
3452 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3453 (properties `((upstream-name . "etrunct")))
3454 (build-system r-build-system)
3455 (home-page "https://cran.r-project.org/web/packages/etrunct")
3456 (synopsis "Computes moments of univariate truncated T distribution")
3457 (description "This package computes moments of univariate truncated
3458 T distribution. There is only one exported function, @code{e_trunct},
3459 which should be seen for details.")
3460 (license license:expat)))
3462 (define-public r-extremes
3469 (uri (cran-uri "extRemes" version))
3472 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3473 (properties `((upstream-name . "extRemes")))
3474 (build-system r-build-system)
3476 `(("r-distillery" ,r-distillery)
3477 ("r-lmoments" ,r-lmoments)))
3478 (home-page "https://www.assessment.ucar.edu/toolkit/")
3479 (synopsis "Extreme value analysis")
3481 "ExtRemes is a suite of functions for carrying out analyses on the
3482 extreme values of a process of interest; be they block maxima over long blocks
3483 or excesses over a high threshold.")
3484 (license license:gpl2+)))
3486 (define-public r-lmtest
3493 (uri (cran-uri "lmtest" version))
3496 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3497 (build-system r-build-system)
3499 `(("r-zoo" ,r-zoo)))
3501 `(("gfortran" ,gfortran)))
3502 (home-page "https://cran.r-project.org/web/packages/lmtest")
3503 (synopsis "Testing linear regression models")
3505 "This package provides a collection of tests, data sets, and examples for
3506 diagnostic checking in linear regression models. Furthermore, some generic
3507 tools for inference in parametric models are provided.")
3508 ;; Either version is okay
3509 (license (list license:gpl2 license:gpl3))))
3511 (define-public r-idr
3517 (uri (cran-uri "idr" version))
3520 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3521 (build-system r-build-system)
3522 (home-page "https://cran.r-project.org/web/packages/idr/")
3523 (synopsis "Irreproducible discovery rate")
3525 "This is a package for estimating the copula mixture model and plotting
3526 correspondence curves in \"Measuring reproducibility of high-throughput
3527 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3528 by Li, Brown, Huang, and Bickel")
3529 (license license:gpl2+)))
3531 (define-public r-inline
3537 (uri (cran-uri "inline" version))
3540 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3541 (build-system r-build-system)
3542 (home-page "https://cran.r-project.org/web/packages/inline")
3543 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3545 "This package provides functionality to dynamically define R functions
3546 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3547 @code{.Call} calling conventions.")
3548 ;; Any version of the LGPL.
3549 (license license:lgpl3+)))
3551 (define-public r-inum
3557 (uri (cran-uri "inum" version))
3560 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3561 (build-system r-build-system)
3563 `(("r-libcoin" ,r-libcoin)))
3564 (home-page "https://cran.r-project.org/web/packages/inum/")
3565 (synopsis "Interval and enum-type representation of vectors")
3567 "This package provides an enum-type representation of vectors and
3568 representation of intervals, including a method of coercing variables
3570 (license license:gpl2)))
3571 (define-public r-invgamma
3577 (uri (cran-uri "invgamma" version))
3580 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3581 (properties `((upstream-name . "invgamma")))
3582 (build-system r-build-system)
3583 (home-page "https://github.com/dkahle/invgamma")
3584 (synopsis "Inverse gamma distribution")
3585 (description "This package provides a light weight implementation of the
3586 standard distribution functions for the inverse gamma distribution, wrapping
3587 those for the gamma distribution in the @code{stats} package.")
3588 (license license:gpl2)))
3590 (define-public r-bdsmatrix
3592 (name "r-bdsmatrix")
3597 (uri (cran-uri "bdsmatrix" version))
3600 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3601 (properties `((upstream-name . "bdsmatrix")))
3602 (build-system r-build-system)
3603 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3604 (synopsis "Routines for block diagonal symmetric matrices")
3606 "This package provides procedures to work with block diagonal symmetric
3607 matrices, a special case of sparse matrices.")
3608 (license license:lgpl2.0)))
3610 (define-public r-bbmle
3613 (version "1.0.23.1")
3617 (uri (cran-uri "bbmle" version))
3620 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3621 (build-system r-build-system)
3623 `(("r-bdsmatrix" ,r-bdsmatrix)
3624 ("r-lattice" ,r-lattice)
3626 ("r-matrix" ,r-matrix)
3627 ("r-mvtnorm" ,r-mvtnorm)
3628 ("r-numderiv" ,r-numderiv)))
3629 (home-page "https://cran.r-project.org/web/packages/bbmle")
3630 (synopsis "Tools for General Maximum Likelihood Estimation")
3632 "This package provides methods and functions for fitting maximum
3633 likelihood models in R. This package modifies and extends the @code{mle}
3634 classes in the @code{stats4} package.")
3635 ;; Any version of the GPL
3636 (license license:gpl2+)))
3638 (define-public r-emdbook
3645 (uri (cran-uri "emdbook" version))
3648 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3649 (build-system r-build-system)
3651 `(("r-bbmle" ,r-bbmle)
3653 ("r-lattice" ,r-lattice)
3655 ("r-plyr" ,r-plyr)))
3656 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3657 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3659 "This package provides auxiliary functions and data sets for \"Ecological
3660 Models and Data\", a book presenting maximum likelihood estimation and related
3661 topics for ecologists (ISBN 978-0-691-12522-0).")
3663 (license (list license:gpl2 license:gpl3))))
3665 (define-public r-lpsolve
3672 (uri (cran-uri "lpSolve" version))
3675 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3676 (properties `((upstream-name . "lpSolve")))
3677 (build-system r-build-system)
3678 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3679 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3681 "Lp_solve is software for solving linear, integer and mixed integer
3682 programs. This implementation supplies a \"wrapper\" function in C and some R
3683 functions that solve general linear/integer problems, assignment problems, and
3684 transportation problems.")
3685 (license license:lgpl2.0)))
3687 (define-public r-limsolve
3694 (uri (cran-uri "limSolve" version))
3697 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3698 (properties `((upstream-name . "limSolve")))
3699 (build-system r-build-system)
3701 `(("r-lpsolve" ,r-lpsolve)
3703 ("r-quadprog" ,r-quadprog)))
3704 (native-inputs `(("gfortran" ,gfortran)))
3705 (home-page "https://cran.r-project.org/web/packages/limSolve")
3706 (synopsis "Solving linear inverse models")
3708 "This package provides functions that:
3711 @item find the minimum/maximum of a linear or quadratic function,
3712 @item sample an underdetermined or overdetermined system,
3713 @item solve a linear system Ax=B for the unknown x.
3716 It includes banded and tridiagonal linear systems. The package calls Fortran
3717 functions from LINPACK.")
3719 (license (list license:gpl2+ license:gpl3+))))
3721 (define-public r-fitdistrplus
3723 (name "r-fitdistrplus")
3728 (uri (cran-uri "fitdistrplus" version))
3731 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3732 (build-system r-build-system)
3734 `(("r-mass" ,r-mass)
3735 ("r-survival" ,r-survival)))
3737 `(("r-knitr" ,r-knitr)))
3738 (home-page "http://riskassessment.r-forge.r-project.org")
3739 (synopsis "Fitting a parametric distribution from data")
3741 "This package extends the @code{fitdistr} function of the MASS package
3742 with several functions to help the fit of a parametric distribution to
3743 non-censored or censored data. Censored data may contain left-censored,
3744 right-censored and interval-censored values, with several lower and upper
3745 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3746 provides moment matching (MME), quantile matching (QME) and maximum
3747 goodness-of-fit estimation (MGE) methods (available only for non-censored
3748 data). Weighted versions of MLE, MME and QME are available.")
3749 (license license:gpl2+)))
3751 (define-public r-energy
3758 (uri (cran-uri "energy" version))
3761 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3762 (build-system r-build-system)
3764 `(("r-boot" ,r-boot)
3766 ("r-rcpp" ,r-rcpp)))
3767 (home-page "https://cran.r-project.org/web/packages/energy")
3768 (synopsis "Multivariate inference via the energy of data")
3770 "This package provides e-statistics (energy) tests and statistics for
3771 multivariate and univariate inference, including distance correlation,
3772 one-sample, two-sample, and multi-sample tests for comparing multivariate
3773 distributions, are implemented. Measuring and testing multivariate
3774 independence based on distance correlation, partial distance correlation,
3775 multivariate goodness-of-fit tests, clustering based on energy distance,
3776 testing for multivariate normality, distance components (disco) for
3777 non-parametric analysis of structured data, and other energy
3778 statistics/methods are implemented.")
3779 (license license:gpl2+)))
3781 (define-public r-suppdists
3783 (name "r-suppdists")
3788 (uri (cran-uri "SuppDists" version))
3791 "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8"))))
3792 (properties `((upstream-name . "SuppDists")))
3793 (build-system r-build-system)
3794 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3795 (synopsis "Supplementary distributions")
3797 "This package provides ten distributions supplementing those built into
3798 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3799 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3800 coefficient, Johnson distributions, normal scores and generalized
3801 hypergeometric distributions. In addition two random number generators of
3802 George Marsaglia are included.")
3803 (license license:gpl2+)))
3805 (define-public r-ksamples
3812 (uri (cran-uri "kSamples" version))
3815 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3816 (properties `((upstream-name . "kSamples")))
3817 (build-system r-build-system)
3819 `(("r-suppdists" ,r-suppdists)))
3820 (home-page "https://cran.r-project.org/web/packages/kSamples")
3821 (synopsis "K-Sample rank tests and their combinations")
3823 "This package provides tools to compares k samples using the
3824 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3825 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3826 test. It computes asymptotic, simulated or (limited) exact P-values, all
3827 valid under randomization, with or without ties, or conditionally under random
3828 sampling from populations, given the observed tie pattern. Except for Steel's
3829 test and the JT test it also combines these tests across several blocks of
3831 (license license:gpl2+)))
3833 (define-public r-cvst
3840 (uri (cran-uri "CVST" version))
3843 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3844 (properties `((upstream-name . "CVST")))
3845 (build-system r-build-system)
3847 `(("r-kernlab" ,r-kernlab)
3848 ("r-matrix" ,r-matrix)))
3849 (home-page "https://cran.r-project.org/web/packages/CVST")
3850 (synopsis "Fast cross-validation via sequential testing")
3852 "This package implements the fast cross-validation via sequential
3853 testing (CVST) procedure. CVST is an improved cross-validation procedure
3854 which uses non-parametric testing coupled with sequential analysis to
3855 determine the best parameter set on linearly increasing subsets of the data.
3856 Additionally to the CVST the package contains an implementation of the
3857 ordinary k-fold cross-validation with a flexible and powerful set of helper
3858 objects and methods to handle the overall model selection process. The
3859 implementations of the Cochran's Q test with permutations and the sequential
3860 testing framework of Wald are generic and can therefore also be used in other
3862 (license license:gpl2+)))
3864 (define-public r-squarem
3871 (uri (cran-uri "SQUAREM" version))
3874 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3875 (properties `((upstream-name . "SQUAREM")))
3876 (build-system r-build-system)
3877 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3878 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3880 "This package provides algorithms for accelerating the convergence of
3881 slow, monotone sequences from smooth, contraction mapping such as the EM
3882 algorithm. It can be used to accelerate any smooth, linearly convergent
3883 acceleration scheme. A tutorial style introduction to this package is
3884 available in a vignette.")
3885 (license license:gpl2+)))
3887 (define-public r-lava
3894 (uri (cran-uri "lava" version))
3897 "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83"))))
3898 (build-system r-build-system)
3900 `(("r-numderiv" ,r-numderiv)
3901 ("r-squarem" ,r-squarem)
3902 ("r-survival" ,r-survival)))
3904 `(("r-knitr" ,r-knitr)))
3905 (home-page "https://github.com/kkholst/lava")
3906 (synopsis "Latent variable models")
3908 "This package provides tools for the estimation and simulation of latent
3910 (license license:gpl3)))
3912 (define-public r-drr
3919 (uri (cran-uri "DRR" version))
3922 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3923 (properties `((upstream-name . "DRR")))
3924 (build-system r-build-system)
3926 `(("r-cvst" ,r-cvst)
3927 ("r-kernlab" ,r-kernlab)
3928 ("r-matrix" ,r-matrix)))
3929 (home-page "https://cran.r-project.org/web/packages/DRR")
3930 (synopsis "Dimensionality reduction via regression")
3932 "This package provides an implementation of dimensionality reduction via
3933 regression using Kernel Ridge Regression.")
3934 (license license:gpl3)))
3936 (define-public r-prodlim
3939 (version "2019.11.13")
3943 (uri (cran-uri "prodlim" version))
3946 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3947 (build-system r-build-system)
3949 `(("r-kernsmooth" ,r-kernsmooth)
3952 ("r-survival" ,r-survival)))
3953 (home-page "https://cran.r-project.org/web/packages/prodlim")
3954 (synopsis "Product-limit estimation for censored event history analysis")
3956 "This package provides a fast and user-friendly implementation of
3957 nonparametric estimators for censored event history (survival) analysis with
3958 the Kaplan-Meier and Aalen-Johansen methods.")
3959 (license license:gpl2+)))
3961 (define-public r-dimred
3968 (uri (cran-uri "dimRed" version))
3971 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3972 (properties `((upstream-name . "dimRed")))
3973 (build-system r-build-system)
3976 ("r-magrittr" ,r-magrittr)))
3977 (home-page "https://github.com/gdkrmr/dimRed")
3978 (synopsis "Framework for dimensionality reduction")
3980 "This package provides a collection of dimensionality reduction
3981 techniques from R packages and provides a common interface for calling the
3983 (license license:gpl3)))
3985 (define-public r-timedate
3988 (version "3043.102")
3992 (uri (cran-uri "timeDate" version))
3995 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3996 (properties `((upstream-name . "timeDate")))
3997 (build-system r-build-system)
3998 (home-page "https://www.rmetrics.org")
3999 (synopsis "Chronological and calendar objects")
4001 "This package provides an environment for teaching \"Financial
4002 Engineering and Computational Finance\" and for managing chronological and
4004 (license license:gpl2+)))
4006 (define-public r-magic
4013 (uri (cran-uri "magic" version))
4016 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4017 (build-system r-build-system)
4019 `(("r-abind" ,r-abind)))
4020 (home-page "https://github.com/RobinHankin/magic.git")
4021 (synopsis "Create and investigate magic squares")
4023 "This package provides a collection of efficient, vectorized algorithms
4024 for the creation and investigation of magic squares and hypercubes, including
4025 a variety of functions for the manipulation and analysis of arbitrarily
4026 dimensioned arrays.")
4027 (license license:gpl2)))
4029 (define-public r-rmysql
4036 (uri (cran-uri "RMySQL" version))
4039 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4040 (properties `((upstream-name . "RMySQL")))
4041 (build-system r-build-system)
4043 `(("mariadb-dev" ,mariadb "dev")
4046 `(("r-dbi" ,r-dbi)))
4047 (home-page "https://github.com/r-dbi/RMySQL")
4048 (synopsis "Database interface and MySQL driver for R")
4050 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4051 package contains an old implementation based on legacy code from S-PLUS which
4052 is being phased out. A modern MySQL client based on Rcpp is available from
4053 the RMariaDB package.")
4054 (license license:gpl2)))
4056 (define-public r-rpostgresql
4058 (name "r-rpostgresql")
4063 (uri (cran-uri "RPostgreSQL" version))
4066 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4067 (properties `((upstream-name . "RPostgreSQL")))
4068 (build-system r-build-system)
4070 `(("postgresql" ,postgresql)))
4072 `(("r-dbi" ,r-dbi)))
4073 (home-page "https://github.com/tomoakin/RPostgreSQL")
4074 (synopsis "R interface to the PostgreSQL database system")
4076 "This package provides a Database Interface (DBI) compliant driver for R
4077 to access PostgreSQL database systems.")
4078 ;; The whole package is released under GPL version 2. It includes code
4079 ;; under the PostgreSQL license.
4080 (license license:gpl2)))
4082 (define-public r-linprog
4089 (uri (cran-uri "linprog" version))
4092 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4093 (build-system r-build-system)
4094 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4095 (home-page "http://linprog.r-forge.r-project.org/")
4096 (synopsis "Linear programming and optimization")
4098 "This package can be used to solve Linear Programming / Linear
4099 Optimization problems by using the simplex algorithm.")
4100 (license license:gpl2+)))
4102 (define-public r-geometry
4109 (uri (cran-uri "geometry" version))
4112 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4113 (build-system r-build-system)
4115 `(("r-magic" ,r-magic)
4116 ("r-linprog" ,r-linprog)
4117 ("r-lpsolve" ,r-lpsolve)
4119 ("r-rcppprogress" ,r-rcppprogress)))
4120 (home-page "http://geometry.r-forge.r-project.org/")
4121 (synopsis "Mesh generator and surface tessellator")
4123 "This package makes the qhull library available in R, in a similar manner
4124 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4125 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4126 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4127 and higher dimensions. It implements the Quickhull algorithm for computing
4128 the convex hull. Qhull does not support constrained Delaunay triangulations,
4129 or mesh generation of non-convex objects, but the package does include some R
4130 functions that allow for this. Currently the package only gives access to
4131 Delaunay triangulation and convex hull computation.")
4132 ;; The Qhull sources are included and are distributed under a custom
4133 ;; non-copyleft license. The R sources are released under GPL version 2.
4134 (license (list license:gpl2
4135 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4137 (define-public r-ddalpha
4144 (uri (cran-uri "ddalpha" version))
4147 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4148 (build-system r-build-system)
4151 ("r-class" ,r-class)
4152 ("r-geometry" ,r-geometry)
4155 ("r-robustbase" ,r-robustbase)
4156 ("r-sfsmisc" ,r-sfsmisc)))
4158 `(("gfortran" ,gfortran)))
4159 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4160 (synopsis "Depth-Based classification and calculation of data depth")
4162 "This package contains procedures for depth-based supervised learning,
4163 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4164 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4165 statistical depth function to a compact low-dimensional space, where the final
4166 classification is done. It also offers an extension to functional data and
4167 routines for calculating certain notions of statistical depth functions. 50
4168 multivariate and 5 functional classification problems are included.")
4169 (license license:gpl2)))
4171 (define-public r-gower
4178 (uri (cran-uri "gower" version))
4181 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4182 (build-system r-build-system)
4183 (home-page "https://github.com/markvanderloo/gower")
4184 (synopsis "Gower's distance")
4186 "This package provides tools to compute Gower's distance (or similarity)
4187 coefficient between records, and to compute the top-n matches between records.
4188 Core algorithms are executed in parallel on systems supporting OpenMP.")
4189 (license license:gpl3)))
4191 (define-public r-rcpproll
4198 (uri (cran-uri "RcppRoll" version))
4201 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4202 (properties `((upstream-name . "RcppRoll")))
4203 (build-system r-build-system)
4205 `(("r-rcpp" ,r-rcpp)))
4206 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4207 (synopsis "Efficient rolling and windowed operations")
4209 "This package provides fast and efficient routines for common rolling /
4210 windowed operations. Routines for the efficient computation of windowed mean,
4211 median, sum, product, minimum, maximum, standard deviation and variance are
4213 (license license:gpl2+)))
4215 (define-public r-ipred
4222 (uri (cran-uri "ipred" version))
4225 "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp"))))
4226 (build-system r-build-system)
4228 `(("r-class" ,r-class)
4231 ("r-prodlim" ,r-prodlim)
4232 ("r-rpart" ,r-rpart)
4233 ("r-survival" ,r-survival)))
4234 (home-page "https://cran.r-project.org/web/packages/ipred")
4235 (synopsis "Improved predictors")
4237 "This package provides improved predictive models by indirect
4238 classification and bagging for classification, regression and survival
4239 problems as well as resampling based estimators of prediction error.")
4240 (license license:gpl2+)))
4242 (define-public r-psych
4249 (uri (cran-uri "psych" version))
4252 "1ibh1ivr280wpmk3qjgm715dk79wx0ikjl9jjjcqs03q6vz4wmdx"))))
4253 (build-system r-build-system)
4255 `(("r-lattice" ,r-lattice)
4256 ("r-mnormt" ,r-mnormt)
4257 ("r-nlme" ,r-nlme)))
4259 `(("r-knitr" ,r-knitr)))
4260 (home-page "https://cran.r-project.org/web/packages/psych/")
4261 (synopsis "Procedures for psychological, psychometric, and personality research")
4263 "This package provides a general purpose toolbox for personality,
4264 psychometric theory and experimental psychology. Functions are primarily for
4265 multivariate analysis and scale construction using factor analysis, principal
4266 component analysis, cluster analysis and reliability analysis, although others
4267 provide basic descriptive statistics. Item Response Theory is done using
4268 factor analysis of tetrachoric and polychoric correlations. Functions for
4269 analyzing data at multiple levels include within and between group statistics,
4270 including correlations and factor analysis. Functions for simulating and
4271 testing particular item and test structures are included. Several functions
4272 serve as a useful front end for structural equation modeling. Graphical
4273 displays of path diagrams, factor analysis and structural equation models are
4274 created using basic graphics.")
4275 (license license:gpl2+)))
4277 (define-public r-generics
4284 (uri (cran-uri "generics" version))
4287 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4288 (build-system r-build-system)
4289 (home-page "https://github.com/r-lib/generics")
4290 (synopsis "Common S3 generics not provided by base R methods")
4292 "In order to reduce potential package dependencies and conflicts,
4293 generics provides a number of commonly used S3 generics that are not provided
4294 by base R methods related to model fitting.")
4295 (license license:gpl2)))
4297 (define-public r-broom
4304 (uri (cran-uri "broom" version))
4307 "1ljcl8mh0yqxw3qxzar482qwbxbcaim1x6y1wm82ws12pfdw0j8n"))))
4308 (build-system r-build-system)
4310 `(("r-backports" ,r-backports)
4311 ("r-dplyr" ,r-dplyr)
4312 ("r-ellipsis" ,r-ellipsis)
4313 ("r-generics" ,r-generics)
4315 ("r-purrr" ,r-purrr)
4316 ("r-rlang" ,r-rlang)
4317 ("r-stringr" ,r-stringr)
4318 ("r-tibble" ,r-tibble)
4319 ("r-tidyr" ,r-tidyr)))
4321 `(("r-knitr" ,r-knitr)))
4322 (home-page "https://github.com/tidyverse/broom")
4323 (synopsis "Convert statistical analysis objects into tidy data frames")
4325 "This package provides tools to convert statistical analysis objects from
4326 R into tidy data frames, so that they can more easily be combined, reshaped
4327 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4328 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4329 summarizes a model's statistical findings such as coefficients of a
4330 regression; @code{augment}, which adds columns to the original data such as
4331 predictions, residuals and cluster assignments; and @code{glance}, which
4332 provides a one-row summary of model-level statistics.")
4333 (license license:expat)))
4335 (define-public r-recipes
4342 (uri (cran-uri "recipes" version))
4345 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4346 (build-system r-build-system)
4348 `(("r-dplyr" ,r-dplyr)
4349 ("r-generics" ,r-generics)
4351 ("r-gower" ,r-gower)
4352 ("r-ipred" ,r-ipred)
4353 ("r-lifecycle" ,r-lifecycle)
4354 ("r-lubridate" ,r-lubridate)
4355 ("r-magrittr" ,r-magrittr)
4356 ("r-matrix" ,r-matrix)
4357 ("r-purrr" ,r-purrr)
4358 ("r-rlang" ,r-rlang)
4359 ("r-tibble" ,r-tibble)
4360 ("r-tidyr" ,r-tidyr)
4361 ("r-tidyselect" ,r-tidyselect)
4362 ("r-timedate" ,r-timedate)
4363 ("r-withr" ,r-withr)))
4365 `(("r-knitr" ,r-knitr)))
4366 (home-page "https://github.com/topepo/recipes")
4367 (synopsis "Preprocessing tools to create design matrices")
4369 "Recipes is an extensible framework to create and preprocess design
4370 matrices. Recipes consist of one or more data manipulation and analysis
4371 \"steps\". Statistical parameters for the steps can be estimated from an
4372 initial data set and then applied to other data sets. The resulting design
4373 matrices can then be used as inputs into statistical or machine learning
4375 (license license:gpl2)))
4377 (define-public r-pdist
4384 (uri (cran-uri "pdist" version))
4387 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4388 (build-system r-build-system)
4389 (home-page "https://github.com/jeffwong/pdist")
4390 (synopsis "Partitioned distance function")
4392 "Pdist computes the euclidean distance between rows of a matrix X and
4393 rows of another matrix Y. Previously, this could be done by binding the two
4394 matrices together and calling @code{dist}, but this creates unnecessary
4395 computation by computing the distances between a row of X and another row of
4396 X, and likewise for Y. Pdist strictly computes distances across the two
4397 matrices, not within the same matrix, making computations significantly faster
4398 for certain use cases.")
4399 (license license:gpl3+)))
4401 (define-public r-ggrepel
4408 (uri (cran-uri "ggrepel" version))
4411 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4412 (build-system r-build-system)
4414 `(("r-ggplot2" ,r-ggplot2)
4416 ("r-rlang" ,r-rlang)
4417 ("r-scales" ,r-scales)))
4419 `(("r-knitr" ,r-knitr))) ; for vignettes
4420 (home-page "https://github.com/slowkow/ggrepel")
4421 (synopsis "Repulsive text and label geometries for ggplot2")
4423 "This package provides text and label geometries for ggplot2 that help to
4424 avoid overlapping text labels. Labels repel away from each other and away
4425 from the data points.")
4426 (license license:gpl3)))
4428 (define-public r-corrplot
4435 (uri (cran-uri "corrplot" version))
4438 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4439 (build-system r-build-system)
4440 (home-page "https://github.com/taiyun/corrplot")
4441 (synopsis "Visualization of a correlation matrix")
4443 "This package provides a graphical display of a correlation matrix or
4444 general matrix. It also contains some algorithms to do matrix reordering. In
4445 addition, corrplot is good at details, including choosing color, text labels,
4446 color labels, layout, etc.")
4447 ;; Any version of the GPL
4448 (license license:gpl2+)))
4450 (define-public r-stringdist
4452 (name "r-stringdist")
4457 (uri (cran-uri "stringdist" version))
4459 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4460 (build-system r-build-system)
4461 (home-page "https://github.com/markvanderloo/stringdist")
4462 (synopsis "Approximate string matching and string distance functions")
4464 "This package implements an approximate string matching version of R's
4465 native @code{match} function. It can calculate various string distances based
4466 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4467 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4468 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4469 can be computed between character vectors while taking proper care of encoding
4470 or between integer vectors representing generic sequences.")
4471 (license license:gpl3+)))
4473 (define-public r-ucminf
4480 (uri (cran-uri "ucminf" version))
4483 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4484 (build-system r-build-system)
4485 (native-inputs `(("gfortran" ,gfortran)))
4486 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4487 (synopsis "General-purpose unconstrained non-linear optimization")
4489 "This package provides an implementation of an algorithm for
4490 general-purpose unconstrained non-linear optimization. The algorithm is of
4491 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4492 search with a trust region type monitoring of the input to the line search
4493 algorithm. The interface of @code{ucminf} is designed for easy interchange
4494 with the package @code{optim}.")
4495 (license license:gpl2+)))
4497 (define-public r-useful
4503 (uri (cran-uri "useful" version))
4506 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4507 (properties `((upstream-name . "useful")))
4508 (build-system r-build-system)
4510 `(("r-assertthat" ,r-assertthat)
4511 ("r-dplyr" ,r-dplyr)
4512 ("r-ggplot2" ,r-ggplot2)
4513 ("r-magrittr" ,r-magrittr)
4514 ("r-matrix" ,r-matrix)
4516 ("r-purrr" ,r-purrr)
4517 ("r-scales" ,r-scales)))
4518 (home-page "https://github.com/jaredlander/useful")
4519 (synopsis "Collection of handy, useful functions")
4520 (description "This package provides a set of little functions that have been
4521 found useful to do little odds and ends such as plotting the results of K-means
4522 clustering, substituting special text characters, viewing parts of a
4523 @code{data.frame}, constructing formulas from text and building design and
4524 response matrices.")
4525 (license license:bsd-3)))
4527 (define-public r-ordinal
4530 (version "2019.12-10")
4534 (uri (cran-uri "ordinal" version))
4537 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4538 (build-system r-build-system)
4540 `(("r-mass" ,r-mass)
4541 ("r-matrix" ,r-matrix)
4542 ("r-numderiv" ,r-numderiv)
4543 ("r-ucminf" ,r-ucminf)))
4544 (home-page "https://github.com/runehaubo/ordinal")
4545 (synopsis "Regression models for ordinal data")
4547 "This package provides an implementation of cumulative link (mixed)
4548 models also known as ordered regression models, proportional odds models,
4549 proportional hazards models for grouped survival times and ordered models.
4550 Estimation is via maximum likelihood and mixed models are fitted with the
4551 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4552 (license license:gpl2+)))
4554 (define-public r-jomo
4561 (uri (cran-uri "jomo" version))
4564 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4565 (build-system r-build-system)
4567 `(("r-lme4" ,r-lme4)
4569 ("r-ordinal" ,r-ordinal)
4570 ("r-survival" ,r-survival)))
4571 (home-page "https://cran.r-project.org/web/packages/jomo/")
4572 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4574 "Similarly to Schafer's package pan, jomo is a package for multilevel
4575 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4576 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4577 possibility of handling binary and categorical data through latent normal
4578 variables, the option to use cluster-specific covariance matrices and to
4579 impute compatibly with the substantive model.")
4580 (license license:gpl2)))
4582 (define-public r-pan
4589 (uri (cran-uri "pan" version))
4592 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4593 (build-system r-build-system)
4594 (native-inputs `(("gfortran" ,gfortran)))
4595 (home-page "https://cran.r-project.org/web/packages/pan/")
4596 (synopsis "Multiple imputation for multivariate panel or clustered data")
4598 "This package implements multiple imputation for multivariate panel or
4600 (license license:gpl3)))
4602 (define-public r-mitml
4609 (uri (cran-uri "mitml" version))
4612 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4613 (build-system r-build-system)
4615 `(("r-haven" ,r-haven)
4619 `(("r-knitr" ,r-knitr)))
4620 (home-page "https://cran.r-project.org/web/packages/mitml/")
4621 (synopsis "Tools for multiple imputation in multilevel modeling")
4623 "This package provides tools for multiple imputation of missing data in
4624 multilevel modeling. It includes a user-friendly interface to the packages
4625 pan and jomo, and several functions for visualization, data management and the
4626 analysis of multiply imputed data sets.")
4627 (license license:gpl2+)))
4629 (define-public r-mice
4636 (uri (cran-uri "mice" version))
4639 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4640 (build-system r-build-system)
4642 `(("r-broom" ,r-broom)
4643 ("r-cpp11" ,r-cpp11)
4644 ("r-dplyr" ,r-dplyr)
4645 ("r-generics" ,r-generics)
4646 ("r-lattice" ,r-lattice)
4648 ("r-rlang" ,r-rlang)
4649 ("r-tidyr" ,r-tidyr)))
4650 (home-page "https://cran.r-project.org/web/packages/mice/")
4651 (synopsis "Multivariate imputation by chained equations")
4653 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4654 implemented by the MICE algorithm as described in @url{Van Buuren and
4655 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4656 variable has its own imputation model. Built-in imputation models are
4657 provided for continuous data (predictive mean matching, normal), binary
4658 data (logistic regression), unordered categorical data (polytomous logistic
4659 regression) and ordered categorical data (proportional odds). MICE can also
4660 impute continuous two-level data (normal model, pan, second-level variables).
4661 Passive imputation can be used to maintain consistency between variables.
4662 Various diagnostic plots are available to inspect the quality of the
4664 ;; Any of these two versions.
4665 (license (list license:gpl2 license:gpl3))))
4667 (define-public r-truncnorm
4669 (name "r-truncnorm")
4674 (uri (cran-uri "truncnorm" version))
4677 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4678 (build-system r-build-system)
4679 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4680 (synopsis "Truncated normal distribution")
4681 (description "This package provides functions for the truncated normal
4682 distribution with mean equal to @code{mean} and standard deviation equal to
4683 @code{sd}. It includes density, distribution, quantile, and expected value
4684 functions, as well as a random generation function.")
4685 (license license:gpl2)))
4687 (define-public r-rsolnp
4694 (uri (cran-uri "Rsolnp" version))
4697 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4698 (properties `((upstream-name . "Rsolnp")))
4699 (build-system r-build-system)
4701 `(("r-truncnorm" ,r-truncnorm)))
4702 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4703 (synopsis "General non-linear optimization")
4704 (description "The Rsolnp package implements a general non-linear augmented
4705 Lagrange multiplier method solver, a @dfn{sequential quadratic
4706 programming} (SQP) based solver).")
4707 ;; Any version of the GPL.
4708 (license license:gpl2+)))
4710 (define-public r-hardyweinberg
4712 (name "r-hardyweinberg")
4717 (uri (cran-uri "HardyWeinberg" version))
4720 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4721 (properties `((upstream-name . "HardyWeinberg")))
4722 (build-system r-build-system)
4724 `(("r-mice" ,r-mice)
4726 ("r-rsolnp" ,r-rsolnp)))
4727 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4728 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4730 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4731 diallelic genetic marker data. All classical tests (chi-square, exact,
4732 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4733 included in the package, as well as functions for power computation and for
4734 the simulation of marker data under equilibrium and disequilibrium. Routines
4735 for dealing with markers on the X-chromosome are included. Functions for
4736 testing equilibrium in the presence of missing data by using multiple
4737 imputation are also provided. Implements several graphics for exploring the
4738 equilibrium status of a large set of diallelic markers: ternary plots with
4739 acceptance regions, log-ratio plots and Q-Q plots.")
4740 (license license:gpl2+)))
4749 (uri (cran-uri "sm" version))
4752 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4753 (build-system r-build-system)
4754 (native-inputs `(("gfortran" ,gfortran)))
4755 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4756 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4758 "This is software accompanying the book 'Applied Smoothing Techniques for
4759 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4760 University Press. It provides smoothing methods for nonparametric regression
4761 and density estimation")
4762 (license license:gpl2+)))
4764 (define-public r-venndiagram
4766 (name "r-venndiagram")
4770 (uri (cran-uri "VennDiagram" version))
4773 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4774 (properties `((upstream-name . "VennDiagram")))
4775 (build-system r-build-system)
4777 `(("r-futile-logger" ,r-futile-logger)))
4778 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4779 (synopsis "Generate High-Resolution Venn and Euler Plots")
4781 "This package provides a set of functions to generate high-resolution
4782 Venn and Euler plots. It includes handling for several special cases,
4783 including two-case scaling, and extensive customization of plot shape and
4785 (license license:gpl2+)))
4787 (define-public r-vioplot
4794 (uri (cran-uri "vioplot" version))
4797 "15vmrm9gwdhfg8mnq8rsg7m59kzc9h53cv96am4ds1dkm56w4n6p"))))
4798 (build-system r-build-system)
4803 `(("r-knitr" ,r-knitr)))
4804 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4805 (synopsis "Violin plot")
4807 "This package provides a violin plot, which is a combination of a box
4808 plot and a kernel density plot.")
4809 (license license:bsd-3)))
4811 (define-public r-rsofia
4817 ;; This package has been removed from CRAN, so we can
4818 ;; only fetch it from the archives.
4819 (uri (string-append "https://cran.r-project.org/src/"
4820 "contrib/Archive/RSofia/RSofia_"
4824 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4825 (properties `((upstream-name . "RSofia")))
4826 (build-system r-build-system)
4828 `(("r-rcpp" ,r-rcpp)))
4829 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4830 (synopsis "Port of sofia-ml to R")
4831 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4832 suite of fast incremental algorithms for machine learning that can be used for
4833 training models for classification or ranking.")
4834 (license license:asl2.0)))
4836 (define-public r-xts
4843 (uri (cran-uri "xts" version))
4846 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4847 (build-system r-build-system)
4848 (propagated-inputs `(("r-zoo" ,r-zoo)))
4849 (home-page "https://github.com/joshuaulrich/xts")
4850 (synopsis "Extensible time series")
4852 "This package provides for uniform handling of R's different time-based
4853 data classes by extending @code{zoo}, maximizing native format information
4854 preservation and allowing for user-level customization and extension, while
4855 simplifying cross-class interoperability.")
4856 (license license:gpl2+)))
4858 (define-public r-performanceanalytics
4860 (name "r-performanceanalytics")
4865 (uri (cran-uri "PerformanceAnalytics" version))
4868 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4870 `((upstream-name . "PerformanceAnalytics")))
4871 (build-system r-build-system)
4873 `(("r-quadprog" ,r-quadprog)
4876 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4877 (synopsis "Econometric tools for performance and risk analysis")
4878 (description "This is a collection of econometric functions for
4879 performance and risk analysis. This package aims to aid practitioners and
4880 researchers in utilizing the latest research in analysis of non-normal return
4881 streams. In general, it is most tested on return (rather than price) data on
4882 a regular scale, but most functions will work with irregular return data as
4883 well, and increasing numbers of functions will work with P&L or price data
4885 ;; Either version may be picked.
4886 (license (list license:gpl2 license:gpl3))))
4888 (define-public r-laeken
4895 (uri (cran-uri "laeken" version))
4898 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4899 (build-system r-build-system)
4901 `(("r-boot" ,r-boot)
4902 ("r-mass" ,r-mass)))
4903 (home-page "https://cran.r-project.org/web/packages/laeken/")
4904 (synopsis "Estimation of indicators on social exclusion and poverty")
4905 (description "This package provides tools for the estimation of indicators
4906 on social exclusion and poverty, as well as an implementation of Pareto tail
4907 modeling for empirical income distributions.")
4908 (license license:gpl2+)))
4910 (define-public r-vcd
4917 (uri (cran-uri "vcd" version))
4920 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4921 (build-system r-build-system)
4923 `(("r-colorspace" ,r-colorspace)
4924 ("r-lmtest" ,r-lmtest)
4925 ("r-mass" ,r-mass)))
4926 (home-page "https://cran.r-project.org/web/packages/vcd/")
4927 (synopsis "Visualizing categorical data")
4928 (description "This package provides visualization techniques, data sets,
4929 summary and inference procedures aimed particularly at categorical data.
4930 Special emphasis is given to highly extensible grid graphics. The package was
4931 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4932 Friendly and is now the main support package for a new book, \"Discrete Data
4933 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4934 (license license:gpl2)))
4936 (define-public r-ica
4943 (uri (cran-uri "ica" version))
4946 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4947 (build-system r-build-system)
4948 (home-page "https://cran.r-project.org/web/packages/ica/")
4949 (synopsis "Independent component analysis")
4950 (description "This package provides tools for @dfn{Independent Component
4951 Analysis} (ICA) using various algorithms: FastICA,
4952 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4953 of Eigenmatrices} (JADE).")
4954 (license license:gpl2+)))
4956 (define-public r-dtw
4963 (uri (cran-uri "dtw" version))
4966 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4967 (build-system r-build-system)
4968 (propagated-inputs `(("r-proxy" ,r-proxy)))
4969 (home-page "http://dtw.r-forge.r-project.org/")
4970 (synopsis "Dynamic Time Warping Algorithms")
4971 (description "This package provides a comprehensive implementation of
4972 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4973 optimal (least cumulative distance) alignment between points of two time
4974 series. Common DTW variants covered include local (slope) and global (window)
4975 constraints, subsequence matches, arbitrary distance definitions,
4976 normalizations, minimum variance matching, and so on.")
4977 (license license:gpl2+)))
4979 (define-public r-sdmtools
4982 (version "1.1-221.2")
4986 (uri (cran-uri "SDMTools" version))
4989 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4990 (properties `((upstream-name . "SDMTools")))
4991 (build-system r-build-system)
4992 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4993 (home-page "https://www.rforge.net/SDMTools/")
4994 (synopsis "Species distribution modelling tools")
4995 (description "This package provides a set of tools for post processing
4996 the outcomes of species distribution modeling exercises. It includes novel
4997 methods for comparing models and tracking changes in distributions through
4998 time. It further includes methods for visualizing outcomes, selecting
4999 thresholds, calculating measures of accuracy and landscape fragmentation
5001 (license license:gpl3+)))
5003 (define-public r-scatterplot3d
5005 (name "r-scatterplot3d")
5010 (uri (cran-uri "scatterplot3d" version))
5013 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5014 (build-system r-build-system)
5015 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5016 (synopsis "3D scatter plot")
5017 (description "This package provides an implementation of scatter plots for
5018 plotting. a three dimensional point cloud.")
5019 (license license:gpl2)))
5021 (define-public r-ggridges
5028 (uri (cran-uri "ggridges" version))
5031 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5032 (build-system r-build-system)
5034 `(("r-ggplot2" ,r-ggplot2)
5036 ("r-scales" ,r-scales)
5037 ("r-withr" ,r-withr)))
5039 `(("r-knitr" ,r-knitr)))
5040 (home-page "https://github.com/clauswilke/ggridges")
5041 (synopsis "Ridgeline plots in ggplot2")
5043 "Ridgeline plots 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-ggjoy
5055 (uri (cran-uri "ggjoy" version))
5058 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5059 (build-system r-build-system)
5061 `(("r-ggplot2" ,r-ggplot2)
5062 ("r-ggridges" ,r-ggridges)))
5063 (home-page "https://github.com/clauswilke/ggjoy")
5064 (synopsis "Joyplots in ggplot2")
5065 (description "Joyplots provide a convenient way of visualizing changes in
5066 distributions over time or space. This package enables the creation of such
5067 plots in @code{ggplot2}.")
5068 (license license:gpl2)))
5070 (define-public r-cli
5077 (uri (cran-uri "cli" version))
5080 "0l1s9yv23bc7mm0hfdlamgz4wjfrisv8aylr65ihjs98jsynrkg3"))))
5081 (build-system r-build-system)
5083 `(("r-glue" ,r-glue)))
5084 (home-page "https://github.com/r-lib/cli#readme")
5085 (synopsis "Helpers for developing command line interfaces")
5086 (description "This package provides a suite of tools designed to build
5087 attractive command line interfaces (CLIs). It includes tools for drawing
5088 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5089 (license license:expat)))
5091 (define-public r-argparser
5093 (name "r-argparser")
5098 (uri (cran-uri "argparser" version))
5101 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5102 (build-system r-build-system)
5103 (home-page "https://bitbucket.org/djhshih/argparser")
5104 (synopsis "Command-line argument parser")
5106 "This package provides a cross-platform command-line argument parser
5107 written purely in R with no external dependencies. It is useful with the
5108 Rscript front-end and facilitates turning an R script into an executable
5110 (license license:gpl3+)))
5112 (define-public r-debugme
5119 (uri (cran-uri "debugme" version))
5122 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5123 (build-system r-build-system)
5124 (propagated-inputs `(("r-crayon" ,r-crayon)))
5125 (home-page "https://github.com/r-lib/debugme#readme")
5126 (synopsis "Debug R packages")
5128 "This package allows the user to specify debug messages as special string
5129 constants, and control debugging of packages via environment variables.")
5130 (license license:expat)))
5132 (define-public r-processx
5139 (uri (cran-uri "processx" version))
5141 (base32 "1z7zag7g041xlhzhkdfl33y2phc877h1pwj9k69p69b967qi6p6k"))))
5142 (build-system r-build-system)
5146 (home-page "https://github.com/r-lib/processx3")
5147 (synopsis "Execute and control system processes")
5149 "This package provides portable tools to run system processes in the
5150 background. It can check if a background process is running; wait on a
5151 background process to finish; get the exit status of finished processes; kill
5152 background processes and their children; restart processes. It can read the
5153 standard output and error of the processes, using non-blocking connections.
5154 @code{processx} can poll a process for standard output or error, with a
5155 timeout. It can also poll several processes at once.")
5156 (license license:expat)))
5158 (define-public r-tsp
5165 (uri (cran-uri "TSP" version))
5168 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5169 (properties `((upstream-name . "TSP")))
5170 (build-system r-build-system)
5171 (propagated-inputs `(("r-foreach" ,r-foreach)))
5172 (home-page "https://cran.r-project.org/web/packages/TSP/")
5173 (synopsis "Traveling salesperson problem (TSP)")
5174 (description "This package provides basic infrastructure and some
5175 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5176 traveling salesman problem).")
5177 (license license:gpl3)))
5179 (define-public r-qap
5186 (uri (cran-uri "qap" version))
5189 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5190 (build-system r-build-system)
5191 (native-inputs `(("gfortran" ,gfortran)))
5192 (home-page "https://cran.r-project.org/web/packages/qap/")
5193 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5194 (description "This package implements heuristics for the @dfn{quadratic
5195 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5197 (license license:gpl3)))
5199 (define-public r-gclus
5206 (uri (cran-uri "gclus" version))
5209 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5210 (build-system r-build-system)
5211 (propagated-inputs `(("r-cluster" ,r-cluster)))
5212 (home-page "https://cran.r-project.org/web/packages/gclus/")
5213 (synopsis "Clustering graphics")
5214 (description "This package orders panels in scatterplot matrices and
5215 parallel coordinate displays by some merit index. It contains various indices
5216 of merit, ordering functions, and enhanced versions of @code{pairs} and
5217 @code{parcoord} which color panels according to their merit level.")
5218 (license license:gpl2+)))
5220 (define-public r-webshot
5227 (uri (cran-uri "webshot" version))
5230 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5231 (build-system r-build-system)
5233 `(("r-callr" ,r-callr)
5234 ("r-jsonlite" ,r-jsonlite)
5235 ("r-magrittr" ,r-magrittr)))
5236 (home-page "https://github.com/wch/webshot/")
5237 (synopsis "Take screenshots of web pages")
5239 "Webshot makes it easy to take screenshots of web pages from within R.
5240 It can also run Shiny applications locally and take screenshots of the
5241 application; and it can render and screenshot static as well as interactive R
5242 Markdown documents.")
5243 (license license:gpl2)))
5245 (define-public r-seriation
5247 (name "r-seriation")
5252 (uri (cran-uri "seriation" version))
5255 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5256 (build-system r-build-system)
5258 `(("r-cluster" ,r-cluster)
5259 ("r-colorspace" ,r-colorspace)
5260 ("r-dendextend" ,r-dendextend)
5261 ("r-gclus" ,r-gclus)
5262 ("r-gplots" ,r-gplots)
5265 ("r-registry" ,r-registry)
5267 (native-inputs `(("gfortran" ,gfortran)))
5268 (home-page "https://s2.smu.edu/IDA/seriation/")
5269 (synopsis "Infrastructure for ordering objects using seriation")
5271 "This package provides infrastructure for seriation with an
5272 implementation of several seriation/sequencing techniques to reorder matrices,
5273 dissimilarity matrices, and dendrograms. It also provides (optimally)
5274 reordered heatmaps, color images and clustering visualizations like
5275 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5277 (license license:gpl3)))
5279 (define-public r-xfun
5286 (uri (cran-uri "xfun" version))
5288 (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y"))))
5289 (build-system r-build-system)
5290 ;; knitr itself depends on xfun
5293 `(("r-knitr" ,r-knitr)))
5294 (home-page "https://github.com/yihui/xfun")
5295 (synopsis "Miscellaneous functions")
5297 "This package provides miscellaneous functions commonly used in other
5298 packages maintained by Yihui Xie.")
5299 (license license:expat)))
5301 (define-public r-utf8
5308 (uri (cran-uri "utf8" version))
5311 "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk"))))
5312 (build-system r-build-system)
5314 `(("r-knitr" ,r-knitr)))
5315 (home-page "https://github.com/patperry/r-utf8")
5316 (synopsis "Unicode text processing")
5318 "This package provides tools to process and print UTF-8 encoded
5319 international text (Unicode). Input, validate, normalize, encode, format, and
5321 (license license:asl2.0)))
5323 (define-public r-zeallot
5330 (uri (cran-uri "zeallot" version))
5333 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5334 (build-system r-build-system)
5335 (home-page "https://github.com/nteetor/zeallot")
5336 (synopsis "Multiple, unpacking, and destructuring assignment")
5338 "This package provides a @code{%<-%} operator to perform multiple,
5339 unpacking, and destructuring assignment in R. The operator unpacks the
5340 right-hand side of an assignment into multiple values and assigns these values
5341 to variables on the left-hand side of the assignment.")
5342 (license license:expat)))
5344 (define-public r-vctrs
5351 (uri (cran-uri "vctrs" version))
5354 "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas"))))
5355 (build-system r-build-system)
5357 `(("r-ellipsis" ,r-ellipsis)
5359 ("r-rlang" ,r-rlang)))
5361 `(("r-knitr" ,r-knitr)))
5362 (home-page "https://github.com/r-lib/vctrs")
5363 (synopsis "Vector helpers")
5365 "There are three main goals to the @code{vctrs} package:
5368 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5369 @code{length()} and @code{class()}. These definitions are paired with a
5370 framework for type-coercion and size-recycling.
5371 @item To define type- and size-stability as desirable function properties, use
5372 them to analyse existing base function, and to propose better alternatives.
5373 This work has been particularly motivated by thinking about the ideal
5374 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5375 @item To provide a new @code{vctr} base class that makes it easy to create new
5376 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5377 a few new @code{vctrs} generics, making implementation considerably simpler
5380 (license license:gpl3)))
5382 (define-public r-pillar
5389 (uri (cran-uri "pillar" version))
5392 "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c"))))
5393 (build-system r-build-system)
5396 ("r-crayon" ,r-crayon)
5397 ("r-ellipsis" ,r-ellipsis)
5398 ("r-fansi" ,r-fansi)
5399 ("r-lifecycle" ,r-lifecycle)
5400 ("r-rlang" ,r-rlang)
5402 ("r-vctrs" ,r-vctrs)))
5404 `(("r-knitr" ,r-knitr)))
5405 (home-page "https://github.com/r-lib/pillar")
5406 (synopsis "Coloured formatting for columns")
5408 "This package provides a @code{pillar} generic designed for formatting
5409 columns of data using the full range of colours provided by modern
5411 (license license:gpl3)))
5413 (define-public r-uuid
5420 (uri (cran-uri "uuid" version))
5423 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5424 (build-system r-build-system)
5425 (home-page "https://www.rforge.net/uuid")
5426 (synopsis "Tools for generating and handling of UUIDs")
5428 "This package provides tools for generating and handling of
5429 @dfn{Universally Unique Identifiers} (UUIDs).")
5430 (license license:expat)))
5432 (define-public r-tinytex
5439 (uri (cran-uri "tinytex" version))
5442 "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p"))))
5443 (build-system r-build-system)
5445 `(("r-xfun" ,r-xfun)))
5446 (home-page "https://github.com/yihui/tinytex")
5447 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5449 "This package provides helper functions to install and maintain the LaTeX
5450 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5451 easy-to-maintain version of TeX Live. This package also contains helper
5452 functions to compile LaTeX documents, and install missing LaTeX packages
5454 (license license:expat)))
5456 (define-public r-tinytest
5463 (uri (cran-uri "tinytest" version))
5466 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5467 (properties `((upstream-name . "tinytest")))
5468 (build-system r-build-system)
5469 (home-page "https://github.com/markvanderloo/tinytest")
5470 (synopsis "Lightweight unit testing framework")
5472 "This package provides a lightweight unit testing framework. Main
5476 @item install tests with the package;
5477 @item test results are treated as data that can be stored and manipulated;
5478 @item test files are R scripts interspersed with test commands, that can be
5480 @item fully automated build-install-test sequence for packages;
5481 @item skip tests when not run locally (e.g. on CRAN);
5482 @item flexible and configurable output printing;
5483 @item compare computed output with output stored with the package;
5484 @item run tests in parallel;
5485 @item extensible by other packages;
5486 @item report side effects.
5489 (license license:gpl3)))
5491 (define-public r-network
5498 (uri (cran-uri "network" version))
5501 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5502 (build-system r-build-system)
5504 `(("r-magrittr" ,r-magrittr)
5505 ("r-tibble" ,r-tibble)))
5506 (home-page "https://statnet.org/")
5507 (synopsis "Classes for relational data")
5509 "This package provides tools to create and modify network objects. The
5510 @code{network} class can represent a range of relational data types, and
5511 supports arbitrary vertex/edge/graph attributes.")
5512 (license license:gpl2+)))
5514 (define-public r-stabs
5521 (uri (cran-uri "stabs" version))
5524 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5525 (build-system r-build-system)
5527 `(("r-knitr" ,r-knitr)))
5528 (home-page "https://github.com/hofnerb/stabs")
5529 (synopsis "Stability selection with error control")
5531 "This package provides resampling procedures to assess the stability of
5532 selected variables with additional finite sample error control for
5533 high-dimensional variable selection procedures such as Lasso or boosting.
5534 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5535 complementary pairs stability selection with improved error bounds
5536 (Shah & Samworth, 2013) are implemented. The package can be combined with
5537 arbitrary user specified variable selection approaches.")
5538 (license license:gpl2)))
5540 (define-public r-rle
5547 (uri (cran-uri "rle" version))
5550 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5551 (properties `((upstream-name . "rle")))
5552 (build-system r-build-system)
5553 (home-page "https://cran.r-project.org/web/packages/rle/")
5554 (synopsis "Common functions for run-length encoded vectors")
5556 "This package provides common @code{base} and @code{stats} methods for
5557 @code{rle} objects, aiming to make it possible to treat them transparently as
5559 (license license:gpl3)))
5561 (define-public r-statnet-common
5563 (name "r-statnet-common")
5568 (uri (cran-uri "statnet.common" version))
5571 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5573 `((upstream-name . "statnet.common")))
5574 (build-system r-build-system)
5576 `(("r-coda" ,r-coda)
5578 (home-page "https://statnet.org")
5579 (synopsis "R scripts and utilities used by the Statnet software")
5580 (description "This package provides non-statistical utilities used by the
5581 software developed by the Statnet Project.")
5582 (license license:gpl3)))
5584 (define-public r-statcheck
5586 (name "r-statcheck")
5591 (uri (cran-uri "statcheck" version))
5594 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5595 (build-system r-build-system)
5597 `(("r-ggplot2" ,r-ggplot2)
5599 ("r-rmarkdown" ,r-rmarkdown)))
5600 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5601 (synopsis "Extract statistics from articles and recompute p-values")
5602 (description "This package can automatically extract statistical
5603 null-hypothesis significant testing (NHST) results from articles and recompute
5604 the p-values based on the reported test statistic and degrees of freedom to
5605 detect possible inconsistencies.")
5606 (license license:gpl2)))
5608 (define-public r-sna
5615 (uri (cran-uri "sna" version))
5618 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5619 (build-system r-build-system)
5621 `(("r-network" ,r-network)
5622 ("r-statnet-common" ,r-statnet-common)))
5623 (home-page "https://statnet.org")
5624 (synopsis "Tools for social network analysis")
5626 "This package provides a range of tools for social network analysis,
5627 including node and graph-level indices, structural distance and covariance
5628 methods, structural equivalence detection, network regression, random graph
5629 generation, and 2D/3D network visualization.")
5630 (license license:gpl2+)))
5632 (define-public r-tfisher
5639 (uri (cran-uri "TFisher" version))
5642 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5643 (properties `((upstream-name . "TFisher")))
5644 (build-system r-build-system)
5646 `(("r-matrix" ,r-matrix)
5647 ("r-mvtnorm" ,r-mvtnorm)
5649 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5650 (synopsis "Optimal thresholding Fisher's p-value combination method")
5652 "This package provides the @dfn{cumulative distribution function} (CDF),
5653 quantile, and statistical power calculator for a collection of thresholding
5654 Fisher's p-value combination methods, including Fisher's p-value combination
5655 method, truncated product method and, in particular, soft-thresholding
5656 Fisher's p-value combination method which is proven to be optimal in some
5657 context of signal detection. The p-value calculator for the omnibus version
5658 of these tests are also included.")
5659 (license license:gpl2)))
5661 (define-public r-ttr
5668 (uri (cran-uri "TTR" version))
5671 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5672 (properties `((upstream-name . "TTR")))
5673 (build-system r-build-system)
5675 `(("r-curl" ,r-curl)
5678 (home-page "https://github.com/joshuaulrich/TTR")
5679 (synopsis "Technical trading rules")
5681 "This package provides functions and data to construct technical trading
5683 (license license:gpl2)))
5685 (define-public r-leaps
5692 (uri (cran-uri "leaps" version))
5695 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5696 (build-system r-build-system)
5697 (native-inputs `(("gfortran" ,gfortran)))
5698 (home-page "https://cran.r-project.org/web/packages/leaps/")
5699 (synopsis "Regression subset selection")
5701 "This package provides tools for regression subset selection, including
5702 exhaustive search.")
5703 (license license:gpl2+)))
5705 (define-public r-splus2r
5712 (uri (cran-uri "splus2R" version))
5715 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5716 (properties `((upstream-name . "splus2R")))
5717 (build-system r-build-system)
5718 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5719 (synopsis "Supplemental S-PLUS functionality in R")
5721 "Currently there are many functions in S-PLUS that are missing in R. To
5722 facilitate the conversion of S-PLUS packages to R packages, this package
5723 provides some missing S-PLUS functionality in R.")
5724 (license license:gpl2)))
5726 (define-public r-ifultools
5728 (name "r-ifultools")
5733 (uri (cran-uri "ifultools" version))
5736 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5737 (build-system r-build-system)
5739 `(("r-mass" ,r-mass)
5740 ("r-splus2r" ,r-splus2r)))
5741 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5742 (synopsis "Insightful research tools")
5743 (description "This package provides C code used by the wmtsa, fractal, and
5745 (license license:gpl2)))
5747 (define-public r-sapa
5754 (uri (cran-uri "sapa" version))
5757 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
5758 (build-system r-build-system)
5760 `(("r-ifultools" ,r-ifultools)
5761 ("r-splus2r" ,r-splus2r)))
5762 (home-page "https://cran.r-project.org/web/packages/sapa/")
5763 (synopsis "Spectral analysis for physical applications")
5764 (description "This package provides software for the book Spectral
5765 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5766 Cambridge University Press, 1993.")
5767 (license license:gpl2)))
5769 (define-public r-aggregation
5771 (name "r-aggregation")
5776 (uri (cran-uri "aggregation" version))
5779 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5780 (build-system r-build-system)
5781 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5782 (synopsis "Methods for p-value aggregation")
5784 "This package contains functionality for performing the following methods
5785 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5786 Fisher's method), and Sidak correction.")
5787 (license license:gpl3)))
5789 (define-public r-quantmod
5796 (uri (cran-uri "quantmod" version))
5799 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5800 (build-system r-build-system)
5802 `(("r-curl" ,r-curl)
5806 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5807 (synopsis "Quantitative financial modelling framework")
5808 (description "This package provides a quantitative financial modelling
5809 framework to allow users to specify, build, trade, and analyse quantitative
5810 financial trading strategies.")
5811 (license license:gpl3)))
5813 (define-public r-tseries
5820 (uri (cran-uri "tseries" version))
5823 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5824 (build-system r-build-system)
5826 `(("r-quadprog" ,r-quadprog)
5827 ("r-quantmod" ,r-quantmod)
5830 `(("gfortran" ,gfortran)))
5831 (home-page "https://cran.r-project.org/web/packages/tseries/")
5832 (synopsis "Time series analysis and computational finance")
5834 "This package provides functions relating to time series analysis and
5835 computational finance.")
5836 (license license:gpl2)))
5838 (define-public r-wmtsa
5845 (uri (cran-uri "wmtsa" version))
5848 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5849 (build-system r-build-system)
5851 `(("r-ifultools" ,r-ifultools)
5853 ("r-splus2r" ,r-splus2r)))
5854 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5855 (synopsis "Wavelet methods for time series analysis")
5857 "This package provides software to accompany the book \"Wavelet Methods
5858 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5859 University Press, 2000.")
5860 (license license:gpl2)))
5862 (define-public r-tsa
5869 (uri (cran-uri "TSA" version))
5872 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5873 (properties `((upstream-name . "TSA")))
5874 (build-system r-build-system)
5876 `(("r-leaps" ,r-leaps)
5877 ("r-locfit" ,r-locfit)
5879 ("r-tseries" ,r-tseries)))
5880 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5881 (synopsis "Time series analysis")
5883 "This package contains R functions and datasets detailed in the book
5884 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5885 Cryer and Kung-Sik Chan.")
5886 (license license:gpl2+)))
5888 (define-public r-extradistr
5890 (name "r-extradistr")
5895 (uri (cran-uri "extraDistr" version))
5898 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5899 (properties `((upstream-name . "extraDistr")))
5900 (build-system r-build-system)
5902 `(("r-rcpp" ,r-rcpp)))
5903 (home-page "https://github.com/twolodzko/extraDistr")
5904 (synopsis "Additional univariate and multivariate distributions")
5906 "This package implements density, distribution functions, quantile
5907 functions and random generation functions for a large number of univariate and
5908 multivariate distributions.")
5909 (license license:gpl2)))
5911 (define-public r-fractal
5918 (uri (cran-uri "fractal" version))
5921 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5922 (build-system r-build-system)
5924 `(("r-ifultools" ,r-ifultools)
5927 ("r-scatterplot3d" ,r-scatterplot3d)
5928 ("r-splus2r" ,r-splus2r)
5929 ("r-wmtsa" ,r-wmtsa)))
5930 (home-page "https://cran.r-project.org/web/packages/fractal/")
5931 (synopsis "Fractal time series modeling and analysis")
5933 "This package provides tools for stochastic fractal and deterministic
5934 chaotic time series analysis.")
5935 (license license:gpl2)))
5937 (define-public r-urca
5944 (uri (cran-uri "urca" version))
5947 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5948 (build-system r-build-system)
5949 (propagated-inputs `(("r-nlme" ,r-nlme)))
5950 (native-inputs `(("gfortran" ,gfortran)))
5951 (home-page "https://cran.r-project.org/web/packages/urca/")
5952 (synopsis "Unit root and cointegration tests for time series data")
5954 "This package provides unit root and cointegration tests encountered in
5955 applied econometric analysis.")
5956 (license license:gpl2+)))
5958 (define-public r-cubature
5965 (uri (cran-uri "cubature" version))
5968 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5969 (build-system r-build-system)
5971 `(("r-rcpp" ,r-rcpp)))
5973 `(("r-knitr" ,r-knitr)))
5974 (home-page "https://github.com/bnaras/cubature")
5975 (synopsis "Adaptive multivariate integration over hypercubes")
5977 "This package is an R wrapper around the cubature C library for adaptive
5978 multivariate integration over hypercubes. This version provides both
5979 @code{hcubature} and @code{pcubature} routines in addition to a vector
5981 ;; The included cubature C library is released under GPLv2+, but the
5982 ;; wrapper declares the license to be GPLv3+.
5983 (license (list license:gpl2+ license:gpl3+))))
5985 (define-public r-trend
5992 (uri (cran-uri "trend" version))
5995 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5996 (build-system r-build-system)
5998 `(("r-extradistr" ,r-extradistr)))
6000 `(("gfortran" ,gfortran)))
6001 (home-page "https://cran.r-project.org/web/packages/trend/")
6002 (synopsis "Non-parametric trend tests and change-point detection")
6004 "The analysis of environmental data often requires the detection of
6005 trends and change-points. This package includes tests for trend
6006 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6007 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6008 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6009 correlation trend test), change-point detection (Lanzante's test procedures,
6010 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6011 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6012 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6013 sample Robust Rank-Order Distributional Test.")
6014 (license license:gpl3)))
6016 (define-public r-expm
6023 (uri (cran-uri "expm" version))
6026 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6027 (build-system r-build-system)
6028 (propagated-inputs `(("r-matrix" ,r-matrix)))
6029 (native-inputs `(("gfortran" ,gfortran)))
6030 (home-page "https://r-forge.r-project.org/projects/expm/")
6031 (synopsis "Tools for matrix exponentials and related quantities")
6033 "This package provides tools for the computation of the matrix
6034 exponential, logarithm, square root, and related quantities.")
6035 (license license:gpl2+)))
6037 (define-public r-complexplus
6039 (name "r-complexplus")
6044 (uri (cran-uri "complexplus" version))
6047 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6048 (build-system r-build-system)
6050 `(("r-expm" ,r-expm)
6051 ("r-matrix" ,r-matrix)))
6052 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6053 (synopsis "Functions of complex or real variables")
6055 "This package extends several functions to the complex domain, including
6056 the matrix exponential and logarithm, and the determinant.")
6057 (license license:gpl2)))
6059 (define-public r-phontools
6061 (name "r-phontools")
6066 (uri (cran-uri "phonTools" version))
6069 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6070 (properties `((upstream-name . "phonTools")))
6071 (build-system r-build-system)
6072 (home-page "http://www.santiagobarreda.com/rscripts.html")
6073 (synopsis "Tools for phonetic and acoustic analyses")
6075 "This package contains tools for the organization, display, and analysis
6076 of the sorts of data frequently encountered in phonetics research and
6077 experimentation, including the easy creation of IPA vowel plots, and the
6078 creation and manipulation of WAVE audio files.")
6079 (license license:bsd-2)))
6088 (uri (cran-uri "np" version))
6091 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6092 (build-system r-build-system)
6094 `(("r-boot" ,r-boot)
6095 ("r-cubature" ,r-cubature)
6096 ("r-quadprog" ,r-quadprog)
6097 ("r-quantreg" ,r-quantreg)))
6098 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6099 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6100 (description "This package provides non-parametric (and semi-parametric)
6101 kernel methods that seamlessly handle a mix of continuous, unordered, and
6102 ordered factor data types.")
6103 ;; Any version of the GPL.
6104 (license license:gpl3+)))
6106 (define-public r-powerplus
6108 (name "r-powerplus")
6113 (uri (cran-uri "powerplus" version))
6116 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6117 (build-system r-build-system)
6119 `(("r-complexplus" ,r-complexplus)
6122 ("r-matrix" ,r-matrix)
6123 ("r-phontools" ,r-phontools)))
6124 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6125 (synopsis "Exponentiation operations")
6127 "This package provides tools for the computation of matrix and scalar
6129 (license license:gpl2)))
6131 (define-public r-egg
6138 (uri (cran-uri "egg" version))
6141 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6142 (properties `((upstream-name . "egg")))
6143 (build-system r-build-system)
6145 `(("r-ggplot2" ,r-ggplot2)
6146 ("r-gridextra" ,r-gridextra)
6147 ("r-gtable" ,r-gtable)))
6148 (home-page "https://cran.r-project.org/web/packages/egg")
6149 (synopsis "Extensions for ggplot2")
6151 "This package provides miscellaneous functions to help customize ggplot2
6152 objects. High-level functions are provided to post-process ggplot2 layouts
6153 and allow alignment between plot panels, as well as setting panel sizes to
6154 fixed values. Other functions include a custom @code{geom}, and helper
6155 functions to enforce symmetric scales or add tags to facetted plots.")
6156 (license license:gpl3)))
6158 (define-public r-heatmaply
6160 (name "r-heatmaply")
6165 (uri (cran-uri "heatmaply" version))
6168 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6169 (build-system r-build-system)
6171 `(("r-assertthat" ,r-assertthat)
6172 ("r-colorspace" ,r-colorspace)
6173 ("r-dendextend" ,r-dendextend)
6175 ("r-ggplot2" ,r-ggplot2)
6176 ("r-htmlwidgets" ,r-htmlwidgets)
6177 ("r-magrittr" ,r-magrittr)
6178 ("r-plotly" ,r-plotly)
6179 ("r-rcolorbrewer" ,r-rcolorbrewer)
6180 ("r-reshape2" ,r-reshape2)
6181 ("r-scales" ,r-scales)
6182 ("r-seriation" ,r-seriation)
6183 ("r-viridis" ,r-viridis)
6184 ("r-webshot" ,r-webshot)))
6186 `(("r-knitr" ,r-knitr)))
6187 (home-page "https://cran.r-project.org/package=heatmaply")
6188 (synopsis "Interactive cluster heat maps using plotly")
6190 "This package enables you to create interactive cluster heatmaps that can
6191 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6192 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6193 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6194 a popular graphical method for visualizing high-dimensional data, in which a
6195 table of numbers is encoded as a grid of colored cells. The rows and columns
6196 of the matrix are ordered to highlight patterns and are often accompanied by
6198 ;; Either version of the license.
6199 (license (list license:gpl2 license:gpl3))))
6208 (uri (cran-uri "h5" version))
6211 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6212 (build-system r-build-system)
6217 `(("which" ,which)))
6219 `(("r-rcpp" ,r-rcpp)))
6220 (home-page "https://github.com/mannau/h5")
6221 (synopsis "Interface to the HDF5 Library")
6223 "This package provides an S4 interface to the HDF5 library supporting
6224 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6225 binary files in a language independent format. The HDF5 format can therefore
6226 be used as an alternative to R's save/load mechanism. Since h5 is able to
6227 access only subsets of stored data it can also handle data sets which do not
6229 (license license:bsd-2)))
6231 (define-public r-cgdsr
6238 (uri (cran-uri "cgdsr" version))
6241 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6242 (build-system r-build-system)
6244 `(("r-httr" ,r-httr)
6245 ("r-r-methodss3" ,r-r-methodss3)
6246 ("r-r-oo" ,r-r-oo)))
6247 (home-page "https://github.com/cBioPortal/cgdsr")
6248 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6250 "This package provides a basic set of R functions for querying the Cancer
6251 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6252 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6253 (license license:lgpl3)))
6255 (define-public r-import
6262 (uri (cran-uri "import" version))
6265 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6266 (build-system r-build-system)
6268 `(("r-knitr" ,r-knitr)))
6269 (home-page "https://github.com/smbache/import")
6270 (synopsis "Import mechanism for R")
6272 "This is an alternative mechanism for importing objects from packages.
6273 The syntax allows for importing multiple objects from a package with a single
6274 command in an expressive way. The import package bridges some of the gap
6275 between using @code{library} (or @code{require}) and direct (single-object)
6276 imports. Furthermore the imported objects are not placed in the current
6277 environment. It is also possible to import objects from stand-alone @code{.R}
6279 (license license:expat)))
6281 (define-public r-shinyace
6288 (uri (cran-uri "shinyAce" version))
6291 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6292 (properties `((upstream-name . "shinyAce")))
6293 (build-system r-build-system)
6295 `(("r-shiny" ,r-shiny)
6296 ("r-jsonlite" ,r-jsonlite)))
6297 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6298 (synopsis "Ace editor bindings for Shiny")
6300 "This package provides Ace editor bindings to enable a rich text editing
6301 environment within Shiny.")
6302 (license license:expat)))
6304 (define-public r-randomizr
6306 (name "r-randomizr")
6311 (uri (cran-uri "randomizr" version))
6314 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6315 (properties `((upstream-name . "randomizr")))
6316 (build-system r-build-system)
6318 `(("r-knitr" ,r-knitr)))
6319 (home-page "https://declaredesign.org/r/randomizr/")
6320 (synopsis "Tools for common forms of random assignment and sampling")
6322 "This package provides tools for generating random assignments for common
6323 experimental designs and random samples for common sampling designs.")
6324 (license license:expat)))
6326 (define-public r-base64url
6328 (name "r-base64url")
6333 (uri (cran-uri "base64url" version))
6336 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6337 (build-system r-build-system)
6339 `(("r-backports" ,r-backports)))
6340 (home-page "https://github.com/mllg/base64url")
6341 (synopsis "Fast and URL-safe base64 encoder and decoder")
6343 "This package provides a URL-safe base64 encoder and decoder. In
6344 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6345 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6346 encoder does not fill the string with trailing @code{=}. The resulting
6347 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6348 and thus are safe to use in URLs or for file names. The package also comes
6349 with a simple base32 encoder/decoder suited for case insensitive file
6351 (license license:gpl3)))
6353 (define-public r-radiant-data
6355 (name "r-radiant-data")
6360 (uri (cran-uri "radiant.data" version))
6363 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6364 (modules '((guix build utils)))
6367 ;; Delete files that are under CC-NC-SA.
6368 (delete-file-recursively "inst/app/tools/help")
6370 (properties `((upstream-name . "radiant.data")))
6371 (build-system r-build-system)
6373 `(("r-base64enc" ,r-base64enc)
6374 ("r-broom" ,r-broom)
6377 ("r-dplyr" ,r-dplyr)
6380 ("r-ggplot2" ,r-ggplot2)
6381 ("r-import" ,r-import)
6382 ("r-jsonlite" ,r-jsonlite)
6383 ("r-knitr" ,r-knitr)
6384 ("r-lubridate" ,r-lubridate)
6385 ("r-magrittr" ,r-magrittr)
6386 ("r-markdown" ,r-markdown)
6388 ("r-patchwork" ,r-patchwork)
6389 ("r-plotly" ,r-plotly)
6390 ("r-psych" ,r-psych)
6391 ("r-randomizr" ,r-randomizr)
6392 ("r-readr" ,r-readr)
6393 ("r-readxl" ,r-readxl)
6394 ("r-rlang" ,r-rlang)
6395 ("r-rmarkdown" ,r-rmarkdown)
6396 ("r-rstudioapi" ,r-rstudioapi)
6397 ("r-scales" ,r-scales)
6398 ("r-shiny" ,r-shiny)
6399 ("r-shinyfiles" ,r-shinyfiles)
6400 ("r-shinyace" ,r-shinyace)
6401 ("r-stringi" ,r-stringi)
6402 ("r-tibble" ,r-tibble)
6403 ("r-tidyr" ,r-tidyr)
6404 ("r-writexl" ,r-writexl)))
6405 (home-page "https://github.com/radiant-rstats/radiant.data")
6406 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6408 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6409 visualizing, summarizing, transforming, and combining data. It also contains
6410 functionality to generate reproducible reports of the analyses conducted in
6412 (license license:agpl3)))
6414 (define-public r-algdesign
6416 (name "r-algdesign")
6421 (uri (cran-uri "AlgDesign" version))
6423 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6424 (properties `((upstream-name . "AlgDesign")))
6425 (build-system r-build-system)
6426 (home-page "https://github.com/jvbraun/AlgDesign")
6427 (synopsis "Algorithmic experimental design")
6429 "This package provides tools to calculate exact and approximate theory
6430 experimental designs for D, A, and I criteria. Very large designs may be
6431 created. Experimental designs may be blocked or blocked designs created from
6432 a candidate list, using several criteria. The blocking can be done when whole
6433 and within plot factors interact.")
6434 (license license:gpl2+)))
6436 (define-public r-signal
6443 (uri (cran-uri "signal" version))
6446 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6447 (build-system r-build-system)
6448 (propagated-inputs `(("r-mass" ,r-mass)))
6449 (native-inputs `(("gfortran" ,gfortran)))
6450 (home-page "https://cran.r-project.org/web/packages/signal/")
6451 (synopsis "Signal processing")
6453 "This package provides a set of signal processing functions originally
6454 written for Matlab and GNU Octave. It includes filter generation utilities,
6455 filtering functions, resampling routines, and visualization of filter models.
6456 It also includes interpolation functions.")
6457 (license license:gpl2)))
6459 (define-public r-gsubfn
6466 (uri (cran-uri "gsubfn" version))
6469 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6470 (build-system r-build-system)
6471 (propagated-inputs `(("r-proto" ,r-proto)))
6472 (home-page "https://code.google.com/archive/p/gsubfn/")
6473 (synopsis "Utilities for strings and function arguments.")
6475 "This package provides @code{gsubfn} which is like @code{gsub} but can
6476 take a replacement function or certain other objects instead of the
6477 replacement string. Matches and back references are input to the replacement
6478 function and replaced by the function output. @code{gsubfn} can be used to
6479 split strings based on content rather than delimiters and for quasi-perl-style
6480 string interpolation. The package also has facilities for translating
6481 formulas to functions and allowing such formulas in function calls instead of
6483 (license license:gpl2+)))
6485 (define-public r-sqldf
6492 (uri (cran-uri "sqldf" version))
6495 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6496 (build-system r-build-system)
6498 `(("r-chron" ,r-chron)
6500 ("r-gsubfn" ,r-gsubfn)
6501 ("r-proto" ,r-proto)
6502 ("r-rsqlite" ,r-rsqlite)))
6503 (home-page "https://github.com/ggrothendieck/sqldf")
6504 (synopsis "Manipulate R data frames using SQL")
6506 "The @code{sqldf} function is typically passed a single argument which is
6507 an SQL select statement where the table names are ordinary R data frame names.
6508 @code{sqldf} transparently sets up a database, imports the data frames into
6509 that database, performs the SQL statement and returns the result using a
6510 heuristic to determine which class to assign to each column of the returned
6511 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6512 used to read filtered files into R even if the original files are larger than
6513 R itself can handle.")
6514 (license license:gpl2)))
6516 (define-public r-abind
6523 (uri (cran-uri "abind" version))
6526 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6527 (build-system r-build-system)
6528 (home-page "https://cran.r-project.org/web/packages/abind/")
6529 (synopsis "Combine multidimensional arrays")
6531 "This package provides tools to combine multidimensional arrays into a
6532 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6533 works with vectors, matrices, and higher-dimensional arrays. It also provides
6534 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6535 extracting and replacing data in arrays.")
6536 (license license:lgpl2.0+)))
6538 (define-public r-prroc
6545 (uri (cran-uri "PRROC" version))
6548 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6549 (properties `((upstream-name . "PRROC")))
6550 (build-system r-build-system)
6551 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6552 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6554 "This package computes the areas under the @dfn{precision-recall} (PR)
6555 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6556 contrast to other implementations, the interpolation between points of the PR
6557 curve is done by a non-linear piecewise function. In addition to the areas
6558 under the curves, the curves themselves can also be computed and plotted by a
6559 specific S3-method.")
6560 (license license:gpl3)))
6562 (define-public r-vim
6569 (uri (cran-uri "VIM" version))
6572 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6573 (properties `((upstream-name . "VIM")))
6574 (build-system r-build-system)
6577 ("r-colorspace" ,r-colorspace)
6578 ("r-data-table" ,r-data-table)
6579 ("r-e1071" ,r-e1071)
6580 ("r-laeken" ,r-laeken)
6581 ("r-magrittr" ,r-magrittr)
6584 ("r-ranger" ,r-ranger)
6586 ("r-robustbase" ,r-robustbase)
6590 `(("r-knitr" ,r-knitr)))
6591 (home-page "https://github.com/alexkowa/VIM")
6592 (synopsis "Visualization and imputation of missing values")
6594 "This package provides tools for the visualization of missing and/or
6595 imputed values are introduced, which can be used for exploring the data and
6596 the structure of the missing and/or imputed values. Depending on this
6597 structure of the missing values, the corresponding methods may help to
6598 identify the mechanism generating the missing values and explore the
6599 data including missing values. In addition, the quality of imputation can be
6600 visually explored using various univariate, bivariate, multiple and
6601 multivariate plot methods.")
6602 (license license:gpl2+)))
6604 (define-public r-fnn
6611 (uri (cran-uri "FNN" version))
6614 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6615 (properties `((upstream-name . "FNN")))
6616 (build-system r-build-system)
6617 (home-page "https://cran.r-project.org/web/packages/FNN")
6618 (synopsis "Fast nearest neighbor search algorithms and applications")
6620 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6621 search algorithms. Related applications including KNN classification,
6622 regression and information measures are implemented.")
6623 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6624 ;; later can be used.
6625 (license license:gpl2+)))
6627 (define-public r-smoother
6634 (uri (cran-uri "smoother" version))
6637 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6638 (build-system r-build-system)
6640 `(("r-ttr" ,r-ttr)))
6641 (home-page "https://cran.r-project.org/web/packages/smoother")
6642 (synopsis "Functions relating to the smoothing of numerical data")
6644 "This package provides a collection of methods for smoothing numerical
6645 data, commencing with a port of the Matlab gaussian window smoothing function.
6646 In addition, several functions typically used in smoothing of financial data
6648 (license license:gpl2)))
6650 (define-public r-riverplot
6652 (name "r-riverplot")
6657 (uri (cran-uri "riverplot" version))
6660 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6661 (build-system r-build-system)
6663 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6665 `(("r-knitr" ,r-knitr)))
6666 (home-page "https://logfc.wordpress.com")
6667 (synopsis "Sankey or ribbon plots")
6669 "Sankey plots are a type of diagram that is convenient to illustrate how
6670 flow of information, resources etc. separates and joins, much like observing
6671 how rivers split and merge. For example, they can be used to compare
6672 different clusterings. This package provides an implementation of Sankey
6674 (license license:gpl2+)))
6676 (define-public r-dyn
6683 (uri (cran-uri "dyn" version))
6686 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6687 (build-system r-build-system)
6689 `(("r-zoo" ,r-zoo)))
6690 (home-page "https://cran.r-project.org/web/packages/dyn")
6691 (synopsis "Time series regression")
6693 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6694 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6695 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6696 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6697 @code{randomForest::randomForest()} and other regression functions, allowing
6698 those functions to be used with time series including specifications that may
6699 contain lags, diffs and missing values.")
