1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020 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 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>
36 ;;; This file is part of GNU Guix.
38 ;;; GNU Guix is free software; you can redistribute it and/or modify it
39 ;;; under the terms of the GNU General Public License as published by
40 ;;; the Free Software Foundation; either version 3 of the License, or (at
41 ;;; your option) any later version.
43 ;;; GNU Guix is distributed in the hope that it will be useful, but
44 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
45 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
46 ;;; GNU General Public License for more details.
48 ;;; You should have received a copy of the GNU General Public License
49 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
51 (define-module (gnu packages cran)
52 #:use-module ((guix licenses) #:prefix license:)
53 #:use-module (guix packages)
54 #:use-module (guix download)
55 #:use-module (guix git-download)
56 #:use-module (guix utils)
57 #:use-module (guix build-system r)
58 #:use-module (gnu packages)
59 #:use-module (gnu packages algebra)
60 #:use-module (gnu packages autotools)
61 #:use-module (gnu packages base)
62 #:use-module (gnu packages bioinformatics)
63 #:use-module (gnu packages c)
64 #:use-module (gnu packages compression)
65 #:use-module (gnu packages curl)
66 #:use-module (gnu packages databases)
67 #:use-module (gnu packages fontutils)
68 #:use-module (gnu packages gcc)
69 #:use-module (gnu packages geo)
70 #:use-module (gnu packages ghostscript)
71 #:use-module (gnu packages gl)
72 #:use-module (gnu packages gnome)
73 #:use-module (gnu packages graph)
74 #:use-module (gnu packages gtk)
75 #:use-module (gnu packages haskell-xyz)
76 #:use-module (gnu packages icu4c)
77 #:use-module (gnu packages image)
78 #:use-module (gnu packages imagemagick)
79 #:use-module (gnu packages java)
80 #:use-module (gnu packages javascript)
81 #:use-module (gnu packages libevent)
82 #:use-module (gnu packages lisp-xyz)
83 #:use-module (gnu packages machine-learning)
84 #:use-module (gnu packages maths)
85 #:use-module (gnu packages mpi)
86 #:use-module (gnu packages multiprecision)
87 #:use-module (gnu packages networking)
88 #:use-module (gnu packages node)
89 #:use-module (gnu packages pcre)
90 #:use-module (gnu packages perl)
91 #:use-module (gnu packages pkg-config)
92 #:use-module (gnu packages pulseaudio) ;libsndfile
93 #:use-module (gnu packages python)
94 #:use-module (gnu packages python-xyz)
95 #:use-module (gnu packages sqlite)
96 #:use-module (gnu packages statistics)
97 #:use-module (gnu packages tcl)
98 #:use-module (gnu packages tls)
99 #:use-module (gnu packages version-control)
100 #:use-module (gnu packages web)
101 #:use-module (gnu packages xml)
102 #:use-module (gnu packages xorg))
104 (define-public r-brio
111 (uri (cran-uri "brio" version))
114 "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb"))))
115 (properties `((upstream-name . "brio")))
116 (build-system r-build-system)
117 (home-page "https://github.com/r-lib/brio")
118 (synopsis "Basic R input output")
120 "This package provides functions to handle basic input output. These
121 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
122 files and provide more explicit control over line endings.")
123 (license license:expat)))
125 (define-public r-diffobj
132 (uri (cran-uri "diffobj" version))
135 "0v18zz14g8ppzmj1d997rdmsfh327ml4wvpmfx168lravdsk5ym2"))))
136 (properties `((upstream-name . "diffobj")))
137 (build-system r-build-system)
138 (propagated-inputs `(("r-crayon" ,r-crayon)))
139 (native-inputs `(("r-knitr" ,r-knitr)))
140 (home-page "https://github.com/brodieG/diffobj")
141 (synopsis "Diffs for R objects")
143 "Generate a colorized diff of two R objects for an intuitive
144 visualization of their differences.")
145 (license license:gpl2+)))
147 (define-public r-waldo
154 (uri (cran-uri "waldo" version))
157 "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz"))))
158 (properties `((upstream-name . "waldo")))
159 (build-system r-build-system)
162 ("r-diffobj" ,r-diffobj)
165 ("r-rematch2" ,r-rematch2)
167 ("r-tibble" ,r-tibble)))
168 (home-page "https://github.com/r-lib/waldo")
169 (synopsis "Find differences between R objects")
171 "Compare complex R objects and reveal the key differences. This package
172 was designed particularly for use in testing packages where being able to
173 quickly isolate key differences makes understanding test failures much
175 (license license:expat)))
177 (define-public r-rticles
184 (uri (cran-uri "rticles" version))
187 "1wbwva5n88dw3vvhcrlzkr58cv03hyx0dqgfmxj7d0dgf4ichr3c"))))
188 (properties `((upstream-name . "rticles")))
189 (build-system r-build-system)
191 `(("r-knitr" ,r-knitr)
192 ("r-rmarkdown" ,r-rmarkdown)
193 ("r-tinytex" ,r-tinytex)
196 (home-page "https://github.com/rstudio/rticles")
197 (synopsis "Article formats for R Markdown")
199 "This package provides a suite of custom R Markdown formats and templates
200 for authoring journal articles and conference submissions.")
201 (license license:gpl3)))
203 (define-public r-bezier
209 (uri (cran-uri "bezier" version))
212 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
213 (build-system r-build-system)
214 (home-page "https://cran.r-project.org/web/packages/bezier/")
215 (synopsis "Bezier curve and spline toolkit")
217 "This package is a toolkit for working with Bezier curves and splines.
218 The package provides functions for point generation, arc length estimation,
219 degree elevation and curve fitting.")
220 (license license:gpl2+)))
229 (uri (cran-uri "V8" version))
232 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
233 (properties `((upstream-name . "V8")))
234 (build-system r-build-system)
237 (modify-phases %standard-phases
238 (add-after 'unpack 'find-v8
239 (lambda* (#:key inputs #:allow-other-keys)
240 (substitute* "configure"
242 (string-append "PKG_LIBS="
243 (assoc-ref inputs "node")
244 "/lib/libnode.so.64\n")))
245 (setenv "INCLUDE_DIR"
247 (assoc-ref inputs "node")
251 (assoc-ref inputs "node") "/lib"))
254 `(("node" ,libnode)))
257 ("r-jsonlite" ,r-jsonlite)
260 `(("r-knitr" ,r-knitr)))
261 (home-page "https://jeroen.cran.dev/V8")
262 (synopsis "Embedded JavaScript and WebAssembly engine for R")
264 "This package provides an R interface to V8: Google's JavaScript and
265 WebAssembly engine.")
266 (license license:expat)))
275 (uri (cran-uri "DOT" version))
278 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
279 (properties `((upstream-name . "DOT")))
280 (build-system r-build-system)
283 (home-page "http://haghish.com/dot")
284 (synopsis "Render and Export DOT Graphs in R")
286 "This package provides tools to render DOT diagram markup language in R
287 and also provides the possibility to export the graphs in PostScript and
288 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
289 programming packages such as @code{knitr} and @code{rmarkdown}.")
290 (license license:expat)))
292 (define-public r-clipr
299 (uri (cran-uri "clipr" version))
302 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
303 (build-system r-build-system)
305 `(("r-knitr" ,r-knitr)))
306 (home-page "https://github.com/mdlincoln/clipr")
307 (synopsis "Read and write from the system clipboard")
309 "This package provides simple utility functions to read from and write to
310 the system clipboards.")
311 (license license:gpl3)))
319 (uri (cran-uri "zoo" version))
322 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
323 (build-system r-build-system)
325 `(("r-lattice" ,r-lattice)))
326 (home-page "http://zoo.R-Forge.R-project.org/")
327 (synopsis "S3 infrastructure for regular and irregular time series")
328 (description "This package contains an S3 class with methods for totally
329 ordered indexed observations. It is particularly aimed at irregular time
330 series of numeric vectors/matrices and factors.")
331 (license license:gpl2+)))
333 (define-public r-ggalluvial
335 (name "r-ggalluvial")
339 (uri (cran-uri "ggalluvial" version))
342 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
343 (properties `((upstream-name . "ggalluvial")))
344 (build-system r-build-system)
346 `(("r-dplyr" ,r-dplyr)
347 ("r-ggplot2" ,r-ggplot2)
348 ("r-lazyeval" ,r-lazyeval)
351 ("r-tidyselect" ,r-tidyselect)))
353 `(("r-knitr" ,r-knitr)))
354 (home-page "http://corybrunson.github.io/ggalluvial/")
355 (synopsis "Alluvial plots for ggplot2")
356 (description "This package provides alluvial plots for @code{ggplot2}.
357 Alluvial plots use variable-width ribbons and stacked bar plots to represent
358 multi-dimensional or repeated-measures data with categorical or ordinal
360 (license license:gpl3)))
362 (define-public r-ggpmisc
368 (uri (cran-uri "ggpmisc" version))
371 "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn"))))
372 (build-system r-build-system)
374 `(("r-broom" ,r-broom)
377 ("r-ggplot2" ,r-ggplot2)
378 ("r-gridextra" ,r-gridextra)
379 ("r-lubridate" ,r-lubridate)
380 ("r-magrittr" ,r-magrittr)
383 ("r-polynom" ,r-polynom)
385 ("r-scales" ,r-scales)
386 ("r-splus2r" ,r-splus2r)
387 ("r-stringr" ,r-stringr)
388 ("r-tibble" ,r-tibble)
392 `(("r-knitr" ,r-knitr)))
393 (home-page "https://www.r4photobiology.info/")
394 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
395 (description "This package provides extensions to @code{ggplot2},
396 respecting the grammar of its graphics paradigm.")
397 (license license:gpl2+)))
399 (define-public r-gprofiler
406 (uri (cran-uri "gProfileR" version))
409 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
410 (properties `((upstream-name . "gProfileR")))
411 (build-system r-build-system)
414 ("r-rcurl" ,r-rcurl)))
415 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
416 (synopsis "Interface to the g:Profiler toolkit")
418 "This package provides tools for functional enrichment analysis,
419 gene identifier conversion and mapping homologous genes across related
420 organisms via the @code{g:Profiler} toolkit.")
421 (license license:gpl2+)))
423 (define-public r-gprofiler2
425 (name "r-gprofiler2")
430 (uri (cran-uri "gprofiler2" version))
433 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
434 (properties `((upstream-name . "gprofiler2")))
435 (build-system r-build-system)
437 `(("r-crosstalk" ,r-crosstalk)
439 ("r-ggplot2" ,r-ggplot2)
440 ("r-gridextra" ,r-gridextra)
441 ("r-jsonlite" ,r-jsonlite)
442 ("r-plotly" ,r-plotly)
445 ("r-viridislite" ,r-viridislite)))
446 (native-inputs `(("r-knitr" ,r-knitr)))
447 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
448 (synopsis "Interface to the g:Profiler toolset")
450 "This package provides a toolset for functional enrichment analysis and
451 visualization, gene/protein/SNP identifier conversion and mapping orthologous
452 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
456 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
458 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
460 @item @code{g:Orth}, orthology search across species;
461 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
462 genes and variant effects.
465 This package is an R interface corresponding to the 2019 update of
466 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
468 (license license:gpl2+)))
470 (define-public r-oenb
477 (uri (cran-uri "oenb" version))
480 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
481 (properties `((upstream-name . "oenb")))
482 (build-system r-build-system)
484 `(("r-dplyr" ,r-dplyr)
486 (native-inputs `(("r-knitr" ,r-knitr)))
487 (home-page "https://github.com/franzmohr/oenb")
488 (synopsis "Tools for the OeNB Data Web Service")
490 "Tools to access data from the data web service of the
491 @acronym{OeNB, Oesterreichische Nationalbank},
492 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
493 (license license:gpl2+)))
495 (define-public r-scales
502 (uri (cran-uri "scales" version))
504 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
505 (build-system r-build-system)
507 `(("r-farver" ,r-farver)
508 ("r-labeling" ,r-labeling)
509 ("r-lifecycle" ,r-lifecycle)
510 ("r-munsell" ,r-munsell)
511 ("r-rcolorbrewer" ,r-rcolorbrewer)
513 ("r-viridislite" ,r-viridislite)))
514 (home-page "https://github.com/hadley/scales")
515 (synopsis "Scale functions for visualization")
517 "This package provides graphical scales that map data to aesthetics, and
518 provides methods for automatically determining breaks and labels for axes and
520 (license license:expat)))
522 (define-public r-pheatmap
529 (uri (cran-uri "pheatmap" version))
532 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
533 (build-system r-build-system)
535 `(("r-gtable" ,r-gtable)
536 ("r-rcolorbrewer" ,r-rcolorbrewer)
537 ("r-scales" ,r-scales)))
538 (home-page "https://cran.r-project.org/web/packages/pheatmap")
539 (synopsis "Pretty heatmaps")
541 "This package provides an implementation of heatmaps that offers more
542 control over dimensions and appearance.")
543 (license license:gpl2+)))
551 (uri (cran-uri "ecp" version))
554 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
555 (build-system r-build-system)
557 `(("r-rcpp" ,r-rcpp)))
558 (home-page "https://cran.r-project.org/web/packages/ecp/")
559 (synopsis "Multiple change-point analysis of multivariate data")
561 "This package implements various procedures for finding multiple
562 change-points. Two methods make use of dynamic programming and pruning, with
563 no distributional assumptions other than the existence of certain absolute
564 moments in one method. Hierarchical and exact search methods are included.
565 All methods return the set of estimated change-points as well as other summary
567 (license license:gpl2+)))
569 (define-public r-ellipsis
576 (uri (cran-uri "ellipsis" version))
579 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
580 (build-system r-build-system)
582 `(("r-rlang" ,r-rlang)))
583 (home-page "https://github.com/hadley/ellipsis")
584 (synopsis "Tools for working with additional arguments")
586 "In S3 generics, it's useful to take @code{...} so that methods can have
587 additional arguments. But this flexibility comes at a cost: misspelled
588 arguments will be silently ignored. The @code{ellipsis} package is an
589 experiment that allows a generic to warn if any arguments passed in @code{...}
591 (license license:gpl3)))
600 (uri (cran-uri "grr" version))
603 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
604 (build-system r-build-system)
605 (home-page "https://cran.r-project.org/web/packages/grr")
606 (synopsis "Alternative implementations of base R functions")
608 "This package provides alternative implementations of some base R
609 functions, including @code{sort}, @code{order}, and @code{match}. The
610 functions are simplified but can be faster or have other advantages.")
611 (license license:gpl3)))
613 (define-public r-matrix-utils
615 (name "r-matrix-utils")
620 (uri (cran-uri "Matrix.utils" version))
623 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
624 (properties `((upstream-name . "Matrix.utils")))
625 (build-system r-build-system)
628 ("r-matrix" ,r-matrix)))
629 (home-page "https://github.com/cvarrichio/Matrix.utils")
631 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
633 "This package implements data manipulation methods such as @code{cast},
634 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
636 (license license:gpl3)))
638 (define-public r-mboost
644 (uri (cran-uri "mboost" version))
647 "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
648 (build-system r-build-system)
650 `(("r-lattice" ,r-lattice)
651 ("r-matrix" ,r-matrix)
653 ("r-partykit" ,r-partykit)
654 ("r-quadprog" ,r-quadprog)
656 ("r-survival" ,r-survival)))
657 (home-page "https://github.com/boost-R/mboost")
658 (synopsis "Model-based boosting")
660 "This package provides a functional gradient descent algorithm (boosting)
661 for optimizing general risk functions utilizing component-wise (penalised)
662 least squares estimates or regression trees as base-learners for fitting
663 generalized linear, additive and interaction models to potentially
664 high-dimensional data.")
665 (license license:gpl2)))
667 (define-public r-shadowtext
669 (name "r-shadowtext")
673 (uri (cran-uri "shadowtext" version))
676 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
677 (properties `((upstream-name . "shadowtext")))
678 (build-system r-build-system)
680 `(("r-ggplot2" ,r-ggplot2)
681 ("r-scales" ,r-scales)))
683 `(("r-knitr" ,r-knitr)))
684 (home-page "https://github.com/GuangchuangYu/shadowtext/")
685 (synopsis "Shadow text grob and layer")
686 (description "This package implements @code{shadowtextGrob()} for
687 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
688 These functions draw text grob with background shadow.")
689 (license license:artistic2.0)))
698 (uri (cran-uri "sys" version))
701 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
702 (build-system r-build-system)
703 (home-page "https://github.com/jeroen/sys")
704 (synopsis "Powerful and reliable tools for running system commands in R")
706 "This package provides drop-in replacements for the base @code{system2()}
707 function with fine control and consistent behavior across platforms. It
708 supports clean interruption, timeout, background tasks, and streaming STDIN /
709 STDOUT / STDERR over binary or text connections. The package also provides
710 functions for evaluating expressions inside a temporary fork. Such
711 evaluations have no side effects on the main R process, and support reliable
712 interrupts and timeouts. This provides the basis for a sandboxing
714 (license license:expat)))
716 (define-public r-ashr
722 (uri (cran-uri "ashr" version))
725 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
726 (properties `((upstream-name . "ashr")))
727 (build-system r-build-system)
729 `(("r-etrunct" ,r-etrunct)
730 ("r-invgamma" ,r-invgamma)
731 ("r-matrix" ,r-matrix)
732 ("r-mixsqp" ,r-mixsqp)
734 ("r-squarem" ,r-squarem)
735 ("r-truncnorm" ,r-truncnorm)))
737 `(("r-knitr" ,r-knitr)))
738 (home-page "https://github.com/stephens999/ashr")
739 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
740 (description "This package implements an empirical Bayes approach for
741 large-scale hypothesis testing and false discovery rate estimation.")
742 (license license:gpl3+)))
744 (define-public r-askpass
751 (uri (cran-uri "askpass" version))
754 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
755 (build-system r-build-system)
756 (propagated-inputs `(("r-sys" ,r-sys)))
757 (home-page "https://github.com/jeroen/askpass")
758 (synopsis "Safe password entry for R")
760 "This package provides cross-platform utilities for prompting the user
761 for credentials or a passphrase, for example to authenticate with a server or
762 read a protected key.")
763 (license license:expat)))
765 (define-public r-vegan
772 (uri (cran-uri "vegan" version))
775 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
776 (build-system r-build-system)
778 `(("r-knitr" ,r-knitr) ; needed for vignettes
779 ("gfortran" ,gfortran)))
781 `(("r-cluster" ,r-cluster)
782 ("r-lattice" ,r-lattice)
785 ("r-permute" ,r-permute)))
786 (home-page "https://cran.r-project.org/web/packages/vegan")
787 (synopsis "Functions for community ecology")
789 "The vegan package provides tools for descriptive community ecology. It
790 has most basic functions of diversity analysis, community ordination and
791 dissimilarity analysis. Most of its multivariate tools can be used for other
792 data types as well.")
793 (license license:gpl2+)))
795 (define-public r-tidyverse
802 (uri (cran-uri "tidyverse" version))
805 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
806 (build-system r-build-system)
808 `(("r-broom" ,r-broom)
810 ("r-crayon" ,r-crayon)
811 ("r-dbplyr" ,r-dbplyr)
813 ("r-forcats" ,r-forcats)
814 ("r-ggplot2" ,r-ggplot2)
818 ("r-jsonlite" ,r-jsonlite)
819 ("r-lubridate" ,r-lubridate)
820 ("r-magrittr" ,r-magrittr)
821 ("r-modelr" ,r-modelr)
822 ("r-pillar" ,r-pillar)
825 ("r-readxl" ,r-readxl)
826 ("r-reprex" ,r-reprex)
828 ("r-rstudioapi" ,r-rstudioapi)
830 ("r-stringr" ,r-stringr)
831 ("r-tibble" ,r-tibble)
834 (home-page "https://tidyverse.tidyverse.org")
835 (synopsis "Install and load packages from the \"Tidyverse\"")
837 "The @code{tidyverse} is a set of packages that work in harmony because
838 they share common data representations and API design. This package is
839 designed to make it easy to install and load multiple tidyverse packages in a
841 (license license:gpl3)))
843 (define-public r-rvest
850 (uri (cran-uri "rvest" version))
852 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
853 (build-system r-build-system)
856 ("r-magrittr" ,r-magrittr)
857 ("r-selectr" ,r-selectr)
860 `(("r-knitr" ,r-knitr)))
861 (home-page "https://github.com/hadley/rvest")
862 (synopsis "Simple web scraping for R")
864 "@code{r-rvest} helps you scrape information from web pages. It is
865 designed to work with @code{magrittr} to make it easy to express common web
866 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
867 (license license:gpl3)))
869 (define-public r-selectr
876 (uri (cran-uri "selectr" version))
878 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
879 (build-system r-build-system)
881 `(("r-stringr" ,r-stringr)
883 (home-page "https://sjp.co.nz/projects/selectr/")
884 (synopsis "Translate CSS selectors to XPath expressions")
886 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
887 expression. This allows you to use CSS selectors when working with the XML
888 package as it can only evaluate XPath expressions. Also provided are
889 convenience functions useful for using CSS selectors on XML nodes. This
890 package is a port of the Python package @code{cssselect}.")
891 (license license:bsd-3)))
893 (define-public r-reprex
900 (uri (cran-uri "reprex" version))
903 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
904 (build-system r-build-system)
906 `(("r-callr" ,r-callr)
910 ("r-rmarkdown" ,r-rmarkdown)
911 ("r-whisker" ,r-whisker)
912 ("r-withr" ,r-withr)))
913 (home-page "https://github.com/tidyverse/reprex")
914 (synopsis "Prepare reproducible R code examples for sharing")
916 "This package provides a convenience wrapper that uses the
917 @code{rmarkdown} package to render small snippets of code to target formats
918 that include both code and output. The goal is to encourage the sharing of
919 small, reproducible, and runnable examples on code-oriented websites or email.
920 @code{reprex} also extracts clean, runnable R code from various common formats,
921 such as copy/paste from an R session.")
922 (license license:expat)))
924 (define-public r-reordercluster
926 (name "r-reordercluster")
930 (uri (cran-uri "ReorderCluster" version))
933 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
934 (build-system r-build-system)
936 `(("r-gplots" ,r-gplots)
938 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
939 (synopsis "Reordering the dendrogram according to the class labels")
940 (description "This package provides tools for performing the leaf reordering
941 for the dendrogram that preserves the hierarchical clustering result and at the
942 same time tries to group instances from the same class together.")
943 (license license:gpl3+)))
945 (define-public r-callr
952 (uri (cran-uri "callr" version))
955 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
956 (build-system r-build-system)
959 ("r-processx" ,r-processx)))
960 (home-page "https://github.com/r-lib/callr#readme")
961 (synopsis "Call R from R")
963 "It is sometimes useful to perform a computation in a separate R process,
964 without affecting the current R process at all. This package does exactly
966 (license license:expat)))
968 (define-public r-readxl
975 (uri (cran-uri "readxl" version))
978 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
979 (build-system r-build-system)
981 `(("r-cellranger" ,r-cellranger)
982 ("r-progress" ,r-progress)
984 ("r-tibble" ,r-tibble)))
985 (home-page "https://readxl.tidyverse.org")
986 (synopsis "Read Excel files")
988 "This package lets you import Excel files into R. It supports
989 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
990 the embedded @code{RapidXML} C++ library.")
991 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
992 ;; 'rapidxml' which is Boost.
993 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
995 (define-public r-modelr
1002 (uri (cran-uri "modelr" version))
1005 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1006 (build-system r-build-system)
1008 `(("r-broom" ,r-broom)
1009 ("r-magrittr" ,r-magrittr)
1010 ("r-purrr" ,r-purrr)
1011 ("r-rlang" ,r-rlang)
1012 ("r-tibble" ,r-tibble)
1013 ("r-tidyr" ,r-tidyr)
1014 ("r-tidyselect" ,r-tidyselect)
1015 ("r-vctrs" ,r-vctrs)))
1016 (home-page "https://github.com/tidyverse/modelr")
1017 (synopsis "Helper functions for modelling in pipelines")
1019 "Functions for modelling that help you seamlessly integrate modelling
1020 into a pipeline of data manipulation and visualisation.")
1021 (license license:gpl3)))
1023 (define-public r-httpuv
1029 (uri (cran-uri "httpuv" version))
1032 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
1033 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1034 ;; only contains fixes for building on Solaris.
1035 (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
1036 (modules '((guix build utils)
1041 (delete-file-recursively "src/libuv")
1042 ;; Cannot unbundle http-parser, because it contains local
1045 (build-system r-build-system)
1048 (modify-phases %standard-phases
1049 (add-after 'unpack 'unbundle-libuv
1050 (lambda* (#:key outputs #:allow-other-keys)
1051 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1052 (("\"libuv/include/uv\\.h\"")
1054 ;; Fix https://github.com/rstudio/httpuv/issues/282
1055 (substitute* "src/http.cpp"
1056 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1057 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1060 `(("libuv" ,libuv)))
1063 ("r-later" ,r-later)
1064 ("r-promises" ,r-promises)
1066 ("r-rcpp" ,r-rcpp)))
1067 (home-page "https://github.com/rstudio/httpuv")
1068 (synopsis "HTTP and WebSocket server library for R")
1070 "The httpuv package provides low-level socket and protocol support for
1071 handling HTTP and WebSocket requests directly from within R. It is primarily
1072 intended as a building block for other packages, rather than making it
1073 particularly easy to create complete web applications using httpuv alone.")
1074 ;; This package includes third-party code that was originally released
1075 ;; under various non-copyleft licenses. Full licensing information can be
1076 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1077 (license license:gpl3+)))
1079 (define-public r-jsonlite
1085 (uri (cran-uri "jsonlite" version))
1088 "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
1089 (build-system r-build-system)
1091 `(("r-knitr" ,r-knitr)))
1092 (home-page "https://arxiv.org/abs/1403.2805")
1093 (synopsis "Robust, high performance JSON parser and generator for R")
1095 "The jsonlite package provides a fast JSON parser and generator optimized
1096 for statistical data and the web. It offers flexible, robust, high
1097 performance tools for working with JSON in R and is particularly powerful for
1098 building pipelines and interacting with a web API. In addition to converting
1099 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1100 and prettify JSON data. The unit tests included with the package verify that
1101 all edge cases are encoded and decoded consistently for use with dynamic data
1102 in systems and applications.")
1103 (license license:expat)))
1105 (define-public r-servr
1111 (uri (cran-uri "servr" version))
1114 "0px75vkc6q4iwbirr27bbrbpv0v9ial7zijnbd6dhjccwxl3x1l3"))))
1115 (build-system r-build-system)
1117 `(("r-httpuv" ,r-httpuv)
1118 ("r-jsonlite" ,r-jsonlite)
1120 ("r-xfun" ,r-xfun)))
1121 (home-page "https://github.com/yihui/servr")
1122 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1124 "Servr provides an HTTP server in R to serve static files, or dynamic
1125 documents that can be converted to HTML files (e.g., R Markdown) under a given
1127 (license license:expat)))
1129 (define-public r-htmltools
1131 (name "r-htmltools")
1135 (uri (cran-uri "htmltools" version))
1138 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
1139 (build-system r-build-system)
1141 `(("r-base64enc" ,r-base64enc)
1142 ("r-digest" ,r-digest)
1143 ("r-rlang" ,r-rlang)))
1144 (home-page "https://cran.r-project.org/web/packages/htmltools")
1145 (synopsis "R tools for HTML")
1147 "This package provides tools for HTML generation and output in R.")
1148 (license license:expat)))
1150 (define-public r-htmlwidgets
1152 (name "r-htmlwidgets")
1156 (uri (cran-uri "htmlwidgets" version))
1159 "0072wlkl58lav3qszzqw6pmx8qra4784r0yb6rx4lg7rbrik6335"))))
1160 (build-system r-build-system)
1162 `(("r-htmltools" ,r-htmltools)
1163 ("r-jsonlite" ,r-jsonlite)
1164 ("r-yaml" ,r-yaml)))
1166 `(("r-knitr" ,r-knitr)))
1167 (home-page "https://github.com/ramnathv/htmlwidgets")
1168 (synopsis "HTML Widgets for R")
1170 "HTML widgets is a framework for creating HTML widgets that render in
1171 various contexts including the R console, R Markdown documents, and Shiny web
1173 (license license:expat)))
1175 (define-public r-htmltable
1177 (name "r-htmltable")
1182 (uri (cran-uri "htmlTable" version))
1184 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1185 (properties `((upstream-name . "htmlTable")))
1186 (build-system r-build-system)
1188 `(("r-checkmate" ,r-checkmate)
1189 ("r-htmltools" ,r-htmltools)
1190 ("r-htmlwidgets" ,r-htmlwidgets)
1191 ("r-knitr" ,r-knitr)
1192 ("r-magrittr" ,r-magrittr)
1193 ("r-rstudioapi" ,r-rstudioapi)
1194 ("r-stringr" ,r-stringr)))
1196 `(("r-knitr" ,r-knitr)))
1197 (home-page "http://gforge.se/packages/")
1198 (synopsis "Advanced tables for Markdown/HTML")
1200 "This package provides functions to build tables with advanced layout
1201 elements such as row spanners, column spanners, table spanners, zebra
1202 striping, and more. While allowing advanced layout, the underlying
1203 CSS-structure is simple in order to maximize compatibility with word
1204 processors such as LibreOffice. The package also contains a few text
1205 formatting functions that help outputting text compatible with HTML or
1207 (license license:gpl3+)))
1209 (define-public r-curl
1215 (uri (cran-uri "curl" version))
1218 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1219 (build-system r-build-system)
1222 (modify-phases %standard-phases
1223 ;; The environment variable CURL_CA_BUNDLE is only respected when
1224 ;; running Windows, so we disable the platform checks.
1225 ;; This can be removed once the libcurl has been patched.
1226 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1228 (substitute* "R/onload.R"
1229 (("if \\(!grepl\\(\"mingw\".*")
1231 (substitute* "src/handle.c"
1232 (("/\\* Only set" m)
1234 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1235 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1242 `(("pkg-config" ,pkg-config)))
1243 (home-page "https://github.com/jeroenooms/curl")
1244 (synopsis "HTTP client for R")
1246 "The @code{curl()} and @code{curl_download()} functions provide highly
1247 configurable drop-in replacements for base @code{url()} and
1248 @code{download.file()} with better performance, support for encryption, gzip
1249 compression, authentication, and other @code{libcurl} goodies. The core of
1250 the package implements a framework for performing fully customized requests
1251 where data can be processed either in memory, on disk, or streaming via the
1252 callback or connection interfaces.")
1253 (license license:expat)))
1255 (define-public r-hwriter
1262 (uri (cran-uri "hwriter" version))
1265 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1266 (build-system r-build-system)
1267 (home-page "https://cran.r-project.org/web/packages/hwriter")
1268 (synopsis "Output R objects in HTML format")
1270 "This package provides easy-to-use and versatile functions to output R
1271 objects in HTML format.")
1272 (license license:lgpl2.1+)))
1274 (define-public r-rjson
1281 (uri (cran-uri "rjson" version))
1284 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1285 (build-system r-build-system)
1286 (home-page "https://cran.r-project.org/web/packages/rjson")
1287 (synopsis "JSON library for R")
1289 "This package provides functions to convert R objects into JSON objects
1291 (license license:gpl2+)))
1293 (define-public r-fastmap
1300 (uri (cran-uri "fastmap" version))
1303 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1304 (properties `((upstream-name . "fastmap")))
1305 (build-system r-build-system)
1306 (home-page "https://r-lib.github.io/fastmap/")
1307 (synopsis "Fast implementation of a key-value store")
1309 "This package provides a fast implementation of a key-value store.
1310 Environments are commonly used as key-value stores, but every time a new key
1311 is used, it is added to R's global symbol table, causing a small amount of
1312 memory leakage. This can be problematic in cases where many different keys
1313 are used. Fastmap avoids this memory leak issue by implementing the map using
1314 data structures in C++.")
1315 (license license:expat)))
1317 (define-public r-shiny
1325 (url "https://github.com/rstudio/shiny")
1326 (commit (string-append "v" version))))
1327 (file-name (git-file-name name version))
1330 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1331 (build-system r-build-system)
1333 `(#:modules ((guix build r-build-system)
1334 (guix build minify-build-system)
1337 #:imported-modules (,@%r-build-system-modules
1338 (guix build minify-build-system))
1340 (modify-phases (@ (guix build r-build-system) %standard-phases)
1341 (add-after 'unpack 'replace-bundled-minified-JavaScript
1342 (lambda* (#:key inputs #:allow-other-keys)
1343 (let ((replace-file (lambda (old new)
1344 (format #t "replacing ~a with ~a\n" old new)
1346 (symlink new old))))
1347 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1348 ;; contain just data. They are not minified code, so we don't
1350 (with-directory-excursion "inst/www/shared"
1351 (replace-file "bootstrap/shim/respond.min.js"
1352 (string-append (assoc-ref inputs "js-respond")
1353 "/share/javascript/respond.min.js"))
1354 (replace-file "bootstrap/shim/html5shiv.min.js"
1355 (string-append (assoc-ref inputs "js-html5shiv")
1356 "/share/javascript/html5shiv.min.js"))
1357 (replace-file "json2-min.js"
1358 (string-append (assoc-ref inputs "js-json2")
1359 "/share/javascript/json2-min.js"))
1360 (replace-file "strftime/strftime-min.js"
1361 (string-append (assoc-ref inputs "js-strftime")
1362 "/share/javascript/strftime.min.js"))
1363 (replace-file "highlight/highlight.pack.js"
1364 (string-append (assoc-ref inputs "js-highlight")
1365 "/share/javascript/highlight.min.js"))
1366 (replace-file "datatables/js/jquery.dataTables.min.js"
1367 (string-append (assoc-ref inputs "js-datatables")
1368 "/share/javascript/jquery.dataTables.min.js"))
1369 (replace-file "selectize/js/selectize.min.js"
1370 (string-append (assoc-ref inputs "js-selectize")
1371 "/share/javascript/selectize.min.js"))
1372 (replace-file "selectize/js/es5-shim.min.js"
1373 (string-append (assoc-ref inputs "js-es5-shim")
1374 "/share/javascript/es5-shim.min.js"))
1375 (for-each (match-lambda
1377 (delete-file target)
1378 (minify source #:target target)))
1379 '(("jqueryui/jquery-ui.js" .
1380 "jqueryui/jquery-ui.min.js")
1381 ("datepicker/js/bootstrap-datepicker.js" .
1382 "datepicker/js/bootstrap-datepicker.min.js")
1383 ("ionrangeslider/js/ion.rangeSlider.js" .
1384 "ionrangeslider/js/ion.rangeSlider.min.js")
1385 ("bootstrap/js/bootstrap.js" .
1386 "bootstrap/js/bootstrap.min.js")
1391 ("legacy/jquery.js" .
1392 "legacy/jquery.min.js")
1393 ("showdown/src/showdown.js" .
1394 "showdown/compressed/showdown.js")))))
1397 `(("r-crayon" ,r-crayon)
1398 ("r-digest" ,r-digest)
1399 ("r-fastmap" ,r-fastmap)
1400 ("r-htmltools" ,r-htmltools)
1401 ("r-httpuv" ,r-httpuv)
1402 ("r-jsonlite" ,r-jsonlite)
1403 ("r-later" ,r-later)
1405 ("r-promises" ,r-promises)
1407 ("r-rlang" ,r-rlang)
1408 ("r-sourcetools" ,r-sourcetools)
1409 ("r-withr" ,r-withr)
1410 ("r-xtable" ,r-xtable)))
1412 `(("js-datatables" ,js-datatables)
1413 ("js-html5shiv" ,js-html5shiv)
1414 ("js-json2" ,js-json2)
1415 ("js-respond" ,js-respond)
1416 ("js-selectize" ,js-selectize)
1417 ("js-strftime" ,js-strftime)
1418 ("js-highlight" ,js-highlight)
1419 ("js-es5-shim" ,js-es5-shim)))
1421 `(("uglify-js" ,uglify-js)
1422 ("gfortran" ,gfortran)))
1423 (home-page "http://shiny.rstudio.com")
1424 (synopsis "Easy interactive web applications with R")
1426 "Makes it incredibly easy to build interactive web applications
1427 with R. Automatic \"reactive\" binding between inputs and outputs and
1428 extensive prebuilt widgets make it possible to build beautiful,
1429 responsive, and powerful applications with minimal effort.")
1430 (license license:artistic2.0)))
1432 ;; This package includes minified JavaScript files. When upgrading please
1433 ;; check that there are no new minified JavaScript files.
1434 (define-public r-shinytree
1436 (name "r-shinytree")
1441 (uri (cran-uri "shinyTree" version))
1444 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1445 (modules '((guix build utils)))
1448 ;; Delete minified JavaScript
1449 (for-each delete-file
1450 '("inst/www/jsTree-3.3.7/libs/require.js"
1451 "inst/www/jsTree-3.3.7/libs/jquery.js"
1452 "inst/www/jsTree-3.3.7/jstree.min.js"))
1454 (properties `((upstream-name . "shinyTree")))
1455 (build-system r-build-system)
1457 `(#:modules ((guix build utils)
1458 (guix build r-build-system)
1462 (modify-phases %standard-phases
1463 (add-after 'unpack 'replace-minified-javascript
1464 (lambda* (#:key inputs #:allow-other-keys)
1465 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1466 (symlink (string-append (assoc-ref inputs "js-requirejs")
1467 "/share/javascript/require.min.js")
1472 `((,(assoc-ref inputs "js-jquery")
1476 (lambda (sources targets)
1477 (for-each (lambda (source target)
1478 (format #t "Processing ~a --> ~a~%"
1480 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1481 (call-with-output-file target
1483 (dump-port minified port)))))
1487 `(("r-htmlwidgets" ,r-htmlwidgets)
1488 ("r-jsonlite" ,r-jsonlite)
1489 ("r-promises" ,r-promises)
1490 ("r-shiny" ,r-shiny)
1491 ("r-stringr" ,r-stringr)))
1493 `(("js-requirejs" ,js-requirejs)))
1495 `(("uglify-js" ,uglify-js)
1499 (uri "https://code.jquery.com/jquery-3.3.1.js")
1502 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1503 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1504 (synopsis "jsTree bindings for Shiny")
1506 "This package exposes R bindings to jsTree, a JavaScript library that
1507 supports interactive trees, to enable rich, editable trees in Shiny.")
1508 (license license:expat)))
1510 (define-public r-shinydashboard
1512 (name "r-shinydashboard")
1516 (uri (cran-uri "shinydashboard" version))
1519 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1520 (build-system r-build-system)
1521 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1522 ;; Regenerate it from the included sources.
1524 `(#:modules ((guix build utils)
1525 (guix build r-build-system)
1528 (modify-phases %standard-phases
1529 (add-after 'unpack 'generate-minified-javascript
1531 (with-directory-excursion "inst/AdminLTE"
1532 (delete-file "app.min.js")
1533 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1534 (call-with-output-file "app.min.js"
1536 (dump-port minified port))))))))))
1538 `(("r-htmltools" ,r-htmltools)
1539 ("r-promises" ,r-promises)
1540 ("r-shiny" ,r-shiny)))
1542 `(("uglify-js" ,uglify-js)))
1543 (home-page "https://rstudio.github.io/shinydashboard/")
1544 (synopsis "Create dashboards with shiny")
1545 (description "This package provides an extension to the Shiny web
1546 application framework for R, making it easy to create attractive dashboards.")
1547 ;; This package includes software that was released under the Expat
1548 ;; license, but the whole package is released under GPL version 2 or
1550 (license license:gpl2+)))
1552 (define-public r-shinyfiles
1554 (name "r-shinyfiles")
1559 (uri (cran-uri "shinyFiles" version))
1561 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1562 (properties `((upstream-name . "shinyFiles")))
1563 (build-system r-build-system)
1566 ("r-htmltools" ,r-htmltools)
1567 ("r-jsonlite" ,r-jsonlite)
1568 ("r-shiny" ,r-shiny)
1569 ("r-tibble" ,r-tibble)))
1570 (home-page "https://github.com/thomasp85/shinyFiles")
1571 (synopsis "Server-side file system viewer for Shiny")
1573 "This package provides functionality for client-side navigation of the
1574 server side file system in shiny apps. In case the app is running locally
1575 this gives the user direct access to the file system without the need to
1576 \"download\" files to a temporary location. Both file and folder selection as
1577 well as file saving is available.")
1578 (license license:gpl2+)))
1580 (define-public r-shinythemes
1582 (name "r-shinythemes")
1587 (uri (cran-uri "shinythemes" version))
1590 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1591 (properties `((upstream-name . "shinythemes")))
1592 (build-system r-build-system)
1593 (propagated-inputs `(("r-shiny" ,r-shiny)))
1594 (home-page "https://rstudio.github.io/shinythemes/")
1595 (synopsis "Themes for Shiny")
1597 "This package provides themes for use with Shiny. It includes several
1598 Bootstrap themes, which are packaged for use with Shiny applications.")
1599 ;; The package is released under version 3 of the GPL, but it includes
1600 ;; source files that are covered by the Expat license. It also includes
1601 ;; fonts under SIL or the ASL.
1602 (license (list license:gpl3 license:expat
1603 license:silofl1.1 license:asl2.0))))
1605 ;; The package sources include minified variants of d3.js and non-minified
1606 ;; source code of d3-jetpack.
1607 (define-public r-d3r
1614 (uri (cran-uri "d3r" version))
1617 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1618 (build-system r-build-system)
1620 `(#:modules ((guix build utils)
1621 (guix build r-build-system)
1624 (modify-phases %standard-phases
1625 (add-after 'unpack 'process-javascript
1626 (lambda* (#:key inputs #:allow-other-keys)
1627 (with-directory-excursion "inst/www/d3/"
1631 `((,(assoc-ref inputs "d3.v3.js")
1632 "v3/dist/d3.min.js")
1633 (,(assoc-ref inputs "d3.v4.js")
1634 "v4/dist/d3.min.js")
1635 (,(assoc-ref inputs "d3.v5.js")
1636 "v5/dist/d3.min.js")
1637 (,(assoc-ref inputs "d3.v6.js")
1638 "v6/dist/d3.min.js"))))
1639 (lambda (sources targets)
1640 (for-each (lambda (source target)
1641 (format #t "Processing ~a --> ~a~%"
1643 (delete-file target)
1644 (invoke "esbuild" source "--minify"
1645 (string-append "--outfile=" target)))
1649 `(("r-dplyr" ,r-dplyr)
1650 ("r-htmltools" ,r-htmltools)
1651 ("r-rlang" ,r-rlang)
1652 ("r-tidyr" ,r-tidyr)))
1654 `(("esbuild" ,esbuild)
1658 (uri "https://d3js.org/d3.v3.js")
1661 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1665 (uri "https://d3js.org/d3.v4.js")
1668 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1672 (uri "https://d3js.org/d3.v5.js")
1675 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1679 (uri "https://d3js.org/d3.v6.js")
1682 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1683 (home-page "https://github.com/timelyportfolio/d3r")
1684 (synopsis "d3.js utilities for R")
1686 "This package provides a suite of functions to help ease the use of the
1687 d3.js visualization library in R. These helpers include
1688 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1689 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1690 R objects into the JSON format that the d3.js library expects.")
1691 (license license:bsd-3)))
1693 ;; We use the latest commit here because the last release was in 2016 while
1694 ;; the latest commit was in 2018.
1695 (define-public r-sankeyd3
1696 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1700 (version (git-version "0.3.2" revision commit))
1705 (url "https://github.com/fbreitwieser/sankeyD3")
1707 (file-name (git-file-name name version))
1710 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1711 (build-system r-build-system)
1714 ("r-htmlwidgets" ,r-htmlwidgets)
1715 ("r-shiny" ,r-shiny)
1716 ("r-magrittr" ,r-magrittr)))
1717 (home-page "https://github.com/fbreitwieser/sankeyD3")
1718 (synopsis "Sankey network graphs from R")
1720 "This package provides an R library to generate Sankey network graphs
1721 in R and Shiny via the D3 visualization library.")
1722 ;; The R code is licensed under GPLv3+. It includes the non-minified
1723 ;; JavaScript source code of d3-sankey, which is released under the
1724 ;; 3-clause BSD license.
1725 (license (list license:gpl3+ license:bsd-3)))))
1727 (define-public r-crosstalk
1729 (name "r-crosstalk")
1734 (uri (cran-uri "crosstalk" version))
1737 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1738 (build-system r-build-system)
1740 `(("r-htmltools" ,r-htmltools)
1741 ("r-jsonlite" ,r-jsonlite)
1742 ("r-lazyeval" ,r-lazyeval)
1744 (home-page "https://rstudio.github.io/crosstalk/")
1745 (synopsis "Inter-widget interactivity for HTML widgets")
1747 "This package provides building blocks for allowing HTML widgets to
1748 communicate with each other, with Shiny or without (i.e. static @code{.html}
1749 files). It currently supports linked brushing and filtering.")
1750 (license license:expat)))
1752 (define-public r-rook
1759 (uri (cran-uri "Rook" version))
1762 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1763 (properties `((upstream-name . "Rook")))
1764 (build-system r-build-system)
1765 (propagated-inputs `(("r-brew" ,r-brew)))
1766 (home-page "https://cran.r-project.org/web/packages/Rook")
1767 (synopsis "Web server interface for R")
1769 "This package contains the Rook specification and convenience software
1770 for building and running Rook applications. A Rook application is an R
1771 reference class object that implements a @code{call} method or an R closure
1772 that takes exactly one argument, an environment, and returns a list with three
1773 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1774 (license license:gpl2)))
1776 (define-public r-miniui
1783 (uri (cran-uri "miniUI" version))
1786 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1787 (properties `((upstream-name . "miniUI")))
1788 (build-system r-build-system)
1790 `(("r-htmltools" ,r-htmltools)
1791 ("r-shiny" ,r-shiny)))
1792 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1793 (synopsis "Shiny UI widgets for small screens")
1795 "This package provides UI widget and layout functions for writing Shiny apps that
1796 work well on small screens.")
1797 (license license:gpl3)))
1799 (define-public r-feather
1806 (uri (cran-uri "feather" version))
1809 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1810 (build-system r-build-system)
1814 ("r-tibble" ,r-tibble)))
1815 (home-page "https://github.com/wesm/feather")
1816 (synopsis "R Bindings to the Feather API")
1817 (description "Read and write feather files, a lightweight binary columnar
1818 data store designed for maximum speed.")
1819 (license license:asl2.0)))
1821 (define-public r-maps
1828 (uri (cran-uri "maps" version))
1831 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1832 (build-system r-build-system)
1833 (home-page "https://cran.r-project.org/web/packages/maps")
1834 (synopsis "Draw geographical maps")
1835 (description "This package provides an R module for display of maps.
1836 Projection code and larger maps are in separate packages (@code{mapproj} and
1838 (license license:gpl2)))
1840 (define-public r-mapproj
1847 (uri (cran-uri "mapproj" version))
1850 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1851 (build-system r-build-system)
1852 (propagated-inputs `(("r-maps" ,r-maps)))
1853 (home-page "https://cran.r-project.org/web/packages/mapproj")
1854 (synopsis "Map projection in R")
1855 (description "This package converts latitude/longitude into projected
1857 (license (list license:gpl2 ; The R interface
1858 (license:non-copyleft ; The C code
1859 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1860 "Lucent Public License Version 1.02")))))
1862 (define-public r-rgooglemaps
1864 (name "r-rgooglemaps")
1869 (uri (cran-uri "RgoogleMaps" version))
1872 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1873 (properties `((upstream-name . "RgoogleMaps")))
1874 (build-system r-build-system)
1878 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1879 (synopsis "Use Google Maps in R")
1880 (description "This package serves two purposes:
1882 @item Provide a comfortable R interface to query the Google server for static
1884 @item Use the map as a background image to overlay plots within R. This
1885 requires proper coordinate scaling.
1887 (license license:gpl2+)))
1889 (define-public r-geosphere
1891 (name "r-geosphere")
1896 (uri (cran-uri "geosphere" version))
1899 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1900 (build-system r-build-system)
1901 (propagated-inputs `(("r-sp" ,r-sp)))
1902 (home-page "https://cran.r-project.org/web/packages/geosphere")
1903 (synopsis "Spherical trigonometry")
1904 (description "This package computes spherical trigonometry for geographic
1905 applications. That is, compute distances and related measures for angular
1906 (longitude/latitude) locations.")
1907 (license license:gpl3+)))
1909 (define-public r-jpeg
1916 (uri (cran-uri "jpeg" version))
1919 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1920 (build-system r-build-system)
1921 (inputs `(("libjpeg" ,libjpeg-turbo)))
1922 (home-page "https://www.rforge.net/jpeg/")
1923 (synopsis "Read and write JPEG images with R")
1924 (description "This package provides a way to read, write and display
1925 bitmap images stored in the JPEG format with R. It can read and write both
1926 files and in-memory raw vectors.")
1927 (license license:gpl2+)))
1929 (define-public r-ggmap
1936 (uri (cran-uri "ggmap" version))
1939 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1940 (build-system r-build-system)
1942 `(("r-bitops" ,r-bitops)
1943 ("r-digest" ,r-digest)
1944 ("r-dplyr" ,r-dplyr)
1945 ("r-ggplot2" ,r-ggplot2)
1949 ("r-magrittr" ,r-magrittr)
1952 ("r-purrr" ,r-purrr)
1953 ("r-rgooglemaps" ,r-rgooglemaps)
1954 ("r-rjson" ,r-rjson)
1955 ("r-scales" ,r-scales)
1956 ("r-stringr" ,r-stringr)
1957 ("r-tibble" ,r-tibble)
1958 ("r-tidyr" ,r-tidyr)))
1959 (home-page "https://github.com/dkahle/ggmap")
1960 (synopsis "Spatial visualization with ggplot2")
1961 (description "This package provides a collection of functions to visualize
1962 spatial data and models on top of static maps from various online sources (e.g
1963 Google Maps and Stamen Maps). It includes tools common to those tasks,
1964 including functions for geolocation and routing.")
1965 (license license:gpl2)))
1967 (define-public r-haven
1974 (uri (cran-uri "haven" version))
1977 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1978 (build-system r-build-system)
1982 `(("r-knitr" ,r-knitr)))
1984 `(("r-forcats" ,r-forcats)
1987 ("r-rlang" ,r-rlang)
1988 ("r-readr" ,r-readr)
1989 ("r-tibble" ,r-tibble)
1990 ("r-tidyselect" ,r-tidyselect)
1991 ("r-vctrs" ,r-vctrs)))
1992 (home-page "https://haven.tidyverse.org")
1993 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1995 "This package lets you mport foreign statistical formats into R via the
1996 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1997 (license license:expat)))
1999 (define-public r-amap
2005 (uri (cran-uri "amap" version))
2008 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2009 (build-system r-build-system)
2011 `(("gfortran" ,gfortran)))
2012 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2013 (synopsis "Another multidimensional analysis package")
2014 (description "This package provides tools for clustering and principal
2015 component analysis (with robust methods, and parallelized functions).")
2016 (license license:gpl2+)))
2018 (define-public r-ape
2025 (uri (cran-uri "ape" version))
2028 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2029 (build-system r-build-system)
2031 `(("r-lattice" ,r-lattice)
2033 ("r-rcpp" ,r-rcpp)))
2034 (home-page "http://ape-package.ird.fr/")
2035 (synopsis "Analyses of phylogenetics and evolution")
2037 "This package provides functions for reading, writing, plotting, and
2038 manipulating phylogenetic trees, analyses of comparative data in a
2039 phylogenetic framework, ancestral character analyses, analyses of
2040 diversification and macroevolution, computing distances from DNA sequences,
2041 and several other tools.")
2042 (license license:gpl2+)))
2044 (define-public r-abbyyr
2051 (uri (cran-uri "abbyyR" version))
2054 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2055 (properties `((upstream-name . "abbyyR")))
2056 (build-system r-build-system)
2058 `(("r-curl" ,r-curl)
2061 ("r-progress" ,r-progress)
2062 ("r-readr" ,r-readr)
2064 (home-page "https://github.com/soodoku/abbyyR")
2065 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2067 "This package provides tools to get text from images of text using Abbyy
2068 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2069 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2070 passports and get the results in a variety of formats including plain text and
2071 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2072 (license license:expat)))
2074 (define-public r-colorspace
2076 (name "r-colorspace")
2081 (uri (cran-uri "colorspace" version))
2083 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2084 (build-system r-build-system)
2086 `(("r-knitr" ,r-knitr)))
2087 (home-page "https://cran.r-project.org/web/packages/colorspace")
2088 (synopsis "Color space manipulation")
2090 "This package carries out a mapping between assorted color spaces
2091 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2092 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2093 colors are provided.")
2094 (license license:bsd-3)))
2096 (define-public r-glue
2103 (uri (cran-uri "glue" version))
2106 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2107 (build-system r-build-system)
2108 ;; knitr depends on glue, so we can't add knitr here to build the
2112 `(("r-knitr" ,r-knitr)))
2113 (home-page "https://github.com/tidyverse/glue")
2114 (synopsis "Interpreted string literals")
2116 "This package provides an implementation of interpreted string literals,
2117 inspired by Python's Literal String Interpolation (PEP-0498) and
2118 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2119 (license license:expat)))
2121 (define-public r-pastecs
2127 (uri (cran-uri "pastecs" version))
2130 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2131 (build-system r-build-system)
2133 `(("r-boot" ,r-boot)))
2134 (home-page "http://www.sciviews.org/pastecs")
2135 (synopsis "Analysis of space-time ecological series")
2137 "This package provides functions for regulation, decomposition and analysis
2138 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2139 initiative to bring PASSTEC 2000 functionalities to R.")
2140 (license license:gpl2+)))
2142 (define-public r-partykit
2148 (uri (cran-uri "partykit" version))
2151 "1jg68rqhk2r0h2hk50xl99zp56b1nfdcam06kfvssqrkgkavkswf"))))
2152 (build-system r-build-system)
2154 `(("r-formula" ,r-formula)
2156 ("r-libcoin" ,r-libcoin)
2157 ("r-mvtnorm" ,r-mvtnorm)
2158 ("r-rpart" ,r-rpart)
2159 ("r-survival" ,r-survival)))
2160 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2161 (synopsis "Toolkit for recursive partytioning")
2163 "This package provides a toolkit with infrastructure for representing,
2164 summarizing, and visualizing tree-structured regression and classification
2166 (license license:gpl2+)))
2168 (define-public r-plogr
2175 (uri (cran-uri "plogr" version))
2178 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2179 (build-system r-build-system)
2180 (home-page "https://github.com/krlmlr/plogr")
2181 (synopsis "R bindings for the plog C++ logging library")
2183 "This package provides the header files for a stripped-down version of
2184 the plog header-only C++ logging library, and a method to log to R's standard
2186 (license license:expat)))
2188 (define-public r-pls
2195 (uri (cran-uri "pls" version))
2197 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2198 (build-system r-build-system)
2199 (home-page "https://mevik.net/work/software/pls.html")
2200 (synopsis "Partial Least Squares and Principal Component Regression")
2202 "The pls package implements multivariate regression methods: Partial Least
2203 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2204 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2207 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2208 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2209 @item multi-response models (or @dfn{PLS2})
2210 @item flexible cross-validation
2211 @item Jackknife variance estimates of regression coefficients
2212 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2213 (R)MSEP, R², and correlation loadings
2214 @item formula interface, modelled after @code{lm()}, with methods for predict,
2215 print, summary, plot, update, etc.
2216 @item extraction functions for coefficients, scores, and loadings
2217 @item MSEP, RMSEP, and R² estimates
2218 @item multiplicative scatter correction (@dfn{MSC})
2220 (license license:gpl2)))
2229 (uri (cran-uri "ps" version))
2231 (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl"))))
2232 (build-system r-build-system)
2233 (home-page "https://ps.r-lib.org")
2234 (synopsis "List, query, and manipulate system processes")
2236 "The ps package implements an API to list, query, and manipulate system
2237 processes. Most of its code is based on the @code{psutil} Python package.")
2238 (license license:bsd-3)))
2240 (define-public r-pkgbuild
2247 (uri (cran-uri "pkgbuild" version))
2249 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
2250 (build-system r-build-system)
2252 `(("r-callr" ,r-callr)
2254 ("r-crayon" ,r-crayon)
2256 ("r-prettyunits" ,r-prettyunits)
2258 ("r-rprojroot" ,r-rprojroot)
2259 ("r-withr" ,r-withr)))
2260 (home-page "https://github.com/r-pkgs/pkgbuild")
2261 (synopsis "Find tools needed to build R packages")
2263 "This package provides functions used to build R packages. It locates
2264 compilers needed to build R packages on various platforms and ensures the PATH
2265 is configured appropriately so R can use them.")
2266 (license license:gpl3)))
2268 (define-public r-pkgload
2275 (uri (cran-uri "pkgload" version))
2278 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2279 (build-system r-build-system)
2282 ("r-crayon" ,r-crayon)
2284 ("r-pkgbuild" ,r-pkgbuild)
2285 ("r-rlang" ,r-rlang)
2286 ("r-rprojroot" ,r-rprojroot)
2287 ("r-rstudioapi" ,r-rstudioapi)
2288 ("r-withr" ,r-withr)))
2289 (home-page "https://github.com/r-lib/pkgload")
2290 (synopsis "Simulate package installation and attach")
2292 "This package simulates the process of installing a package and then
2293 attaching it. This is a key part of the @code{devtools} package as it allows
2294 you to rapidly iterate while developing a package.")
2295 (license license:gpl3)))
2297 (define-public r-rcpp
2304 (uri (cran-uri "Rcpp" version))
2306 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2307 (build-system r-build-system)
2308 (home-page "http://www.rcpp.org")
2309 (synopsis "Seamless R and C++ integration")
2311 "The Rcpp package provides R functions as well as C++ classes which offer
2312 a seamless integration of R and C++. Many R data types and objects can be
2313 mapped back and forth to C++ equivalents which facilitates both writing of new
2314 code as well as easier integration of third-party libraries. Documentation
2315 about Rcpp is provided by several vignettes included in this package, via the
2316 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2317 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2318 @code{citation(\"Rcpp\")} for details on these last two.")
2319 (license license:gpl2+)))
2321 (define-public r-bindr
2328 (uri (cran-uri "bindr" version))
2331 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2332 (build-system r-build-system)
2333 (home-page "https://github.com/krlmlr/bindr")
2334 (synopsis "Parametrized active bindings")
2336 "This package provides a simple interface for creating active bindings
2337 where the bound function accepts additional arguments.")
2338 (license license:expat)))
2340 (define-public r-bindrcpp
2347 (uri (cran-uri "bindrcpp" version))
2350 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2351 (build-system r-build-system)
2353 `(("r-bindr" ,r-bindr)
2354 ("r-plogr" ,r-plogr)
2355 ("r-rcpp" ,r-rcpp)))
2356 (home-page "https://github.com/krlmlr/bindrcpp")
2357 (synopsis "Rcpp interface to active bindings")
2359 "This package provides an easy way to fill an environment with active
2360 bindings that call a C++ function.")
2361 (license license:expat)))
2363 (define-public r-bisquerna
2365 (name "r-bisquerna")
2369 (uri (cran-uri "BisqueRNA" version))
2372 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2373 (properties `((upstream-name . "BisqueRNA")))
2374 (build-system r-build-system)
2376 `(("r-biobase" ,r-biobase)
2377 ("r-limsolve" ,r-limsolve)))
2378 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2379 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2380 (description "This package provides tools to accurately estimate cell type
2381 abundances from heterogeneous bulk expression. A reference-based method
2382 utilizes single-cell information to generate a signature matrix and
2383 transformation of bulk expression for accurate regression based estimates.
2384 A marker-based method utilizes known cell-specific marker genes to measure
2385 relative abundances across samples.")
2386 (license license:gpl3)))
2388 (define-public r-auc
2395 (uri (cran-uri "AUC" version))
2398 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2399 (properties `((upstream-name . "AUC")))
2400 (build-system r-build-system)
2401 (home-page "https://cran.r-project.org/web/packages/AUC")
2402 (synopsis "Compute the area under the curve of selected measures")
2404 "This package includes functions to compute the area under the curve of
2405 selected measures: the area under the sensitivity curve (AUSEC), the area
2406 under the specificity curve (AUSPC), the area under the accuracy
2407 curve (AUACC), and the area under the receiver operating characteristic
2408 curve (AUROC). The curves can also be visualized. Support for partial areas
2410 (license license:gpl2+)))
2412 (define-public r-calibrate
2414 (name "r-calibrate")
2419 (uri (cran-uri "calibrate" version))
2421 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2422 (build-system r-build-system)
2424 `(("r-mass" ,r-mass)))
2425 (home-page "https://cran.r-project.org/web/packages/calibrate")
2426 (synopsis "Calibration of scatterplot and biplot axes")
2428 "This is a package for drawing calibrated scales with tick marks
2429 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2430 (license license:gpl2)))
2432 (define-public r-shape
2439 (uri (cran-uri "shape" version))
2442 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2443 (build-system r-build-system)
2444 (home-page "https://cran.r-project.org/web/packages/shape")
2445 (synopsis "Functions for plotting graphical shapes")
2447 "This package provides functions for plotting graphical shapes such as
2448 ellipses, circles, cylinders, arrows, ...")
2449 (license license:gpl3+)))
2451 (define-public r-globaloptions
2453 (name "r-globaloptions")
2458 (uri (cran-uri "GlobalOptions" version))
2460 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2461 (properties `((upstream-name . "GlobalOptions")))
2462 (build-system r-build-system)
2464 `(("r-knitr" ,r-knitr)))
2465 (home-page "https://github.com/jokergoo/GlobalOptions")
2466 (synopsis "Generate functions to get or set global options")
2468 "This package provides more controls on the option values such as
2469 validation and filtering on the values, making options invisible or private.")
2470 (license license:gpl2+)))
2472 (define-public r-circlize
2479 (uri (cran-uri "circlize" version))
2482 "1s84xl7kv3qc1261xxaq4aqh64gwywhacsf5nh6yf8djw0d1w42d"))))
2483 (build-system r-build-system)
2485 `(("r-colorspace" ,r-colorspace)
2486 ("r-globaloptions" ,r-globaloptions)
2487 ("r-shape" ,r-shape)))
2489 `(("r-knitr" ,r-knitr)))
2490 (home-page "https://github.com/jokergoo/circlize")
2491 (synopsis "Circular visualization")
2493 "Circular layout is an efficient way to visualise huge amounts of
2494 information. This package provides an implementation of circular layout
2495 generation in R as well as an enhancement of available software. Its
2496 flexibility is based on the usage of low-level graphics functions such that
2497 self-defined high-level graphics can be easily implemented by users for
2498 specific purposes. Together with the seamless connection between the powerful
2499 computational and visual environment in R, it gives users more convenience and
2500 freedom to design figures for better understanding complex patterns behind
2501 multi-dimensional data.")
2502 (license license:gpl2+)))
2504 (define-public r-powerlaw
2511 (uri (cran-uri "poweRlaw" version))
2513 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2514 (properties `((upstream-name . "poweRlaw")))
2515 (build-system r-build-system)
2517 `(("r-pracma" ,r-pracma)))
2519 `(("r-knitr" ,r-knitr)))
2520 (home-page "https://github.com/csgillespie/poweRlaw")
2521 (synopsis "Tools for the analysis of heavy tailed distributions")
2523 "This package provides an implementation of maximum likelihood estimators
2524 for a variety of heavy tailed distributions, including both the discrete and
2525 continuous power law distributions. Additionally, a goodness-of-fit based
2526 approach is used to estimate the lower cut-off for the scaling region.")
2527 ;; Any of these GPL versions.
2528 (license (list license:gpl2 license:gpl3))))
2530 (define-public r-compare
2537 (uri (cran-uri "compare" version))
2540 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2541 (build-system r-build-system)
2542 (home-page "https://cran.r-project.org/web/packages/compare")
2543 (synopsis "Comparing objects for differences")
2545 "This package provides functions to compare a model object to a
2546 comparison object. If the objects are not identical, the functions can be
2547 instructed to explore various modifications of the objects (e.g., sorting
2548 rows, dropping names) to see if the modified versions are identical.")
2549 (license license:gpl2+)))
2551 (define-public r-dendextend
2553 (name "r-dendextend")
2558 (uri (cran-uri "dendextend" version))
2561 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2562 (build-system r-build-system)
2564 `(("r-ggplot2" ,r-ggplot2)
2565 ("r-magrittr" ,r-magrittr)
2566 ("r-viridis" ,r-viridis)))
2568 `(("r-knitr" ,r-knitr)))
2569 (home-page "https://cran.r-project.org/web/packages/dendextend")
2570 (synopsis "Extending 'dendrogram' functionality in R")
2572 "This package offers a set of functions for extending @code{dendrogram}
2573 objects in R, letting you visualize and compare trees of hierarchical
2574 clusterings. You can adjust a tree's graphical parameters (the color, size,
2575 type, etc of its branches, nodes and labels) and visually and statistically
2576 compare different dendrograms to one another.")
2577 ;; Any of these versions
2578 (license (list license:gpl2 license:gpl3))))
2580 (define-public r-getoptlong
2582 (name "r-getoptlong")
2587 (uri (cran-uri "GetoptLong" version))
2590 "0l9pa9dx8pcg3j7jn4b9k98g7r5vdsvnmf6apnifzm57mc0vlkg6"))))
2591 (properties `((upstream-name . "GetoptLong")))
2592 (build-system r-build-system)
2596 `(("r-crayon" ,r-crayon)
2597 ("r-globaloptions" ,r-globaloptions)
2598 ("r-rjson" ,r-rjson)))
2600 `(("r-knitr" ,r-knitr)))
2601 (home-page "https://github.com/jokergoo/GetoptLong")
2602 (synopsis "Parsing command-line arguments and variable interpolation")
2604 "This is yet another command-line argument parser which wraps the
2605 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2606 use in R. It also provides a simple way for variable interpolation in R.")
2607 (license license:gpl2+)))
2609 (define-public r-fastmatch
2611 (name "r-fastmatch")
2616 (uri (cran-uri "fastmatch" version))
2619 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2620 (build-system r-build-system)
2621 (home-page "https://www.rforge.net/fastmatch")
2622 (synopsis "Fast match function")
2624 "This package provides a fast @code{match} replacement for cases that
2625 require repeated look-ups. It is slightly faster that R's built-in
2626 @code{match} function on first match against a table, but extremely fast on
2627 any subsequent lookup as it keeps the hash table in memory.")
2628 (license license:gpl2)))
2637 (uri (cran-uri "ff" version))
2640 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
2641 (build-system r-build-system)
2642 (propagated-inputs `(("r-bit" ,r-bit)))
2643 (home-page "http://ff.r-forge.r-project.org/")
2644 (synopsis "Memory-efficient storage of large data on disk and access functions")
2646 "This package provides data structures that are stored on disk but
2647 behave (almost) as if they were in RAM by transparently mapping only a section
2649 ;; error Architecture not supported.
2650 (supported-systems (delete "aarch64-linux" %supported-systems))
2651 (license license:gpl2)))
2653 (define-public r-ffbase
2660 (uri (cran-uri "ffbase" version))
2663 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2664 (build-system r-build-system)
2667 ("r-fastmatch" ,r-fastmatch)
2669 (home-page "https://github.com/edwindj/ffbase")
2670 (synopsis "Basic statistical functions for package 'ff'")
2672 "This package extends the out of memory vectors of @code{ff} with
2673 statistical functions and other utilities to ease their usage.")
2674 (license license:gpl3)))
2676 (define-public r-prettyunits
2678 (name "r-prettyunits")
2683 (uri (cran-uri "prettyunits" version))
2686 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2687 (build-system r-build-system)
2688 (home-page "https://github.com/gaborcsardi/prettyunits")
2689 (synopsis "Pretty, human readable formatting of quantities")
2691 "This package provides tools for pretty, human readable formatting of
2693 (license license:expat)))
2695 (define-public r-reshape
2702 (uri (cran-uri "reshape" version))
2705 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2706 (build-system r-build-system)
2708 `(("r-plyr" ,r-plyr)
2709 ("r-rcpp" ,r-rcpp)))
2710 (home-page "http://had.co.nz/reshape")
2711 (synopsis "Flexibly reshape data")
2713 "Flexibly restructure and aggregate data using just two functions:
2714 @code{melt} and @code{cast}. This package provides them.")
2715 (license license:expat)))
2717 (define-public r-restrserve
2719 (name "r-restrserve")
2724 (uri (cran-uri "RestRserve" version))
2726 (base32 "07mm65yxzpwlg6x3lsggj41v8nl4m6v9mszhqjpgj19v3yxvwgi0"))))
2727 (build-system r-build-system)
2729 `(("r-checkmate" ,r-checkmate)
2730 ("r-jsonlite" ,r-jsonlite)
2734 ("r-rserve" ,r-rserve)
2735 ("r-uuid" ,r-uuid)))
2737 `(("r-knitr" ,r-knitr)))
2738 (home-page "https://restrserve.org")
2739 (synopsis "R web API framework")
2741 "RestRserve is an R web API framework for building high-performance AND
2742 robust microservices and app backends. With Rserve backend on UNIX-like
2743 systems it is parallel by design. It will handle incoming requests in
2744 parallel - each request in a separate fork.")
2745 (license license:gpl2+)))
2747 (define-public r-progress
2754 (uri (cran-uri "progress" version))
2757 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2758 (build-system r-build-system)
2760 `(("r-crayon" ,r-crayon)
2762 ("r-prettyunits" ,r-prettyunits)
2764 (home-page "https://github.com/gaborcsardi/progress")
2765 (synopsis "Terminal progress bars")
2767 "This package provides configurable progress bars. They may include
2768 percentage, elapsed time, and/or the estimated completion time. They work in
2769 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2770 package also provides a C++ API, that works with or without Rcpp.")
2771 (license license:expat)))
2773 (define-public r-ggally
2780 (uri (cran-uri "GGally" version))
2783 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2784 (properties `((upstream-name . "GGally")))
2785 (build-system r-build-system)
2787 `(("libressl" ,libressl)))
2789 `(("r-ggplot2" ,r-ggplot2)
2790 ("r-gtable" ,r-gtable)
2791 ("r-lifecycle" ,r-lifecycle)
2793 ("r-progress" ,r-progress)
2794 ("r-rcolorbrewer" ,r-rcolorbrewer)
2795 ("r-reshape" ,r-reshape)
2796 ("r-rlang" ,r-rlang)
2797 ("r-scales" ,r-scales)))
2798 (home-page "https://ggobi.github.io/ggally")
2799 (synopsis "Extension to ggplot2")
2801 "The R package ggplot2 is a plotting system based on the grammar of
2802 graphics. GGally extends ggplot2 by adding several functions to reduce the
2803 complexity of combining geometric objects with transformed data. Some of
2804 these functions include a pairwise plot matrix, a two group pairwise plot
2805 matrix, a parallel coordinates plot, a survival plot, and several functions to
2807 (license license:gpl2+)))
2809 (define-public r-proxy
2816 (uri (cran-uri "proxy" version))
2819 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2820 (build-system r-build-system)
2821 (home-page "https://cran.r-project.org/web/packages/proxy")
2822 (synopsis "Distance and similarity measures")
2824 "This package provides an extensible framework for the efficient
2825 calculation of auto- and cross-proximities, along with implementations of the
2826 most popular ones.")
2827 (license license:gpl2)))
2836 (uri (cran-uri "sp" version))
2838 (base32 "0zzw1gfic5b311vrbkmmmaap3yllgd192af067l5ymm885jqm1zs"))))
2839 (build-system r-build-system)
2841 `(("r-lattice" ,r-lattice)))
2842 (home-page "https://cran.r-project.org/web/packages/sp")
2843 (synopsis "Classes and methods for spatial data")
2845 "This package provides classes and methods for spatial data; the classes
2846 document where the spatial location information resides, for 2D or 3D data.
2847 Utility functions are provided, e.g. for plotting data as maps, spatial
2848 selection, as well as methods for retrieving coordinates, for subsetting,
2849 print, summary, etc.")
2850 (license license:gpl2+)))
2852 (define-public r-laplacesdemon
2854 (name "r-laplacesdemon")
2859 (uri (cran-uri "LaplacesDemon" version))
2861 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
2862 (properties `((upstream-name . "LaplacesDemon")))
2863 (build-system r-build-system)
2864 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
2865 (synopsis "Complete environment for Bayesian inference")
2867 "This package provides a complete environment for Bayesian inference using
2868 a variety of different samplers.")
2869 (license license:expat)))
2871 (define-public r-rmtstat
2878 (uri (cran-uri "RMTstat" version))
2881 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2882 (properties `((upstream-name . "RMTstat")))
2883 (build-system r-build-system)
2884 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2885 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2887 "This package provides functions for working with the Tracy-Widom laws
2888 and other distributions related to the eigenvalues of large Wishart
2890 (license license:bsd-3)))
2892 (define-public r-rmpi
2898 (uri (cran-uri "Rmpi" version))
2901 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2902 (properties `((upstream-name . "Rmpi")))
2903 (build-system r-build-system)
2905 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2906 #:phases (modify-phases %standard-phases
2907 (add-before 'install 'mpi-setup
2910 `(("openmpi" ,openmpi)))
2912 `(("pkg-config" ,pkg-config)))
2913 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2914 (synopsis "R interface to message-passing interface (MPI)")
2916 "This package provides an interface (wrapper) to MPI APIs. It also
2917 provides an interactive R manager and worker environment.")
2918 (license license:gpl2+)))
2920 (define-public r-lmoments
2927 (uri (cran-uri "Lmoments" version))
2930 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2931 (properties `((upstream-name . "Lmoments")))
2932 (build-system r-build-system)
2934 `(("r-rcpp" ,r-rcpp)
2935 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2936 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2937 (synopsis "L-moments and quantile mixtures")
2939 "This package contains functions to estimate L-moments and trimmed
2940 L-moments from the data. It also contains functions to estimate the
2941 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2942 quantile mixture from L-moments and trimmed L-moments.")
2943 (license license:gpl2)))
2945 (define-public r-distillery
2947 (name "r-distillery")
2952 (uri (cran-uri "distillery" version))
2955 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
2956 (build-system r-build-system)
2957 (home-page "https://ral.ucar.edu/staff/ericg/")
2958 (synopsis "Functions for confidence intervals and object information")
2960 "This package provides some very simple method functions for confidence
2961 interval calculation and to distill pertinent information from a potentially
2962 complex object; primarily used in common with the packages extRemes and
2964 (license license:gpl2+)))
2966 (define-public r-etrunct
2972 (uri (cran-uri "etrunct" version))
2975 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
2976 (properties `((upstream-name . "etrunct")))
2977 (build-system r-build-system)
2978 (home-page "https://cran.r-project.org/web/packages/etrunct")
2979 (synopsis "Computes moments of univariate truncated T distribution")
2980 (description "This package computes moments of univariate truncated
2981 T distribution. There is only one exported function, @code{e_trunct},
2982 which should be seen for details.")
2983 (license license:expat)))
2985 (define-public r-extremes
2992 (uri (cran-uri "extRemes" version))
2995 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
2996 (properties `((upstream-name . "extRemes")))
2997 (build-system r-build-system)
2999 `(("r-distillery" ,r-distillery)
3000 ("r-lmoments" ,r-lmoments)))
3001 (home-page "https://www.assessment.ucar.edu/toolkit/")
3002 (synopsis "Extreme value analysis")
3004 "ExtRemes is a suite of functions for carrying out analyses on the
3005 extreme values of a process of interest; be they block maxima over long blocks
3006 or excesses over a high threshold.")
3007 (license license:gpl2+)))
3009 (define-public r-lmtest
3016 (uri (cran-uri "lmtest" version))
3019 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3020 (build-system r-build-system)
3022 `(("r-zoo" ,r-zoo)))
3024 `(("gfortran" ,gfortran)))
3025 (home-page "https://cran.r-project.org/web/packages/lmtest")
3026 (synopsis "Testing linear regression models")
3028 "This package provides a collection of tests, data sets, and examples for
3029 diagnostic checking in linear regression models. Furthermore, some generic
3030 tools for inference in parametric models are provided.")
3031 ;; Either version is okay
3032 (license (list license:gpl2 license:gpl3))))
3034 (define-public r-idr
3040 (uri (cran-uri "idr" version))
3043 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3044 (build-system r-build-system)
3045 (home-page "https://cran.r-project.org/web/packages/idr/")
3046 (synopsis "Irreproducible discovery rate")
3048 "This is a package for estimating the copula mixture model and plotting
3049 correspondence curves in \"Measuring reproducibility of high-throughput
3050 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3051 by Li, Brown, Huang, and Bickel")
3052 (license license:gpl2+)))
3054 (define-public r-inline
3060 (uri (cran-uri "inline" version))
3063 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3064 (build-system r-build-system)
3065 (home-page "https://cran.r-project.org/web/packages/inline")
3066 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3068 "This package provides functionality to dynamically define R functions
3069 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3070 @code{.Call} calling conventions.")
3071 ;; Any version of the LGPL.
3072 (license license:lgpl3+)))
3074 (define-public r-inum
3080 (uri (cran-uri "inum" version))
3083 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
3084 (build-system r-build-system)
3086 `(("r-libcoin" ,r-libcoin)))
3087 (home-page "https://cran.r-project.org/web/packages/inum/")
3088 (synopsis "Interval and enum-type representation of vectors")
3090 "This package provides an enum-type representation of vectors and
3091 representation of intervals, including a method of coercing variables
3093 (license license:gpl2)))
3094 (define-public r-invgamma
3100 (uri (cran-uri "invgamma" version))
3103 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3104 (properties `((upstream-name . "invgamma")))
3105 (build-system r-build-system)
3106 (home-page "https://github.com/dkahle/invgamma")
3107 (synopsis "Inverse gamma distribution")
3108 (description "This package provides a light weight implementation of the
3109 standard distribution functions for the inverse gamma distribution, wrapping
3110 those for the gamma distribution in the @code{stats} package.")
3111 (license license:gpl2)))
3113 (define-public r-bdsmatrix
3115 (name "r-bdsmatrix")
3120 (uri (cran-uri "bdsmatrix" version))
3123 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3124 (properties `((upstream-name . "bdsmatrix")))
3125 (build-system r-build-system)
3126 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3127 (synopsis "Routines for block diagonal symmetric matrices")
3129 "This package provides procedures to work with block diagonal symmetric
3130 matrices, a special case of sparse matrices.")
3131 (license license:lgpl2.0)))
3133 (define-public r-bbmle
3136 (version "1.0.23.1")
3140 (uri (cran-uri "bbmle" version))
3143 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3144 (build-system r-build-system)
3146 `(("r-bdsmatrix" ,r-bdsmatrix)
3147 ("r-lattice" ,r-lattice)
3149 ("r-matrix" ,r-matrix)
3150 ("r-mvtnorm" ,r-mvtnorm)
3151 ("r-numderiv" ,r-numderiv)))
3152 (home-page "https://cran.r-project.org/web/packages/bbmle")
3153 (synopsis "Tools for General Maximum Likelihood Estimation")
3155 "This package provides methods and functions for fitting maximum
3156 likelihood models in R. This package modifies and extends the @code{mle}
3157 classes in the @code{stats4} package.")
3158 ;; Any version of the GPL
3159 (license license:gpl2+)))
3161 (define-public r-emdbook
3168 (uri (cran-uri "emdbook" version))
3171 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3172 (build-system r-build-system)
3174 `(("r-bbmle" ,r-bbmle)
3176 ("r-lattice" ,r-lattice)
3178 ("r-plyr" ,r-plyr)))
3179 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3180 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3182 "This package provides auxiliary functions and data sets for \"Ecological
3183 Models and Data\", a book presenting maximum likelihood estimation and related
3184 topics for ecologists (ISBN 978-0-691-12522-0).")
3186 (license (list license:gpl2 license:gpl3))))
3188 (define-public r-lpsolve
3195 (uri (cran-uri "lpSolve" version))
3198 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3199 (properties `((upstream-name . "lpSolve")))
3200 (build-system r-build-system)
3201 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3202 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3204 "Lp_solve is software for solving linear, integer and mixed integer
3205 programs. This implementation supplies a \"wrapper\" function in C and some R
3206 functions that solve general linear/integer problems, assignment problems, and
3207 transportation problems.")
3208 (license license:lgpl2.0)))
3210 (define-public r-limsolve
3217 (uri (cran-uri "limSolve" version))
3220 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3221 (properties `((upstream-name . "limSolve")))
3222 (build-system r-build-system)
3224 `(("r-lpsolve" ,r-lpsolve)
3226 ("r-quadprog" ,r-quadprog)))
3227 (native-inputs `(("gfortran" ,gfortran)))
3228 (home-page "https://cran.r-project.org/web/packages/limSolve")
3229 (synopsis "Solving linear inverse models")
3231 "This package provides functions that:
3234 @item find the minimum/maximum of a linear or quadratic function,
3235 @item sample an underdetermined or overdetermined system,
3236 @item solve a linear system Ax=B for the unknown x.
3239 It includes banded and tridiagonal linear systems. The package calls Fortran
3240 functions from LINPACK.")
3242 (license (list license:gpl2+ license:gpl3+))))
3244 (define-public r-fitdistrplus
3246 (name "r-fitdistrplus")
3251 (uri (cran-uri "fitdistrplus" version))
3254 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3255 (build-system r-build-system)
3257 `(("r-mass" ,r-mass)
3258 ("r-survival" ,r-survival)))
3260 `(("r-knitr" ,r-knitr)))
3261 (home-page "http://riskassessment.r-forge.r-project.org")
3262 (synopsis "Fitting a parametric distribution from data")
3264 "This package extends the @code{fitdistr} function of the MASS package
3265 with several functions to help the fit of a parametric distribution to
3266 non-censored or censored data. Censored data may contain left-censored,
3267 right-censored and interval-censored values, with several lower and upper
3268 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3269 provides moment matching (MME), quantile matching (QME) and maximum
3270 goodness-of-fit estimation (MGE) methods (available only for non-censored
3271 data). Weighted versions of MLE, MME and QME are available.")
