1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
38 ;;; This file is part of GNU Guix.
40 ;;; GNU Guix is free software; you can redistribute it and/or modify it
41 ;;; under the terms of the GNU General Public License as published by
42 ;;; the Free Software Foundation; either version 3 of the License, or (at
43 ;;; your option) any later version.
45 ;;; GNU Guix is distributed in the hope that it will be useful, but
46 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
47 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
48 ;;; GNU General Public License for more details.
50 ;;; You should have received a copy of the GNU General Public License
51 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
53 (define-module (gnu packages cran)
54 #:use-module ((guix licenses) #:prefix license:)
55 #:use-module (guix packages)
56 #:use-module (guix download)
57 #:use-module (guix git-download)
58 #:use-module (guix utils)
59 #:use-module (guix build-system gnu)
60 #:use-module (guix build-system r)
61 #:use-module (gnu packages)
62 #:use-module (gnu packages algebra)
63 #:use-module (gnu packages autotools)
64 #:use-module (gnu packages base)
65 #:use-module (gnu packages bioinformatics)
66 #:use-module (gnu packages c)
67 #:use-module (gnu packages compression)
68 #:use-module (gnu packages crypto)
69 #:use-module (gnu packages curl)
70 #:use-module (gnu packages databases)
71 #:use-module (gnu packages fontutils)
72 #:use-module (gnu packages fribidi)
73 #:use-module (gnu packages gcc)
74 #:use-module (gnu packages geo)
75 #:use-module (gnu packages ghostscript)
76 #:use-module (gnu packages gl)
77 #:use-module (gnu packages gnome)
78 #:use-module (gnu packages graph)
79 #:use-module (gnu packages gtk)
80 #:use-module (gnu packages haskell-xyz)
81 #:use-module (gnu packages icu4c)
82 #:use-module (gnu packages image)
83 #:use-module (gnu packages imagemagick)
84 #:use-module (gnu packages java)
85 #:use-module (gnu packages javascript)
86 #:use-module (gnu packages libevent)
87 #:use-module (gnu packages lisp-xyz)
88 #:use-module (gnu packages machine-learning)
89 #:use-module (gnu packages maths)
90 #:use-module (gnu packages mpi)
91 #:use-module (gnu packages multiprecision)
92 #:use-module (gnu packages networking)
93 #:use-module (gnu packages node)
94 #:use-module (gnu packages pcre)
95 #:use-module (gnu packages pdf)
96 #:use-module (gnu packages perl)
97 #:use-module (gnu packages pkg-config)
98 #:use-module (gnu packages pulseaudio) ;libsndfile
99 #:use-module (gnu packages python)
100 #:use-module (gnu packages python-xyz)
101 #:use-module (gnu packages sqlite)
102 #:use-module (gnu packages statistics)
103 #:use-module (gnu packages tcl)
104 #:use-module (gnu packages textutils)
105 #:use-module (gnu packages tls)
106 #:use-module (gnu packages version-control)
107 #:use-module (gnu packages web)
108 #:use-module (gnu packages xml)
109 #:use-module (gnu packages xorg))
111 (define-public r-brio
118 (uri (cran-uri "brio" version))
121 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
122 (properties `((upstream-name . "brio")))
123 (build-system r-build-system)
124 (home-page "https://github.com/r-lib/brio")
125 (synopsis "Basic R input output")
127 "This package provides functions to handle basic input output. These
128 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
129 files and provide more explicit control over line endings.")
130 (license license:expat)))
132 (define-public r-cachem
139 (uri (cran-uri "cachem" version))
142 "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh"))))
143 (properties `((upstream-name . "cachem")))
144 (build-system r-build-system)
146 `(("r-fastmap" ,r-fastmap)
147 ("r-rlang" ,r-rlang)))
148 (home-page "https://cachem.r-lib.org/")
149 (synopsis "Cache R objects with automatic pruning")
151 "This package provides key-value stores with automatic pruning. Caches
152 can limit either their total size or the age of the oldest object (or both),
153 automatically pruning objects to maintain the constraints.")
154 (license license:expat)))
156 (define-public r-diffobj
163 (uri (cran-uri "diffobj" version))
166 "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q"))))
167 (properties `((upstream-name . "diffobj")))
168 (build-system r-build-system)
169 (propagated-inputs `(("r-crayon" ,r-crayon)))
170 (native-inputs `(("r-knitr" ,r-knitr)))
171 (home-page "https://github.com/brodieG/diffobj")
172 (synopsis "Diffs for R objects")
174 "Generate a colorized diff of two R objects for an intuitive
175 visualization of their differences.")
176 (license license:gpl2+)))
178 (define-public r-waldo
185 (uri (cran-uri "waldo" version))
188 "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr"))))
189 (properties `((upstream-name . "waldo")))
190 (build-system r-build-system)
193 ("r-diffobj" ,r-diffobj)
196 ("r-rematch2" ,r-rematch2)
198 ("r-tibble" ,r-tibble)))
199 (home-page "https://github.com/r-lib/waldo")
200 (synopsis "Find differences between R objects")
202 "Compare complex R objects and reveal the key differences. This package
203 was designed particularly for use in testing packages where being able to
204 quickly isolate key differences makes understanding test failures much
206 (license license:expat)))
208 (define-public r-rticles
215 (uri (cran-uri "rticles" version))
218 "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818"))))
219 (properties `((upstream-name . "rticles")))
220 (build-system r-build-system)
222 `(("r-knitr" ,r-knitr)
223 ("r-rmarkdown" ,r-rmarkdown)
224 ("r-tinytex" ,r-tinytex)
227 (home-page "https://github.com/rstudio/rticles")
228 (synopsis "Article formats for R Markdown")
230 "This package provides a suite of custom R Markdown formats and templates
231 for authoring journal articles and conference submissions.")
232 (license license:gpl3)))
234 (define-public r-bezier
240 (uri (cran-uri "bezier" version))
243 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
244 (build-system r-build-system)
245 (home-page "https://cran.r-project.org/web/packages/bezier/")
246 (synopsis "Bezier curve and spline toolkit")
248 "This package is a toolkit for working with Bezier curves and splines.
249 The package provides functions for point generation, arc length estimation,
250 degree elevation and curve fitting.")
251 (license license:gpl2+)))
260 (uri (cran-uri "V8" version))
263 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
264 (properties `((upstream-name . "V8")))
265 (build-system r-build-system)
268 (modify-phases %standard-phases
269 (add-after 'unpack 'find-v8
270 (lambda* (#:key inputs #:allow-other-keys)
271 (substitute* "configure"
273 (string-append "PKG_LIBS="
274 (assoc-ref inputs "node")
275 "/lib/libnode.so.64\n")))
276 (setenv "INCLUDE_DIR"
278 (assoc-ref inputs "node")
282 (assoc-ref inputs "node") "/lib"))
285 `(("node" ,libnode)))
288 ("r-jsonlite" ,r-jsonlite)
291 `(("r-knitr" ,r-knitr)))
292 (home-page "https://jeroen.cran.dev/V8")
293 (synopsis "Embedded JavaScript and WebAssembly engine for R")
295 "This package provides an R interface to V8: Google's JavaScript and
296 WebAssembly engine.")
297 (license license:expat)))
306 (uri (cran-uri "DOT" version))
309 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
310 (properties `((upstream-name . "DOT")))
311 (build-system r-build-system)
314 (home-page "http://haghish.com/dot")
315 (synopsis "Render and Export DOT Graphs in R")
317 "This package provides tools to render DOT diagram markup language in R
318 and also provides the possibility to export the graphs in PostScript and
319 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
320 programming packages such as @code{knitr} and @code{rmarkdown}.")
321 (license license:expat)))
323 (define-public r-clipr
330 (uri (cran-uri "clipr" version))
333 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
334 (build-system r-build-system)
336 `(("r-knitr" ,r-knitr)))
337 (home-page "https://github.com/mdlincoln/clipr")
338 (synopsis "Read and write from the system clipboard")
340 "This package provides simple utility functions to read from and write to
341 the system clipboards.")