6701 (license license:gpl2+)))
6703 (define-public r-catdap
6710 (uri (cran-uri "catdap" version))
6713 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6714 (build-system r-build-system)
6716 `(("gfortran" ,gfortran)))
6717 (home-page "https://cran.r-project.org/web/packages/catdap/")
6718 (synopsis "Tools for categorical data analysis")
6720 "This package provides functions for analyzing multivariate data.
6721 Dependencies of the distribution of the specified variable (response
6722 variable) to other variables (explanatory variables) are derived and
6723 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6724 (license license:gpl2+)))
6726 (define-public r-arules
6733 (uri (cran-uri "arules" version))
6736 "0m80kndfbannw8h53nqdd5wl8h33q2z259aa1cp1nwadaxf9fc1q"))))
6737 (build-system r-build-system)
6739 `(("r-matrix" ,r-matrix)))
6740 (home-page "https://github.com/mhahsler/arules")
6741 (synopsis "Mining association rules and frequent itemsets")
6743 "This package provides an infrastructure for representing, manipulating
6744 and analyzing transaction data and patterns (frequent itemsets and association rules).
6745 It also provides C implementations of the association mining algorithms Apriori
6747 (license license:gpl3)))
6749 (define-public r-parsedate
6751 (name "r-parsedate")
6756 (uri (cran-uri "parsedate" version))
6759 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6760 (build-system r-build-system)
6762 `(("r-rematch2" ,r-rematch2)))
6763 (home-page "https://github.com/gaborcsardi/parsedate")
6765 "Recognize and parse dates in various formats")
6767 "This package provides three functions for dealing with dates:
6768 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6769 time formats, @code{parse_date} parses dates in unspecified formats,
6770 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6771 (license license:gpl2)))
6773 (define-public r-abc-data
6780 (uri (cran-uri "abc.data" version))
6783 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6784 (properties `((upstream-name . "abc.data")))
6785 (build-system r-build-system)
6786 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6787 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6789 "This package contains data which are used by functions of the abc
6790 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6791 algorithms for performing parameter estimation, model selection, and
6793 (license license:gpl3+)))
6795 (define-public r-abc
6802 (uri (cran-uri "abc" version))
6805 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6806 (build-system r-build-system)
6808 `(("r-abc-data" ,r-abc-data)
6809 ("r-locfit" ,r-locfit)
6812 ("r-quantreg" ,r-quantreg)))
6813 (home-page "https://cran.r-project.org/web/packages/abc/")
6814 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6816 "This package implements several @dfn{Approximate Bayesian
6817 Computation} (ABC) algorithms for performing parameter estimation, model
6818 selection, and goodness-of-fit. Cross-validation tools are also available for
6819 measuring the accuracy of ABC estimates, and to calculate the
6820 misclassification probabilities of different models.")
6821 (license license:gpl3+)))
6823 (define-public r-zip
6830 (uri (cran-uri "zip" version))
6833 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6834 (build-system r-build-system)
6835 (home-page "https://github.com/gaborcsardi/zip")
6836 (synopsis "Cross-platform Zip compression")
6838 "This package provides a cross-platform Zip compression library for R.
6839 It is a replacement for the @code{zip} function, that does not require any
6840 additional external tools on any platform.")
6841 (license license:cc0)))
6843 (define-public r-openxlsx
6850 (uri (cran-uri "openxlsx" version))
6853 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6854 (build-system r-build-system)
6856 `(("r-rcpp" ,r-rcpp)
6857 ("r-stringi" ,r-stringi)
6860 `(("r-knitr" ,r-knitr)))
6861 (home-page "https://github.com/awalker89/openxlsx")
6862 (synopsis "Read, write and edit XLSX files")
6864 "This package simplifies the creation of Excel @code{.xlsx} files by
6865 providing a high level interface to writing, styling and editing worksheets.
6866 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6867 and @code{XLConnect} packages with the added benefit of removing the
6868 dependency on Java.")
6869 (license license:gpl3)))
6871 (define-public r-rio
6878 (uri (cran-uri "rio" version))
6881 "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d"))))
6882 (build-system r-build-system)
6884 `(("r-curl" ,r-curl)
6885 ("r-data-table" ,r-data-table)
6886 ("r-foreign" ,r-foreign)
6887 ("r-haven" ,r-haven)
6888 ("r-openxlsx" ,r-openxlsx)
6889 ("r-readxl" ,r-readxl)
6890 ("r-tibble" ,r-tibble)))
6892 `(("r-knitr" ,r-knitr)))
6893 (home-page "https://github.com/leeper/rio")
6894 (synopsis "Swiss-army knife for data I/O")
6896 "This package provides streamlined data import and export infrastructure
6897 by making assumptions that the user is probably willing to make: @code{import}
6898 and @code{export} determine the data structure from the file extension,
6899 reasonable defaults are used for data import and export (e.g.,
6900 @code{stringsAsFactors=FALSE}), web-based import is natively
6901 supported (including from SSL/HTTPS), compressed files can be read directly
6902 without explicit decompression, and fast import packages are used where
6903 appropriate. An additional convenience function, @code{convert}, provides a
6904 simple method for converting between file types.")
6905 (license license:gpl2)))
6907 (define-public r-maptools
6914 (uri (cran-uri "maptools" version))
6917 "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l"))))
6918 (build-system r-build-system)
6920 `(("r-foreign" ,r-foreign)
6921 ("r-lattice" ,r-lattice)
6923 (home-page "https://r-forge.r-project.org/projects/maptools/")
6924 (synopsis "Tools for reading and handling spatial objects")
6926 "This package provides a set of tools for manipulating and reading
6927 geographic data, in particular ESRI Shapefiles. It includes binary access to
6928 GSHHG shoreline files. The package also provides interface wrappers for
6929 exchanging spatial objects with other R packages.")
6930 ;; The C source files from shapelib are released under the Expat license.
6931 ;; The R code is released under GPL version 2 or later.
6932 (license (list license:gpl2+
6935 (define-public r-later
6942 (uri (cran-uri "later" version))
6945 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6946 (build-system r-build-system)
6950 ("r-rlang" ,r-rlang)))
6952 `(("r-knitr" ,r-knitr)))
6953 (home-page "https://github.com/r-lib/later")
6954 (synopsis "Utilities for delaying function execution")
6956 "This package provides tools to execute arbitrary R or C functions some
6957 time after the current time, after the R execution stack has emptied.")
6958 (license license:gpl2+)))
6960 (define-public r-promises
6967 (uri (cran-uri "promises" version))
6970 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
6971 (build-system r-build-system)
6973 `(("r-later" ,r-later)
6974 ("r-magrittr" ,r-magrittr)
6977 ("r-rlang" ,r-rlang)))
6979 `(("r-knitr" ,r-knitr)))
6980 (home-page "https://rstudio.github.io/promises")
6981 (synopsis "Abstractions for promise-based asynchronous programming")
6983 "This package provides fundamental abstractions for doing asynchronous
6984 programming in R using promises. Asynchronous programming is useful for
6985 allowing a single R process to orchestrate multiple tasks in the background
6986 while also attending to something else. Semantics are similar to JavaScript
6987 promises, but with a syntax that is idiomatic R.")
6988 (license license:expat)))
6990 (define-public r-dosnow
6997 (uri (cran-uri "doSNOW" version))
7000 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
7001 (properties `((upstream-name . "doSNOW")))
7002 (build-system r-build-system)
7004 `(("r-foreach" ,r-foreach)
7005 ("r-iterators" ,r-iterators)
7006 ("r-snow" ,r-snow)))
7007 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7008 (synopsis "Foreach parallel adaptor for the snow package")
7010 "This package provides a parallel backend for the @code{%dopar%} function
7011 using the @code{snow} package.")
7012 (license license:gpl2)))
7014 (define-public r-fst
7021 (uri (cran-uri "fst" version))
7024 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7025 (properties `((upstream-name . "fst")))
7026 (build-system r-build-system)
7027 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7028 (home-page "http://www.fstpackage.org")
7029 (synopsis "Fast serialization of data frames")
7031 "The fst package for R provides a fast, easy and flexible way to
7032 serialize data frames. With access speeds of multiple GB/s, fst is
7033 specifically designed to unlock the potential of high speed solid state disks.
7034 Data frames stored in the fst format have full random access, both in column
7035 and rows. The fst format allows for random access of stored data and
7036 compression with the LZ4 and ZSTD compressors.")
7037 (license license:agpl3)))
7039 (define-public r-snowfall
7042 (version "1.84-6.1")
7045 (uri (cran-uri "snowfall" version))
7047 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7048 (build-system r-build-system)
7050 `(("r-snow" ,r-snow)))
7051 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7052 (synopsis "Easier cluster computing")
7053 (description "This package is a usability wrapper around snow for easier
7054 development of parallel R programs. This package offers e.g. extended error
7055 checks, and additional functions. All functions work in sequential mode, too,
7056 if no cluster is present or wished. The package is also designed as connector
7057 to the cluster management tool @code{sfCluster}, but can also used without
7059 (license license:gpl2+)))
7061 (define-public r-rgexf
7068 (uri (cran-uri "rgexf" version))
7071 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7074 ;; Delete minified JavaScript files
7075 (for-each delete-file
7076 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7077 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7078 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7080 (properties `((upstream-name . "rgexf")))
7081 (build-system r-build-system)
7083 `(#:modules ((guix build utils)
7084 (guix build r-build-system)
7088 (modify-phases %standard-phases
7089 (add-after 'unpack 'process-javascript
7090 (lambda* (#:key inputs #:allow-other-keys)
7091 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7092 (with-directory-excursion "inst/gexf-js/js/"
7096 `((,(assoc-ref inputs "js-jquery")
7097 "jquery-2.0.2.min.js")
7098 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7099 "jquery-ui-1.10.3.custom.min.js")
7100 (,(assoc-ref inputs "js-jquery-mousewheel")
7101 "jquery.mousewheel.min.js"))))
7102 (lambda (sources targets)
7103 (for-each (lambda (source target)
7104 (format #true "Processing ~a --> ~a~%"
7106 (invoke "esbuild" source "--minify"
7107 (string-append "--outfile=" target)))
7111 `(("r-igraph" ,r-igraph)
7112 ("r-servr" ,r-servr)
7115 `(("r-knitr" ,r-knitr)
7116 ("esbuild" ,esbuild)
7121 (uri "https://code.jquery.com/jquery-2.0.2.js")
7124 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7128 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7131 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7132 ("js-jquery-mousewheel"
7135 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7136 3.0.6/jquery.mousewheel.js")
7139 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7140 (home-page "https://gvegayon.github.io/rgexf")
7141 (synopsis "Build, import and export GEXF graph files")
7143 "Create, read and write GEXF (Graph Exchange XML Format) graph
7144 files (used in Gephi and others). It allows the user to easily build/read
7145 graph files including attributes, GEXF visual attributes (such as color, size,
7146 and position), network dynamics (for both edges and nodes) and edge weighting.
7147 Users can build/handle graphs element-by-element or massively through
7148 data-frames, visualize the graph on a web browser through gexf-js (a
7149 JavaScript library) and interact with the igraph package.")
7150 (license license:expat)))
7152 (define-public r-data-tree
7154 (name "r-data-tree")
7159 (uri (cran-uri "data.tree" version))
7162 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7163 (properties `((upstream-name . "data.tree")))
7164 (build-system r-build-system)
7167 ("r-stringi" ,r-stringi)))
7169 `(("r-knitr" ,r-knitr)))
7170 (home-page "https://github.com/gluc/data.tree")
7171 (synopsis "General purpose hierarchical data structure")
7173 "Create tree structures from hierarchical data, and traverse the tree in
7174 various orders. Aggregate, cumulate, print, plot, convert to and from
7175 data.frame and more. This is useful for decision trees, machine learning,
7176 finance, conversion from and to JSON, and many other applications.")
7177 (license license:gpl2+)))
7179 (define-public r-collapsibletree
7181 (name "r-collapsibletree")
7186 (uri (cran-uri "collapsibleTree" version))
7189 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7192 ;; Delete minified JavaScript file
7193 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7196 `((upstream-name . "collapsibleTree")))
7197 (build-system r-build-system)
7200 (modify-phases %standard-phases
7201 (add-after 'unpack 'process-javascript
7202 (lambda* (#:key inputs #:allow-other-keys)
7203 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7204 (let ((source (assoc-ref inputs "d3.v4.js"))
7205 (target "d3.min.js"))
7206 (format #t "Processing ~a --> ~a~%"
7208 (invoke "esbuild" source "--minify"
7209 (string-append "--outfile=" target)))))))))
7211 `(("r-data-tree" ,r-data-tree)
7212 ("r-htmlwidgets" ,r-htmlwidgets)))
7214 `(("esbuild" ,esbuild)
7218 (uri "https://d3js.org/d3.v4.js")
7221 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7222 (home-page "https://github.com/AdeelK93/collapsibleTree")
7223 (synopsis "Interactive collapsible tree diagrams using D3.js")
7225 "This is a package for interactive Reingold-Tilford tree diagrams created
7226 using D3.js, where every node can be expanded and collapsed by clicking on it.
7227 Tooltips and color gradients can be mapped to nodes using a numeric column in
7228 the source data frame.")
7229 (license license:gpl3+)))
7231 (define-public r-rappdirs
7238 (uri (cran-uri "rappdirs" version))
7241 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7242 (build-system r-build-system)
7243 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7244 (synopsis "Determine where to save data, caches, and logs")
7246 "This package provides an easy way to determine which directories on the
7247 user's computer should be used to save data, caches and logs. It is a port of
7248 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7249 (license license:expat)))
7251 (define-public r-rastervis
7253 (name "r-rastervis")
7258 (uri (cran-uri "rasterVis" version))
7261 "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w"))))
7262 (properties `((upstream-name . "rasterVis")))
7263 (build-system r-build-system)
7265 `(("r-hexbin" ,r-hexbin)
7266 ("r-lattice" ,r-lattice)
7267 ("r-latticeextra" ,r-latticeextra)
7268 ("r-raster" ,r-raster)
7269 ("r-rcolorbrewer" ,r-rcolorbrewer)
7271 ("r-terra" ,r-terra)
7272 ("r-viridislite" ,r-viridislite)
7274 (home-page "https://oscarperpinan.github.io/rastervis/")
7275 (synopsis "Visualization methods for raster data")
7277 "This package provides methods for enhanced visualization and interaction
7278 with raster data. It implements visualization methods for quantitative data
7279 and categorical data, both for univariate and multivariate rasters. It also
7280 provides methods to display spatiotemporal rasters, and vector fields.")
7281 (license license:gpl3)))
7283 (define-public r-rentrez
7290 (uri (cran-uri "rentrez" version))
7293 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7294 (properties `((upstream-name . "rentrez")))
7295 (build-system r-build-system)
7297 `(("r-httr" ,r-httr)
7298 ("r-jsonlite" ,r-jsonlite)
7301 `(("r-knitr" ,r-knitr)))
7302 (home-page "https://docs.ropensci.org/rentrez/")
7303 (synopsis "Entrez in R")
7305 "This package provides an R interface to the NCBI's EUtils API,
7306 allowing users to search databases like GenBank PubMed, process the results of
7307 those searches and pull data into their R sessions.")
7308 (license license:expat)))
7310 (define-public r-renv
7317 (uri (cran-uri "renv" version))
7320 "0jlsf6vfvqhr4i35xy3xf1ixkfillivzy3wbpl6ca9vyjpnhiwj1"))))
7321 (properties `((upstream-name . "renv")))
7322 (build-system r-build-system)
7324 `(("r-knitr" ,r-knitr)))
7325 (home-page "https://rstudio.github.io/renv")
7326 (synopsis "Project environments")
7328 "This package provides a dependency management toolkit for R. Using
7329 renv, you can create and manage project-local R libraries, save the state of
7330 these libraries to a lockfile, and later restore your library as required.
7331 Together, these tools can help make your projects more isolated, portable, and
7333 (license license:expat)))
7335 (define-public r-learnr
7342 (uri (cran-uri "learnr" version))
7345 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7346 (build-system r-build-system)
7348 `(("r-checkmate" ,r-checkmate)
7349 ("r-ellipsis" ,r-ellipsis)
7350 ("r-evaluate" ,r-evaluate)
7351 ("r-htmltools" ,r-htmltools)
7352 ("r-htmlwidgets" ,r-htmlwidgets)
7353 ("r-jsonlite" ,r-jsonlite)
7354 ("r-knitr" ,r-knitr)
7355 ("r-markdown" ,r-markdown)
7356 ("r-rappdirs" ,r-rappdirs)
7358 ("r-rmarkdown" ,r-rmarkdown)
7359 ("r-rprojroot" ,r-rprojroot)
7360 ("r-shiny" ,r-shiny)
7361 ("r-withr" ,r-withr)))
7362 (home-page "https://rstudio.github.io/learnr/")
7363 (synopsis "Interactive tutorials for R")
7365 "This package provides tools to create interactive tutorials using R
7366 Markdown. Use a combination of narrative, figures, videos, exercises, and
7367 quizzes to create self-paced tutorials for learning about R and R packages.")
7368 (license license:asl2.0)))
7370 (define-public r-analytics
7372 (name "r-analytics")
7377 (uri (cran-uri "analytics" version))
7380 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7381 (build-system r-build-system)
7384 ("r-cluster" ,r-cluster)
7385 ("r-fractal" ,r-fractal)
7386 ("r-lmtest" ,r-lmtest)
7389 ("r-powerplus" ,r-powerplus)
7390 ("r-robust" ,r-robust)
7391 ("r-trend" ,r-trend)
7395 (home-page "https://cran.r-project.org/web/packages/analytics/")
7396 (synopsis "Collection of data analysis tools")
7398 "This package is a collection of data analysis tools. It includes tools
7399 for regression outlier detection in a fitted linear model, stationary
7400 bootstrap using a truncated geometric distribution, a comprehensive test for
7401 weak stationarity, column means by group, weighted biplots, and a heuristic to
7402 obtain a better initial configuration in non-metric MDS.")
7403 (license license:gpl2)))
7405 (define-public r-reticulate
7407 (name "r-reticulate")
7412 (uri (cran-uri "reticulate" version))
7415 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7416 (build-system r-build-system)
7417 (inputs `(("python" ,python)))
7419 `(("r-rappdirs" ,r-rappdirs)
7420 ("r-jsonlite" ,r-jsonlite)
7421 ("r-matrix" ,r-matrix)
7422 ("r-rcpp" ,r-rcpp)))
7424 `(("r-knitr" ,r-knitr)))
7425 (home-page "https://github.com/rstudio/reticulate")
7426 (synopsis "R interface to Python")
7428 "This package provides an interface from R to Python modules, classes,
7429 and functions. When calling into Python, R data types are automatically
7430 converted to their equivalent Python types. When values are returned from
7431 Python to R they are converted back to R types.")
7432 (license license:asl2.0)))
7434 (define-public r-bibtex
7441 (uri (cran-uri "bibtex" version))
7444 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7445 (build-system r-build-system)
7446 (propagated-inputs `(("r-stringr" ,r-stringr)))
7447 (home-page "https://github.com/romainfrancois/bibtex")
7448 (synopsis "Bibtex parser")
7449 (description "This package provides a utility for R to parse a bibtex
7451 (license license:gpl2+)))
7453 (define-public r-ggseqlogo
7455 (name "r-ggseqlogo")
7460 (uri (cran-uri "ggseqlogo" version))
7463 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7464 (build-system r-build-system)
7465 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7466 (home-page "https://github.com/omarwagih/ggseqlogo")
7467 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7469 "The range of functions provided by this package makes it possible to
7470 draw highly versatile genomic sequence logos. Features include, but are not
7471 limited to, modifying colour schemes and fonts used to draw the logo,
7472 generating multiple logo plots, and aiding the visualisation with annotations.
7473 Sequence logos can easily be combined with other ggplot2 plots.")
7474 ;; Unspecified version of the LGPL.
7475 (license license:lgpl3+)))
7477 (define-public r-ggsci
7484 (uri (cran-uri "ggsci" version))
7487 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7488 (build-system r-build-system)
7490 `(("r-ggplot2" ,r-ggplot2)
7491 ("r-scales" ,r-scales)))
7492 (home-page "https://nanx.me/ggsci/")
7493 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7495 "This package provides a collection of ggplot2 color palettes inspired by
7496 plots in scientific journals, data visualization libraries, science fiction
7497 movies, and TV shows.")
7498 (license license:gpl3)))
7500 (define-public r-ggsignif
7507 (uri (cran-uri "ggsignif" version))
7510 "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh"))))
7511 (build-system r-build-system)
7513 `(("r-knitr" ,r-knitr)))
7515 `(("r-ggplot2" ,r-ggplot2)))
7516 (home-page "https://github.com/const-ae/ggsignif")
7517 (synopsis "Significance brackets for ggplot2")
7519 "Enrich your ggplots with group-wise comparisons. This package provides
7520 an easy way to indicate if two groups are significantly different. Commonly
7521 this is shown by a bracket on top connecting the groups of interest which
7522 itself is annotated with the level of significance. The package provides a
7523 single layer that takes the groups for comparison and the test as arguments
7524 and adds the annotation to the plot.")
7525 (license license:gpl3)))
7527 (define-public r-rstatix
7534 (uri (cran-uri "rstatix" version))
7537 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
7538 (properties `((upstream-name . "rstatix")))
7539 (build-system r-build-system)
7541 `(("r-broom" ,r-broom)
7543 ("r-corrplot" ,r-corrplot)
7544 ("r-dplyr" ,r-dplyr)
7545 ("r-generics" ,r-generics)
7546 ("r-magrittr" ,r-magrittr)
7547 ("r-purrr" ,r-purrr)
7548 ("r-rlang" ,r-rlang)
7549 ("r-tibble" ,r-tibble)
7550 ("r-tidyr" ,r-tidyr)
7551 ("r-tidyselect" ,r-tidyselect)))
7552 (home-page "https://rpkgs.datanovia.com/rstatix/")
7553 (synopsis "Pipe-friendly framework for basic statistical tests")
7555 "This package provides a simple and intuitive pipe-friendly framework,
7556 coherent with the @code{tidyverse} design philosophy, for performing basic
7557 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7558 correlation analyses. The output of each test is automatically transformed
7559 into a tidy data frame to facilitate visualization. Additional functions are
7560 available for reshaping, reordering, manipulating and visualizing correlation
7562 (license license:gpl2)))
7564 (define-public r-ggpubr
7571 (uri (cran-uri "ggpubr" version))
7574 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7575 (build-system r-build-system)
7577 `(("r-cowplot" ,r-cowplot)
7578 ("r-dplyr" ,r-dplyr)
7579 ("r-ggplot2" ,r-ggplot2)
7580 ("r-ggrepel" ,r-ggrepel)
7581 ("r-ggsci" ,r-ggsci)
7582 ("r-ggsignif" ,r-ggsignif)
7584 ("r-gridextra" ,r-gridextra)
7585 ("r-magrittr" ,r-magrittr)
7586 ("r-polynom" ,r-polynom)
7587 ("r-purrr" ,r-purrr)
7588 ("r-rlang" ,r-rlang)
7589 ("r-scales" ,r-scales)
7590 ("r-rstatix" ,r-rstatix)
7591 ("r-tibble" ,r-tibble)
7592 ("r-tidyr" ,r-tidyr)))
7593 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7594 (synopsis "ggplot2-based publication-ready plots")
7596 "The ggplot2 package is an excellent and flexible package for elegant
7597 data visualization in R. However the default generated plots require some
7598 formatting before we can send them for publication. The ggpubr package
7599 provides some easy-to-use functions for creating and customizing ggplot2-based
7600 publication-ready plots.")
7601 (license license:gpl2)))
7603 (define-public r-ellipse
7610 (uri (cran-uri "ellipse" version))
7613 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7614 (build-system r-build-system)
7615 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7616 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7618 "This package contains various routines for drawing ellipses and
7619 ellipse-like confidence regions, implementing the plots described in Murdoch
7620 and Chow (1996), A graphical display of large correlation matrices, The
7621 American Statistician 50, 178-180. There are also routines implementing the
7622 profile plots described in Bates and Watts (1988), Nonlinear Regression
7623 Analysis and its Applications.")
7624 (license license:gpl2+)))
7626 (define-public r-flashclust
7628 (name "r-flashclust")
7633 (uri (cran-uri "flashClust" version))
7636 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7637 (properties `((upstream-name . "flashClust")))
7638 (build-system r-build-system)
7639 (native-inputs `(("gfortran" ,gfortran)))
7640 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7641 (synopsis "Implementation of optimal hierarchical clustering")
7643 "This package provides a fast implementation of hierarchical
7645 (license license:gpl2+)))
7647 (define-public r-factominer
7649 (name "r-factominer")
7654 (uri (cran-uri "FactoMineR" version))
7657 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7658 (properties `((upstream-name . "FactoMineR")))
7659 (build-system r-build-system)
7662 ("r-cluster" ,r-cluster)
7664 ("r-ellipse" ,r-ellipse)
7665 ("r-flashclust" ,r-flashclust)
7666 ("r-ggplot2" ,r-ggplot2)
7667 ("r-ggrepel" ,r-ggrepel)
7668 ("r-lattice" ,r-lattice)
7669 ("r-leaps" ,r-leaps)
7671 ("r-scatterplot3d" ,r-scatterplot3d)))
7673 `(("r-knitr" ,r-knitr)))
7674 (home-page "http://factominer.free.fr")
7675 (synopsis "Multivariate exploratory data analysis and data mining")
7677 "This package provides exploratory data analysis methods to summarize,
7678 visualize and describe datasets. The main principal component methods are
7679 available, those with the largest potential in terms of applications:
7680 principal component analysis (PCA) when variables are quantitative,
7681 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7682 variables are categorical, Multiple Factor Analysis when variables are
7683 structured in groups, etc. and hierarchical cluster analysis.")
7684 (license license:gpl2+)))
7686 (define-public r-factoextra
7688 (name "r-factoextra")
7693 (uri (cran-uri "factoextra" version))
7696 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7697 (build-system r-build-system)
7699 `(("r-abind" ,r-abind)
7700 ("r-cluster" ,r-cluster)
7701 ("r-dendextend" ,r-dendextend)
7702 ("r-factominer" ,r-factominer)
7703 ("r-ggplot2" ,r-ggplot2)
7704 ("r-ggpubr" ,r-ggpubr)
7705 ("r-ggrepel" ,r-ggrepel)
7706 ("r-reshape2" ,r-reshape2)
7707 ("r-tidyr" ,r-tidyr)))
7708 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7709 (synopsis "Extract and visualize the results of multivariate data analyses")
7711 "This package provides some easy-to-use functions to extract and
7712 visualize the output of multivariate data analyses, including
7713 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7714 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7715 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7716 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7717 packages. It contains also functions for simplifying some clustering analysis
7718 steps and provides ggplot2-based elegant data visualization.")
7719 (license license:gpl2)))
7721 (define-public r-fansi
7728 (uri (cran-uri "fansi" version))
7731 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7732 (build-system r-build-system)
7734 `(("r-knitr" ,r-knitr))) ; for vignettes
7735 (home-page "https://github.com/brodieG/fansi")
7736 (synopsis "ANSI control sequence aware string functions")
7738 "This package provides counterparts to R string manipulation functions
7739 that account for the effects of ANSI text formatting control sequences.")
7740 (license license:gpl2+)))
7742 (define-public r-nbclust
7749 (uri (cran-uri "NbClust" version))
7752 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7753 (properties `((upstream-name . "NbClust")))
7754 (build-system r-build-system)
7755 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7756 (synopsis "Determine the best number of clusters in a data set")
7758 "NbClust provides 30 indexes for determining the optimal number of
7759 clusters in a data set and offers the best clustering scheme from different
7760 results to the user.")
7761 (license license:gpl2)))
7763 (define-public r-hdf5r
7770 (uri (cran-uri "hdf5r" version))
7773 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7774 (build-system r-build-system)
7779 `(("r-bit64" ,r-bit64)
7782 `(("r-knitr" ,r-knitr)))
7783 (home-page "https://hhoeflin.github.io/hdf5r")
7784 (synopsis "Interface to the HDF5 binary data format")
7786 "HDF5 is a data model, library and file format for storing and managing
7787 large amounts of data. This package provides a nearly feature complete,
7788 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7789 functionality is added so that HDF5 objects behave very similar to their
7790 corresponding R counterparts.")
7791 (license license:asl2.0)))
7793 (define-public r-itertools
7795 (name "r-itertools")
7800 (uri (cran-uri "itertools" version))
7803 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7804 (build-system r-build-system)
7806 `(("r-iterators" ,r-iterators)))
7807 (home-page "https://cran.r-project.org/web/packages/itertools/")
7808 (synopsis "Iterator tools")
7810 "This package provides various tools for creating iterators, many
7811 patterned after functions in the Python @code{itertools} module, and others
7812 patterned after functions in the snow package.")
7813 (license license:gpl2)))
7815 (define-public r-polynom
7822 (uri (cran-uri "polynom" version))
7825 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7826 (build-system r-build-system)
7827 (home-page "https://cran.r-project.org/web/packages/polynom/")
7828 (synopsis "Functions for univariate polynomial manipulations")
7830 "This package provides a collection of functions to implement a class for
7831 univariate polynomial manipulations.")
7832 (license license:gpl2)))
7834 (define-public r-gbrd
7841 (uri (cran-uri "gbRd" version))
7844 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7845 (properties `((upstream-name . "gbRd")))
7846 (build-system r-build-system)
7847 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7848 (synopsis "Utilities for processing Rd objects and files")
7850 "This package provides utilities for processing Rd objects and files.
7851 Extract argument descriptions and other parts of the help pages of
7853 (license license:gpl2+)))
7855 (define-public r-rjags
7862 (uri (cran-uri "rjags" version))
7865 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7866 (build-system r-build-system)
7868 `(("r-coda" ,r-coda)))
7872 `(("pkg-config" ,pkg-config)))
7873 (home-page "http://mcmc-jags.sourceforge.net")
7874 (synopsis "Bayesian graphical models using MCMC")
7876 "This package provides an R interface to the JAGS MCMC library. JAGS is
7877 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7878 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7879 (license license:gpl2)))
7881 (define-public r-rbibutils
7883 (name "r-rbibutils")
7888 (uri (cran-uri "rbibutils" version))
7891 "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44"))))
7892 (properties `((upstream-name . "rbibutils")))
7893 (build-system r-build-system)
7894 (home-page "https://geobosh.github.io/rbibutils/")
7895 (synopsis "Convert between bibliography formats")
7897 "This package converts between a number of bibliography formats,
7898 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7899 utilities and supports all bibliography formats and character encodings
7900 implemented in bibutils.")
7901 (license license:gpl2)))
7903 (define-public r-rdpack
7910 (uri (cran-uri "Rdpack" version))
7913 "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
7914 (properties `((upstream-name . "Rdpack")))
7915 (build-system r-build-system)
7917 `(("r-rbibutils" ,r-rbibutils)))
7918 (home-page "https://github.com/GeoBosh/Rdpack")
7919 (synopsis "Update and manipulate Rd documentation objects")
7921 "This package provides functions for manipulation of R documentation
7922 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7923 updating Rd documentation for functions, methods and classes; it also includes
7924 Rd macros for citations and import of references from bibtex files for use in
7925 Rd files and roxygen2 comments, as well as many functions for manipulation of
7926 references and Rd files.")
7927 (license license:gpl2+)))
7929 (define-public r-officer
7936 (uri (cran-uri "officer" version))
7939 "1j3bv4j8x5ijj0j447vpdsk4p8pl3ncwdwnns6n3plfrqgsf3vsg"))))
7940 (build-system r-build-system)
7947 `(("r-knitr" ,r-knitr)))
7948 (home-page "https://davidgohel.github.io/officer")
7949 (synopsis "Manipulation of Word and PowerPoint documents")
7951 "This package provides tools to access and manipulate Word and PowerPoint
7952 documents from R. The package focuses on tabular and graphical reporting from
7953 R; it also provides two functions that let users get document content into
7954 data objects. A set of functions lets add and remove images, tables and
7955 paragraphs of text in new or existing documents. When working with PowerPoint
7956 presentations, slides can be added or removed; shapes inside slides can also
7957 be added or removed. When working with Word documents, a cursor can be used
7958 to help insert or delete content at a specific location in the document.")
7959 (license license:gpl3)))
7961 (define-public r-profilemodel
7963 (name "r-profilemodel")
7968 (uri (cran-uri "profileModel" version))
7971 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7972 (properties `((upstream-name . "profileModel")))
7973 (build-system r-build-system)
7974 (home-page "https://github.com/ikosmidis/profileModel")
7975 (synopsis "Profiling inference functions for various model classes")
7977 "This package provides tools that can be used to calculate, evaluate,
7978 plot and use for inference the profiles of *arbitrary* inference functions for
7979 arbitrary @code{glm}-like fitted models with linear predictors. More information
7980 on the methods that are implemented can be found in Kosmidis (2008)
7981 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7982 (license license:gpl2+)))
7984 (define-public r-brglm
7991 (uri (cran-uri "brglm" version))
7994 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7995 (properties `((upstream-name . "brglm")))
7996 (build-system r-build-system)
7998 `(("r-profilemodel" ,r-profilemodel)))
7999 (home-page "https://github.com/ikosmidis/brglm")
8000 (synopsis "Bias reduction in binomial-response generalized linear models")
8002 "Fit generalized linear models with binomial responses using either an
8003 adjusted-score approach to bias reduction or maximum penalized likelihood
8004 where penalization is by Jeffreys invariant prior. These procedures return
8005 estimates with improved frequentist properties (bias, mean squared error) that
8006 are always finite even in cases where the maximum likelihood estimates are
8007 infinite (data separation). Fitting takes place by fitting generalized linear
8008 models on iteratively updated pseudo-data. The interface is essentially the
8009 same as @code{glm}. More flexibility is provided by the fact that custom
8010 pseudo-data representations can be specified and used for model fitting.
8011 Functions are provided for the construction of confidence intervals for the
8012 reduced-bias estimates.")
8013 (license license:gpl2+)))
8015 (define-public r-entropy
8022 (uri (cran-uri "entropy" version))
8025 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8026 (properties `((upstream-name . "entropy")))
8027 (build-system r-build-system)
8028 (home-page "https://www.strimmerlab.org/software/entropy/")
8029 (synopsis "Estimation of entropy, mutual information and related quantities")
8031 "This package implements various estimators of entropy, such as the
8032 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8033 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8034 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8035 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8036 mutual information, and chi-squared statistic of independence. In addition
8037 there are functions for discretizing continuous random variables.")
8038 (license license:gpl3+)))
8040 (define-public r-abn
8047 (uri (cran-uri "abn" version))
8050 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8051 (build-system r-build-system)
8055 `(("r-lme4" ,r-lme4)
8058 ("r-rcpparmadillo" ,r-rcpparmadillo)
8059 ("r-rjags" ,r-rjags)))
8060 (home-page "https://r-bayesian-networks.org/")
8061 (synopsis "Modelling multivariate data with additive bayesian networks")
8063 "Bayesian network analysis is a form of probabilistic graphical models
8064 which derives from empirical data a directed acyclic graph, DAG, describing
8065 the dependency structure between random variables. An additive Bayesian
8066 network model consists of a form of a DAG where each node comprises a
8067 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8068 equivalent to Bayesian multivariate regression using graphical modelling, they
8069 generalises the usual multivariable regression, GLM, to multiple dependent
8070 variables. This package provides routines to help determine optimal Bayesian
8071 network models for a given data set, where these models are used to identify
8072 statistical dependencies in messy, complex data.")
8073 (license license:gpl2+)))
8075 (define-public r-acd
8082 (uri (cran-uri "ACD" version))
8085 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8086 (properties `((upstream-name . "ACD")))
8087 (build-system r-build-system)
8088 (home-page "https://cran.r-project.org/web/packages/ACD/")
8089 (synopsis "Categorical data analysis with complete or missing responses")
8091 "This package provides tools for categorical data analysis with complete
8092 or missing responses.")
8093 (license license:gpl2+)))
8095 (define-public r-acdm
8102 (uri (cran-uri "ACDm" version))
8105 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8106 (properties `((upstream-name . "ACDm")))
8107 (build-system r-build-system)
8109 `(("r-dplyr" ,r-dplyr)
8110 ("r-ggplot2" ,r-ggplot2)
8112 ("r-rsolnp" ,r-rsolnp)
8114 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8115 (synopsis "Tools for Autoregressive Conditional Duration Models")
8117 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8118 and Russell, 1998) models. It creates trade, price or volume durations from
8119 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8121 (license license:gpl2+)))
8123 (define-public r-overlap
8130 (uri (cran-uri "overlap" version))
8133 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8134 (build-system r-build-system)
8135 (home-page "https://cran.r-project.org/web/packages/overlap/")
8136 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8138 "This package provides functions to fit kernel density functions to data
8139 on temporal activity patterns of animals; estimate coefficients of overlapping
8140 of densities for two species; and calculate bootstrap estimates of confidence
8142 (license license:gpl3+)))
8144 (define-public r-snakecase
8146 (name "r-snakecase")
8151 (uri (cran-uri "snakecase" version))
8154 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8155 (build-system r-build-system)
8157 `(("r-stringi" ,r-stringi)
8158 ("r-stringr" ,r-stringr)))
8159 (home-page "https://github.com/Tazinho/snakecase")
8160 (synopsis "Convert strings into any case")
8162 "This package provides a consistent, flexible and easy to use tool to
8163 parse and convert strings into cases like snake or camel among others.")
8164 (license license:gpl3)))
8166 (define-public r-prediction
8168 (name "r-prediction")
8173 (uri (cran-uri "prediction" version))
8176 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8177 (build-system r-build-system)
8179 `(("r-data-table" ,r-data-table)))
8180 (home-page "https://github.com/leeper/prediction")
8181 (synopsis "Tidy, type-safe prediction methods")
8183 "This package provides the @code{prediction()} function, a type-safe
8184 alternative to @code{predict()} that always returns a data frame. The package
8185 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8186 from the @code{stats} package, as well as numerous other model classes from
8187 other add-on packages.")
8188 (license license:expat)))
8190 (define-public r-insight
8197 (uri (cran-uri "insight" version))
8200 "03b7kd17h25mi1si40ibcp3jpasyqpj51mr8js0ywywyfw7909j1"))))
8201 (build-system r-build-system)
8203 `(("r-knitr" ,r-knitr)))
8204 (home-page "https://easystats.github.io/insight/")
8205 (synopsis "Easy access to model information for various model objects")
8207 "This package provides a tool to provide an easy, intuitive and
8208 consistent access to information contained in various R models, like model
8209 formulas, model terms, information about random effects, data that was used to
8210 fit the model or data from response variables. The package mainly revolves
8211 around two types of functions: Functions that find (the names of) information,
8212 starting with @code{find_}, and functions that get the underlying data,
8213 starting with @code{get_}. The package has a consistent syntax and works with
8214 many different model objects, where otherwise functions to access these
8215 information are missing.")
8216 (license license:gpl3)))
8218 (define-public r-sjlabelled
8220 (name "r-sjlabelled")
8225 (uri (cran-uri "sjlabelled" version))
8228 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8229 (build-system r-build-system)
8231 `(("r-insight" ,r-insight)))
8233 `(("r-knitr" ,r-knitr)))
8234 (home-page "https://github.com/strengejacke/sjlabelled")
8235 (synopsis "Labelled data utility functions")
8237 "This package provides a collection of functions dealing with labelled
8238 data, like reading and writing data between R and other statistical software
8239 packages. This includes easy ways to get, set or change value and variable
8240 label attributes, to convert labelled vectors into factors or numeric (and
8241 vice versa), or to deal with multiple declared missing values.")
8242 (license license:gpl3)))
8244 (define-public r-sjmisc
8251 (uri (cran-uri "sjmisc" version))
8254 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8255 (build-system r-build-system)
8257 `(("r-dplyr" ,r-dplyr)
8258 ("r-insight" ,r-insight)
8259 ("r-magrittr" ,r-magrittr)
8260 ("r-purrr" ,r-purrr)
8261 ("r-rlang" ,r-rlang)
8262 ("r-sjlabelled" ,r-sjlabelled)
8263 ("r-tidyselect" ,r-tidyselect)))
8265 `(("r-knitr" ,r-knitr)))
8266 (home-page "https://github.com/strengejacke/sjmisc")
8267 (synopsis "Data and variable transformation functions")
8269 "This package is a collection of miscellaneous utility functions,
8270 supporting data transformation tasks like recoding, dichotomizing or grouping
8271 variables, setting and replacing missing values. The data transformation
8272 functions also support labelled data, and all integrate seamlessly into a
8273 tidyverse workflow.")
8274 (license license:gpl3)))
8276 (define-public r-nortest
8283 (uri (cran-uri "nortest" version))
8286 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8287 (build-system r-build-system)
8288 (home-page "https://cran.r-project.org/web/packages/nortest/")
8289 (synopsis "Tests for normality")
8291 "This package provides five omnibus tests for testing the composite
8292 hypothesis of normality.")
8293 (license license:gpl2+)))
8295 (define-public r-moonbook
8302 (uri (cran-uri "moonBook" version))
8305 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8306 (properties `((upstream-name . "moonBook")))
8307 (build-system r-build-system)
8309 `(("r-magrittr" ,r-magrittr)
8310 ("r-nortest" ,r-nortest)
8311 ("r-sjmisc" ,r-sjmisc)
8312 ("r-stringr" ,r-stringr)
8313 ("r-survival" ,r-survival)
8314 ("r-ztable" ,r-ztable)))
8316 `(("r-knitr" ,r-knitr)))
8317 (home-page "https://github.com/cardiomoon/moonBook")
8318 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8320 "This package provides several analysis-related functions for the book
8321 entitled \"R statistics and graph for medical articles\" (written in Korean),
8322 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8324 (license license:gpl2)))
8326 (define-public r-flextable
8328 (name "r-flextable")
8333 (uri (cran-uri "flextable" version))
8336 "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma"))))
8337 (build-system r-build-system)
8339 `(("r-base64enc" ,r-base64enc)
8340 ("r-data-table" ,r-data-table)
8341 ("r-gdtools" ,r-gdtools)
8342 ("r-htmltools" ,r-htmltools)
8343 ("r-knitr" ,r-knitr)
8344 ("r-officer" ,r-officer)
8345 ("r-rlang" ,r-rlang)
8346 ("r-rmarkdown" ,r-rmarkdown)
8348 ("r-xml2" ,r-xml2)))
8350 `(("r-knitr" ,r-knitr)))
8351 (home-page "https://davidgohel.github.io/flextable")
8352 (synopsis "Functions for tabular reporting")
8354 "This package provides tools to create pretty tables for HTML documents
8355 and other formats. Functions are provided to let users create tables, modify
8356 and format their content. It extends the @code{officer} package and can be
8357 used within R markdown documents when rendering to HTML and to Word
8359 (license license:gpl3)))
8361 (define-public r-writexl
8368 (uri (cran-uri "writexl" version))
8371 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8372 (build-system r-build-system)
8373 (inputs `(("zlib" ,zlib)))
8374 (home-page "https://github.com/ropensci/writexl")
8375 (synopsis "Export data frames to xlsx format")
8377 "This package provides a data frame to xlsx exporter based on
8379 (license license:bsd-2)))
8381 (define-public r-biasedurn
8383 (name "r-biasedurn")
8388 (uri (cran-uri "BiasedUrn" version))
8391 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8392 (properties `((upstream-name . "BiasedUrn")))
8393 (build-system r-build-system)
8394 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8395 (synopsis "Biased Urn model distributions")
8397 "This package provides statistical models of biased sampling in the form
8398 of univariate and multivariate noncentral hypergeometric distributions,
8399 including Wallenius' noncentral hypergeometric distribution and Fisher's
8400 noncentral hypergeometric distribution (also called extended hypergeometric
8402 (license license:gpl3)))
8404 (define-public r-goplot
8411 (uri (cran-uri "GOplot" version))
8414 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8415 (properties `((upstream-name . "GOplot")))
8416 (build-system r-build-system)
8418 `(("r-ggdendro" ,r-ggdendro)
8419 ("r-ggplot2" ,r-ggplot2)
8420 ("r-gridextra" ,r-gridextra)
8421 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8422 (home-page "https://github.com/wencke/wencke.github.io")
8423 (synopsis "Visualization of functional analysis data")
8425 "This package provides an implementation of multilayered visualizations
8426 for enhanced graphical representation of functional analysis data. It
8427 combines and integrates omics data derived from expression and functional
8428 annotation enrichment analyses. Its plotting functions have been developed
8429 with an hierarchical structure in mind: starting from a general overview to
8430 identify the most enriched categories (modified bar plot, bubble plot) to a
8431 more detailed one displaying different types of relevant information for the
8432 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8433 Venn diagram, heatmap).")
8434 (license license:gpl2)))
8436 (define-public r-getopt
8443 (uri (cran-uri "getopt" version))
8446 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8447 (build-system r-build-system)
8448 (home-page "https://github.com/trevorld/getopt")
8449 (synopsis "Command-line option processor for R")
8451 "This package is designed to be used with Rscript to write shebang
8452 scripts that accept short and long options. Many users will prefer to
8453 use the packages @code{optparse} or @code{argparse} which add extra
8454 features like automatically generated help options and usage texts,
8455 support for default values, positional argument support, etc.")
8456 (license license:gpl2+)))
8458 (define-public r-findpython
8460 (name "r-findpython")
8465 (uri (cran-uri "findpython" version))
8468 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8469 (build-system r-build-system)
8470 (home-page "https://github.com/trevorld/findpython")
8471 (synopsis "Functions to find an acceptable Python binary")
8473 "This package was designed to find an acceptable Python binary that
8474 matches version and feature constraints.")
8475 (license license:expat)))
8477 ;; This in not the same as "r-argparser"
8478 (define-public r-argparse
8485 (uri (cran-uri "argparse" version))
8488 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8489 (build-system r-build-system)
8490 (inputs `(("python" ,python)))
8492 `(("r-findpython" ,r-findpython)
8493 ("r-jsonlite" ,r-jsonlite)
8496 `(("r-knitr" ,r-knitr)))
8497 (home-page "https://github.com/trevorld/argparse")
8498 (synopsis "Command line optional and positional argument parser")
8500 "This package provides a command line parser to be used with Rscript to
8501 write shebang scripts that gracefully accept positional and optional arguments
8502 and automatically generate usage notices.")
8503 (license license:gpl2+)))
8505 (define-public r-hash
8512 (uri (cran-uri "hash" version))
8515 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8516 (build-system r-build-system)
8517 (home-page "https://cran.r-project.org/web/packages/hash/")
8518 (synopsis "Implementation of hash/associated arrays/dictionaries")
8520 "This package implements a data structure similar to hashes in Perl and
8521 dictionaries in Python but with a purposefully R flavor. For objects of
8522 appreciable size, access using hashes outperforms native named lists and
8524 (license license:gpl2+)))
8526 (define-public r-orddom
8533 (uri (cran-uri "orddom" version))
8536 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8537 (build-system r-build-system)
8538 (propagated-inputs `(("r-psych" ,r-psych)))
8539 (home-page "https://cran.r-project.org/web/packages/orddom/")
8540 (synopsis "Ordinal dominance statistics")
8542 "This package provides tools to compute ordinal, statistics and effect
8543 sizes as an alternative to mean comparison: Cliff's delta or success rate
8544 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8545 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8546 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8547 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8548 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8549 Group (Non-)Overlap considerations.")
8550 (license license:gpl2)))
8552 (define-public r-deriv
8559 (uri (cran-uri "Deriv" version))
8562 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
8563 (properties `((upstream-name . "Deriv")))
8564 (build-system r-build-system)
8565 (home-page "https://cran.r-project.org/web/packages/Deriv")
8566 (synopsis "Symbolic differentiation")
8568 "This package provides an R-based solution for symbolic differentiation.
8569 It admits user-defined functions as well as function substitution in arguments
8570 of functions to be differentiated. Some symbolic simplification is part of
8572 (license license:gpl3+)))
8574 (define-public r-doby
8581 (uri (cran-uri "doBy" version))
8584 "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00"))))
8585 (properties `((upstream-name . "doBy")))
8586 (build-system r-build-system)
8588 `(("r-broom" ,r-broom)
8589 ("r-deriv" ,r-deriv)
8590 ("r-dplyr" ,r-dplyr)
8591 ("r-ggplot2" ,r-ggplot2)
8592 ("r-magrittr" ,r-magrittr)
8594 ("r-matrix" ,r-matrix)
8595 ("r-pbkrtest" ,r-pbkrtest)
8596 ("r-tibble" ,r-tibble)))
8598 `(("r-knitr" ,r-knitr)))
8599 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8600 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8602 "This package contains:
8605 @item facilities for working with grouped data: @code{do}
8606 something to data stratified @code{by} some variables.
8607 @item implementations of least-squares means, general linear contrasts, and
8608 @item miscellaneous other utilities.
8610 (license license:gpl2+)))
8612 (define-public r-refgenome
8614 (name "r-refgenome")
8619 (uri (cran-uri "refGenome" version))
8622 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8623 (properties `((upstream-name . "refGenome")))
8624 (build-system r-build-system)
8628 ("r-rsqlite" ,r-rsqlite)))
8629 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8631 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8633 "This package contains functionality for importing and managing of
8634 downloaded genome annotation data from the Ensembl genome browser (European
8635 Bioinformatics Institute) and from the UCSC genome browser (University of
8636 California, Santa Cruz) and annotation routines for genomic positions and
8637 splice site positions.")
8638 (license license:gpl2)))
8640 (define-public r-basix
8647 (uri (cran-uri "BASIX" version))
8650 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8651 (properties `((upstream-name . "BASIX")))
8652 (build-system r-build-system)
8653 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8654 (synopsis "Efficient C/C++ toolset for R")
8656 "BASIX provides some efficient C/C++ implementations of native R
8657 procedures to speed up calculations in R.")
8658 (license license:gpl2)))
8660 (define-public r-blockfest
8662 (name "r-blockfest")
8667 (uri (cran-uri "BlockFeST" version))
8670 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
8671 (properties `((upstream-name . "BlockFeST")))
8672 (build-system r-build-system)
8673 (propagated-inputs `(("r-basix" ,r-basix)))
8674 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8675 (synopsis "Bayesian calculation of region-specific fixation index")
8677 "This package provides an R implementation of an extension of the
8678 BayeScan software for codominant markers, adding the option to group
8679 individual SNPs into pre-defined blocks. A typical application of this new
8680 approach is the identification of genomic regions, genes, or gene sets
8681 containing one or more SNPs that evolved under directional selection.")
8682 (license license:gpl2)))
8684 (define-public r-proc
8687 (version "1.17.0.1")
8691 (uri (cran-uri "pROC" version))
8694 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8695 (properties `((upstream-name . "pROC")))
8696 (build-system r-build-system)
8698 `(("r-plyr" ,r-plyr)
8699 ("r-rcpp" ,r-rcpp)))
8700 (home-page "https://web.expasy.org/pROC/")
8701 (synopsis "Display and analyze ROC curves")
8703 "This package provides tools for visualizing, smoothing and comparing
8704 receiver operating characteristic (ROC curves). The area under the
8705 curve (AUC) can be compared with statistical tests based on U-statistics or
8706 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8707 (license license:gpl3+)))
8709 (define-public r-rootsolve
8711 (name "r-rootsolve")
8716 (uri (cran-uri "rootSolve" version))
8719 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8720 (properties `((upstream-name . "rootSolve")))
8721 (build-system r-build-system)
8722 (native-inputs `(("gfortran" ,gfortran)))
8723 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8724 (synopsis "Tools for the analysis of ordinary differential equations")
8726 "This package provides routines to find the root of nonlinear functions,
8727 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8728 differential equations} (ODE). It includes routines that:
8731 @item generate gradient and jacobian matrices (full and banded),
8732 @item find roots of non-linear equations by the Newton-Raphson method,
8733 @item estimate steady-state conditions of a system of (differential) equations
8734 in full, banded or sparse form, using the Newton-Raphson method, or by
8735 dynamically running,
8736 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8737 and 3-D partial differential equations, that have been converted to ordinary
8738 differential equations by numerical differencing (using the method-of-lines
8741 (license license:gpl2+)))
8743 (define-public r-abcanalysis
8745 (name "r-abcanalysis")
8750 (uri (cran-uri "ABCanalysis" version))
8752 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8753 (properties `((upstream-name . "ABCanalysis")))
8754 (build-system r-build-system)
8755 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8756 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8757 (synopsis "Computed ABC Analysis")
8759 "Multivariate data sets often differ in several factors or derived statistical
8760 parameters, which have to be selected for a valid interpretation. Basing this
8761 selection on traditional statistical limits leads occasionally to the perception
8762 of losing information from a data set. This package provides tools to calculate
8763 these limits on the basis of the mathematical properties of the distribution of
8764 the analyzed items.")
8765 (license license:gpl3)))
8767 (define-public r-slam
8774 (uri (cran-uri "slam" version))
8776 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8777 (build-system r-build-system)
8778 (home-page "https://cran.r-project.org/web/packages/slam/")
8779 (synopsis "Sparse lightweight arrays and matrices")
8781 "This package contains data structures and algorithms for sparse arrays and matrices,
8782 based on index arrays and simple triplet representations, respectively.")
8783 (license license:gpl2)))
8785 (define-public r-manipulatewidget
8787 (name "r-manipulatewidget")
8792 (uri (cran-uri "manipulateWidget" version))
8794 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8796 `((upstream-name . "manipulateWidget")))
8797 (build-system r-build-system)
8799 `(("r-base64enc" ,r-base64enc)
8800 ("r-codetools" ,r-codetools)
8801 ("r-htmltools" ,r-htmltools)
8802 ("r-htmlwidgets" ,r-htmlwidgets)
8803 ("r-knitr" ,r-knitr)
8804 ("r-miniui" ,r-miniui)
8805 ("r-shiny" ,r-shiny)
8806 ("r-webshot" ,r-webshot)))
8807 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8808 (synopsis "Add even more interactivity to interactive charts")
8810 "This package lets you create in just a few lines of R code a nice user interface to
8811 modify the data or the graphical parameters of one or multiple interactive
8812 charts. It is useful to quickly explore visually some data or for package
8813 developers to generate user interfaces easy to maintain.")
8814 (license license:gpl2+)))
8823 (uri (cran-uri "A3" version))
8825 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8826 (properties `((upstream-name . "A3")))
8827 (build-system r-build-system)
8829 `(("r-pbapply" ,r-pbapply)
8830 ("r-xtable" ,r-xtable)))
8831 (home-page "https://cran.r-project.org/web/packages/A3/")
8832 (synopsis "Error metrics for predictive models")
8834 "This package supplies tools for tabulating and analyzing the results of predictive
8835 models. The methods employed are applicable to virtually any predictive model
8836 and make comparisons between different methodologies straightforward.")
8837 (license license:gpl2+)))
8839 (define-public r-infotheo
8846 (uri (cran-uri "infotheo" version))
8849 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8850 (build-system r-build-system)
8851 (home-page "http://homepage.meyerp.com/software")
8852 (synopsis "Information-theoretic measures")
8854 "This package implements various measures of information theory based on
8855 several entropy estimators.")
8856 (license license:gpl3+)))
8858 (define-public r-abcoptim
8865 (uri (cran-uri "ABCoptim" version))
8867 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8868 (properties `((upstream-name . "ABCoptim")))
8869 (build-system r-build-system)
8870 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8871 (home-page "https://github.com/gvegayon/ABCoptim/")
8872 (synopsis "Optimization of Artificial Bee Colony algorithm")
8874 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8875 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8876 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8877 algorithms, and uses only common control parameters such as colony size and
8878 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8879 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8880 This version is a work-in-progress and is written in R code.")
8881 (license license:expat)))
8883 (define-public r-abcp2
8890 (uri (cran-uri "ABCp2" version))
8892 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8893 (properties `((upstream-name . "ABCp2")))
8894 (build-system r-build-system)
8895 (propagated-inputs `(("r-mass" ,r-mass)))
8896 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8897 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8899 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8900 Poisson, and Gamma distribution and estimates the proportional paternity of the
8901 second male (P2) based on the best fit distribution.")
8902 (license license:gpl2)))
8904 (define-public r-abcrf
8911 (uri (cran-uri "abcrf" version))
8913 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8914 (build-system r-build-system)
8916 `(("r-doparallel" ,r-doparallel)
8917 ("r-foreach" ,r-foreach)
8919 ("r-matrixstats" ,r-matrixstats)
8920 ("r-ranger" ,r-ranger)
8922 ("r-rcpparmadillo" ,r-rcpparmadillo)
8923 ("r-readr" ,r-readr)
8924 ("r-stringr" ,r-stringr)))
8925 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8926 (synopsis "Approximate bayesian computation via random forests")
8928 "This package performs approximate bayesian computation (ABC) model choice and
8929 parameter inference via random forests. This machine learning tool named random
8930 forests (RF) can conduct selection among the highly complex models covered by
8932 (license license:gpl2+)))
8934 (define-public r-abctools
8941 (uri (cran-uri "abctools" version))
8943 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8944 (build-system r-build-system)
8947 ("r-abind" ,r-abind)
8948 ("r-hmisc" ,r-hmisc)
8949 ("r-plyr" ,r-plyr)))
8950 (home-page "https://github.com/dennisprangle/abctools/")
8951 (synopsis "Tools for ABC analyses")
8953 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8954 including summary statistic selection and assessing coverage. This includes
8955 recent dimension reduction algorithms to tune the choice of summary statistics,
8956 and coverage methods to tune the choice of threshold.")
8957 (license license:gpl2+)))
8959 (define-public r-ggstance
8966 (uri (cran-uri "ggstance" version))
8968 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8969 (build-system r-build-system)
8971 `(("r-ggplot2" ,r-ggplot2)
8973 ("r-rlang" ,r-rlang)
8974 ("r-withr" ,r-withr)))
8975 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8976 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8978 "This package is a @code{r-ggplot2} extension that provides flipped components:
8980 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8981 @item vertical versions of @code{r-ggplot2} positions.
8983 (license license:gpl3)))
8985 (define-public r-mosaiccore
8987 (name "r-mosaiccore")
8992 (uri (cran-uri "mosaicCore" version))
8994 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8995 (properties `((upstream-name . "mosaicCore")))
8996 (build-system r-build-system)
8998 `(("r-dplyr" ,r-dplyr)
9000 ("r-rlang" ,r-rlang)
9001 ("r-tidyr" ,r-tidyr)))
9002 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
9003 (synopsis "Common utilities for mosaic family packages")
9005 "Common utilities used in other Mosaic family packages are collected here.")
9006 (license license:gpl2+)))
9008 (define-public r-labelled
9015 (uri (cran-uri "labelled" version))
9018 "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg"))))
9019 (properties `((upstream-name . "labelled")))
9020 (build-system r-build-system)
9022 `(("r-dplyr" ,r-dplyr)
9023 ("r-haven" ,r-haven)
9024 ("r-lifecycle" ,r-lifecycle)
9025 ("r-rlang" ,r-rlang)
9026 ("r-stringr" ,r-stringr)
9027 ("r-tidyr" ,r-tidyr)
9028 ("r-vctrs" ,r-vctrs)))
9030 `(("r-knitr" ,r-knitr)))
9031 (home-page "http://larmarange.github.io/labelled/")
9032 (synopsis "Manipulating labelled data")
9034 "This package provides useful functions to deal with the
9035 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9037 (license license:gpl3)))
9039 (define-public r-ggformula
9041 (name "r-ggformula")
9046 (uri (cran-uri "ggformula" version))
9048 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9049 (build-system r-build-system)
9051 `(("r-ggforce" ,r-ggforce)
9052 ("r-ggplot2" ,r-ggplot2)
9053 ("r-ggridges" ,r-ggridges)
9054 ("r-ggstance" ,r-ggstance)
9055 ("r-labelled" ,r-labelled)
9056 ("r-magrittr" ,r-magrittr)
9057 ("r-mosaiccore" ,r-mosaiccore)
9058 ("r-rlang" ,r-rlang)
9059 ("r-scales" ,r-scales)
9060 ("r-stringr" ,r-stringr)
9061 ("r-tibble" ,r-tibble)))
9063 `(("r-knitr" ,r-knitr)))
9064 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9065 (synopsis "Formula interface for the @code{r-ggplot2}")
9067 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9068 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9069 and extends the excellent simplicity of the lattice-graphics formula interface,
9070 while providing the intuitive capabilities of @code{r-ggplot2}.")
9071 (license license:expat)))
9073 (define-public r-mosaicdata
9075 (name "r-mosaicdata")
9080 (uri (cran-uri "mosaicData" version))
9082 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9083 (properties `((upstream-name . "mosaicData")))
9084 (build-system r-build-system)
9085 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9086 (synopsis "Data sets for project Mosaic")
9088 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9089 used to teach mathematics, statistics, computation and modeling.")
9090 (license license:gpl2+)))
9092 (define-public r-raster
9099 (uri (cran-uri "raster" version))
9102 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9103 (build-system r-build-system)
9105 `(("r-rcpp" ,r-rcpp)
9107 (home-page "https://www.rspatial.org/")
9108 (synopsis "Geographic data analysis and modeling")
9110 "The package implements basic and high-level functions for reading,
9111 writing, manipulating, analyzing and modeling of gridded spatial data.
9112 Processing of very large files is supported.")
9113 (license license:gpl3+)))
9115 (define-public r-mosaic
9122 (uri (cran-uri "mosaic" version))
9124 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9125 (build-system r-build-system)
9127 `(("r-broom" ,r-broom)
9128 ("r-dplyr" ,r-dplyr)
9129 ("r-ggdendro" ,r-ggdendro)
9130 ("r-ggformula" ,r-ggformula)
9131 ("r-ggplot2" ,r-ggplot2)
9132 ("r-ggrepel" ,r-ggrepel)
9134 ("r-gridextra" ,r-gridextra)
9135 ("r-lattice" ,r-lattice)
9136 ("r-latticeextra" ,r-latticeextra)
9137 ("r-lazyeval" ,r-lazyeval)
9139 ("r-matrix" ,r-matrix)
9140 ("r-mosaiccore" ,r-mosaiccore)
9141 ("r-mosaicdata" ,r-mosaicdata)
9142 ("r-readr" ,r-readr)
9143 ("r-tidyr" ,r-tidyr)))
9145 `(("r-knitr" ,r-knitr)))
9146 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9147 (synopsis "Mathematics, statistics, and computation teaching utilities")
9149 "This package contain data sets and utilities from
9150 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9151 statistics, computation and modeling. Project MOSAIC is a community of
9152 educators working to tie together aspects of quantitative work that students
9153 in science, technology, engineering and mathematics will need in their
9154 professional lives, but which are usually taught in isolation, if at all.")
9155 (license license:gpl2+)))
9157 (define-public r-abd
9164 (uri (cran-uri "abd" version))
9166 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9167 (build-system r-build-system)
9169 `(("r-lattice" ,r-lattice)
9170 ("r-mosaic" ,r-mosaic)
9171 ("r-nlme" ,r-nlme)))
9172 (home-page "https://cran.r-project.org/web/packages/abd/")
9173 (synopsis "Analysis of biological data")
9175 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9176 biological data by Michael Whitlock and Dolph Schluter.")
9177 (license license:gpl2)))
9179 (define-public r-svgui
9186 (uri (cran-uri "svGUI" version))
9188 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9189 (properties `((upstream-name . "svGUI")))
9190 (build-system r-build-system)
9191 (home-page "https://github.com/SciViews/svGUI/")
9192 (synopsis "Functions for managing GUI clients in R")
9194 "The SciViews @code{svGUI} package eases the management of Graphical User
9195 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9196 centralizes info about GUI elements currently used, and it dispatches GUI
9197 calls to the particular toolkits in use in function of the context.")
9198 (license license:gpl2)))
9200 (define-public r-svdialogs
9202 (name "r-svdialogs")
9207 (uri (cran-uri "svDialogs" version))
9209 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9210 (properties `((upstream-name . "svDialogs")))
9211 (build-system r-build-system)
9214 ("zenity" ,zenity)))
9216 `(("r-rstudioapi" ,r-rstudioapi)
9217 ("r-svgui" ,r-svgui)))
9218 (home-page "https://github.com/SciViews/svDialogs/")
9219 (synopsis "Portable dialog boxes")
9221 "This package helps to construct standard dialog boxes for your GUI, including
9222 message boxes, input boxes, list, file or directory selection, and others. In
9223 case R cannot display GUI dialog boxes, a simpler command line version of these
9224 interactive elements is also provided as a fallback solution.")
9225 (license license:gpl2)))
9227 (define-public r-abe
9234 (uri (cran-uri "abe" version))
9237 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9238 (build-system r-build-system)
9239 (home-page "https://cran.r-project.org/web/packages/abe/")
9240 (synopsis "Augmented backward elimination")
9242 "This package performs augmented backward elimination and checks the
9243 stability of the obtained model. Augmented backward elimination combines
9244 significance or information based criteria with the change in estimate to
9245 either select the optimal model for prediction purposes or to serve as a tool
9246 to obtain a practically sound, highly interpretable model.")
9247 (license license:gpl2+)))
9249 (define-public r-abf2
9256 (uri (cran-uri "abf2" version))
9258 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9259 (build-system r-build-system)
9260 (home-page "https://cran.r-project.org/web/packages/abf2/")
9261 (synopsis "Load gap-free axon @code{r-abf2} files")
9263 "This package loads electrophysiology data from ABF2 files, as created by
9264 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9265 mode are currently supported.")
9266 (license license:artistic2.0)))
9268 (define-public r-abhgenotyper
9270 (name "r-abhgenotyper")
9275 (uri (cran-uri "ABHgenotypeR" version))
9277 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9278 (properties `((upstream-name . "ABHgenotypeR")))
9279 (build-system r-build-system)
9281 `(("r-ggplot2" ,r-ggplot2)
9282 ("r-reshape2" ,r-reshape2)))
9283 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9284 (synopsis "Visualize and manipulate ABH genotypes")
9286 "The @code{r-abhgenotyper} package provides simple imputation,
9287 error-correction and plotting capacities for genotype data. The package is
9288 supposed to serve as an intermediate but independent analysis tool between the
9289 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9290 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9291 genotypes as \"graphical genotypes\".")
9292 (license license:gpl3)))
9294 (define-public r-furrr
9301 (uri (cran-uri "furrr" version))
9304 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9305 (build-system r-build-system)
9307 `(("r-ellipsis" ,r-ellipsis)
9308 ("r-future" ,r-future)
9309 ("r-globals" ,r-globals)
9310 ("r-lifecycle" ,r-lifecycle)
9311 ("r-purrr" ,r-purrr)
9312 ("r-rlang" ,r-rlang)
9313 ("r-vctrs" ,r-vctrs)))
9314 (home-page "https://github.com/DavisVaughan/furrr")
9315 (synopsis "Apply mapping functions in parallel using futures")
9317 "This package provides implementations of the family of @code{map()}
9318 functions from the @code{purrr} package that can be resolved using any
9319 @code{future}-supported backend, e.g. parallel on the local machine or
9320 distributed on a compute cluster.")
9321 (license license:lgpl2.1+)))
9323 (define-public r-abjutils
9330 (uri (cran-uri "abjutils" version))
9332 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9333 (build-system r-build-system)
9335 `(("r-dplyr" ,r-dplyr)
9336 ("r-magrittr" ,r-magrittr)
9337 ("r-purrr" ,r-purrr)
9338 ("r-rlang" ,r-rlang)
9339 ("r-rstudioapi" ,r-rstudioapi)
9340 ("r-stringi" ,r-stringi)
9341 ("r-stringr" ,r-stringr)
9342 ("r-tidyr" ,r-tidyr)))
9343 (home-page "https://github.com/abjur/abjutils/")
9344 (synopsis "Collection of tools for jurimetrical analysis")
9346 "This package implements general purpose tools, such as functions for
9347 sampling and basic manipulation of Brazilian lawsuits identification number.
9348 It also implements functions for text cleaning, such as accentuation
9350 (license license:expat)))
9352 (define-public r-abnormality
9354 (name "r-abnormality")
9359 (uri (cran-uri "abnormality" version))
9361 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9362 (build-system r-build-system)
9364 `(("r-mass" ,r-mass)
9365 ("r-matrix" ,r-matrix)))
9366 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9367 (synopsis "Measure a subject's abnormality with respect to a reference population")
9369 "This package contains functions to implement the methodology and
9370 considerations laid out by Marks et al. in the article \"Measuring abnormality
9371 in high dimensional spaces: applications in biomechanical gait analysis\".
9372 Using high-dimensional datasets to measure a subject's overall level of
9373 abnormality as compared to a reference population is often needed in outcomes
9375 (license license:expat)))
9377 (define-public r-abodoutlier
9379 (name "r-abodoutlier")
9384 (uri (cran-uri "abodOutlier" version))
9386 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9387 (properties `((upstream-name . "abodOutlier")))
9388 (build-system r-build-system)
9390 `(("r-cluster" ,r-cluster)))
9391 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9392 (synopsis "Angle-based outlier detection")
9394 "This package performs angle-based outlier detection on a given data
9395 frame. It offers three methods to process data:
9397 @item full but slow implementation using all the data that has cubic
9399 @item a fully randomized method;
9400 @item a method using k-nearest neighbours.
9402 These algorithms are well suited for high dimensional data outlier
9404 (license license:expat)))
9406 (define-public r-abps
9413 (uri (cran-uri "ABPS" version))
9415 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9416 (properties `((upstream-name . "ABPS")))
9417 (build-system r-build-system)
9418 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9419 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9420 (synopsis "Abnormal blood profile score to detect blood doping")
9422 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9423 The ABPS is a part of the Athlete biological passport program of the World
9424 anti-doping agency, which combines several blood parameters into a single
9425 score in order to detect blood doping. The package also contains functions to
9426 calculate other scores used in anti-doping programs, such as the ratio of
9427 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9428 (license license:gpl2+)))
9430 (define-public r-parmigene
9432 (name "r-parmigene")
9437 (uri (cran-uri "parmigene" version))
9440 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9441 (build-system r-build-system)
9442 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9443 (synopsis "Mutual information estimation for gene network reconstruction")
9445 "This package provides a parallel estimation of the mutual information
9446 based on entropy estimates from k-nearest neighbors distances and algorithms
9447 for the reconstruction of gene regulatory networks.")
9448 (license license:agpl3+)))
9450 (define-public r-pscl
9457 (uri (cran-uri "pscl" version))
9459 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9460 (build-system r-build-system)
9462 `(("r-mass" ,r-mass)))
9463 (home-page "https://github.com/atahk/pscl/")
9464 (synopsis "Political science computational laboratory")
9466 "The @code{pscl} is an R package providing classes and methods for:
9468 @item Bayesian analysis of roll call data (item-response models);
9469 @item elementary Bayesian statistics;
9470 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9472 @item utility functions.
9474 (license license:gpl2)))
9476 (define-public r-accelmissing
9478 (name "r-accelmissing")
9483 (uri (cran-uri "accelmissing" version))
9485 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9486 (build-system r-build-system)
9488 `(("r-mice" ,r-mice)
9489 ("r-pscl" ,r-pscl)))
9490 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9491 (synopsis "Missing value imputation for accelerometer data")
9493 "This package provides a statistical method to impute the missing values in
9494 accelerometer data. The methodology includes both parametric and
9495 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9496 model. It also provides multiple functions to preprocess the accelerometer data
9497 previous to the missing data imputation. These include detecting the wearing
9498 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9499 (license license:gpl2+)))
9501 (define-public r-mhsmm
9508 (uri (cran-uri "mhsmm" version))
9510 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9511 (build-system r-build-system)
9512 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9513 (home-page "https://github.com/jaredo/mhsmm/")
9514 (synopsis "Inference for hidden Markov and semi-Markov models")
9516 "The @code{r-mhsmm} package implements estimation and prediction methods for
9517 hidden Markov and semi-Markov models for multiple observation sequences. Such
9518 techniques are of interest when observed data is thought to be dependent on some
9519 unobserved (or hidden) state. Also, this package is suitable for equidistant
9520 time series data, with multivariate and/or missing data. Allows user defined
9521 emission distributions.")
9522 (license license:gpl2+)))
9524 (define-public r-nleqslv
9531 (uri (cran-uri "nleqslv" version))
9533 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9534 (build-system r-build-system)
9535 (native-inputs `(("gfortran" ,gfortran)))
9536 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9537 (synopsis "Solve systems of nonlinear equations")
9539 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9540 Broyden or a Newton method with a choice of global strategies such as line
9541 search and trust region. There are options for using a numerical or user
9542 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9543 singular or ill-conditioned Jacobian.")
9544 (license license:gpl2+)))
9546 (define-public r-physicalactivity
9548 (name "r-physicalactivity")
9553 (uri (cran-uri "PhysicalActivity" version))
9555 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9557 `((upstream-name . "PhysicalActivity")))
9558 (build-system r-build-system)
9559 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9560 (synopsis "Processing accelerometer data for physical activity measurement")
9562 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9563 for classification of monitored wear and nonwear time intervals in accelerometer
9564 data collected to assess physical activity. The package also contains functions
9565 for making plots of accelerometer data and obtaining the summary of various
9566 information including daily monitor wear time and the mean monitor wear time
9567 during valid days. The revised package version 0.2-1 improved the functions
9568 regarding speed, robustness and add better support for time zones and daylight
9569 saving. In addition, several functions were added:
9571 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9572 @item the @code{markPAI} can categorize physical activity intensity level based
9573 on user-defined cut-points of accelerometer counts.
9575 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9576 @code{queryActigraph} functions.")
9577 (license license:gpl3+)))
9579 (define-public r-acc
9586 (uri (cran-uri "acc" version))
9588 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9589 (build-system r-build-system)
9591 `(("r-circlize" ,r-circlize)
9593 ("r-ggplot2" ,r-ggplot2)
9594 ("r-iterators" ,r-iterators)
9595 ("r-mhsmm" ,r-mhsmm)
9596 ("r-nleqslv" ,r-nleqslv)
9597 ("r-physicalactivity" ,r-physicalactivity)
9599 ("r-r-utils" ,r-r-utils)
9601 ("r-rcpparmadillo" ,r-rcpparmadillo)
9602 ("r-rsqlite" ,r-rsqlite)
9604 (home-page "https://cran.r-project.org/web/packages/acc/")
9605 (synopsis "Exploring accelerometer data")
9607 "This package processes accelerometer data from uni-axial and tri-axial devices
9608 and generates data summaries. Also, includes functions to plot, analyze, and
9609 simulate accelerometer data.")
9610 (license license:gpl2+)))
9612 (define-public r-rbenchmark
9614 (name "r-rbenchmark")
9619 (uri (cran-uri "rbenchmark" version))
9621 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9622 (build-system r-build-system)
9623 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9624 (synopsis "Benchmarking routine for R")
9626 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9627 and is intended to facilitate benchmarking of arbitrary R code. The library
9628 consists of just one function, benchmark, which is a simple wrapper around
9629 system.time. Given a specification of the benchmarking process (counts of
9630 replications, evaluation environment) and an arbitrary number of expressions,
9631 benchmark evaluates each of the expressions in the specified environment,
9632 replicating the evaluation as many times as specified, and returning the results
9633 conveniently wrapped into a data frame.")
9634 (license license:gpl2+)))
9636 (define-public r-mitools
9643 (uri (cran-uri "mitools" version))
9646 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9647 (build-system r-build-system)
9648 (propagated-inputs `(("r-dbi" ,r-dbi)))
9649 (home-page "https://cran.r-project.org/web/packages/mitools/")
9650 (synopsis "Tools for multiple imputation of missing data")
9652 "This package provides tools to perform analyses and combine results from
9653 multiple-imputation datasets.")
9654 (license license:gpl2)))
9656 (define-public r-mixsqp
9662 (uri (cran-uri "mixsqp" version))
9665 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9666 (properties `((upstream-name . "mixsqp")))
9667 (build-system r-build-system)
9669 `(("r-irlba" ,r-irlba)
9671 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9673 `(("r-knitr" ,r-knitr)))
9674 (home-page "https://github.com/stephenslab/mixsqp")
9676 "Sequential quadratic programming for maximum-likelihood estimation")
9678 "This package provides an optimization method based on sequential
9679 quadratic programming for maximum likelihood estimation of the mixture
9680 proportions in a finite mixture model where the component densities are
9681 known. The algorithm is expected to obtain solutions that are at least
9682 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9683 are expected to arrive at solutions more quickly when the number of
9684 samples is large and the number of mixture components is not too large.")
9685 (license license:expat)))
9687 (define-public r-magick
9694 (uri (cran-uri "magick" version))
9697 "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf"))))
9698 (build-system r-build-system)
9700 `(("imagemagick" ,imagemagick)
9703 `(("r-curl" ,r-curl)
9704 ("r-magrittr" ,r-magrittr)
9705 ("r-rcpp" ,r-rcpp)))
9707 `(("pkg-config" ,pkg-config)
9708 ("r-knitr" ,r-knitr)))
9709 (home-page "https://github.com/ropensci/magick")
9710 (synopsis "Advanced graphics and image-processing in R")
9712 "This package provides bindings to ImageMagick, a comprehensive image
9713 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9714 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9715 operations are vectorized via the Magick++ STL meaning they operate either on
9716 a single frame or a series of frames for working with layers, collages, or
9717 animation. In RStudio, images are automatically previewed when printed to the
9718 console, resulting in an interactive editing environment.")
9719 (license license:expat)))
9721 (define-public r-survey
9728 (uri (cran-uri "survey" version))
9731 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9732 (build-system r-build-system)
9734 `(("r-lattice" ,r-lattice)
9735 ("r-matrix" ,r-matrix)
9736 ("r-minqa" ,r-minqa)
9737 ("r-mitools" ,r-mitools)
9738 ("r-numderiv" ,r-numderiv)
9739 ("r-survival" ,r-survival)))
9740 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9741 (synopsis "Analysis of complex survey samples")
9743 "This package provides tools for the analysis of complex survey samples.
9744 The provided features include: summary statistics, two-sample tests, rank
9745 tests, generalised linear models, cumulative link models, Cox models,
9746 loglinear models, and general maximum pseudolikelihood estimation for
9747 multistage stratified, cluster-sampled, unequally weighted survey samples;
9748 variances by Taylor series linearisation or replicate weights;
9749 post-stratification, calibration, and raking; two-phase subsampling designs;
9750 graphics; PPS sampling without replacement; principal components, and factor
9752 ;; Either version of the GPL.
9753 (license (list license:gpl2 license:gpl3))))
9755 (define-public r-gee
9762 (uri (cran-uri "gee" version))
9765 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9766 (properties `((upstream-name . "gee")))
9767 (build-system r-build-system)
9769 `(("gfortran" ,gfortran)))
9770 (home-page "https://cran.r-project.org/web/packages/gee/")
9771 (synopsis "Generalized estimation equation solver")
9773 "This package provides a solver for generalized estimation equations.")
9774 (license license:gpl2)))
9776 (define-public r-tab
9783 (uri (cran-uri "tab" version))
9786 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9787 (properties `((upstream-name . "tab")))
9788 (build-system r-build-system)
9790 `(("r-dplyr" ,r-dplyr)
9792 ("r-knitr" ,r-knitr)
9794 ("r-survey" ,r-survey)
9795 ("r-survival" ,r-survival)
9796 ("r-xtable" ,r-xtable)))
9797 (home-page "https://cran.r-project.org/web/packages/tab/")
9798 (synopsis "Create summary tables for statistical reports")
9800 "This package contains functions for creating various types of summary
9801 tables, e.g. comparing characteristics across levels of a categorical variable
9802 and summarizing fitted generalized linear models, generalized estimating
9803 equations, and Cox proportional hazards models. Functions are available to
9804 handle data from simple random samples as well as complex surveys.")