3272 (license license:gpl2+)))
3274 (define-public r-energy
3281 (uri (cran-uri "energy" version))
3284 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3285 (build-system r-build-system)
3287 `(("r-boot" ,r-boot)
3288 ("r-rcpp" ,r-rcpp)))
3289 (home-page "https://cran.r-project.org/web/packages/energy")
3290 (synopsis "Multivariate inference via the energy of data")
3292 "This package provides e-statistics (energy) tests and statistics for
3293 multivariate and univariate inference, including distance correlation,
3294 one-sample, two-sample, and multi-sample tests for comparing multivariate
3295 distributions, are implemented. Measuring and testing multivariate
3296 independence based on distance correlation, partial distance correlation,
3297 multivariate goodness-of-fit tests, clustering based on energy distance,
3298 testing for multivariate normality, distance components (disco) for
3299 non-parametric analysis of structured data, and other energy
3300 statistics/methods are implemented.")
3301 (license license:gpl2+)))
3303 (define-public r-suppdists
3305 (name "r-suppdists")
3310 (uri (cran-uri "SuppDists" version))
3313 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3314 (properties `((upstream-name . "SuppDists")))
3315 (build-system r-build-system)
3316 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3317 (synopsis "Supplementary distributions")
3319 "This package provides ten distributions supplementing those built into
3320 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3321 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3322 coefficient, Johnson distributions, normal scores and generalized
3323 hypergeometric distributions. In addition two random number generators of
3324 George Marsaglia are included.")
3325 (license license:gpl2+)))
3327 (define-public r-ksamples
3334 (uri (cran-uri "kSamples" version))
3337 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3338 (properties `((upstream-name . "kSamples")))
3339 (build-system r-build-system)
3341 `(("r-suppdists" ,r-suppdists)))
3342 (home-page "https://cran.r-project.org/web/packages/kSamples")
3343 (synopsis "K-Sample rank tests and their combinations")
3345 "This package provides tools to compares k samples using the
3346 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3347 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3348 test. It computes asymptotic, simulated or (limited) exact P-values, all
3349 valid under randomization, with or without ties, or conditionally under random
3350 sampling from populations, given the observed tie pattern. Except for Steel's
3351 test and the JT test it also combines these tests across several blocks of
3353 (license license:gpl2+)))
3355 (define-public r-cvst
3362 (uri (cran-uri "CVST" version))
3365 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3366 (properties `((upstream-name . "CVST")))
3367 (build-system r-build-system)
3369 `(("r-kernlab" ,r-kernlab)
3370 ("r-matrix" ,r-matrix)))
3371 (home-page "https://cran.r-project.org/web/packages/CVST")
3372 (synopsis "Fast cross-validation via sequential testing")
3374 "This package implements the fast cross-validation via sequential
3375 testing (CVST) procedure. CVST is an improved cross-validation procedure
3376 which uses non-parametric testing coupled with sequential analysis to
3377 determine the best parameter set on linearly increasing subsets of the data.
3378 Additionally to the CVST the package contains an implementation of the
3379 ordinary k-fold cross-validation with a flexible and powerful set of helper
3380 objects and methods to handle the overall model selection process. The
3381 implementations of the Cochran's Q test with permutations and the sequential
3382 testing framework of Wald are generic and can therefore also be used in other
3384 (license license:gpl2+)))
3386 (define-public r-squarem
3393 (uri (cran-uri "SQUAREM" version))
3396 "1f0j5pbsz2wi7dfl8h8gvdl991bjywiwkd2f6z0xgkh87kl5y0b4"))))
3397 (properties `((upstream-name . "SQUAREM")))
3398 (build-system r-build-system)
3399 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3400 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3402 "This package provides algorithms for accelerating the convergence of
3403 slow, monotone sequences from smooth, contraction mapping such as the EM
3404 algorithm. It can be used to accelerate any smooth, linearly convergent
3405 acceleration scheme. A tutorial style introduction to this package is
3406 available in a vignette.")
3407 (license license:gpl2+)))
3409 (define-public r-lava
3416 (uri (cran-uri "lava" version))
3419 "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d"))))
3420 (build-system r-build-system)
3422 `(("r-numderiv" ,r-numderiv)
3423 ("r-squarem" ,r-squarem)
3424 ("r-survival" ,r-survival)))
3426 `(("r-knitr" ,r-knitr)))
3427 (home-page "https://github.com/kkholst/lava")
3428 (synopsis "Latent variable models")
3430 "This package provides tools for the estimation and simulation of latent
3432 (license license:gpl3)))
3434 (define-public r-drr
3441 (uri (cran-uri "DRR" version))
3444 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3445 (properties `((upstream-name . "DRR")))
3446 (build-system r-build-system)
3448 `(("r-cvst" ,r-cvst)
3449 ("r-kernlab" ,r-kernlab)
3450 ("r-matrix" ,r-matrix)))
3451 (home-page "https://cran.r-project.org/web/packages/DRR")
3452 (synopsis "Dimensionality reduction via regression")
3454 "This package provides an implementation of dimensionality reduction via
3455 regression using Kernel Ridge Regression.")
3456 (license license:gpl3)))
3458 (define-public r-prodlim
3461 (version "2019.11.13")
3465 (uri (cran-uri "prodlim" version))
3468 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3469 (build-system r-build-system)
3471 `(("r-kernsmooth" ,r-kernsmooth)
3474 ("r-survival" ,r-survival)))
3475 (home-page "https://cran.r-project.org/web/packages/prodlim")
3476 (synopsis "Product-limit estimation for censored event history analysis")
3478 "This package provides a fast and user-friendly implementation of
3479 nonparametric estimators for censored event history (survival) analysis with
3480 the Kaplan-Meier and Aalen-Johansen methods.")
3481 (license license:gpl2+)))
3483 (define-public r-dimred
3490 (uri (cran-uri "dimRed" version))
3493 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3494 (properties `((upstream-name . "dimRed")))
3495 (build-system r-build-system)
3498 ("r-magrittr" ,r-magrittr)))
3499 (home-page "https://github.com/gdkrmr/dimRed")
3500 (synopsis "Framework for dimensionality reduction")
3502 "This package provides a collection of dimensionality reduction
3503 techniques from R packages and provides a common interface for calling the
3505 (license license:gpl3)))
3507 (define-public r-timedate
3510 (version "3043.102")
3514 (uri (cran-uri "timeDate" version))
3517 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3518 (properties `((upstream-name . "timeDate")))
3519 (build-system r-build-system)
3520 (home-page "https://www.rmetrics.org")
3521 (synopsis "Chronological and calendar objects")
3523 "This package provides an environment for teaching \"Financial
3524 Engineering and Computational Finance\" and for managing chronological and
3526 (license license:gpl2+)))
3528 (define-public r-magic
3535 (uri (cran-uri "magic" version))
3538 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3539 (build-system r-build-system)
3541 `(("r-abind" ,r-abind)))
3542 (home-page "https://github.com/RobinHankin/magic.git")
3543 (synopsis "Create and investigate magic squares")
3545 "This package provides a collection of efficient, vectorized algorithms
3546 for the creation and investigation of magic squares and hypercubes, including
3547 a variety of functions for the manipulation and analysis of arbitrarily
3548 dimensioned arrays.")
3549 (license license:gpl2)))
3551 (define-public r-rmysql
3558 (uri (cran-uri "RMySQL" version))
3561 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3562 (properties `((upstream-name . "RMySQL")))
3563 (build-system r-build-system)
3565 `(("mariadb-dev" ,mariadb "dev")
3568 `(("r-dbi" ,r-dbi)))
3569 (home-page "https://github.com/r-dbi/RMySQL")
3570 (synopsis "Database interface and MySQL driver for R")
3572 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3573 package contains an old implementation based on legacy code from S-PLUS which
3574 is being phased out. A modern MySQL client based on Rcpp is available from
3575 the RMariaDB package.")
3576 (license license:gpl2)))
3578 (define-public r-rpostgresql
3580 (name "r-rpostgresql")
3585 (uri (cran-uri "RPostgreSQL" version))
3588 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3589 (properties `((upstream-name . "RPostgreSQL")))
3590 (build-system r-build-system)
3592 `(("postgresql" ,postgresql)))
3594 `(("r-dbi" ,r-dbi)))
3595 (home-page "https://github.com/tomoakin/RPostgreSQL")
3596 (synopsis "R interface to the PostgreSQL database system")
3598 "This package provides a Database Interface (DBI) compliant driver for R
3599 to access PostgreSQL database systems.")
3600 ;; The whole package is released under GPL version 2. It includes code
3601 ;; under the PostgreSQL license.
3602 (license license:gpl2)))
3604 (define-public r-linprog
3611 (uri (cran-uri "linprog" version))
3614 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3615 (build-system r-build-system)
3616 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3617 (home-page "http://linprog.r-forge.r-project.org/")
3618 (synopsis "Linear programming and optimization")
3620 "This package can be used to solve Linear Programming / Linear
3621 Optimization problems by using the simplex algorithm.")
3622 (license license:gpl2+)))
3624 (define-public r-geometry
3631 (uri (cran-uri "geometry" version))
3634 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3635 (build-system r-build-system)
3637 `(("r-magic" ,r-magic)
3638 ("r-linprog" ,r-linprog)
3639 ("r-lpsolve" ,r-lpsolve)
3641 ("r-rcppprogress" ,r-rcppprogress)))
3642 (home-page "http://geometry.r-forge.r-project.org/")
3643 (synopsis "Mesh generator and surface tessellator")
3645 "This package makes the qhull library available in R, in a similar manner
3646 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3647 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3648 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3649 and higher dimensions. It implements the Quickhull algorithm for computing
3650 the convex hull. Qhull does not support constrained Delaunay triangulations,
3651 or mesh generation of non-convex objects, but the package does include some R
3652 functions that allow for this. Currently the package only gives access to
3653 Delaunay triangulation and convex hull computation.")
3654 ;; The Qhull sources are included and are distributed under a custom
3655 ;; non-copyleft license. The R sources are released under GPL version 2.
3656 (license (list license:gpl2
3657 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3659 (define-public r-ddalpha
3666 (uri (cran-uri "ddalpha" version))
3669 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3670 (build-system r-build-system)
3673 ("r-class" ,r-class)
3674 ("r-geometry" ,r-geometry)
3677 ("r-robustbase" ,r-robustbase)
3678 ("r-sfsmisc" ,r-sfsmisc)))
3680 `(("gfortran" ,gfortran)))
3681 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3682 (synopsis "Depth-Based classification and calculation of data depth")
3684 "This package contains procedures for depth-based supervised learning,
3685 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3686 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3687 statistical depth function to a compact low-dimensional space, where the final
3688 classification is done. It also offers an extension to functional data and
3689 routines for calculating certain notions of statistical depth functions. 50
3690 multivariate and 5 functional classification problems are included.")
3691 (license license:gpl2)))
3693 (define-public r-gower
3700 (uri (cran-uri "gower" version))
3703 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3704 (build-system r-build-system)
3705 (home-page "https://github.com/markvanderloo/gower")
3706 (synopsis "Gower's distance")
3708 "This package provides tools to compute Gower's distance (or similarity)
3709 coefficient between records, and to compute the top-n matches between records.
3710 Core algorithms are executed in parallel on systems supporting OpenMP.")
3711 (license license:gpl3)))
3713 (define-public r-rcpproll
3720 (uri (cran-uri "RcppRoll" version))
3723 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3724 (properties `((upstream-name . "RcppRoll")))
3725 (build-system r-build-system)
3727 `(("r-rcpp" ,r-rcpp)))
3728 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3729 (synopsis "Efficient rolling and windowed operations")
3731 "This package provides fast and efficient routines for common rolling /
3732 windowed operations. Routines for the efficient computation of windowed mean,
3733 median, sum, product, minimum, maximum, standard deviation and variance are
3735 (license license:gpl2+)))
3737 (define-public r-ipred
3744 (uri (cran-uri "ipred" version))
3747 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3748 (build-system r-build-system)
3750 `(("r-class" ,r-class)
3753 ("r-prodlim" ,r-prodlim)
3754 ("r-rpart" ,r-rpart)
3755 ("r-survival" ,r-survival)))
3756 (home-page "https://cran.r-project.org/web/packages/ipred")
3757 (synopsis "Improved predictors")
3759 "This package provides improved predictive models by indirect
3760 classification and bagging for classification, regression and survival
3761 problems as well as resampling based estimators of prediction error.")
3762 (license license:gpl2+)))
3764 (define-public r-psych
3771 (uri (cran-uri "psych" version))
3774 "0wdh580a0psbdil28n0d85hnp42wmn11hcbnihjq8r7h54drgzpn"))))
3775 (build-system r-build-system)
3777 `(("r-lattice" ,r-lattice)
3778 ("r-mnormt" ,r-mnormt)
3779 ("r-nlme" ,r-nlme)))
3780 (home-page "https://cran.r-project.org/web/packages/psych/")
3781 (synopsis "Procedures for psychological, psychometric, and personality research")
3783 "This package provides a general purpose toolbox for personality,
3784 psychometric theory and experimental psychology. Functions are primarily for
3785 multivariate analysis and scale construction using factor analysis, principal
3786 component analysis, cluster analysis and reliability analysis, although others
3787 provide basic descriptive statistics. Item Response Theory is done using
3788 factor analysis of tetrachoric and polychoric correlations. Functions for
3789 analyzing data at multiple levels include within and between group statistics,
3790 including correlations and factor analysis. Functions for simulating and
3791 testing particular item and test structures are included. Several functions
3792 serve as a useful front end for structural equation modeling. Graphical
3793 displays of path diagrams, factor analysis and structural equation models are
3794 created using basic graphics.")
3795 (license license:gpl2+)))
3797 (define-public r-generics
3804 (uri (cran-uri "generics" version))
3807 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
3808 (build-system r-build-system)
3809 (home-page "https://github.com/r-lib/generics")
3810 (synopsis "Common S3 generics not provided by base R methods")
3812 "In order to reduce potential package dependencies and conflicts,
3813 generics provides a number of commonly used S3 generics that are not provided
3814 by base R methods related to model fitting.")
3815 (license license:gpl2)))
3817 (define-public r-broom
3824 (uri (cran-uri "broom" version))
3827 "18qkgw5f46cfr8sc7r9a261ivn3s4w88sdj653gaa20723179300"))))
3828 (build-system r-build-system)
3830 `(("r-backports" ,r-backports)
3831 ("r-dplyr" ,r-dplyr)
3832 ("r-ellipsis" ,r-ellipsis)
3833 ("r-generics" ,r-generics)
3835 ("r-purrr" ,r-purrr)
3836 ("r-rlang" ,r-rlang)
3837 ("r-stringr" ,r-stringr)
3838 ("r-tibble" ,r-tibble)
3839 ("r-tidyr" ,r-tidyr)))
3841 `(("r-knitr" ,r-knitr)))
3842 (home-page "https://github.com/tidyverse/broom")
3843 (synopsis "Convert statistical analysis objects into tidy data frames")
3845 "This package provides tools to convert statistical analysis objects from
3846 R into tidy data frames, so that they can more easily be combined, reshaped
3847 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3848 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3849 summarizes a model's statistical findings such as coefficients of a
3850 regression; @code{augment}, which adds columns to the original data such as
3851 predictions, residuals and cluster assignments; and @code{glance}, which
3852 provides a one-row summary of model-level statistics.")
3853 (license license:expat)))
3855 (define-public r-recipes
3862 (uri (cran-uri "recipes" version))
3865 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
3866 (build-system r-build-system)
3868 `(("r-dplyr" ,r-dplyr)
3869 ("r-generics" ,r-generics)
3871 ("r-gower" ,r-gower)
3872 ("r-ipred" ,r-ipred)
3873 ("r-lifecycle" ,r-lifecycle)
3874 ("r-lubridate" ,r-lubridate)
3875 ("r-magrittr" ,r-magrittr)
3876 ("r-matrix" ,r-matrix)
3877 ("r-purrr" ,r-purrr)
3878 ("r-rlang" ,r-rlang)
3879 ("r-tibble" ,r-tibble)
3880 ("r-tidyr" ,r-tidyr)
3881 ("r-tidyselect" ,r-tidyselect)
3882 ("r-timedate" ,r-timedate)
3883 ("r-withr" ,r-withr)))
3885 `(("r-knitr" ,r-knitr)))
3886 (home-page "https://github.com/topepo/recipes")
3887 (synopsis "Preprocessing tools to create design matrices")
3889 "Recipes is an extensible framework to create and preprocess design
3890 matrices. Recipes consist of one or more data manipulation and analysis
3891 \"steps\". Statistical parameters for the steps can be estimated from an
3892 initial data set and then applied to other data sets. The resulting design
3893 matrices can then be used as inputs into statistical or machine learning
3895 (license license:gpl2)))
3897 (define-public r-pdist
3904 (uri (cran-uri "pdist" version))
3907 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3908 (build-system r-build-system)
3909 (home-page "https://github.com/jeffwong/pdist")
3910 (synopsis "Partitioned distance function")
3912 "Pdist computes the euclidean distance between rows of a matrix X and
3913 rows of another matrix Y. Previously, this could be done by binding the two
3914 matrices together and calling @code{dist}, but this creates unnecessary
3915 computation by computing the distances between a row of X and another row of
3916 X, and likewise for Y. Pdist strictly computes distances across the two
3917 matrices, not within the same matrix, making computations significantly faster
3918 for certain use cases.")
3919 (license license:gpl3+)))
3921 (define-public r-ggrepel
3928 (uri (cran-uri "ggrepel" version))
3931 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3932 (build-system r-build-system)
3934 `(("r-ggplot2" ,r-ggplot2)
3936 ("r-scales" ,r-scales)))
3938 `(("r-knitr" ,r-knitr))) ; for vignettes
3939 (home-page "https://github.com/slowkow/ggrepel")
3940 (synopsis "Repulsive text and label geometries for ggplot2")
3942 "This package provides text and label geometries for ggplot2 that help to
3943 avoid overlapping text labels. Labels repel away from each other and away
3944 from the data points.")
3945 (license license:gpl3)))
3947 (define-public r-corrplot
3954 (uri (cran-uri "corrplot" version))
3957 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3958 (build-system r-build-system)
3959 (home-page "https://github.com/taiyun/corrplot")
3960 (synopsis "Visualization of a correlation matrix")
3962 "This package provides a graphical display of a correlation matrix or
3963 general matrix. It also contains some algorithms to do matrix reordering. In
3964 addition, corrplot is good at details, including choosing color, text labels,
3965 color labels, layout, etc.")
3966 ;; Any version of the GPL
3967 (license license:gpl2+)))
3969 (define-public r-stringdist
3971 (name "r-stringdist")
3976 (uri (cran-uri "stringdist" version))
3978 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
3979 (build-system r-build-system)
3980 (home-page "https://github.com/markvanderloo/stringdist")
3981 (synopsis "Approximate string matching and string distance functions")
3983 "This package implements an approximate string matching version of R's
3984 native @code{match} function. It can calculate various string distances based
3985 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
3986 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3987 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3988 can be computed between character vectors while taking proper care of encoding
3989 or between integer vectors representing generic sequences.")
3990 (license license:gpl3+)))
3992 (define-public r-ucminf
3999 (uri (cran-uri "ucminf" version))
4002 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4003 (build-system r-build-system)
4004 (native-inputs `(("gfortran" ,gfortran)))
4005 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4006 (synopsis "General-purpose unconstrained non-linear optimization")
4008 "This package provides an implementation of an algorithm for
4009 general-purpose unconstrained non-linear optimization. The algorithm is of
4010 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4011 search with a trust region type monitoring of the input to the line search
4012 algorithm. The interface of @code{ucminf} is designed for easy interchange
4013 with the package @code{optim}.")
4014 (license license:gpl2+)))
4016 (define-public r-useful
4022 (uri (cran-uri "useful" version))
4025 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4026 (properties `((upstream-name . "useful")))
4027 (build-system r-build-system)
4029 `(("r-assertthat" ,r-assertthat)
4030 ("r-dplyr" ,r-dplyr)
4031 ("r-ggplot2" ,r-ggplot2)
4032 ("r-magrittr" ,r-magrittr)
4033 ("r-matrix" ,r-matrix)
4035 ("r-purrr" ,r-purrr)
4036 ("r-scales" ,r-scales)))
4037 (home-page "https://github.com/jaredlander/useful")
4038 (synopsis "Collection of handy, useful functions")
4039 (description "This package provides a set of little functions that have been
4040 found useful to do little odds and ends such as plotting the results of K-means
4041 clustering, substituting special text characters, viewing parts of a
4042 @code{data.frame}, constructing formulas from text and building design and
4043 response matrices.")
4044 (license license:bsd-3)))
4046 (define-public r-ordinal
4049 (version "2019.12-10")
4053 (uri (cran-uri "ordinal" version))
4056 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4057 (build-system r-build-system)
4059 `(("r-mass" ,r-mass)
4060 ("r-matrix" ,r-matrix)
4061 ("r-numderiv" ,r-numderiv)
4062 ("r-ucminf" ,r-ucminf)))
4063 (home-page "https://github.com/runehaubo/ordinal")
4064 (synopsis "Regression models for ordinal data")
4066 "This package provides an implementation of cumulative link (mixed)
4067 models also known as ordered regression models, proportional odds models,
4068 proportional hazards models for grouped survival times and ordered models.
4069 Estimation is via maximum likelihood and mixed models are fitted with the
4070 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4071 (license license:gpl2+)))
4073 (define-public r-jomo
4080 (uri (cran-uri "jomo" version))
4083 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4084 (build-system r-build-system)
4086 `(("r-lme4" ,r-lme4)
4088 ("r-ordinal" ,r-ordinal)
4089 ("r-survival" ,r-survival)))
4090 (home-page "https://cran.r-project.org/web/packages/jomo/")
4091 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4093 "Similarly to Schafer's package pan, jomo is a package for multilevel
4094 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4095 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4096 possibility of handling binary and categorical data through latent normal
4097 variables, the option to use cluster-specific covariance matrices and to
4098 impute compatibly with the substantive model.")
4099 (license license:gpl2)))
4101 (define-public r-pan
4108 (uri (cran-uri "pan" version))
4111 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4112 (build-system r-build-system)
4113 (native-inputs `(("gfortran" ,gfortran)))
4114 (home-page "https://cran.r-project.org/web/packages/pan/")
4115 (synopsis "Multiple imputation for multivariate panel or clustered data")
4117 "This package implements multiple imputation for multivariate panel or
4119 (license license:gpl3)))
4121 (define-public r-mitml
4128 (uri (cran-uri "mitml" version))
4131 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
4132 (build-system r-build-system)
4134 `(("r-haven" ,r-haven)
4137 (home-page "https://cran.r-project.org/web/packages/mitml/")
4138 (synopsis "Tools for multiple imputation in multilevel modeling")
4140 "This package provides tools for multiple imputation of missing data in
4141 multilevel modeling. It includes a user-friendly interface to the packages
4142 pan and jomo, and several functions for visualization, data management and the
4143 analysis of multiply imputed data sets.")
4144 (license license:gpl2+)))
4146 (define-public r-mice
4153 (uri (cran-uri "mice" version))
4156 "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap"))))
4157 (build-system r-build-system)
4159 `(("r-broom" ,r-broom)
4160 ("r-cpp11" ,r-cpp11)
4161 ("r-dplyr" ,r-dplyr)
4162 ("r-generics" ,r-generics)
4163 ("r-lattice" ,r-lattice)
4165 ("r-rlang" ,r-rlang)
4166 ("r-tidyr" ,r-tidyr)))
4167 (home-page "https://cran.r-project.org/web/packages/mice/")
4168 (synopsis "Multivariate imputation by chained equations")
4170 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4171 implemented by the MICE algorithm as described in @url{Van Buuren and
4172 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4173 variable has its own imputation model. Built-in imputation models are
4174 provided for continuous data (predictive mean matching, normal), binary
4175 data (logistic regression), unordered categorical data (polytomous logistic
4176 regression) and ordered categorical data (proportional odds). MICE can also
4177 impute continuous two-level data (normal model, pan, second-level variables).
4178 Passive imputation can be used to maintain consistency between variables.
4179 Various diagnostic plots are available to inspect the quality of the
4181 ;; Any of these two versions.
4182 (license (list license:gpl2 license:gpl3))))
4184 (define-public r-truncnorm
4186 (name "r-truncnorm")
4191 (uri (cran-uri "truncnorm" version))
4194 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4195 (build-system r-build-system)
4196 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4197 (synopsis "Truncated normal distribution")
4198 (description "This package provides functions for the truncated normal
4199 distribution with mean equal to @code{mean} and standard deviation equal to
4200 @code{sd}. It includes density, distribution, quantile, and expected value
4201 functions, as well as a random generation function.")
4202 (license license:gpl2)))
4204 (define-public r-rsolnp
4211 (uri (cran-uri "Rsolnp" version))
4214 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4215 (properties `((upstream-name . "Rsolnp")))
4216 (build-system r-build-system)
4218 `(("r-truncnorm" ,r-truncnorm)))
4219 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4220 (synopsis "General non-linear optimization")
4221 (description "The Rsolnp package implements a general non-linear augmented
4222 Lagrange multiplier method solver, a @dfn{sequential quadratic
4223 programming} (SQP) based solver).")
4224 ;; Any version of the GPL.
4225 (license license:gpl2+)))
4227 (define-public r-hardyweinberg
4229 (name "r-hardyweinberg")
4234 (uri (cran-uri "HardyWeinberg" version))
4237 "0l93r1hkr483hp4yd7rm7mdkgl5lp0nkvv0inahj3r1cplgfxpvs"))))
4238 (properties `((upstream-name . "HardyWeinberg")))
4239 (build-system r-build-system)
4241 `(("r-mice" ,r-mice)
4243 ("r-rsolnp" ,r-rsolnp)))
4244 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4245 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4247 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4248 diallelic genetic marker data. All classical tests (chi-square, exact,
4249 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4250 included in the package, as well as functions for power computation and for
4251 the simulation of marker data under equilibrium and disequilibrium. Routines
4252 for dealing with markers on the X-chromosome are included. Functions for
4253 testing equilibrium in the presence of missing data by using multiple
4254 imputation are also provided. Implements several graphics for exploring the
4255 equilibrium status of a large set of diallelic markers: ternary plots with
4256 acceptance regions, log-ratio plots and Q-Q plots.")
4257 (license license:gpl2+)))
4266 (uri (cran-uri "sm" version))
4269 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4270 (build-system r-build-system)
4271 (native-inputs `(("gfortran" ,gfortran)))
4272 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4273 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4275 "This is software accompanying the book 'Applied Smoothing Techniques for
4276 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4277 University Press. It provides smoothing methods for nonparametric regression
4278 and density estimation")
4279 (license license:gpl2+)))
4281 (define-public r-venndiagram
4283 (name "r-venndiagram")
4287 (uri (cran-uri "VennDiagram" version))
4290 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4291 (properties `((upstream-name . "VennDiagram")))
4292 (build-system r-build-system)
4294 `(("r-futile-logger" ,r-futile-logger)))
4295 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4296 (synopsis "Generate High-Resolution Venn and Euler Plots")
4298 "This package provides a set of functions to generate high-resolution
4299 Venn and Euler plots. It includes handling for several special cases,
4300 including two-case scaling, and extensive customization of plot shape and
4302 (license license:gpl2+)))
4304 (define-public r-vioplot
4311 (uri (cran-uri "vioplot" version))
4314 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4315 (build-system r-build-system)
4320 `(("r-knitr" ,r-knitr)))
4321 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4322 (synopsis "Violin plot")
4324 "This package provides a violin plot, which is a combination of a box
4325 plot and a kernel density plot.")
4326 (license license:bsd-3)))
4328 (define-public r-rsofia
4334 ;; This package has been removed from CRAN, so we can
4335 ;; only fetch it from the archives.
4336 (uri (string-append "https://cran.r-project.org/src/"
4337 "contrib/Archive/RSofia/RSofia_"
4341 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4342 (properties `((upstream-name . "RSofia")))
4343 (build-system r-build-system)
4345 `(("r-rcpp" ,r-rcpp)))
4346 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4347 (synopsis "Port of sofia-ml to R")
4348 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4349 suite of fast incremental algorithms for machine learning that can be used for
4350 training models for classification or ranking.")
4351 (license license:asl2.0)))
4353 (define-public r-xts
4360 (uri (cran-uri "xts" version))
4363 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4364 (build-system r-build-system)
4365 (propagated-inputs `(("r-zoo" ,r-zoo)))
4366 (home-page "https://github.com/joshuaulrich/xts")
4367 (synopsis "Extensible time series")
4369 "This package provides for uniform handling of R's different time-based
4370 data classes by extending @code{zoo}, maximizing native format information
4371 preservation and allowing for user-level customization and extension, while
4372 simplifying cross-class interoperability.")
4373 (license license:gpl2+)))
4375 (define-public r-performanceanalytics
4377 (name "r-performanceanalytics")
4382 (uri (cran-uri "PerformanceAnalytics" version))
4385 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4387 `((upstream-name . "PerformanceAnalytics")))
4388 (build-system r-build-system)
4390 `(("r-quadprog" ,r-quadprog)
4393 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4394 (synopsis "Econometric tools for performance and risk analysis")
4395 (description "This is a collection of econometric functions for
4396 performance and risk analysis. This package aims to aid practitioners and
4397 researchers in utilizing the latest research in analysis of non-normal return
4398 streams. In general, it is most tested on return (rather than price) data on
4399 a regular scale, but most functions will work with irregular return data as
4400 well, and increasing numbers of functions will work with P&L or price data
4402 ;; Either version may be picked.
4403 (license (list license:gpl2 license:gpl3))))
4405 (define-public r-laeken
4412 (uri (cran-uri "laeken" version))
4415 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4416 (build-system r-build-system)
4418 `(("r-boot" ,r-boot)
4419 ("r-mass" ,r-mass)))
4420 (home-page "https://cran.r-project.org/web/packages/laeken/")
4421 (synopsis "Estimation of indicators on social exclusion and poverty")
4422 (description "This package provides tools for the estimation of indicators
4423 on social exclusion and poverty, as well as an implementation of Pareto tail
4424 modeling for empirical income distributions.")
4425 (license license:gpl2+)))
4427 (define-public r-vcd
4434 (uri (cran-uri "vcd" version))
4437 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4438 (build-system r-build-system)
4440 `(("r-colorspace" ,r-colorspace)
4441 ("r-lmtest" ,r-lmtest)
4442 ("r-mass" ,r-mass)))
4443 (home-page "https://cran.r-project.org/web/packages/vcd/")
4444 (synopsis "Visualizing categorical data")
4445 (description "This package provides visualization techniques, data sets,
4446 summary and inference procedures aimed particularly at categorical data.
4447 Special emphasis is given to highly extensible grid graphics. The package was
4448 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4449 Friendly and is now the main support package for a new book, \"Discrete Data
4450 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4451 (license license:gpl2)))
4453 (define-public r-ica
4460 (uri (cran-uri "ica" version))
4463 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4464 (build-system r-build-system)
4465 (home-page "https://cran.r-project.org/web/packages/ica/")
4466 (synopsis "Independent component analysis")
4467 (description "This package provides tools for @dfn{Independent Component
4468 Analysis} (ICA) using various algorithms: FastICA,
4469 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4470 of Eigenmatrices} (JADE).")
4471 (license license:gpl2+)))
4473 (define-public r-dtw
4480 (uri (cran-uri "dtw" version))
4483 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4484 (build-system r-build-system)
4485 (propagated-inputs `(("r-proxy" ,r-proxy)))
4486 (home-page "http://dtw.r-forge.r-project.org/")
4487 (synopsis "Dynamic Time Warping Algorithms")
4488 (description "This package provides a comprehensive implementation of
4489 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4490 optimal (least cumulative distance) alignment between points of two time
4491 series. Common DTW variants covered include local (slope) and global (window)
4492 constraints, subsequence matches, arbitrary distance definitions,
4493 normalizations, minimum variance matching, and so on.")
4494 (license license:gpl2+)))
4496 (define-public r-sdmtools
4499 (version "1.1-221.2")
4503 (uri (cran-uri "SDMTools" version))
4506 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4507 (properties `((upstream-name . "SDMTools")))
4508 (build-system r-build-system)
4509 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4510 (home-page "https://www.rforge.net/SDMTools/")
4511 (synopsis "Species distribution modelling tools")
4512 (description "This package provides a set of tools for post processing
4513 the outcomes of species distribution modeling exercises. It includes novel
4514 methods for comparing models and tracking changes in distributions through
4515 time. It further includes methods for visualizing outcomes, selecting
4516 thresholds, calculating measures of accuracy and landscape fragmentation
4518 (license license:gpl3+)))
4520 (define-public r-scatterplot3d
4522 (name "r-scatterplot3d")
4527 (uri (cran-uri "scatterplot3d" version))
4530 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4531 (build-system r-build-system)
4532 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4533 (synopsis "3D scatter plot")
4534 (description "This package provides an implementation of scatter plots for
4535 plotting. a three dimensional point cloud.")
4536 (license license:gpl2)))
4538 (define-public r-ggridges
4545 (uri (cran-uri "ggridges" version))
4548 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4549 (build-system r-build-system)
4551 `(("r-ggplot2" ,r-ggplot2)
4553 ("r-scales" ,r-scales)
4554 ("r-withr" ,r-withr)))
4555 (home-page "https://github.com/clauswilke/ggridges")
4556 (synopsis "Ridgeline plots in ggplot2")
4558 "Ridgeline plots provide a convenient way of visualizing changes in
4559 distributions over time or space. This package enables the creation of such
4560 plots in @code{ggplot2}.")
4561 (license license:gpl2)))
4563 (define-public r-ggjoy
4570 (uri (cran-uri "ggjoy" version))
4573 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4574 (build-system r-build-system)
4576 `(("r-ggplot2" ,r-ggplot2)
4577 ("r-ggridges" ,r-ggridges)))
4578 (home-page "https://github.com/clauswilke/ggjoy")
4579 (synopsis "Joyplots in ggplot2")
4580 (description "Joyplots provide a convenient way of visualizing changes in
4581 distributions over time or space. This package enables the creation of such
4582 plots in @code{ggplot2}.")
4583 (license license:gpl2)))
4585 (define-public r-cli
4592 (uri (cran-uri "cli" version))
4595 "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr"))))
4596 (build-system r-build-system)
4598 `(("r-assertthat" ,r-assertthat)
4599 ("r-crayon" ,r-crayon)
4600 ("r-fansi" ,r-fansi)
4601 ("r-glue" ,r-glue)))
4602 (home-page "https://github.com/r-lib/cli#readme")
4603 (synopsis "Helpers for developing command line interfaces")
4604 (description "This package provides a suite of tools designed to build
4605 attractive command line interfaces (CLIs). It includes tools for drawing
4606 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4607 (license license:expat)))
4609 (define-public r-argparser
4611 (name "r-argparser")
4616 (uri (cran-uri "argparser" version))
4619 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4620 (build-system r-build-system)
4621 (home-page "https://bitbucket.org/djhshih/argparser")
4622 (synopsis "Command-line argument parser")
4624 "This package provides a cross-platform command-line argument parser
4625 written purely in R with no external dependencies. It is useful with the
4626 Rscript front-end and facilitates turning an R script into an executable
4628 (license license:gpl3+)))
4630 (define-public r-debugme
4637 (uri (cran-uri "debugme" version))
4640 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4641 (build-system r-build-system)
4642 (propagated-inputs `(("r-crayon" ,r-crayon)))
4643 (home-page "https://github.com/r-lib/debugme#readme")
4644 (synopsis "Debug R packages")
4646 "This package allows the user to specify debug messages as special string
4647 constants, and control debugging of packages via environment variables.")
4648 (license license:expat)))
4650 (define-public r-processx
4657 (uri (cran-uri "processx" version))
4659 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
4660 (build-system r-build-system)
4664 (home-page "https://github.com/r-lib/processx3")
4665 (synopsis "Execute and control system processes")
4667 "This package provides portable tools to run system processes in the
4668 background. It can check if a background process is running; wait on a
4669 background process to finish; get the exit status of finished processes; kill
4670 background processes and their children; restart processes. It can read the
4671 standard output and error of the processes, using non-blocking connections.
4672 @code{processx} can poll a process for standard output or error, with a
4673 timeout. It can also poll several processes at once.")
4674 (license license:expat)))
4676 (define-public r-tsp
4683 (uri (cran-uri "TSP" version))
4686 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4687 (properties `((upstream-name . "TSP")))
4688 (build-system r-build-system)
4689 (propagated-inputs `(("r-foreach" ,r-foreach)))
4690 (home-page "https://cran.r-project.org/web/packages/TSP/")
4691 (synopsis "Traveling salesperson problem (TSP)")
4692 (description "This package provides basic infrastructure and some
4693 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4694 traveling salesman problem).")
4695 (license license:gpl3)))
4697 (define-public r-qap
4704 (uri (cran-uri "qap" version))
4707 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4708 (build-system r-build-system)
4709 (native-inputs `(("gfortran" ,gfortran)))
4710 (home-page "https://cran.r-project.org/web/packages/qap/")
4711 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4712 (description "This package implements heuristics for the @dfn{quadratic
4713 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4715 (license license:gpl3)))
4717 (define-public r-gclus
4724 (uri (cran-uri "gclus" version))
4727 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4728 (build-system r-build-system)
4729 (propagated-inputs `(("r-cluster" ,r-cluster)))
4730 (home-page "https://cran.r-project.org/web/packages/gclus/")
4731 (synopsis "Clustering graphics")
4732 (description "This package orders panels in scatterplot matrices and
4733 parallel coordinate displays by some merit index. It contains various indices
4734 of merit, ordering functions, and enhanced versions of @code{pairs} and
4735 @code{parcoord} which color panels according to their merit level.")
4736 (license license:gpl2+)))
4738 (define-public r-webshot
4745 (uri (cran-uri "webshot" version))
4748 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4749 (build-system r-build-system)
4751 `(("r-callr" ,r-callr)
4752 ("r-jsonlite" ,r-jsonlite)
4753 ("r-magrittr" ,r-magrittr)))
4754 (home-page "https://github.com/wch/webshot/")
4755 (synopsis "Take screenshots of web pages")
4757 "Webshot makes it easy to take screenshots of web pages from within R.
4758 It can also run Shiny applications locally and take screenshots of the
4759 application; and it can render and screenshot static as well as interactive R
4760 Markdown documents.")
4761 (license license:gpl2)))
4763 (define-public r-seriation
4765 (name "r-seriation")
4770 (uri (cran-uri "seriation" version))
4773 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
4774 (build-system r-build-system)
4776 `(("r-cluster" ,r-cluster)
4777 ("r-colorspace" ,r-colorspace)
4778 ("r-dendextend" ,r-dendextend)
4779 ("r-gclus" ,r-gclus)
4780 ("r-gplots" ,r-gplots)
4783 ("r-registry" ,r-registry)
4785 (native-inputs `(("gfortran" ,gfortran)))
4786 (home-page "https://s2.smu.edu/IDA/seriation/")
4787 (synopsis "Infrastructure for ordering objects using seriation")
4789 "This package provides infrastructure for seriation with an
4790 implementation of several seriation/sequencing techniques to reorder matrices,
4791 dissimilarity matrices, and dendrograms. It also provides (optimally)
4792 reordered heatmaps, color images and clustering visualizations like
4793 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4795 (license license:gpl3)))
4797 (define-public r-xfun
4804 (uri (cran-uri "xfun" version))
4806 (base32 "15yyigkl1g9w9d7097hrm94dxn1af333ywr5xdw78qqrw6npn0iv"))))
4807 (build-system r-build-system)
4808 ;; knitr itself depends on xfun
4811 `(("r-knitr" ,r-knitr)))
4812 (home-page "https://github.com/yihui/xfun")
4813 (synopsis "Miscellaneous functions")
4815 "This package provides miscellaneous functions commonly used in other
4816 packages maintained by Yihui Xie.")
4817 (license license:expat)))
4819 (define-public r-utf8
4826 (uri (cran-uri "utf8" version))
4829 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4830 (build-system r-build-system)
4831 (home-page "https://github.com/patperry/r-utf8")
4832 (synopsis "Unicode text processing")
4834 "This package provides tools to process and print UTF-8 encoded
4835 international text (Unicode). Input, validate, normalize, encode, format, and
4837 (license license:asl2.0)))
4839 (define-public r-zeallot
4846 (uri (cran-uri "zeallot" version))
4849 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4850 (build-system r-build-system)
4851 (home-page "https://github.com/nteetor/zeallot")
4852 (synopsis "Multiple, unpacking, and destructuring assignment")
4854 "This package provides a @code{%<-%} operator to perform multiple,
4855 unpacking, and destructuring assignment in R. The operator unpacks the
4856 right-hand side of an assignment into multiple values and assigns these values
4857 to variables on the left-hand side of the assignment.")
4858 (license license:expat)))
4860 (define-public r-vctrs
4867 (uri (cran-uri "vctrs" version))
4870 "1k1mcq7jkpc55dsm0wb4k8asc1irvmi5884v3ap4sabf22c5sq0i"))))
4871 (build-system r-build-system)
4873 `(("r-digest" ,r-digest)
4874 ("r-ellipsis" ,r-ellipsis)
4876 ("r-rlang" ,r-rlang)))
4878 `(("r-knitr" ,r-knitr)))
4879 (home-page "https://github.com/r-lib/vctrs")
4880 (synopsis "Vector helpers")
4882 "There are three main goals to the @code{vctrs} package:
4885 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4886 @code{length()} and @code{class()}. These definitions are paired with a
4887 framework for type-coercion and size-recycling.
4888 @item To define type- and size-stability as desirable function properties, use
4889 them to analyse existing base function, and to propose better alternatives.
4890 This work has been particularly motivated by thinking about the ideal
4891 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4892 @item To provide a new @code{vctr} base class that makes it easy to create new
4893 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4894 a few new @code{vctrs} generics, making implementation considerably simpler
4897 (license license:gpl3)))
4899 (define-public r-pillar
4906 (uri (cran-uri "pillar" version))
4909 "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd"))))
4910 (build-system r-build-system)
4913 ("r-crayon" ,r-crayon)
4914 ("r-ellipsis" ,r-ellipsis)
4915 ("r-fansi" ,r-fansi)
4916 ("r-lifecycle" ,r-lifecycle)
4917 ("r-rlang" ,r-rlang)
4919 ("r-vctrs" ,r-vctrs)))
4920 (home-page "https://github.com/r-lib/pillar")
4921 (synopsis "Coloured formatting for columns")
4923 "This package provides a @code{pillar} generic designed for formatting
4924 columns of data using the full range of colours provided by modern
4926 (license license:gpl3)))
4928 (define-public r-uuid
4935 (uri (cran-uri "uuid" version))
4938 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4939 (build-system r-build-system)
4940 (home-page "https://www.rforge.net/uuid")
4941 (synopsis "Tools for generating and handling of UUIDs")
4943 "This package provides tools for generating and handling of
4944 @dfn{Universally Unique Identifiers} (UUIDs).")
4945 (license license:expat)))
4947 (define-public r-tinytex
4954 (uri (cran-uri "tinytex" version))
4957 "10hbc9h1fsw91w5f4fjcaqy68b3n1wr6pml01fnkf3pdjiri5sj0"))))
4958 (build-system r-build-system)
4960 `(("r-xfun" ,r-xfun)))
4961 (home-page "https://github.com/yihui/tinytex")
4962 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4964 "This package provides helper functions to install and maintain the LaTeX
4965 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4966 easy-to-maintain version of TeX Live. This package also contains helper
4967 functions to compile LaTeX documents, and install missing LaTeX packages
4969 (license license:expat)))
4971 (define-public r-network
4978 (uri (cran-uri "network" version))
4981 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
4982 (build-system r-build-system)
4984 `(("r-magrittr" ,r-magrittr)
4985 ("r-tibble" ,r-tibble)))
4986 (home-page "https://statnet.org/")
4987 (synopsis "Classes for relational data")
4989 "This package provides tools to create and modify network objects. The
4990 @code{network} class can represent a range of relational data types, and
4991 supports arbitrary vertex/edge/graph attributes.")
4992 (license license:gpl2+)))
4994 (define-public r-stabs
5001 (uri (cran-uri "stabs" version))
5004 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
5005 (build-system r-build-system)
5006 (home-page "https://github.com/hofnerb/stabs")
5007 (synopsis "Stability selection with error control")
5009 "This package provides resampling procedures to assess the stability of
5010 selected variables with additional finite sample error control for
5011 high-dimensional variable selection procedures such as Lasso or boosting.
5012 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5013 complementary pairs stability selection with improved error bounds
5014 (Shah & Samworth, 2013) are implemented. The package can be combined with
5015 arbitrary user specified variable selection approaches.")
5016 (license license:gpl2)))
5018 (define-public r-rle
5025 (uri (cran-uri "rle" version))
5028 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5029 (properties `((upstream-name . "rle")))
5030 (build-system r-build-system)
5031 (home-page "https://cran.r-project.org/web/packages/rle/")
5032 (synopsis "Common functions for run-length encoded vectors")
5034 "This package provides common @code{base} and @code{stats} methods for
5035 @code{rle} objects, aiming to make it possible to treat them transparently as
5037 (license license:gpl3)))
5039 (define-public r-statnet-common
5041 (name "r-statnet-common")
5046 (uri (cran-uri "statnet.common" version))
5049 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5051 `((upstream-name . "statnet.common")))
5052 (build-system r-build-system)
5054 `(("r-coda" ,r-coda)
5056 (home-page "https://statnet.org")
5057 (synopsis "R scripts and utilities used by the Statnet software")
5058 (description "This package provides non-statistical utilities used by the
5059 software developed by the Statnet Project.")
5060 (license license:gpl3)))
5062 (define-public r-statcheck
5064 (name "r-statcheck")
5069 (uri (cran-uri "statcheck" version))
5072 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5073 (build-system r-build-system)
5075 `(("r-ggplot2" ,r-ggplot2)
5077 ("r-rmarkdown" ,r-rmarkdown)))
5078 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5079 (synopsis "Extract statistics from articles and recompute p-values")
5080 (description "This package can automatically extract statistical
5081 null-hypothesis significant testing (NHST) results from articles and recompute
5082 the p-values based on the reported test statistic and degrees of freedom to
5083 detect possible inconsistencies.")
5084 (license license:gpl2)))
5086 (define-public r-sna
5093 (uri (cran-uri "sna" version))
5096 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5097 (build-system r-build-system)
5099 `(("r-network" ,r-network)
5100 ("r-statnet-common" ,r-statnet-common)))
5101 (home-page "https://statnet.org")
5102 (synopsis "Tools for social network analysis")
5104 "This package provides a range of tools for social network analysis,
5105 including node and graph-level indices, structural distance and covariance
5106 methods, structural equivalence detection, network regression, random graph
5107 generation, and 2D/3D network visualization.")
5108 (license license:gpl2+)))
5110 (define-public r-tfisher
5117 (uri (cran-uri "TFisher" version))
5120 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5121 (properties `((upstream-name . "TFisher")))
5122 (build-system r-build-system)
5124 `(("r-matrix" ,r-matrix)
5125 ("r-mvtnorm" ,r-mvtnorm)
5127 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5128 (synopsis "Optimal thresholding Fisher's p-value combination method")
5130 "This package provides the @dfn{cumulative distribution function} (CDF),
5131 quantile, and statistical power calculator for a collection of thresholding
5132 Fisher's p-value combination methods, including Fisher's p-value combination
5133 method, truncated product method and, in particular, soft-thresholding
5134 Fisher's p-value combination method which is proven to be optimal in some
5135 context of signal detection. The p-value calculator for the omnibus version
5136 of these tests are also included.")
5137 (license license:gpl2)))
5139 (define-public r-ttr
5146 (uri (cran-uri "TTR" version))
5149 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5150 (properties `((upstream-name . "TTR")))
5151 (build-system r-build-system)
5153 `(("r-curl" ,r-curl)
5156 (home-page "https://github.com/joshuaulrich/TTR")
5157 (synopsis "Technical trading rules")
5159 "This package provides functions and data to construct technical trading
5161 (license license:gpl2)))
5163 (define-public r-leaps
5170 (uri (cran-uri "leaps" version))
5173 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5174 (build-system r-build-system)
5175 (native-inputs `(("gfortran" ,gfortran)))
5176 (home-page "https://cran.r-project.org/web/packages/leaps/")
5177 (synopsis "Regression subset selection")
5179 "This package provides tools for regression subset selection, including
5180 exhaustive search.")
5181 (license license:gpl2+)))
5183 (define-public r-splus2r
5190 (uri (cran-uri "splus2R" version))
5193 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
5194 (properties `((upstream-name . "splus2R")))
5195 (build-system r-build-system)
5196 (native-inputs `(("gfortran" ,gfortran)))
5197 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5198 (synopsis "Supplemental S-PLUS functionality in R")
5200 "Currently there are many functions in S-PLUS that are missing in R. To
5201 facilitate the conversion of S-PLUS packages to R packages, this package
5202 provides some missing S-PLUS functionality in R.")
5203 (license license:gpl2)))
5205 (define-public r-ifultools
5207 (name "r-ifultools")
5212 (uri (cran-uri "ifultools" version))
5215 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5216 (build-system r-build-system)
5218 `(("r-mass" ,r-mass)
5219 ("r-splus2r" ,r-splus2r)))
5220 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5221 (synopsis "Insightful research tools")
5222 (description "This package provides C code used by the wmtsa, fractal, and
5224 (license license:gpl2)))
5226 (define-public r-sapa
5233 (uri (cran-uri "sapa" version))
5236 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5237 (build-system r-build-system)
5239 `(("r-ifultools" ,r-ifultools)
5240 ("r-splus2r" ,r-splus2r)))
5241 (home-page "https://cran.r-project.org/web/packages/sapa/")
5242 (synopsis "Spectral analysis for physical applications")
5243 (description "This package provides software for the book Spectral
5244 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5245 Cambridge University Press, 1993.")
5246 (license license:gpl2)))
5248 (define-public r-aggregation
5250 (name "r-aggregation")
5255 (uri (cran-uri "aggregation" version))
5258 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5259 (build-system r-build-system)
5260 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5261 (synopsis "Methods for p-value aggregation")
5263 "This package contains functionality for performing the following methods
5264 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5265 Fisher's method), and Sidak correction.")
5266 (license license:gpl3)))
5268 (define-public r-quantmod
5275 (uri (cran-uri "quantmod" version))
5278 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5279 (build-system r-build-system)
5281 `(("r-curl" ,r-curl)
5285 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5286 (synopsis "Quantitative financial modelling framework")
5287 (description "This package provides a quantitative financial modelling
5288 framework to allow users to specify, build, trade, and analyse quantitative
5289 financial trading strategies.")
5290 (license license:gpl3)))
5292 (define-public r-tseries
5299 (uri (cran-uri "tseries" version))
5302 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5303 (build-system r-build-system)
5305 `(("r-quadprog" ,r-quadprog)
5306 ("r-quantmod" ,r-quantmod)
5309 `(("gfortran" ,gfortran)))
5310 (home-page "https://cran.r-project.org/web/packages/tseries/")
5311 (synopsis "Time series analysis and computational finance")
5313 "This package provides functions relating to time series analysis and
5314 computational finance.")
5315 (license license:gpl2)))
5317 (define-public r-wmtsa
5324 (uri (cran-uri "wmtsa" version))
5327 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5328 (build-system r-build-system)
5330 `(("r-ifultools" ,r-ifultools)
5332 ("r-splus2r" ,r-splus2r)))
5333 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5334 (synopsis "Wavelet methods for time series analysis")
5336 "This package provides software to accompany the book \"Wavelet Methods
5337 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5338 University Press, 2000.")
5339 (license license:gpl2)))
5341 (define-public r-tsa
5348 (uri (cran-uri "TSA" version))
5351 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5352 (properties `((upstream-name . "TSA")))
5353 (build-system r-build-system)
5355 `(("r-leaps" ,r-leaps)
5356 ("r-locfit" ,r-locfit)
5358 ("r-tseries" ,r-tseries)))
5359 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5360 (synopsis "Time series analysis")
5362 "This package contains R functions and datasets detailed in the book
5363 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5364 Cryer and Kung-Sik Chan.")
5365 (license license:gpl2+)))
5367 (define-public r-extradistr
5369 (name "r-extradistr")
5374 (uri (cran-uri "extraDistr" version))
5377 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5378 (properties `((upstream-name . "extraDistr")))
5379 (build-system r-build-system)
5381 `(("r-rcpp" ,r-rcpp)))
5382 (home-page "https://github.com/twolodzko/extraDistr")
5383 (synopsis "Additional univariate and multivariate distributions")
5385 "This package implements density, distribution functions, quantile
5386 functions and random generation functions for a large number of univariate and
5387 multivariate distributions.")
5388 (license license:gpl2)))
5390 (define-public r-fractal
5397 (uri (cran-uri "fractal" version))
5400 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5401 (build-system r-build-system)
5403 `(("r-ifultools" ,r-ifultools)
5406 ("r-scatterplot3d" ,r-scatterplot3d)
5407 ("r-splus2r" ,r-splus2r)
5408 ("r-wmtsa" ,r-wmtsa)))
5409 (home-page "https://cran.r-project.org/web/packages/fractal/")
5410 (synopsis "Fractal time series modeling and analysis")
5412 "This package provides tools for stochastic fractal and deterministic
5413 chaotic time series analysis.")
5414 (license license:gpl2)))
5416 (define-public r-urca
5423 (uri (cran-uri "urca" version))
5426 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5427 (build-system r-build-system)
5428 (propagated-inputs `(("r-nlme" ,r-nlme)))
5429 (native-inputs `(("gfortran" ,gfortran)))
5430 (home-page "https://cran.r-project.org/web/packages/urca/")
5431 (synopsis "Unit root and cointegration tests for time series data")
5433 "This package provides unit root and cointegration tests encountered in
5434 applied econometric analysis.")
5435 (license license:gpl2+)))
5437 (define-public r-cubature
5444 (uri (cran-uri "cubature" version))
5447 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5448 (build-system r-build-system)
5450 `(("r-rcpp" ,r-rcpp)))
5452 `(("r-knitr" ,r-knitr)))
5453 (home-page "https://github.com/bnaras/cubature")
5454 (synopsis "Adaptive multivariate integration over hypercubes")
5456 "This package is an R wrapper around the cubature C library for adaptive
5457 multivariate integration over hypercubes. This version provides both
5458 @code{hcubature} and @code{pcubature} routines in addition to a vector
5460 ;; The included cubature C library is released under GPLv2+, but the
5461 ;; wrapper declares the license to be GPLv3+.
5462 (license (list license:gpl2+ license:gpl3+))))
5464 (define-public r-trend
5471 (uri (cran-uri "trend" version))
5474 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5475 (build-system r-build-system)
5477 `(("r-extradistr" ,r-extradistr)))
5479 `(("gfortran" ,gfortran)))
5480 (home-page "https://cran.r-project.org/web/packages/trend/")
5481 (synopsis "Non-parametric trend tests and change-point detection")
5483 "The analysis of environmental data often requires the detection of
5484 trends and change-points. This package includes tests for trend
5485 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5486 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5487 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5488 correlation trend test), change-point detection (Lanzante's test procedures,
5489 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5490 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5491 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5492 sample Robust Rank-Order Distributional Test.")
5493 (license license:gpl3)))
5495 (define-public r-expm
5502 (uri (cran-uri "expm" version))
5505 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5506 (build-system r-build-system)
5507 (propagated-inputs `(("r-matrix" ,r-matrix)))
5508 (native-inputs `(("gfortran" ,gfortran)))
5509 (home-page "https://r-forge.r-project.org/projects/expm/")
5510 (synopsis "Tools for matrix exponentials and related quantities")
5512 "This package provides tools for the computation of the matrix
5513 exponential, logarithm, square root, and related quantities.")
5514 (license license:gpl2+)))
5516 (define-public r-complexplus
5518 (name "r-complexplus")
5523 (uri (cran-uri "complexplus" version))
5526 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5527 (build-system r-build-system)
5529 `(("r-expm" ,r-expm)
5530 ("r-matrix" ,r-matrix)))
5531 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5532 (synopsis "Functions of complex or real variables")
5534 "This package extends several functions to the complex domain, including
5535 the matrix exponential and logarithm, and the determinant.")
5536 (license license:gpl2)))
5538 (define-public r-phontools
5540 (name "r-phontools")
5545 (uri (cran-uri "phonTools" version))
5548 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5549 (properties `((upstream-name . "phonTools")))
5550 (build-system r-build-system)
5551 (home-page "http://www.santiagobarreda.com/rscripts.html")
5552 (synopsis "Tools for phonetic and acoustic analyses")
5554 "This package contains tools for the organization, display, and analysis
5555 of the sorts of data frequently encountered in phonetics research and
5556 experimentation, including the easy creation of IPA vowel plots, and the
5557 creation and manipulation of WAVE audio files.")
5558 (license license:bsd-2)))
5567 (uri (cran-uri "np" version))
5570 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5571 (build-system r-build-system)
5573 `(("r-boot" ,r-boot)
5574 ("r-cubature" ,r-cubature)
5575 ("r-quadprog" ,r-quadprog)
5576 ("r-quantreg" ,r-quantreg)))
5577 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5578 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5579 (description "This package provides non-parametric (and semi-parametric)
5580 kernel methods that seamlessly handle a mix of continuous, unordered, and
5581 ordered factor data types.")
5582 ;; Any version of the GPL.
5583 (license license:gpl3+)))
5585 (define-public r-powerplus
5587 (name "r-powerplus")
5592 (uri (cran-uri "powerplus" version))
5595 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5596 (build-system r-build-system)
5598 `(("r-complexplus" ,r-complexplus)
5601 ("r-matrix" ,r-matrix)
5602 ("r-phontools" ,r-phontools)))
5603 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5604 (synopsis "Exponentiation operations")
5606 "This package provides tools for the computation of matrix and scalar
5608 (license license:gpl2)))
5610 (define-public r-egg
5617 (uri (cran-uri "egg" version))
5620 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5621 (properties `((upstream-name . "egg")))
5622 (build-system r-build-system)
5624 `(("r-ggplot2" ,r-ggplot2)
5625 ("r-gridextra" ,r-gridextra)
5626 ("r-gtable" ,r-gtable)))
5627 (home-page "https://cran.r-project.org/web/packages/egg")
5628 (synopsis "Extensions for ggplot2")
5630 "This package provides miscellaneous functions to help customize ggplot2
5631 objects. High-level functions are provided to post-process ggplot2 layouts
5632 and allow alignment between plot panels, as well as setting panel sizes to
5633 fixed values. Other functions include a custom @code{geom}, and helper
5634 functions to enforce symmetric scales or add tags to facetted plots.")
5635 (license license:gpl3)))
5637 (define-public r-heatmaply
5639 (name "r-heatmaply")
5644 (uri (cran-uri "heatmaply" version))
5647 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5648 (build-system r-build-system)
5650 `(("r-assertthat" ,r-assertthat)
5651 ("r-colorspace" ,r-colorspace)
5652 ("r-dendextend" ,r-dendextend)
5654 ("r-ggplot2" ,r-ggplot2)
5655 ("r-htmlwidgets" ,r-htmlwidgets)
5656 ("r-magrittr" ,r-magrittr)
5657 ("r-plotly" ,r-plotly)
5658 ("r-rcolorbrewer" ,r-rcolorbrewer)
5659 ("r-reshape2" ,r-reshape2)
5660 ("r-scales" ,r-scales)
5661 ("r-seriation" ,r-seriation)
5662 ("r-viridis" ,r-viridis)
5663 ("r-webshot" ,r-webshot)))
5665 `(("r-knitr" ,r-knitr)))
5666 (home-page "https://cran.r-project.org/package=heatmaply")
5667 (synopsis "Interactive cluster heat maps using plotly")
5669 "This package enables you to create interactive cluster heatmaps that can
5670 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5671 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5672 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5673 a popular graphical method for visualizing high-dimensional data, in which a
5674 table of numbers is encoded as a grid of colored cells. The rows and columns
5675 of the matrix are ordered to highlight patterns and are often accompanied by
5677 ;; Either version of the license.
5678 (license (list license:gpl2 license:gpl3))))
5687 (uri (cran-uri "h5" version))
5690 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5691 (build-system r-build-system)
5696 `(("which" ,which)))
5698 `(("r-rcpp" ,r-rcpp)))
5699 (home-page "https://github.com/mannau/h5")
5700 (synopsis "Interface to the HDF5 Library")
5702 "This package provides an S4 interface to the HDF5 library supporting
5703 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5704 binary files in a language independent format. The HDF5 format can therefore
5705 be used as an alternative to R's save/load mechanism. Since h5 is able to
5706 access only subsets of stored data it can also handle data sets which do not
5708 (license license:bsd-2)))
5710 (define-public r-cgdsr
5717 (uri (cran-uri "cgdsr" version))
5720 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5721 (build-system r-build-system)
5723 `(("r-httr" ,r-httr)
5724 ("r-r-methodss3" ,r-r-methodss3)
5725 ("r-r-oo" ,r-r-oo)))
5726 (home-page "https://github.com/cBioPortal/cgdsr")
5727 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5729 "This package provides a basic set of R functions for querying the Cancer
5730 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5731 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5732 (license license:lgpl3)))
5734 (define-public r-import
5741 (uri (cran-uri "import" version))
5744 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
5745 (build-system r-build-system)
5747 `(("r-knitr" ,r-knitr)))
5748 (home-page "https://github.com/smbache/import")
5749 (synopsis "Import mechanism for R")
5751 "This is an alternative mechanism for importing objects from packages.
5752 The syntax allows for importing multiple objects from a package with a single
5753 command in an expressive way. The import package bridges some of the gap
5754 between using @code{library} (or @code{require}) and direct (single-object)
5755 imports. Furthermore the imported objects are not placed in the current
5756 environment. It is also possible to import objects from stand-alone @code{.R}
5758 (license license:expat)))
5760 (define-public r-shinyace
5767 (uri (cran-uri "shinyAce" version))
5770 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5771 (properties `((upstream-name . "shinyAce")))
5772 (build-system r-build-system)
5774 `(("r-shiny" ,r-shiny)
5775 ("r-jsonlite" ,r-jsonlite)))
5776 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5777 (synopsis "Ace editor bindings for Shiny")
5779 "This package provides Ace editor bindings to enable a rich text editing
5780 environment within Shiny.")
5781 (license license:expat)))
5783 (define-public r-randomizr
5785 (name "r-randomizr")
5790 (uri (cran-uri "randomizr" version))
5793 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5794 (properties `((upstream-name . "randomizr")))
5795 (build-system r-build-system)
5797 `(("r-knitr" ,r-knitr)))
5798 (home-page "https://declaredesign.org/r/randomizr/")
5799 (synopsis "Tools for common forms of random assignment and sampling")
5801 "This package provides tools for generating random assignments for common
5802 experimental designs and random samples for common sampling designs.")
5803 (license license:expat)))
5805 (define-public r-base64url
5807 (name "r-base64url")
5812 (uri (cran-uri "base64url" version))
5815 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5816 (build-system r-build-system)
5818 `(("r-backports" ,r-backports)))
5819 (home-page "https://github.com/mllg/base64url")
5820 (synopsis "Fast and URL-safe base64 encoder and decoder")
5822 "This package provides a URL-safe base64 encoder and decoder. In
5823 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5824 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5825 encoder does not fill the string with trailing @code{=}. The resulting
5826 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5827 and thus are safe to use in URLs or for file names. The package also comes
5828 with a simple base32 encoder/decoder suited for case insensitive file
5830 (license license:gpl3)))
5832 (define-public r-radiant-data
5834 (name "r-radiant-data")
5839 (uri (cran-uri "radiant.data" version))
5842 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
5843 (modules '((guix build utils)))
5846 ;; Delete files that are under CC-NC-SA.
5847 (delete-file-recursively "inst/app/tools/help")
5849 (properties `((upstream-name . "radiant.data")))
5850 (build-system r-build-system)
5852 `(("r-base64enc" ,r-base64enc)
5853 ("r-broom" ,r-broom)
5856 ("r-dplyr" ,r-dplyr)
5859 ("r-ggplot2" ,r-ggplot2)
5860 ("r-import" ,r-import)
5861 ("r-jsonlite" ,r-jsonlite)
5862 ("r-knitr" ,r-knitr)
5863 ("r-lubridate" ,r-lubridate)
5864 ("r-magrittr" ,r-magrittr)
5865 ("r-markdown" ,r-markdown)
5867 ("r-patchwork" ,r-patchwork)
5868 ("r-plotly" ,r-plotly)
5869 ("r-psych" ,r-psych)
5870 ("r-randomizr" ,r-randomizr)
5871 ("r-readr" ,r-readr)
5872 ("r-readxl" ,r-readxl)
5873 ("r-rlang" ,r-rlang)
5874 ("r-rmarkdown" ,r-rmarkdown)
5875 ("r-rstudioapi" ,r-rstudioapi)
5876 ("r-scales" ,r-scales)
5877 ("r-shiny" ,r-shiny)
5878 ("r-shinyfiles" ,r-shinyfiles)
5879 ("r-shinyace" ,r-shinyace)
5880 ("r-stringi" ,r-stringi)
5881 ("r-tibble" ,r-tibble)
5882 ("r-tidyr" ,r-tidyr)
5883 ("r-writexl" ,r-writexl)))
5884 (home-page "https://github.com/radiant-rstats/radiant.data")
5885 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5887 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5888 visualizing, summarizing, transforming, and combining data. It also contains
5889 functionality to generate reproducible reports of the analyses conducted in
5891 (license license:agpl3)))
5893 (define-public r-algdesign
5895 (name "r-algdesign")
5900 (uri (cran-uri "AlgDesign" version))
5902 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5903 (properties `((upstream-name . "AlgDesign")))
5904 (build-system r-build-system)
5905 (home-page "https://github.com/jvbraun/AlgDesign")
5906 (synopsis "Algorithmic experimental design")
5908 "This package provides tools to calculate exact and approximate theory
5909 experimental designs for D, A, and I criteria. Very large designs may be
5910 created. Experimental designs may be blocked or blocked designs created from
5911 a candidate list, using several criteria. The blocking can be done when whole
5912 and within plot factors interact.")
5913 (license license:gpl2+)))
5915 (define-public r-signal
5922 (uri (cran-uri "signal" version))
5925 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5926 (build-system r-build-system)
5927 (propagated-inputs `(("r-mass" ,r-mass)))
5928 (native-inputs `(("gfortran" ,gfortran)))
5929 (home-page "https://cran.r-project.org/web/packages/signal/")
5930 (synopsis "Signal processing")
5932 "This package provides a set of signal processing functions originally
5933 written for Matlab and GNU Octave. It includes filter generation utilities,
5934 filtering functions, resampling routines, and visualization of filter models.
5935 It also includes interpolation functions.")
5936 (license license:gpl2)))
5938 (define-public r-gsubfn
5945 (uri (cran-uri "gsubfn" version))
5948 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5949 (build-system r-build-system)
5950 (propagated-inputs `(("r-proto" ,r-proto)))
5951 (home-page "https://code.google.com/archive/p/gsubfn/")
5952 (synopsis "Utilities for strings and function arguments.")
5954 "This package provides @code{gsubfn} which is like @code{gsub} but can
5955 take a replacement function or certain other objects instead of the
5956 replacement string. Matches and back references are input to the replacement
5957 function and replaced by the function output. @code{gsubfn} can be used to
5958 split strings based on content rather than delimiters and for quasi-perl-style
5959 string interpolation. The package also has facilities for translating
5960 formulas to functions and allowing such formulas in function calls instead of
5962 (license license:gpl2+)))
5964 (define-public r-sqldf
5971 (uri (cran-uri "sqldf" version))
5974 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5975 (build-system r-build-system)
5977 `(("r-chron" ,r-chron)
5979 ("r-gsubfn" ,r-gsubfn)
5980 ("r-proto" ,r-proto)
5981 ("r-rsqlite" ,r-rsqlite)))
5982 (home-page "https://github.com/ggrothendieck/sqldf")
5983 (synopsis "Manipulate R data frames using SQL")
5985 "The @code{sqldf} function is typically passed a single argument which is
5986 an SQL select statement where the table names are ordinary R data frame names.
5987 @code{sqldf} transparently sets up a database, imports the data frames into
5988 that database, performs the SQL statement and returns the result using a
5989 heuristic to determine which class to assign to each column of the returned
5990 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5991 used to read filtered files into R even if the original files are larger than
5992 R itself can handle.")
5993 (license license:gpl2)))
5995 (define-public r-abind
6002 (uri (cran-uri "abind" version))
6005 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6006 (build-system r-build-system)
6007 (home-page "https://cran.r-project.org/web/packages/abind/")
6008 (synopsis "Combine multidimensional arrays")
6010 "This package provides tools to combine multidimensional arrays into a
6011 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6012 works with vectors, matrices, and higher-dimensional arrays. It also provides
6013 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6014 extracting and replacing data in arrays.")
6015 (license license:lgpl2.0+)))
6017 (define-public r-prroc
6024 (uri (cran-uri "PRROC" version))
6027 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6028 (properties `((upstream-name . "PRROC")))
6029 (build-system r-build-system)
6030 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6031 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6033 "This package computes the areas under the @dfn{precision-recall} (PR)
6034 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6035 contrast to other implementations, the interpolation between points of the PR
6036 curve is done by a non-linear piecewise function. In addition to the areas
6037 under the curves, the curves themselves can also be computed and plotted by a
6038 specific S3-method.")
6039 (license license:gpl3)))
6041 (define-public r-vim
6048 (uri (cran-uri "VIM" version))
6051 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
6052 (properties `((upstream-name . "VIM")))
6053 (build-system r-build-system)
6056 ("r-colorspace" ,r-colorspace)
6057 ("r-data-table" ,r-data-table)
6058 ("r-e1071" ,r-e1071)
6059 ("r-laeken" ,r-laeken)
6060 ("r-magrittr" ,r-magrittr)
6063 ("r-ranger" ,r-ranger)
6065 ("r-robustbase" ,r-robustbase)
6069 `(("r-knitr" ,r-knitr)))
6070 (home-page "https://github.com/alexkowa/VIM")
6071 (synopsis "Visualization and imputation of missing values")
6073 "This package provides tools for the visualization of missing and/or
6074 imputed values are introduced, which can be used for exploring the data and
6075 the structure of the missing and/or imputed values. Depending on this
6076 structure of the missing values, the corresponding methods may help to
6077 identify the mechanism generating the missing values and explore the
6078 data including missing values. In addition, the quality of imputation can be
6079 visually explored using various univariate, bivariate, multiple and
6080 multivariate plot methods.")
6081 (license license:gpl2+)))
6083 (define-public r-fnn
6090 (uri (cran-uri "FNN" version))
6093 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6094 (properties `((upstream-name . "FNN")))
6095 (build-system r-build-system)
6096 (home-page "https://cran.r-project.org/web/packages/FNN")
6097 (synopsis "Fast nearest neighbor search algorithms and applications")
6099 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6100 search algorithms. Related applications including KNN classification,
6101 regression and information measures are implemented.")
6102 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6103 ;; later can be used.
6104 (license license:gpl2+)))
6106 (define-public r-smoother
6113 (uri (cran-uri "smoother" version))
6116 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6117 (build-system r-build-system)
6119 `(("r-ttr" ,r-ttr)))
6120 (home-page "https://cran.r-project.org/web/packages/smoother")
6121 (synopsis "Functions relating to the smoothing of numerical data")
6123 "This package provides a collection of methods for smoothing numerical
6124 data, commencing with a port of the Matlab gaussian window smoothing function.
6125 In addition, several functions typically used in smoothing of financial data
6127 (license license:gpl2)))
6129 (define-public r-riverplot
6131 (name "r-riverplot")
6136 (uri (cran-uri "riverplot" version))
6139 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
6140 (build-system r-build-system)
6141 (home-page "https://logfc.wordpress.com")
6142 (synopsis "Sankey or ribbon plots")
6144 "Sankey plots are a type of diagram that is convenient to illustrate how
6145 flow of information, resources etc. separates and joins, much like observing
6146 how rivers split and merge. For example, they can be used to compare
6147 different clusterings. This package provides an implementation of Sankey
6149 (license license:gpl2+)))
6151 (define-public r-dyn
6158 (uri (cran-uri "dyn" version))
6161 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6162 (build-system r-build-system)
6164 `(("r-zoo" ,r-zoo)))
6165 (home-page "https://cran.r-project.org/web/packages/dyn")
6166 (synopsis "Time series regression")
6168 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6169 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6170 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6171 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6172 @code{randomForest::randomForest()} and other regression functions, allowing
6173 those functions to be used with time series including specifications that may
6174 contain lags, diffs and missing values.")
6176 (license license:gpl2+)))
6178 (define-public r-catdap
6185 (uri (cran-uri "catdap" version))
6188 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6189 (build-system r-build-system)
6191 `(("gfortran" ,gfortran)))
6192 (home-page "https://cran.r-project.org/web/packages/catdap/")
6193 (synopsis "Tools for categorical data analysis")
6195 "This package provides functions for analyzing multivariate data.
6196 Dependencies of the distribution of the specified variable (response
6197 variable) to other variables (explanatory variables) are derived and
6198 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6199 (license license:gpl2+)))
6201 (define-public r-arules
6208 (uri (cran-uri "arules" version))
6211 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6212 (build-system r-build-system)
6214 `(("r-matrix" ,r-matrix)))
6215 (home-page "https://github.com/mhahsler/arules")
6216 (synopsis "Mining association rules and frequent itemsets")
6218 "This package provides an infrastructure for representing, manipulating
6219 and analyzing transaction data and patterns (frequent itemsets and association rules).
6220 It also provides C implementations of the association mining algorithms Apriori
6222 (license license:gpl3)))
6224 (define-public r-parsedate
6226 (name "r-parsedate")
6231 (uri (cran-uri "parsedate" version))
6234 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6235 (build-system r-build-system)
6237 `(("r-rematch2" ,r-rematch2)))
6238 (home-page "https://github.com/gaborcsardi/parsedate")
6240 "Recognize and parse dates in various formats")
6242 "This package provides three functions for dealing with dates:
6243 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6244 time formats, @code{parse_date} parses dates in unspecified formats,
6245 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6246 (license license:gpl2)))
6248 (define-public r-abc-data
6255 (uri (cran-uri "abc.data" version))
6258 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6259 (properties `((upstream-name . "abc.data")))
6260 (build-system r-build-system)
6261 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6262 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6264 "This package contains data which are used by functions of the abc
6265 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6266 algorithms for performing parameter estimation, model selection, and
6268 (license license:gpl3+)))
6270 (define-public r-abc
6277 (uri (cran-uri "abc" version))
6280 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6281 (build-system r-build-system)
6283 `(("r-abc-data" ,r-abc-data)
6284 ("r-locfit" ,r-locfit)
6287 ("r-quantreg" ,r-quantreg)))
6288 (home-page "https://cran.r-project.org/web/packages/abc/")
6289 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6291 "This package implements several @dfn{Approximate Bayesian
6292 Computation} (ABC) algorithms for performing parameter estimation, model
6293 selection, and goodness-of-fit. Cross-validation tools are also available for
6294 measuring the accuracy of ABC estimates, and to calculate the
6295 misclassification probabilities of different models.")
6296 (license license:gpl3+)))
6298 (define-public r-zip
6305 (uri (cran-uri "zip" version))
6308 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6309 (build-system r-build-system)
6310 (home-page "https://github.com/gaborcsardi/zip")
6311 (synopsis "Cross-platform Zip compression")
6313 "This package provides a cross-platform Zip compression library for R.
6314 It is a replacement for the @code{zip} function, that does not require any
6315 additional external tools on any platform.")
6316 (license license:cc0)))
6318 (define-public r-openxlsx
6325 (uri (cran-uri "openxlsx" version))
6328 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6329 (build-system r-build-system)
6331 `(("r-rcpp" ,r-rcpp)
6332 ("r-stringi" ,r-stringi)
6335 `(("r-knitr" ,r-knitr)))
6336 (home-page "https://github.com/awalker89/openxlsx")
6337 (synopsis "Read, write and edit XLSX files")
6339 "This package simplifies the creation of Excel @code{.xlsx} files by
6340 providing a high level interface to writing, styling and editing worksheets.
6341 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6342 and @code{XLConnect} packages with the added benefit of removing the
6343 dependency on Java.")
6344 (license license:gpl3)))
6346 (define-public r-rio
6353 (uri (cran-uri "rio" version))
6356 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6357 (build-system r-build-system)
6359 `(("r-curl" ,r-curl)
6360 ("r-data-table" ,r-data-table)
6361 ("r-foreign" ,r-foreign)
6362 ("r-haven" ,r-haven)
6363 ("r-openxlsx" ,r-openxlsx)
6364 ("r-readxl" ,r-readxl)
6365 ("r-tibble" ,r-tibble)))
6366 (home-page "https://github.com/leeper/rio")
6367 (synopsis "Swiss-army knife for data I/O")
6369 "This package provides streamlined data import and export infrastructure
6370 by making assumptions that the user is probably willing to make: @code{import}
6371 and @code{export} determine the data structure from the file extension,
6372 reasonable defaults are used for data import and export (e.g.,
6373 @code{stringsAsFactors=FALSE}), web-based import is natively
6374 supported (including from SSL/HTTPS), compressed files can be read directly
6375 without explicit decompression, and fast import packages are used where
6376 appropriate. An additional convenience function, @code{convert}, provides a
6377 simple method for converting between file types.")
6378 (license license:gpl2)))
6380 (define-public r-maptools
6387 (uri (cran-uri "maptools" version))
6390 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6391 (build-system r-build-system)
6393 `(("r-foreign" ,r-foreign)
6394 ("r-lattice" ,r-lattice)
6396 (home-page "https://r-forge.r-project.org/projects/maptools/")
6397 (synopsis "Tools for reading and handling spatial objects")
6399 "This package provides a set of tools for manipulating and reading
6400 geographic data, in particular ESRI Shapefiles. It includes binary access to
6401 GSHHG shoreline files. The package also provides interface wrappers for
6402 exchanging spatial objects with other R packages.")
6403 ;; The C source files from shapelib are released under the Expat license.
6404 ;; The R code is released under GPL version 2 or later.
6405 (license (list license:gpl2+
6408 (define-public r-later
6415 (uri (cran-uri "later" version))
6418 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6419 (build-system r-build-system)
6423 ("r-rlang" ,r-rlang)))
6425 `(("r-knitr" ,r-knitr)))
6426 (home-page "https://github.com/r-lib/later")
6427 (synopsis "Utilities for delaying function execution")
6429 "This package provides tools to execute arbitrary R or C functions some
6430 time after the current time, after the R execution stack has emptied.")
6431 (license license:gpl2+)))
6433 (define-public r-promises
6440 (uri (cran-uri "promises" version))
6443 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6444 (build-system r-build-system)
6446 `(("r-later" ,r-later)
6447 ("r-magrittr" ,r-magrittr)
6450 ("r-rlang" ,r-rlang)))
6452 `(("r-knitr" ,r-knitr)))
6453 (home-page "https://rstudio.github.io/promises")
6454 (synopsis "Abstractions for promise-based asynchronous programming")
6456 "This package provides fundamental abstractions for doing asynchronous
6457 programming in R using promises. Asynchronous programming is useful for
6458 allowing a single R process to orchestrate multiple tasks in the background
6459 while also attending to something else. Semantics are similar to JavaScript
6460 promises, but with a syntax that is idiomatic R.")
6461 (license license:expat)))
6463 (define-public r-dosnow
6470 (uri (cran-uri "doSNOW" version))
6473 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6474 (properties `((upstream-name . "doSNOW")))
6475 (build-system r-build-system)
6477 `(("r-foreach" ,r-foreach)
6478 ("r-iterators" ,r-iterators)
6479 ("r-snow" ,r-snow)))
6480 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6481 (synopsis "Foreach parallel adaptor for the snow package")
6483 "This package provides a parallel backend for the @code{%dopar%} function
6484 using the @code{snow} package.")
6485 (license license:gpl2)))
6487 (define-public r-snowfall
6490 (version "1.84-6.1")
6493 (uri (cran-uri "snowfall" version))
6495 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6496 (build-system r-build-system)
6498 `(("r-snow" ,r-snow)))
6499 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6500 (synopsis "Easier cluster computing")
6501 (description "This package is a usability wrapper around snow for easier
6502 development of parallel R programs. This package offers e.g. extended error
6503 checks, and additional functions. All functions work in sequential mode, too,
6504 if no cluster is present or wished. The package is also designed as connector
6505 to the cluster management tool @code{sfCluster}, but can also used without
6507 (license license:gpl2+)))
6509 (define-public r-rappdirs
6516 (uri (cran-uri "rappdirs" version))
6519 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6520 (build-system r-build-system)
6521 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6522 (synopsis "Determine where to save data, caches, and logs")
6524 "This package provides an easy way to determine which directories on the
6525 user's computer should be used to save data, caches and logs. It is a port of
6526 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6527 (license license:expat)))
6529 (define-public r-renv
6536 (uri (cran-uri "renv" version))
6539 "0k31x19gzpffb701c76p840cip10c0dh8yv3wcs30gqi0ag1g77l"))))
6540 (properties `((upstream-name . "renv")))
6541 (build-system r-build-system)
6543 `(("r-knitr" ,r-knitr)))
6544 (home-page "https://rstudio.github.io/renv")
6545 (synopsis "Project environments")
6547 "This package provides a dependency management toolkit for R. Using
6548 renv, you can create and manage project-local R libraries, save the state of
6549 these libraries to a lockfile, and later restore your library as required.