342 (license license:gpl3)))
350 (uri (cran-uri "zoo" version))
353 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
354 (build-system r-build-system)
356 `(("r-lattice" ,r-lattice)))
357 (home-page "http://zoo.R-Forge.R-project.org/")
358 (synopsis "S3 infrastructure for regular and irregular time series")
359 (description "This package contains an S3 class with methods for totally
360 ordered indexed observations. It is particularly aimed at irregular time
361 series of numeric vectors/matrices and factors.")
362 (license license:gpl2+)))
364 (define-public r-ggalluvial
366 (name "r-ggalluvial")
370 (uri (cran-uri "ggalluvial" version))
373 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
374 (properties `((upstream-name . "ggalluvial")))
375 (build-system r-build-system)
377 `(("r-dplyr" ,r-dplyr)
378 ("r-ggplot2" ,r-ggplot2)
379 ("r-lazyeval" ,r-lazyeval)
382 ("r-tidyselect" ,r-tidyselect)))
384 `(("r-knitr" ,r-knitr)))
385 (home-page "http://corybrunson.github.io/ggalluvial/")
386 (synopsis "Alluvial plots for ggplot2")
387 (description "This package provides alluvial plots for @code{ggplot2}.
388 Alluvial plots use variable-width ribbons and stacked bar plots to represent
389 multi-dimensional or repeated-measures data with categorical or ordinal
391 (license license:gpl3)))
393 (define-public r-ggpmisc
399 (uri (cran-uri "ggpmisc" version))
402 "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v"))))
403 (build-system r-build-system)
405 `(("r-dplyr" ,r-dplyr)
406 ("r-generics" ,r-generics)
408 ("r-ggplot2" ,r-ggplot2)
409 ("r-gridextra" ,r-gridextra)
410 ("r-lubridate" ,r-lubridate)
411 ("r-magrittr" ,r-magrittr)
414 ("r-polynom" ,r-polynom)
416 ("r-scales" ,r-scales)
417 ("r-splus2r" ,r-splus2r)
418 ("r-stringr" ,r-stringr)
419 ("r-tibble" ,r-tibble)
423 `(("r-knitr" ,r-knitr)))
424 (home-page "https://www.r4photobiology.info/")
425 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
426 (description "This package provides extensions to @code{ggplot2},
427 respecting the grammar of its graphics paradigm.")
428 (license license:gpl2+)))
430 (define-public r-gprofiler
437 (uri (cran-uri "gProfileR" version))
440 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
441 (properties `((upstream-name . "gProfileR")))
442 (build-system r-build-system)
445 ("r-rcurl" ,r-rcurl)))
446 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
447 (synopsis "Interface to the g:Profiler toolkit")
449 "This package provides tools for functional enrichment analysis,
450 gene identifier conversion and mapping homologous genes across related
451 organisms via the @code{g:Profiler} toolkit.")
452 (license license:gpl2+)))
454 (define-public r-gprofiler2
456 (name "r-gprofiler2")
461 (uri (cran-uri "gprofiler2" version))
464 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
465 (properties `((upstream-name . "gprofiler2")))
466 (build-system r-build-system)
468 `(("r-crosstalk" ,r-crosstalk)
470 ("r-ggplot2" ,r-ggplot2)
471 ("r-gridextra" ,r-gridextra)
472 ("r-jsonlite" ,r-jsonlite)
473 ("r-plotly" ,r-plotly)
476 ("r-viridislite" ,r-viridislite)))
477 (native-inputs `(("r-knitr" ,r-knitr)))
478 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
479 (synopsis "Interface to the g:Profiler toolset")
481 "This package provides a toolset for functional enrichment analysis and
482 visualization, gene/protein/SNP identifier conversion and mapping orthologous
483 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
487 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
489 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
491 @item @code{g:Orth}, orthology search across species;
492 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
493 genes and variant effects.
496 This package is an R interface corresponding to the 2019 update of
497 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
499 (license license:gpl2+)))
501 (define-public r-oenb
508 (uri (cran-uri "oenb" version))
511 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
512 (properties `((upstream-name . "oenb")))
513 (build-system r-build-system)
515 `(("r-dplyr" ,r-dplyr)
517 (native-inputs `(("r-knitr" ,r-knitr)))
518 (home-page "https://github.com/franzmohr/oenb")
519 (synopsis "Tools for the OeNB Data Web Service")
521 "Tools to access data from the data web service of the
522 @acronym{OeNB, Oesterreichische Nationalbank},
523 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
524 (license license:gpl2+)))
526 (define-public r-scales
533 (uri (cran-uri "scales" version))
535 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
536 (build-system r-build-system)
538 `(("r-farver" ,r-farver)
539 ("r-labeling" ,r-labeling)
540 ("r-lifecycle" ,r-lifecycle)
541 ("r-munsell" ,r-munsell)
542 ("r-rcolorbrewer" ,r-rcolorbrewer)
544 ("r-viridislite" ,r-viridislite)))
545 (home-page "https://github.com/hadley/scales")
546 (synopsis "Scale functions for visualization")
548 "This package provides graphical scales that map data to aesthetics, and
549 provides methods for automatically determining breaks and labels for axes and
551 (license license:expat)))
553 (define-public r-pheatmap
560 (uri (cran-uri "pheatmap" version))
563 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
564 (build-system r-build-system)
566 `(("r-gtable" ,r-gtable)
567 ("r-rcolorbrewer" ,r-rcolorbrewer)
568 ("r-scales" ,r-scales)))
569 (home-page "https://cran.r-project.org/web/packages/pheatmap")
570 (synopsis "Pretty heatmaps")
572 "This package provides an implementation of heatmaps that offers more
573 control over dimensions and appearance.")
574 (license license:gpl2+)))
582 (uri (cran-uri "ecp" version))
585 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
586 (build-system r-build-system)
588 `(("r-rcpp" ,r-rcpp)))
589 (home-page "https://cran.r-project.org/web/packages/ecp/")
590 (synopsis "Multiple change-point analysis of multivariate data")
592 "This package implements various procedures for finding multiple
593 change-points. Two methods make use of dynamic programming and pruning, with
594 no distributional assumptions other than the existence of certain absolute
595 moments in one method. Hierarchical and exact search methods are included.
596 All methods return the set of estimated change-points as well as other summary
598 (license license:gpl2+)))
600 (define-public r-ellipsis
607 (uri (cran-uri "ellipsis" version))
610 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
611 (build-system r-build-system)
613 `(("r-rlang" ,r-rlang)))
614 (home-page "https://github.com/hadley/ellipsis")
615 (synopsis "Tools for working with additional arguments")
617 "In S3 generics, it's useful to take @code{...} so that methods can have
618 additional arguments. But this flexibility comes at a cost: misspelled
619 arguments will be silently ignored. The @code{ellipsis} package is an
620 experiment that allows a generic to warn if any arguments passed in @code{...}
622 (license license:gpl3)))
631 (uri (cran-uri "grr" version))
634 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
635 (build-system r-build-system)
636 (home-page "https://cran.r-project.org/web/packages/grr")
637 (synopsis "Alternative implementations of base R functions")
639 "This package provides alternative implementations of some base R
640 functions, including @code{sort}, @code{order}, and @code{match}. The
641 functions are simplified but can be faster or have other advantages.")