9805 (license license:gpl3+)))
9807 (define-public r-dvmisc
9814 (uri (cran-uri "dvmisc" version))
9816 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9817 (build-system r-build-system)
9819 `(("r-cubature" ,r-cubature)
9820 ("r-data-table" ,r-data-table)
9821 ("r-dplyr" ,r-dplyr)
9822 ("r-ggplot2" ,r-ggplot2)
9824 ("r-mvtnorm" ,r-mvtnorm)
9825 ("r-pracma" ,r-pracma)
9826 ("r-rbenchmark" ,r-rbenchmark)
9828 ("r-survey" ,r-survey)
9830 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9831 (synopsis "Faster computation of common statistics and miscellaneous functions")
9833 "This package implements faster versions of base R functions (e.g. mean, standard
9834 deviation, covariance, weighted mean), mostly written in C++, along with
9835 miscellaneous functions for various purposes (e.g. create the histogram with
9836 fitted probability density function or probability mass function curve, create
9837 the body mass index groups, assess the linearity assumption in logistic
9839 (license license:gpl2)))
9841 (define-public r-accelerometry
9843 (name "r-accelerometry")
9848 (uri (cran-uri "accelerometry" version))
9850 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9851 (build-system r-build-system)
9853 `(("r-dvmisc" ,r-dvmisc)
9854 ("r-rcpp" ,r-rcpp)))
9855 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9856 (synopsis "Functions for processing accelerometer data")
9858 "This package provides a collection of functions that perform operations on
9859 time-series accelerometer data, such as identify the non-wear time, flag minutes
9860 that are part of an activity bout, and find the maximum 10-minute average count
9861 value. The functions are generally very flexible, allowing for a variety of
9862 algorithms to be implemented.")
9863 (license license:gpl3)))
9865 (define-public r-absim
9872 (uri (cran-uri "AbSim" version))
9874 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9875 (properties `((upstream-name . "AbSim")))
9876 (build-system r-build-system)
9879 ("r-powerlaw" ,r-powerlaw)))
9880 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9881 (synopsis "Time resolved simulations of antibody repertoires")
9883 "This package provides simulation methods for the evolution of antibody repertoires.
9884 The heavy and light chain variable region of both human and C57BL/6 mice can
9885 be simulated in a time-dependent fashion. Both single lineages using one set of
9886 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9887 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9888 Upon completion, the main loop of the algorithm begins, with each iteration
9889 representing one simulated time step. Various mutation events are possible at
9890 each time step, contributing to a diverse final repertoire.")
9891 (license license:gpl2)))
9893 (define-public r-quic
9900 (uri (cran-uri "QUIC" version))
9902 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9903 (properties `((upstream-name . "QUIC")))
9904 (build-system r-build-system)
9905 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9906 (synopsis "Regularized sparse inverse covariance matrix estimation")
9908 "This package implements the regularized Gaussian maximum likelihood
9909 estimation of the inverse of a covariance matrix. It uses Newton's method and
9910 coordinate descent to solve the regularized inverse covariance matrix
9911 estimation problem.")
9912 ;; The project home page states that the release is under GPLv3 or later.
9913 ;; The CRAN page only says GPL-3.
9914 (license license:gpl3+)))
9916 (define-public r-abundant
9923 (uri (cran-uri "abundant" version))
9925 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9926 (build-system r-build-system)
9928 `(("r-quic" ,r-quic)))
9929 (home-page "https://cran.r-project.org/web/packages/abundant/")
9930 (synopsis "Abundant regression and high-dimensional principal fitted components")
9932 "This package provides tools to fit and predict with the high-dimensional
9933 principal fitted components model. This model is described by Cook, Forzani,
9934 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9935 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9936 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9937 (license license:gpl2+)))
9939 (define-public r-ac3net
9946 (uri (cran-uri "Ac3net" version))
9948 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9949 (properties `((upstream-name . "Ac3net")))
9950 (build-system r-build-system)
9952 `(("r-data-table" ,r-data-table)))
9953 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9954 (synopsis "Inferring directional conservative causal core gene networks")
9955 (description "This package infers directional Conservative causal core
9956 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9957 directional network.")
9958 (license license:gpl3+)))
9960 (define-public r-aca
9967 (uri (cran-uri "ACA" version))
9969 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9970 (properties `((upstream-name . "ACA")))
9971 (build-system r-build-system)
9972 (home-page "https://cran.r-project.org/web/packages/ACA/")
9973 (synopsis "Abrupt change-point or aberration detection in point series")
9975 "This package offers an interactive function for the detection of breakpoints in
9977 ;; Any version of the GPL
9978 (license (list license:gpl2+ license:gpl3+))))
9980 (define-public r-acceptancesampling
9982 (name "r-acceptancesampling")
9987 (uri (cran-uri "AcceptanceSampling" version))
9989 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9991 `((upstream-name . "AcceptanceSampling")))
9992 (build-system r-build-system)
9993 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9994 (synopsis "Creation and evaluation of acceptance sampling plans")
9996 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9997 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9998 in quality control and improvement. International standards of acceptance
9999 sampling provide sampling plans for specific circumstances. The aim of this
10000 package is to provide an easy-to-use interface to visualize single, double or
10001 multiple sampling plans. In addition, methods have been provided to enable the
10002 user to assess sampling plans against pre-specified levels of performance, as
10003 measured by the probability of acceptance for a given level of quality in the
10005 (license license:gpl3+)))
10007 (define-public r-acclma
10014 (uri (cran-uri "ACCLMA" version))
10016 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
10017 (properties `((upstream-name . "ACCLMA")))
10018 (build-system r-build-system)
10019 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10020 (synopsis "ACC & LMA graph plotting")
10022 "This package contains a function that imports data from a @acronym{CSV,
10023 Comma-Separated Values} file, or uses manually entered data from the format (x,
10024 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10025 Curve} vs @acronym{LOI, Line of Independence} graph and
10026 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10027 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10028 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10029 string) was passed, a manual data entry window is opened. The header parameter
10030 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10031 a header row or not. The dataset should contain only one independent variable
10032 (x) and one dependent variable (y) and can contain a weight for each
10034 (license license:gpl2)))
10036 (define-public r-aspi
10043 (uri (cran-uri "aspi" version))
10045 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10046 (build-system r-build-system)
10048 "https://cran.r-project.org/web/packages/aspi/")
10050 "Analysis of symmetry of parasitic infections")
10052 "This package provides tools for the analysis and visualization of bilateral
10053 asymmetry in parasitic infections.")
10054 (license license:gpl3+)))
10056 (define-public r-sandwich
10058 (name "r-sandwich")
10063 (uri (cran-uri "sandwich" version))
10066 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10067 (build-system r-build-system)
10069 `(("r-zoo" ,r-zoo)))
10070 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10071 (synopsis "Robust Covariance Matrix Estimators")
10073 "This package provides model-robust standard error estimators for
10074 cross-sectional, time series, clustered, panel, and longitudinal data.")
10075 ;; Either version of the license.
10076 (license (list license:gpl2 license:gpl3))))
10078 (define-public r-th-data
10085 (uri (cran-uri "TH.data" version))
10088 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10089 (properties `((upstream-name . "TH.data")))
10090 (build-system r-build-system)
10092 `(("r-mass" ,r-mass)
10093 ("r-survival" ,r-survival)))
10094 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10095 (synopsis "Shared data sets")
10097 "This package contains supporting data sets that are used in other
10098 packages maintained by Torsten Hothorn.")
10099 (license license:gpl3)))
10101 (define-public r-multcomp
10103 (name "r-multcomp")
10108 (uri (cran-uri "multcomp" version))
10111 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10112 (build-system r-build-system)
10114 `(("r-codetools" ,r-codetools)
10115 ("r-mvtnorm" ,r-mvtnorm)
10116 ("r-sandwich" ,r-sandwich)
10117 ("r-survival" ,r-survival)
10118 ("r-th-data" ,r-th-data)))
10119 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10120 (synopsis "Simultaneous inference in general parametric models")
10122 "Simultaneous tests and confidence intervals for general linear
10123 hypotheses in parametric models, including linear, generalized linear, linear
10124 mixed effects, and survival models. The package includes demos reproducing
10125 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10126 Hothorn, Westfall, 2010, CRC Press).")
10127 (license license:gpl2)))
10129 (define-public r-emmeans
10132 (version "1.5.5-1")
10136 (uri (cran-uri "emmeans" version))
10139 "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz"))))
10140 (build-system r-build-system)
10142 `(("r-estimability" ,r-estimability)
10143 ("r-mvtnorm" ,r-mvtnorm)
10144 ("r-numderiv" ,r-numderiv)
10146 ("r-xtable" ,r-xtable)))
10148 `(("r-knitr" ,r-knitr)))
10149 (home-page "https://github.com/rvlenth/emmeans")
10150 (synopsis "Estimated marginal means, aka least-squares means")
10152 "This package provides tools to obtain @dfn{estimated marginal
10153 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10154 be used to compute contrasts or linear functions of EMMs, trends, and
10155 comparisons of slopes.")
10156 ;; Either version of the license.
10157 (license (list license:gpl2 license:gpl3))))
10159 (define-public r-pwr
10166 (uri (cran-uri "pwr" version))
10169 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10170 (build-system r-build-system)
10172 `(("r-knitr" ,r-knitr)))
10173 (home-page "https://github.com/heliosdrm/pwr")
10174 (synopsis "Basic functions for power analysis")
10176 "This package provides power analysis functions along the lines of
10178 (license license:gpl3+)))
10180 (define-public r-libcoin
10187 (uri (cran-uri "libcoin" version))
10189 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10190 (build-system r-build-system)
10191 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10192 (home-page "https://cran.r-project.org/web/packages/libcoin")
10193 (synopsis "Linear test statistics for permutation inference")
10195 "This package provides basic infrastructure for linear test statistics
10196 and permutation inference in the framework of Strasser and Weber (1999).")
10197 (license license:gpl2)))
10199 (define-public r-coin
10206 (uri (cran-uri "coin" version))
10209 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10210 (build-system r-build-system)
10212 `(("r-libcoin" ,r-libcoin)
10213 ("r-matrixstats" ,r-matrixstats)
10214 ("r-modeltools" ,r-modeltools)
10215 ("r-multcomp" ,r-multcomp)
10216 ("r-mvtnorm" ,r-mvtnorm)
10217 ("r-survival" ,r-survival)))
10218 (home-page "http://coin.r-forge.r-project.org")
10219 (synopsis "Conditional inference procedures in a permutation test framework")
10221 "This package provides conditional inference procedures for the general
10222 independence problem including two-sample, K-sample (non-parametric ANOVA),
10223 correlation, censored, ordered and multivariate problems.")
10224 (license license:gpl2)))
10226 (define-public r-bayesplot
10228 (name "r-bayesplot")
10233 (uri (cran-uri "bayesplot" version))
10236 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10237 (build-system r-build-system)
10239 `(("pandoc" ,pandoc)
10240 ("pandoc-citeproc" ,pandoc-citeproc)))
10242 `(("r-knitr" ,r-knitr)))
10244 `(("r-dplyr" ,r-dplyr)
10245 ("r-ggplot2" ,r-ggplot2)
10246 ("r-ggridges" ,r-ggridges)
10248 ("r-reshape2" ,r-reshape2)
10249 ("r-rlang" ,r-rlang)
10250 ("r-tibble" ,r-tibble)
10251 ("r-tidyselect" ,r-tidyselect)))
10252 (home-page "https://mc-stan.org/bayesplot")
10253 (synopsis "Plotting for Bayesian models")
10255 "This package provides plotting functions for posterior analysis, model
10256 checking, and MCMC diagnostics. The package is designed not only to provide
10257 convenient functionality for users, but also a common set of functions that
10258 can be easily used by developers working on a variety of R packages for
10259 Bayesian modeling.")
10260 (license license:gpl3+)))
10262 (define-public r-tmb
10269 (uri (cran-uri "TMB" version))
10272 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10273 (properties `((upstream-name . "TMB")))
10274 (build-system r-build-system)
10276 `(("r-matrix" ,r-matrix)
10277 ("r-rcppeigen" ,r-rcppeigen)))
10278 (home-page "http://tmb-project.org")
10279 (synopsis "Template model builder: a general random effect tool")
10281 "With this tool, a user should be able to quickly implement complex
10282 random effect models through simple C++ templates. The package combines
10283 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10284 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10285 from R) to obtain an efficient implementation of the applied Laplace
10286 approximation with exact derivatives. Key features are: Automatic sparseness
10287 detection, parallelism through BLAS and parallel user templates.")
10288 (license license:gpl2)))
10290 (define-public r-sjstats
10297 (uri (cran-uri "sjstats" version))
10299 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10300 (build-system r-build-system)
10302 `(("r-bayestestr" ,r-bayestestr)
10303 ("r-broom" ,r-broom)
10304 ("r-dplyr" ,r-dplyr)
10305 ("r-effectsize" ,r-effectsize)
10306 ("r-emmeans" ,r-emmeans)
10307 ("r-insight" ,r-insight)
10309 ("r-magrittr" ,r-magrittr)
10311 ("r-modelr" ,r-modelr)
10312 ("r-parameters" ,r-parameters)
10313 ("r-performance" ,r-performance)
10314 ("r-purrr" ,r-purrr)
10315 ("r-rlang" ,r-rlang)
10316 ("r-sjlabelled" ,r-sjlabelled)
10317 ("r-sjmisc" ,r-sjmisc)
10318 ("r-tidyr" ,r-tidyr)))
10319 (home-page "https://github.com/strengejacke/sjstats")
10320 (synopsis "Functions for common statistical computations")
10322 "This package provides a collection of convenient functions for common
10323 statistical computations, which are not directly provided by R's @code{base}
10324 or @code{stats} packages. This package aims at providing, first, shortcuts
10325 for statistical measures, which otherwise could only be calculated with
10326 additional effort. Second, these shortcut functions are generic, and can be
10327 applied not only to vectors, but also to other objects as well. The focus of
10328 most functions lies on summary statistics or fit measures for regression
10329 models, including generalized linear models, mixed effects models and Bayesian
10331 (license license:gpl3)))
10333 (define-public r-glmmtmb
10336 (version "1.0.2.1")
10340 (uri (cran-uri "glmmTMB" version))
10343 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10344 (properties `((upstream-name . "glmmTMB")))
10345 (build-system r-build-system)
10347 `(("r-lme4" ,r-lme4)
10348 ("r-matrix" ,r-matrix)
10350 ("r-rcppeigen" ,r-rcppeigen)
10353 `(("r-knitr" ,r-knitr))) ; for vignettes
10354 (home-page "https://github.com/glmmTMB")
10355 (synopsis "Generalized linear mixed models")
10357 "Fit linear and generalized linear mixed models with various extensions,
10358 including zero-inflation. The models are fitted using maximum likelihood
10359 estimation via the Template Model Builder. Random effects are assumed to be
10360 Gaussian on the scale of the linear predictor and are integrated out using the
10361 Laplace approximation. Gradients are calculated using automatic
10363 (license license:agpl3+)))
10365 (define-public r-bayestestr
10367 (name "r-bayestestr")
10372 (uri (cran-uri "bayestestR" version))
10375 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10376 (properties `((upstream-name . "bayestestR")))
10377 (build-system r-build-system)
10379 `(("r-insight" ,r-insight)))
10381 `(("r-knitr" ,r-knitr)))
10382 (home-page "https://github.com/easystats/bayestestR")
10383 (synopsis "Describe Bayesian models and posterior distributions")
10385 "This package provides utilities to understand and describe posterior
10386 distributions and Bayesian models. It includes point-estimates such as
10387 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10388 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10389 ROPE percentage and pd).")
10390 (license license:gpl3)))
10392 (define-public r-performance
10394 (name "r-performance")
10399 (uri (cran-uri "performance" version))
10402 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10403 (build-system r-build-system)
10405 `(("r-bayestestr" ,r-bayestestr)
10406 ("r-insight" ,r-insight)))
10407 (home-page "https://easystats.github.io/performance/")
10408 (synopsis "Assessment of regression models performance")
10410 "This package provides utilities for computing measures to assess model
10411 quality, which are not directly provided by R's @code{base} or @code{stats}
10412 packages. These include e.g. measures like r-squared, intraclass correlation
10413 coefficient, root mean squared error or functions to check models for
10414 overdispersion, singularity or zero-inflation and more. Functions apply to a
10415 large variety of regression models, including generalized linear models, mixed
10416 effects models and Bayesian models.")
10417 (license license:gpl3)))
10419 (define-public r-ggeffects
10421 (name "r-ggeffects")
10426 (uri (cran-uri "ggeffects" version))
10429 "0qh8x8yi8gkb5x7zfxmb1c689k7bhc1f5947yymny34j7xdsb9s8"))))
10430 (build-system r-build-system)
10432 `(("r-insight" ,r-insight)
10434 ("r-sjlabelled" ,r-sjlabelled)))
10436 `(("r-knitr" ,r-knitr)))
10437 (home-page "https://github.com/strengejacke/ggeffects")
10438 (synopsis "Create tidy data frames of marginal effects for ggplot")
10440 "This package provides tools to compute marginal effects from statistical
10441 models and return the result as tidy data frames. These data frames are ready
10442 to use with the @code{ggplot2} package. Marginal effects can be calculated
10443 for many different models. Interaction terms, splines and polynomial terms
10444 are also supported. The two main functions are @code{ggpredict()} and
10445 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10446 results using @code{ggplot2}.")
10447 (license license:gpl3)))
10449 (define-public r-effectsize
10451 (name "r-effectsize")
10452 (version "0.4.4-1")
10456 (uri (cran-uri "effectsize" version))
10459 "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb"))))
10460 (properties `((upstream-name . "effectsize")))
10461 (build-system r-build-system)
10463 `(("r-bayestestr" ,r-bayestestr)
10464 ("r-insight" ,r-insight)
10465 ("r-parameters" ,r-parameters)))
10467 `(("r-knitr" ,r-knitr)))
10468 (home-page "https://github.com/easystats/effectsize")
10469 (synopsis "Indices of effect size and standardized parameters")
10471 "This package provides utilities to work with indices of effect size and
10472 standardized parameters for a wide variety of models, allowing computation and
10473 conversion of indices such as Cohen's d, r, odds, etc.")
10474 (license license:gpl3)))
10476 (define-public r-sjplot
10483 (uri (cran-uri "sjPlot" version))
10485 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10486 (properties `((upstream-name . "sjPlot")))
10487 (build-system r-build-system)
10489 `(("r-bayestestr" ,r-bayestestr)
10490 ("r-dplyr" ,r-dplyr)
10491 ("r-effectsize" ,r-effectsize)
10492 ("r-ggeffects" ,r-ggeffects)
10493 ("r-ggplot2" ,r-ggplot2)
10494 ("r-insight" ,r-insight)
10495 ("r-knitr" ,r-knitr)
10497 ("r-parameters" ,r-parameters)
10498 ("r-performance" ,r-performance)
10499 ("r-purrr" ,r-purrr)
10500 ("r-rlang" ,r-rlang)
10501 ("r-scales" ,r-scales)
10502 ("r-sjlabelled" ,r-sjlabelled)
10503 ("r-sjmisc" ,r-sjmisc)
10504 ("r-sjstats" ,r-sjstats)
10505 ("r-tidyr" ,r-tidyr)))
10507 `(("r-knitr" ,r-knitr)))
10508 (home-page "https://strengejacke.github.io/sjPlot/")
10509 (synopsis "Data visualization for statistics in social science")
10511 "This package represents a collection of plotting and table output
10512 functions for data visualization. Results of various statistical
10513 analyses (that are commonly used in social sciences) can be visualized using
10514 this package, including simple and cross tabulated frequencies, histograms,
10515 box plots, (generalized) linear models, mixed effects models, principal
10516 component analysis and correlation matrices, cluster analyses, scatter plots,
10517 stacked scales, effects plots of regression models (including interaction
10518 terms) and much more. This package supports labelled data.")
10519 (license license:gpl3)))
10521 (define-public r-ini
10528 (uri (cran-uri "ini" version))
10531 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10532 (build-system r-build-system)
10533 (home-page "https://github.com/dvdscripter/ini")
10534 (synopsis "Read and write configuration files")
10536 "This package provides tools to parse simple @code{.ini} configuration
10537 files to an structured list. Users can manipulate this resulting list with
10538 @code{lapply()} functions. This same structured list can be used to write
10539 back to file after modifications.")
10540 (license license:gpl3)))
10542 (define-public r-gitcreds
10544 (name "r-gitcreds")
10549 (uri (cran-uri "gitcreds" version))
10552 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10553 (properties `((upstream-name . "gitcreds")))
10554 (build-system r-build-system)
10555 (inputs `(("git" ,git-minimal)))
10556 (native-inputs `(("r-knitr" ,r-knitr)))
10557 (home-page "https://github.com/r-lib/gitcreds")
10558 (synopsis "Query git credentials from R")
10560 "Query, set, and delete credentials from the git credential store.
10561 Manage GitHub tokens and other git credentials. This package is to be used by
10562 other packages that need to authenticate to GitHub and/or other git
10564 (license license:expat)))
10566 (define-public r-gh
10573 (uri (cran-uri "gh" version))
10576 "16xa1qb1r28f8yc6ybjrxiq2zigxj886dp9k29jpsn5091xbzkq0"))))
10577 (build-system r-build-system)
10580 ("r-gitcreds" ,r-gitcreds)
10583 ("r-jsonlite" ,r-jsonlite)))
10585 `(("r-knitr" ,r-knitr)))
10586 (home-page "https://github.com/r-lib/gh#readme")
10587 (synopsis "Access the GitHub API via R")
10589 "This package provides a minimal R client to access the GitHub API.")
10590 (license license:expat)))
10592 (define-public r-fs
10599 (uri (cran-uri "fs" version))
10602 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10603 (build-system r-build-system)
10605 `(("r-knitr" ,r-knitr)))
10606 (home-page "https://fs.r-lib.org")
10607 (synopsis "Cross-platform file system operations based on libuv")
10609 "This package provides a cross-platform interface to file system
10610 operations, built on top of the libuv C library.")
10611 (license license:gpl3)))
10613 (define-public r-clisymbols
10615 (name "r-clisymbols")
10620 (uri (cran-uri "clisymbols" version))
10623 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10624 (build-system r-build-system)
10625 (home-page "https://github.com/gaborcsardi/clisymbols")
10626 (synopsis "Unicode symbols at the R prompt")
10628 "This package provides a small subset of Unicode symbols, that are useful
10629 when building command line applications. They fall back to alternatives on
10630 terminals that do not support Unicode.")
10631 (license license:expat)))
10633 (define-public r-credentials
10635 (name "r-credentials")
10640 (uri (cran-uri "credentials" version))
10643 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10644 (properties `((upstream-name . "credentials")))
10645 (build-system r-build-system)
10648 (modify-phases %standard-phases
10649 (add-after 'unpack 'setenv-HOME
10651 ;; This is necessary because git looks for $HOME/.gitconfig
10652 (setenv "HOME" "/tmp")
10655 `(("git" ,git-minimal)))
10657 `(("r-askpass" ,r-askpass)
10659 ("r-jsonlite" ,r-jsonlite)
10660 ("r-openssl" ,r-openssl)
10663 `(("r-knitr" ,r-knitr)))
10664 (home-page "https://docs.ropensci.org/credentials/")
10665 (synopsis "Tools for managing SSH and Git credentials")
10667 "This package assists you in setting up and retrieving of HTTPS and SSH
10668 credentials for use with git and other services. For HTTPS remotes the
10669 package interfaces the @command{git-credential} utility which @command{git}
10670 uses to store HTTP usernames and passwords. For SSH remotes this package
10671 provides convenient functions to find or generate appropriate SSH keys. The
10672 package both helps the user to setup a local git installation, and also
10673 provides a back-end for git/ssh client libraries to authenticate with existing
10674 user credentials.")
10675 (license license:expat)))
10677 (define-public r-gert
10684 (uri (cran-uri "gert" version))
10687 "1fh72p92wj83yv1ch77jms6k1gjqfji8cmgw23vpxd0p8l9jj4h7"))))
10688 (properties `((upstream-name . "gert")))
10689 (build-system r-build-system)
10691 `(("libgit2" ,libgit2)
10694 `(("r-askpass" ,r-askpass)
10695 ("r-credentials" ,r-credentials)
10696 ("r-openssl" ,r-openssl)
10697 ("r-rstudioapi" ,r-rstudioapi)
10701 `(("pkg-config" ,pkg-config)
10702 ("r-knitr" ,r-knitr)))
10703 (home-page "https://docs.ropensci.org/gert/")
10704 (synopsis "Simple Git client for R")
10706 "This package provides a simple git client for R based on libgit2 with
10707 support for SSH and HTTPS remotes. All functions in gert use basic R data
10708 types (such as vectors and data-frames) for their arguments and return values.
10709 User credentials are shared with command line git through the
10710 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10711 (license license:expat)))
10713 (define-public r-usethis
10720 (uri (cran-uri "usethis" version))
10723 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10724 (build-system r-build-system)
10727 ("r-clipr" ,r-clipr)
10728 ("r-crayon" ,r-crayon)
10735 ("r-jsonlite" ,r-jsonlite)
10736 ("r-lifecycle" ,r-lifecycle)
10737 ("r-purrr" ,r-purrr)
10738 ("r-rappdirs" ,r-rappdirs)
10739 ("r-rlang" ,r-rlang)
10740 ("r-rprojroot" ,r-rprojroot)
10741 ("r-rstudioapi" ,r-rstudioapi)
10742 ("r-whisker" ,r-whisker)
10743 ("r-withr" ,r-withr)
10744 ("r-yaml" ,r-yaml)))
10745 (home-page "https://github.com/r-lib/usethis")
10746 (synopsis "Automate R package and project setup")
10748 "This package helps you to automate R package and project setup tasks
10749 that are otherwise performed manually. This includes setting up unit testing,
10750 test coverage, continuous integration, Git, GitHub integration, licenses,
10751 Rcpp, RStudio projects, and more.")
10752 (license license:gpl3)))
10754 (define-public r-sessioninfo
10756 (name "r-sessioninfo")
10761 (uri (cran-uri "sessioninfo" version))
10764 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10765 (build-system r-build-system)
10768 ("r-withr" ,r-withr)))
10769 (home-page "https://github.com/r-lib/sessioninfo#readme")
10770 (synopsis "R session information")
10772 "This package provides tools to query and print information about the
10773 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10774 more information about packages, and where they were installed from.")
10775 (license license:gpl2)))
10777 (define-public r-remotes
10784 (uri (cran-uri "remotes" version))
10787 "0f35648bdxhvplcfj80r4hfj5w21f1s01kcz6b29d098c1mnfzb7"))))
10788 (build-system r-build-system)
10790 `(("r-knitr" ,r-knitr)))
10791 (home-page "https://github.com/r-lib/remotes#readme")
10792 (synopsis "R package installation from remote repositories")
10794 "Download and install R packages stored in GitHub, BitBucket, or plain
10795 subversion or git repositories. This package is a lightweight replacement of
10796 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10797 the code was copied over from @code{devtools}.")
10798 (license license:gpl2+)))
10800 (define-public r-xopen
10807 (uri (cran-uri "xopen" version))
10810 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10811 (build-system r-build-system)
10813 `(("r-processx" ,r-processx)))
10814 (home-page "https://github.com/r-lib/xopen#readme")
10815 (synopsis "Open system files, URLs, anything")
10817 "This package provides a cross-platform solution to open files,
10818 directories or URLs with their associated programs.")
10819 (license license:expat)))
10821 (define-public r-rcmdcheck
10823 (name "r-rcmdcheck")
10828 (uri (cran-uri "rcmdcheck" version))
10831 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10832 (build-system r-build-system)
10834 `(("r-callr" ,r-callr)
10836 ("r-crayon" ,r-crayon)
10838 ("r-digest" ,r-digest)
10839 ("r-pkgbuild" ,r-pkgbuild)
10840 ("r-prettyunits" ,r-prettyunits)
10842 ("r-rprojroot" ,r-rprojroot)
10843 ("r-sessioninfo" ,r-sessioninfo)
10844 ("r-withr" ,r-withr)
10845 ("r-xopen" ,r-xopen)))
10846 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10847 (synopsis "Run R CMD check from R and capture results")
10849 "Run @code{R CMD check} from R programmatically, and capture the results
10850 of the individual checks.")
10851 (license license:expat)))
10853 (define-public r-rapportools
10855 (name "r-rapportools")
10860 (uri (cran-uri "rapportools" version))
10863 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10864 (build-system r-build-system)
10866 `(("r-pander" ,r-pander)
10868 ("r-reshape" ,r-reshape)))
10869 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10870 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10872 "This package provides helper functions that act as wrappers to more
10873 advanced statistical methods with the advantage of having sane defaults for
10875 (license license:agpl3+)))
10877 (define-public r-pander
10884 (uri (cran-uri "pander" version))
10887 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10888 (build-system r-build-system)
10890 `(("r-digest" ,r-digest)
10891 ("r-rcpp" ,r-rcpp)))
10892 (home-page "https://rapporter.github.io/pander")
10893 (synopsis "Render R objects into Pandoc's markdown")
10895 "The main aim of the pander R package is to provide a minimal and easy
10896 tool for rendering R objects into Pandoc's markdown. The package is also
10897 capable of exporting/converting complex Pandoc documents (reports) in various
10899 ;; This package is licensed under either the AGPLv3+ or the very rarely
10901 (license license:agpl3+)))
10903 (define-public r-summarytools
10905 (name "r-summarytools")
10910 (uri (cran-uri "summarytools" version))
10913 "0ig7vgjvldbndwhky1bsi38zifr9ji8xvvfqbfffplac08llvrbr"))))
10914 (build-system r-build-system)
10916 `(("r-base64enc" ,r-base64enc)
10917 ("r-checkmate" ,r-checkmate)
10918 ("r-dplyr" ,r-dplyr)
10919 ("r-htmltools" ,r-htmltools)
10920 ("r-lubridate" ,r-lubridate)
10921 ("r-magick" ,r-magick)
10922 ("r-matrixstats" ,r-matrixstats)
10923 ("r-pander" ,r-pander)
10925 ("r-rapportools" ,r-rapportools)
10926 ("r-tibble" ,r-tibble)
10927 ("r-tidyr" ,r-tidyr)))
10929 `(("r-knitr" ,r-knitr)))
10930 (home-page "https://github.com/dcomtois/summarytools")
10931 (synopsis "Tools to quickly and neatly summarize data")
10933 "This package provides tools for data frame summaries, cross-tabulations,
10934 weight-enabled frequency tables and common univariate statistics in concise
10935 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10936 good point-of-entry for exploring data, both for experienced and new R
10938 (license license:gpl2)))
10940 (define-public r-lsei
10947 (uri (cran-uri "lsei" version))
10950 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10951 (build-system r-build-system)
10953 `(("gfortran" ,gfortran)))
10954 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10955 (synopsis "Solve regression problems under equality/inequality constraints")
10957 "It contains functions that solve least squares linear regression
10958 problems under linear equality/inequality constraints. Functions for solving
10959 quadratic programming problems are also available, which transform such
10960 problems into least squares ones first.")
10961 (license license:gpl2+)))
10963 (define-public r-npsurv
10970 (uri (cran-uri "npsurv" version))
10973 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10974 (build-system r-build-system)
10976 `(("r-lsei" ,r-lsei)))
10977 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10978 (synopsis "Nonparametric survival analysis")
10980 "This package contains functions for non-parametric survival analysis of
10981 exact and interval-censored observations.")
10982 (license license:gpl2+)))
10984 (define-public r-clusteval
10986 (name "r-clusteval")
10991 (uri (cran-uri "clusteval" version))
10994 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10995 (build-system r-build-system)
10997 `(("r-mvtnorm" ,r-mvtnorm)
10998 ("r-rcpp" ,r-rcpp)))
10999 (home-page "https://cran.r-project.org/web/packages/clusteval/")
11000 (synopsis "Evaluation of clustering algorithms")
11002 "This R package provides a suite of tools to evaluate clustering
11003 algorithms, clusterings, and individual clusters.")
11004 (license license:expat)))
11006 (define-public r-tweedie
11013 (uri (cran-uri "tweedie" version))
11016 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
11017 (build-system r-build-system)
11018 (native-inputs `(("gfortran" ,gfortran)))
11019 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11020 (synopsis "Evaluation of Tweedie exponential family models")
11022 "Maximum likelihood computations for Tweedie families, including the
11023 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11024 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11025 and related methods.")
11026 (license license:gpl2+)))
11028 (define-public r-rcppgsl
11035 (uri (cran-uri "RcppGSL" version))
11037 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11038 (properties `((upstream-name . "RcppGSL")))
11039 (build-system r-build-system)
11041 `(("r-rcpp" ,r-rcpp)
11043 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11044 (synopsis "Rcpp integration for GSL vectors and matrices")
11046 "The GNU Scientific Library (or GSL) is a collection of numerical
11047 routines for scientific computing. It is particularly useful for C and C++
11048 programs as it provides a standard C interface to a wide range of mathematical
11049 routines. There are over 1000 functions in total with an extensive test
11050 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11051 structures and R using concepts from Rcpp which is itself a package that eases
11052 the interfaces between R and C++.")
11053 (license license:gpl2+)))
11055 (define-public r-mvabund
11062 (uri (cran-uri "mvabund" version))
11065 "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
11066 (build-system r-build-system)
11068 `(("r-mass" ,r-mass)
11070 ("r-rcppgsl" ,r-rcppgsl)
11071 ("r-statmod" ,r-statmod)
11072 ("r-tweedie" ,r-tweedie)))
11073 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11074 (synopsis "Statistical methods for analysing multivariate abundance data")
11076 "This package provides a set of tools for displaying, modeling and
11077 analysing multivariate abundance data in community ecology.")
11078 (license license:lgpl2.1+)))
11080 (define-public r-afex
11087 (uri (cran-uri "afex" version))
11090 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11091 (build-system r-build-system)
11095 ("r-lmertest" ,r-lmertest)
11096 ("r-pbkrtest" ,r-pbkrtest)
11097 ("r-reshape2" ,r-reshape2)))
11099 `(("r-knitr" ,r-knitr)))
11100 (home-page "https://afex.singmann.science/")
11101 (synopsis "Analysis of factorial experiments")
11103 "This package provides convenience functions for analyzing factorial
11104 experiments using ANOVA or mixed models.")
11105 (license license:gpl2+)))
11107 (define-public r-lmertest
11109 (name "r-lmertest")
11114 (uri (cran-uri "lmerTest" version))
11117 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11118 (properties `((upstream-name . "lmerTest")))
11119 (build-system r-build-system)
11121 `(("r-ggplot2" ,r-ggplot2)
11124 ("r-numderiv" ,r-numderiv)))
11125 (home-page "https://github.com/runehaubo/lmerTestR")
11126 (synopsis "Tests in linear mixed effects models")
11128 "This package provides p-values in type I, II or III anova and summary
11129 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11130 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11131 package. Model selection methods include step, drop1 and anova-like tables
11132 for random effects (ranova). Methods for Least-Square means (LS-means) and
11133 tests of linear contrasts of fixed effects are also available.")
11134 (license license:gpl2+)))
11136 (define-public r-r2glmm
11143 (uri (cran-uri "r2glmm" version))
11146 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11147 (build-system r-build-system)
11149 `(("r-afex" ,r-afex)
11150 ("r-data-table" ,r-data-table)
11151 ("r-dplyr" ,r-dplyr)
11152 ("r-ggplot2" ,r-ggplot2)
11153 ("r-gridextra" ,r-gridextra)
11154 ("r-lmertest" ,r-lmertest)
11156 ("r-matrix" ,r-matrix)
11158 ("r-pbkrtest" ,r-pbkrtest)))
11159 (home-page "https://github.com/bcjaeger/r2glmm")
11160 (synopsis "Compute R squared for mixed (multilevel) models")
11162 "This package computes model and semi partial R squared with confidence
11163 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11164 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11165 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11167 (license license:gpl2)))
11169 (define-public r-weights
11176 (uri (cran-uri "weights" version))
11179 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11180 (build-system r-build-system)
11182 `(("r-gdata" ,r-gdata)
11183 ("r-hmisc" ,r-hmisc)
11184 ("r-mice" ,r-mice)))
11186 "https://cran.r-project.org/web/packages/weights/")
11187 (synopsis "Weighting and weighted statistics")
11188 (description "This package Provides a variety of functions for producing
11189 simple weighted statistics, such as weighted Pearson's correlations, partial
11190 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11191 includes some software for quickly recoding survey data and plotting point
11192 estimates from interaction terms in regressions (and multiply imputed
11193 regressions). NOTE: Weighted partial correlation calculations pulled to
11195 (license license:gpl2+)))
11197 (define-public r-rcppannoy
11199 (name "r-rcppannoy")
11204 (uri (cran-uri "RcppAnnoy" version))
11207 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11208 (properties `((upstream-name . "RcppAnnoy")))
11209 (build-system r-build-system)
11211 `(("r-rcpp" ,r-rcpp)))
11212 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11213 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11215 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11216 for efficient memory usage as well an ability to load from and save to disk.
11217 This package provides an R interface.")
11218 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11220 (license (list license:gpl2+ license:asl2.0))))
11222 (define-public r-rcpphnsw
11224 (name "r-rcpphnsw")
11229 (uri (cran-uri "RcppHNSW" version))
11232 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11233 (properties `((upstream-name . "RcppHNSW")))
11234 (build-system r-build-system)
11235 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11236 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11237 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11239 "Hnswlib is a C++ library for approximate nearest neighbors. This
11240 package provides a minimal R interface by relying on the Rcpp package.")
11241 ;; hnswlib is released under Version 2.0 of the Apache License.
11242 (license (list license:gpl3 license:asl2.0))))
11244 (define-public r-rcppparallel
11246 (name "r-rcppparallel")
11251 (uri (cran-uri "RcppParallel" version))
11254 "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki"))))
11255 (properties `((upstream-name . "RcppParallel")))
11256 (build-system r-build-system)
11257 (home-page "https://rcppcore.github.io/RcppParallel/")
11258 (synopsis "Parallel programming tools for Rcpp")
11260 "This package provides high level functions for parallel programming with
11261 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11262 the work of a standard serial @code{for} loop into a parallel one and the
11263 @code{parallelReduce()} function can be used for accumulating aggregates or
11265 (license license:gpl2)))
11267 (define-public r-ncdf4
11274 (uri (cran-uri "ncdf4" version))
11277 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11278 (build-system r-build-system)
11280 `(("netcdf" ,netcdf)
11282 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11283 (synopsis "R interface to Unidata netCDF format data files")
11285 "This package provides a high-level R interface to data files written
11286 using Unidata's netCDF library (version 4 or earlier), which are binary data
11287 files that are portable across platforms and include metadata information in
11288 addition to the data sets. Using this package, netCDF files can be opened and
11289 data sets read in easily. It is also easy to create new netCDF dimensions,
11290 variables, and files, in either version 3 or 4 format, and manipulate existing
11292 (license license:gpl3+)))
11294 (define-public r-biocmanager
11296 (name "r-biocmanager")
11297 (version "1.30.12")
11301 (uri (cran-uri "BiocManager" version))
11303 (base32 "0c2anza01pc36manj3cvycbq8p57qpq18dsimk3y3gpks70hhqf3"))))
11304 (properties `((upstream-name . "BiocManager")))
11305 (build-system r-build-system)
11307 `(("r-knitr" ,r-knitr)))
11308 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11309 (synopsis "Access the Bioconductor project package repository")
11311 "This package provides a convenient tool to install and update
11312 Bioconductor packages.")
11313 (license license:artistic2.0)))
11315 (define-public r-rgl
11318 (version "0.105.22")
11322 (uri (cran-uri "rgl" version))
11325 "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz"))))
11326 (build-system r-build-system)
11328 `(("pkg-config" ,pkg-config)
11329 ("r-knitr" ,r-knitr)))
11331 `(("freetype" ,freetype)
11338 `(("r-crosstalk" ,r-crosstalk)
11339 ("r-htmltools" ,r-htmltools)
11340 ("r-htmlwidgets" ,r-htmlwidgets)
11341 ("r-jsonlite" ,r-jsonlite)
11342 ("r-knitr" ,r-knitr)
11343 ("r-magrittr" ,r-magrittr)
11344 ("r-manipulatewidget" ,r-manipulatewidget)
11345 ("r-shiny" ,r-shiny)))
11346 (home-page "https://r-forge.r-project.org/projects/rgl/")
11347 (synopsis "3D visualization using OpenGL")
11349 "This package provides medium to high level functions for 3D interactive graphics,
11350 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11351 as functions for constructing representations of geometric
11352 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11353 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11354 image formats, including PNG, Postscript, SVG, PGF.")
11355 ;; Any version of the GPL.
11356 (license (list license:gpl2+ license:gpl3+))))
11358 (define-public r-multicool
11360 (name "r-multicool")
11365 (uri (cran-uri "multicool" version))
11368 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11369 (build-system r-build-system)
11370 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11371 (home-page "https://cran.r-project.org/web/packages/multicool/")
11372 (synopsis "Permutations of multisets in cool-lex order")
11374 "This package provides a set of tools to permute multisets without loops
11375 or hash tables and to generate integer partitions. Cool-lex order is similar
11376 to colexicographical order.")
11377 (license license:gpl2)))
11379 (define-public r-misc3d
11386 (uri (cran-uri "misc3d" version))
11389 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11390 (build-system r-build-system)
11391 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11392 (synopsis "Miscellaneous 3D Plots")
11394 "This package provides a collection of miscellaneous 3d plots, including
11396 ;; Any version of the GPL.
11397 (license (list license:gpl2+ license:gpl3+))))
11399 (define-public r-ks
11406 (uri (cran-uri "ks" version))
11408 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11409 (build-system r-build-system)
11412 ("r-kernlab" ,r-kernlab)
11413 ("r-kernsmooth" ,r-kernsmooth)
11414 ("r-matrix" ,r-matrix)
11415 ("r-mclust" ,r-mclust)
11417 ("r-multicool" ,r-multicool)
11418 ("r-mvtnorm" ,r-mvtnorm)
11419 ("r-plot3d" ,r-plot3d)))
11420 (home-page "https://www.mvstat.net/tduong/")
11421 (synopsis "Kernel smoothing")
11423 "This package provides kernel smoothers for univariate and multivariate
11424 data, including density functions, density derivatives, cumulative
11425 distributions, modal clustering, discriminant analysis, and two-sample
11426 hypothesis testing.")
11427 ;; Either version of the GPL.
11428 (license (list license:gpl2 license:gpl3))))
11430 (define-public r-feature
11437 (uri (cran-uri "feature" version))
11440 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11441 (build-system r-build-system)
11444 ("r-plot3d" ,r-plot3d)))
11446 `(("r-knitr" ,r-knitr)))
11447 (home-page "https://www.mvstat.net/tduong/")
11448 (synopsis "Inferential feature significance for kernel density estimation")
11450 "The feature package contains functions to display and compute kernel
11451 density estimates, significant gradient and significant curvature regions.
11452 Significant gradient and/or curvature regions often correspond to significant
11453 features (e.g. local modes).")
11454 ;; Either version of the GPL.
11455 (license (list license:gpl2 license:gpl3))))
11457 (define-public r-arm
11464 (uri (cran-uri "arm" version))
11467 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11468 (build-system r-build-system)
11470 `(("r-abind" ,r-abind)
11472 ("r-hmisc" ,r-hmisc)
11475 ("r-matrix" ,r-matrix)
11476 ("r-nlme" ,r-nlme)))
11477 (home-page "https://cran.r-project.org/web/packages/arm/")
11478 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11480 "This package provides functions to accompany A. Gelman and J. Hill,
11481 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11482 University Press, 2007.")
11483 (license license:gpl3+)))
11485 (define-public r-circular
11487 (name "r-circular")
11492 (uri (cran-uri "circular" version))
11495 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11496 (build-system r-build-system)
11498 `(("r-boot" ,r-boot)
11499 ("r-mvtnorm" ,r-mvtnorm)))
11501 `(("gfortran" ,gfortran)))
11502 (home-page "https://cran.r-project.org/web/packages/circular/")
11503 (synopsis "Circular statistics")
11505 "This package provides tools for circular statistics, from \"Topics in
11506 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11508 (license license:gpl2+)))
11510 (define-public r-activity
11512 (name "r-activity")
11517 (uri (cran-uri "activity" version))
11520 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
11521 (build-system r-build-system)
11523 `(("r-circular" ,r-circular)
11524 ("r-insol" ,r-insol)
11525 ("r-pbapply" ,r-pbapply)))
11526 (home-page "https://cran.r-project.org/web/packages/activity/")
11527 (synopsis "Animal activity statistics")
11529 "This package provides functions to fit kernel density functions to
11530 animal activity time data; plot activity distributions; quantify overall
11531 levels of activity; statistically compare activity metrics through
11532 bootstrapping; and evaluate variation in linear variables with time (or other
11533 circular variables).")
11534 (license license:gpl3)))
11536 (define-public r-ouch
11543 (uri (cran-uri "ouch" version))
11546 "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q"))))
11547 (build-system r-build-system)
11548 (propagated-inputs `(("r-subplex" ,r-subplex)))
11549 (home-page "https://kingaa.github.io/ouch/")
11550 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11552 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11553 for evolution along a phylogenetic tree.")
11554 (license license:gpl2+)))
11556 (define-public r-fmsb
11563 (uri (cran-uri "fmsb" version))
11566 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11567 (build-system r-build-system)
11568 (home-page "http://minato.sip21c.org/msb/")
11569 (synopsis "Functions for medical statistics book with demographic data")
11571 "This package provides several utility functions for the book entitled
11572 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11573 Japan, 2007) with Japanese demographic data and some demographic analysis
11574 related functions.")
11575 (license license:gpl2+)))
11577 (define-public r-stabledist
11579 (name "r-stabledist")
11584 (uri (cran-uri "stabledist" version))
11587 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11588 (build-system r-build-system)
11589 (home-page "https://www.rmetrics.org")
11590 (synopsis "Stable distribution functions")
11592 "This package provides density, probability and quantile functions, and
11593 random number generation for (skew) stable distributions, using the
11594 parametrizations of Nolan.")
11595 (license license:gpl2+)))
11597 (define-public r-gsl
11604 (uri (cran-uri "gsl" version))
11607 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11608 (build-system r-build-system)
11611 (home-page "https://cran.r-project.org/web/packages/gsl")
11612 (synopsis "Wrapper for the GNU Scientific Library")
11614 "This package provides an R wrapper for the special functions and quasi
11615 random number generators of the GNU Scientific Library.")
11616 (license license:gpl2+)))
11618 (define-public r-adgoftest
11620 (name "r-adgoftest")
11625 (uri (cran-uri "ADGofTest" version))
11628 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11629 (properties `((upstream-name . "ADGofTest")))
11630 (build-system r-build-system)
11631 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11632 (synopsis "Anderson-Darling GoF test")
11634 "This package provides an implementation of the Anderson-Darling GoF test
11635 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11636 Anderson-Darling Distribution\".")
11637 ;; Any version of the GPL.
11638 (license license:gpl3+)))
11640 (define-public r-sodium
11647 (uri (cran-uri "sodium" version))
11650 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11651 (properties `((upstream-name . "sodium")))
11652 (build-system r-build-system)
11654 `(("libsodium" ,libsodium)))
11656 `(("pkg-config" ,pkg-config)
11657 ("r-knitr" ,r-knitr)))
11658 (home-page "https://github.com/jeroen/sodium")
11659 (synopsis "R bindings to the libsodium crypto library")
11661 "This package provides bindings to libsodium: a library for encryption,
11662 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11663 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11664 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11665 (license license:expat)))
11667 (define-public r-softimpute
11669 (name "r-softimpute")
11674 (uri (cran-uri "softImpute" version))
11677 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11678 (properties `((upstream-name . "softImpute")))
11679 (build-system r-build-system)
11681 `(("r-matrix" ,r-matrix)))
11683 `(("gfortran" ,gfortran)))
11684 (home-page "https://cran.r-project.org/web/packages/softImpute")
11685 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11687 "This package provides iterative methods for matrix completion that use
11688 nuclear-norm regularization. The package includes procedures for centering
11689 and scaling rows, columns or both, and for computing low-rank @dfn{single
11690 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11692 (license license:gpl2)))
11694 (define-public r-fftwtools
11696 (name "r-fftwtools")
11701 (uri (cran-uri "fftwtools" version))
11704 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
11705 (build-system r-build-system)
11706 (inputs `(("fftw" ,fftw)))
11708 `(("pkg-config" ,pkg-config)))
11709 (home-page "https://github.com/krahim/fftwtools")
11710 (synopsis "Wrapper for FFTW3")
11712 "This package provides a wrapper for several FFTW functions. It provides
11713 access to the two-dimensional FFT, the multivariate FFT, and the
11714 one-dimensional real to complex FFT using the FFTW3 library. The package
11715 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11716 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11717 The FFT functions have a parameter that allows them to not return the
11718 redundant complex conjugate when the input is real data.")
11719 (license license:gpl2+)))
11721 (define-public r-tiff
11728 (uri (cran-uri "tiff" version))
11731 "18m17g5q3nz4v4wrqxnb129b1j02873g2vknddczkklf1pvq4x2b"))))
11732 (build-system r-build-system)
11734 `(("libtiff" ,libtiff)
11735 ("libjpeg" ,libjpeg-turbo)
11738 `(("pkg-config" ,pkg-config)))
11739 (home-page "https://www.rforge.net/tiff/")
11740 (synopsis "Read and write TIFF images")
11742 "This package provides an easy and simple way to read, write and display
11743 bitmap images stored in the TIFF format. It can read and write both files and
11744 in-memory raw vectors.")
11745 ;; Either of these two license versions.
11746 (license (list license:gpl2 license:gpl3))))
11748 (define-public r-nlp
11755 (uri (cran-uri "NLP" version))
11758 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11759 (properties `((upstream-name . "NLP")))
11760 (build-system r-build-system)
11761 (home-page "https://cran.r-project.org/web/packages/NLP/")
11762 (synopsis "Natural language processing infrastructure")
11764 "This package provides basic classes and methods for Natural Language
11766 (license license:gpl3)))
11768 (define-public r-tm
11775 (uri (cran-uri "tm" version))
11778 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11779 (properties `((upstream-name . "tm")))
11780 (build-system r-build-system)
11786 ("r-xml2" ,r-xml2)))
11787 (home-page "http://tm.r-forge.r-project.org/")
11788 (synopsis "Text mining package")
11790 "This package provides a framework for text mining applications within R.")
11791 (license license:gpl3)))
11793 (define-public r-waveslim
11795 (name "r-waveslim")
11800 (uri (cran-uri "waveslim" version))
11803 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11804 (build-system r-build-system)
11806 `(("gfortran" ,gfortran)))
11807 (home-page "http://waveslim.blogspot.com")
11808 (synopsis "Basic wavelet routines for signal processing")
11810 "This package provides basic wavelet routines for time series (1D),
11811 image (2D) and array (3D) analysis. The code provided here is based on
11812 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11813 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11814 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11815 pairs (Selesnick 2001, 2002).")
11816 (license license:bsd-3)))
11818 (define-public r-wordcloud
11820 (name "r-wordcloud")
11825 (uri (cran-uri "wordcloud" version))
11828 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11829 (build-system r-build-system)
11831 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11833 ;; The "tm" package is only "suggested" according to CRAN, but the
11834 ;; wordcloud package cannot be loaded without it.
11836 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11837 (synopsis "Word clouds")
11839 "This package provides functionality to create pretty word clouds,
11840 visualize differences and similarity between documents, and avoid
11841 over-plotting in scatter plots with text.")
11842 (license license:lgpl2.1)))
11844 (define-public r-colorramps
11846 (name "r-colorramps")
11851 (uri (cran-uri "colorRamps" version))
11854 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11855 (properties `((upstream-name . "colorRamps")))
11856 (build-system r-build-system)
11857 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11858 (synopsis "Build color tables")
11859 (description "This package provides features to build gradient color
11861 ;; Any version of the GPL
11862 (license license:gpl3+)))
11864 (define-public r-tidytree
11866 (name "r-tidytree")
11871 (uri (cran-uri "tidytree" version))
11873 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11874 (build-system r-build-system)
11877 ("r-dplyr" ,r-dplyr)
11878 ("r-lazyeval" ,r-lazyeval)
11879 ("r-magrittr" ,r-magrittr)
11880 ("r-rlang" ,r-rlang)
11881 ("r-tibble" ,r-tibble)))
11883 `(("r-knitr" ,r-knitr)))
11884 (home-page "https://github.com/GuangchuangYu/tidytree")
11885 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11887 "Phylogenetic trees generally contain multiple components including nodes,
11888 edges, branches and associated data. This package provides an approach to
11889 convert tree objects to tidy data frames. It also provides tidy interfaces to
11890 manipulate tree data.")
11891 (license license:artistic2.0)))
11893 (define-public r-rvcheck
11900 (uri (cran-uri "rvcheck" version))
11902 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11903 (build-system r-build-system)
11905 `(("r-biocmanager" ,r-biocmanager)
11906 ("r-rlang" ,r-rlang)))
11907 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11908 (synopsis "R package version check")
11910 "This package provides tools to check the latest release version of R and
11911 R packages (on CRAN, Bioconductor or Github).")
11912 (license license:artistic2.0)))
11914 (define-public r-docopt
11921 (uri (cran-uri "docopt" version))
11924 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11925 (build-system r-build-system)
11926 (home-page "https://github.com/docopt/docopt.R")
11927 (synopsis "Command-line interface specification language")
11929 "This package enables you to define a command-line interface by just
11930 giving it a description in the specific format.")
11931 (license license:expat)))
11933 (define-public r-sparsesvd
11935 (name "r-sparsesvd")
11940 (uri (cran-uri "sparsesvd" version))
11943 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11944 (build-system r-build-system)
11945 (propagated-inputs `(("r-matrix" ,r-matrix)))
11946 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11947 (synopsis "Sparse truncated singular value decomposition")
11949 "This package provides a Wrapper around the SVDLIBC library
11950 for (truncated) singular value decomposition of a sparse matrix. Currently,
11951 only sparse real matrices in Matrix package format are supported.")
11952 ;; SVDLIBC is released under BSD-2. The R interface is released under
11954 (license (list license:bsd-3 license:bsd-2))))
11956 (define-public r-speedglm
11958 (name "r-speedglm")
11963 (uri (cran-uri "speedglm" version))
11966 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11967 (build-system r-build-system)
11969 `(("r-mass" ,r-mass)
11970 ("r-matrix" ,r-matrix)))
11971 (home-page "https://cran.r-project.org/web/packages/speedglm")
11972 (synopsis "Fit linear and generalized linear models to large data sets")
11974 "This package provides tools for fitting linear models and generalized
11975 linear models to large data sets by updating algorithms.")
11976 ;; Any version of the GPL
11977 (license license:gpl2+)))
11979 (define-public r-densityclust
11981 (name "r-densityclust")
11986 (uri (cran-uri "densityClust" version))
11989 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11990 (properties `((upstream-name . "densityClust")))
11991 (build-system r-build-system)
11994 ("r-ggplot2" ,r-ggplot2)
11995 ("r-ggrepel" ,r-ggrepel)
11996 ("r-gridextra" ,r-gridextra)
11997 ("r-rcolorbrewer" ,r-rcolorbrewer)
11999 ("r-rtsne" ,r-rtsne)))
12000 (home-page "https://cran.r-project.org/web/packages/densityClust")
12001 (synopsis "Clustering by fast search and find of density peaks")
12003 "This package provides an improved implementation (based on k-nearest
12004 neighbors) of the density peak clustering algorithm, originally described by
12005 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
12006 large datasets (> 100,000 samples) very efficiently.")
12007 (license license:gpl2+)))
12009 (define-public r-combinat
12011 (name "r-combinat")
12016 (uri (cran-uri "combinat" version))
12019 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12020 (build-system r-build-system)
12021 (home-page "https://cran.r-project.org/web/packages/combinat")
12022 (synopsis "Combinatorics utilities")
12023 (description "This package provides assorted routines for combinatorics.")
12024 (license license:gpl2)))
12026 (define-public r-qlcmatrix
12028 (name "r-qlcmatrix")
12033 (uri (cran-uri "qlcMatrix" version))
12036 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12037 (properties `((upstream-name . "qlcMatrix")))
12038 (build-system r-build-system)
12040 `(("r-docopt" ,r-docopt)
12041 ("r-matrix" ,r-matrix)
12043 ("r-sparsesvd" ,r-sparsesvd)))
12044 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12045 (synopsis "Sparse matrix functions for quantitative language comparison")
12047 "This package provides an extension of the functionality of the Matrix
12048 package for using sparse matrices. Some of the functions are very general,
12049 while other are highly specific for the special data format used for
12050 @dfn{quantitative language comparison} (QLC).")
12051 (license license:gpl3)))
12053 (define-public r-ddrtree
12060 (uri (cran-uri "DDRTree" version))
12063 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12064 (properties `((upstream-name . "DDRTree")))
12065 (build-system r-build-system)
12068 ("r-irlba" ,r-irlba)
12070 ("r-rcppeigen" ,r-rcppeigen)))
12071 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12072 (synopsis "Learning principal graphs with DDRTree")
12074 "This package provides an implementation of the framework of
12075 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12076 dimensional space while constructs a principal tree which passes through the
12077 middle of the data simultaneously. DDRTree shows superiority to
12078 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12079 intrinsic structure of single cell genomics data. In general, it could be
12080 used to reconstruct the temporal progression as well as the bifurcation
12081 structure of any data type.")
12082 (license license:asl2.0)))
12084 (define-public r-corpcor
12091 (uri (cran-uri "corpcor" version))
12094 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12095 (build-system r-build-system)
12096 (home-page "http://strimmerlab.org/software/corpcor/")
12097 (synopsis "Efficient estimation of covariance and (partial) correlation")
12099 "This package implements a James-Stein-type shrinkage estimator for the
12100 covariance matrix, with separate shrinkage for variances and correlations.
12101 Furthermore, functions are available for fast singular value decomposition,
12102 for computing the pseudoinverse, and for checking the rank and positive
12103 definiteness of a matrix.")
12104 (license license:gpl3+)))
12106 (define-public r-rspectra
12108 (name "r-rspectra")
12113 (uri (cran-uri "RSpectra" version))
12116 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12117 (properties `((upstream-name . "RSpectra")))
12118 (build-system r-build-system)
12120 `(("r-matrix" ,r-matrix)
12122 ("r-rcppeigen" ,r-rcppeigen)))
12123 (home-page "https://github.com/yixuan/RSpectra")
12124 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12126 "This package provides an R interface to the Spectra library for
12127 large-scale eigenvalue and SVD problems. It is typically used to compute a
12128 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12129 which is usually more efficient than @code{eigen()} if k << n.")
12131 (license license:mpl2.0)))
12133 (define-public r-vbsr
12140 (uri (cran-uri "vbsr" version))
12143 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12144 (build-system r-build-system)
12145 (home-page "https://cran.r-project.org/web/packages/vbsr")
12146 (synopsis "Variational Bayes spike regression regularized linear models")
12148 "This package provides an efficient algorithm for solving ultra-sparse
12149 regularized regression models using a variational Bayes algorithm with a spike
12150 prior. The algorithm is solved on a path, with coordinate updates, and is
12151 capable of generating very sparse models. Very general model
12152 diagnostics for controlling type-1 errors are also provided.")
12153 (license license:gpl2)))
12155 (define-public r-flare
12162 (uri (cran-uri "flare" version))
12165 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12166 (build-system r-build-system)
12168 `(("r-igraph" ,r-igraph)
12169 ("r-lattice" ,r-lattice)
12171 ("r-matrix" ,r-matrix)))
12172 (home-page "https://cran.r-project.org/web/packages/flare")
12173 (synopsis "Family of Lasso regression implementations")
12175 "This package provides implementations of a family of Lasso variants
12176 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12177 high dimensional sparse linear models.")
12178 (license license:gpl2)))
12180 (define-public r-lassopv
12187 (uri (cran-uri "lassopv" version))
12190 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12191 (build-system r-build-system)
12192 (propagated-inputs `(("r-lars" ,r-lars)))
12193 (home-page "https://github.com/lingfeiwang/lassopv")
12194 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12196 "This package enables you to estimate the p-values for predictors x
12197 against target variable y in Lasso regression, using the regularization
12198 strength when each predictor enters the active set of regularization path for
12199 the first time as the statistic.")
12200 (license license:gpl3)))
12202 (define-public r-splitstackshape
12204 (name "r-splitstackshape")
12209 (uri (cran-uri "splitstackshape" version))
12212 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12213 (build-system r-build-system)
12215 `(("r-data-table" ,r-data-table)))
12216 (home-page "https://github.com/mrdwab/splitstackshape")
12217 (synopsis "Stack and reshape datasets after splitting concatenated values")
12219 "Online data collection tools like Google Forms often export
12220 multiple-response questions with data concatenated in cells. The
12221 @code{concat.split} (cSplit) family of functions provided by this package
12222 splits such data into separate cells. This package also includes functions to
12223 stack groups of columns and to reshape wide data, even when the data are
12224 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12225 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12227 (license license:gpl3)))
12229 (define-public r-tfmpvalue
12231 (name "r-tfmpvalue")
12236 (uri (cran-uri "TFMPvalue" version))
12239 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12240 (properties `((upstream-name . "TFMPvalue")))
12241 (build-system r-build-system)
12242 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12243 (home-page "https://github.com/ge11232002/TFMPvalue")
12244 (synopsis "P-value computation for position weight matrices")
12246 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12247 identification from sequence/alignments, we are interested in the significance
12248 of certain match scores. TFMPvalue provides the accurate calculation of a
12249 p-value with a score threshold for position weight matrices, or the score with
12250 a given p-value. It is an interface to code originally made available by
12251 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12252 Touzet and Varre (2007).")
12253 (license license:gpl2)))
12255 (define-public r-rnifti
12262 (uri (cran-uri "RNifti" version))
12265 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12266 (properties `((upstream-name . "RNifti")))
12267 (build-system r-build-system)
12268 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12269 (home-page "https://github.com/jonclayden/RNifti")
12270 (synopsis "Fast R and C++ access to NIfTI images")
12272 "This package provides very fast read and write access to images stored
12273 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12274 compiled C and interpreted R code. It also provides a C/C++ API that can be
12275 used by other packages.")
12276 (license license:gpl2)))
12278 (define-public r-shades
12285 (uri (cran-uri "shades" version))
12288 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12289 (build-system r-build-system)
12290 (home-page "https://github.com/jonclayden/shades")
12291 (synopsis "Simple color manipulation")
12293 "This package provides functions for easily manipulating colors,
12294 creating color scales and calculating color distances.")
12295 (license license:bsd-3)))
12297 (define-public r-ore
12304 (uri (cran-uri "ore" version))
12306 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12307 (build-system r-build-system)
12308 (home-page "https://github.com/jonclayden/ore")
12309 (synopsis "R interface to the Onigmo regular expression library")
12311 "This package provides an alternative to R's built-in functionality for
12312 handling regular expressions, based on the Onigmo library. It offers
12313 first-class compiled regex objects, partial matching and function-based
12314 substitutions, amongst other features.")
12315 (license license:bsd-3)))
12317 (define-public r-reportr
12324 (uri (cran-uri "reportr" version))
12327 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12328 (build-system r-build-system)
12329 (propagated-inputs `(("r-ore" ,r-ore)))
12330 (home-page "https://github.com/jonclayden/reportr")
12331 (synopsis "General message and error reporting system")
12333 "This package provides a system for reporting messages, which offers
12334 certain useful features over the standard R system, such as the incorporation
12335 of output consolidation, message filtering, assertions, expression
12336 substitution, automatic generation of stack traces for debugging, and
12337 conditional reporting based on the current \"output level\".")
12338 (license license:gpl2)))
12340 (define-public r-tractor-base
12342 (name "r-tractor-base")
12343 (version "3.3.3.1")
12347 (uri (cran-uri "tractor.base" version))
12350 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12351 (properties `((upstream-name . "tractor.base")))
12352 (build-system r-build-system)
12355 ("r-reportr" ,r-reportr)
12356 ("r-rnifti" ,r-rnifti)
12357 ("r-shades" ,r-shades)))
12358 (home-page "https://www.tractor-mri.org.uk")
12359 (synopsis "Read, manipulate and visualize magnetic resonance images")
12361 "This package provides functions for working with magnetic resonance
12362 images. It supports reading and writing of popular file formats (DICOM,
12363 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12364 visualization; flexible image manipulation; metadata and sparse image
12366 (license license:gpl2)))
12368 (define-public r-grimport
12370 (name "r-grimport")
12375 (uri (cran-uri "grImport" version))
12378 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12379 (properties `((upstream-name . "grImport")))
12380 (build-system r-build-system)
12382 `(("ghostscript" ,ghostscript)))
12384 `(("r-xml" ,r-xml)))
12385 (home-page "https://cran.r-project.org/web/packages/grImport")
12386 (synopsis "Convert, import, and draw PostScript pictures")
12388 "This package provides functions for converting, importing, and drawing
12389 PostScript pictures in R plots.")
12390 (license license:gpl2+)))
12392 (define-public r-grimport2
12394 (name "r-grimport2")
12399 (uri (cran-uri "grImport2" version))
12402 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12403 (properties `((upstream-name . "grImport2")))
12404 (build-system r-build-system)
12406 `(("r-base64enc" ,r-base64enc)
12410 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12411 (synopsis "Import SVG graphics")
12413 "This package provides functions for importing external vector images and
12414 drawing them as part of R plots. This package is different from the
12415 @code{grImport} package because, where that package imports PostScript format
12416 images, this package imports SVG format images. Furthermore, this package
12417 imports a specific subset of SVG, so external images must be preprocessed
12418 using a package like @code{rsvg} to produce SVG that this package can import.
12419 SVG features that are not supported by R graphics, such as gradient fills, can
12420 be imported and then exported via the @code{gridSVG} package.")
12421 (license license:gpl2+)))
12423 (define-public r-kohonen
12430 (uri (cran-uri "kohonen" version))
12433 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12434 (build-system r-build-system)
12436 `(("r-rcpp" ,r-rcpp)))
12437 (home-page "https://cran.r-project.org/web/packages/kohonen")
12438 (synopsis "Supervised and unsupervised self-organising maps")
12440 "This package provides functions to train @dfn{self-organising
12441 maps} (SOMs). Also interrogation of the maps and prediction using trained
12442 maps are supported. The name of the package refers to Teuvo Kohonen, the
12443 inventor of the SOM.")
12444 (license license:gpl2+)))
12446 (define-public r-nnls
12453 (uri (cran-uri "nnls" version))
12456 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12457 (build-system r-build-system)
12458 (native-inputs `(("gfortran" ,gfortran)))
12459 (home-page "https://cran.r-project.org/web/packages/nnls")
12460 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12462 "This package provides an R interface to the Lawson-Hanson implementation
12463 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12464 the combination of non-negative and non-positive constraints.")
12465 (license license:gpl2+)))
12467 (define-public r-iso
12470 (version "0.0-18.1")
12474 (uri (cran-uri "Iso" version))
12477 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12478 (properties `((upstream-name . "Iso")))
12479 (build-system r-build-system)
12480 (native-inputs `(("gfortran" ,gfortran)))
12481 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12482 (synopsis "Functions to perform isotonic regression")
12484 "This package provides support for linear order and unimodal
12485 order (univariate) isotonic regression and bivariate isotonic regression with
12486 linear order on both variables.")
12487 (license license:gpl2+)))
12489 (define-public r-chemometricswithr
12491 (name "r-chemometricswithr")
12496 (uri (cran-uri "ChemometricsWithR" version))
12499 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12501 `((upstream-name . "ChemometricsWithR")))
12502 (build-system r-build-system)
12504 `(("r-devtools" ,r-devtools)
12505 ("r-kohonen" ,r-kohonen)
12508 (home-page "https://github.com/rwehrens/CWR")
12509 (synopsis "Chemometrics with R")
12511 "This package provides functions and scripts used in the book
12512 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12513 Life Sciences\" by Ron Wehrens, Springer (2011).")
12514 (license license:gpl2+)))
12516 (define-public r-als
12523 (uri (cran-uri "ALS" version))
12526 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12527 (properties `((upstream-name . "ALS")))
12528 (build-system r-build-system)
12531 ("r-nnls" ,r-nnls)))
12532 (home-page "https://cran.r-project.org/web/packages/ALS")
12533 (synopsis "Multivariate curve resolution alternating least squares")
12535 "Alternating least squares is often used to resolve components
12536 contributing to data with a bilinear structure; the basic technique may be
12537 extended to alternating constrained least squares. This package provides an
12538 implementation of @dfn{multivariate curve resolution alternating least
12539 squares} (MCR-ALS).
12541 Commonly applied constraints include unimodality, non-negativity, and
12542 normalization of components. Several data matrices may be decomposed
12543 simultaneously by assuming that one of the two matrices in the bilinear
12544 decomposition is shared between datasets.")
12545 (license license:gpl2+)))
12547 (define-public r-strucchange
12549 (name "r-strucchange")
12554 (uri (cran-uri "strucchange" version))
12557 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12558 (build-system r-build-system)
12560 `(("r-sandwich" ,r-sandwich)
12562 (home-page "https://cran.r-project.org/web/packages/strucchange")
12563 (synopsis "Testing, monitoring, and dating structural changes")
12565 "This package provides tools for testing, monitoring and dating
12566 structural changes in (linear) regression models. It features tests/methods
12567 from the generalized fluctuation test framework as well as from the F
12568 test (Chow test) framework. This includes methods to fit, plot and test
12569 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12570 statistics, respectively. It is possible to monitor incoming data online
12571 using fluctuation processes. Finally, the breakpoints in regression models
12572 with structural changes can be estimated together with confidence intervals.
12573 Emphasis is always given to methods for visualizing the data.")
12574 ;; Either of these two GPL versions
12575 (license (list license:gpl2 license:gpl3))))
12577 (define-public r-pixmap
12584 (uri (cran-uri "pixmap" version))
12587 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12588 (build-system r-build-system)
12589 (home-page "https://cran.r-project.org/web/packages/pixmap")
12590 (synopsis "Tools for bitmap images")
12592 "This package provides functions for importing, exporting, plotting and
12593 other manipulations of bitmapped images.")
12594 (license license:gpl2)))
12596 (define-public r-rapidjsonr
12598 (name "r-rapidjsonr")
12603 (uri (cran-uri "rapidjsonr" version))
12606 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12607 (build-system r-build-system)
12608 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12609 (synopsis "JSON parser")
12611 "This package provides JSON parsing capability through the Rapidjson
12613 (license license:expat)))
12615 (define-public r-ontologyindex
12617 (name "r-ontologyindex")
12622 (uri (cran-uri "ontologyIndex" version))
12625 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12626 (properties `((upstream-name . "ontologyIndex")))
12627 (build-system r-build-system)
12629 `(("r-knitr" ,r-knitr)))
12630 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12631 (synopsis "Functions for processing ontologies in R")
12633 "This package provides functions for reading ontologies into R as lists
12634 and manipulating sets of ontological terms.")
12635 (license license:gpl2+)))
12637 (define-public r-gargle
12644 (uri (cran-uri "gargle" version))
12647 "03y29dzz54bw9px5k8a72vmc000lcyrkc5l0izkqcciyi9ijkr3w"))))
12648 (build-system r-build-system)
12654 ("r-jsonlite" ,r-jsonlite)
12655 ("r-rappdirs" ,r-rappdirs)
12656 ("r-rlang" ,r-rlang)
12657 ("r-rstudioapi" ,r-rstudioapi)
12658 ("r-withr" ,r-withr)))
12660 `(("r-knitr" ,r-knitr)))
12661 (home-page "https://gargle.r-lib.org")
12662 (synopsis "Utilities for working with Google APIs")
12664 "This package provides utilities for working with Google APIs. This
12665 includes functions and classes for handling common credential types and for
12666 preparing, executing, and processing HTTP requests.")
12667 (license license:expat)))
12669 (define-public r-bigrquery
12671 (name "r-bigrquery")
12676 (uri (cran-uri "bigrquery" version))
12679 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12680 (build-system r-build-system)
12682 `(("r-assertthat" ,r-assertthat)
12683 ("r-bit64" ,r-bit64)
12686 ("r-gargle" ,r-gargle)
12689 ("r-jsonlite" ,r-jsonlite)
12690 ("r-prettyunits" ,r-prettyunits)
12691 ("r-progress" ,r-progress)
12692 ("r-rapidjsonr" ,r-rapidjsonr)
12694 ("r-rlang" ,r-rlang)
12695 ("r-tibble" ,r-tibble)))
12696 (home-page "https://github.com/rstats-db/bigrquery")
12697 (synopsis "R interface to Google's BigQuery API")
12699 "This package provides an R interface to Google's BigQuery database.")
12700 (license license:gpl3)))
12702 (define-public r-gmp
12709 (uri (cran-uri "gmp" version))
12712 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12713 (build-system r-build-system)
12716 (modify-phases %standard-phases
12717 (add-after 'unpack 'set-CC
12718 (lambda _ (setenv "CC" "gcc") #t)))))
12719 (inputs `(("gmp" ,gmp)))
12720 (home-page "https://cran.r-project.org/web/packages/gmp")
12721 (synopsis "Multiple precision arithmetic")
12723 "This package supports multiple precision arithmetic (big integers and
12724 rationals, prime number tests, matrix computation), \"arithmetic without
12725 limitations\" using the GNU Multiple Precision library.")
12726 ;; Any version of the GPL.
12727 (license license:gpl3+)))
12729 (define-public r-rmpfr
12736 (uri (cran-uri "Rmpfr" version))
12739 "1m9wwwch9wg886147brr2zfih65yfdfs3vmfvim1w6jykycasc9a"))))
12740 (properties `((upstream-name . "Rmpfr")))
12741 (build-system r-build-system)
12746 `(("r-gmp" ,r-gmp)))
12748 `(("pkg-config" ,pkg-config)))
12749 (home-page "http://rmpfr.r-forge.r-project.org/")
12750 (synopsis "R bindings to the MPFR library")
12752 "This package supports arithmetic (via S4 classes and methods) for
12753 arbitrary precision floating point numbers, including transcendental
12754 functions. To this end, the package interfaces with the @dfn{Multiple
12755 Precision Floating-Point Reliable} (MPFR) library.")
12756 (license license:gpl2+)))
12758 (define-public r-assertive-base
12760 (name "r-assertive-base")
12765 (uri (cran-uri "assertive.base" version))
12768 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12770 `((upstream-name . "assertive.base")))
12771 (build-system r-build-system)
12772 (home-page "https://bitbucket.org/richierocks/assertive.base")
12773 (synopsis "Core of the assertive package")
12775 "This package provides a minimal set of predicates and assertions used by
12776 the assertive package. This is mainly for use by other package developers who
12777 want to include run-time testing features in their own packages.")
12778 (license license:gpl3+)))
12780 (define-public r-assertive-properties
12782 (name "r-assertive-properties")
12787 (uri (cran-uri "assertive.properties" version))
12790 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12792 `((upstream-name . "assertive.properties")))
12793 (build-system r-build-system)
12795 `(("r-assertive-base" ,r-assertive-base)))
12796 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12797 (synopsis "Assertions to check properties of variables")
12799 "This package provides a set of predicates and assertions for checking
12800 the properties of variables, such as length, names and attributes. This is
12801 mainly for use by other package developers who want to include run-time
12802 testing features in their own packages.")
12803 (license license:gpl3+)))
12805 (define-public r-assertive-numbers
12807 (name "r-assertive-numbers")
12812 (uri (cran-uri "assertive.numbers" version))
12815 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12817 `((upstream-name . "assertive.numbers")))
12818 (build-system r-build-system)
12820 `(("r-assertive-base" ,r-assertive-base)))
12821 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12822 (synopsis "Assertions to check properties of numbers")
12824 "This package provides a set of predicates and assertions for checking
12825 the properties of numbers. This is mainly for use by other package developers
12826 who want to include run-time testing features in their own packages.")
12827 (license license:gpl3+)))
12829 (define-public r-assertive-sets
12831 (name "r-assertive-sets")
12836 (uri (cran-uri "assertive.sets" version))
12839 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12841 `((upstream-name . "assertive.sets")))
12842 (build-system r-build-system)
12844 `(("r-assertive-base" ,r-assertive-base)))
12845 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12846 (synopsis "Assertions to check properties of sets")
12848 "This package provides a set of predicates and assertions for checking
12849 the properties of sets. This is mainly for use by other package developers
12850 who want to include run-time testing features in their own packages.")
12851 (license license:gpl3+)))
12853 (define-public r-assertive-matrices
12855 (name "r-assertive-matrices")
12860 (uri (cran-uri "assertive.matrices" version))
12863 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12865 `((upstream-name . "assertive.matrices")))
12866 (build-system r-build-system)
12868 `(("r-assertive-base" ,r-assertive-base)))
12869 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12870 (synopsis "Assertions to check properties of matrices")
12872 "This package provides a set of predicates and assertions for checking
12873 the properties of matrices. This is mainly for use by other package
12874 developers who want to include run-time testing features in their own
12876 (license license:gpl3+)))
12878 (define-public r-assertive-models
12880 (name "r-assertive-models")
12885 (uri (cran-uri "assertive.models" version))
12888 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12890 `((upstream-name . "assertive.models")))
12891 (build-system r-build-system)
12893 `(("r-assertive-base" ,r-assertive-base)))
12894 (home-page "https://bitbucket.org/richierocks/assertive.models")
12895 (synopsis "Assertions to check properties of models")
12897 "This package provides a set of predicates and assertions for checking
12898 the properties of models. This is mainly for use by other package developers
12899 who want to include run-time testing features in their own packages.")
12900 (license license:gpl3+)))
12902 (define-public r-assertive-reflection
12904 (name "r-assertive-reflection")
12909 (uri (cran-uri "assertive.reflection" version))
12912 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12914 `((upstream-name . "assertive.reflection")))
12915 (build-system r-build-system)
12917 `(("r-assertive-base" ,r-assertive-base)))
12918 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12919 (synopsis "Assertions for checking the state of R")
12921 "This package provides a set of predicates and assertions for checking
12922 the state and capabilities of R, the operating system it is running on, and
12923 the IDE being used. This is mainly for use by other package developers who
12924 want to include run-time testing features in their own packages.")
12925 (license license:gpl3+)))
12927 (define-public r-assertive-types
12929 (name "r-assertive-types")
12934 (uri (cran-uri "assertive.types" version))
12937 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12939 `((upstream-name . "assertive.types")))
12940 (build-system r-build-system)
12942 `(("r-assertive-base" ,r-assertive-base)
12943 ("r-assertive-properties" ,r-assertive-properties)
12944 ("r-codetools" ,r-codetools)))
12945 (home-page "https://bitbucket.org/richierocks/assertive.types")
12946 (synopsis "Assertions to check types of variables")
12948 "This package provides a set of predicates and assertions for checking
12949 the types of variables. This is mainly for use by other package developers
12950 who want to include run-time testing features in their own packages.")
12951 (license license:gpl3+)))
12953 (define-public r-assertive-files
12955 (name "r-assertive-files")
12960 (uri (cran-uri "assertive.files" version))
12963 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12965 `((upstream-name . "assertive.files")))
12966 (build-system r-build-system)
12968 `(("r-assertive-base" ,r-assertive-base)
12969 ("r-assertive-numbers" ,r-assertive-numbers)))
12970 (home-page "https://bitbucket.org/richierocks/assertive.files")
12971 (synopsis "Assertions to check properties of files")
12973 "This package provides a set of predicates and assertions for checking
12974 the properties of files and connections. This is mainly for use by other
12975 package developers who want to include run-time testing features in their own
12977 (license license:gpl3+)))
12979 (define-public r-assertive-code
12981 (name "r-assertive-code")
12986 (uri (cran-uri "assertive.code" version))
12989 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12991 `((upstream-name . "assertive.code")))
12992 (build-system r-build-system)
12994 `(("r-assertive-base" ,r-assertive-base)
12995 ("r-assertive-properties" ,r-assertive-properties)
12996 ("r-assertive-types" ,r-assertive-types)))
12997 (home-page "https://bitbucket.org/richierocks/assertive.code")
12998 (synopsis "Assertions to check properties of code")
13000 "This package provides a set of predicates and assertions for checking
13001 the properties of code. This is mainly for use by other package developers
13002 who want to include run-time testing features in their own packages.")
13003 (license license:gpl3+)))
13005 (define-public r-assertive-datetimes
13007 (name "r-assertive-datetimes")
13012 (uri (cran-uri "assertive.datetimes" version))
13015 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
13017 `((upstream-name . "assertive.datetimes")))
13018 (build-system r-build-system)
13020 `(("r-assertive-base" ,r-assertive-base)
13021 ("r-assertive-types" ,r-assertive-types)))
13022 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13023 (synopsis "Assertions to check properties of dates and times")
13025 "This package provides a set of predicates and assertions for checking
13026 the properties of dates and times. This is mainly for use by other package
13027 developers who want to include run-time testing features in their own
13029 (license license:gpl3+)))
13031 (define-public r-assertive-strings
13033 (name "r-assertive-strings")
13038 (uri (cran-uri "assertive.strings" version))
13041 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13043 `((upstream-name . "assertive.strings")))
13044 (build-system r-build-system)
13046 `(("r-assertive-base" ,r-assertive-base)
13047 ("r-assertive-types" ,r-assertive-types)
13048 ("r-stringi" ,r-stringi)))
13049 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13050 (synopsis "Assertions to check properties of strings")
13052 "This package provides a set of predicates and assertions for checking
13053 the properties of strings. This is mainly for use by other package developers
13054 who want to include run-time testing features in their own packages.")