6550 Together, these tools can help make your projects more isolated, portable, and
6552 (license license:expat)))
6554 (define-public r-learnr
6561 (uri (cran-uri "learnr" version))
6564 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6565 (build-system r-build-system)
6567 `(("r-checkmate" ,r-checkmate)
6568 ("r-ellipsis" ,r-ellipsis)
6569 ("r-evaluate" ,r-evaluate)
6570 ("r-htmltools" ,r-htmltools)
6571 ("r-htmlwidgets" ,r-htmlwidgets)
6572 ("r-jsonlite" ,r-jsonlite)
6573 ("r-knitr" ,r-knitr)
6574 ("r-markdown" ,r-markdown)
6575 ("r-rappdirs" ,r-rappdirs)
6577 ("r-rmarkdown" ,r-rmarkdown)
6578 ("r-rprojroot" ,r-rprojroot)
6579 ("r-shiny" ,r-shiny)
6580 ("r-withr" ,r-withr)))
6581 (home-page "https://rstudio.github.io/learnr/")
6582 (synopsis "Interactive tutorials for R")
6584 "This package provides tools to create interactive tutorials using R
6585 Markdown. Use a combination of narrative, figures, videos, exercises, and
6586 quizzes to create self-paced tutorials for learning about R and R packages.")
6587 (license license:asl2.0)))
6589 (define-public r-analytics
6591 (name "r-analytics")
6596 (uri (cran-uri "analytics" version))
6599 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6600 (build-system r-build-system)
6603 ("r-cluster" ,r-cluster)
6604 ("r-fractal" ,r-fractal)
6605 ("r-lmtest" ,r-lmtest)
6608 ("r-powerplus" ,r-powerplus)
6609 ("r-robust" ,r-robust)
6610 ("r-trend" ,r-trend)
6614 (home-page "https://cran.r-project.org/web/packages/analytics/")
6615 (synopsis "Collection of data analysis tools")
6617 "This package is a collection of data analysis tools. It includes tools
6618 for regression outlier detection in a fitted linear model, stationary
6619 bootstrap using a truncated geometric distribution, a comprehensive test for
6620 weak stationarity, column means by group, weighted biplots, and a heuristic to
6621 obtain a better initial configuration in non-metric MDS.")
6622 (license license:gpl2)))
6624 (define-public r-reticulate
6626 (name "r-reticulate")
6631 (uri (cran-uri "reticulate" version))
6634 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
6635 (build-system r-build-system)
6636 (inputs `(("python" ,python)))
6638 `(("r-rappdirs" ,r-rappdirs)
6639 ("r-jsonlite" ,r-jsonlite)
6640 ("r-matrix" ,r-matrix)
6641 ("r-rcpp" ,r-rcpp)))
6643 `(("r-knitr" ,r-knitr)))
6644 (home-page "https://github.com/rstudio/reticulate")
6645 (synopsis "R interface to Python")
6647 "This package provides an interface from R to Python modules, classes,
6648 and functions. When calling into Python, R data types are automatically
6649 converted to their equivalent Python types. When values are returned from
6650 Python to R they are converted back to R types.")
6651 (license license:asl2.0)))
6653 (define-public r-bibtex
6660 (uri (cran-uri "bibtex" version))
6663 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
6664 (build-system r-build-system)
6665 (propagated-inputs `(("r-stringr" ,r-stringr)))
6666 (home-page "https://github.com/romainfrancois/bibtex")
6667 (synopsis "Bibtex parser")
6668 (description "This package provides a utility for R to parse a bibtex
6670 (license license:gpl2+)))
6672 (define-public r-ggseqlogo
6674 (name "r-ggseqlogo")
6679 (uri (cran-uri "ggseqlogo" version))
6682 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6683 (build-system r-build-system)
6684 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6685 (home-page "https://github.com/omarwagih/ggseqlogo")
6686 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6688 "The range of functions provided by this package makes it possible to
6689 draw highly versatile genomic sequence logos. Features include, but are not
6690 limited to, modifying colour schemes and fonts used to draw the logo,
6691 generating multiple logo plots, and aiding the visualisation with annotations.
6692 Sequence logos can easily be combined with other ggplot2 plots.")
6693 ;; Unspecified version of the LGPL.
6694 (license license:lgpl3+)))
6696 (define-public r-ggsci
6703 (uri (cran-uri "ggsci" version))
6706 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6707 (build-system r-build-system)
6709 `(("r-ggplot2" ,r-ggplot2)
6710 ("r-scales" ,r-scales)))
6711 (home-page "https://nanx.me/ggsci/")
6712 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6714 "This package provides a collection of ggplot2 color palettes inspired by
6715 plots in scientific journals, data visualization libraries, science fiction
6716 movies, and TV shows.")
6717 (license license:gpl3)))
6719 (define-public r-ggsignif
6726 (uri (cran-uri "ggsignif" version))
6729 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6730 (build-system r-build-system)
6732 `(("r-knitr" ,r-knitr)))
6734 `(("r-ggplot2" ,r-ggplot2)))
6735 (home-page "https://github.com/const-ae/ggsignif")
6736 (synopsis "Significance brackets for ggplot2")
6738 "Enrich your ggplots with group-wise comparisons. This package provides
6739 an easy way to indicate if two groups are significantly different. Commonly
6740 this is shown by a bracket on top connecting the groups of interest which
6741 itself is annotated with the level of significance. The package provides a
6742 single layer that takes the groups for comparison and the test as arguments
6743 and adds the annotation to the plot.")
6744 (license license:gpl3)))
6746 (define-public r-rstatix
6753 (uri (cran-uri "rstatix" version))
6756 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6757 (properties `((upstream-name . "rstatix")))
6758 (build-system r-build-system)
6760 `(("r-broom" ,r-broom)
6762 ("r-corrplot" ,r-corrplot)
6763 ("r-dplyr" ,r-dplyr)
6764 ("r-generics" ,r-generics)
6765 ("r-magrittr" ,r-magrittr)
6766 ("r-purrr" ,r-purrr)
6767 ("r-rlang" ,r-rlang)
6768 ("r-tibble" ,r-tibble)
6769 ("r-tidyr" ,r-tidyr)
6770 ("r-tidyselect" ,r-tidyselect)))
6771 (home-page "https://rpkgs.datanovia.com/rstatix/")
6772 (synopsis "Pipe-friendly framework for basic statistical tests")
6774 "This package provides a simple and intuitive pipe-friendly framework,
6775 coherent with the @code{tidyverse} design philosophy, for performing basic
6776 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6777 correlation analyses. The output of each test is automatically transformed
6778 into a tidy data frame to facilitate visualization. Additional functions are
6779 available for reshaping, reordering, manipulating and visualizing correlation
6781 (license license:gpl2)))
6783 (define-public r-ggpubr
6790 (uri (cran-uri "ggpubr" version))
6793 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6794 (build-system r-build-system)
6796 `(("r-cowplot" ,r-cowplot)
6797 ("r-dplyr" ,r-dplyr)
6798 ("r-ggplot2" ,r-ggplot2)
6799 ("r-ggrepel" ,r-ggrepel)
6800 ("r-ggsci" ,r-ggsci)
6801 ("r-ggsignif" ,r-ggsignif)
6803 ("r-gridextra" ,r-gridextra)
6804 ("r-magrittr" ,r-magrittr)
6805 ("r-polynom" ,r-polynom)
6806 ("r-purrr" ,r-purrr)
6807 ("r-rlang" ,r-rlang)
6808 ("r-scales" ,r-scales)
6809 ("r-rstatix" ,r-rstatix)
6810 ("r-tibble" ,r-tibble)
6811 ("r-tidyr" ,r-tidyr)))
6812 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6813 (synopsis "ggplot2-based publication-ready plots")
6815 "The ggplot2 package is an excellent and flexible package for elegant
6816 data visualization in R. However the default generated plots require some
6817 formatting before we can send them for publication. The ggpubr package
6818 provides some easy-to-use functions for creating and customizing ggplot2-based
6819 publication-ready plots.")
6820 (license license:gpl2)))
6822 (define-public r-ellipse
6829 (uri (cran-uri "ellipse" version))
6832 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6833 (build-system r-build-system)
6834 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6835 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6837 "This package contains various routines for drawing ellipses and
6838 ellipse-like confidence regions, implementing the plots described in Murdoch
6839 and Chow (1996), A graphical display of large correlation matrices, The
6840 American Statistician 50, 178-180. There are also routines implementing the
6841 profile plots described in Bates and Watts (1988), Nonlinear Regression
6842 Analysis and its Applications.")
6843 (license license:gpl2+)))
6845 (define-public r-flashclust
6847 (name "r-flashclust")
6852 (uri (cran-uri "flashClust" version))
6855 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6856 (properties `((upstream-name . "flashClust")))
6857 (build-system r-build-system)
6858 (native-inputs `(("gfortran" ,gfortran)))
6859 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6860 (synopsis "Implementation of optimal hierarchical clustering")
6862 "This package provides a fast implementation of hierarchical
6864 (license license:gpl2+)))
6866 (define-public r-factominer
6868 (name "r-factominer")
6873 (uri (cran-uri "FactoMineR" version))
6876 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6877 (properties `((upstream-name . "FactoMineR")))
6878 (build-system r-build-system)
6881 ("r-cluster" ,r-cluster)
6882 ("r-ellipse" ,r-ellipse)
6883 ("r-flashclust" ,r-flashclust)
6884 ("r-ggplot2" ,r-ggplot2)
6885 ("r-ggrepel" ,r-ggrepel)
6886 ("r-lattice" ,r-lattice)
6887 ("r-leaps" ,r-leaps)
6889 ("r-scatterplot3d" ,r-scatterplot3d)))
6890 (home-page "http://factominer.free.fr")
6891 (synopsis "Multivariate exploratory data analysis and data mining")
6893 "This package provides exploratory data analysis methods to summarize,
6894 visualize and describe datasets. The main principal component methods are
6895 available, those with the largest potential in terms of applications:
6896 principal component analysis (PCA) when variables are quantitative,
6897 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6898 variables are categorical, Multiple Factor Analysis when variables are
6899 structured in groups, etc. and hierarchical cluster analysis.")
6900 (license license:gpl2+)))
6902 (define-public r-factoextra
6904 (name "r-factoextra")
6909 (uri (cran-uri "factoextra" version))
6912 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6913 (build-system r-build-system)
6915 `(("r-abind" ,r-abind)
6916 ("r-cluster" ,r-cluster)
6917 ("r-dendextend" ,r-dendextend)
6918 ("r-factominer" ,r-factominer)
6919 ("r-ggplot2" ,r-ggplot2)
6920 ("r-ggpubr" ,r-ggpubr)
6921 ("r-ggrepel" ,r-ggrepel)
6922 ("r-reshape2" ,r-reshape2)
6923 ("r-tidyr" ,r-tidyr)))
6924 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6925 (synopsis "Extract and visualize the results of multivariate data analyses")
6927 "This package provides some easy-to-use functions to extract and
6928 visualize the output of multivariate data analyses, including
6929 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6930 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6931 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6932 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6933 packages. It contains also functions for simplifying some clustering analysis
6934 steps and provides ggplot2-based elegant data visualization.")
6935 (license license:gpl2)))
6937 (define-public r-fansi
6944 (uri (cran-uri "fansi" version))
6947 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6948 (build-system r-build-system)
6950 `(("r-knitr" ,r-knitr))) ; for vignettes
6951 (home-page "https://github.com/brodieG/fansi")
6952 (synopsis "ANSI control sequence aware string functions")
6954 "This package provides counterparts to R string manipulation functions
6955 that account for the effects of ANSI text formatting control sequences.")
6956 (license license:gpl2+)))
6958 (define-public r-nbclust
6965 (uri (cran-uri "NbClust" version))
6968 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6969 (properties `((upstream-name . "NbClust")))
6970 (build-system r-build-system)
6971 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6972 (synopsis "Determine the best number of clusters in a data set")
6974 "NbClust provides 30 indexes for determining the optimal number of
6975 clusters in a data set and offers the best clustering scheme from different
6976 results to the user.")
6977 (license license:gpl2)))
6979 (define-public r-hdf5r
6986 (uri (cran-uri "hdf5r" version))
6989 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6990 (build-system r-build-system)
6995 `(("r-bit64" ,r-bit64)
6998 `(("r-knitr" ,r-knitr)))
6999 (home-page "https://hhoeflin.github.io/hdf5r")
7000 (synopsis "Interface to the HDF5 binary data format")
7002 "HDF5 is a data model, library and file format for storing and managing
7003 large amounts of data. This package provides a nearly feature complete,
7004 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7005 functionality is added so that HDF5 objects behave very similar to their
7006 corresponding R counterparts.")
7007 (license license:asl2.0)))
7009 (define-public r-itertools
7011 (name "r-itertools")
7016 (uri (cran-uri "itertools" version))
7019 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7020 (build-system r-build-system)
7022 `(("r-iterators" ,r-iterators)))
7023 (home-page "https://cran.r-project.org/web/packages/itertools/")
7024 (synopsis "Iterator tools")
7026 "This package provides various tools for creating iterators, many
7027 patterned after functions in the Python @code{itertools} module, and others
7028 patterned after functions in the snow package.")
7029 (license license:gpl2)))
7031 (define-public r-polynom
7038 (uri (cran-uri "polynom" version))
7041 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7042 (build-system r-build-system)
7043 (home-page "https://cran.r-project.org/web/packages/polynom/")
7044 (synopsis "Functions for univariate polynomial manipulations")
7046 "This package provides a collection of functions to implement a class for
7047 univariate polynomial manipulations.")
7048 (license license:gpl2)))
7050 (define-public r-gbrd
7057 (uri (cran-uri "gbRd" version))
7060 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7061 (properties `((upstream-name . "gbRd")))
7062 (build-system r-build-system)
7063 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7064 (synopsis "Utilities for processing Rd objects and files")
7066 "This package provides utilities for processing Rd objects and files.
7067 Extract argument descriptions and other parts of the help pages of
7069 (license license:gpl2+)))
7071 (define-public r-rjags
7078 (uri (cran-uri "rjags" version))
7081 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7082 (build-system r-build-system)
7084 `(("r-coda" ,r-coda)))
7088 `(("pkg-config" ,pkg-config)))
7089 (home-page "http://mcmc-jags.sourceforge.net")
7090 (synopsis "Bayesian graphical models using MCMC")
7092 "This package provides an R interface to the JAGS MCMC library. JAGS is
7093 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7094 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7095 (license license:gpl2)))
7097 (define-public r-rbibutils
7099 (name "r-rbibutils")
7104 (uri (cran-uri "rbibutils" version))
7107 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7108 (properties `((upstream-name . "rbibutils")))
7109 (build-system r-build-system)
7110 (home-page "https://geobosh.github.io/rbibutils/")
7111 (synopsis "Convert between bibliography formats")
7113 "This package converts between a number of bibliography formats,
7114 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7115 utilities and supports all bibliography formats and character encodings
7116 implemented in bibutils.")
7117 (license license:gpl2)))
7119 (define-public r-rdpack
7126 (uri (cran-uri "Rdpack" version))
7129 "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16"))))
7130 (properties `((upstream-name . "Rdpack")))
7131 (build-system r-build-system)
7133 `(("r-rbibutils" ,r-rbibutils)
7134 ("r-gbrd" ,r-gbrd)))
7135 (home-page "https://github.com/GeoBosh/Rdpack")
7136 (synopsis "Update and manipulate Rd documentation objects")
7138 "This package provides functions for manipulation of R documentation
7139 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7140 updating Rd documentation for functions, methods and classes; it also includes
7141 Rd macros for citations and import of references from bibtex files for use in
7142 Rd files and roxygen2 comments, as well as many functions for manipulation of
7143 references and Rd files.")
7144 (license license:gpl2+)))
7146 (define-public r-officer
7153 (uri (cran-uri "officer" version))
7156 "1s9hrkdx105c1plpxywv68bmp8hvvxbdizhwx81fxr79fhj62x5j"))))
7157 (build-system r-build-system)
7159 `(("r-magrittr" ,r-magrittr)
7165 `(("r-knitr" ,r-knitr)))
7166 (home-page "https://davidgohel.github.io/officer")
7167 (synopsis "Manipulation of Word and PowerPoint documents")
7169 "This package provides tools to access and manipulate Word and PowerPoint
7170 documents from R. The package focuses on tabular and graphical reporting from
7171 R; it also provides two functions that let users get document content into
7172 data objects. A set of functions lets add and remove images, tables and
7173 paragraphs of text in new or existing documents. When working with PowerPoint
7174 presentations, slides can be added or removed; shapes inside slides can also
7175 be added or removed. When working with Word documents, a cursor can be used
7176 to help insert or delete content at a specific location in the document.")
7177 (license license:gpl3)))
7179 (define-public r-profilemodel
7181 (name "r-profilemodel")
7186 (uri (cran-uri "profileModel" version))
7189 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
7190 (properties `((upstream-name . "profileModel")))
7191 (build-system r-build-system)
7192 (home-page "https://github.com/ikosmidis/profileModel")
7193 (synopsis "Profiling inference functions for various model classes")
7195 "This package provides tools that can be used to calculate, evaluate,
7196 plot and use for inference the profiles of *arbitrary* inference functions for
7197 arbitrary @code{glm}-like fitted models with linear predictors. More information
7198 on the methods that are implemented can be found in Kosmidis (2008)
7199 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7200 (license license:gpl2+)))
7202 (define-public r-brglm
7209 (uri (cran-uri "brglm" version))
7212 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7213 (properties `((upstream-name . "brglm")))
7214 (build-system r-build-system)
7216 `(("r-profilemodel" ,r-profilemodel)))
7217 (home-page "https://github.com/ikosmidis/brglm")
7218 (synopsis "Bias reduction in binomial-response generalized linear models")
7220 "Fit generalized linear models with binomial responses using either an
7221 adjusted-score approach to bias reduction or maximum penalized likelihood
7222 where penalization is by Jeffreys invariant prior. These procedures return
7223 estimates with improved frequentist properties (bias, mean squared error) that
7224 are always finite even in cases where the maximum likelihood estimates are
7225 infinite (data separation). Fitting takes place by fitting generalized linear
7226 models on iteratively updated pseudo-data. The interface is essentially the
7227 same as @code{glm}. More flexibility is provided by the fact that custom
7228 pseudo-data representations can be specified and used for model fitting.
7229 Functions are provided for the construction of confidence intervals for the
7230 reduced-bias estimates.")
7231 (license license:gpl2+)))
7233 (define-public r-entropy
7240 (uri (cran-uri "entropy" version))
7243 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
7244 (properties `((upstream-name . "entropy")))
7245 (build-system r-build-system)
7246 (home-page "https://www.strimmerlab.org/software/entropy/")
7247 (synopsis "Estimation of entropy, mutual information and related quantities")
7249 "This package implements various estimators of entropy, such as the
7250 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
7251 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
7252 estimator. It also offers an R interface to the NSB estimator. Furthermore,
7253 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
7254 mutual information, and chi-squared statistic of independence. In addition
7255 there are functions for discretizing continuous random variables.")
7256 (license license:gpl3+)))
7258 (define-public r-abn
7265 (uri (cran-uri "abn" version))
7268 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
7269 (build-system r-build-system)
7273 `(("r-lme4" ,r-lme4)
7276 ("r-rcpparmadillo" ,r-rcpparmadillo)
7277 ("r-rjags" ,r-rjags)))
7278 (home-page "https://r-bayesian-networks.org/")
7279 (synopsis "Modelling multivariate data with additive bayesian networks")
7281 "Bayesian network analysis is a form of probabilistic graphical models
7282 which derives from empirical data a directed acyclic graph, DAG, describing
7283 the dependency structure between random variables. An additive Bayesian
7284 network model consists of a form of a DAG where each node comprises a
7285 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
7286 equivalent to Bayesian multivariate regression using graphical modelling, they
7287 generalises the usual multivariable regression, GLM, to multiple dependent
7288 variables. This package provides routines to help determine optimal Bayesian
7289 network models for a given data set, where these models are used to identify
7290 statistical dependencies in messy, complex data.")
7291 (license license:gpl2+)))
7293 (define-public r-acd
7300 (uri (cran-uri "ACD" version))
7303 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7304 (properties `((upstream-name . "ACD")))
7305 (build-system r-build-system)
7306 (home-page "https://cran.r-project.org/web/packages/ACD/")
7307 (synopsis "Categorical data analysis with complete or missing responses")
7309 "This package provides tools for categorical data analysis with complete
7310 or missing responses.")
7311 (license license:gpl2+)))
7313 (define-public r-acdm
7320 (uri (cran-uri "ACDm" version))
7323 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7324 (properties `((upstream-name . "ACDm")))
7325 (build-system r-build-system)
7327 `(("r-dplyr" ,r-dplyr)
7328 ("r-ggplot2" ,r-ggplot2)
7330 ("r-rsolnp" ,r-rsolnp)
7332 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7333 (synopsis "Tools for Autoregressive Conditional Duration Models")
7335 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7336 and Russell, 1998) models. It creates trade, price or volume durations from
7337 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7339 (license license:gpl2+)))
7341 (define-public r-overlap
7348 (uri (cran-uri "overlap" version))
7351 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7352 (build-system r-build-system)
7353 (home-page "https://cran.r-project.org/web/packages/overlap/")
7354 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7356 "This package provides functions to fit kernel density functions to data
7357 on temporal activity patterns of animals; estimate coefficients of overlapping
7358 of densities for two species; and calculate bootstrap estimates of confidence
7360 (license license:gpl3+)))
7362 (define-public r-snakecase
7364 (name "r-snakecase")
7369 (uri (cran-uri "snakecase" version))
7372 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7373 (build-system r-build-system)
7375 `(("r-stringi" ,r-stringi)
7376 ("r-stringr" ,r-stringr)))
7377 (home-page "https://github.com/Tazinho/snakecase")
7378 (synopsis "Convert strings into any case")
7380 "This package provides a consistent, flexible and easy to use tool to
7381 parse and convert strings into cases like snake or camel among others.")
7382 (license license:gpl3)))
7384 (define-public r-prediction
7386 (name "r-prediction")
7391 (uri (cran-uri "prediction" version))
7394 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7395 (build-system r-build-system)
7397 `(("r-data-table" ,r-data-table)))
7398 (home-page "https://github.com/leeper/prediction")
7399 (synopsis "Tidy, type-safe prediction methods")
7401 "This package provides the @code{prediction()} function, a type-safe
7402 alternative to @code{predict()} that always returns a data frame. The package
7403 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7404 from the @code{stats} package, as well as numerous other model classes from
7405 other add-on packages.")
7406 (license license:expat)))
7408 (define-public r-insight
7415 (uri (cran-uri "insight" version))
7418 "1m95xfvai1kbzqxdggjvdbk6ax2dg4v2lrfpqn7v607g2n77n2k0"))))
7419 (build-system r-build-system)
7421 `(("r-knitr" ,r-knitr)))
7422 (home-page "https://easystats.github.io/insight/")
7423 (synopsis "Easy access to model information for various model objects")
7425 "This package provides a tool to provide an easy, intuitive and
7426 consistent access to information contained in various R models, like model
7427 formulas, model terms, information about random effects, data that was used to
7428 fit the model or data from response variables. The package mainly revolves
7429 around two types of functions: Functions that find (the names of) information,
7430 starting with @code{find_}, and functions that get the underlying data,
7431 starting with @code{get_}. The package has a consistent syntax and works with
7432 many different model objects, where otherwise functions to access these
7433 information are missing.")
7434 (license license:gpl3)))
7436 (define-public r-sjlabelled
7438 (name "r-sjlabelled")
7443 (uri (cran-uri "sjlabelled" version))
7446 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
7447 (build-system r-build-system)
7449 `(("r-insight" ,r-insight)))
7451 `(("r-knitr" ,r-knitr)))
7452 (home-page "https://github.com/strengejacke/sjlabelled")
7453 (synopsis "Labelled data utility functions")
7455 "This package provides a collection of functions dealing with labelled
7456 data, like reading and writing data between R and other statistical software
7457 packages. This includes easy ways to get, set or change value and variable
7458 label attributes, to convert labelled vectors into factors or numeric (and
7459 vice versa), or to deal with multiple declared missing values.")
7460 (license license:gpl3)))
7462 (define-public r-sjmisc
7469 (uri (cran-uri "sjmisc" version))
7472 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7473 (build-system r-build-system)
7475 `(("r-dplyr" ,r-dplyr)
7476 ("r-insight" ,r-insight)
7477 ("r-magrittr" ,r-magrittr)
7478 ("r-purrr" ,r-purrr)
7479 ("r-rlang" ,r-rlang)
7480 ("r-sjlabelled" ,r-sjlabelled)
7481 ("r-tidyselect" ,r-tidyselect)))
7483 `(("r-knitr" ,r-knitr)))
7484 (home-page "https://github.com/strengejacke/sjmisc")
7485 (synopsis "Data and variable transformation functions")
7487 "This package is a collection of miscellaneous utility functions,
7488 supporting data transformation tasks like recoding, dichotomizing or grouping
7489 variables, setting and replacing missing values. The data transformation
7490 functions also support labelled data, and all integrate seamlessly into a
7491 tidyverse workflow.")
7492 (license license:gpl3)))
7494 (define-public r-nortest
7501 (uri (cran-uri "nortest" version))
7504 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7505 (build-system r-build-system)
7506 (home-page "https://cran.r-project.org/web/packages/nortest/")
7507 (synopsis "Tests for normality")
7509 "This package provides five omnibus tests for testing the composite
7510 hypothesis of normality.")
7511 (license license:gpl2+)))
7513 (define-public r-moonbook
7520 (uri (cran-uri "moonBook" version))
7523 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7524 (properties `((upstream-name . "moonBook")))
7525 (build-system r-build-system)
7527 `(("r-magrittr" ,r-magrittr)
7528 ("r-nortest" ,r-nortest)
7529 ("r-purrr" ,r-purrr)
7530 ("r-sjmisc" ,r-sjmisc)
7531 ("r-stringr" ,r-stringr)
7532 ("r-survival" ,r-survival)))
7533 (home-page "https://github.com/cardiomoon/moonBook")
7534 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7536 "This package provides several analysis-related functions for the book
7537 entitled \"R statistics and graph for medical articles\" (written in Korean),
7538 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7540 (license license:gpl2)))
7542 (define-public r-flextable
7544 (name "r-flextable")
7549 (uri (cran-uri "flextable" version))
7552 "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li"))))
7553 (build-system r-build-system)
7555 `(("r-base64enc" ,r-base64enc)
7556 ("r-data-table" ,r-data-table)
7557 ("r-gdtools" ,r-gdtools)
7558 ("r-htmltools" ,r-htmltools)
7559 ("r-knitr" ,r-knitr)
7560 ("r-officer" ,r-officer)
7561 ("r-rlang" ,r-rlang)
7562 ("r-rmarkdown" ,r-rmarkdown)
7564 ("r-xml2" ,r-xml2)))
7566 `(("r-knitr" ,r-knitr)))
7567 (home-page "https://davidgohel.github.io/flextable")
7568 (synopsis "Functions for tabular reporting")
7570 "This package provides tools to create pretty tables for HTML documents
7571 and other formats. Functions are provided to let users create tables, modify
7572 and format their content. It extends the @code{officer} package and can be
7573 used within R markdown documents when rendering to HTML and to Word
7575 (license license:gpl3)))
7577 (define-public r-writexl
7584 (uri (cran-uri "writexl" version))
7587 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7588 (build-system r-build-system)
7589 (inputs `(("zlib" ,zlib)))
7590 (home-page "https://github.com/ropensci/writexl")
7591 (synopsis "Export data frames to xlsx format")
7593 "This package provides a data frame to xlsx exporter based on
7595 (license license:bsd-2)))
7597 (define-public r-biasedurn
7599 (name "r-biasedurn")
7604 (uri (cran-uri "BiasedUrn" version))
7607 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7608 (properties `((upstream-name . "BiasedUrn")))
7609 (build-system r-build-system)
7610 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7611 (synopsis "Biased Urn model distributions")
7613 "This package provides statistical models of biased sampling in the form
7614 of univariate and multivariate noncentral hypergeometric distributions,
7615 including Wallenius' noncentral hypergeometric distribution and Fisher's
7616 noncentral hypergeometric distribution (also called extended hypergeometric
7618 (license license:gpl3)))
7620 (define-public r-goplot
7627 (uri (cran-uri "GOplot" version))
7630 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7631 (properties `((upstream-name . "GOplot")))
7632 (build-system r-build-system)
7634 `(("r-ggdendro" ,r-ggdendro)
7635 ("r-ggplot2" ,r-ggplot2)
7636 ("r-gridextra" ,r-gridextra)
7637 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7638 (home-page "https://github.com/wencke/wencke.github.io")
7639 (synopsis "Visualization of functional analysis data")
7641 "This package provides an implementation of multilayered visualizations
7642 for enhanced graphical representation of functional analysis data. It
7643 combines and integrates omics data derived from expression and functional
7644 annotation enrichment analyses. Its plotting functions have been developed
7645 with an hierarchical structure in mind: starting from a general overview to
7646 identify the most enriched categories (modified bar plot, bubble plot) to a
7647 more detailed one displaying different types of relevant information for the
7648 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7649 Venn diagram, heatmap).")
7650 (license license:gpl2)))
7652 (define-public r-getopt
7659 (uri (cran-uri "getopt" version))
7662 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7663 (build-system r-build-system)
7664 (home-page "https://github.com/trevorld/getopt")
7665 (synopsis "Command-line option processor for R")
7667 "This package is designed to be used with Rscript to write shebang
7668 scripts that accept short and long options. Many users will prefer to
7669 use the packages @code{optparse} or @code{argparse} which add extra
7670 features like automatically generated help options and usage texts,
7671 support for default values, positional argument support, etc.")
7672 (license license:gpl2+)))
7674 (define-public r-findpython
7676 (name "r-findpython")
7681 (uri (cran-uri "findpython" version))
7684 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7685 (build-system r-build-system)
7686 (home-page "https://github.com/trevorld/findpython")
7687 (synopsis "Functions to find an acceptable Python binary")
7689 "This package was designed to find an acceptable Python binary that
7690 matches version and feature constraints.")
7691 (license license:expat)))
7693 ;; This in not the same as "r-argparser"
7694 (define-public r-argparse
7701 (uri (cran-uri "argparse" version))
7704 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
7705 (build-system r-build-system)
7706 (inputs `(("python" ,python)))
7708 `(("r-findpython" ,r-findpython)
7709 ("r-jsonlite" ,r-jsonlite)
7712 `(("r-knitr" ,r-knitr)))
7713 (home-page "https://github.com/trevorld/argparse")
7714 (synopsis "Command line optional and positional argument parser")
7716 "This package provides a command line parser to be used with Rscript to
7717 write shebang scripts that gracefully accept positional and optional arguments
7718 and automatically generate usage notices.")
7719 (license license:gpl2+)))
7721 (define-public r-hash
7728 (uri (cran-uri "hash" version))
7731 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7732 (build-system r-build-system)
7733 (home-page "https://cran.r-project.org/web/packages/hash/")
7734 (synopsis "Implementation of hash/associated arrays/dictionaries")
7736 "This package implements a data structure similar to hashes in Perl and
7737 dictionaries in Python but with a purposefully R flavor. For objects of
7738 appreciable size, access using hashes outperforms native named lists and
7740 (license license:gpl2+)))
7742 (define-public r-orddom
7749 (uri (cran-uri "orddom" version))
7752 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7753 (build-system r-build-system)
7754 (propagated-inputs `(("r-psych" ,r-psych)))
7755 (home-page "https://cran.r-project.org/web/packages/orddom/")
7756 (synopsis "Ordinal dominance statistics")
7758 "This package provides tools to compute ordinal, statistics and effect
7759 sizes as an alternative to mean comparison: Cliff's delta or success rate
7760 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7761 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7762 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7763 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7764 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7765 Group (Non-)Overlap considerations.")
7766 (license license:gpl2)))
7768 (define-public r-deriv
7775 (uri (cran-uri "Deriv" version))
7778 "1fzchsignpb7cpizbf6l8v9k1nkmaf4r4j3mnxz0csl2g2npi1xc"))))
7779 (properties `((upstream-name . "Deriv")))
7780 (build-system r-build-system)
7781 (home-page "https://cran.r-project.org/web/packages/Deriv")
7782 (synopsis "Symbolic differentiation")
7784 "This package provides an R-based solution for symbolic differentiation.
7785 It admits user-defined functions as well as function substitution in arguments
7786 of functions to be differentiated. Some symbolic simplification is part of
7788 (license license:gpl3+)))
7790 (define-public r-doby
7797 (uri (cran-uri "doBy" version))
7800 "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg"))))
7801 (properties `((upstream-name . "doBy")))
7802 (build-system r-build-system)
7804 `(("r-broom" ,r-broom)
7805 ("r-deriv" ,r-deriv)
7806 ("r-dplyr" ,r-dplyr)
7807 ("r-ggplot2" ,r-ggplot2)
7808 ("r-magrittr" ,r-magrittr)
7810 ("r-matrix" ,r-matrix)
7811 ("r-pbkrtest" ,r-pbkrtest)
7812 ("r-tibble" ,r-tibble)))
7814 `(("r-knitr" ,r-knitr)))
7815 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7816 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7818 "This package contains:
7821 @item facilities for working with grouped data: @code{do}
7822 something to data stratified @code{by} some variables.
7823 @item implementations of least-squares means, general linear contrasts, and
7824 @item miscellaneous other utilities.
7826 (license license:gpl2+)))
7828 (define-public r-refgenome
7830 (name "r-refgenome")
7835 (uri (cran-uri "refGenome" version))
7838 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7839 (properties `((upstream-name . "refGenome")))
7840 (build-system r-build-system)
7844 ("r-rsqlite" ,r-rsqlite)))
7845 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7847 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7849 "This package contains functionality for importing and managing of
7850 downloaded genome annotation data from the Ensembl genome browser (European
7851 Bioinformatics Institute) and from the UCSC genome browser (University of
7852 California, Santa Cruz) and annotation routines for genomic positions and
7853 splice site positions.")
7854 (license license:gpl2)))
7856 (define-public r-basix
7863 (uri (cran-uri "BASIX" version))
7866 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7867 (properties `((upstream-name . "BASIX")))
7868 (build-system r-build-system)
7869 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7870 (synopsis "Efficient C/C++ toolset for R")
7872 "BASIX provides some efficient C/C++ implementations of native R
7873 procedures to speed up calculations in R.")
7874 (license license:gpl2)))
7876 (define-public r-blockfest
7878 (name "r-blockfest")
7883 (uri (cran-uri "BlockFeST" version))
7886 "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5"))))
7887 (properties `((upstream-name . "BlockFeST")))
7888 (build-system r-build-system)
7889 (propagated-inputs `(("r-basix" ,r-basix)))
7890 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7891 (synopsis "Bayesian calculation of region-specific fixation index")
7893 "This package provides an R implementation of an extension of the
7894 BayeScan software for codominant markers, adding the option to group
7895 individual SNPs into pre-defined blocks. A typical application of this new
7896 approach is the identification of genomic regions, genes, or gene sets
7897 containing one or more SNPs that evolved under directional selection.")
7898 (license license:gpl2)))
7900 (define-public r-proc
7907 (uri (cran-uri "pROC" version))
7910 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7911 (properties `((upstream-name . "pROC")))
7912 (build-system r-build-system)
7914 `(("r-plyr" ,r-plyr)
7915 ("r-rcpp" ,r-rcpp)))
7916 (home-page "https://web.expasy.org/pROC/")
7917 (synopsis "Display and analyze ROC curves")
7919 "This package provides tools for visualizing, smoothing and comparing
7920 receiver operating characteristic (ROC curves). The area under the
7921 curve (AUC) can be compared with statistical tests based on U-statistics or
7922 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7923 (license license:gpl3+)))
7925 (define-public r-rootsolve
7927 (name "r-rootsolve")
7932 (uri (cran-uri "rootSolve" version))
7935 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7936 (properties `((upstream-name . "rootSolve")))
7937 (build-system r-build-system)
7938 (native-inputs `(("gfortran" ,gfortran)))
7939 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7940 (synopsis "Tools for the analysis of ordinary differential equations")
7942 "This package provides routines to find the root of nonlinear functions,
7943 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7944 differential equations} (ODE). It includes routines that:
7947 @item generate gradient and jacobian matrices (full and banded),
7948 @item find roots of non-linear equations by the Newton-Raphson method,
7949 @item estimate steady-state conditions of a system of (differential) equations
7950 in full, banded or sparse form, using the Newton-Raphson method, or by
7951 dynamically running,
7952 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7953 and 3-D partial differential equations, that have been converted to ordinary
7954 differential equations by numerical differencing (using the method-of-lines
7957 (license license:gpl2+)))
7959 (define-public r-abcanalysis
7961 (name "r-abcanalysis")
7966 (uri (cran-uri "ABCanalysis" version))
7968 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7969 (properties `((upstream-name . "ABCanalysis")))
7970 (build-system r-build-system)
7971 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7972 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7973 (synopsis "Computed ABC Analysis")
7975 "Multivariate data sets often differ in several factors or derived statistical
7976 parameters, which have to be selected for a valid interpretation. Basing this
7977 selection on traditional statistical limits leads occasionally to the perception
7978 of losing information from a data set. This package provides tools to calculate
7979 these limits on the basis of the mathematical properties of the distribution of
7980 the analyzed items.")
7981 (license license:gpl3)))
7983 (define-public r-slam
7990 (uri (cran-uri "slam" version))
7992 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
7993 (build-system r-build-system)
7994 (home-page "https://cran.r-project.org/web/packages/slam/")
7995 (synopsis "Sparse lightweight arrays and matrices")
7997 "This package contains data structures and algorithms for sparse arrays and matrices,
7998 based on index arrays and simple triplet representations, respectively.")
7999 (license license:gpl2)))
8001 (define-public r-manipulatewidget
8003 (name "r-manipulatewidget")
8008 (uri (cran-uri "manipulateWidget" version))
8010 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8012 `((upstream-name . "manipulateWidget")))
8013 (build-system r-build-system)
8015 `(("r-base64enc" ,r-base64enc)
8016 ("r-codetools" ,r-codetools)
8017 ("r-htmltools" ,r-htmltools)
8018 ("r-htmlwidgets" ,r-htmlwidgets)
8019 ("r-knitr" ,r-knitr)
8020 ("r-miniui" ,r-miniui)
8021 ("r-shiny" ,r-shiny)
8022 ("r-webshot" ,r-webshot)))
8023 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8024 (synopsis "Add even more interactivity to interactive charts")
8026 "This package lets you create in just a few lines of R code a nice user interface to
8027 modify the data or the graphical parameters of one or multiple interactive
8028 charts. It is useful to quickly explore visually some data or for package
8029 developers to generate user interfaces easy to maintain.")
8030 (license license:gpl2+)))
8039 (uri (cran-uri "A3" version))
8041 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8042 (properties `((upstream-name . "A3")))
8043 (build-system r-build-system)
8045 `(("r-pbapply" ,r-pbapply)
8046 ("r-xtable" ,r-xtable)))
8047 (home-page "https://cran.r-project.org/web/packages/A3/")
8048 (synopsis "Error metrics for predictive models")
8050 "This package supplies tools for tabulating and analyzing the results of predictive
8051 models. The methods employed are applicable to virtually any predictive model
8052 and make comparisons between different methodologies straightforward.")
8053 (license license:gpl2+)))
8055 (define-public r-infotheo
8062 (uri (cran-uri "infotheo" version))
8065 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8066 (build-system r-build-system)
8067 (home-page "http://homepage.meyerp.com/software")
8068 (synopsis "Information-theoretic measures")
8070 "This package implements various measures of information theory based on
8071 several entropy estimators.")
8072 (license license:gpl3+)))
8074 (define-public r-abcoptim
8081 (uri (cran-uri "ABCoptim" version))
8083 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8084 (properties `((upstream-name . "ABCoptim")))
8085 (build-system r-build-system)
8086 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8087 (home-page "https://github.com/gvegayon/ABCoptim/")
8088 (synopsis "Optimization of Artificial Bee Colony algorithm")
8090 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8091 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8092 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8093 algorithms, and uses only common control parameters such as colony size and
8094 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8095 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8096 This version is a work-in-progress and is written in R code.")
8097 (license license:expat)))
8099 (define-public r-abcp2
8106 (uri (cran-uri "ABCp2" version))
8108 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8109 (properties `((upstream-name . "ABCp2")))
8110 (build-system r-build-system)
8111 (propagated-inputs `(("r-mass" ,r-mass)))
8112 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8113 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8115 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8116 Poisson, and Gamma distribution and estimates the proportional paternity of the
8117 second male (P2) based on the best fit distribution.")
8118 (license license:gpl2)))
8120 (define-public r-abcrf
8127 (uri (cran-uri "abcrf" version))
8129 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8130 (build-system r-build-system)
8132 `(("r-doparallel" ,r-doparallel)
8133 ("r-foreach" ,r-foreach)
8135 ("r-matrixstats" ,r-matrixstats)
8136 ("r-ranger" ,r-ranger)
8138 ("r-rcpparmadillo" ,r-rcpparmadillo)
8139 ("r-readr" ,r-readr)
8140 ("r-stringr" ,r-stringr)))
8141 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8142 (synopsis "Approximate bayesian computation via random forests")
8144 "This package performs approximate bayesian computation (ABC) model choice and
8145 parameter inference via random forests. This machine learning tool named random
8146 forests (RF) can conduct selection among the highly complex models covered by
8148 (license license:gpl2+)))
8150 (define-public r-abctools
8157 (uri (cran-uri "abctools" version))
8159 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8160 (build-system r-build-system)
8163 ("r-abind" ,r-abind)
8164 ("r-hmisc" ,r-hmisc)
8165 ("r-plyr" ,r-plyr)))
8166 (home-page "https://github.com/dennisprangle/abctools/")
8167 (synopsis "Tools for ABC analyses")
8169 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8170 including summary statistic selection and assessing coverage. This includes
8171 recent dimension reduction algorithms to tune the choice of summary statistics,
8172 and coverage methods to tune the choice of threshold.")
8173 (license license:gpl2+)))
8175 (define-public r-ggstance
8182 (uri (cran-uri "ggstance" version))
8184 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
8185 (build-system r-build-system)
8187 `(("r-ggplot2" ,r-ggplot2)
8189 ("r-rlang" ,r-rlang)
8190 ("r-withr" ,r-withr)))
8191 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8192 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8194 "This package is a @code{r-ggplot2} extension that provides flipped components:
8196 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8197 @item vertical versions of @code{r-ggplot2} positions.
8199 (license license:gpl3)))
8201 (define-public r-mosaiccore
8203 (name "r-mosaiccore")
8208 (uri (cran-uri "mosaicCore" version))
8210 (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj"))))
8211 (properties `((upstream-name . "mosaicCore")))
8212 (build-system r-build-system)
8214 `(("r-dplyr" ,r-dplyr)
8216 ("r-rlang" ,r-rlang)
8217 ("r-tidyr" ,r-tidyr)))
8218 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8219 (synopsis "Common utilities for mosaic family packages")
8221 "Common utilities used in other Mosaic family packages are collected here.")
8222 (license license:gpl2+)))
8224 (define-public r-ggformula
8226 (name "r-ggformula")
8231 (uri (cran-uri "ggformula" version))
8233 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
8234 (build-system r-build-system)
8236 `(("r-ggforce" ,r-ggforce)
8237 ("r-ggplot2" ,r-ggplot2)
8238 ("r-ggstance" ,r-ggstance)
8239 ("r-magrittr" ,r-magrittr)
8240 ("r-mosaiccore" ,r-mosaiccore)
8241 ("r-rlang" ,r-rlang)
8242 ("r-stringr" ,r-stringr)
8243 ("r-tibble" ,r-tibble)))
8244 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
8245 (synopsis "Formula interface for the @code{r-ggplot2}")
8247 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
8248 gf_density(), and so on, bring the formula interface to ggplot(). This captures
8249 and extends the excellent simplicity of the lattice-graphics formula interface,
8250 while providing the intuitive capabilities of @code{r-ggplot2}.")
8251 (license license:expat)))
8253 (define-public r-mosaicdata
8255 (name "r-mosaicdata")
8260 (uri (cran-uri "mosaicData" version))
8262 (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji"))))
8263 (properties `((upstream-name . "mosaicData")))
8264 (build-system r-build-system)
8265 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
8266 (synopsis "Data sets for project Mosaic")
8268 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
8269 used to teach mathematics, statistics, computation and modeling.")
8270 (license license:gpl2+)))
8272 (define-public r-raster
8279 (uri (cran-uri "raster" version))
8282 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
8283 (build-system r-build-system)
8285 `(("r-rcpp" ,r-rcpp)
8287 (home-page "https://www.rspatial.org/")
8288 (synopsis "Geographic data analysis and modeling")
8290 "The package implements basic and high-level functions for reading,
8291 writing, manipulating, analyzing and modeling of gridded spatial data.
8292 Processing of very large files is supported.")
8293 (license license:gpl3+)))
8295 (define-public r-mosaic
8302 (uri (cran-uri "mosaic" version))
8304 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8305 (build-system r-build-system)
8307 `(("r-broom" ,r-broom)
8308 ("r-dplyr" ,r-dplyr)
8309 ("r-ggdendro" ,r-ggdendro)
8310 ("r-ggformula" ,r-ggformula)
8311 ("r-ggplot2" ,r-ggplot2)
8312 ("r-ggrepel" ,r-ggrepel)
8314 ("r-gridextra" ,r-gridextra)
8315 ("r-lattice" ,r-lattice)
8316 ("r-latticeextra" ,r-latticeextra)
8317 ("r-lazyeval" ,r-lazyeval)
8319 ("r-matrix" ,r-matrix)
8320 ("r-mosaiccore" ,r-mosaiccore)
8321 ("r-mosaicdata" ,r-mosaicdata)
8322 ("r-readr" ,r-readr)
8323 ("r-tidyr" ,r-tidyr)))
8325 `(("r-knitr" ,r-knitr)))
8326 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8327 (synopsis "Mathematics, statistics, and computation teaching utilities")
8329 "This package contain data sets and utilities from
8330 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8331 statistics, computation and modeling. Project MOSAIC is a community of
8332 educators working to tie together aspects of quantitative work that students
8333 in science, technology, engineering and mathematics will need in their
8334 professional lives, but which are usually taught in isolation, if at all.")
8335 (license license:gpl2+)))
8337 (define-public r-abd
8344 (uri (cran-uri "abd" version))
8346 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8347 (build-system r-build-system)
8349 `(("r-lattice" ,r-lattice)
8350 ("r-mosaic" ,r-mosaic)
8351 ("r-nlme" ,r-nlme)))
8352 (home-page "https://cran.r-project.org/web/packages/abd/")
8353 (synopsis "Analysis of biological data")
8355 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8356 biological data by Michael Whitlock and Dolph Schluter.")
8357 (license license:gpl2)))
8359 (define-public r-svgui
8366 (uri (cran-uri "svGUI" version))
8368 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8369 (properties `((upstream-name . "svGUI")))
8370 (build-system r-build-system)
8371 (home-page "https://github.com/SciViews/svGUI/")
8372 (synopsis "Functions for managing GUI clients in R")
8374 "The SciViews @code{svGUI} package eases the management of Graphical User
8375 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8376 centralizes info about GUI elements currently used, and it dispatches GUI
8377 calls to the particular toolkits in use in function of the context.")
8378 (license license:gpl2)))
8380 (define-public r-svdialogs
8382 (name "r-svdialogs")
8387 (uri (cran-uri "svDialogs" version))
8389 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8390 (properties `((upstream-name . "svDialogs")))
8391 (build-system r-build-system)
8394 ("zenity" ,zenity)))
8396 `(("r-rstudioapi" ,r-rstudioapi)
8397 ("r-svgui" ,r-svgui)))
8398 (home-page "https://github.com/SciViews/svDialogs/")
8399 (synopsis "Portable dialog boxes")
8401 "This package helps to construct standard dialog boxes for your GUI, including
8402 message boxes, input boxes, list, file or directory selection, and others. In
8403 case R cannot display GUI dialog boxes, a simpler command line version of these
8404 interactive elements is also provided as a fallback solution.")
8405 (license license:gpl2)))
8407 (define-public r-abe
8414 (uri (cran-uri "abe" version))
8417 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8418 (build-system r-build-system)
8419 (home-page "https://cran.r-project.org/web/packages/abe/")
8420 (synopsis "Augmented backward elimination")
8422 "This package performs augmented backward elimination and checks the
8423 stability of the obtained model. Augmented backward elimination combines
8424 significance or information based criteria with the change in estimate to
8425 either select the optimal model for prediction purposes or to serve as a tool
8426 to obtain a practically sound, highly interpretable model.")
8427 (license license:gpl2+)))
8429 (define-public r-abf2
8436 (uri (cran-uri "abf2" version))
8438 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8439 (build-system r-build-system)
8440 (home-page "https://cran.r-project.org/web/packages/abf2/")
8441 (synopsis "Load gap-free axon @code{r-abf2} files")
8443 "This package loads electrophysiology data from ABF2 files, as created by
8444 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8445 mode are currently supported.")
8446 (license license:artistic2.0)))
8448 (define-public r-abhgenotyper
8450 (name "r-abhgenotyper")
8455 (uri (cran-uri "ABHgenotypeR" version))
8457 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8458 (properties `((upstream-name . "ABHgenotypeR")))
8459 (build-system r-build-system)
8461 `(("r-ggplot2" ,r-ggplot2)
8462 ("r-reshape2" ,r-reshape2)))
8463 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8464 (synopsis "Visualize and manipulate ABH genotypes")
8466 "The @code{r-abhgenotyper} package provides simple imputation,
8467 error-correction and plotting capacities for genotype data. The package is
8468 supposed to serve as an intermediate but independent analysis tool between the
8469 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8470 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8471 genotypes as \"graphical genotypes\".")
8472 (license license:gpl3)))
8474 (define-public r-furrr
8481 (uri (cran-uri "furrr" version))
8484 "16s6sgfgh1ayzhf3kvpy9vhsd5h6p57waj1xgbksgdmf4j1wkcq7"))))
8485 (build-system r-build-system)
8487 `(("r-ellipsis" ,r-ellipsis)
8488 ("r-future" ,r-future)
8489 ("r-globals" ,r-globals)
8490 ("r-lifecycle" ,r-lifecycle)
8491 ("r-purrr" ,r-purrr)
8492 ("r-rlang" ,r-rlang)
8493 ("r-vctrs" ,r-vctrs)))
8494 (home-page "https://github.com/DavisVaughan/furrr")
8495 (synopsis "Apply mapping functions in parallel using futures")
8497 "This package provides implementations of the family of @code{map()}
8498 functions from the @code{purrr} package that can be resolved using any
8499 @code{future}-supported backend, e.g. parallel on the local machine or
8500 distributed on a compute cluster.")
8501 (license license:lgpl2.1+)))
8503 (define-public r-abjutils
8510 (uri (cran-uri "abjutils" version))
8512 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8513 (build-system r-build-system)
8515 `(("r-dplyr" ,r-dplyr)
8516 ("r-magrittr" ,r-magrittr)
8517 ("r-purrr" ,r-purrr)
8518 ("r-rlang" ,r-rlang)
8519 ("r-rstudioapi" ,r-rstudioapi)
8520 ("r-stringi" ,r-stringi)
8521 ("r-stringr" ,r-stringr)
8522 ("r-tidyr" ,r-tidyr)))
8523 (home-page "https://github.com/abjur/abjutils/")
8524 (synopsis "Collection of tools for jurimetrical analysis")
8526 "This package implements general purpose tools, such as functions for
8527 sampling and basic manipulation of Brazilian lawsuits identification number.
8528 It also implements functions for text cleaning, such as accentuation
8530 (license license:expat)))
8532 (define-public r-abnormality
8534 (name "r-abnormality")
8539 (uri (cran-uri "abnormality" version))
8541 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8542 (build-system r-build-system)
8544 `(("r-mass" ,r-mass)
8545 ("r-matrix" ,r-matrix)))
8546 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8547 (synopsis "Measure a subject's abnormality with respect to a reference population")
8549 "This package contains functions to implement the methodology and
8550 considerations laid out by Marks et al. in the article \"Measuring abnormality
8551 in high dimensional spaces: applications in biomechanical gait analysis\".
8552 Using high-dimensional datasets to measure a subject's overall level of
8553 abnormality as compared to a reference population is often needed in outcomes
8555 (license license:expat)))
8557 (define-public r-abodoutlier
8559 (name "r-abodoutlier")
8564 (uri (cran-uri "abodOutlier" version))
8566 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8567 (properties `((upstream-name . "abodOutlier")))
8568 (build-system r-build-system)
8570 `(("r-cluster" ,r-cluster)))
8571 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8572 (synopsis "Angle-based outlier detection")
8574 "This package performs angle-based outlier detection on a given data
8575 frame. It offers three methods to process data:
8577 @item full but slow implementation using all the data that has cubic
8579 @item a fully randomized method;
8580 @item a method using k-nearest neighbours.
8582 These algorithms are well suited for high dimensional data outlier
8584 (license license:expat)))
8586 (define-public r-abps
8593 (uri (cran-uri "ABPS" version))
8595 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8596 (properties `((upstream-name . "ABPS")))
8597 (build-system r-build-system)
8598 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8599 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8600 (synopsis "Abnormal blood profile score to detect blood doping")
8602 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8603 The ABPS is a part of the Athlete biological passport program of the World
8604 anti-doping agency, which combines several blood parameters into a single
8605 score in order to detect blood doping. The package also contains functions to
8606 calculate other scores used in anti-doping programs, such as the ratio of
8607 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8608 (license license:gpl2+)))
8610 (define-public r-parmigene
8612 (name "r-parmigene")
8617 (uri (cran-uri "parmigene" version))
8620 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8621 (build-system r-build-system)
8622 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8623 (synopsis "Mutual information estimation for gene network reconstruction")
8625 "This package provides a parallel estimation of the mutual information
8626 based on entropy estimates from k-nearest neighbors distances and algorithms
8627 for the reconstruction of gene regulatory networks.")
8628 (license license:agpl3+)))
8630 (define-public r-pscl
8637 (uri (cran-uri "pscl" version))
8639 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8640 (build-system r-build-system)
8642 `(("r-mass" ,r-mass)))
8643 (home-page "https://github.com/atahk/pscl/")
8644 (synopsis "Political science computational laboratory")
8646 "The @code{pscl} is an R package providing classes and methods for:
8648 @item Bayesian analysis of roll call data (item-response models);
8649 @item elementary Bayesian statistics;
8650 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8652 @item utility functions.
8654 (license license:gpl2)))
8656 (define-public r-accelmissing
8658 (name "r-accelmissing")
8663 (uri (cran-uri "accelmissing" version))
8665 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8666 (build-system r-build-system)
8668 `(("r-mice" ,r-mice)
8669 ("r-pscl" ,r-pscl)))
8670 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8671 (synopsis "Missing value imputation for accelerometer data")
8673 "This package provides a statistical method to impute the missing values in
8674 accelerometer data. The methodology includes both parametric and
8675 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8676 model. It also provides multiple functions to preprocess the accelerometer data
8677 previous to the missing data imputation. These include detecting the wearing
8678 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8679 (license license:gpl2+)))
8681 (define-public r-mhsmm
8688 (uri (cran-uri "mhsmm" version))
8690 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8691 (build-system r-build-system)
8692 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8693 (home-page "https://github.com/jaredo/mhsmm/")
8694 (synopsis "Inference for hidden Markov and semi-Markov models")
8696 "The @code{r-mhsmm} package implements estimation and prediction methods for
8697 hidden Markov and semi-Markov models for multiple observation sequences. Such
8698 techniques are of interest when observed data is thought to be dependent on some
8699 unobserved (or hidden) state. Also, this package is suitable for equidistant
8700 time series data, with multivariate and/or missing data. Allows user defined
8701 emission distributions.")
8702 (license license:gpl2+)))
8704 (define-public r-nleqslv
8711 (uri (cran-uri "nleqslv" version))
8713 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8714 (build-system r-build-system)
8715 (native-inputs `(("gfortran" ,gfortran)))
8716 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8717 (synopsis "Solve systems of nonlinear equations")
8719 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8720 Broyden or a Newton method with a choice of global strategies such as line
8721 search and trust region. There are options for using a numerical or user
8722 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8723 singular or ill-conditioned Jacobian.")
8724 (license license:gpl2+)))
8726 (define-public r-physicalactivity
8728 (name "r-physicalactivity")
8733 (uri (cran-uri "PhysicalActivity" version))
8735 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8737 `((upstream-name . "PhysicalActivity")))
8738 (build-system r-build-system)
8739 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8740 (synopsis "Procesing accelerometer data for physical activity measurement")
8742 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8743 for classification of monitor wear and nonwear time intervals in accelerometer
8744 data collected to assess physical activity. The package also contains functions
8745 for making plots of accelerometer data and obtaining the summary of various
8746 information including daily monitor wear time and the mean monitor wear time
8747 during valid days. The revised package version 0.2-1 improved the functions
8748 regarding speed, robustness and add better support for time zones and daylight
8749 saving. In addition, several functions were added:
8751 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8752 @item the @code{markPAI} can categorize physical activity intensity level based
8753 on user-defined cut-points of accelerometer counts.
8755 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8756 @code{queryActigraph} functions.")
8757 (license license:gpl3+)))
8759 (define-public r-acc
8766 (uri (cran-uri "acc" version))
8768 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8769 (build-system r-build-system)
8771 `(("r-circlize" ,r-circlize)
8773 ("r-ggplot2" ,r-ggplot2)
8774 ("r-iterators" ,r-iterators)
8775 ("r-mhsmm" ,r-mhsmm)
8776 ("r-nleqslv" ,r-nleqslv)
8777 ("r-physicalactivity" ,r-physicalactivity)
8779 ("r-r-utils" ,r-r-utils)
8781 ("r-rcpparmadillo" ,r-rcpparmadillo)
8782 ("r-rsqlite" ,r-rsqlite)
8784 (home-page "https://cran.r-project.org/web/packages/acc/")
8785 (synopsis "Exploring accelerometer data")
8787 "This package processes accelerometer data from uni-axial and tri-axial devices
8788 and generates data summaries. Also, includes functions to plot, analyze, and
8789 simulate accelerometer data.")
8790 (license license:gpl2+)))
8792 (define-public r-rbenchmark
8794 (name "r-rbenchmark")
8799 (uri (cran-uri "rbenchmark" version))
8801 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8802 (build-system r-build-system)
8803 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8804 (synopsis "Benchmarking routine for R")
8806 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8807 and is intended to facilitate benchmarking of arbitrary R code. The library
8808 consists of just one function, benchmark, which is a simple wrapper around
8809 system.time. Given a specification of the benchmarking process (counts of
8810 replications, evaluation environment) and an arbitrary number of expressions,
8811 benchmark evaluates each of the expressions in the specified environment,
8812 replicating the evaluation as many times as specified, and returning the results
8813 conveniently wrapped into a data frame.")
8814 (license license:gpl2+)))
8816 (define-public r-mitools
8823 (uri (cran-uri "mitools" version))
8826 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8827 (build-system r-build-system)
8828 (propagated-inputs `(("r-dbi" ,r-dbi)))
8829 (home-page "https://cran.r-project.org/web/packages/mitools/")
8830 (synopsis "Tools for multiple imputation of missing data")
8832 "This package provides tools to perform analyses and combine results from
8833 multiple-imputation datasets.")
8834 (license license:gpl2)))
8836 (define-public r-mixsqp
8842 (uri (cran-uri "mixsqp" version))
8845 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
8846 (properties `((upstream-name . "mixsqp")))
8847 (build-system r-build-system)
8849 `(("r-irlba" ,r-irlba)
8851 ("r-rcpparmadillo" ,r-rcpparmadillo)))
8853 `(("r-knitr" ,r-knitr)))
8854 (home-page "https://github.com/stephenslab/mixsqp")
8856 "Sequential quadratic programming for maximum-likelihood estimation")
8858 "This package provides an optimization method based on sequential
8859 quadratic programming for maximum likelihood estimation of the mixture
8860 proportions in a finite mixture model where the component densities are
8861 known. The algorithm is expected to obtain solutions that are at least
8862 as accurate as the state-of-the-art MOSEK interior-point solver, and they
8863 are expected to arrive at solutions more quickly when the number of
8864 samples is large and the number of mixture components is not too large.")
8865 (license license:expat)))
8867 (define-public r-magick
8874 (uri (cran-uri "magick" version))
8877 "0myvryya7b4bbw0hs4jqflrbdffmg78kz28gbybw3yc7zwc7sqxx"))))
8878 (build-system r-build-system)
8880 `(("imagemagick" ,imagemagick)
8883 `(("r-curl" ,r-curl)
8884 ("r-magrittr" ,r-magrittr)
8885 ("r-rcpp" ,r-rcpp)))
8887 `(("pkg-config" ,pkg-config)
8888 ("r-knitr" ,r-knitr)))
8889 (home-page "https://github.com/ropensci/magick")
8890 (synopsis "Advanced graphics and image-processing in R")
8892 "This package provides bindings to ImageMagick, a comprehensive image
8893 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8894 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8895 operations are vectorized via the Magick++ STL meaning they operate either on
8896 a single frame or a series of frames for working with layers, collages, or
8897 animation. In RStudio, images are automatically previewed when printed to the
8898 console, resulting in an interactive editing environment.")
8899 (license license:expat)))
8901 (define-public r-survey
8908 (uri (cran-uri "survey" version))
8911 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8912 (build-system r-build-system)
8914 `(("r-lattice" ,r-lattice)
8915 ("r-matrix" ,r-matrix)
8916 ("r-minqa" ,r-minqa)
8917 ("r-mitools" ,r-mitools)
8918 ("r-numderiv" ,r-numderiv)
8919 ("r-survival" ,r-survival)))
8920 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8921 (synopsis "Analysis of complex survey samples")
8923 "This package provides tools for the analysis of complex survey samples.
8924 The provided features include: summary statistics, two-sample tests, rank
8925 tests, generalised linear models, cumulative link models, Cox models,
8926 loglinear models, and general maximum pseudolikelihood estimation for
8927 multistage stratified, cluster-sampled, unequally weighted survey samples;
8928 variances by Taylor series linearisation or replicate weights;
8929 post-stratification, calibration, and raking; two-phase subsampling designs;
8930 graphics; PPS sampling without replacement; principal components, and factor
8932 ;; Either version of the GPL.
8933 (license (list license:gpl2 license:gpl3))))
8935 (define-public r-gee
8942 (uri (cran-uri "gee" version))
8945 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8946 (properties `((upstream-name . "gee")))
8947 (build-system r-build-system)
8949 `(("gfortran" ,gfortran)))
8950 (home-page "https://cran.r-project.org/web/packages/gee/")
8951 (synopsis "Generalized estimation equation solver")
8953 "This package provides a solver for generalized estimation equations.")
8954 (license license:gpl2)))
8956 (define-public r-tab
8963 (uri (cran-uri "tab" version))
8966 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8967 (properties `((upstream-name . "tab")))
8968 (build-system r-build-system)
8970 `(("r-dplyr" ,r-dplyr)
8972 ("r-knitr" ,r-knitr)
8974 ("r-survey" ,r-survey)
8975 ("r-survival" ,r-survival)
8976 ("r-xtable" ,r-xtable)))
8977 (home-page "https://cran.r-project.org/web/packages/tab/")
8978 (synopsis "Create summary tables for statistical reports")
8980 "This package contains functions for creating various types of summary
8981 tables, e.g. comparing characteristics across levels of a categorical variable
8982 and summarizing fitted generalized linear models, generalized estimating
8983 equations, and Cox proportional hazards models. Functions are available to
8984 handle data from simple random samples as well as complex surveys.")
8985 (license license:gpl3+)))
8987 (define-public r-dvmisc
8994 (uri (cran-uri "dvmisc" version))
8996 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8997 (build-system r-build-system)
8999 `(("r-cubature" ,r-cubature)
9000 ("r-data-table" ,r-data-table)
9001 ("r-dplyr" ,r-dplyr)
9002 ("r-ggplot2" ,r-ggplot2)
9004 ("r-mvtnorm" ,r-mvtnorm)
9005 ("r-pracma" ,r-pracma)
9006 ("r-rbenchmark" ,r-rbenchmark)
9008 ("r-survey" ,r-survey)
9010 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9011 (synopsis "Faster computation of common statistics and miscellaneous functions")
9013 "This package implements faster versions of base R functions (e.g. mean, standard
9014 deviation, covariance, weighted mean), mostly written in C++, along with
9015 miscellaneous functions for various purposes (e.g. create the histogram with
9016 fitted probability density function or probability mass function curve, create
9017 the body mass index groups, assess the linearity assumption in logistic
9019 (license license:gpl2)))
9021 (define-public r-accelerometry
9023 (name "r-accelerometry")
9028 (uri (cran-uri "accelerometry" version))
9030 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9031 (build-system r-build-system)
9033 `(("r-dvmisc" ,r-dvmisc)
9034 ("r-rcpp" ,r-rcpp)))
9035 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9036 (synopsis "Functions for processing accelerometer data")
9038 "This package provides a collection of functions that perform operations on
9039 time-series accelerometer data, such as identify the non-wear time, flag minutes
9040 that are part of an activity bout, and find the maximum 10-minute average count
9041 value. The functions are generally very flexible, allowing for a variety of
9042 algorithms to be implemented.")
9043 (license license:gpl3)))
9045 (define-public r-absim
9052 (uri (cran-uri "AbSim" version))
9054 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9055 (properties `((upstream-name . "AbSim")))
9056 (build-system r-build-system)
9059 ("r-powerlaw" ,r-powerlaw)))
9060 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9061 (synopsis "Time resolved simulations of antibody repertoires")
9063 "This package provides simulation methods for the evolution of antibody repertoires.
9064 The heavy and light chain variable region of both human and C57BL/6 mice can
9065 be simulated in a time-dependent fashion. Both single lineages using one set of
9066 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9067 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9068 Upon completion, the main loop of the algorithm begins, with each iteration
9069 representing one simulated time step. Various mutation events are possible at
9070 each time step, contributing to a diverse final repertoire.")
9071 (license license:gpl2)))
9073 (define-public r-quic
9080 (uri (cran-uri "QUIC" version))
9082 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9083 (properties `((upstream-name . "QUIC")))
9084 (build-system r-build-system)
9085 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9086 (synopsis "Regularized sparse inverse covariance matrix estimation")
9088 "This package implements the regularized Gaussian maximum likelihood
9089 estimation of the inverse of a covariance matrix. It uses Newton's method and
9090 coordinate descent to solve the regularized inverse covariance matrix
9091 estimation problem.")
9092 ;; The project home page states that the release is under GPLv3 or later.
9093 ;; The CRAN page only says GPL-3.
9094 (license license:gpl3+)))
9096 (define-public r-abundant
9103 (uri (cran-uri "abundant" version))
9105 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9106 (build-system r-build-system)
9108 `(("r-quic" ,r-quic)))
9109 (home-page "https://cran.r-project.org/web/packages/abundant/")
9110 (synopsis "Abundant regression and high-dimensional principal fitted components")
9112 "This package provides tools to fit and predict with the high-dimensional
9113 principal fitted components model. This model is described by Cook, Forzani,
9114 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9115 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9116 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9117 (license license:gpl2+)))
9119 (define-public r-ac3net
9126 (uri (cran-uri "Ac3net" version))
9128 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9129 (properties `((upstream-name . "Ac3net")))
9130 (build-system r-build-system)
9132 `(("r-data-table" ,r-data-table)))
9133 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9134 (synopsis "Inferring directional conservative causal core gene networks")
9135 (description "This package infers directional Conservative causal core
9136 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9137 directional network.")
9138 (license license:gpl3+)))
9140 (define-public r-aca
9147 (uri (cran-uri "ACA" version))
9149 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9150 (properties `((upstream-name . "ACA")))
9151 (build-system r-build-system)
9152 (home-page "https://cran.r-project.org/web/packages/ACA/")
9153 (synopsis "Abrupt change-point or aberration detection in point series")
9155 "This package offers an interactive function for the detection of breakpoints in
9157 ;; Any version of the GPL
9158 (license (list license:gpl2+ license:gpl3+))))
9160 (define-public r-acceptancesampling
9162 (name "r-acceptancesampling")
9167 (uri (cran-uri "AcceptanceSampling" version))
9169 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9171 `((upstream-name . "AcceptanceSampling")))
9172 (build-system r-build-system)
9173 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9174 (synopsis "Creation and evaluation of acceptance sampling plans")
9176 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9177 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9178 in quality control and improvement. International standards of acceptance
9179 sampling provide sampling plans for specific circumstances. The aim of this
9180 package is to provide an easy-to-use interface to visualize single, double or
9181 multiple sampling plans. In addition, methods have been provided to enable the
9182 user to assess sampling plans against pre-specified levels of performance, as
9183 measured by the probability of acceptance for a given level of quality in the
9185 (license license:gpl3+)))
9187 (define-public r-acclma
9194 (uri (cran-uri "ACCLMA" version))
9196 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
9197 (properties `((upstream-name . "ACCLMA")))
9198 (build-system r-build-system)
9199 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
9200 (synopsis "ACC & LMA graph plotting")
9202 "This package contains a function that imports data from a @acronym{CSV,
9203 Comma-Separated Values} file, or uses manually entered data from the format (x,
9204 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
9205 Curve} vs @acronym{LOI, Line of Independence} graph and
9206 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
9207 function is @code{plotLMA} (source file, header) that takes a data set and plots the
9208 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
9209 string) was passed, a manual data entry window is opened. The header parameter
9210 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
9211 a header row or not. The dataset should contain only one independent variable
9212 (x) and one dependent variable (y) and can contain a weight for each
9214 (license license:gpl2)))
9216 (define-public r-aspi
9223 (uri (cran-uri "aspi" version))
9225 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
9226 (build-system r-build-system)
9228 "https://cran.r-project.org/web/packages/aspi/")
9230 "Analysis of symmetry of parasitic infections")
9232 "This package provides tools for the analysis and visualization of bilateral
9233 asymmetry in parasitic infections.")
9234 (license license:gpl3+)))
9236 (define-public r-sandwich
9243 (uri (cran-uri "sandwich" version))
9246 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
9247 (build-system r-build-system)
9249 `(("r-zoo" ,r-zoo)))
9250 (home-page "https://cran.r-project.org/web/packages/sandwich/")
9251 (synopsis "Robust Covariance Matrix Estimators")
9253 "This package provides model-robust standard error estimators for
9254 cross-sectional, time series, clustered, panel, and longitudinal data.")
9255 ;; Either version of the license.
9256 (license (list license:gpl2 license:gpl3))))
9258 (define-public r-th-data
9265 (uri (cran-uri "TH.data" version))
9268 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
9269 (properties `((upstream-name . "TH.data")))
9270 (build-system r-build-system)
9272 `(("r-mass" ,r-mass)
9273 ("r-survival" ,r-survival)))
9274 (home-page "https://cran.r-project.org/web/packages/TH.data/")
9275 (synopsis "Shared data sets")
9277 "This package contains supporting data sets that are used in other
9278 packages maintained by Torsten Hothorn.")
9279 (license license:gpl3)))
9281 (define-public r-multcomp
9288 (uri (cran-uri "multcomp" version))
9291 "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr"))))
9292 (build-system r-build-system)
9294 `(("r-codetools" ,r-codetools)
9295 ("r-mvtnorm" ,r-mvtnorm)
9296 ("r-sandwich" ,r-sandwich)
9297 ("r-survival" ,r-survival)
9298 ("r-th-data" ,r-th-data)))
9299 (home-page "https://cran.r-project.org/web/packages/multcomp/")
9300 (synopsis "Simultaneous inference in general parametric models")
9302 "Simultaneous tests and confidence intervals for general linear
9303 hypotheses in parametric models, including linear, generalized linear, linear
9304 mixed effects, and survival models. The package includes demos reproducing
9305 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
9306 Hothorn, Westfall, 2010, CRC Press).")
9307 (license license:gpl2)))
9309 (define-public r-emmeans
9316 (uri (cran-uri "emmeans" version))
9319 "0ndbjhglycdycppz9lbj3vhiqv2mp0z6h4w8fbyjziqx15ai5h59"))))
9320 (build-system r-build-system)
9322 `(("r-estimability" ,r-estimability)
9323 ("r-mvtnorm" ,r-mvtnorm)
9324 ("r-numderiv" ,r-numderiv)
9326 ("r-xtable" ,r-xtable)))
9328 `(("r-knitr" ,r-knitr)))
9329 (home-page "https://github.com/rvlenth/emmeans")
9330 (synopsis "Estimated marginal means, aka least-squares means")
9332 "This package provides tools to obtain @dfn{estimated marginal
9333 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9334 be used to compute contrasts or linear functions of EMMs, trends, and
9335 comparisons of slopes.")
9336 ;; Either version of the license.
9337 (license (list license:gpl2 license:gpl3))))
9339 (define-public r-pwr
9346 (uri (cran-uri "pwr" version))
9349 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9350 (build-system r-build-system)
9352 `(("r-knitr" ,r-knitr)))
9353 (home-page "https://github.com/heliosdrm/pwr")
9354 (synopsis "Basic functions for power analysis")
9356 "This package provides power analysis functions along the lines of
9358 (license license:gpl3+)))
9360 (define-public r-libcoin
9367 (uri (cran-uri "libcoin" version))
9369 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9370 (build-system r-build-system)
9371 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9372 (home-page "https://cran.r-project.org/web/packages/libcoin")
9373 (synopsis "Linear test statistics for permutation inference")
9375 "This package provides basic infrastructure for linear test statistics
9376 and permutation inference in the framework of Strasser and Weber (1999).")
9377 (license license:gpl2)))
9379 (define-public r-coin
9386 (uri (cran-uri "coin" version))
9389 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9390 (build-system r-build-system)
9392 `(("r-libcoin" ,r-libcoin)
9393 ("r-matrixstats" ,r-matrixstats)
9394 ("r-modeltools" ,r-modeltools)
9395 ("r-multcomp" ,r-multcomp)
9396 ("r-mvtnorm" ,r-mvtnorm)
9397 ("r-survival" ,r-survival)))
9398 (home-page "http://coin.r-forge.r-project.org")
9399 (synopsis "Conditional inference procedures in a permutation test framework")
9401 "This package provides conditional inference procedures for the general
9402 independence problem including two-sample, K-sample (non-parametric ANOVA),
9403 correlation, censored, ordered and multivariate problems.")
9404 (license license:gpl2)))
9406 (define-public r-bayesplot
9408 (name "r-bayesplot")
9413 (uri (cran-uri "bayesplot" version))
9416 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9417 (build-system r-build-system)
9419 `(("pandoc" ,pandoc)
9420 ("pandoc-citeproc" ,pandoc-citeproc)))
9422 `(("r-knitr" ,r-knitr)))
9424 `(("r-dplyr" ,r-dplyr)
9425 ("r-ggplot2" ,r-ggplot2)
9426 ("r-ggridges" ,r-ggridges)
9428 ("r-reshape2" ,r-reshape2)
9429 ("r-rlang" ,r-rlang)
9430 ("r-tibble" ,r-tibble)
9431 ("r-tidyselect" ,r-tidyselect)))
9432 (home-page "https://mc-stan.org/bayesplot")
9433 (synopsis "Plotting for Bayesian models")
9435 "This package provides plotting functions for posterior analysis, model
9436 checking, and MCMC diagnostics. The package is designed not only to provide
9437 convenient functionality for users, but also a common set of functions that
9438 can be easily used by developers working on a variety of R packages for
9439 Bayesian modeling.")
9440 (license license:gpl3+)))
9442 (define-public r-tmb
9449 (uri (cran-uri "TMB" version))
9452 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9453 (properties `((upstream-name . "TMB")))
9454 (build-system r-build-system)
9456 `(("r-matrix" ,r-matrix)
9457 ("r-rcppeigen" ,r-rcppeigen)))
9458 (home-page "http://tmb-project.org")
9459 (synopsis "Template model builder: a general random effect tool")
9461 "With this tool, a user should be able to quickly implement complex
9462 random effect models through simple C++ templates. The package combines
9463 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9464 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9465 from R) to obtain an efficient implementation of the applied Laplace
9466 approximation with exact derivatives. Key features are: Automatic sparseness
9467 detection, parallelism through BLAS and parallel user templates.")
9468 (license license:gpl2)))
9470 (define-public r-sjstats
9477 (uri (cran-uri "sjstats" version))
9479 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9480 (build-system r-build-system)
9482 `(("r-bayestestr" ,r-bayestestr)
9483 ("r-broom" ,r-broom)
9484 ("r-dplyr" ,r-dplyr)
9485 ("r-effectsize" ,r-effectsize)
9486 ("r-emmeans" ,r-emmeans)
9487 ("r-insight" ,r-insight)
9489 ("r-magrittr" ,r-magrittr)
9491 ("r-modelr" ,r-modelr)
9492 ("r-parameters" ,r-parameters)
9493 ("r-performance" ,r-performance)
9494 ("r-purrr" ,r-purrr)
9495 ("r-rlang" ,r-rlang)
9496 ("r-sjlabelled" ,r-sjlabelled)
9497 ("r-sjmisc" ,r-sjmisc)
9498 ("r-tidyr" ,r-tidyr)))
9499 (home-page "https://github.com/strengejacke/sjstats")
9500 (synopsis "Functions for common statistical computations")
9502 "This package provides a collection of convenient functions for common
9503 statistical computations, which are not directly provided by R's @code{base}
9504 or @code{stats} packages. This package aims at providing, first, shortcuts
9505 for statistical measures, which otherwise could only be calculated with
9506 additional effort. Second, these shortcut functions are generic, and can be
9507 applied not only to vectors, but also to other objects as well. The focus of
9508 most functions lies on summary statistics or fit measures for regression
9509 models, including generalized linear models, mixed effects models and Bayesian
9511 (license license:gpl3)))
9513 (define-public r-glmmtmb
9520 (uri (cran-uri "glmmTMB" version))
9523 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9524 (properties `((upstream-name . "glmmTMB")))
9525 (build-system r-build-system)
9527 `(("r-lme4" ,r-lme4)
9528 ("r-matrix" ,r-matrix)
9530 ("r-rcppeigen" ,r-rcppeigen)
9533 `(("r-knitr" ,r-knitr))) ; for vignettes
9534 (home-page "https://github.com/glmmTMB")
9535 (synopsis "Generalized linear mixed models")
9537 "Fit linear and generalized linear mixed models with various extensions,
9538 including zero-inflation. The models are fitted using maximum likelihood
9539 estimation via the Template Model Builder. Random effects are assumed to be
9540 Gaussian on the scale of the linear predictor and are integrated out using the
9541 Laplace approximation. Gradients are calculated using automatic
9543 (license license:agpl3+)))
9545 (define-public r-bayestestr
9547 (name "r-bayestestr")
9552 (uri (cran-uri "bayestestR" version))
9555 "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw"))))
9556 (properties `((upstream-name . "bayestestR")))
9557 (build-system r-build-system)
9559 `(("r-insight" ,r-insight)))
9561 `(("r-knitr" ,r-knitr)))
9562 (home-page "https://github.com/easystats/bayestestR")
9563 (synopsis "Describe Bayesian models and posterior distributions")
9565 "This package provides utilities to understand and describe posterior
9566 distributions and Bayesian models. It includes point-estimates such as
9567 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9568 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9569 ROPE percentage and pd).")
9570 (license license:gpl3)))
9572 (define-public r-performance
9574 (name "r-performance")
9579 (uri (cran-uri "performance" version))
9582 "0ai1pp6k0pmmjgpj7hc53s0h258c4mljln8lv3nd9r7kzrmic0gc"))))
9583 (build-system r-build-system)
9585 `(("r-bayestestr" ,r-bayestestr)
9586 ("r-insight" ,r-insight)))
9587 (home-page "https://easystats.github.io/performance/")
9588 (synopsis "Assessment of regression models performance")
9590 "This package provides utilities for computing measures to assess model
9591 quality, which are not directly provided by R's @code{base} or @code{stats}
9592 packages. These include e.g. measures like r-squared, intraclass correlation
9593 coefficient, root mean squared error or functions to check models for
9594 overdispersion, singularity or zero-inflation and more. Functions apply to a
9595 large variety of regression models, including generalized linear models, mixed
9596 effects models and Bayesian models.")
9597 (license license:gpl3)))
9599 (define-public r-ggeffects
9601 (name "r-ggeffects")
9606 (uri (cran-uri "ggeffects" version))
9609 "18diwssc5vij5g7zh9mv0ppcv3xgfi2jqzfx9srxfahg05sr1xdq"))))
9610 (build-system r-build-system)
9612 `(("r-insight" ,r-insight)
9614 ("r-sjlabelled" ,r-sjlabelled)))
9616 `(("r-knitr" ,r-knitr)))
9617 (home-page "https://github.com/strengejacke/ggeffects")
9618 (synopsis "Create tidy data frames of marginal effects for ggplot")
9620 "This package provides tools to compute marginal effects from statistical
9621 models and return the result as tidy data frames. These data frames are ready
9622 to use with the @code{ggplot2} package. Marginal effects can be calculated
9623 for many different models. Interaction terms, splines and polynomial terms
9624 are also supported. The two main functions are @code{ggpredict()} and
9625 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9626 results using @code{ggplot2}.")