642 (license license:gpl3)))
644 (define-public r-matrix-utils
646 (name "r-matrix-utils")
651 (uri (cran-uri "Matrix.utils" version))
654 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
655 (properties `((upstream-name . "Matrix.utils")))
656 (build-system r-build-system)
659 ("r-matrix" ,r-matrix)))
660 (home-page "https://github.com/cvarrichio/Matrix.utils")
662 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
664 "This package implements data manipulation methods such as @code{cast},
665 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
667 (license license:gpl3)))
669 (define-public r-mboost
675 (uri (cran-uri "mboost" version))
678 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
679 (build-system r-build-system)
681 `(("r-lattice" ,r-lattice)
682 ("r-matrix" ,r-matrix)
684 ("r-partykit" ,r-partykit)
685 ("r-quadprog" ,r-quadprog)
687 ("r-survival" ,r-survival)))
688 (home-page "https://github.com/boost-R/mboost")
689 (synopsis "Model-based boosting")
691 "This package provides a functional gradient descent algorithm (boosting)
692 for optimizing general risk functions utilizing component-wise (penalised)
693 least squares estimates or regression trees as base-learners for fitting
694 generalized linear, additive and interaction models to potentially
695 high-dimensional data.")
696 (license license:gpl2)))
698 (define-public r-shadowtext
700 (name "r-shadowtext")
704 (uri (cran-uri "shadowtext" version))
707 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
708 (properties `((upstream-name . "shadowtext")))
709 (build-system r-build-system)
711 `(("r-ggplot2" ,r-ggplot2)
712 ("r-scales" ,r-scales)))
714 `(("r-knitr" ,r-knitr)))
715 (home-page "https://github.com/GuangchuangYu/shadowtext/")
716 (synopsis "Shadow text grob and layer")
717 (description "This package implements @code{shadowtextGrob()} for
718 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
719 These functions draw text grob with background shadow.")
720 (license license:artistic2.0)))
729 (uri (cran-uri "sys" version))
732 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
733 (build-system r-build-system)
734 (home-page "https://github.com/jeroen/sys")
735 (synopsis "Powerful and reliable tools for running system commands in R")
737 "This package provides drop-in replacements for the base @code{system2()}
738 function with fine control and consistent behavior across platforms. It
739 supports clean interruption, timeout, background tasks, and streaming STDIN /
740 STDOUT / STDERR over binary or text connections. The package also provides
741 functions for evaluating expressions inside a temporary fork. Such
742 evaluations have no side effects on the main R process, and support reliable
743 interrupts and timeouts. This provides the basis for a sandboxing
745 (license license:expat)))
747 (define-public r-ashr
753 (uri (cran-uri "ashr" version))
756 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
757 (properties `((upstream-name . "ashr")))
758 (build-system r-build-system)
760 `(("r-etrunct" ,r-etrunct)
761 ("r-invgamma" ,r-invgamma)
762 ("r-matrix" ,r-matrix)
763 ("r-mixsqp" ,r-mixsqp)
765 ("r-squarem" ,r-squarem)
766 ("r-truncnorm" ,r-truncnorm)))
768 `(("r-knitr" ,r-knitr)))
769 (home-page "https://github.com/stephens999/ashr")
770 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
771 (description "This package implements an empirical Bayes approach for
772 large-scale hypothesis testing and false discovery rate estimation.")
773 (license license:gpl3+)))
775 (define-public r-askpass
782 (uri (cran-uri "askpass" version))
785 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
786 (build-system r-build-system)
787 (propagated-inputs `(("r-sys" ,r-sys)))
788 (home-page "https://github.com/jeroen/askpass")
789 (synopsis "Safe password entry for R")
791 "This package provides cross-platform utilities for prompting the user
792 for credentials or a passphrase, for example to authenticate with a server or
793 read a protected key.")
794 (license license:expat)))
796 (define-public r-vegan
803 (uri (cran-uri "vegan" version))
806 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
807 (build-system r-build-system)
809 `(("r-knitr" ,r-knitr) ; needed for vignettes
810 ("gfortran" ,gfortran)))
812 `(("r-cluster" ,r-cluster)
813 ("r-lattice" ,r-lattice)
816 ("r-permute" ,r-permute)))
817 (home-page "https://cran.r-project.org/web/packages/vegan")
818 (synopsis "Functions for community ecology")
820 "The vegan package provides tools for descriptive community ecology. It
821 has most basic functions of diversity analysis, community ordination and
822 dissimilarity analysis. Most of its multivariate tools can be used for other
823 data types as well.")
824 (license license:gpl2+)))
826 (define-public r-tidyverse
833 (uri (cran-uri "tidyverse" version))
836 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
837 (build-system r-build-system)
839 `(("r-broom" ,r-broom)
841 ("r-crayon" ,r-crayon)
842 ("r-dbplyr" ,r-dbplyr)
844 ("r-forcats" ,r-forcats)
845 ("r-ggplot2" ,r-ggplot2)
849 ("r-jsonlite" ,r-jsonlite)
850 ("r-lubridate" ,r-lubridate)
851 ("r-magrittr" ,r-magrittr)
852 ("r-modelr" ,r-modelr)
853 ("r-pillar" ,r-pillar)
856 ("r-readxl" ,r-readxl)
857 ("r-reprex" ,r-reprex)
859 ("r-rstudioapi" ,r-rstudioapi)
861 ("r-stringr" ,r-stringr)
862 ("r-tibble" ,r-tibble)
865 (home-page "https://tidyverse.tidyverse.org")
866 (synopsis "Install and load packages from the \"Tidyverse\"")
868 "The @code{tidyverse} is a set of packages that work in harmony because
869 they share common data representations and API design. This package is
870 designed to make it easy to install and load multiple tidyverse packages in a
872 (license license:gpl3)))
874 (define-public r-rvest
881 (uri (cran-uri "rvest" version))
883 (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53"))))
884 (build-system r-build-system)
887 ("r-lifecycle" ,r-lifecycle)
888 ("r-magrittr" ,r-magrittr)
890 ("r-selectr" ,r-selectr)
891 ("r-tibble" ,r-tibble)
894 `(("r-knitr" ,r-knitr)))
895 (home-page "https://github.com/hadley/rvest")
896 (synopsis "Simple web scraping for R")
898 "@code{r-rvest} helps you scrape information from web pages. It is
899 designed to work with @code{magrittr} to make it easy to express common web
900 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
901 (license license:gpl3)))
903 (define-public r-selectr
910 (uri (cran-uri "selectr" version))
912 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
913 (build-system r-build-system)
915 `(("r-stringr" ,r-stringr)
917 (home-page "https://sjp.co.nz/projects/selectr/")
918 (synopsis "Translate CSS selectors to XPath expressions")
920 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
921 expression. This allows you to use CSS selectors when working with the XML
922 package as it can only evaluate XPath expressions. Also provided are
923 convenience functions useful for using CSS selectors on XML nodes. This
924 package is a port of the Python package @code{cssselect}.")
925 (license license:bsd-3)))
927 (define-public r-reprex
934 (uri (cran-uri "reprex" version))
937 "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh"))))
938 (build-system r-build-system)
940 `(("r-callr" ,r-callr)
947 ("r-rmarkdown" ,r-rmarkdown)
948 ("r-rstudioapi" ,r-rstudioapi)
949 ("r-withr" ,r-withr)))
951 `(("r-knitr" ,r-knitr)))
952 (home-page "https://github.com/tidyverse/reprex")
953 (synopsis "Prepare reproducible R code examples for sharing")
955 "This package provides a convenience wrapper that uses the
956 @code{rmarkdown} package to render small snippets of code to target formats
957 that include both code and output. The goal is to encourage the sharing of
958 small, reproducible, and runnable examples on code-oriented websites or email.
959 @code{reprex} also extracts clean, runnable R code from various common formats,
960 such as copy/paste from an R session.")
961 (license license:expat)))
963 (define-public r-reordercluster
965 (name "r-reordercluster")
969 (uri (cran-uri "ReorderCluster" version))
972 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
973 (build-system r-build-system)
975 `(("r-gplots" ,r-gplots)
977 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
978 (synopsis "Reordering the dendrogram according to the class labels")
979 (description "This package provides tools for performing the leaf reordering
980 for the dendrogram that preserves the hierarchical clustering result and at the
981 same time tries to group instances from the same class together.")