13055 (license license:gpl3+)))
13057 (define-public r-assertive-data-us
13059 (name "r-assertive-data-us")
13064 (uri (cran-uri "assertive.data.us" version))
13067 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13069 `((upstream-name . "assertive.data.us")))
13070 (build-system r-build-system)
13072 `(("r-assertive-base" ,r-assertive-base)
13073 ("r-assertive-strings" ,r-assertive-strings)))
13074 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13075 (synopsis "Assertions to check properties of strings")
13077 "This package provides a set of predicates and assertions for checking
13078 the properties of US-specific complex data types. This is mainly for use by
13079 other package developers who want to include run-time testing features in
13080 their own packages.")
13081 (license license:gpl3+)))
13083 (define-public r-assertive-data-uk
13085 (name "r-assertive-data-uk")
13090 (uri (cran-uri "assertive.data.uk" version))
13093 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13095 `((upstream-name . "assertive.data.uk")))
13096 (build-system r-build-system)
13098 `(("r-assertive-base" ,r-assertive-base)
13099 ("r-assertive-strings" ,r-assertive-strings)))
13100 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13101 (synopsis "Assertions to check properties of strings")
13103 "This package provides a set of predicates and assertions for checking
13104 the properties of UK-specific complex data types. This is mainly for use by
13105 other package developers who want to include run-time testing features in
13106 their own packages.")
13107 (license license:gpl3+)))
13109 (define-public r-assertive-data
13111 (name "r-assertive-data")
13116 (uri (cran-uri "assertive.data" version))
13119 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13121 `((upstream-name . "assertive.data")))
13122 (build-system r-build-system)
13124 `(("r-assertive-base" ,r-assertive-base)
13125 ("r-assertive-strings" ,r-assertive-strings)))
13126 (home-page "https://bitbucket.org/richierocks/assertive.data")
13127 (synopsis "Assertions to check properties of data")
13129 "This package provides a set of predicates and assertions for checking
13130 the properties of (country independent) complex data types. This is mainly
13131 for use by other package developers who want to include run-time testing
13132 features in their own packages.")
13133 (license license:gpl3+)))
13135 (define-public r-assertive
13137 (name "r-assertive")
13142 (uri (cran-uri "assertive" version))
13145 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13146 (build-system r-build-system)
13148 `(("r-assertive-base" ,r-assertive-base)
13149 ("r-assertive-code" ,r-assertive-code)
13150 ("r-assertive-data" ,r-assertive-data)
13151 ("r-assertive-data-uk" ,r-assertive-data-uk)
13152 ("r-assertive-data-us" ,r-assertive-data-us)
13153 ("r-assertive-datetimes" ,r-assertive-datetimes)
13154 ("r-assertive-files" ,r-assertive-files)
13155 ("r-assertive-matrices" ,r-assertive-matrices)
13156 ("r-assertive-models" ,r-assertive-models)
13157 ("r-assertive-numbers" ,r-assertive-numbers)
13158 ("r-assertive-properties" ,r-assertive-properties)
13159 ("r-assertive-reflection" ,r-assertive-reflection)
13160 ("r-assertive-sets" ,r-assertive-sets)
13161 ("r-assertive-strings" ,r-assertive-strings)
13162 ("r-assertive-types" ,r-assertive-types)
13163 ("r-knitr" ,r-knitr)))
13165 `(("r-knitr" ,r-knitr)))
13166 (home-page "https://bitbucket.org/richierocks/assertive")
13167 (synopsis "Readable check functions to ensure code integrity")
13169 "This package provides lots of predicates (@code{is_*} functions) to
13170 check the state of your variables, and assertions (@code{assert_*} functions)
13171 to throw errors if they aren't in the right form.")
13172 (license license:gpl3+)))
13174 (define-public r-dotcall64
13176 (name "r-dotcall64")
13181 (uri (cran-uri "dotCall64" version))
13184 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
13185 (properties `((upstream-name . "dotCall64")))
13186 (build-system r-build-system)
13187 (native-inputs `(("gfortran" ,gfortran)))
13188 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13189 (synopsis "Enhanced foreign function interface supporting long vectors")
13191 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13192 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13193 supports long vectors, arguments of type 64-bit integer, and provides a
13194 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13195 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13196 (license license:gpl2+)))
13198 (define-public r-spam
13205 (uri (cran-uri "spam" version))
13207 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13208 (build-system r-build-system)
13210 `(("r-dotcall64" ,r-dotcall64)))
13212 `(("gfortran" ,gfortran)
13213 ("r-knitr" ,r-knitr)))
13214 (home-page "https://www.math.uzh.ch/pages/spam/")
13215 (synopsis "Sparse matrix algebra")
13217 "This package provides a set of functions for sparse matrix algebra.
13218 Differences with other sparse matrix packages are:
13221 @item it only supports (essentially) one sparse matrix format;
13222 @item it is based on transparent and simple structure(s);
13223 @item it is tailored for MCMC calculations within G(M)RF;
13224 @item and it is fast and scalable (with the extension package @code{spam64}).
13226 ;; Either of these licenses
13227 (license (list license:bsd-3 license:lgpl2.0))))
13229 (define-public r-fields
13236 (uri (cran-uri "fields" version))
13238 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13239 (build-system r-build-system)
13241 `(("r-maps" ,r-maps)
13242 ("r-spam" ,r-spam)))
13244 `(("gfortran" ,gfortran)))
13245 (home-page "https://www.image.ucar.edu/fields")
13246 (synopsis "Tools for spatial data")
13248 "This is a package for curve, surface and function fitting with an
13249 emphasis on splines, spatial data and spatial statistics. The major methods
13250 include cubic, and thin plate splines, Kriging, and compactly supported
13251 covariance functions for large data sets.")
13252 (license license:gpl2+)))
13254 (define-public r-spatialextremes
13256 (name "r-spatialextremes")
13261 (uri (cran-uri "SpatialExtremes" version))
13264 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13266 `((upstream-name . "SpatialExtremes")))
13267 (build-system r-build-system)
13269 `(("r-fields" ,r-fields)
13270 ("r-maps" ,r-maps)))
13271 (home-page "http://spatialextremes.r-forge.r-project.org/")
13272 (synopsis "Modelling spatial extremes")
13274 "This package provides tools for the statistical modelling of spatial
13275 extremes using max-stable processes, copula or Bayesian hierarchical models.
13276 More precisely, this package allows (conditional) simulations from various
13277 parametric max-stable models, analysis of the extremal spatial dependence, the
13278 fitting of such processes using composite likelihoods or least square (simple
13279 max-stable processes only), model checking and selection and prediction.")
13280 (license license:gpl2+)))
13282 (define-public r-drc
13289 (uri (cran-uri "drc" version))
13292 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13293 (build-system r-build-system)
13296 ("r-gtools" ,r-gtools)
13298 ("r-multcomp" ,r-multcomp)
13299 ("r-plotrix" ,r-plotrix)
13300 ("r-scales" ,r-scales)))
13301 (home-page "https://cran.r-project.org/web/packages/drc")
13302 (synopsis "Analysis of dose-response curves")
13304 "This package provides a suite of flexible and versatile model fitting
13305 and after-fitting functions for the analysis of dose-response data.")
13306 (license license:gpl2+)))
13308 (define-public r-rmeta
13315 (uri (cran-uri "rmeta" version))
13318 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13319 (build-system r-build-system)
13320 (home-page "https://cran.r-project.org/web/packages/rmeta")
13321 (synopsis "Tools for meta-analysis")
13323 "This package provides functions for simple fixed and random effects
13324 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13325 draws standard summary plots, funnel plots, and computes summaries and tests
13326 for association and heterogeneity.")
13327 (license license:gpl2)))
13329 (define-public r-bootstrap
13331 (name "r-bootstrap")
13336 (uri (cran-uri "bootstrap" version))
13339 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13340 (build-system r-build-system)
13341 (native-inputs `(("gfortran" ,gfortran)))
13342 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13343 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13345 "This package provides software and data for the book \"An Introduction
13346 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13347 This package is primarily provided for projects already based on it, and for
13348 support of the book. New projects should preferentially use the recommended
13349 package \"boot\".")
13350 (license license:bsd-3)))
13352 (define-public r-survivalroc
13354 (name "r-survivalroc")
13359 (uri (cran-uri "survivalROC" version))
13362 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13363 (properties `((upstream-name . "survivalROC")))
13364 (build-system r-build-system)
13365 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13366 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13368 "Compute time-dependent ROC curve from censored survival data using
13369 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13370 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13371 (license license:gpl2+)))
13373 (define-public r-longitudinal
13375 (name "r-longitudinal")
13380 (uri (cran-uri "longitudinal" version))
13383 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13384 (build-system r-build-system)
13385 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13386 (home-page "http://strimmerlab.org/software/longitudinal/")
13387 (synopsis "Analysis of multiple time course data")
13389 "This package contains general data structures and functions for
13390 longitudinal data with multiple variables, repeated measurements, and
13391 irregularly spaced time points. It also implements a shrinkage estimator of
13392 dynamical correlation and dynamical covariance.")
13393 (license license:gpl3+)))
13395 (define-public r-genenet
13402 (uri (cran-uri "GeneNet" version))
13405 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13406 (properties `((upstream-name . "GeneNet")))
13407 (build-system r-build-system)
13409 `(("r-corpcor" ,r-corpcor)
13410 ("r-fdrtool" ,r-fdrtool)
13411 ("r-longitudinal" ,r-longitudinal)))
13412 (home-page "http://strimmerlab.org/software/genenet/")
13413 (synopsis "Modeling and inferring gene networks")
13415 "This package analyzes gene expression (time series) data with focus on
13416 the inference of gene networks. In particular, GeneNet implements the methods
13417 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13418 for learning large-scale gene association networks (including assignment of
13419 putative directions).")
13420 (license license:gpl3+)))
13422 (define-public r-rbamtools
13424 (name "r-rbamtools")
13425 (version "2.16.17")
13429 (uri (cran-uri "rbamtools" version))
13432 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13433 (build-system r-build-system)
13434 (inputs `(("zlib" ,zlib)))
13436 `(("r-refgenome" ,r-refgenome)))
13437 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13438 (synopsis "Read and write BAM (binary alignment) files")
13440 "This package provides an R interface to functions of the SAMtools
13442 (license license:artistic2.0)))
13444 (define-public r-protviz
13451 (uri (cran-uri "protViz" version))
13454 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13455 (properties `((upstream-name . "protViz")))
13456 (build-system r-build-system)
13457 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13458 (home-page "https://github.com/protViz/protViz/")
13459 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13461 "This package helps with quality checks, visualizations and analysis of
13462 mass spectrometry data, coming from proteomics experiments. The package is
13463 developed, tested and used at the Functional Genomics Center Zurich, where it
13464 is used mainly for prototyping, teaching, and having fun with proteomics data.
13465 But it can also be used to do data analysis for small scale data sets.")
13466 (license license:gpl3)))
13468 (define-public r-cmprsk
13475 (uri (cran-uri "cmprsk" version))
13477 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13478 (build-system r-build-system)
13480 `(("r-survival" ,r-survival)))
13482 `(("gfortran" ,gfortran)))
13483 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13484 (synopsis "Subdistribution analysis of competing risks")
13486 "This package provides tool for estimation, testing and regression
13487 modeling of subdistribution functions in competing risks, as described in
13488 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13489 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13490 A proportional hazards model for the subdistribution of a competing risk,
13491 JASA, 94:496-509.")
13492 (license license:gpl2+)))
13494 (define-public r-etm
13501 (uri (cran-uri "etm" version))
13504 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13505 (build-system r-build-system)
13507 `(("r-data-table" ,r-data-table)
13508 ("r-lattice" ,r-lattice)
13510 ("r-rcpparmadillo" ,r-rcpparmadillo)
13511 ("r-survival" ,r-survival)))
13512 (home-page "https://cran.r-project.org/web/packages/etm")
13513 (synopsis "Empirical transition matrix")
13515 "The @dfn{empirical transition matrix} (etm) package estimates
13516 the matrix of transition probabilities for any time-inhomogeneous multistate
13517 model with finite state space using the Aalen-Johansen estimator.")
13518 (license license:expat)))
13520 (define-public r-epi
13527 (uri (cran-uri "Epi" version))
13530 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
13531 (properties `((upstream-name . "Epi")))
13532 (build-system r-build-system)
13534 `(("r-cmprsk" ,r-cmprsk)
13535 ("r-data-table" ,r-data-table)
13536 ("r-dplyr" ,r-dplyr)
13539 ("r-matrix" ,r-matrix)
13541 ("r-numderiv" ,r-numderiv)
13543 ("r-purrr" ,r-purrr)
13544 ("r-survival" ,r-survival)
13546 (home-page "https://BendixCarstensen.com/Epi/")
13547 (synopsis "Statistical analysis in epidemiology")
13549 "This package provides functions for demographic and epidemiological
13550 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13551 particular representation, manipulation and simulation of multistate data -
13552 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13553 @code{etm} and @code{cmprsk} packages. It also contains functions for
13554 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13555 data and some useful functions for tabulation and plotting, as well as a
13556 number of epidemiological data sets.")
13557 (license license:gpl2)))
13559 (define-public r-ppls
13562 (version "1.6-1.1")
13566 (uri (cran-uri "ppls" version))
13569 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13570 (build-system r-build-system)
13571 (propagated-inputs `(("r-mass" ,r-mass)))
13572 (home-page "https://cran.r-project.org/web/packages/ppls")
13573 (synopsis "Penalized partial least squares")
13575 "This package contains linear and nonlinear regression methods based on
13576 partial least squares and penalization techniques. Model parameters are
13577 selected via cross-validation, and confidence intervals ans tests for the
13578 regression coefficients can be conducted via jackknifing.")
13579 (license license:gpl2+)))
13581 (define-public r-huge
13584 (version "1.3.4.1")
13588 (uri (cran-uri "huge" version))
13590 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13591 (build-system r-build-system)
13593 `(("r-igraph" ,r-igraph)
13595 ("r-matrix" ,r-matrix)
13597 ("r-rcppeigen" ,r-rcppeigen)))
13598 (home-page "https://cran.r-project.org/web/packages/huge")
13599 (synopsis "High-dimensional undirected graph estimation")
13601 "This package provides a general framework for high-dimensional
13602 undirected graph estimation. It integrates data preprocessing, neighborhood
13603 screening, graph estimation, and model selection techniques into a pipeline.")
13604 (license license:gpl2)))
13606 (define-public r-parcor
13613 (uri (cran-uri "parcor" version))
13616 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13617 (build-system r-build-system)
13620 ("r-genenet" ,r-genenet)
13621 ("r-glmnet" ,r-glmnet)
13623 ("r-ppls" ,r-ppls)))
13624 (home-page "https://cran.r-project.org/web/packages/parcor")
13625 (synopsis "Regularized estimation of partial correlation matrices")
13627 "This package estimates the matrix of partial correlations based on
13628 different regularized regression methods: lasso, adaptive lasso, PLS, and
13629 Ridge Regression. In addition, the package provides model selection for
13630 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13631 (license license:gpl2+)))
13633 (define-public r-mcmc
13640 (uri (cran-uri "mcmc" version))
13643 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13644 (build-system r-build-system)
13645 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13646 (synopsis "Markov chain Monte Carlo")
13648 "This package simulates continuous distributions of random vectors using
13649 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13650 function that evaluates the log unnormalized density. Algorithms are random
13651 walk Metropolis algorithm (function @code{metrop}), simulated
13652 tempering (function @code{temper}), and morphometric random walk
13653 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13654 by change of variable.")
13655 (license license:expat)))
13657 (define-public r-listenv
13664 (uri (cran-uri "listenv" version))
13667 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13668 (build-system r-build-system)
13670 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13671 (home-page "https://github.com/HenrikBengtsson/listenv")
13672 (synopsis "Environments behaving (almost) as lists")
13674 "This package implements list environments. List environments are
13675 environments that have list-like properties. For instance, the elements of a
13676 list environment are ordered and can be accessed and iterated over using index
13678 (license license:lgpl2.1+)))
13680 (define-public r-globals
13687 (uri (cran-uri "globals" version))
13690 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13691 (build-system r-build-system)
13693 `(("r-codetools" ,r-codetools)))
13694 (home-page "https://github.com/HenrikBengtsson/globals")
13695 (synopsis "Identify global objects in R expressions")
13697 "This package provides tools to identify global (\"unknown\" or \"free\")
13698 objects in R expressions by code inspection using various strategies, e.g.
13699 conservative or liberal. The objective of this package is to make it as
13700 simple as possible to identify global objects for the purpose of exporting
13701 them in distributed compute environments.")
13702 (license license:lgpl2.1+)))
13704 (define-public r-parallelly
13706 (name "r-parallelly")
13711 (uri (cran-uri "parallelly" version))
13714 "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6"))))
13715 (properties `((upstream-name . "parallelly")))
13716 (build-system r-build-system)
13717 (home-page "https://github.com/HenrikBengtsson/parallelly")
13718 (synopsis "Enhancements of the parallel package")
13720 "This package provides utility functions that enhance the @code{parallel}
13721 package and support the built-in parallel backends of the @code{future}
13722 package. For example, @code{availableCores} gives the number of CPU cores
13723 available to your R process as given by R options and environment variables,
13724 including those set by job schedulers on high-performance compute clusters.
13725 If none is set, it will fall back to @code{parallel::detectCores}. Another
13726 example is @code{makeClusterPSOCK}, which is backward compatible with
13727 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13728 remote cluster workers without the need for configuring the firewall to do
13729 port-forwarding to your local computer.")
13730 (license license:lgpl2.1+)))
13732 (define-public r-future
13739 (uri (cran-uri "future" version))
13742 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13743 (build-system r-build-system)
13745 `(("r-digest" ,r-digest)
13746 ("r-globals" ,r-globals)
13747 ("r-listenv" ,r-listenv)
13748 ("r-parallelly" ,r-parallelly)))
13750 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13751 (home-page "https://github.com/HenrikBengtsson/future")
13752 (synopsis "Unified parallel and distributed processing in R")
13754 "The purpose of this package is to provide a lightweight and unified
13755 Future API for sequential and parallel processing of R expression via futures.
13756 This package implements sequential, multicore, multisession, and cluster
13757 futures. With these, R expressions can be evaluated on the local machine, in
13758 parallel a set of local machines, or distributed on a mix of local and remote
13759 machines. Extensions to this package implement additional backends for
13760 processing futures via compute cluster schedulers etc. Because of its unified
13761 API, there is no need to modify any code in order to switch from sequential on
13762 the local machine to, say, distributed processing on a remote compute cluster.")
13763 (license license:lgpl2.1+)))
13765 (define-public r-future-apply
13767 (name "r-future-apply")
13772 (uri (cran-uri "future.apply" version))
13775 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13776 (properties `((upstream-name . "future.apply")))
13777 (build-system r-build-system)
13779 `(("r-future" ,r-future)
13780 ("r-globals" ,r-globals)))
13782 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13783 (home-page "https://github.com/HenrikBengtsson/future.apply")
13784 (synopsis "Apply function to elements in parallel using futures")
13786 "This package provides implementations of @code{apply()},
13787 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13788 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13789 can be resolved using any future-supported backend, e.g. parallel on the local
13790 machine or distributed on a compute cluster.")
13791 (license license:gpl2+)))
13793 (define-public r-rsvd
13800 (uri (cran-uri "rsvd" version))
13803 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13804 (build-system r-build-system)
13806 `(("r-matrix" ,r-matrix)))
13807 (home-page "https://github.com/erichson/rSVD")
13808 (synopsis "Randomized singular value decomposition")
13810 "Low-rank matrix decompositions are fundamental tools and widely used for
13811 data analysis, dimension reduction, and data compression. Classically, highly
13812 accurate deterministic matrix algorithms are used for this task. However, the
13813 emergence of large-scale data has severely challenged our computational
13814 ability to analyze big data. The concept of randomness has been demonstrated
13815 as an effective strategy to quickly produce approximate answers to familiar
13816 problems such as the @dfn{singular value decomposition} (SVD). This package
13817 provides several randomized matrix algorithms such as the randomized singular
13818 value decomposition (@code{rsvd}), randomized principal component
13819 analysis (@code{rpca}), randomized robust principal component
13820 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13821 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13822 functions are provided.")
13823 (license license:gpl3+)))
13825 (define-public r-sloop
13832 (uri (cran-uri "sloop" version))
13835 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13836 (build-system r-build-system)
13838 `(("r-codetools" ,r-codetools)
13839 ("r-crayon" ,r-crayon)
13840 ("r-purrr" ,r-purrr)
13841 ("r-rlang" ,r-rlang)
13842 ("r-tibble" ,r-tibble)))
13843 (home-page "https://github.com/r-lib/sloop")
13844 (synopsis "Helpers for object-oriented programming in R")
13846 "This package provides a collection of helper functions designed to
13847 help you to better understand object oriented programming in R, particularly
13849 (license license:gpl3)))
13851 (define-public r-capushe
13858 (uri (cran-uri "capushe" version))
13861 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13862 (build-system r-build-system)
13863 (propagated-inputs `(("r-mass" ,r-mass)))
13864 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13865 (synopsis "Calibrating penalties using slope heuristics")
13867 "This package provides tools for the calibration of penalized criteria
13868 for model selection. The calibration methods available are based on the slope
13870 (license license:gpl2+)))
13872 (define-public r-dorng
13879 (uri (cran-uri "doRNG" version))
13882 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13883 (properties `((upstream-name . "doRNG")))
13884 (build-system r-build-system)
13886 `(("r-foreach" ,r-foreach)
13887 ("r-iterators" ,r-iterators)
13888 ("r-rngtools" ,r-rngtools)))
13889 (home-page "https://renozao.github.io/doRNG/")
13890 (synopsis "Generic reproducible parallel backend for foreach loops")
13892 "This package provides functions to perform reproducible parallel
13893 @code{foreach} loops, using independent random streams as generated by
13894 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13895 convert standard @code{%dopar%} loops into fully reproducible loops,
13896 independently of the number of workers, the task scheduling strategy, or the
13897 chosen parallel environment and associated foreach backend.")
13898 (license license:gpl2+)))
13900 (define-public r-blockmodeling
13902 (name "r-blockmodeling")
13907 (uri (cran-uri "blockmodeling" version))
13910 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13911 (build-system r-build-system)
13913 `(("r-matrix" ,r-matrix)))
13914 (native-inputs `(("gfortran" ,gfortran)))
13915 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13916 (synopsis "Generalized and classical blockmodeling of valued networks")
13918 "This package is primarily meant as an implementation of generalized
13919 blockmodeling for valued networks. In addition, measures of similarity or
13920 dissimilarity based on structural equivalence and regular equivalence (REGE
13921 algorithms) can be computed and partitioned matrices can be plotted.")
13922 (license license:gpl2+)))
13924 (define-public r-upsetr
13931 (uri (cran-uri "UpSetR" version))
13934 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13935 (properties `((upstream-name . "UpSetR")))
13936 (build-system r-build-system)
13938 `(("r-ggplot2" ,r-ggplot2)
13939 ("r-gridextra" ,r-gridextra)
13941 ("r-scales" ,r-scales)))
13942 (home-page "https://github.com/hms-dbmi/UpSetR")
13943 (synopsis "Visualize intersecting sets")
13945 "This package provides a more scalable alternative to Venn and Euler
13946 diagrams for visualizing intersecting sets. Create visualizations of
13947 intersecting sets using a novel matrix design, along with visualizations of
13948 several common set, element and attribute related tasks.")
13949 (license license:expat)))
13951 ;; This package includes a JavaScript file, which is not minified. When
13952 ;; upgrading please check that there are no new minified JavaScript files.
13953 (define-public r-shinybs
13960 (uri (cran-uri "shinyBS" version))
13963 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13964 (properties `((upstream-name . "shinyBS")))
13965 (build-system r-build-system)
13966 ;; The tests spawn Shiny browser apps. They cannot be run
13967 ;; non-interactively.
13968 (arguments '(#:tests? #f))
13970 `(("r-htmltools" ,r-htmltools)
13971 ("r-shiny" ,r-shiny)))
13972 (home-page "https://ebailey78.github.io/shinyBS/")
13973 (synopsis "Twitter Bootstrap components for Shiny")
13975 "This package adds additional Twitter Bootstrap components to Shiny.")
13976 (license license:gpl3)))
13978 (define-public r-shinyjqui
13980 (name "r-shinyjqui")
13985 (uri (cran-uri "shinyjqui" version))
13988 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
13991 (delete-file "inst/www/shinyjqui.min.js")))))
13992 (properties `((upstream-name . "shinyjqui")))
13993 (build-system r-build-system)
13996 (modify-phases %standard-phases
13997 (add-after 'unpack 'process-javascript
13998 (lambda* (#:key inputs #:allow-other-keys)
13999 (with-directory-excursion "inst/www/"
14000 (let ((source "shinyjqui.js")
14001 (target "shinyjqui.min.js"))
14002 (format #true "Processing ~a --> ~a~%"
14004 (invoke "esbuild" source "--minify"
14005 (string-append "--outfile=" target)))))))))
14007 `(("r-htmltools" ,r-htmltools)
14008 ("r-htmlwidgets" ,r-htmlwidgets)
14009 ("r-jsonlite" ,r-jsonlite)
14010 ("r-shiny" ,r-shiny)))
14012 `(("r-knitr" ,r-knitr)
14013 ("esbuild" ,esbuild)))
14014 (home-page "https://github.com/yang-tang/shinyjqui")
14015 (synopsis "jQuery UI interactions and effects for Shiny")
14017 "This is an extension to Shiny that brings interactions and animation
14018 effects from the jQuery UI library.")
14019 (license license:expat)))
14021 (define-public r-outliers
14023 (name "r-outliers")
14028 (uri (cran-uri "outliers" version))
14031 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14032 (build-system r-build-system)
14033 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14034 (synopsis "Tests for outliers")
14036 "This package provides a collection of some tests commonly used for
14037 identifying outliers.")
14038 (license license:gpl2+)))
14040 (define-public r-bayesm
14047 (uri (cran-uri "bayesm" version))
14049 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14050 (build-system r-build-system)
14052 `(("r-rcpp" ,r-rcpp)
14053 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14054 (home-page "http://www.perossi.org/home/bsm-1")
14055 (synopsis "Bayesian inference for marketing/micro-econometrics")
14057 "This package covers many important models used in marketing and
14058 micro-econometrics applications, including Bayes Regression (univariate or
14059 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14060 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14061 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14062 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14063 Estimation with normal base, Hierarchical Linear Models with normal prior and
14064 covariates, Hierarchical Linear Models with a mixture of normals prior and
14065 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14066 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14067 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14068 analysis of choice-based conjoint data, Bayesian treatment of linear
14069 instrumental variables models, Analysis of Multivariate Ordinal survey data
14070 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14071 Coefficient Logit Models.")
14072 (license license:gpl2+)))
14074 (define-public r-tensora
14081 (uri (cran-uri "tensorA" version))
14084 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14085 (properties `((upstream-name . "tensorA")))
14086 (build-system r-build-system)
14087 (home-page "http://www.stat.boogaart.de/tensorA")
14088 (synopsis "Advanced tensor arithmetic with named indices")
14090 "This package provides convenience functions for advanced linear algebra
14091 with tensors and computation with datasets of tensors on a higher level
14092 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14093 co- and contravariate indices, and parallel computations on sequences of
14095 (license license:gpl2+)))
14097 (define-public r-rarpack
14104 (uri (cran-uri "rARPACK" version))
14107 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14108 (properties `((upstream-name . "rARPACK")))
14109 (build-system r-build-system)
14110 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14111 (home-page "https://github.com/yixuan/rARPACK")
14112 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14114 "This package was previously an R wrapper of the ARPACK library, and now
14115 a shell of the R package RSpectra, an R interface to the Spectra library for
14116 solving large scale eigenvalue/vector problems. The current version of
14117 rARPACK simply imports and exports the functions provided by RSpectra. New
14118 users of rARPACK are advised to switch to the RSpectra package.")
14119 (license license:bsd-3)))
14121 (define-public r-compositions
14123 (name "r-compositions")
14128 (uri (cran-uri "compositions" version))
14131 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14132 (build-system r-build-system)
14134 `(("r-bayesm" ,r-bayesm)
14136 ("r-robustbase" ,r-robustbase)
14137 ("r-tensora" ,r-tensora)))
14139 `(("r-knitr" ,r-knitr)))
14140 (home-page "http://www.stat.boogaart.de/compositions")
14141 (synopsis "Compositional data analysis")
14143 "This package provides functions for the consistent analysis of
14144 compositional data (e.g. portions of substances) and positive
14145 numbers (e.g. concentrations).")
14146 (license license:gpl2+)))
14148 (define-public r-cobs
14155 (uri (cran-uri "cobs" version))
14158 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14159 (build-system r-build-system)
14161 `(("r-quantreg" ,r-quantreg)
14162 ("r-sparsem" ,r-sparsem)))
14163 (home-page "https://cran.r-project.org/web/packages/cobs")
14164 (synopsis "Constrained B-Splines (sparse matrix based)")
14166 "This package provides qualitatively constrained (regression) smoothing
14167 splines via linear programming and sparse matrices.")
14168 (license license:gpl2+)))
14170 (define-public r-drimpute
14172 (name "r-drimpute")
14177 (uri (cran-uri "DrImpute" version))
14180 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14181 (properties `((upstream-name . "DrImpute")))
14182 (build-system r-build-system)
14184 `(("r-rcpp" ,r-rcpp)
14185 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14186 (home-page "https://github.com/ikwak2/DrImpute")
14187 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14189 "This is an R package for imputing dropout events. Many statistical
14190 methods in cell type identification, visualization and lineage reconstruction
14191 do not account for dropout events. DrImpute can improve the performance of
14192 such software by imputing dropout events.")
14193 (license license:gpl3)))
14195 (define-public r-gamlss-dist
14197 (name "r-gamlss-dist")
14202 (uri (cran-uri "gamlss.dist" version))
14204 (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc"))))
14205 (properties `((upstream-name . "gamlss.dist")))
14206 (build-system r-build-system)
14207 (propagated-inputs `(("r-mass" ,r-mass)))
14208 (home-page "http://www.gamlss.org/")
14209 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14211 "This package provides a set of distributions which can be used for
14212 modelling the response variables in Generalized Additive Models for Location
14213 Scale and Shape. The distributions can be continuous, discrete or mixed
14214 distributions. Extra distributions can be created, by transforming, any
14215 continuous distribution defined on the real line, to a distribution defined on
14216 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14217 transformation, respectively.")
14218 ;; Either version of the GPL.
14219 (license (list license:gpl2 license:gpl3))))
14221 ;; This package includes JavaScript files, which are not minified. When
14222 ;; upgrading please check that there are no new minified JavaScript files.
14223 (define-public r-shinyjs
14230 (uri (cran-uri "shinyjs" version))
14233 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14234 (build-system r-build-system)
14236 `(("r-digest" ,r-digest)
14237 ("r-htmltools" ,r-htmltools)
14238 ("r-jsonlite" ,r-jsonlite)
14239 ("r-shiny" ,r-shiny)))
14241 `(("r-knitr" ,r-knitr)))
14242 (home-page "https://deanattali.com/shinyjs")
14243 (synopsis "Improve the user experience of your Shiny apps")
14245 "Perform common useful JavaScript operations in Shiny apps that will
14246 greatly improve your apps without having to know any JavaScript. Examples
14247 include: hiding an element, disabling an input, resetting an input back to its
14248 original value, delaying code execution by a few seconds, and many more useful
14249 functions for both the end user and the developer. Shinyjs can also be used
14250 to easily call your own custom JavaScript functions from R.")
14251 (license license:agpl3+)))
14253 ;; This package includes minified JavaScript files. When upgrading please
14254 ;; check that there are no new minified JavaScript files.
14255 (define-public r-colourpicker
14257 (name "r-colourpicker")
14262 (uri (cran-uri "colourpicker" version))
14265 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14266 (build-system r-build-system)
14268 `(#:modules ((guix build utils)
14269 (guix build r-build-system)
14273 (modify-phases %standard-phases
14274 (add-after 'unpack 'process-javascript
14275 (lambda* (#:key inputs #:allow-other-keys)
14276 (with-directory-excursion "inst"
14280 `((,(assoc-ref inputs "js-salvattore")
14281 "examples/colourInput/www/salvattore.min.js")
14282 (,(assoc-ref inputs "js-jquery")
14283 "htmlwidgets/lib/jquery/jquery.min.js")
14284 ("www/shared/colourpicker/js/colourpicker.js"
14285 "www/shared/colourpicker/js/colourpicker.min.js"))))
14286 (lambda (sources targets)
14287 (for-each (lambda (source target)
14288 (format #t "Processing ~a --> ~a~%"
14290 (delete-file target)
14291 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14292 (call-with-output-file target
14294 (dump-port minified port)))))
14295 sources targets))))
14298 `(("r-ggplot2" ,r-ggplot2)
14299 ("r-htmltools" ,r-htmltools)
14300 ("r-htmlwidgets" ,r-htmlwidgets)
14301 ("r-jsonlite" ,r-jsonlite)
14302 ("r-miniui" ,r-miniui)
14303 ("r-shiny" ,r-shiny)
14304 ("r-shinyjs" ,r-shinyjs)))
14306 `(("r-knitr" ,r-knitr)
14307 ("uglify-js" ,uglify-js)
14311 (uri "https://code.jquery.com/jquery-3.3.1.js")
14314 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14318 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14321 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14322 (home-page "https://github.com/daattali/colourpicker")
14323 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14325 "This package provides a color picker that can be used as an input in
14326 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14327 custom color palettes, and many more options. A plot color helper tool is
14328 available as an RStudio Addin, which helps you pick colors to use in your
14329 plots. A more generic color picker RStudio Addin is also provided to let you
14330 select colors to use in your R code.")
14331 (license license:expat)))
14333 (define-public r-ggextra
14340 (uri (cran-uri "ggExtra" version))
14343 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14344 (properties `((upstream-name . "ggExtra")))
14345 (build-system r-build-system)
14347 `(("r-colourpicker" ,r-colourpicker)
14348 ("r-ggplot2" ,r-ggplot2)
14349 ("r-gtable" ,r-gtable)
14350 ("r-miniui" ,r-miniui)
14352 ("r-scales" ,r-scales)
14353 ("r-shiny" ,r-shiny)
14354 ("r-shinyjs" ,r-shinyjs)))
14356 `(("r-knitr" ,r-knitr)))
14357 (home-page "https://github.com/daattali/ggExtra")
14358 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14360 "This package is a collection of functions and layers to enhance ggplot2.
14361 The flagship function is @code{ggMarginal()}, which can be used to add
14362 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14363 (license license:expat)))
14365 (define-public r-minpack-lm
14367 (name "r-minpack-lm")
14372 (uri (cran-uri "minpack.lm" version))
14375 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14376 (properties `((upstream-name . "minpack.lm")))
14377 (build-system r-build-system)
14378 (native-inputs `(("gfortran" ,gfortran)))
14379 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14380 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14382 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14383 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14384 problems by a modification of the Levenberg-Marquardt algorithm, with support
14385 for lower and upper parameter bounds. The implementation can be used via
14386 @code{nls}-like calls using the @code{nlsLM} function.")
14387 (license license:gpl3)))
14389 (define-public r-moments
14396 (uri (cran-uri "moments" version))
14399 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14400 (build-system r-build-system)
14401 (home-page "https://cran.r-project.org/web/packages/moments")
14402 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14404 "This package provides functions to calculate: moments, Pearson's
14405 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14406 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14407 (license license:gpl2+)))
14409 (define-public r-msir
14416 (uri (cran-uri "msir" version))
14419 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14420 (build-system r-build-system)
14422 `(("r-mclust" ,r-mclust)))
14424 `(("r-knitr" ,r-knitr)))
14425 (home-page "https://cran.r-project.org/web/packages/msir")
14426 (synopsis "Model-based sliced inverse regression")
14428 "This is an R package for dimension reduction based on finite Gaussian
14429 mixture modeling of inverse regression.")
14430 (license license:gpl2+)))
14432 (define-public r-pbivnorm
14434 (name "r-pbivnorm")
14439 (uri (cran-uri "pbivnorm" version))
14442 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14443 (build-system r-build-system)
14444 (native-inputs `(("gfortran" ,gfortran)))
14445 (home-page "https://github.com/brentonk/pbivnorm")
14446 (synopsis "Vectorized bivariate normal CDF")
14448 "This package provides a vectorized R function for calculating
14449 probabilities from a standard bivariate normal CDF.")
14450 (license license:gpl2+)))
14452 (define-public r-lavaan
14459 (uri (cran-uri "lavaan" version))
14462 "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0"))))
14463 (build-system r-build-system)
14465 `(("r-mass" ,r-mass)
14466 ("r-mnormt" ,r-mnormt)
14467 ("r-numderiv" ,r-numderiv)
14468 ("r-pbivnorm" ,r-pbivnorm)))
14469 (home-page "https://lavaan.ugent.be")
14470 (synopsis "Latent variable analysis")
14472 "This package provides tools to fit a variety of latent variable models,
14473 including confirmatory factor analysis, structural equation modeling and
14474 latent growth curve models.")
14475 (license license:gpl2+)))
14477 (define-public r-nonnest2
14479 (name "r-nonnest2")
14484 (uri (cran-uri "nonnest2" version))
14487 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14488 (build-system r-build-system)
14490 `(("r-compquadform" ,r-compquadform)
14491 ("r-lavaan" ,r-lavaan)
14492 ("r-mvtnorm" ,r-mvtnorm)
14493 ("r-sandwich" ,r-sandwich)))
14495 `(("r-knitr" ,r-knitr)))
14496 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14497 (synopsis "Tests of non-nested models")
14499 "This package allows for testing of non-nested models. It includes tests
14500 of model distinguishability and of model fit that can be applied to both
14501 nested and non-nested models. The package also includes functionality to
14502 obtain confidence intervals associated with AIC and BIC.")
14503 ;; Either version of the GPL.
14504 (license (list license:gpl2 license:gpl3))))
14506 (define-public r-penalized
14508 (name "r-penalized")
14513 (uri (cran-uri "penalized" version))
14516 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14517 (build-system r-build-system)
14519 `(("r-rcpp" ,r-rcpp)
14520 ("r-rcpparmadillo" ,r-rcpparmadillo)
14521 ("r-survival" ,r-survival)))
14522 (home-page "https://cran.r-project.org/web/packages/penalized/")
14523 (synopsis "Penalized estimation in GLMs and in the Cox model")
14525 "This package provides tools for fitting possibly high dimensional
14526 penalized regression models. The penalty structure can be any combination of
14527 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14528 constraint on the regression coefficients. The supported regression models
14529 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14530 model. Cross-validation routines allow optimization of the tuning
14532 (license license:gpl2+)))
14534 (define-public r-zim
14541 (uri (cran-uri "ZIM" version))
14544 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14545 (properties `((upstream-name . "ZIM")))
14546 (build-system r-build-system)
14547 (propagated-inputs `(("r-mass" ,r-mass)))
14548 (home-page "https://github.com/biostatstudio/ZIM")
14549 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14551 "Analyze count time series with excess zeros. Two types of statistical
14552 models are supported: Markov regression and state-space models. They are also
14553 known as observation-driven and parameter-driven models respectively in the
14554 time series literature. The functions used for Markov regression or
14555 observation-driven models can also be used to fit ordinary regression models
14556 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14557 negative binomial (ZINB) assumption. The package also contains miscellaneous
14558 functions to compute density, distribution, quantile, and generate random
14559 numbers from ZIP and ZINB distributions.")
14560 (license license:gpl3)))
14562 (define-public r-nor1mix
14569 (uri (cran-uri "nor1mix" version))
14572 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14573 (build-system r-build-system)
14574 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14575 (synopsis "Normal (1-d) mixture models")
14577 "This package provides S3 classes and methods for one-dimensional normal
14578 mixture models, for, e.g., density estimation or clustering algorithms
14579 research and teaching; it provides the widely used Marron-Wand densities. It
14580 also provides tools for efficient random number generation and graphics.")
14581 (license license:gpl2+)))
14583 (define-public r-beanplot
14585 (name "r-beanplot")
14590 (uri (cran-uri "beanplot" version))
14593 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14594 (build-system r-build-system)
14595 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14596 (synopsis "Visualization via beanplots")
14598 "This package provides beanplots, an alternative to
14599 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14601 (license license:gpl2)))
14603 (define-public r-pbdzmq
14610 (uri (cran-uri "pbdZMQ" version))
14613 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14614 (properties `((upstream-name . "pbdZMQ")))
14615 (build-system r-build-system)
14617 `(("zeromq" ,zeromq)
14620 `(("pkg-config" ,pkg-config)))
14621 (home-page "https://pbdr.org/")
14622 (synopsis "R interface to ZeroMQ")
14624 "ZeroMQ is a well-known library for high-performance asynchronous
14625 messaging in scalable, distributed applications. This package provides high
14626 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14627 interactive client/server programming frameworks. A few wrapper functions
14628 compatible with @code{rzmq} are also provided.")
14629 (license license:gpl3)))
14631 (define-public r-repr
14638 (uri (cran-uri "repr" version))
14641 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14642 (build-system r-build-system)
14644 `(("r-base64enc" ,r-base64enc)
14645 ("r-htmltools" ,r-htmltools)
14646 ("r-jsonlite" ,r-jsonlite)
14647 ("r-pillar" ,r-pillar)))
14648 (home-page "https://cran.r-project.org/web/packages/repr/")
14649 (synopsis "Serializable representations")
14651 "This package provides string and binary representations of objects for
14652 several formats and MIME types.")
14653 (license license:gpl3)))
14655 (define-public r-irdisplay
14657 (name "r-irdisplay")
14662 (uri (cran-uri "IRdisplay" version))
14665 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14666 (properties `((upstream-name . "IRdisplay")))
14667 (build-system r-build-system)
14669 `(("r-repr" ,r-repr)))
14670 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14671 (synopsis "Jupyter display machinery")
14673 "This package provides an interface to the rich display capabilities of
14674 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14675 running IRkernel session.")
14676 (license license:expat)))
14678 (define-public r-irkernel
14680 (name "r-irkernel")
14685 (uri (cran-uri "IRkernel" version))
14688 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14689 (properties `((upstream-name . "IRkernel")))
14690 (build-system r-build-system)
14693 (modify-phases %standard-phases
14694 (add-after 'install 'install-kernelspec
14695 (lambda* (#:key outputs #:allow-other-keys)
14696 (let ((out (assoc-ref outputs "out")))
14697 (setenv "HOME" "/tmp")
14698 (invoke "jupyter" "kernelspec" "install"
14701 (string-append out "/site-library/IRkernel/kernelspec"))
14702 ;; Record the absolute file name of the 'R' executable in
14704 (substitute* (string-append out "/share/jupyter"
14705 "/kernels/ir/kernel.json")
14707 (string-append "[\"" (which "R") "\",")))
14710 `(("jupyter" ,jupyter)))
14712 `(("r-crayon" ,r-crayon)
14713 ("r-digest" ,r-digest)
14714 ("r-evaluate" ,r-evaluate)
14715 ("r-irdisplay" ,r-irdisplay)
14716 ("r-jsonlite" ,r-jsonlite)
14717 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14718 ("r-minimal" ,r-minimal)
14719 ("r-pbdzmq" ,r-pbdzmq)
14721 ("r-uuid" ,r-uuid)))
14722 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14723 (synopsis "Native R kernel for Jupyter")
14725 "The R kernel for the Jupyter environment executes R code which the
14726 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14728 (license license:expat)))
14730 (define-public r-gmodels
14737 (uri (cran-uri "gmodels" version))
14740 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14741 (build-system r-build-system)
14743 `(("r-gdata" ,r-gdata)
14744 ("r-mass" ,r-mass)))
14745 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14746 (synopsis "Various R programming tools for model fitting")
14748 "This package provides various R programming tools for model fitting.")
14749 (license license:gpl2)))
14751 (define-public r-apcluster
14753 (name "r-apcluster")
14758 (uri (cran-uri "apcluster" version))
14761 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14762 (build-system r-build-system)
14764 `(("r-matrix" ,r-matrix)
14765 ("r-rcpp" ,r-rcpp)))
14766 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14767 (synopsis "Affinity propagation clustering")
14769 "This package implements affinity propagation clustering introduced by
14770 Frey and Dueck (2007). The package further provides leveraged affinity
14771 propagation and an algorithm for exemplar-based agglomerative clustering that
14772 can also be used to join clusters obtained from affinity propagation. Various
14773 plotting functions are available for analyzing clustering results.")
14774 (license license:gpl2+)))
14776 (define-public r-valr
14783 (uri (cran-uri "valr" version))
14786 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14787 (build-system r-build-system)
14789 `(("r-broom" ,r-broom)
14790 ("r-dplyr" ,r-dplyr)
14791 ("r-ggplot2" ,r-ggplot2)
14793 ("r-readr" ,r-readr)
14794 ("r-rlang" ,r-rlang)
14795 ("r-stringr" ,r-stringr)
14796 ("r-tibble" ,r-tibble)))
14798 `(("r-knitr" ,r-knitr)))
14799 (home-page "https://github.com/rnabioco/valr")
14800 (synopsis "Genome interval arithmetic in R")
14802 "This package enables you to read and manipulate genome intervals and
14803 signals. It provides functionality similar to command-line tool suites within
14804 R, enabling interactive analysis and visualization of genome-scale data.")
14805 (license license:expat)))
14807 (define-public r-rematch2
14809 (name "r-rematch2")
14814 (uri (cran-uri "rematch2" version))
14817 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14818 (build-system r-build-system)
14820 `(("r-tibble" ,r-tibble)))
14821 (home-page "https://github.com/r-lib/rematch2")
14822 (synopsis "Tidy output from regular expression matching")
14824 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14825 return the match results in tidy data frames.")
14826 (license license:expat)))
14828 (define-public r-picante
14835 (uri (cran-uri "picante" version))
14838 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14839 (build-system r-build-system)
14843 ("r-vegan" ,r-vegan)))
14844 (home-page "https://cran.r-project.org/web/packages/picante/")
14845 (synopsis "Integrating phylogenies and ecology")
14847 "This package provides functions for phylocom integration, community
14848 analyses, null-models, traits and evolution. It implements numerous
14849 ecophylogenetic approaches including measures of community phylogenetic and
14850 trait diversity, phylogenetic signal, estimation of trait values for
14851 unobserved taxa, null models for community and phylogeny randomizations, and
14852 utility functions for data input/output and phylogeny plotting. A full
14853 description of package functionality and methods are provided by Kembel et
14855 (license license:gpl2)))
14857 (define-public r-reinforcelearn
14859 (name "r-reinforcelearn")
14864 (uri (cran-uri "reinforcelearn" version))
14867 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14868 (build-system r-build-system)
14870 `(("r-checkmate" ,r-checkmate)
14872 ("r-purrr" ,r-purrr)
14874 (home-page "https://markusdumke.github.io/reinforcelearn")
14875 (synopsis "Reinforcement learning")
14877 "This package implements reinforcement learning environments and
14878 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14879 can be used with function approximation, eligibility traces (Singh & Sutton,
14880 1996) and experience replay (Mnih et al., 2013).")
14881 (license license:expat)))
14883 (define-public r-lemon
14890 (uri (cran-uri "lemon" version))
14893 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14894 (build-system r-build-system)
14896 `(("r-ggplot2" ,r-ggplot2)
14897 ("r-gridextra" ,r-gridextra)
14898 ("r-gtable" ,r-gtable)
14899 ("r-knitr" ,r-knitr)
14900 ("r-lattice" ,r-lattice)
14902 ("r-rlang" ,r-rlang)
14903 ("r-scales" ,r-scales)))
14905 `(("r-knitr" ,r-knitr)))
14906 (home-page "https://github.com/stefanedwards/lemon")
14907 (synopsis "Freshen up your ggplot2 plots")
14909 "This package provides functions for working with legends and axis lines
14910 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14912 (license license:gpl3)))
14914 (define-public r-wgaim
14921 (uri (cran-uri "wgaim" version))
14923 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14924 (build-system r-build-system)
14926 `(("r-ggplot2" ,r-ggplot2)
14928 (home-page "https://cran.r-project.org/web/packages/wgaim")
14929 (synopsis "Whole genome average interval mapping for QTL detection")
14931 "This package integrates sophisticated mixed modelling methods with a
14932 whole genome approach to detecting significant QTL in linkage maps.")
14933 (license license:gpl2+)))
14935 (define-public r-bedr
14942 (uri (cran-uri "bedr" version))
14945 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14946 (build-system r-build-system)
14948 `(("r-data-table" ,r-data-table)
14949 ("r-r-utils" ,r-r-utils)
14950 ("r-testthat" ,r-testthat)
14951 ("r-venndiagram" ,r-venndiagram)
14954 ("bedtools" ,bedtools)
14955 ("htslib" ,htslib))) ; for tabix
14957 `(("r-knitr" ,r-knitr))) ; for vignettes
14958 (home-page "https://cran.r-project.org/web/packages/bedr")
14959 (synopsis "Genomic region processing")
14961 "This package is for genomic regions processing using command line tools
14962 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14963 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14964 The bedr package's API enhances access to these tools as well as offers
14965 additional utilities for genomic regions processing.")
14966 (license license:gpl2)))
14968 (define-public r-sets
14975 (uri (cran-uri "sets" version))
14978 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14979 (properties `((upstream-name . "sets")))
14980 (build-system r-build-system)
14981 (home-page "https://cran.r-project.org/web/packages/sets")
14982 (synopsis "Sets, generalized sets, customizable sets and intervals")
14984 "This package provides data structures and basic operations for ordinary
14985 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14986 customizable sets, and intervals.")
14987 (license license:gpl2)))
14989 (define-public r-partitions
14991 (name "r-partitions")
14996 (uri (cran-uri "partitions" version))
14999 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
15000 (build-system r-build-system)
15003 ("r-polynom" ,r-polynom)
15004 ("r-sets" ,r-sets)))
15005 (home-page "https://cran.r-project.org/web/packages/partitions")
15006 (synopsis "Additive partitions of integers")
15008 "This package provides tools to enumerates the partitions, unequal
15009 partitions, and restricted partitions of an integer; the three corresponding
15010 partition functions are also given.")
15011 ;; Any version of the GPL
15012 (license license:gpl2+)))
15014 (define-public r-brobdingnag
15016 (name "r-brobdingnag")
15021 (uri (cran-uri "Brobdingnag" version))
15024 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15025 (properties `((upstream-name . "Brobdingnag")))
15026 (build-system r-build-system)
15027 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15028 (synopsis "Very large numbers in R")
15030 "This package handles very large numbers in R. Real numbers are held
15031 using their natural logarithms, plus a logical flag indicating sign. The
15032 package includes a vignette that gives a step-by-step introduction to using S4
15034 ;; Any version of the GPL
15035 (license license:gpl2+)))
15037 (define-public r-untb
15044 (uri (cran-uri "untb" version))
15047 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15048 (build-system r-build-system)
15050 `(("r-brobdingnag" ,r-brobdingnag)
15051 ("r-partitions" ,r-partitions)
15052 ("r-polynom" ,r-polynom)))
15053 (home-page "https://github.com/RobinHankin/untb.git")
15054 (synopsis "Ecological drift under the UNTB")
15056 "This package provides numerical simulations, and visualizations, of
15057 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15058 (license license:gpl2+)))
15060 (define-public r-stepwise
15062 (name "r-stepwise")
15067 (uri (cran-uri "stepwise" version))
15070 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15071 (build-system r-build-system)
15072 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15073 (synopsis "Stepwise detection of recombination breakpoints")
15075 "This package provides a stepwise approach to identifying recombination
15076 breakpoints in a genomic sequence alignment.")
15077 (license license:gpl2+)))
15079 (define-public r-snpmaxsel
15081 (name "r-snpmaxsel")
15086 (uri (cran-uri "SNPmaxsel" version))
15089 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15090 (properties `((upstream-name . "SNPmaxsel")))
15091 (build-system r-build-system)
15093 `(("r-combinat" ,r-combinat)
15094 ("r-mvtnorm" ,r-mvtnorm)))
15095 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15096 (synopsis "Maximally selected statistics for SNP data")
15098 "This package implements asymptotic methods related to maximally selected
15099 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15101 (license license:gpl2+)))
15103 (define-public r-acsnminer
15105 (name "r-acsnminer")
15106 (version "0.16.8.25")
15109 (uri (cran-uri "ACSNMineR" version))
15112 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15113 (properties `((upstream-name . "ACSNMineR")))
15114 (build-system r-build-system)
15116 `(("r-ggplot2" ,r-ggplot2)
15117 ("r-gridextra" ,r-gridextra)))
15118 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15119 (synopsis "Gene enrichment analysis")
15121 "This package provides tools to compute and represent gene set enrichment
15122 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15123 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15124 enrichment can be run with hypergeometric test or Fisher exact test, and can
15125 use multiple corrections. Visualization of data can be done either by
15126 barplots or heatmaps.")
15127 (license license:gpl2+)))
15129 (define-public r-seqinr
15136 (uri (cran-uri "seqinr" version))
15139 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15140 (build-system r-build-system)
15142 `(("r-ade4" ,r-ade4)
15143 ("r-segmented" ,r-segmented)))
15146 (home-page "http://seqinr.r-forge.r-project.org/")
15147 (synopsis "Biological sequences retrieval and analysis")
15149 "This package provides tools for exploratory data analysis and data
15150 visualization of biological sequence (DNA and protein) data. It also includes
15151 utilities for sequence data management under the ACNUC system.")
15152 (license license:gpl2+)))
15154 (define-public r-units
15161 (uri (cran-uri "units" version))
15164 "0wwndzjjgqj795xvx1jwa86nwd8adfiwj0pn15yyzzk9baky2axw"))))
15165 (build-system r-build-system)
15167 `(("udunits" ,udunits)))
15169 `(("r-rcpp" ,r-rcpp)))
15171 `(("r-knitr" ,r-knitr)))
15172 (home-page "https://github.com/r-quantities/units/")
15173 (synopsis "Measurement Units for R Vectors")
15175 "This package provides support for measurement units in R vectors,
15176 matrices and arrays: automatic propagation, conversion, derivation and
15177 simplification of units; raising errors in case of unit incompatibility. It
15178 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15180 (license license:gpl2)))
15182 (define-public r-udunits2
15184 (name "r-udunits2")
15189 (uri (cran-uri "udunits2" version))
15192 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15193 (properties `((upstream-name . "udunits2")))
15194 (build-system r-build-system)
15196 `(("udunits" ,udunits)))
15197 (home-page "https://cran.r-project.org/package=udunits2")
15198 (synopsis "Udunits-2 bindings for R")
15200 "This package provides simple bindings to Unidata's udunits library.")
15201 (license license:gpl2)))
15203 (define-public r-classint
15205 (name "r-classint")
15210 (uri (cran-uri "classInt" version))
15213 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15214 (properties `((upstream-name . "classInt")))
15215 (build-system r-build-system)
15217 `(("r-class" ,r-class)
15218 ("r-e1071" ,r-e1071)
15219 ("r-kernsmooth" ,r-kernsmooth)))
15221 `(("gfortran" ,gfortran)
15222 ("r-knitr" ,r-knitr)))
15223 (home-page "https://github.com/r-spatial/classInt/")
15224 (synopsis "Choose univariate class intervals")
15226 "This package provides selected commonly used methods for choosing
15227 univariate class intervals for mapping or other graphics purposes.")
15228 (license license:gpl2+)))
15230 (define-public r-spdata
15237 (uri (cran-uri "spData" version))
15240 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15241 (properties `((upstream-name . "spData")))
15242 (build-system r-build-system)
15244 `(("r-raster" ,r-raster)
15246 (home-page "https://github.com/Nowosad/spData")
15247 (synopsis "Datasets for spatial analysis")
15249 "This a package containing diverse spatial datasets for demonstrating,
15250 benchmarking and teaching spatial data analysis. It includes R data of class
15251 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15252 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15253 of the datasets are designed to illustrate specific analysis techniques.
15254 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15255 illustrate point pattern analysis techniques.")
15256 (license license:cc0)))
15258 (define-public r-learnbayes
15260 (name "r-learnbayes")
15265 (uri (cran-uri "LearnBayes" version))
15268 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15269 (properties `((upstream-name . "LearnBayes")))
15270 (build-system r-build-system)
15271 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15272 (synopsis "Functions for learning Bayesian inference")
15274 "This package provides a collection of functions helpful in learning the
15275 basic tenets of Bayesian statistical inference. It contains functions for
15276 summarizing basic one and two parameter posterior distributions and predictive
15277 distributions. It contains MCMC algorithms for summarizing posterior
15278 distributions defined by the user. It also contains functions for regression
15279 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15281 (license license:gpl2+)))
15283 (define-public r-deldir
15290 (uri (cran-uri "deldir" version))
15293 "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
15294 (build-system r-build-system)
15295 (native-inputs `(("gfortran" ,gfortran)))
15296 (home-page "https://cran.r-project.org/web/packages/deldir")
15297 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15299 "This package provides tools for calculating the Delaunay triangulation
15300 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15301 of a planar point set. It plots triangulations and tessellations in various
15302 ways, clips tessellations to sub-windows, calculates perimeters of
15303 tessellations, and summarizes information about the tiles of the
15305 (license license:gpl2+)))
15307 (define-public r-sf
15314 (uri (cran-uri "sf" version))
15317 "096gg2hbynn6mv3w8n69x987fklg5rrgd0d4nbqaw7vhg1jhlmqi"))))
15318 (build-system r-build-system)
15326 `(("r-classint" ,r-classint)
15328 ("r-magrittr" ,r-magrittr)
15330 ("r-units" ,r-units)))
15332 `(("pkg-config" ,pkg-config)
15333 ("r-knitr" ,r-knitr)))
15334 (home-page "https://github.com/r-spatial/sf/")
15335 (synopsis "Simple features for R")
15337 "This package provides support for simple features, a standardized way to
15338 encode spatial vector data. It binds to GDAL for reading and writing data, to
15339 GEOS for geometrical operations, and to PROJ for projection conversions and
15340 datum transformations.")
15341 ;; Either of these licenses
15342 (license (list license:gpl2 license:expat))))
15344 (define-public r-spdep
15351 (uri (cran-uri "spdep" version))
15354 "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1"))))
15355 (build-system r-build-system)
15357 `(("r-boot" ,r-boot)
15359 ("r-deldir" ,r-deldir)
15361 ("r-gmodels" ,r-gmodels)
15362 ("r-learnbayes" ,r-learnbayes)
15364 ("r-matrix" ,r-matrix)
15368 ("r-spdata" ,r-spdata)))
15370 `(("r-knitr" ,r-knitr)))
15371 (home-page "https://github.com/r-spatial/spdep/")
15372 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15374 "This package provides a collection of functions to create spatial
15375 weights matrix objects from polygon contiguities, from point patterns by
15376 distance and tessellations, for summarizing these objects, and for permitting
15377 their use in spatial data analysis, including regional aggregation by minimum
15379 (license license:gpl2+)))
15381 (define-public r-adegenet
15383 (name "r-adegenet")
15388 (uri (cran-uri "adegenet" version))
15391 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15392 (build-system r-build-system)
15394 `(("r-ade4" ,r-ade4)
15397 ("r-dplyr" ,r-dplyr)
15398 ("r-ggplot2" ,r-ggplot2)
15399 ("r-igraph" ,r-igraph)
15401 ("r-reshape2" ,r-reshape2)
15402 ("r-seqinr" ,r-seqinr)
15403 ("r-shiny" ,r-shiny)
15404 ("r-spdep" ,r-spdep)
15405 ("r-vegan" ,r-vegan)))
15406 (home-page "https://github.com/thibautjombart/adegenet")
15407 (synopsis "Exploratory analysis of genetic and genomic data")
15409 "This package provides a toolset for the exploration of genetic and
15410 genomic data. Adegenet provides formal (S4) classes for storing and handling
15411 various genetic data, including genetic markers with varying ploidy and
15412 hierarchical population structure (@code{genind} class), alleles counts by
15413 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15414 also implements original multivariate methods (DAPC, sPCA), graphics,
15415 statistical tests, simulation tools, distance and similarity measures, and
15416 several spatial methods. A range of both empirical and simulated datasets is
15417 also provided to illustrate various methods.")
15418 (license license:gpl2+)))
15420 (define-public r-pegas
15427 (uri (cran-uri "pegas" version))
15429 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15430 (build-system r-build-system)
15432 `(("r-adegenet" ,r-adegenet)
15434 (home-page "http://ape-package.ird.fr/pegas.html")
15435 (synopsis "Population and evolutionary genetics analysis system")
15437 "This package provides functions for reading, writing, plotting,
15438 analysing, and manipulating allelic and haplotypic data, including from VCF
15439 files, and for the analysis of population nucleotide sequences and
15440 micro-satellites including coalescent analyses, linkage disequilibrium,
15441 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15442 minimum spanning tree and network, and median-joining networks.")
15443 (license license:gpl2+)))
15445 (define-public r-rmetasim
15447 (name "r-rmetasim")
15452 (uri (cran-uri "rmetasim" version))
15455 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15456 (build-system r-build-system)
15458 `(("r-ade4" ,r-ade4)
15459 ("r-adegenet" ,r-adegenet)
15460 ("r-gtools" ,r-gtools)
15461 ("r-pegas" ,r-pegas)))
15462 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15463 (synopsis "Individual-based population genetic simulation environment")
15465 "This package provides an interface between R and the metasim simulation
15466 engine. The simulation environment is documented in: Strand, A.(2002),
15467 Metasim 1.0: an individual-based environment for simulating population
15468 genetics of complex population dynamics.")
15470 (license license:gpl2+)))
15472 (define-public r-genetics
15474 (name "r-genetics")
15475 (version "1.3.8.1.3")
15479 (uri (cran-uri "genetics" version))
15482 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
15483 (build-system r-build-system)
15485 `(("r-combinat" ,r-combinat)
15486 ("r-gdata" ,r-gdata)
15487 ("r-gtools" ,r-gtools)
15489 ("r-mvtnorm" ,r-mvtnorm)))
15490 (home-page "https://cran.r-project.org/web/packages/genetics/")
15491 (synopsis "Population genetics")
15493 "This package provides classes and methods for handling genetic data.
15494 It includes classes to represent genotypes and haplotypes at single markers up
15495 to multiple markers on multiple chromosomes. Function include allele
15496 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15497 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15498 and testing for linkage disequilibrium, ...")
15499 ;; Any GPL version.
15500 (license license:gpl2+)))
15502 (define-public r-snp-plotter
15504 (name "r-snp-plotter")
15509 (uri (cran-uri "snp.plotter" version))
15512 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15513 (properties `((upstream-name . "snp.plotter")))
15514 (build-system r-build-system)
15515 (propagated-inputs `(("r-genetics" ,r-genetics)))
15516 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15517 (synopsis "Plot p-values using single SNP and/or haplotype data")
15519 "This package helps you create plots of p-values using single SNP and/or
15520 haplotype data. Main features of the package include options to display a
15521 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15522 datasets simultaneously. Plots can be created using global and/or individual
15523 haplotype p-values along with single SNP p-values. Images are created as
15524 either PDF/EPS files.")
15525 (license license:gpl2+)))
15527 (define-public r-polspline
15529 (name "r-polspline")
15534 (uri (cran-uri "polspline" version))
15536 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15537 (build-system r-build-system)
15538 (native-inputs `(("gfortran" ,gfortran)))
15539 (home-page "https://cran.r-project.org/web/packages/polspline/")
15540 (synopsis "Polynomial spline routines")
15542 "This package provides routines for the polynomial spline fitting
15543 routines hazard regression, hazard estimation with flexible tails, logspline,
15544 lspec, polyclass, and polymars.")
15545 (license license:gpl2+)))
15547 (define-public r-rms
15554 (uri (cran-uri "rms" version))
15556 (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h"))))
15557 (build-system r-build-system)
15559 `(("r-cluster" ,r-cluster)
15560 ("r-digest" ,r-digest)
15561 ("r-ggplot2" ,r-ggplot2)
15562 ("r-hmisc" ,r-hmisc)
15563 ("r-htmltable" ,r-htmltable)
15564 ("r-htmltools" ,r-htmltools)
15565 ("r-lattice" ,r-lattice)
15567 ("r-multcomp" ,r-multcomp)
15569 ("r-polspline" ,r-polspline)
15570 ("r-quantreg" ,r-quantreg)
15571 ("r-rpart" ,r-rpart)
15572 ("r-sparsem" ,r-sparsem)
15573 ("r-survival" ,r-survival)))
15574 (native-inputs `(("gfortran" ,gfortran)))
15575 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15576 (synopsis "Regression modeling strategies")
15578 "This is a package for regression modeling, testing, estimation,
15579 validation, graphics, prediction, and typesetting by storing enhanced model
15580 design attributes in the fit. The rms package is a collection of functions
15581 that assist with and streamline modeling. It also contains functions for
15582 binary and ordinal logistic regression models, ordinal models for continuous Y
15583 with a variety of distribution families, and the Buckley-James multiple
15584 regression model for right-censored responses, and implements penalized
15585 maximum likelihood estimation for logistic and ordinary linear models. The
15586 package works with almost any regression model, but it was especially written
15587 to work with binary or ordinal regression models, Cox regression, accelerated
15588 failure time models, ordinary linear models, the Buckley-James model,
15589 generalized least squares for serially or spatially correlated observations,
15590 generalized linear models, and quantile regression.")
15591 (license license:gpl2+)))
15593 (define-public r-arsenal
15600 (uri (cran-uri "arsenal" version))
15603 "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn"))))
15604 (properties `((upstream-name . "arsenal")))
15605 (build-system r-build-system)
15606 (propagated-inputs `(("r-knitr" ,r-knitr)))
15607 (native-inputs `(("r-knitr" ,r-knitr)))
15608 (home-page "https://github.com/mayoverse/arsenal")
15609 (synopsis "Functions for large-scale statistical summaries")
15611 "This package provides an arsenal of R functions for large-scale
15612 statistical summaries, which are streamlined to work within the latest
15613 reporting tools in R and RStudio and which use formulas and versatile
15614 summary statistics for summary tables and models. The primary functions
15618 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15619 levels of one or more categorical variables;
15620 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15621 across two time points;
15622 @item @code{modelsum}, which performs simple model fits on one or more
15623 endpoints for many variables (univariate or adjusted for covariates);
15624 @item @code{freqlist}, a powerful frequency table across many categorical
15626 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15627 @item @code{write2}, a function to output tables to a document.
15630 (license license:gpl2+)))
15632 (define-public r-haplo-stats
15634 (name "r-haplo-stats")
15639 (uri (cran-uri "haplo.stats" version))
15642 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15643 (properties `((upstream-name . "haplo.stats")))
15644 (build-system r-build-system)
15646 `(("r-arsenal" ,r-arsenal)
15649 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15650 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15651 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15653 "This package provides routines for the analysis of indirectly measured
15654 haplotypes. The statistical methods assume that all subjects are unrelated
15655 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15656 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15657 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15658 examples in the vignette.")
15659 (license license:gpl2+)))
15661 (define-public r-bqtl
15668 (uri (cran-uri "bqtl" version))
15671 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15672 (build-system r-build-system)
15673 (native-inputs `(("gfortran" ,gfortran)))
15674 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15675 (synopsis "Bayesian QTL mapping toolkit")
15677 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15678 lines. It includes maximum likelihood and Bayesian tools.")
15679 (license license:gpl2+)))
15681 (define-public r-ibdreg
15688 (uri (cran-uri "ibdreg" version))
15691 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15692 (build-system r-build-system)
15693 (home-page "https://www.mayo.edu/research/labs/\
15694 statistical-genetics-genetic-epidemiology/software")
15695 (synopsis "Regression methods for IBD linkage with covariates")
15697 "This package provides a method to test genetic linkage with covariates
15698 by regression methods with response IBD sharing for relative pairs. Account
15699 for correlations of IBD statistics and covariates for relative pairs within
15700 the same pedigree.")
15701 (license license:gpl2+)))
15703 (define-public r-dlmap
15710 (uri (cran-uri "dlmap" version))
15713 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15714 (build-system r-build-system)
15716 `(("r-ibdreg" ,r-ibdreg)
15720 ("r-wgaim" ,r-wgaim)))
15721 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15722 (synopsis "Detection localization mapping for QTL")
15724 "This is package for QTL mapping in a mixed model framework with separate
15725 detection and localization stages. The first stage detects the number of QTL
15726 on each chromosome based on the genetic variation due to grouped markers on
15727 the chromosome; the second stage uses this information to determine the most
15728 likely QTL positions. The mixed model can accommodate general fixed and
15729 random effects, including spatial effects in field trials and pedigree
15730 effects. It is applicable to backcrosses, doubled haploids, recombinant
15731 inbred lines, F2 intercrosses, and association mapping populations.")
15732 (license license:gpl2)))
15734 (define-public r-hwde
15741 (uri (cran-uri "hwde" version))
15744 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15745 (build-system r-build-system)
15746 (home-page "https://cran.r-project.org/web/packages/hwde/")
15747 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15749 "This package fits models for genotypic disequilibria, as described in
15750 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15751 terms are available that account for first order interactions between loci.
15752 It also implements, for a single locus in a single population, a conditional
15753 exact test for Hardy-Weinberg equilibrium.")
15754 (license license:gpl2+)))
15756 (define-public r-tdthap
15763 (uri (cran-uri "tdthap" version))
15766 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15767 (build-system r-build-system)
15768 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15769 (synopsis "TDT tests for extended haplotypes")
15771 "Functions and examples are provided for transmission/disequilibrium
15772 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15773 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15774 (license license:artistic2.0)))
15776 (define-public r-sparql
15782 (uri (cran-uri "SPARQL" version))
15785 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15786 (properties `((upstream-name . "SPARQL")))
15787 (build-system r-build-system)
15789 `(("r-rcurl" ,r-rcurl)
15791 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15792 (synopsis "SPARQL client for R")
15793 (description "This package provides an interface to use SPARQL to pose
15794 SELECT or UPDATE queries to an end-point.")
15795 ;; The only license indication is found in the DESCRIPTION file,
15796 ;; which states GPL-3. So we cannot assume GPLv3+.
15797 (license license:gpl3)))
15799 (define-public r-bookdown
15801 (name "r-bookdown")
15805 (uri (cran-uri "bookdown" version))
15808 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15809 (build-system r-build-system)
15811 `(("r-htmltools" ,r-htmltools)
15812 ("r-knitr" ,r-knitr)
15813 ("r-rmarkdown" ,r-rmarkdown)
15814 ("r-tinytex" ,r-tinytex)
15817 ("pandoc" ,pandoc)))
15818 (home-page "https://github.com/rstudio/bookdown")
15819 (synopsis "Authoring books and technical documents with R markdown")
15820 (description "This package provides output formats and utilities for
15821 authoring books and technical documents with R Markdown.")
15822 (license license:gpl3)))
15824 (define-public r-optparse
15826 (name "r-optparse")
15831 (uri (cran-uri "optparse" version))
15834 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15835 (build-system r-build-system)
15837 `(("r-getopt" ,r-getopt)))
15839 `(("r-knitr" ,r-knitr)))
15840 (home-page "https://github.com/trevorld/optparse")
15841 (synopsis "Command line option parser")
15843 "This package provides a command line parser inspired by Python's
15844 @code{optparse} library to be used with Rscript to write shebang scripts
15845 that accept short and long options.")
15846 (license license:gpl2+)))
15848 (define-public r-kernlab
15855 (uri (cran-uri "kernlab" version))
15857 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15858 (build-system r-build-system)
15859 (home-page "https://cran.r-project.org/web/packages/kernlab")
15860 (synopsis "Kernel-based machine learning tools")
15862 "This package provides kernel-based machine learning methods for
15863 classification, regression, clustering, novelty detection, quantile regression
15864 and dimensionality reduction. Among other methods @code{kernlab} includes
15865 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15867 (license license:gpl2)))
15869 (define-public r-hierfstat
15871 (name "r-hierfstat")
15876 (uri (cran-uri "hierfstat" version))
15879 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15880 (build-system r-build-system)
15882 `(("r-ade4" ,r-ade4)
15883 ("r-adegenet" ,r-adegenet)
15884 ("r-gaston" ,r-gaston)
15885 ("r-gtools" ,r-gtools)))
15887 `(("r-knitr" ,r-knitr)))
15888 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15889 (synopsis "Estimation and tests of hierarchical F-statistics")
15891 "This package allows the estimation of hierarchical F-statistics from
15892 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15893 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15894 are also given to test via randomisations the significance of each F and
15895 variance components, using the likelihood-ratio statistics G.")
15896 (license license:gpl2+)))
15898 (define-public r-hapassoc
15900 (name "r-hapassoc")
15905 (uri (cran-uri "hapassoc" version))
15908 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15909 (build-system r-build-system)
15910 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15911 (synopsis "Inference of trait associations with SNP haplotypes")
15913 "Hapassoc performs likelihood inference of trait associations with
15914 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15915 functions are developed primarily for data collected in cohort or
15916 cross-sectional studies. They can accommodate uncertain haplotype phase and
15917 handle missing genotypes at some SNPs.")
15918 (license license:gpl2)))
15920 (define-public r-sampling
15922 (name "r-sampling")
15927 (uri (cran-uri "sampling" version))
15930 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15931 (build-system r-build-system)
15933 `(("r-lpsolve" ,r-lpsolve)
15934 ("r-mass" ,r-mass)))
15935 (home-page "https://cran.r-project.org/web/packages/sampling/")
15936 (synopsis "Survey sampling")
15938 "This package provides functions for drawing and calibrating samples.")
15939 (license license:gpl2+)))
15941 (define-public r-r2html
15948 (uri (cran-uri "R2HTML" version))
15951 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15952 (properties `((upstream-name . "R2HTML")))
15953 (build-system r-build-system)
15954 (home-page "https://github.com/nalimilan/R2HTML")
15955 (synopsis "HTML export for R objects")
15957 "This package includes HTML functions and methods to write in an HTML
15958 file. Thus, making HTML reports is easy. It includes a function that allows
15959 redirection on the fly, which appears to be very useful for teaching purposes,
15960 as the student can keep a copy of the produced output to keep all that they
15961 did during the course. The package comes with a vignette describing how to
15962 write HTML reports for statistical analysis. Finally, a driver for Sweave
15963 parses HTML flat files containing R code and to automatically write
15964 the corresponding outputs (tables and graphs).")
15965 (license license:gpl2+)))
15967 (define-public r-rjava
15974 (uri (cran-uri "rJava" version))
15977 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15978 (properties `((upstream-name . "rJava")))
15979 (build-system r-build-system)
15981 `(#:modules ((guix build utils)
15982 (guix build r-build-system)
15985 (modify-phases %standard-phases
15986 (add-after 'unpack 'set-JAVA_HOME
15987 (lambda* (#:key inputs #:allow-other-keys)
15988 (let ((jdk (assoc-ref inputs "jdk")))
15989 (setenv "JAVA_HOME" jdk)
15990 (setenv "JAVA" (which "java"))
15991 (setenv "JAR" (which "jar"))
15992 (setenv "JAVAC" (which "javac"))
15993 (setenv "JAVAH" (which "javah"))
15994 (setenv "JAVA_CPPFLAGS"
15995 (string-append "-I" jdk "/include "
15996 "-I" jdk "/include/linux"))
15997 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15998 ((lib) (setenv "JAVA_LIBS" lib))
15999 (_ (error "Could not find libjvm.so"))))
16003 ("jdk" ,icedtea-8 "jdk")
16006 (home-page "https://www.rforge.net/rJava/")
16007 (synopsis "Low-Level R to Java interface")
16009 "This package provides a low-level interface to the Java VM very much
16010 like .C/.Call and friends. It allows the creation of objects, calling methods
16011 and accessing fields.")
16012 (license license:gpl2)))
16014 (define-public r-svmisc
16021 (uri (cran-uri "svMisc" version))
16024 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
16025 (properties `((upstream-name . "svMisc")))
16026 (build-system r-build-system)
16027 (home-page "https://github.com/SciViews/svMisc")
16028 (synopsis "Miscellaneous functions for SciViews")
16030 "This package provides miscellaneous functions for SciViews or general
16031 use, including tools to manage a temporary environment attached to the search
16032 path for temporary variables you do not want to @code{save()} or
16033 @code{load()}; test the current platform; showing progress bars, etc.")
16034 (license license:gpl2)))
16036 (define-public r-xyz
16043 (uri (cran-uri "xyz" version))
16046 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16047 (build-system r-build-system)
16049 `(("r-rcpp" ,r-rcpp)))
16050 (home-page "https://cran.r-project.org/web/packages/xyz/")
16051 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16053 "High dimensional interaction search by brute force requires a quadratic
16054 computational cost in the number of variables. The xyz algorithm provably
16055 finds strong interactions in almost linear time. For details of the algorithm
16056 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16057 interaction search in high-dimensional data.")
16058 ;; Any version of the GPL.
16059 (license license:gpl2+)))
16061 (define-public r-rttf2pt1
16063 (name "r-rttf2pt1")
16068 (uri (cran-uri "Rttf2pt1" version))
16071 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16072 (properties `((upstream-name . "Rttf2pt1")))
16073 (build-system r-build-system)
16074 (home-page "https://github.com/wch/Rttf2pt1")
16075 (synopsis "Font conversion utility")
16077 "This package contains the program @code{ttf2pt1}, for use with the
16078 @code{extrafont} package.")
16079 ;; Most of the files are covered under the Expat license. Some files are
16080 ;; covered under BSD-3. Deviations for individual files are recorded in
16081 ;; the LICENSE file.
16082 (license (list license:bsd-3 license:expat
16083 (license:non-copyleft "file://LICENSE")))))
16085 (define-public r-extrafontdb
16087 (name "r-extrafontdb")
16092 (uri (cran-uri "extrafontdb" version))
16095 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16096 (build-system r-build-system)
16097 (home-page "https://github.com/wch/extrafontdb")
16098 (synopsis "Database for the extrafont package")
16100 "This package holds the database for the @code{extrafont} package.")
16101 (license license:gpl2)))
16103 (define-public r-extrafont
16105 (name "r-extrafont")
16110 (uri (cran-uri "extrafont" version))
16113 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16114 (build-system r-build-system)
16116 `(("r-extrafontdb" ,r-extrafontdb)
16117 ("r-rttf2pt1" ,r-rttf2pt1)))
16118 (home-page "https://github.com/wch/extrafont")
16119 (synopsis "Tools for using fonts in R")
16121 "The extrafont package makes it easier to use fonts other than the basic
16122 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16123 used with PDF or PostScript output files. There are two hurdles for using
16124 fonts in PDF (or Postscript) output files:
16127 @item Making R aware of the font and the dimensions of the characters.
16128 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16129 properly on a device that doesn't have the font. This is usually needed if
16130 you want to print the PDF file or share it with others.
16133 The extrafont package makes both of these things easier.")
16134 (license license:gpl2)))
16136 (define-public r-xkcd
16143 (uri (cran-uri "xkcd" version))
16146 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16147 (build-system r-build-system)
16149 `(("r-extrafont" ,r-extrafont)
16150 ("r-ggplot2" ,r-ggplot2)
16151 ("r-hmisc" ,r-hmisc)))
16152 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16153 (synopsis "Plot ggplot2 graphics in the XKCD style")
16155 "This package provides the means to plot ggplot2 graphs in the style of
16156 the XKCD web comic.")
16157 (license license:gpl3)))
16159 (define-public r-msigdbr
16166 (uri (cran-uri "msigdbr" version))
16169 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16170 (build-system r-build-system)
16172 `(("r-dplyr" ,r-dplyr)
16173 ("r-magrittr" ,r-magrittr)
16174 ("r-rlang" ,r-rlang)
16175 ("r-tibble" ,r-tibble)
16176 ("r-tidyselect" ,r-tidyselect)))
16178 `(("r-knitr" ,r-knitr)))
16179 (home-page "https://github.com/igordot/msigdbr")
16180 (synopsis "MSigDB gene sets for multiple organisms")
16182 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16183 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16184 software in a standard R data frame with key-value pairs. Included are the
16185 original human gene symbols and Entrez IDs as well as the equivalents for
16186 various frequently studied model organisms such as mouse, rat, pig, fly, and
16188 ;; The package is covered under the Expat license, but the upstream MSigDB
16189 ;; files are made available under the Creative Commons Attribution 4.0
16190 ;; International license.