9627 (license license:gpl3)))
9629 (define-public r-effectsize
9631 (name "r-effectsize")
9636 (uri (cran-uri "effectsize" version))
9639 "1rbl63b1c7z9llznnwvclqrcgdd4hfmc7y66v7raqqf2a4nadqa5"))))
9640 (properties `((upstream-name . "effectsize")))
9641 (build-system r-build-system)
9643 `(("r-bayestestr" ,r-bayestestr)
9644 ("r-insight" ,r-insight)
9645 ("r-parameters" ,r-parameters)))
9647 `(("r-knitr" ,r-knitr)))
9648 (home-page "https://github.com/easystats/effectsize")
9649 (synopsis "Indices of effect size and standardized parameters")
9651 "This package provides utilities to work with indices of effect size and
9652 standardized parameters for a wide variety of models, allowing computation and
9653 conversion of indices such as Cohen's d, r, odds, etc.")
9654 (license license:gpl3)))
9656 (define-public r-sjplot
9663 (uri (cran-uri "sjPlot" version))
9665 (base32 "1dn9nvvp4jd45kwr4rpp2abf7xdpdmiv41rr3fkdb32a136bzx4b"))))
9666 (properties `((upstream-name . "sjPlot")))
9667 (build-system r-build-system)
9669 `(("r-bayestestr" ,r-bayestestr)
9670 ("r-dplyr" ,r-dplyr)
9671 ("r-effectsize" ,r-effectsize)
9672 ("r-ggeffects" ,r-ggeffects)
9673 ("r-ggplot2" ,r-ggplot2)
9674 ("r-insight" ,r-insight)
9675 ("r-knitr" ,r-knitr)
9677 ("r-parameters" ,r-parameters)
9678 ("r-performance" ,r-performance)
9679 ("r-purrr" ,r-purrr)
9680 ("r-rlang" ,r-rlang)
9681 ("r-scales" ,r-scales)
9682 ("r-sjlabelled" ,r-sjlabelled)
9683 ("r-sjmisc" ,r-sjmisc)
9684 ("r-sjstats" ,r-sjstats)
9685 ("r-tidyr" ,r-tidyr)))
9687 `(("r-knitr" ,r-knitr)))
9688 (home-page "https://strengejacke.github.io/sjPlot/")
9689 (synopsis "Data visualization for statistics in social science")
9691 "This package represents a collection of plotting and table output
9692 functions for data visualization. Results of various statistical
9693 analyses (that are commonly used in social sciences) can be visualized using
9694 this package, including simple and cross tabulated frequencies, histograms,
9695 box plots, (generalized) linear models, mixed effects models, principal
9696 component analysis and correlation matrices, cluster analyses, scatter plots,
9697 stacked scales, effects plots of regression models (including interaction
9698 terms) and much more. This package supports labelled data.")
9699 (license license:gpl3)))
9701 (define-public r-ini
9708 (uri (cran-uri "ini" version))
9711 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9712 (build-system r-build-system)
9713 (home-page "https://github.com/dvdscripter/ini")
9714 (synopsis "Read and write configuration files")
9716 "This package provides tools to parse simple @code{.ini} configuration
9717 files to an structured list. Users can manipulate this resulting list with
9718 @code{lapply()} functions. This same structured list can be used to write
9719 back to file after modifications.")
9720 (license license:gpl3)))
9722 (define-public r-gitcreds
9729 (uri (cran-uri "gitcreds" version))
9732 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
9733 (properties `((upstream-name . "gitcreds")))
9734 (build-system r-build-system)
9735 (inputs `(("git" ,git-minimal)))
9736 (native-inputs `(("r-knitr" ,r-knitr)))
9737 (home-page "https://github.com/r-lib/gitcreds")
9738 (synopsis "Query git credentials from R")
9740 "Query, set, and delete credentials from the git credential store.
9741 Manage GitHub tokens and other git credentials. This package is to be used by
9742 other packages that need to authenticate to GitHub and/or other git
9744 (license license:expat)))
9753 (uri (cran-uri "gh" version))
9756 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
9757 (build-system r-build-system)
9760 ("r-gitcreds" ,r-gitcreds)
9763 ("r-jsonlite" ,r-jsonlite)))
9765 `(("r-knitr" ,r-knitr)))
9766 (home-page "https://github.com/r-lib/gh#readme")
9767 (synopsis "Access the GitHub API via R")
9769 "This package provides a minimal R client to access the GitHub API.")
9770 (license license:expat)))
9779 (uri (cran-uri "fs" version))
9782 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9783 (build-system r-build-system)
9785 `(("r-knitr" ,r-knitr)))
9786 (home-page "https://fs.r-lib.org")
9787 (synopsis "Cross-platform file system operations based on libuv")
9789 "This package provides a cross-platform interface to file system
9790 operations, built on top of the libuv C library.")
9791 (license license:gpl3)))
9793 (define-public r-clisymbols
9795 (name "r-clisymbols")
9800 (uri (cran-uri "clisymbols" version))
9803 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9804 (build-system r-build-system)
9805 (home-page "https://github.com/gaborcsardi/clisymbols")
9806 (synopsis "Unicode symbols at the R prompt")
9808 "This package provides a small subset of Unicode symbols, that are useful
9809 when building command line applications. They fall back to alternatives on
9810 terminals that do not support Unicode.")
9811 (license license:expat)))
9813 (define-public r-usethis
9820 (uri (cran-uri "usethis" version))
9823 "09lk04kycvf5x9ggrb6pwc7bx5mzqxwialm2w9vn1a0w0gh2gcfc"))))
9824 (build-system r-build-system)
9827 ("r-clipr" ,r-clipr)
9828 ("r-crayon" ,r-crayon)
9833 ("r-git2r" ,r-git2r)
9835 ("r-purrr" ,r-purrr)
9836 ("r-rematch2" ,r-rematch2)
9837 ("r-rlang" ,r-rlang)
9838 ("r-rprojroot" ,r-rprojroot)
9839 ("r-rstudioapi" ,r-rstudioapi)
9840 ("r-whisker" ,r-whisker)
9841 ("r-withr" ,r-withr)
9842 ("r-yaml" ,r-yaml)))
9843 (home-page "https://github.com/r-lib/usethis")
9844 (synopsis "Automate R package and project setup")
9846 "This package helps you to automate R package and project setup tasks
9847 that are otherwise performed manually. This includes setting up unit testing,
9848 test coverage, continuous integration, Git, GitHub integration, licenses,
9849 Rcpp, RStudio projects, and more.")
9850 (license license:gpl3)))
9852 (define-public r-sessioninfo
9854 (name "r-sessioninfo")
9859 (uri (cran-uri "sessioninfo" version))
9862 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9863 (build-system r-build-system)
9866 ("r-withr" ,r-withr)))
9867 (home-page "https://github.com/r-lib/sessioninfo#readme")
9868 (synopsis "R session information")
9870 "This package provides tools to query and print information about the
9871 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9872 more information about packages, and where they were installed from.")
9873 (license license:gpl2)))
9875 (define-public r-remotes
9882 (uri (cran-uri "remotes" version))
9885 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9886 (build-system r-build-system)
9888 `(("r-knitr" ,r-knitr)))
9889 (home-page "https://github.com/r-lib/remotes#readme")
9890 (synopsis "R package installation from remote repositories")
9892 "Download and install R packages stored in GitHub, BitBucket, or plain
9893 subversion or git repositories. This package is a lightweight replacement of
9894 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9895 the code was copied over from @code{devtools}.")
9896 (license license:gpl2+)))
9898 (define-public r-xopen
9905 (uri (cran-uri "xopen" version))
9908 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9909 (build-system r-build-system)
9911 `(("r-processx" ,r-processx)))
9912 (home-page "https://github.com/r-lib/xopen#readme")
9913 (synopsis "Open system files, URLs, anything")
9915 "This package provides a cross-platform solution to open files,
9916 directories or URLs with their associated programs.")
9917 (license license:expat)))
9919 (define-public r-rcmdcheck
9921 (name "r-rcmdcheck")
9926 (uri (cran-uri "rcmdcheck" version))
9929 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9930 (build-system r-build-system)
9932 `(("r-callr" ,r-callr)
9934 ("r-crayon" ,r-crayon)
9936 ("r-digest" ,r-digest)
9937 ("r-pkgbuild" ,r-pkgbuild)
9938 ("r-prettyunits" ,r-prettyunits)
9940 ("r-rprojroot" ,r-rprojroot)
9941 ("r-sessioninfo" ,r-sessioninfo)
9942 ("r-withr" ,r-withr)
9943 ("r-xopen" ,r-xopen)))
9944 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9945 (synopsis "Run R CMD check from R and capture results")
9947 "Run @code{R CMD check} from R programmatically, and capture the results
9948 of the individual checks.")
9949 (license license:expat)))
9951 (define-public r-rapportools
9953 (name "r-rapportools")
9958 (uri (cran-uri "rapportools" version))
9961 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9962 (build-system r-build-system)
9964 `(("r-pander" ,r-pander)
9966 ("r-reshape" ,r-reshape)))
9967 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9968 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9970 "This package provides helper functions that act as wrappers to more
9971 advanced statistical methods with the advantage of having sane defaults for
9973 (license license:agpl3+)))
9975 (define-public r-pander
9982 (uri (cran-uri "pander" version))
9985 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9986 (build-system r-build-system)
9988 `(("r-digest" ,r-digest)
9989 ("r-rcpp" ,r-rcpp)))
9990 (home-page "https://rapporter.github.io/pander")
9991 (synopsis "Render R objects into Pandoc's markdown")
9993 "The main aim of the pander R package is to provide a minimal and easy
9994 tool for rendering R objects into Pandoc's markdown. The package is also
9995 capable of exporting/converting complex Pandoc documents (reports) in various
9997 ;; This package is licensed under either the AGPLv3+ or the very rarely
9999 (license license:agpl3+)))
10001 (define-public r-summarytools
10003 (name "r-summarytools")
10008 (uri (cran-uri "summarytools" version))
10011 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
10012 (build-system r-build-system)
10014 `(("r-base64enc" ,r-base64enc)
10015 ("r-checkmate" ,r-checkmate)
10016 ("r-dplyr" ,r-dplyr)
10017 ("r-htmltools" ,r-htmltools)
10018 ("r-lubridate" ,r-lubridate)
10019 ("r-magick" ,r-magick)
10020 ("r-matrixstats" ,r-matrixstats)
10021 ("r-pander" ,r-pander)
10023 ("r-rapportools" ,r-rapportools)
10024 ("r-tibble" ,r-tibble)
10025 ("r-tidyr" ,r-tidyr)))
10026 (home-page "https://github.com/dcomtois/summarytools")
10027 (synopsis "Tools to quickly and neatly summarize data")
10029 "This package provides tools for data frame summaries, cross-tabulations,
10030 weight-enabled frequency tables and common univariate statistics in concise
10031 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10032 good point-of-entry for exploring data, both for experienced and new R
10034 (license license:gpl2)))
10036 (define-public r-lsei
10043 (uri (cran-uri "lsei" version))
10046 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10047 (build-system r-build-system)
10049 `(("gfortran" ,gfortran)))
10050 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10051 (synopsis "Solve regression problems under equality/inequality constraints")
10053 "It contains functions that solve least squares linear regression
10054 problems under linear equality/inequality constraints. Functions for solving
10055 quadratic programming problems are also available, which transform such
10056 problems into least squares ones first.")
10057 (license license:gpl2+)))
10059 (define-public r-npsurv
10066 (uri (cran-uri "npsurv" version))
10069 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10070 (build-system r-build-system)
10072 `(("r-lsei" ,r-lsei)))
10073 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10074 (synopsis "Nonparametric survival analysis")
10076 "This package contains functions for non-parametric survival analysis of
10077 exact and interval-censored observations.")
10078 (license license:gpl2+)))
10080 (define-public r-clusteval
10082 (name "r-clusteval")
10087 (uri (cran-uri "clusteval" version))
10090 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10091 (build-system r-build-system)
10093 `(("r-mvtnorm" ,r-mvtnorm)
10094 ("r-rcpp" ,r-rcpp)))
10095 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10096 (synopsis "Evaluation of clustering algorithms")
10098 "This R package provides a suite of tools to evaluate clustering
10099 algorithms, clusterings, and individual clusters.")
10100 (license license:expat)))
10102 (define-public r-tweedie
10109 (uri (cran-uri "tweedie" version))
10112 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
10113 (build-system r-build-system)
10114 (native-inputs `(("gfortran" ,gfortran)))
10115 (home-page "https://cran.r-project.org/web/packages/tweedie/")
10116 (synopsis "Evaluation of Tweedie exponential family models")
10118 "Maximum likelihood computations for Tweedie families, including the
10119 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
10120 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
10121 and related methods.")
10122 (license license:gpl2+)))
10124 (define-public r-rcppgsl
10131 (uri (cran-uri "RcppGSL" version))
10133 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
10134 (properties `((upstream-name . "RcppGSL")))
10135 (build-system r-build-system)
10137 `(("r-rcpp" ,r-rcpp)
10139 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
10140 (synopsis "Rcpp integration for GSL vectors and matrices")
10142 "The GNU Scientific Library (or GSL) is a collection of numerical
10143 routines for scientific computing. It is particularly useful for C and C++
10144 programs as it provides a standard C interface to a wide range of mathematical
10145 routines. There are over 1000 functions in total with an extensive test
10146 suite. The RcppGSL package provides an easy-to-use interface between GSL data
10147 structures and R using concepts from Rcpp which is itself a package that eases
10148 the interfaces between R and C++.")
10149 (license license:gpl2+)))
10151 (define-public r-mvabund
10158 (uri (cran-uri "mvabund" version))
10161 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
10162 (build-system r-build-system)
10164 `(("r-mass" ,r-mass)
10166 ("r-rcppgsl" ,r-rcppgsl)
10167 ("r-statmod" ,r-statmod)
10168 ("r-tweedie" ,r-tweedie)))
10169 (home-page "https://cran.r-project.org/web/packages/mvabund/")
10170 (synopsis "Statistical methods for analysing multivariate abundance data")
10172 "This package provides a set of tools for displaying, modeling and
10173 analysing multivariate abundance data in community ecology.")
10174 (license license:lgpl2.1+)))
10176 (define-public r-afex
10183 (uri (cran-uri "afex" version))
10186 "0c47bq2llzw2b4avhkxyhmf1m2zjh9jsjiw2kww9n1bhwqsyr4ci"))))
10187 (build-system r-build-system)
10191 ("r-lmertest" ,r-lmertest)
10192 ("r-pbkrtest" ,r-pbkrtest)
10193 ("r-reshape2" ,r-reshape2)))
10195 `(("r-knitr" ,r-knitr)))
10196 (home-page "https://afex.singmann.science/")
10197 (synopsis "Analysis of factorial experiments")
10199 "This package provides convenience functions for analyzing factorial
10200 experiments using ANOVA or mixed models.")
10201 (license license:gpl2+)))
10203 (define-public r-lmertest
10205 (name "r-lmertest")
10210 (uri (cran-uri "lmerTest" version))
10213 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
10214 (properties `((upstream-name . "lmerTest")))
10215 (build-system r-build-system)
10217 `(("r-ggplot2" ,r-ggplot2)
10220 ("r-numderiv" ,r-numderiv)))
10221 (home-page "https://github.com/runehaubo/lmerTestR")
10222 (synopsis "Tests in linear mixed effects models")
10224 "This package provides p-values in type I, II or III anova and summary
10225 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
10226 method. A Kenward-Roger method is also available via the @code{pbkrtest}
10227 package. Model selection methods include step, drop1 and anova-like tables
10228 for random effects (ranova). Methods for Least-Square means (LS-means) and
10229 tests of linear contrasts of fixed effects are also available.")
10230 (license license:gpl2+)))
10232 (define-public r-r2glmm
10239 (uri (cran-uri "r2glmm" version))
10242 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
10243 (build-system r-build-system)
10245 `(("r-afex" ,r-afex)
10246 ("r-data-table" ,r-data-table)
10247 ("r-dplyr" ,r-dplyr)
10248 ("r-ggplot2" ,r-ggplot2)
10249 ("r-gridextra" ,r-gridextra)
10250 ("r-lmertest" ,r-lmertest)
10252 ("r-matrix" ,r-matrix)
10254 ("r-pbkrtest" ,r-pbkrtest)))
10255 (home-page "https://github.com/bcjaeger/r2glmm")
10256 (synopsis "Compute R squared for mixed (multilevel) models")
10258 "This package computes model and semi partial R squared with confidence
10259 limits for the linear and generalized linear mixed model (LMM and GLMM). The
10260 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
10261 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
10263 (license license:gpl2)))
10265 (define-public r-weights
10272 (uri (cran-uri "weights" version))
10275 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
10276 (build-system r-build-system)
10278 `(("r-gdata" ,r-gdata)
10279 ("r-hmisc" ,r-hmisc)
10280 ("r-mice" ,r-mice)))
10282 "https://cran.r-project.org/web/packages/weights/")
10283 (synopsis "Weighting and weighted statistics")
10284 (description "This package Provides a variety of functions for producing
10285 simple weighted statistics, such as weighted Pearson's correlations, partial
10286 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
10287 includes some software for quickly recoding survey data and plotting point
10288 estimates from interaction terms in regressions (and multiply imputed
10289 regressions). NOTE: Weighted partial correlation calculations pulled to
10291 (license license:gpl2+)))
10293 (define-public r-rcppannoy
10295 (name "r-rcppannoy")
10300 (uri (cran-uri "RcppAnnoy" version))
10303 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
10304 (properties `((upstream-name . "RcppAnnoy")))
10305 (build-system r-build-system)
10307 `(("r-rcpp" ,r-rcpp)))
10308 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
10309 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
10311 "Annoy is a small C++ library for Approximate Nearest Neighbors written
10312 for efficient memory usage as well an ability to load from and save to disk.
10313 This package provides an R interface.")
10314 ;; Annoy is released under ASL 2.0, but this wrapper is released under
10316 (license (list license:gpl2+ license:asl2.0))))
10318 (define-public r-rcpphnsw
10320 (name "r-rcpphnsw")
10325 (uri (cran-uri "RcppHNSW" version))
10328 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
10329 (properties `((upstream-name . "RcppHNSW")))
10330 (build-system r-build-system)
10331 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10332 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
10333 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
10335 "Hnswlib is a C++ library for approximate nearest neighbors. This
10336 package provides a minimal R interface by relying on the Rcpp package.")
10337 ;; hnswlib is released under Version 2.0 of the Apache License.
10338 (license (list license:gpl3 license:asl2.0))))
10340 (define-public r-rcppparallel
10342 (name "r-rcppparallel")
10347 (uri (cran-uri "RcppParallel" version))
10350 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10351 (properties `((upstream-name . "RcppParallel")))
10352 (build-system r-build-system)
10353 (home-page "https://rcppcore.github.io/RcppParallel/")
10354 (synopsis "Parallel programming tools for Rcpp")
10356 "This package provides high level functions for parallel programming with
10357 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10358 the work of a standard serial @code{for} loop into a parallel one and the
10359 @code{parallelReduce()} function can be used for accumulating aggregates or
10361 (license license:gpl2)))
10363 (define-public r-ncdf4
10370 (uri (cran-uri "ncdf4" version))
10373 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10374 (build-system r-build-system)
10376 `(("netcdf" ,netcdf)
10378 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10379 (synopsis "R interface to Unidata netCDF format data files")
10381 "This package provides a high-level R interface to data files written
10382 using Unidata's netCDF library (version 4 or earlier), which are binary data
10383 files that are portable across platforms and include metadata information in
10384 addition to the data sets. Using this package, netCDF files can be opened and
10385 data sets read in easily. It is also easy to create new netCDF dimensions,
10386 variables, and files, in either version 3 or 4 format, and manipulate existing
10388 (license license:gpl3+)))
10390 (define-public r-biocmanager
10392 (name "r-biocmanager")
10393 (version "1.30.10")
10397 (uri (cran-uri "BiocManager" version))
10399 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10400 (properties `((upstream-name . "BiocManager")))
10401 (build-system r-build-system)
10402 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10403 (synopsis "Access the Bioconductor project package repository")
10405 "This package provides a convenient tool to install and update
10406 Bioconductor packages.")
10407 (license license:artistic2.0)))
10409 (define-public r-rgl
10412 (version "0.100.54")
10416 (uri (cran-uri "rgl" version))
10419 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10420 (build-system r-build-system)
10422 `(("pkg-config" ,pkg-config)))
10424 `(("freetype" ,freetype)
10431 `(("r-crosstalk" ,r-crosstalk)
10432 ("r-htmltools" ,r-htmltools)
10433 ("r-htmlwidgets" ,r-htmlwidgets)
10434 ("r-jsonlite" ,r-jsonlite)
10435 ("r-knitr" ,r-knitr)
10436 ("r-magrittr" ,r-magrittr)
10437 ("r-manipulatewidget" ,r-manipulatewidget)
10438 ("r-shiny" ,r-shiny)))
10439 (home-page "https://r-forge.r-project.org/projects/rgl/")
10440 (synopsis "3D visualization using OpenGL")
10442 "This package provides medium to high level functions for 3D interactive graphics,
10443 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10444 as functions for constructing representations of geometric
10445 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10446 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10447 image formats, including PNG, Postscript, SVG, PGF.")
10448 ;; Any version of the GPL.
10449 (license (list license:gpl2+ license:gpl3+))))
10451 (define-public r-multicool
10453 (name "r-multicool")
10458 (uri (cran-uri "multicool" version))
10461 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10462 (build-system r-build-system)
10463 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10464 (home-page "https://cran.r-project.org/web/packages/multicool/")
10465 (synopsis "Permutations of multisets in cool-lex order")
10467 "This package provides a set of tools to permute multisets without loops
10468 or hash tables and to generate integer partitions. Cool-lex order is similar
10469 to colexicographical order.")
10470 (license license:gpl2)))
10472 (define-public r-misc3d
10479 (uri (cran-uri "misc3d" version))
10482 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
10483 (build-system r-build-system)
10484 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10485 (synopsis "Miscellaneous 3D Plots")
10487 "This package provides a collection of miscellaneous 3d plots, including
10489 ;; Any version of the GPL.
10490 (license (list license:gpl2+ license:gpl3+))))
10492 (define-public r-ks
10499 (uri (cran-uri "ks" version))
10501 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10502 (build-system r-build-system)
10505 ("r-kernlab" ,r-kernlab)
10506 ("r-kernsmooth" ,r-kernsmooth)
10507 ("r-matrix" ,r-matrix)
10508 ("r-mclust" ,r-mclust)
10510 ("r-multicool" ,r-multicool)
10511 ("r-mvtnorm" ,r-mvtnorm)))
10512 (home-page "http://www.mvstat.net/tduong/")
10513 (synopsis "Kernel smoothing")
10515 "This package provides kernel smoothers for univariate and multivariate
10516 data, including density functions, density derivatives, cumulative
10517 distributions, modal clustering, discriminant analysis, and two-sample
10518 hypothesis testing.")
10519 ;; Either version of the GPL.
10520 (license (list license:gpl2 license:gpl3))))
10522 (define-public r-feature
10529 (uri (cran-uri "feature" version))
10532 "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1"))))
10533 (build-system r-build-system)
10537 `(("r-knitr" ,r-knitr)))
10538 (home-page "http://www.mvstat.net/tduong/")
10539 (synopsis "Inferential feature significance for kernel density estimation")
10541 "The feature package contains functions to display and compute kernel
10542 density estimates, significant gradient and significant curvature regions.
10543 Significant gradient and/or curvature regions often correspond to significant
10544 features (e.g. local modes).")
10545 ;; Either version of the GPL.
10546 (license (list license:gpl2 license:gpl3))))
10548 (define-public r-arm
10555 (uri (cran-uri "arm" version))
10558 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10559 (build-system r-build-system)
10561 `(("r-abind" ,r-abind)
10563 ("r-hmisc" ,r-hmisc)
10566 ("r-matrix" ,r-matrix)
10567 ("r-nlme" ,r-nlme)))
10568 (home-page "https://cran.r-project.org/web/packages/arm/")
10569 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10571 "This package provides functions to accompany A. Gelman and J. Hill,
10572 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10573 University Press, 2007.")
10574 (license license:gpl3+)))
10576 (define-public r-circular
10578 (name "r-circular")
10583 (uri (cran-uri "circular" version))
10586 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10587 (build-system r-build-system)
10589 `(("r-boot" ,r-boot)
10590 ("r-mvtnorm" ,r-mvtnorm)))
10592 `(("gfortran" ,gfortran)))
10593 (home-page "https://cran.r-project.org/web/packages/circular/")
10594 (synopsis "Circular statistics")
10596 "This package provides tools for circular statistics, from \"Topics in
10597 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10599 (license license:gpl2+)))
10601 (define-public r-activity
10603 (name "r-activity")
10608 (uri (cran-uri "activity" version))
10611 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10612 (build-system r-build-system)
10614 `(("r-circular" ,r-circular)
10615 ("r-insol" ,r-insol)
10616 ("r-pbapply" ,r-pbapply)))
10617 (home-page "https://cran.r-project.org/web/packages/activity/")
10618 (synopsis "Animal activity statistics")
10620 "This package provides functions to fit kernel density functions to
10621 animal activity time data; plot activity distributions; quantify overall
10622 levels of activity; statistically compare activity metrics through
10623 bootstrapping; and evaluate variation in linear variables with time (or other
10624 circular variables).")
10625 (license license:gpl3)))
10627 (define-public r-ouch
10634 (uri (cran-uri "ouch" version))
10637 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10638 (build-system r-build-system)
10639 (propagated-inputs `(("r-subplex" ,r-subplex)))
10640 (home-page "https://kingaa.github.io/ouch/")
10641 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10643 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10644 for evolution along a phylogenetic tree.")
10645 (license license:gpl2+)))
10647 (define-public r-fmsb
10654 (uri (cran-uri "fmsb" version))
10657 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10658 (build-system r-build-system)
10659 (home-page "http://minato.sip21c.org/msb/")
10660 (synopsis "Functions for medical statistics book with demographic data")
10662 "This package provides several utility functions for the book entitled
10663 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10664 Japan, 2007) with Japanese demographic data and some demographic analysis
10665 related functions.")
10666 (license license:gpl2+)))
10668 (define-public r-stabledist
10670 (name "r-stabledist")
10675 (uri (cran-uri "stabledist" version))
10678 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10679 (build-system r-build-system)
10680 (home-page "https://www.rmetrics.org")
10681 (synopsis "Stable distribution functions")
10683 "This package provides density, probability and quantile functions, and
10684 random number generation for (skew) stable distributions, using the
10685 parametrizations of Nolan.")
10686 (license license:gpl2+)))
10688 (define-public r-gsl
10695 (uri (cran-uri "gsl" version))
10698 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10699 (build-system r-build-system)
10702 (home-page "https://cran.r-project.org/web/packages/gsl")
10703 (synopsis "Wrapper for the GNU Scientific Library")
10705 "This package provides an R wrapper for the special functions and quasi
10706 random number generators of the GNU Scientific Library.")
10707 (license license:gpl2+)))
10709 (define-public r-adgoftest
10711 (name "r-adgoftest")
10716 (uri (cran-uri "ADGofTest" version))
10719 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10720 (properties `((upstream-name . "ADGofTest")))
10721 (build-system r-build-system)
10722 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10723 (synopsis "Anderson-Darling GoF test")
10725 "This package provides an implementation of the Anderson-Darling GoF test
10726 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10727 Anderson-Darling Distribution\".")
10728 ;; Any version of the GPL.
10729 (license license:gpl3+)))
10731 (define-public r-softimpute
10733 (name "r-softimpute")
10738 (uri (cran-uri "softImpute" version))
10741 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10742 (properties `((upstream-name . "softImpute")))
10743 (build-system r-build-system)
10745 `(("r-matrix" ,r-matrix)))
10747 `(("gfortran" ,gfortran)))
10748 (home-page "https://cran.r-project.org/web/packages/softImpute")
10749 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10751 "This package provides iterative methods for matrix completion that use
10752 nuclear-norm regularization. The package includes procedures for centering
10753 and scaling rows, columns or both, and for computing low-rank @dfn{single
10754 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10756 (license license:gpl2)))
10758 (define-public r-fftwtools
10760 (name "r-fftwtools")
10765 (uri (cran-uri "fftwtools" version))
10768 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9"))))
10769 (build-system r-build-system)
10770 (inputs `(("fftw" ,fftw)))
10771 (home-page "https://github.com/krahim/fftwtools")
10772 (synopsis "Wrapper for FFTW3")
10774 "This package provides a wrapper for several FFTW functions. It provides
10775 access to the two-dimensional FFT, the multivariate FFT, and the
10776 one-dimensional real to complex FFT using the FFTW3 library. The package
10777 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10778 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10779 The FFT functions have a parameter that allows them to not return the
10780 redundant complex conjugate when the input is real data.")
10781 (license license:gpl2+)))
10783 (define-public r-tiff
10790 (uri (cran-uri "tiff" version))
10793 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10794 (build-system r-build-system)
10796 `(("libtiff" ,libtiff)
10797 ("libjpeg" ,libjpeg-turbo)
10799 (home-page "https://www.rforge.net/tiff/")
10800 (synopsis "Read and write TIFF images")
10802 "This package provides an easy and simple way to read, write and display
10803 bitmap images stored in the TIFF format. It can read and write both files and
10804 in-memory raw vectors.")
10805 ;; Either of these two license versions.
10806 (license (list license:gpl2 license:gpl3))))
10808 (define-public r-nlp
10815 (uri (cran-uri "NLP" version))
10818 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
10819 (properties `((upstream-name . "NLP")))
10820 (build-system r-build-system)
10821 (home-page "https://cran.r-project.org/web/packages/NLP/")
10822 (synopsis "Natural language processing infrastructure")
10824 "This package provides basic classes and methods for Natural Language
10826 (license license:gpl3)))
10828 (define-public r-tm
10835 (uri (cran-uri "tm" version))
10838 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10839 (properties `((upstream-name . "tm")))
10840 (build-system r-build-system)
10846 ("r-xml2" ,r-xml2)))
10847 (home-page "http://tm.r-forge.r-project.org/")
10848 (synopsis "Text mining package")
10850 "This package provides a framework for text mining applications within R.")
10851 (license license:gpl3)))
10853 (define-public r-waveslim
10855 (name "r-waveslim")
10860 (uri (cran-uri "waveslim" version))
10863 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10864 (build-system r-build-system)
10866 `(("gfortran" ,gfortran)))
10867 (home-page "http://waveslim.blogspot.com")
10868 (synopsis "Basic wavelet routines for signal processing")
10870 "This package provides basic wavelet routines for time series (1D),
10871 image (2D) and array (3D) analysis. The code provided here is based on
10872 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10873 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10874 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10875 pairs (Selesnick 2001, 2002).")
10876 (license license:bsd-3)))
10878 (define-public r-wordcloud
10880 (name "r-wordcloud")
10885 (uri (cran-uri "wordcloud" version))
10888 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10889 (build-system r-build-system)
10891 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10893 ;; The "tm" package is only "suggested" according to CRAN, but the
10894 ;; wordcloud package cannot be loaded without it.
10896 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10897 (synopsis "Word clouds")
10899 "This package provides functionality to create pretty word clouds,
10900 visualize differences and similarity between documents, and avoid
10901 over-plotting in scatter plots with text.")
10902 (license license:lgpl2.1)))
10904 (define-public r-colorramps
10906 (name "r-colorramps")
10911 (uri (cran-uri "colorRamps" version))
10914 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10915 (properties `((upstream-name . "colorRamps")))
10916 (build-system r-build-system)
10917 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10918 (synopsis "Build color tables")
10919 (description "This package provides features to build gradient color
10921 ;; Any version of the GPL
10922 (license license:gpl3+)))
10924 (define-public r-tidytree
10926 (name "r-tidytree")
10931 (uri (cran-uri "tidytree" version))
10933 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10934 (build-system r-build-system)
10937 ("r-dplyr" ,r-dplyr)
10938 ("r-lazyeval" ,r-lazyeval)
10939 ("r-magrittr" ,r-magrittr)
10940 ("r-rlang" ,r-rlang)
10941 ("r-tibble" ,r-tibble)))
10943 `(("r-knitr" ,r-knitr)))
10944 (home-page "https://github.com/GuangchuangYu/tidytree")
10945 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10947 "Phylogenetic trees generally contain multiple components including nodes,
10948 edges, branches and associated data. This package provides an approach to
10949 convert tree objects to tidy data frames. It also provides tidy interfaces to
10950 manipulate tree data.")
10951 (license license:artistic2.0)))
10953 (define-public r-rvcheck
10960 (uri (cran-uri "rvcheck" version))
10962 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10963 (build-system r-build-system)
10965 `(("r-biocmanager" ,r-biocmanager)
10966 ("r-rlang" ,r-rlang)))
10967 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10968 (synopsis "R package version check")
10970 "This package provides tools to check the latest release version of R and
10971 R packages (on CRAN, Bioconductor or Github).")
10972 (license license:artistic2.0)))
10974 (define-public r-docopt
10981 (uri (cran-uri "docopt" version))
10984 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10985 (build-system r-build-system)
10986 (home-page "https://github.com/docopt/docopt.R")
10987 (synopsis "Command-line interface specification language")
10989 "This package enables you to define a command-line interface by just
10990 giving it a description in the specific format.")
10991 (license license:expat)))
10993 (define-public r-sparsesvd
10995 (name "r-sparsesvd")
11000 (uri (cran-uri "sparsesvd" version))
11003 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11004 (build-system r-build-system)
11005 (propagated-inputs `(("r-matrix" ,r-matrix)))
11006 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11007 (synopsis "Sparse truncated singular value decomposition")
11009 "This package provides a Wrapper around the SVDLIBC library
11010 for (truncated) singular value decomposition of a sparse matrix. Currently,
11011 only sparse real matrices in Matrix package format are supported.")
11012 ;; SVDLIBC is released under BSD-2. The R interface is released under
11014 (license (list license:bsd-3 license:bsd-2))))
11016 (define-public r-speedglm
11018 (name "r-speedglm")
11023 (uri (cran-uri "speedglm" version))
11026 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
11027 (build-system r-build-system)
11029 `(("r-mass" ,r-mass)
11030 ("r-matrix" ,r-matrix)))
11031 (home-page "https://cran.r-project.org/web/packages/speedglm")
11032 (synopsis "Fit linear and generalized linear models to large data sets")
11034 "This package provides tools for fitting linear models and generalized
11035 linear models to large data sets by updating algorithms.")
11036 ;; Any version of the GPL
11037 (license license:gpl2+)))
11039 (define-public r-densityclust
11041 (name "r-densityclust")
11046 (uri (cran-uri "densityClust" version))
11049 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11050 (properties `((upstream-name . "densityClust")))
11051 (build-system r-build-system)
11054 ("r-ggplot2" ,r-ggplot2)
11055 ("r-ggrepel" ,r-ggrepel)
11056 ("r-gridextra" ,r-gridextra)
11057 ("r-rcolorbrewer" ,r-rcolorbrewer)
11059 ("r-rtsne" ,r-rtsne)))
11060 (home-page "https://cran.r-project.org/web/packages/densityClust")
11061 (synopsis "Clustering by fast search and find of density peaks")
11063 "This package provides an improved implementation (based on k-nearest
11064 neighbors) of the density peak clustering algorithm, originally described by
11065 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11066 large datasets (> 100,000 samples) very efficiently.")
11067 (license license:gpl2+)))
11069 (define-public r-combinat
11071 (name "r-combinat")
11076 (uri (cran-uri "combinat" version))
11079 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
11080 (build-system r-build-system)
11081 (home-page "https://cran.r-project.org/web/packages/combinat")
11082 (synopsis "Combinatorics utilities")
11083 (description "This package provides assorted routines for combinatorics.")
11084 (license license:gpl2)))
11086 (define-public r-qlcmatrix
11088 (name "r-qlcmatrix")
11093 (uri (cran-uri "qlcMatrix" version))
11096 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
11097 (properties `((upstream-name . "qlcMatrix")))
11098 (build-system r-build-system)
11100 `(("r-docopt" ,r-docopt)
11101 ("r-matrix" ,r-matrix)
11103 ("r-sparsesvd" ,r-sparsesvd)))
11104 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
11105 (synopsis "Sparse matrix functions for quantitative language comparison")
11107 "This package provides an extension of the functionality of the Matrix
11108 package for using sparse matrices. Some of the functions are very general,
11109 while other are highly specific for the special data format used for
11110 @dfn{quantitative language comparison} (QLC).")
11111 (license license:gpl3)))
11113 (define-public r-ddrtree
11120 (uri (cran-uri "DDRTree" version))
11123 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
11124 (properties `((upstream-name . "DDRTree")))
11125 (build-system r-build-system)
11128 ("r-irlba" ,r-irlba)
11130 ("r-rcppeigen" ,r-rcppeigen)))
11131 (home-page "https://cran.r-project.org/web/packages/DDRTree")
11132 (synopsis "Learning principal graphs with DDRTree")
11134 "This package provides an implementation of the framework of
11135 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
11136 dimensional space while constructs a principal tree which passes through the
11137 middle of the data simultaneously. DDRTree shows superiority to
11138 alternatives (Wishbone, DPT) for inferring the ordering as well as the
11139 intrinsic structure of single cell genomics data. In general, it could be
11140 used to reconstruct the temporal progression as well as the bifurcation
11141 structure of any data type.")
11142 (license license:asl2.0)))
11144 (define-public r-corpcor
11151 (uri (cran-uri "corpcor" version))
11154 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
11155 (build-system r-build-system)
11156 (home-page "http://strimmerlab.org/software/corpcor/")
11157 (synopsis "Efficient estimation of covariance and (partial) correlation")
11159 "This package implements a James-Stein-type shrinkage estimator for the
11160 covariance matrix, with separate shrinkage for variances and correlations.
11161 Furthermore, functions are available for fast singular value decomposition,
11162 for computing the pseudoinverse, and for checking the rank and positive
11163 definiteness of a matrix.")
11164 (license license:gpl3+)))
11166 (define-public r-rspectra
11168 (name "r-rspectra")
11173 (uri (cran-uri "RSpectra" version))
11176 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
11177 (properties `((upstream-name . "RSpectra")))
11178 (build-system r-build-system)
11180 `(("r-matrix" ,r-matrix)
11182 ("r-rcppeigen" ,r-rcppeigen)))
11183 (home-page "https://github.com/yixuan/RSpectra")
11184 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
11186 "This package provides an R interface to the Spectra library for
11187 large-scale eigenvalue and SVD problems. It is typically used to compute a
11188 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
11189 which is usually more efficient than @code{eigen()} if k << n.")
11191 (license license:mpl2.0)))
11193 (define-public r-vbsr
11200 (uri (cran-uri "vbsr" version))
11203 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
11204 (build-system r-build-system)
11205 (home-page "https://cran.r-project.org/web/packages/vbsr")
11206 (synopsis "Variational Bayes spike regression regularized linear models")
11208 "This package provides an efficient algorithm for solving ultra-sparse
11209 regularized regression models using a variational Bayes algorithm with a spike
11210 prior. The algorithm is solved on a path, with coordinate updates, and is
11211 capable of generating very sparse models. Very general model
11212 diagnostics for controlling type-1 errors are also provided.")
11213 (license license:gpl2)))
11215 (define-public r-flare
11218 (version "1.6.0.2")
11222 (uri (cran-uri "flare" version))
11225 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
11226 (build-system r-build-system)
11228 `(("r-igraph" ,r-igraph)
11229 ("r-lattice" ,r-lattice)
11231 ("r-matrix" ,r-matrix)))
11232 (home-page "https://cran.r-project.org/web/packages/flare")
11233 (synopsis "Family of Lasso regression implementations")
11235 "This package provides implementations of a family of Lasso variants
11236 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
11237 high dimensional sparse linear models.")
11238 (license license:gpl2)))
11240 (define-public r-lassopv
11247 (uri (cran-uri "lassopv" version))
11250 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
11251 (build-system r-build-system)
11252 (propagated-inputs `(("r-lars" ,r-lars)))
11253 (home-page "https://github.com/lingfeiwang/lassopv")
11254 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
11256 "This package enables you to estimate the p-values for predictors x
11257 against target variable y in Lasso regression, using the regularization
11258 strength when each predictor enters the active set of regularization path for
11259 the first time as the statistic.")
11260 (license license:gpl3)))
11262 (define-public r-splitstackshape
11264 (name "r-splitstackshape")
11269 (uri (cran-uri "splitstackshape" version))
11272 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
11273 (build-system r-build-system)
11275 `(("r-data-table" ,r-data-table)))
11276 (home-page "https://github.com/mrdwab/splitstackshape")
11277 (synopsis "Stack and reshape datasets after splitting concatenated values")
11279 "Online data collection tools like Google Forms often export
11280 multiple-response questions with data concatenated in cells. The
11281 @code{concat.split} (cSplit) family of functions provided by this package
11282 splits such data into separate cells. This package also includes functions to
11283 stack groups of columns and to reshape wide data, even when the data are
11284 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
11285 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
11287 (license license:gpl3)))
11289 (define-public r-tfmpvalue
11291 (name "r-tfmpvalue")
11296 (uri (cran-uri "TFMPvalue" version))
11299 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
11300 (properties `((upstream-name . "TFMPvalue")))
11301 (build-system r-build-system)
11302 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11303 (home-page "https://github.com/ge11232002/TFMPvalue")
11304 (synopsis "P-value computation for position weight matrices")
11306 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
11307 identification from sequence/alignments, we are interested in the significance
11308 of certain match scores. TFMPvalue provides the accurate calculation of a
11309 p-value with a score threshold for position weight matrices, or the score with
11310 a given p-value. It is an interface to code originally made available by
11311 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
11312 Touzet and Varre (2007).")
11313 (license license:gpl2)))
11315 (define-public r-rnifti
11322 (uri (cran-uri "RNifti" version))
11325 "02jdxz3w423k9b5wldky4pnnq0cs2zlfi52jxjw1mk24z756j692"))))
11326 (properties `((upstream-name . "RNifti")))
11327 (build-system r-build-system)
11328 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11329 (home-page "https://github.com/jonclayden/RNifti")
11330 (synopsis "Fast R and C++ access to NIfTI images")
11332 "This package provides very fast read and write access to images stored
11333 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
11334 compiled C and interpreted R code. It also provides a C/C++ API that can be
11335 used by other packages.")
11336 (license license:gpl2)))
11338 (define-public r-shades
11345 (uri (cran-uri "shades" version))
11348 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11349 (build-system r-build-system)
11350 (home-page "https://github.com/jonclayden/shades")
11351 (synopsis "Simple color manipulation")
11353 "This package provides functions for easily manipulating colors,
11354 creating color scales and calculating color distances.")
11355 (license license:bsd-3)))
11357 (define-public r-ore
11364 (uri (cran-uri "ore" version))
11366 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11367 (build-system r-build-system)
11368 (home-page "https://github.com/jonclayden/ore")
11369 (synopsis "R interface to the Onigmo regular expression library")
11371 "This package provides an alternative to R's built-in functionality for
11372 handling regular expressions, based on the Onigmo library. It offers
11373 first-class compiled regex objects, partial matching and function-based
11374 substitutions, amongst other features.")
11375 (license license:bsd-3)))
11377 (define-public r-reportr
11384 (uri (cran-uri "reportr" version))
11387 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11388 (build-system r-build-system)
11389 (propagated-inputs `(("r-ore" ,r-ore)))
11390 (home-page "https://github.com/jonclayden/reportr")
11391 (synopsis "General message and error reporting system")
11393 "This package provides a system for reporting messages, which offers
11394 certain useful features over the standard R system, such as the incorporation
11395 of output consolidation, message filtering, assertions, expression
11396 substitution, automatic generation of stack traces for debugging, and
11397 conditional reporting based on the current \"output level\".")
11398 (license license:gpl2)))
11400 (define-public r-tractor-base
11402 (name "r-tractor-base")
11407 (uri (cran-uri "tractor.base" version))
11410 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11411 (properties `((upstream-name . "tractor.base")))
11412 (build-system r-build-system)
11415 ("r-reportr" ,r-reportr)
11416 ("r-rnifti" ,r-rnifti)
11417 ("r-shades" ,r-shades)))
11418 (home-page "https://www.tractor-mri.org.uk")
11419 (synopsis "Read, manipulate and visualize magnetic resonance images")
11421 "This package provides functions for working with magnetic resonance
11422 images. It supports reading and writing of popular file formats (DICOM,
11423 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11424 visualization; flexible image manipulation; metadata and sparse image
11426 (license license:gpl2)))
11428 (define-public r-grimport
11430 (name "r-grimport")
11435 (uri (cran-uri "grImport" version))
11438 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11439 (properties `((upstream-name . "grImport")))
11440 (build-system r-build-system)
11442 `(("ghostscript" ,ghostscript)))
11444 `(("r-xml" ,r-xml)))
11445 (home-page "https://cran.r-project.org/web/packages/grImport")
11446 (synopsis "Convert, import, and draw PostScript pictures")
11448 "This package provides functions for converting, importing, and drawing
11449 PostScript pictures in R plots.")
11450 (license license:gpl2+)))
11452 (define-public r-grimport2
11454 (name "r-grimport2")
11459 (uri (cran-uri "grImport2" version))
11462 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11463 (properties `((upstream-name . "grImport2")))
11464 (build-system r-build-system)
11466 `(("r-base64enc" ,r-base64enc)
11470 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11471 (synopsis "Import SVG graphics")
11473 "This package provides functions for importing external vector images and
11474 drawing them as part of R plots. This package is different from the
11475 @code{grImport} package because, where that package imports PostScript format
11476 images, this package imports SVG format images. Furthermore, this package
11477 imports a specific subset of SVG, so external images must be preprocessed
11478 using a package like @code{rsvg} to produce SVG that this package can import.
11479 SVG features that are not supported by R graphics, such as gradient fills, can
11480 be imported and then exported via the @code{gridSVG} package.")
11481 (license license:gpl2+)))
11483 (define-public r-kohonen
11490 (uri (cran-uri "kohonen" version))
11493 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11494 (build-system r-build-system)
11496 `(("r-rcpp" ,r-rcpp)))
11497 (home-page "https://cran.r-project.org/web/packages/kohonen")
11498 (synopsis "Supervised and unsupervised self-organising maps")
11500 "This package provides functions to train @dfn{self-organising
11501 maps} (SOMs). Also interrogation of the maps and prediction using trained
11502 maps are supported. The name of the package refers to Teuvo Kohonen, the
11503 inventor of the SOM.")
11504 (license license:gpl2+)))
11506 (define-public r-nnls
11513 (uri (cran-uri "nnls" version))
11516 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11517 (build-system r-build-system)
11518 (native-inputs `(("gfortran" ,gfortran)))
11519 (home-page "https://cran.r-project.org/web/packages/nnls")
11520 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11522 "This package provides an R interface to the Lawson-Hanson implementation
11523 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11524 the combination of non-negative and non-positive constraints.")
11525 (license license:gpl2+)))
11527 (define-public r-iso
11530 (version "0.0-18.1")
11534 (uri (cran-uri "Iso" version))
11537 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11538 (properties `((upstream-name . "Iso")))
11539 (build-system r-build-system)
11540 (native-inputs `(("gfortran" ,gfortran)))
11541 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11542 (synopsis "Functions to perform isotonic regression")
11544 "This package provides support for linear order and unimodal
11545 order (univariate) isotonic regression and bivariate isotonic regression with
11546 linear order on both variables.")
11547 (license license:gpl2+)))
11549 (define-public r-chemometricswithr
11551 (name "r-chemometricswithr")
11556 (uri (cran-uri "ChemometricsWithR" version))
11559 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11561 `((upstream-name . "ChemometricsWithR")))
11562 (build-system r-build-system)
11564 `(("r-devtools" ,r-devtools)
11565 ("r-kohonen" ,r-kohonen)
11568 (home-page "https://github.com/rwehrens/CWR")
11569 (synopsis "Chemometrics with R")
11571 "This package provides functions and scripts used in the book
11572 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11573 Life Sciences\" by Ron Wehrens, Springer (2011).")
11574 (license license:gpl2+)))
11576 (define-public r-als
11583 (uri (cran-uri "ALS" version))
11586 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11587 (properties `((upstream-name . "ALS")))
11588 (build-system r-build-system)
11591 ("r-nnls" ,r-nnls)))
11592 (home-page "https://cran.r-project.org/web/packages/ALS")
11593 (synopsis "Multivariate curve resolution alternating least squares")
11595 "Alternating least squares is often used to resolve components
11596 contributing to data with a bilinear structure; the basic technique may be
11597 extended to alternating constrained least squares. This package provides an
11598 implementation of @dfn{multivariate curve resolution alternating least
11599 squares} (MCR-ALS).
11601 Commonly applied constraints include unimodality, non-negativity, and
11602 normalization of components. Several data matrices may be decomposed
11603 simultaneously by assuming that one of the two matrices in the bilinear
11604 decomposition is shared between datasets.")
11605 (license license:gpl2+)))
11607 (define-public r-strucchange
11609 (name "r-strucchange")
11614 (uri (cran-uri "strucchange" version))
11617 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11618 (build-system r-build-system)
11620 `(("r-sandwich" ,r-sandwich)
11622 (home-page "https://cran.r-project.org/web/packages/strucchange")
11623 (synopsis "Testing, monitoring, and dating structural changes")
11625 "This package provides tools for testing, monitoring and dating
11626 structural changes in (linear) regression models. It features tests/methods
11627 from the generalized fluctuation test framework as well as from the F
11628 test (Chow test) framework. This includes methods to fit, plot and test
11629 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11630 statistics, respectively. It is possible to monitor incoming data online
11631 using fluctuation processes. Finally, the breakpoints in regression models
11632 with structural changes can be estimated together with confidence intervals.
11633 Emphasis is always given to methods for visualizing the data.")
11634 ;; Either of these two GPL versions
11635 (license (list license:gpl2 license:gpl3))))
11637 (define-public r-pixmap
11644 (uri (cran-uri "pixmap" version))
11647 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11648 (build-system r-build-system)
11649 (home-page "https://cran.r-project.org/web/packages/pixmap")
11650 (synopsis "Tools for bitmap images")
11652 "This package provides functions for importing, exporting, plotting and
11653 other manipulations of bitmapped images.")
11654 (license license:gpl2)))
11656 (define-public r-rapidjsonr
11658 (name "r-rapidjsonr")
11663 (uri (cran-uri "rapidjsonr" version))
11666 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11667 (build-system r-build-system)
11668 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11669 (synopsis "JSON parser")
11671 "This package provides JSON parsing capability through the Rapidjson
11673 (license license:expat)))
11675 (define-public r-ontologyindex
11677 (name "r-ontologyindex")
11682 (uri (cran-uri "ontologyIndex" version))
11685 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11686 (properties `((upstream-name . "ontologyIndex")))
11687 (build-system r-build-system)
11688 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11689 (synopsis "Functions for processing ontologies in R")
11691 "This package provides functions for reading ontologies into R as lists
11692 and manipulating sets of ontological terms.")
11693 (license license:gpl2+)))
11695 (define-public r-gargle
11702 (uri (cran-uri "gargle" version))
11705 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11706 (build-system r-build-system)
11711 ("r-jsonlite" ,r-jsonlite)
11712 ("r-rlang" ,r-rlang)
11713 ("r-withr" ,r-withr)))
11715 `(("r-knitr" ,r-knitr)))
11716 (home-page "https://gargle.r-lib.org")
11717 (synopsis "Utilities for working with Google APIs")
11719 "This package provides utilities for working with Google APIs. This
11720 includes functions and classes for handling common credential types and for
11721 preparing, executing, and processing HTTP requests.")
11722 (license license:expat)))
11724 (define-public r-bigrquery
11726 (name "r-bigrquery")
11731 (uri (cran-uri "bigrquery" version))
11734 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
11735 (build-system r-build-system)
11737 `(("r-assertthat" ,r-assertthat)
11738 ("r-bit64" ,r-bit64)
11741 ("r-gargle" ,r-gargle)
11744 ("r-jsonlite" ,r-jsonlite)
11745 ("r-prettyunits" ,r-prettyunits)
11746 ("r-progress" ,r-progress)
11747 ("r-rapidjsonr" ,r-rapidjsonr)
11749 ("r-rlang" ,r-rlang)
11750 ("r-tibble" ,r-tibble)))
11751 (home-page "https://github.com/rstats-db/bigrquery")
11752 (synopsis "R interface to Google's BigQuery API")
11754 "This package provides an R interface to Google's BigQuery database.")
11755 (license license:gpl3)))
11757 (define-public r-gmp
11764 (uri (cran-uri "gmp" version))
11767 "11rl7qmfrpp1974f0vzsi3zjyx147wlb82ydxak2b60khfvhrn90"))))
11768 (build-system r-build-system)
11771 (modify-phases %standard-phases
11772 (add-after 'unpack 'set-CC
11773 (lambda _ (setenv "CC" "gcc") #t)))))
11774 (inputs `(("gmp" ,gmp)))
11775 (home-page "https://cran.r-project.org/web/packages/gmp")
11776 (synopsis "Multiple precision arithmetic")
11778 "This package supports multiple precision arithmetic (big integers and
11779 rationals, prime number tests, matrix computation), \"arithmetic without
11780 limitations\" using the GNU Multiple Precision library.")
11781 ;; Any version of the GPL.
11782 (license license:gpl3+)))
11784 (define-public r-rmpfr
11791 (uri (cran-uri "Rmpfr" version))
11794 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11795 (properties `((upstream-name . "Rmpfr")))
11796 (build-system r-build-system)
11801 `(("r-gmp" ,r-gmp)))
11803 `(("pkg-config" ,pkg-config)))
11804 (home-page "http://rmpfr.r-forge.r-project.org/")
11805 (synopsis "R bindings to the MPFR library")
11807 "This package supports arithmetic (via S4 classes and methods) for
11808 arbitrary precision floating point numbers, including transcendental
11809 functions. To this end, the package interfaces with the @dfn{Multiple
11810 Precision Floating-Point Reliable} (MPFR) library.")
11811 (license license:gpl2+)))
11813 (define-public r-assertive-base
11815 (name "r-assertive-base")
11820 (uri (cran-uri "assertive.base" version))
11823 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11825 `((upstream-name . "assertive.base")))
11826 (build-system r-build-system)
11827 (home-page "https://bitbucket.org/richierocks/assertive.base")
11828 (synopsis "Core of the assertive package")
11830 "This package provides a minimal set of predicates and assertions used by
11831 the assertive package. This is mainly for use by other package developers who
11832 want to include run-time testing features in their own packages.")
11833 (license license:gpl3+)))
11835 (define-public r-assertive-properties
11837 (name "r-assertive-properties")
11842 (uri (cran-uri "assertive.properties" version))
11845 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11847 `((upstream-name . "assertive.properties")))
11848 (build-system r-build-system)
11850 `(("r-assertive-base" ,r-assertive-base)))
11851 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11852 (synopsis "Assertions to check properties of variables")
11854 "This package provides a set of predicates and assertions for checking
11855 the properties of variables, such as length, names and attributes. This is
11856 mainly for use by other package developers who want to include run-time
11857 testing features in their own packages.")
11858 (license license:gpl3+)))
11860 (define-public r-assertive-numbers
11862 (name "r-assertive-numbers")
11867 (uri (cran-uri "assertive.numbers" version))
11870 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11872 `((upstream-name . "assertive.numbers")))
11873 (build-system r-build-system)
11875 `(("r-assertive-base" ,r-assertive-base)))
11876 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11877 (synopsis "Assertions to check properties of numbers")
11879 "This package provides a set of predicates and assertions for checking
11880 the properties of numbers. This is mainly for use by other package developers
11881 who want to include run-time testing features in their own packages.")
11882 (license license:gpl3+)))
11884 (define-public r-assertive-sets
11886 (name "r-assertive-sets")
11891 (uri (cran-uri "assertive.sets" version))
11894 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11896 `((upstream-name . "assertive.sets")))
11897 (build-system r-build-system)
11899 `(("r-assertive-base" ,r-assertive-base)))
11900 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11901 (synopsis "Assertions to check properties of sets")
11903 "This package provides a set of predicates and assertions for checking
11904 the properties of sets. This is mainly for use by other package developers
11905 who want to include run-time testing features in their own packages.")
11906 (license license:gpl3+)))
11908 (define-public r-assertive-matrices
11910 (name "r-assertive-matrices")
11915 (uri (cran-uri "assertive.matrices" version))
11918 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11920 `((upstream-name . "assertive.matrices")))
11921 (build-system r-build-system)
11923 `(("r-assertive-base" ,r-assertive-base)))
11924 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11925 (synopsis "Assertions to check properties of matrices")
11927 "This package provides a set of predicates and assertions for checking
11928 the properties of matrices. This is mainly for use by other package
11929 developers who want to include run-time testing features in their own
11931 (license license:gpl3+)))
11933 (define-public r-assertive-models
11935 (name "r-assertive-models")
11940 (uri (cran-uri "assertive.models" version))
11943 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11945 `((upstream-name . "assertive.models")))
11946 (build-system r-build-system)
11948 `(("r-assertive-base" ,r-assertive-base)))
11949 (home-page "https://bitbucket.org/richierocks/assertive.models")
11950 (synopsis "Assertions to check properties of models")
11952 "This package provides a set of predicates and assertions for checking
11953 the properties of models. This is mainly for use by other package developers
11954 who want to include run-time testing features in their own packages.")
11955 (license license:gpl3+)))
11957 (define-public r-assertive-reflection
11959 (name "r-assertive-reflection")
11964 (uri (cran-uri "assertive.reflection" version))
11967 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11969 `((upstream-name . "assertive.reflection")))
11970 (build-system r-build-system)
11972 `(("r-assertive-base" ,r-assertive-base)))
11973 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11974 (synopsis "Assertions for checking the state of R")
11976 "This package provides a set of predicates and assertions for checking
11977 the state and capabilities of R, the operating system it is running on, and
11978 the IDE being used. This is mainly for use by other package developers who
11979 want to include run-time testing features in their own packages.")
11980 (license license:gpl3+)))
11982 (define-public r-assertive-types
11984 (name "r-assertive-types")
11989 (uri (cran-uri "assertive.types" version))
11992 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11994 `((upstream-name . "assertive.types")))
11995 (build-system r-build-system)
11997 `(("r-assertive-base" ,r-assertive-base)
11998 ("r-assertive-properties" ,r-assertive-properties)
11999 ("r-codetools" ,r-codetools)))
12000 (home-page "https://bitbucket.org/richierocks/assertive.types")
12001 (synopsis "Assertions to check types of variables")
12003 "This package provides a set of predicates and assertions for checking
12004 the types of variables. This is mainly for use by other package developers
12005 who want to include run-time testing features in their own packages.")
12006 (license license:gpl3+)))
12008 (define-public r-assertive-files
12010 (name "r-assertive-files")
12015 (uri (cran-uri "assertive.files" version))
12018 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12020 `((upstream-name . "assertive.files")))
12021 (build-system r-build-system)
12023 `(("r-assertive-base" ,r-assertive-base)
12024 ("r-assertive-numbers" ,r-assertive-numbers)))
12025 (home-page "https://bitbucket.org/richierocks/assertive.files")
12026 (synopsis "Assertions to check properties of files")
12028 "This package provides a set of predicates and assertions for checking
12029 the properties of files and connections. This is mainly for use by other
12030 package developers who want to include run-time testing features in their own
12032 (license license:gpl3+)))
12034 (define-public r-assertive-code
12036 (name "r-assertive-code")
12041 (uri (cran-uri "assertive.code" version))
12044 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12046 `((upstream-name . "assertive.code")))
12047 (build-system r-build-system)
12049 `(("r-assertive-base" ,r-assertive-base)
12050 ("r-assertive-properties" ,r-assertive-properties)
12051 ("r-assertive-types" ,r-assertive-types)))
12052 (home-page "https://bitbucket.org/richierocks/assertive.code")
12053 (synopsis "Assertions to check properties of code")
12055 "This package provides a set of predicates and assertions for checking
12056 the properties of code. This is mainly for use by other package developers
12057 who want to include run-time testing features in their own packages.")
12058 (license license:gpl3+)))
12060 (define-public r-assertive-datetimes
12062 (name "r-assertive-datetimes")
12067 (uri (cran-uri "assertive.datetimes" version))
12070 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
12072 `((upstream-name . "assertive.datetimes")))
12073 (build-system r-build-system)
12075 `(("r-assertive-base" ,r-assertive-base)
12076 ("r-assertive-types" ,r-assertive-types)))
12077 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
12078 (synopsis "Assertions to check properties of dates and times")
12080 "This package provides a set of predicates and assertions for checking
12081 the properties of dates and times. This is mainly for use by other package
12082 developers who want to include run-time testing features in their own
12084 (license license:gpl3+)))
12086 (define-public r-assertive-strings
12088 (name "r-assertive-strings")
12093 (uri (cran-uri "assertive.strings" version))
12096 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
12098 `((upstream-name . "assertive.strings")))
12099 (build-system r-build-system)
12101 `(("r-assertive-base" ,r-assertive-base)
12102 ("r-assertive-types" ,r-assertive-types)
12103 ("r-stringi" ,r-stringi)))
12104 (home-page "https://bitbucket.org/richierocks/assertive.strings")
12105 (synopsis "Assertions to check properties of strings")
12107 "This package provides a set of predicates and assertions for checking
12108 the properties of strings. This is mainly for use by other package developers
12109 who want to include run-time testing features in their own packages.")
12110 (license license:gpl3+)))
12112 (define-public r-assertive-data-us
12114 (name "r-assertive-data-us")
12119 (uri (cran-uri "assertive.data.us" version))
12122 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
12124 `((upstream-name . "assertive.data.us")))
12125 (build-system r-build-system)
12127 `(("r-assertive-base" ,r-assertive-base)
12128 ("r-assertive-strings" ,r-assertive-strings)))
12129 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
12130 (synopsis "Assertions to check properties of strings")
12132 "This package provides a set of predicates and assertions for checking
12133 the properties of US-specific complex data types. This is mainly for use by
12134 other package developers who want to include run-time testing features in
12135 their own packages.")
12136 (license license:gpl3+)))
12138 (define-public r-assertive-data-uk
12140 (name "r-assertive-data-uk")
12145 (uri (cran-uri "assertive.data.uk" version))
12148 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
12150 `((upstream-name . "assertive.data.uk")))
12151 (build-system r-build-system)
12153 `(("r-assertive-base" ,r-assertive-base)
12154 ("r-assertive-strings" ,r-assertive-strings)))
12155 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
12156 (synopsis "Assertions to check properties of strings")
12158 "This package provides a set of predicates and assertions for checking
12159 the properties of UK-specific complex data types. This is mainly for use by
12160 other package developers who want to include run-time testing features in
12161 their own packages.")
12162 (license license:gpl3+)))
12164 (define-public r-assertive-data
12166 (name "r-assertive-data")
12171 (uri (cran-uri "assertive.data" version))
12174 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
12176 `((upstream-name . "assertive.data")))
12177 (build-system r-build-system)
12179 `(("r-assertive-base" ,r-assertive-base)
12180 ("r-assertive-strings" ,r-assertive-strings)))
12181 (home-page "https://bitbucket.org/richierocks/assertive.data")
12182 (synopsis "Assertions to check properties of data")
12184 "This package provides a set of predicates and assertions for checking
12185 the properties of (country independent) complex data types. This is mainly
12186 for use by other package developers who want to include run-time testing
12187 features in their own packages.")
12188 (license license:gpl3+)))
12190 (define-public r-assertive
12192 (name "r-assertive")
12197 (uri (cran-uri "assertive" version))
12200 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
12201 (build-system r-build-system)
12203 `(("r-assertive-base" ,r-assertive-base)
12204 ("r-assertive-code" ,r-assertive-code)
12205 ("r-assertive-data" ,r-assertive-data)
12206 ("r-assertive-data-uk" ,r-assertive-data-uk)
12207 ("r-assertive-data-us" ,r-assertive-data-us)
12208 ("r-assertive-datetimes" ,r-assertive-datetimes)
12209 ("r-assertive-files" ,r-assertive-files)
12210 ("r-assertive-matrices" ,r-assertive-matrices)
12211 ("r-assertive-models" ,r-assertive-models)
12212 ("r-assertive-numbers" ,r-assertive-numbers)
12213 ("r-assertive-properties" ,r-assertive-properties)
12214 ("r-assertive-reflection" ,r-assertive-reflection)
12215 ("r-assertive-sets" ,r-assertive-sets)
12216 ("r-assertive-strings" ,r-assertive-strings)
12217 ("r-assertive-types" ,r-assertive-types)
12218 ("r-knitr" ,r-knitr)))
12220 `(("r-knitr" ,r-knitr)))
12221 (home-page "https://bitbucket.org/richierocks/assertive")
12222 (synopsis "Readable check functions to ensure code integrity")
12224 "This package provides lots of predicates (@code{is_*} functions) to
12225 check the state of your variables, and assertions (@code{assert_*} functions)
12226 to throw errors if they aren't in the right form.")
12227 (license license:gpl3+)))
12229 (define-public r-dotcall64
12231 (name "r-dotcall64")
12236 (uri (cran-uri "dotCall64" version))
12239 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
12240 (properties `((upstream-name . "dotCall64")))
12241 (build-system r-build-system)
12242 (native-inputs `(("gfortran" ,gfortran)))
12243 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
12244 (synopsis "Enhanced foreign function interface supporting long vectors")
12246 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
12247 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
12248 supports long vectors, arguments of type 64-bit integer, and provides a
12249 mechanism to avoid unnecessary copies of read-only and write-only arguments.
12250 This makes it a convenient and fast interface to C/C++ and Fortran code.")
12251 (license license:gpl2+)))
12253 (define-public r-spam
12260 (uri (cran-uri "spam" version))
12262 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
12263 (build-system r-build-system)
12265 `(("r-dotcall64" ,r-dotcall64)))
12266 (native-inputs `(("gfortran" ,gfortran)))
12267 (home-page "https://www.math.uzh.ch/pages/spam/")
12268 (synopsis "Sparse matrix algebra")
12270 "This package provides a set of functions for sparse matrix algebra.
12271 Differences with other sparse matrix packages are:
12274 @item it only supports (essentially) one sparse matrix format;
12275 @item it is based on transparent and simple structure(s);
12276 @item it is tailored for MCMC calculations within G(M)RF;
12277 @item and it is fast and scalable (with the extension package @code{spam64}).
12279 ;; Either of these licenses
12280 (license (list license:bsd-3 license:lgpl2.0))))
12282 (define-public r-fields
12289 (uri (cran-uri "fields" version))
12291 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
12292 (build-system r-build-system)
12294 `(("r-maps" ,r-maps)
12295 ("r-spam" ,r-spam)))
12297 `(("gfortran" ,gfortran)))
12298 (home-page "https://www.image.ucar.edu/fields")
12299 (synopsis "Tools for spatial data")
12301 "This is a package for curve, surface and function fitting with an
12302 emphasis on splines, spatial data and spatial statistics. The major methods
12303 include cubic, and thin plate splines, Kriging, and compactly supported
12304 covariance functions for large data sets.")
12305 (license license:gpl2+)))
12307 (define-public r-spatialextremes
12309 (name "r-spatialextremes")
12314 (uri (cran-uri "SpatialExtremes" version))
12317 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
12319 `((upstream-name . "SpatialExtremes")))
12320 (build-system r-build-system)
12322 `(("r-fields" ,r-fields)
12323 ("r-maps" ,r-maps)))
12324 (home-page "http://spatialextremes.r-forge.r-project.org/")
12325 (synopsis "Modelling spatial extremes")
12327 "This package provides tools for the statistical modelling of spatial
12328 extremes using max-stable processes, copula or Bayesian hierarchical models.
12329 More precisely, this package allows (conditional) simulations from various
12330 parametric max-stable models, analysis of the extremal spatial dependence, the
12331 fitting of such processes using composite likelihoods or least square (simple
12332 max-stable processes only), model checking and selection and prediction.")
12333 (license license:gpl2+)))
12335 (define-public r-drc
12342 (uri (cran-uri "drc" version))
12345 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
12346 (build-system r-build-system)
12349 ("r-gtools" ,r-gtools)
12351 ("r-multcomp" ,r-multcomp)
12352 ("r-plotrix" ,r-plotrix)
12353 ("r-scales" ,r-scales)))
12354 (home-page "https://cran.r-project.org/web/packages/drc")
12355 (synopsis "Analysis of dose-response curves")
12357 "This package provides a suite of flexible and versatile model fitting
12358 and after-fitting functions for the analysis of dose-response data.")
12359 (license license:gpl2+)))
12361 (define-public r-rmeta
12368 (uri (cran-uri "rmeta" version))
12371 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12372 (build-system r-build-system)
12373 (home-page "https://cran.r-project.org/web/packages/rmeta")
12374 (synopsis "Tools for meta-analysis")
12376 "This package provides functions for simple fixed and random effects
12377 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12378 draws standard summary plots, funnel plots, and computes summaries and tests
12379 for association and heterogeneity.")
12380 (license license:gpl2)))
12382 (define-public r-bootstrap
12384 (name "r-bootstrap")
12389 (uri (cran-uri "bootstrap" version))
12392 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12393 (build-system r-build-system)
12394 (native-inputs `(("gfortran" ,gfortran)))
12395 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12396 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12398 "This package provides software and data for the book \"An Introduction
12399 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12400 This package is primarily provided for projects already based on it, and for
12401 support of the book. New projects should preferentially use the recommended
12402 package \"boot\".")
12403 (license license:bsd-3)))
12405 (define-public r-survivalroc
12407 (name "r-survivalroc")
12412 (uri (cran-uri "survivalROC" version))
12415 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12416 (properties `((upstream-name . "survivalROC")))
12417 (build-system r-build-system)
12418 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12419 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12421 "Compute time-dependent ROC curve from censored survival data using
12422 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12423 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12424 (license license:gpl2+)))
12426 (define-public r-longitudinal
12428 (name "r-longitudinal")
12433 (uri (cran-uri "longitudinal" version))
12436 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12437 (build-system r-build-system)
12438 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12439 (home-page "http://strimmerlab.org/software/longitudinal/")
12440 (synopsis "Analysis of multiple time course data")
12442 "This package contains general data structures and functions for
12443 longitudinal data with multiple variables, repeated measurements, and
12444 irregularly spaced time points. It also implements a shrinkage estimator of
12445 dynamical correlation and dynamical covariance.")
12446 (license license:gpl3+)))
12448 (define-public r-genenet
12455 (uri (cran-uri "GeneNet" version))
12458 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12459 (properties `((upstream-name . "GeneNet")))
12460 (build-system r-build-system)
12462 `(("r-corpcor" ,r-corpcor)
12463 ("r-fdrtool" ,r-fdrtool)
12464 ("r-longitudinal" ,r-longitudinal)))
12465 (home-page "http://strimmerlab.org/software/genenet/")
12466 (synopsis "Modeling and inferring gene networks")
12468 "This package analyzes gene expression (time series) data with focus on
12469 the inference of gene networks. In particular, GeneNet implements the methods
12470 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12471 for learning large-scale gene association networks (including assignment of
12472 putative directions).")
12473 (license license:gpl3+)))
12475 (define-public r-rbamtools
12477 (name "r-rbamtools")
12478 (version "2.16.17")
12482 (uri (cran-uri "rbamtools" version))
12485 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12486 (build-system r-build-system)
12487 (inputs `(("zlib" ,zlib)))
12489 `(("r-refgenome" ,r-refgenome)))
12490 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12491 (synopsis "Read and write BAM (binary alignment) files")
12493 "This package provides an R interface to functions of the SAMtools
12495 (license license:artistic2.0)))
12497 (define-public r-protviz
12504 (uri (cran-uri "protViz" version))
12507 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12508 (properties `((upstream-name . "protViz")))
12509 (build-system r-build-system)
12510 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12511 (home-page "https://github.com/protViz/protViz/")
12512 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12514 "This package helps with quality checks, visualizations and analysis of
12515 mass spectrometry data, coming from proteomics experiments. The package is
12516 developed, tested and used at the Functional Genomics Center Zurich, where it
12517 is used mainly for prototyping, teaching, and having fun with proteomics data.
12518 But it can also be used to do data analysis for small scale data sets.")
12519 (license license:gpl3)))
12521 (define-public r-cmprsk
12528 (uri (cran-uri "cmprsk" version))
12530 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12531 (build-system r-build-system)
12533 `(("r-survival" ,r-survival)))
12535 `(("gfortran" ,gfortran)))
12536 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12537 (synopsis "Subdistribution analysis of competing risks")
12539 "This package provides tool for estimation, testing and regression
12540 modeling of subdistribution functions in competing risks, as described in
12541 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12542 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12543 A proportional hazards model for the subdistribution of a competing risk,
12544 JASA, 94:496-509.")
12545 (license license:gpl2+)))
12547 (define-public r-etm
12554 (uri (cran-uri "etm" version))
12557 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
12558 (build-system r-build-system)
12560 `(("r-data-table" ,r-data-table)
12561 ("r-lattice" ,r-lattice)
12563 ("r-rcpparmadillo" ,r-rcpparmadillo)
12564 ("r-survival" ,r-survival)))
12565 (home-page "https://cran.r-project.org/web/packages/etm")
12566 (synopsis "Empirical transition matrix")
12568 "The @dfn{empirical transition matrix} (etm) package estimates
12569 the matrix of transition probabilities for any time-inhomogeneous multistate
12570 model with finite state space using the Aalen-Johansen estimator.")
12571 (license license:expat)))
12573 (define-public r-epi
12580 (uri (cran-uri "Epi" version))
12583 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12584 (properties `((upstream-name . "Epi")))
12585 (build-system r-build-system)
12587 `(("r-cmprsk" ,r-cmprsk)
12588 ("r-data-table" ,r-data-table)
12591 ("r-matrix" ,r-matrix)
12593 ("r-numderiv" ,r-numderiv)
12595 ("r-survival" ,r-survival)
12597 (home-page "https://BendixCarstensen.com/Epi/")
12598 (synopsis "Statistical analysis in epidemiology")
12600 "This package provides functions for demographic and epidemiological
12601 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12602 particular representation, manipulation and simulation of multistate data -
12603 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12604 @code{etm} and @code{cmprsk} packages. It also contains functions for
12605 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12606 data and some useful functions for tabulation and plotting, as well as a
12607 number of epidemiological data sets.")
12608 (license license:gpl2)))
12610 (define-public r-ppls
12613 (version "1.6-1.1")
12617 (uri (cran-uri "ppls" version))
12620 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12621 (build-system r-build-system)
12622 (propagated-inputs `(("r-mass" ,r-mass)))
12623 (home-page "https://cran.r-project.org/web/packages/ppls")
12624 (synopsis "Penalized partial least squares")
12626 "This package contains linear and nonlinear regression methods based on
12627 partial least squares and penalization techniques. Model parameters are
12628 selected via cross-validation, and confidence intervals ans tests for the
12629 regression coefficients can be conducted via jackknifing.")
12630 (license license:gpl2+)))
12632 (define-public r-huge
12635 (version "1.3.4.1")
12639 (uri (cran-uri "huge" version))
12641 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12642 (build-system r-build-system)
12644 `(("r-igraph" ,r-igraph)
12646 ("r-matrix" ,r-matrix)
12648 ("r-rcppeigen" ,r-rcppeigen)))
12649 (home-page "https://cran.r-project.org/web/packages/huge")
12650 (synopsis "High-dimensional undirected graph estimation")
12652 "This package provides a general framework for high-dimensional
12653 undirected graph estimation. It integrates data preprocessing, neighborhood
12654 screening, graph estimation, and model selection techniques into a pipeline.")
12655 (license license:gpl2)))
12657 (define-public r-parcor
12664 (uri (cran-uri "parcor" version))
12667 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12668 (build-system r-build-system)
12671 ("r-genenet" ,r-genenet)
12672 ("r-glmnet" ,r-glmnet)
12674 ("r-ppls" ,r-ppls)))
12675 (home-page "https://cran.r-project.org/web/packages/parcor")
12676 (synopsis "Regularized estimation of partial correlation matrices")
12678 "This package estimates the matrix of partial correlations based on
12679 different regularized regression methods: lasso, adaptive lasso, PLS, and
12680 Ridge Regression. In addition, the package provides model selection for
12681 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12682 (license license:gpl2+)))
12684 (define-public r-mcmc
12691 (uri (cran-uri "mcmc" version))
12694 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12695 (build-system r-build-system)
12696 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12697 (synopsis "Markov chain Monte Carlo")
12699 "This package simulates continuous distributions of random vectors using
12700 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12701 function that evaluates the log unnormalized density. Algorithms are random
12702 walk Metropolis algorithm (function @code{metrop}), simulated
12703 tempering (function @code{temper}), and morphometric random walk
12704 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12705 by change of variable.")
12706 (license license:expat)))
12708 (define-public r-listenv
12715 (uri (cran-uri "listenv" version))
12718 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12719 (build-system r-build-system)
12721 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12722 (home-page "https://github.com/HenrikBengtsson/listenv")
12723 (synopsis "Environments behaving (almost) as lists")
12725 "This package implements list environments. List environments are
12726 environments that have list-like properties. For instance, the elements of a
12727 list environment are ordered and can be accessed and iterated over using index
12729 (license license:lgpl2.1+)))
12731 (define-public r-globals
12738 (uri (cran-uri "globals" version))
12741 "1ch9m7fxclfhfa38b743wcm7w1bkx9kmivc6l7phpbgs6h9jhrcc"))))
12742 (build-system r-build-system)
12744 `(("r-codetools" ,r-codetools)))
12745 (home-page "https://github.com/HenrikBengtsson/globals")
12746 (synopsis "Identify global objects in R expressions")
12748 "This package provides tools to identify global (\"unknown\" or \"free\")
12749 objects in R expressions by code inspection using various strategies, e.g.
12750 conservative or liberal. The objective of this package is to make it as
12751 simple as possible to identify global objects for the purpose of exporting
12752 them in distributed compute environments.")
12753 (license license:lgpl2.1+)))
12755 (define-public r-parallelly
12757 (name "r-parallelly")
12762 (uri (cran-uri "parallelly" version))
12765 "1hlr81khr7z4x9gprymdh19mdq3nw6wm8d2795sd2pa3ya6phnb0"))))
12766 (properties `((upstream-name . "parallelly")))
12767 (build-system r-build-system)
12768 (home-page "https://github.com/HenrikBengtsson/parallelly")
12769 (synopsis "Enhancements of the parallel package")
12771 "This package provides utility functions that enhance the @code{parallel}
12772 package and support the built-in parallel backends of the @code{future}
12773 package. For example, @code{availableCores} gives the number of CPU cores
12774 available to your R process as given by R options and environment variables,
12775 including those set by job schedulers on high-performance compute clusters.
12776 If none is set, it will fall back to @code{parallel::detectCores}. Another
12777 example is @code{makeClusterPSOCK}, which is backward compatible with
12778 @code{parallel::makePSOCKcluster} while doing a better job in setting up
12779 remote cluster workers without the need for configuring the firewall to do
12780 port-forwarding to your local computer.")
12781 (license license:lgpl2.1+)))
12783 (define-public r-future
12790 (uri (cran-uri "future" version))
12793 "12f483h7g172ygafbg7h43vykv0f7xz9miwqf5q8dyv7gpgqi5fl"))))
12794 (build-system r-build-system)
12796 `(("r-digest" ,r-digest)
12797 ("r-globals" ,r-globals)
12798 ("r-listenv" ,r-listenv)))
12800 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12801 (home-page "https://github.com/HenrikBengtsson/future")
12802 (synopsis "Unified parallel and distributed processing in R")
12804 "The purpose of this package is to provide a lightweight and unified
12805 Future API for sequential and parallel processing of R expression via futures.
12806 This package implements sequential, multicore, multisession, and cluster
12807 futures. With these, R expressions can be evaluated on the local machine, in
12808 parallel a set of local machines, or distributed on a mix of local and remote
12809 machines. Extensions to this package implement additional backends for
12810 processing futures via compute cluster schedulers etc. Because of its unified
12811 API, there is no need to modify any code in order to switch from sequential on
12812 the local machine to, say, distributed processing on a remote compute cluster.")
12813 (license license:lgpl2.1+)))
12815 (define-public r-future-apply
12817 (name "r-future-apply")
12822 (uri (cran-uri "future.apply" version))
12825 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12826 (properties `((upstream-name . "future.apply")))
12827 (build-system r-build-system)
12829 `(("r-future" ,r-future)
12830 ("r-globals" ,r-globals)))
12832 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12833 (home-page "https://github.com/HenrikBengtsson/future.apply")
12834 (synopsis "Apply function to elements in parallel using futures")
12836 "This package provides implementations of @code{apply()},
12837 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12838 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12839 can be resolved using any future-supported backend, e.g. parallel on the local
12840 machine or distributed on a compute cluster.")
12841 (license license:gpl2+)))
12843 (define-public r-rsvd
12850 (uri (cran-uri "rsvd" version))
12853 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12854 (build-system r-build-system)
12856 `(("r-matrix" ,r-matrix)))
12857 (home-page "https://github.com/erichson/rSVD")
12858 (synopsis "Randomized singular value decomposition")
12860 "Low-rank matrix decompositions are fundamental tools and widely used for
12861 data analysis, dimension reduction, and data compression. Classically, highly
12862 accurate deterministic matrix algorithms are used for this task. However, the
12863 emergence of large-scale data has severely challenged our computational
12864 ability to analyze big data. The concept of randomness has been demonstrated
12865 as an effective strategy to quickly produce approximate answers to familiar
12866 problems such as the @dfn{singular value decomposition} (SVD). This package
12867 provides several randomized matrix algorithms such as the randomized singular
12868 value decomposition (@code{rsvd}), randomized principal component
12869 analysis (@code{rpca}), randomized robust principal component
12870 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12871 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12872 functions are provided.")