982 (license license:gpl3+)))
984 (define-public r-callr
991 (uri (cran-uri "callr" version))
994 "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6"))))
995 (build-system r-build-system)
998 ("r-processx" ,r-processx)))
999 (home-page "https://github.com/r-lib/callr#readme")
1000 (synopsis "Call R from R")
1002 "It is sometimes useful to perform a computation in a separate R process,
1003 without affecting the current R process at all. This package does exactly
1005 (license license:expat)))
1007 (define-public r-readxl
1014 (uri (cran-uri "readxl" version))
1017 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1018 (build-system r-build-system)
1020 `(("r-cellranger" ,r-cellranger)
1021 ("r-progress" ,r-progress)
1023 ("r-tibble" ,r-tibble)))
1024 (home-page "https://readxl.tidyverse.org")
1025 (synopsis "Read Excel files")
1027 "This package lets you import Excel files into R. It supports
1028 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1029 the embedded @code{RapidXML} C++ library.")
1030 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1031 ;; 'rapidxml' which is Boost.
1032 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1034 (define-public r-modelr
1041 (uri (cran-uri "modelr" version))
1044 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1045 (build-system r-build-system)
1047 `(("r-broom" ,r-broom)
1048 ("r-magrittr" ,r-magrittr)
1049 ("r-purrr" ,r-purrr)
1050 ("r-rlang" ,r-rlang)
1051 ("r-tibble" ,r-tibble)
1052 ("r-tidyr" ,r-tidyr)
1053 ("r-tidyselect" ,r-tidyselect)
1054 ("r-vctrs" ,r-vctrs)))
1055 (home-page "https://github.com/tidyverse/modelr")
1056 (synopsis "Helper functions for modelling in pipelines")
1058 "Functions for modelling that help you seamlessly integrate modelling
1059 into a pipeline of data manipulation and visualisation.")
1060 (license license:gpl3)))
1062 (define-public r-httpuv
1068 (uri (cran-uri "httpuv" version))
1071 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1072 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1073 ;; only contains fixes for building on Solaris.
1074 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1075 (modules '((guix build utils)))
1078 (delete-file-recursively "src/libuv")
1079 ;; Cannot unbundle http-parser, because it contains local
1082 (build-system r-build-system)
1085 (modify-phases %standard-phases
1086 (add-after 'unpack 'unbundle-libuv
1087 (lambda* (#:key outputs #:allow-other-keys)
1088 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1089 (("\"libuv/include/uv\\.h\"")
1091 ;; Fix https://github.com/rstudio/httpuv/issues/282
1092 (substitute* "src/http.cpp"
1093 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1094 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1097 `(("libuv" ,libuv)))
1100 ("r-later" ,r-later)
1101 ("r-promises" ,r-promises)
1103 ("r-rcpp" ,r-rcpp)))
1104 (home-page "https://github.com/rstudio/httpuv")
1105 (synopsis "HTTP and WebSocket server library for R")
1107 "The httpuv package provides low-level socket and protocol support for
1108 handling HTTP and WebSocket requests directly from within R. It is primarily
1109 intended as a building block for other packages, rather than making it
1110 particularly easy to create complete web applications using httpuv alone.")
1111 ;; This package includes third-party code that was originally released
1112 ;; under various non-copyleft licenses. Full licensing information can be
1113 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1114 (license license:gpl3+)))
1116 (define-public r-jsonlite
1122 (uri (cran-uri "jsonlite" version))
1125 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1126 (build-system r-build-system)
1128 `(("r-knitr" ,r-knitr)))
1129 (home-page "https://arxiv.org/abs/1403.2805")
1130 (synopsis "Robust, high performance JSON parser and generator for R")
1132 "The jsonlite package provides a fast JSON parser and generator optimized
1133 for statistical data and the web. It offers flexible, robust, high
1134 performance tools for working with JSON in R and is particularly powerful for
1135 building pipelines and interacting with a web API. In addition to converting
1136 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1137 and prettify JSON data. The unit tests included with the package verify that
1138 all edge cases are encoded and decoded consistently for use with dynamic data
1139 in systems and applications.")
1140 (license license:expat)))
1142 (define-public r-servr
1148 (uri (cran-uri "servr" version))
1151 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1152 (build-system r-build-system)
1154 `(("r-httpuv" ,r-httpuv)
1155 ("r-jsonlite" ,r-jsonlite)
1157 ("r-xfun" ,r-xfun)))
1158 (home-page "https://github.com/yihui/servr")
1159 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1161 "Servr provides an HTTP server in R to serve static files, or dynamic
1162 documents that can be converted to HTML files (e.g., R Markdown) under a given
1164 (license license:expat)))
1166 (define-public r-htmltools
1168 (name "r-htmltools")
1172 (uri (cran-uri "htmltools" version))
1175 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1176 (build-system r-build-system)
1178 `(("r-base64enc" ,r-base64enc)
1179 ("r-digest" ,r-digest)
1180 ("r-rlang" ,r-rlang)))
1181 (home-page "https://cran.r-project.org/web/packages/htmltools")
1182 (synopsis "R tools for HTML")
1184 "This package provides tools for HTML generation and output in R.")
1185 (license license:expat)))
1187 (define-public r-htmlwidgets
1189 (name "r-htmlwidgets")
1193 (uri (cran-uri "htmlwidgets" version))
1196 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1197 (build-system r-build-system)
1199 `(("r-htmltools" ,r-htmltools)
1200 ("r-jsonlite" ,r-jsonlite)
1201 ("r-yaml" ,r-yaml)))
1203 `(("r-knitr" ,r-knitr)))
1204 (home-page "https://github.com/ramnathv/htmlwidgets")
1205 (synopsis "HTML Widgets for R")
1207 "HTML widgets is a framework for creating HTML widgets that render in
1208 various contexts including the R console, R Markdown documents, and Shiny web
1210 (license license:expat)))
1212 (define-public r-htmltable
1214 (name "r-htmltable")
1219 (uri (cran-uri "htmlTable" version))
1221 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1222 (properties `((upstream-name . "htmlTable")))
1223 (build-system r-build-system)
1225 `(("r-checkmate" ,r-checkmate)
1226 ("r-htmltools" ,r-htmltools)
1227 ("r-htmlwidgets" ,r-htmlwidgets)
1228 ("r-knitr" ,r-knitr)
1229 ("r-magrittr" ,r-magrittr)
1230 ("r-rstudioapi" ,r-rstudioapi)
1231 ("r-stringr" ,r-stringr)))
1233 `(("r-knitr" ,r-knitr)))
1234 (home-page "http://gforge.se/packages/")
1235 (synopsis "Advanced tables for Markdown/HTML")
1237 "This package provides functions to build tables with advanced layout
1238 elements such as row spanners, column spanners, table spanners, zebra
1239 striping, and more. While allowing advanced layout, the underlying
1240 CSS-structure is simple in order to maximize compatibility with word
1241 processors such as LibreOffice. The package also contains a few text
1242 formatting functions that help outputting text compatible with HTML or
1244 (license license:gpl3+)))
1246 (define-public r-curl
1252 (uri (cran-uri "curl" version))
1255 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1256 (build-system r-build-system)
1259 (modify-phases %standard-phases
1260 ;; The environment variable CURL_CA_BUNDLE is only respected when
1261 ;; running Windows, so we disable the platform checks.
1262 ;; This can be removed once the libcurl has been patched.
1263 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1265 (substitute* "R/onload.R"
1266 (("if \\(!grepl\\(\"mingw\".*")
1268 (substitute* "src/handle.c"
1269 (("/\\* Only set" m)
1271 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1272 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1279 `(("pkg-config" ,pkg-config)))
1280 (home-page "https://github.com/jeroenooms/curl")
1281 (synopsis "HTTP client for R")
1283 "The @code{curl()} and @code{curl_download()} functions provide highly
1284 configurable drop-in replacements for base @code{url()} and
1285 @code{download.file()} with better performance, support for encryption, gzip
1286 compression, authentication, and other @code{libcurl} goodies. The core of
1287 the package implements a framework for performing fully customized requests
1288 where data can be processed either in memory, on disk, or streaming via the
1289 callback or connection interfaces.")