16191 (license (list license:expat license:cc-by4.0))))
16193 (define-public r-gridgraphics
16195 (name "r-gridgraphics")
16200 (uri (cran-uri "gridGraphics" version))
16203 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16204 (properties `((upstream-name . "gridGraphics")))
16205 (build-system r-build-system)
16206 (home-page "https://github.com/pmur002/gridgraphics")
16207 (synopsis "Redraw base graphics using @code{grid} graphics")
16209 "This package provides functions to convert a page of plots drawn with
16210 the @code{graphics} package into identical output drawn with the @code{grid}
16211 package. The result looks like the original @code{graphics}-based plot, but
16212 consists of @code{grid} grobs and viewports that can then be manipulated with
16213 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16214 (license license:gpl2+)))
16216 (define-public r-farver
16223 (uri (cran-uri "farver" version))
16226 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
16227 (build-system r-build-system)
16228 (home-page "https://github.com/thomasp85/farver")
16229 (synopsis "Vectorized color conversion and comparison")
16231 "The encoding of color can be handled in many different ways, using
16232 different color spaces. As different color spaces have different uses,
16233 efficient conversion between these representations are important. This
16234 package provides a set of functions that gives access to very fast color space
16235 conversion and comparisons implemented in C++, and offers 100-fold speed
16236 improvements over the @code{convertColor} function in the @code{grDevices}
16238 (license license:expat)))
16240 (define-public r-ggplotify
16242 (name "r-ggplotify")
16247 (uri (cran-uri "ggplotify" version))
16250 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16251 (build-system r-build-system)
16253 `(("r-ggplot2" ,r-ggplot2)
16254 ("r-gridgraphics" ,r-gridgraphics)
16255 ("r-rvcheck" ,r-rvcheck)))
16257 `(("r-knitr" ,r-knitr)))
16258 (home-page "https://github.com/GuangchuangYu/ggplotify")
16259 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16261 "This package provides tools to convert plot function calls (using
16262 expression or formula) to @code{grob} or @code{ggplot} objects that are
16263 compatible with the @code{grid} and @code{ggplot2} environment. With this
16264 package, we are able to e.g. use @code{cowplot} to align plots produced by
16265 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16266 converting them to @code{ggplot} objects.")
16267 (license license:artistic2.0)))
16269 (define-public r-triebeard
16271 (name "r-triebeard")
16276 (uri (cran-uri "triebeard" version))
16279 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16280 (build-system r-build-system)
16281 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16282 (home-page "https://github.com/Ironholds/triebeard/")
16283 (synopsis "Radix trees in Rcpp")
16285 "Radix trees, or tries, are key-value data structures optimized for
16286 efficient lookups, similar in purpose to hash tables. This package provides
16287 an implementation of radix trees for use in R programming and in developing
16288 packages with Rcpp.")
16289 (license license:expat)))
16291 (define-public r-tweenr
16298 (uri (cran-uri "tweenr" version))
16301 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
16302 (build-system r-build-system)
16304 `(("r-farver" ,r-farver)
16305 ("r-magrittr" ,r-magrittr)
16307 ("r-rlang" ,r-rlang)))
16308 (home-page "https://github.com/thomasp85/tweenr")
16309 (synopsis "Interpolate data for smooth animations")
16311 "In order to create smooth animation between states of data, tweening is
16312 necessary. This package provides a range of functions for creating tweened
16313 data that can be used as basis for animation. Furthermore it adds a number of
16314 vectorized interpolaters for common R data types such as numeric, date and
16316 (license license:expat)))
16318 (define-public r-polyclip
16320 (name "r-polyclip")
16325 (uri (cran-uri "polyclip" version))
16328 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16329 (build-system r-build-system)
16330 (native-inputs `(("pkg-config" ,pkg-config)))
16331 (home-page "http://www.angusj.com/delphi/clipper.php")
16332 (synopsis "Polygon clipping")
16334 "This package provides an R port of the library Clipper. It performs
16335 polygon clipping operations (intersection, union, set minus, set difference)
16336 for polygonal regions of arbitrary complexity, including holes. It computes
16337 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16338 dilations) for polygonal regions and polygonal lines. It computes the
16339 Minkowski Sum of general polygons. There is a function for removing
16340 self-intersections from polygon data.")
16341 (license license:boost1.0)))
16343 (define-public r-urltools
16345 (name "r-urltools")
16350 (uri (cran-uri "urltools" version))
16353 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16354 (build-system r-build-system)
16356 `(("r-rcpp" ,r-rcpp)
16357 ("r-triebeard" ,r-triebeard)))
16358 (home-page "https://github.com/Ironholds/urltools/")
16359 (synopsis "Vectorized tools for URL handling and parsing")
16361 "This package provides a toolkit for all URL-handling needs, including
16362 encoding and decoding, parsing, parameter extraction and modification. All
16363 functions are designed to be both fast and entirely vectorized. It is
16364 intended to be useful for people dealing with web-related datasets, such as
16365 server-side logs, although may be useful for other situations involving large
16367 (license license:expat)))
16369 (define-public r-ggforce
16376 (uri (cran-uri "ggforce" version))
16379 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
16380 (build-system r-build-system)
16382 `(("r-ggplot2" ,r-ggplot2)
16383 ("r-gtable" ,r-gtable)
16385 ("r-polyclip" ,r-polyclip)
16387 ("r-rcppeigen" ,r-rcppeigen)
16388 ("r-rlang" ,r-rlang)
16389 ("r-scales" ,r-scales)
16390 ("r-tidyselect" ,r-tidyselect)
16391 ("r-tweenr" ,r-tweenr)
16392 ("r-withr" ,r-withr)))
16393 (home-page "https://ggforce.data-imaginist.com")
16394 (synopsis "Accelerating ggplot2")
16396 "The aim of the ggplot2 package is to aid in visual data investigations.
16397 This focus has led to a lack of facilities for composing specialized plots.
16398 This package aims to be a collection of mainly new statistics and geometries
16399 that fills this gap.")
16400 (license license:expat)))
16402 (define-public r-europepmc
16404 (name "r-europepmc")
16409 (uri (cran-uri "europepmc" version))
16412 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16413 (build-system r-build-system)
16415 `(("r-dplyr" ,r-dplyr)
16417 ("r-jsonlite" ,r-jsonlite)
16419 ("r-progress" ,r-progress)
16420 ("r-purrr" ,r-purrr)
16421 ("r-rlang" ,r-rlang)
16422 ("r-tibble" ,r-tibble)
16423 ("r-tidyr" ,r-tidyr)
16424 ("r-urltools" ,r-urltools)
16425 ("r-xml2" ,r-xml2)))
16427 `(("r-knitr" ,r-knitr)))
16428 (home-page "https://github.com/ropensci/europepmc/")
16429 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16431 "This package provides an R Client for the
16432 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16433 Service}. It gives access to both metadata on life science literature and
16434 open access full texts. Europe PMC indexes all PubMed content and other
16435 literature sources including Agricola, a bibliographic database of citations
16436 to the agricultural literature, or Biological Patents. In addition to
16437 bibliographic metadata, the client allows users to fetch citations and
16438 reference lists. Links between life-science literature and other EBI
16439 databases, including ENA, PDB or ChEMBL are also accessible.")
16440 (license license:gpl3)))
16442 (define-public r-ggraph
16449 (uri (cran-uri "ggraph" version))
16452 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
16453 (build-system r-build-system)
16455 `(("r-digest" ,r-digest)
16456 ("r-dplyr" ,r-dplyr)
16457 ("r-ggforce" ,r-ggforce)
16458 ("r-ggplot2" ,r-ggplot2)
16459 ("r-ggrepel" ,r-ggrepel)
16460 ("r-graphlayouts" ,r-graphlayouts)
16461 ("r-gtable" ,r-gtable)
16462 ("r-igraph" ,r-igraph)
16465 ("r-rlang" ,r-rlang)
16466 ("r-scales" ,r-scales)
16467 ("r-tidygraph" ,r-tidygraph)
16468 ("r-viridis" ,r-viridis)
16469 ("r-withr" ,r-withr)))
16471 `(("r-knitr" ,r-knitr)))
16472 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16473 (synopsis "Implementation of grammar of graphics for graphs and networks")
16475 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16476 graph and network visualizations due to its reliance on tabular data input.
16477 The ggraph package is an extension of the ggplot2 API tailored to graph
16478 visualizations and provides the same flexible approach to building up plots
16480 (license license:gpl3)))
16482 (define-public r-gkmsvm
16489 (uri (cran-uri "gkmSVM" version))
16492 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
16493 (properties `((upstream-name . "gkmSVM")))
16494 (build-system r-build-system)
16496 `(("r-kernlab" ,r-kernlab)
16499 ("r-seqinr" ,r-seqinr)))
16500 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
16501 (synopsis "Gapped-kmer support vector machine")
16503 "This R package provides tools for training gapped-kmer SVM classifiers
16504 for DNA and protein sequences. This package supports several sequence
16505 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
16506 (license license:gpl2+)))
16508 (define-public r-varselrf
16510 (name "r-varselrf")
16515 (uri (cran-uri "varSelRF" version))
16518 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16519 (properties `((upstream-name . "varSelRF")))
16520 (build-system r-build-system)
16522 `(("r-randomforest" ,r-randomforest)))
16523 (home-page "https://www.ligarto.org/rdiaz/software/software")
16524 (synopsis "Variable selection using random forests")
16526 "This package provides tools for the variable selection from random
16527 forests using both backwards variable elimination (for the selection of small
16528 sets of non-redundant variables) and selection based on the importance
16529 spectrum (somewhat similar to scree plots; for the selection of large,
16530 potentially highly-correlated variables). The main applications are in
16531 high-dimensional data (e.g., microarray data, and other genomics and
16532 proteomics applications).")
16533 (license license:gpl2+)))
16535 (define-public r-pamr
16542 (uri (cran-uri "pamr" version))
16545 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16546 (build-system r-build-system)
16548 `(("r-cluster" ,r-cluster)
16549 ("r-survival" ,r-survival)))
16550 (native-inputs `(("gfortran" ,gfortran)))
16551 (home-page "https://cran.r-project.org/web/packages/pamr/")
16552 (synopsis "Prediction Analysis for Microarrays")
16554 "This package provides some functions for sample classification in
16556 (license license:gpl2)))
16558 (define-public r-rda
16561 (version "1.0.2-2.1")
16565 (uri (cran-uri "rda" version))
16568 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16569 (build-system r-build-system)
16570 (home-page "https://cran.r-project.org/web/packages/rda/")
16571 (synopsis "Shrunken centroids regularized discriminant analysis")
16573 "This package provides tools for shrunken centroids regularized
16574 discriminant analysis for the purpose of classifying high dimensional data.")
16575 (license license:gpl2+)))
16577 (define-public r-ggvis
16584 (uri (cran-uri "ggvis" version))
16587 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16588 (build-system r-build-system)
16590 `(("r-assertthat" ,r-assertthat)
16591 ("r-dplyr" ,r-dplyr)
16592 ("r-htmltools" ,r-htmltools)
16593 ("r-jsonlite" ,r-jsonlite)
16594 ("r-magrittr" ,r-magrittr)
16595 ("r-rlang" ,r-rlang)
16596 ("r-shiny" ,r-shiny)))
16597 (home-page "https://ggvis.rstudio.com/")
16598 (synopsis "Interactive grammar of graphics")
16600 "This package is a data visualization package for R providing an
16601 implementation of an interactive grammar of graphics, taking the best parts of
16602 ggplot2, combining them with the reactive framework of Shiny and drawing web
16603 graphics using Vega.")
16604 (license license:gpl2)))
16606 (define-public r-gbm
16613 (uri (cran-uri "gbm" version))
16616 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16617 (build-system r-build-system)
16619 `(("r-lattice" ,r-lattice)
16620 ("r-survival" ,r-survival)))
16622 `(("r-knitr" ,r-knitr)))
16623 (home-page "https://github.com/gbm-developers/gbm")
16624 (synopsis "Generalized boosted regression models")
16626 "This package is an implementation of extensions to Freund and Schapire's
16627 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16628 regression methods for least squares, absolute loss, t-distribution loss,
16629 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16630 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16631 and Learning to Rank measures (LambdaMart).")
16632 (license license:gpl2+)))
16634 (define-public r-threejs
16641 (uri (cran-uri "threejs" version))
16644 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16645 (build-system r-build-system)
16647 `(#:modules ((guix build utils)
16648 (guix build r-build-system)
16652 (modify-phases %standard-phases
16653 (add-after 'unpack 'process-javascript
16654 (lambda* (#:key inputs #:allow-other-keys)
16655 (with-directory-excursion "inst"
16659 `((,(assoc-ref inputs "js-jquery")
16660 "htmlwidgets/lib/jquery/jquery.min.js")
16661 (,(assoc-ref inputs "js-threejs-111")
16662 "htmlwidgets/lib/threejs-111/three.min.js"))))
16663 (lambda (sources targets)
16664 (for-each (lambda (source target)
16665 (format #t "Processing ~a --> ~a~%"
16667 (delete-file target)
16668 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16669 (call-with-output-file target
16671 (dump-port minified port)))))
16672 sources targets))))
16675 `(("r-base64enc" ,r-base64enc)
16676 ("r-crosstalk" ,r-crosstalk)
16677 ("r-htmlwidgets" ,r-htmlwidgets)
16678 ("r-igraph" ,r-igraph)))
16680 `(("uglify-js" ,uglify-js)
16684 (uri "https://code.jquery.com/jquery-1.12.4.js")
16687 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16691 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16694 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16695 (home-page "https://bwlewis.github.io/rthreejs")
16696 (synopsis "Interactive 3D scatter plots, networks and globes")
16698 "Create interactive 3D scatter plots, network plots, and globes in R
16699 using the three.js visualization library.")
16700 (license license:expat)))
16702 (define-public r-mlbench
16709 (uri (cran-uri "mlbench" version))
16712 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16713 (build-system r-build-system)
16714 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16715 (synopsis "Machine learning benchmark problems")
16717 "This package provides a collection of artificial and real-world machine
16718 learning benchmark problems, including, e.g., several data sets from the UCI
16720 (license license:gpl2)))
16722 (define-public r-mpm
16729 (uri (cran-uri "mpm" version))
16732 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16733 (build-system r-build-system)
16735 `(("r-kernsmooth" ,r-kernsmooth)
16736 ("r-mass" ,r-mass)))
16737 (home-page "http://mpm.r-forge.r-project.org")
16738 (synopsis "Multivariate projection methods")
16740 "This is a package for exploratory graphical analysis of multivariate
16741 data, specifically gene expression data with different projection methods:
16742 principal component analysis, correspondence analysis, spectral map
16744 (license license:gpl2+)))
16746 (define-public r-png
16752 (uri (cran-uri "png" version))
16755 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16756 (build-system r-build-system)
16758 `(("libpng" ,libpng)
16760 (home-page "https://www.rforge.net/png/")
16761 (synopsis "Read and write PNG images")
16763 "This package provides an easy and simple way to read, write and display
16764 bitmap images stored in the PNG format. It can read and write both files and
16765 in-memory raw vectors.")
16766 ;; Any of these GPL versions.
16767 (license (list license:gpl2 license:gpl3))))
16769 (define-public r-ggcorrplot
16771 (name "r-ggcorrplot")
16776 (uri (cran-uri "ggcorrplot" version))
16779 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16780 (build-system r-build-system)
16782 `(("r-ggplot2" ,r-ggplot2)
16783 ("r-reshape2" ,r-reshape2)))
16784 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16785 (synopsis "Visualization of a correlation matrix using ggplot2")
16787 "The ggcorrplot package can be used to visualize easily a correlation
16788 matrix using ggplot2. It provides a solution for reordering the correlation
16789 matrix and displays the significance level on the plot. It also includes a
16790 function for computing a matrix of correlation p-values.")
16791 (license license:gpl2)))
16793 (define-public r-gridtext
16795 (name "r-gridtext")
16800 (uri (cran-uri "gridtext" version))
16803 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16804 (properties `((upstream-name . "gridtext")))
16805 (build-system r-build-system)
16807 `(("r-jpeg" ,r-jpeg)
16808 ("r-markdown" ,r-markdown)
16811 ("r-rcurl" ,r-rcurl)
16812 ("r-rlang" ,r-rlang)
16813 ("r-stringr" ,r-stringr)
16814 ("r-xml2" ,r-xml2)))
16815 (home-page "https://wilkelab.org/gridtext/")
16816 (synopsis "Improved text rendering support for Grid graphics")
16818 "This package provides support for rendering of formatted text using Grid
16819 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16820 inline CSS directives, and it can be rendered both with and without word
16822 (license license:expat)))
16824 (define-public r-ggtext
16831 (uri (cran-uri "ggtext" version))
16834 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16835 (properties `((upstream-name . "ggtext")))
16836 (build-system r-build-system)
16838 `(("r-ggplot2" ,r-ggplot2)
16839 ("r-gridtext" ,r-gridtext)
16840 ("r-rlang" ,r-rlang)
16841 ("r-scales" ,r-scales)))
16842 (native-inputs `(("r-knitr" ,r-knitr)))
16843 (home-page "https://wilkelab.org/ggtext/")
16844 (synopsis "Improved text rendering support for ggplot2")
16846 "This package provides a ggplot2 extension that enables the rendering of
16847 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16848 etc.). Text boxes with automatic word wrap are also supported.")
16849 (license license:gpl2)))
16851 ;; This package includes minified JavaScript files. When upgrading please
16852 ;; check that there are no new minified JavaScript files.
16853 (define-public r-flexdashboard
16855 (name "r-flexdashboard")
16860 (uri (cran-uri "flexdashboard" version))
16863 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16864 (modules '((guix build utils)))
16867 ;; Delete bundled minified JavaScript files
16868 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16869 (delete-file "inst/www/sly/sly.min.js")
16870 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16871 (delete-file "inst/www/prism/prism.js")
16873 (build-system r-build-system)
16875 `(#:modules ((guix build utils)
16876 (guix build r-build-system)
16880 (ice-9 textual-ports))
16882 (modify-phases %standard-phases
16883 (add-after 'unpack 'process-javascript
16884 (lambda* (#:key inputs #:allow-other-keys)
16885 (with-directory-excursion "inst"
16886 ;; Concatenate all components of prism.js
16887 (let ((contents (string-join
16888 (map (lambda (name)
16889 (call-with-input-file
16890 (assoc-ref inputs name)
16894 "js-prism-line-numbers"))
16896 (call-with-output-file "prism-src.js"
16897 (cut display contents <>)))
16901 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16902 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16904 "www/sly/sly.min.js")
16906 "www/prism/prism.js")
16907 (,(assoc-ref inputs "js-raphael")
16908 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16909 (,(assoc-ref inputs "js-featherlight")
16910 "www/featherlight/featherlight.min.js"))))
16911 (lambda (sources targets)
16912 (for-each (lambda (source target)
16913 (format #t "Processing ~a --> ~a~%"
16915 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16916 (call-with-output-file target
16918 (dump-port minified port)))))
16919 sources targets))))
16922 `(("r-htmltools" ,r-htmltools)
16923 ("r-htmlwidgets" ,r-htmlwidgets)
16924 ("r-jsonlite" ,r-jsonlite)
16925 ("r-knitr" ,r-knitr)
16926 ("r-rmarkdown" ,r-rmarkdown)
16927 ("r-shiny" ,r-shiny)))
16929 `(("uglify-js" ,uglify-js)
16933 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16936 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16940 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16943 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16947 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16950 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16951 ("js-prism-line-numbers"
16954 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16957 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16961 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16964 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16965 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16966 (synopsis "R Markdown format for flexible dashboards")
16968 "This package provides an R Markdown format for converting an R Markdown
16969 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16970 of its components to the containing web page.")
16971 (license license:expat)))
16973 (define-public r-preseqr
16980 (uri (cran-uri "preseqR" version))
16983 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16984 (properties `((upstream-name . "preseqR")))
16985 (build-system r-build-system)
16987 `(("r-polynom" ,r-polynom)))
16988 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16989 (synopsis "Predicting species accumulation curves")
16991 "This package can be used to predict the r-species accumulation
16992 curve (r-SAC), which is the number of species represented at least r times as
16993 a function of the sampling effort. When r = 1, the curve is known as the
16994 species accumulation curve, or the library complexity curve in high-throughput
16995 genomic sequencing. The package includes both parametric and nonparametric
16996 methods, as described by Deng C, et al. (2018).")
16997 (license license:gpl3)))
16999 (define-public r-mapplots
17001 (name "r-mapplots")
17006 (uri (cran-uri "mapplots" version))
17009 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
17010 (build-system r-build-system)
17011 (home-page "https://cran.r-project.org/web/packages/mapplots/")
17012 (synopsis "Data visualization on maps")
17014 "This package helps you create simple maps; add sub-plots like pie plots
17015 to a map or any other plot; format, plot and export gridded data. The package
17016 was developed for displaying fisheries data but most functions can be used for
17017 more generic data visualisation.")
17018 (license license:gpl2+)))
17020 (define-public r-pmcmr
17027 (uri (cran-uri "PMCMR" version))
17030 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
17031 (properties `((upstream-name . "PMCMR")))
17032 (build-system r-build-system)
17033 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
17034 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
17036 "This is a deprecated package for calculating pairwise multiple
17037 comparisons of mean rank sums. This package is superseded by the novel
17038 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
17039 compatibility of dependent packages for some time.")
17040 (license license:gpl3+)))
17042 (define-public r-downloader
17044 (name "r-downloader")
17049 (uri (cran-uri "downloader" version))
17052 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17053 (build-system r-build-system)
17055 `(("r-digest" ,r-digest)))
17056 (home-page "https://github.com/wch/downloader")
17057 (synopsis "Download files over HTTP and HTTPS")
17059 "This package provides a wrapper for the @code{download.file} function,
17060 making it possible to download files over HTTPS across platforms. The
17061 @code{RCurl} package provides this functionality (and much more) but has
17062 external dependencies. This package has is implemented purely in R.")
17063 (license license:gpl2)))
17065 (define-public r-rex
17072 (uri (cran-uri "rex" version))
17075 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17076 (build-system r-build-system)
17078 `(("r-lazyeval" ,r-lazyeval)))
17080 `(("r-knitr" ,r-knitr)))
17081 (home-page "https://github.com/kevinushey/rex")
17082 (synopsis "Friendly regular expressions")
17084 "This package provides a friendly interface for the construction of
17085 regular expressions. Regular expressions are a very powerful feature, however
17086 they are often difficult to interpret. Rex allows you to build complex
17087 regular expressions from human readable expressions")
17088 (license license:expat)))
17090 (define-public r-xmlparsedata
17092 (name "r-xmlparsedata")
17097 (uri (cran-uri "xmlparsedata" version))
17100 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
17101 (properties `((upstream-name . "xmlparsedata")))
17102 (build-system r-build-system)
17103 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17104 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17106 "This package provides tools to convert the output of
17107 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17108 @code{XPath}, and is easier to manipulate in general.")
17109 (license license:expat)))
17111 (define-public r-cyclocomp
17113 (name "r-cyclocomp")
17118 (uri (cran-uri "cyclocomp" version))
17121 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17122 (properties `((upstream-name . "cyclocomp")))
17123 (build-system r-build-system)
17125 `(("r-callr" ,r-callr)
17126 ("r-crayon" ,r-crayon)
17128 ("r-remotes" ,r-remotes)
17129 ("r-withr" ,r-withr)))
17130 (home-page "https://github.com/MangoTheCat/cyclocomp")
17131 (synopsis "Cyclomatic complexity of R code")
17133 "Cyclomatic complexity is a software metric, used to indicate the
17134 complexity of a program. It is a quantitative measure of the number of
17135 linearly independent paths through a program's source code. This package
17136 provides tools to compute this metric.")
17137 (license license:expat)))
17139 (define-public r-lintr
17146 (uri (cran-uri "lintr" version))
17149 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17150 (properties `((upstream-name . "lintr")))
17151 (build-system r-build-system)
17153 `(("r-codetools" ,r-codetools)
17154 ("r-crayon" ,r-crayon)
17155 ("r-cyclocomp" ,r-cyclocomp)
17156 ("r-digest" ,r-digest)
17158 ("r-jsonlite" ,r-jsonlite)
17159 ("r-knitr" ,r-knitr)
17161 ("r-rstudioapi" ,r-rstudioapi)
17162 ("r-testthat" ,r-testthat)
17164 ("r-xmlparsedata" ,r-xmlparsedata)))
17165 (home-page "https://github.com/jimhester/lintr")
17166 (synopsis "Linter for R code")
17167 (description "This package checks adherence to a given style, syntax
17168 errors and possible semantic issues. It supports on the fly checking of R
17169 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17170 (license license:expat)))
17172 (define-public r-sctransform
17174 (name "r-sctransform")
17179 (uri (cran-uri "sctransform" version))
17182 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17183 (build-system r-build-system)
17185 `(("r-future" ,r-future)
17186 ("r-future-apply" ,r-future-apply)
17187 ("r-ggplot2" ,r-ggplot2)
17188 ("r-gridextra" ,r-gridextra)
17190 ("r-matrix" ,r-matrix)
17191 ("r-matrixstats" ,r-matrixstats)
17193 ("r-rcpparmadillo" ,r-rcpparmadillo)
17194 ("r-reshape2" ,r-reshape2)))
17195 (home-page "https://github.com/ChristophH/sctransform")
17196 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17198 "This package provides a normalization method for single-cell UMI count
17199 data using a variance stabilizing transformation. The transformation is based
17200 on a negative binomial regression model with regularized parameters. As part
17201 of the same regression framework, this package also provides functions for
17202 batch correction, and data correction.")
17203 (license license:gpl3)))
17205 (define-public r-styler
17212 (uri (cran-uri "styler" version))
17215 "10fj4cnazicb2z9djbv5pszcmrf7wbzagbjvksffqpdc5vbbbw5x"))))
17216 (build-system r-build-system)
17218 `(("r-backports" ,r-backports)
17220 ("r-magrittr" ,r-magrittr)
17221 ("r-purrr" ,r-purrr)
17222 ("r-r-cache" ,r-r-cache)
17223 ("r-rematch2" ,r-rematch2)
17224 ("r-rlang" ,r-rlang)
17225 ("r-rprojroot" ,r-rprojroot)
17226 ("r-tibble" ,r-tibble)
17227 ("r-withr" ,r-withr)
17228 ("r-xfun" ,r-xfun)))
17230 `(("r-knitr" ,r-knitr)))
17231 (home-page "https://github.com/r-lib/styler")
17232 (synopsis "Non-invasive pretty printing of R code")
17234 "This is a package for pretty-printing R code without changing the user's
17235 formatting intent.")
17236 (license license:gpl3)))
17238 (define-public r-scrime
17245 (uri (cran-uri "scrime" version))
17248 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17249 (build-system r-build-system)
17250 (home-page "https://cran.r-project.org/web/packages/scrime/")
17251 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17253 "This package provides tools for the analysis of high-dimensional data
17254 developed/implemented at the group \"Statistical Complexity Reduction In
17255 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17256 the functions can also be applied to other types of categorical data.")
17257 (license license:gpl2)))
17259 (define-public r-pbmcapply
17261 (name "r-pbmcapply")
17266 (uri (cran-uri "pbmcapply" version))
17269 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17270 (build-system r-build-system)
17271 (home-page "https://github.com/kvnkuang/pbmcapply")
17272 (synopsis "Track the progress of apply procedures with a progress bar")
17274 "This light-weight package helps you track and visualize the progress of
17275 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17276 (license license:expat)))
17278 (define-public r-blme
17285 (uri (cran-uri "blme" version))
17288 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17289 (build-system r-build-system)
17290 (propagated-inputs `(("r-lme4" ,r-lme4)))
17291 (home-page "https://github.com/vdorie/blme")
17292 (synopsis "Bayesian linear mixed-effects models")
17294 "This package provides tools for maximum a posteriori estimation for
17295 linear and generalized linear mixed-effects models in a Bayesian setting. It
17296 extends the lme4 package.")
17297 (license license:gpl2+)))
17299 (define-public r-batchtools
17301 (name "r-batchtools")
17306 (uri (cran-uri "batchtools" version))
17309 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17310 (build-system r-build-system)
17312 `(("r-backports" ,r-backports)
17313 ("r-base64url" ,r-base64url)
17315 ("r-checkmate" ,r-checkmate)
17316 ("r-data-table" ,r-data-table)
17317 ("r-digest" ,r-digest)
17319 ("r-progress" ,r-progress)
17321 ("r-rappdirs" ,r-rappdirs)
17322 ("r-stringi" ,r-stringi)
17323 ("r-withr" ,r-withr)))
17325 `(("r-knitr" ,r-knitr)))
17326 (home-page "https://github.com/mllg/batchtools")
17327 (synopsis "Tools for computation on batch systems")
17329 "As a successor of the packages BatchJobs and BatchExperiments, this
17330 package provides a parallel implementation of the Map function for high
17331 performance computing systems managed by various schedulers. A multicore and
17332 socket mode allow the parallelization on a local machines, and multiple
17333 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17334 the package provides an abstraction mechanism to define large-scale computer
17335 experiments in a well-organized and reproducible way.")
17336 (license license:lgpl3)))
17338 (define-public r-clue
17345 (uri (cran-uri "clue" version))
17348 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17349 (build-system r-build-system)
17350 (propagated-inputs `(("r-cluster" ,r-cluster)))
17351 (home-page "https://cran.r-project.org/web/packages/clue/")
17352 (synopsis "Tools for analyzing cluster ensembles")
17353 (description "Cluster ensembles are collections of individual solutions to
17354 a given clustering problem which are useful or necessary to consider in a wide
17355 range of applications. This R package provides an extensible computational
17356 environment for creating and analyzing cluster ensembles, with basic data
17357 structures for representing partitions and hierarchies, and facilities for
17358 computing on them, including methods for measuring proximity and obtaining
17359 consensus and secondary clusterings.")
17360 (license license:gpl2)))
17362 (define-public r-sitmo
17369 (uri (cran-uri "sitmo" version))
17372 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17373 (build-system r-build-system)
17374 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17375 (home-page "https://github.com/coatless/sitmo/")
17376 (synopsis "Parallel pseudo random number generator header files")
17378 "This package provides two high quality and fast PPRNGs that may be used
17379 in an OpenMP parallel environment. In addition, there is a generator for one
17380 dimensional low-discrepancy sequence.")
17381 (license license:expat)))
17383 (define-public r-dqrng
17390 (uri (cran-uri "dqrng" version))
17393 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17394 (build-system r-build-system)
17398 ("r-sitmo" ,r-sitmo)))
17399 (home-page "https://www.daqana.org/dqrng")
17400 (synopsis "Fast pseudo random number generators")
17402 "Several fast random number generators are provided as C++ header-only
17403 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17404 Additionally, fast functions for generating random numbers according to a
17405 uniform, normal and exponential distribution are included. The latter two use
17406 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17407 functions are exported to R and as a C++ interface and are enabled for use
17408 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17409 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17410 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17411 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17412 ;; whole is distributed under the terms of the AGPL 3.
17413 (license license:agpl3)))
17415 (define-public r-ingredients
17417 (name "r-ingredients")
17422 (uri (cran-uri "ingredients" version))
17425 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17426 (properties `((upstream-name . "ingredients")))
17427 (build-system r-build-system)
17429 `(("r-ggplot2" ,r-ggplot2)
17430 ("r-gridextra" ,r-gridextra)
17431 ("r-scales" ,r-scales)))
17432 (native-inputs `(("r-knitr" ,r-knitr)))
17433 (home-page "https://ModelOriented.github.io/ingredients/")
17434 (synopsis "Effects and importances of model ingredients")
17436 "This is a collection of tools for assessment of feature importance and
17437 feature effects. Key functions are:
17440 @item @code{feature_importance()} for assessment of global level feature
17442 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17443 @item @code{partial_dependence()} for partial dependence plots,
17444 @item @code{conditional_dependence()} for conditional dependence plots,
17445 @item @code{accumulated_dependence()} for accumulated local effects plots,
17446 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17447 aggregation of ceteris paribus profiles,
17448 @item generic @code{print()} and @code{plot()} for better usability of
17449 selected explainers,
17450 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17451 @item generic @code{describe()} for explanations in natural language.
17453 (license license:gpl3)))
17455 (define-public r-ibreakdown
17457 (name "r-ibreakdown")
17462 (uri (cran-uri "iBreakDown" version))
17465 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17466 (properties `((upstream-name . "iBreakDown")))
17467 (build-system r-build-system)
17468 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17469 (native-inputs `(("r-knitr" ,r-knitr)))
17470 (home-page "https://ModelOriented.github.io/iBreakDown/")
17471 (synopsis "Model agnostic instance level variable attributions")
17473 "This package provides a model agnostic tool for decomposition of
17474 predictions from black boxes. It supports additive attributions and
17475 attributions with interactions. The Break Down Table shows contributions of
17476 every variable to a final prediction. The Break Down Plot presents variable
17477 contributions in a concise graphical way. This package works for
17478 classification and regression models.")
17479 (license license:gpl3)))
17481 (define-public r-dae
17488 (uri (cran-uri "dae" version))
17491 "102fgbdpn7yvm1zj180cv4sr1096sz35d4gndsv7w9kriqyi1c1l"))))
17492 (build-system r-build-system)
17494 `(("r-ggplot2" ,r-ggplot2)
17495 ("r-plyr" ,r-plyr)))
17497 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17498 (home-page "http://chris.brien.name")
17499 (synopsis "Functions useful in the design and ANOVA of experiments")
17501 "This package provides functions useful in the design and ANOVA of
17502 experiments. The content falls into the following groupings:
17506 @item factor manipulation functions,
17507 @item design functions,
17508 @item ANOVA functions,
17509 @item matrix functions,
17510 @item projector and canonical efficiency functions, and
17511 @item miscellaneous functions.
17514 There is a vignette called @code{DesignNotes} describing how to use the design
17515 functions for randomizing and assessing designs. The ANOVA functions
17516 facilitate the extraction of information when the @code{Error} function has
17517 been used in the call to @code{aov}.")
17518 (license license:gpl2)))
17520 (define-public r-dalex
17527 (uri (cran-uri "DALEX" version))
17530 "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn"))))
17531 (properties `((upstream-name . "DALEX")))
17532 (build-system r-build-system)
17534 `(("r-ggplot2" ,r-ggplot2)
17535 ("r-ibreakdown" ,r-ibreakdown)
17536 ("r-ingredients" ,r-ingredients)))
17537 (home-page "https://pbiecek.github.io/DALEX/")
17538 (synopsis "Descriptive machine learning explanations")
17540 "Machine Learning models are widely used and have various applications in
17541 classification or regression. Models created with boosting, bagging, stacking
17542 or similar techniques are often used due to their high performance, but such
17543 black-box models usually lack interpretability. The DALEX package contains
17544 various explainers that help to understand the link between input variables
17545 and model output.")
17546 ;; Any version of the GPL
17547 (license license:gpl3+)))
17549 (define-public r-enrichr
17556 (uri (cran-uri "enrichR" version))
17559 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17560 (properties `((upstream-name . "enrichR")))
17561 (build-system r-build-system)
17563 `(("r-ggplot2" ,r-ggplot2)
17565 ("r-rjson" ,r-rjson)))
17567 `(("r-knitr" ,r-knitr)))
17568 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17569 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17571 "This package provides an R interface to all Enrichr databases, a
17572 web-based tool for analyzing gene sets and returns any enrichment of common
17573 annotated biological functions.")
17574 (license license:gpl2+)))
17576 (define-public r-plot3d
17583 (uri (cran-uri "plot3D" version))
17586 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17587 (properties `((upstream-name . "plot3D")))
17588 (build-system r-build-system)
17589 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17590 (home-page "https://cran.r-project.org/web/packages/plot3D")
17591 (synopsis "Plot multi-dimensional data")
17593 "This package provides functions for viewing 2D and 3D data, including
17594 perspective plots, slice plots, surface plots, scatter plots, etc. It
17595 includes data sets from oceanography.")
17596 (license license:gpl3+)))
17598 (define-public r-ggfortify
17600 (name "r-ggfortify")
17605 (uri (cran-uri "ggfortify" version))
17608 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17609 (build-system r-build-system)
17611 `(("r-dplyr" ,r-dplyr)
17612 ("r-ggplot2" ,r-ggplot2)
17613 ("r-gridextra" ,r-gridextra)
17614 ("r-scales" ,r-scales)
17615 ("r-stringr" ,r-stringr)
17616 ("r-tibble" ,r-tibble)
17617 ("r-tidyr" ,r-tidyr)))
17619 `(("r-knitr" ,r-knitr)))
17620 (home-page "https://github.com/sinhrks/ggfortify")
17621 (synopsis "Data visualization tools for statistical analysis results")
17623 "This package provides unified plotting tools for statistics commonly
17624 used, such as GLM, time series, PCA families, clustering and survival
17625 analysis. The package offers a single plotting interface for these analysis
17626 results and plots in a unified style using the @code{ggplot2} package.")
17627 (license license:gpl2)))
17629 (define-public r-refmanager
17631 (name "r-refmanager")
17636 (uri (cran-uri "RefManageR" version))
17639 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17640 (properties `((upstream-name . "RefManageR")))
17641 (build-system r-build-system)
17643 `(("r-httr" ,r-httr)
17644 ("r-jsonlite" ,r-jsonlite)
17645 ("r-lubridate" ,r-lubridate)
17647 ("r-stringr" ,r-stringr)
17648 ("r-xml2" ,r-xml2)))
17650 `(("r-knitr" ,r-knitr)))
17651 (home-page "https://github.com/ropensci/RefManageR/")
17652 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17654 "This package provides tools for importing and working with bibliographic
17655 references. It greatly enhances the @code{bibentry} class by providing a
17656 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17657 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17658 by various formats for name lists (author by last names, translator by full
17659 names, etc.). Entries can be updated, combined, sorted, printed in a number
17660 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17661 into R and converted to @code{BibEntry} objects.")
17662 ;; Any of these licenses may be picked.
17663 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17665 (define-public r-citr
17672 (uri (cran-uri "citr" version))
17675 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17676 (build-system r-build-system)
17678 `(("r-assertthat" ,r-assertthat)
17681 ("r-miniui" ,r-miniui)
17682 ("r-refmanager" ,r-refmanager)
17683 ("r-rstudioapi" ,r-rstudioapi)
17684 ("r-shiny" ,r-shiny)
17685 ("r-shinyjs" ,r-shinyjs)
17686 ("r-yaml" ,r-yaml)))
17687 (home-page "https://github.com/crsh/citr")
17688 (synopsis "RStudio add-in to insert Markdown citations")
17690 "This package provides functions and an RStudio add-in that search a
17691 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17692 the current document.")
17693 (license license:expat)))
17695 (define-public r-xgboost
17698 (version "1.3.2.1")
17702 (uri (cran-uri "xgboost" version))
17705 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17706 (build-system r-build-system)
17708 `(("r-data-table" ,r-data-table)
17709 ("r-magrittr" ,r-magrittr)
17710 ("r-matrix" ,r-matrix)))
17712 `(("r-knitr" ,r-knitr)))
17713 (home-page "https://github.com/dmlc/xgboost")
17714 (synopsis "Extreme gradient boosting")
17716 "This package provides an R interface to Extreme Gradient Boosting, which
17717 is an efficient implementation of the gradient boosting framework from Chen
17718 and Guestrin (2016). The package includes efficient linear model solver and
17719 tree learning algorithms. The package can automatically do parallel
17720 computation on a single machine. It supports various objective functions,
17721 including regression, classification and ranking. The package is made to be
17722 extensible, so that users are also allowed to define their own objectives
17724 (license license:asl2.0)))
17726 (define-public r-umap
17729 (version "0.2.7.0")
17733 (uri (cran-uri "umap" version))
17736 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17737 (build-system r-build-system)
17739 `(("r-openssl" ,r-openssl)
17741 ("r-reticulate" ,r-reticulate)
17742 ("r-rspectra" ,r-rspectra)))
17744 `(("r-knitr" ,r-knitr)))
17745 (home-page "https://github.com/tkonopka/umap")
17746 (synopsis "Uniform manifold approximation and projection")
17748 "Uniform manifold approximation and projection is a technique for
17749 dimension reduction. This package provides an interface to the UMAP algorithm
17750 in R, including a translation of the original algorithm into R.")
17751 (license license:expat)))
17753 (define-public r-uwot
17760 (uri (cran-uri "uwot" version))
17763 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17764 (build-system r-build-system)
17766 `(("r-dqrng" ,r-dqrng)
17768 ("r-irlba" ,r-irlba)
17769 ("r-matrix" ,r-matrix)
17771 ("r-rcppannoy" ,r-rcppannoy)
17772 ("r-rcppprogress" ,r-rcppprogress)
17773 ("r-rspectra" ,r-rspectra)))
17774 (home-page "https://github.com/jlmelville/uwot")
17775 (synopsis "Uniform manifold approximation and projection")
17777 "This package provides an implementation of the Uniform Manifold
17778 Approximation and Projection dimensionality reduction by McInnes et
17779 al. (2018). It also provides means to transform new data and to carry out
17780 supervised dimensionality reduction. An implementation of the related
17781 LargeVis method of Tang et al. (2016) is also provided.")
17782 (license license:gpl3)))
17784 (define-public r-kableextra
17786 (name "r-kableextra")
17791 (uri (cran-uri "kableExtra" version))
17794 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
17795 (properties `((upstream-name . "kableExtra")))
17796 (build-system r-build-system)
17798 `(("r-digest" ,r-digest)
17800 ("r-htmltools" ,r-htmltools)
17801 ("r-knitr" ,r-knitr)
17802 ("r-magrittr" ,r-magrittr)
17803 ("r-rmarkdown" ,r-rmarkdown)
17804 ("r-rstudioapi" ,r-rstudioapi)
17805 ("r-rvest" ,r-rvest)
17806 ("r-scales" ,r-scales)
17807 ("r-stringr" ,r-stringr)
17808 ("r-svglite" ,r-svglite)
17809 ("r-viridislite" ,r-viridislite)
17810 ("r-webshot" ,r-webshot)
17811 ("r-xml2" ,r-xml2)))
17813 `(("r-knitr" ,r-knitr)))
17814 (home-page "https://haozhu233.github.io/kableExtra/")
17815 (synopsis "Construct complex tables with pipe syntax")
17817 "Build complex HTML or LaTeX tables using @code{kable()} from
17818 @code{knitr} and the piping syntax from @code{magrittr}. The function
17819 @code{kable()} is a light weight table generator coming from @code{knitr}.
17820 This package simplifies the way to manipulate the HTML or LaTeX codes
17821 generated by @code{kable()} and allows users to construct complex tables and
17822 customize styles using a readable syntax.")
17823 (license license:expat)))
17825 (define-public r-glasso
17832 (uri (cran-uri "glasso" version))
17834 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17835 (build-system r-build-system)
17836 (native-inputs `(("gfortran" ,gfortran)))
17837 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17838 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17840 "This is a package for estimation of a sparse inverse covariance matrix
17841 using a lasso (L1) penalty. Facilities are provided for estimates along a
17842 path of values for the regularization parameter.")
17843 (license license:gpl2)))
17845 (define-public r-rhpcblasctl
17847 (name "r-rhpcblasctl")
17848 (version "0.20-137")
17852 (uri (cran-uri "RhpcBLASctl" version))
17855 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17856 (properties `((upstream-name . "RhpcBLASctl")))
17857 (build-system r-build-system)
17858 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17859 (synopsis "Control the number of threads on BLAS")
17861 "This package allows you to control the number of threads the BLAS
17862 library uses. It is also possible to control the number of threads in
17864 (license license:agpl3+)))
17866 (define-public r-lda
17873 (uri (cran-uri "lda" version))
17876 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17877 (build-system r-build-system)
17878 (home-page "https://cran.r-project.org/web/packages/lda/")
17879 (synopsis "Collapsed Gibbs sampling methods for topic models")
17881 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17882 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17883 mixed-membership stochastic blockmodel. Inference for all of these models is
17884 implemented via a fast collapsed Gibbs sampler written in C. Utility
17885 functions for reading/writing data typically used in topic models, as well as
17886 tools for examining posterior distributions are also included.")
17887 ;; Any version of the LGPL
17888 (license license:lgpl3+)))
17890 (define-public r-rann-l1
17897 (uri (cran-uri "RANN.L1" version))
17900 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17901 (properties `((upstream-name . "RANN.L1")))
17902 (build-system r-build-system)
17903 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17904 (synopsis "Fast nearest neighbour search using L1 metric")
17906 "This package provides tools to find the k nearest neighbours for every
17907 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17908 library. There is support for approximate as well as exact searches, fixed
17909 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17910 computed using the L1 (Manhattan, taxicab) metric.")
17911 (license license:gpl3+)))
17913 (define-public r-leiden
17920 (uri (cran-uri "leiden" version))
17923 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17924 (properties `((upstream-name . "leiden")))
17925 (build-system r-build-system)
17927 `(("r-igraph" ,r-igraph)
17928 ("r-matrix" ,r-matrix)
17929 ("r-reticulate" ,r-reticulate)))
17931 `(("r-knitr" ,r-knitr)))
17932 (home-page "https://github.com/TomKellyGenetics/leiden")
17933 (synopsis "R implementation of Leiden clustering algorithm")
17935 "This package implements the Python @code{leidenalg} module to be called
17936 in R. It enables clustering using the Leiden algorithm for partitioning a
17937 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17938 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17939 (license license:gpl3)))
17941 (define-public r-patchwork
17943 (name "r-patchwork")
17948 (uri (cran-uri "patchwork" version))
17951 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17952 (build-system r-build-system)
17954 `(("r-ggplot2" ,r-ggplot2)
17955 ("r-gtable" ,r-gtable)))
17957 `(("r-knitr" ,r-knitr)))
17958 (home-page "https://github.com/thomasp85/patchwork")
17959 (synopsis "Compose ggplot2 plots")
17961 "The @code{ggplot2} package provides a strong API for sequentially
17962 building up a plot, but does not concern itself with composition of multiple
17963 plots. Patchwork is a package that expands the API to allow for arbitrarily
17964 complex composition of plots by providing mathematical operators for combining
17966 (license license:expat)))
17968 (define-public r-liger
17975 (uri (git-reference
17976 (url "https://github.com/MacoskoLab/liger")
17977 (commit (string-append "v" version))))
17978 (file-name (git-file-name name version))
17981 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17982 (modules '((guix build utils)))
17985 (delete-file "inst/java/ModularityOptimizer.jar")
17987 (build-system r-build-system)
17990 (modify-phases %standard-phases
17991 (add-after 'unpack 'build-java-part
17992 (lambda* (#:key inputs #:allow-other-keys)
17993 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17994 (for-each (lambda (file) (invoke "javac" file))
17995 (find-files "." "\\.java$"))
17996 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17997 (find-files "." "\\.class$"))
18000 `(("r-cowplot" ,r-cowplot)
18001 ("r-dosnow" ,r-dosnow)
18002 ("r-dplyr" ,r-dplyr)
18004 ("r-foreach" ,r-foreach)
18005 ("r-ggplot2" ,r-ggplot2)
18006 ("r-ggrepel" ,r-ggrepel)
18007 ("r-hmisc" ,r-hmisc)
18009 ("r-irlba" ,r-irlba)
18010 ("r-matrix" ,r-matrix)
18011 ("r-mclust" ,r-mclust)
18012 ("r-patchwork" ,r-patchwork)
18014 ("r-rann-l1" ,r-rann-l1)
18016 ("r-rcpparmadillo" ,r-rcpparmadillo)
18017 ("r-riverplot" ,r-riverplot)
18018 ("r-rtsne" ,r-rtsne)
18019 ("r-snow" ,r-snow)))
18021 `(("jdk" ,icedtea "jdk")
18022 ;; See https://github.com/MacoskoLab/liger/issues/96
18023 ;; The optimizer is released under the Expat license.
18027 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
18030 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
18032 ("r-knitr" ,r-knitr))) ; for vignettes
18033 (home-page "https://github.com/MacoskoLab/liger")
18034 (synopsis "Integrate and analyze multiple single-cell datasets")
18036 "LIGER is a package for integrating and analyzing multiple single-cell
18037 datasets, developed and maintained by the Macosko lab. It relies on
18038 integrative non-negative matrix factorization to identify shared and
18039 dataset-specific factors.")
18040 (license license:gpl3)))
18042 (define-public r-harmony
18049 (uri (git-reference
18050 (url "https://github.com/immunogenomics/harmony")
18052 (file-name (git-file-name name version))
18055 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18056 (modules '((guix build utils)))
18059 (for-each delete-file '("config.status" "configure"))
18061 (build-system r-build-system)
18063 `(("r-cowplot" ,r-cowplot)
18064 ("r-dplyr" ,r-dplyr)
18065 ("r-ggplot2" ,r-ggplot2)
18066 ("r-irlba" ,r-irlba)
18067 ("r-matrix" ,r-matrix)
18069 ("r-rcpparmadillo" ,r-rcpparmadillo)
18070 ("r-rcppprogress" ,r-rcppprogress)
18071 ("r-rlang" ,r-rlang)
18072 ("r-tibble" ,r-tibble)
18073 ("r-tidyr" ,r-tidyr)))
18075 `(("autoconf" ,autoconf)))
18076 (home-page "https://github.com/immunogenomics/harmony")
18077 (synopsis "Integration of single cell sequencing data")
18079 "This package provides an implementation of the Harmony algorithm for
18080 single cell integration, described in Korsunsky et al
18081 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18082 function and interfaces to external frameworks.")
18083 (license license:gpl3)))
18085 (define-public r-covr
18092 (uri (cran-uri "covr" version))
18094 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18095 (properties `((upstream-name . "covr")))
18096 (build-system r-build-system)
18098 `(("r-crayon" ,r-crayon)
18099 ("r-digest" ,r-digest)
18101 ("r-jsonlite" ,r-jsonlite)
18103 ("r-withr" ,r-withr)
18104 ("r-yaml" ,r-yaml)))
18106 `(("r-knitr" ,r-knitr))) ; for vignettes
18107 (home-page "https://github.com/r-lib/covr")
18108 (synopsis "Test coverage for R packages")
18110 "Thisp package enables you to track and report code coverage for your
18111 package and (optionally) upload the results to a coverage service. Code
18112 coverage is a measure of the amount of code being exercised by a set of tests.
18113 It is an indirect measure of test quality and completeness. This package is
18114 compatible with any testing methodology or framework and tracks coverage of
18115 both R code and compiled C/C++/FORTRAN code.")
18116 (license license:gpl3)))
18118 (define-public r-systemfonts
18120 (name "r-systemfonts")
18125 (uri (cran-uri "systemfonts" version))
18128 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18129 (properties `((upstream-name . "systemfonts")))
18130 (build-system r-build-system)
18132 `(("r-cpp11" ,r-cpp11)))
18134 `(("fontconfig" ,fontconfig)
18137 `(("pkg-config" ,pkg-config)
18138 ("r-knitr" ,r-knitr)))
18139 (home-page "https://github.com/r-lib/systemfonts")
18140 (synopsis "System native font finding")
18142 "This package provides system native access to the font catalogue. As
18143 font handling varies between systems it is difficult to correctly locate
18144 installed fonts across different operating systems. The 'systemfonts' package
18145 provides bindings to the native libraries for finding font files that can then
18146 be used further by e.g. graphic devices.")
18147 (license license:expat)))
18149 (define-public r-graphlayouts
18151 (name "r-graphlayouts")
18156 (uri (cran-uri "graphlayouts" version))
18159 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18160 (properties `((upstream-name . "graphlayouts")))
18161 (build-system r-build-system)
18163 `(("r-igraph" ,r-igraph)
18165 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18166 (home-page "https://github.com/schochastics/graphlayouts")
18167 (synopsis "Additional layout algorithms for network visualizations")
18169 "This package provides several layout algorithms to visualize networks
18170 which are not part of the igraph library. Most are based on the concept of
18171 stress majorization by Gansner et al. (2004)
18172 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18173 emphasize hidden group structures in networks or focus on specific nodes.")
18174 (license license:expat)))
18176 (define-public r-terra
18183 (uri (cran-uri "terra" version))
18186 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18187 (properties `((upstream-name . "terra")))
18188 (build-system r-build-system)
18193 ("sqlite" ,sqlite) ; needed for proj
18196 `(("r-raster" ,r-raster)
18197 ("r-rcpp" ,r-rcpp)))
18199 `(("pkg-config" ,pkg-config)))
18200 (home-page "https://rspatial.org/terra")
18201 (synopsis "Spatial data analysis")
18203 "This package provides methods for spatial data analysis, especially
18204 raster data. The included methods allow for low-level data manipulation as
18205 well as high-level global, local, zonal, and focal computation. The predict
18206 and interpolate methods facilitate the use of regression type (interpolation,
18207 machine learning) models for spatial prediction. Processing of very large
18208 files is supported.")
18209 (license license:gpl3+)))
18211 (define-public r-tidygraph
18213 (name "r-tidygraph")
18218 (uri (cran-uri "tidygraph" version))
18221 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18222 (properties `((upstream-name . "tidygraph")))
18223 (build-system r-build-system)
18225 `(("r-dplyr" ,r-dplyr)
18226 ("r-igraph" ,r-igraph)
18227 ("r-magrittr" ,r-magrittr)
18228 ("r-pillar" ,r-pillar)
18231 ("r-rlang" ,r-rlang)
18232 ("r-tibble" ,r-tibble)
18233 ("r-tidyr" ,r-tidyr)))
18234 (home-page "https://github.com/thomasp85/tidygraph")
18235 (synopsis "Tidy API for graph manipulation")
18237 "This package provides a graph implementation that can be thought of as
18238 two tidy data frames describing node and edge data respectively. It provides
18239 an approach to manipulate these two virtual data frames using the API defined
18240 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18241 common graph algorithms.")
18242 (license license:expat)))
18244 (define-public r-soupx
18245 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18249 (version (git-version "0.3.1" revision commit))
18253 (uri (git-reference
18254 (url "https://github.com/constantAmateur/SoupX")
18256 (file-name (git-file-name name version))
18259 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18260 (properties `((upstream-name . "SoupX")))
18261 (build-system r-build-system)
18263 `(("r-ggplot2" ,r-ggplot2)
18264 ("r-matrix" ,r-matrix)
18265 ("r-seurat" ,r-seurat)))
18266 (home-page "https://github.com/constantAmateur/SoupX")
18267 (synopsis "Single cell mRNA Soup eXterminator")
18269 "This package provides a package for quantifying, profiling and
18270 removing cell free mRNA contamination (the \"soup\") from droplet based single
18271 cell RNA-seq experiments.")
18272 (license license:gpl2))))
18274 (define-public r-assertr
18281 (uri (cran-uri "assertr" version))
18284 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18285 (build-system r-build-system)
18287 `(("r-dplyr" ,r-dplyr)
18289 ("r-rlang" ,r-rlang)))
18291 `(("r-knitr" ,r-knitr))) ; needed for vignette
18292 (home-page "https://github.com/ropensci/assertr")
18293 (synopsis "Assertive programming for R analysis pipelines")
18295 "This package provides functionality to assert conditions that have to be
18296 met so that errors in data used in analysis pipelines can fail quickly. It is
18297 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18299 (license license:expat)))
18301 (define-public r-parameters
18303 (name "r-parameters")
18308 (uri (cran-uri "parameters" version))
18311 "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm"))))
18312 (properties `((upstream-name . "parameters")))
18313 (build-system r-build-system)
18315 `(("r-bayestestr" ,r-bayestestr)
18316 ("r-insight" ,r-insight)))
18318 `(("r-knitr" ,r-knitr)))
18319 (home-page "https://cran.r-project.org/web/packages/parameters")
18320 (synopsis "Processing of model parameters")
18322 "This package provides utilities for processing the parameters of various
18323 statistical models. Beyond computing p values, CIs, and other indices for a
18324 wide variety of models, this package implements features like standardization
18325 or bootstrapping of parameters and models, feature reduction (feature
18326 extraction and variable selection) as well as conversion between indices of
18328 (license license:gpl3)))
18330 (define-public r-rgdal
18337 (uri (cran-uri "rgdal" version))
18339 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18340 (properties `((upstream-name . "rgdal")))
18341 (build-system r-build-system)
18349 `(("pkg-config" ,pkg-config)
18350 ("r-knitr" ,r-knitr)))
18351 (home-page "http://rgdal.r-forge.r-project.org")
18352 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18354 "This package provides bindings to the Geospatial Data Abstraction
18355 Library (GDAL) and access to projection/transformation operations from the
18357 (license license:gpl2+)))
18359 (define-public r-insol
18366 (uri (cran-uri "insol" version))
18369 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18370 (properties `((upstream-name . "insol")))
18371 (build-system r-build-system)
18373 `(("r-raster" ,r-raster)))
18375 `(("gfortran" ,gfortran)))
18376 (home-page "https://meteoexploration.com/R/insol/index.html")
18377 (synopsis "Tools for calculating solar radiation")
18379 "This package provides functions to compute insolation on tilted
18380 surfaces, computes atmospheric transmittance and related parameters such as:
18381 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18382 time, vector in the direction of the sun, vector normal to surface, and some
18383 atmospheric physics.")
18384 (license license:gpl2+)))
18386 (define-public r-lifecycle
18388 (name "r-lifecycle")
18393 (uri (cran-uri "lifecycle" version))
18396 "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3"))))
18397 (properties `((upstream-name . "lifecycle")))
18398 (build-system r-build-system)
18400 `(("r-glue" ,r-glue)
18401 ("r-rlang" ,r-rlang)))
18403 `(("r-knitr" ,r-knitr))) ; for vignettes
18404 (home-page "https://github.com/r-lib/lifecycle")
18405 (synopsis "Manage the life cycle of your package functions")
18407 "Manage the life cycle of your exported functions with shared
18408 conventions, documentation badges, and non-invasive deprecation warnings. The
18409 lifecycle package defines four development stages (experimental, maturing,
18410 stable, and questioning) and three deprecation stages (soft-deprecated,
18411 deprecated, and defunct). It makes it easy to insert badges corresponding to
18412 these stages in your documentation. Usage of deprecated functions are
18413 signalled with increasing levels of non-invasive verbosity.")
18414 (license license:gpl3)))
18416 (define-public r-assertable
18418 (name "r-assertable")
18423 (uri (cran-uri "assertable" version))
18426 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18427 (build-system r-build-system)
18429 `(("r-data-table" ,r-data-table)))
18431 `(("r-knitr" ,r-knitr)))
18432 (home-page "https://cran.r-project.org/web/packages/assertable/")
18433 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18434 (description "This package provides simple, flexible assertions on
18435 data.frame or data.table objects with verbose output for vetting. While other
18436 assertion packages apply towards more general use-cases, @code{assertable} is
18437 tailored towards tabular data. It includes functions to check variable names
18438 and values, whether the dataset contains all combinations of a given set of
18439 unique identifiers, and whether it is a certain length. In addition,
18440 @code{assertable} includes utility functions to check the existence of target
18441 files and to efficiently import multiple tabular data files into one
18443 (license license:gpl3)))
18445 (define-public r-quadprog
18447 (name "r-quadprog")
18452 (uri (cran-uri "quadprog" version))
18454 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18455 (build-system r-build-system)
18457 `(("gfortran" ,gfortran)))
18458 (home-page "https://cran.r-project.org/web/packages/quadprog")
18459 (synopsis "Functions to solve quadratic programming problems")
18461 "This package contains routines and documentation for solving quadratic
18462 programming problems.")
18463 (license license:gpl3+)))
18465 (define-public r-desolve
18472 (uri (cran-uri "deSolve" version))
18474 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18475 (properties `((upstream-name . "deSolve")))
18476 (build-system r-build-system)
18478 `(("gfortran" ,gfortran)))
18479 (home-page "https://desolve.r-forge.r-project.org/")
18480 (synopsis "Solvers for initial value problems of differential equations")
18481 (description "This package provides functions that solve initial value
18482 problems of a system of first-order @dfn{ordinary differential
18483 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18484 @dfn{differential algebraic equations} (DAE), and of delay differential
18485 equations. The functions provide an interface to the FORTRAN functions
18486 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18487 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18488 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18489 time steps. The package contains routines designed for solving ODEs resulting
18490 from 1-D, 2-D and 3-D partial differential equations that have been converted
18491 to ODEs by numerical differencing.")
18492 (license license:gpl2+)))
18494 (define-public r-pracma
18500 (uri (cran-uri "pracma" version))
18502 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18503 (build-system r-build-system)
18504 (home-page "https://cran.r-project.org/web/packages/pracma/")
18505 (synopsis "Practical numerical math functions")
18506 (description "This package provides functions for numerical analysis and
18507 linear algebra, numerical optimization, differential equations, plus some
18508 special functions. It uses Matlab function names where appropriate to simplify
18510 (license license:gpl3+)))
18512 (define-public r-subplex
18519 (uri (cran-uri "subplex" version))
18522 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18523 (build-system r-build-system)
18525 `(("gfortran" ,gfortran)))
18526 (home-page "https://cran.r-project.org/web/packages/subplex")
18527 (synopsis "Unconstrained optimization using the subplex algorithm")
18529 "This package implements the Subplex optimization algorithm.
18530 It solves unconstrained optimization problems using a simplex method on
18531 subspaces. The method is well suited for optimizing objective functions that
18532 are noisy or are discontinuous at the solution.")
18533 (license license:gpl3+)))
18535 (define-public r-txtplot
18542 (uri (cran-uri "txtplot" version))
18545 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18546 (build-system r-build-system)
18547 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18548 (synopsis "Text-based plotting")
18549 (description "This package provides functions to produce rudimentary ASCII
18550 graphics directly in the terminal window. This package provides a basic
18551 plotting function (and equivalents of curve, density, acf and barplot) as well
18552 as a boxplot function.")
18553 (license license:lgpl3+)))
18555 (define-public r-bio3d
18562 (uri (cran-uri "bio3d" version))
18565 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18566 (properties `((upstream-name . "bio3d")))
18567 (build-system r-build-system)
18568 (inputs `(("zlib" ,zlib)))
18569 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18570 (home-page "http://thegrantlab.org/bio3d/")
18571 (synopsis "Biological structure analysis")
18573 "This package provides utilities to process, organize and explore protein
18574 structure, sequence and dynamics data. Features include the ability to read
18575 and write structure, sequence and dynamic trajectory data, perform sequence
18576 and structure database searches, data summaries, atom selection, alignment,
18577 superposition, rigid core identification, clustering, torsion analysis,
18578 distance matrix analysis, structure and sequence conservation analysis, normal
18579 mode analysis, principal component analysis of heterogeneous structure data,
18580 and correlation network analysis from normal mode and molecular dynamics data.
18581 In addition, various utility functions are provided to enable the statistical
18582 and graphical power of the R environment to work with biological sequence and
18584 (license license:gpl2+)))
18586 (define-public r-bios2cor
18588 (name "r-bios2cor")
18593 (uri (cran-uri "Bios2cor" version))
18596 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18597 (properties `((upstream-name . "Bios2cor")))
18598 (build-system r-build-system)
18600 `(("r-bigmemory" ,r-bigmemory)
18601 ("r-bio3d" ,r-bio3d)
18602 ("r-circular" ,r-circular)
18603 ("r-igraph" ,r-igraph)))
18604 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18605 (synopsis "From biological sequences and simulations to correlation analysis")
18607 "This package provides utilities for computation and analysis of
18608 correlation/covariation in multiple sequence alignments and in side chain
18609 motions during molecular dynamics simulations. Features include the
18610 computation of correlation/covariation scores using a variety of scoring
18611 functions between either sequence positions in alignments or side chain
18612 dihedral angles in molecular dynamics simulations and utilities to analyze the
18613 correlation/covariation matrix through a variety of tools including network
18614 representation and principal components analysis. In addition, several
18615 utility functions are based on the R graphical environment to provide friendly
18616 tools for help in data interpretation.")
18617 (license license:gpl2+)))
18619 ;; This package includes minified JavaScript files. When upgrading please
18620 ;; check that there are no new minified JavaScript files.
18621 (define-public r-networkd3
18623 (name "r-networkd3")
18628 (uri (cran-uri "networkD3" version))
18631 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18634 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18636 (properties `((upstream-name . "networkD3")))
18637 (build-system r-build-system)
18639 `(#:modules ((guix build utils)
18640 (guix build r-build-system)
18644 (modify-phases %standard-phases
18645 (add-after 'unpack 'process-javascript
18646 (lambda* (#:key inputs #:allow-other-keys)
18647 (with-directory-excursion "inst/htmlwidgets/lib/"
18651 `((,(assoc-ref inputs "d3.v4.js")
18652 "d3-4.5.0/d3.min.js"))))
18653 (lambda (sources targets)
18654 (for-each (lambda (source target)
18655 (format #t "Processing ~a --> ~a~%"
18657 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18658 (call-with-output-file target
18660 (dump-port minified port)))))
18661 sources targets))))
18664 `(("uglify-js" ,uglify-js)
18665 ;; NOTE: Make sure that this version of d3 is still valid when
18666 ;; upgrading the package.
18670 (uri "https://d3js.org/d3.v4.js")
18673 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18675 `(("r-htmlwidgets" ,r-htmlwidgets)
18676 ("r-igraph" ,r-igraph)
18677 ("r-magrittr" ,r-magrittr)))
18678 (home-page "https://cran.r-project.org/package=networkD3")
18679 (synopsis "D3 JavaScript network graphs from R")
18681 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18683 (license license:gpl3+)))
18685 (define-public r-aasea
18692 (uri (cran-uri "aaSEA" version))
18695 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18696 (properties `((upstream-name . "aaSEA")))
18697 (build-system r-build-system)
18699 `(("r-bios2cor" ,r-bios2cor)
18701 ("r-hmisc" ,r-hmisc)
18702 ("r-magrittr" ,r-magrittr)
18703 ("r-networkd3" ,r-networkd3)
18704 ("r-plotly" ,r-plotly)
18705 ("r-seqinr" ,r-seqinr)
18706 ("r-shiny" ,r-shiny)
18707 ("r-shinydashboard" ,r-shinydashboard)))
18708 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18709 (synopsis "Amino acid substitution effect analyzer")
18711 "Given a protein multiple sequence alignment, it is a daunting task to
18712 assess the effects of substitutions along sequence length. The aaSEA package
18713 is intended to help researchers to rapidly analyze property changes caused by
18714 single, multiple and correlated amino acid substitutions in proteins.")
18715 (license license:gpl3)))
18717 (define-public r-abacus
18724 (uri (cran-uri "ABACUS" version))
18727 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18728 (properties `((upstream-name . "ABACUS")))
18729 (build-system r-build-system)
18731 `(("r-ggplot2" ,r-ggplot2)
18732 ("r-shiny" ,r-shiny)))
18733 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18734 (synopsis "Apps-based activities for communicating and understanding statistics")
18736 "This package provides a set of Shiny apps for effective communication
18737 and understanding in statistics. The current version includes properties of
18738 normal distribution, properties of sampling distribution, one-sample z and t
18739 tests, two samples independent (unpaired) t test and analysis of variance.")
18740 (license license:gpl3)))
18742 (define-public r-abc-rap
18749 (uri (cran-uri "ABC.RAP" version))
18752 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18753 (properties `((upstream-name . "ABC.RAP")))
18754 (build-system r-build-system)
18755 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18756 (synopsis "Array-based CpG region analysis pipeline")
18758 "This package aims to identify candidate genes that are differentially
18759 methylated between cases and controls. It applies Student's t-test and delta
18760 beta analysis to identify candidate genes containing multiple CpG sites.")
18761 (license license:gpl3)))
18763 (define-public r-abcadm
18770 (uri (cran-uri "abcADM" version))
18773 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18774 (properties `((upstream-name . "abcADM")))
18775 (build-system r-build-system)
18778 ("r-rcpp" ,r-rcpp)))
18779 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18780 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18782 "This package provides tools to estimate parameters of accumulated
18783 damage (load duration) models based on failure time data under a Bayesian
18784 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18785 long-term reliability under stochastic load profiles.")
18786 (license license:gpl3)))
18788 (define-public r-rglpk
18795 (uri (cran-uri "Rglpk" version))
18798 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18799 (properties `((upstream-name . "Rglpk")))
18800 (build-system r-build-system)
18802 `(("r-slam" ,r-slam)))
18805 (home-page "https://r-forge.r-project.org/projects/rglp/")
18806 (synopsis "R interface to the GNU Linear Programming Kit")
18808 "This package provides an R interface to the GNU Linear Programming Kit,
18809 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18810 integer linear programming} (MILP) and other related problems.")
18812 (license (list license:gpl2 license:gpl3))))
18814 (define-public r-abcdefba
18816 (name "r-abcdefba")
18821 (uri (cran-uri "abcdeFBA" version))
18824 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18825 (properties `((upstream-name . "abcdeFBA")))
18826 (build-system r-build-system)
18828 `(("r-corrplot" ,r-corrplot)
18829 ("r-lattice" ,r-lattice)
18831 ("r-rglpk" ,r-rglpk)))
18832 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18833 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18835 "This package provides functions for Constraint Based Simulation using
18836 Flux Balance Analysis and informative analysis of the data generated during
18838 (license license:gpl2)))
18840 (define-public r-abcrlda
18847 (uri (cran-uri "abcrlda" version))
18850 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18851 (properties `((upstream-name . "abcrlda")))
18852 (build-system r-build-system)
18853 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18854 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18856 "This package offers methods to perform @dfn{asymptotically
18857 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18858 cost-sensitive binary classification. The bias-correction is an estimate of
18859 the bias term added to regularized discriminant analysis that minimizes the
18861 (license license:gpl3)))
18863 (define-public r-abemus
18870 (uri (cran-uri "abemus" version))
18873 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18874 (properties `((upstream-name . "abemus")))
18875 (build-system r-build-system)
18877 `(("r-data-table" ,r-data-table)))
18878 (home-page "https://cran.r-project.org/web/packages/abemus/")
18879 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18881 "This package provides an implementation of @dfn{Adaptive Base Error
18882 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18883 platform-specific genetic knowledge and empirical signal to readily detect and
18884 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18885 cell free DNA} (cfDNA).")
18886 (license license:gpl3)))
18888 ;; This package includes minified JavaScript files. When upgrading please
18889 ;; check that there are no new minified JavaScript files.
18890 (define-public r-rintrojs
18892 (name "r-rintrojs")
18897 (uri (cran-uri "rintrojs" version))
18900 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18901 (properties `((upstream-name . "rintrojs")))
18902 (build-system r-build-system)
18904 `(#:modules ((guix build utils)
18905 (guix build r-build-system)
18909 (modify-phases %standard-phases
18910 (add-after 'unpack 'process-javascript
18911 (lambda* (#:key inputs #:allow-other-keys)
18912 (with-directory-excursion "inst/javascript/introjs/"
18916 `((,(assoc-ref inputs "intro.js")
18918 (lambda (sources targets)
18919 (for-each (lambda (source target)
18920 (format #t "Processing ~a --> ~a~%"
18922 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18923 (call-with-output-file target
18925 (dump-port minified port)))))
18926 sources targets))))
18929 `(("uglify-js" ,uglify-js)
18933 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18936 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18938 `(("r-jsonlite" ,r-jsonlite)
18939 ("r-shiny" ,r-shiny)))
18940 (home-page "https://github.com/carlganz/rintrojs")
18941 (synopsis "Wrapper for the Intro.js library")
18943 "This package provides a wrapper for the @url{http://www.introjs.com,
18944 Intro.js} library. This package makes it easy to include step-by-step
18945 introductions, and clickable hints in a Shiny application. It supports both
18946 static introductions in the UI, and programmatic introductions from the
18948 (license license:agpl3+)))
18950 (define-public r-sysfonts
18952 (name "r-sysfonts")
18957 (uri (cran-uri "sysfonts" version))
18960 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18961 (properties `((upstream-name . "sysfonts")))
18962 (build-system r-build-system)
18964 `(("freetype" ,freetype)
18968 `(("pkg-config" ,pkg-config)))
18969 (home-page "https://github.com/yixuan/sysfonts")
18970 (synopsis "Loading fonts into R")
18972 "This is a package to simplify loading of system fonts and Google Fonts
18973 into R, in order to support other packages.")
18974 (license license:gpl2)))
18976 (define-public r-showtextdb
18978 (name "r-showtextdb")
18983 (uri (cran-uri "showtextdb" version))
18986 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18987 (properties `((upstream-name . "showtextdb")))
18988 (build-system r-build-system)
18990 `(("r-sysfonts" ,r-sysfonts)))
18991 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18992 (synopsis "Font files for the 'showtext' package")
18994 "This package provides font files that can be used by the @code{showtext}
18996 (license license:asl2.0)))
18998 (define-public r-showtext
19000 (name "r-showtext")
19005 (uri (cran-uri "showtext" version))
19008 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
19009 (properties `((upstream-name . "showtext")))
19010 (build-system r-build-system)
19012 `(("freetype" ,freetype)
19016 `(("r-showtextdb" ,r-showtextdb)
19017 ("r-sysfonts" ,r-sysfonts)))
19019 `(("pkg-config" ,pkg-config)
19020 ("r-knitr" ,r-knitr)))
19021 (home-page "https://github.com/yixuan/showtext")
19022 (synopsis "Using fonts more easily in R graphs")
19024 "This package aims to make it easy to use various types of
19025 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
19026 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
19027 will be converted into polygons or raster images, hence after the plot has
19028 been created, it no longer relies on the font files. No external software
19029 such as Ghostscript is needed to use this package.")
19030 (license license:asl2.0)))
19032 (define-public r-emojifont
19034 (name "r-emojifont")
19039 (uri (cran-uri "emojifont" version))
19042 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
19043 (properties `((upstream-name . "emojifont")))
19044 (build-system r-build-system)
19046 `(("r-ggplot2" ,r-ggplot2)
19047 ("r-proto" ,r-proto)
19048 ("r-showtext" ,r-showtext)
19049 ("r-sysfonts" ,r-sysfonts)))
19050 (home-page "https://guangchuangyu.github.io/emojifont")
19051 (synopsis "Emoji and Font Awesome in R graphics")
19053 "This package enables the use of emoji and the Font Awesome glyphs in
19054 both base and ggplot2 graphics.")
19055 (license license:artistic2.0)))
19057 (define-public r-abstractr
19059 (name "r-abstractr")
19064 (uri (cran-uri "abstractr" version))
19067 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19068 (properties `((upstream-name . "abstractr")))
19069 (build-system r-build-system)
19071 `(("r-colourpicker" ,r-colourpicker)
19072 ("r-emojifont" ,r-emojifont)
19073 ("r-ggplot2" ,r-ggplot2)
19074 ("r-gridextra" ,r-gridextra)
19075 ("r-rintrojs" ,r-rintrojs)
19076 ("r-shiny" ,r-shiny)
19077 ("r-shinythemes" ,r-shinythemes)))
19078 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19079 (synopsis "R-Shiny application for creating visual abstracts")
19081 "This package provides an R Shiny application to create visual abstracts
19082 for original research. A variety of user defined options and formatting are
19084 (license license:gpl3)))
19086 (define-public r-qgam
19093 (uri (cran-uri "qgam" version))
19096 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19097 (properties `((upstream-name . "qgam")))
19098 (build-system r-build-system)
19100 `(("r-doparallel" ,r-doparallel)
19103 ("r-shiny" ,r-shiny)))
19104 (native-inputs `(("r-knitr" ,r-knitr)))
19105 (home-page "https://cran.r-project.org/web/packages/qgam/")
19106 (synopsis "Smooth additive quantile regression models")
19108 "This package provides smooth additive quantile regression models, fitted
19109 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19110 the smoothing parameters are estimated automatically by marginal loss
19111 minimization, while the regression coefficients are estimated using either
19112 PIRLS or Newton algorithm. The learning rate is determined so that the
19113 Bayesian credible intervals of the estimated effects have approximately the
19114 correct coverage. The main function is @code{qgam()} which is similar to
19115 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19116 regression models.")
19117 (license license:gpl2+)))
19119 (define-public r-abtest
19126 (uri (cran-uri "abtest" version))
19129 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19130 (properties `((upstream-name . "abtest")))
19131 (build-system r-build-system)
19133 `(("r-matrix" ,r-matrix)
19134 ("r-mvtnorm" ,r-mvtnorm)
19135 ("r-plotrix" ,r-plotrix)
19137 ("r-rcolorbrewer" ,r-rcolorbrewer)
19140 ("r-truncnorm" ,r-truncnorm)))
19141 (home-page "https://cran.r-project.org/web/packages/abtest/")
19142 (synopsis "Bayesian A/B testing")
19144 "This package provides functions for Bayesian A/B testing including prior
19145 elicitation options based on Kass and Vaidyanathan (1992)
19146 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19147 (license license:gpl2+)))
19149 (define-public r-accept
19156 (uri (cran-uri "accept" version))
19159 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19160 (properties `((upstream-name . "accept")))
19161 (build-system r-build-system)
19163 `(("r-dplyr" ,r-dplyr)
19164 ("r-extrafont" ,r-extrafont)
19166 ("r-plotly" ,r-plotly)
19167 ("r-stringr" ,r-stringr)
19168 ("r-viridis" ,r-viridis)))
19169 (home-page "https://cran.r-project.org/web/packages/accept/")
19170 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19172 "This package allows clinicians to predict the rate and severity of
19173 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19174 Disease} (COPD) patients, based on the clinical prediction model published in
19175 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19176 (license license:gpl3)))
19178 (define-public r-smpracticals
19180 (name "r-smpracticals")
19185 (uri (cran-uri "SMPracticals" version))
19188 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19189 (properties `((upstream-name . "SMPracticals")))
19190 (build-system r-build-system)
19192 `(("r-ellipse" ,r-ellipse)
19195 ("r-survival" ,r-survival)))
19196 (home-page "http://statwww.epfl.ch/davison/SM/")
19197 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19199 "This package contains the datasets and a few functions for use with the
19200 practicals outlined in Appendix A of the book Statistical Models (Davison,
19201 2003, Cambridge University Press). The practicals themselves can be found at
19202 @url{http://statwww.epfl.ch/davison/SM/}.")
19203 (license license:gpl2+)))
19205 (define-public r-fgui
19212 (uri (cran-uri "fgui" version))
19215 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19216 (properties `((upstream-name . "fgui")))
19217 (build-system r-build-system)
19219 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19220 (synopsis "Create GUI for R functions")
19222 "Rapidly create a GUI for a function you created by automatically
19223 creating widgets for arguments of the function. This package automatically
19224 parses help routines for context-sensitive help to these arguments. The
19225 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19226 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19227 incorporated into the interface for greater customization for the more
19229 ;; Any version of the GPL.
19230 (license (list license:gpl2+ license:gpl3+))))
19232 (define-public r-tcltk2
19239 (uri (cran-uri "tcltk2" version))
19242 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19243 (properties `((upstream-name . "tcltk2")))
19244 (build-system r-build-system)
19248 (home-page "https://www.sciviews.org/SciViews-R")
19249 (synopsis "Tcl/Tk additions")
19251 "This package provides a series of additional Tcl commands and Tk widgets
19252 with style and various functions to supplement the tcltk package")
19253 (license license:lgpl3)))
19255 (define-public r-accrual
19262 (uri (cran-uri "accrual" version))
19265 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19266 (properties `((upstream-name . "accrual")))
19267 (build-system r-build-system)
19269 `(("r-fgui" ,r-fgui)
19270 ("r-smpracticals" ,r-smpracticals)
19271 ("r-tcltk2" ,r-tcltk2)))
19272 (home-page "https://cran.r-project.org/web/packages/accrual/")
19273 (synopsis "Bayesian accrual prediction")
19275 "Subject recruitment for medical research is challenging. Slow patient
19276 accrual leads to delay in research. Accrual monitoring during the process of
19277 recruitment is critical. Researchers need reliable tools to manage the
19278 accrual rate. This package provides an implementation of a Bayesian method
19279 that integrates researcher's experience on previous trials and data from the
19280 current study, providing reliable prediction on accrual rate for clinical
19281 studies. It provides functions for Bayesian accrual prediction which can be
19282 easily used by statisticians and clinical researchers.")