12873 (license license:gpl3+)))
12875 (define-public r-sloop
12882 (uri (cran-uri "sloop" version))
12885 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12886 (build-system r-build-system)
12888 `(("r-codetools" ,r-codetools)
12889 ("r-crayon" ,r-crayon)
12890 ("r-purrr" ,r-purrr)
12891 ("r-rlang" ,r-rlang)
12892 ("r-tibble" ,r-tibble)))
12893 (home-page "https://github.com/r-lib/sloop")
12894 (synopsis "Helpers for object-oriented programming in R")
12896 "This package provides a collection of helper functions designed to
12897 help you to better understand object oriented programming in R, particularly
12899 (license license:gpl3)))
12901 (define-public r-capushe
12908 (uri (cran-uri "capushe" version))
12911 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12912 (build-system r-build-system)
12913 (propagated-inputs `(("r-mass" ,r-mass)))
12914 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12915 (synopsis "Calibrating penalties using slope heuristics")
12917 "This package provides tools for the calibration of penalized criteria
12918 for model selection. The calibration methods available are based on the slope
12920 (license license:gpl2+)))
12922 (define-public r-dorng
12929 (uri (cran-uri "doRNG" version))
12932 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12933 (properties `((upstream-name . "doRNG")))
12934 (build-system r-build-system)
12936 `(("r-foreach" ,r-foreach)
12937 ("r-iterators" ,r-iterators)
12938 ("r-rngtools" ,r-rngtools)))
12939 (home-page "https://renozao.github.io/doRNG/")
12940 (synopsis "Generic reproducible parallel backend for foreach loops")
12942 "This package provides functions to perform reproducible parallel
12943 @code{foreach} loops, using independent random streams as generated by
12944 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12945 convert standard @code{%dopar%} loops into fully reproducible loops,
12946 independently of the number of workers, the task scheduling strategy, or the
12947 chosen parallel environment and associated foreach backend.")
12948 (license license:gpl2+)))
12950 (define-public r-blockmodeling
12952 (name "r-blockmodeling")
12957 (uri (cran-uri "blockmodeling" version))
12960 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12961 (build-system r-build-system)
12963 `(("r-matrix" ,r-matrix)))
12964 (native-inputs `(("gfortran" ,gfortran)))
12965 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12966 (synopsis "Generalized and classical blockmodeling of valued networks")
12968 "This package is primarily meant as an implementation of generalized
12969 blockmodeling for valued networks. In addition, measures of similarity or
12970 dissimilarity based on structural equivalence and regular equivalence (REGE
12971 algorithms) can be computed and partitioned matrices can be plotted.")
12972 (license license:gpl2+)))
12974 (define-public r-upsetr
12981 (uri (cran-uri "UpSetR" version))
12984 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12985 (properties `((upstream-name . "UpSetR")))
12986 (build-system r-build-system)
12988 `(("r-ggplot2" ,r-ggplot2)
12989 ("r-gridextra" ,r-gridextra)
12991 ("r-scales" ,r-scales)))
12992 (home-page "https://github.com/hms-dbmi/UpSetR")
12993 (synopsis "Visualize intersecting sets")
12995 "This package provides a more scalable alternative to Venn and Euler
12996 diagrams for visualizing intersecting sets. Create visualizations of
12997 intersecting sets using a novel matrix design, along with visualizations of
12998 several common set, element and attribute related tasks.")
12999 (license license:expat)))
13001 ;; This package includes a JavaScript file, which is not minified. When
13002 ;; upgrading please check that there are no new minified JavaScript files.
13003 (define-public r-shinybs
13010 (uri (cran-uri "shinyBS" version))
13013 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13014 (properties `((upstream-name . "shinyBS")))
13015 (build-system r-build-system)
13016 ;; The tests spawn Shiny browser apps. They cannot be run
13017 ;; non-interactively.
13018 (arguments '(#:tests? #f))
13020 `(("r-htmltools" ,r-htmltools)
13021 ("r-shiny" ,r-shiny)))
13022 (home-page "https://ebailey78.github.io/shinyBS/")
13023 (synopsis "Twitter Bootstrap components for Shiny")
13025 "This package adds additional Twitter Bootstrap components to Shiny.")
13026 (license license:gpl3)))
13028 (define-public r-outliers
13030 (name "r-outliers")
13035 (uri (cran-uri "outliers" version))
13038 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
13039 (build-system r-build-system)
13040 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
13041 (synopsis "Tests for outliers")
13043 "This package provides a collection of some tests commonly used for
13044 identifying outliers.")
13045 (license license:gpl2+)))
13047 (define-public r-bayesm
13054 (uri (cran-uri "bayesm" version))
13056 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
13057 (build-system r-build-system)
13059 `(("r-rcpp" ,r-rcpp)
13060 ("r-rcpparmadillo" ,r-rcpparmadillo)))
13061 (home-page "http://www.perossi.org/home/bsm-1")
13062 (synopsis "Bayesian inference for marketing/micro-econometrics")
13064 "This package covers many important models used in marketing and
13065 micro-econometrics applications, including Bayes Regression (univariate or
13066 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
13067 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
13068 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
13069 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
13070 Estimation with normal base, Hierarchical Linear Models with normal prior and
13071 covariates, Hierarchical Linear Models with a mixture of normals prior and
13072 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
13073 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
13074 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
13075 analysis of choice-based conjoint data, Bayesian treatment of linear
13076 instrumental variables models, Analysis of Multivariate Ordinal survey data
13077 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
13078 Coefficient Logit Models.")
13079 (license license:gpl2+)))
13081 (define-public r-tensora
13088 (uri (cran-uri "tensorA" version))
13091 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
13092 (properties `((upstream-name . "tensorA")))
13093 (build-system r-build-system)
13094 (home-page "http://www.stat.boogaart.de/tensorA")
13095 (synopsis "Advanced tensor arithmetic with named indices")
13097 "This package provides convenience functions for advanced linear algebra
13098 with tensors and computation with datasets of tensors on a higher level
13099 abstraction. It includes Einstein and Riemann summing conventions, dragging,
13100 co- and contravariate indices, and parallel computations on sequences of
13102 (license license:gpl2+)))
13104 (define-public r-rarpack
13111 (uri (cran-uri "rARPACK" version))
13114 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
13115 (properties `((upstream-name . "rARPACK")))
13116 (build-system r-build-system)
13117 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
13118 (home-page "https://github.com/yixuan/rARPACK")
13119 (synopsis "Solvers for large scale eigenvalue and SVD problems")
13121 "This package was previously an R wrapper of the ARPACK library, and now
13122 a shell of the R package RSpectra, an R interface to the Spectra library for
13123 solving large scale eigenvalue/vector problems. The current version of
13124 rARPACK simply imports and exports the functions provided by RSpectra. New
13125 users of rARPACK are advised to switch to the RSpectra package.")
13126 (license license:bsd-3)))
13128 (define-public r-compositions
13130 (name "r-compositions")
13135 (uri (cran-uri "compositions" version))
13138 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
13139 (build-system r-build-system)
13141 `(("r-bayesm" ,r-bayesm)
13143 ("r-robustbase" ,r-robustbase)
13144 ("r-tensora" ,r-tensora)))
13146 `(("r-knitr" ,r-knitr)))
13147 (home-page "http://www.stat.boogaart.de/compositions")
13148 (synopsis "Compositional data analysis")
13150 "This package provides functions for the consistent analysis of
13151 compositional data (e.g. portions of substances) and positive
13152 numbers (e.g. concentrations).")
13153 (license license:gpl2+)))
13155 (define-public r-cobs
13162 (uri (cran-uri "cobs" version))
13165 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
13166 (build-system r-build-system)
13168 `(("r-quantreg" ,r-quantreg)
13169 ("r-sparsem" ,r-sparsem)))
13170 (home-page "https://cran.r-project.org/web/packages/cobs")
13171 (synopsis "Constrained B-Splines (sparse matrix based)")
13173 "This package provides qualitatively constrained (regression) smoothing
13174 splines via linear programming and sparse matrices.")
13175 (license license:gpl2+)))
13177 (define-public r-drimpute
13179 (name "r-drimpute")
13184 (uri (cran-uri "DrImpute" version))
13187 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
13188 (properties `((upstream-name . "DrImpute")))
13189 (build-system r-build-system)
13191 `(("r-rcpp" ,r-rcpp)
13192 ("r-rcpparmadillo" ,r-rcpparmadillo)))
13193 (home-page "https://github.com/ikwak2/DrImpute")
13194 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
13196 "This is an R package for imputing dropout events. Many statistical
13197 methods in cell type identification, visualization and lineage reconstruction
13198 do not account for dropout events. DrImpute can improve the performance of
13199 such software by imputing dropout events.")
13200 (license license:gpl3)))
13202 (define-public r-gamlss-dist
13204 (name "r-gamlss-dist")
13209 (uri (cran-uri "gamlss.dist" version))
13211 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
13212 (properties `((upstream-name . "gamlss.dist")))
13213 (build-system r-build-system)
13214 (propagated-inputs `(("r-mass" ,r-mass)))
13215 (home-page "http://www.gamlss.org/")
13216 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
13218 "This package provides a set of distributions which can be used for
13219 modelling the response variables in Generalized Additive Models for Location
13220 Scale and Shape. The distributions can be continuous, discrete or mixed
13221 distributions. Extra distributions can be created, by transforming, any
13222 continuous distribution defined on the real line, to a distribution defined on
13223 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
13224 transformation, respectively.")
13225 ;; Either version of the GPL.
13226 (license (list license:gpl2 license:gpl3))))
13228 ;; This package includes JavaScript files, which are not minified. When
13229 ;; upgrading please check that there are no new minified JavaScript files.
13230 (define-public r-shinyjs
13237 (uri (cran-uri "shinyjs" version))
13240 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
13241 (build-system r-build-system)
13243 `(("r-digest" ,r-digest)
13244 ("r-htmltools" ,r-htmltools)
13245 ("r-jsonlite" ,r-jsonlite)
13246 ("r-shiny" ,r-shiny)))
13248 `(("r-knitr" ,r-knitr)))
13249 (home-page "https://deanattali.com/shinyjs")
13250 (synopsis "Improve the user experience of your Shiny apps")
13252 "Perform common useful JavaScript operations in Shiny apps that will
13253 greatly improve your apps without having to know any JavaScript. Examples
13254 include: hiding an element, disabling an input, resetting an input back to its
13255 original value, delaying code execution by a few seconds, and many more useful
13256 functions for both the end user and the developer. Shinyjs can also be used
13257 to easily call your own custom JavaScript functions from R.")
13258 (license license:agpl3+)))
13260 ;; This package includes minified JavaScript files. When upgrading please
13261 ;; check that there are no new minified JavaScript files.
13262 (define-public r-colourpicker
13264 (name "r-colourpicker")
13269 (uri (cran-uri "colourpicker" version))
13272 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
13273 (build-system r-build-system)
13275 `(#:modules ((guix build utils)
13276 (guix build r-build-system)
13280 (modify-phases %standard-phases
13281 (add-after 'unpack 'process-javascript
13282 (lambda* (#:key inputs #:allow-other-keys)
13283 (with-directory-excursion "inst"
13287 `((,(assoc-ref inputs "js-salvattore")
13288 "examples/colourInput/www/salvattore.min.js")
13289 (,(assoc-ref inputs "js-jquery")
13290 "htmlwidgets/lib/jquery/jquery.min.js")
13291 ("www/shared/colourpicker/js/colourpicker.js"
13292 "www/shared/colourpicker/js/colourpicker.min.js"))))
13293 (lambda (sources targets)
13294 (for-each (lambda (source target)
13295 (format #t "Processing ~a --> ~a~%"
13297 (delete-file target)
13298 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13299 (call-with-output-file target
13301 (dump-port minified port)))))
13302 sources targets))))
13305 `(("r-ggplot2" ,r-ggplot2)
13306 ("r-htmltools" ,r-htmltools)
13307 ("r-htmlwidgets" ,r-htmlwidgets)
13308 ("r-jsonlite" ,r-jsonlite)
13309 ("r-miniui" ,r-miniui)
13310 ("r-shiny" ,r-shiny)
13311 ("r-shinyjs" ,r-shinyjs)))
13313 `(("r-knitr" ,r-knitr)
13314 ("uglify-js" ,uglify-js)
13318 (uri "https://code.jquery.com/jquery-3.3.1.js")
13321 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
13325 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
13328 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
13329 (home-page "https://github.com/daattali/colourpicker")
13330 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
13332 "This package provides a color picker that can be used as an input in
13333 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
13334 custom color palettes, and many more options. A plot color helper tool is
13335 available as an RStudio Addin, which helps you pick colors to use in your
13336 plots. A more generic color picker RStudio Addin is also provided to let you
13337 select colors to use in your R code.")
13338 (license license:expat)))
13340 (define-public r-ggextra
13347 (uri (cran-uri "ggExtra" version))
13350 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
13351 (properties `((upstream-name . "ggExtra")))
13352 (build-system r-build-system)
13354 `(("r-colourpicker" ,r-colourpicker)
13355 ("r-ggplot2" ,r-ggplot2)
13356 ("r-gtable" ,r-gtable)
13357 ("r-miniui" ,r-miniui)
13359 ("r-scales" ,r-scales)
13360 ("r-shiny" ,r-shiny)
13361 ("r-shinyjs" ,r-shinyjs)))
13363 `(("r-knitr" ,r-knitr)))
13364 (home-page "https://github.com/daattali/ggExtra")
13365 (synopsis "Marginal histograms for ggplot2 and other enhancements")
13367 "This package is a collection of functions and layers to enhance ggplot2.
13368 The flagship function is @code{ggMarginal()}, which can be used to add
13369 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
13370 (license license:expat)))
13372 (define-public r-minpack-lm
13374 (name "r-minpack-lm")
13379 (uri (cran-uri "minpack.lm" version))
13382 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13383 (properties `((upstream-name . "minpack.lm")))
13384 (build-system r-build-system)
13385 (native-inputs `(("gfortran" ,gfortran)))
13386 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13387 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13389 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13390 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13391 problems by a modification of the Levenberg-Marquardt algorithm, with support
13392 for lower and upper parameter bounds. The implementation can be used via
13393 @code{nls}-like calls using the @code{nlsLM} function.")
13394 (license license:gpl3)))
13396 (define-public r-moments
13403 (uri (cran-uri "moments" version))
13406 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13407 (build-system r-build-system)
13408 (home-page "https://cran.r-project.org/web/packages/moments")
13409 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13411 "This package provides functions to calculate: moments, Pearson's
13412 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13413 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13414 (license license:gpl2+)))
13416 (define-public r-msir
13423 (uri (cran-uri "msir" version))
13426 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13427 (build-system r-build-system)
13429 `(("r-mclust" ,r-mclust)))
13430 (home-page "https://cran.r-project.org/web/packages/msir")
13431 (synopsis "Model-based sliced inverse regression")
13433 "This is an R package for dimension reduction based on finite Gaussian
13434 mixture modeling of inverse regression.")
13435 (license license:gpl2+)))
13437 (define-public r-pbivnorm
13439 (name "r-pbivnorm")
13444 (uri (cran-uri "pbivnorm" version))
13447 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13448 (build-system r-build-system)
13449 (native-inputs `(("gfortran" ,gfortran)))
13450 (home-page "https://github.com/brentonk/pbivnorm")
13451 (synopsis "Vectorized bivariate normal CDF")
13453 "This package provides a vectorized R function for calculating
13454 probabilities from a standard bivariate normal CDF.")
13455 (license license:gpl2+)))
13457 (define-public r-lavaan
13464 (uri (cran-uri "lavaan" version))
13467 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13468 (build-system r-build-system)
13470 `(("r-mass" ,r-mass)
13471 ("r-mnormt" ,r-mnormt)
13472 ("r-numderiv" ,r-numderiv)
13473 ("r-pbivnorm" ,r-pbivnorm)))
13474 (home-page "http://lavaan.ugent.be")
13475 (synopsis "Latent variable analysis")
13477 "This package provides tools to fit a variety of latent variable models,
13478 including confirmatory factor analysis, structural equation modeling and
13479 latent growth curve models.")
13480 (license license:gpl2+)))
13482 (define-public r-nonnest2
13484 (name "r-nonnest2")
13489 (uri (cran-uri "nonnest2" version))
13492 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13493 (build-system r-build-system)
13495 `(("r-compquadform" ,r-compquadform)
13496 ("r-lavaan" ,r-lavaan)
13497 ("r-mvtnorm" ,r-mvtnorm)
13498 ("r-sandwich" ,r-sandwich)))
13500 `(("r-knitr" ,r-knitr)))
13501 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13502 (synopsis "Tests of non-nested models")
13504 "This package allows for testing of non-nested models. It includes tests
13505 of model distinguishability and of model fit that can be applied to both
13506 nested and non-nested models. The package also includes functionality to
13507 obtain confidence intervals associated with AIC and BIC.")
13508 ;; Either version of the GPL.
13509 (license (list license:gpl2 license:gpl3))))
13511 (define-public r-penalized
13513 (name "r-penalized")
13518 (uri (cran-uri "penalized" version))
13521 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13522 (build-system r-build-system)
13524 `(("r-rcpp" ,r-rcpp)
13525 ("r-rcpparmadillo" ,r-rcpparmadillo)
13526 ("r-survival" ,r-survival)))
13527 (home-page "https://cran.r-project.org/web/packages/penalized/")
13528 (synopsis "Penalized estimation in GLMs and in the Cox model")
13530 "This package provides tools for fitting possibly high dimensional
13531 penalized regression models. The penalty structure can be any combination of
13532 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13533 constraint on the regression coefficients. The supported regression models
13534 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13535 model. Cross-validation routines allow optimization of the tuning
13537 (license license:gpl2+)))
13539 (define-public r-zim
13546 (uri (cran-uri "ZIM" version))
13549 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13550 (properties `((upstream-name . "ZIM")))
13551 (build-system r-build-system)
13552 (propagated-inputs `(("r-mass" ,r-mass)))
13553 (home-page "https://github.com/biostatstudio/ZIM")
13554 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13556 "Analyze count time series with excess zeros. Two types of statistical
13557 models are supported: Markov regression and state-space models. They are also
13558 known as observation-driven and parameter-driven models respectively in the
13559 time series literature. The functions used for Markov regression or
13560 observation-driven models can also be used to fit ordinary regression models
13561 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13562 negative binomial (ZINB) assumption. The package also contains miscellaneous
13563 functions to compute density, distribution, quantile, and generate random
13564 numbers from ZIP and ZINB distributions.")
13565 (license license:gpl3)))
13567 (define-public r-nor1mix
13574 (uri (cran-uri "nor1mix" version))
13577 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13578 (build-system r-build-system)
13579 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13580 (synopsis "Normal (1-d) mixture models")
13582 "This package provides S3 classes and methods for one-dimensional normal
13583 mixture models, for, e.g., density estimation or clustering algorithms
13584 research and teaching; it provides the widely used Marron-Wand densities. It
13585 also provides tools for efficient random number generation and graphics.")
13586 (license license:gpl2+)))
13588 (define-public r-beanplot
13590 (name "r-beanplot")
13595 (uri (cran-uri "beanplot" version))
13598 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13599 (build-system r-build-system)
13600 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13601 (synopsis "Visualization via beanplots")
13603 "This package provides beanplots, an alternative to
13604 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13606 (license license:gpl2)))
13608 (define-public r-pbdzmq
13611 (version "0.3-3.1")
13615 (uri (cran-uri "pbdZMQ" version))
13618 "08qmrzazadkyxlqc8830r0pckaq10l3fgj1f198xy6wwrm2lf0wy"))))
13619 (properties `((upstream-name . "pbdZMQ")))
13620 (build-system r-build-system)
13622 `(("zeromq" ,zeromq)
13625 `(("pkg-config" ,pkg-config)))
13626 (home-page "https://pbdr.org/")
13627 (synopsis "R interface to ZeroMQ")
13629 "ZeroMQ is a well-known library for high-performance asynchronous
13630 messaging in scalable, distributed applications. This package provides high
13631 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13632 interactive client/server programming frameworks. A few wrapper functions
13633 compatible with @code{rzmq} are also provided.")
13634 (license license:gpl3)))
13636 (define-public r-repr
13643 (uri (cran-uri "repr" version))
13646 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13647 (build-system r-build-system)
13649 `(("r-base64enc" ,r-base64enc)
13650 ("r-htmltools" ,r-htmltools)
13651 ("r-jsonlite" ,r-jsonlite)
13652 ("r-pillar" ,r-pillar)))
13653 (home-page "https://cran.r-project.org/web/packages/repr/")
13654 (synopsis "Serializable representations")
13656 "This package provides string and binary representations of objects for
13657 several formats and MIME types.")
13658 (license license:gpl3)))
13660 (define-public r-irdisplay
13662 (name "r-irdisplay")
13667 (uri (cran-uri "IRdisplay" version))
13670 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13671 (properties `((upstream-name . "IRdisplay")))
13672 (build-system r-build-system)
13674 `(("r-repr" ,r-repr)))
13675 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13676 (synopsis "Jupyter display machinery")
13678 "This package provides an interface to the rich display capabilities of
13679 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13680 running IRkernel session.")
13681 (license license:expat)))
13683 (define-public r-irkernel
13685 (name "r-irkernel")
13690 (uri (cran-uri "IRkernel" version))
13693 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13694 (properties `((upstream-name . "IRkernel")))
13695 (build-system r-build-system)
13698 (modify-phases %standard-phases
13699 (add-after 'install 'install-kernelspec
13700 (lambda* (#:key outputs #:allow-other-keys)
13701 (let ((out (assoc-ref outputs "out")))
13702 (setenv "HOME" "/tmp")
13703 (invoke "jupyter" "kernelspec" "install"
13706 (string-append out "/site-library/IRkernel/kernelspec"))
13707 ;; Record the absolute file name of the 'R' executable in
13709 (substitute* (string-append out "/share/jupyter"
13710 "/kernels/ir/kernel.json")
13712 (string-append "[\"" (which "R") "\",")))
13715 `(("jupyter" ,jupyter)))
13717 `(("r-crayon" ,r-crayon)
13718 ("r-digest" ,r-digest)
13719 ("r-evaluate" ,r-evaluate)
13720 ("r-irdisplay" ,r-irdisplay)
13721 ("r-jsonlite" ,r-jsonlite)
13722 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13723 ("r-minimal" ,r-minimal)
13724 ("r-pbdzmq" ,r-pbdzmq)
13726 ("r-uuid" ,r-uuid)))
13727 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13728 (synopsis "Native R kernel for Jupyter")
13730 "The R kernel for the Jupyter environment executes R code which the
13731 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13733 (license license:expat)))
13735 (define-public r-gmodels
13742 (uri (cran-uri "gmodels" version))
13745 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13746 (build-system r-build-system)
13748 `(("r-gdata" ,r-gdata)
13749 ("r-mass" ,r-mass)))
13750 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13751 (synopsis "Various R programming tools for model fitting")
13753 "This package provides various R programming tools for model fitting.")
13754 (license license:gpl2)))
13756 (define-public r-apcluster
13758 (name "r-apcluster")
13763 (uri (cran-uri "apcluster" version))
13766 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13767 (build-system r-build-system)
13769 `(("r-matrix" ,r-matrix)
13770 ("r-rcpp" ,r-rcpp)))
13771 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13772 (synopsis "Affinity propagation clustering")
13774 "This package implements affinity propagation clustering introduced by
13775 Frey and Dueck (2007). The package further provides leveraged affinity
13776 propagation and an algorithm for exemplar-based agglomerative clustering that
13777 can also be used to join clusters obtained from affinity propagation. Various
13778 plotting functions are available for analyzing clustering results.")
13779 (license license:gpl2+)))
13781 (define-public r-valr
13788 (uri (cran-uri "valr" version))
13791 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
13792 (build-system r-build-system)
13794 `(("r-broom" ,r-broom)
13795 ("r-dplyr" ,r-dplyr)
13796 ("r-ggplot2" ,r-ggplot2)
13798 ("r-readr" ,r-readr)
13799 ("r-rlang" ,r-rlang)
13800 ("r-stringr" ,r-stringr)
13801 ("r-tibble" ,r-tibble)))
13803 `(("r-knitr" ,r-knitr)))
13804 (home-page "https://github.com/rnabioco/valr")
13805 (synopsis "Genome interval arithmetic in R")
13807 "This package enables you to read and manipulate genome intervals and
13808 signals. It provides functionality similar to command-line tool suites within
13809 R, enabling interactive analysis and visualization of genome-scale data.")
13810 (license license:expat)))
13812 (define-public r-rematch2
13814 (name "r-rematch2")
13819 (uri (cran-uri "rematch2" version))
13822 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13823 (build-system r-build-system)
13825 `(("r-tibble" ,r-tibble)))
13826 (home-page "https://github.com/r-lib/rematch2")
13827 (synopsis "Tidy output from regular expression matching")
13829 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13830 return the match results in tidy data frames.")
13831 (license license:expat)))
13833 (define-public r-picante
13840 (uri (cran-uri "picante" version))
13843 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13844 (build-system r-build-system)
13848 ("r-vegan" ,r-vegan)))
13849 (home-page "https://cran.r-project.org/web/packages/picante/")
13850 (synopsis "Integrating phylogenies and ecology")
13852 "This package provides functions for phylocom integration, community
13853 analyses, null-models, traits and evolution. It implements numerous
13854 ecophylogenetic approaches including measures of community phylogenetic and
13855 trait diversity, phylogenetic signal, estimation of trait values for
13856 unobserved taxa, null models for community and phylogeny randomizations, and
13857 utility functions for data input/output and phylogeny plotting. A full
13858 description of package functionality and methods are provided by Kembel et
13860 (license license:gpl2)))
13862 (define-public r-reinforcelearn
13864 (name "r-reinforcelearn")
13869 (uri (cran-uri "reinforcelearn" version))
13872 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13873 (build-system r-build-system)
13875 `(("r-checkmate" ,r-checkmate)
13877 ("r-purrr" ,r-purrr)
13879 (home-page "https://markusdumke.github.io/reinforcelearn")
13880 (synopsis "Reinforcement learning")
13882 "This package implements reinforcement learning environments and
13883 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13884 can be used with function approximation, eligibility traces (Singh & Sutton,
13885 1996) and experience replay (Mnih et al., 2013).")
13886 (license license:expat)))
13888 (define-public r-lemon
13895 (uri (cran-uri "lemon" version))
13898 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13899 (build-system r-build-system)
13901 `(("r-ggplot2" ,r-ggplot2)
13902 ("r-gridextra" ,r-gridextra)
13903 ("r-gtable" ,r-gtable)
13904 ("r-knitr" ,r-knitr)
13905 ("r-lattice" ,r-lattice)
13907 ("r-rlang" ,r-rlang)
13908 ("r-scales" ,r-scales)))
13910 `(("r-knitr" ,r-knitr)))
13911 (home-page "https://github.com/stefanedwards/lemon")
13912 (synopsis "Freshen up your ggplot2 plots")
13914 "This package provides functions for working with legends and axis lines
13915 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13917 (license license:gpl3)))
13919 (define-public r-wgaim
13926 (uri (cran-uri "wgaim" version))
13928 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13929 (build-system r-build-system)
13931 `(("r-ggplot2" ,r-ggplot2)
13933 (home-page "https://cran.r-project.org/web/packages/wgaim")
13934 (synopsis "Whole genome average interval mapping for QTL detection")
13936 "This package integrates sophisticated mixed modelling methods with a
13937 whole genome approach to detecting significant QTL in linkage maps.")
13938 (license license:gpl2+)))
13940 (define-public r-bedr
13947 (uri (cran-uri "bedr" version))
13950 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13951 (build-system r-build-system)
13953 `(("r-data-table" ,r-data-table)
13954 ("r-r-utils" ,r-r-utils)
13955 ("r-testthat" ,r-testthat)
13956 ("r-venndiagram" ,r-venndiagram)
13959 ("bedtools" ,bedtools)
13960 ("htslib" ,htslib))) ; for tabix
13962 `(("r-knitr" ,r-knitr))) ; for vignettes
13963 (home-page "https://cran.r-project.org/web/packages/bedr")
13964 (synopsis "Genomic region processing")
13966 "This package is for genomic regions processing using command line tools
13967 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13968 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13969 The bedr package's API enhances access to these tools as well as offers
13970 additional utilities for genomic regions processing.")
13971 (license license:gpl2)))
13973 (define-public r-sets
13980 (uri (cran-uri "sets" version))
13983 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13984 (properties `((upstream-name . "sets")))
13985 (build-system r-build-system)
13986 (home-page "https://cran.r-project.org/web/packages/sets")
13987 (synopsis "Sets, generalized sets, customizable sets and intervals")
13989 "This package provides data structures and basic operations for ordinary
13990 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13991 customizable sets, and intervals.")
13992 (license license:gpl2)))
13994 (define-public r-partitions
13996 (name "r-partitions")
14001 (uri (cran-uri "partitions" version))
14004 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14005 (build-system r-build-system)
14008 ("r-polynom" ,r-polynom)
14009 ("r-sets" ,r-sets)))
14010 (home-page "https://cran.r-project.org/web/packages/partitions")
14011 (synopsis "Additive partitions of integers")
14013 "This package provides tools to enumerates the partitions, unequal
14014 partitions, and restricted partitions of an integer; the three corresponding
14015 partition functions are also given.")
14016 ;; Any version of the GPL
14017 (license license:gpl2+)))
14019 (define-public r-brobdingnag
14021 (name "r-brobdingnag")
14026 (uri (cran-uri "Brobdingnag" version))
14029 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
14030 (properties `((upstream-name . "Brobdingnag")))
14031 (build-system r-build-system)
14032 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
14033 (synopsis "Very large numbers in R")
14035 "This package handles very large numbers in R. Real numbers are held
14036 using their natural logarithms, plus a logical flag indicating sign. The
14037 package includes a vignette that gives a step-by-step introduction to using S4
14039 ;; Any version of the GPL
14040 (license license:gpl2+)))
14042 (define-public r-untb
14049 (uri (cran-uri "untb" version))
14052 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
14053 (build-system r-build-system)
14055 `(("r-brobdingnag" ,r-brobdingnag)
14056 ("r-partitions" ,r-partitions)
14057 ("r-polynom" ,r-polynom)))
14058 (home-page "https://github.com/RobinHankin/untb.git")
14059 (synopsis "Ecological drift under the UNTB")
14061 "This package provides numerical simulations, and visualizations, of
14062 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
14063 (license license:gpl2+)))
14065 (define-public r-stepwise
14067 (name "r-stepwise")
14072 (uri (cran-uri "stepwise" version))
14075 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
14076 (build-system r-build-system)
14077 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
14078 (synopsis "Stepwise detection of recombination breakpoints")
14080 "This package provides a stepwise approach to identifying recombination
14081 breakpoints in a genomic sequence alignment.")
14082 (license license:gpl2+)))
14084 (define-public r-snpmaxsel
14086 (name "r-snpmaxsel")
14091 (uri (cran-uri "SNPmaxsel" version))
14094 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
14095 (properties `((upstream-name . "SNPmaxsel")))
14096 (build-system r-build-system)
14098 `(("r-combinat" ,r-combinat)
14099 ("r-mvtnorm" ,r-mvtnorm)))
14100 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
14101 (synopsis "Maximally selected statistics for SNP data")
14103 "This package implements asymptotic methods related to maximally selected
14104 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
14106 (license license:gpl2+)))
14108 (define-public r-acsnminer
14110 (name "r-acsnminer")
14111 (version "0.16.8.25")
14114 (uri (cran-uri "ACSNMineR" version))
14117 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
14118 (properties `((upstream-name . "ACSNMineR")))
14119 (build-system r-build-system)
14121 `(("r-ggplot2" ,r-ggplot2)
14122 ("r-gridextra" ,r-gridextra)))
14123 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
14124 (synopsis "Gene enrichment analysis")
14126 "This package provides tools to compute and represent gene set enrichment
14127 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
14128 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
14129 enrichment can be run with hypergeometric test or Fisher exact test, and can
14130 use multiple corrections. Visualization of data can be done either by
14131 barplots or heatmaps.")
14132 (license license:gpl2+)))
14134 (define-public r-seqinr
14141 (uri (cran-uri "seqinr" version))
14144 "0pw035h17dmic8m0pb73fbyf6p4jbwggxjk5vpjlybn8dwd0rk93"))))
14145 (build-system r-build-system)
14147 `(("r-ade4" ,r-ade4)
14148 ("r-segmented" ,r-segmented)))
14151 (home-page "http://seqinr.r-forge.r-project.org/")
14152 (synopsis "Biological sequences retrieval and analysis")
14154 "This package provides tools for exploratory data analysis and data
14155 visualization of biological sequence (DNA and protein) data. It also includes
14156 utilities for sequence data management under the ACNUC system.")
14157 (license license:gpl2+)))
14159 (define-public r-units
14166 (uri (cran-uri "units" version))
14169 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
14170 (build-system r-build-system)
14172 `(("udunits" ,udunits)))
14174 `(("r-rcpp" ,r-rcpp)))
14176 `(("r-knitr" ,r-knitr)))
14177 (home-page "https://github.com/r-quantities/units/")
14178 (synopsis "Measurement Units for R Vectors")
14180 "This package provides support for measurement units in R vectors,
14181 matrices and arrays: automatic propagation, conversion, derivation and
14182 simplification of units; raising errors in case of unit incompatibility. It
14183 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
14185 (license license:gpl2)))
14187 (define-public r-classint
14189 (name "r-classint")
14194 (uri (cran-uri "classInt" version))
14197 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
14198 (properties `((upstream-name . "classInt")))
14199 (build-system r-build-system)
14201 `(("r-class" ,r-class)
14202 ("r-e1071" ,r-e1071)
14203 ("r-kernsmooth" ,r-kernsmooth)))
14205 `(("gfortran" ,gfortran)
14206 ("r-knitr" ,r-knitr)))
14207 (home-page "https://github.com/r-spatial/classInt/")
14208 (synopsis "Choose univariate class intervals")
14210 "This package provides selected commonly used methods for choosing
14211 univariate class intervals for mapping or other graphics purposes.")
14212 (license license:gpl2+)))
14214 (define-public r-spdata
14221 (uri (cran-uri "spData" version))
14224 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
14225 (properties `((upstream-name . "spData")))
14226 (build-system r-build-system)
14228 `(("r-raster" ,r-raster)
14230 (home-page "https://github.com/Nowosad/spData")
14231 (synopsis "Datasets for spatial analysis")
14233 "This a package containing diverse spatial datasets for demonstrating,
14234 benchmarking and teaching spatial data analysis. It includes R data of class
14235 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
14236 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
14237 of the datasets are designed to illustrate specific analysis techniques.
14238 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
14239 illustrate point pattern analysis techniques.")
14240 (license license:cc0)))
14242 (define-public r-learnbayes
14244 (name "r-learnbayes")
14249 (uri (cran-uri "LearnBayes" version))
14252 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
14253 (properties `((upstream-name . "LearnBayes")))
14254 (build-system r-build-system)
14255 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
14256 (synopsis "Functions for learning Bayesian inference")
14258 "This package provides a collection of functions helpful in learning the
14259 basic tenets of Bayesian statistical inference. It contains functions for
14260 summarizing basic one and two parameter posterior distributions and predictive
14261 distributions. It contains MCMC algorithms for summarizing posterior
14262 distributions defined by the user. It also contains functions for regression
14263 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
14265 (license license:gpl2+)))
14267 (define-public r-deldir
14274 (uri (cran-uri "deldir" version))
14277 "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
14278 (build-system r-build-system)
14279 (native-inputs `(("gfortran" ,gfortran)))
14280 (home-page "https://cran.r-project.org/web/packages/deldir")
14281 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
14283 "This package provides tools for calculating the Delaunay triangulation
14284 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
14285 of a planar point set. It plots triangulations and tessellations in various
14286 ways, clips tessellations to sub-windows, calculates perimeters of
14287 tessellations, and summarizes information about the tiles of the
14289 (license license:gpl2+)))
14291 (define-public r-sf
14298 (uri (cran-uri "sf" version))
14301 "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
14302 (build-system r-build-system)
14310 `(("r-classint" ,r-classint)
14312 ("r-magrittr" ,r-magrittr)
14314 ("r-units" ,r-units)))
14316 `(("pkg-config" ,pkg-config)
14317 ("r-knitr" ,r-knitr)))
14318 (home-page "https://github.com/r-spatial/sf/")
14319 (synopsis "Simple features for R")
14321 "This package provides support for simple features, a standardized way to
14322 encode spatial vector data. It binds to GDAL for reading and writing data, to
14323 GEOS for geometrical operations, and to PROJ for projection conversions and
14324 datum transformations.")
14325 ;; Either of these licenses
14326 (license (list license:gpl2 license:expat))))
14328 (define-public r-spdep
14335 (uri (cran-uri "spdep" version))
14338 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
14339 (build-system r-build-system)
14341 `(("r-boot" ,r-boot)
14343 ("r-deldir" ,r-deldir)
14345 ("r-gmodels" ,r-gmodels)
14346 ("r-learnbayes" ,r-learnbayes)
14348 ("r-matrix" ,r-matrix)
14352 ("r-spdata" ,r-spdata)))
14354 `(("r-knitr" ,r-knitr)))
14355 (home-page "https://github.com/r-spatial/spdep/")
14356 (synopsis "Spatial dependence: weighting schemes, statistics and models")
14358 "This package provides a collection of functions to create spatial
14359 weights matrix objects from polygon contiguities, from point patterns by
14360 distance and tessellations, for summarizing these objects, and for permitting
14361 their use in spatial data analysis, including regional aggregation by minimum
14363 (license license:gpl2+)))
14365 (define-public r-adegenet
14367 (name "r-adegenet")
14372 (uri (cran-uri "adegenet" version))
14375 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
14376 (build-system r-build-system)
14378 `(("r-ade4" ,r-ade4)
14381 ("r-dplyr" ,r-dplyr)
14382 ("r-ggplot2" ,r-ggplot2)
14383 ("r-igraph" ,r-igraph)
14385 ("r-reshape2" ,r-reshape2)
14386 ("r-seqinr" ,r-seqinr)
14387 ("r-shiny" ,r-shiny)
14388 ("r-spdep" ,r-spdep)
14389 ("r-vegan" ,r-vegan)))
14390 (home-page "https://github.com/thibautjombart/adegenet")
14391 (synopsis "Exploratory analysis of genetic and genomic data")
14393 "This package provides a toolset for the exploration of genetic and
14394 genomic data. Adegenet provides formal (S4) classes for storing and handling
14395 various genetic data, including genetic markers with varying ploidy and
14396 hierarchical population structure (@code{genind} class), alleles counts by
14397 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14398 also implements original multivariate methods (DAPC, sPCA), graphics,
14399 statistical tests, simulation tools, distance and similarity measures, and
14400 several spatial methods. A range of both empirical and simulated datasets is
14401 also provided to illustrate various methods.")
14402 (license license:gpl2+)))
14404 (define-public r-pegas
14411 (uri (cran-uri "pegas" version))
14413 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
14414 (build-system r-build-system)
14416 `(("r-adegenet" ,r-adegenet)
14418 (home-page "http://ape-package.ird.fr/pegas.html")
14419 (synopsis "Population and evolutionary genetics analysis system")
14421 "This package provides functions for reading, writing, plotting,
14422 analysing, and manipulating allelic and haplotypic data, including from VCF
14423 files, and for the analysis of population nucleotide sequences and
14424 micro-satellites including coalescent analyses, linkage disequilibrium,
14425 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14426 minimum spanning tree and network, and median-joining networks.")
14427 (license license:gpl2+)))
14429 (define-public r-rmetasim
14431 (name "r-rmetasim")
14436 (uri (cran-uri "rmetasim" version))
14439 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14440 (build-system r-build-system)
14442 `(("r-ade4" ,r-ade4)
14443 ("r-adegenet" ,r-adegenet)
14444 ("r-gtools" ,r-gtools)
14445 ("r-pegas" ,r-pegas)))
14446 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14447 (synopsis "Individual-based population genetic simulation environment")
14449 "This package provides an interface between R and the metasim simulation
14450 engine. The simulation environment is documented in: Strand, A.(2002),
14451 Metasim 1.0: an individual-based environment for simulating population
14452 genetics of complex population dynamics.")
14454 (license license:gpl2+)))
14456 (define-public r-genetics
14458 (name "r-genetics")
14459 (version "1.3.8.1.2")
14463 (uri (cran-uri "genetics" version))
14466 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14467 (build-system r-build-system)
14469 `(("r-combinat" ,r-combinat)
14470 ("r-gdata" ,r-gdata)
14471 ("r-gtools" ,r-gtools)
14473 ("r-mvtnorm" ,r-mvtnorm)))
14474 (home-page "https://cran.r-project.org/web/packages/genetics/")
14475 (synopsis "Population genetics")
14477 "This package provides classes and methods for handling genetic data.
14478 It includes classes to represent genotypes and haplotypes at single markers up
14479 to multiple markers on multiple chromosomes. Function include allele
14480 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14481 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14482 and testing for linkage disequilibrium, ...")
14483 ;; Any GPL version.
14484 (license license:gpl2+)))
14486 (define-public r-snp-plotter
14488 (name "r-snp-plotter")
14493 (uri (cran-uri "snp.plotter" version))
14496 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14497 (properties `((upstream-name . "snp.plotter")))
14498 (build-system r-build-system)
14499 (propagated-inputs `(("r-genetics" ,r-genetics)))
14500 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14501 (synopsis "Plot p-values using single SNP and/or haplotype data")
14503 "This package helps you create plots of p-values using single SNP and/or
14504 haplotype data. Main features of the package include options to display a
14505 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14506 datasets simultaneously. Plots can be created using global and/or individual
14507 haplotype p-values along with single SNP p-values. Images are created as
14508 either PDF/EPS files.")
14509 (license license:gpl2+)))
14511 (define-public r-polspline
14513 (name "r-polspline")
14518 (uri (cran-uri "polspline" version))
14520 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14521 (build-system r-build-system)
14522 (native-inputs `(("gfortran" ,gfortran)))
14523 (home-page "https://cran.r-project.org/web/packages/polspline/")
14524 (synopsis "Polynomial spline routines")
14526 "This package provides routines for the polynomial spline fitting
14527 routines hazard regression, hazard estimation with flexible tails, logspline,
14528 lspec, polyclass, and polymars.")
14529 (license license:gpl2+)))
14531 (define-public r-rms
14538 (uri (cran-uri "rms" version))
14540 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14541 (build-system r-build-system)
14543 `(("r-cluster" ,r-cluster)
14544 ("r-digest" ,r-digest)
14545 ("r-ggplot2" ,r-ggplot2)
14546 ("r-hmisc" ,r-hmisc)
14547 ("r-htmltable" ,r-htmltable)
14548 ("r-htmltools" ,r-htmltools)
14549 ("r-lattice" ,r-lattice)
14551 ("r-multcomp" ,r-multcomp)
14553 ("r-polspline" ,r-polspline)
14554 ("r-quantreg" ,r-quantreg)
14555 ("r-rpart" ,r-rpart)
14556 ("r-sparsem" ,r-sparsem)
14557 ("r-survival" ,r-survival)))
14558 (native-inputs `(("gfortran" ,gfortran)))
14559 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14560 (synopsis "Regression modeling strategies")
14562 "This is a package for regression modeling, testing, estimation,
14563 validation, graphics, prediction, and typesetting by storing enhanced model
14564 design attributes in the fit. The rms package is a collection of functions
14565 that assist with and streamline modeling. It also contains functions for
14566 binary and ordinal logistic regression models, ordinal models for continuous Y
14567 with a variety of distribution families, and the Buckley-James multiple
14568 regression model for right-censored responses, and implements penalized
14569 maximum likelihood estimation for logistic and ordinary linear models. The
14570 package works with almost any regression model, but it was especially written
14571 to work with binary or ordinal regression models, Cox regression, accelerated
14572 failure time models, ordinary linear models, the Buckley-James model,
14573 generalized least squares for serially or spatially correlated observations,
14574 generalized linear models, and quantile regression.")
14575 (license license:gpl2+)))
14577 (define-public r-arsenal
14584 (uri (cran-uri "arsenal" version))
14587 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14588 (properties `((upstream-name . "arsenal")))
14589 (build-system r-build-system)
14590 (propagated-inputs `(("r-knitr" ,r-knitr)))
14591 (native-inputs `(("r-knitr" ,r-knitr)))
14592 (home-page "https://github.com/mayoverse/arsenal")
14593 (synopsis "Functions for large-scale statistical summaries")
14595 "This package provides an arsenal of R functions for large-scale
14596 statistical summaries, which are streamlined to work within the latest
14597 reporting tools in R and RStudio and which use formulas and versatile
14598 summary statistics for summary tables and models. The primary functions
14602 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14603 levels of one or more categorical variables;
14604 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14605 across two time points;
14606 @item @code{modelsum}, which performs simple model fits on one or more
14607 endpoints for many variables (univariate or adjusted for covariates);
14608 @item @code{freqlist}, a powerful frequency table across many categorical
14610 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14611 @item @code{write2}, a function to output tables to a document.
14614 (license license:gpl2+)))
14616 (define-public r-haplo-stats
14618 (name "r-haplo-stats")
14623 (uri (cran-uri "haplo.stats" version))
14626 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
14627 (properties `((upstream-name . "haplo.stats")))
14628 (build-system r-build-system)
14630 `(("r-arsenal" ,r-arsenal)
14633 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14634 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14635 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14637 "This package provides routines for the analysis of indirectly measured
14638 haplotypes. The statistical methods assume that all subjects are unrelated
14639 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14640 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14641 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14642 examples in the vignette.")
14643 (license license:gpl2+)))
14645 (define-public r-bqtl
14652 (uri (cran-uri "bqtl" version))
14655 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14656 (build-system r-build-system)
14657 (native-inputs `(("gfortran" ,gfortran)))
14658 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14659 (synopsis "Bayesian QTL mapping toolkit")
14661 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14662 lines. It includes maximum likelihood and Bayesian tools.")
14663 (license license:gpl2+)))
14665 (define-public r-ibdreg
14672 (uri (cran-uri "ibdreg" version))
14675 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14676 (build-system r-build-system)
14677 (home-page "https://www.mayo.edu/research/labs/\
14678 statistical-genetics-genetic-epidemiology/software")
14679 (synopsis "Regression methods for IBD linkage with covariates")
14681 "This package provides a method to test genetic linkage with covariates
14682 by regression methods with response IBD sharing for relative pairs. Account
14683 for correlations of IBD statistics and covariates for relative pairs within
14684 the same pedigree.")
14685 (license license:gpl2+)))
14687 (define-public r-dlmap
14694 (uri (cran-uri "dlmap" version))
14697 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14698 (build-system r-build-system)
14700 `(("r-ibdreg" ,r-ibdreg)
14704 ("r-wgaim" ,r-wgaim)))
14705 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14706 (synopsis "Detection localization mapping for QTL")
14708 "This is package for QTL mapping in a mixed model framework with separate
14709 detection and localization stages. The first stage detects the number of QTL
14710 on each chromosome based on the genetic variation due to grouped markers on
14711 the chromosome; the second stage uses this information to determine the most
14712 likely QTL positions. The mixed model can accommodate general fixed and
14713 random effects, including spatial effects in field trials and pedigree
14714 effects. It is applicable to backcrosses, doubled haploids, recombinant
14715 inbred lines, F2 intercrosses, and association mapping populations.")
14716 (license license:gpl2)))
14718 (define-public r-ldheatmap
14720 (name "r-ldheatmap")
14725 (uri (cran-uri "LDheatmap" version))
14728 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
14729 (properties `((upstream-name . "LDheatmap")))
14730 (build-system r-build-system)
14732 `(("r-genetics" ,r-genetics)
14734 ("r-snpstats" ,r-snpstats)))
14735 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14736 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14738 "This package provides tools to produce a graphical display, as a heat
14739 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14740 optionally include the physical locations or genetic map distances of each SNP
14742 (license license:gpl3)))
14744 (define-public r-hwde
14751 (uri (cran-uri "hwde" version))
14754 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14755 (build-system r-build-system)
14756 (home-page "https://cran.r-project.org/web/packages/hwde/")
14757 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14759 "This package fits models for genotypic disequilibria, as described in
14760 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14761 terms are available that account for first order interactions between loci.
14762 It also implements, for a single locus in a single population, a conditional
14763 exact test for Hardy-Weinberg equilibrium.")
14764 (license license:gpl2+)))
14766 (define-public r-tdthap
14773 (uri (cran-uri "tdthap" version))
14776 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14777 (build-system r-build-system)
14778 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14779 (synopsis "TDT tests for extended haplotypes")
14781 "Functions and examples are provided for transmission/disequilibrium
14782 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14783 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14784 (license license:artistic2.0)))
14786 (define-public r-sparql
14792 (uri (cran-uri "SPARQL" version))
14795 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14796 (properties `((upstream-name . "SPARQL")))
14797 (build-system r-build-system)
14799 `(("r-rcurl" ,r-rcurl)
14801 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14802 (synopsis "SPARQL client for R")
14803 (description "This package provides an interface to use SPARQL to pose
14804 SELECT or UPDATE queries to an end-point.")
14805 ;; The only license indication is found in the DESCRIPTION file,
14806 ;; which states GPL-3. So we cannot assume GPLv3+.
14807 (license license:gpl3)))
14809 (define-public r-bookdown
14811 (name "r-bookdown")
14815 (uri (cran-uri "bookdown" version))
14818 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
14819 (build-system r-build-system)
14821 `(("r-htmltools" ,r-htmltools)
14822 ("r-knitr" ,r-knitr)
14823 ("r-rmarkdown" ,r-rmarkdown)
14824 ("r-tinytex" ,r-tinytex)
14827 ("pandoc" ,pandoc)))
14828 (home-page "https://github.com/rstudio/bookdown")
14829 (synopsis "Authoring books and technical documents with R markdown")
14830 (description "This package provides output formats and utilities for
14831 authoring books and technical documents with R Markdown.")
14832 (license license:gpl3)))
14834 (define-public r-optparse
14836 (name "r-optparse")
14841 (uri (cran-uri "optparse" version))
14844 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14845 (build-system r-build-system)
14847 `(("r-getopt" ,r-getopt)))
14849 `(("r-knitr" ,r-knitr)))
14850 (home-page "https://github.com/trevorld/optparse")
14851 (synopsis "Command line option parser")
14853 "This package provides a command line parser inspired by Python's
14854 @code{optparse} library to be used with Rscript to write shebang scripts
14855 that accept short and long options.")
14856 (license license:gpl2+)))
14858 (define-public r-kernlab
14865 (uri (cran-uri "kernlab" version))
14867 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14868 (build-system r-build-system)
14869 (home-page "https://cran.r-project.org/web/packages/kernlab")
14870 (synopsis "Kernel-based machine learning tools")
14872 "This package provides kernel-based machine learning methods for
14873 classification, regression, clustering, novelty detection, quantile regression
14874 and dimensionality reduction. Among other methods @code{kernlab} includes
14875 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14877 (license license:gpl2)))
14879 (define-public r-hierfstat
14881 (name "r-hierfstat")
14886 (uri (cran-uri "hierfstat" version))
14889 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14890 (build-system r-build-system)
14892 `(("r-ade4" ,r-ade4)
14893 ("r-adegenet" ,r-adegenet)
14894 ("r-gaston" ,r-gaston)
14895 ("r-gtools" ,r-gtools)))
14897 `(("r-knitr" ,r-knitr)))
14898 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14899 (synopsis "Estimation and tests of hierarchical F-statistics")
14901 "This package allows the estimation of hierarchical F-statistics from
14902 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14903 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14904 are also given to test via randomisations the significance of each F and
14905 variance components, using the likelihood-ratio statistics G.")
14906 (license license:gpl2+)))
14908 (define-public r-hapassoc
14910 (name "r-hapassoc")
14915 (uri (cran-uri "hapassoc" version))
14918 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14919 (build-system r-build-system)
14920 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14921 (synopsis "Inference of trait associations with SNP haplotypes")
14923 "Hapassoc performs likelihood inference of trait associations with
14924 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14925 functions are developed primarily for data collected in cohort or
14926 cross-sectional studies. They can accommodate uncertain haplotype phase and
14927 handle missing genotypes at some SNPs.")
14928 (license license:gpl2)))
14930 (define-public r-sampling
14932 (name "r-sampling")
14937 (uri (cran-uri "sampling" version))
14940 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14941 (build-system r-build-system)
14943 `(("r-lpsolve" ,r-lpsolve)
14944 ("r-mass" ,r-mass)))
14945 (home-page "https://cran.r-project.org/web/packages/sampling/")
14946 (synopsis "Survey sampling")
14948 "This package provides functions for drawing and calibrating samples.")
14949 (license license:gpl2+)))
14951 (define-public r-r2html
14958 (uri (cran-uri "R2HTML" version))
14961 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14962 (properties `((upstream-name . "R2HTML")))
14963 (build-system r-build-system)
14964 (home-page "https://github.com/nalimilan/R2HTML")
14965 (synopsis "HTML export for R objects")
14967 "This package includes HTML functions and methods to write in an HTML
14968 file. Thus, making HTML reports is easy. It includes a function that allows
14969 redirection on the fly, which appears to be very useful for teaching purposes,
14970 as the student can keep a copy of the produced output to keep all that they
14971 did during the course. The package comes with a vignette describing how to
14972 write HTML reports for statistical analysis. Finally, a driver for Sweave
14973 parses HTML flat files containing R code and to automatically write
14974 the corresponding outputs (tables and graphs).")
14975 (license license:gpl2+)))
14977 (define-public r-rjava
14984 (uri (cran-uri "rJava" version))
14987 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14988 (properties `((upstream-name . "rJava")))
14989 (build-system r-build-system)
14991 `(#:modules ((guix build utils)
14992 (guix build r-build-system)
14995 (modify-phases %standard-phases
14996 (add-after 'unpack 'set-JAVA_HOME
14997 (lambda* (#:key inputs #:allow-other-keys)
14998 (let ((jdk (assoc-ref inputs "jdk")))
14999 (setenv "JAVA_HOME" jdk)
15000 (setenv "JAVA" (which "java"))
15001 (setenv "JAR" (which "jar"))
15002 (setenv "JAVAC" (which "javac"))
15003 (setenv "JAVAH" (which "javah"))
15004 (setenv "JAVA_CPPFLAGS"
15005 (string-append "-I" jdk "/include "
15006 "-I" jdk "/include/linux"))
15007 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15008 ((lib) (setenv "JAVA_LIBS" lib))
15009 (_ (error "Could not find libjvm.so"))))
15013 ("jdk" ,icedtea-8 "jdk")
15016 (home-page "https://www.rforge.net/rJava/")
15017 (synopsis "Low-Level R to Java interface")
15019 "This package provides a low-level interface to the Java VM very much
15020 like .C/.Call and friends. It allows the creation of objects, calling methods
15021 and accessing fields.")
15022 (license license:gpl2)))
15024 (define-public r-svmisc
15031 (uri (cran-uri "svMisc" version))
15034 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
15035 (properties `((upstream-name . "svMisc")))
15036 (build-system r-build-system)
15037 (home-page "https://github.com/SciViews/svMisc")
15038 (synopsis "Miscellaneous functions for SciViews")
15040 "This package provides miscellaneous functions for SciViews or general
15041 use, including tools to manage a temporary environment attached to the search
15042 path for temporary variables you do not want to @code{save()} or
15043 @code{load()}; test the current platform; showing progress bars, etc.")
15044 (license license:gpl2)))
15046 (define-public r-xyz
15053 (uri (cran-uri "xyz" version))
15056 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
15057 (build-system r-build-system)
15059 `(("r-rcpp" ,r-rcpp)))
15060 (home-page "https://cran.r-project.org/web/packages/xyz/")
15061 (synopsis "Algorithm for fast interaction search in high-dimensional data")
15063 "High dimensional interaction search by brute force requires a quadratic
15064 computational cost in the number of variables. The xyz algorithm provably
15065 finds strong interactions in almost linear time. For details of the algorithm
15066 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
15067 interaction search in high-dimensional data.")
15068 ;; Any version of the GPL.
15069 (license license:gpl2+)))
15071 (define-public r-rttf2pt1
15073 (name "r-rttf2pt1")
15078 (uri (cran-uri "Rttf2pt1" version))
15081 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
15082 (properties `((upstream-name . "Rttf2pt1")))
15083 (build-system r-build-system)
15084 (home-page "https://github.com/wch/Rttf2pt1")
15085 (synopsis "Font conversion utility")
15087 "This package contains the program @code{ttf2pt1}, for use with the
15088 @code{extrafont} package.")
15089 ;; Most of the files are covered under the Expat license. Some files are
15090 ;; covered under BSD-3. Deviations for individual files are recorded in
15091 ;; the LICENSE file.
15092 (license (list license:bsd-3 license:expat
15093 (license:non-copyleft "file://LICENSE")))))
15095 (define-public r-extrafontdb
15097 (name "r-extrafontdb")
15102 (uri (cran-uri "extrafontdb" version))
15105 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
15106 (build-system r-build-system)
15107 (home-page "https://github.com/wch/extrafontdb")
15108 (synopsis "Database for the extrafont package")
15110 "This package holds the database for the @code{extrafont} package.")
15111 (license license:gpl2)))
15113 (define-public r-extrafont
15115 (name "r-extrafont")
15120 (uri (cran-uri "extrafont" version))
15123 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
15124 (build-system r-build-system)
15126 `(("r-extrafontdb" ,r-extrafontdb)
15127 ("r-rttf2pt1" ,r-rttf2pt1)))
15128 (home-page "https://github.com/wch/extrafont")
15129 (synopsis "Tools for using fonts in R")
15131 "The extrafont package makes it easier to use fonts other than the basic
15132 PostScript fonts that R uses. Fonts that are imported into extrafont can be
15133 used with PDF or PostScript output files. There are two hurdles for using
15134 fonts in PDF (or Postscript) output files:
15137 @item Making R aware of the font and the dimensions of the characters.
15138 @item Embedding the fonts in the PDF file so that the PDF can be displayed
15139 properly on a device that doesn't have the font. This is usually needed if
15140 you want to print the PDF file or share it with others.
15143 The extrafont package makes both of these things easier.")
15144 (license license:gpl2)))
15146 (define-public r-xkcd
15153 (uri (cran-uri "xkcd" version))
15156 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
15157 (build-system r-build-system)
15159 `(("r-extrafont" ,r-extrafont)
15160 ("r-ggplot2" ,r-ggplot2)
15161 ("r-hmisc" ,r-hmisc)))
15162 (home-page "https://cran.r-project.org/web/packages/xkcd/")
15163 (synopsis "Plot ggplot2 graphics in the XKCD style")
15165 "This package provides the means to plot ggplot2 graphs in the style of
15166 the XKCD web comic.")
15167 (license license:gpl3)))
15169 (define-public r-msigdbr
15176 (uri (cran-uri "msigdbr" version))
15179 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
15180 (build-system r-build-system)
15182 `(("r-dplyr" ,r-dplyr)
15183 ("r-magrittr" ,r-magrittr)
15184 ("r-rlang" ,r-rlang)
15185 ("r-tibble" ,r-tibble)
15186 ("r-tidyselect" ,r-tidyselect)))
15188 `(("r-knitr" ,r-knitr)))
15189 (home-page "https://github.com/igordot/msigdbr")
15190 (synopsis "MSigDB gene sets for multiple organisms")
15192 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
15193 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
15194 software in a standard R data frame with key-value pairs. Included are the
15195 original human gene symbols and Entrez IDs as well as the equivalents for
15196 various frequently studied model organisms such as mouse, rat, pig, fly, and
15198 ;; The package is covered under the Expat license, but the upstream MSigDB
15199 ;; files are made available under the Creative Commons Attribution 4.0
15200 ;; International license.
15201 (license (list license:expat license:cc-by4.0))))
15203 (define-public r-gridgraphics
15205 (name "r-gridgraphics")
15210 (uri (cran-uri "gridGraphics" version))
15213 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
15214 (properties `((upstream-name . "gridGraphics")))
15215 (build-system r-build-system)
15216 (home-page "https://github.com/pmur002/gridgraphics")
15217 (synopsis "Redraw base graphics using @code{grid} graphics")
15219 "This package provides functions to convert a page of plots drawn with
15220 the @code{graphics} package into identical output drawn with the @code{grid}
15221 package. The result looks like the original @code{graphics}-based plot, but
15222 consists of @code{grid} grobs and viewports that can then be manipulated with
15223 @code{grid} functions (e.g., edit grobs and revisit viewports).")
15224 (license license:gpl2+)))
15226 (define-public r-farver
15233 (uri (cran-uri "farver" version))
15236 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
15237 (build-system r-build-system)
15238 (home-page "https://github.com/thomasp85/farver")
15239 (synopsis "Vectorized color conversion and comparison")
15241 "The encoding of color can be handled in many different ways, using
15242 different color spaces. As different color spaces have different uses,
15243 efficient conversion between these representations are important. This
15244 package provides a set of functions that gives access to very fast color space
15245 conversion and comparisons implemented in C++, and offers 100-fold speed
15246 improvements over the @code{convertColor} function in the @code{grDevices}
15248 (license license:expat)))
15250 (define-public r-ggplotify
15252 (name "r-ggplotify")
15257 (uri (cran-uri "ggplotify" version))
15260 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
15261 (build-system r-build-system)
15263 `(("r-ggplot2" ,r-ggplot2)
15264 ("r-gridgraphics" ,r-gridgraphics)
15265 ("r-rvcheck" ,r-rvcheck)))
15267 `(("r-knitr" ,r-knitr)))
15268 (home-page "https://github.com/GuangchuangYu/ggplotify")
15269 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
15271 "This package provides tools to convert plot function calls (using
15272 expression or formula) to @code{grob} or @code{ggplot} objects that are
15273 compatible with the @code{grid} and @code{ggplot2} environment. With this
15274 package, we are able to e.g. use @code{cowplot} to align plots produced by
15275 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
15276 converting them to @code{ggplot} objects.")
15277 (license license:artistic2.0)))
15279 (define-public r-triebeard
15281 (name "r-triebeard")
15286 (uri (cran-uri "triebeard" version))
15289 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
15290 (build-system r-build-system)
15291 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15292 (home-page "https://github.com/Ironholds/triebeard/")
15293 (synopsis "Radix trees in Rcpp")
15295 "Radix trees, or tries, are key-value data structures optimized for
15296 efficient lookups, similar in purpose to hash tables. This package provides
15297 an implementation of radix trees for use in R programming and in developing
15298 packages with Rcpp.")
15299 (license license:expat)))
15301 (define-public r-tweenr
15308 (uri (cran-uri "tweenr" version))
15311 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
15312 (build-system r-build-system)
15314 `(("r-farver" ,r-farver)
15315 ("r-magrittr" ,r-magrittr)
15317 ("r-rlang" ,r-rlang)))
15318 (home-page "https://github.com/thomasp85/tweenr")
15319 (synopsis "Interpolate data for smooth animations")
15321 "In order to create smooth animation between states of data, tweening is
15322 necessary. This package provides a range of functions for creating tweened
15323 data that can be used as basis for animation. Furthermore it adds a number of
15324 vectorized interpolaters for common R data types such as numeric, date and
15326 (license license:expat)))
15328 (define-public r-polyclip
15330 (name "r-polyclip")
15335 (uri (cran-uri "polyclip" version))
15338 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
15339 (build-system r-build-system)
15340 (native-inputs `(("pkg-config" ,pkg-config)))
15341 (home-page "http://www.angusj.com/delphi/clipper.php")
15342 (synopsis "Polygon clipping")
15344 "This package provides an R port of the library Clipper. It performs
15345 polygon clipping operations (intersection, union, set minus, set difference)
15346 for polygonal regions of arbitrary complexity, including holes. It computes
15347 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15348 dilations) for polygonal regions and polygonal lines. It computes the
15349 Minkowski Sum of general polygons. There is a function for removing
15350 self-intersections from polygon data.")
15351 (license license:boost1.0)))
15353 (define-public r-urltools
15355 (name "r-urltools")
15360 (uri (cran-uri "urltools" version))
15363 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15364 (build-system r-build-system)
15366 `(("r-rcpp" ,r-rcpp)
15367 ("r-triebeard" ,r-triebeard)))
15368 (home-page "https://github.com/Ironholds/urltools/")
15369 (synopsis "Vectorized tools for URL handling and parsing")
15371 "This package provides a toolkit for all URL-handling needs, including
15372 encoding and decoding, parsing, parameter extraction and modification. All
15373 functions are designed to be both fast and entirely vectorized. It is
15374 intended to be useful for people dealing with web-related datasets, such as
15375 server-side logs, although may be useful for other situations involving large
15377 (license license:expat)))
15379 (define-public r-ggforce
15386 (uri (cran-uri "ggforce" version))
15389 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15390 (build-system r-build-system)
15392 `(("r-ggplot2" ,r-ggplot2)
15393 ("r-gtable" ,r-gtable)
15395 ("r-polyclip" ,r-polyclip)
15397 ("r-rcppeigen" ,r-rcppeigen)
15398 ("r-rlang" ,r-rlang)
15399 ("r-scales" ,r-scales)
15400 ("r-tidyselect" ,r-tidyselect)
15401 ("r-tweenr" ,r-tweenr)
15402 ("r-withr" ,r-withr)))
15403 (home-page "https://ggforce.data-imaginist.com")
15404 (synopsis "Accelerating ggplot2")
15406 "The aim of the ggplot2 package is to aid in visual data investigations.
15407 This focus has led to a lack of facilities for composing specialized plots.
15408 Thi package aims to be a collection of mainly new statistics and geometries
15409 that fills this gap.")
15410 (license license:expat)))
15412 (define-public r-europepmc
15414 (name "r-europepmc")
15419 (uri (cran-uri "europepmc" version))
15422 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15423 (build-system r-build-system)
15425 `(("r-dplyr" ,r-dplyr)
15427 ("r-jsonlite" ,r-jsonlite)
15429 ("r-progress" ,r-progress)
15430 ("r-purrr" ,r-purrr)
15431 ("r-rlang" ,r-rlang)
15432 ("r-tibble" ,r-tibble)
15433 ("r-tidyr" ,r-tidyr)
15434 ("r-urltools" ,r-urltools)
15435 ("r-xml2" ,r-xml2)))
15437 `(("r-knitr" ,r-knitr)))
15438 (home-page "https://github.com/ropensci/europepmc/")
15439 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15441 "This package provides an R Client for the
15442 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15443 Service}. It gives access to both metadata on life science literature and
15444 open access full texts. Europe PMC indexes all PubMed content and other
15445 literature sources including Agricola, a bibliographic database of citations
15446 to the agricultural literature, or Biological Patents. In addition to
15447 bibliographic metadata, the client allows users to fetch citations and
15448 reference lists. Links between life-science literature and other EBI
15449 databases, including ENA, PDB or ChEMBL are also accessible.")
15450 (license license:gpl3)))
15452 (define-public r-ggraph
15459 (uri (cran-uri "ggraph" version))
15462 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15463 (build-system r-build-system)
15465 `(("r-digest" ,r-digest)
15466 ("r-dplyr" ,r-dplyr)
15467 ("r-ggforce" ,r-ggforce)
15468 ("r-ggplot2" ,r-ggplot2)
15469 ("r-ggrepel" ,r-ggrepel)
15470 ("r-graphlayouts" ,r-graphlayouts)
15471 ("r-gtable" ,r-gtable)
15472 ("r-igraph" ,r-igraph)
15475 ("r-rlang" ,r-rlang)
15476 ("r-scales" ,r-scales)
15477 ("r-tidygraph" ,r-tidygraph)
15478 ("r-viridis" ,r-viridis)))
15480 `(("r-knitr" ,r-knitr)))
15481 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15482 (synopsis "Implementation of grammar of graphics for graphs and networks")
15484 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15485 graph and network visualizations due to its reliance on tabular data input.
15486 The ggraph package is an extension of the ggplot2 API tailored to graph
15487 visualizations and provides the same flexible approach to building up plots
15489 (license license:gpl3)))
15491 (define-public r-varselrf
15493 (name "r-varselrf")
15498 (uri (cran-uri "varSelRF" version))
15501 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15502 (properties `((upstream-name . "varSelRF")))
15503 (build-system r-build-system)
15505 `(("r-randomforest" ,r-randomforest)))
15506 (home-page "https://www.ligarto.org/rdiaz/software/software")
15507 (synopsis "Variable selection using random forests")
15509 "This package provides tools for the variable selection from random
15510 forests using both backwards variable elimination (for the selection of small
15511 sets of non-redundant variables) and selection based on the importance
15512 spectrum (somewhat similar to scree plots; for the selection of large,
15513 potentially highly-correlated variables). The main applications are in
15514 high-dimensional data (e.g., microarray data, and other genomics and
15515 proteomics applications).")
15516 (license license:gpl2+)))
15518 (define-public r-pamr
15525 (uri (cran-uri "pamr" version))
15528 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15529 (build-system r-build-system)
15531 `(("r-cluster" ,r-cluster)
15532 ("r-survival" ,r-survival)))
15533 (native-inputs `(("gfortran" ,gfortran)))
15534 (home-page "https://cran.r-project.org/web/packages/pamr/")
15535 (synopsis "Prediction Analysis for Microarrays")
15537 "This package provides some functions for sample classification in
15539 (license license:gpl2)))
15541 (define-public r-rda
15544 (version "1.0.2-2.1")
15548 (uri (cran-uri "rda" version))
15551 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15552 (build-system r-build-system)
15553 (home-page "https://cran.r-project.org/web/packages/rda/")
15554 (synopsis "Shrunken centroids regularized discriminant analysis")
15556 "This package provides tools for shrunken centroids regularized
15557 discriminant analysis for the purpose of classifying high dimensional data.")
15558 (license license:gpl2+)))
15560 (define-public r-ggvis
15567 (uri (cran-uri "ggvis" version))
15570 "1k40mkfxj66qvwbsp849maihv6vxkdprhhzjkwffwn0lwl78lsz1"))))
15571 (build-system r-build-system)
15573 `(("r-assertthat" ,r-assertthat)
15574 ("r-dplyr" ,r-dplyr)
15575 ("r-htmltools" ,r-htmltools)
15576 ("r-jsonlite" ,r-jsonlite)
15577 ("r-lazyeval" ,r-lazyeval)
15578 ("r-magrittr" ,r-magrittr)
15579 ("r-shiny" ,r-shiny)))
15580 (home-page "https://ggvis.rstudio.com/")
15581 (synopsis "Interactive grammar of graphics")
15583 "This package is a data visualization package for R providing an
15584 implementation of an interactive grammar of graphics, taking the best parts of
15585 ggplot2, combining them with the reactive framework of Shiny and drawing web
15586 graphics using Vega.")
15587 (license license:gpl2)))
15589 (define-public r-gbm
15596 (uri (cran-uri "gbm" version))
15599 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15600 (build-system r-build-system)
15602 `(("r-lattice" ,r-lattice)
15603 ("r-survival" ,r-survival)))
15605 `(("r-knitr" ,r-knitr)))
15606 (home-page "https://github.com/gbm-developers/gbm")
15607 (synopsis "Generalized boosted regression models")
15609 "This package is an implementation of extensions to Freund and Schapire's
15610 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15611 regression methods for least squares, absolute loss, t-distribution loss,
15612 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15613 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15614 and Learning to Rank measures (LambdaMart).")
15615 (license license:gpl2+)))
15617 (define-public r-threejs
15624 (uri (cran-uri "threejs" version))
15627 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15628 (build-system r-build-system)
15630 `(#:modules ((guix build utils)
15631 (guix build r-build-system)
15635 (modify-phases %standard-phases
15636 (add-after 'unpack 'process-javascript
15637 (lambda* (#:key inputs #:allow-other-keys)
15638 (with-directory-excursion "inst"
15642 `((,(assoc-ref inputs "js-jquery")
15643 "htmlwidgets/lib/jquery/jquery.min.js")
15644 (,(assoc-ref inputs "js-threejs-111")
15645 "htmlwidgets/lib/threejs-111/three.min.js"))))
15646 (lambda (sources targets)
15647 (for-each (lambda (source target)
15648 (format #t "Processing ~a --> ~a~%"
15650 (delete-file target)
15651 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15652 (call-with-output-file target
15654 (dump-port minified port)))))
15655 sources targets))))
15658 `(("r-base64enc" ,r-base64enc)
15659 ("r-crosstalk" ,r-crosstalk)
15660 ("r-htmlwidgets" ,r-htmlwidgets)
15661 ("r-igraph" ,r-igraph)))
15663 `(("uglify-js" ,uglify-js)
15667 (uri "https://code.jquery.com/jquery-1.12.4.js")
15670 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15674 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15677 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15678 (home-page "https://bwlewis.github.io/rthreejs")
15679 (synopsis "Interactive 3D scatter plots, networks and globes")
15681 "Create interactive 3D scatter plots, network plots, and globes in R
15682 using the three.js visualization library.")
15683 (license license:expat)))
15685 (define-public r-mlbench
15692 (uri (cran-uri "mlbench" version))
15695 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15696 (build-system r-build-system)
15697 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15698 (synopsis "Machine learning benchmark problems")
15700 "This package provides a collection of artificial and real-world machine
15701 learning benchmark problems, including, e.g., several data sets from the UCI
15703 (license license:gpl2)))
15705 (define-public r-mpm
15712 (uri (cran-uri "mpm" version))
15715 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15716 (build-system r-build-system)
15718 `(("r-kernsmooth" ,r-kernsmooth)
15719 ("r-mass" ,r-mass)))
15720 (home-page "http://mpm.r-forge.r-project.org")
15721 (synopsis "Multivariate projection methods")
15723 "This is a package for exploratory graphical analysis of multivariate
15724 data, specifically gene expression data with different projection methods:
15725 principal component analysis, correspondence analysis, spectral map
15727 (license license:gpl2+)))
15729 (define-public r-png
15735 (uri (cran-uri "png" version))
15738 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15739 (build-system r-build-system)
15741 `(("libpng" ,libpng)
15743 (home-page "https://www.rforge.net/png/")
15744 (synopsis "Read and write PNG images")
15746 "This package provides an easy and simple way to read, write and display
15747 bitmap images stored in the PNG format. It can read and write both files and
15748 in-memory raw vectors.")
15749 ;; Any of these GPL versions.
15750 (license (list license:gpl2 license:gpl3))))
15752 (define-public r-ggcorrplot
15754 (name "r-ggcorrplot")
15759 (uri (cran-uri "ggcorrplot" version))
15762 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15763 (build-system r-build-system)
15765 `(("r-ggplot2" ,r-ggplot2)
15766 ("r-reshape2" ,r-reshape2)))
15767 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15768 (synopsis "Visualization of a correlation matrix using ggplot2")
15770 "The ggcorrplot package can be used to visualize easily a correlation
15771 matrix using ggplot2. It provides a solution for reordering the correlation
15772 matrix and displays the significance level on the plot. It also includes a
15773 function for computing a matrix of correlation p-values.")
15774 (license license:gpl2)))
15776 ;; This package includes minified JavaScript files. When upgrading please
15777 ;; check that there are no new minified JavaScript files.
15778 (define-public r-flexdashboard
15780 (name "r-flexdashboard")
15785 (uri (cran-uri "flexdashboard" version))
15788 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15789 (modules '((guix build utils)))
15792 ;; Delete bundled minified JavaScript files
15793 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15794 (delete-file "inst/www/sly/sly.min.js")
15795 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15796 (delete-file "inst/www/prism/prism.js")
15798 (build-system r-build-system)
15800 `(#:modules ((guix build utils)
15801 (guix build r-build-system)
15805 (ice-9 textual-ports))
15807 (modify-phases %standard-phases
15808 (add-after 'unpack 'process-javascript
15809 (lambda* (#:key inputs #:allow-other-keys)
15810 (with-directory-excursion "inst"
15811 ;; Concatenate all components of prism.js
15812 (let ((contents (string-join
15813 (map (lambda (name)
15814 (call-with-input-file
15815 (assoc-ref inputs name)
15819 "js-prism-line-numbers"))
15821 (call-with-output-file "prism-src.js"
15822 (cut display contents <>)))
15826 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15827 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15829 "www/sly/sly.min.js")
15831 "www/prism/prism.js")
15832 (,(assoc-ref inputs "js-raphael")
15833 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15834 (,(assoc-ref inputs "js-featherlight")
15835 "www/featherlight/featherlight.min.js"))))
15836 (lambda (sources targets)
15837 (for-each (lambda (source target)
15838 (format #t "Processing ~a --> ~a~%"
15840 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15841 (call-with-output-file target
15843 (dump-port minified port)))))
15844 sources targets))))
15847 `(("r-htmltools" ,r-htmltools)
15848 ("r-htmlwidgets" ,r-htmlwidgets)
15849 ("r-jsonlite" ,r-jsonlite)
15850 ("r-knitr" ,r-knitr)
15851 ("r-rmarkdown" ,r-rmarkdown)
15852 ("r-shiny" ,r-shiny)))
15854 `(("uglify-js" ,uglify-js)
15858 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15861 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15865 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15868 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15872 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15875 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15876 ("js-prism-line-numbers"
15879 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15882 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15886 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15889 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15890 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15891 (synopsis "R Markdown format for flexible dashboards")
15893 "This package provides an R Markdown format for converting an R Markdown
15894 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15895 of its components to the containing web page.")
15896 (license license:expat)))
15898 (define-public r-preseqr
15905 (uri (cran-uri "preseqR" version))
15908 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15909 (properties `((upstream-name . "preseqR")))
15910 (build-system r-build-system)
15912 `(("r-polynom" ,r-polynom)))
15913 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15914 (synopsis "Predicting species accumulation curves")
15916 "This package can be used to predict the r-species accumulation
15917 curve (r-SAC), which is the number of species represented at least r times as
15918 a function of the sampling effort. When r = 1, the curve is known as the
15919 species accumulation curve, or the library complexity curve in high-throughput
15920 genomic sequencing. The package includes both parametric and nonparametric
15921 methods, as described by Deng C, et al. (2018).")
15922 (license license:gpl3)))
15924 (define-public r-mapplots
15926 (name "r-mapplots")
15931 (uri (cran-uri "mapplots" version))
15934 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15935 (build-system r-build-system)
15936 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15937 (synopsis "Data visualization on maps")
15939 "This package helps you create simple maps; add sub-plots like pie plots
15940 to a map or any other plot; format, plot and export gridded data. The package
15941 was developed for displaying fisheries data but most functions can be used for
15942 more generic data visualisation.")
15943 (license license:gpl2+)))
15945 (define-public r-pmcmr
15952 (uri (cran-uri "PMCMR" version))
15955 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15956 (properties `((upstream-name . "PMCMR")))
15957 (build-system r-build-system)
15958 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15959 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15961 "This is a deprecated package for calculating pairwise multiple
15962 comparisons of mean rank sums. This package is superseded by the novel
15963 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15964 compatibility of dependent packages for some time.")
15965 (license license:gpl3+)))
15967 (define-public r-downloader
15969 (name "r-downloader")
15974 (uri (cran-uri "downloader" version))
15977 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15978 (build-system r-build-system)
15980 `(("r-digest" ,r-digest)))
15981 (home-page "https://github.com/wch/downloader")
15982 (synopsis "Download files over HTTP and HTTPS")
15984 "This package provides a wrapper for the @code{download.file} function,
15985 making it possible to download files over HTTPS across platforms. The
15986 @code{RCurl} package provides this functionality (and much more) but has
15987 external dependencies. This package has is implemented purely in R.")
15988 (license license:gpl2)))
15990 (define-public r-rex
15997 (uri (cran-uri "rex" version))
16000 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
16001 (build-system r-build-system)
16003 `(("r-lazyeval" ,r-lazyeval)))
16005 `(("r-knitr" ,r-knitr)))
16006 (home-page "https://github.com/kevinushey/rex")
16007 (synopsis "Friendly regular expressions")
16009 "This package provides a friendly interface for the construction of
16010 regular expressions. Regular expressions are a very powerful feature, however
16011 they are often difficult to interpret. Rex allows you to build complex
16012 regular expressions from human readable expressions")
16013 (license license:expat)))
16015 (define-public r-xmlparsedata
16017 (name "r-xmlparsedata")
16022 (uri (cran-uri "xmlparsedata" version))
16025 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
16026 (properties `((upstream-name . "xmlparsedata")))
16027 (build-system r-build-system)
16028 (home-page "https://github.com/r-lib/xmlparsedata#readme")
16029 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
16031 "This package provides tools to convert the output of
16032 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
16033 @code{XPath}, and is easier to manipulate in general.")
16034 (license license:expat)))
16036 (define-public r-cyclocomp
16038 (name "r-cyclocomp")
16043 (uri (cran-uri "cyclocomp" version))
16046 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
16047 (properties `((upstream-name . "cyclocomp")))
16048 (build-system r-build-system)
16050 `(("r-callr" ,r-callr)
16051 ("r-crayon" ,r-crayon)
16053 ("r-remotes" ,r-remotes)
16054 ("r-withr" ,r-withr)))
16055 (home-page "https://github.com/MangoTheCat/cyclocomp")
16056 (synopsis "Cyclomatic complexity of R code")
16058 "Cyclomatic complexity is a software metric, used to indicate the
16059 complexity of a program. It is a quantitative measure of the number of
16060 linearly independent paths through a program's source code. This package
16061 provides tools to compute this metric.")