1290 (license license:expat)))
1292 (define-public r-hwriter
1299 (uri (cran-uri "hwriter" version))
1302 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1303 (build-system r-build-system)
1304 (home-page "https://cran.r-project.org/web/packages/hwriter")
1305 (synopsis "Output R objects in HTML format")
1307 "This package provides easy-to-use and versatile functions to output R
1308 objects in HTML format.")
1309 (license license:lgpl2.1+)))
1311 (define-public r-rjson
1318 (uri (cran-uri "rjson" version))
1321 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1322 (build-system r-build-system)
1323 (home-page "https://cran.r-project.org/web/packages/rjson")
1324 (synopsis "JSON library for R")
1326 "This package provides functions to convert R objects into JSON objects
1328 (license license:gpl2+)))
1330 (define-public r-fastmap
1337 (uri (cran-uri "fastmap" version))
1340 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1341 (properties `((upstream-name . "fastmap")))
1342 (build-system r-build-system)
1343 (home-page "https://r-lib.github.io/fastmap/")
1344 (synopsis "Fast implementation of a key-value store")
1346 "This package provides a fast implementation of a key-value store.
1347 Environments are commonly used as key-value stores, but every time a new key
1348 is used, it is added to R's global symbol table, causing a small amount of
1349 memory leakage. This can be problematic in cases where many different keys
1350 are used. Fastmap avoids this memory leak issue by implementing the map using
1351 data structures in C++.")
1352 (license license:expat)))
1354 (define-public r-fastghquad
1356 (name "r-fastghquad")
1361 (uri (cran-uri "fastGHQuad" version))
1364 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1365 (properties `((upstream-name . "fastGHQuad")))
1366 (build-system r-build-system)
1368 `(("r-rcpp" ,r-rcpp)))
1369 (home-page "https://github.com/awblocker/fastGHQuad")
1370 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1372 "This package implements numerically-stable Gauss-Hermite quadrature
1373 rules and utility functions for adaptive GH quadrature.")
1374 (license license:expat)))
1376 (define-public r-rstpm2
1383 (uri (cran-uri "rstpm2" version))
1386 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1387 (properties `((upstream-name . "rstpm2")))
1388 (build-system r-build-system)
1390 `(("r-bbmle" ,r-bbmle)
1392 ("r-desolve" ,r-desolve)
1393 ("r-fastghquad" ,r-fastghquad)
1396 ("r-rcpparmadillo" ,r-rcpparmadillo)
1397 ("r-survival" ,r-survival)))
1399 `(("gfortran" ,gfortran)))
1400 (home-page "https://github.com/mclements/rstpm2")
1401 (synopsis "Link-based survival models")
1403 "This package provides R implementations of @dfn{generalized survival
1404 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1405 multi-state models.")
1406 ;; One of these licenses
1407 (license (list license:gpl2 license:gpl3))))
1409 ;; This package includes minified JavaScript files. When upgrading please
1410 ;; check that there are no new minified JavaScript files.
1411 (define-public r-jquerylib
1413 (name "r-jquerylib")
1418 (uri (cran-uri "jquerylib" version))
1421 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1423 '(for-each delete-file
1424 '("inst/lib/jquery-1.12.4.min.js"
1425 "inst/lib/jquery-2.2.4.min.js"
1426 "inst/lib/jquery-3.5.1.min.js")))))
1427 (properties `((upstream-name . "jquerylib")))
1428 (build-system r-build-system)
1430 `(#:modules ((guix build utils)
1431 (guix build r-build-system)
1434 (modify-phases %standard-phases
1435 (add-after 'unpack 'process-javascript
1436 (lambda* (#:key inputs #:allow-other-keys)
1437 (with-directory-excursion "inst/lib/"
1441 `(("jquery-1.12.4.js"
1442 "jquery-1.12.4.min.js")
1444 "jquery-2.2.4.min.js")
1446 "jquery-3.5.1.min.js"))))
1447 (lambda (sources targets)
1448 (for-each (lambda (source target)
1449 (format #t "Processing ~a --> ~a~%"
1451 (invoke "esbuild" source "--minify"
1452 (string-append "--outfile=" target)))
1453 sources targets)))))))))
1455 `(("r-htmltools" ,r-htmltools)))
1457 `(("esbuild" ,esbuild)))
1458 (home-page "https://cran.r-project.org/package=jquerylib")
1459 (synopsis "Obtain jQuery as an HTML dependency object")
1461 "Obtain any major version of jQuery and use it in any webpage generated
1462 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1463 need to use this package directly, but other R packages (e.g. shiny,
1464 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1466 (license license:expat)))
1468 (define-public r-sass
1475 (uri (cran-uri "sass" version))
1478 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1479 (properties `((upstream-name . "sass")))
1480 (build-system r-build-system)
1482 `(("r-digest" ,r-digest)
1484 ("r-htmltools" ,r-htmltools)
1486 ("r-rappdirs" ,r-rappdirs)
1487 ("r-rlang" ,r-rlang)))
1488 (native-inputs `(("r-knitr" ,r-knitr)))
1489 (home-page "https://github.com/rstudio/sass")
1490 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1492 "This package provides an SCSS compiler, powered by the libsass library.
1493 With this, R developers can use variables, inheritance, and functions to
1494 generate dynamic style sheets. The package uses the Sass CSS extension
1495 language, which is stable, powerful, and CSS compatible.")
1496 (license license:expat)))
1498 ;; This package includes minified JavaScript files. When upgrading please
1499 ;; check that there are no new minified JavaScript files.
1500 (define-public r-bslib
1507 (uri (cran-uri "bslib" version))
1510 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1512 '(for-each delete-file
1513 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1514 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1515 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1516 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1517 (properties `((upstream-name . "bslib")))
1518 (build-system r-build-system)
1520 `(#:modules ((guix build utils)
1521 (guix build r-build-system)
1524 (modify-phases %standard-phases
1525 (add-after 'unpack 'process-javascript
1526 (lambda* (#:key inputs #:allow-other-keys)
1527 (with-directory-excursion "inst/lib/"
1531 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1532 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1533 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1534 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1535 ("bs-sass/assets/javascripts/bootstrap.js"
1536 "bs-sass/assets/javascripts/bootstrap.min.js")
1537 (,(assoc-ref inputs "js-bootstrap-bundle")
1538 "bs/dist/js/bootstrap.bundle.min.js"))))
1539 (lambda (sources targets)
1540 (for-each (lambda (source target)
1541 (format #t "Processing ~a --> ~a~%"
1543 (invoke "esbuild" source "--minify"
1544 (string-append "--outfile=" target)))
1545 sources targets)))))))))
1547 `(("r-digest" ,r-digest)
1548 ("r-htmltools" ,r-htmltools)
1549 ("r-jquerylib" ,r-jquerylib)
1550 ("r-jsonlite" ,r-jsonlite)
1551 ("r-magrittr" ,r-magrittr)
1552 ("r-rlang" ,r-rlang)
1553 ("r-sass" ,r-sass)))
1555 `(("esbuild" ,esbuild)
1556 ("js-bootstrap-bundle"
1559 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1562 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1563 (home-page "https://rstudio.github.io/bslib/")
1564 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1566 "This package simplifies custom CSS styling of both shiny and rmarkdown
1567 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1568 various Bootswatch themes. An interactive widget is also provided for
1569 previewing themes in real time.")
1570 (license license:expat)))
1572 ;; This package includes minified JavaScript files. When upgrading please
1573 ;; check that there are no new minified JavaScript files.