19283 (license license:gpl2)))
19285 (define-public r-accrued
19292 (uri (cran-uri "accrued" version))
19295 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19296 (properties `((upstream-name . "accrued")))
19297 (build-system r-build-system)
19298 (home-page "https://cran.r-project.org/web/packages/accrued/")
19299 (synopsis "Data quality visualization tools for partially accruing data")
19301 "This is a package for visualizing data quality of partially accruing
19303 (license license:gpl3)))
19305 (define-public r-mda
19312 (uri (cran-uri "mda" version))
19315 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19316 (properties `((upstream-name . "mda")))
19317 (build-system r-build-system)
19318 (propagated-inputs `(("r-class" ,r-class)))
19319 (native-inputs `(("gfortran" ,gfortran)))
19320 (home-page "https://cran.r-project.org/web/packages/mda/")
19321 (synopsis "Mixture and flexible discriminant analysis")
19323 "This is a package for mixture and flexible discriminant analysis,
19324 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19325 (license license:gpl2)))
19327 (define-public r-elasticnet
19329 (name "r-elasticnet")
19334 (uri (cran-uri "elasticnet" version))
19337 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19338 (properties `((upstream-name . "elasticnet")))
19339 (build-system r-build-system)
19341 `(("r-lars" ,r-lars)))
19342 (home-page "http://users.stat.umn.edu/~zouxx019/")
19343 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19345 "This package provides functions for fitting the entire solution path of
19346 the Elastic-Net and also provides functions for estimating sparse Principal
19347 Components. The Lasso solution paths can be computed by the same function.")
19348 (license license:gpl2+)))
19350 (define-public r-sparselda
19352 (name "r-sparselda")
19357 (uri (cran-uri "sparseLDA" version))
19360 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19361 (properties `((upstream-name . "sparseLDA")))
19362 (build-system r-build-system)
19364 `(("r-elasticnet" ,r-elasticnet)
19367 (home-page "https://www.imm.dtu.dk/~lkhc/")
19368 (synopsis "Sparse discriminant analysis")
19370 "This package performs sparse linear discriminant analysis for Gaussians
19371 and mixture of Gaussian models.")
19372 (license license:gpl2+)))
19374 (define-public r-accsda
19381 (uri (cran-uri "accSDA" version))
19384 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19385 (properties `((upstream-name . "accSDA")))
19386 (build-system r-build-system)
19388 `(("r-ggplot2" ,r-ggplot2)
19389 ("r-ggthemes" ,r-ggthemes)
19390 ("r-gridextra" ,r-gridextra)
19392 ("r-rarpack" ,r-rarpack)
19393 ("r-sparselda" ,r-sparselda)))
19394 (home-page "https://github.com/gumeo/accSDA/wiki")
19395 (synopsis "Accelerated sparse discriminant analysis")
19397 "This package provides an implementation of sparse linear discriminant
19398 analysis, which is a supervised classification method for multiple classes.
19399 Various novel optimization approaches to this problem are implemented
19400 including @dfn{alternating direction method of multipliers} (ADMM),
19401 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19402 Functions for performing cross validation are also supplied along with basic
19403 prediction and plotting functions. @dfn{Sparse zero variance
19404 discriminant} (SZVD) analysis is also included in the package.")
19405 (license license:gpl2+)))
19407 (define-public r-ace2fastq
19409 (name "r-ace2fastq")
19414 (uri (cran-uri "ace2fastq" version))
19417 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19418 (properties `((upstream-name . "ace2fastq")))
19419 (build-system r-build-system)
19421 `(("r-stringr" ,r-stringr)))
19422 (home-page "https://github.com/c5sire/ace2fastq")
19423 (synopsis "ACE file to FASTQ converter")
19425 "The ACE file format is used in genomics to store contigs from sequencing
19426 machines. This tools converts it into FASTQ format. Both formats contain the
19427 sequence characters and their corresponding quality information. Unlike the
19428 FASTQ file, the ACE file stores the quality values numerically. The
19429 conversion algorithm uses the standard Sanger formula. The package
19430 facilitates insertion into pipelines, and content inspection.")
19431 (license license:gpl3)))
19433 (define-public r-rngwell
19440 (uri (cran-uri "rngWELL" version))
19443 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19444 (properties `((upstream-name . "rngWELL")))
19445 (build-system r-build-system)
19446 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19447 (synopsis "Toolbox for WELL random number generators")
19449 "This is a dedicated package to WELL pseudo random generators, which were
19450 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19451 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19452 (license license:bsd-3)))
19454 (define-public r-randtoolbox
19456 (name "r-randtoolbox")
19461 (uri (cran-uri "randtoolbox" version))
19464 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19465 (properties `((upstream-name . "randtoolbox")))
19466 (build-system r-build-system)
19468 `(("r-rngwell" ,r-rngwell)))
19470 `(("gfortran" ,gfortran)))
19471 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19472 (synopsis "Toolbox for pseudo and quasi random number generation")
19474 "This package provides
19477 @item pseudo random generators, such as general linear
19478 congruential generators, multiple recursive generators and generalized
19479 feedback shift register (SF-Mersenne Twister algorithm and WELL
19482 @item quasi random generators, such as the Torus algorithm, the Sobol
19483 sequence, the Halton sequence (including the Van der Corput sequence), and
19485 @item some generator tests: the gap test, the serial test, the poker test.
19488 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19489 (license license:bsd-3)))
19491 (define-public r-lhs
19498 (uri (cran-uri "lhs" version))
19501 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19502 (properties `((upstream-name . "lhs")))
19503 (build-system r-build-system)
19504 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19506 `(("r-knitr" ,r-knitr)))
19507 (home-page "https://github.com/bertcarnell/lhs")
19508 (synopsis "Latin Hypercube Samples")
19510 "This package provides a number of methods for creating and augmenting
19511 Latin Hypercube Samples.")
19512 (license license:gpl3)))
19514 (define-public r-acebayes
19516 (name "r-acebayes")
19521 (uri (cran-uri "acebayes" version))
19524 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19525 (properties `((upstream-name . "acebayes")))
19526 (build-system r-build-system)
19528 `(("r-compare" ,r-compare)
19530 ("r-randtoolbox" ,r-randtoolbox)
19532 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19533 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19534 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19536 "Finding an optimal Bayesian experimental design involves maximizing an
19537 objective function given by the expectation of some appropriately chosen
19538 utility function with respect to the joint distribution of unknown
19539 quantities (including responses). This objective function is usually not
19540 available in closed form and the design space can be continuous and of high
19541 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19542 to maximise an approximation to the expectation of the utility function.")
19543 (license license:gpl2)))
19545 (define-public r-acet
19552 (uri (cran-uri "ACEt" version))
19555 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19556 (properties `((upstream-name . "ACEt")))
19557 (build-system r-build-system)
19562 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19563 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19564 (synopsis "Estimating dynamic heritability and twin model comparison")
19566 "This package supports twin models that are able to estimate the dynamic
19567 behaviour of the variance components in the classical twin models with respect
19568 to age using B-splines and P-splines.")
19569 (license license:gpl2+)))
19571 (define-public r-acfmperiod
19573 (name "r-acfmperiod")
19578 (uri (cran-uri "acfMPeriod" version))
19581 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19582 (properties `((upstream-name . "acfMPeriod")))
19583 (build-system r-build-system)
19585 `(("r-mass" ,r-mass)))
19586 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19587 (synopsis "Estimation of the ACF from the M-periodogram")
19589 "This package support non-robust and robust computations of the sample
19590 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19591 univariate and multivariate processes. The methodology consists in reversing
19592 the diagonalization procedure involving the periodogram or the
19593 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19594 ACOVF or the ACF as discussed in Fuller (1995)
19595 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19596 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19597 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19598 (license license:gpl2+)))
19600 (define-public r-gamlss-data
19602 (name "r-gamlss-data")
19607 (uri (cran-uri "gamlss.data" version))
19610 "1cjb2n5i5mnhmb5qbqycdbfg65j7nxb9s74yihqs9kpa39byrzcq"))))
19611 (properties `((upstream-name . "gamlss.data")))
19612 (build-system r-build-system)
19613 (home-page "http://www.gamlss.org/")
19614 (synopsis "GAMLSS data")
19616 "This package provides data used as examples to demonstrate GAMLSS
19618 ;; Either version of the license
19619 (license (list license:gpl2 license:gpl3))))
19621 (define-public r-gamlss
19628 (uri (cran-uri "gamlss" version))
19631 "06mh00jjxnqwknbv777hawjk0zm81ixrp35fg59mrlqz8y3p2w3j"))))
19632 (properties `((upstream-name . "gamlss")))
19633 (build-system r-build-system)
19635 `(("r-gamlss-data" ,r-gamlss-data)
19636 ("r-gamlss-dist" ,r-gamlss-dist)
19639 ("r-survival" ,r-survival)))
19640 (home-page "http://www.gamlss.org/")
19641 (synopsis "Generalized additive models for location scale and shape")
19643 "This package provides functions for fitting the generalized additive
19644 models for location scale and shape introduced by Rigby and
19645 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19646 use a distributional regression approach where all the parameters of the
19647 conditional distribution of the response variable are modelled using
19648 explanatory variables.")
19649 ;; Either version of the license
19650 (license (list license:gpl2 license:gpl3))))
19652 (define-public r-acid
19659 (uri (cran-uri "acid" version))
19662 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19663 (properties `((upstream-name . "acid")))
19664 (build-system r-build-system)
19666 `(("r-gamlss" ,r-gamlss)
19667 ("r-gamlss-dist" ,r-gamlss-dist)
19668 ("r-hmisc" ,r-hmisc)))
19669 (home-page "https://cran.r-project.org/web/packages/acid/")
19670 (synopsis "Analysing conditional income distributions")
19672 "This package provides functions for the analysis of income distributions
19673 for subgroups of the population as defined by a set of variables like age,
19674 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19675 distribution as well as functions for moments, inequality measures, entropy
19676 measures and polarisation measures of income distributions. This package thus
19677 aides the analysis of income inequality by offering tools for the exploratory
19678 analysis of income distributions at the disaggregated level.")
19679 (license license:gpl3)))
19681 (define-public r-acm4r
19688 (uri (cran-uri "acm4r" version))
19691 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19692 (properties `((upstream-name . "acm4r")))
19693 (build-system r-build-system)
19694 (propagated-inputs `(("r-mass" ,r-mass)))
19695 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19696 (synopsis "Align-and-count method comparisons of RFLP data")
19698 "This is a package to compare sequence fragment lengths or molecular
19699 weights from pairs of lanes. The number of matching bands in the
19700 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19701 the align-and-count method.")
19702 ;; Any version of the GPL
19703 (license (list license:gpl2+ license:gpl3+))))
19705 (define-public r-filelock
19707 (name "r-filelock")
19712 (uri (cran-uri "filelock" version))
19715 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19716 (properties `((upstream-name . "filelock")))
19717 (build-system r-build-system)
19718 (home-page "https://github.com/r-lib/filelock")
19719 (synopsis "Portable file locking")
19721 "This library lets you place an exclusive or shared lock on a file using
19722 the appropriate system call provided by the underlying operating system.")
19723 (license license:expat)))
19725 (define-public r-filematrix
19727 (name "r-filematrix")
19732 (uri (cran-uri "filematrix" version))
19735 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19736 (properties `((upstream-name . "filematrix")))
19737 (build-system r-build-system)
19738 ;; These inputs are needed for vignettes
19740 `(("r-knitr" ,r-knitr)
19741 ("r-rmarkdown" ,r-rmarkdown)
19742 ("pandoc-citeproc" ,pandoc-citeproc)))
19743 (home-page "https://github.com/andreyshabalin/filematrix")
19744 (synopsis "File-backed matrix class with convenient read and write access")
19746 "This package provides an interface for working with large matrices
19747 stored in files, not in computer memory. It supports multiple non-character
19748 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19749 byte real values). Access to parts of the matrix is done by indexing, exactly
19750 as with usual R matrices. It supports very large matrices; the package has
19751 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19752 columns, ad allows for quick addition of extra columns to a filematrix.")
19753 (license license:lgpl3)))
19755 (define-public r-acmeeqtl
19757 (name "r-acmeeqtl")
19762 (uri (cran-uri "ACMEeqtl" version))
19765 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19766 (properties `((upstream-name . "ACMEeqtl")))
19767 (build-system r-build-system)
19769 `(("r-filematrix" ,r-filematrix)))
19770 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19771 (synopsis "Estimation of interpretable eQTL effect sizes")
19773 "This package provides a non-linear model, termed ACME, that reflects a
19774 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19775 With non-linear least-squares algorithm the maximum likelihood parameters can
19776 be estimated. The ACME model provides interpretable effect size estimates and
19777 p-values with well controlled Type-I error.")
19778 (license license:lgpl3)))
19780 (define-public r-acmer
19787 (uri (cran-uri "acmeR" version))
19790 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19791 (properties `((upstream-name . "acmeR")))
19792 (build-system r-build-system)
19793 (propagated-inputs `(("r-foreign" ,r-foreign)))
19794 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19795 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19797 "This package provides an implementation of the ACME estimator, described
19798 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19799 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19800 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19801 as carcasses age; variable bleed-through at successive searches; and interval
19802 mortality estimates. The package provides, based on search data, functions
19803 for estimating the mortality inflation factor in Frequentist and Bayesian
19805 (license license:expat)))
19807 (define-public r-r-huge
19814 (uri (cran-uri "R.huge" version))
19817 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19818 (properties `((upstream-name . "R.huge")))
19819 (build-system r-build-system)
19821 `(("r-r-methodss3" ,r-r-methodss3)
19823 ("r-r-utils" ,r-r-utils)))
19824 (home-page "https://github.com/HenrikBengtsson/R.huge")
19825 (synopsis "Methods for accessing huge amounts of data")
19827 "This is a deprecated package for accessing huge amounts of data.
19828 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19829 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19830 the @code{aroma.affymetrix} package.")
19831 (license license:lgpl2.1+)))
19833 (define-public r-r-filesets
19835 (name "r-r-filesets")
19840 (uri (cran-uri "R.filesets" version))
19843 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19844 (properties `((upstream-name . "R.filesets")))
19845 (build-system r-build-system)
19847 `(("r-digest" ,r-digest)
19848 ("r-r-cache" ,r-r-cache)
19849 ("r-r-methodss3" ,r-r-methodss3)
19851 ("r-r-utils" ,r-r-utils)))
19852 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19853 (synopsis "Easy handling of and access to files")
19855 "This package provides classes and methods to locate, setup, subset,
19856 navigate and iterate file sets, i.e. sets of files located in one or more
19857 directories on the file system. The API is designed such that these classes
19858 can be extended via inheritance to provide a richer API for special file
19859 formats. Moreover, a specific name format is defined such that filenames and
19860 directories can be considered to have full names which consists of a name
19861 followed by comma-separated tags. This adds additional flexibility to
19862 identify file sets and individual files.")
19863 (license license:lgpl2.1+)))
19865 (define-public r-r-devices
19867 (name "r-r-devices")
19872 (uri (cran-uri "R.devices" version))
19875 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19876 (properties `((upstream-name . "R.devices")))
19877 (build-system r-build-system)
19879 `(("r-base64enc" ,r-base64enc)
19880 ("r-r-methodss3" ,r-r-methodss3)
19882 ("r-r-utils" ,r-r-utils)))
19883 (home-page "https://github.com/HenrikBengtsson/R.devices")
19884 (synopsis "Unified handling of graphics devices")
19886 "This package provides functions for creating plots and image files in a
19887 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19888 Default device options as well as scales and aspect ratios are controlled in a
19889 uniform way across all device types. Switching output format requires minimal
19890 changes in code. This package is ideal for large-scale batch processing,
19891 because it will never leave open graphics devices or incomplete image files
19892 behind, even on errors or user interrupts.")
19893 (license license:lgpl2.1+)))
19895 (define-public r-acnr
19902 (uri (cran-uri "acnr" version))
19905 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19906 (properties `((upstream-name . "acnr")))
19907 (build-system r-build-system)
19908 (home-page "https://github.com/mpierrejean/acnr")
19909 (synopsis "Annotated copy-number regions")
19911 "This package provides SNP array data from different types of copy-number
19912 regions. These regions were identified manually by the authors of the package
19913 and may be used to generate realistic data sets with known truth.")
19914 (license license:lgpl2.1+)))
19916 (define-public r-acopula
19923 (uri (cran-uri "acopula" version))
19926 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19927 (properties `((upstream-name . "acopula")))
19928 (build-system r-build-system)
19929 (home-page "https://cran.r-project.org/web/packages/acopula/")
19930 (synopsis "Modelling dependence with multivariate Archimax copulas")
19932 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19933 package provides definitions of several parametric families of generator and
19934 dependence function, computes CDF and PDF, estimates parameters, tests for
19935 goodness of fit, generates random sample and checks copula properties for
19936 custom constructs. In the 2-dimensional case explicit formulas for density
19937 are used, contrary to higher dimensions when all derivatives are linearly
19938 approximated. Several non-archimax families (normal, FGM, Plackett) are
19939 provided as well.")
19940 (license license:gpl2)))
19942 (define-public r-tuner
19949 (uri (cran-uri "tuneR" version))
19952 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19953 (properties `((upstream-name . "tuneR")))
19954 (build-system r-build-system)
19955 (propagated-inputs `(("r-signal" ,r-signal)))
19956 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19957 (synopsis "Analysis of music and speech")
19959 "This is a package for the analysis of music and speech. Analyze music
19960 and speech, extract features like MFCCs, handle wave files and their
19961 representation in various ways, read MP3, read MIDI, perform steps of a
19962 transcription, ...")
19963 ;; Either of these versions.
19964 (license (list license:gpl2 license:gpl3))))
19966 (define-public r-seewave
19973 (uri (cran-uri "seewave" version))
19976 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19977 (properties `((upstream-name . "seewave")))
19978 (build-system r-build-system)
19980 `(("libsndfile" ,libsndfile)))
19982 `(("r-tuner" ,r-tuner)))
19983 (home-page "http://rug.mnhn.fr/seewave")
19984 (synopsis "Sound analysis and synthesis")
19986 "This package provides functions for analysing, manipulating, displaying,
19987 editing and synthesizing time waves (particularly sound). This package
19988 processes time analysis (oscillograms and envelopes), spectral content,
19989 resonance quality factor, entropy, cross correlation and autocorrelation,
19990 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19991 and 3D spectrograms and many other analyses.")
19992 (license license:gpl2+)))
19994 (define-public r-acousticndlcoder
19996 (name "r-acousticndlcoder")
20001 (uri (cran-uri "AcousticNDLCodeR" version))
20004 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
20006 `((upstream-name . "AcousticNDLCodeR")))
20007 (build-system r-build-system)
20009 `(("r-seewave" ,r-seewave)
20010 ("r-tuner" ,r-tuner)
20012 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
20013 (synopsis "Coding sound files for use with NDL")
20015 "Make acoustic cues to use with the R package @code{ndl}.
20016 The package implements functions used in the PLoS ONE paper \"Words from
20017 spontaneous conversational speech can be recognized with human-like accuracy
20018 by an error-driven learning algorithm that discriminates between meanings
20019 straight from smart acoustic features, bypassing the phoneme as recognition
20020 unit.\" @url{doi:10.1371/journal.pone.0174623}")
20021 (license license:gpl2+)))
20023 (define-public r-acp
20030 (uri (cran-uri "acp" version))
20033 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
20034 (properties `((upstream-name . "acp")))
20035 (build-system r-build-system)
20037 `(("r-quantmod" ,r-quantmod)
20038 ("r-tseries" ,r-tseries)))
20039 (home-page "https://cran.r-project.org/web/packages/acp/")
20040 (synopsis "Autoregressive conditional Poisson")
20042 "This package supports the analysis of count data exhibiting
20043 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
20044 model (ACP(p,q)) proposed by Heinen (2003).")
20045 (license license:gpl2)))
20047 (define-public r-ada
20054 (uri (cran-uri "ada" version))
20057 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20058 (properties `((upstream-name . "ada")))
20059 (build-system r-build-system)
20060 (propagated-inputs `(("r-rpart" ,r-rpart)))
20061 (home-page "https://cran.r-project.org/web/packages/ada/")
20062 (synopsis "Stochastic boosting")
20064 "This package provides a straightforward, well-documented, and broad
20065 boosting routine for classification, ideally suited for small to
20066 moderate-sized data sets. It performs discrete, real, and gentle boost under
20067 both exponential and logistic loss on a given data set.")
20068 ;; Any version of the GPL.
20069 (license (list license:gpl2+ license:gpl3+))))
20071 (define-public r-genalg
20078 (uri (cran-uri "genalg" version))
20081 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20082 (properties `((upstream-name . "genalg")))
20083 (build-system r-build-system)
20084 (home-page "https://github.com/egonw/genalg")
20085 (synopsis "R based genetic algorithm")
20087 "This package provides an R based genetic algorithm for binary and
20088 floating point chromosomes.")
20089 (license license:gpl2)))
20091 (define-public r-kernelfactory
20093 (name "r-kernelfactory")
20098 (uri (cran-uri "kernelFactory" version))
20101 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20102 (properties `((upstream-name . "kernelFactory")))
20103 (build-system r-build-system)
20106 ("r-genalg" ,r-genalg)
20107 ("r-kernlab" ,r-kernlab)
20108 ("r-randomforest" ,r-randomforest)))
20109 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20110 (synopsis "Ensemble of kernel machines")
20112 "Kernel factory is an ensemble method where each base classifier (random
20113 forest) is fit on the kernel matrix of a subset of the training data.")
20114 (license license:gpl2+)))
20116 (define-public r-dummies
20123 (uri (cran-uri "dummies" version))
20126 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20127 (properties `((upstream-name . "dummies")))
20128 (build-system r-build-system)
20129 (home-page "https://decisionpatterns.com")
20130 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20132 "This package lets you expand factors, characters and other eligible
20133 classes into dummy/indicator variables.")
20134 (license license:gpl2+)))
20136 (define-public r-acrm
20143 (uri (cran-uri "aCRM" version))
20146 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20147 (properties `((upstream-name . "aCRM")))
20148 (build-system r-build-system)
20151 ("r-dummies" ,r-dummies)
20152 ("r-kernelfactory" ,r-kernelfactory)
20153 ("r-randomforest" ,r-randomforest)))
20154 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20155 (synopsis "Convenience functions for analytical customer relationship management")
20157 "This package provides convenience functions for data preparation and
20158 modeling often used in @dfn{analytical customer relationship
20159 management} (aCRM).")
20160 (license license:gpl2+)))
20162 (define-public r-treeclust
20164 (name "r-treeclust")
20169 (uri (cran-uri "treeClust" version))
20172 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20173 (properties `((upstream-name . "treeClust")))
20174 (build-system r-build-system)
20176 `(("r-cluster" ,r-cluster)
20177 ("r-rpart" ,r-rpart)))
20178 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20179 (synopsis "Cluster distances through trees")
20181 "This package provides tools to create a measure of inter-point
20182 dissimilarity useful for clustering mixed data, and, optionally, perform the
20184 (license license:gpl2+)))
20186 (define-public r-acrosstic
20188 (name "r-acrosstic")
20193 (uri (cran-uri "AcrossTic" version))
20196 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20197 (properties `((upstream-name . "AcrossTic")))
20198 (build-system r-build-system)
20200 `(("r-lpsolve" ,r-lpsolve)
20201 ("r-treeclust" ,r-treeclust)))
20202 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20203 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20205 "This is a package for constructing minimum-cost regular spanning
20206 subgraph as part of a non-parametric two-sample test for equality of
20208 (license license:gpl2+)))
20210 (define-public r-acrt
20217 (uri (cran-uri "acrt" version))
20220 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20221 (properties `((upstream-name . "acrt")))
20222 (build-system r-build-system)
20224 `(("r-rcpp" ,r-rcpp)
20225 ("r-rcppeigen" ,r-rcppeigen)
20226 ("r-sandwich" ,r-sandwich)))
20227 (home-page "https://cran.r-project.org/web/packages/acrt/")
20228 (synopsis "Autocorrelation robust testing")
20230 "This package provides functions for testing affine hypotheses on the
20231 regression coefficient vector in regression models with autocorrelated
20233 (license license:gpl2)))
20235 (define-public r-acs
20242 (uri (cran-uri "acs" version))
20245 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20246 (properties `((upstream-name . "acs")))
20247 (build-system r-build-system)
20249 `(("r-httr" ,r-httr)
20252 ("r-stringr" ,r-stringr)
20254 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20255 (synopsis "Work with data from the US Census")
20257 "This package provides a general toolkit for downloading, managing,
20258 analyzing, and presenting data from the
20259 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20260 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20261 American Community Survey (ACS). Confidence intervals provided with ACS data
20262 are converted to standard errors to be bundled with estimates in complex
20263 @code{acs} objects. The package provides new methods to conduct standard
20264 operations on @code{acs} objects and present/plot data in statistically
20265 appropriate ways.")
20266 (license license:gpl3)))
20268 (define-public r-acss-data
20270 (name "r-acss-data")
20275 (uri (cran-uri "acss.data" version))
20278 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20279 (properties `((upstream-name . "acss.data")))
20280 (build-system r-build-system)
20281 (home-page "http://complexitycalculator.com/methodology.html")
20282 (synopsis "Data for algorithmic complexity of short strings")
20284 "This is a data only package providing the algorithmic complexity of
20285 short strings, computed using the coding theorem method. For a given set of
20286 symbols in a string, all possible or a large number of random samples of
20287 Turing machines with a given number of states (e.g., 5) and number of symbols
20288 corresponding to the number of symbols in the strings were simulated until
20289 they reached a halting state or failed to end. This package contains data on
20290 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20291 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20292 distribution of the halting states.")
20293 (license license:gpl2+)))
20295 (define-public r-acss
20302 (uri (cran-uri "acss" version))
20305 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20306 (properties `((upstream-name . "acss")))
20307 (build-system r-build-system)
20309 `(("r-acss-data" ,r-acss-data)
20311 (home-page "http://complexitycalculator.com/methodology.html")
20312 (synopsis "Algorithmic complexity for short strings")
20314 "The main purpose of this package is to provide the algorithmic
20315 complexity for short strings, an approximation of the Kolmogorov Complexity of
20316 a short string using the coding theorem method. While the database containing
20317 the complexity is provided in the data only package @code{acss.data}, this
20318 package provides functions accessing the data such as @code{prob_random}
20319 returning the posterior probability that a given string was produced by a
20320 random process. In addition, two traditional (but problematic) measures of
20321 complexity are also provided: entropy and change complexity.")
20322 (license license:gpl2+)))
20324 (define-public r-acswr
20331 (uri (cran-uri "ACSWR" version))
20334 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20335 (properties `((upstream-name . "ACSWR")))
20336 (build-system r-build-system)
20338 `(("r-mass" ,r-mass)))
20339 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20340 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20342 "This is a companion package for the book \"A Course in Statistics with
20343 R\" (ISBN 978-1-119-15272-9.)")
20344 (license license:gpl2)))
20346 (define-public r-alabama
20349 (version "2015.3-1")
20353 (uri (cran-uri "alabama" version))
20356 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20357 (properties `((upstream-name . "alabama")))
20358 (build-system r-build-system)
20359 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20360 (home-page "https://cran.r-project.org/web/packages/alabama/")
20361 (synopsis "Constrained nonlinear optimization")
20363 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20364 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20365 constraints. Linear or nonlinear equality and inequality constraints are
20367 (license license:gpl2+)))
20369 (define-public r-gdina
20376 (uri (cran-uri "GDINA" version))
20379 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20380 (properties `((upstream-name . "GDINA")))
20381 (build-system r-build-system)
20383 `(("r-alabama" ,r-alabama)
20384 ("r-ggplot2" ,r-ggplot2)
20386 ("r-nloptr" ,r-nloptr)
20387 ("r-numderiv" ,r-numderiv)
20389 ("r-rcpparmadillo" ,r-rcpparmadillo)
20390 ("r-rsolnp" ,r-rsolnp)
20391 ("r-shiny" ,r-shiny)
20392 ("r-shinydashboard" ,r-shinydashboard)))
20394 `(("r-knitr" ,r-knitr)))
20395 (home-page "https://github.com/Wenchao-Ma/GDINA")
20396 (synopsis "Generalized DINA model framework")
20398 "This package provides a set of psychometric tools for cognitive
20399 diagnosis modeling based on the generalized deterministic inputs, noisy and
20400 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20401 and its extensions, including the sequential G-DINA model by Ma and de la
20402 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20403 polytomous G-DINA model by Chen and de la Torre
20404 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20405 distribution can be independent, saturated, higher-order, loglinear smoothed
20406 or structured. Q-matrix validation, item and model fit statistics, model
20407 comparison at test and item level and differential item functioning can also
20408 be conducted. A graphical user interface is also provided.")
20409 (license license:gpl3)))
20411 (define-public r-actcd
20418 (uri (cran-uri "ACTCD" version))
20421 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20422 (properties `((upstream-name . "ACTCD")))
20423 (build-system r-build-system)
20425 `(("r-gdina" ,r-gdina)
20426 ("r-r-methodss3" ,r-r-methodss3)))
20428 `(("gfortran" ,gfortran)))
20429 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20430 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20432 "This is a package supporting cluster analysis for cognitive diagnosis
20433 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20434 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20435 sum-scores, cluster analysis techniques can be used to classify examinees into
20436 latent classes based on their attribute patterns. In addition to the
20437 algorithms used to classify data, three labeling approaches are proposed to
20438 label clusters so that examinees' attribute profiles can be obtained.")
20439 (license license:gpl2+)))
20441 (define-public r-ineq
20448 (uri (cran-uri "ineq" version))
20451 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20452 (properties `((upstream-name . "ineq")))
20453 (build-system r-build-system)
20454 (home-page "https://cran.r-project.org/web/packages/ineq/")
20455 (synopsis "Measuring inequality, concentration, and poverty")
20457 "This package provides tools for measuring inequality, concentration, and
20458 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20459 ;; Either of these two versions.
20460 (license (list license:gpl2 license:gpl3))))
20462 (define-public r-actfrag
20469 (uri (cran-uri "ActFrag" version))
20472 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20473 (properties `((upstream-name . "ActFrag")))
20474 (build-system r-build-system)
20476 `(("r-accelerometry" ,r-accelerometry)
20477 ("r-dplyr" ,r-dplyr)
20479 ("r-survival" ,r-survival)
20480 ("r-tidyr" ,r-tidyr)))
20481 (home-page "https://github.com/junruidi/ActFrag")
20482 (synopsis "Activity fragmentation metrics extraction")
20484 "This package provides functions to extract commonly used fragmentation
20485 metrics to quantify time accumulation strategies based on minute level
20486 actigraphy-measured activity counts data.")
20487 (license license:gpl3)))
20489 (define-public r-ash
20496 (uri (cran-uri "ash" version))
20499 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20500 (properties `((upstream-name . "ash")))
20501 (build-system r-build-system)
20502 (native-inputs `(("gfortran" ,gfortran)))
20503 (home-page "https://cran.r-project.org/web/packages/ash/")
20504 (synopsis "David Scott's ASH routines")
20506 "This package provides David Scott's ASH routines ported from S-PLUS to
20508 (license license:gpl2+)))
20510 (define-public r-hdrcde
20517 (uri (cran-uri "hdrcde" version))
20520 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20521 (properties `((upstream-name . "hdrcde")))
20522 (build-system r-build-system)
20525 ("r-ggplot2" ,r-ggplot2)
20526 ("r-kernsmooth" ,r-kernsmooth)
20528 ("r-locfit" ,r-locfit)
20529 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20530 (native-inputs `(("gfortran" ,gfortran)))
20531 (home-page "http://pkg.robjhyndman.com/hdrcde")
20532 (synopsis "Highest density regions and conditional density estimation")
20534 "This is a package for the computation of highest density regions in one
20535 and two dimensions, kernel estimation of univariate density functions
20536 conditional on one covariate, and multimodal regression.")
20537 (license license:gpl3)))
20539 (define-public r-rainbow
20546 (uri (cran-uri "rainbow" version))
20549 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20550 (properties `((upstream-name . "rainbow")))
20551 (build-system r-build-system)
20553 `(("r-cluster" ,r-cluster)
20554 ("r-colorspace" ,r-colorspace)
20555 ("r-hdrcde" ,r-hdrcde)
20558 ("r-pcapp" ,r-pcapp)))
20559 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20560 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20562 "This is a package for visualizing functional data and identifying
20563 functional outliers with bagplots, boxplots and rainbow plots.")
20564 (license license:gpl3)))
20566 (define-public r-fds
20573 (uri (cran-uri "fds" version))
20576 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20577 (properties `((upstream-name . "fds")))
20578 (build-system r-build-system)
20580 `(("r-rainbow" ,r-rainbow)
20581 ("r-rcurl" ,r-rcurl)))
20582 (home-page "https://cran.r-project.org/web/packages/fds/")
20583 (synopsis "Functional data sets")
20584 (description "This package contains a list of functional time series,
20585 sliced functional time series, and functional data sets. Functional time
20586 series is a special type of functional data observed over time. Sliced
20587 functional time series is a special type of functional time series with a time
20588 variable observed over time.")
20589 (license license:gpl2+)))
20591 (define-public r-fda
20598 (uri (cran-uri "fda" version))
20601 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20602 (properties `((upstream-name . "fda")))
20603 (build-system r-build-system)
20606 ("r-matrix" ,r-matrix)))
20607 (home-page "https://www.functionaldata.org")
20608 (synopsis "Functional data analysis")
20610 "These functions were developed to support functional data analysis as
20611 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20612 Analysis. The package includes data sets and script files working many
20614 (license license:gpl2+)))
20616 (define-public r-actigraphy
20618 (name "r-actigraphy")
20623 (uri (cran-uri "Actigraphy" version))
20626 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20627 (properties `((upstream-name . "Actigraphy")))
20628 (build-system r-build-system)
20630 `(("r-fda" ,r-fda)))
20631 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20632 (synopsis "Actigraphy data analysis")
20634 "This package provides tools for functional linear modeling and analysis
20635 of actigraphy data.")
20636 (license license:asl2.0)))
20638 (define-public r-activedriver
20640 (name "r-activedriver")
20645 (uri (cran-uri "ActiveDriver" version))
20648 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20649 (properties `((upstream-name . "ActiveDriver")))
20650 (build-system r-build-system)
20652 `(("r-mass" ,r-mass)))
20653 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20654 (synopsis "Tools for finding cancer driver proteins")
20656 "This package provides a mutation analysis tool that discovers cancer
20657 driver genes with frequent mutations in protein signalling sites such as
20658 post-translational modifications (phosphorylation, ubiquitination, etc). The
20659 Poisson generalized linear regression model identifies genes where cancer
20660 mutations in signalling sites are more frequent than expected from the
20661 sequence of the entire gene. Integration of mutations with signalling
20662 information helps find new driver genes and propose candidate mechanisms to
20664 (license license:gpl2+)))
20666 (define-public r-activitycounts
20668 (name "r-activitycounts")
20673 (uri (cran-uri "activityCounts" version))
20676 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20678 `((upstream-name . "activityCounts")))
20679 (build-system r-build-system)
20681 `(("r-lubridate" ,r-lubridate)
20682 ("r-magrittr" ,r-magrittr)
20683 ("r-seewave" ,r-seewave)
20684 ("r-signal" ,r-signal)
20685 ("r-tibble" ,r-tibble)))
20686 (home-page "https://github.com/walkabillylab/activityCounts")
20687 (synopsis "Generate ActiLife counts")
20689 "ActiLife generates activity counts from data collected by Actigraph
20690 accelerometers. Actigraph is one of the most common research-grade
20691 accelerometers. There is considerable research validating and developing
20692 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20693 counts are proprietary and difficult to implement if researchers use different
20694 accelerometer brands. The code creates ActiLife counts from raw acceleration
20695 data for different accelerometer brands.")
20696 (license license:gpl3)))
20698 (define-public r-activityindex
20700 (name "r-activityindex")
20705 (uri (cran-uri "ActivityIndex" version))
20708 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20709 (properties `((upstream-name . "ActivityIndex")))
20710 (build-system r-build-system)
20712 `(("r-data-table" ,r-data-table)
20713 ("r-matrixstats" ,r-matrixstats)
20714 ("r-r-utils" ,r-r-utils)))
20716 `(("r-knitr" ,r-knitr)))
20717 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20718 (synopsis "Activity Index calculation using raw accelerometry data")
20720 "This is a package to read raw accelerometry from GT3X+ accelerometry
20721 data and plain table data to calculate the Activity Index from Bai et
20722 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20723 (license license:gpl3)))
20725 (define-public r-activpal
20727 (name "r-activpal")
20732 (uri (cran-uri "activPAL" version))
20735 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20736 (properties `((upstream-name . "activPAL")))
20737 (build-system r-build-system)
20739 `(("r-devtools" ,r-devtools)
20740 ("r-dplyr" ,r-dplyr)
20741 ("r-ggplot2" ,r-ggplot2)
20742 ("r-lubridate" ,r-lubridate)
20743 ("r-magrittr" ,r-magrittr)
20744 ("r-tidyr" ,r-tidyr)))
20745 (home-page "https://cran.r-project.org/web/packages/activPAL")
20746 (synopsis "Processing and chart generation from activPAL events files")
20748 "This package contains functions to generate pre-defined summary
20749 statistics from activPAL events files. The package also contains functions to
20750 produce informative graphics that visualize physical activity behaviour and
20751 trends. This includes generating graphs that align physical activity
20752 behaviour with additional time based observations described by other data
20753 sets, such as sleep diaries and continuous glucose monitoring data.")
20754 (license license:gpl3)))
20756 (define-public r-activpalprocessing
20758 (name "r-activpalprocessing")
20763 (uri (cran-uri "activpalProcessing" version))
20766 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20768 `((upstream-name . "activpalProcessing")))
20769 (build-system r-build-system)
20771 `(("r-chron" ,r-chron)))
20772 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20773 (synopsis "Process activPAL events files")
20775 "This package performs estimation of physical activity and sedentary
20776 behavior variables from activPAL events files.")
20777 ;; Either version of the GPL.
20778 (license (list license:gpl2 license:gpl3))))
20780 (define-public r-actogrammr
20782 (name "r-actogrammr")
20787 (uri (cran-uri "actogrammr" version))
20790 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20791 (properties `((upstream-name . "actogrammr")))
20792 (build-system r-build-system)
20794 `(("r-dplyr" ,r-dplyr)
20795 ("r-ggplot2" ,r-ggplot2)
20796 ("r-lubridate" ,r-lubridate)
20797 ("r-readr" ,r-readr)
20798 ("r-tidyr" ,r-tidyr)))
20799 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20800 (synopsis "Read in activity data and plot actograms")
20802 "Read in activity measurements from standard file formats used by
20803 circadian rhythm researchers, currently only ClockLab format, and process and
20804 plot the data. The central type of plot is the actogram, as first described
20805 in \"Activity and distribution of certain wild mice in relation to biotic
20806 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20807 (license license:gpl3)))
20809 (define-public r-expint
20816 (uri (cran-uri "expint" version))
20819 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20820 (properties `((upstream-name . "expint")))
20821 (build-system r-build-system)
20822 (home-page "https://gitlab.com/vigou3/expint")
20823 (synopsis "Exponential integral and incomplete Gamma function")
20825 "This package provides the exponential integrals @code{E_1(x)},
20826 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20827 function @code{G(a, x)} defined for negative values of its first argument.
20828 The package also gives easy access to the underlying C routines through an
20829 API; see the package vignette for details.")
20830 (license license:gpl2+)))
20832 (define-public r-actuar
20839 (uri (cran-uri "actuar" version))
20842 "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y"))))
20843 (properties `((upstream-name . "actuar")))
20844 (build-system r-build-system)
20845 (propagated-inputs `(("r-expint" ,r-expint)))
20846 (home-page "https://gitlab.com/vigou3/actuar")
20847 (synopsis "Actuarial functions and heavy tailed distributions")
20849 "This package provides functions and data sets for actuarial science:
20850 modeling of loss distributions; risk theory and ruin theory; simulation of
20851 compound models, discrete mixtures and compound hierarchical models;
20852 credibility theory. It boasts support for many additional probability
20853 distributions to model insurance loss amounts and loss frequency: 19
20854 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20855 distribution; zero-truncated and zero-modified extensions of the standard
20856 discrete distributions. It also supports phase-type distributions commonly
20857 used to compute ruin probabilities.")
20858 (license license:gpl2+)))
20860 (define-public r-bmp
20867 (uri (cran-uri "bmp" version))
20870 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20871 (properties `((upstream-name . "bmp")))
20872 (build-system r-build-system)
20873 (home-page "https://cran.r-project.org/web/packages/bmp/")
20874 (synopsis "Read Bitmap (BMP) images")
20876 "This package provides pure R tools to read BMP format images. It is
20877 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20878 (license license:gpl2+)))
20880 (define-public r-readbitmap
20882 (name "r-readbitmap")
20887 (uri (cran-uri "readbitmap" version))
20890 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20891 (properties `((upstream-name . "readbitmap")))
20892 (build-system r-build-system)
20894 `(("libjpeg" ,libjpeg-turbo)
20895 ("libpng" ,libpng)))
20900 ("r-tiff" ,r-tiff)))
20901 (home-page "https://github.com/jefferis/readbitmap")
20902 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20904 "This package provides tools to identify and read BMP, JPEG, PNG, and
20905 TIFF format bitmap images. Identification defaults to the use of the magic
20906 number embedded in the file rather than the file extension.")
20907 (license license:gpl2+)))
20909 (define-public r-imager
20916 (uri (cran-uri "imager" version))
20919 "1kzl93l6k9i4528bbycbqxdn28mj7hnx0fbxisva859xl1wys5c5"))))
20920 (properties `((upstream-name . "imager")))
20921 (build-system r-build-system)
20924 ("libtiff" ,libtiff)
20928 `(("r-downloader" ,r-downloader)
20929 ("r-igraph" ,r-igraph)
20931 ("r-magrittr" ,r-magrittr)
20933 ("r-purrr" ,r-purrr)
20935 ("r-readbitmap" ,r-readbitmap)
20936 ("r-stringr" ,r-stringr)))
20938 `(("pkg-config" ,pkg-config)
20939 ("r-knitr" ,r-knitr)))
20940 (home-page "https://dahtah.github.io/imager/")
20941 (synopsis "Image processing library")
20943 "This is a package for fast image processing for images in up to 4
20944 dimensions (two spatial dimensions, one time/depth dimension, one color
20945 dimension). It provides most traditional image processing tools (filtering,
20946 morphology, transformations, etc.) as well as various functions for easily
20947 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20948 simple, modern C++ library for image processing.")
20949 (license license:lgpl3)))
20951 (define-public r-acuityview
20953 (name "r-acuityview")
20958 (uri (cran-uri "AcuityView" version))
20961 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20962 (properties `((upstream-name . "AcuityView")))
20963 (build-system r-build-system)
20965 `(("r-fftwtools" ,r-fftwtools)
20966 ("r-imager" ,r-imager)
20967 ("r-plotrix" ,r-plotrix)))
20968 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20969 (synopsis "Display scenes as seen by an animal with less acute vision")
20971 "This package provides a simple method for representing a visual scene as
20972 it may be seen by an animal with less acute vision.")
20973 (license license:gpl2+)))
20975 (define-public r-caret
20982 (uri (cran-uri "caret" version))
20985 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20986 (build-system r-build-system)
20988 `(("r-foreach" ,r-foreach)
20989 ("r-ggplot2" ,r-ggplot2)
20990 ("r-lattice" ,r-lattice)
20991 ("r-modelmetrics" ,r-modelmetrics)
20995 ("r-recipes" ,r-recipes)
20996 ("r-reshape2" ,r-reshape2)
20997 ("r-withr" ,r-withr)))
20999 `(("r-knitr" ,r-knitr)))
21000 (home-page "https://github.com/topepo/caret")
21001 (synopsis "Classification and regression training")
21003 "This package provides miscellaneous functions for training and plotting
21004 classification and regression models.")
21005 (license license:gpl2+)))
21007 (define-public r-adabag
21014 (uri (cran-uri "adabag" version))
21017 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
21018 (properties `((upstream-name . "adabag")))
21019 (build-system r-build-system)
21021 `(("r-caret" ,r-caret)
21022 ("r-doparallel" ,r-doparallel)
21023 ("r-foreach" ,r-foreach)
21024 ("r-rpart" ,r-rpart)))
21025 (home-page "https://cran.r-project.org/web/packages/adabag/")
21026 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
21028 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
21029 Breiman's Bagging algorithm using classification trees as individual
21030 classifiers. Once these classifiers have been trained, they can be used to
21031 predict on new data. Also, cross validation estimation of the error can be
21033 (license license:gpl2+)))
21035 (define-public r-adagio
21042 (uri (cran-uri "adagio" version))
21045 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21046 (properties `((upstream-name . "adagio")))
21047 (build-system r-build-system)
21048 (native-inputs `(("gfortran" ,gfortran)))
21049 (home-page "https://cran.r-project.org/web/packages/adagio/")
21050 (synopsis "Discrete and global optimization routines")
21052 "This package provides methods and algorithms for discrete optimization,
21053 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21054 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21056 (license license:gpl3+)))
21058 (define-public r-univoutl
21060 (name "r-univoutl")
21065 (uri (cran-uri "univOutl" version))
21068 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
21069 (properties `((upstream-name . "univOutl")))
21070 (build-system r-build-system)
21072 `(("r-hmisc" ,r-hmisc)
21073 ("r-robustbase" ,r-robustbase)))
21074 (home-page "https://github.com/marcellodo/univOutl")
21075 (synopsis "Detection of univariate outliers")
21077 "This package provides well-known outlier detection techniques in the
21078 univariate case. Methods to deal with skewed distribution are included too.
21079 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21080 historical data is implemented as well. When available, survey weights can be
21081 used in outliers detection.")
21082 (license license:gpl2+)))
21084 (define-public r-tolerance
21086 (name "r-tolerance")
21091 (uri (cran-uri "tolerance" version))
21094 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21095 (properties `((upstream-name . "tolerance")))
21096 (build-system r-build-system)
21098 `(("r-mass" ,r-mass)
21100 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21101 (synopsis "Statistical tolerance intervals and regions")
21103 "This package provides functions for estimating tolerance
21104 limits (intervals) for various univariate distributions (binomial, Cauchy,
21105 discrete Pareto, exponential, two-parameter exponential, extreme value,
21106 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21107 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21108 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21109 nonparametric tolerance intervals, tolerance bands for regression
21110 settings (linear regression, nonlinear regression, nonparametric regression,
21111 and multivariate regression), and analysis of variance tolerance intervals.
21112 Visualizations are also available for most of these settings.")
21113 (license license:gpl2+)))
21115 (define-public r-additivitytests
21117 (name "r-additivitytests")
21122 (uri (cran-uri "additivityTests" version))
21125 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21127 `((upstream-name . "additivityTests")))
21128 (build-system r-build-system)
21129 (home-page "https://github.com/simecek/additivityTests")
21130 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21132 "This package provides an implementation of the Tukey, Mandel,
21133 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21134 (license license:gpl3)))
21136 (define-public r-flexclust
21138 (name "r-flexclust")
21143 (uri (cran-uri "flexclust" version))
21146 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21147 (properties `((upstream-name . "flexclust")))
21148 (build-system r-build-system)
21150 `(("r-class" ,r-class)
21151 ("r-lattice" ,r-lattice)
21152 ("r-modeltools" ,r-modeltools)))
21153 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21154 (synopsis "Flexible cluster algorithms")
21156 "The main function @code{kcca} implements a general framework for
21157 k-centroids cluster analysis supporting arbitrary distance measures and
21158 centroid computation. Further cluster methods include hard competitive
21159 learning, neural gas, and QT clustering. There are numerous visualization
21160 methods for cluster results (neighborhood graphs, convex cluster hulls,
21161 barcharts of centroids, ...), and bootstrap methods for the analysis of
21162 cluster stability.")
21163 (license license:gpl2)))
21165 (define-public r-biclust
21172 (uri (cran-uri "biclust" version))
21175 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21176 (properties `((upstream-name . "biclust")))
21177 (build-system r-build-system)
21179 `(("r-additivitytests" ,r-additivitytests)
21180 ("r-colorspace" ,r-colorspace)
21181 ("r-flexclust" ,r-flexclust)
21182 ("r-ggplot2" ,r-ggplot2)
21183 ("r-lattice" ,r-lattice)
21185 ("r-tidyr" ,r-tidyr)))
21186 (home-page "https://cran.r-project.org/web/packages/biclust/")
21187 (synopsis "BiCluster algorithms")
21189 "The main function @code{biclust()} provides several algorithms to find
21190 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21191 In addition, the package provides methods for data
21192 preprocessing (normalization and discretization), visualization, and
21193 validation of bicluster solutions.")
21194 (license license:gpl3)))
21196 (define-public r-icge
21203 (uri (cran-uri "ICGE" version))
21206 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21207 (properties `((upstream-name . "ICGE")))
21208 (build-system r-build-system)
21210 `(("r-cluster" ,r-cluster)
21211 ("r-mass" ,r-mass)))
21212 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21213 (synopsis "Cluster estimation and identification of atypical units")
21215 "ICGE is a package that helps to estimate the number of real clusters in
21216 data as well as to identify atypical units. The underlying methods are based
21217 on distances rather than on unit x variables.")
21218 (license license:gpl2+)))
21220 (define-public r-depth
21223 (version "2.1-1.1")
21227 (uri (cran-uri "depth" version))
21230 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21231 (properties `((upstream-name . "depth")))
21232 (build-system r-build-system)
21234 `(("r-abind" ,r-abind)
21235 ("r-circular" ,r-circular)
21238 `(("gfortran" ,gfortran)))
21239 (home-page "https://cran.r-project.org/web/packages/depth/")
21240 (synopsis "Nonparametric depth functions for multivariate analysis")
21242 "This package provides tools for depth functions methodology applied to
21243 multivariate analysis. Besides allowing calculation of depth values and
21244 depth-based location estimators, the package includes functions or drawing
21245 contour plots and perspective plots of depth functions. Euclidean and
21246 spherical depths are supported.")
21247 (license license:gpl2)))
21249 (define-public r-archetypes
21251 (name "r-archetypes")
21252 (version "2.2-0.1")
21256 (uri (cran-uri "archetypes" version))
21259 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21260 (properties `((upstream-name . "archetypes")))
21261 (build-system r-build-system)
21263 `(("r-modeltools" ,r-modeltools)
21264 ("r-nnls" ,r-nnls)))
21265 (home-page "https://cran.r-project.org/web/packages/archetypes")
21266 (synopsis "Archetypal analysis")
21268 "The main function @code{archetypes} implements a framework for
21269 archetypal analysis supporting arbitrary problem solving mechanisms for the
21270 different conceptual parts of the algorithm.")
21271 (license license:gpl2+)))
21273 (define-public r-shapes
21280 (uri (cran-uri "shapes" version))
21283 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
21284 (properties `((upstream-name . "shapes")))
21285 (build-system r-build-system)
21287 `(("r-mass" ,r-mass)
21288 ("r-minpack-lm" ,r-minpack-lm)
21290 ("r-scatterplot3d" ,r-scatterplot3d)))
21291 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21292 (synopsis "Statistical shape analysis")
21294 "This package provides routines for the statistical analysis of landmark
21295 shapes, including Procrustes analysis, graphical displays, principal
21296 components analysis, permutation and bootstrap tests, thin-plate spline
21297 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21298 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21299 Edition), John Wiley and Sons.")
21300 (license license:gpl2)))
21302 (define-public r-anthropometry
21304 (name "r-anthropometry")
21309 (uri (cran-uri "Anthropometry" version))
21312 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21313 (properties `((upstream-name . "Anthropometry")))
21314 (build-system r-build-system)
21316 `(("r-archetypes" ,r-archetypes)
21317 ("r-biclust" ,r-biclust)
21318 ("r-cluster" ,r-cluster)
21319 ("r-depth" ,r-depth)
21324 ("r-shapes" ,r-shapes)))
21326 `(("r-knitr" ,r-knitr)))
21327 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21328 (synopsis "Statistical methods for anthropometric data")
21330 "This package provides statistical methods especially developed to
21331 analyze anthropometric data. These methods are aimed at providing effective
21332 solutions to some commons problems related to Ergonomics and Anthropometry.
21333 They are based on clustering, the statistical concept of data depth,
21334 statistical shape analysis and archetypal analysis.")
21335 (license license:gpl2+)))
21337 (define-public r-adamethods
21339 (name "r-adamethods")
21344 (uri (cran-uri "adamethods" version))
21347 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21348 (properties `((upstream-name . "adamethods")))
21349 (build-system r-build-system)
21351 `(("r-anthropometry" ,r-anthropometry)
21352 ("r-archetypes" ,r-archetypes)
21354 ("r-foreach" ,r-foreach)
21356 ("r-tolerance" ,r-tolerance)
21357 ("r-univoutl" ,r-univoutl)))
21358 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21359 (synopsis "Archetypoid algorithms and anomaly detection")
21361 "This package is a collection of several algorithms to obtain
21362 archetypoids with small and large databases and with both classical
21363 multivariate data and functional data (univariate and multivariate). Some of
21364 these algorithms also detect anomalies (outliers).")
21365 (license license:gpl2+)))
21367 (define-public r-idpmisc
21374 (uri (cran-uri "IDPmisc" version))
21377 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21378 (properties `((upstream-name . "IDPmisc")))
21379 (build-system r-build-system)
21381 `(("r-lattice" ,r-lattice)))
21382 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21383 (synopsis "Functions for data analyses and visualization")
21385 "This package provides different high-level graphics functions for
21386 displaying large datasets, displaying circular data in a very flexible way,
21387 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21388 2D-plots, creating figures with differently colored margin and plot region.
21389 In addition, the package contains auxiliary functions for data manipulation
21390 like omitting observations with irregular values or selecting data by logical
21391 vectors, which include NAs. Other functions are especially useful in
21392 spectroscopy and analyses of environmental data: robust baseline fitting,
21393 finding peaks in spectra, converting humidity measures.")
21394 (license license:gpl3+)))
21396 (define-public r-qqman
21403 (uri (cran-uri "qqman" version))
21406 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21407 (properties `((upstream-name . "qqman")))
21408 (build-system r-build-system)
21410 `(("r-calibrate" ,r-calibrate)))
21411 (home-page "https://cran.r-project.org/web/packages/qqman/")
21412 (synopsis "Q-Q and Manhattan plots for GWAS data")
21414 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21415 from PLINK results.")
21416 (license license:gpl3)))
21418 (define-public r-ggplot-multistats
21420 (name "r-ggplot-multistats")
21425 (uri (cran-uri "ggplot.multistats" version))
21428 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21430 `((upstream-name . "ggplot.multistats")))
21431 (build-system r-build-system)
21433 `(("r-ggplot2" ,r-ggplot2)
21434 ("r-hexbin" ,r-hexbin)
21435 ("r-rlang" ,r-rlang)
21436 ("r-scales" ,r-scales)))
21437 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21438 (synopsis "Multiple summary statistics for binned stats/geometries")
21440 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21441 which functions similar to its singular form, but allows the use of multiple
21442 statistics per bin. Those statistics can be mapped to multiple bin
21444 (license license:gpl3)))
21446 (define-public r-knn-covertree
21448 (name "r-knn-covertree")
21453 (uri (cran-uri "knn.covertree" version))
21456 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21457 (properties `((upstream-name . "knn.covertree")))
21458 (build-system r-build-system)
21460 `(("r-matrix" ,r-matrix)
21462 ("r-rcppeigen" ,r-rcppeigen)))
21463 (home-page "https://github.com/flying-sheep/knn.covertree")
21464 (synopsis "Accurate kNN Implementation with multiple distance measures")
21466 "Similarly to the FNN package, this package allows calculation of the k
21467 nearest neighbors (kNN) of a data matrix. The implementation is based on
21468 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21469 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21470 (license license:agpl3+)))
21472 (define-public r-poibin
21479 (uri (cran-uri "poibin" version))
21482 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21483 (properties `((upstream-name . "poibin")))
21484 (build-system r-build-system)
21485 (home-page "https://cran.r-project.org/web/packages/poibin/")
21486 (synopsis "Poisson binomial distribution")
21488 "This package provides an implementation of both the exact and
21489 approximation methods for computing the @dfn{cumulative distribution
21490 function} (CDF) of the Poisson binomial distribution. It also provides the
21491 @dfn{probability mass function} (PMF), quantile function, and random number
21492 generation for the Poisson binomial distribution.")
21493 (license license:gpl2)))
21495 (define-public r-diagram
21502 (uri (cran-uri "diagram" version))
21505 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21506 (properties `((upstream-name . "diagram")))
21507 (build-system r-build-system)
21509 `(("r-shape" ,r-shape)))
21510 (home-page "https://cran.r-project.org/web/packages/diagram/")
21511 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21513 "This package provides tools to visualize simple graphs (networks) based
21514 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21515 electrical networks, etc. It also includes supporting material for the book
21516 \"A practical guide to ecological modelling - using R as a simulation
21517 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21518 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21519 Francesca Mazzia (2012).")
21520 (license license:gpl2+)))
21522 (define-public r-lim
21529 (uri (cran-uri "LIM" version))
21532 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21533 (properties `((upstream-name . "LIM")))
21534 (build-system r-build-system)
21536 `(("r-diagram" ,r-diagram)
21537 ("r-limsolve" ,r-limsolve)))
21538 (home-page "https://cran.r-project.org/web/packages/LIM/")
21539 (synopsis "Linear inverse model examples and solution methods")
21541 "This package provides functions that read and solve linear inverse
21542 problems (food web problems, linear programming problems).")
21543 (license license:gpl2+)))
21545 (define-public r-shinycssloaders
21547 (name "r-shinycssloaders")
21552 (uri (cran-uri "shinycssloaders" version))
21555 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21557 `((upstream-name . "shinycssloaders")))
21558 (build-system r-build-system)
21560 `(("r-digest" ,r-digest)
21562 ("r-shiny" ,r-shiny)))
21563 (home-page "https://github.com/andrewsali/shinycssloaders")
21564 (synopsis "Add CSS loading animations to Shiny outputs")
21566 "This package provides tools to create a lightweight Shiny wrapper for
21567 the css-loaders created by Luke Hass
21568 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21569 automatically show a loader when the output is (re)calculating.")
21570 (license license:gpl3)))
21572 (define-public r-rsvg
21579 (uri (cran-uri "rsvg" version))
21582 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21583 (properties `((upstream-name . "rsvg")))
21584 (build-system r-build-system)
21586 `(("librsvg" ,librsvg)
21589 `(("pkg-config" ,pkg-config)
21590 ("r-knitr" ,r-knitr)))
21591 (home-page "https://github.com/jeroen/rsvg#readme")
21592 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21594 "This package allows you to render vector-based SVG images into
21595 high-quality custom-size bitmap arrays using the librsvg2 library. The
21596 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21597 addition, the package can convert images directly to various formats such as
21598 PDF or PostScript.")
21599 (license license:expat)))
21601 (define-public r-influencer
21603 (name "r-influencer")
21608 (uri (cran-uri "influenceR" version))
21611 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21612 (properties `((upstream-name . "influenceR")))
21613 (build-system r-build-system)
21615 `(("r-igraph" ,r-igraph)
21616 ("r-matrix" ,r-matrix)))
21617 (home-page "https://github.com/rcc-uchicago/influenceR")
21618 (synopsis "Tools to quantify structural importance of nodes in a network")
21620 "This package provides functionality to compute various node centrality
21621 measures on networks. Included are functions to compute betweenness
21622 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21623 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21624 algorithm to identify key players, and Valente's bridging metric. The
21625 betweenness, Key Players, and bridging implementations are parallelized with
21627 (license license:gpl2)))
21629 (define-public r-emplik
21636 (uri (cran-uri "emplik" version))
21639 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21640 (properties `((upstream-name . "emplik")))
21641 (build-system r-build-system)
21643 `(("r-quantreg" ,r-quantreg)))
21644 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21645 (synopsis "Empirical likelihood ratio for censored/truncated data")
21647 "This package provides empirical likelihood ratio tests for
21648 means/quantiles/hazards from possibly censored and/or truncated data. It also
21650 (license license:gpl2+)))
21652 (define-public r-imputeyn
21654 (name "r-imputeyn")
21659 (uri (cran-uri "imputeYn" version))
21662 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21663 (properties `((upstream-name . "imputeYn")))
21664 (build-system r-build-system)
21666 `(("r-boot" ,r-boot)
21667 ("r-emplik" ,r-emplik)
21668 ("r-mvtnorm" ,r-mvtnorm)
21669 ("r-quadprog" ,r-quadprog)
21670 ("r-survival" ,r-survival)))
21671 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21672 (synopsis "Impute last largest censored observation under weighted least squares")
21674 "This package allows for the imputation of the last largest censored
21675 observantions. This method brings less bias and more efficient estimates for
21677 (license license:gpl2)))
21679 (define-public r-adapenetclass
21681 (name "r-adapenetclass")
21686 (uri (cran-uri "AdapEnetClass" version))
21689 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21690 (properties `((upstream-name . "AdapEnetClass")))
21691 (build-system r-build-system)
21693 `(("r-glmnet" ,r-glmnet)
21694 ("r-imputeyn" ,r-imputeyn)
21696 ("r-quadprog" ,r-quadprog)))
21697 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21698 (synopsis "Class of adaptive elastic net methods for censored data")
21700 "This package provides methods for variable selection for AFT models.")
21701 (license license:gpl2)))
21703 (define-public r-flock
21710 (uri (cran-uri "flock" version))
21713 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21714 (properties `((upstream-name . "flock")))
21715 (build-system r-build-system)
21716 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21717 (home-page "https://cran.r-project.org/web/packages/flock/")
21718 (synopsis "Process synchronization using file locks")
21720 "This package implements synchronization between R processes (spawned by
21721 using the @code{parallel} package for instance) using file locks. It supports
21722 both exclusive and shared locking.")
21723 (license license:asl2.0)))
21725 (define-public r-archivist
21727 (name "r-archivist")
21732 (uri (cran-uri "archivist" version))
21735 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21736 (properties `((upstream-name . "archivist")))
21737 (build-system r-build-system)
21740 ("r-digest" ,r-digest)
21741 ("r-flock" ,r-flock)
21743 ("r-lubridate" ,r-lubridate)
21744 ("r-magrittr" ,r-magrittr)
21745 ("r-rcurl" ,r-rcurl)
21746 ("r-rsqlite" ,r-rsqlite)))
21748 `(("r-knitr" ,r-knitr)))
21749 (home-page "https://pbiecek.github.io/archivist/")
21750 (synopsis "Tools for storing, restoring and searching for R objects")
21752 "Data exploration and modelling is a process in which a lot of data
21753 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21754 statistical models, different versions of data sets and different versions of
21755 results. Archivist helps to store and manage artifacts created in R. It
21756 allows you to store selected artifacts as binary files together with their
21757 metadata and relations. Archivist allows sharing artifacts with others. It
21758 can look for already created artifacts by using its class, name, date of the
21759 creation or other properties. It also makes it easy to restore such
21761 (license license:gpl2)))
21763 (define-public r-versions
21765 (name "r-versions")
21770 (uri (cran-uri "versions" version))
21773 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21774 (properties `((upstream-name . "versions")))
21775 (build-system r-build-system)
21776 (home-page "https://cran.r-project.org/web/packages/versions/")
21777 (synopsis "Query and install specific versions of CRAN packages")
21779 "This package allows you to install specified versions of R packages
21780 hosted on CRAN and provides functions to list available versions and the
21781 versions of currently installed packages.")
21782 (license license:bsd-3)))
21784 (define-public r-adapr
21791 (uri (cran-uri "adapr" version))
21794 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21795 (properties `((upstream-name . "adapr")))
21796 (build-system r-build-system)
21798 `(("r-archivist" ,r-archivist)
21799 ("r-devtools" ,r-devtools)
21800 ("r-digest" ,r-digest)
21801 ("r-doparallel" ,r-doparallel)
21802 ("r-gdata" ,r-gdata)
21803 ("r-ggplot2" ,r-ggplot2)
21804 ("r-git2r" ,r-git2r)
21805 ("r-igraph" ,r-igraph)
21806 ("r-knitr" ,r-knitr)
21807 ("r-plotly" ,r-plotly)
21809 ("r-rmarkdown" ,r-rmarkdown)
21810 ("r-shiny" ,r-shiny)
21811 ("r-shinydashboard" ,r-shinydashboard)
21812 ("r-versions" ,r-versions)))
21813 (home-page "https://cran.r-project.org/web/packages/adapr/")
21814 (synopsis "Implementation of an accountable data analysis process")
21816 "This package tracks reading and writing within R scripts that are
21817 organized into a directed acyclic graph. It contains an interactive Shiny
21818 application @code{adaprApp()}. It uses Git and file hashes to track version
21819 histories of inputs and outputs.")
21820 (license license:lgpl2.0)))
21822 (define-public r-adapsamp
21824 (name "r-adapsamp")
21829 (uri (cran-uri "AdapSamp" version))
21832 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21833 (properties `((upstream-name . "AdapSamp")))
21834 (build-system r-build-system)
21835 (propagated-inputs `(("r-pracma" ,r-pracma)))
21836 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21837 (synopsis "Adaptive sampling algorithms")
21839 "For distributions whose probability density functions are log-concave,
21840 the adaptive rejection sampling algorithm can be used to build envelope
21841 functions for sampling. For others, the modified adaptive rejection sampling
21842 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21843 adaptive slice sampling algorithm can be used. This R package mainly includes
21844 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21845 @code{rASS()}. These functions can realize sampling based on the algorithms
21847 (license license:gpl2)))
21849 (define-public r-adaptalint
21851 (name "r-adaptalint")
21856 (uri (cran-uri "adaptalint" version))
21859 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21860 (properties `((upstream-name . "adaptalint")))
21861 (build-system r-build-system)
21863 `(("r-dplyr" ,r-dplyr)
21864 ("r-lintr" ,r-lintr)
21865 ("r-purrr" ,r-purrr)))
21866 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21867 (synopsis "Check R code style")
21869 "This package provides tools to infer the code style (which style rules
21870 are followed and which ones are not) from one package and use it to check
21871 another. This makes it easier to find and correct the most important problems
21873 (license license:gpl3)))
21875 (define-public r-fracdiff
21877 (name "r-fracdiff")
21882 (uri (cran-uri "fracdiff" version))
21885 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21886 (properties `((upstream-name . "fracdiff")))
21887 (build-system r-build-system)
21888 (home-page "https://github.com/mmaechler/fracdiff")
21890 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21892 "This package provides tools for the maximum likelihood estimation of the
21893 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21894 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21895 (license license:gpl2+)))
21897 (define-public r-forecast
21899 (name "r-forecast")
21904 (uri (cran-uri "forecast" version))
21907 "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
21908 (properties `((upstream-name . "forecast")))
21909 (build-system r-build-system)
21911 `(("r-colorspace" ,r-colorspace)
21912 ("r-fracdiff" ,r-fracdiff)
21913 ("r-ggplot2" ,r-ggplot2)
21914 ("r-lmtest" ,r-lmtest)
21915 ("r-magrittr" ,r-magrittr)
21918 ("r-rcpparmadillo" ,r-rcpparmadillo)
21919 ("r-timedate" ,r-timedate)
21920 ("r-tseries" ,r-tseries)
21924 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21925 (home-page "https://pkg.robjhyndman.com/forecast/")
21926 (synopsis "Forecasting functions for time series and linear models")
21928 "This package provides methods and tools for displaying and analysing
21929 univariate time series forecasts including exponential smoothing via state
21930 space models and automatic ARIMA modelling.")
21931 (license license:gpl3)))
21933 (define-public r-xmisc
21940 (uri (cran-uri "Xmisc" version))
21943 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21944 (properties `((upstream-name . "Xmisc")))
21945 (build-system r-build-system)
21946 (home-page "https://cran.r-project.org/package=Xmisc")
21948 "Xiaobei's miscellaneous classes and functions")
21950 "This package provides Xiaobei's miscellaneous classes and functions,
21951 which are useful when developing R packages for @dfn{object oriented
21952 programming} (OOP) using R Reference Class.")
21953 (license license:gpl2+)))
21955 (define-public r-proxyc
21962 (uri (cran-uri "proxyC" version))
21965 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21966 (properties `((upstream-name . "proxyC")))
21967 (build-system r-build-system)
21969 `(("r-matrix" ,r-matrix)
21971 ("r-rcpparmadillo" ,r-rcpparmadillo)
21972 ("r-rcppparallel" ,r-rcppparallel)))
21973 (home-page "https://cran.r-project.org/package=proxyC")
21974 (synopsis "Compute proximity in large sparse matrices")
21976 "This package provides efficient tools to compute the proximity between
21977 rows or columns of large matrices. Functions are optimised for large sparse
21978 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21979 similarity/distance measures, computation of correlation, cosine similarity
21980 and Euclidean distance is particularly fast.")
21981 (license license:gpl3)))
21983 (define-public r-isocodes
21985 (name "r-isocodes")
21986 (version "2021.02.24")
21990 (uri (cran-uri "ISOcodes" version))
21993 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
21994 (properties `((upstream-name . "ISOcodes")))
21995 (build-system r-build-system)
21996 (home-page "https://cran.r-project.org/package=ISOcodes")
21997 (synopsis "Selected ISO codes")
21999 "This package provides ISO language, territory, currency, script and
22000 character codes. It provides ISO 639 language codes, ISO 3166 territory
22001 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
22002 character codes as well as the UN M.49 area codes.")
22003 (license license:gpl2)))
22005 (define-public r-stopwords
22007 (name "r-stopwords")
22012 (uri (cran-uri "stopwords" version))
22015 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
22016 (properties `((upstream-name . "stopwords")))
22017 (build-system r-build-system)
22019 `(("r-isocodes" ,r-isocodes)))
22020 (home-page "https://github.com/quanteda/stopwords")
22021 (synopsis "Multilingual stopword lists")
22023 "This package provides multiple sources of stopwords, for use in text
22024 analysis and natural language processing.")
22025 (license license:expat)))
22027 (define-public r-spacyr
22034 (uri (cran-uri "spacyr" version))
22037 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
22038 (properties `((upstream-name . "spacyr")))
22039 (build-system r-build-system)
22041 `(("r-data-table" ,r-data-table)
22042 ("r-reticulate" ,r-reticulate)))
22043 (home-page "https://spacyr.quanteda.io")
22044 (synopsis "R wrapper for the spaCy NLP library")
22046 "This package provides an R wrapper to the Python @dfn{natural language
22047 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22048 (license license:gpl3)))
22050 (define-public r-snowballc
22052 (name "r-snowballc")
22057 (uri (cran-uri "SnowballC" version))
22060 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22061 (properties `((upstream-name . "SnowballC")))
22062 (build-system r-build-system)
22063 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22064 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22066 "This package provides an R interface to the C @code{libstemmer} library
22067 that implements Porter's word stemming algorithm for collapsing words to a
22068 common root to aid comparison of vocabulary. Currently supported languages
22069 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22070 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22071 (license license:bsd-3)))
22073 (define-public r-quanteda
22075 (name "r-quanteda")
22080 (uri (cran-uri "quanteda" version))
22083 "0b1jfkdhpsg5jhjz4p0nf4cmi9p8w40wv3i2f17jf2x1n1y2hjj8"))))
22084 (properties `((upstream-name . "quanteda")))
22085 (build-system r-build-system)
22087 `(("r-fastmatch" ,r-fastmatch)
22088 ("r-magrittr" ,r-magrittr)
22089 ("r-matrix" ,r-matrix)
22091 ("r-rcpparmadillo" ,r-rcpparmadillo)
22092 ("r-rcppparallel" ,r-rcppparallel)
22093 ("r-snowballc" ,r-snowballc)
22094 ("r-stopwords" ,r-stopwords)
22095 ("r-stringi" ,r-stringi)
22097 ("r-yaml" ,r-yaml)))
22099 `(("r-knitr" ,r-knitr)))
22100 (home-page "https://quanteda.io")
22101 (synopsis "Quantitative analysis of textual data")
22103 "This package provides a fast, flexible, and comprehensive framework for
22104 quantitative text analysis in R. It provides functionality for corpus
22105 management, creating and manipulating tokens and ngrams, exploring keywords in
22106 context, forming and manipulating sparse matrices of documents by features and
22107 feature co-occurrences, analyzing keywords, computing feature similarities and
22108 distances, applying content dictionaries, applying supervised and unsupervised
22109 machine learning, visually representing text and text analyses, and more.")
22110 (license license:gpl3)))
22112 (define-public r-topicmodels
22114 (name "r-topicmodels")
22119 (uri (cran-uri "topicmodels" version))
22122 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22123 (properties `((upstream-name . "topicmodels")))
22124 (build-system r-build-system)
22128 `(("r-modeltools" ,r-modeltools)
22131 (home-page "https://cran.r-project.org/package=topicmodels")
22132 (synopsis "Topic models")
22134 "This package provides an interface to the C code for @dfn{Latent
22135 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22136 David M. Blei and co-authors and the C++ code for fitting LDA models using
22137 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22138 (license license:gpl2)))
22140 (define-public r-stm
22147 (uri (cran-uri "stm" version))
22150 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22151 (properties `((upstream-name . "stm")))
22152 (build-system r-build-system)
22154 `(("r-data-table" ,r-data-table)
22155 ("r-glmnet" ,r-glmnet)
22157 ("r-matrix" ,r-matrix)
22158 ("r-matrixstats" ,r-matrixstats)
22159 ("r-quadprog" ,r-quadprog)
22160 ("r-quanteda" ,r-quanteda)
22162 ("r-rcpparmadillo" ,r-rcpparmadillo)
22164 ("r-stringr" ,r-stringr)))
22165 (home-page "http://www.structuraltopicmodel.com/")
22166 (synopsis "Estimation of the Structural Topic Model")
22168 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22169 topic models with document-level covariates. The package also includes tools
22170 for model selection, visualization, and estimation of topic-covariate
22172 (license license:expat)))
22174 (define-public r-polycor
22181 (uri (cran-uri "polycor" version))
22184 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22185 (properties `((upstream-name . "polycor")))
22186 (build-system r-build-system)
22188 `(("r-matrix" ,r-matrix)
22189 ("r-mvtnorm" ,r-mvtnorm)))
22190 (home-page "https://r-forge.r-project.org/projects/polycor/")
22191 (synopsis "Polychoric and polyserial correlations")
22193 "This package provides tools to compute polychoric and polyserial
22194 correlations by quick \"two-step\" methods or ML, optionally with standard
22195 errors; tetrachoric and biserial correlations are special cases.")
22196 (license license:gpl2+)))
22198 (define-public r-msm
22205 (uri (cran-uri "msm" version))
22208 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22209 (properties `((upstream-name . "msm")))
22210 (build-system r-build-system)
22212 `(("r-expm" ,r-expm)
22213 ("r-mvtnorm" ,r-mvtnorm)
22214 ("r-survival" ,r-survival)))
22215 (home-page "https://github.com/chjackson/msm")
22216 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22218 "This package provides functions for fitting continuous-time Markov and
22219 hidden Markov multi-state models to longitudinal data. It was designed for
22220 processes observed at arbitrary times in continuous time (panel data) but some
22221 other observation schemes are supported. Both Markov transition rates and the
22222 hidden Markov output process can be modelled in terms of covariates, which may
22223 be constant or piecewise-constant in time.")
22224 (license license:gpl2+)))
22226 (define-public r-ltm
22233 (uri (cran-uri "ltm" version))
22236 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22237 (properties `((upstream-name . "ltm")))
22238 (build-system r-build-system)
22240 `(("r-mass" ,r-mass)
22242 ("r-polycor" ,r-polycor)))
22243 (home-page "https://github.com/drizopoulos/ltm")
22244 (synopsis "Latent trait models under IRT")
22246 "This is a package supporting the analysis of multivariate dichotomous
22247 and polytomous data using latent trait models under the Item Response Theory
22248 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22249 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22251 (license license:gpl2+)))
22253 (define-public r-mi
22260 (uri (cran-uri "mi" version))
22263 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22264 (properties `((upstream-name . "mi")))
22265 (build-system r-build-system)
22268 ("r-matrix" ,r-matrix)))
22269 (home-page "http://www.stat.columbia.edu/~gelman/")
22270 (synopsis "Missing data imputation and model checking")
22272 "This package provides functions for data manipulation, imputing missing
22273 values in an approximate Bayesian framework, diagnostics of the models used to
22274 generate the imputations, confidence-building mechanisms to validate some of
22275 the assumptions of the imputation algorithm, and functions to analyze multiply
22276 imputed data sets with the appropriate degree of sampling uncertainty.")
22277 (license license:gpl2+)))
22279 (define-public r-matrixcalc
22281 (name "r-matrixcalc")
22286 (uri (cran-uri "matrixcalc" version))
22289 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22290 (properties `((upstream-name . "matrixcalc")))
22291 (build-system r-build-system)
22292 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22293 (synopsis "Collection of functions for matrix calculations")
22295 "This package provides a collection of functions to support matrix
22296 calculations for probability, econometric and numerical analysis. There are
22297 additional functions that are comparable to APL functions which are useful for
22298 actuarial models such as pension mathematics.")
22299 (license license:gpl2+)))
22301 (define-public r-sem
22308 (uri (cran-uri "sem" version))
22311 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22312 (properties `((upstream-name . "sem")))
22313 (build-system r-build-system)
22315 `(("r-boot" ,r-boot)
22317 ("r-matrixcalc" ,r-matrixcalc)
22319 (home-page "https://cran.r-project.org/package=sem")
22320 (synopsis "Structural equation models")
22322 "This package provides functions for fitting general linear structural
22323 equation models (with observed and latent variables) using the RAM approach,
22324 and for fitting structural equations in observed-variable models by two-stage
22326 (license license:gpl2+)))
22328 (define-public r-semtools
22330 (name "r-semtools")
22335 (uri (cran-uri "semTools" version))
22338 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22339 (properties `((upstream-name . "semTools")))
22340 (build-system r-build-system)
22342 `(("r-lavaan" ,r-lavaan)))
22343 (home-page "https://github.com/simsem/semTools/wiki")
22344 (synopsis "Useful tools for structural equation modeling")
22346 "This package provides useful tools for structural equation modeling.")
22347 (license license:gpl2+)))
22349 (define-public r-regsem
22356 (uri (cran-uri "regsem" version))
22359 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22360 (properties `((upstream-name . "regsem")))
22361 (build-system r-build-system)
22363 `(("r-lavaan" ,r-lavaan)
22365 ("r-rcpparmadillo" ,r-rcpparmadillo)
22366 ("r-rsolnp" ,r-rsolnp)))
22368 `(("r-knitr" ,r-knitr)))
22369 (home-page "https://cran.r-project.org/package=regsem")
22370 (synopsis "Regularized structural equation modeling")
22372 "This package uses both ridge and lasso penalties (and extensions) to
22373 penalize specific parameters in structural equation models. The package
22374 offers additional cost functions, cross validation, and other extensions
22375 beyond traditional structural equation models. It also contains a function to
22376 perform @dfn{exploratory mediation} (XMed).")
22377 (license license:gpl2+)))
22379 (define-public r-stanheaders
22381 (name "r-stanheaders")
22382 (version "2.21.0-7")
22386 (uri (cran-uri "StanHeaders" version))
22389 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22390 (properties `((upstream-name . "StanHeaders")))
22391 (build-system r-build-system)
22392 (inputs `(("pandoc" ,pandoc)))
22394 `(("r-rcppeigen" ,r-rcppeigen)
22395 ("r-rcppparallel" ,r-rcppparallel)))
22397 `(("gfortran" ,gfortran)
22398 ("r-knitr" ,r-knitr))) ; for vignettes
22399 (home-page "https://mc-stan.org/")
22400 (synopsis "C++ header files for Stan")
22402 "The C++ header files of the Stan project are provided by this package.
22403 There is a shared object containing part of the @code{CVODES} library, but it
22404 is not accessible from R. @code{r-stanheaders} is only useful for developers
22405 who want to utilize the @code{LinkingTo} directive of their package's
22406 DESCRIPTION file to build on the Stan library without incurring unnecessary
22409 The Stan project develops a probabilistic programming language that implements
22410 full or approximate Bayesian statistical inference via Markov Chain Monte
22411 Carlo or variational methods and implements (optionally penalized) maximum
22412 likelihood estimation via optimization. The Stan library includes an advanced
22413 automatic differentiation scheme, templated statistical and linear algebra
22414 functions that can handle the automatically differentiable scalar types (and
22415 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22416 package provides user-facing R functions to parse, compile, test, estimate,
22417 and analyze Stan models.")
22418 (license license:bsd-3)))
22420 (define-public r-rpf
22427 (uri (cran-uri "rpf" version))
22430 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22431 (properties `((upstream-name . "rpf")))
22432 (build-system r-build-system)
22434 `(("r-lifecycle" ,r-lifecycle)
22435 ("r-mvtnorm" ,r-mvtnorm)
22437 ("r-rcppeigen" ,r-rcppeigen)))
22439 `(("r-knitr" ,r-knitr)))
22440 (home-page "https://github.com/jpritikin/rpf")
22441 (synopsis "Response probability functions")
22443 "The purpose of this package is to factor out logic and math common to
22444 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22445 core support code suitable for more specialized IRT packages to build upon.
22446 Complete access to optimized C functions is made available with
22447 @code{R_RegisterCCallable()}.")