16062 (license license:expat)))
16064 (define-public r-lintr
16071 (uri (cran-uri "lintr" version))
16074 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
16075 (properties `((upstream-name . "lintr")))
16076 (build-system r-build-system)
16078 `(("r-codetools" ,r-codetools)
16079 ("r-crayon" ,r-crayon)
16080 ("r-cyclocomp" ,r-cyclocomp)
16081 ("r-digest" ,r-digest)
16083 ("r-jsonlite" ,r-jsonlite)
16084 ("r-knitr" ,r-knitr)
16086 ("r-rstudioapi" ,r-rstudioapi)
16087 ("r-testthat" ,r-testthat)
16089 ("r-xmlparsedata" ,r-xmlparsedata)))
16090 (home-page "https://github.com/jimhester/lintr")
16091 (synopsis "Linter for R code")
16092 (description "This package checks adherence to a given style, syntax
16093 errors and possible semantic issues. It supports on the fly checking of R
16094 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
16095 (license license:expat)))
16097 (define-public r-sctransform
16099 (name "r-sctransform")
16104 (uri (cran-uri "sctransform" version))
16107 "0b8ni8dzlcikjm2bx5w8yi9vygx0qqxjrmnsy4kf7d1h03n2sxwa"))))
16108 (build-system r-build-system)
16110 `(("r-future" ,r-future)
16111 ("r-future-apply" ,r-future-apply)
16112 ("r-ggplot2" ,r-ggplot2)
16113 ("r-gridextra" ,r-gridextra)
16115 ("r-matrix" ,r-matrix)
16116 ("r-matrixstats" ,r-matrixstats)
16118 ("r-rcpparmadillo" ,r-rcpparmadillo)
16119 ("r-reshape2" ,r-reshape2)))
16120 (home-page "https://github.com/ChristophH/sctransform")
16121 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
16123 "This package provides a normalization method for single-cell UMI count
16124 data using a variance stabilizing transformation. The transformation is based
16125 on a negative binomial regression model with regularized parameters. As part
16126 of the same regression framework, this package also provides functions for
16127 batch correction, and data correction.")
16128 (license license:gpl3)))
16130 (define-public r-styler
16137 (uri (cran-uri "styler" version))
16140 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
16141 (build-system r-build-system)
16143 `(("r-backports" ,r-backports)
16145 ("r-magrittr" ,r-magrittr)
16146 ("r-purrr" ,r-purrr)
16147 ("r-r-cache" ,r-r-cache)
16148 ("r-rematch2" ,r-rematch2)
16149 ("r-rlang" ,r-rlang)
16150 ("r-rprojroot" ,r-rprojroot)
16151 ("r-tibble" ,r-tibble)
16152 ("r-withr" ,r-withr)
16153 ("r-xfun" ,r-xfun)))
16154 (home-page "https://github.com/r-lib/styler")
16155 (synopsis "Non-invasive pretty printing of R code")
16157 "This is a package for pretty-printing R code without changing the user's
16158 formatting intent.")
16159 (license license:gpl3)))
16161 (define-public r-scrime
16168 (uri (cran-uri "scrime" version))
16171 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
16172 (build-system r-build-system)
16173 (home-page "https://cran.r-project.org/web/packages/scrime/")
16174 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
16176 "This package provides tools for the analysis of high-dimensional data
16177 developed/implemented at the group \"Statistical Complexity Reduction In
16178 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
16179 the functions can also be applied to other types of categorical data.")
16180 (license license:gpl2)))
16182 (define-public r-pbmcapply
16184 (name "r-pbmcapply")
16189 (uri (cran-uri "pbmcapply" version))
16192 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
16193 (build-system r-build-system)
16194 (home-page "https://github.com/kvnkuang/pbmcapply")
16195 (synopsis "Track the progress of apply procedures with a progress bar")
16197 "This light-weight package helps you track and visualize the progress of
16198 parallel versions of vectorized R functions of the @code{mc*apply} family.")
16199 (license license:expat)))
16201 (define-public r-blme
16208 (uri (cran-uri "blme" version))
16211 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
16212 (build-system r-build-system)
16213 (propagated-inputs `(("r-lme4" ,r-lme4)))
16214 (home-page "https://github.com/vdorie/blme")
16215 (synopsis "Bayesian linear mixed-effects models")
16217 "This package provides tools for maximum a posteriori estimation for
16218 linear and generalized linear mixed-effects models in a Bayesian setting. It
16219 extends the lme4 package.")
16220 (license license:gpl2+)))
16222 (define-public r-batchtools
16224 (name "r-batchtools")
16229 (uri (cran-uri "batchtools" version))
16232 "1b78r70gm4a0wzjr367hqx2rfphfkbppp14d0l5zs2fvyz166lsx"))))
16233 (build-system r-build-system)
16235 `(("r-backports" ,r-backports)
16236 ("r-base64url" ,r-base64url)
16238 ("r-checkmate" ,r-checkmate)
16239 ("r-data-table" ,r-data-table)
16240 ("r-digest" ,r-digest)
16242 ("r-progress" ,r-progress)
16244 ("r-rappdirs" ,r-rappdirs)
16245 ("r-stringi" ,r-stringi)
16246 ("r-withr" ,r-withr)))
16248 `(("r-knitr" ,r-knitr)))
16249 (home-page "https://github.com/mllg/batchtools")
16250 (synopsis "Tools for computation on batch systems")
16252 "As a successor of the packages BatchJobs and BatchExperiments, this
16253 package provides a parallel implementation of the Map function for high
16254 performance computing systems managed by various schedulers. A multicore and
16255 socket mode allow the parallelization on a local machines, and multiple
16256 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
16257 the package provides an abstraction mechanism to define large-scale computer
16258 experiments in a well-organized and reproducible way.")
16259 (license license:lgpl3)))
16261 (define-public r-clue
16268 (uri (cran-uri "clue" version))
16271 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
16272 (build-system r-build-system)
16273 (propagated-inputs `(("r-cluster" ,r-cluster)))
16274 (home-page "https://cran.r-project.org/web/packages/clue/")
16275 (synopsis "Tools for analyzing cluster ensembles")
16276 (description "Cluster ensembles are collections of individual solutions to
16277 a given clustering problem which are useful or necessary to consider in a wide
16278 range of applications. This R package provides an extensible computational
16279 environment for creating and analyzing cluster ensembles, with basic data
16280 structures for representing partitions and hierarchies, and facilities for
16281 computing on them, including methods for measuring proximity and obtaining
16282 consensus and secondary clusterings.")
16283 (license license:gpl2)))
16285 (define-public r-sitmo
16292 (uri (cran-uri "sitmo" version))
16295 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
16296 (build-system r-build-system)
16297 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16298 (home-page "https://github.com/coatless/sitmo/")
16299 (synopsis "Parallel pseudo random number generator header files")
16301 "This package provides two high quality and fast PPRNGs that may be used
16302 in an OpenMP parallel environment. In addition, there is a generator for one
16303 dimensional low-discrepancy sequence.")
16304 (license license:expat)))
16306 (define-public r-dqrng
16313 (uri (cran-uri "dqrng" version))
16316 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
16317 (build-system r-build-system)
16321 ("r-sitmo" ,r-sitmo)))
16322 (home-page "https://www.daqana.org/dqrng")
16323 (synopsis "Fast pseudo random number generators")
16325 "Several fast random number generators are provided as C++ header-only
16326 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
16327 Additionally, fast functions for generating random numbers according to a
16328 uniform, normal and exponential distribution are included. The latter two use
16329 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
16330 functions are exported to R and as a C++ interface and are enabled for use
16331 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
16332 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
16333 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
16334 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
16335 ;; whole is distributed under the terms of the AGPL 3.
16336 (license license:agpl3)))
16338 (define-public r-ingredients
16340 (name "r-ingredients")
16345 (uri (cran-uri "ingredients" version))
16348 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16349 (properties `((upstream-name . "ingredients")))
16350 (build-system r-build-system)
16352 `(("r-ggplot2" ,r-ggplot2)
16353 ("r-gridextra" ,r-gridextra)
16354 ("r-scales" ,r-scales)))
16355 (native-inputs `(("r-knitr" ,r-knitr)))
16356 (home-page "https://ModelOriented.github.io/ingredients/")
16357 (synopsis "Effects and importances of model ingredients")
16359 "This is a collection of tools for assessment of feature importance and
16360 feature effects. Key functions are:
16363 @item @code{feature_importance()} for assessment of global level feature
16365 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16366 @item @code{partial_dependence()} for partial dependence plots,
16367 @item @code{conditional_dependence()} for conditional dependence plots,
16368 @item @code{accumulated_dependence()} for accumulated local effects plots,
16369 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16370 aggregation of ceteris paribus profiles,
16371 @item generic @code{print()} and @code{plot()} for better usability of
16372 selected explainers,
16373 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16374 @item generic @code{describe()} for explanations in natural language.
16376 (license license:gpl3)))
16378 (define-public r-ibreakdown
16380 (name "r-ibreakdown")
16385 (uri (cran-uri "iBreakDown" version))
16388 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16389 (properties `((upstream-name . "iBreakDown")))
16390 (build-system r-build-system)
16391 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16392 (native-inputs `(("r-knitr" ,r-knitr)))
16393 (home-page "https://ModelOriented.github.io/iBreakDown/")
16394 (synopsis "Model agnostic instance level variable attributions")
16396 "This package provides a model agnostic tool for decomposition of
16397 predictions from black boxes. It supports additive attributions and
16398 attributions with interactions. The Break Down Table shows contributions of
16399 every variable to a final prediction. The Break Down Plot presents variable
16400 contributions in a concise graphical way. This package works for
16401 classification and regression models.")
16402 (license license:gpl3)))
16404 (define-public r-dae
16411 (uri (cran-uri "dae" version))
16414 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16415 (build-system r-build-system)
16417 `(("r-ggplot2" ,r-ggplot2)
16418 ("r-plyr" ,r-plyr)))
16420 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16421 (home-page "http://chris.brien.name")
16422 (synopsis "Functions useful in the design and ANOVA of experiments")
16424 "This package provides functions useful in the design and ANOVA of
16425 experiments. The content falls into the following groupings:
16429 @item factor manipulation functions,
16430 @item design functions,
16431 @item ANOVA functions,
16432 @item matrix functions,
16433 @item projector and canonical efficiency functions, and
16434 @item miscellaneous functions.
16437 There is a vignette called @code{DesignNotes} describing how to use the design
16438 functions for randomizing and assessing designs. The ANOVA functions
16439 facilitate the extraction of information when the @code{Error} function has
16440 been used in the call to @code{aov}.")
16441 (license license:gpl2)))
16443 (define-public r-dalex
16450 (uri (cran-uri "DALEX" version))
16453 "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98"))))
16454 (properties `((upstream-name . "DALEX")))
16455 (build-system r-build-system)
16457 `(("r-ggplot2" ,r-ggplot2)
16458 ("r-ibreakdown" ,r-ibreakdown)
16459 ("r-ingredients" ,r-ingredients)))
16460 (home-page "https://pbiecek.github.io/DALEX/")
16461 (synopsis "Descriptive machine learning explanations")
16463 "Machine Learning models are widely used and have various applications in
16464 classification or regression. Models created with boosting, bagging, stacking
16465 or similar techniques are often used due to their high performance, but such
16466 black-box models usually lack interpretability. The DALEX package contains
16467 various explainers that help to understand the link between input variables
16468 and model output.")
16469 ;; Any version of the GPL
16470 (license license:gpl3+)))
16472 (define-public r-enrichr
16479 (uri (cran-uri "enrichR" version))
16482 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16483 (properties `((upstream-name . "enrichR")))
16484 (build-system r-build-system)
16486 `(("r-httr" ,r-httr)
16487 ("r-rjson" ,r-rjson)))
16488 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16489 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16491 "This package provides an R interface to all Enrichr databases, a
16492 web-based tool for analyzing gene sets and returns any enrichment of common
16493 annotated biological functions.")
16494 (license license:gpl2+)))
16496 (define-public r-plot3d
16503 (uri (cran-uri "plot3D" version))
16506 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16507 (properties `((upstream-name . "plot3D")))
16508 (build-system r-build-system)
16509 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16510 (home-page "https://cran.r-project.org/web/packages/plot3D")
16511 (synopsis "Plot multi-dimensional data")
16513 "This package provides functions for viewing 2D and 3D data, including
16514 perspective plots, slice plots, surface plots, scatter plots, etc. It
16515 includes data sets from oceanography.")
16516 (license license:gpl3+)))
16518 (define-public r-ggfortify
16520 (name "r-ggfortify")
16525 (uri (cran-uri "ggfortify" version))
16528 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
16529 (build-system r-build-system)
16531 `(("r-dplyr" ,r-dplyr)
16532 ("r-ggplot2" ,r-ggplot2)
16533 ("r-gridextra" ,r-gridextra)
16534 ("r-scales" ,r-scales)
16535 ("r-stringr" ,r-stringr)
16536 ("r-tibble" ,r-tibble)
16537 ("r-tidyr" ,r-tidyr)))
16539 `(("r-knitr" ,r-knitr)))
16540 (home-page "https://github.com/sinhrks/ggfortify")
16541 (synopsis "Data visualization tools for statistical analysis results")
16543 "This package provides unified plotting tools for statistics commonly
16544 used, such as GLM, time series, PCA families, clustering and survival
16545 analysis. The package offers a single plotting interface for these analysis
16546 results and plots in a unified style using the @code{ggplot2} package.")
16547 (license license:gpl2)))
16549 (define-public r-refmanager
16551 (name "r-refmanager")
16556 (uri (cran-uri "RefManageR" version))
16559 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16560 (properties `((upstream-name . "RefManageR")))
16561 (build-system r-build-system)
16563 `(("r-bibtex" ,r-bibtex)
16565 ("r-jsonlite" ,r-jsonlite)
16566 ("r-lubridate" ,r-lubridate)
16568 ("r-stringr" ,r-stringr)
16569 ("r-xml2" ,r-xml2)))
16570 (home-page "https://github.com/ropensci/RefManageR/")
16571 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16573 "This package provides tools for importing and working with bibliographic
16574 references. It greatly enhances the @code{bibentry} class by providing a
16575 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16576 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16577 by various formats for name lists (author by last names, translator by full
16578 names, etc.). Entries can be updated, combined, sorted, printed in a number
16579 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16580 into R and converted to @code{BibEntry} objects.")
16581 ;; Any of these licenses may be picked.
16582 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16584 (define-public r-citr
16591 (uri (cran-uri "citr" version))
16594 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16595 (build-system r-build-system)
16597 `(("r-assertthat" ,r-assertthat)
16600 ("r-miniui" ,r-miniui)
16601 ("r-refmanager" ,r-refmanager)
16602 ("r-rstudioapi" ,r-rstudioapi)
16603 ("r-shiny" ,r-shiny)
16604 ("r-shinyjs" ,r-shinyjs)
16605 ("r-yaml" ,r-yaml)))
16606 (home-page "https://github.com/crsh/citr")
16607 (synopsis "RStudio add-in to insert Markdown citations")
16609 "This package provides functions and an RStudio add-in that search a
16610 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16611 the current document.")
16612 (license license:expat)))
16614 (define-public r-xgboost
16617 (version "1.2.0.1")
16621 (uri (cran-uri "xgboost" version))
16624 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16625 (build-system r-build-system)
16627 `(("r-data-table" ,r-data-table)
16628 ("r-magrittr" ,r-magrittr)
16629 ("r-matrix" ,r-matrix)
16630 ("r-stringi" ,r-stringi)))
16632 `(("r-knitr" ,r-knitr)))
16633 (home-page "https://github.com/dmlc/xgboost")
16634 (synopsis "Extreme gradient boosting")
16636 "This package provides an R interface to Extreme Gradient Boosting, which
16637 is an efficient implementation of the gradient boosting framework from Chen
16638 and Guestrin (2016). The package includes efficient linear model solver and
16639 tree learning algorithms. The package can automatically do parallel
16640 computation on a single machine. It supports various objective functions,
16641 including regression, classification and ranking. The package is made to be
16642 extensible, so that users are also allowed to define their own objectives
16644 (license license:asl2.0)))
16646 (define-public r-umap
16649 (version "0.2.6.0")
16653 (uri (cran-uri "umap" version))
16656 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16657 (build-system r-build-system)
16659 `(("r-openssl" ,r-openssl)
16661 ("r-reticulate" ,r-reticulate)
16662 ("r-rspectra" ,r-rspectra)))
16664 `(("r-knitr" ,r-knitr)))
16665 (home-page "https://github.com/tkonopka/umap")
16666 (synopsis "Uniform manifold approximation and projection")
16668 "Uniform manifold approximation and projection is a technique for
16669 dimension reduction. This package provides an interface to the UMAP algorithm
16670 in R, including a translation of the original algorithm into R.")
16671 (license license:expat)))
16673 (define-public r-uwot
16680 (uri (cran-uri "uwot" version))
16683 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16684 (build-system r-build-system)
16686 `(("r-dqrng" ,r-dqrng)
16688 ("r-irlba" ,r-irlba)
16689 ("r-matrix" ,r-matrix)
16691 ("r-rcppannoy" ,r-rcppannoy)
16692 ("r-rcppprogress" ,r-rcppprogress)
16693 ("r-rspectra" ,r-rspectra)))
16694 (home-page "https://github.com/jlmelville/uwot")
16695 (synopsis "Uniform manifold approximation and projection")
16697 "This package provides an implementation of the Uniform Manifold
16698 Approximation and Projection dimensionality reduction by McInnes et
16699 al. (2018). It also provides means to transform new data and to carry out
16700 supervised dimensionality reduction. An implementation of the related
16701 LargeVis method of Tang et al. (2016) is also provided.")
16702 (license license:gpl3)))
16704 (define-public r-kableextra
16706 (name "r-kableextra")
16711 (uri (cran-uri "kableExtra" version))
16714 "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf"))))
16715 (properties `((upstream-name . "kableExtra")))
16716 (build-system r-build-system)
16718 `(("r-digest" ,r-digest)
16720 ("r-htmltools" ,r-htmltools)
16721 ("r-knitr" ,r-knitr)
16722 ("r-magrittr" ,r-magrittr)
16723 ("r-rmarkdown" ,r-rmarkdown)
16724 ("r-rstudioapi" ,r-rstudioapi)
16725 ("r-rvest" ,r-rvest)
16726 ("r-scales" ,r-scales)
16727 ("r-stringr" ,r-stringr)
16728 ("r-viridislite" ,r-viridislite)
16729 ("r-webshot" ,r-webshot)
16730 ("r-xml2" ,r-xml2)))
16732 `(("r-knitr" ,r-knitr)))
16733 (home-page "https://haozhu233.github.io/kableExtra/")
16734 (synopsis "Construct complex tables with pipe syntax")
16736 "Build complex HTML or LaTeX tables using @code{kable()} from
16737 @code{knitr} and the piping syntax from @code{magrittr}. The function
16738 @code{kable()} is a light weight table generator coming from @code{knitr}.
16739 This package simplifies the way to manipulate the HTML or LaTeX codes
16740 generated by @code{kable()} and allows users to construct complex tables and
16741 customize styles using a readable syntax.")
16742 (license license:expat)))
16744 (define-public r-glasso
16751 (uri (cran-uri "glasso" version))
16753 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16754 (build-system r-build-system)
16755 (native-inputs `(("gfortran" ,gfortran)))
16756 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16757 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16759 "This is a package for estimation of a sparse inverse covariance matrix
16760 using a lasso (L1) penalty. Facilities are provided for estimates along a
16761 path of values for the regularization parameter.")
16762 (license license:gpl2)))
16764 (define-public r-rhpcblasctl
16766 (name "r-rhpcblasctl")
16767 (version "0.20-137")
16771 (uri (cran-uri "RhpcBLASctl" version))
16774 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16775 (properties `((upstream-name . "RhpcBLASctl")))
16776 (build-system r-build-system)
16777 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16778 (synopsis "Control the number of threads on BLAS")
16780 "This package allows you to control the number of threads the BLAS
16781 library uses. It is also possible to control the number of threads in
16783 (license license:agpl3+)))
16785 (define-public r-lda
16792 (uri (cran-uri "lda" version))
16795 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16796 (build-system r-build-system)
16797 (home-page "https://cran.r-project.org/web/packages/lda/")
16798 (synopsis "Collapsed Gibbs sampling methods for topic models")
16800 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16801 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16802 mixed-membership stochastic blockmodel. Inference for all of these models is
16803 implemented via a fast collapsed Gibbs sampler written in C. Utility
16804 functions for reading/writing data typically used in topic models, as well as
16805 tools for examining posterior distributions are also included.")
16806 ;; Any version of the LGPL
16807 (license license:lgpl3+)))
16809 (define-public r-rann-l1
16816 (uri (cran-uri "RANN.L1" version))
16819 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16820 (properties `((upstream-name . "RANN.L1")))
16821 (build-system r-build-system)
16822 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16823 (synopsis "Fast nearest neighbour search using L1 metric")
16825 "This package provides tools to find the k nearest neighbours for every
16826 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16827 library. There is support for approximate as well as exact searches, fixed
16828 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16829 computed using the L1 (Manhattan, taxicab) metric.")
16830 (license license:gpl3+)))
16832 (define-public r-leiden
16839 (uri (cran-uri "leiden" version))
16842 "0cj98s1d9771dahn2xwdb1hpkw51jsfmgvzpam34c7i57fj37hn2"))))
16843 (properties `((upstream-name . "leiden")))
16844 (build-system r-build-system)
16846 `(("r-igraph" ,r-igraph)
16847 ("r-matrix" ,r-matrix)
16848 ("r-reticulate" ,r-reticulate)))
16850 `(("r-knitr" ,r-knitr)))
16851 (home-page "https://github.com/TomKellyGenetics/leiden")
16852 (synopsis "R implementation of Leiden clustering algorithm")
16854 "This package implements the Python @code{leidenalg} module to be called
16855 in R. It enables clustering using the Leiden algorithm for partitioning a
16856 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16857 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16858 (license license:gpl3)))
16860 (define-public r-patchwork
16862 (name "r-patchwork")
16867 (uri (cran-uri "patchwork" version))
16870 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16871 (build-system r-build-system)
16873 `(("r-ggplot2" ,r-ggplot2)
16874 ("r-gtable" ,r-gtable)))
16876 `(("r-knitr" ,r-knitr)))
16877 (home-page "https://github.com/thomasp85/patchwork")
16878 (synopsis "Compose ggplot2 plots")
16880 "The @code{ggplot2} package provides a strong API for sequentially
16881 building up a plot, but does not concern itself with composition of multiple
16882 plots. Patchwork is a package that expands the API to allow for arbitrarily
16883 complex composition of plots by providing mathematical operators for combining
16885 (license license:expat)))
16887 (define-public r-liger
16894 (uri (git-reference
16895 (url "https://github.com/MacoskoLab/liger")
16896 (commit (string-append "v" version))))
16897 (file-name (git-file-name name version))
16900 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16901 (modules '((guix build utils)))
16904 (delete-file "inst/java/ModularityOptimizer.jar")
16906 (build-system r-build-system)
16909 (modify-phases %standard-phases
16910 (add-after 'unpack 'build-java-part
16911 (lambda* (#:key inputs #:allow-other-keys)
16912 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16913 (for-each (lambda (file) (invoke "javac" file))
16914 (find-files "." "\\.java$"))
16915 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16916 (find-files "." "\\.class$"))
16919 `(("r-cowplot" ,r-cowplot)
16920 ("r-dosnow" ,r-dosnow)
16921 ("r-dplyr" ,r-dplyr)
16923 ("r-foreach" ,r-foreach)
16924 ("r-ggplot2" ,r-ggplot2)
16925 ("r-ggrepel" ,r-ggrepel)
16926 ("r-hmisc" ,r-hmisc)
16928 ("r-irlba" ,r-irlba)
16929 ("r-matrix" ,r-matrix)
16930 ("r-mclust" ,r-mclust)
16931 ("r-patchwork" ,r-patchwork)
16933 ("r-rann-l1" ,r-rann-l1)
16935 ("r-rcpparmadillo" ,r-rcpparmadillo)
16936 ("r-riverplot" ,r-riverplot)
16937 ("r-rtsne" ,r-rtsne)
16938 ("r-snow" ,r-snow)))
16940 `(("jdk" ,icedtea "jdk")
16941 ;; See https://github.com/MacoskoLab/liger/issues/96
16942 ;; The optimizer is released under the Expat license.
16946 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16949 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16951 ("r-knitr" ,r-knitr))) ; for vignettes
16952 (home-page "https://github.com/MacoskoLab/liger")
16953 (synopsis "Integrate and analyze multiple single-cell datasets")
16955 "LIGER is a package for integrating and analyzing multiple single-cell
16956 datasets, developed and maintained by the Macosko lab. It relies on
16957 integrative non-negative matrix factorization to identify shared and
16958 dataset-specific factors.")
16959 (license license:gpl3)))
16961 (define-public r-harmony
16968 (uri (git-reference
16969 (url "https://github.com/immunogenomics/harmony")
16971 (file-name (git-file-name name version))
16974 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16975 (modules '((guix build utils)))
16978 (for-each delete-file '("config.status" "configure"))
16980 (build-system r-build-system)
16982 `(("r-cowplot" ,r-cowplot)
16983 ("r-dplyr" ,r-dplyr)
16984 ("r-ggplot2" ,r-ggplot2)
16985 ("r-irlba" ,r-irlba)
16986 ("r-matrix" ,r-matrix)
16988 ("r-rcpparmadillo" ,r-rcpparmadillo)
16989 ("r-rcppprogress" ,r-rcppprogress)
16990 ("r-rlang" ,r-rlang)
16991 ("r-tibble" ,r-tibble)
16992 ("r-tidyr" ,r-tidyr)))
16994 `(("autoconf" ,autoconf)))
16995 (home-page "https://github.com/immunogenomics/harmony")
16996 (synopsis "Integration of single cell sequencing data")
16998 "This package provides an implementation of the Harmony algorithm for
16999 single cell integration, described in Korsunsky et al
17000 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
17001 function and interfaces to external frameworks.")
17002 (license license:gpl3)))
17004 (define-public r-covr
17011 (uri (cran-uri "covr" version))
17013 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
17014 (properties `((upstream-name . "covr")))
17015 (build-system r-build-system)
17017 `(("r-crayon" ,r-crayon)
17018 ("r-digest" ,r-digest)
17020 ("r-jsonlite" ,r-jsonlite)
17022 ("r-withr" ,r-withr)
17023 ("r-yaml" ,r-yaml)))
17025 `(("r-knitr" ,r-knitr))) ; for vignettes
17026 (home-page "https://github.com/r-lib/covr")
17027 (synopsis "Test coverage for R packages")
17029 "Thisp package enables you to track and report code coverage for your
17030 package and (optionally) upload the results to a coverage service. Code
17031 coverage is a measure of the amount of code being exercised by a set of tests.
17032 It is an indirect measure of test quality and completeness. This package is
17033 compatible with any testing methodology or framework and tracks coverage of
17034 both R code and compiled C/C++/FORTRAN code.")
17035 (license license:gpl3)))
17037 (define-public r-systemfonts
17039 (name "r-systemfonts")
17044 (uri (cran-uri "systemfonts" version))
17047 "12hdvv66kkd3b4rs82blc3c4ifz2dw1048sqpkbz6vkk1zqpc53x"))))
17048 (properties `((upstream-name . "systemfonts")))
17049 (build-system r-build-system)
17051 `(("r-cpp11" ,r-cpp11)))
17053 `(("fontconfig" ,fontconfig)
17056 `(("pkg-config" ,pkg-config)
17057 ("r-knitr" ,r-knitr)))
17058 (home-page "https://github.com/r-lib/systemfonts")
17059 (synopsis "System native font finding")
17061 "This package provides system native access to the font catalogue. As
17062 font handling varies between systems it is difficult to correctly locate
17063 installed fonts across different operating systems. The 'systemfonts' package
17064 provides bindings to the native libraries for finding font files that can then
17065 be used further by e.g. graphic devices.")
17066 (license license:expat)))
17068 (define-public r-graphlayouts
17070 (name "r-graphlayouts")
17075 (uri (cran-uri "graphlayouts" version))
17078 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
17079 (properties `((upstream-name . "graphlayouts")))
17080 (build-system r-build-system)
17082 `(("r-igraph" ,r-igraph)
17084 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17085 (home-page "https://github.com/schochastics/graphlayouts")
17086 (synopsis "Additional layout algorithms for network visualizations")
17088 "This package provides several layout algorithms to visualize networks
17089 which are not part of the igraph library. Most are based on the concept of
17090 stress majorization by Gansner et al. (2004)
17091 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
17092 emphasize hidden group structures in networks or focus on specific nodes.")
17093 (license license:expat)))
17095 (define-public r-tidygraph
17097 (name "r-tidygraph")
17102 (uri (cran-uri "tidygraph" version))
17105 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
17106 (properties `((upstream-name . "tidygraph")))
17107 (build-system r-build-system)
17109 `(("r-dplyr" ,r-dplyr)
17110 ("r-igraph" ,r-igraph)
17111 ("r-magrittr" ,r-magrittr)
17112 ("r-pillar" ,r-pillar)
17115 ("r-rlang" ,r-rlang)
17116 ("r-tibble" ,r-tibble)
17117 ("r-tidyr" ,r-tidyr)))
17118 (home-page "https://github.com/thomasp85/tidygraph")
17119 (synopsis "Tidy API for graph manipulation")
17121 "This package provides a graph implementation that can be thought of as
17122 two tidy data frames describing node and edge data respectively. It provides
17123 an approach to manipulate these two virtual data frames using the API defined
17124 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
17125 common graph algorithms.")
17126 (license license:expat)))
17128 (define-public r-soupx
17129 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
17133 (version (git-version "0.3.1" revision commit))
17137 (uri (git-reference
17138 (url "https://github.com/constantAmateur/SoupX")
17140 (file-name (git-file-name name version))
17143 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
17144 (properties `((upstream-name . "SoupX")))
17145 (build-system r-build-system)
17147 `(("r-ggplot2" ,r-ggplot2)
17148 ("r-matrix" ,r-matrix)
17149 ("r-seurat" ,r-seurat)))
17150 (home-page "https://github.com/constantAmateur/SoupX")
17151 (synopsis "Single cell mRNA Soup eXterminator")
17153 "This package provides a package for quantifying, profiling and
17154 removing cell free mRNA contamination (the \"soup\") from droplet based single
17155 cell RNA-seq experiments.")
17156 (license license:gpl2))))
17158 (define-public r-assertr
17165 (uri (cran-uri "assertr" version))
17168 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
17169 (build-system r-build-system)
17171 `(("r-dplyr" ,r-dplyr)
17173 ("r-rlang" ,r-rlang)))
17175 `(("r-knitr" ,r-knitr))) ; needed for vignette
17176 (home-page "https://github.com/ropensci/assertr")
17177 (synopsis "Assertive programming for R analysis pipelines")
17179 "This package provides functionality to assert conditions that have to be
17180 met so that errors in data used in analysis pipelines can fail quickly. It is
17181 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
17183 (license license:expat)))
17185 (define-public r-parameters
17187 (name "r-parameters")
17192 (uri (cran-uri "parameters" version))
17195 "17jjmy1qnx25ldvasrwhmal45nl1sr8qjxprbi8fcjwra9af6cr6"))))
17196 (properties `((upstream-name . "parameters")))
17197 (build-system r-build-system)
17199 `(("r-bayestestr" ,r-bayestestr)
17200 ("r-insight" ,r-insight)))
17202 `(("r-knitr" ,r-knitr)))
17203 (home-page "https://cran.r-project.org/web/packages/parameters")
17204 (synopsis "Processing of model parameters")
17206 "This package provides utilities for processing the parameters of various
17207 statistical models. Beyond computing p values, CIs, and other indices for a
17208 wide variety of models, this package implements features like standardization
17209 or bootstrapping of parameters and models, feature reduction (feature
17210 extraction and variable selection) as well as conversion between indices of
17212 (license license:gpl3)))
17214 (define-public r-rgdal
17221 (uri (cran-uri "rgdal" version))
17223 (base32 "1pr267sh0v6cympdg12yny51cmn4r20s5sjq2hqymn4kphcpqijk"))))
17224 (properties `((upstream-name . "rgdal")))
17225 (build-system r-build-system)
17233 `(("pkg-config" ,pkg-config)
17234 ("r-knitr" ,r-knitr)))
17235 (home-page "http://rgdal.r-forge.r-project.org")
17236 (synopsis "Bindings for the Geospatial Data Abstraction Library")
17238 "This package provides bindings to the Geospatial Data Abstraction
17239 Library (GDAL) and access to projection/transformation operations from the
17241 (license license:gpl2+)))
17243 (define-public r-insol
17250 (uri (cran-uri "insol" version))
17253 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
17254 (properties `((upstream-name . "insol")))
17255 (build-system r-build-system)
17257 `(("r-raster" ,r-raster)))
17259 `(("gfortran" ,gfortran)))
17260 (home-page "https://meteoexploration.com/R/insol/index.html")
17261 (synopsis "Tools for calculating solar radiation")
17263 "This package provides functions to compute insolation on tilted
17264 surfaces, computes atmospheric transmittance and related parameters such as:
17265 Earth radius vector, declination, sunset and sunrise, daylength, equation of
17266 time, vector in the direction of the sun, vector normal to surface, and some
17267 atmospheric physics.")
17268 (license license:gpl2+)))
17270 (define-public r-lifecycle
17272 (name "r-lifecycle")
17277 (uri (cran-uri "lifecycle" version))
17280 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
17281 (properties `((upstream-name . "lifecycle")))
17282 (build-system r-build-system)
17284 `(("r-glue" ,r-glue)
17285 ("r-rlang" ,r-rlang)))
17287 `(("r-knitr" ,r-knitr))) ; for vignettes
17288 (home-page "https://github.com/r-lib/lifecycle")
17289 (synopsis "Manage the life cycle of your package functions")
17291 "Manage the life cycle of your exported functions with shared
17292 conventions, documentation badges, and non-invasive deprecation warnings. The
17293 lifecycle package defines four development stages (experimental, maturing,
17294 stable, and questioning) and three deprecation stages (soft-deprecated,
17295 deprecated, and defunct). It makes it easy to insert badges corresponding to
17296 these stages in your documentation. Usage of deprecated functions are
17297 signalled with increasing levels of non-invasive verbosity.")
17298 (license license:gpl3)))
17300 (define-public r-assertable
17302 (name "r-assertable")
17307 (uri (cran-uri "assertable" version))
17310 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
17311 (build-system r-build-system)
17313 `(("r-data-table" ,r-data-table)))
17314 (home-page "https://cran.r-project.org/web/packages/assertable/")
17315 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
17316 (description "This package provides simple, flexible assertions on
17317 data.frame or data.table objects with verbose output for vetting. While other
17318 assertion packages apply towards more general use-cases, @code{assertable} is
17319 tailored towards tabular data. It includes functions to check variable names
17320 and values, whether the dataset contains all combinations of a given set of
17321 unique identifiers, and whether it is a certain length. In addition,
17322 @code{assertable} includes utility functions to check the existence of target
17323 files and to efficiently import multiple tabular data files into one
17325 (license license:gpl3)))
17327 (define-public r-quadprog
17329 (name "r-quadprog")
17334 (uri (cran-uri "quadprog" version))
17336 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
17337 (build-system r-build-system)
17339 `(("gfortran" ,gfortran)))
17340 (home-page "https://cran.r-project.org/web/packages/quadprog")
17341 (synopsis "Functions to solve quadratic programming problems")
17343 "This package contains routines and documentation for solving quadratic
17344 programming problems.")
17345 (license license:gpl3+)))
17347 (define-public r-desolve
17354 (uri (cran-uri "deSolve" version))
17356 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17357 (properties `((upstream-name . "deSolve")))
17358 (build-system r-build-system)
17360 `(("gfortran" ,gfortran)))
17361 (home-page "https://desolve.r-forge.r-project.org/")
17362 (synopsis "Solvers for initial value problems of differential equations")
17363 (description "This package provides functions that solve initial value
17364 problems of a system of first-order @dfn{ordinary differential
17365 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17366 @dfn{differential algebraic equations} (DAE), and of delay differential
17367 equations. The functions provide an interface to the FORTRAN functions
17368 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17369 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17370 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17371 time steps. The package contains routines designed for solving ODEs resulting
17372 from 1-D, 2-D and 3-D partial differential equations that have been converted
17373 to ODEs by numerical differencing.")
17374 (license license:gpl2+)))
17376 (define-public r-pracma
17382 (uri (cran-uri "pracma" version))
17384 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17385 (build-system r-build-system)
17386 (home-page "https://cran.r-project.org/web/packages/pracma/")
17387 (synopsis "Practical numerical math functions")
17388 (description "This package provides functions for numerical analysis and
17389 linear algebra, numerical optimization, differential equations, plus some
17390 special functions. It uses Matlab function names where appropriate to simplify
17392 (license license:gpl3+)))
17394 (define-public r-subplex
17401 (uri (cran-uri "subplex" version))
17404 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17405 (build-system r-build-system)
17407 `(("gfortran" ,gfortran)))
17408 (home-page "https://cran.r-project.org/web/packages/subplex")
17409 (synopsis "Unconstrained optimization using the subplex algorithm")
17411 "This package implements the Subplex optimization algorithm.
17412 It solves unconstrained optimization problems using a simplex method on
17413 subspaces. The method is well suited for optimizing objective functions that
17414 are noisy or are discontinuous at the solution.")
17415 (license license:gpl3+)))
17417 (define-public r-txtplot
17424 (uri (cran-uri "txtplot" version))
17427 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17428 (build-system r-build-system)
17429 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17430 (synopsis "Text-based plotting")
17431 (description "This package provides functions to produce rudimentary ASCII
17432 graphics directly in the terminal window. This package provides a basic
17433 plotting function (and equivalents of curve, density, acf and barplot) as well
17434 as a boxplot function.")
17435 (license license:lgpl3+)))
17437 (define-public r-bio3d
17444 (uri (cran-uri "bio3d" version))
17447 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17448 (properties `((upstream-name . "bio3d")))
17449 (build-system r-build-system)
17450 (inputs `(("zlib" ,zlib)))
17451 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17452 (home-page "http://thegrantlab.org/bio3d/")
17453 (synopsis "Biological structure analysis")
17455 "This package provides utilities to process, organize and explore protein
17456 structure, sequence and dynamics data. Features include the ability to read
17457 and write structure, sequence and dynamic trajectory data, perform sequence
17458 and structure database searches, data summaries, atom selection, alignment,
17459 superposition, rigid core identification, clustering, torsion analysis,
17460 distance matrix analysis, structure and sequence conservation analysis, normal
17461 mode analysis, principal component analysis of heterogeneous structure data,
17462 and correlation network analysis from normal mode and molecular dynamics data.
17463 In addition, various utility functions are provided to enable the statistical
17464 and graphical power of the R environment to work with biological sequence and
17466 (license license:gpl2+)))
17468 (define-public r-bios2cor
17470 (name "r-bios2cor")
17475 (uri (cran-uri "Bios2cor" version))
17478 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
17479 (properties `((upstream-name . "Bios2cor")))
17480 (build-system r-build-system)
17482 `(("r-bigmemory" ,r-bigmemory)
17483 ("r-bio3d" ,r-bio3d)
17484 ("r-circular" ,r-circular)
17485 ("r-igraph" ,r-igraph)))
17486 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17487 (synopsis "From biological sequences and simulations to correlation analysis")
17489 "This package provides utilities for computation and analysis of
17490 correlation/covariation in multiple sequence alignments and in side chain
17491 motions during molecular dynamics simulations. Features include the
17492 computation of correlation/covariation scores using a variety of scoring
17493 functions between either sequence positions in alignments or side chain
17494 dihedral angles in molecular dynamics simulations and utilities to analyze the
17495 correlation/covariation matrix through a variety of tools including network
17496 representation and principal components analysis. In addition, several
17497 utility functions are based on the R graphical environment to provide friendly
17498 tools for help in data interpretation.")
17499 (license license:gpl2+)))
17501 ;; This package includes minified JavaScript files. When upgrading please
17502 ;; check that there are no new minified JavaScript files.
17503 (define-public r-networkd3
17505 (name "r-networkd3")
17510 (uri (cran-uri "networkD3" version))
17513 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17516 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17518 (properties `((upstream-name . "networkD3")))
17519 (build-system r-build-system)
17521 `(#:modules ((guix build utils)
17522 (guix build r-build-system)
17526 (modify-phases %standard-phases
17527 (add-after 'unpack 'process-javascript
17528 (lambda* (#:key inputs #:allow-other-keys)
17529 (with-directory-excursion "inst/htmlwidgets/lib/"
17533 `((,(assoc-ref inputs "d3.v4.js")
17534 "d3-4.5.0/d3.min.js"))))
17535 (lambda (sources targets)
17536 (for-each (lambda (source target)
17537 (format #t "Processing ~a --> ~a~%"
17539 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17540 (call-with-output-file target
17542 (dump-port minified port)))))
17543 sources targets))))
17546 `(("uglify-js" ,uglify-js)
17547 ;; NOTE: Make sure that this version of d3 is still valid when
17548 ;; upgrading the package.
17552 (uri "https://d3js.org/d3.v4.js")
17555 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17557 `(("r-htmlwidgets" ,r-htmlwidgets)
17558 ("r-igraph" ,r-igraph)
17559 ("r-magrittr" ,r-magrittr)))
17560 (home-page "https://cran.r-project.org/package=networkD3")
17561 (synopsis "D3 JavaScript network graphs from R")
17563 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17565 (license license:gpl3+)))
17567 (define-public r-aasea
17574 (uri (cran-uri "aaSEA" version))
17577 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17578 (properties `((upstream-name . "aaSEA")))
17579 (build-system r-build-system)
17581 `(("r-bios2cor" ,r-bios2cor)
17583 ("r-hmisc" ,r-hmisc)
17584 ("r-magrittr" ,r-magrittr)
17585 ("r-networkd3" ,r-networkd3)
17586 ("r-plotly" ,r-plotly)
17587 ("r-seqinr" ,r-seqinr)
17588 ("r-shiny" ,r-shiny)
17589 ("r-shinydashboard" ,r-shinydashboard)))
17590 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17591 (synopsis "Amino acid substitution effect analyzer")
17593 "Given a protein multiple sequence alignment, it is a daunting task to
17594 assess the effects of substitutions along sequence length. The aaSEA package
17595 is intended to help researchers to rapidly analyze property changes caused by
17596 single, multiple and correlated amino acid substitutions in proteins.")
17597 (license license:gpl3)))
17599 (define-public r-abacus
17606 (uri (cran-uri "ABACUS" version))
17609 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17610 (properties `((upstream-name . "ABACUS")))
17611 (build-system r-build-system)
17613 `(("r-ggplot2" ,r-ggplot2)
17614 ("r-shiny" ,r-shiny)))
17615 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17616 (synopsis "Apps-based activities for communicating and understanding statistics")
17618 "This package provides a set of Shiny apps for effective communication
17619 and understanding in statistics. The current version includes properties of
17620 normal distribution, properties of sampling distribution, one-sample z and t
17621 tests, two samples independent (unpaired) t test and analysis of variance.")
17622 (license license:gpl3)))
17624 (define-public r-abc-rap
17631 (uri (cran-uri "ABC.RAP" version))
17634 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17635 (properties `((upstream-name . "ABC.RAP")))
17636 (build-system r-build-system)
17637 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17638 (synopsis "Array-based CpG region analysis pipeline")
17640 "This package aims to identify candidate genes that are differentially
17641 methylated between cases and controls. It applies Student's t-test and delta
17642 beta analysis to identify candidate genes containing multiple CpG sites.")
17643 (license license:gpl3)))
17645 (define-public r-abcadm
17652 (uri (cran-uri "abcADM" version))
17655 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17656 (properties `((upstream-name . "abcADM")))
17657 (build-system r-build-system)
17660 ("r-rcpp" ,r-rcpp)))
17661 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17662 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17664 "This package provides tools to estimate parameters of accumulated
17665 damage (load duration) models based on failure time data under a Bayesian
17666 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17667 long-term reliability under stochastic load profiles.")
17668 (license license:gpl3)))
17670 (define-public r-rglpk
17677 (uri (cran-uri "Rglpk" version))
17680 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17681 (properties `((upstream-name . "Rglpk")))
17682 (build-system r-build-system)
17684 `(("r-slam" ,r-slam)))
17687 (home-page "https://r-forge.r-project.org/projects/rglp/")
17688 (synopsis "R interface to the GNU Linear Programming Kit")
17690 "This package provides an R interface to the GNU Linear Programming Kit,
17691 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17692 integer linear programming} (MILP) and other related problems.")
17694 (license (list license:gpl2 license:gpl3))))
17696 (define-public r-abcdefba
17698 (name "r-abcdefba")
17703 (uri (cran-uri "abcdeFBA" version))
17706 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17707 (properties `((upstream-name . "abcdeFBA")))
17708 (build-system r-build-system)
17710 `(("r-corrplot" ,r-corrplot)
17711 ("r-lattice" ,r-lattice)
17713 ("r-rglpk" ,r-rglpk)))
17714 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17715 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17717 "This package provides functions for Constraint Based Simulation using
17718 Flux Balance Analysis and informative analysis of the data generated during
17720 (license license:gpl2)))
17722 (define-public r-abcrlda
17729 (uri (cran-uri "abcrlda" version))
17732 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17733 (properties `((upstream-name . "abcrlda")))
17734 (build-system r-build-system)
17735 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17736 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17738 "This package offers methods to perform @dfn{asymptotically
17739 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17740 cost-sensitive binary classification. The bias-correction is an estimate of
17741 the bias term added to regularized discriminant analysis that minimizes the
17743 (license license:gpl3)))
17745 (define-public r-abemus
17752 (uri (cran-uri "abemus" version))
17755 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17756 (properties `((upstream-name . "abemus")))
17757 (build-system r-build-system)
17759 `(("r-data-table" ,r-data-table)))
17760 (home-page "https://cran.r-project.org/web/packages/abemus/")
17761 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17763 "This package provides an implementation of @dfn{Adaptive Base Error
17764 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17765 platform-specific genetic knowledge and empirical signal to readily detect and
17766 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17767 cell free DNA} (cfDNA).")
17768 (license license:gpl3)))
17770 ;; This package includes minified JavaScript files. When upgrading please
17771 ;; check that there are no new minified JavaScript files.
17772 (define-public r-rintrojs
17774 (name "r-rintrojs")
17779 (uri (cran-uri "rintrojs" version))
17782 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17783 (properties `((upstream-name . "rintrojs")))
17784 (build-system r-build-system)
17786 `(#:modules ((guix build utils)
17787 (guix build r-build-system)
17791 (modify-phases %standard-phases
17792 (add-after 'unpack 'process-javascript
17793 (lambda* (#:key inputs #:allow-other-keys)
17794 (with-directory-excursion "inst/javascript/introjs/"
17798 `((,(assoc-ref inputs "intro.js")
17800 (lambda (sources targets)
17801 (for-each (lambda (source target)
17802 (format #t "Processing ~a --> ~a~%"
17804 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17805 (call-with-output-file target
17807 (dump-port minified port)))))
17808 sources targets))))
17811 `(("uglify-js" ,uglify-js)
17815 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17818 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17820 `(("r-jsonlite" ,r-jsonlite)
17821 ("r-shiny" ,r-shiny)))
17822 (home-page "https://github.com/carlganz/rintrojs")
17823 (synopsis "Wrapper for the Intro.js library")
17825 "This package provides a wrapper for the @url{http://www.introjs.com,
17826 Intro.js} library. This package makes it easy to include step-by-step
17827 introductions, and clickable hints in a Shiny application. It supports both
17828 static introductions in the UI, and programmatic introductions from the
17830 (license license:agpl3+)))
17832 (define-public r-sysfonts
17834 (name "r-sysfonts")
17839 (uri (cran-uri "sysfonts" version))
17842 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17843 (properties `((upstream-name . "sysfonts")))
17844 (build-system r-build-system)
17846 `(("freetype" ,freetype)
17850 `(("pkg-config" ,pkg-config)))
17851 (home-page "https://github.com/yixuan/sysfonts")
17852 (synopsis "Loading fonts into R")
17854 "This is a package to simplify loading of system fonts and Google Fonts
17855 into R, in order to support other packages.")
17856 (license license:gpl2)))
17858 (define-public r-showtextdb
17860 (name "r-showtextdb")
17865 (uri (cran-uri "showtextdb" version))
17868 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17869 (properties `((upstream-name . "showtextdb")))
17870 (build-system r-build-system)
17872 `(("r-sysfonts" ,r-sysfonts)))
17873 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17874 (synopsis "Font files for the 'showtext' package")
17876 "This package provides font files that can be used by the @code{showtext}
17878 (license license:asl2.0)))
17880 (define-public r-showtext
17882 (name "r-showtext")
17887 (uri (cran-uri "showtext" version))
17890 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17891 (properties `((upstream-name . "showtext")))
17892 (build-system r-build-system)
17894 `(("freetype" ,freetype)
17898 `(("r-showtextdb" ,r-showtextdb)
17899 ("r-sysfonts" ,r-sysfonts)))
17901 `(("pkg-config" ,pkg-config)
17902 ("r-knitr" ,r-knitr)))
17903 (home-page "https://github.com/yixuan/showtext")
17904 (synopsis "Using fonts more easily in R graphs")
17906 "This package aims to make it easy to use various types of
17907 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17908 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17909 will be converted into polygons or raster images, hence after the plot has
17910 been created, it no longer relies on the font files. No external software
17911 such as Ghostscript is needed to use this package.")
17912 (license license:asl2.0)))
17914 (define-public r-emojifont
17916 (name "r-emojifont")
17921 (uri (cran-uri "emojifont" version))
17924 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17925 (properties `((upstream-name . "emojifont")))
17926 (build-system r-build-system)
17928 `(("r-ggplot2" ,r-ggplot2)
17929 ("r-proto" ,r-proto)
17930 ("r-showtext" ,r-showtext)
17931 ("r-sysfonts" ,r-sysfonts)))
17932 (home-page "https://guangchuangyu.github.io/emojifont")
17933 (synopsis "Emoji and Font Awesome in R graphics")
17935 "This package enables the use of emoji and the Font Awesome glyphs in
17936 both base and ggplot2 graphics.")
17937 (license license:artistic2.0)))
17939 (define-public r-abstractr
17941 (name "r-abstractr")
17946 (uri (cran-uri "abstractr" version))
17949 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17950 (properties `((upstream-name . "abstractr")))
17951 (build-system r-build-system)
17953 `(("r-colourpicker" ,r-colourpicker)
17954 ("r-emojifont" ,r-emojifont)
17955 ("r-ggplot2" ,r-ggplot2)
17956 ("r-gridextra" ,r-gridextra)
17957 ("r-rintrojs" ,r-rintrojs)
17958 ("r-shiny" ,r-shiny)
17959 ("r-shinythemes" ,r-shinythemes)))
17960 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17961 (synopsis "R-Shiny application for creating visual abstracts")
17963 "This package provides an R Shiny application to create visual abstracts
17964 for original research. A variety of user defined options and formatting are
17966 (license license:gpl3)))
17968 (define-public r-qgam
17975 (uri (cran-uri "qgam" version))
17978 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17979 (properties `((upstream-name . "qgam")))
17980 (build-system r-build-system)
17982 `(("r-doparallel" ,r-doparallel)
17985 ("r-shiny" ,r-shiny)))
17986 (native-inputs `(("r-knitr" ,r-knitr)))
17987 (home-page "https://cran.r-project.org/web/packages/qgam/")
17988 (synopsis "Smooth additive quantile regression models")
17990 "This package provides smooth additive quantile regression models, fitted
17991 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17992 the smoothing parameters are estimated automatically by marginal loss
17993 minimization, while the regression coefficients are estimated using either
17994 PIRLS or Newton algorithm. The learning rate is determined so that the
17995 Bayesian credible intervals of the estimated effects have approximately the
17996 correct coverage. The main function is @code{qgam()} which is similar to
17997 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17998 regression models.")
17999 (license license:gpl2+)))
18001 (define-public r-abtest
18008 (uri (cran-uri "abtest" version))
18011 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
18012 (properties `((upstream-name . "abtest")))
18013 (build-system r-build-system)
18015 `(("r-matrix" ,r-matrix)
18016 ("r-mvtnorm" ,r-mvtnorm)
18017 ("r-plotrix" ,r-plotrix)
18019 ("r-rcolorbrewer" ,r-rcolorbrewer)
18022 ("r-truncnorm" ,r-truncnorm)))
18023 (home-page "https://cran.r-project.org/web/packages/abtest/")
18024 (synopsis "Bayesian A/B testing")
18026 "This package provides functions for Bayesian A/B testing including prior
18027 elicitation options based on Kass and Vaidyanathan (1992)
18028 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
18029 (license license:gpl2+)))
18031 (define-public r-accept
18038 (uri (cran-uri "accept" version))
18041 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
18042 (properties `((upstream-name . "accept")))
18043 (build-system r-build-system)
18045 `(("r-dplyr" ,r-dplyr)
18046 ("r-extrafont" ,r-extrafont)
18048 ("r-plotly" ,r-plotly)
18049 ("r-stringr" ,r-stringr)
18050 ("r-viridis" ,r-viridis)))
18051 (home-page "https://cran.r-project.org/web/packages/accept/")
18052 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
18054 "This package allows clinicians to predict the rate and severity of
18055 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
18056 Disease} (COPD) patients, based on the clinical prediction model published in
18057 Adibi et al. (2019) @url{doi:10.1101/651901}.")
18058 (license license:gpl3)))
18060 (define-public r-smpracticals
18062 (name "r-smpracticals")
18067 (uri (cran-uri "SMPracticals" version))
18070 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
18071 (properties `((upstream-name . "SMPracticals")))
18072 (build-system r-build-system)
18074 `(("r-ellipse" ,r-ellipse)
18077 ("r-survival" ,r-survival)))
18078 (home-page "http://statwww.epfl.ch/davison/SM/")
18079 (synopsis "Practicals for use with Davison (2003) Statistical Models")
18081 "This package contains the datasets and a few functions for use with the
18082 practicals outlined in Appendix A of the book Statistical Models (Davison,
18083 2003, Cambridge University Press). The practicals themselves can be found at
18084 @url{http://statwww.epfl.ch/davison/SM/}.")
18085 (license license:gpl2+)))
18087 (define-public r-fgui
18094 (uri (cran-uri "fgui" version))
18097 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
18098 (properties `((upstream-name . "fgui")))
18099 (build-system r-build-system)
18101 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
18102 (synopsis "Create GUI for R functions")
18104 "Rapidly create a GUI for a function you created by automatically
18105 creating widgets for arguments of the function. This package automatically
18106 parses help routines for context-sensitive help to these arguments. The
18107 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
18108 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
18109 incorporated into the interface for greater customization for the more
18111 ;; Any version of the GPL.
18112 (license (list license:gpl2+ license:gpl3+))))
18114 (define-public r-tcltk2
18121 (uri (cran-uri "tcltk2" version))
18124 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
18125 (properties `((upstream-name . "tcltk2")))
18126 (build-system r-build-system)
18130 (home-page "https://www.sciviews.org/SciViews-R")
18131 (synopsis "Tcl/Tk additions")
18133 "This package provides a series of additional Tcl commands and Tk widgets
18134 with style and various functions to supplement the tcltk package")
18135 (license license:lgpl3)))
18137 (define-public r-accrual
18144 (uri (cran-uri "accrual" version))
18147 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
18148 (properties `((upstream-name . "accrual")))
18149 (build-system r-build-system)
18151 `(("r-fgui" ,r-fgui)
18152 ("r-smpracticals" ,r-smpracticals)
18153 ("r-tcltk2" ,r-tcltk2)))
18154 (home-page "https://cran.r-project.org/web/packages/accrual/")
18155 (synopsis "Bayesian accrual prediction")
18157 "Subject recruitment for medical research is challenging. Slow patient
18158 accrual leads to delay in research. Accrual monitoring during the process of
18159 recruitment is critical. Researchers need reliable tools to manage the
18160 accrual rate. This package provides an implementation of a Bayesian method
18161 that integrates researcher's experience on previous trials and data from the
18162 current study, providing reliable prediction on accrual rate for clinical
18163 studies. It provides functions for Bayesian accrual prediction which can be
18164 easily used by statisticians and clinical researchers.")
18165 (license license:gpl2)))
18167 (define-public r-accrued
18174 (uri (cran-uri "accrued" version))
18177 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
18178 (properties `((upstream-name . "accrued")))
18179 (build-system r-build-system)
18180 (home-page "https://cran.r-project.org/web/packages/accrued/")
18181 (synopsis "Data quality visualization tools for partially accruing data")
18183 "This is a package for visualizing data quality of partially accruing
18185 (license license:gpl3)))
18187 (define-public r-mda
18194 (uri (cran-uri "mda" version))
18197 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
18198 (properties `((upstream-name . "mda")))
18199 (build-system r-build-system)
18200 (propagated-inputs `(("r-class" ,r-class)))
18201 (native-inputs `(("gfortran" ,gfortran)))
18202 (home-page "https://cran.r-project.org/web/packages/mda/")
18203 (synopsis "Mixture and flexible discriminant analysis")
18205 "This is a package for mixture and flexible discriminant analysis,
18206 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
18207 (license license:gpl2)))
18209 (define-public r-elasticnet
18211 (name "r-elasticnet")
18216 (uri (cran-uri "elasticnet" version))
18219 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
18220 (properties `((upstream-name . "elasticnet")))
18221 (build-system r-build-system)
18223 `(("r-lars" ,r-lars)))
18224 (home-page "http://users.stat.umn.edu/~zouxx019/")
18225 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
18227 "This package provides functions for fitting the entire solution path of
18228 the Elastic-Net and also provides functions for estimating sparse Principal
18229 Components. The Lasso solution paths can be computed by the same function.")
18230 (license license:gpl2+)))
18232 (define-public r-sparselda
18234 (name "r-sparselda")
18239 (uri (cran-uri "sparseLDA" version))
18242 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
18243 (properties `((upstream-name . "sparseLDA")))
18244 (build-system r-build-system)
18246 `(("r-elasticnet" ,r-elasticnet)
18249 (home-page "https://www.imm.dtu.dk/~lkhc/")
18250 (synopsis "Sparse discriminant analysis")
18252 "This package performs sparse linear discriminant analysis for Gaussians
18253 and mixture of Gaussian models.")
18254 (license license:gpl2+)))
18256 (define-public r-accsda
18263 (uri (cran-uri "accSDA" version))
18266 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
18267 (properties `((upstream-name . "accSDA")))
18268 (build-system r-build-system)
18270 `(("r-ggplot2" ,r-ggplot2)
18271 ("r-ggthemes" ,r-ggthemes)
18272 ("r-gridextra" ,r-gridextra)
18274 ("r-rarpack" ,r-rarpack)
18275 ("r-sparselda" ,r-sparselda)))
18276 (home-page "https://github.com/gumeo/accSDA/wiki")
18277 (synopsis "Accelerated sparse discriminant analysis")
18279 "This package provides an implementation of sparse linear discriminant
18280 analysis, which is a supervised classification method for multiple classes.
18281 Various novel optimization approaches to this problem are implemented
18282 including @dfn{alternating direction method of multipliers} (ADMM),
18283 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
18284 Functions for performing cross validation are also supplied along with basic
18285 prediction and plotting functions. @dfn{Sparse zero variance
18286 discriminant} (SZVD) analysis is also included in the package.")
18287 (license license:gpl2+)))
18289 (define-public r-ace2fastq
18291 (name "r-ace2fastq")
18296 (uri (cran-uri "ace2fastq" version))
18299 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
18300 (properties `((upstream-name . "ace2fastq")))
18301 (build-system r-build-system)
18303 `(("r-stringr" ,r-stringr)))
18304 (home-page "https://github.com/c5sire/ace2fastq")
18305 (synopsis "ACE file to FASTQ converter")
18307 "The ACE file format is used in genomics to store contigs from sequencing
18308 machines. This tools converts it into FASTQ format. Both formats contain the
18309 sequence characters and their corresponding quality information. Unlike the
18310 FASTQ file, the ACE file stores the quality values numerically. The
18311 conversion algorithm uses the standard Sanger formula. The package
18312 facilitates insertion into pipelines, and content inspection.")
18313 (license license:gpl3)))
18315 (define-public r-rngwell
18322 (uri (cran-uri "rngWELL" version))
18325 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
18326 (properties `((upstream-name . "rngWELL")))
18327 (build-system r-build-system)
18328 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
18329 (synopsis "Toolbox for WELL random number generators")
18331 "This is a dedicated package to WELL pseudo random generators, which were
18332 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
18333 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
18334 (license license:bsd-3)))
18336 (define-public r-randtoolbox
18338 (name "r-randtoolbox")
18343 (uri (cran-uri "randtoolbox" version))
18346 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
18347 (properties `((upstream-name . "randtoolbox")))
18348 (build-system r-build-system)
18350 `(("r-rngwell" ,r-rngwell)))
18352 `(("gfortran" ,gfortran)))
18353 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18354 (synopsis "Toolbox for pseudo and quasi random number generation")
18356 "This package provides
18359 @item pseudo random generators, such as general linear
18360 congruential generators, multiple recursive generators and generalized
18361 feedback shift register (SF-Mersenne Twister algorithm and WELL
18364 @item quasi random generators, such as the Torus algorithm, the Sobol
18365 sequence, the Halton sequence (including the Van der Corput sequence), and
18367 @item some generator tests: the gap test, the serial test, the poker test.
18370 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18371 (license license:bsd-3)))
18373 (define-public r-lhs
18380 (uri (cran-uri "lhs" version))
18383 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
18384 (properties `((upstream-name . "lhs")))
18385 (build-system r-build-system)
18386 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18388 `(("r-knitr" ,r-knitr)))
18389 (home-page "https://github.com/bertcarnell/lhs")
18390 (synopsis "Latin Hypercube Samples")
18392 "This package provides a number of methods for creating and augmenting
18393 Latin Hypercube Samples.")
18394 (license license:gpl3)))
18396 (define-public r-acebayes
18398 (name "r-acebayes")
18403 (uri (cran-uri "acebayes" version))
18406 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
18407 (properties `((upstream-name . "acebayes")))
18408 (build-system r-build-system)
18410 `(("r-compare" ,r-compare)
18412 ("r-randtoolbox" ,r-randtoolbox)
18414 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18415 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18416 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18418 "Finding an optimal Bayesian experimental design involves maximizing an
18419 objective function given by the expectation of some appropriately chosen
18420 utility function with respect to the joint distribution of unknown
18421 quantities (including responses). This objective function is usually not
18422 available in closed form and the design space can be continuous and of high
18423 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18424 to maximise an approximation to the expectation of the utility function.")
18425 (license license:gpl2)))
18427 (define-public r-acet
18434 (uri (cran-uri "ACEt" version))
18437 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
18438 (properties `((upstream-name . "ACEt")))
18439 (build-system r-build-system)
18444 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18445 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18446 (synopsis "Estimating dynamic heritability and twin model comparison")
18448 "This package supports twin models that are able to estimate the dynamic
18449 behaviour of the variance components in the classical twin models with respect
18450 to age using B-splines and P-splines.")
18451 (license license:gpl2+)))
18453 (define-public r-acfmperiod
18455 (name "r-acfmperiod")
18460 (uri (cran-uri "acfMPeriod" version))
18463 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18464 (properties `((upstream-name . "acfMPeriod")))
18465 (build-system r-build-system)
18467 `(("r-mass" ,r-mass)))
18468 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18469 (synopsis "Estimation of the ACF from the M-periodogram")
18471 "This package support non-robust and robust computations of the sample
18472 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18473 univariate and multivariate processes. The methodology consists in reversing
18474 the diagonalization procedure involving the periodogram or the
18475 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18476 ACOVF or the ACF as discussed in Fuller (1995)
18477 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18478 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18479 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18480 (license license:gpl2+)))
18482 (define-public r-gamlss-data
18484 (name "r-gamlss-data")
18489 (uri (cran-uri "gamlss.data" version))
18492 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18493 (properties `((upstream-name . "gamlss.data")))
18494 (build-system r-build-system)
18495 (home-page "http://www.gamlss.org/")
18496 (synopsis "GAMLSS data")
18498 "This package provides data used as examples to demonstrate GAMLSS
18500 ;; Either version of the license
18501 (license (list license:gpl2 license:gpl3))))
18503 (define-public r-gamlss
18510 (uri (cran-uri "gamlss" version))
18513 "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
18514 (properties `((upstream-name . "gamlss")))
18515 (build-system r-build-system)
18517 `(("r-gamlss-data" ,r-gamlss-data)
18518 ("r-gamlss-dist" ,r-gamlss-dist)
18521 ("r-survival" ,r-survival)))
18522 (home-page "http://www.gamlss.org/")
18523 (synopsis "Generalized additive models for location scale and shape")
18525 "This package provides functions for fitting the generalized additive
18526 models for location scale and shape introduced by Rigby and
18527 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18528 use a distributional regression approach where all the parameters of the
18529 conditional distribution of the response variable are modelled using
18530 explanatory variables.")
18531 ;; Either version of the license
18532 (license (list license:gpl2 license:gpl3))))
18534 (define-public r-acid
18541 (uri (cran-uri "acid" version))
18544 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18545 (properties `((upstream-name . "acid")))
18546 (build-system r-build-system)
18548 `(("r-gamlss" ,r-gamlss)
18549 ("r-gamlss-dist" ,r-gamlss-dist)
18550 ("r-hmisc" ,r-hmisc)))
18551 (home-page "https://cran.r-project.org/web/packages/acid/")
18552 (synopsis "Analysing conditional income distributions")
18554 "This package provides functions for the analysis of income distributions
18555 for subgroups of the population as defined by a set of variables like age,
18556 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18557 distribution as well as functions for moments, inequality measures, entropy
18558 measures and polarisation measures of income distributions. This package thus
18559 aides the analysis of income inequality by offering tools for the exploratory
18560 analysis of income distributions at the disaggregated level.")
18561 (license license:gpl3)))
18563 (define-public r-acm4r
18570 (uri (cran-uri "acm4r" version))
18573 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18574 (properties `((upstream-name . "acm4r")))
18575 (build-system r-build-system)
18576 (propagated-inputs `(("r-mass" ,r-mass)))
18577 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18578 (synopsis "Align-and-count method comparisons of RFLP data")
18580 "This is a package to compare sequence fragment lengths or molecular
18581 weights from pairs of lanes. The number of matching bands in the
18582 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18583 the align-and-count method.")
18584 ;; Any version of the GPL
18585 (license (list license:gpl2+ license:gpl3+))))
18587 (define-public r-filematrix
18589 (name "r-filematrix")
18594 (uri (cran-uri "filematrix" version))
18597 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18598 (properties `((upstream-name . "filematrix")))
18599 (build-system r-build-system)
18600 ;; These inputs are needed for vignettes
18602 `(("r-knitr" ,r-knitr)
18603 ("r-rmarkdown" ,r-rmarkdown)
18604 ("pandoc-citeproc" ,pandoc-citeproc)))
18605 (home-page "https://github.com/andreyshabalin/filematrix")
18606 (synopsis "File-backed matrix class with convenient read and write access")
18608 "This package provides an interface for working with large matrices
18609 stored in files, not in computer memory. It supports multiple non-character
18610 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18611 byte real values). Access to parts of the matrix is done by indexing, exactly
18612 as with usual R matrices. It supports very large matrices; the package has
18613 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18614 columns, ad allows for quick addition of extra columns to a filematrix.")
18615 (license license:lgpl3)))
18617 (define-public r-acmeeqtl
18619 (name "r-acmeeqtl")
18624 (uri (cran-uri "ACMEeqtl" version))
18627 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18628 (properties `((upstream-name . "ACMEeqtl")))
18629 (build-system r-build-system)
18631 `(("r-filematrix" ,r-filematrix)))
18632 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18633 (synopsis "Estimation of interpretable eQTL effect sizes")
18635 "This package provides a non-linear model, termed ACME, that reflects a
18636 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18637 With non-linear least-squares algorithm the maximum likelihood parameters can
18638 be estimated. The ACME model provides interpretable effect size estimates and
18639 p-values with well controlled Type-I error.")
18640 (license license:lgpl3)))
18642 (define-public r-acmer
18649 (uri (cran-uri "acmeR" version))
18652 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18653 (properties `((upstream-name . "acmeR")))
18654 (build-system r-build-system)
18655 (propagated-inputs `(("r-foreign" ,r-foreign)))
18656 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18657 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18659 "This package provides an implementation of the ACME estimator, described
18660 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18661 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18662 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18663 as carcasses age; variable bleed-through at successive searches; and interval
18664 mortality estimates. The package provides, based on search data, functions
18665 for estimating the mortality inflation factor in Frequentist and Bayesian
18667 (license license:expat)))
18669 (define-public r-r-huge
18676 (uri (cran-uri "R.huge" version))
18679 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18680 (properties `((upstream-name . "R.huge")))
18681 (build-system r-build-system)
18683 `(("r-r-methodss3" ,r-r-methodss3)
18685 ("r-r-utils" ,r-r-utils)))
18686 (home-page "https://github.com/HenrikBengtsson/R.huge")
18687 (synopsis "Methods for accessing huge amounts of data")
18689 "This is a deprecated package for accessing huge amounts of data.
18690 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18691 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18692 the @code{aroma.affymetrix} package.")
18693 (license license:lgpl2.1+)))
18695 (define-public r-r-filesets
18697 (name "r-r-filesets")
18702 (uri (cran-uri "R.filesets" version))
18705 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18706 (properties `((upstream-name . "R.filesets")))
18707 (build-system r-build-system)
18709 `(("r-digest" ,r-digest)
18710 ("r-r-cache" ,r-r-cache)
18711 ("r-r-methodss3" ,r-r-methodss3)
18713 ("r-r-utils" ,r-r-utils)))
18714 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18715 (synopsis "Easy handling of and access to files")
18717 "This package provides classes and methods to locate, setup, subset,
18718 navigate and iterate file sets, i.e. sets of files located in one or more
18719 directories on the file system. The API is designed such that these classes
18720 can be extended via inheritance to provide a richer API for special file
18721 formats. Moreover, a specific name format is defined such that filenames and
18722 directories can be considered to have full names which consists of a name
18723 followed by comma-separated tags. This adds additional flexibility to
18724 identify file sets and individual files.")
18725 (license license:lgpl2.1+)))
18727 (define-public r-r-devices
18729 (name "r-r-devices")
18734 (uri (cran-uri "R.devices" version))
18737 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18738 (properties `((upstream-name . "R.devices")))
18739 (build-system r-build-system)
18741 `(("r-base64enc" ,r-base64enc)
18742 ("r-r-methodss3" ,r-r-methodss3)
18744 ("r-r-utils" ,r-r-utils)))
18745 (home-page "https://github.com/HenrikBengtsson/R.devices")
18746 (synopsis "Unified handling of graphics devices")
18748 "This package provides functions for creating plots and image files in a
18749 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18750 Default device options as well as scales and aspect ratios are controlled in a
18751 uniform way across all device types. Switching output format requires minimal
18752 changes in code. This package is ideal for large-scale batch processing,
18753 because it will never leave open graphics devices or incomplete image files
18754 behind, even on errors or user interrupts.")
18755 (license license:lgpl2.1+)))
18757 (define-public r-acnr
18764 (uri (cran-uri "acnr" version))
18767 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18768 (properties `((upstream-name . "acnr")))
18769 (build-system r-build-system)
18770 (home-page "https://github.com/mpierrejean/acnr")
18771 (synopsis "Annotated copy-number regions")
18773 "This package provides SNP array data from different types of copy-number
18774 regions. These regions were identified manually by the authors of the package
18775 and may be used to generate realistic data sets with known truth.")
18776 (license license:lgpl2.1+)))
18778 (define-public r-acopula
18785 (uri (cran-uri "acopula" version))
18788 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18789 (properties `((upstream-name . "acopula")))
18790 (build-system r-build-system)
18791 (home-page "https://cran.r-project.org/web/packages/acopula/")
18792 (synopsis "Modelling dependence with multivariate Archimax copulas")
18794 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18795 package provides definitions of several parametric families of generator and
18796 dependence function, computes CDF and PDF, estimates parameters, tests for
18797 goodness of fit, generates random sample and checks copula properties for
18798 custom constructs. In the 2-dimensional case explicit formulas for density
18799 are used, contrary to higher dimensions when all derivatives are linearly
18800 approximated. Several non-archimax families (normal, FGM, Plackett) are
18801 provided as well.")
18802 (license license:gpl2)))
18804 (define-public r-tuner
18811 (uri (cran-uri "tuneR" version))
18814 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18815 (properties `((upstream-name . "tuneR")))
18816 (build-system r-build-system)
18817 (propagated-inputs `(("r-signal" ,r-signal)))
18818 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18819 (synopsis "Analysis of music and speech")
18821 "This is a package for the analysis of music and speech. Analyze music
18822 and speech, extract features like MFCCs, handle wave files and their
18823 representation in various ways, read MP3, read MIDI, perform steps of a
18824 transcription, ...")
18825 ;; Either of these versions.
18826 (license (list license:gpl2 license:gpl3))))
18828 (define-public r-seewave
18835 (uri (cran-uri "seewave" version))
18838 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18839 (properties `((upstream-name . "seewave")))
18840 (build-system r-build-system)
18842 `(("libsndfile" ,libsndfile)))
18844 `(("r-tuner" ,r-tuner)))
18845 (home-page "http://rug.mnhn.fr/seewave")
18846 (synopsis "Sound analysis and synthesis")
18848 "This package provides functions for analysing, manipulating, displaying,
18849 editing and synthesizing time waves (particularly sound). This package
18850 processes time analysis (oscillograms and envelopes), spectral content,
18851 resonance quality factor, entropy, cross correlation and autocorrelation,
18852 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18853 and 3D spectrograms and many other analyses.")
18854 (license license:gpl2+)))
18856 (define-public r-acousticndlcoder
18858 (name "r-acousticndlcoder")
18863 (uri (cran-uri "AcousticNDLCodeR" version))
18866 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18868 `((upstream-name . "AcousticNDLCodeR")))
18869 (build-system r-build-system)
18871 `(("r-seewave" ,r-seewave)
18872 ("r-tuner" ,r-tuner)
18874 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18875 (synopsis "Coding sound files for use with NDL")
18877 "Make acoustic cues to use with the R package @code{ndl}.
18878 The package implements functions used in the PLoS ONE paper \"Words from
18879 spontaneous conversational speech can be recognized with human-like accuracy
18880 by an error-driven learning algorithm that discriminates between meanings
18881 straight from smart acoustic features, bypassing the phoneme as recognition
18882 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18883 (license license:gpl2+)))
18885 (define-public r-acp
18892 (uri (cran-uri "acp" version))
18895 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18896 (properties `((upstream-name . "acp")))
18897 (build-system r-build-system)
18899 `(("r-quantmod" ,r-quantmod)
18900 ("r-tseries" ,r-tseries)))
18901 (home-page "https://cran.r-project.org/web/packages/acp/")
18902 (synopsis "Autoregressive conditional Poisson")
18904 "This package supports the analysis of count data exhibiting
18905 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18906 model (ACP(p,q)) proposed by Heinen (2003).")
18907 (license license:gpl2)))
18909 (define-public r-ada
18916 (uri (cran-uri "ada" version))
18919 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18920 (properties `((upstream-name . "ada")))
18921 (build-system r-build-system)
18922 (propagated-inputs `(("r-rpart" ,r-rpart)))
18923 (home-page "https://cran.r-project.org/web/packages/ada/")
18924 (synopsis "Stochastic boosting")
18926 "This package provides a straightforward, well-documented, and broad
18927 boosting routine for classification, ideally suited for small to
18928 moderate-sized data sets. It performs discrete, real, and gentle boost under
18929 both exponential and logistic loss on a given data set.")
18930 ;; Any version of the GPL.
18931 (license (list license:gpl2+ license:gpl3+))))
18933 (define-public r-genalg
18940 (uri (cran-uri "genalg" version))
18943 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18944 (properties `((upstream-name . "genalg")))
18945 (build-system r-build-system)
18946 (home-page "https://github.com/egonw/genalg")
18947 (synopsis "R based genetic algorithm")
18949 "This package provides an R based genetic algorithm for binary and
18950 floating point chromosomes.")
18951 (license license:gpl2)))
18953 (define-public r-kernelfactory
18955 (name "r-kernelfactory")
18960 (uri (cran-uri "kernelFactory" version))
18963 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18964 (properties `((upstream-name . "kernelFactory")))
18965 (build-system r-build-system)
18968 ("r-genalg" ,r-genalg)
18969 ("r-kernlab" ,r-kernlab)
18970 ("r-randomforest" ,r-randomforest)))
18971 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18972 (synopsis "Ensemble of kernel machines")
18974 "Kernel factory is an ensemble method where each base classifier (random
18975 forest) is fit on the kernel matrix of a subset of the training data.")
18976 (license license:gpl2+)))
18978 (define-public r-dummies
18985 (uri (cran-uri "dummies" version))
18988 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18989 (properties `((upstream-name . "dummies")))
18990 (build-system r-build-system)
18991 (home-page "https://decisionpatterns.com")
18992 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18994 "This package lets you expand factors, characters and other eligible
18995 classes into dummy/indicator variables.")
18996 (license license:gpl2+)))
18998 (define-public r-acrm
19005 (uri (cran-uri "aCRM" version))
19008 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
19009 (properties `((upstream-name . "aCRM")))
19010 (build-system r-build-system)
19013 ("r-dummies" ,r-dummies)
19014 ("r-kernelfactory" ,r-kernelfactory)
19015 ("r-randomforest" ,r-randomforest)))
19016 (home-page "https://cran.r-project.org/web/packages/aCRM/")
19017 (synopsis "Convenience functions for analytical customer relationship management")
19019 "This package provides convenience functions for data preparation and
19020 modeling often used in @dfn{analytical customer relationship
19021 management} (aCRM).")
19022 (license license:gpl2+)))
19024 (define-public r-treeclust
19026 (name "r-treeclust")
19031 (uri (cran-uri "treeClust" version))
19034 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
19035 (properties `((upstream-name . "treeClust")))
19036 (build-system r-build-system)
19038 `(("r-cluster" ,r-cluster)
19039 ("r-rpart" ,r-rpart)))
19040 (home-page "https://cran.r-project.org/web/packages/treeClust/")
19041 (synopsis "Cluster distances through trees")
19043 "This package provides tools to create a measure of inter-point
19044 dissimilarity useful for clustering mixed data, and, optionally, perform the
19046 (license license:gpl2+)))
19048 (define-public r-acrosstic
19050 (name "r-acrosstic")
19055 (uri (cran-uri "AcrossTic" version))
19058 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
19059 (properties `((upstream-name . "AcrossTic")))
19060 (build-system r-build-system)
19062 `(("r-lpsolve" ,r-lpsolve)
19063 ("r-treeclust" ,r-treeclust)))
19064 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
19065 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
19067 "This is a package for constructing minimum-cost regular spanning
19068 subgraph as part of a non-parametric two-sample test for equality of
19070 (license license:gpl2+)))
19072 (define-public r-acrt
19079 (uri (cran-uri "acrt" version))
19082 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
19083 (properties `((upstream-name . "acrt")))
19084 (build-system r-build-system)
19086 `(("r-rcpp" ,r-rcpp)
19087 ("r-rcppeigen" ,r-rcppeigen)
19088 ("r-sandwich" ,r-sandwich)))
19089 (home-page "https://cran.r-project.org/web/packages/acrt/")
19090 (synopsis "Autocorrelation robust testing")
19092 "This package provides functions for testing affine hypotheses on the
19093 regression coefficient vector in regression models with autocorrelated
19095 (license license:gpl2)))
19097 (define-public r-acs
19104 (uri (cran-uri "acs" version))
19107 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
19108 (properties `((upstream-name . "acs")))
19109 (build-system r-build-system)
19111 `(("r-httr" ,r-httr)
19114 ("r-stringr" ,r-stringr)
19116 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
19117 (synopsis "Work with data from the US Census")
19119 "This package provides a general toolkit for downloading, managing,
19120 analyzing, and presenting data from the
19121 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
19122 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
19123 American Community Survey (ACS). Confidence intervals provided with ACS data
19124 are converted to standard errors to be bundled with estimates in complex
19125 @code{acs} objects. The package provides new methods to conduct standard
19126 operations on @code{acs} objects and present/plot data in statistically
19127 appropriate ways.")
19128 (license license:gpl3)))
19130 (define-public r-acss-data
19132 (name "r-acss-data")
19137 (uri (cran-uri "acss.data" version))
19140 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
19141 (properties `((upstream-name . "acss.data")))
19142 (build-system r-build-system)
19143 (home-page "http://complexitycalculator.com/methodology.html")
19144 (synopsis "Data for algorithmic complexity of short strings")
19146 "This is a data only package providing the algorithmic complexity of
19147 short strings, computed using the coding theorem method. For a given set of
19148 symbols in a string, all possible or a large number of random samples of
19149 Turing machines with a given number of states (e.g., 5) and number of symbols
19150 corresponding to the number of symbols in the strings were simulated until
19151 they reached a halting state or failed to end. This package contains data on
19152 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
19153 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
19154 distribution of the halting states.")
19155 (license license:gpl2+)))
19157 (define-public r-acss
19164 (uri (cran-uri "acss" version))
19167 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
19168 (properties `((upstream-name . "acss")))
19169 (build-system r-build-system)
19171 `(("r-acss-data" ,r-acss-data)
19173 (home-page "http://complexitycalculator.com/methodology.html")
19174 (synopsis "Algorithmic complexity for short strings")
19176 "The main purpose of this package is to provide the algorithmic
19177 complexity for short strings, an approximation of the Kolmogorov Complexity of
19178 a short string using the coding theorem method. While the database containing
19179 the complexity is provided in the data only package @code{acss.data}, this
19180 package provides functions accessing the data such as @code{prob_random}
19181 returning the posterior probability that a given string was produced by a
19182 random process. In addition, two traditional (but problematic) measures of
19183 complexity are also provided: entropy and change complexity.")