1574 (define-public r-shiny
1582 (url "https://github.com/rstudio/shiny")
1583 (commit (string-append "v" version))))
1584 (file-name (git-file-name name version))
1587 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1589 '(for-each delete-file
1590 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1591 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1592 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1593 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1594 "inst/www/shared/highlight/highlight.pack.js"
1595 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1596 "inst/www/shared/jquery.min.js"
1597 "inst/www/shared/jqueryui/jquery-ui.min.js"
1598 "inst/www/shared/legacy/jquery.min.js"
1599 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1600 "inst/www/shared/selectize/js/selectize.min.js"
1601 "inst/www/shared/shiny.min.js"
1602 "inst/www/shared/showdown/compressed/showdown.js"
1603 "inst/www/shared/strftime/strftime-min.js")))))
1604 (build-system r-build-system)
1606 `(#:modules ((guix build r-build-system)
1607 (guix build minify-build-system)
1610 #:imported-modules (,@%r-build-system-modules
1611 (guix build minify-build-system))
1613 (modify-phases (@ (guix build r-build-system) %standard-phases)
1614 (add-after 'unpack 'replace-bundled-minified-JavaScript
1615 (lambda* (#:key inputs #:allow-other-keys)
1616 (let ((replace-file (lambda (old new)
1617 (format #t "replacing ~a with ~a\n" old new)
1618 (symlink new old))))
1619 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1620 ;; contain just data. They are not minified code, so we don't
1622 (with-directory-excursion "inst/www/shared"
1623 (replace-file "strftime/strftime-min.js"
1624 (string-append (assoc-ref inputs "js-strftime")
1625 "/share/javascript/strftime.min.js"))
1626 (replace-file "highlight/highlight.pack.js"
1627 (string-append (assoc-ref inputs "js-highlight")
1628 "/share/javascript/highlight.min.js"))
1629 (replace-file "datatables/js/jquery.dataTables.min.js"
1630 (string-append (assoc-ref inputs "js-datatables")
1631 "/share/javascript/jquery.dataTables.min.js"))
1632 (replace-file "selectize/js/selectize.min.js"
1633 (string-append (assoc-ref inputs "js-selectize")
1634 "/share/javascript/selectize.min.js"))
1635 (for-each (match-lambda
1637 (minify source #:target target)))
1638 `(("jqueryui/jquery-ui.js" .
1639 "jqueryui/jquery-ui.min.js")
1640 ("datepicker/js/bootstrap-datepicker.js" .
1641 "datepicker/js/bootstrap-datepicker.min.js")
1642 ("ionrangeslider/js/ion.rangeSlider.js" .
1643 "ionrangeslider/js/ion.rangeSlider.min.js")
1644 ("bootstrap/js/bootstrap.js" .
1645 "bootstrap/js/bootstrap.min.js")
1646 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1647 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1652 ("legacy/jquery.js" .
1653 "legacy/jquery.min.js")
1654 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1655 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1656 ("showdown/src/showdown.js" .
1657 "showdown/compressed/showdown.js"))))))))))
1659 `(("r-bslib" ,r-bslib)
1660 ("r-cachem" ,r-cachem)
1661 ("r-commonmark" ,r-commonmark)
1662 ("r-crayon" ,r-crayon)
1663 ("r-digest" ,r-digest)
1664 ("r-ellipsis" ,r-ellipsis)
1665 ("r-fastmap" ,r-fastmap)
1667 ("r-htmltools" ,r-htmltools)
1668 ("r-httpuv" ,r-httpuv)
1669 ("r-jsonlite" ,r-jsonlite)
1670 ("r-later" ,r-later)
1671 ("r-lifecycle" ,r-lifecycle)
1673 ("r-promises" ,r-promises)
1675 ("r-rlang" ,r-rlang)
1676 ("r-sourcetools" ,r-sourcetools)
1677 ("r-withr" ,r-withr)
1678 ("r-xtable" ,r-xtable)))
1680 `(("js-datatables" ,js-datatables)
1681 ("js-selectize" ,js-selectize)
1682 ("js-strftime" ,js-strftime)
1683 ("js-highlight" ,js-highlight)))
1685 `(("uglify-js" ,uglify-js)
1686 ("gfortran" ,gfortran)
1687 ("js-bootstrap-accessibility"
1690 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1691 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1694 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1695 (home-page "https://shiny.rstudio.com")
1696 (synopsis "Easy interactive web applications with R")
1698 "Makes it incredibly easy to build interactive web applications
1699 with R. Automatic \"reactive\" binding between inputs and outputs and
1700 extensive prebuilt widgets make it possible to build beautiful,
1701 responsive, and powerful applications with minimal effort.")
1702 (license license:artistic2.0)))
1704 ;; This package includes minified JavaScript files. When upgrading please
1705 ;; check that there are no new minified JavaScript files.
1706 (define-public r-shinytree
1708 (name "r-shinytree")
1713 (uri (cran-uri "shinyTree" version))
1716 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1717 (modules '((guix build utils)))
1720 ;; Delete minified JavaScript
1721 (for-each delete-file
1722 '("inst/www/jsTree-3.3.7/libs/require.js"
1723 "inst/www/jsTree-3.3.7/libs/jquery.js"
1724 "inst/www/jsTree-3.3.7/jstree.min.js"))
1726 (properties `((upstream-name . "shinyTree")))
1727 (build-system r-build-system)
1729 `(#:modules ((guix build utils)
1730 (guix build r-build-system)
1734 (modify-phases %standard-phases
1735 (add-after 'unpack 'replace-minified-javascript
1736 (lambda* (#:key inputs #:allow-other-keys)
1737 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1738 (symlink (string-append (assoc-ref inputs "js-requirejs")
1739 "/share/javascript/require.min.js")
1744 `((,(assoc-ref inputs "js-jquery")
1748 (lambda (sources targets)
1749 (for-each (lambda (source target)
1750 (format #t "Processing ~a --> ~a~%"
1752 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1753 (call-with-output-file target
1755 (dump-port minified port)))))
1759 `(("r-htmlwidgets" ,r-htmlwidgets)
1760 ("r-jsonlite" ,r-jsonlite)
1761 ("r-promises" ,r-promises)
1762 ("r-shiny" ,r-shiny)
1763 ("r-stringr" ,r-stringr)))
1765 `(("js-requirejs" ,js-requirejs)))
1767 `(("uglify-js" ,uglify-js)
1771 (uri "https://code.jquery.com/jquery-3.3.1.js")
1774 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1775 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1776 (synopsis "jsTree bindings for Shiny")
1778 "This package exposes R bindings to jsTree, a JavaScript library that
1779 supports interactive trees, to enable rich, editable trees in Shiny.")
1780 (license license:expat)))
1782 (define-public r-shinydashboard
1784 (name "r-shinydashboard")
1788 (uri (cran-uri "shinydashboard" version))
1791 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1792 (build-system r-build-system)
1793 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1794 ;; Regenerate it from the included sources.
1796 `(#:modules ((guix build utils)
1797 (guix build r-build-system)
1800 (modify-phases %standard-phases
1801 (add-after 'unpack 'generate-minified-javascript
1803 (with-directory-excursion "inst/AdminLTE"
1804 (delete-file "app.min.js")
1805 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1806 (call-with-output-file "app.min.js"
1808 (dump-port minified port))))))))))
1810 `(("r-htmltools" ,r-htmltools)
1811 ("r-promises" ,r-promises)
1812 ("r-shiny" ,r-shiny)))
1814 `(("uglify-js" ,uglify-js)))
1815 (home-page "https://rstudio.github.io/shinydashboard/")
1816 (synopsis "Create dashboards with shiny")
1817 (description "This package provides an extension to the Shiny web
1818 application framework for R, making it easy to create attractive dashboards.")