22448 (license license:gpl3+)))
22450 (define-public r-openmx
22457 (uri (cran-uri "OpenMx" version))
22460 "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj"))))
22461 (properties `((upstream-name . "OpenMx")))
22462 (build-system r-build-system)
22465 ("r-digest" ,r-digest)
22466 ("r-lifecycle" ,r-lifecycle)
22468 ("r-matrix" ,r-matrix)
22470 ("r-rcppeigen" ,r-rcppeigen)
22472 ("r-stanheaders" ,r-stanheaders)))
22473 (native-inputs `(("gfortran" ,gfortran)))
22474 (home-page "http://openmx.ssri.psu.edu")
22475 (synopsis "Extended structural equation modelling")
22477 "This package allows for the estimation of a wide variety of advanced
22478 multivariate statistical models. It consists of a library of functions and
22479 optimizers that allow you to quickly and flexibly define an SEM model and
22480 estimate parameters given observed data.")
22481 (license license:asl2.0)))
22483 (define-public r-kutils
22490 (uri (cran-uri "kutils" version))
22493 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22494 (properties `((upstream-name . "kutils")))
22495 (build-system r-build-system)
22497 `(("r-foreign" ,r-foreign)
22498 ("r-openxlsx" ,r-openxlsx)
22500 ("r-runit" ,r-runit)
22501 ("r-xtable" ,r-xtable)))
22502 (home-page "https://cran.r-project.org/package=kutils")
22503 (synopsis "Project management tools")
22505 "This package provides tools for data importation, recoding, and
22506 inspection. There are functions to create new project folders, R code
22507 templates, create uniquely named output directories, and to quickly obtain a
22508 visual summary for each variable in a data frame. The main feature here is
22509 the systematic implementation of the \"variable key\" framework for data
22510 importation and recoding.")
22511 (license license:gpl2)))
22513 (define-public r-rockchalk
22515 (name "r-rockchalk")
22516 (version "1.8.144")
22520 (uri (cran-uri "rockchalk" version))
22523 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22524 (properties `((upstream-name . "rockchalk")))
22525 (build-system r-build-system)
22527 `(("r-cardata" ,r-cardata)
22528 ("r-kutils" ,r-kutils)
22530 ("r-mass" ,r-mass)))
22531 (home-page "https://cran.r-project.org/package=rockchalk")
22532 (synopsis "Regression estimation and presentation")
22534 "This package provides a collection of functions for interpretation and
22535 presentation of regression analysis. These functions are used to produce the
22536 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22537 includes regression diagnostics, regression tables, and plots of interactions
22538 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22539 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22540 fairly comprehensive overview.")
22541 (license license:gpl3+)))
22543 (define-public r-lisreltor
22545 (name "r-lisreltor")
22550 (uri (cran-uri "lisrelToR" version))
22553 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22554 (properties `((upstream-name . "lisrelToR")))
22555 (build-system r-build-system)
22556 (home-page "https://cran.r-project.org/package=lisrelToR")
22557 (synopsis "Import output from LISREL into R")
22559 "This is an unofficial package aimed at automating the import of LISREL
22561 (license license:gpl2)))
22563 (define-public r-bdgraph
22570 (uri (cran-uri "BDgraph" version))
22573 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22574 (properties `((upstream-name . "BDgraph")))
22575 (build-system r-build-system)
22577 `(("r-igraph" ,r-igraph)))
22578 (home-page "https://www.uva.nl/profile/a.mohammadi")
22579 (synopsis "Bayesian structure learning in graphical models")
22581 "This package provides statistical tools for Bayesian structure learning
22582 in undirected graphical models for continuous, discrete, and mixed data. It
22583 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22584 on a continuous-time birth-death process.")
22585 (license license:gpl2+)))
22587 (define-public r-d3network
22589 (name "r-d3network")
22590 (version "0.5.2.1")
22594 (uri (cran-uri "d3Network" version))
22597 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22598 (properties `((upstream-name . "d3Network")))
22599 (build-system r-build-system)
22601 `(("r-plyr" ,r-plyr)
22602 ("r-rjson" ,r-rjson)
22603 ("r-whisker" ,r-whisker)))
22604 (home-page "http://christophergandrud.github.io/d3Network/")
22605 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22607 "This package is intended to make it easy to create D3 JavaScript
22608 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22609 (license license:gpl3+)))
22611 (define-public r-qgraph
22618 (uri (cran-uri "qgraph" version))
22621 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22622 (properties `((upstream-name . "qgraph")))
22623 (build-system r-build-system)
22625 `(("r-abind" ,r-abind)
22626 ("r-colorspace" ,r-colorspace)
22627 ("r-corpcor" ,r-corpcor)
22628 ("r-dplyr" ,r-dplyr)
22629 ("r-fdrtool" ,r-fdrtool)
22630 ("r-ggplot2" ,r-ggplot2)
22631 ("r-glasso" ,r-glasso)
22632 ("r-gtools" ,r-gtools)
22633 ("r-hmisc" ,r-hmisc)
22634 ("r-igraph" ,r-igraph)
22636 ("r-lavaan" ,r-lavaan)
22637 ("r-matrix" ,r-matrix)
22638 ("r-pbapply" ,r-pbapply)
22641 ("r-psych" ,r-psych)
22643 ("r-reshape2" ,r-reshape2)))
22644 (home-page "http://sachaepskamp.com/qgraph/")
22645 (synopsis "Weighted network visualization and analysis")
22647 "This package implements tools for weighted network visualization and
22648 analysis, as well as Gaussian graphical model computation. It contains graph
22649 plotting methods, and tools for psychometric data visualization and graphical
22650 model estimation. See Epskamp et al. (2012)
22651 @url{doi:10.18637/jss.v048.i04}.")
22652 (license license:gpl2)))
22654 (define-public r-semplot
22661 (uri (cran-uri "semPlot" version))
22664 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22665 (properties `((upstream-name . "semPlot")))
22666 (build-system r-build-system)
22668 `(("r-colorspace" ,r-colorspace)
22669 ("r-corpcor" ,r-corpcor)
22670 ("r-igraph" ,r-igraph)
22671 ("r-lavaan" ,r-lavaan)
22672 ("r-lisreltor" ,r-lisreltor)
22673 ("r-openmx" ,r-openmx)
22675 ("r-qgraph" ,r-qgraph)
22676 ("r-regsem" ,r-regsem)
22677 ("r-rockchalk" ,r-rockchalk)
22680 (home-page "https://github.com/SachaEpskamp/semPlot")
22681 (synopsis "Unified visualizations of structural equation models")
22683 "Structural equation modeling (SEM) has a long history of representing
22684 models graphically as path diagrams. The semPlot package for R fills the gap
22685 between advanced, but time-consuming, graphical software and the limited
22686 graphics produced automatically by SEM software. In addition, semPlot offers
22687 more functionality than drawing path diagrams: it can act as a common ground
22688 for importing SEM results into R. Any result usable as input to semPlot can
22689 also be represented in any of the three popular SEM frame-works, as well as
22690 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22691 (license license:gpl2)))
22693 (define-public r-cdm
22700 (uri (cran-uri "CDM" version))
22703 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22704 (properties `((upstream-name . "CDM")))
22705 (build-system r-build-system)
22707 `(("r-mvtnorm" ,r-mvtnorm)
22708 ("r-polycor" ,r-polycor)
22710 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22712 "https://github.com/alexanderrobitzsch/CDM")
22713 (synopsis "Cognitive diagnosis modeling")
22715 "This package provides functions for cognitive diagnosis modeling and
22716 multidimensional item response modeling for dichotomous and polytomous item
22717 responses. It enables the estimation of the DINA and DINO model, the multiple
22718 group (polytomous) GDINA model, the multiple choice DINA model, the general
22719 diagnostic model (GDM), the structured latent class model (SLCA), and
22720 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22721 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22722 estimation and the package structure. For tutorials on how to use the CDM
22723 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22724 well as Ravand and Robitzsch (2015).")
22725 (license license:gpl2+)))
22727 (define-public r-tam
22734 (uri (cran-uri "TAM" version))
22737 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22738 (properties `((upstream-name . "TAM")))
22739 (build-system r-build-system)
22743 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22744 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22745 (synopsis "Test analysis modules")
22747 "This package includes tools for marginal maximum likelihood estimation
22748 and joint maximum likelihood estimation for unidimensional and
22749 multidimensional item response models. The package functionality covers the
22750 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22751 multi-faceted Rasch model, nominal item response model, structured latent
22752 class model, mixture distribution IRT models, and located latent class models.
22753 Latent regression models and plausible value imputation are also supported.")
22754 (license license:gpl2+)))
22756 (define-public r-erm
22763 (uri (cran-uri "eRm" version))
22766 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
22767 (properties `((upstream-name . "eRm")))
22768 (build-system r-build-system)
22770 `(("r-colorspace" ,r-colorspace)
22771 ("r-lattice" ,r-lattice)
22773 ("r-matrix" ,r-matrix)
22774 ("r-psych" ,r-psych)))
22775 (native-inputs `(("gfortran" ,gfortran)))
22776 (home-page "https://cran.r-project.org/package=eRm")
22777 (synopsis "Extended Rasch modeling")
22779 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22780 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22781 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22782 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22783 data matrix. Additional features are the ML estimation of the person
22784 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22785 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22786 infit and outfit measures, ICC and other plots, automated stepwise item
22787 elimination, and a simulation module for various binary data matrices.")
22788 (license license:gpl3)))
22790 (define-public r-irtoys
22797 (uri (cran-uri "irtoys" version))
22800 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22801 (properties `((upstream-name . "irtoys")))
22802 (build-system r-build-system)
22806 (home-page "https://cran.r-project.org/package=irtoys")
22807 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22809 "This package provides a collection of functions useful in learning and
22810 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22811 programs. It provides basic CTT analysis, a simple common interface to the
22812 estimation of item parameters in IRT models for binary responses with three
22813 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22814 EAP, WLE, plausible values), item and person fit statistics, scaling
22815 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22816 array of parametric and non-parametric (kernel) plots. It estimates and plots
22817 Haberman's interaction model when all items are dichotomously scored.")
22818 (license license:gpl2+)))
22820 (define-public r-iheatmapr
22822 (name "r-iheatmapr")
22827 (uri (cran-uri "iheatmapr" version))
22830 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22831 (properties `((upstream-name . "iheatmapr")))
22832 (build-system r-build-system)
22834 `(("r-fastcluster" ,r-fastcluster)
22835 ("r-ggdendro" ,r-ggdendro)
22836 ("r-htmlwidgets" ,r-htmlwidgets)
22837 ("r-jsonlite" ,r-jsonlite)
22838 ("r-knitr" ,r-knitr)
22839 ("r-magrittr" ,r-magrittr)
22840 ("r-rcolorbrewer" ,r-rcolorbrewer)
22841 ("r-scales" ,r-scales)))
22843 `(("r-knitr" ,r-knitr)))
22844 (home-page "https://docs.ropensci.org/iheatmapr")
22845 (synopsis "Interactive, Complex Heatmaps")
22847 "iheatmapr is an R package for building complex, interactive heatmaps
22848 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22849 subplots along the rows or columns of the main heatmap add more information
22850 about each row or column. For example, a one column additional heatmap may
22851 indicate what group a particular row or column belongs to. Complex heatmaps
22852 may also include multiple side by side heatmaps which show different types of
22853 data for the same conditions. Interactivity can improve complex heatmaps by
22854 providing tooltips with information about each cell and enabling zooming into
22855 interesting features. iheatmapr uses the plotly library for interactivity.")
22856 (license license:expat)))
22858 (define-public r-packrat
22865 (uri (cran-uri "packrat" version))
22868 "01cn2vf95nc8bh0hh8imkn030yra3hx64q1fb8jwsr52p9s397fr"))))
22869 (properties `((upstream-name . "packrat")))
22870 (build-system r-build-system)
22871 (home-page "https://github.com/rstudio/packrat/")
22872 (synopsis "Dependency management R projects")
22874 "This package provides a dependency manager for R projects that allows
22875 you to manage the R packages your project depends on in an isolated, portable,
22876 and reproducible way.")
22877 (license license:gpl2)))
22879 (define-public r-rsconnect
22881 (name "r-rsconnect")
22886 (uri (cran-uri "rsconnect" version))
22889 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22890 (properties `((upstream-name . "rsconnect")))
22891 (build-system r-build-system)
22893 `(("r-curl" ,r-curl)
22894 ("r-digest" ,r-digest)
22895 ("r-jsonlite" ,r-jsonlite)
22896 ("r-openssl" ,r-openssl)
22897 ("r-packrat" ,r-packrat)
22898 ("r-rstudioapi" ,r-rstudioapi)
22899 ("r-yaml" ,r-yaml)))
22900 (home-page "https://github.com/rstudio/rsconnect")
22901 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22903 "This package provides a programmatic deployment interface for RPubs,
22904 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22905 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22906 (license license:gpl2)))
22908 ;; This package includes minified JavaScript files. When upgrading please
22909 ;; check that there are no new minified JavaScript files.
22910 (define-public r-dygraphs
22912 (name "r-dygraphs")
22913 (version "1.1.1.6")
22917 (uri (cran-uri "dygraphs" version))
22920 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22921 (properties `((upstream-name . "dygraphs")))
22922 (build-system r-build-system)
22924 `(#:modules ((guix build utils)
22925 (guix build r-build-system)
22929 (modify-phases %standard-phases
22930 (add-after 'unpack 'process-javascript
22931 (lambda* (#:key inputs #:allow-other-keys)
22932 (with-directory-excursion "inst/htmlwidgets/lib/"
22936 `(("dygraphs/dygraph-combined-dev.js"
22937 "dygraph-combined.js")
22938 (,(assoc-ref inputs "js-jquery")
22939 "jquery/jquery.min.js")
22940 (,(assoc-ref inputs "js-fquarter")
22941 "fquarter/moment-fquarter.min.js"))))
22942 (lambda (sources targets)
22943 (for-each (lambda (source target)
22944 (format #t "Processing ~a --> ~a~%"
22946 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22947 (call-with-output-file target
22949 (dump-port minified port)))))
22950 sources targets))))
22953 `(("uglify-js" ,uglify-js)
22954 ;; They actually use version 1.11.1, but this more recent version
22955 ;; should be just fine.
22959 (uri "https://code.jquery.com/jquery-1.12.4.js")
22962 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22966 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22967 "moment-fquarter/1.0.1/moment-fquarter.js"))
22970 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22972 `(("r-htmltools" ,r-htmltools)
22973 ("r-htmlwidgets" ,r-htmlwidgets)
22974 ("r-magrittr" ,r-magrittr)
22977 (home-page "https://github.com/rstudio/dygraphs")
22978 (synopsis "Interface to Dygraphs interactive time series charting library")
22980 "This package provides an R interface to the dygraphs JavaScript charting
22981 library (a copy of which is included in the package). It provides rich
22982 facilities for charting time-series data in R, including highly configurable
22983 series- and axis-display and interactive features like zoom/pan and
22984 series/point highlighting.")
22985 (license license:expat)))
22987 (define-public r-shinystan
22989 (name "r-shinystan")
22994 (uri (cran-uri "shinystan" version))
22997 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22998 (properties `((upstream-name . "shinystan")))
22999 (build-system r-build-system)
23001 `(("r-bayesplot" ,r-bayesplot)
23002 ("r-colourpicker" ,r-colourpicker)
23004 ("r-dygraphs" ,r-dygraphs)
23005 ("r-ggplot2" ,r-ggplot2)
23006 ("r-gridextra" ,r-gridextra)
23007 ("r-gtools" ,r-gtools)
23008 ("r-markdown" ,r-markdown)
23009 ("r-reshape2" ,r-reshape2)
23010 ("r-rsconnect" ,r-rsconnect)
23011 ("r-rstan" ,r-rstan)
23012 ("r-shiny" ,r-shiny)
23013 ("r-shinyjs" ,r-shinyjs)
23014 ("r-shinythemes" ,r-shinythemes)
23015 ("r-threejs" ,r-threejs)
23016 ("r-xtable" ,r-xtable)
23018 (home-page "https://mc-stan.org/")
23019 (synopsis "Interactive visual and numerical analysis for Bayesian models")
23021 "This package provides a graphical user interface for interactive
23022 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
23023 for analyzing a posterior sample. The interface is powered by the Shiny web
23024 application framework and works with the output of MCMC programs written in
23025 any programming language (and has extended functionality for Stan models fit
23026 using the @code{rstan} and @code{rstanarm} packages).")
23027 (license license:gpl3+)))
23029 (define-public r-rstantools
23031 (name "r-rstantools")
23036 (uri (cran-uri "rstantools" version))
23039 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23040 (properties `((upstream-name . "rstantools")))
23041 (build-system r-build-system)
23042 (inputs `(("pandoc" ,pandoc)))
23044 `(("r-desc" ,r-desc)
23046 ("r-rcppparallel" ,r-rcppparallel)))
23048 `(("r-knitr" ,r-knitr)))
23049 (home-page "https://mc-stan.org/rstantools/")
23050 (synopsis "Tools for developing R packages interfacing with Stan")
23052 "This package provides various tools for developers of R packages
23053 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23054 up the required package structure, S3 generics and default methods to unify
23055 function naming across Stan-based R packages, and vignettes with
23056 recommendations for developers.")
23057 (license license:gpl3+)))
23059 (define-public r-loo
23066 (uri (cran-uri "loo" version))
23068 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23069 (properties `((upstream-name . "loo")))
23070 (build-system r-build-system)
23072 `(("pandoc" ,pandoc)
23073 ("pandoc-citeproc" ,pandoc-citeproc)))
23075 `(("r-checkmate" ,r-checkmate)
23076 ("r-matrixstats" ,r-matrixstats)))
23078 `(("r-knitr" ,r-knitr)))
23079 (home-page "https://mc-stan.org/loo/")
23080 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23082 "This package provides an implementation of efficient approximate
23083 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23084 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23085 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23086 procedure for regularizing importance weights. As a byproduct of the
23087 calculations, we also obtain approximate standard errors for estimated
23088 predictive errors and for the comparison of predictive errors between models.
23089 The package also provides methods for using stacking and other model weighting
23090 techniques to average Bayesian predictive distributions.")
23091 (license license:gpl3+)))
23093 (define-public r-rstan
23100 (uri (cran-uri "rstan" version))
23103 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23104 (properties `((upstream-name . "rstan")))
23105 (build-system r-build-system)
23108 (modify-phases %standard-phases
23109 (add-before 'install 'set-timezone
23110 ;; This package is picky about timezones.
23111 (lambda* (#:key inputs #:allow-other-keys)
23112 (setenv "TZ" "UTC+1")
23114 (string-append (assoc-ref inputs "tzdata")
23115 "/share/zoneinfo"))
23118 `(("tzdata" ,tzdata-for-tests)
23120 ("r-knitr" ,r-knitr)))
23123 ("r-ggplot2" ,r-ggplot2)
23124 ("r-gridextra" ,r-gridextra)
23125 ("r-inline" ,r-inline)
23127 ("r-pkgbuild" ,r-pkgbuild)
23129 ("r-rcppeigen" ,r-rcppeigen)
23130 ("r-rcppparallel" ,r-rcppparallel)
23131 ("r-stanheaders" ,r-stanheaders)
23133 ("r-withr" ,r-withr)))
23134 (home-page "https://discourse.mc-stan.org/")
23135 (synopsis "R interface to Stan")
23137 "User-facing R functions are provided to parse, compile, test, estimate,
23138 and analyze Stan models by accessing the header-only Stan library provided by
23139 the StanHeaders package. The Stan project develops a probabilistic
23140 programming language that implements full Bayesian statistical inference via
23141 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23142 approximation, and (optionally penalized) maximum likelihood estimation via
23143 optimization. In all three cases, automatic differentiation is used to
23144 quickly and accurately evaluate gradients without burdening the user with the
23145 need to derive the partial derivatives.")
23146 (license license:gpl3+)))
23148 (define-public r-rstanarm
23150 (name "r-rstanarm")
23155 (uri (cran-uri "rstanarm" version))
23158 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23159 (properties `((upstream-name . "rstanarm")))
23160 (build-system r-build-system)
23162 `(("pandoc" ,pandoc)
23163 ("pandoc-citeproc" ,pandoc-citeproc)))
23165 `(("r-bayesplot" ,r-bayesplot)
23167 ("r-ggplot2" ,r-ggplot2)
23170 ("r-matrix" ,r-matrix)
23173 ("r-rcppeigen" ,r-rcppeigen)
23174 ("r-rcppparallel" ,r-rcppparallel)
23175 ("r-rstan" ,r-rstan)
23176 ("r-rstantools" ,r-rstantools)
23177 ("r-shinystan" ,r-shinystan)
23178 ("r-stanheaders" ,r-stanheaders)
23179 ("r-survival" ,r-survival)))
23181 `(("r-knitr" ,r-knitr)))
23182 (home-page "https://mc-stan.org/rstanarm/")
23183 (synopsis "Bayesian applied regression modeling via Stan")
23185 "This package estimates previously compiled regression models using the
23186 @code{rstan} package, which provides the R interface to the Stan C++ library
23187 for Bayesian estimation. Users specify models via the customary R syntax with
23188 a formula and @code{data.frame} plus some additional arguments for priors.")
23189 (license license:gpl3+)))
23191 (define-public r-kendall
23198 (uri (cran-uri "Kendall" version))
23201 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23202 (properties `((upstream-name . "Kendall")))
23203 (build-system r-build-system)
23205 `(("r-boot" ,r-boot)))
23207 `(("gfortran" ,gfortran)))
23208 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23209 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23211 "This package computes the Kendall rank correlation and Mann-Kendall
23213 (license license:gpl2+)))
23215 (define-public r-keyring
23222 (uri (cran-uri "keyring" version))
23225 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23226 (properties `((upstream-name . "keyring")))
23227 (build-system r-build-system)
23229 `(("r-assertthat" ,r-assertthat)
23230 ("r-filelock" ,r-filelock)
23231 ("r-getpass" ,r-getpass)
23232 ("r-openssl" ,r-openssl)
23234 ("r-rappdirs" ,r-rappdirs)
23235 ("r-sodium" ,r-sodium)
23236 ("r-yaml" ,r-yaml)))
23237 (native-inputs `(("pkg-config" ,pkg-config)))
23238 (home-page "https://github.com/r-lib/keyring")
23239 (synopsis "Access the system credential store from R")
23241 "This package provides a platform-independent API to access the operating
23242 system's credential store. It currently supports Keychain on macOS,
23243 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23244 simple, platform independent store implemented with environment variables.
23245 Additional storage back-ends can be added easily.")
23246 (license license:expat)))
23248 (define-public r-zyp
23251 (version "0.10-1.1")
23255 (uri (cran-uri "zyp" version))
23258 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23259 (properties `((upstream-name . "zyp")))
23260 (build-system r-build-system)
23262 `(("r-kendall" ,r-kendall)))
23263 (home-page "https://cran.r-project.org/web/packages/zyp/")
23264 (synopsis "Zhang + Yue-Pilon Trends Package")
23266 "This package contains an efficient implementation of Sen's slope
23267 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23268 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23270 (license license:lgpl2.1)))
23272 (define-public r-rlinsolve
23274 (name "r-rlinsolve")
23279 (uri (cran-uri "Rlinsolve" version))
23282 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23283 (properties `((upstream-name . "Rlinsolve")))
23284 (build-system r-build-system)
23286 `(("r-matrix" ,r-matrix)
23288 ("r-rcpparmadillo" ,r-rcpparmadillo)
23289 ("r-rdpack" ,r-rdpack)))
23290 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23291 (synopsis "Iterative solvers for (sparse) linear system of equations")
23293 "Solving a system of linear equations is one of the most fundamental
23294 computational problems for many fields of mathematical studies, such as
23295 regression problems from statistics or numerical partial differential
23296 equations. This package provides basic stationary iterative solvers such as
23297 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23298 Nonstationary, also known as Krylov subspace methods are also provided.
23299 Sparse matrix computation is also supported in that solving large and sparse
23300 linear systems can be manageable using the @code{Matrix} package along with
23301 @code{RcppArmadillo}.")
23302 (license license:gpl3+)))
23304 (define-public r-zvcv
23311 (uri (cran-uri "ZVCV" version))
23314 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23315 (properties `((upstream-name . "ZVCV")))
23316 (build-system r-build-system)
23318 `(("r-abind" ,r-abind)
23320 ("r-dplyr" ,r-dplyr)
23321 ("r-glmnet" ,r-glmnet)
23322 ("r-magrittr" ,r-magrittr)
23323 ("r-mvtnorm" ,r-mvtnorm)
23325 ("r-rcpparmadillo" ,r-rcpparmadillo)
23326 ("r-rlinsolve" ,r-rlinsolve)))
23327 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23328 (synopsis "Zero-Variance Control Variates")
23330 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23331 to reduce the variance of Monte Carlo estimators of expectations using the
23332 derivatives of the log target. Once the derivatives are available, the only
23333 additional computational effort is in solving a linear regression problem.
23334 This method has been extended to higher dimensions using regularisation. This
23335 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23336 samples, derivatives and function evaluations are available. Additional
23337 functions for applying ZV-CV to two estimators for the normalising constant of
23338 the posterior distribution in Bayesian statistics are also supplied.")
23339 (license license:gpl2+)))
23341 (define-public r-ztype
23348 (uri (cran-uri "ztype" version))
23351 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23352 (properties `((upstream-name . "ztype")))
23353 (build-system r-build-system)
23355 `(("r-assertthat" ,r-assertthat)
23356 ("r-dplyr" ,r-dplyr)
23357 ("r-ggplot2" ,r-ggplot2)
23358 ("r-lubridate" ,r-lubridate)
23359 ("r-magrittr" ,r-magrittr)
23360 ("r-rvest" ,r-rvest)
23361 ("r-stringr" ,r-stringr)))
23362 (home-page "https://cran.r-project.org/web/packages/ztype/")
23363 (synopsis "Run a Ztype game loaded with R functions")
23365 "How fast can you type R functions on your keyboard? Find out by running
23366 a @code{zty.pe} game: export R functions as instructions to type to destroy
23367 opponents' vessels.")
23368 (license license:gpl3)))
23370 (define-public r-zseq
23377 (uri (cran-uri "Zseq" version))
23380 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23381 (properties `((upstream-name . "Zseq")))
23382 (build-system r-build-system)
23384 `(("r-gmp" ,r-gmp)))
23385 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23386 (synopsis "Integer sequence generator")
23388 "This package generates well-known integer sequences. The @code{gmp}
23389 package is adopted for computing with arbitrarily large numbers. Every
23390 function has a hyperlink to its corresponding item in the @dfn{On-Line
23391 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23392 (license license:gpl3+)))
23394 (define-public r-isoband
23401 (uri (cran-uri "isoband" version))
23404 "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn"))))
23405 (properties `((upstream-name . "isoband")))
23406 (build-system r-build-system)
23408 `(("r-knitr" ,r-knitr)))
23409 (home-page "https://github.com/wilkelab/isoband")
23410 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23412 "This package provides a fast C++ implementation to generate contour
23413 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23414 containing elevation data.")
23415 (license license:expat)))
23417 (define-public r-ppcor
23424 (uri (cran-uri "ppcor" version))
23427 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23428 (properties `((upstream-name . "ppcor")))
23429 (build-system r-build-system)
23431 `(("r-mass" ,r-mass)))
23432 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23433 (synopsis "Partial and semi-partial correlation")
23435 "This package provides users not only with a function to readily
23436 calculate the higher-order partial and semi-partial correlations but also with
23437 statistics and p-values of the correlation coefficients.")
23438 (license license:gpl2)))
23440 (define-public r-hrbrthemes
23442 (name "r-hrbrthemes")
23447 (uri (cran-uri "hrbrthemes" version))
23449 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23450 (properties `((upstream-name . "hrbrthemes")))
23451 (build-system r-build-system)
23453 `(("r-extrafont" ,r-extrafont)
23454 ("r-gdtools" ,r-gdtools)
23455 ("r-ggplot2" ,r-ggplot2)
23456 ("r-htmltools" ,r-htmltools)
23457 ("r-knitr" ,r-knitr)
23458 ("r-magrittr" ,r-magrittr)
23459 ("r-rmarkdown" ,r-rmarkdown)
23460 ("r-scales" ,r-scales)))
23462 `(("r-knitr" ,r-knitr)))
23463 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23464 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23466 "This package provides a compilation of extra @code{ggplot2} themes,
23467 scales and utilities, including a spell check function for plot label fields
23468 and an overall emphasis on typography.")
23469 (license license:expat)))
23471 (define-public r-crochet
23478 (uri (cran-uri "crochet" version))
23481 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23482 (build-system r-build-system)
23484 `(("r-knitr" ,r-knitr)))
23485 (home-page "https://github.com/agrueneberg/crochet")
23486 (synopsis "Implementation Helper for Matrix-Like Types")
23488 "Functions to help implement the extraction / subsetting / indexing
23489 function @code{[} and replacement function @code{[<-} of custom matrix-like
23490 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23491 as possible (with tests to prove it).")
23492 (license license:expat)))
23494 (define-public r-boa
23497 (version "1.1.8-2")
23501 (uri (cran-uri "boa" version))
23504 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23505 (properties `((upstream-name . "boa")))
23506 (build-system r-build-system)
23507 (home-page "https://www.jstatsoft.org/v21/i11")
23508 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23510 "This package provides a menu-driven program and library of functions for
23511 carrying out convergence diagnostics and statistical and graphical analysis of
23512 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23513 (license license:gpl2+)))
23515 (define-public r-httpcode
23517 (name "r-httpcode")
23521 (uri (cran-uri "httpcode" version))
23524 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23525 (build-system r-build-system)
23526 (home-page "https://github.com/sckott/httpcode")
23527 (synopsis "HTTP status code helper")
23528 (description "@code{httpcode} provides functionality for finding and
23529 explaining the meaning of @code{HTTP} status codes. Functions are included for
23530 searching for codes by full or partial number, by message, and to get
23531 appropriate dog and cat images for many status codes.")
23532 (license license:expat)))
23534 (define-public r-latex2exp
23536 (name "r-latex2exp")
23540 (uri (cran-uri "latex2exp" version))
23543 "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg"))))
23544 (build-system r-build-system)
23546 `(("r-stringr" ,r-stringr)
23547 ("r-magrittr" ,r-magrittr)))
23549 `(("r-knitr" ,r-knitr)))
23550 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23551 (synopsis "Use LaTeX expressions in plots")
23552 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23553 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23554 rendered as text, axis labels, etc. throughout R's plotting system.")
23555 (license license:expat)))
23557 (define-public r-oai
23563 (uri (cran-uri "oai" version))
23566 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23567 (build-system r-build-system)
23569 `(("r-xml2" ,r-xml2)
23572 ("r-stringr" ,r-stringr)
23573 ("r-tibble" ,r-tibble)))
23574 (home-page "https://github.com/ropensci/oai/")
23575 (synopsis "General purpose OAI-PMH services client")
23576 (description "@code{oai} provides a general purpose client to work with
23577 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23578 service. Functions are provided to work with the OAI-PMH verbs:
23579 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23580 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23581 (license license:expat)))
23583 (define-public r-argon2
23590 (uri (cran-uri "argon2" version))
23593 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23594 (properties `((upstream-name . "argon2")))
23595 (build-system r-build-system)
23596 (home-page "https://github.com/wrathematics/argon2")
23597 (synopsis "Secure password hashing based on the argon2 algorithm")
23599 "This package provides utilities for secure password hashing via the
23600 argon2 algorithm.")
23601 (license license:bsd-2)))
23603 (define-public r-getpass
23610 (uri (cran-uri "getPass" version))
23613 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23614 (properties `((upstream-name . "getPass")))
23615 (build-system r-build-system)
23617 `(("r-rstudioapi" ,r-rstudioapi)))
23618 (home-page "https://github.com/wrathematics/getPass")
23619 (synopsis "Masked user input")
23621 "This package provides a micro-package for reading \"passwords\", i.e.
23622 reading user input with masking, so that the input is not displayed as it is
23623 typed. Currently, RStudio, the command line (every OS), and any platform
23624 where tcltk is present are supported.")
23625 (license license:bsd-2)))
23627 (define-public r-remoter
23634 (uri (cran-uri "remoter" version))
23637 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23638 (properties `((upstream-name . "remoter")))
23639 (build-system r-build-system)
23641 `(("r-argon2" ,r-argon2)
23642 ("r-getpass" ,r-getpass)
23643 ("r-pbdzmq" ,r-pbdzmq)
23645 (home-page "https://github.com/RBigData/remoter")
23646 (synopsis "Control a remote R session from a local one")
23648 "This package provides a set of utilities for client/server computing
23649 with R, controlling a remote R session (the server) from a local one (the
23651 (license license:bsd-2)))
23653 (define-public r-asd
23660 (uri (cran-uri "asd" version))
23663 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23664 (properties `((upstream-name . "asd")))
23665 (build-system r-build-system)
23667 `(("r-mvtnorm" ,r-mvtnorm)))
23668 (home-page "https://cran.r-project.org/web/packages/asd")
23669 (synopsis "Simulations for Adaptive Seamless Designs")
23671 "This package provdes means to run simulations for adaptive seamless
23672 designs with and without early outcomes for treatment selection and
23673 subpopulation type designs.")
23674 (license license:gpl3)))
23676 (define-public r-nbconvertr
23678 (name "r-nbconvertr")
23683 (uri (cran-uri "nbconvertR" version))
23686 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23687 (properties `((upstream-name . "nbconvertR")))
23688 (build-system r-build-system)
23690 `(("jupyter" ,python-nbconvert)
23691 ("pandoc" ,pandoc)))
23692 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23693 (synopsis "Vignette engine wrapping Jupyter notebooks")
23695 "This package calls the Jupyter script @code{nbconvert} to create
23696 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23697 containing rich text, code, and its output. Code cells can be edited and
23698 evaluated interactively.")
23699 (license license:gpl3)))
23701 (define-public r-bridgesampling
23703 (name "r-bridgesampling")
23708 (uri (cran-uri "bridgesampling" version))
23711 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23713 `((upstream-name . "bridgesampling")))
23714 (build-system r-build-system)
23716 `(("r-brobdingnag" ,r-brobdingnag)
23718 ("r-matrix" ,r-matrix)
23719 ("r-mvtnorm" ,r-mvtnorm)
23720 ("r-scales" ,r-scales)
23721 ("r-stringr" ,r-stringr)))
23723 `(("r-knitr" ,r-knitr)))
23724 (home-page "https://github.com/quentingronau/bridgesampling")
23725 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23727 "This package provides functions for estimating marginal likelihoods,
23728 Bayes factors, posterior model probabilities, and normalizing constants in
23729 general, via different versions of bridge sampling.")
23730 (license license:gpl2+)))
23732 (define-public r-tea
23739 (uri (cran-uri "tea" version))
23742 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23744 `((upstream-name . "tea")))
23745 (build-system r-build-system)
23747 `(("r-matrix" ,r-matrix)))
23748 (home-page "https://cran.r-project.org/web/packages/tea/")
23749 (synopsis "Threshold estimation approaches")
23751 "This package provides different approaches for selecting the threshold
23752 in generalized Pareto distributions. Most of them are based on minimizing the
23753 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23754 Others are heuristically motivated by searching for stable sample paths, i.e.
23755 a nearly constant region of the tail index estimator with respect to k, which
23756 is the number of data in the tail. The third class is motivated by graphical
23757 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23758 is also implemented here.")
23759 (license license:gpl3)))
23761 (define-public r-awsmethods
23763 (name "r-awsmethods")
23768 (uri (cran-uri "awsMethods" version))
23771 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23773 `((upstream-name . "awsMethods")))
23774 (build-system r-build-system)
23775 (home-page "http://www.wias-berlin.de/software/imaging/")
23776 (synopsis "Class and methods definitions")
23778 "This package defines the generic method @code{extract} and provides
23779 @code{openMP} support as needed in several packages like
23780 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23781 (license license:gpl2+)))
23783 (define-public r-aws
23790 (uri (cran-uri "aws" version))
23793 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23795 `((upstream-name . "aws")))
23796 (build-system r-build-system)
23798 `(("r-awsmethods" ,r-awsmethods)
23801 `(("gfortran" ,gfortran)))
23802 (home-page "https://cran.r-project.org/web/packages/aws/")
23803 (synopsis "Adaptive weights smoothing")
23805 "This package provides a collection of R-functions implementing adaptive
23806 smoothing procedures in 1D, 2D and 3D. This includes the
23807 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23808 Confidence Intervals} (ICI), variational approaches, and a non-local means
23810 (license license:gpl2+)))
23812 (define-public r-sgloptim
23814 (name "r-sgloptim")
23819 (uri (cran-uri "sglOptim" version))
23822 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23824 `((upstream-name . "sglOptim")))
23825 (build-system r-build-system)
23828 ("r-doparallel" ,r-doparallel)
23829 ("r-foreach" ,r-foreach)
23830 ("r-matrix" ,r-matrix)
23832 ("r-rcpparmadillo" ,r-rcpparmadillo)
23833 ("r-rcppprogress" ,r-rcppprogress)))
23835 `(("r-knitr" ,r-knitr)))
23836 (home-page "https://github.com/nielsrhansen/sglOptim")
23837 (synopsis "Generic sparse group Lasso solver")
23839 "This package provides a fast generic solver for sparse group lasso
23840 optimization problems. The loss (objective) function must be defined in a C++
23841 module. The optimization problem is solved using a coordinate gradient
23842 descent algorithm. Convergence of the algorithm is established and the
23843 algorithm is applicable to a broad class of loss functions. Use of parallel
23844 computing for cross validation and subsampling is supported through the
23845 @code{foreach} and @code{doParallel} packages.")
23846 (license license:gpl2+)))
23848 (define-public r-grouped
23855 (uri (cran-uri "grouped" version))
23858 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23860 `((upstream-name . "grouped")))
23861 (build-system r-build-system)
23863 `(("r-mass" ,r-mass)))
23864 (home-page "https://cran.r-project.org/web/packages/grouped/")
23865 (synopsis "Regression analysis of grouped and coarse data")
23867 "This package provides regression models for grouped and coarse data,
23868 under the coarsened at random assumption.")
23869 (license license:gpl2+)))
23871 (define-public r-stam
23878 (uri (cran-uri "stam" version))
23881 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23883 `((upstream-name . "stam")))
23884 (build-system r-build-system)
23888 (home-page "https://cran.r-project.org/web/packages/stam")
23889 (synopsis "Spatio-temporal analysis and modelling")
23891 "This package provides various methods to conduct Spatio-Temporal
23892 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23893 Inferred Spatio-Temporal Modelling.")
23894 (license license:gpl2+)))
23896 (define-public r-dcv
23903 (uri (cran-uri "dcv" version))
23906 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23908 `((upstream-name . "dcv")))
23909 (build-system r-build-system)
23911 `(("r-lmtest" ,r-lmtest)))
23912 (home-page "https://cran.r-project.org/web/packages/dcv/")
23913 (synopsis "Conventional cross-validation statistics for climate-growth model")
23915 "This package performs several conventional cross-validation statistical
23916 methods for climate-growth model in the climate reconstruction from tree
23917 rings, including Sign Test statistic, Reduction of Error statistic, Product
23918 Mean Test, Durbin-Watson statistic etc.")
23919 (license license:gpl2)))
23921 (define-public r-rcdd
23928 (uri (cran-uri "rcdd" version))
23931 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23933 `((upstream-name . "rcdd")))
23934 (build-system r-build-system)
23937 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23938 (synopsis "Computational geometry")
23940 "This package converts back and forth between two representations of a
23941 convex polytope: as solution of a set of linear equalities and inequalities
23942 and as convex hull of set of points and rays. Also does linear programming
23943 and redundant generator elimination. All functions can use exact
23944 infinite-precision rational arithmetic.")
23945 (license license:gpl2)))
23947 (define-public r-rxnat
23954 (uri (cran-uri "Rxnat" version))
23957 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23959 `((upstream-name . "Rxnat")))
23960 (build-system r-build-system)
23962 `(("r-dplyr" ,r-dplyr)
23964 ("r-rcurl" ,r-rcurl)
23965 ("r-tibble" ,r-tibble)))
23967 `(("r-knitr" ,r-knitr)))
23968 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23969 (synopsis "Queries and extracts images from neuroimaging datasets")
23971 "This package allows communication with the Extensible Neuroimaging
23972 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23974 (license license:gpl2)))
23976 (define-public r-rserve
23983 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23984 version ".tar.gz"))
23987 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23988 (build-system r-build-system)
23991 (modify-phases %standard-phases
23992 (add-before 'install 'install-server-binary
23993 ;; Makevars tries to install to R's store directory.
23994 (lambda* (#:key outputs #:allow-other-keys)
23995 (let* ((out (assoc-ref outputs "out"))
23996 (bin (string-append out "/bin")))
23997 (substitute* "src/Makevars.in"
23998 (("\\$\\(R_HOME\\)") out))
23999 (mkdir-p bin)))))))
24001 `(("r-checkmate" ,r-checkmate)
24003 ("r-jsonlite" ,r-jsonlite)
24004 ("r-knitr" ,r-knitr)
24007 ("r-uuid" ,r-uuid)))
24009 `(("openssl" ,openssl)
24011 (home-page "https://github.com/s-u/Rserve")
24013 "Server providing access to R from many languages and systems")
24015 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
24016 binary requests to be sent to R. Every connection has a separate workspace
24017 and working directory. Client-side implementations are available for popular
24018 languages such as C/C++ and Java, allowing any application to use facilities
24019 of R without the need of linking to R code. Rserve supports remote
24020 connection, user authentication and file transfer. A simple R client is
24021 included in this package as well.")
24022 (license license:gpl2)))
24024 (define-public r-gamm4
24031 (uri (cran-uri "gamm4" version))
24034 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
24035 (properties `((upstream-name . "gamm4")))
24036 (build-system r-build-system)
24038 `(("r-lme4" ,r-lme4)
24039 ("r-matrix" ,r-matrix)
24040 ("r-mgcv" ,r-mgcv)))
24041 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24042 (synopsis "Generalized additive mixed models using mgcv and lme4")
24044 "Estimate generalized additive mixed models via a version of function
24045 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24047 (license license:gpl2+)))
24049 (define-public r-optimx
24052 (version "2020-4.2")
24056 (uri (cran-uri "optimx" version))
24059 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24060 (properties `((upstream-name . "optimx")))
24061 (build-system r-build-system)
24062 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24063 (native-inputs `(("r-knitr" ,r-knitr)))
24064 (home-page "https://cran.r-project.org/web/packages/optimx/")
24065 (synopsis "Expanded replacement and extension of the optim function")
24067 "This package provides a replacement and extension of the @code{optim}
24068 function to call to several function minimization codes in R in a single
24069 statement. These methods handle smooth, possibly box constrained functions of
24070 several or many parameters. Note that the function @code{optimr} was prepared
24071 to simplify the incorporation of minimization codes going forward. This
24072 package also implements some utility codes and some extra solvers, including
24073 safeguarded Newton methods. Many methods previously separate are now included
24075 (license license:gpl2)))
24077 (define-public r-projpred
24079 (name "r-projpred")
24084 (uri (cran-uri "projpred" version))
24087 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24088 (properties `((upstream-name . "projpred")))
24089 (build-system r-build-system)
24091 `(("r-dplyr" ,r-dplyr)
24092 ("r-gamm4" ,r-gamm4)
24093 ("r-ggplot2" ,r-ggplot2)
24096 ("r-magrittr" ,r-magrittr)
24099 ("r-optimx" ,r-optimx)
24101 ("r-rcpparmadillo" ,r-rcpparmadillo)
24102 ("r-rngtools" ,r-rngtools)
24103 ("r-rstantools" ,r-rstantools)
24104 ("r-tidyverse" ,r-tidyverse)))
24105 (native-inputs `(("r-knitr" ,r-knitr)))
24106 (home-page "https://mc-stan.org/projpred/")
24107 (synopsis "Projection predictive feature selection")
24109 "This package performs projection predictive feature selection for
24110 generalized linear models and generalized linear and additive multilevel
24111 models. The package is compatible with the @code{rstanarm} and @code{brms}
24112 packages, but other reference models can also be used. See the package
24113 vignette for more information and examples.")
24114 (license license:gpl3)))
24116 (define-public r-brms
24123 (uri (cran-uri "brms" version))
24126 "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1"))))
24127 (properties `((upstream-name . "brms")))
24128 (build-system r-build-system)
24130 `(("r-abind" ,r-abind)
24131 ("r-backports" ,r-backports)
24132 ("r-bayesplot" ,r-bayesplot)
24133 ("r-bridgesampling" ,r-bridgesampling)
24135 ("r-future" ,r-future)
24136 ("r-ggplot2" ,r-ggplot2)
24139 ("r-matrix" ,r-matrix)
24140 ("r-matrixstats" ,r-matrixstats)
24142 ("r-nleqslv" ,r-nleqslv)
24144 ("r-projpred" ,r-projpred)
24146 ("r-rstan" ,r-rstan)
24147 ("r-rstantools" ,r-rstantools)
24148 ("r-shinystan" ,r-shinystan)))
24149 (native-inputs `(("r-knitr" ,r-knitr)))
24151 "https://github.com/paul-buerkner/brms")
24153 "Bayesian Regression Models using 'Stan'")
24155 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24156 using 'Stan' for full Bayesian inference. A wide range of distributions and
24157 link functions are supported, allowing users to fit -- among others -- linear,
24158 robust linear, count data, survival, response times, ordinal, zero-inflated,
24159 hurdle, and even self-defined mixture models all in a multilevel context.
24160 Further modeling options include non-linear and smooth terms, auto-correlation
24161 structures, censored data, meta-analytic standard errors, and quite a few
24162 more. In addition, all parameters of the response distribution can be
24163 predicted in order to perform distributional regression. Prior specifications
24164 are flexible and explicitly encourage users to apply prior distributions that
24165 actually reflect their beliefs. Model fit can easily be assessed and compared
24166 with posterior predictive checks and leave-one-out cross-validation.")
24167 (license license:gpl2)))
24169 (define-public r-mstate
24176 (uri (cran-uri "mstate" version))
24179 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24180 (properties `((upstream-name . "mstate")))
24181 (build-system r-build-system)
24183 `(("r-data-table" ,r-data-table)
24184 ("r-lattice" ,r-lattice)
24185 ("r-magrittr" ,r-magrittr)
24186 ("r-rcolorbrewer" ,r-rcolorbrewer)
24187 ("r-rlang" ,r-rlang)
24188 ("r-survival" ,r-survival)
24189 ("r-viridis" ,r-viridis)))
24191 `(("r-knitr" ,r-knitr)))
24193 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24195 "Data Preparation, Estimation and Prediction in Multi-State Models")
24197 "Contains functions for data preparation, descriptives, hazard estimation
24198 and prediction with Aalen-Johansen or simulation in competing risks and
24199 multi-state models.")
24200 (license license:gpl2+)))
24202 (define-public r-scatterpie
24204 (name "r-scatterpie")
24209 (uri (cran-uri "scatterpie" version))
24212 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24213 (properties `((upstream-name . "scatterpie")))
24214 (build-system r-build-system)
24216 `(("r-ggforce" ,r-ggforce)
24217 ("r-ggplot2" ,r-ggplot2)
24218 ("r-rlang" ,r-rlang)
24219 ("r-rvcheck" ,r-rvcheck)
24220 ("r-tidyr" ,r-tidyr)))
24222 `(("r-knitr" ,r-knitr)))
24223 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24224 (synopsis "Scatter pie plot")
24226 "This package creates scatterpie plots, especially useful for plotting
24228 (license license:artistic2.0)))
24230 (define-public r-scrypt
24237 (uri (cran-uri "scrypt" version))
24240 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24241 (properties `((upstream-name . "scrypt")))
24242 (build-system r-build-system)
24244 `(("r-rcpp" ,r-rcpp)))
24245 (home-page "https://github.com/rstudio/rscrypt")
24246 (synopsis "Key derivation functions for R based on Scrypt")
24248 "This package provides functions for working with the scrypt key
24249 derivation functions. Scrypt is a password-based key derivation function
24250 created by Colin Percival. The algorithm was specifically designed to make it
24251 costly to perform large-scale custom hardware attacks by requiring large
24252 amounts of memory.")
24253 (license license:bsd-2)))
24255 (define-public r-boruta
24262 (uri (cran-uri "Boruta" version))
24265 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24266 (properties `((upstream-name . "Boruta")))
24267 (build-system r-build-system)
24268 (propagated-inputs `(("r-ranger" ,r-ranger)))
24269 (home-page "https://gitlab.com/mbq/Boruta/")
24270 (synopsis "Wrapper algorithm for all relevant feature selection")
24272 "This package provides an all relevant feature selection wrapper
24273 algorithm. It finds relevant features by comparing original attributes'
24274 importance with importance achievable at random, estimated using their
24275 permuted copies (shadows).")
24276 (license license:gpl2+)))
24278 (define-public r-directlabels
24280 (name "r-directlabels")
24281 (version "2021.1.13")
24285 (uri (cran-uri "directlabels" version))
24288 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24289 (build-system r-build-system)
24291 `(("r-quadprog" ,r-quadprog)))
24293 `(("r-knitr" ,r-knitr)))
24294 (home-page "http://directlabels.r-forge.r-project.org/")
24295 (synopsis "Direct labels for multicolor plots")
24297 "This package provides an extensible framework for automatically placing
24298 direct labels onto multicolor plots. Label positions are described using
24299 positioning methods that can be re-used across several different plots. There
24300 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24301 inferring an appropriate positioning method.")
24302 (license license:gpl3)))
24304 (define-public r-lsd
24311 (uri (cran-uri "LSD" version))
24313 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24314 (properties `((upstream-name . "LSD")))
24315 (build-system r-build-system)
24316 (home-page "https://cran.r-project.org/web/packages/LSD/")
24317 (synopsis "Lots of superior depictions tool creates colorful plots")
24319 "This package creates lots of colorful plots in a multitude of variations.
24320 Try a demo of the LSD by running @code{demotour()}.")
24322 (license (list license:gpl2 license:gpl3))))
24324 (define-public r-phylogram
24326 (name "r-phylogram")
24331 (uri (cran-uri "phylogram" version))
24333 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24334 (properties `((upstream-name . "phylogram")))
24335 (build-system r-build-system)
24336 (propagated-inputs `(("r-ape" ,r-ape)))
24337 (home-page "https://github.com/ropensci/phylogram/")
24338 (synopsis "Dendrograms for evolutionary analysis")
24340 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24341 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24342 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24343 as well as several tools for command-line tree manipulation and import/export
24344 via Newick parenthetic text. This improves accessibility to the comprehensive
24345 range of object-specific analytical and tree-visualization functions found
24346 across a wide array of bioinformatic R packages.")
24347 (license license:gpl3)))
24349 (define-public r-kmer
24356 (uri (cran-uri "kmer" version))
24358 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24359 (properties `((upstream-name . "kmer")))
24360 (build-system r-build-system)
24362 `(("r-openssl" ,r-openssl)
24363 ("r-phylogram" ,r-phylogram)
24364 ("r-rcpp" ,r-rcpp)))
24365 (home-page "https://github.com/shaunpwilkinson/kmer/")
24366 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24368 "@code{r-kmer} is an R package for rapidly computing distance matrices
24369 and clustering large sequence datasets using fast alignment-free k-mer
24370 counting and recursive k-means partitioning.")
24371 (license license:gpl3)))
24373 (define-public r-hardhat
24380 (uri (cran-uri "hardhat" version))
24383 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24384 (properties `((upstream-name . "hardhat")))
24385 (build-system r-build-system)
24387 `(("r-glue" ,r-glue)
24388 ("r-rlang" ,r-rlang)
24389 ("r-tibble" ,r-tibble)
24390 ("r-vctrs" ,r-vctrs)))
24392 `(("r-knitr" ,r-knitr)))
24393 (home-page "https://github.com/tidymodels/hardhat")
24394 (synopsis "Construct modeling packages")
24396 "Building modeling packages is hard. A large amount of effort generally
24397 goes into providing an implementation for a new method that is efficient,
24398 fast, and correct, but often less emphasis is put on the user interface. A
24399 good interface requires specialized knowledge about S3 methods and formulas,
24400 which the average package developer might not have. The goal of
24401 @code{hardhat} is to reduce the burden around building new modeling packages
24402 by providing functionality for preprocessing, predicting, and validating
24404 (license license:expat)))
24406 (define-public r-lightgbm
24408 (name "r-lightgbm")
24413 (uri (cran-uri "lightgbm" version))
24416 "0aw1zcrg7nhddfaif9544hn8g8qcylv6vzpkf8d3kl07nzvgxkvj"))))
24417 (properties `((upstream-name . "lightgbm")))
24418 (build-system r-build-system)
24420 `(("r-data-table" ,r-data-table)
24421 ("r-jsonlite" ,r-jsonlite)
24422 ("r-matrix" ,r-matrix)
24424 (home-page "https://github.com/Microsoft/LightGBM")
24425 (synopsis "Light gradient boosting machine")
24427 "Tree based algorithms can be improved by introducing boosting
24428 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24429 al. (2017). This package offers an R interface to work with it. It is
24430 designed to be distributed and efficient with the following goals:
24433 @item Faster training speed and higher efficiency;
24434 @item lower memory usage;
24435 @item better accuracy;
24436 @item parallel learning supported; and
24437 @item capable of handling large-scale data.
24440 (license license:expat)))
24442 (define-public r-shapforxgboost
24444 (name "r-shapforxgboost")
24449 (uri (cran-uri "SHAPforxgboost" version))
24452 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
24454 `((upstream-name . "SHAPforxgboost")))
24455 (build-system r-build-system)
24457 `(("r-bbmisc" ,r-bbmisc)
24458 ("r-data-table" ,r-data-table)
24459 ("r-ggextra" ,r-ggextra)
24460 ("r-ggforce" ,r-ggforce)
24461 ("r-ggplot2" ,r-ggplot2)
24462 ("r-ggpubr" ,r-ggpubr)
24463 ("r-rcolorbrewer" ,r-rcolorbrewer)
24464 ("r-xgboost" ,r-xgboost)))
24466 `(("r-knitr" ,r-knitr)))
24467 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24468 (synopsis "SHAP Plots for XGBoost")
24470 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24471 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24472 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24473 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24475 (license license:expat)))
24477 (define-public r-rismed
24484 (uri (cran-uri "RISmed" version))
24487 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24488 (properties `((upstream-name . "RISmed")))
24489 (build-system r-build-system)
24490 (home-page "https://cran.r-project.org/web/packages/RISmed")
24491 (synopsis "Download content from NCBI databases")
24493 "This package provides a set of tools to extract bibliographic
24494 content from the National Center for Biotechnology Information (NCBI)
24495 databases, including PubMed. The name RISmed is a portmanteau of
24496 RIS (for Research Information Systems, a common tag format for
24497 bibliographic data) and PubMed.")
24498 (license license:gpl2+)))
24500 (define-public r-semver
24507 (uri (cran-uri "semver" version))
24510 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24511 (properties `((upstream-name . "semver")))
24512 (build-system r-build-system)
24514 `(("r-assertthat" ,r-assertthat)
24515 ("r-rcpp" ,r-rcpp)))
24516 (native-inputs `(("r-knitr" ,r-knitr)))
24517 (home-page "https://github.com/johndharrison/semver")
24518 (synopsis "Parser for Semantic Versioning 2.0.0")
24520 "This package provides tools and functions for parsing, rendering and
24521 operating on semantic version strings. Semantic versioning is a simple set of
24522 rules and requirements that dictate how version numbers are assigned and
24523 incremented as outlined at @url{http://semver.org}.")
24524 (license license:expat)))
24526 (define-public r-binman
24533 (uri (cran-uri "binman" version))
24536 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24537 (properties `((upstream-name . "binman")))
24538 (build-system r-build-system)
24540 `(("r-assertthat" ,r-assertthat)
24542 ("r-jsonlite" ,r-jsonlite)
24543 ("r-rappdirs" ,r-rappdirs)
24544 ("r-semver" ,r-semver)
24546 ("r-yaml" ,r-yaml)))
24547 (native-inputs `(("r-knitr" ,r-knitr)))
24548 (home-page "https://github.com/ropensci/binman")
24549 (synopsis "Binary download manager")
24551 "This package provides tools and functions for managing the download of
24552 binary files. Binary repositories are defined in the YAML format. Defining
24553 new pre-download, download and post-download templates allow additional
24554 repositories to be added.")
24555 (license license:expat)))
24557 (define-public r-wdman
24564 (uri (cran-uri "wdman" version))
24567 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24568 (properties `((upstream-name . "wdman")))
24569 (build-system r-build-system)
24571 `(("r-assertthat" ,r-assertthat)
24572 ("r-binman" ,r-binman)
24573 ("r-processx" ,r-processx)
24574 ("r-semver" ,r-semver)
24575 ("r-yaml" ,r-yaml)))
24576 (native-inputs `(("r-knitr" ,r-knitr)))
24577 (home-page "https://docs.ropensci.org/wdman/")
24578 (synopsis "Webdriver/Selenium binary manager")
24580 "There are a number of binary files associated with the
24581 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24582 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24583 @url{https://github.com/mozilla/geckodriver},
24584 @url{http://phantomjs.org/download.html}, and
24585 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24586 more information). This package provides functions to download these binaries
24587 and to manage processes involving them.")
24588 (license license:expat)))
24590 (define-public r-rselenium
24592 (name "r-rselenium")
24597 (uri (cran-uri "RSelenium" version))
24600 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24601 (properties `((upstream-name . "RSelenium")))
24602 (build-system r-build-system)
24604 `(("r-binman" ,r-binman)
24605 ("r-catools" ,r-catools)
24607 ("r-openssl" ,r-openssl)
24608 ("r-wdman" ,r-wdman)
24610 (native-inputs `(("r-knitr" ,r-knitr)))
24611 (home-page "https://docs.ropensci.org/RSelenium/")
24612 (synopsis "R bindings for Selenium WebDriver")
24614 "This package provides a set of R bindings for the Selenium 2.0
24615 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24616 information) using the @code{JsonWireProtocol} (see
24617 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24618 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24619 a user would either locally or on a remote machine using the Selenium server
24620 it marks a leap forward in terms of web browser automation. Selenium
24621 automates web browsers (commonly referred to as browsers). Using RSelenium
24622 you can automate browsers locally or remotely.")
24623 (license license:agpl3+)))
24625 (define-public r-conquer
24632 (uri (cran-uri "conquer" version))
24635 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24636 (properties `((upstream-name . "conquer")))
24637 (build-system r-build-system)
24639 `(("r-matrix" ,r-matrix)
24640 ("r-matrixstats" ,r-matrixstats)
24642 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24643 (home-page "https://github.com/XiaoouPan/conquer")
24644 (synopsis "Convolution-type smoothed quantile regression")
24646 "This package provides fast and accurate convolution-type smoothed
24647 quantile regression, implemented using Barzilai-Borwein gradient descent with
24648 a Huber regression warm start. Confidence intervals for regression
24649 coefficients are constructed using multiplier bootstrap.")
24650 (license license:gpl3)))
24652 (define-public r-fastshap
24654 (name "r-fastshap")
24659 (uri (cran-uri "fastshap" version))
24662 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24663 (properties `((upstream-name . "fastshap")))
24664 (build-system r-build-system)
24666 `(("r-abind" ,r-abind)
24667 ("r-ggplot2" ,r-ggplot2)
24668 ("r-gridextra" ,r-gridextra)
24669 ("r-matrixstats" ,r-matrixstats)
24672 ("r-rcpparmadillo" ,r-rcpparmadillo)
24673 ("r-tibble" ,r-tibble)))
24674 (home-page "https://github.com/bgreenwell/fastshap")
24675 (synopsis "Fast approximate Shapley values")
24677 "This package computes fast (relative to other implementations)
24678 approximate Shapley values for any supervised learning model. Shapley values
24679 help to explain the predictions from any black box model using ideas from game
24680 theory; see @url{Strumbel and Kononenko (2014),
24681 doi.org/10.1007/s10115-013-0679-x} for details.")
24682 (license license:gpl2+)))
24684 (define-public r-metrics
24691 (uri (cran-uri "Metrics" version))
24694 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24695 (properties `((upstream-name . "Metrics")))
24696 (build-system r-build-system)
24697 (home-page "https://github.com/mfrasco/Metrics")
24698 (synopsis "Evaluation metrics for machine learning")
24700 "This package provides an implementation of evaluation metrics in R that
24701 are commonly used in supervised machine learning. It implements metrics for
24702 regression, time series, binary classification, classification, and
24703 information retrieval problems. It has zero dependencies and a consistent,
24704 simple interface for all functions.")
24705 (license license:bsd-3)))
24707 (define-public r-iml
24714 (uri (cran-uri "iml" version))
24717 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24718 (properties `((upstream-name . "iml")))
24719 (build-system r-build-system)
24721 `(("r-checkmate" ,r-checkmate)
24722 ("r-data-table" ,r-data-table)
24723 ("r-formula" ,r-formula)
24724 ("r-future" ,r-future)
24725 ("r-future-apply" ,r-future-apply)
24726 ("r-ggplot2" ,r-ggplot2)
24727 ("r-gridextra" ,r-gridextra)
24728 ("r-metrics" ,r-metrics)
24729 ("r-prediction" ,r-prediction)
24731 (native-inputs `(("r-knitr" ,r-knitr)))
24732 (home-page "https://github.com/christophM/iml")
24733 (synopsis "Interpretable machine learning")
24735 "This package provides interpretability methods to analyze the behavior
24736 and predictions of any machine learning model. Implemented methods are:
24739 @item Feature importance described by Fisher et al. (2018),
24740 @item accumulated local effects plots described by Apley (2018),
24741 @item partial dependence plots described by Friedman (2001),
24742 @item individual conditional expectation ('ice') plots described by Goldstein
24743 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24744 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24745 @item the Shapley Value described by Strumbelj et. al (2014)
24746 @url{https://doi.org/10.1007/s10115-013-0679-x},
24747 @item feature interactions described by Friedman et. al
24748 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24751 (license license:expat)))
24753 (define-public r-goftest
24760 (uri (cran-uri "goftest" version))
24763 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24764 (properties `((upstream-name . "goftest")))
24765 (build-system r-build-system)
24766 (home-page "https://github.com/baddstats/goftest")
24767 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24769 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24770 goodness-of-fit for continuous univariate distributions, using efficient
24772 (license license:gpl2+)))
24774 (define-public r-tensor
24781 (uri (cran-uri "tensor" version))
24784 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24785 (properties `((upstream-name . "tensor")))
24786 (build-system r-build-system)
24787 (home-page "https://cran.r-project.org/web/packages/tensor/")
24788 (synopsis "Tensor product of arrays")
24790 "The tensor product of two arrays is notionally an outer product of the
24791 arrays collapsed in specific extents by summing along the appropriate
24792 diagonals. This package allows you to compute the tensor product of arrays.")
24793 (license license:gpl2+)))
24795 (define-public r-spatstat-utils
24797 (name "r-spatstat-utils")
24802 (uri (cran-uri "spatstat.utils" version))
24805 "18gqsc1a85pk69aifi10wprv1c0lci3zxp4wqjb27dlmlbz6jdgd"))))
24807 `((upstream-name . "spatstat.utils")))
24808 (build-system r-build-system)
24809 (home-page "http://www.spatstat.org")
24810 (synopsis "Utility functions for spatstat")
24812 "This package contains utility functions for the @code{spatstat} package
24813 which may also be useful for other purposes.")
24814 (license license:gpl2+)))
24816 (define-public r-spatstat-sparse
24818 (name "r-spatstat-sparse")
24823 (uri (cran-uri "spatstat.sparse" version))
24826 "1iqrpazb88s4w208adf2qgm4ajwz3kwqck65k9g5l28zw9jcxyr7"))))
24828 `((upstream-name . "spatstat.sparse")))
24829 (build-system r-build-system)
24831 `(("r-abind" ,r-abind)
24832 ("r-matrix" ,r-matrix)
24833 ("r-spatstat-utils" ,r-spatstat-utils)
24834 ("r-tensor" ,r-tensor)))
24835 (home-page "http://spatstat.org/")
24836 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
24838 "This package defines sparse three-dimensional arrays and supports
24839 standard operations on them. The package also includes utility functions for
24840 matrix calculations that are common in statistics, such as quadratic forms.")
24841 (license license:gpl2+)))
24843 (define-public r-spatstat-data
24845 (name "r-spatstat-data")
24850 (uri (cran-uri "spatstat.data" version))
24853 "0csmz5vjaxnznkbsfah8qd3v8p0y56jvis01ialxzvf71snl160v"))))
24854 (properties `((upstream-name . "spatstat.data")))
24855 (build-system r-build-system)
24857 `(("r-matrix" ,r-matrix)
24858 ("r-spatstat-utils" ,r-spatstat-utils)))
24859 (home-page "http://www.spatstat.org")
24860 (synopsis "Datasets for spatstat")
24862 "This package contains all the datasets for the @code{spatstat}
24864 (license license:gpl2+)))
24866 (define-public r-spatstat-geom
24868 (name "r-spatstat-geom")
24873 (uri (cran-uri "spatstat.geom" version))
24876 "1r7nlgh62apchidg28fxq1a22iv1b29y5xmsg1kjwfvkbq8zxsvh"))))
24877 (properties `((upstream-name . "spatstat.geom")))
24878 (build-system r-build-system)
24880 `(("r-deldir" ,r-deldir)
24881 ("r-polyclip" ,r-polyclip)
24882 ("r-spatstat-data" ,r-spatstat-data)
24883 ("r-spatstat-utils" ,r-spatstat-utils)))
24884 (home-page "http://spatstat.org/")
24885 (synopsis "Geometrical functionality of the spatstat package")
24887 "This is a subset of the original spatstat package, containing the
24888 user-level code from spatstat which performs geometrical operations, except
24889 for the geometry of linear networks.")
24890 (license license:gpl2+)))
24892 (define-public r-spatstat-core
24894 (name "r-spatstat-core")
24899 (uri (cran-uri "spatstat.core" version))
24902 "19wv27nfx48xkqa1amys4jf93k0d8xns20p84n5kqyibscdsksgx"))))
24903 (properties `((upstream-name . "spatstat.core")))
24904 (build-system r-build-system)
24906 `(("r-abind" ,r-abind)
24907 ("r-goftest" ,r-goftest)
24908 ("r-matrix" ,r-matrix)
24911 ("r-rpart" ,r-rpart)
24912 ("r-spatstat-data" ,r-spatstat-data)
24913 ("r-spatstat-geom" ,r-spatstat-geom)
24914 ("r-spatstat-sparse" ,r-spatstat-sparse)
24915 ("r-spatstat-utils" ,r-spatstat-utils)
24916 ("r-tensor" ,r-tensor)))
24917 (home-page "http://spatstat.org/")
24918 (synopsis "Core functionality of the spatstat package")
24920 "This is a subset of the original spatstat package, containing all of the
24921 user-level code from spatstat, except for the code for linear networks.")
24922 (license license:gpl2+)))
24924 (define-public r-spatstat-linnet
24926 (name "r-spatstat-linnet")
24931 (uri (cran-uri "spatstat.linnet" version))
24934 "1ia0qgggddiwhhyd3q516f3p6by0p4xnq26wqz7410n2ja60bbb4"))))
24936 `((upstream-name . "spatstat.linnet")))
24937 (build-system r-build-system)
24939 `(("r-matrix" ,r-matrix)
24940 ("r-spatstat-core" ,r-spatstat-core)
24941 ("r-spatstat-data" ,r-spatstat-data)
24942 ("r-spatstat-geom" ,r-spatstat-geom)
24943 ("r-spatstat-utils" ,r-spatstat-utils)))
24944 (home-page "http://spatstat.org/")
24945 (synopsis "Linear networks functionality of the spatstat package")
24947 "This is a subset of the spatstat package, containing its functionality
24948 for spatial data on a linear network.")
24949 (license license:gpl2+)))
24951 (define-public r-spatstat
24953 (name "r-spatstat")
24958 (uri (cran-uri "spatstat" version))
24961 "0vr5md53247v6crvjvg9m82vc6h914zzvkzfkga8x79hv35ii4as"))))
24962 (properties `((upstream-name . "spatstat")))
24963 (build-system r-build-system)
24965 `(("r-spatstat-core" ,r-spatstat-core)
24966 ("r-spatstat-data" ,r-spatstat-data)
24967 ("r-spatstat-geom" ,r-spatstat-geom)
24968 ("r-spatstat-linnet" ,r-spatstat-linnet)
24969 ("r-spatstat-utils" ,r-spatstat-utils)))
24970 (home-page "http://www.spatstat.org")
24971 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24973 "This package provides a comprehensive toolbox for analysing Spatial
24974 Point Patterns. It is focused mainly on two-dimensional point patterns,
24975 including multitype/marked points, in any spatial region. It also supports
24976 three-dimensional point patterns, space-time point patterns in any number of
24977 dimensions, point patterns on a linear network, and patterns of other
24978 geometrical objects. It supports spatial covariate data such as pixel images
24979 and contains over 2000 functions for plotting spatial data, exploratory data
24980 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24981 formal inference.")
24982 (license license:gpl2+)))
24984 (define-public r-gaston
24991 (uri (cran-uri "gaston" version))
24994 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24995 (properties `((upstream-name . "gaston")))
24996 (build-system r-build-system)
24997 (inputs `(("zlib" ,zlib)))
24999 `(("r-rcpp" ,r-rcpp)
25000 ("r-rcppeigen" ,r-rcppeigen)
25001 ("r-rcppparallel" ,r-rcppparallel)))
25002 (native-inputs `(("r-knitr" ,r-knitr)))
25003 (home-page "https://cran.r-project.org/web/packages/gaston/")
25004 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
25006 "This is a package for the manipulation of genetic data (SNPs).
25007 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
25008 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
25009 for linear mixed models (AIREML).")
25010 (license license:gpl3)))
25012 (define-public r-cpp11
25019 (uri (cran-uri "cpp11" version))
25022 "1m31yq3kn5wqvm0ahj08kb4bszbbhfybx3l2x975cjzgv3058h8x"))))
25023 (properties `((upstream-name . "cpp11")))
25024 (build-system r-build-system)
25025 (native-inputs `(("r-knitr" ,r-knitr)))
25026 (home-page "https://github.com/r-lib/cpp11")
25027 (synopsis "C++11 Interface for R's C Interface")
25029 "This package provides a header only, C++11 interface to R's C interface.
25030 Compared to other approaches @code{cpp11} strives to be safe against long
25031 jumps from the C API as well as C++ exceptions, conform to normal R function
25032 semantics and supports interaction with @code{ALTREP} vectors.")
25033 (license license:expat)))
25035 (define-public r-rcppziggurat
25037 (name "r-rcppziggurat")
25042 (uri (cran-uri "RcppZiggurat" version))
25045 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
25046 (properties `((upstream-name . "RcppZiggurat")))
25047 (build-system r-build-system)
25049 `(("r-rcpp" ,r-rcpp)
25050 ("r-rcppgsl" ,r-rcppgsl)))
25051 (native-inputs `(("r-knitr" ,r-knitr)))
25052 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
25053 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
25055 "The Ziggurat generator for normally distributed random numbers,
25056 originally proposed by Marsaglia and Tsang (2000,
25057 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
25058 times starting with Leong et al (2005,
25059 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
25060 aggregation for comparing different implementations in order to provide a
25061 'faster but good enough' alternative for use with R and C++ code.")
25062 (license license:gpl2+)))
25064 (define-public r-rfast
25071 (uri (cran-uri "Rfast" version))
25074 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
25075 (properties `((upstream-name . "Rfast")))
25076 (build-system r-build-system)
25078 `(("r-rcpp" ,r-rcpp)
25079 ("r-rcpparmadillo" ,r-rcpparmadillo)
25080 ("r-rcppziggurat" ,r-rcppziggurat)))
25081 (home-page "https://github.com/RfastOfficial/Rfast")
25082 (synopsis "Collection of efficient and fast R functions")
25084 "This package provides a collection of fast (utility) functions for data
25085 analysis. Column- and row- wise means, medians, variances, minimums,
25086 maximums, many t, F and G-square tests, many regressions (normal, logistic,
25087 Poisson), are some of the many fast functions.")
25088 (license license:gpl2+)))
25090 (define-public r-clusterr
25092 (name "r-clusterr")
25097 (uri (cran-uri "ClusterR" version))
25100 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
25101 (properties `((upstream-name . "ClusterR")))
25102 (build-system r-build-system)
25104 `(("r-ggplot2" ,r-ggplot2)
25106 ("r-gtools" ,r-gtools)
25108 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25109 (native-inputs `(("r-knitr" ,r-knitr)))
25110 (home-page "https://github.com/mlampros/ClusterR")
25111 (synopsis "Clustering")
25113 "This package provides Gaussian mixture models, k-means,
25114 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
25115 option to plot, validate, predict (new data) and estimate the optimal number
25116 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
25117 the computationally intensive parts of the functions. For more information,
25121 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
25122 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
25123 @url{https://doi.org/10.18637/jss.v001.i04};
25124 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
25125 Library, @url{https://doi.org/10.1145/1772690.1772862};
25126 @item \"Armadillo: a template-based C++ library
25127 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
25128 Software, @url{https://doi.org/10.21105/joss.00026};
25129 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
25130 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
25131 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
25134 (license license:gpl3)))
25136 (define-public r-spectrum
25138 (name "r-spectrum")
25143 (uri (cran-uri "Spectrum" version))
25146 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25147 (properties `((upstream-name . "Spectrum")))
25148 (build-system r-build-system)
25150 `(("r-clusterr" ,r-clusterr)
25151 ("r-diptest" ,r-diptest)
25152 ("r-ggplot2" ,r-ggplot2)
25153 ("r-rfast" ,r-rfast)))
25154 (native-inputs `(("r-knitr" ,r-knitr)))
25155 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25156 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25158 "This package provides a self-tuning spectral clustering method for
25159 single or multi-view data. Spectrum uses a new type of adaptive density aware
25160 kernel that strengthens connections in the graph based on common nearest
25161 neighbours. It uses a tensor product graph data integration and diffusion
25162 procedure to integrate different data sources and reduce noise. Spectrum uses
25163 either the eigengap or multimodality gap heuristics to determine the number of
25164 clusters. The method is sufficiently flexible so that a wide range of
25165 Gaussian and non-Gaussian structures can be clustered with automatic selection
25167 (license license:agpl3+)))
25169 (define-public r-nabor
25176 (uri (cran-uri "nabor" version))
25179 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25180 (properties `((upstream-name . "nabor")))
25181 (build-system r-build-system)
25185 ("r-rcppeigen" ,r-rcppeigen)))
25186 (home-page "https://cran.r-project.org/web/packages/nabor/")
25187 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25189 "This package provides an R wrapper for libnabo, an exact or approximate
25190 k nearest neighbour library which is optimised for low dimensional
25191 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25192 designed as a drop-in replacement for the RANN function @code{nn2}. In
25193 addition, objects which include the k-d tree search structure can be returned
25194 to speed up repeated queries of the same set of target points.")
25195 (license license:bsd-3)))
25197 (define-public r-muhaz
25200 (version "1.2.6.3")
25204 (uri (cran-uri "muhaz" version))
25207 "1lzc8arbpcxgfap3dfsgq8crpp1cxd9qlbrhvyvl79zgpxjqx4q2"))))
25208 (properties `((upstream-name . "muhaz")))
25209 (build-system r-build-system)
25211 `(("r-survival" ,r-survival)))
25213 `(("gfortran" ,gfortran)))
25214 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25215 (synopsis "Hazard function estimation in survival analysis")
25217 "This package produces a smooth estimate of the hazard function for
25219 ;; Any version of the GPL.
25220 (license license:gpl3+)))
25222 (define-public r-flexsurv
25224 (name "r-flexsurv")
25229 (uri (cran-uri "flexsurv" version))
25232 "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9"))))
25233 (properties `((upstream-name . "flexsurv")))
25234 (build-system r-build-system)
25236 `(("r-assertthat" ,r-assertthat)
25237 ("r-desolve" ,r-desolve)
25238 ("r-dplyr" ,r-dplyr)
25239 ("r-generics" ,r-generics)
25240 ("r-magrittr" ,r-magrittr)
25241 ("r-matrix" ,r-matrix)
25242 ("r-mstate" ,r-mstate)
25243 ("r-muhaz" ,r-muhaz)
25244 ("r-mvtnorm" ,r-mvtnorm)
25245 ("r-numderiv" ,r-numderiv)
25246 ("r-purrr" ,r-purrr)
25247 ("r-quadprog" ,r-quadprog)
25249 ("r-rlang" ,r-rlang)
25250 ("r-rstpm2" ,r-rstpm2)
25251 ("r-survival" ,r-survival)
25252 ("r-tibble" ,r-tibble)
25253 ("r-tidyr" ,r-tidyr)
25254 ("r-tidyselect" ,r-tidyselect)))
25256 `(("r-knitr" ,r-knitr)))
25257 (home-page "https://github.com/chjackson/flexsurv-dev")
25258 (synopsis "Flexible parametric survival and multi-state models")
25260 "This package provides flexible parametric models for time-to-event data,
25261 including the Royston-Parmar spline model, generalized gamma and generalized F
25262 distributions. Any user-defined parametric distribution can be fitted, given
25263 at least an R function defining the probability density or hazard. There are
25264 also tools for fitting and predicting from fully parametric multi-state
25266 (license license:gpl2+)))
25268 (define-public r-transphylo
25270 (name "r-transphylo")
25275 (uri (cran-uri "TransPhylo" version))
25278 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25279 (properties `((upstream-name . "TransPhylo")))
25280 (build-system r-build-system)
25283 ("r-rcpp" ,r-rcpp)))
25285 `(("r-knitr" ,r-knitr)))
25286 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25287 (synopsis "Inference of transmission tree from a dated phylogeny")
25289 "This is a package to infer transmission trees from a dated phylogeny.
25290 It includes methods to simulate and analyze outbreaks. The methodology is
25291 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25292 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25293 (license license:gpl2+)))
25295 (define-public r-km-ci
25302 (uri (cran-uri "km.ci" version))
25305 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25306 (properties `((upstream-name . "km.ci")))
25307 (build-system r-build-system)
25309 `(("r-survival" ,r-survival)))
25310 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25311 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25313 "This package computes various @dfn{confidence intervals} (CI) for the
25314 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25315 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25316 Nair and Hall and Wellner.")
25317 (license license:gpl2+)))
25319 (define-public r-kmsurv
25326 (uri (cran-uri "KMsurv" version))
25329 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25330 (properties `((upstream-name . "KMsurv")))
25331 (build-system r-build-system)
25332 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25333 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25335 "This package provides data sets and functions for Klein and Moeschberger
25336 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25338 (license license:gpl3+)))
25340 (define-public r-survmisc
25342 (name "r-survmisc")
25347 (uri (cran-uri "survMisc" version))
25350 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25351 (properties `((upstream-name . "survMisc")))
25352 (build-system r-build-system)
25354 `(("r-data-table" ,r-data-table)
25355 ("r-ggplot2" ,r-ggplot2)
25356 ("r-gridextra" ,r-gridextra)
25357 ("r-km-ci" ,r-km-ci)
25358 ("r-kmsurv" ,r-kmsurv)
25359 ("r-knitr" ,r-knitr)
25360 ("r-survival" ,r-survival)
25361 ("r-xtable" ,r-xtable)
25364 `(("r-knitr" ,r-knitr)))
25365 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25366 (synopsis "Miscellaneous functions for survival data")
25368 "This package provides a collection of functions to help in the analysis
25369 of right-censored survival data. These extend the methods available in
25370 the @code{survival} package.")
25371 (license license:gpl2)))
25373 (define-public r-exactranktests
25375 (name "r-exactranktests")
25380 (uri (cran-uri "exactRankTests" version))
25383 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25385 `((upstream-name . "exactRankTests")))
25386 (build-system r-build-system)
25387 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25388 (synopsis "Exact distributions for rank and permutation tests")
25390 "This package computes exact conditional p-values and quantiles using an
25391 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25392 (license license:gpl2+)))
25394 (define-public r-maxstat
25401 (uri (cran-uri "maxstat" version))
25404 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25405 (properties `((upstream-name . "maxstat")))
25406 (build-system r-build-system)
25408 `(("r-exactranktests" ,r-exactranktests)
25409 ("r-mvtnorm" ,r-mvtnorm)))
25410 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25411 (synopsis "Maximally selected rank statistics")
25413 "This package provides maximally selected rank statistics with several
25414 p-value approximations.")