19184 (license license:gpl2+)))
19186 (define-public r-acswr
19193 (uri (cran-uri "ACSWR" version))
19196 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
19197 (properties `((upstream-name . "ACSWR")))
19198 (build-system r-build-system)
19200 `(("r-mass" ,r-mass)))
19201 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
19202 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
19204 "This is a companion package for the book \"A Course in Statistics with
19205 R\" (ISBN 978-1-119-15272-9.)")
19206 (license license:gpl2)))
19208 (define-public r-alabama
19211 (version "2015.3-1")
19215 (uri (cran-uri "alabama" version))
19218 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
19219 (properties `((upstream-name . "alabama")))
19220 (build-system r-build-system)
19221 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
19222 (home-page "https://cran.r-project.org/web/packages/alabama/")
19223 (synopsis "Constrained nonlinear optimization")
19225 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
19226 Algorithm; it is used for optimizing smooth nonlinear objective functions with
19227 constraints. Linear or nonlinear equality and inequality constraints are
19229 (license license:gpl2+)))
19231 (define-public r-gdina
19238 (uri (cran-uri "GDINA" version))
19241 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
19242 (properties `((upstream-name . "GDINA")))
19243 (build-system r-build-system)
19245 `(("r-alabama" ,r-alabama)
19246 ("r-ggplot2" ,r-ggplot2)
19248 ("r-nloptr" ,r-nloptr)
19249 ("r-numderiv" ,r-numderiv)
19251 ("r-rcpparmadillo" ,r-rcpparmadillo)
19252 ("r-rsolnp" ,r-rsolnp)
19253 ("r-shiny" ,r-shiny)
19254 ("r-shinydashboard" ,r-shinydashboard)))
19256 `(("r-knitr" ,r-knitr)))
19257 (home-page "https://github.com/Wenchao-Ma/GDINA")
19258 (synopsis "Generalized DINA model framework")
19260 "This package provides a set of psychometric tools for cognitive
19261 diagnosis modeling based on the generalized deterministic inputs, noisy and
19262 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
19263 and its extensions, including the sequential G-DINA model by Ma and de la
19264 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
19265 polytomous G-DINA model by Chen and de la Torre
19266 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
19267 distribution can be independent, saturated, higher-order, loglinear smoothed
19268 or structured. Q-matrix validation, item and model fit statistics, model
19269 comparison at test and item level and differential item functioning can also
19270 be conducted. A graphical user interface is also provided.")
19271 (license license:gpl3)))
19273 (define-public r-actcd
19280 (uri (cran-uri "ACTCD" version))
19283 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
19284 (properties `((upstream-name . "ACTCD")))
19285 (build-system r-build-system)
19287 `(("r-gdina" ,r-gdina)
19288 ("r-r-methodss3" ,r-r-methodss3)))
19290 `(("gfortran" ,gfortran)))
19291 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
19292 (synopsis "Asymptotic classification theory for cognitive diagnosis")
19294 "This is a package supporting cluster analysis for cognitive diagnosis
19295 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
19296 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
19297 sum-scores, cluster analysis techniques can be used to classify examinees into
19298 latent classes based on their attribute patterns. In addition to the
19299 algorithms used to classify data, three labeling approaches are proposed to
19300 label clusters so that examinees' attribute profiles can be obtained.")
19301 (license license:gpl2+)))
19303 (define-public r-ineq
19310 (uri (cran-uri "ineq" version))
19313 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
19314 (properties `((upstream-name . "ineq")))
19315 (build-system r-build-system)
19316 (home-page "https://cran.r-project.org/web/packages/ineq/")
19317 (synopsis "Measuring inequality, concentration, and poverty")
19319 "This package provides tools for measuring inequality, concentration, and
19320 poverty measures. It provides both empirical and theoretical Lorenz curves.")
19321 ;; Either of these two versions.
19322 (license (list license:gpl2 license:gpl3))))
19324 (define-public r-actfrag
19331 (uri (cran-uri "ActFrag" version))
19334 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
19335 (properties `((upstream-name . "ActFrag")))
19336 (build-system r-build-system)
19338 `(("r-accelerometry" ,r-accelerometry)
19339 ("r-dplyr" ,r-dplyr)
19341 ("r-survival" ,r-survival)
19342 ("r-tidyr" ,r-tidyr)))
19343 (home-page "https://github.com/junruidi/ActFrag")
19344 (synopsis "Activity fragmentation metrics extraction")
19346 "This package provides functions to extract commonly used fragmentation
19347 metrics to quantify time accumulation strategies based on minute level
19348 actigraphy-measured activity counts data.")
19349 (license license:gpl3)))
19351 (define-public r-ash
19358 (uri (cran-uri "ash" version))
19361 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
19362 (properties `((upstream-name . "ash")))
19363 (build-system r-build-system)
19364 (native-inputs `(("gfortran" ,gfortran)))
19365 (home-page "https://cran.r-project.org/web/packages/ash/")
19366 (synopsis "David Scott's ASH routines")
19368 "This package provides David Scott's ASH routines ported from S-PLUS to
19370 (license license:gpl2+)))
19372 (define-public r-hdrcde
19379 (uri (cran-uri "hdrcde" version))
19382 "0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab"))))
19383 (properties `((upstream-name . "hdrcde")))
19384 (build-system r-build-system)
19387 ("r-ggplot2" ,r-ggplot2)
19388 ("r-kernsmooth" ,r-kernsmooth)
19390 ("r-locfit" ,r-locfit)
19391 ("r-rcolorbrewer" ,r-rcolorbrewer)))
19392 (native-inputs `(("gfortran" ,gfortran)))
19393 (home-page "http://pkg.robjhyndman.com/hdrcde")
19394 (synopsis "Highest density regions and conditional density estimation")
19396 "This is a package for the computation of highest density regions in one
19397 and two dimensions, kernel estimation of univariate density functions
19398 conditional on one covariate, and multimodal regression.")
19399 (license license:gpl3)))
19401 (define-public r-rainbow
19408 (uri (cran-uri "rainbow" version))
19411 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
19412 (properties `((upstream-name . "rainbow")))
19413 (build-system r-build-system)
19415 `(("r-cluster" ,r-cluster)
19416 ("r-colorspace" ,r-colorspace)
19417 ("r-hdrcde" ,r-hdrcde)
19420 ("r-pcapp" ,r-pcapp)))
19421 (home-page "https://cran.r-project.org/web/packages/rainbow/")
19422 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
19424 "This is a package for visualizing functional data and identifying
19425 functional outliers with bagplots, boxplots and rainbow plots.")
19426 (license license:gpl3)))
19428 (define-public r-fds
19435 (uri (cran-uri "fds" version))
19438 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
19439 (properties `((upstream-name . "fds")))
19440 (build-system r-build-system)
19442 `(("r-rainbow" ,r-rainbow)
19443 ("r-rcurl" ,r-rcurl)))
19444 (home-page "https://cran.r-project.org/web/packages/fds/")
19445 (synopsis "Functional data sets")
19446 (description "This package contains a list of functional time series,
19447 sliced functional time series, and functional data sets. Functional time
19448 series is a special type of functional data observed over time. Sliced
19449 functional time series is a special type of functional time series with a time
19450 variable observed over time.")
19451 (license license:gpl2+)))
19453 (define-public r-fda
19456 (version "5.1.5.1")
19460 (uri (cran-uri "fda" version))
19463 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19464 (properties `((upstream-name . "fda")))
19465 (build-system r-build-system)
19467 `(("r-matrix" ,r-matrix)))
19468 (home-page "https://www.functionaldata.org")
19469 (synopsis "Functional data analysis")
19471 "These functions were developed to support functional data analysis as
19472 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19473 Analysis. The package includes data sets and script files working many
19475 (license license:gpl2+)))
19477 (define-public r-actigraphy
19479 (name "r-actigraphy")
19484 (uri (cran-uri "Actigraphy" version))
19487 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19488 (properties `((upstream-name . "Actigraphy")))
19489 (build-system r-build-system)
19491 `(("r-fda" ,r-fda)))
19492 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19493 (synopsis "Actigraphy data analysis")
19495 "This package provides tools for functional linear modeling and analysis
19496 of actigraphy data.")
19497 (license license:asl2.0)))
19499 (define-public r-activedriver
19501 (name "r-activedriver")
19506 (uri (cran-uri "ActiveDriver" version))
19509 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19510 (properties `((upstream-name . "ActiveDriver")))
19511 (build-system r-build-system)
19513 `(("r-mass" ,r-mass)))
19514 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19515 (synopsis "Tools for finding cancer driver proteins")
19517 "This package provides a mutation analysis tool that discovers cancer
19518 driver genes with frequent mutations in protein signalling sites such as
19519 post-translational modifications (phosphorylation, ubiquitination, etc). The
19520 Poisson generalized linear regression model identifies genes where cancer
19521 mutations in signalling sites are more frequent than expected from the
19522 sequence of the entire gene. Integration of mutations with signalling
19523 information helps find new driver genes and propose candidate mechanisms to
19525 (license license:gpl2+)))
19527 (define-public r-activitycounts
19529 (name "r-activitycounts")
19534 (uri (cran-uri "activityCounts" version))
19537 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19539 `((upstream-name . "activityCounts")))
19540 (build-system r-build-system)
19542 `(("r-lubridate" ,r-lubridate)
19543 ("r-magrittr" ,r-magrittr)
19544 ("r-seewave" ,r-seewave)
19545 ("r-signal" ,r-signal)
19546 ("r-tibble" ,r-tibble)))
19547 (home-page "https://github.com/walkabillylab/activityCounts")
19548 (synopsis "Generate ActiLife counts")
19550 "ActiLife generates activity counts from data collected by Actigraph
19551 accelerometers. Actigraph is one of the most common research-grade
19552 accelerometers. There is considerable research validating and developing
19553 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19554 counts are proprietary and difficult to implement if researchers use different
19555 accelerometer brands. The code creates ActiLife counts from raw acceleration
19556 data for different accelerometer brands.")
19557 (license license:gpl3)))
19559 (define-public r-activityindex
19561 (name "r-activityindex")
19566 (uri (cran-uri "ActivityIndex" version))
19569 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19570 (properties `((upstream-name . "ActivityIndex")))
19571 (build-system r-build-system)
19573 `(("r-data-table" ,r-data-table)
19574 ("r-matrixstats" ,r-matrixstats)
19575 ("r-r-utils" ,r-r-utils)))
19576 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19577 (synopsis "Activity Index calculation using raw accelerometry data")
19579 "This is a package to read raw accelerometry from GT3X+ accelerometry
19580 data and plain table data to calculate the Activity Index from Bai et
19581 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19582 (license license:gpl3)))
19584 (define-public r-activpal
19586 (name "r-activpal")
19591 (uri (cran-uri "activPAL" version))
19594 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19595 (properties `((upstream-name . "activPAL")))
19596 (build-system r-build-system)
19598 `(("r-devtools" ,r-devtools)
19599 ("r-dplyr" ,r-dplyr)
19600 ("r-ggplot2" ,r-ggplot2)
19601 ("r-lubridate" ,r-lubridate)
19602 ("r-magrittr" ,r-magrittr)
19603 ("r-tidyr" ,r-tidyr)))
19604 (home-page "https://cran.r-project.org/web/packages/activPAL")
19605 (synopsis "Processing and chart generation from activPAL events files")
19607 "This package contains functions to generate pre-defined summary
19608 statistics from activPAL events files. The package also contains functions to
19609 produce informative graphics that visualize physical activity behaviour and
19610 trends. This includes generating graphs that align physical activity
19611 behaviour with additional time based observations described by other data
19612 sets, such as sleep diaries and continuous glucose monitoring data.")
19613 (license license:gpl3)))
19615 (define-public r-activpalprocessing
19617 (name "r-activpalprocessing")
19622 (uri (cran-uri "activpalProcessing" version))
19625 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19627 `((upstream-name . "activpalProcessing")))
19628 (build-system r-build-system)
19630 `(("r-chron" ,r-chron)))
19631 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19632 (synopsis "Process activPAL events files")
19634 "This package performs estimation of physical activity and sedentary
19635 behavior variables from activPAL events files.")
19636 ;; Either version of the GPL.
19637 (license (list license:gpl2 license:gpl3))))
19639 (define-public r-actogrammr
19641 (name "r-actogrammr")
19646 (uri (cran-uri "actogrammr" version))
19649 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19650 (properties `((upstream-name . "actogrammr")))
19651 (build-system r-build-system)
19653 `(("r-dplyr" ,r-dplyr)
19654 ("r-ggplot2" ,r-ggplot2)
19655 ("r-lubridate" ,r-lubridate)
19656 ("r-readr" ,r-readr)
19657 ("r-tidyr" ,r-tidyr)))
19658 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19659 (synopsis "Read in activity data and plot actograms")
19661 "Read in activity measurements from standard file formats used by
19662 circadian rhythm researchers, currently only ClockLab format, and process and
19663 plot the data. The central type of plot is the actogram, as first described
19664 in \"Activity and distribution of certain wild mice in relation to biotic
19665 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19666 (license license:gpl3)))
19668 (define-public r-expint
19675 (uri (cran-uri "expint" version))
19678 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19679 (properties `((upstream-name . "expint")))
19680 (build-system r-build-system)
19681 (home-page "https://gitlab.com/vigou3/expint")
19682 (synopsis "Exponential integral and incomplete Gamma function")
19684 "This package provides the exponential integrals @code{E_1(x)},
19685 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19686 function @code{G(a, x)} defined for negative values of its first argument.
19687 The package also gives easy access to the underlying C routines through an
19688 API; see the package vignette for details.")
19689 (license license:gpl2+)))
19691 (define-public r-actuar
19698 (uri (cran-uri "actuar" version))
19701 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19702 (properties `((upstream-name . "actuar")))
19703 (build-system r-build-system)
19704 (propagated-inputs `(("r-expint" ,r-expint)))
19705 (home-page "https://gitlab.com/vigou3/actuar")
19706 (synopsis "Actuarial functions and heavy tailed distributions")
19708 "This package provides functions and data sets for actuarial science:
19709 modeling of loss distributions; risk theory and ruin theory; simulation of
19710 compound models, discrete mixtures and compound hierarchical models;
19711 credibility theory. It boasts support for many additional probability
19712 distributions to model insurance loss amounts and loss frequency: 19
19713 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19714 distribution; zero-truncated and zero-modified extensions of the standard
19715 discrete distributions. It also supports phase-type distributions commonly
19716 used to compute ruin probabilities.")
19717 (license license:gpl2+)))
19719 (define-public r-bmp
19726 (uri (cran-uri "bmp" version))
19729 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19730 (properties `((upstream-name . "bmp")))
19731 (build-system r-build-system)
19732 (home-page "https://cran.r-project.org/web/packages/bmp/")
19733 (synopsis "Read Bitmap (BMP) images")
19735 "This package provides pure R tools to read BMP format images. It is
19736 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19737 (license license:gpl2+)))
19739 (define-public r-readbitmap
19741 (name "r-readbitmap")
19746 (uri (cran-uri "readbitmap" version))
19749 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19750 (properties `((upstream-name . "readbitmap")))
19751 (build-system r-build-system)
19753 `(("libjpeg" ,libjpeg-turbo)
19754 ("libpng" ,libpng)))
19759 ("r-tiff" ,r-tiff)))
19760 (home-page "https://github.com/jefferis/readbitmap")
19761 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19763 "This package provides tools to identify and read BMP, JPEG, PNG, and
19764 TIFF format bitmap images. Identification defaults to the use of the magic
19765 number embedded in the file rather than the file extension.")
19766 (license license:gpl2+)))
19768 (define-public r-imager
19775 (uri (cran-uri "imager" version))
19778 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19779 (properties `((upstream-name . "imager")))
19780 (build-system r-build-system)
19783 ("libtiff" ,libtiff)
19787 `(("r-downloader" ,r-downloader)
19788 ("r-igraph" ,r-igraph)
19790 ("r-magrittr" ,r-magrittr)
19792 ("r-purrr" ,r-purrr)
19794 ("r-readbitmap" ,r-readbitmap)
19795 ("r-stringr" ,r-stringr)))
19797 `(("pkg-config" ,pkg-config)
19798 ("r-knitr" ,r-knitr)))
19799 (home-page "https://dahtah.github.io/imager/")
19800 (synopsis "Image processing library")
19802 "This is a package for fast image processing for images in up to 4
19803 dimensions (two spatial dimensions, one time/depth dimension, one color
19804 dimension). It provides most traditional image processing tools (filtering,
19805 morphology, transformations, etc.) as well as various functions for easily
19806 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19807 simple, modern C++ library for image processing.")
19808 (license license:lgpl3)))
19810 (define-public r-acuityview
19812 (name "r-acuityview")
19817 (uri (cran-uri "AcuityView" version))
19820 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19821 (properties `((upstream-name . "AcuityView")))
19822 (build-system r-build-system)
19824 `(("r-fftwtools" ,r-fftwtools)
19825 ("r-imager" ,r-imager)
19826 ("r-plotrix" ,r-plotrix)))
19827 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19828 (synopsis "Display scenes as seen by an animal with less acute vision")
19830 "This package provides a simple method for representing a visual scene as
19831 it may be seen by an animal with less acute vision.")
19832 (license license:gpl2+)))
19834 (define-public r-caret
19841 (uri (cran-uri "caret" version))
19844 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19845 (build-system r-build-system)
19847 `(("r-foreach" ,r-foreach)
19848 ("r-ggplot2" ,r-ggplot2)
19849 ("r-lattice" ,r-lattice)
19850 ("r-modelmetrics" ,r-modelmetrics)
19854 ("r-recipes" ,r-recipes)
19855 ("r-reshape2" ,r-reshape2)
19856 ("r-withr" ,r-withr)))
19858 `(("r-knitr" ,r-knitr)))
19859 (home-page "https://github.com/topepo/caret")
19860 (synopsis "Classification and regression training")
19862 "This package provides miscellaneous functions for training and plotting
19863 classification and regression models.")
19864 (license license:gpl2+)))
19866 (define-public r-adabag
19873 (uri (cran-uri "adabag" version))
19876 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19877 (properties `((upstream-name . "adabag")))
19878 (build-system r-build-system)
19880 `(("r-caret" ,r-caret)
19881 ("r-doparallel" ,r-doparallel)
19882 ("r-foreach" ,r-foreach)
19883 ("r-rpart" ,r-rpart)))
19884 (home-page "https://cran.r-project.org/web/packages/adabag/")
19885 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19887 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19888 Breiman's Bagging algorithm using classification trees as individual
19889 classifiers. Once these classifiers have been trained, they can be used to
19890 predict on new data. Also, cross validation estimation of the error can be
19892 (license license:gpl2+)))
19894 (define-public r-adagio
19901 (uri (cran-uri "adagio" version))
19904 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19905 (properties `((upstream-name . "adagio")))
19906 (build-system r-build-system)
19907 (native-inputs `(("gfortran" ,gfortran)))
19908 (home-page "https://cran.r-project.org/web/packages/adagio/")
19909 (synopsis "Discrete and global optimization routines")
19911 "This package provides methods and algorithms for discrete optimization,
19912 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19913 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19915 (license license:gpl3+)))
19917 (define-public r-univoutl
19919 (name "r-univoutl")
19924 (uri (cran-uri "univOutl" version))
19927 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19928 (properties `((upstream-name . "univOutl")))
19929 (build-system r-build-system)
19931 `(("r-hmisc" ,r-hmisc)
19932 ("r-robustbase" ,r-robustbase)))
19933 (home-page "https://github.com/marcellodo/univOutl")
19934 (synopsis "Detection of univariate outliers")
19936 "This package provides well-known outlier detection techniques in the
19937 univariate case. Methods to deal with skewed distribution are included too.
19938 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19939 historical data is implemented as well. When available, survey weights can be
19940 used in outliers detection.")
19941 (license license:gpl2+)))
19943 (define-public r-tolerance
19945 (name "r-tolerance")
19950 (uri (cran-uri "tolerance" version))
19953 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19954 (properties `((upstream-name . "tolerance")))
19955 (build-system r-build-system)
19957 `(("r-mass" ,r-mass)
19959 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19960 (synopsis "Statistical tolerance intervals and regions")
19962 "This package provides functions for estimating tolerance
19963 limits (intervals) for various univariate distributions (binomial, Cauchy,
19964 discrete Pareto, exponential, two-parameter exponential, extreme value,
19965 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19966 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19967 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19968 nonparametric tolerance intervals, tolerance bands for regression
19969 settings (linear regression, nonlinear regression, nonparametric regression,
19970 and multivariate regression), and analysis of variance tolerance intervals.
19971 Visualizations are also available for most of these settings.")
19972 (license license:gpl2+)))
19974 (define-public r-additivitytests
19976 (name "r-additivitytests")
19981 (uri (cran-uri "additivityTests" version))
19984 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19986 `((upstream-name . "additivityTests")))
19987 (build-system r-build-system)
19988 (home-page "https://github.com/simecek/additivityTests")
19989 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19991 "This package provides an implementation of the Tukey, Mandel,
19992 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19993 (license license:gpl3)))
19995 (define-public r-flexclust
19997 (name "r-flexclust")
20002 (uri (cran-uri "flexclust" version))
20005 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
20006 (properties `((upstream-name . "flexclust")))
20007 (build-system r-build-system)
20009 `(("r-class" ,r-class)
20010 ("r-lattice" ,r-lattice)
20011 ("r-modeltools" ,r-modeltools)))
20012 (home-page "https://cran.r-project.org/web/packages/flexclust/")
20013 (synopsis "Flexible cluster algorithms")
20015 "The main function @code{kcca} implements a general framework for
20016 k-centroids cluster analysis supporting arbitrary distance measures and
20017 centroid computation. Further cluster methods include hard competitive
20018 learning, neural gas, and QT clustering. There are numerous visualization
20019 methods for cluster results (neighborhood graphs, convex cluster hulls,
20020 barcharts of centroids, ...), and bootstrap methods for the analysis of
20021 cluster stability.")
20022 (license license:gpl2)))
20024 (define-public r-biclust
20031 (uri (cran-uri "biclust" version))
20034 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
20035 (properties `((upstream-name . "biclust")))
20036 (build-system r-build-system)
20038 `(("r-additivitytests" ,r-additivitytests)
20039 ("r-colorspace" ,r-colorspace)
20040 ("r-flexclust" ,r-flexclust)
20041 ("r-ggplot2" ,r-ggplot2)
20042 ("r-lattice" ,r-lattice)
20044 ("r-tidyr" ,r-tidyr)))
20045 (home-page "https://cran.r-project.org/web/packages/biclust/")
20046 (synopsis "BiCluster algorithms")
20048 "The main function @code{biclust()} provides several algorithms to find
20049 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
20050 In addition, the package provides methods for data
20051 preprocessing (normalization and discretization), visualization, and
20052 validation of bicluster solutions.")
20053 (license license:gpl3)))
20055 (define-public r-icge
20062 (uri (cran-uri "ICGE" version))
20065 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
20066 (properties `((upstream-name . "ICGE")))
20067 (build-system r-build-system)
20069 `(("r-cluster" ,r-cluster)
20070 ("r-mass" ,r-mass)))
20071 (home-page "https://cran.r-project.org/web/packages/ICGE/")
20072 (synopsis "Cluster estimation and identification of atypical units")
20074 "ICGE is a package that helps to estimate the number of real clusters in
20075 data as well as to identify atypical units. The underlying methods are based
20076 on distances rather than on unit x variables.")
20077 (license license:gpl2+)))
20079 (define-public r-depth
20082 (version "2.1-1.1")
20086 (uri (cran-uri "depth" version))
20089 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
20090 (properties `((upstream-name . "depth")))
20091 (build-system r-build-system)
20093 `(("r-abind" ,r-abind)
20094 ("r-circular" ,r-circular)
20097 `(("gfortran" ,gfortran)))
20098 (home-page "https://cran.r-project.org/web/packages/depth/")
20099 (synopsis "Nonparametric depth functions for multivariate analysis")
20101 "This package provides tools for depth functions methodology applied to
20102 multivariate analysis. Besides allowing calculation of depth values and
20103 depth-based location estimators, the package includes functions or drawing
20104 contour plots and perspective plots of depth functions. Euclidean and
20105 spherical depths are supported.")
20106 (license license:gpl2)))
20108 (define-public r-archetypes
20110 (name "r-archetypes")
20111 (version "2.2-0.1")
20115 (uri (cran-uri "archetypes" version))
20118 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
20119 (properties `((upstream-name . "archetypes")))
20120 (build-system r-build-system)
20122 `(("r-modeltools" ,r-modeltools)
20123 ("r-nnls" ,r-nnls)))
20124 (home-page "https://cran.r-project.org/web/packages/archetypes")
20125 (synopsis "Archetypal analysis")
20127 "The main function @code{archetypes} implements a framework for
20128 archetypal analysis supporting arbitrary problem solving mechanisms for the
20129 different conceptual parts of the algorithm.")
20130 (license license:gpl2+)))
20132 (define-public r-shapes
20139 (uri (cran-uri "shapes" version))
20142 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
20143 (properties `((upstream-name . "shapes")))
20144 (build-system r-build-system)
20146 `(("r-mass" ,r-mass)
20147 ("r-minpack-lm" ,r-minpack-lm)
20149 ("r-scatterplot3d" ,r-scatterplot3d)))
20150 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
20151 (synopsis "Statistical shape analysis")
20153 "This package provides routines for the statistical analysis of landmark
20154 shapes, including Procrustes analysis, graphical displays, principal
20155 components analysis, permutation and bootstrap tests, thin-plate spline
20156 transformation grids and comparing covariance matrices. See Dryden, I.L. and
20157 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
20158 Edition), John Wiley and Sons.")
20159 (license license:gpl2)))
20161 (define-public r-anthropometry
20163 (name "r-anthropometry")
20168 (uri (cran-uri "Anthropometry" version))
20171 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
20172 (properties `((upstream-name . "Anthropometry")))
20173 (build-system r-build-system)
20175 `(("r-archetypes" ,r-archetypes)
20176 ("r-biclust" ,r-biclust)
20177 ("r-cluster" ,r-cluster)
20178 ("r-depth" ,r-depth)
20183 ("r-shapes" ,r-shapes)))
20185 `(("r-knitr" ,r-knitr)))
20186 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
20187 (synopsis "Statistical methods for anthropometric data")
20189 "This package provides statistical methods especially developed to
20190 analyze anthropometric data. These methods are aimed at providing effective
20191 solutions to some commons problems related to Ergonomics and Anthropometry.
20192 They are based on clustering, the statistical concept of data depth,
20193 statistical shape analysis and archetypal analysis.")
20194 (license license:gpl2+)))
20196 (define-public r-adamethods
20198 (name "r-adamethods")
20203 (uri (cran-uri "adamethods" version))
20206 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
20207 (properties `((upstream-name . "adamethods")))
20208 (build-system r-build-system)
20210 `(("r-anthropometry" ,r-anthropometry)
20211 ("r-archetypes" ,r-archetypes)
20213 ("r-foreach" ,r-foreach)
20215 ("r-tolerance" ,r-tolerance)
20216 ("r-univoutl" ,r-univoutl)))
20217 (home-page "https://cran.r-project.org/web/packages/adamethods/")
20218 (synopsis "Archetypoid algorithms and anomaly detection")
20220 "This package is a collection of several algorithms to obtain
20221 archetypoids with small and large databases and with both classical
20222 multivariate data and functional data (univariate and multivariate). Some of
20223 these algorithms also detect anomalies (outliers).")
20224 (license license:gpl2+)))
20226 (define-public r-idpmisc
20233 (uri (cran-uri "IDPmisc" version))
20236 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
20237 (properties `((upstream-name . "IDPmisc")))
20238 (build-system r-build-system)
20240 `(("r-lattice" ,r-lattice)))
20241 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
20242 (synopsis "Functions for data analyses and visualization")
20244 "This package provides different high-level graphics functions for
20245 displaying large datasets, displaying circular data in a very flexible way,
20246 finding local maxima, brewing color ramps, drawing nice arrows, zooming
20247 2D-plots, creating figures with differently colored margin and plot region.
20248 In addition, the package contains auxiliary functions for data manipulation
20249 like omitting observations with irregular values or selecting data by logical
20250 vectors, which include NAs. Other functions are especially useful in
20251 spectroscopy and analyses of environmental data: robust baseline fitting,
20252 finding peaks in spectra, converting humidity measures.")
20253 (license license:gpl3+)))
20255 (define-public r-qqman
20262 (uri (cran-uri "qqman" version))
20265 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
20266 (properties `((upstream-name . "qqman")))
20267 (build-system r-build-system)
20269 `(("r-calibrate" ,r-calibrate)))
20270 (home-page "https://cran.r-project.org/web/packages/qqman/")
20271 (synopsis "Q-Q and Manhattan plots for GWAS data")
20273 "This package allows you to create Q-Q and Manhattan plots for GWAS data
20274 from PLINK results.")
20275 (license license:gpl3)))
20277 (define-public r-ggplot-multistats
20279 (name "r-ggplot-multistats")
20284 (uri (cran-uri "ggplot.multistats" version))
20287 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
20289 `((upstream-name . "ggplot.multistats")))
20290 (build-system r-build-system)
20292 `(("r-ggplot2" ,r-ggplot2)
20293 ("r-hexbin" ,r-hexbin)
20294 ("r-rlang" ,r-rlang)
20295 ("r-scales" ,r-scales)))
20296 (home-page "https://github.com/flying-sheep/ggplot.multistats")
20297 (synopsis "Multiple summary statistics for binned stats/geometries")
20299 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
20300 which functions similar to its singular form, but allows the use of multiple
20301 statistics per bin. Those statistics can be mapped to multiple bin
20303 (license license:gpl3)))
20305 (define-public r-knn-covertree
20307 (name "r-knn-covertree")
20312 (uri (cran-uri "knn.covertree" version))
20315 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
20316 (properties `((upstream-name . "knn.covertree")))
20317 (build-system r-build-system)
20319 `(("r-matrix" ,r-matrix)
20321 ("r-rcppeigen" ,r-rcppeigen)))
20322 (home-page "https://github.com/flying-sheep/knn.covertree")
20323 (synopsis "Accurate kNN Implementation with multiple distance measures")
20325 "Similarly to the FNN package, this package allows calculation of the k
20326 nearest neighbors (kNN) of a data matrix. The implementation is based on
20327 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
20328 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
20329 (license license:agpl3+)))
20331 (define-public r-poibin
20338 (uri (cran-uri "poibin" version))
20341 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
20342 (properties `((upstream-name . "poibin")))
20343 (build-system r-build-system)
20344 (home-page "https://cran.r-project.org/web/packages/poibin/")
20345 (synopsis "Poisson binomial distribution")
20347 "This package provides an implementation of both the exact and
20348 approximation methods for computing the @dfn{cumulative distribution
20349 function} (CDF) of the Poisson binomial distribution. It also provides the
20350 @dfn{probability mass function} (PMF), quantile function, and random number
20351 generation for the Poisson binomial distribution.")
20352 (license license:gpl2)))
20354 (define-public r-diagram
20361 (uri (cran-uri "diagram" version))
20364 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
20365 (properties `((upstream-name . "diagram")))
20366 (build-system r-build-system)
20368 `(("r-shape" ,r-shape)))
20369 (home-page "https://cran.r-project.org/web/packages/diagram/")
20370 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
20372 "This package provides tools to visualize simple graphs (networks) based
20373 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
20374 electrical networks, etc. It also includes supporting material for the book
20375 \"A practical guide to ecological modelling - using R as a simulation
20376 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
20377 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
20378 Francesca Mazzia (2012).")
20379 (license license:gpl2+)))
20381 (define-public r-lim
20388 (uri (cran-uri "LIM" version))
20391 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
20392 (properties `((upstream-name . "LIM")))
20393 (build-system r-build-system)
20395 `(("r-diagram" ,r-diagram)
20396 ("r-limsolve" ,r-limsolve)))
20397 (home-page "https://cran.r-project.org/web/packages/LIM/")
20398 (synopsis "Linear inverse model examples and solution methods")
20400 "This package provides functions that read and solve linear inverse
20401 problems (food web problems, linear programming problems).")
20402 (license license:gpl2+)))
20404 (define-public r-shinycssloaders
20406 (name "r-shinycssloaders")
20411 (uri (cran-uri "shinycssloaders" version))
20414 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
20416 `((upstream-name . "shinycssloaders")))
20417 (build-system r-build-system)
20419 `(("r-digest" ,r-digest)
20421 ("r-shiny" ,r-shiny)))
20422 (home-page "https://github.com/andrewsali/shinycssloaders")
20423 (synopsis "Add CSS loading animations to Shiny outputs")
20425 "This package provides tools to create a lightweight Shiny wrapper for
20426 the css-loaders created by Luke Hass
20427 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
20428 automatically show a loader when the output is (re)calculating.")
20429 (license license:gpl3)))
20431 (define-public r-rsvg
20438 (uri (cran-uri "rsvg" version))
20441 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
20442 (properties `((upstream-name . "rsvg")))
20443 (build-system r-build-system)
20445 `(("librsvg" ,librsvg)
20448 `(("pkg-config" ,pkg-config)
20449 ("r-knitr" ,r-knitr)))
20450 (home-page "https://github.com/jeroen/rsvg#readme")
20451 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20453 "This package allows you to render vector-based SVG images into
20454 high-quality custom-size bitmap arrays using the librsvg2 library. The
20455 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20456 addition, the package can convert images directly to various formats such as
20457 PDF or PostScript.")
20458 (license license:expat)))
20460 (define-public r-influencer
20462 (name "r-influencer")
20467 (uri (cran-uri "influenceR" version))
20470 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20471 (properties `((upstream-name . "influenceR")))
20472 (build-system r-build-system)
20474 `(("r-igraph" ,r-igraph)
20475 ("r-matrix" ,r-matrix)))
20476 (home-page "https://github.com/rcc-uchicago/influenceR")
20477 (synopsis "Tools to quantify structural importance of nodes in a network")
20479 "This package provides functionality to compute various node centrality
20480 measures on networks. Included are functions to compute betweenness
20481 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20482 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20483 algorithm to identify key players, and Valente's bridging metric. The
20484 betweenness, Key Players, and bridging implementations are parallelized with
20486 (license license:gpl2)))
20488 (define-public r-emplik
20495 (uri (cran-uri "emplik" version))
20498 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20499 (properties `((upstream-name . "emplik")))
20500 (build-system r-build-system)
20502 `(("r-quantreg" ,r-quantreg)))
20503 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20504 (synopsis "Empirical likelihood ratio for censored/truncated data")
20506 "This package provides empirical likelihood ratio tests for
20507 means/quantiles/hazards from possibly censored and/or truncated data. It also
20509 (license license:gpl2+)))
20511 (define-public r-imputeyn
20513 (name "r-imputeyn")
20518 (uri (cran-uri "imputeYn" version))
20521 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20522 (properties `((upstream-name . "imputeYn")))
20523 (build-system r-build-system)
20525 `(("r-boot" ,r-boot)
20526 ("r-emplik" ,r-emplik)
20527 ("r-mvtnorm" ,r-mvtnorm)
20528 ("r-quadprog" ,r-quadprog)
20529 ("r-survival" ,r-survival)))
20530 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20531 (synopsis "Impute last largest censored observation under weighted least squares")
20533 "This package allows for the imputation of the last largest censored
20534 observantions. This method brings less bias and more efficient estimates for
20536 (license license:gpl2)))
20538 (define-public r-adapenetclass
20540 (name "r-adapenetclass")
20545 (uri (cran-uri "AdapEnetClass" version))
20548 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20549 (properties `((upstream-name . "AdapEnetClass")))
20550 (build-system r-build-system)
20552 `(("r-glmnet" ,r-glmnet)
20553 ("r-imputeyn" ,r-imputeyn)
20555 ("r-quadprog" ,r-quadprog)))
20556 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20557 (synopsis "Class of adaptive elastic net methods for censored data")
20559 "This package provides methods for variable selection for AFT models.")
20560 (license license:gpl2)))
20562 (define-public r-flock
20569 (uri (cran-uri "flock" version))
20572 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20573 (properties `((upstream-name . "flock")))
20574 (build-system r-build-system)
20575 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20576 (home-page "https://cran.r-project.org/web/packages/flock/")
20577 (synopsis "Process synchronization using file locks")
20579 "This package implements synchronization between R processes (spawned by
20580 using the @code{parallel} package for instance) using file locks. It supports
20581 both exclusive and shared locking.")
20582 (license license:asl2.0)))
20584 (define-public r-archivist
20586 (name "r-archivist")
20591 (uri (cran-uri "archivist" version))
20594 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20595 (properties `((upstream-name . "archivist")))
20596 (build-system r-build-system)
20599 ("r-digest" ,r-digest)
20600 ("r-flock" ,r-flock)
20602 ("r-lubridate" ,r-lubridate)
20603 ("r-magrittr" ,r-magrittr)
20604 ("r-rcurl" ,r-rcurl)
20605 ("r-rsqlite" ,r-rsqlite)))
20606 (home-page "https://pbiecek.github.io/archivist/")
20607 (synopsis "Tools for storing, restoring and searching for R objects")
20609 "Data exploration and modelling is a process in which a lot of data
20610 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20611 statistical models, different versions of data sets and different versions of
20612 results. Archivist helps to store and manage artifacts created in R. It
20613 allows you to store selected artifacts as binary files together with their
20614 metadata and relations. Archivist allows sharing artifacts with others. It
20615 can look for already created artifacts by using its class, name, date of the
20616 creation or other properties. It also makes it easy to restore such
20618 (license license:gpl2)))
20620 (define-public r-versions
20622 (name "r-versions")
20627 (uri (cran-uri "versions" version))
20630 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20631 (properties `((upstream-name . "versions")))
20632 (build-system r-build-system)
20633 (home-page "https://cran.r-project.org/web/packages/versions/")
20634 (synopsis "Query and install specific versions of CRAN packages")
20636 "This package allows you to install specified versions of R packages
20637 hosted on CRAN and provides functions to list available versions and the
20638 versions of currently installed packages.")
20639 (license license:bsd-3)))
20641 (define-public r-adapr
20648 (uri (cran-uri "adapr" version))
20651 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20652 (properties `((upstream-name . "adapr")))
20653 (build-system r-build-system)
20655 `(("r-archivist" ,r-archivist)
20656 ("r-devtools" ,r-devtools)
20657 ("r-digest" ,r-digest)
20658 ("r-doparallel" ,r-doparallel)
20659 ("r-gdata" ,r-gdata)
20660 ("r-ggplot2" ,r-ggplot2)
20661 ("r-git2r" ,r-git2r)
20662 ("r-igraph" ,r-igraph)
20663 ("r-knitr" ,r-knitr)
20664 ("r-plotly" ,r-plotly)
20666 ("r-rmarkdown" ,r-rmarkdown)
20667 ("r-shiny" ,r-shiny)
20668 ("r-shinydashboard" ,r-shinydashboard)
20669 ("r-versions" ,r-versions)))
20670 (home-page "https://cran.r-project.org/web/packages/adapr/")
20671 (synopsis "Implementation of an accountable data analysis process")
20673 "This package tracks reading and writing within R scripts that are
20674 organized into a directed acyclic graph. It contains an interactive Shiny
20675 application @code{adaprApp()}. It uses Git and file hashes to track version
20676 histories of inputs and outputs.")
20677 (license license:lgpl2.0)))
20679 (define-public r-adapsamp
20681 (name "r-adapsamp")
20686 (uri (cran-uri "AdapSamp" version))
20689 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20690 (properties `((upstream-name . "AdapSamp")))
20691 (build-system r-build-system)
20692 (propagated-inputs `(("r-pracma" ,r-pracma)))
20693 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20694 (synopsis "Adaptive sampling algorithms")
20696 "For distributions whose probability density functions are log-concave,
20697 the adaptive rejection sampling algorithm can be used to build envelope
20698 functions for sampling. For others, the modified adaptive rejection sampling
20699 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20700 adaptive slice sampling algorithm can be used. This R package mainly includes
20701 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20702 @code{rASS()}. These functions can realize sampling based on the algorithms
20704 (license license:gpl2)))
20706 (define-public r-adaptalint
20708 (name "r-adaptalint")
20713 (uri (cran-uri "adaptalint" version))
20716 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20717 (properties `((upstream-name . "adaptalint")))
20718 (build-system r-build-system)
20720 `(("r-dplyr" ,r-dplyr)
20721 ("r-lintr" ,r-lintr)
20722 ("r-purrr" ,r-purrr)))
20723 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20724 (synopsis "Check R code style")
20726 "This package provides tools to infer the code style (which style rules
20727 are followed and which ones are not) from one package and use it to check
20728 another. This makes it easier to find and correct the most important problems
20730 (license license:gpl3)))
20732 (define-public r-fracdiff
20734 (name "r-fracdiff")
20739 (uri (cran-uri "fracdiff" version))
20742 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20743 (properties `((upstream-name . "fracdiff")))
20744 (build-system r-build-system)
20745 (home-page "https://github.com/mmaechler/fracdiff")
20747 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20749 "This package provides tools for the maximum likelihood estimation of the
20750 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20751 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20752 (license license:gpl2+)))
20754 (define-public r-forecast
20756 (name "r-forecast")
20761 (uri (cran-uri "forecast" version))
20764 "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
20765 (properties `((upstream-name . "forecast")))
20766 (build-system r-build-system)
20768 `(("r-colorspace" ,r-colorspace)
20769 ("r-fracdiff" ,r-fracdiff)
20770 ("r-ggplot2" ,r-ggplot2)
20771 ("r-lmtest" ,r-lmtest)
20772 ("r-magrittr" ,r-magrittr)
20775 ("r-rcpparmadillo" ,r-rcpparmadillo)
20776 ("r-timedate" ,r-timedate)
20777 ("r-tseries" ,r-tseries)
20781 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20782 (home-page "https://pkg.robjhyndman.com/forecast/")
20783 (synopsis "Forecasting functions for time series and linear models")
20785 "This package provides methods and tools for displaying and analysing
20786 univariate time series forecasts including exponential smoothing via state
20787 space models and automatic ARIMA modelling.")
20788 (license license:gpl3)))
20790 (define-public r-xmisc
20797 (uri (cran-uri "Xmisc" version))
20800 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20801 (properties `((upstream-name . "Xmisc")))
20802 (build-system r-build-system)
20803 (home-page "https://cran.r-project.org/package=Xmisc")
20805 "Xiaobei's miscellaneous classes and functions")
20807 "This package provides Xiaobei's miscellaneous classes and functions,
20808 which are useful when developing R packages for @dfn{object oriented
20809 programming} (OOP) using R Reference Class.")
20810 (license license:gpl2+)))
20812 (define-public r-proxyc
20819 (uri (cran-uri "proxyC" version))
20822 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20823 (properties `((upstream-name . "proxyC")))
20824 (build-system r-build-system)
20826 `(("r-matrix" ,r-matrix)
20828 ("r-rcpparmadillo" ,r-rcpparmadillo)
20829 ("r-rcppparallel" ,r-rcppparallel)))
20830 (home-page "https://cran.r-project.org/package=proxyC")
20831 (synopsis "Compute proximity in large sparse matrices")
20833 "This package provides efficient tools to compute the proximity between
20834 rows or columns of large matrices. Functions are optimised for large sparse
20835 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20836 similarity/distance measures, computation of correlation, cosine similarity
20837 and Euclidean distance is particularly fast.")
20838 (license license:gpl3)))
20840 (define-public r-isocodes
20842 (name "r-isocodes")
20843 (version "2020.03.16")
20847 (uri (cran-uri "ISOcodes" version))
20850 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20851 (properties `((upstream-name . "ISOcodes")))
20852 (build-system r-build-system)
20853 (home-page "https://cran.r-project.org/package=ISOcodes")
20854 (synopsis "Selected ISO codes")
20856 "This package provides ISO language, territory, currency, script and
20857 character codes. It provides ISO 639 language codes, ISO 3166 territory
20858 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20859 character codes as well as the UN M.49 area codes.")
20860 (license license:gpl2)))
20862 (define-public r-stopwords
20864 (name "r-stopwords")
20869 (uri (cran-uri "stopwords" version))
20872 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20873 (properties `((upstream-name . "stopwords")))
20874 (build-system r-build-system)
20876 `(("r-desc" ,r-desc)
20877 ("r-isocodes" ,r-isocodes)
20878 ("r-usethis" ,r-usethis)))
20879 (home-page "https://github.com/quanteda/stopwords")
20880 (synopsis "Multilingual stopword lists")
20882 "This package provides multiple sources of stopwords, for use in text
20883 analysis and natural language processing.")
20884 (license license:expat)))
20886 (define-public r-spacyr
20893 (uri (cran-uri "spacyr" version))
20896 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20897 (properties `((upstream-name . "spacyr")))
20898 (build-system r-build-system)
20900 `(("r-data-table" ,r-data-table)
20901 ("r-reticulate" ,r-reticulate)))
20902 (home-page "https://spacyr.quanteda.io")
20903 (synopsis "R wrapper for the spaCy NLP library")
20905 "This package provides an R wrapper to the Python @dfn{natural language
20906 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20907 (license license:gpl3)))
20909 (define-public r-snowballc
20911 (name "r-snowballc")
20916 (uri (cran-uri "SnowballC" version))
20919 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20920 (properties `((upstream-name . "SnowballC")))
20921 (build-system r-build-system)
20922 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20923 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20925 "This package provides an R interface to the C @code{libstemmer} library
20926 that implements Porter's word stemming algorithm for collapsing words to a
20927 common root to aid comparison of vocabulary. Currently supported languages
20928 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20929 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20930 (license license:bsd-3)))
20932 (define-public r-quanteda
20934 (name "r-quanteda")
20939 (uri (cran-uri "quanteda" version))
20942 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
20943 (properties `((upstream-name . "quanteda")))
20944 (build-system r-build-system)
20946 `(("r-data-table" ,r-data-table)
20947 ("r-digest" ,r-digest)
20948 ("r-extrafont" ,r-extrafont)
20949 ("r-fastmatch" ,r-fastmatch)
20950 ("r-ggplot2" ,r-ggplot2)
20951 ("r-ggrepel" ,r-ggrepel)
20952 ("r-jsonlite" ,r-jsonlite)
20953 ("r-magrittr" ,r-magrittr)
20954 ("r-matrix" ,r-matrix)
20955 ("r-network" ,r-network)
20956 ("r-proxyc" ,r-proxyc)
20958 ("r-rcpparmadillo" ,r-rcpparmadillo)
20959 ("r-rcppparallel" ,r-rcppparallel)
20961 ("r-snowballc" ,r-snowballc)
20962 ("r-stopwords" ,r-stopwords)
20963 ("r-stringi" ,r-stringi)
20965 ("r-yaml" ,r-yaml)))
20967 `(("r-knitr" ,r-knitr)))
20968 (home-page "https://quanteda.io")
20969 (synopsis "Quantitative analysis of textual data")
20971 "This package provides a fast, flexible, and comprehensive framework for
20972 quantitative text analysis in R. It provides functionality for corpus
20973 management, creating and manipulating tokens and ngrams, exploring keywords in
20974 context, forming and manipulating sparse matrices of documents by features and
20975 feature co-occurrences, analyzing keywords, computing feature similarities and
20976 distances, applying content dictionaries, applying supervised and unsupervised
20977 machine learning, visually representing text and text analyses, and more.")
20978 (license license:gpl3)))
20980 (define-public r-topicmodels
20982 (name "r-topicmodels")
20987 (uri (cran-uri "topicmodels" version))
20990 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20991 (properties `((upstream-name . "topicmodels")))
20992 (build-system r-build-system)
20996 `(("r-modeltools" ,r-modeltools)
20999 (home-page "https://cran.r-project.org/package=topicmodels")
21000 (synopsis "Topic models")
21002 "This package provides an interface to the C code for @dfn{Latent
21003 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
21004 David M. Blei and co-authors and the C++ code for fitting LDA models using
21005 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
21006 (license license:gpl2)))
21008 (define-public r-stm
21015 (uri (cran-uri "stm" version))
21018 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
21019 (properties `((upstream-name . "stm")))
21020 (build-system r-build-system)
21022 `(("r-data-table" ,r-data-table)
21023 ("r-glmnet" ,r-glmnet)
21025 ("r-matrix" ,r-matrix)
21026 ("r-matrixstats" ,r-matrixstats)
21027 ("r-quadprog" ,r-quadprog)
21028 ("r-quanteda" ,r-quanteda)
21030 ("r-rcpparmadillo" ,r-rcpparmadillo)
21032 ("r-stringr" ,r-stringr)))
21033 (home-page "http://www.structuraltopicmodel.com/")
21034 (synopsis "Estimation of the Structural Topic Model")
21036 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
21037 topic models with document-level covariates. The package also includes tools
21038 for model selection, visualization, and estimation of topic-covariate
21040 (license license:expat)))
21042 (define-public r-polycor
21049 (uri (cran-uri "polycor" version))
21052 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
21053 (properties `((upstream-name . "polycor")))
21054 (build-system r-build-system)
21056 `(("r-matrix" ,r-matrix)
21057 ("r-mvtnorm" ,r-mvtnorm)))
21058 (home-page "https://r-forge.r-project.org/projects/polycor/")
21059 (synopsis "Polychoric and polyserial correlations")
21061 "This package provides tools to compute polychoric and polyserial
21062 correlations by quick \"two-step\" methods or ML, optionally with standard
21063 errors; tetrachoric and biserial correlations are special cases.")
21064 (license license:gpl2+)))
21066 (define-public r-msm
21073 (uri (cran-uri "msm" version))
21076 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
21077 (properties `((upstream-name . "msm")))
21078 (build-system r-build-system)
21080 `(("r-expm" ,r-expm)
21081 ("r-mvtnorm" ,r-mvtnorm)
21082 ("r-survival" ,r-survival)))
21083 (home-page "https://github.com/chjackson/msm")
21084 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
21086 "This package provides functions for fitting continuous-time Markov and
21087 hidden Markov multi-state models to longitudinal data. It was designed for
21088 processes observed at arbitrary times in continuous time (panel data) but some
21089 other observation schemes are supported. Both Markov transition rates and the
21090 hidden Markov output process can be modelled in terms of covariates, which may
21091 be constant or piecewise-constant in time.")
21092 (license license:gpl2+)))
21094 (define-public r-ltm
21101 (uri (cran-uri "ltm" version))
21104 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
21105 (properties `((upstream-name . "ltm")))
21106 (build-system r-build-system)
21108 `(("r-mass" ,r-mass)
21110 ("r-polycor" ,r-polycor)))
21111 (home-page "https://github.com/drizopoulos/ltm")
21112 (synopsis "Latent trait models under IRT")
21114 "This is a package supporting the analysis of multivariate dichotomous
21115 and polytomous data using latent trait models under the Item Response Theory
21116 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
21117 Three-Parameter, the Graded Response, and the Generalized Partial Credit
21119 (license license:gpl2+)))
21121 (define-public r-mi
21128 (uri (cran-uri "mi" version))
21131 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
21132 (properties `((upstream-name . "mi")))
21133 (build-system r-build-system)
21136 ("r-matrix" ,r-matrix)))
21137 (home-page "http://www.stat.columbia.edu/~gelman/")
21138 (synopsis "Missing data imputation and model checking")
21140 "This package provides functions for data manipulation, imputing missing
21141 values in an approximate Bayesian framework, diagnostics of the models used to
21142 generate the imputations, confidence-building mechanisms to validate some of
21143 the assumptions of the imputation algorithm, and functions to analyze multiply
21144 imputed data sets with the appropriate degree of sampling uncertainty.")
21145 (license license:gpl2+)))
21147 (define-public r-matrixcalc
21149 (name "r-matrixcalc")
21154 (uri (cran-uri "matrixcalc" version))
21157 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
21158 (properties `((upstream-name . "matrixcalc")))
21159 (build-system r-build-system)
21160 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
21161 (synopsis "Collection of functions for matrix calculations")
21163 "This package provides a collection of functions to support matrix
21164 calculations for probability, econometric and numerical analysis. There are
21165 additional functions that are comparable to APL functions which are useful for
21166 actuarial models such as pension mathematics.")
21167 (license license:gpl2+)))
21169 (define-public r-sem
21176 (uri (cran-uri "sem" version))
21179 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
21180 (properties `((upstream-name . "sem")))
21181 (build-system r-build-system)
21183 `(("r-boot" ,r-boot)
21185 ("r-matrixcalc" ,r-matrixcalc)
21187 (home-page "https://cran.r-project.org/package=sem")
21188 (synopsis "Structural equation models")
21190 "This package provides functions for fitting general linear structural
21191 equation models (with observed and latent variables) using the RAM approach,
21192 and for fitting structural equations in observed-variable models by two-stage
21194 (license license:gpl2+)))
21196 (define-public r-semtools
21198 (name "r-semtools")
21203 (uri (cran-uri "semTools" version))
21206 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
21207 (properties `((upstream-name . "semTools")))
21208 (build-system r-build-system)
21210 `(("r-lavaan" ,r-lavaan)))
21211 (home-page "https://github.com/simsem/semTools/wiki")
21212 (synopsis "Useful tools for structural equation modeling")
21214 "This package provides useful tools for structural equation modeling.")
21215 (license license:gpl2+)))
21217 (define-public r-regsem
21224 (uri (cran-uri "regsem" version))
21227 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
21228 (properties `((upstream-name . "regsem")))
21229 (build-system r-build-system)
21231 `(("r-lavaan" ,r-lavaan)
21233 ("r-rcpparmadillo" ,r-rcpparmadillo)
21234 ("r-rsolnp" ,r-rsolnp)))
21236 `(("r-knitr" ,r-knitr)))
21237 (home-page "https://cran.r-project.org/package=regsem")
21238 (synopsis "Regularized structural equation modeling")
21240 "This package uses both ridge and lasso penalties (and extensions) to
21241 penalize specific parameters in structural equation models. The package
21242 offers additional cost functions, cross validation, and other extensions
21243 beyond traditional structural equation models. It also contains a function to
21244 perform @dfn{exploratory mediation} (XMed).")
21245 (license license:gpl2+)))
21247 (define-public r-stanheaders
21249 (name "r-stanheaders")
21250 (version "2.21.0-6")
21254 (uri (cran-uri "StanHeaders" version))
21257 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
21258 (properties `((upstream-name . "StanHeaders")))
21259 (build-system r-build-system)
21260 (inputs `(("pandoc" ,pandoc)))
21262 `(("r-rcppeigen" ,r-rcppeigen)
21263 ("r-rcppparallel" ,r-rcppparallel)))
21265 `(("gfortran" ,gfortran)
21266 ("r-knitr" ,r-knitr))) ; for vignettes
21267 (home-page "https://mc-stan.org/")
21268 (synopsis "C++ header files for Stan")
21270 "The C++ header files of the Stan project are provided by this package.
21271 There is a shared object containing part of the @code{CVODES} library, but it
21272 is not accessible from R. @code{r-stanheaders} is only useful for developers
21273 who want to utilize the @code{LinkingTo} directive of their package's
21274 DESCRIPTION file to build on the Stan library without incurring unnecessary
21277 The Stan project develops a probabilistic programming language that implements
21278 full or approximate Bayesian statistical inference via Markov Chain Monte
21279 Carlo or variational methods and implements (optionally penalized) maximum
21280 likelihood estimation via optimization. The Stan library includes an advanced
21281 automatic differentiation scheme, templated statistical and linear algebra
21282 functions that can handle the automatically differentiable scalar types (and
21283 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
21284 package provides user-facing R functions to parse, compile, test, estimate,
21285 and analyze Stan models.")
21286 (license license:bsd-3)))
21288 (define-public r-rpf
21295 (uri (cran-uri "rpf" version))
21298 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
21299 (properties `((upstream-name . "rpf")))
21300 (build-system r-build-system)
21302 `(("r-lifecycle" ,r-lifecycle)
21303 ("r-mvtnorm" ,r-mvtnorm)
21305 ("r-rcppeigen" ,r-rcppeigen)))
21307 `(("r-knitr" ,r-knitr)))
21308 (home-page "https://github.com/jpritikin/rpf")
21309 (synopsis "Response probability functions")
21311 "The purpose of this package is to factor out logic and math common to
21312 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
21313 core support code suitable for more specialized IRT packages to build upon.
21314 Complete access to optimized C functions is made available with
21315 @code{R_RegisterCCallable()}.")
21316 (license license:gpl3+)))
21318 (define-public r-openmx
21325 (uri (cran-uri "OpenMx" version))
21328 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
21329 (properties `((upstream-name . "OpenMx")))
21330 (build-system r-build-system)
21333 ("r-digest" ,r-digest)
21334 ("r-lifecycle" ,r-lifecycle)
21336 ("r-matrix" ,r-matrix)
21338 ("r-rcppeigen" ,r-rcppeigen)
21340 ("r-stanheaders" ,r-stanheaders)))
21341 (native-inputs `(("gfortran" ,gfortran)))
21342 (home-page "http://openmx.ssri.psu.edu")
21343 (synopsis "Extended structural equation modelling")
21345 "This package allows for the estimation of a wide variety of advanced
21346 multivariate statistical models. It consists of a library of functions and
21347 optimizers that allow you to quickly and flexibly define an SEM model and
21348 estimate parameters given observed data.")
21349 (license license:asl2.0)))
21351 (define-public r-kutils
21358 (uri (cran-uri "kutils" version))
21361 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
21362 (properties `((upstream-name . "kutils")))
21363 (build-system r-build-system)
21365 `(("r-foreign" ,r-foreign)
21366 ("r-openxlsx" ,r-openxlsx)
21368 ("r-runit" ,r-runit)
21369 ("r-xtable" ,r-xtable)))
21370 (home-page "https://cran.r-project.org/package=kutils")
21371 (synopsis "Project management tools")
21373 "This package provides tools for data importation, recoding, and
21374 inspection. There are functions to create new project folders, R code
21375 templates, create uniquely named output directories, and to quickly obtain a
21376 visual summary for each variable in a data frame. The main feature here is
21377 the systematic implementation of the \"variable key\" framework for data
21378 importation and recoding.")
21379 (license license:gpl2)))
21381 (define-public r-rockchalk
21383 (name "r-rockchalk")
21384 (version "1.8.144")
21388 (uri (cran-uri "rockchalk" version))
21391 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
21392 (properties `((upstream-name . "rockchalk")))
21393 (build-system r-build-system)
21395 `(("r-cardata" ,r-cardata)
21396 ("r-kutils" ,r-kutils)
21398 ("r-mass" ,r-mass)))
21399 (home-page "https://cran.r-project.org/package=rockchalk")
21400 (synopsis "Regression estimation and presentation")
21402 "This package provides a collection of functions for interpretation and
21403 presentation of regression analysis. These functions are used to produce the
21404 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
21405 includes regression diagnostics, regression tables, and plots of interactions
21406 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
21407 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
21408 fairly comprehensive overview.")
21409 (license license:gpl3+)))
21411 (define-public r-lisreltor
21413 (name "r-lisreltor")
21418 (uri (cran-uri "lisrelToR" version))
21421 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
21422 (properties `((upstream-name . "lisrelToR")))
21423 (build-system r-build-system)
21424 (home-page "https://cran.r-project.org/package=lisrelToR")
21425 (synopsis "Import output from LISREL into R")
21427 "This is an unofficial package aimed at automating the import of LISREL
21429 (license license:gpl2)))
21431 (define-public r-bdgraph
21438 (uri (cran-uri "BDgraph" version))
21441 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
21442 (properties `((upstream-name . "BDgraph")))
21443 (build-system r-build-system)
21445 `(("r-igraph" ,r-igraph)))
21446 (home-page "https://www.uva.nl/profile/a.mohammadi")
21447 (synopsis "Bayesian structure learning in graphical models")
21449 "This package provides statistical tools for Bayesian structure learning
21450 in undirected graphical models for continuous, discrete, and mixed data. It
21451 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
21452 on a continuous-time birth-death process.")
21453 (license license:gpl2+)))
21455 (define-public r-d3network
21457 (name "r-d3network")
21458 (version "0.5.2.1")
21462 (uri (cran-uri "d3Network" version))
21465 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21466 (properties `((upstream-name . "d3Network")))
21467 (build-system r-build-system)
21469 `(("r-plyr" ,r-plyr)
21470 ("r-rjson" ,r-rjson)
21471 ("r-whisker" ,r-whisker)))
21472 (home-page "http://christophergandrud.github.io/d3Network/")
21473 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21475 "This package is intended to make it easy to create D3 JavaScript
21476 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21477 (license license:gpl3+)))
21479 (define-public r-qgraph
21486 (uri (cran-uri "qgraph" version))
21489 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21490 (properties `((upstream-name . "qgraph")))
21491 (build-system r-build-system)
21493 `(("r-abind" ,r-abind)
21494 ("r-bdgraph" ,r-bdgraph)
21495 ("r-colorspace" ,r-colorspace)
21496 ("r-corpcor" ,r-corpcor)
21497 ("r-d3network" ,r-d3network)
21498 ("r-dplyr" ,r-dplyr)
21499 ("r-fdrtool" ,r-fdrtool)
21500 ("r-ggplot2" ,r-ggplot2)
21501 ("r-ggraph" ,r-ggraph)
21502 ("r-glasso" ,r-glasso)
21503 ("r-gtools" ,r-gtools)
21504 ("r-hmisc" ,r-hmisc)
21506 ("r-igraph" ,r-igraph)
21508 ("r-lavaan" ,r-lavaan)
21509 ("r-matrix" ,r-matrix)
21510 ("r-pbapply" ,r-pbapply)
21513 ("r-psych" ,r-psych)
21515 ("r-reshape2" ,r-reshape2)
21516 ("r-tidygraph" ,r-tidygraph)))
21517 (home-page "http://sachaepskamp.com/qgraph/")
21518 (synopsis "Weighted network visualization and analysis")
21520 "This package implements tools for weighted network visualization and
21521 analysis, as well as Gaussian graphical model computation. It contains graph
21522 plotting methods, and tools for psychometric data visualization and graphical
21523 model estimation. See Epskamp et al. (2012)
21524 @url{doi:10.18637/jss.v048.i04}.")
21525 (license license:gpl2)))
21527 (define-public r-semplot
21534 (uri (cran-uri "semPlot" version))
21537 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21538 (properties `((upstream-name . "semPlot")))
21539 (build-system r-build-system)
21541 `(("r-colorspace" ,r-colorspace)
21542 ("r-corpcor" ,r-corpcor)
21543 ("r-igraph" ,r-igraph)
21544 ("r-lavaan" ,r-lavaan)
21545 ("r-lisreltor" ,r-lisreltor)
21546 ("r-openmx" ,r-openmx)
21548 ("r-qgraph" ,r-qgraph)
21549 ("r-regsem" ,r-regsem)
21550 ("r-rockchalk" ,r-rockchalk)
21553 (home-page "https://github.com/SachaEpskamp/semPlot")
21554 (synopsis "Unified visualizations of structural equation models")
21556 "Structural equation modeling (SEM) has a long history of representing
21557 models graphically as path diagrams. The semPlot package for R fills the gap
21558 between advanced, but time-consuming, graphical software and the limited
21559 graphics produced automatically by SEM software. In addition, semPlot offers
21560 more functionality than drawing path diagrams: it can act as a common ground
21561 for importing SEM results into R. Any result usable as input to semPlot can
21562 also be represented in any of the three popular SEM frame-works, as well as
21563 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21564 (license license:gpl2)))
21566 (define-public r-cdm
21573 (uri (cran-uri "CDM" version))
21576 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21577 (properties `((upstream-name . "CDM")))
21578 (build-system r-build-system)
21580 `(("r-mvtnorm" ,r-mvtnorm)
21581 ("r-polycor" ,r-polycor)
21583 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21585 "https://github.com/alexanderrobitzsch/CDM")
21586 (synopsis "Cognitive diagnosis modeling")
21588 "This package provides functions for cognitive diagnosis modeling and
21589 multidimensional item response modeling for dichotomous and polytomous item
21590 responses. It enables the estimation of the DINA and DINO model, the multiple
21591 group (polytomous) GDINA model, the multiple choice DINA model, the general
21592 diagnostic model (GDM), the structured latent class model (SLCA), and
21593 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21594 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21595 estimation and the package structure. For tutorials on how to use the CDM
21596 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21597 well as Ravand and Robitzsch (2015).")
21598 (license license:gpl2+)))
21600 (define-public r-tam
21607 (uri (cran-uri "TAM" version))
21610 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21611 (properties `((upstream-name . "TAM")))
21612 (build-system r-build-system)
21616 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21617 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21618 (synopsis "Test analysis modules")
21620 "This package includes tools for marginal maximum likelihood estimation
21621 and joint maximum likelihood estimation for unidimensional and
21622 multidimensional item response models. The package functionality covers the
21623 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21624 multi-faceted Rasch model, nominal item response model, structured latent
21625 class model, mixture distribution IRT models, and located latent class models.
21626 Latent regression models and plausible value imputation are also supported.")
21627 (license license:gpl2+)))
21629 (define-public r-erm
21636 (uri (cran-uri "eRm" version))
21639 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21640 (properties `((upstream-name . "eRm")))
21641 (build-system r-build-system)
21643 `(("r-colorspace" ,r-colorspace)
21644 ("r-lattice" ,r-lattice)
21646 ("r-matrix" ,r-matrix)
21647 ("r-psych" ,r-psych)))
21648 (native-inputs `(("gfortran" ,gfortran)))
21649 (home-page "https://cran.r-project.org/package=eRm")
21650 (synopsis "Extended Rasch modeling")
21652 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21653 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21654 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21655 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21656 data matrix. Additional features are the ML estimation of the person
21657 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21658 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21659 infit and outfit measures, ICC and other plots, automated stepwise item
21660 elimination, and a simulation module for various binary data matrices.")
21661 (license license:gpl3)))
21663 (define-public r-irtoys
21670 (uri (cran-uri "irtoys" version))
21673 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21674 (properties `((upstream-name . "irtoys")))
21675 (build-system r-build-system)
21679 (home-page "https://cran.r-project.org/package=irtoys")
21680 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21682 "This package provides a collection of functions useful in learning and
21683 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21684 programs. It provides basic CTT analysis, a simple common interface to the
21685 estimation of item parameters in IRT models for binary responses with three
21686 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21687 EAP, WLE, plausible values), item and person fit statistics, scaling
21688 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21689 array of parametric and non-parametric (kernel) plots. It estimates and plots
21690 Haberman's interaction model when all items are dichotomously scored.")
21691 (license license:gpl2+)))
21693 (define-public r-iheatmapr
21695 (name "r-iheatmapr")
21700 (uri (cran-uri "iheatmapr" version))
21703 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
21704 (properties `((upstream-name . "iheatmapr")))
21705 (build-system r-build-system)
21707 `(("r-fastcluster" ,r-fastcluster)
21708 ("r-ggdendro" ,r-ggdendro)
21709 ("r-htmlwidgets" ,r-htmlwidgets)
21710 ("r-jsonlite" ,r-jsonlite)
21711 ("r-knitr" ,r-knitr)
21712 ("r-magrittr" ,r-magrittr)
21713 ("r-rcolorbrewer" ,r-rcolorbrewer)
21714 ("r-scales" ,r-scales)))
21716 `(("r-knitr" ,r-knitr)))
21717 (home-page "https://docs.ropensci.org/iheatmapr")
21718 (synopsis "Interactive, Complex Heatmaps")
21720 "iheatmapr is an R package for building complex, interactive heatmaps
21721 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21722 subplots along the rows or columns of the main heatmap add more information
21723 about each row or column. For example, a one column additional heatmap may
21724 indicate what group a particular row or column belongs to. Complex heatmaps
21725 may also include multiple side by side heatmaps which show different types of
21726 data for the same conditions. Interactivity can improve complex heatmaps by
21727 providing tooltips with information about each cell and enabling zooming into
21728 interesting features. iheatmapr uses the plotly library for interactivity.")
21729 (license license:expat)))
21731 (define-public r-packrat
21738 (uri (cran-uri "packrat" version))
21741 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21742 (properties `((upstream-name . "packrat")))
21743 (build-system r-build-system)
21744 (home-page "https://github.com/rstudio/packrat/")
21745 (synopsis "Dependency management R projects")
21747 "This package provides a dependency manager for R projects that allows
21748 you to manage the R packages your project depends on in an isolated, portable,
21749 and reproducible way.")
21750 (license license:gpl2)))
21752 (define-public r-rsconnect
21754 (name "r-rsconnect")
21759 (uri (cran-uri "rsconnect" version))
21762 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21763 (properties `((upstream-name . "rsconnect")))
21764 (build-system r-build-system)
21766 `(("r-curl" ,r-curl)
21767 ("r-digest" ,r-digest)
21768 ("r-jsonlite" ,r-jsonlite)
21769 ("r-openssl" ,r-openssl)
21770 ("r-packrat" ,r-packrat)
21771 ("r-rstudioapi" ,r-rstudioapi)
21772 ("r-yaml" ,r-yaml)))
21773 (home-page "https://github.com/rstudio/rsconnect")
21774 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21776 "This package provides a programmatic deployment interface for RPubs,
21777 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21778 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21779 (license license:gpl2)))
21781 ;; This package includes minified JavaScript files. When upgrading please
21782 ;; check that there are no new minified JavaScript files.
21783 (define-public r-dygraphs
21785 (name "r-dygraphs")
21786 (version "1.1.1.6")
21790 (uri (cran-uri "dygraphs" version))
21793 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21794 (properties `((upstream-name . "dygraphs")))
21795 (build-system r-build-system)
21797 `(#:modules ((guix build utils)
21798 (guix build r-build-system)
21802 (modify-phases %standard-phases
21803 (add-after 'unpack 'process-javascript
21804 (lambda* (#:key inputs #:allow-other-keys)
21805 (with-directory-excursion "inst/htmlwidgets/lib/"
21809 `(("dygraphs/dygraph-combined-dev.js"
21810 "dygraph-combined.js")
21811 (,(assoc-ref inputs "js-jquery")
21812 "jquery/jquery.min.js")
21813 (,(assoc-ref inputs "js-fquarter")
21814 "fquarter/moment-fquarter.min.js"))))
21815 (lambda (sources targets)
21816 (for-each (lambda (source target)
21817 (format #t "Processing ~a --> ~a~%"
21819 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21820 (call-with-output-file target
21822 (dump-port minified port)))))
21823 sources targets))))
21826 `(("uglify-js" ,uglify-js)
21827 ;; They actually use version 1.11.1, but this more recent version
21828 ;; should be just fine.
21832 (uri "https://code.jquery.com/jquery-1.12.4.js")
21835 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21839 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21840 "moment-fquarter/1.0.1/moment-fquarter.js"))
21843 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21845 `(("r-htmltools" ,r-htmltools)
21846 ("r-htmlwidgets" ,r-htmlwidgets)
21847 ("r-magrittr" ,r-magrittr)
21850 (home-page "https://github.com/rstudio/dygraphs")
21851 (synopsis "Interface to Dygraphs interactive time series charting library")
21853 "This package provides an R interface to the dygraphs JavaScript charting
21854 library (a copy of which is included in the package). It provides rich
21855 facilities for charting time-series data in R, including highly configurable
21856 series- and axis-display and interactive features like zoom/pan and
21857 series/point highlighting.")
21858 (license license:expat)))
21860 (define-public r-shinystan
21862 (name "r-shinystan")
21867 (uri (cran-uri "shinystan" version))
21870 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21871 (properties `((upstream-name . "shinystan")))
21872 (build-system r-build-system)
21874 `(("r-bayesplot" ,r-bayesplot)
21875 ("r-colourpicker" ,r-colourpicker)
21877 ("r-dygraphs" ,r-dygraphs)
21878 ("r-ggplot2" ,r-ggplot2)
21879 ("r-gridextra" ,r-gridextra)
21880 ("r-gtools" ,r-gtools)
21881 ("r-markdown" ,r-markdown)
21882 ("r-reshape2" ,r-reshape2)
21883 ("r-rsconnect" ,r-rsconnect)
21884 ("r-rstan" ,r-rstan)
21885 ("r-shiny" ,r-shiny)
21886 ("r-shinyjs" ,r-shinyjs)
21887 ("r-shinythemes" ,r-shinythemes)
21888 ("r-threejs" ,r-threejs)
21889 ("r-xtable" ,r-xtable)
21891 (home-page "https://mc-stan.org/")
21892 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21894 "This package provides a graphical user interface for interactive
21895 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21896 for analyzing a posterior sample. The interface is powered by the Shiny web
21897 application framework and works with the output of MCMC programs written in
21898 any programming language (and has extended functionality for Stan models fit
21899 using the @code{rstan} and @code{rstanarm} packages).")
21900 (license license:gpl3+)))
21902 (define-public r-rstantools
21904 (name "r-rstantools")
21909 (uri (cran-uri "rstantools" version))
21912 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21913 (properties `((upstream-name . "rstantools")))
21914 (build-system r-build-system)
21915 (inputs `(("pandoc" ,pandoc)))
21917 `(("r-desc" ,r-desc)
21919 ("r-rcppparallel" ,r-rcppparallel)))
21921 `(("r-knitr" ,r-knitr)))
21922 (home-page "https://mc-stan.org/rstantools/")
21923 (synopsis "Tools for developing R packages interfacing with Stan")
21925 "This package provides various tools for developers of R packages
21926 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21927 up the required package structure, S3 generics and default methods to unify
21928 function naming across Stan-based R packages, and vignettes with
21929 recommendations for developers.")
21930 (license license:gpl3+)))
21932 (define-public r-loo
21939 (uri (cran-uri "loo" version))
21941 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21942 (properties `((upstream-name . "loo")))
21943 (build-system r-build-system)
21945 `(("pandoc" ,pandoc)
21946 ("pandoc-citeproc" ,pandoc-citeproc)))
21948 `(("r-checkmate" ,r-checkmate)
21949 ("r-matrixstats" ,r-matrixstats)))
21951 `(("r-knitr" ,r-knitr)))
21952 (home-page "https://mc-stan.org/loo/")
21953 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21955 "This package provides an implementation of efficient approximate
21956 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21957 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21958 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21959 procedure for regularizing importance weights. As a byproduct of the
21960 calculations, we also obtain approximate standard errors for estimated
21961 predictive errors and for the comparison of predictive errors between models.
21962 The package also provides methods for using stacking and other model weighting
21963 techniques to average Bayesian predictive distributions.")
21964 (license license:gpl3+)))
21966 (define-public r-rstan
21973 (uri (cran-uri "rstan" version))
21976 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21977 (properties `((upstream-name . "rstan")))
21978 (build-system r-build-system)
21981 (modify-phases %standard-phases
21982 (add-before 'install 'set-timezone
21983 ;; This package is picky about timezones.
21984 (lambda* (#:key inputs #:allow-other-keys)
21985 (setenv "TZ" "UTC+1")
21987 (string-append (assoc-ref inputs "tzdata")
21988 "/share/zoneinfo"))
21991 `(("tzdata" ,tzdata-for-tests)
21993 ("r-knitr" ,r-knitr)))
21996 ("r-ggplot2" ,r-ggplot2)
21997 ("r-gridextra" ,r-gridextra)
21998 ("r-inline" ,r-inline)
22000 ("r-pkgbuild" ,r-pkgbuild)
22002 ("r-rcppeigen" ,r-rcppeigen)
22003 ("r-rcppparallel" ,r-rcppparallel)
22004 ("r-stanheaders" ,r-stanheaders)
22006 ("r-withr" ,r-withr)))
22007 (home-page "https://discourse.mc-stan.org/")
22008 (synopsis "R interface to Stan")
22010 "User-facing R functions are provided to parse, compile, test, estimate,
22011 and analyze Stan models by accessing the header-only Stan library provided by
22012 the StanHeaders package. The Stan project develops a probabilistic
22013 programming language that implements full Bayesian statistical inference via
22014 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
22015 approximation, and (optionally penalized) maximum likelihood estimation via
22016 optimization. In all three cases, automatic differentiation is used to
22017 quickly and accurately evaluate gradients without burdening the user with the
22018 need to derive the partial derivatives.")
22019 (license license:gpl3+)))
22021 (define-public r-rstanarm
22023 (name "r-rstanarm")
22028 (uri (cran-uri "rstanarm" version))
22031 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
22032 (properties `((upstream-name . "rstanarm")))
22033 (build-system r-build-system)
22035 `(("pandoc" ,pandoc)
22036 ("pandoc-citeproc" ,pandoc-citeproc)))
22038 `(("r-bayesplot" ,r-bayesplot)
22040 ("r-ggplot2" ,r-ggplot2)
22043 ("r-matrix" ,r-matrix)
22046 ("r-rcppeigen" ,r-rcppeigen)
22047 ("r-rcppparallel" ,r-rcppparallel)
22048 ("r-rstan" ,r-rstan)
22049 ("r-rstantools" ,r-rstantools)
22050 ("r-shinystan" ,r-shinystan)
22051 ("r-stanheaders" ,r-stanheaders)
22052 ("r-survival" ,r-survival)))
22054 `(("r-knitr" ,r-knitr)))
22055 (home-page "https://mc-stan.org/rstanarm/")
22056 (synopsis "Bayesian applied regression modeling via Stan")
22058 "This package estimates previously compiled regression models using the
22059 @code{rstan} package, which provides the R interface to the Stan C++ library
22060 for Bayesian estimation. Users specify models via the customary R syntax with
22061 a formula and @code{data.frame} plus some additional arguments for priors.")
22062 (license license:gpl3+)))
22064 (define-public r-kendall
22071 (uri (cran-uri "Kendall" version))
22074 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
22075 (properties `((upstream-name . "Kendall")))
22076 (build-system r-build-system)
22078 `(("r-boot" ,r-boot)))
22080 `(("gfortran" ,gfortran)))
22081 (home-page "https://cran.r-project.org/web/packages/Kendall/")
22082 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
22084 "This package computes the Kendall rank correlation and Mann-Kendall
22086 (license license:gpl2+)))
22088 (define-public r-zyp
22091 (version "0.10-1.1")
22095 (uri (cran-uri "zyp" version))
22098 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
22099 (properties `((upstream-name . "zyp")))
22100 (build-system r-build-system)
22102 `(("r-kendall" ,r-kendall)))
22103 (home-page "https://cran.r-project.org/web/packages/zyp/")
22104 (synopsis "Zhang + Yue-Pilon Trends Package")
22106 "This package contains an efficient implementation of Sen's slope
22107 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
22108 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
22110 (license license:lgpl2.1)))
22112 (define-public r-rlinsolve
22114 (name "r-rlinsolve")
22119 (uri (cran-uri "Rlinsolve" version))
22122 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
22123 (properties `((upstream-name . "Rlinsolve")))
22124 (build-system r-build-system)
22126 `(("r-matrix" ,r-matrix)
22128 ("r-rcpparmadillo" ,r-rcpparmadillo)
22129 ("r-rdpack" ,r-rdpack)))
22130 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
22131 (synopsis "Iterative solvers for (sparse) linear system of equations")
22133 "Solving a system of linear equations is one of the most fundamental
22134 computational problems for many fields of mathematical studies, such as
22135 regression problems from statistics or numerical partial differential
22136 equations. This package provides basic stationary iterative solvers such as
22137 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
22138 Nonstationary, also known as Krylov subspace methods are also provided.
22139 Sparse matrix computation is also supported in that solving large and sparse
22140 linear systems can be manageable using the @code{Matrix} package along with
22141 @code{RcppArmadillo}.")
22142 (license license:gpl3+)))
22144 (define-public r-zvcv
22151 (uri (cran-uri "ZVCV" version))
22154 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
22155 (properties `((upstream-name . "ZVCV")))
22156 (build-system r-build-system)
22158 `(("r-abind" ,r-abind)
22160 ("r-dplyr" ,r-dplyr)
22161 ("r-glmnet" ,r-glmnet)
22162 ("r-magrittr" ,r-magrittr)
22163 ("r-mvtnorm" ,r-mvtnorm)
22165 ("r-rcpparmadillo" ,r-rcpparmadillo)
22166 ("r-rlinsolve" ,r-rlinsolve)))
22167 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
22168 (synopsis "Zero-Variance Control Variates")
22170 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
22171 to reduce the variance of Monte Carlo estimators of expectations using the
22172 derivatives of the log target. Once the derivatives are available, the only
22173 additional computational effort is in solving a linear regression problem.
22174 This method has been extended to higher dimensions using regularisation. This
22175 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
22176 samples, derivatives and function evaluations are available. Additional
22177 functions for applying ZV-CV to two estimators for the normalising constant of
22178 the posterior distribution in Bayesian statistics are also supplied.")
22179 (license license:gpl2+)))
22181 (define-public r-ztype
22188 (uri (cran-uri "ztype" version))
22191 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
22192 (properties `((upstream-name . "ztype")))
22193 (build-system r-build-system)
22195 `(("r-assertthat" ,r-assertthat)
22196 ("r-dplyr" ,r-dplyr)
22197 ("r-ggplot2" ,r-ggplot2)
22198 ("r-lubridate" ,r-lubridate)
22199 ("r-magrittr" ,r-magrittr)
22200 ("r-rvest" ,r-rvest)
22201 ("r-stringr" ,r-stringr)))
22202 (home-page "https://cran.r-project.org/web/packages/ztype/")
22203 (synopsis "Run a Ztype game loaded with R functions")
22205 "How fast can you type R functions on your keyboard? Find out by running
22206 a @code{zty.pe} game: export R functions as instructions to type to destroy
22207 opponents' vessels.")