1819 ;; This package includes software that was released under the Expat
1820 ;; license, but the whole package is released under GPL version 2 or
1822 (license license:gpl2+)))
1824 (define-public r-shinyfiles
1826 (name "r-shinyfiles")
1831 (uri (cran-uri "shinyFiles" version))
1833 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1834 (properties `((upstream-name . "shinyFiles")))
1835 (build-system r-build-system)
1838 ("r-htmltools" ,r-htmltools)
1839 ("r-jsonlite" ,r-jsonlite)
1840 ("r-shiny" ,r-shiny)
1841 ("r-tibble" ,r-tibble)))
1842 (home-page "https://github.com/thomasp85/shinyFiles")
1843 (synopsis "Server-side file system viewer for Shiny")
1845 "This package provides functionality for client-side navigation of the
1846 server side file system in shiny apps. In case the app is running locally
1847 this gives the user direct access to the file system without the need to
1848 \"download\" files to a temporary location. Both file and folder selection as
1849 well as file saving is available.")
1850 (license license:gpl2+)))
1852 (define-public r-shinythemes
1854 (name "r-shinythemes")
1859 (uri (cran-uri "shinythemes" version))
1862 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1863 (properties `((upstream-name . "shinythemes")))
1864 (build-system r-build-system)
1865 (propagated-inputs `(("r-shiny" ,r-shiny)))
1866 (home-page "https://rstudio.github.io/shinythemes/")
1867 (synopsis "Themes for Shiny")
1869 "This package provides themes for use with Shiny. It includes several
1870 Bootstrap themes, which are packaged for use with Shiny applications.")
1871 ;; The package is released under version 3 of the GPL, but it includes
1872 ;; source files that are covered by the Expat license. It also includes
1873 ;; fonts under SIL or the ASL.
1874 (license (list license:gpl3 license:expat
1875 license:silofl1.1 license:asl2.0))))
1877 ;; The package sources include minified variants of d3.js and non-minified
1878 ;; source code of d3-jetpack.
1879 (define-public r-d3r
1886 (uri (cran-uri "d3r" version))
1889 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1890 (build-system r-build-system)
1892 `(#:modules ((guix build utils)
1893 (guix build r-build-system)
1896 (modify-phases %standard-phases
1897 (add-after 'unpack 'process-javascript
1898 (lambda* (#:key inputs #:allow-other-keys)
1899 (with-directory-excursion "inst/www/d3/"
1903 `((,(assoc-ref inputs "d3.v3.js")
1904 "v3/dist/d3.min.js")
1905 (,(assoc-ref inputs "d3.v4.js")
1906 "v4/dist/d3.min.js")
1907 (,(assoc-ref inputs "d3.v5.js")
1908 "v5/dist/d3.min.js")
1909 (,(assoc-ref inputs "d3.v6.js")
1910 "v6/dist/d3.min.js"))))
1911 (lambda (sources targets)
1912 (for-each (lambda (source target)
1913 (format #t "Processing ~a --> ~a~%"
1915 (delete-file target)
1916 (invoke "esbuild" source "--minify"
1917 (string-append "--outfile=" target)))
1921 `(("r-dplyr" ,r-dplyr)
1922 ("r-htmltools" ,r-htmltools)
1923 ("r-rlang" ,r-rlang)
1924 ("r-tidyr" ,r-tidyr)))
1926 `(("esbuild" ,esbuild)
1930 (uri "https://d3js.org/d3.v3.js")
1933 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1937 (uri "https://d3js.org/d3.v4.js")
1940 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1944 (uri "https://d3js.org/d3.v5.js")
1947 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1951 (uri "https://d3js.org/d3.v6.js")
1954 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1955 (home-page "https://github.com/timelyportfolio/d3r")
1956 (synopsis "d3.js utilities for R")
1958 "This package provides a suite of functions to help ease the use of the
1959 d3.js visualization library in R. These helpers include
1960 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1961 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1962 R objects into the JSON format that the d3.js library expects.")
1963 (license license:bsd-3)))
1965 ;; We use the latest commit here because the last release was in 2016 while
1966 ;; the latest commit was in 2018.
1967 (define-public r-sankeyd3
1968 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1972 (version (git-version "0.3.2" revision commit))
1977 (url "https://github.com/fbreitwieser/sankeyD3")
1979 (file-name (git-file-name name version))
1982 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1983 (build-system r-build-system)
1986 ("r-htmlwidgets" ,r-htmlwidgets)
1987 ("r-shiny" ,r-shiny)
1988 ("r-magrittr" ,r-magrittr)))
1989 (home-page "https://github.com/fbreitwieser/sankeyD3")
1990 (synopsis "Sankey network graphs from R")
1992 "This package provides an R library to generate Sankey network graphs
1993 in R and Shiny via the D3 visualization library.")
1994 ;; The R code is licensed under GPLv3+. It includes the non-minified
1995 ;; JavaScript source code of d3-sankey, which is released under the
1996 ;; 3-clause BSD license.
1997 (license (list license:gpl3+ license:bsd-3)))))
1999 (define-public r-wesanderson
2001 (name "r-wesanderson")
2006 (uri (cran-uri "wesanderson" version))
2009 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2010 (properties `((upstream-name . "wesanderson")))
2011 (build-system r-build-system)
2012 (home-page "https://github.com/karthik/wesanderson")
2013 (synopsis "Wes Anderson color palette generator")
2015 "This package provides color palettes that have been generated mostly
2016 from Wes Anderson movies.")
2017 (license license:expat)))
2019 (define-public r-gg-gap
2026 (uri (cran-uri "gg.gap" version))
2029 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2030 (properties `((upstream-name . "gg.gap")))
2031 (build-system r-build-system)
2033 `(("r-cowplot" ,r-cowplot)
2034 ("r-ggplot2" ,r-ggplot2)))
2035 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2036 (synopsis "Define segments on the y-axis for ggplot2")
2038 "The @code{gg.gap} function enables you to define segments for the y-axis
2039 in a ggplot2 plot.")
2040 (license license:gpl3)))
2042 (define-public r-tablerdash
2044 (name "r-tablerdash")
2049 (uri (cran-uri "tablerDash" version))
2052 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2055 ;; Delete minified JavaScript
2056 (for-each delete-file
2057 '("inst/tablerDash-0.1.0/require.min.js"
2058 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2060 (properties `((upstream-name . "tablerDash")))
2061 (build-system r-build-system)
2063 `(#:modules ((guix build utils)
2064 (guix build r-build-system)
2067 (modify-phases %standard-phases
2068 (add-after 'unpack 'process-javascript
2069 (lambda* (#:key inputs #:allow-other-keys)
2070 (with-directory-excursion "inst"
2074 `((,(assoc-ref inputs "js-requirejs")
2075 "tablerDash-0.1.0/require.min.js")
2076 (,(assoc-ref inputs "js-bootstrap")
2077 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2078 (lambda (sources targets)
2079 (for-each (lambda (source target)
2080 (format #t "Processing ~a --> ~a~%"
2082 (invoke "esbuild" source "--minify"
2083 (string-append "--outfile=" target)))
2087 `(("r-htmltools" ,r-htmltools)
2088 ("r-knitr" ,r-knitr)
2089 ("r-shiny" ,r-shiny)))
2091 `(("esbuild" ,esbuild)
2095 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2098 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2102 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2103 v4.0.0/dist/js/bootstrap.bundle.js")
2106 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2107 (home-page "https://rinterface.github.io/tablerDash/")
2108 (synopsis "Tabler API for Shiny")
2110 "This package provides an R interface to the
2111 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2112 4 dashboard template. There are different layouts available such as a one
2113 page dashboard or a multi-page template, where the navigation menu is
2114 contained in the navigation bar.")