25415 (license license:gpl2+)))
25417 (define-public r-survminer
25419 (name "r-survminer")
25424 (uri (cran-uri "survminer" version))
25427 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
25428 (properties `((upstream-name . "survminer")))
25429 (build-system r-build-system)
25431 `(("r-broom" ,r-broom)
25432 ("r-dplyr" ,r-dplyr)
25433 ("r-ggplot2" ,r-ggplot2)
25434 ("r-ggpubr" ,r-ggpubr)
25435 ("r-ggtext" ,r-ggtext)
25436 ("r-gridextra" ,r-gridextra)
25437 ("r-magrittr" ,r-magrittr)
25438 ("r-maxstat" ,r-maxstat)
25439 ("r-purrr" ,r-purrr)
25440 ("r-rlang" ,r-rlang)
25441 ("r-scales" ,r-scales)
25442 ("r-survival" ,r-survival)
25443 ("r-survmisc" ,r-survmisc)
25444 ("r-tibble" ,r-tibble)
25445 ("r-tidyr" ,r-tidyr)))
25447 `(("r-knitr" ,r-knitr)))
25448 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25449 (synopsis "Drawing survival curves using ggplot2")
25451 "This package contains the function @code{ggsurvplot()} for easily
25452 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25453 risk' table and 'censoring count plot'. Other functions are also available to
25454 plot adjusted curves for Cox model and to visually examine Cox model
25456 (license license:gpl2)))
25458 (define-public r-forge
25465 (uri (cran-uri "forge" version))
25468 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25469 (properties `((upstream-name . "forge")))
25470 (build-system r-build-system)
25472 `(("r-magrittr" ,r-magrittr)
25473 ("r-rlang" ,r-rlang)))
25474 (home-page "https://cran.r-project.org/web/packages/forge/")
25475 (synopsis "Cast values into shape")
25477 "This package provides helper functions with a consistent interface to
25478 coerce and verify the types and shapes of values for input checking.")
25479 (license license:asl2.0)))
25481 (define-public r-config
25488 (uri (cran-uri "config" version))
25491 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25492 (properties `((upstream-name . "config")))
25493 (build-system r-build-system)
25495 `(("r-yaml" ,r-yaml)))
25497 `(("r-knitr" ,r-knitr)))
25498 (home-page "https://github.com/rstudio/config")
25499 (synopsis "Manage environment specific configuration values")
25501 "This package lets you manage configuration values across multiple
25502 environments (e.g. development, test, production). It reads values using a
25503 function that determines the current environment and returns the appropriate
25505 (license license:gpl3)))
25507 (define-public r-adaptivesparsity
25509 (name "r-adaptivesparsity")
25513 (uri (cran-uri "AdaptiveSparsity" version))
25516 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25518 `((upstream-name . "AdaptiveSparsity")))
25519 (build-system r-build-system)
25522 (modify-phases %standard-phases
25523 (add-after 'unpack 'link-against-armadillo
25525 (substitute* "src/Makevars"
25526 (("PKG_LIBS=" prefix)
25527 (string-append prefix "-larmadillo")))
25530 `(("r-mass" ,r-mass)
25531 ("r-matrix" ,r-matrix)
25533 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25535 `(("armadillo" ,armadillo)))
25536 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25537 (synopsis "Adaptive sparsity models")
25539 "This package implements the Figueiredo machine learning algorithm for
25540 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25541 geometric models.")
25542 (license license:lgpl3+)))
25544 (define-public r-diffusionmap
25546 (name "r-diffusionmap")
25551 (uri (cran-uri "diffusionMap" version))
25554 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25555 (properties `((upstream-name . "diffusionMap")))
25556 (build-system r-build-system)
25558 `(("r-igraph" ,r-igraph)
25559 ("r-matrix" ,r-matrix)
25560 ("r-scatterplot3d" ,r-scatterplot3d)))
25561 (home-page "https://www.r-project.org")
25562 (synopsis "Diffusion map")
25563 (description "This package implements the diffusion map method of data
25564 parametrization, including creation and visualization of diffusion maps,
25565 clustering with diffusion K-means and regression using the adaptive regression
25567 (license license:gpl2)))
25569 (define-public r-igraph
25576 (uri (cran-uri "igraph" version))
25579 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25580 (build-system r-build-system)
25582 `(("gfortran" ,gfortran)))
25586 ("libxml2" ,libxml2)
25589 `(("r-magrittr" ,r-magrittr)
25590 ("r-matrix" ,r-matrix)
25591 ("r-pkgconfig" ,r-pkgconfig)))
25592 (home-page "https://igraph.org")
25593 (synopsis "Network analysis and visualization")
25595 "This package provides routines for simple graphs and network analysis.
25596 It can handle large graphs very well and provides functions for generating
25597 random and regular graphs, graph visualization, centrality methods and much
25599 (license license:gpl2+)))
25601 (define-public r-workflows
25603 (name "r-workflows")
25608 (uri (cran-uri "workflows" version))
25611 "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz"))))
25612 (properties `((upstream-name . "workflows")))
25613 (build-system r-build-system)
25616 ("r-ellipsis" ,r-ellipsis)
25617 ("r-generics" ,r-generics)
25619 ("r-hardhat" ,r-hardhat)
25620 ("r-parsnip" ,r-parsnip)
25621 ("r-rlang" ,r-rlang)
25622 ("r-tidyselect" ,r-tidyselect)
25623 ("r-vctrs" ,r-vctrs)))
25625 `(("r-knitr" ,r-knitr)))
25626 (home-page "https://github.com/tidymodels/workflows")
25627 (synopsis "Modeling workflows")
25629 "A workflow is an object that can bundle together your pre-processing,
25630 modeling, and post-processing requests. For example, if you have a
25631 @code{recipe} and @code{parsnip} model, these can be combined into a
25632 workflow. The advantages are:
25635 @item You don’t have to keep track of separate objects in your workspace.
25636 @item The recipe prepping and model fitting can be executed using a single
25637 call to @code{fit()}.
25638 @item If you have custom tuning parameter settings, these can be defined using
25639 a simpler interface when combined with @code{tune}.
25640 @item In the future, workflows will be able to add post-processing operations,
25641 such as modifying the probability cutoff for two-class models.
25644 (license license:expat)))
25646 (define-public r-gpfit
25653 (uri (cran-uri "GPfit" version))
25656 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25657 (properties `((upstream-name . "GPfit")))
25658 (build-system r-build-system)
25660 `(("r-lattice" ,r-lattice)
25662 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25663 (synopsis "Gaussian Processes modeling")
25665 "This package provides a computationally stable approach of fitting a
25666 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25667 (license license:gpl2)))
25669 (define-public r-yardstick
25671 (name "r-yardstick")
25676 (uri (cran-uri "yardstick" version))
25679 "13b0lyj2k0r568mwlyz9yvp9156rzlj4jqnjazaffh9vwqh4whir"))))
25680 (properties `((upstream-name . "yardstick")))
25681 (build-system r-build-system)
25683 `(("r-dplyr" ,r-dplyr)
25684 ("r-generics" ,r-generics)
25686 ("r-rlang" ,r-rlang)
25687 ("r-tidyselect" ,r-tidyselect)
25688 ("r-vctrs" ,r-vctrs)))
25690 `(("r-knitr" ,r-knitr)))
25691 (home-page "https://github.com/tidymodels/yardstick")
25692 (synopsis "Tidy characterizations of model performance")
25694 "This package provides tidy tools for quantifying how well a model fits
25695 to a data set such as confusion matrices, class probability curve summaries,
25696 and regression metrics (e.g., RMSE).")
25697 (license license:gpl2)))
25699 (define-public r-warp
25706 (uri (cran-uri "warp" version))
25709 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25710 (properties `((upstream-name . "warp")))
25711 (build-system r-build-system)
25712 (native-inputs `(("r-knitr" ,r-knitr)))
25713 (home-page "https://github.com/DavisVaughan/warp")
25714 (synopsis "Group dates")
25716 "This package provides tooling to group dates by a variety of periods
25717 including: yearly, monthly, by second, by week of the month, and more. The
25718 groups are defined in such a way that they also represent the distance between
25719 dates in terms of the period. This extracts valuable information that can be
25720 used in further calculations that rely on a specific temporal spacing between
25722 (license license:expat)))
25724 (define-public r-slider
25731 (uri (cran-uri "slider" version))
25734 "1jijh8f3qcn8fa677sqvgl2fb4r5vca1cw4l2vbcqscxb2hr4bqw"))))
25735 (properties `((upstream-name . "slider")))
25736 (build-system r-build-system)
25738 `(("r-ellipsis" ,r-ellipsis)
25740 ("r-rlang" ,r-rlang)
25741 ("r-vctrs" ,r-vctrs)
25742 ("r-warp" ,r-warp)))
25743 (native-inputs `(("r-knitr" ,r-knitr)))
25744 (home-page "https://github.com/DavisVaughan/slider")
25745 (synopsis "Sliding window functions")
25747 "This package provides type-stable rolling window functions over any R
25748 data type. Cumulative and expanding windows are also supported. For more
25749 advanced usage, an index can be used as a secondary vector that defines how
25750 sliding windows are to be created.")
25751 (license license:expat)))
25753 (define-public r-rsample
25760 (uri (cran-uri "rsample" version))
25763 "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c"))))
25764 (properties `((upstream-name . "rsample")))
25765 (build-system r-build-system)
25767 `(("r-dplyr" ,r-dplyr)
25768 ("r-ellipsis" ,r-ellipsis)
25769 ("r-furrr" ,r-furrr)
25770 ("r-generics" ,r-generics)
25771 ("r-purrr" ,r-purrr)
25772 ("r-rlang" ,r-rlang)
25773 ("r-slider" ,r-slider)
25774 ("r-tibble" ,r-tibble)
25775 ("r-tidyr" ,r-tidyr)
25776 ("r-tidyselect" ,r-tidyselect)
25777 ("r-vctrs" ,r-vctrs)))
25779 `(("r-knitr" ,r-knitr)))
25780 (home-page "https://rsample.tidymodels.org")
25781 (synopsis "General resampling infrastructure")
25783 "This package provides classes and functions to create and summarize
25784 different types of resampling objects (e.g. bootstrap, cross-validation).")
25785 (license license:gpl2)))
25787 (define-public r-dicedesign
25789 (name "r-dicedesign")
25794 (uri (cran-uri "DiceDesign" version))
25797 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
25798 (properties `((upstream-name . "DiceDesign")))
25799 (build-system r-build-system)
25800 (home-page "http://dice.emse.fr/")
25801 (synopsis "Designs of computer experiments")
25803 "This package provides tools to create some specific @code{Space-Filling
25804 Design} (SFD) and to test their quality.")
25805 (license license:gpl3)))
25807 (define-public r-dials
25814 (uri (cran-uri "dials" version))
25817 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25818 (properties `((upstream-name . "dials")))
25819 (build-system r-build-system)
25821 `(("r-dicedesign" ,r-dicedesign)
25822 ("r-dplyr" ,r-dplyr)
25824 ("r-purrr" ,r-purrr)
25825 ("r-rlang" ,r-rlang)
25826 ("r-scales" ,r-scales)
25827 ("r-tibble" ,r-tibble)
25828 ("r-vctrs" ,r-vctrs)
25829 ("r-withr" ,r-withr)))
25830 (native-inputs `(("r-knitr" ,r-knitr)))
25831 (home-page "https://dials.tidymodels.org/")
25832 (synopsis "Tools for creating tuning parameter values")
25834 "Many models contain tuning parameters (i.e. parameters that cannot be
25835 directly estimated from the data). These tools can be used to define objects
25836 for creating, simulating, or validating values for such parameters.")
25837 (license license:gpl2)))
25839 (define-public r-tune
25846 (uri (cran-uri "tune" version))
25849 "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293"))))
25850 (properties `((upstream-name . "tune")))
25851 (build-system r-build-system)
25854 ("r-dials" ,r-dials)
25855 ("r-dplyr" ,r-dplyr)
25856 ("r-foreach" ,r-foreach)
25857 ("r-generics" ,r-generics)
25858 ("r-ggplot2" ,r-ggplot2)
25860 ("r-gpfit" ,r-gpfit)
25861 ("r-parsnip" ,r-parsnip)
25862 ("r-purrr" ,r-purrr)
25863 ("r-recipes" ,r-recipes)
25864 ("r-rlang" ,r-rlang)
25865 ("r-rsample" ,r-rsample)
25866 ("r-tibble" ,r-tibble)
25867 ("r-tidyr" ,r-tidyr)
25868 ("r-vctrs" ,r-vctrs)
25869 ("r-workflows" ,r-workflows)
25870 ("r-yardstick" ,r-yardstick)))
25871 (home-page "https://github.com/tidymodels/tune")
25872 (synopsis "Tidy tuning tools")
25874 "The ability to tune models is important. @code{tune} contains functions
25875 and classes to be used in conjunction with other @code{tidymodels} packages
25876 for finding reasonable values of hyper-parameters in models, pre-processing
25877 methods, and post-processing steps.")
25878 (license license:expat)))
25880 (define-public r-workflowsets
25882 (name "r-workflowsets")
25887 (uri (cran-uri "workflowsets" version))
25890 "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p"))))
25891 (properties `((upstream-name . "workflowsets")))
25892 (build-system r-build-system)
25895 ("r-dplyr" ,r-dplyr)
25896 ("r-ggplot2" ,r-ggplot2)
25897 ("r-prettyunits" ,r-prettyunits)
25898 ("r-purrr" ,r-purrr)
25899 ("r-rlang" ,r-rlang)
25900 ("r-rsample" ,r-rsample)
25901 ("r-tibble" ,r-tibble)
25902 ("r-tidyr" ,r-tidyr)
25904 ("r-vctrs" ,r-vctrs)
25905 ("r-withr" ,r-withr)
25906 ("r-workflows" ,r-workflows)))
25908 `(("r-knitr" ,r-knitr)))
25909 (home-page "https://github.com/tidymodels/workflowsets")
25910 (synopsis "Create a collection of tidymodels workflows")
25912 "A workflow is a combination of a model and preprocessors (e.g, a
25913 formula, recipe, etc.). In order to try different combinations of these, an
25914 object can be created that contains many workflows. There are functions to
25915 create workflows en masse as well as training them and visualizing the
25917 (license license:expat)))
25919 (define-public r-tidyposterior
25921 (name "r-tidyposterior")
25926 (uri (cran-uri "tidyposterior" version))
25929 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
25930 (properties `((upstream-name . "tidyposterior")))
25931 (build-system r-build-system)
25933 `(("r-dplyr" ,r-dplyr)
25934 ("r-generics" ,r-generics)
25935 ("r-ggplot2" ,r-ggplot2)
25936 ("r-purrr" ,r-purrr)
25937 ("r-rlang" ,r-rlang)
25938 ("r-rsample" ,r-rsample)
25939 ("r-rstanarm" ,r-rstanarm)
25940 ("r-tibble" ,r-tibble)
25941 ("r-tidyr" ,r-tidyr)
25943 ("r-vctrs" ,r-vctrs)
25944 ("r-workflowsets" ,r-workflowsets)))
25946 `(("r-knitr" ,r-knitr)))
25947 (home-page "https://tidyposterior.tidymodels.org")
25948 (synopsis "Bayesian analysis to compare models using resampling statistics")
25950 "This package can be used to conduct post hoc analyses of resampling
25951 results generated by models. For example, if two models are evaluated with
25952 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25953 are 10 paired statistics. These can be used to make comparisons between
25954 models without involving a test set.")
25955 (license license:gpl2)))
25957 (define-public r-tidypredict
25959 (name "r-tidypredict")
25964 (uri (cran-uri "tidypredict" version))
25967 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25968 (properties `((upstream-name . "tidypredict")))
25969 (build-system r-build-system)
25971 `(("r-dplyr" ,r-dplyr)
25972 ("r-generics" ,r-generics)
25973 ("r-knitr" ,r-knitr)
25974 ("r-purrr" ,r-purrr)
25975 ("r-rlang" ,r-rlang)
25976 ("r-stringr" ,r-stringr)
25977 ("r-tibble" ,r-tibble)
25978 ("r-tidyr" ,r-tidyr)))
25980 `(("r-knitr" ,r-knitr)))
25981 (home-page "https://tidypredict.tidymodels.org")
25982 (synopsis "Run predictions inside the database")
25984 "This package parses a fitted R model object, and returns a formula in
25985 Tidy Eval code that calculates the predictions. It works with several
25986 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25987 final SQL translation of the algorithm. It currently supports @code{lm()},
25988 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25989 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25990 (license license:gpl3)))
25992 (define-public r-janeaustenr
25994 (name "r-janeaustenr")
25999 (uri (cran-uri "janeaustenr" version))
26002 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
26003 (properties `((upstream-name . "janeaustenr")))
26004 (build-system r-build-system)
26005 (home-page "https://github.com/juliasilge/janeaustenr")
26006 (synopsis "Jane Austen's complete novels")
26008 "This package provides the full texts for Jane Austen's six completed
26009 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
26010 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
26011 and \"Persuasion\".")
26012 (license license:expat)))
26014 (define-public r-tokenizers
26016 (name "r-tokenizers")
26021 (uri (cran-uri "tokenizers" version))
26024 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
26025 (properties `((upstream-name . "tokenizers")))
26026 (build-system r-build-system)
26028 `(("r-rcpp" ,r-rcpp)
26029 ("r-snowballc" ,r-snowballc)
26030 ("r-stringi" ,r-stringi)))
26032 `(("r-knitr" ,r-knitr)))
26033 (home-page "https://lincolnmullen.com/software/tokenizers/")
26034 (synopsis "Fast, consistent tokenization of natural language text")
26036 "This is a package for converting natural language text into tokens.
26037 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
26038 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
26039 Treebank, regular expressions, as well as functions for counting characters,
26040 words, and sentences, and a function for splitting longer texts into separate
26041 documents, each with the same number of words. The tokenizers have a
26042 consistent interface, and the package is built on the @code{stringi} and
26043 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
26044 (license license:expat)))
26046 (define-public r-hunspell
26048 (name "r-hunspell")
26053 (uri (cran-uri "hunspell" version))
26056 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
26057 (properties `((upstream-name . "hunspell")))
26058 (build-system r-build-system)
26060 `(("r-digest" ,r-digest)
26061 ("r-rcpp" ,r-rcpp)))
26063 `(("r-knitr" ,r-knitr)))
26064 (home-page "https://github.com/ropensci/hunspell#readme")
26065 (synopsis "High-performance stemmer, tokenizer, and spell checker")
26067 "This package provides a low-level spell checker and morphological
26068 analyzer based on the famous @code{hunspell} library. The package can analyze
26069 or check individual words as well as parse text, LaTeX, HTML or XML documents.
26070 For a more user-friendly interface use the @code{spelling} package which
26071 builds on this package to automate checking of files, documentation and
26072 vignettes in all common formats.")
26073 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
26074 ;; MPL; in addition to these licenses the rest of the R wrapper is also
26075 ;; available under the Expat license.
26076 (license (list license:gpl2
26081 (define-public r-tidytext
26083 (name "r-tidytext")
26088 (uri (cran-uri "tidytext" version))
26091 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
26092 (properties `((upstream-name . "tidytext")))
26093 (build-system r-build-system)
26095 `(("r-dplyr" ,r-dplyr)
26096 ("r-generics" ,r-generics)
26097 ("r-hunspell" ,r-hunspell)
26098 ("r-janeaustenr" ,r-janeaustenr)
26099 ("r-lifecycle" ,r-lifecycle)
26100 ("r-matrix" ,r-matrix)
26101 ("r-purrr" ,r-purrr)
26102 ("r-rlang" ,r-rlang)
26103 ("r-stringr" ,r-stringr)
26104 ("r-tibble" ,r-tibble)
26105 ("r-tokenizers" ,r-tokenizers)
26106 ("r-vctrs" ,r-vctrs)))
26108 `(("r-knitr" ,r-knitr)))
26109 (home-page "https://github.com/juliasilge/tidytext")
26110 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
26112 "This is a package for text mining for word processing and sentiment
26113 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
26114 (license license:expat)))
26116 (define-public r-parsnip
26123 (uri (cran-uri "parsnip" version))
26126 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
26127 (properties `((upstream-name . "parsnip")))
26128 (build-system r-build-system)
26130 `(("r-dplyr" ,r-dplyr)
26131 ("r-generics" ,r-generics)
26132 ("r-globals" ,r-globals)
26134 ("r-magrittr" ,r-magrittr)
26135 ("r-prettyunits" ,r-prettyunits)
26136 ("r-purrr" ,r-purrr)
26137 ("r-rlang" ,r-rlang)
26138 ("r-tibble" ,r-tibble)
26139 ("r-tidyr" ,r-tidyr)
26140 ("r-vctrs" ,r-vctrs)))
26142 `(("r-knitr" ,r-knitr)))
26143 (home-page "https://parsnip.tidymodels.org")
26144 (synopsis "Common API to modeling and analysis functions")
26146 "This package provides a common interface to allow users to specify a
26147 model without having to remember the different argument names across different
26148 functions or computational engines (e.g. R, Spark, Stan, etc).")
26149 (license license:gpl2)))
26151 (define-public r-infer
26158 (uri (cran-uri "infer" version))
26161 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
26162 (properties `((upstream-name . "infer")))
26163 (build-system r-build-system)
26165 `(("r-dplyr" ,r-dplyr)
26166 ("r-ggplot2" ,r-ggplot2)
26168 ("r-magrittr" ,r-magrittr)
26169 ("r-purrr" ,r-purrr)
26170 ("r-rlang" ,r-rlang)
26171 ("r-tibble" ,r-tibble)))
26173 `(("r-knitr" ,r-knitr)))
26174 (home-page "https://github.com/tidymodels/infer")
26175 (synopsis "Tidy statistical inference")
26177 "The objective of this package is to perform inference using an
26178 expressive statistical grammar that coheres with the Tidy design framework.")
26179 (license license:cc0)))
26181 (define-public r-modeldata
26183 (name "r-modeldata")
26188 (uri (cran-uri "modeldata" version))
26191 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
26192 (properties `((upstream-name . "modeldata")))
26193 (build-system r-build-system)
26194 (home-page "https://modeldata.tidymodels.org")
26195 (synopsis "Data sets useful for modeling packages")
26197 "This package provides data sets used for demonstrating or testing
26198 model-related packages.")
26199 (license license:expat)))
26201 (define-public r-tidymodels
26203 (name "r-tidymodels")
26208 (uri (cran-uri "tidymodels" version))
26211 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26212 (properties `((upstream-name . "tidymodels")))
26213 (build-system r-build-system)
26215 `(("r-broom" ,r-broom)
26217 ("r-dials" ,r-dials)
26218 ("r-dplyr" ,r-dplyr)
26219 ("r-ggplot2" ,r-ggplot2)
26220 ("r-infer" ,r-infer)
26221 ("r-magrittr" ,r-magrittr)
26222 ("r-modeldata" ,r-modeldata)
26223 ("r-parsnip" ,r-parsnip)
26224 ("r-purrr" ,r-purrr)
26225 ("r-recipes" ,r-recipes)
26226 ("r-rlang" ,r-rlang)
26227 ("r-rsample" ,r-rsample)
26228 ("r-rstudioapi" ,r-rstudioapi)
26229 ("r-tibble" ,r-tibble)
26230 ("r-tidyr" ,r-tidyr)
26232 ("r-workflows" ,r-workflows)
26233 ("r-yardstick" ,r-yardstick)))
26235 `(("r-knitr" ,r-knitr)
26236 ("r-rmarkdown" ,r-rmarkdown)
26238 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26239 (home-page "https://github.com/tidymodels/tidymodels")
26240 (synopsis "Tidy collection for modeling and statistical analysis")
26242 "The tidy modeling \"verse\" is a collection of packages for modeling and
26243 statistical analysis that share the underlying design philosophy, grammar, and
26244 data structures of the tidyverse.")
26245 (license license:gpl3)))
26247 (define-public r-lsa
26254 (uri (cran-uri "lsa" version))
26257 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
26258 (properties `((upstream-name . "lsa")))
26259 (build-system r-build-system)
26261 `(("r-snowballc" ,r-snowballc)))
26262 (home-page "https://cran.r-project.org/package=lsa")
26263 (synopsis "Latent semantic analysis")
26265 "The basic idea of latent semantic analysis (LSA) is, that text do have a
26266 higher order (=latent semantic) structure which, however, is obscured by word
26267 usage (e.g. through the use of synonyms or polysemy). By using conceptual
26268 indices that are derived statistically via a truncated singular value
26269 decomposition (a two-mode factor analysis) over a given document-term matrix,
26270 this variability problem can be overcome.")
26271 (license license:gpl2+)))
26273 (define-public r-mlecens
26280 (uri (cran-uri "MLEcens" version))
26283 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26284 (properties `((upstream-name . "MLEcens")))
26285 (build-system r-build-system)
26286 (home-page "http://stat.ethz.ch/~maathuis/")
26287 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26289 "This package contains functions to compute the nonparametric
26290 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26291 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26292 To be more precise, we consider the situation where we observe a set of
26293 rectangles that are known to contain the unobservable realizations of (X,Y).
26294 We compute the MLE based on such a set of rectangles. The methods can also be
26295 used for univariate censored data (see data set @code{cosmesis}), and for
26296 censored data with competing risks (see data set @code{menopause}). The
26297 package also provides functions to visualize the observed data and the MLE.")
26298 (license license:gpl2+)))
26300 (define-public r-metafor
26307 (uri (cran-uri "metafor" version))
26310 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26311 (properties `((upstream-name . "metafor")))
26312 (build-system r-build-system)
26314 `(("r-matrix" ,r-matrix)
26315 ("r-nlme" ,r-nlme)))
26316 (home-page "https://cran.r-project.org/web/packages/metafor/")
26317 (synopsis "Meta-analysis package for R")
26319 "This package provides a comprehensive collection of functions for
26320 conducting meta-analyses in R. The package includes functions to calculate
26321 various effect sizes or outcome measures, fit fixed-, random-, and
26322 mixed-effects models to such data, carry out moderator and meta-regression
26323 analyses, and create various types of meta-analytical plots (e.g., forest,
26324 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26325 and person-time data, the package also provides functions that implement
26326 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26327 a variety of suitable generalized linear (mixed-effects) models (i.e.
26328 mixed-effects logistic and Poisson regression models). Finally, the package
26329 provides functionality for fitting meta-analytic multivariate/multilevel
26330 models that account for non-independent sampling errors and/or true
26331 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26332 endpoints, or other forms of clustering). Network meta-analyses and
26333 meta-analyses accounting for known correlation structures (e.g. due to
26334 phylogenetic relatedness) can also be conducted.")
26335 (license license:gpl2+)))
26337 (define-public r-altmeta
26344 (uri (cran-uri "altmeta" version))
26347 "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
26348 (properties `((upstream-name . "altmeta")))
26349 (build-system r-build-system)
26351 `(("r-coda" ,r-coda)
26353 ("r-matrix" ,r-matrix)
26354 ("r-metafor" ,r-metafor)
26355 ("r-rjags" ,r-rjags)))
26356 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26357 (synopsis "Alternative meta-analysis methods")
26359 "This package provides alternative statistical methods for meta-analysis,
26363 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26364 relative risks, and risk differences
26365 @item heterogeneity tests and measures that are robust to outliers;
26366 @item measures, tests, and visualization tools for publication bias or
26367 small-study effects;
26368 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26369 specificities, etc.;
26370 @item meta-analysis methods for synthesizing proportions;
26371 @item models for multivariate meta-analysis.
26374 (license license:gpl2+)))
26376 (define-public r-perm
26379 (version "1.0-0.0")
26383 (uri (cran-uri "perm" version))
26386 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26387 (properties `((upstream-name . "perm")))
26388 (build-system r-build-system)
26389 (home-page "https://cran.r-project.org/web/packages/perm/")
26390 (synopsis "Exact or asymptotic permutation tests")
26392 "This package provides several methods for performing permutation tests.
26393 It has three main functions, to perform linear permutation tests. These tests
26394 are tests where the test statistic is the sum of the product of a
26395 covariate (usually group indicator) and the scores.")
26396 ;; Any version of the GPL
26397 (license license:gpl2+)))
26399 (define-public r-qtl
26406 (uri (cran-uri "qtl" version))
26409 "098mgmfj8ndi8yipr9b3f6gbbh78cgp9j7y561nlnhrnyc8bsih9"))))
26410 (build-system r-build-system)
26411 (home-page "https://rqtl.org/")
26412 (synopsis "R package for analyzing QTL experiments in genetics")
26413 (description "R/qtl is an extension library for the R statistics system.
26414 It is used to analyze experimental crosses for identifying genes contributing
26415 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26417 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26418 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26420 (license license:gpl3)))
26422 (define-public r-qtl2
26428 (uri (cran-uri "qtl2" version))
26430 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26431 (build-system r-build-system)
26433 `(("r-data-table" ,r-data-table)
26434 ("r-jsonlite" ,r-jsonlite)
26436 ("r-rcppeigen" ,r-rcppeigen)
26437 ("r-rsqlite" ,r-rsqlite)
26438 ("r-yaml" ,r-yaml)))
26439 (home-page "https://kbroman.org/qtl2/")
26440 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26442 "This package provides a set of tools to perform @dfn{Quantitative Trait
26443 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26444 @code{R/qtl} package to better handle high-dimensional data and complex cross
26445 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26446 (license license:gpl3)))
26448 (define-public r-seqminer
26450 (name "r-seqminer")
26455 (uri (cran-uri "seqminer" version))
26458 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26459 (build-system r-build-system)
26462 (home-page "http://seqminer.genomic.codes")
26463 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26465 "This package provides tools to integrate nucleotide sequencing
26466 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26467 ;; Any version of the GPL is acceptable
26468 (license (list license:gpl2+ license:gpl3+))))
26470 (define-public r-maldiquant
26472 (name "r-maldiquant")
26477 (uri (cran-uri "MALDIquant" version))
26480 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26481 (properties `((upstream-name . "MALDIquant")))
26482 (build-system r-build-system)
26483 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26484 (synopsis "Quantitative analysis of mass spectrometry data")
26486 "This package provides a complete analysis pipeline for matrix-assisted
26487 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26488 two-dimensional mass spectrometry data. In addition to commonly used plotting
26489 and processing methods it includes distinctive features, namely baseline
26490 subtraction methods such as morphological filters (TopHat) or the
26491 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26492 alignment using warping functions, handling of replicated measurements as well
26493 as allowing spectra with different resolutions.")
26494 (license license:gpl3+)))
26496 (define-public r-scattermore
26498 (name "r-scattermore")
26503 (uri (cran-uri "scattermore" version))
26506 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26507 (properties `((upstream-name . "scattermore")))
26508 (build-system r-build-system)
26510 `(("r-ggplot2" ,r-ggplot2)
26511 ("r-scales" ,r-scales)))
26512 (home-page "https://github.com/exaexa/scattermore")
26513 (synopsis "Scatterplots with more points")
26515 "This package provides C-based tools for converting large scatterplot
26516 data to rasters. It speeds up plotting of data with millions of points.")
26517 (license license:gpl3+)))
26519 (define-public r-seuratobject
26521 (name "r-seuratobject")
26526 (uri (cran-uri "SeuratObject" version))
26529 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26530 (properties `((upstream-name . "SeuratObject")))
26531 (build-system r-build-system)
26533 `(("r-matrix" ,r-matrix)
26535 ("r-rcppeigen" ,r-rcppeigen)
26536 ("r-rlang" ,r-rlang)
26537 ("r-sctransform" ,r-sctransform)))
26538 (home-page "https://satijalab.org/seurat")
26539 (synopsis "Data structures for single cell data")
26541 "This package defines S4 classes for single-cell genomic data and
26542 associated information, such as dimensionality reduction embeddings,
26543 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26544 access methods and R-native hooks to ensure the Seurat object is familiar to
26546 (license license:gpl3)))
26548 (define-public r-seurat
26554 (uri (cran-uri "Seurat" version))
26557 "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
26558 (properties `((upstream-name . "Seurat")))
26559 (build-system r-build-system)
26561 `(("r-cluster" ,r-cluster)
26562 ("r-cowplot" ,r-cowplot)
26563 ("r-fitdistrplus" ,r-fitdistrplus)
26564 ("r-future" ,r-future)
26565 ("r-future-apply" ,r-future-apply)
26566 ("r-ggplot2" ,r-ggplot2)
26567 ("r-ggrepel" ,r-ggrepel)
26568 ("r-ggridges" ,r-ggridges)
26571 ("r-igraph" ,r-igraph)
26572 ("r-irlba" ,r-irlba)
26573 ("r-jsonlite" ,r-jsonlite)
26574 ("r-kernsmooth" ,r-kernsmooth)
26575 ("r-leiden" ,r-leiden)
26576 ("r-lmtest" ,r-lmtest)
26578 ("r-matrix" ,r-matrix)
26579 ("r-matrixstats" ,r-matrixstats)
26580 ("r-miniui" ,r-miniui)
26581 ("r-patchwork" ,r-patchwork)
26582 ("r-pbapply" ,r-pbapply)
26583 ("r-plotly" ,r-plotly)
26586 ("r-rcolorbrewer" ,r-rcolorbrewer)
26588 ("r-rcppannoy" ,r-rcppannoy)
26589 ("r-rcppeigen" ,r-rcppeigen)
26590 ("r-rcppprogress" ,r-rcppprogress)
26591 ("r-reticulate" ,r-reticulate)
26592 ("r-rlang" ,r-rlang)
26594 ("r-rtsne" ,r-rtsne)
26595 ("r-scales" ,r-scales)
26596 ("r-scattermore" ,r-scattermore)
26597 ("r-sctransform" ,r-sctransform)
26598 ("r-seuratobject" ,r-seuratobject)
26599 ("r-shiny" ,r-shiny)
26600 ("r-spatstat-core" ,r-spatstat-core)
26601 ("r-spatstat-geom" ,r-spatstat-geom)
26602 ("r-tibble" ,r-tibble)
26603 ("r-uwot" ,r-uwot)))
26604 (home-page "http://www.satijalab.org/seurat")
26605 (synopsis "Seurat is an R toolkit for single cell genomics")
26607 "This package is an R package designed for QC, analysis, and
26608 exploration of single cell RNA-seq data. It easily enables widely-used
26609 analytical techniques, including the identification of highly variable genes,
26610 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26611 algorithms; density clustering, hierarchical clustering, k-means, and the
26612 discovery of differentially expressed genes and markers.")
26613 (license license:gpl3)))
26615 (define-public r-phangorn
26617 (name "r-phangorn")
26622 (uri (cran-uri "phangorn" version))
26625 "08yqz8qlw960x4b52wzrm22f242xnpc8695pjkhy7bi1nzm303ga"))))
26626 (build-system r-build-system)
26629 ("r-fastmatch" ,r-fastmatch)
26630 ("r-igraph" ,r-igraph)
26631 ("r-magrittr" ,r-magrittr)
26632 ("r-matrix" ,r-matrix)
26633 ("r-quadprog" ,r-quadprog)
26634 ("r-rcpp" ,r-rcpp)))
26636 `(("r-knitr" ,r-knitr)))
26637 (home-page "https://github.com/KlausVigo/phangorn")
26638 (synopsis "Phylogenetic analysis in R")
26640 "Phangorn is a package for phylogenetic analysis in R. It supports
26641 estimation of phylogenetic trees and networks using Maximum Likelihood,
26642 Maximum Parsimony, distance methods and Hadamard conjugation.")
26643 (license license:gpl2+)))
26645 (define-public r-diversitree
26647 (name "r-diversitree")
26652 (uri (cran-uri "diversitree" version))
26655 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26656 (build-system r-build-system)
26658 `(("gfortran" ,gfortran)))
26659 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26662 ("r-desolve" ,r-desolve)
26664 ("r-subplex" ,r-subplex)))
26665 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26666 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26667 (description "This package contains a number of comparative \"phylogenetic\"
26668 methods, mostly focusing on analysing diversification and character evolution.
26669 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26670 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26671 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26672 include Markov models of discrete and continuous trait evolution and constant
26673 rate speciation and extinction.")
26674 (license license:gpl2+)))
26676 (define-public r-calculus
26678 (name "r-calculus")
26683 (uri (cran-uri "calculus" version))
26686 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26687 (properties `((upstream-name . "calculus")))
26688 (build-system r-build-system)
26690 `(("r-rcpp" ,r-rcpp)))
26692 `(("r-knitr" ,r-knitr)))
26693 (home-page "https://github.com/eguidotti/calculus")
26694 (synopsis "High dimensional numerical and symbolic calculus")
26696 "Efficient C++ optimized functions for numerical and symbolic calculus.
26697 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26698 convention, fast computation of the Levi-Civita symbol and generalized
26699 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26700 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26701 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26702 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26703 parabolic or user defined by custom scale factors.")
26704 (license license:gpl3)))
26706 (define-public r-decon
26713 (uri (cran-uri "decon" version))
26716 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26717 (properties `((upstream-name . "decon")))
26718 (build-system r-build-system)
26720 `(("gfortran" ,gfortran)))
26722 "https://cran.r-project.org/web/packages/decon/")
26723 (synopsis "Deconvolution Estimation in Measurement Error Models")
26725 "This package contains a collection of functions to deal with
26726 nonparametric measurement error problems using deconvolution
26727 kernel methods. We focus two measurement error models in the
26728 package: (1) an additive measurement error model, where the
26729 goal is to estimate the density or distribution function from
26730 contaminated data; (2) nonparametric regression model with
26731 errors-in-variables. The R functions allow the measurement errors
26732 to be either homoscedastic or heteroscedastic. To make the
26733 deconvolution estimators computationally more efficient in R,
26734 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26735 density estimation with error-free data to the deconvolution
26736 kernel estimation. Several methods for the selection of the
26737 data-driven smoothing parameter are also provided in the package.
26738 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26739 estimation in measurement error models: The R package decon.
26740 Journal of Statistical Software, 39(10), 1-24.")
26741 (license license:gpl3+)))
26743 (define-public r-locpol
26750 (uri (cran-uri "locpol" version))
26753 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26754 (properties `((upstream-name . "locpol")))
26755 (build-system r-build-system)
26757 "https://cran.r-project.org/web/packages/locpol/")
26758 (synopsis "Kernel Local Polynomial Regression")
26760 "Computes local polynomial estimators for the regression and
26761 also density. It comprises several different utilities to handle
26762 kernel estimators.")
26763 (license license:gpl2+)))
26765 (define-public r-lpme
26772 (uri (cran-uri "lpme" version))
26775 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26776 (properties `((upstream-name . "lpme")))
26777 (build-system r-build-system)
26779 `(("r-decon" ,r-decon)
26780 ("r-flexmix" ,r-flexmix)
26781 ("r-locpol" ,r-locpol)
26783 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26785 "https://cran.r-project.org/web/packages/lpme/")
26786 (synopsis "Nonparametric Estimation of Measurement Error Models")
26788 "Provide nonparametric methods for mean regression model,
26789 modal regression and conditional density estimation in the
26790 presence/absence of measurement error. Bandwidth selection is
26791 also provided for each method.")
26792 (license license:gpl2+)))
26794 (define-public r-aws-signature
26796 (name "r-aws-signature")
26801 (uri (cran-uri "aws.signature" version))
26804 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26805 (properties `((upstream-name . "aws.signature")))
26806 (build-system r-build-system)
26808 `(("r-base64enc" ,r-base64enc)
26809 ("r-digest" ,r-digest)))
26810 (home-page "https://github.com/cloudyr/aws.signature")
26811 (synopsis "Amazon Web Services Request Signatures")
26813 "This package generates version 2 and 4 request signatures for Amazon Web
26814 Services (AWS) and provides a mechanism for retrieving credentials from
26815 environment variables, AWS credentials files, and EC2 instance metadata. For
26816 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26817 (license license:gpl2+)))
26819 (define-public r-aws-s3
26826 (uri (cran-uri "aws.s3" version))
26829 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26830 (properties `((upstream-name . "aws.s3")))
26831 (build-system r-build-system)
26833 `(("r-aws-signature" ,r-aws-signature)
26834 ("r-base64enc" ,r-base64enc)
26836 ("r-digest" ,r-digest)
26838 ("r-xml2" ,r-xml2)))
26839 (home-page "https://github.com/cloudyr/aws.s3")
26840 (synopsis "AWS S3 Client Package")
26842 "This package provides a simple client package for the Amazon Web
26843 Services (AWS) Simple Storage Service (S3) REST API.")
26844 (license license:gpl2+)))
26846 (define-public r-lgr
26852 (uri (cran-uri "lgr" version))
26855 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26856 (build-system r-build-system)
26860 `(("r-knitr" ,r-knitr)))
26861 (home-page "https://s-fleck.github.io/lgr/")
26862 (synopsis "Fully featured logging framework")
26863 (description "This package offers a flexible, feature-rich yet
26864 light-weight logging framework based on @code{R6} classes. It supports
26865 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26866 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26867 well as email and push notifications.")
26868 (license license:expat)))
26870 (define-public r-mlr3measures
26872 (name "r-mlr3measures")
26876 (uri (cran-uri "mlr3measures" version))
26879 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26880 (build-system r-build-system)
26882 `(("r-checkmate" ,r-checkmate)
26883 ("r-prroc" ,r-prroc)))
26884 (home-page "https://mlr3measures.mlr-org.com/")
26885 (synopsis "Performance measures for mlr3")
26886 (description "This package implements multiple performance measures for
26887 supervised learning. It includes over 40 measures for regression and
26888 classification. Additionally, meta information about the performance measures
26889 can be queried, e.g. what the best and worst possible performances scores
26891 (license license:lgpl3)))
26893 (define-public r-mlr3misc
26895 (name "r-mlr3misc")
26899 (uri (cran-uri "mlr3misc" version))
26902 "0mzicqs8rhzppyd7v3ljqs35k8pp7p2jg5cs7hx21mxr831bwsys"))))
26903 (build-system r-build-system)
26905 `(("r-backports" ,r-backports)
26906 ("r-checkmate" ,r-checkmate)
26907 ("r-data-table" ,r-data-table)
26909 (home-page "https://mlr3misc.mlr-org.com/")
26910 (synopsis "Helper functions for mlr3")
26911 (description "@code{mlr3misc} provides frequently used helper functions
26912 and assertions used in @code{mlr3} and its companion packages. It comes with
26913 helper functions for functional programming, for printing, to work with
26914 @code{data.table}, as well as some generally useful @code{R6} classes. This
26915 package also supersedes the package @code{BBmisc}.")
26916 (license license:lgpl3)))
26918 (define-public r-paradox
26924 (uri (cran-uri "paradox" version))
26927 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
26928 (build-system r-build-system)
26930 `(("r-backports" ,r-backports)
26931 ("r-checkmate" ,r-checkmate)
26932 ("r-data-table" ,r-data-table)
26933 ("r-mlr3misc" ,r-mlr3misc)
26935 (home-page "https://paradox.mlr-org.com/")
26936 (synopsis "Define and work with parameter spaces for complex algorithms")
26937 (description "With this package it is possible to define parameter spaces,
26938 constraints and dependencies for arbitrary algorithms, and to program on such
26939 spaces. It also includes statistical designs and random samplers. Objects are
26940 implemented as @code{R6} classes.")
26941 (license license:lgpl3)))
26943 (define-public r-mlr3
26949 (uri (cran-uri "mlr3" version))
26952 "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl"))))
26953 (build-system r-build-system)
26956 ("r-backports" ,r-backports)
26957 ("r-checkmate" ,r-checkmate)
26958 ("r-data-table" ,r-data-table)
26959 ("r-digest" ,r-digest)
26960 ("r-future-apply" ,r-future-apply)
26962 ("r-mlbench" ,r-mlbench)
26963 ("r-mlr3measures" ,r-mlr3measures)
26964 ("r-mlr3misc" ,r-mlr3misc)
26965 ("r-palmerpenguins" ,r-palmerpenguins)
26966 ("r-paradox" ,r-paradox)
26967 ("r-parallelly" ,r-parallelly)
26968 ("r-uuid" ,r-uuid)))
26969 (home-page "https://mlr3.mlr-org.com/")
26970 (synopsis "Machine Learning in R - Next Generation")
26971 (description "@code{mlr3} enables efficient, object-oriented programming
26972 on the building blocks of machine learning. It provides @code{R6} objects for
26973 tasks, learners, resamplings, and measures. The package is geared towards
26974 scalability and larger datasets by supporting parallelization and out-of-memory
26975 data-backends like databases. While @code{mlr3} focuses on the core
26976 computational operations, add-on packages provide additional functionality.")
26977 (license license:lgpl3)))
26979 (define-public r-mlr3learners
26981 (name "r-mlr3learners")
26985 (uri (cran-uri "mlr3learners" version))
26988 "02v4y32yn1m0akkqzhfg65ib21rgy9iz8db4kdcrvi949clkxnfk"))))
26989 (build-system r-build-system)
26991 `(("r-data-table" ,r-data-table)
26993 ("r-mlr3misc" ,r-mlr3misc)
26994 ("r-paradox" ,r-paradox)
26996 (home-page "https://mlr3learners.mlr-org.com/")
26997 (synopsis "Recommended Learners for @code{mlr3}")
26998 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26999 with interfaces to essential machine learning packages on CRAN. This includes,
27000 but is not limited to: (penalized) linear and logistic regression, linear and
27001 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
27002 vector machines, and gradient boosting.")
27003 (license license:lgpl3)))
27005 (define-public r-bbotk
27012 (uri (cran-uri "bbotk" version))
27015 "0bd9nxfgsj4ixpgky1mj6knb8l8nivvxpqpyw8vgpkj0za7gp4gr"))))
27016 (properties `((upstream-name . "bbotk")))
27017 (build-system r-build-system)
27019 `(("r-checkmate" ,r-checkmate)
27020 ("r-data-table" ,r-data-table)
27022 ("r-mlr3misc" ,r-mlr3misc)
27023 ("r-paradox" ,r-paradox)
27026 `(("r-knitr" ,r-knitr)))
27027 (home-page "https://bbotk.mlr-org.com")
27028 (synopsis "Black-Box Optimization Toolkit")
27029 (description "This package provides a common framework for optimization of
27030 black-box functions for other packages, e.g. @code{mlr3}. It offers various
27031 optimization methods e.g. grid search, random search and generalized simulated
27033 (license license:lgpl3)))
27035 (define-public r-mlr3tuning
27037 (name "r-mlr3tuning")
27041 (uri (cran-uri "mlr3tuning" version))
27044 "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv"))))
27045 (build-system r-build-system)
27047 `(("r-bbotk" ,r-bbotk)
27048 ("r-checkmate" ,r-checkmate)
27049 ("r-data-table" ,r-data-table)
27052 ("r-mlr3misc" ,r-mlr3misc)
27053 ("r-paradox" ,r-paradox)
27055 (home-page "https://mlr3tuning.mlr-org.com/")
27056 (synopsis "Tuning for @code{mlr3}")
27057 (description "@code{mlr3tuning} implements methods for hyperparameter
27058 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
27059 termination criteria can be set and combined. The class @code{AutoTuner} provides a
27060 convenient way to perform nested resampling in combination with @code{mlr3}.")
27061 (license license:lgpl3)))
27063 (define-public r-fontliberation
27065 (name "r-fontliberation")
27070 (uri (cran-uri "fontLiberation" version))
27073 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
27075 `((upstream-name . "fontLiberation")))
27076 (build-system r-build-system)
27077 (home-page "https://cran.r-project.org/package=fontLiberation")
27078 (synopsis "Liberation fonts")
27080 "This package provides a placeholder for the Liberation fontset intended
27081 for the fontquiver package. This fontset covers the 12 combinations of
27082 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
27083 supported in R graphics devices.")
27084 (license license:silofl1.1)))
27086 (define-public r-fontbitstreamvera
27088 (name "r-fontbitstreamvera")
27093 (uri (cran-uri "fontBitstreamVera" version))
27096 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
27098 `((upstream-name . "fontBitstreamVera")))
27099 (build-system r-build-system)
27100 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
27101 (synopsis "Fonts for fontquiver")
27103 "This package is a placeholder for the Bitstream Vera font. It is
27104 intended for the fontquiver package.")
27106 (license:fsdg-compatible
27107 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
27108 "The Font Software may be sold as part of a larger software package but
27109 no copy of one or more of the Font Software typefaces may be sold by
27112 (define-public r-fontquiver
27114 (name "r-fontquiver")
27119 (uri (cran-uri "fontquiver" version))
27122 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
27123 (properties `((upstream-name . "fontquiver")))
27124 (build-system r-build-system)
27126 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
27127 ("r-fontliberation" ,r-fontliberation)))
27128 (home-page "https://cran.r-project.org/package=fontquiver")
27129 (synopsis "Set of installed fonts")
27131 "This package provides a set of fonts. This is useful when you want to
27132 avoid system fonts to make sure your outputs are reproducible.")
27133 (license license:gpl3)))
27135 (define-public r-freetypeharfbuzz
27137 (name "r-freetypeharfbuzz")
27142 (uri (cran-uri "freetypeharfbuzz" version))
27145 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
27147 `((upstream-name . "freetypeharfbuzz")))
27148 (build-system r-build-system)
27151 (modify-phases %standard-phases
27152 (add-after 'unpack 'prepare-static-libraries
27153 (lambda* (#:key inputs #:allow-other-keys)
27154 (mkdir-p "src/target/include")
27155 (let ((freetype (assoc-ref inputs "static-freetype"))
27156 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
27157 (substitute* "src/Makevars.in"
27158 (("include @MK_FILE@") "") ; do not build static libs
27159 (("^HB_STATIC_LIB =.*")
27160 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
27161 (("^FT_STATIC_LIB =.*")
27162 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
27163 (copy-recursively (string-append freetype "/include")
27164 "src/target/include")
27165 (copy-recursively (string-append harfbuzz "/include")
27166 "src/target/include")))))))
27168 `(("r-fontquiver" ,r-fontquiver)))
27169 ;; This may defeat the purpose of this package as our versions of freetype
27170 ;; and harfbuzz obviously differ from the tarballs offered by this
27171 ;; project. On the other hand, Guix arguably does a better job at
27172 ;; "ensur[ing] deterministic computation".
27174 `(("static-freetype"
27176 (inherit (static-package freetype))
27178 `(#:configure-flags
27179 (list "--enable-static=yes"
27184 "--without-harfbuzz")))))
27187 (inherit (static-package harfbuzz))
27189 `(#:tests? #false ; fail because shared library is disabled
27191 (list "--enable-static=yes"
27192 "--enable-shared=no"
27194 "--with-freetype=yes"
27197 "--without-fontconfig"
27198 "--without-glib")))))))
27201 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27202 (synopsis "Deterministic computation of text box metrics")
27204 "Unlike other tools that dynamically link to the Cairo stack,
27205 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27206 harfbuzz libraries. This ensures deterministic computation of text box
27207 extents for situations where reproducible results are crucial (for instance
27208 unit tests of graphics).")
27209 (license license:gpl3)))
27211 (define-public r-vdiffr
27218 (uri (cran-uri "vdiffr" version))
27221 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27224 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27225 (properties `((upstream-name . "vdiffr")))
27226 (build-system r-build-system)
27229 (modify-phases %standard-phases
27230 (add-after 'unpack 'process-javascript
27231 (lambda* (#:key inputs #:allow-other-keys)
27232 (with-directory-excursion "inst/htmlwidgets/lib/"
27233 (let ((source (assoc-ref inputs "js-jquery"))
27234 (target "jquery.min.js"))
27235 (format #true "Processing ~a --> ~a~%"
27237 (invoke "esbuild" source "--minify"
27238 (string-append "--outfile=" target)))))))))
27240 `(("freetype" ,freetype)
27241 ("harfbuzz" ,harfbuzz)))
27244 ("r-devtools" ,r-devtools)
27245 ("r-diffobj" ,r-diffobj)
27246 ("r-fontquiver" ,r-fontquiver)
27247 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27248 ("r-gdtools" ,r-gdtools)
27250 ("r-htmltools" ,r-htmltools)
27251 ("r-htmlwidgets" ,r-htmlwidgets)
27252 ("r-purrr" ,r-purrr)
27255 ("r-rlang" ,r-rlang)
27256 ("r-shiny" ,r-shiny)
27257 ("r-testthat" ,r-testthat)
27258 ("r-usethis" ,r-usethis)
27259 ("r-xml2" ,r-xml2)))
27261 `(("esbuild" ,esbuild)
27265 (uri "https://code.jquery.com/jquery-1.12.4.js")
27268 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27269 (home-page "https://github.com/r-lib/vdiffr")
27270 (synopsis "Visual regression testing and graphical diffing")
27272 "This package is an extension to the testthat package that makes it easy
27273 to add graphical unit tests. It provides a Shiny application to manage the
27275 (license license:gpl3)))
27277 (define-public r-highlight
27279 (name "r-highlight")
27284 (uri (cran-uri "highlight" version))
27287 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27288 (properties `((upstream-name . "highlight")))
27289 (build-system r-build-system)
27290 (home-page "https://github.com/hadley/highlight")
27291 (synopsis "Syntax highlighter for R code")
27293 "This package provides a syntax highlighter for R code based on the
27294 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27295 includes a custom Sweave driver performing syntax highlighting of R code
27297 (license license:gpl3+)))
27299 (define-public r-clustree
27301 (name "r-clustree")
27306 (uri (cran-uri "clustree" version))
27309 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27310 (properties `((upstream-name . "clustree")))
27311 (build-system r-build-system)
27313 `(("r-checkmate" ,r-checkmate)
27314 ("r-dplyr" ,r-dplyr)
27315 ("r-ggplot2" ,r-ggplot2)
27316 ("r-ggraph" ,r-ggraph)
27317 ("r-ggrepel" ,r-ggrepel)
27318 ("r-igraph" ,r-igraph)
27319 ("r-rlang" ,r-rlang)
27320 ("r-tidygraph" ,r-tidygraph)
27321 ("r-viridis" ,r-viridis)))
27323 `(("r-knitr" ,r-knitr)))
27324 (home-page "https://github.com/lazappi/clustree")
27325 (synopsis "Visualize clusterings at different resolutions")
27327 "Deciding what resolution to use can be a difficult question when
27328 approaching a clustering analysis. One way to approach this problem is to
27329 look at how samples move as the number of clusters increases. This package
27330 allows you to produce clustering trees, a visualization for interrogating
27331 clusterings as resolution increases.")
27332 (license license:gpl3)))
27334 (define-public r-textshaping
27336 (name "r-textshaping")
27341 (uri (cran-uri "textshaping" version))
27344 "0yl3cv6r8k27h4lzbrsikjydhz94skdjmxx4zqzihvb7h3jfnlpn"))))
27345 (properties `((upstream-name . "textshaping")))
27346 (build-system r-build-system)
27348 `(("freetype" ,freetype)
27349 ("fribidi" ,fribidi)
27350 ("harfbuzz" ,harfbuzz)
27353 `(("r-cpp11" ,r-cpp11)
27354 ("r-systemfonts" ,r-systemfonts)))
27356 `(("pkg-config" ,pkg-config)
27357 ("r-knitr" ,r-knitr)))
27358 (home-page "https://github.com/r-lib/textshaping")
27359 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27361 "This package provides access to the text shaping functionality in the
27362 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27363 is a low-level utility package mainly for graphic devices that expands upon
27364 the font tool-set provided by the @code{systemfonts} package.")
27365 (license license:expat)))
27367 (define-public r-ragg
27374 (uri (cran-uri "ragg" version))
27377 "0q28bwjdxpxm1wlkd8sxdf1m1q8wp4mmzp83d3m09nyy90ydkd8w"))))
27378 (properties `((upstream-name . "ragg")))
27379 (build-system r-build-system)
27381 `(("freetype" ,freetype)
27382 ("libjpeg" ,libjpeg-turbo)
27384 ("libtiff" ,libtiff)
27387 `(("r-systemfonts" ,r-systemfonts)
27388 ("r-textshaping" ,r-textshaping)))
27390 `(("pkg-config" ,pkg-config)))
27391 (home-page "https://ragg.r-lib.org")
27392 (synopsis "Graphic devices based on AGG")
27394 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27395 drawing library. The ragg package provides a set of graphic devices based on
27396 AGG to use as alternative to the raster devices provided through the
27397 @code{grDevices} package.")
27398 (license license:expat)))
27400 (define-public r-downlit
27407 (uri (cran-uri "downlit" version))
27410 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27411 (properties `((upstream-name . "downlit")))
27412 (build-system r-build-system)
27414 `(("r-brio" ,r-brio)
27415 ("r-digest" ,r-digest)
27416 ("r-evaluate" ,r-evaluate)
27417 ("r-fansi" ,r-fansi)
27418 ("r-rlang" ,r-rlang)
27419 ("r-vctrs" ,r-vctrs)
27420 ("r-yaml" ,r-yaml)))
27421 (home-page "https://downlit.r-lib.org/")
27422 (synopsis "Syntax highlighting and automatic linking")
27424 "This package provides syntax highlighting of R code, specifically
27425 designed for the needs of RMarkdown packages like @code{pkgdown},
27426 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27427 to their documentation on the web, and automatic translation of ANSI escapes
27428 in output to the equivalent HTML.")
27429 (license license:expat)))
27431 (define-public r-pkgdown
27438 (uri (cran-uri "pkgdown" version))
27441 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27442 (properties `((upstream-name . "pkgdown")))
27443 (build-system r-build-system)
27444 (inputs `(("pandoc" ,pandoc)))
27446 `(("r-callr" ,r-callr)
27447 ("r-crayon" ,r-crayon)
27449 ("r-digest" ,r-digest)
27450 ("r-downlit" ,r-downlit)
27453 ("r-magrittr" ,r-magrittr)
27454 ("r-memoise" ,r-memoise)
27455 ("r-openssl" ,r-openssl)
27456 ("r-purrr" ,r-purrr)
27458 ("r-rematch2" ,r-rematch2)
27459 ("r-rlang" ,r-rlang)
27460 ("r-rmarkdown" ,r-rmarkdown)
27461 ("r-tibble" ,r-tibble)
27462 ("r-whisker" ,r-whisker)
27463 ("r-withr" ,r-withr)
27465 ("r-yaml" ,r-yaml)))
27467 `(("r-knitr" ,r-knitr)))
27468 (home-page "https://pkgdown.r-lib.org")
27469 (synopsis "Make static HTML documentation for an R package")
27471 "The goal of this package is to generate an attractive and useful website
27472 from a source package. @code{pkgdown} converts your documentation, vignettes,
27473 README file, and more to HTML making it easy to share information about your
27475 (license license:expat)))
27477 (define-public r-prereg
27484 (uri (cran-uri "prereg" version))
27487 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
27488 (properties `((upstream-name . "prereg")))
27489 (build-system r-build-system)
27491 `(("r-rmarkdown" ,r-rmarkdown)))
27492 (home-page "https://github.com/crsh/prereg")
27494 "R Markdown Templates to preregister Scientific Studies")
27496 "This package provides a collection of templates to author
27497 preregistration documents for scientific studies in PDF format.")
27498 (license license:gpl3)))
27500 (define-public r-ez
27507 (uri (cran-uri "ez" version))
27510 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
27511 (properties `((upstream-name . "ez")))
27512 (build-system r-build-system)
27515 ("r-ggplot2" ,r-ggplot2)
27518 ("r-matrix" ,r-matrix)
27521 ("r-reshape2" ,r-reshape2)
27522 ("r-scales" ,r-scales)
27523 ("r-stringr" ,r-stringr)))
27524 (home-page "https://github.com/mike-lawrence/ez")
27525 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
27527 "Facilitates easy analysis of factorial experiments, including purely
27528 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
27529 and mixed within-and-between-Ss designs. The functions in this package aim to
27530 provide simple, intuitive and consistent specification of data analysis and
27531 visualization. Visualization functions also include design visualization for
27532 pre-analysis data auditing, and correlation matrix visualization. Finally,
27533 this package includes functions for non-parametric analysis, including
27534 permutation tests and bootstrap resampling. The bootstrap function obtains
27535 predictions either by cell means or by more advanced/powerful mixed effects
27536 models, yielding predictions and confidence intervals that may be easily
27537 visualized at any level of the experiment's design.")
27538 (license license:gpl2+)))
27540 (define-public r-qdapregex
27542 (name "r-qdapregex")
27547 (uri (cran-uri "qdapRegex" version))
27550 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
27551 (properties `((upstream-name . "qdapRegex")))
27552 (build-system r-build-system)
27553 (propagated-inputs `(("r-stringi" ,r-stringi)))
27555 "https://trinker.github.com/qdapRegex/")
27557 "Regular Expression Removal, Extraction, and Replacement Tools")
27559 "This package provides a collection of regular expression tools
27560 associated with the @code{qdap} package that may be useful outside of the
27561 context of discourse analysis. Tools include removal/extraction/replacement of
27562 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
27563 percentages, citations, person tags, phone numbers, times, and zip codes.")
27564 (license license:gpl2)))
27566 (define-public r-mgsub
27573 (uri (cran-uri "mgsub" version))
27576 "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr"))))
27577 (properties `((upstream-name . "mgsub")))
27578 (build-system r-build-system)
27579 (native-inputs `(("r-knitr" ,r-knitr)))
27581 "https://cran.r-project.org/package=mgsub")
27583 "Safe, Multiple, Simultaneous String Substitution")
27585 "Designed to enable simultaneous substitution in strings in a safe
27586 fashion. Safe means it does not rely on placeholders (which can cause errors
27587 in same length matches).")
27588 (license license:expat)))
27590 (define-public r-textshape
27592 (name "r-textshape")
27597 (uri (cran-uri "textshape" version))
27600 "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
27601 (properties `((upstream-name . "textshape")))
27602 (build-system r-build-system)
27604 `(("r-data-table" ,r-data-table)
27606 ("r-stringi" ,r-stringi)))
27607 (home-page "https://github.com/trinker/textshape")
27608 (synopsis "Tools for Reshaping Text")
27610 "Tools that can be used to reshape and restructure text data.")
27611 (license license:gpl2)))
27613 (define-public r-syuzhet
27620 (uri (cran-uri "syuzhet" version))
27623 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
27624 (properties `((upstream-name . "syuzhet")))
27625 (build-system r-build-system)
27627 `(("r-dplyr" ,r-dplyr)
27630 ("r-rlang" ,r-rlang)
27631 ("r-textshape" ,r-textshape)
27632 ("r-tidyr" ,r-tidyr)
27634 (native-inputs `(("r-knitr" ,r-knitr)))
27635 (home-page "https://github.com/mjockers/syuzhet")
27637 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
27639 "Extracts sentiment and sentiment-derived plot arcs from text using a
27640 variety of sentiment dictionaries conveniently packaged for consumption by R
27641 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
27642 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
27643 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
27644 M. and Turney, Peter D. Applicable references are available in
27645 @file{README.md} and in the documentation for the @code{get_sentiment}
27646 function. The package also provides a hack for implementing Stanford's coreNLP
27647 sentiment parser. The package provides several methods for plot arc
27649 (license license:gpl3)))
27651 (define-public r-lexicon
27658 (uri (cran-uri "lexicon" version))
27661 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
27662 (properties `((upstream-name . "lexicon")))
27663 (build-system r-build-system)
27665 `(("r-data-table" ,r-data-table)
27666 ("r-syuzhet" ,r-syuzhet)))
27667 (home-page "https://github.com/trinker/lexicon")
27668 (synopsis "Lexicons for Text Analysis")
27670 "This package provides a collection of lexical hash tables, dictionaries,
27672 (license license:gpl3)))
27674 (define-public r-english
27681 (uri (cran-uri "english" version))
27684 "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1"))))
27685 (properties `((upstream-name . "english")))
27686 (build-system r-build-system)
27687 (native-inputs `(("r-knitr" ,r-knitr)))
27689 "https://cran.r-project.org/package=english")
27690 (synopsis "Translate Integers into English")
27692 "Allow numbers to be presented in an English language version, one, two,
27693 three, ... Ordinals are also available, first, second, third, ... and
27694 indefinite article choice, \"a\" or \"an\".")
27695 (license license:gpl2)))
27697 (define-public r-textclean
27699 (name "r-textclean")
27704 (uri (cran-uri "textclean" version))
27707 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
27708 (properties `((upstream-name . "textclean")))
27709 (build-system r-build-system)
27711 `(("r-data-table" ,r-data-table)
27712 ("r-english" ,r-english)
27714 ("r-lexicon" ,r-lexicon)
27715 ("r-mgsub" ,r-mgsub)
27716 ("r-qdapregex" ,r-qdapregex)
27717 ("r-stringi" ,r-stringi)
27718 ("r-textshape" ,r-textshape)))
27720 "https://github.com/trinker/textclean")
27721 (synopsis "Text Cleaning Tools")
27723 "Tools to clean and process text. Tools are geared at checking for
27724 substrings that are not optimal for analysis and replacing or removing them
27725 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
27726 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
27727 extracting them into new variables. For example, emoticons are often used in
27728 text but not always easily handled by analysis algorithms. The
27729 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
27730 (license license:gpl2)))
27732 (define-public r-striprtf
27734 (name "r-striprtf")
27739 (uri (cran-uri "striprtf" version))
27742 "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd"))))
27743 (properties `((upstream-name . "striprtf")))
27744 (build-system r-build-system)
27746 `(("r-magrittr" ,r-magrittr)
27748 ("r-stringr" ,r-stringr)))
27749 (home-page "https://github.com/kota7/striprtf")
27750 (synopsis "Extract Text from RTF File")
27752 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
27753 (license license:expat)))
27755 (define-public r-ndjson
27762 (uri (cran-uri "ndjson" version))
27765 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
27766 (modules '((guix build utils)))
27769 ;; unvendor gzstream
27770 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
27772 (properties `((upstream-name . "ndjson")))
27773 (build-system r-build-system)
27776 (modify-phases %standard-phases
27777 (add-after 'unpack 'use-system-gzstream
27778 (lambda* (#:key inputs #:allow-other-keys)
27779 (substitute* "src/Makevars"
27780 (("PKG_LIBS = " all)
27781 (string-append all "-lgzstream ")))
27783 (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream)))
27785 `(("r-data-table" ,r-data-table)
27787 ("r-tibble" ,r-tibble)))
27788 (home-page "https://gitlab.com/hrbrmstr/ndjson")
27790 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
27792 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
27793 modern ndjson files contain large numbers of records. These constructs may not
27794 be columnar in nature, but it is often useful to read in these files and
27795 \"flatten\" the structure out to enable working with the data in an R
27796 @code{data.frame}-like context. Functions are provided that make it possible
27797 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
27798 validate the format of the records or create \"flat\" @code{data.table}
27799 structures from them.")
27800 (license license:expat)))
27802 (define-public r-streamr
27809 (uri (cran-uri "streamR" version))
27812 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
27813 (properties `((upstream-name . "streamR")))
27814 (build-system r-build-system)
27816 `(("r-ndjson" ,r-ndjson)
27817 ("r-rcurl" ,r-rcurl)
27818 ("r-rjson" ,r-rjson)))
27820 "https://cran.r-project.org/package=streamR")
27822 "Access to Twitter Streaming API via R")
27824 "This package provides functions to access Twitter's filter, sample, and
27825 user streams, and to parse the output into data frames.")
27826 (license license:gpl2)))
27828 (define-public r-readods
27835 (uri (cran-uri "readODS" version))
27838 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
27839 (properties `((upstream-name . "readODS")))
27840 (build-system r-build-system)
27842 `(("r-cellranger" ,r-cellranger)
27843 ("r-readr" ,r-readr)
27844 ("r-stringi" ,r-stringi)
27845 ("r-xml2" ,r-xml2)))
27846 (native-inputs `(("r-knitr" ,r-knitr)))
27848 "https://cran.r-project.org/package=readODS")
27849 (synopsis "Read and Write ODS Files")
27851 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
27852 Also support writing data frame into ODS file.")
27853 (license license:gpl3)))
27855 (define-public r-qpdf
27862 (uri (cran-uri "qpdf" version))
27865 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
27866 (modules '((guix build utils)))
27869 ;; unvendor libqpdf
27870 (delete-file-recursively "src/libqpdf")
27871 (delete-file-recursively "src/include/qpdf")
27873 (properties `((upstream-name . "qpdf")))
27874 (build-system r-build-system)
27877 (modify-phases %standard-phases
27878 (add-after 'unpack 'configure
27880 (setenv "EXTERNAL_QPDF" "1")
27886 `(("r-askpass" ,r-askpass)
27888 ("r-rcpp" ,r-rcpp)))
27889 (native-inputs `(("pkg-config" ,pkg-config)))
27890 (home-page "https://github.com/ropensci/qpdf")
27892 "Split, Combine and Compress PDF Files")
27894 "Content-preserving transformations transformations of PDF files such as
27895 split, combine, and compress. This package interfaces directly to the
27896 @code{qpdf} C++ API and does not require any command line utilities. Note that
27897 @code{qpdf} does not read actual content from PDF files: to extract text and
27898 data you need the @code{pdftools} package.")
27899 (license license:asl2.0)))
27901 (define-public r-pdftools
27903 (name "r-pdftools")
27908 (uri (cran-uri "pdftools" version))
27911 "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx"))))
27912 (properties `((upstream-name . "pdftools")))
27913 (build-system r-build-system)
27916 ("poppler" ,poppler)))
27918 `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp)))
27919 (native-inputs `(("pkg-config" ,pkg-config)))
27921 "https://docs.ropensci.org/pdftools/")
27923 "Text Extraction, Rendering and Converting of PDF Documents")
27925 "Utilities based on @code{libpoppler} for extracting text, fonts,
27926 attachments and metadata from a PDF file. Also supports high quality rendering
27927 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
27928 further processing in R.")
27929 (license license:expat)))
27931 (define-public r-antiword
27933 (name "r-antiword")
27938 (uri (cran-uri "antiword" version))
27941 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
27942 (modules '((guix build utils)))
27945 ;; unvendor libantiword
27946 (delete-file-recursively "src")
27948 (properties `((upstream-name . "antiword")))
27949 (build-system r-build-system)
27952 (modify-phases %standard-phases
27953 (add-after 'unpack 'use-system-antiword
27954 (lambda* (#:key inputs #:allow-other-keys)
27955 (substitute* "R/antiword.R"
27956 (("system.file\\(\"bin\", package = \"antiword\"\\)")
27957 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
27959 (inputs `(("antiword" ,antiword)))
27960 (propagated-inputs `(("r-sys" ,r-sys)))
27962 "https://github.com/ropensci/antiword#readme")
27964 "Extract Text from Microsoft Word Documents")
27966 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
27967 documents. The utility only supports the old @code{doc} format, not the new
27968 xml based @code{docx} format. Use the @code{xml2} package to read the
27970 (license license:gpl2)))
27972 (define-public r-readtext
27974 (name "r-readtext")
27979 (uri (cran-uri "readtext" version))
27982 "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y"))))
27983 (properties `((upstream-name . "readtext")))
27984 (build-system r-build-system)
27986 `(("r-antiword" ,r-antiword)
27987 ("r-data-table" ,r-data-table)
27988 ("r-digest" ,r-digest)
27990 ("r-jsonlite" ,r-jsonlite)
27991 ("r-pdftools" ,r-pdftools)
27992 ("r-readods" ,r-readods)
27993 ("r-readxl" ,r-readxl)
27994 ("r-streamr" ,r-streamr)
27995 ("r-stringi" ,r-stringi)
27996 ("r-striprtf" ,r-striprtf)
27997 ("r-tibble" ,r-tibble)
27998 ("r-xml2" ,r-xml2)))
27999 (native-inputs `(("r-knitr" ,r-knitr)))
28001 "https://github.com/quanteda/readtext")
28003 "Import and Handling for Plain and Formatted Text Files")
28005 "This package provides functions for importing and handling text files
28006 and formatted text files with additional meta-data, such including @code{.csv},
28007 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
28008 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
28009 (license license:gpl3)))
28011 (define-public r-packcircles
28013 (name "r-packcircles")
28018 (uri (cran-uri "packcircles" version))
28021 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
28022 (properties `((upstream-name . "packcircles")))
28023 (build-system r-build-system)
28024 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28025 (native-inputs `(("r-knitr" ,r-knitr)))
28027 "https://github.com/mbedward/packcircles")
28028 (synopsis "Circle Packing")
28030 "Algorithms to find arrangements of non-overlapping circles.")
28031 (license license:expat)))
28033 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
28035 (define-public r-lwgeom
28042 (uri (cran-uri "lwgeom" version))
28045 "1733iwinn426bcmgjxp4j0scvbz35rvqkanmw7g7f47l6j7w14vn"))))
28046 (properties `((upstream-name . "lwgeom")))
28047 (build-system r-build-system)
28054 `(("r-rcpp" ,r-rcpp)
28056 ("r-units" ,r-units)))
28057 (native-inputs `(("pkg-config" ,pkg-config)))
28058 (home-page "https://github.com/r-spatial/lwgeom/")
28059 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
28061 "Access to selected functions found in
28062 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
28063 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
28064 (license license:gpl2)))
28066 (define-public r-stars
28073 (uri (cran-uri "stars" version))
28076 "0w2svw02ywvclq0nsnjns1n0rfr54q7x30y64y14n7zfr969ly1n"))))
28077 (properties `((upstream-name . "stars")))
28078 (build-system r-build-system)
28080 `(("r-abind" ,r-abind)
28081 ("r-classint" ,r-classint)
28082 ("r-lwgeom" ,r-lwgeom)
28083 ("r-rlang" ,r-rlang)
28085 ("r-units" ,r-units)))
28086 (native-inputs `(("r-knitr" ,r-knitr)))
28087 (home-page "https://r-spatial.github.io/stars/")
28089 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
28091 "Reading, manipulating, writing and plotting spatiotemporal arrays
28092 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
28093 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
28094 (license license:asl2.0)))
28096 (define-public r-tmaptools
28098 (name "r-tmaptools")
28103 (uri (cran-uri "tmaptools" version))
28106 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
28107 (properties `((upstream-name . "tmaptools")))
28108 (build-system r-build-system)
28110 `(("r-dichromat" ,r-dichromat)
28111 ("r-lwgeom" ,r-lwgeom)
28112 ("r-magrittr" ,r-magrittr)
28113 ("r-rcolorbrewer" ,r-rcolorbrewer)
28115 ("r-stars" ,r-stars)
28116 ("r-units" ,r-units)
28117 ("r-viridislite" ,r-viridislite)
28120 "https://github.com/mtennekes/tmaptools")
28121 (synopsis "Thematic Map Tools")
28123 "Set of tools for reading and processing spatial data. The aim is to
28124 supply the workflow to create thematic maps. This package also facilitates
28125 @code{tmap}, the package for visualizing thematic maps.")
28126 (license license:gpl3)))
28128 (define-public r-rworldmap
28130 (name "r-rworldmap")
28135 (uri (cran-uri "rworldmap" version))
28138 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
28139 (properties `((upstream-name . "rworldmap")))
28140 (build-system r-build-system)
28142 `(("r-fields" ,r-fields)
28143 ("r-maptools" ,r-maptools)
28146 "https://github.com/AndySouth/rworldmap/")
28147 (synopsis "Mapping Global Data")
28149 "Enables mapping of country level and gridded user datasets.")
28150 (license license:gpl2+)))
28152 (define-public r-rtweet
28159 (uri (cran-uri "rtweet" version))
28162 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
28163 (properties `((upstream-name . "rtweet")))
28164 (build-system r-build-system)
28166 `(("r-httpuv" ,r-httpuv)
28168 ("r-jsonlite" ,r-jsonlite)
28169 ("r-magrittr" ,r-magrittr)
28170 ("r-progress" ,r-progress)
28172 ("r-tibble" ,r-tibble)))
28173 (native-inputs `(("r-knitr" ,r-knitr)))
28175 "https://docs.ropensci.org/rtweet/")
28176 (synopsis "Collecting Twitter Data")
28178 "An implementation of calls designed to collect and organize Twitter data
28179 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
28180 Application Program Interfaces (API)}.")
28181 (license license:expat)))
28183 (define-public r-intervals
28185 (name "r-intervals")
28190 (uri (cran-uri "intervals" version))
28193 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
28194 (properties `((upstream-name . "intervals")))
28195 (build-system r-build-system)
28196 (home-page "https://github.com/edzer/intervals")
28198 "Tools for Working with Points and Intervals")
28200 "Tools for working with and comparing sets of points and intervals.")
28201 (license license:artistic2.0)))
28203 (define-public r-eyelinker
28205 (name "r-eyelinker")
28210 (uri (cran-uri "eyelinker" version))
28213 "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2"))))
28214 (properties `((upstream-name . "eyelinker")))
28215 (build-system r-build-system)
28217 `(("r-intervals" ,r-intervals)
28218 ("r-readr" ,r-readr)
28219 ("r-stringi" ,r-stringi)
28220 ("r-stringr" ,r-stringr)
28221 ("r-tibble" ,r-tibble)))
28222 (native-inputs `(("r-knitr" ,r-knitr)))
28224 "https://github.com/a-hurst/eyelinker")
28226 "Import ASC Files from EyeLink Eye Trackers")
28228 "Imports plain-text ASC data files from EyeLink eye trackers into
28229 (relatively) tidy data frames for analysis and visualization.")
28230 (license license:gpl3)))
28232 (define-public r-btm
28239 (uri (cran-uri "BTM" version))
28242 "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb"))))
28243 (properties `((upstream-name . "BTM")))
28244 (build-system r-build-system)
28245 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28246 (home-page "https://github.com/bnosac/BTM")
28247 (synopsis "Biterm Topic Models for Short Text")
28249 "Biterm Topic Models find topics in collections of short texts. It is a
28250 word co-occurrence based topic model that learns topics by modeling word-word
28251 co-occurrences patterns which are called biterms. This in contrast to
28252 traditional topic models like Latent Dirichlet Allocation and Probabilistic
28253 Latent Semantic Analysis which are word-document co-occurrence topic models. A
28254 biterm consists of two words co-occurring in the same short text window. This
28255 context window can for example be a twitter message, a short answer on a
28256 survey, a sentence of a text or a document identifier. The techniques are
28257 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
28258 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
28259 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
28261 (license license:asl2.0)))
28263 (define-public r-textplot
28265 (name "r-textplot")
28270 (uri (cran-uri "textplot" version))
28273 "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy"))))
28274 (properties `((upstream-name . "textplot")))
28275 (build-system r-build-system)
28277 `(("r-data-table" ,r-data-table)
28278 ("r-lattice" ,r-lattice)
28279 ("r-matrix" ,r-matrix)))
28280 (native-inputs `(("r-knitr" ,r-knitr)))
28281 (home-page "https://github.com/bnosac/textplot")
28282 (synopsis "Text Plots")
28284 "Visualise complex relations in texts. This is done by providing
28285 functionalities for displaying text co-occurrence networks, text correlation
28286 networks, dependency relationships as well as text clustering. Feel free to
28287 join the effort of providing interesting text visualisations.")
28288 (license license:gpl2)))
28290 (define-public r-gsa
28297 (uri (cran-uri "GSA" version))
28300 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
28301 (properties `((upstream-name . "GSA")))
28302 (build-system r-build-system)
28303 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
28304 (synopsis "Gene set analysis")
28305 (description "This package lets you determine the significance of
28306 pre-defined sets of genes with respect to an outcome variable, such as a group
28307 indicator, a quantitative variable or a survival time.")
28308 ;; Any version of the LGPL
28309 (license license:lgpl3+)))
28311 (define-public r-samr
28318 (uri (cran-uri "samr" version))
28321 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
28322 (properties `((upstream-name . "samr")))
28323 (build-system r-build-system)
28326 ("r-impute" ,r-impute)
28327 ("r-matrixstats" ,r-matrixstats)
28328 ("r-openxlsx" ,r-openxlsx)
28329 ("r-shiny" ,r-shiny)
28330 ("r-shinyfiles" ,r-shinyfiles)))
28331 (native-inputs `(("gfortran" ,gfortran)))
28332 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
28333 (synopsis "Significance analysis of Microarrays")
28335 "This is a package for significance analysis of Microarrays for
28336 differential expression analysis, RNAseq data and related problems.")
28337 ;; Any version of the LGPL
28338 (license license:lgpl3+)))
28340 (define-public r-randomforestsrc
28342 (name "r-randomforestsrc")
28347 (uri (cran-uri "randomForestSRC" version))
28350 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
28352 `((upstream-name . "randomForestSRC")))
28353 (build-system r-build-system)
28354 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
28355 (synopsis "Random forests for survival, regression, and classification")
28357 "This package implements fast OpenMP parallel computing of Breiman's
28358 random forests for survival, competing risks, regression and classification
28359 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
28360 It handles missing data and now includes multivariate, unsupervised forests,
28361 quantile regression and solutions for class imbalanced data. It provides a
28362 fast interface using subsampling and confidence regions for variable
28364 (license license:gpl3+)))