22208 (license license:gpl3)))
22210 (define-public r-zseq
22217 (uri (cran-uri "Zseq" version))
22220 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
22221 (properties `((upstream-name . "Zseq")))
22222 (build-system r-build-system)
22224 `(("r-gmp" ,r-gmp)))
22225 (home-page "https://cran.r-project.org/web/packages/Zseq/")
22226 (synopsis "Integer sequence generator")
22228 "This package generates well-known integer sequences. The @code{gmp}
22229 package is adopted for computing with arbitrarily large numbers. Every
22230 function has a hyperlink to its corresponding item in the @dfn{On-Line
22231 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
22232 (license license:gpl3+)))
22234 (define-public r-isoband
22241 (uri (cran-uri "isoband" version))
22244 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
22245 (properties `((upstream-name . "isoband")))
22246 (build-system r-build-system)
22248 `(("r-testthat" ,r-testthat)))
22250 `(("r-knitr" ,r-knitr)))
22251 (home-page "https://github.com/wilkelab/isoband")
22252 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
22254 "This package provides a fast C++ implementation to generate contour
22255 lines (isolines) and contour polygons (isobands) from regularly spaced grids
22256 containing elevation data.")
22257 (license license:expat)))
22259 (define-public r-ppcor
22266 (uri (cran-uri "ppcor" version))
22269 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
22270 (properties `((upstream-name . "ppcor")))
22271 (build-system r-build-system)
22273 `(("r-mass" ,r-mass)))
22274 (home-page "https://cran.r-project.org/web/packages/ppcor/")
22275 (synopsis "Partial and semi-partial correlation")
22277 "This package provides users not only with a function to readily
22278 calculate the higher-order partial and semi-partial correlations but also with
22279 statistics and p-values of the correlation coefficients.")
22280 (license license:gpl2)))
22282 (define-public r-hrbrthemes
22284 (name "r-hrbrthemes")
22289 (uri (cran-uri "hrbrthemes" version))
22291 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
22292 (properties `((upstream-name . "hrbrthemes")))
22293 (build-system r-build-system)
22295 `(("r-extrafont" ,r-extrafont)
22296 ("r-gdtools" ,r-gdtools)
22297 ("r-ggplot2" ,r-ggplot2)
22298 ("r-htmltools" ,r-htmltools)
22299 ("r-knitr" ,r-knitr)
22300 ("r-magrittr" ,r-magrittr)
22301 ("r-rmarkdown" ,r-rmarkdown)
22302 ("r-scales" ,r-scales)))
22304 `(("r-knitr" ,r-knitr)))
22305 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
22306 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
22308 "This package provides a compilation of extra @code{ggplot2} themes,
22309 scales and utilities, including a spell check function for plot label fields
22310 and an overall emphasis on typography.")
22311 (license license:expat)))
22313 (define-public r-crochet
22320 (uri (cran-uri "crochet" version))
22323 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
22324 (build-system r-build-system)
22326 `(("r-knitr" ,r-knitr)))
22327 (home-page "https://github.com/agrueneberg/crochet")
22328 (synopsis "Implementation Helper for Matrix-Like Types")
22330 "Functions to help implement the extraction / subsetting / indexing
22331 function @code{[} and replacement function @code{[<-} of custom matrix-like
22332 types (based on S3, S4, etc.), modeled as closely to the base matrix class
22333 as possible (with tests to prove it).")
22334 (license license:expat)))
22336 (define-public r-boa
22339 (version "1.1.8-2")
22343 (uri (cran-uri "boa" version))
22346 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
22347 (properties `((upstream-name . "boa")))
22348 (build-system r-build-system)
22349 (home-page "http://www.jstatsoft.org/v21/i11")
22350 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
22352 "This package provides a menu-driven program and library of functions for
22353 carrying out convergence diagnostics and statistical and graphical analysis of
22354 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
22355 (license license:gpl2+)))
22357 (define-public r-httpcode
22359 (name "r-httpcode")
22363 (uri (cran-uri "httpcode" version))
22366 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
22367 (build-system r-build-system)
22368 (home-page "https://github.com/sckott/httpcode")
22369 (synopsis "HTTP status code helper")
22370 (description "@code{httpcode} provides functionality for finding and
22371 explaining the meaning of @code{HTTP} status codes. Functions are included for
22372 searching for codes by full or partial number, by message, and to get
22373 appropriate dog and cat images for many status codes.")
22374 (license license:expat)))
22376 (define-public r-latex2exp
22378 (name "r-latex2exp")
22382 (uri (cran-uri "latex2exp" version))
22385 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
22386 (build-system r-build-system)
22388 `(("r-stringr" ,r-stringr)
22389 ("r-magrittr" ,r-magrittr)))
22390 (home-page "https://github.com/stefano-meschiari/latex2exp/")
22391 (synopsis "Use LaTeX expressions in plots")
22392 (description "@code{latex2exp} parses and converts LaTeX math formulas to
22393 R's plotmath expressions, used to enter mathematical formulas and symbols to be
22394 rendered as text, axis labels, etc. throughout R's plotting system.")
22395 (license license:expat)))
22397 (define-public r-oai
22403 (uri (cran-uri "oai" version))
22406 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
22407 (build-system r-build-system)
22409 `(("r-xml2" ,r-xml2)
22412 ("r-stringr" ,r-stringr)
22413 ("r-tibble" ,r-tibble)))
22414 (home-page "https://github.com/ropensci/oai/")
22415 (synopsis "General purpose OAI-PMH services client")
22416 (description "@code{oai} provides a general purpose client to work with
22417 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
22418 service. Functions are provided to work with the OAI-PMH verbs:
22419 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
22420 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
22421 (license license:expat)))
22423 (define-public r-argon2
22430 (uri (cran-uri "argon2" version))
22433 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
22434 (properties `((upstream-name . "argon2")))
22435 (build-system r-build-system)
22436 (home-page "https://github.com/wrathematics/argon2")
22437 (synopsis "Secure password hashing based on the argon2 algorithm")
22439 "This package provides utilities for secure password hashing via the
22440 argon2 algorithm.")
22441 (license license:bsd-2)))
22443 (define-public r-getpass
22450 (uri (cran-uri "getPass" version))
22453 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
22454 (properties `((upstream-name . "getPass")))
22455 (build-system r-build-system)
22457 `(("r-rstudioapi" ,r-rstudioapi)))
22458 (home-page "https://github.com/wrathematics/getPass")
22459 (synopsis "Masked user input")
22461 "This package provides a micro-package for reading \"passwords\", i.e.
22462 reading user input with masking, so that the input is not displayed as it is
22463 typed. Currently, RStudio, the command line (every OS), and any platform
22464 where tcltk is present are supported.")
22465 (license license:bsd-2)))
22467 (define-public r-remoter
22474 (uri (cran-uri "remoter" version))
22477 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22478 (properties `((upstream-name . "remoter")))
22479 (build-system r-build-system)
22481 `(("r-argon2" ,r-argon2)
22482 ("r-getpass" ,r-getpass)
22483 ("r-pbdzmq" ,r-pbdzmq)
22485 (home-page "https://github.com/RBigData/remoter")
22486 (synopsis "Control a remote R session from a local one")
22488 "This package provides a set of utilities for client/server computing
22489 with R, controlling a remote R session (the server) from a local one (the
22491 (license license:bsd-2)))
22493 (define-public r-asd
22500 (uri (cran-uri "asd" version))
22503 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22504 (properties `((upstream-name . "asd")))
22505 (build-system r-build-system)
22507 `(("r-mvtnorm" ,r-mvtnorm)))
22508 (home-page "https://cran.r-project.org/web/packages/asd")
22509 (synopsis "Simulations for Adaptive Seamless Designs")
22511 "This package provdes means to run simulations for adaptive seamless
22512 designs with and without early outcomes for treatment selection and
22513 subpopulation type designs.")
22514 (license license:gpl3)))
22516 (define-public r-nbconvertr
22518 (name "r-nbconvertr")
22523 (uri (cran-uri "nbconvertR" version))
22526 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22527 (properties `((upstream-name . "nbconvertR")))
22528 (build-system r-build-system)
22530 `(("jupyter" ,python-nbconvert)
22531 ("pandoc" ,pandoc)))
22532 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22533 (synopsis "Vignette engine wrapping Jupyter notebooks")
22535 "This package calls the Jupyter script @code{nbconvert} to create
22536 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22537 containing rich text, code, and its output. Code cells can be edited and
22538 evaluated interactively.")
22539 (license license:gpl3)))
22541 (define-public r-bridgesampling
22543 (name "r-bridgesampling")
22548 (uri (cran-uri "bridgesampling" version))
22551 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22553 `((upstream-name . "bridgesampling")))
22554 (build-system r-build-system)
22556 `(("r-brobdingnag" ,r-brobdingnag)
22558 ("r-matrix" ,r-matrix)
22559 ("r-mvtnorm" ,r-mvtnorm)
22560 ("r-scales" ,r-scales)
22561 ("r-stringr" ,r-stringr)))
22563 `(("r-knitr" ,r-knitr)))
22564 (home-page "https://github.com/quentingronau/bridgesampling")
22565 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22567 "This package provides functions for estimating marginal likelihoods,
22568 Bayes factors, posterior model probabilities, and normalizing constants in
22569 general, via different versions of bridge sampling.")
22570 (license license:gpl2+)))
22572 (define-public r-tea
22579 (uri (cran-uri "tea" version))
22582 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22584 `((upstream-name . "tea")))
22585 (build-system r-build-system)
22587 `(("r-matrix" ,r-matrix)))
22588 (home-page "https://cran.r-project.org/web/packages/tea/")
22589 (synopsis "Threshold estimation approaches")
22591 "This package provides different approaches for selecting the threshold
22592 in generalized Pareto distributions. Most of them are based on minimizing the
22593 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
22594 Others are heuristically motivated by searching for stable sample paths, i.e.
22595 a nearly constant region of the tail index estimator with respect to k, which
22596 is the number of data in the tail. The third class is motivated by graphical
22597 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22598 is also implemented here.")
22599 (license license:gpl3)))
22601 (define-public r-awsmethods
22603 (name "r-awsmethods")
22608 (uri (cran-uri "awsMethods" version))
22611 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22613 `((upstream-name . "awsMethods")))
22614 (build-system r-build-system)
22615 (home-page "http://www.wias-berlin.de/software/imaging/")
22616 (synopsis "Class and methods definitions")
22618 "This package defines the generic method @code{extract} and provides
22619 @code{openMP} support as needed in several packages like
22620 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22621 (license license:gpl2+)))
22623 (define-public r-aws
22630 (uri (cran-uri "aws" version))
22633 "1mwg1q7l4a07g5aa9c6kh3fpl9lakk01pbzlk7ixbpy12yfvj9nm"))))
22635 `((upstream-name . "aws")))
22636 (build-system r-build-system)
22638 `(("r-awsmethods" ,r-awsmethods)
22641 `(("gfortran" ,gfortran)))
22642 (home-page "https://cran.r-project.org/web/packages/aws/")
22643 (synopsis "Adaptive weights smoothing")
22645 "This package provides a collection of R-functions implementing adaptive
22646 smoothing procedures in 1D, 2D and 3D. This includes the
22647 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22648 Confidence Intervals} (ICI), variational approaches, and a non-local means
22650 (license license:gpl2+)))
22652 (define-public r-sgloptim
22654 (name "r-sgloptim")
22659 (uri (cran-uri "sglOptim" version))
22662 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22664 `((upstream-name . "sglOptim")))
22665 (build-system r-build-system)
22668 ("r-doparallel" ,r-doparallel)
22669 ("r-foreach" ,r-foreach)
22670 ("r-matrix" ,r-matrix)
22672 ("r-rcpparmadillo" ,r-rcpparmadillo)
22673 ("r-rcppprogress" ,r-rcppprogress)))
22675 `(("r-knitr" ,r-knitr)))
22676 (home-page "https://github.com/nielsrhansen/sglOptim")
22677 (synopsis "Generic sparse group Lasso solver")
22679 "This package provides a fast generic solver for sparse group lasso
22680 optimization problems. The loss (objective) function must be defined in a C++
22681 module. The optimization problem is solved using a coordinate gradient
22682 descent algorithm. Convergence of the algorithm is established and the
22683 algorithm is applicable to a broad class of loss functions. Use of parallel
22684 computing for cross validation and subsampling is supported through the
22685 @code{foreach} and @code{doParallel} packages.")
22686 (license license:gpl2+)))
22688 (define-public r-grouped
22695 (uri (cran-uri "grouped" version))
22698 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22700 `((upstream-name . "grouped")))
22701 (build-system r-build-system)
22703 `(("r-mass" ,r-mass)))
22704 (home-page "https://cran.r-project.org/web/packages/grouped/")
22705 (synopsis "Regression analysis of grouped and coarse data")
22707 "This package provides regression models for grouped and coarse data,
22708 under the coarsened at random assumption.")
22709 (license license:gpl2+)))
22711 (define-public r-stam
22718 (uri (cran-uri "stam" version))
22721 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22723 `((upstream-name . "stam")))
22724 (build-system r-build-system)
22728 (home-page "https://cran.r-project.org/web/packages/stam")
22729 (synopsis "Spatio-temporal analysis and modelling")
22731 "This package provides various methods to conduct Spatio-Temporal
22732 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22733 Inferred Spatio-Temporal Modelling.")
22734 (license license:gpl2+)))
22736 (define-public r-dcv
22743 (uri (cran-uri "dcv" version))
22746 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22748 `((upstream-name . "dcv")))
22749 (build-system r-build-system)
22751 `(("r-lmtest" ,r-lmtest)))
22752 (home-page "https://cran.r-project.org/web/packages/dcv/")
22753 (synopsis "Conventional cross-validation statistics for climate-growth model")
22755 "This package performs several conventional cross-validation statistical
22756 methods for climate-growth model in the climate reconstruction from tree
22757 rings, including Sign Test statistic, Reduction of Error statistic, Product
22758 Mean Test, Durbin-Watson statistic etc.")
22759 (license license:gpl2)))
22761 (define-public r-rcdd
22768 (uri (cran-uri "rcdd" version))
22771 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22773 `((upstream-name . "rcdd")))
22774 (build-system r-build-system)
22777 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22778 (synopsis "Computational geometry")
22780 "This package converts back and forth between two representations of a
22781 convex polytope: as solution of a set of linear equalities and inequalities
22782 and as convex hull of set of points and rays. Also does linear programming
22783 and redundant generator elimination. All functions can use exact
22784 infinite-precision rational arithmetic.")
22785 (license license:gpl2)))
22787 (define-public r-rxnat
22794 (uri (cran-uri "Rxnat" version))
22797 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
22799 `((upstream-name . "Rxnat")))
22800 (build-system r-build-system)
22802 `(("r-dplyr" ,r-dplyr)
22804 ("r-rcurl" ,r-rcurl)
22805 ("r-tibble" ,r-tibble)))
22807 `(("r-knitr" ,r-knitr)))
22808 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22809 (synopsis "Queries and extracts images from neuroimaging datasets")
22811 "This package allows communication with the Extensible Neuroimaging
22812 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22814 (license license:gpl2)))
22816 (define-public r-rserve
22823 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22824 version ".tar.gz"))
22827 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22828 (build-system r-build-system)
22830 `(("r-checkmate" ,r-checkmate)
22832 ("r-jsonlite" ,r-jsonlite)
22833 ("r-knitr" ,r-knitr)
22836 ("r-uuid" ,r-uuid)))
22838 `(("openssl" ,openssl)
22840 (home-page "https://github.com/s-u/Rserve")
22842 "Server providing access to R from many languages and systems")
22844 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22845 binary requests to be sent to R. Every connection has a separate workspace
22846 and working directory. Client-side implementations are available for popular
22847 languages such as C/C++ and Java, allowing any application to use facilities
22848 of R without the need of linking to R code. Rserve supports remote
22849 connection, user authentication and file transfer. A simple R client is
22850 included in this package as well.")
22851 (license license:gpl2)))
22853 (define-public r-gamm4
22860 (uri (cran-uri "gamm4" version))
22863 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
22864 (properties `((upstream-name . "gamm4")))
22865 (build-system r-build-system)
22867 `(("r-lme4" ,r-lme4)
22868 ("r-matrix" ,r-matrix)
22869 ("r-mgcv" ,r-mgcv)))
22870 (home-page "https://cran.r-project.org/web/packages/gamm4/")
22871 (synopsis "Generalized additive mixed models using mgcv and lme4")
22873 "Estimate generalized additive mixed models via a version of function
22874 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
22876 (license license:gpl2+)))
22878 (define-public r-optimx
22881 (version "2020-4.2")
22885 (uri (cran-uri "optimx" version))
22888 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
22889 (properties `((upstream-name . "optimx")))
22890 (build-system r-build-system)
22891 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
22892 (native-inputs `(("r-knitr" ,r-knitr)))
22893 (home-page "https://cran.r-project.org/web/packages/optimx/")
22894 (synopsis "Expanded replacement and extension of the optim function")
22896 "This package provides a replacement and extension of the @code{optim}
22897 function to call to several function minimization codes in R in a single
22898 statement. These methods handle smooth, possibly box constrained functions of
22899 several or many parameters. Note that the function @code{optimr} was prepared
22900 to simplify the incorporation of minimization codes going forward. This
22901 package also implements some utility codes and some extra solvers, including
22902 safeguarded Newton methods. Many methods previously separate are now included
22904 (license license:gpl2)))
22906 (define-public r-projpred
22908 (name "r-projpred")
22913 (uri (cran-uri "projpred" version))
22916 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
22917 (properties `((upstream-name . "projpred")))
22918 (build-system r-build-system)
22920 `(("r-dplyr" ,r-dplyr)
22921 ("r-gamm4" ,r-gamm4)
22922 ("r-ggplot2" ,r-ggplot2)
22925 ("r-magrittr" ,r-magrittr)
22928 ("r-optimx" ,r-optimx)
22930 ("r-rcpparmadillo" ,r-rcpparmadillo)
22931 ("r-rngtools" ,r-rngtools)
22932 ("r-rstantools" ,r-rstantools)
22933 ("r-tidyverse" ,r-tidyverse)))
22934 (native-inputs `(("r-knitr" ,r-knitr)))
22935 (home-page "https://mc-stan.org/projpred/")
22936 (synopsis "Projection predictive feature selection")
22938 "This package performs projection predictive feature selection for
22939 generalized linear models and generalized linear and additive multilevel
22940 models. The package is compatible with the @code{rstanarm} and @code{brms}
22941 packages, but other reference models can also be used. See the package
22942 vignette for more information and examples.")
22943 (license license:gpl3)))
22945 (define-public r-brms
22952 (uri (cran-uri "brms" version))
22955 "0s8dl1xm3bpivfv3hw94zv9cifjg8cgs5137yd8d755kc2v0fdmf"))))
22956 (properties `((upstream-name . "brms")))
22957 (build-system r-build-system)
22959 `(("r-abind" ,r-abind)
22960 ("r-backports" ,r-backports)
22961 ("r-bayesplot" ,r-bayesplot)
22962 ("r-bridgesampling" ,r-bridgesampling)
22964 ("r-future" ,r-future)
22965 ("r-ggplot2" ,r-ggplot2)
22968 ("r-matrix" ,r-matrix)
22969 ("r-matrixstats" ,r-matrixstats)
22971 ("r-nleqslv" ,r-nleqslv)
22974 ("r-rstan" ,r-rstan)
22975 ("r-rstantools" ,r-rstantools)
22976 ("r-shinystan" ,r-shinystan)))
22977 (native-inputs `(("r-knitr" ,r-knitr)))
22979 "https://github.com/paul-buerkner/brms")
22981 "Bayesian Regression Models using 'Stan'")
22983 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22984 using 'Stan' for full Bayesian inference. A wide range of distributions and
22985 link functions are supported, allowing users to fit -- among others -- linear,
22986 robust linear, count data, survival, response times, ordinal, zero-inflated,
22987 hurdle, and even self-defined mixture models all in a multilevel context.
22988 Further modeling options include non-linear and smooth terms, auto-correlation
22989 structures, censored data, meta-analytic standard errors, and quite a few
22990 more. In addition, all parameters of the response distribution can be
22991 predicted in order to perform distributional regression. Prior specifications
22992 are flexible and explicitly encourage users to apply prior distributions that
22993 actually reflect their beliefs. Model fit can easily be assessed and compared
22994 with posterior predictive checks and leave-one-out cross-validation.")
22995 (license license:gpl2)))
22997 (define-public r-mstate
23004 (uri (cran-uri "mstate" version))
23007 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
23008 (properties `((upstream-name . "mstate")))
23009 (build-system r-build-system)
23011 `(("r-rcolorbrewer" ,r-rcolorbrewer)
23012 ("r-survival" ,r-survival)))
23014 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
23016 "Data Preparation, Estimation and Prediction in Multi-State Models")
23018 "Contains functions for data preparation, descriptives, hazard estimation
23019 and prediction with Aalen-Johansen or simulation in competing risks and
23020 multi-state models.")
23021 (license license:gpl2+)))
23023 (define-public r-scatterpie
23025 (name "r-scatterpie")
23030 (uri (cran-uri "scatterpie" version))
23033 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
23034 (properties `((upstream-name . "scatterpie")))
23035 (build-system r-build-system)
23037 `(("r-ggforce" ,r-ggforce)
23038 ("r-ggplot2" ,r-ggplot2)
23039 ("r-rlang" ,r-rlang)
23040 ("r-rvcheck" ,r-rvcheck)
23041 ("r-tidyr" ,r-tidyr)))
23043 `(("r-knitr" ,r-knitr)))
23044 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
23045 (synopsis "Scatter pie plot")
23047 "This package creates scatterpie plots, especially useful for plotting
23049 (license license:artistic2.0)))
23051 (define-public r-boruta
23058 (uri (cran-uri "Boruta" version))
23061 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
23062 (properties `((upstream-name . "Boruta")))
23063 (build-system r-build-system)
23064 (propagated-inputs `(("r-ranger" ,r-ranger)))
23065 (home-page "https://gitlab.com/mbq/Boruta/")
23066 (synopsis "Wrapper algorithm for all relevant feature selection")
23068 "This package provides an all relevant feature selection wrapper
23069 algorithm. It finds relevant features by comparing original attributes'
23070 importance with importance achievable at random, estimated using their
23071 permuted copies (shadows).")
23072 (license license:gpl2+)))
23074 (define-public r-directlabels
23076 (name "r-directlabels")
23077 (version "2020.6.17")
23081 (uri (cran-uri "directlabels" version))
23084 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
23085 (build-system r-build-system)
23087 `(("r-quadprog" ,r-quadprog)))
23089 `(("r-knitr" ,r-knitr)))
23090 (home-page "http://directlabels.r-forge.r-project.org/")
23091 (synopsis "Direct labels for multicolor plots")
23093 "This package provides an extensible framework for automatically placing
23094 direct labels onto multicolor plots. Label positions are described using
23095 positioning methods that can be re-used across several different plots. There
23096 are heuristics for examining @code{trellis} and @code{ggplot} objects and
23097 inferring an appropriate positioning method.")
23098 (license license:gpl3)))
23100 (define-public r-lsd
23107 (uri (cran-uri "LSD" version))
23109 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
23110 (properties `((upstream-name . "LSD")))
23111 (build-system r-build-system)
23112 (home-page "https://cran.r-project.org/web/packages/LSD/")
23113 (synopsis "Lots of superior depictions tool creates colorful plots")
23115 "This package creates lots of colorful plots in a multitude of variations.
23116 Try a demo of the LSD by running @code{demotour()}.")
23118 (license (list license:gpl2 license:gpl3))))
23120 (define-public r-phylogram
23122 (name "r-phylogram")
23127 (uri (cran-uri "phylogram" version))
23129 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
23130 (properties `((upstream-name . "phylogram")))
23131 (build-system r-build-system)
23132 (propagated-inputs `(("r-ape" ,r-ape)))
23133 (home-page "https://github.com/ropensci/phylogram/")
23134 (synopsis "Dendrograms for evolutionary analysis")
23136 "The @code{r-phylogram} package is a tool for for developing phylogenetic
23137 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
23138 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
23139 as well as several tools for command-line tree manipulation and import/export
23140 via Newick parenthetic text. This improves accessibility to the comprehensive
23141 range of object-specific analytical and tree-visualization functions found
23142 across a wide array of bioinformatic R packages.")
23143 (license license:gpl3)))
23145 (define-public r-kmer
23152 (uri (cran-uri "kmer" version))
23154 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
23155 (properties `((upstream-name . "kmer")))
23156 (build-system r-build-system)
23158 `(("r-openssl" ,r-openssl)
23159 ("r-phylogram" ,r-phylogram)
23160 ("r-rcpp" ,r-rcpp)))
23161 (home-page "https://github.com/shaunpwilkinson/kmer/")
23162 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
23164 "@code{r-kmer} is an R package for rapidly computing distance matrices
23165 and clustering large sequence datasets using fast alignment-free k-mer
23166 counting and recursive k-means partitioning.")
23167 (license license:gpl3)))
23169 (define-public r-hardhat
23176 (uri (cran-uri "hardhat" version))
23179 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
23180 (properties `((upstream-name . "hardhat")))
23181 (build-system r-build-system)
23183 `(("r-glue" ,r-glue)
23184 ("r-rlang" ,r-rlang)
23185 ("r-tibble" ,r-tibble)
23186 ("r-vctrs" ,r-vctrs)))
23188 `(("r-knitr" ,r-knitr)))
23189 (home-page "https://github.com/tidymodels/hardhat")
23190 (synopsis "Construct modeling packages")
23192 "Building modeling packages is hard. A large amount of effort generally
23193 goes into providing an implementation for a new method that is efficient,
23194 fast, and correct, but often less emphasis is put on the user interface. A
23195 good interface requires specialized knowledge about S3 methods and formulas,
23196 which the average package developer might not have. The goal of
23197 @code{hardhat} is to reduce the burden around building new modeling packages
23198 by providing functionality for preprocessing, predicting, and validating
23200 (license license:expat)))
23202 (define-public r-shapforxgboost
23204 (name "r-shapforxgboost")
23209 (uri (cran-uri "SHAPforxgboost" version))
23212 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
23214 `((upstream-name . "SHAPforxgboost")))
23215 (build-system r-build-system)
23217 `(("r-bbmisc" ,r-bbmisc)
23218 ("r-data-table" ,r-data-table)
23219 ("r-ggextra" ,r-ggextra)
23220 ("r-ggforce" ,r-ggforce)
23221 ("r-ggplot2" ,r-ggplot2)
23222 ("r-ggpubr" ,r-ggpubr)
23223 ("r-rcolorbrewer" ,r-rcolorbrewer)
23224 ("r-xgboost" ,r-xgboost)))
23225 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
23226 (synopsis "SHAP Plots for XGBoost")
23228 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
23229 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
23230 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
23231 and force plot. It relies on the @code{XGBoost} package to produce SHAP
23233 (license license:expat)))
23235 (define-public r-rismed
23242 (uri (cran-uri "RISmed" version))
23245 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
23246 (properties `((upstream-name . "RISmed")))
23247 (build-system r-build-system)
23248 (home-page "https://cran.r-project.org/web/packages/RISmed")
23249 (synopsis "Download content from NCBI databases")
23251 "This package provides a set of tools to extract bibliographic
23252 content from the National Center for Biotechnology Information (NCBI)
23253 databases, including PubMed. The name RISmed is a portmanteau of
23254 RIS (for Research Information Systems, a common tag format for
23255 bibliographic data) and PubMed.")
23256 (license license:gpl2+)))
23258 (define-public r-semver
23265 (uri (cran-uri "semver" version))
23268 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
23269 (properties `((upstream-name . "semver")))
23270 (build-system r-build-system)
23272 `(("r-assertthat" ,r-assertthat)
23273 ("r-rcpp" ,r-rcpp)))
23274 (native-inputs `(("r-knitr" ,r-knitr)))
23275 (home-page "https://github.com/johndharrison/semver")
23276 (synopsis "Parser for Semantic Versioning 2.0.0")
23278 "This package provides tools and functions for parsing, rendering and
23279 operating on semantic version strings. Semantic versioning is a simple set of
23280 rules and requirements that dictate how version numbers are assigned and
23281 incremented as outlined at @url{http://semver.org}.")
23282 (license license:expat)))
23284 (define-public r-binman
23291 (uri (cran-uri "binman" version))
23294 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
23295 (properties `((upstream-name . "binman")))
23296 (build-system r-build-system)
23298 `(("r-assertthat" ,r-assertthat)
23300 ("r-jsonlite" ,r-jsonlite)
23301 ("r-rappdirs" ,r-rappdirs)
23302 ("r-semver" ,r-semver)
23304 ("r-yaml" ,r-yaml)))
23305 (native-inputs `(("r-knitr" ,r-knitr)))
23306 (home-page "https://github.com/ropensci/binman")
23307 (synopsis "Binary download manager")
23309 "This package provides tools and functions for managing the download of
23310 binary files. Binary repositories are defined in the YAML format. Defining
23311 new pre-download, download and post-download templates allow additional
23312 repositories to be added.")
23313 (license license:expat)))
23315 (define-public r-wdman
23322 (uri (cran-uri "wdman" version))
23325 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
23326 (properties `((upstream-name . "wdman")))
23327 (build-system r-build-system)
23329 `(("r-assertthat" ,r-assertthat)
23330 ("r-binman" ,r-binman)
23331 ("r-processx" ,r-processx)
23332 ("r-semver" ,r-semver)
23333 ("r-yaml" ,r-yaml)))
23334 (native-inputs `(("r-knitr" ,r-knitr)))
23335 (home-page "https://docs.ropensci.org/wdman/")
23336 (synopsis "Webdriver/Selenium binary manager")
23338 "There are a number of binary files associated with the
23339 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
23340 @url{https://sites.google.com/a/chromium.org/chromedriver/},
23341 @url{https://github.com/mozilla/geckodriver},
23342 @url{http://phantomjs.org/download.html}, and
23343 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
23344 more information). This package provides functions to download these binaries
23345 and to manage processes involving them.")
23346 (license license:expat)))
23348 (define-public r-rselenium
23350 (name "r-rselenium")
23355 (uri (cran-uri "RSelenium" version))
23358 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
23359 (properties `((upstream-name . "RSelenium")))
23360 (build-system r-build-system)
23362 `(("r-binman" ,r-binman)
23363 ("r-catools" ,r-catools)
23365 ("r-openssl" ,r-openssl)
23366 ("r-wdman" ,r-wdman)
23368 (native-inputs `(("r-knitr" ,r-knitr)))
23369 (home-page "https://docs.ropensci.org/RSelenium/")
23370 (synopsis "R bindings for Selenium WebDriver")
23372 "This package provides a set of R bindings for the Selenium 2.0
23373 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
23374 information) using the @code{JsonWireProtocol} (see
23375 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
23376 information). Selenium 2.0 WebDriver allows driving a web browser natively as
23377 a user would either locally or on a remote machine using the Selenium server
23378 it marks a leap forward in terms of web browser automation. Selenium
23379 automates web browsers (commonly referred to as browsers). Using RSelenium
23380 you can automate browsers locally or remotely.")
23381 (license license:agpl3+)))
23383 (define-public r-conquer
23390 (uri (cran-uri "conquer" version))
23393 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
23394 (properties `((upstream-name . "conquer")))
23395 (build-system r-build-system)
23397 `(("r-matrix" ,r-matrix)
23398 ("r-matrixstats" ,r-matrixstats)
23400 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23401 (home-page "https://github.com/XiaoouPan/conquer")
23402 (synopsis "Convolution-type smoothed quantile regression")
23404 "This package provides fast and accurate convolution-type smoothed
23405 quantile regression, implemented using Barzilai-Borwein gradient descent with
23406 a Huber regression warm start. Confidence intervals for regression
23407 coefficients are constructed using multiplier bootstrap.")
23408 (license license:gpl3)))
23410 (define-public r-fastshap
23412 (name "r-fastshap")
23417 (uri (cran-uri "fastshap" version))
23420 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
23421 (properties `((upstream-name . "fastshap")))
23422 (build-system r-build-system)
23424 `(("r-abind" ,r-abind)
23425 ("r-ggplot2" ,r-ggplot2)
23426 ("r-gridextra" ,r-gridextra)
23427 ("r-matrixstats" ,r-matrixstats)
23430 ("r-rcpparmadillo" ,r-rcpparmadillo)
23431 ("r-tibble" ,r-tibble)))
23432 (home-page "https://github.com/bgreenwell/fastshap")
23433 (synopsis "Fast approximate Shapley values")
23435 "This package computes fast (relative to other implementations)
23436 approximate Shapley values for any supervised learning model. Shapley values
23437 help to explain the predictions from any black box model using ideas from game
23438 theory; see @url{Strumbel and Kononenko (2014),
23439 doi.org/10.1007/s10115-013-0679-x} for details.")
23440 (license license:gpl2+)))
23442 (define-public r-metrics
23449 (uri (cran-uri "Metrics" version))
23452 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
23453 (properties `((upstream-name . "Metrics")))
23454 (build-system r-build-system)
23455 (home-page "https://github.com/mfrasco/Metrics")
23456 (synopsis "Evaluation metrics for machine learning")
23458 "This package provides an implementation of evaluation metrics in R that
23459 are commonly used in supervised machine learning. It implements metrics for
23460 regression, time series, binary classification, classification, and
23461 information retrieval problems. It has zero dependencies and a consistent,
23462 simple interface for all functions.")
23463 (license license:bsd-3)))
23465 (define-public r-iml
23472 (uri (cran-uri "iml" version))
23475 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
23476 (properties `((upstream-name . "iml")))
23477 (build-system r-build-system)
23479 `(("r-checkmate" ,r-checkmate)
23480 ("r-data-table" ,r-data-table)
23481 ("r-formula" ,r-formula)
23482 ("r-future" ,r-future)
23483 ("r-future-apply" ,r-future-apply)
23484 ("r-ggplot2" ,r-ggplot2)
23485 ("r-gridextra" ,r-gridextra)
23486 ("r-metrics" ,r-metrics)
23487 ("r-prediction" ,r-prediction)
23489 (native-inputs `(("r-knitr" ,r-knitr)))
23490 (home-page "https://github.com/christophM/iml")
23491 (synopsis "Interpretable machine learning")
23493 "This package provides interpretability methods to analyze the behavior
23494 and predictions of any machine learning model. Implemented methods are:
23497 @item Feature importance described by Fisher et al. (2018),
23498 @item accumulated local effects plots described by Apley (2018),
23499 @item partial dependence plots described by Friedman (2001),
23500 @item individual conditional expectation ('ice') plots described by Goldstein
23501 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
23502 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
23503 @item the Shapley Value described by Strumbelj et. al (2014)
23504 @url{https://doi.org/10.1007/s10115-013-0679-x},
23505 @item feature interactions described by Friedman et. al
23506 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
23509 (license license:expat)))
23511 (define-public r-goftest
23518 (uri (cran-uri "goftest" version))
23521 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23522 (properties `((upstream-name . "goftest")))
23523 (build-system r-build-system)
23524 (home-page "https://github.com/baddstats/goftest")
23525 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23527 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23528 goodness-of-fit for continuous univariate distributions, using efficient
23530 (license license:gpl2+)))
23532 (define-public r-tensor
23539 (uri (cran-uri "tensor" version))
23542 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23543 (properties `((upstream-name . "tensor")))
23544 (build-system r-build-system)
23545 (home-page "https://cran.r-project.org/web/packages/tensor/")
23546 (synopsis "Tensor product of arrays")
23548 "The tensor product of two arrays is notionally an outer product of the
23549 arrays collapsed in specific extents by summing along the appropriate
23550 diagonals. This package allows you to compute the tensor product of arrays.")
23551 (license license:gpl2+)))
23553 (define-public r-spatstat-utils
23555 (name "r-spatstat-utils")
23560 (uri (cran-uri "spatstat.utils" version))
23563 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23565 `((upstream-name . "spatstat.utils")))
23566 (build-system r-build-system)
23567 (home-page "http://www.spatstat.org")
23568 (synopsis "Utility functions for spatstat")
23570 "This package contains utility functions for the @code{spatstat} package
23571 which may also be useful for other purposes.")
23572 (license license:gpl2+)))
23574 (define-public r-spatstat-data
23576 (name "r-spatstat-data")
23581 (uri (cran-uri "spatstat.data" version))
23584 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23585 (properties `((upstream-name . "spatstat.data")))
23586 (build-system r-build-system)
23588 `(("r-matrix" ,r-matrix)
23589 ("r-spatstat-utils" ,r-spatstat-utils)))
23590 (home-page "http://www.spatstat.org")
23591 (synopsis "Datasets for spatstat")
23593 "This package contains all the datasets for the @code{spatstat}
23595 (license license:gpl2+)))
23597 (define-public r-spatstat
23599 (name "r-spatstat")
23604 (uri (cran-uri "spatstat" version))
23607 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23608 (properties `((upstream-name . "spatstat")))
23609 (build-system r-build-system)
23611 `(("r-abind" ,r-abind)
23612 ("r-deldir" ,r-deldir)
23613 ("r-goftest" ,r-goftest)
23614 ("r-matrix" ,r-matrix)
23617 ("r-polyclip" ,r-polyclip)
23618 ("r-rpart" ,r-rpart)
23619 ("r-spatstat-data" ,r-spatstat-data)
23620 ("r-spatstat-utils" ,r-spatstat-utils)
23621 ("r-tensor" ,r-tensor)))
23622 (home-page "http://www.spatstat.org")
23623 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23625 "This package provides a comprehensive toolbox for analysing Spatial
23626 Point Patterns. It is focused mainly on two-dimensional point patterns,
23627 including multitype/marked points, in any spatial region. It also supports
23628 three-dimensional point patterns, space-time point patterns in any number of
23629 dimensions, point patterns on a linear network, and patterns of other
23630 geometrical objects. It supports spatial covariate data such as pixel images
23631 and contains over 2000 functions for plotting spatial data, exploratory data
23632 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23633 formal inference.")
23634 (license license:gpl2+)))
23636 (define-public r-gaston
23643 (uri (cran-uri "gaston" version))
23646 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
23647 (properties `((upstream-name . "gaston")))
23648 (build-system r-build-system)
23649 (inputs `(("zlib" ,zlib)))
23651 `(("r-rcpp" ,r-rcpp)
23652 ("r-rcppeigen" ,r-rcppeigen)
23653 ("r-rcppparallel" ,r-rcppparallel)))
23654 (native-inputs `(("r-knitr" ,r-knitr)))
23655 (home-page "https://cran.r-project.org/web/packages/gaston/")
23656 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23658 "This is a package for the manipulation of genetic data (SNPs).
23659 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23660 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23661 for linear mixed models (AIREML).")
23662 (license license:gpl3)))
23664 (define-public r-cpp11
23671 (uri (cran-uri "cpp11" version))
23674 "1avcip33bldzz0rhkl43b4sljrbb8i24684xxmr9il5bijcpyy97"))))
23675 (properties `((upstream-name . "cpp11")))
23676 (build-system r-build-system)
23677 (native-inputs `(("r-knitr" ,r-knitr)))
23678 (home-page "https://github.com/r-lib/cpp11")
23679 (synopsis "C++11 Interface for R's C Interface")
23681 "This package provides a header only, C++11 interface to R's C interface.
23682 Compared to other approaches @code{cpp11} strives to be safe against long
23683 jumps from the C API as well as C++ exceptions, conform to normal R function
23684 semantics and supports interaction with @code{ALTREP} vectors.")
23685 (license license:expat)))
23687 (define-public r-rcppziggurat
23689 (name "r-rcppziggurat")
23694 (uri (cran-uri "RcppZiggurat" version))
23697 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
23698 (properties `((upstream-name . "RcppZiggurat")))
23699 (build-system r-build-system)
23701 `(("r-rcpp" ,r-rcpp)
23702 ("r-rcppgsl" ,r-rcppgsl)))
23703 (native-inputs `(("r-knitr" ,r-knitr)))
23704 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23705 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23707 "The Ziggurat generator for normally distributed random numbers,
23708 originally proposed by Marsaglia and Tsang (2000,
23709 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23710 times starting with Leong et al (2005,
23711 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23712 aggregation for comparing different implementations in order to provide a
23713 'faster but good enough' alternative for use with R and C++ code.")
23714 (license license:gpl2+)))
23716 (define-public r-rfast
23723 (uri (cran-uri "Rfast" version))
23726 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
23727 (properties `((upstream-name . "Rfast")))
23728 (build-system r-build-system)
23730 `(("r-rcpp" ,r-rcpp)
23731 ("r-rcpparmadillo" ,r-rcpparmadillo)
23732 ("r-rcppziggurat" ,r-rcppziggurat)))
23733 (home-page "https://github.com/RfastOfficial/Rfast")
23734 (synopsis "Collection of efficient and fast R functions")
23736 "This package provides a collection of fast (utility) functions for data
23737 analysis. Column- and row- wise means, medians, variances, minimums,
23738 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23739 Poisson), are some of the many fast functions.")
23740 (license license:gpl2+)))
23742 (define-public r-clusterr
23744 (name "r-clusterr")
23749 (uri (cran-uri "ClusterR" version))
23752 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23753 (properties `((upstream-name . "ClusterR")))
23754 (build-system r-build-system)
23756 `(("r-ggplot2" ,r-ggplot2)
23758 ("r-gtools" ,r-gtools)
23760 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23761 (native-inputs `(("r-knitr" ,r-knitr)))
23762 (home-page "https://github.com/mlampros/ClusterR")
23763 (synopsis "Clustering")
23765 "This package provides Gaussian mixture models, k-means,
23766 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23767 option to plot, validate, predict (new data) and estimate the optimal number
23768 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23769 the computationally intensive parts of the functions. For more information,
23773 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23774 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23775 @url{https://doi.org/10.18637/jss.v001.i04};
23776 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23777 Library, @url{https://doi.org/10.1145/1772690.1772862};
23778 @item \"Armadillo: a template-based C++ library
23779 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23780 Software, @url{https://doi.org/10.21105/joss.00026};
23781 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23782 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23783 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23786 (license license:gpl3)))
23788 (define-public r-spectrum
23790 (name "r-spectrum")
23795 (uri (cran-uri "Spectrum" version))
23798 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23799 (properties `((upstream-name . "Spectrum")))
23800 (build-system r-build-system)
23802 `(("r-clusterr" ,r-clusterr)
23803 ("r-diptest" ,r-diptest)
23804 ("r-ggplot2" ,r-ggplot2)
23805 ("r-rfast" ,r-rfast)))
23806 (native-inputs `(("r-knitr" ,r-knitr)))
23807 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23808 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23810 "This package provides a self-tuning spectral clustering method for
23811 single or multi-view data. Spectrum uses a new type of adaptive density aware
23812 kernel that strengthens connections in the graph based on common nearest
23813 neighbours. It uses a tensor product graph data integration and diffusion
23814 procedure to integrate different data sources and reduce noise. Spectrum uses
23815 either the eigengap or multimodality gap heuristics to determine the number of
23816 clusters. The method is sufficiently flexible so that a wide range of
23817 Gaussian and non-Gaussian structures can be clustered with automatic selection
23819 (license license:agpl3+)))
23821 (define-public r-nabor
23828 (uri (cran-uri "nabor" version))
23831 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23832 (properties `((upstream-name . "nabor")))
23833 (build-system r-build-system)
23837 ("r-rcppeigen" ,r-rcppeigen)))
23838 (home-page "https://cran.r-project.org/web/packages/nabor/")
23839 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23841 "This package provides an R wrapper for libnabo, an exact or approximate
23842 k nearest neighbour library which is optimised for low dimensional
23843 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23844 designed as a drop-in replacement for the RANN function @code{nn2}. In
23845 addition, objects which include the k-d tree search structure can be returned
23846 to speed up repeated queries of the same set of target points.")
23847 (license license:bsd-3)))
23849 (define-public r-muhaz
23852 (version "1.2.6.1")
23856 (uri (cran-uri "muhaz" version))
23859 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23860 (properties `((upstream-name . "muhaz")))
23861 (build-system r-build-system)
23863 `(("r-survival" ,r-survival)))
23865 `(("gfortran" ,gfortran)))
23866 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23867 (synopsis "Hazard function estimation in survival analysis")
23869 "This package produces a smooth estimate of the hazard function for
23871 ;; Any version of the GPL.
23872 (license license:gpl3+)))
23874 (define-public r-flexsurv
23876 (name "r-flexsurv")
23881 (uri (cran-uri "flexsurv" version))
23884 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23885 (properties `((upstream-name . "flexsurv")))
23886 (build-system r-build-system)
23888 `(("r-desolve" ,r-desolve)
23889 ("r-mstate" ,r-mstate)
23890 ("r-muhaz" ,r-muhaz)
23891 ("r-mvtnorm" ,r-mvtnorm)
23892 ("r-quadprog" ,r-quadprog)
23894 ("r-survival" ,r-survival)
23895 ("r-tibble" ,r-tibble)
23896 ("r-tidyr" ,r-tidyr)))
23898 `(("r-knitr" ,r-knitr)))
23899 (home-page "https://github.com/chjackson/flexsurv-dev")
23900 (synopsis "Flexible parametric survival and multi-state models")
23902 "This package provides flexible parametric models for time-to-event data,
23903 including the Royston-Parmar spline model, generalized gamma and generalized F
23904 distributions. Any user-defined parametric distribution can be fitted, given
23905 at least an R function defining the probability density or hazard. There are
23906 also tools for fitting and predicting from fully parametric multi-state
23908 (license license:gpl2+)))
23910 (define-public r-transphylo
23912 (name "r-transphylo")
23917 (uri (cran-uri "TransPhylo" version))
23920 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23921 (properties `((upstream-name . "TransPhylo")))
23922 (build-system r-build-system)
23925 ("r-rcpp" ,r-rcpp)))
23927 `(("r-knitr" ,r-knitr)))
23928 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23929 (synopsis "Inference of transmission tree from a dated phylogeny")
23931 "This is a package to infer transmission trees from a dated phylogeny.
23932 It includes methods to simulate and analyze outbreaks. The methodology is
23933 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23934 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23935 (license license:gpl2+)))
23937 (define-public r-km-ci
23944 (uri (cran-uri "km.ci" version))
23947 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23948 (properties `((upstream-name . "km.ci")))
23949 (build-system r-build-system)
23951 `(("r-survival" ,r-survival)))
23952 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23953 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23955 "This package computes various @dfn{confidence intervals} (CI) for the
23956 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23957 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23958 Nair and Hall and Wellner.")
23959 (license license:gpl2+)))
23961 (define-public r-kmsurv
23968 (uri (cran-uri "KMsurv" version))
23971 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23972 (properties `((upstream-name . "KMsurv")))
23973 (build-system r-build-system)
23974 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23975 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23977 "This package provides data sets and functions for Klein and Moeschberger
23978 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23980 (license license:gpl3+)))
23982 (define-public r-survmisc
23984 (name "r-survmisc")
23989 (uri (cran-uri "survMisc" version))
23992 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23993 (properties `((upstream-name . "survMisc")))
23994 (build-system r-build-system)
23996 `(("r-data-table" ,r-data-table)
23997 ("r-ggplot2" ,r-ggplot2)
23998 ("r-gridextra" ,r-gridextra)
23999 ("r-km-ci" ,r-km-ci)
24000 ("r-kmsurv" ,r-kmsurv)
24001 ("r-knitr" ,r-knitr)
24002 ("r-survival" ,r-survival)
24003 ("r-xtable" ,r-xtable)
24006 `(("r-knitr" ,r-knitr)))
24007 (home-page "https://cran.r-project.org/web/packages/survMisc/")
24008 (synopsis "Miscellaneous functions for survival data")
24010 "This package provides a collection of functions to help in the analysis
24011 of right-censored survival data. These extend the methods available in
24012 the @code{survival} package.")
24013 (license license:gpl2)))
24015 (define-public r-exactranktests
24017 (name "r-exactranktests")
24022 (uri (cran-uri "exactRankTests" version))
24025 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
24027 `((upstream-name . "exactRankTests")))
24028 (build-system r-build-system)
24029 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
24030 (synopsis "Exact distributions for rank and permutation tests")
24032 "This package computes exact conditional p-values and quantiles using an
24033 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
24034 (license license:gpl2+)))
24036 (define-public r-maxstat
24043 (uri (cran-uri "maxstat" version))
24046 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
24047 (properties `((upstream-name . "maxstat")))
24048 (build-system r-build-system)
24050 `(("r-exactranktests" ,r-exactranktests)
24051 ("r-mvtnorm" ,r-mvtnorm)))
24052 (home-page "https://cran.r-project.org/web/packages/maxstat/")
24053 (synopsis "Maximally selected rank statistics")
24055 "This package provides maximally selected rank statistics with several
24056 p-value approximations.")
24057 (license license:gpl2+)))
24059 (define-public r-survminer
24061 (name "r-survminer")
24066 (uri (cran-uri "survminer" version))
24069 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
24070 (properties `((upstream-name . "survminer")))
24071 (build-system r-build-system)
24073 `(("r-broom" ,r-broom)
24074 ("r-dplyr" ,r-dplyr)
24075 ("r-ggplot2" ,r-ggplot2)
24076 ("r-ggpubr" ,r-ggpubr)
24077 ("r-gridextra" ,r-gridextra)
24078 ("r-magrittr" ,r-magrittr)
24079 ("r-maxstat" ,r-maxstat)
24080 ("r-purrr" ,r-purrr)
24081 ("r-rlang" ,r-rlang)
24082 ("r-scales" ,r-scales)
24083 ("r-survival" ,r-survival)
24084 ("r-survmisc" ,r-survmisc)
24085 ("r-tibble" ,r-tibble)
24086 ("r-tidyr" ,r-tidyr)))
24088 `(("r-knitr" ,r-knitr)))
24089 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
24090 (synopsis "Drawing survival curves using ggplot2")
24092 "This package contains the function @code{ggsurvplot()} for easily
24093 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
24094 risk' table and 'censoring count plot'. Other functions are also available to
24095 plot adjusted curves for Cox model and to visually examine Cox model
24097 (license license:gpl2)))
24099 (define-public r-forge
24106 (uri (cran-uri "forge" version))
24109 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
24110 (properties `((upstream-name . "forge")))
24111 (build-system r-build-system)
24113 `(("r-magrittr" ,r-magrittr)
24114 ("r-rlang" ,r-rlang)))
24115 (home-page "https://cran.r-project.org/web/packages/forge/")
24116 (synopsis "Cast values into shape")
24118 "This package provides helper functions with a consistent interface to
24119 coerce and verify the types and shapes of values for input checking.")
24120 (license license:asl2.0)))
24122 (define-public r-config
24129 (uri (cran-uri "config" version))
24132 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
24133 (properties `((upstream-name . "config")))
24134 (build-system r-build-system)
24136 `(("r-yaml" ,r-yaml)))
24138 `(("r-knitr" ,r-knitr)))
24139 (home-page "https://github.com/rstudio/config")
24140 (synopsis "Manage environment specific configuration values")
24142 "This package lets you manage configuration values across multiple
24143 environments (e.g. development, test, production). It reads values using a
24144 function that determines the current environment and returns the appropriate
24146 (license license:gpl3)))
24148 (define-public r-adaptivesparsity
24150 (name "r-adaptivesparsity")
24154 (uri (cran-uri "AdaptiveSparsity" version))
24157 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
24159 `((upstream-name . "AdaptiveSparsity")))
24160 (build-system r-build-system)
24163 (modify-phases %standard-phases
24164 (add-after 'unpack 'link-against-armadillo
24166 (substitute* "src/Makevars"
24167 (("PKG_LIBS=" prefix)
24168 (string-append prefix "-larmadillo")))
24171 `(("r-mass" ,r-mass)
24172 ("r-matrix" ,r-matrix)
24174 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24176 `(("armadillo" ,armadillo)))
24177 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
24178 (synopsis "Adaptive sparsity models")
24180 "This package implements the Figueiredo machine learning algorithm for
24181 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
24182 geometric models.")
24183 (license license:lgpl3+)))
24185 (define-public r-diffusionmap
24187 (name "r-diffusionmap")
24192 (uri (cran-uri "diffusionMap" version))
24195 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
24196 (properties `((upstream-name . "diffusionMap")))
24197 (build-system r-build-system)
24199 `(("r-igraph" ,r-igraph)
24200 ("r-matrix" ,r-matrix)
24201 ("r-scatterplot3d" ,r-scatterplot3d)))
24202 (home-page "https://www.r-project.org")
24203 (synopsis "Diffusion map")
24204 (description "This package implements the diffusion map method of data
24205 parametrization, including creation and visualization of diffusion maps,
24206 clustering with diffusion K-means and regression using the adaptive regression
24208 (license license:gpl2)))
24210 (define-public r-igraph
24217 (uri (cran-uri "igraph" version))
24220 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
24221 (build-system r-build-system)
24223 `(("gfortran" ,gfortran)))
24227 ("libxml2" ,libxml2)
24230 `(("r-magrittr" ,r-magrittr)
24231 ("r-matrix" ,r-matrix)
24232 ("r-pkgconfig" ,r-pkgconfig)))
24233 (home-page "https://igraph.org")
24234 (synopsis "Network analysis and visualization")
24236 "This package provides routines for simple graphs and network analysis.
24237 It can handle large graphs very well and provides functions for generating
24238 random and regular graphs, graph visualization, centrality methods and much
24240 (license license:gpl2+)))
24242 (define-public r-workflows
24244 (name "r-workflows")
24249 (uri (cran-uri "workflows" version))
24252 "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9"))))
24253 (properties `((upstream-name . "workflows")))
24254 (build-system r-build-system)
24257 ("r-ellipsis" ,r-ellipsis)
24258 ("r-generics" ,r-generics)
24260 ("r-hardhat" ,r-hardhat)
24261 ("r-parsnip" ,r-parsnip)
24262 ("r-rlang" ,r-rlang)
24263 ("r-tidyselect" ,r-tidyselect)))
24265 `(("r-knitr" ,r-knitr)))
24266 (home-page "https://github.com/tidymodels/workflows")
24267 (synopsis "Modeling workflows")
24269 "A workflow is an object that can bundle together your pre-processing,
24270 modeling, and post-processing requests. For example, if you have a
24271 @code{recipe} and @code{parsnip} model, these can be combined into a
24272 workflow. The advantages are:
24275 @item You don’t have to keep track of separate objects in your workspace.
24276 @item The recipe prepping and model fitting can be executed using a single
24277 call to @code{fit()}.
24278 @item If you have custom tuning parameter settings, these can be defined using
24279 a simpler interface when combined with @code{tune}.
24280 @item In the future, workflows will be able to add post-processing operations,
24281 such as modifying the probability cutoff for two-class models.
24284 (license license:expat)))
24286 (define-public r-gpfit
24293 (uri (cran-uri "GPfit" version))
24296 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
24297 (properties `((upstream-name . "GPfit")))
24298 (build-system r-build-system)
24300 `(("r-lattice" ,r-lattice)
24302 (home-page "https://cran.r-project.org/web/packages/GPfit/")
24303 (synopsis "Gaussian Processes modeling")
24305 "This package provides a computationally stable approach of fitting a
24306 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
24307 (license license:gpl2)))
24309 (define-public r-yardstick
24311 (name "r-yardstick")
24316 (uri (cran-uri "yardstick" version))
24319 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
24320 (properties `((upstream-name . "yardstick")))
24321 (build-system r-build-system)
24323 `(("r-dplyr" ,r-dplyr)
24324 ("r-generics" ,r-generics)
24326 ("r-rlang" ,r-rlang)
24327 ("r-tidyselect" ,r-tidyselect)))
24329 `(("r-knitr" ,r-knitr)))
24330 (home-page "https://github.com/tidymodels/yardstick")
24331 (synopsis "Tidy characterizations of model performance")
24333 "This package provides tidy tools for quantifying how well a model fits
24334 to a data set such as confusion matrices, class probability curve summaries,
24335 and regression metrics (e.g., RMSE).")
24336 (license license:gpl2)))
24338 (define-public r-warp
24345 (uri (cran-uri "warp" version))
24348 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
24349 (properties `((upstream-name . "warp")))
24350 (build-system r-build-system)
24351 (native-inputs `(("r-knitr" ,r-knitr)))
24352 (home-page "https://github.com/DavisVaughan/warp")
24353 (synopsis "Group dates")
24355 "This package provides tooling to group dates by a variety of periods
24356 including: yearly, monthly, by second, by week of the month, and more. The
24357 groups are defined in such a way that they also represent the distance between
24358 dates in terms of the period. This extracts valuable information that can be
24359 used in further calculations that rely on a specific temporal spacing between
24361 (license license:expat)))
24363 (define-public r-slider
24370 (uri (cran-uri "slider" version))
24373 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
24374 (properties `((upstream-name . "slider")))
24375 (build-system r-build-system)
24377 `(("r-glue" ,r-glue)
24378 ("r-rlang" ,r-rlang)
24379 ("r-vctrs" ,r-vctrs)
24380 ("r-warp" ,r-warp)))
24381 (native-inputs `(("r-knitr" ,r-knitr)))
24382 (home-page "https://github.com/DavisVaughan/slider")
24383 (synopsis "Sliding window functions")
24385 "This package provides type-stable rolling window functions over any R
24386 data type. Cumulative and expanding windows are also supported. For more
24387 advanced usage, an index can be used as a secondary vector that defines how
24388 sliding windows are to be created.")
24389 (license license:expat)))
24391 (define-public r-rsample
24398 (uri (cran-uri "rsample" version))
24401 "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i"))))
24402 (properties `((upstream-name . "rsample")))
24403 (build-system r-build-system)
24405 `(("r-dplyr" ,r-dplyr)
24406 ("r-ellipsis" ,r-ellipsis)
24407 ("r-furrr" ,r-furrr)
24408 ("r-generics" ,r-generics)
24409 ("r-modeldata" ,r-modeldata)
24410 ("r-purrr" ,r-purrr)
24411 ("r-rlang" ,r-rlang)
24412 ("r-slider" ,r-slider)
24413 ("r-tibble" ,r-tibble)
24414 ("r-tidyr" ,r-tidyr)
24415 ("r-tidyselect" ,r-tidyselect)
24416 ("r-vctrs" ,r-vctrs)))
24418 `(("r-knitr" ,r-knitr)))
24419 (home-page "https://rsample.tidymodels.org")
24420 (synopsis "General resampling infrastructure")
24422 "This package provides classes and functions to create and summarize
24423 different types of resampling objects (e.g. bootstrap, cross-validation).")
24424 (license license:gpl2)))
24426 (define-public r-dicedesign
24428 (name "r-dicedesign")
24433 (uri (cran-uri "DiceDesign" version))
24436 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
24437 (properties `((upstream-name . "DiceDesign")))
24438 (build-system r-build-system)
24439 (home-page "http://dice.emse.fr/")
24440 (synopsis "Designs of computer experiments")
24442 "This package provides tools to create some specific @code{Space-Filling
24443 Design} (SFD) and to test their quality.")
24444 (license license:gpl3)))
24446 (define-public r-dials
24453 (uri (cran-uri "dials" version))
24456 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
24457 (properties `((upstream-name . "dials")))
24458 (build-system r-build-system)
24460 `(("r-dicedesign" ,r-dicedesign)
24461 ("r-dplyr" ,r-dplyr)
24463 ("r-purrr" ,r-purrr)
24464 ("r-rlang" ,r-rlang)
24465 ("r-scales" ,r-scales)
24466 ("r-tibble" ,r-tibble)
24467 ("r-vctrs" ,r-vctrs)
24468 ("r-withr" ,r-withr)))
24469 (native-inputs `(("r-knitr" ,r-knitr)))
24470 (home-page "https://dials.tidymodels.org/")
24471 (synopsis "Tools for creating tuning parameter values")
24473 "Many models contain tuning parameters (i.e. parameters that cannot be
24474 directly estimated from the data). These tools can be used to define objects
24475 for creating, simulating, or validating values for such parameters.")
24476 (license license:gpl2)))
24478 (define-public r-tune
24485 (uri (cran-uri "tune" version))
24488 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
24489 (properties `((upstream-name . "tune")))
24490 (build-system r-build-system)
24493 ("r-crayon" ,r-crayon)
24494 ("r-dials" ,r-dials)
24495 ("r-dplyr" ,r-dplyr)
24496 ("r-foreach" ,r-foreach)
24497 ("r-ggplot2" ,r-ggplot2)
24499 ("r-gpfit" ,r-gpfit)
24500 ("r-hardhat" ,r-hardhat)
24501 ("r-lifecycle" ,r-lifecycle)
24502 ("r-parsnip" ,r-parsnip)
24503 ("r-purrr" ,r-purrr)
24504 ("r-recipes" ,r-recipes)
24505 ("r-rlang" ,r-rlang)
24506 ("r-rsample" ,r-rsample)
24507 ("r-tibble" ,r-tibble)
24508 ("r-tidyr" ,r-tidyr)
24509 ("r-vctrs" ,r-vctrs)
24510 ("r-workflows" ,r-workflows)
24511 ("r-yardstick" ,r-yardstick)))
24512 (home-page "https://github.com/tidymodels/tune")
24513 (synopsis "Tidy tuning tools")
24515 "The ability to tune models is important. @code{tune} contains functions
24516 and classes to be used in conjunction with other @code{tidymodels} packages
24517 for finding reasonable values of hyper-parameters in models, pre-processing
24518 methods, and post-processing steps.")
24519 (license license:expat)))
24521 (define-public r-tidyposterior
24523 (name "r-tidyposterior")
24528 (uri (cran-uri "tidyposterior" version))
24531 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
24532 (properties `((upstream-name . "tidyposterior")))
24533 (build-system r-build-system)
24535 `(("r-dplyr" ,r-dplyr)
24536 ("r-generics" ,r-generics)
24537 ("r-ggplot2" ,r-ggplot2)
24538 ("r-lifecycle" ,r-lifecycle)
24539 ("r-purrr" ,r-purrr)
24540 ("r-rlang" ,r-rlang)
24541 ("r-rsample" ,r-rsample)
24542 ("r-rstanarm" ,r-rstanarm)
24543 ("r-tibble" ,r-tibble)
24544 ("r-tidyr" ,r-tidyr)
24545 ("r-vctrs" ,r-vctrs)))
24547 `(("r-knitr" ,r-knitr)))
24548 (home-page "https://tidyposterior.tidymodels.org")
24549 (synopsis "Bayesian analysis to compare models using resampling statistics")
24551 "This package can be used to conduct post hoc analyses of resampling
24552 results generated by models. For example, if two models are evaluated with
24553 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
24554 are 10 paired statistics. These can be used to make comparisons between
24555 models without involving a test set.")
24556 (license license:gpl2)))
24558 (define-public r-tidypredict
24560 (name "r-tidypredict")
24565 (uri (cran-uri "tidypredict" version))
24568 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
24569 (properties `((upstream-name . "tidypredict")))
24570 (build-system r-build-system)
24572 `(("r-dplyr" ,r-dplyr)
24573 ("r-generics" ,r-generics)
24574 ("r-knitr" ,r-knitr)
24575 ("r-purrr" ,r-purrr)
24576 ("r-rlang" ,r-rlang)
24577 ("r-stringr" ,r-stringr)
24578 ("r-tibble" ,r-tibble)
24579 ("r-tidyr" ,r-tidyr)))
24581 `(("r-knitr" ,r-knitr)))
24582 (home-page "https://tidypredict.tidymodels.org")
24583 (synopsis "Run predictions inside the database")
24585 "This package parses a fitted R model object, and returns a formula in
24586 Tidy Eval code that calculates the predictions. It works with several
24587 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
24588 final SQL translation of the algorithm. It currently supports @code{lm()},
24589 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
24590 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
24591 (license license:gpl3)))
24593 (define-public r-janeaustenr
24595 (name "r-janeaustenr")
24600 (uri (cran-uri "janeaustenr" version))
24603 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
24604 (properties `((upstream-name . "janeaustenr")))
24605 (build-system r-build-system)
24606 (home-page "https://github.com/juliasilge/janeaustenr")
24607 (synopsis "Jane Austen's complete novels")
24609 "This package provides the full texts for Jane Austen's six completed
24610 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
24611 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
24612 and \"Persuasion\".")
24613 (license license:expat)))
24615 (define-public r-tokenizers
24617 (name "r-tokenizers")
24622 (uri (cran-uri "tokenizers" version))
24625 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
24626 (properties `((upstream-name . "tokenizers")))
24627 (build-system r-build-system)
24629 `(("r-rcpp" ,r-rcpp)
24630 ("r-snowballc" ,r-snowballc)
24631 ("r-stringi" ,r-stringi)))
24633 `(("r-knitr" ,r-knitr)))
24634 (home-page "https://lincolnmullen.com/software/tokenizers/")
24635 (synopsis "Fast, consistent tokenization of natural language text")
24637 "This is a package for converting natural language text into tokens.
24638 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
24639 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
24640 Treebank, regular expressions, as well as functions for counting characters,
24641 words, and sentences, and a function for splitting longer texts into separate
24642 documents, each with the same number of words. The tokenizers have a
24643 consistent interface, and the package is built on the @code{stringi} and
24644 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
24645 (license license:expat)))
24647 (define-public r-hunspell
24649 (name "r-hunspell")
24654 (uri (cran-uri "hunspell" version))
24657 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24658 (properties `((upstream-name . "hunspell")))
24659 (build-system r-build-system)
24661 `(("r-digest" ,r-digest)
24662 ("r-rcpp" ,r-rcpp)))
24664 `(("r-knitr" ,r-knitr)))
24665 (home-page "https://github.com/ropensci/hunspell#readme")
24666 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24668 "This package provides a low-level spell checker and morphological
24669 analyzer based on the famous @code{hunspell} library. The package can analyze
24670 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24671 For a more user-friendly interface use the @code{spelling} package which
24672 builds on this package to automate checking of files, documentation and
24673 vignettes in all common formats.")
24674 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24675 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24676 ;; available under the Expat license.
24677 (license (list license:gpl2
24682 (define-public r-tidytext
24684 (name "r-tidytext")
24689 (uri (cran-uri "tidytext" version))
24692 "0xmjkab7p13ncfglf3a9hvndf8fh96mmxw3l7hcpbnaq9qkiwk29"))))
24693 (properties `((upstream-name . "tidytext")))
24694 (build-system r-build-system)
24696 `(("r-dplyr" ,r-dplyr)
24697 ("r-generics" ,r-generics)
24698 ("r-hunspell" ,r-hunspell)
24699 ("r-janeaustenr" ,r-janeaustenr)
24700 ("r-matrix" ,r-matrix)
24701 ("r-purrr" ,r-purrr)
24702 ("r-rlang" ,r-rlang)
24703 ("r-stringr" ,r-stringr)
24704 ("r-tibble" ,r-tibble)
24705 ("r-tokenizers" ,r-tokenizers)))
24707 `(("r-knitr" ,r-knitr)))
24708 (home-page "https://github.com/juliasilge/tidytext")
24709 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24711 "This is a package for text mining for word processing and sentiment
24712 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24713 (license license:expat)))
24715 (define-public r-parsnip
24722 (uri (cran-uri "parsnip" version))
24725 "1134840xisvkkrbkh5kvx24vxp7sx06124svy573a9m4h8c492sr"))))
24726 (properties `((upstream-name . "parsnip")))
24727 (build-system r-build-system)
24729 `(("r-dplyr" ,r-dplyr)
24730 ("r-generics" ,r-generics)
24731 ("r-globals" ,r-globals)
24733 ("r-magrittr" ,r-magrittr)
24734 ("r-prettyunits" ,r-prettyunits)
24735 ("r-purrr" ,r-purrr)
24736 ("r-rlang" ,r-rlang)
24737 ("r-tibble" ,r-tibble)
24738 ("r-tidyr" ,r-tidyr)
24739 ("r-vctrs" ,r-vctrs)))
24741 `(("r-knitr" ,r-knitr)))
24742 (home-page "https://parsnip.tidymodels.org")
24743 (synopsis "Common API to modeling and analysis functions")
24745 "This package provides a common interface to allow users to specify a
24746 model without having to remember the different argument names across different
24747 functions or computational engines (e.g. R, Spark, Stan, etc).")
24748 (license license:gpl2)))
24750 (define-public r-infer
24757 (uri (cran-uri "infer" version))
24760 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24761 (properties `((upstream-name . "infer")))
24762 (build-system r-build-system)
24764 `(("r-dplyr" ,r-dplyr)
24765 ("r-ggplot2" ,r-ggplot2)
24767 ("r-magrittr" ,r-magrittr)
24768 ("r-purrr" ,r-purrr)
24769 ("r-rlang" ,r-rlang)
24770 ("r-tibble" ,r-tibble)))
24772 `(("r-knitr" ,r-knitr)))
24773 (home-page "https://github.com/tidymodels/infer")
24774 (synopsis "Tidy statistical inference")
24776 "The objective of this package is to perform inference using an
24777 expressive statistical grammar that coheres with the Tidy design framework.")
24778 (license license:cc0)))
24780 (define-public r-modeldata
24782 (name "r-modeldata")
24787 (uri (cran-uri "modeldata" version))
24790 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
24791 (properties `((upstream-name . "modeldata")))
24792 (build-system r-build-system)
24793 (home-page "https://modeldata.tidymodels.org")
24794 (synopsis "Data sets useful for modeling packages")
24796 "This package provides data sets used for demonstrating or testing
24797 model-related packages.")
24798 (license license:expat)))
24800 (define-public r-tidymodels
24802 (name "r-tidymodels")
24807 (uri (cran-uri "tidymodels" version))
24810 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24811 (properties `((upstream-name . "tidymodels")))
24812 (build-system r-build-system)
24814 `(("r-broom" ,r-broom)
24816 ("r-crayon" ,r-crayon)
24817 ("r-dials" ,r-dials)
24818 ("r-dplyr" ,r-dplyr)
24819 ("r-ggplot2" ,r-ggplot2)
24820 ("r-infer" ,r-infer)
24821 ("r-magrittr" ,r-magrittr)
24822 ("r-modeldata" ,r-modeldata)
24823 ("r-parsnip" ,r-parsnip)
24824 ("r-purrr" ,r-purrr)
24825 ("r-recipes" ,r-recipes)
24826 ("r-rlang" ,r-rlang)
24827 ("r-rsample" ,r-rsample)
24828 ("r-rstudioapi" ,r-rstudioapi)
24829 ("r-tibble" ,r-tibble)
24830 ("r-tidyr" ,r-tidyr)
24832 ("r-workflows" ,r-workflows)
24833 ("r-yardstick" ,r-yardstick)))
24835 `(("r-knitr" ,r-knitr)
24836 ("r-rmarkdown" ,r-rmarkdown)
24838 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24839 (home-page "https://github.com/tidymodels/tidymodels")
24840 (synopsis "Tidy collection for modeling and statistical analysis")
24842 "The tidy modeling \"verse\" is a collection of packages for modeling and
24843 statistical analysis that share the underlying design philosophy, grammar, and
24844 data structures of the tidyverse.")
24845 (license license:gpl3)))
24847 (define-public r-mlecens
24854 (uri (cran-uri "MLEcens" version))
24857 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24858 (properties `((upstream-name . "MLEcens")))
24859 (build-system r-build-system)
24860 (home-page "http://stat.ethz.ch/~maathuis/")
24861 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24863 "This package contains functions to compute the nonparametric
24864 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24865 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24866 To be more precise, we consider the situation where we observe a set of
24867 rectangles that are known to contain the unobservable realizations of (X,Y).
24868 We compute the MLE based on such a set of rectangles. The methods can also be
24869 used for univariate censored data (see data set @code{cosmesis}), and for
24870 censored data with competing risks (see data set @code{menopause}). The
24871 package also provides functions to visualize the observed data and the MLE.")
24872 (license license:gpl2+)))
24874 (define-public r-perm
24877 (version "1.0-0.0")
24881 (uri (cran-uri "perm" version))
24884 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24885 (properties `((upstream-name . "perm")))
24886 (build-system r-build-system)
24887 (home-page "https://cran.r-project.org/web/packages/perm/")
24888 (synopsis "Exact or asymptotic permutation tests")
24890 "This package provides several methods for performing permutation tests.
24891 It has three main functions, to perform linear permutation tests. These tests
24892 are tests where the test statistic is the sum of the product of a
24893 covariate (usually group indicator) and the scores.")
24894 ;; Any version of the GPL
24895 (license license:gpl2+)))
24897 (define-public r-qtl
24904 (uri (cran-uri "qtl" version))
24907 "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
24908 (build-system r-build-system)
24909 (home-page "https://rqtl.org/")
24910 (synopsis "R package for analyzing QTL experiments in genetics")
24911 (description "R/qtl is an extension library for the R statistics system.
24912 It is used to analyze experimental crosses for identifying genes contributing
24913 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
24915 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
24916 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
24918 (license license:gpl3)))
24920 (define-public r-qtl2
24923 (version "0.22-11")
24926 (uri (cran-uri "qtl2" version))
24928 (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
24929 (build-system r-build-system)
24931 `(("r-data-table" ,r-data-table)
24932 ("r-jsonlite" ,r-jsonlite)
24934 ("r-rcppeigen" ,r-rcppeigen)
24935 ("r-rsqlite" ,r-rsqlite)
24936 ("r-yaml" ,r-yaml)))
24937 (home-page "https://kbroman.org/qtl2/")
24938 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
24940 "This package provides a set of tools to perform @dfn{Quantitative Trait
24941 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
24942 @code{R/qtl} package to better handle high-dimensional data and complex cross
24943 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
24944 (license license:gpl3)))
24946 (define-public r-seqminer
24948 (name "r-seqminer")
24953 (uri (cran-uri "seqminer" version))
24956 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
24957 (build-system r-build-system)
24960 (home-page "http://seqminer.genomic.codes")
24961 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
24963 "This package provides tools to integrate nucleotide sequencing
24964 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
24965 ;; Any version of the GPL is acceptable
24966 (license (list license:gpl2+ license:gpl3+))))
24968 (define-public r-maldiquant
24970 (name "r-maldiquant")
24975 (uri (cran-uri "MALDIquant" version))
24978 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
24979 (properties `((upstream-name . "MALDIquant")))
24980 (build-system r-build-system)
24981 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
24982 (synopsis "Quantitative analysis of mass spectrometry data")
24984 "This package provides a complete analysis pipeline for matrix-assisted
24985 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
24986 two-dimensional mass spectrometry data. In addition to commonly used plotting
24987 and processing methods it includes distinctive features, namely baseline
24988 subtraction methods such as morphological filters (TopHat) or the
24989 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
24990 alignment using warping functions, handling of replicated measurements as well
24991 as allowing spectra with different resolutions.")
24992 (license license:gpl3+)))
24994 (define-public r-seurat
25000 (uri (cran-uri "Seurat" version))
25003 "048vnj0c3mrwhr6yq3jqhgnkg68w99nj1ccsmgnd8rl694w26spj"))))
25004 (properties `((upstream-name . "Seurat")))
25005 (build-system r-build-system)
25007 `(("r-cluster" ,r-cluster)
25008 ("r-cowplot" ,r-cowplot)
25009 ("r-fitdistrplus" ,r-fitdistrplus)
25010 ("r-future" ,r-future)
25011 ("r-future-apply" ,r-future-apply)
25012 ("r-ggplot2" ,r-ggplot2)
25013 ("r-ggrepel" ,r-ggrepel)
25014 ("r-ggridges" ,r-ggridges)
25017 ("r-igraph" ,r-igraph)
25018 ("r-irlba" ,r-irlba)
25019 ("r-jsonlite" ,r-jsonlite)
25020 ("r-kernsmooth" ,r-kernsmooth)
25021 ("r-leiden" ,r-leiden)
25022 ("r-lmtest" ,r-lmtest)
25024 ("r-matrix" ,r-matrix)
25025 ("r-matrixstats" ,r-matrixstats)
25026 ("r-miniui" ,r-miniui)
25027 ("r-patchwork" ,r-patchwork)
25028 ("r-pbapply" ,r-pbapply)
25029 ("r-plotly" ,r-plotly)
25032 ("r-rcolorbrewer" ,r-rcolorbrewer)
25034 ("r-rcppannoy" ,r-rcppannoy)
25035 ("r-rcppeigen" ,r-rcppeigen)
25036 ("r-rcppprogress" ,r-rcppprogress)
25037 ("r-reticulate" ,r-reticulate)
25038 ("r-rlang" ,r-rlang)
25041 ("r-rtsne" ,r-rtsne)
25042 ("r-scales" ,r-scales)
25043 ("r-sctransform" ,r-sctransform)
25044 ("r-shiny" ,r-shiny)
25045 ("r-spatstat" ,r-spatstat)
25046 ("r-tibble" ,r-tibble)
25047 ("r-uwot" ,r-uwot)))
25048 (home-page "http://www.satijalab.org/seurat")
25049 (synopsis "Seurat is an R toolkit for single cell genomics")
25051 "This package is an R package designed for QC, analysis, and
25052 exploration of single cell RNA-seq data. It easily enables widely-used
25053 analytical techniques, including the identification of highly variable genes,
25054 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
25055 algorithms; density clustering, hierarchical clustering, k-means, and the
25056 discovery of differentially expressed genes and markers.")
25057 (license license:gpl3)))
25059 (define-public r-phangorn
25061 (name "r-phangorn")
25066 (uri (cran-uri "phangorn" version))
25069 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
25070 (build-system r-build-system)
25073 ("r-fastmatch" ,r-fastmatch)
25074 ("r-igraph" ,r-igraph)
25075 ("r-magrittr" ,r-magrittr)
25076 ("r-matrix" ,r-matrix)
25077 ("r-quadprog" ,r-quadprog)
25078 ("r-rcpp" ,r-rcpp)))
25079 (home-page "https://github.com/KlausVigo/phangorn")
25080 (synopsis "Phylogenetic analysis in R")
25082 "Phangorn is a package for phylogenetic analysis in R. It supports
25083 estimation of phylogenetic trees and networks using Maximum Likelihood,
25084 Maximum Parsimony, distance methods and Hadamard conjugation.")
25085 (license license:gpl2+)))
25087 (define-public r-diversitree
25089 (name "r-diversitree")
25094 (uri (cran-uri "diversitree" version))
25097 "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
25098 (build-system r-build-system)
25100 `(("gfortran" ,gfortran)))
25101 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
25104 ("r-desolve" ,r-desolve)
25106 ("r-subplex" ,r-subplex)))
25107 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
25108 (synopsis "Comparative 'phylogenetic' analyses of diversification")
25109 (description "This package contains a number of comparative \"phylogenetic\"
25110 methods, mostly focusing on analysing diversification and character evolution.
25111 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
25112 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
25113 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
25114 include Markov models of discrete and continuous trait evolution and constant
25115 rate speciation and extinction.")
25116 (license license:gpl2+)))
25118 (define-public r-absfiltergsea
25120 (name "r-absfiltergsea")
25125 (uri (cran-uri "AbsFilterGSEA" version))
25127 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
25128 (properties `((upstream-name . "AbsFilterGSEA")))
25129 (build-system r-build-system)
25131 `(("r-biobase" ,r-biobase)
25132 ("r-deseq" ,r-deseq)
25133 ("r-limma" ,r-limma)
25135 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25136 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
25137 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
25139 "This package provides a function that performs gene-permuting of a gene-set
25140 enrichment analysis (GSEA) calculation with or without the absolute filtering.
25141 Without filtering, users can perform (original) two-tailed or one-tailed
25143 (license license:gpl2)))
25145 (define-public r-calculus
25147 (name "r-calculus")
25152 (uri (cran-uri "calculus" version))
25155 "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp"))))
25156 (properties `((upstream-name . "calculus")))
25157 (build-system r-build-system)
25159 `(("r-rcpp" ,r-rcpp)))
25160 (home-page "https://github.com/eguidotti/calculus")
25161 (synopsis "High dimensional numerical and symbolic calculus")
25163 "Efficient C++ optimized functions for numerical and symbolic calculus.
25164 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
25165 convention, fast computation of the Levi-Civita symbol and generalized
25166 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
25167 accurate high-order derivatives, differential operators (Gradient, Jacobian,
25168 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
25169 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
25170 parabolic or user defined by custom scale factors.")
25171 (license license:gpl3)))
25173 (define-public r-aws-signature
25175 (name "r-aws-signature")
25180 (uri (cran-uri "aws.signature" version))
25183 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
25184 (properties `((upstream-name . "aws.signature")))
25185 (build-system r-build-system)
25187 `(("r-base64enc" ,r-base64enc)
25188 ("r-digest" ,r-digest)))
25189 (home-page "https://github.com/cloudyr/aws.signature")
25190 (synopsis "Amazon Web Services Request Signatures")
25192 "This package generates version 2 and 4 request signatures for Amazon Web
25193 Services (AWS) and provides a mechanism for retrieving credentials from
25194 environment variables, AWS credentials files, and EC2 instance metadata. For
25195 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
25196 (license license:gpl2+)))
25198 (define-public r-aws-s3
25205 (uri (cran-uri "aws.s3" version))
25208 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
25209 (properties `((upstream-name . "aws.s3")))
25210 (build-system r-build-system)
25212 `(("r-aws-signature" ,r-aws-signature)
25213 ("r-base64enc" ,r-base64enc)
25215 ("r-digest" ,r-digest)
25217 ("r-xml2" ,r-xml2)))
25218 (home-page "https://github.com/cloudyr/aws.s3")
25219 (synopsis "AWS S3 Client Package")
25221 "This package provides a simple client package for the Amazon Web
25222 Services (AWS) Simple Storage Service (S3) REST API.")
25223 (license license:gpl2+)))