2115 (license license:gpl2+)))
2117 (define-public r-spelling
2124 (uri (cran-uri "spelling" version))
2127 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2128 (properties `((upstream-name . "spelling")))
2129 (build-system r-build-system)
2131 `(("r-commonmark" ,r-commonmark)
2132 ("r-hunspell" ,r-hunspell)
2133 ("r-knitr" ,r-knitr)
2134 ("r-xml2" ,r-xml2)))
2135 (home-page "https://docs.ropensci.org/spelling/")
2136 (synopsis "Tools for spell checking in R")
2138 "This is an R package for spell checking common document formats
2139 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2140 utilities to automate checking of documentation and vignettes as a unit test
2141 during @code{R CMD check}. Both British and American English are supported
2142 out of the box and other languages can be added. In addition, packages may
2143 define a wordlist to allow custom terminology without having to abuse
2145 (license license:expat)))
2147 (define-public r-crosstalk
2149 (name "r-crosstalk")
2154 (uri (cran-uri "crosstalk" version))
2157 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2158 (build-system r-build-system)
2160 `(("r-htmltools" ,r-htmltools)
2161 ("r-jsonlite" ,r-jsonlite)
2162 ("r-lazyeval" ,r-lazyeval)
2164 (home-page "https://rstudio.github.io/crosstalk/")
2165 (synopsis "Inter-widget interactivity for HTML widgets")
2167 "This package provides building blocks for allowing HTML widgets to
2168 communicate with each other, with Shiny or without (i.e. static @code{.html}
2169 files). It currently supports linked brushing and filtering.")
2170 (license license:expat)))
2172 (define-public r-rook
2179 (uri (cran-uri "Rook" version))
2182 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2183 (properties `((upstream-name . "Rook")))
2184 (build-system r-build-system)
2185 (propagated-inputs `(("r-brew" ,r-brew)))
2186 (home-page "https://cran.r-project.org/web/packages/Rook")
2187 (synopsis "Web server interface for R")
2189 "This package contains the Rook specification and convenience software
2190 for building and running Rook applications. A Rook application is an R
2191 reference class object that implements a @code{call} method or an R closure
2192 that takes exactly one argument, an environment, and returns a list with three
2193 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2194 (license license:gpl2)))
2196 (define-public r-miniui
2203 (uri (cran-uri "miniUI" version))
2206 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2207 (properties `((upstream-name . "miniUI")))
2208 (build-system r-build-system)
2210 `(("r-htmltools" ,r-htmltools)
2211 ("r-shiny" ,r-shiny)))
2212 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2213 (synopsis "Shiny UI widgets for small screens")
2215 "This package provides UI widget and layout functions for writing Shiny apps that
2216 work well on small screens.")
2217 (license license:gpl3)))
2219 (define-public r-feather
2226 (uri (cran-uri "feather" version))
2229 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2230 (build-system r-build-system)
2234 ("r-tibble" ,r-tibble)))
2235 (home-page "https://github.com/wesm/feather")
2236 (synopsis "R Bindings to the Feather API")
2237 (description "Read and write feather files, a lightweight binary columnar
2238 data store designed for maximum speed.")
2239 (license license:asl2.0)))
2241 (define-public r-maps
2248 (uri (cran-uri "maps" version))
2251 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2252 (build-system r-build-system)
2253 (home-page "https://cran.r-project.org/web/packages/maps")
2254 (synopsis "Draw geographical maps")
2255 (description "This package provides an R module for display of maps.
2256 Projection code and larger maps are in separate packages (@code{mapproj} and
2258 (license license:gpl2)))
2260 (define-public r-mapproj
2267 (uri (cran-uri "mapproj" version))
2270 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2271 (build-system r-build-system)
2272 (propagated-inputs `(("r-maps" ,r-maps)))
2273 (home-page "https://cran.r-project.org/web/packages/mapproj")
2274 (synopsis "Map projection in R")
2275 (description "This package converts latitude/longitude into projected
2277 (license (list license:gpl2 ; The R interface
2278 (license:non-copyleft ; The C code
2279 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2280 "Lucent Public License Version 1.02")))))
2282 (define-public r-rgooglemaps
2284 (name "r-rgooglemaps")
2289 (uri (cran-uri "RgoogleMaps" version))
2292 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2293 (properties `((upstream-name . "RgoogleMaps")))
2294 (build-system r-build-system)
2298 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2299 (synopsis "Use Google Maps in R")
2300 (description "This package serves two purposes:
2302 @item Provide a comfortable R interface to query the Google server for static
2304 @item Use the map as a background image to overlay plots within R. This
2305 requires proper coordinate scaling.
2307 (license license:gpl2+)))
2309 (define-public r-geosphere
2311 (name "r-geosphere")
2316 (uri (cran-uri "geosphere" version))
2319 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2320 (build-system r-build-system)
2321 (propagated-inputs `(("r-sp" ,r-sp)))
2322 (home-page "https://cran.r-project.org/web/packages/geosphere")
2323 (synopsis "Spherical trigonometry")
2324 (description "This package computes spherical trigonometry for geographic
2325 applications. That is, compute distances and related measures for angular
2326 (longitude/latitude) locations.")
2327 (license license:gpl3+)))
2329 (define-public r-jpeg
2336 (uri (cran-uri "jpeg" version))
2339 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2340 (build-system r-build-system)
2341 (inputs `(("libjpeg" ,libjpeg-turbo)))
2342 (home-page "https://www.rforge.net/jpeg/")
2343 (synopsis "Read and write JPEG images with R")
2344 (description "This package provides a way to read, write and display
2345 bitmap images stored in the JPEG format with R. It can read and write both
2346 files and in-memory raw vectors.")
2347 (license license:gpl2+)))
2349 (define-public r-ggmap
2356 (uri (cran-uri "ggmap" version))
2359 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2360 (build-system r-build-system)
2362 `(("r-bitops" ,r-bitops)
2363 ("r-digest" ,r-digest)
2364 ("r-dplyr" ,r-dplyr)
2365 ("r-ggplot2" ,r-ggplot2)
2369 ("r-magrittr" ,r-magrittr)
2372 ("r-purrr" ,r-purrr)
2373 ("r-rgooglemaps" ,r-rgooglemaps)
2374 ("r-rjson" ,r-rjson)
2375 ("r-scales" ,r-scales)
2376 ("r-stringr" ,r-stringr)
2377 ("r-tibble" ,r-tibble)
2378 ("r-tidyr" ,r-tidyr)))
2379 (home-page "https://github.com/dkahle/ggmap")
2380 (synopsis "Spatial visualization with ggplot2")
2381 (description "This package provides a collection of functions to visualize
2382 spatial data and models on top of static maps from various online sources (e.g
2383 Google Maps and Stamen Maps). It includes tools common to those tasks,
2384 including functions for geolocation and routing.")
2385 (license license:gpl2)))
2387 (define-public r-haven
2394 (uri (cran-uri "haven" version))
2397 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2398 (modules '((guix build utils)))
2401 ;; unvendor readstat
2402 (delete-file-recursively "src/readstat")
2404 (build-system r-build-system)
2407 (modify-phases %standard-phases
2408 (add-after 'unpack 'unbundle-readstat
2410 ;; Not required, since we’re not building readstat.
2411 (substitute* "src/Makevars"
2412 (("-lz") "-lreadstat"))
2415 `(("readstat" ,readstat)))
2417 `(("r-knitr" ,r-knitr)))
2419 `(("r-forcats" ,r-forcats)
2422 ("r-rlang" ,r-rlang)
2423 ("r-readr" ,r-readr)
2424 ("r-tibble" ,r-tibble)
2425 ("r-tidyselect" ,r-tidyselect)
2426 ("r-vctrs" ,r-vctrs)))
2427 (home-page "https://haven.tidyverse.org")
2428 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2430 "This package lets you mport foreign statistical formats into R via the
2431 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2432 (license license:expat)))
2434 (define-public r-amap
2440 (uri (cran-uri "amap" version))
2443 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2444 (build-system r-build-system)
2446 `(("gfortran" ,gfortran)))
2447 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2448 (synopsis "Another multidimensional analysis package")
2449 (description "This package provides tools for clustering and principal
2450 component analysis (with robust methods, and parallelized functions).")
2451 (license license:gpl2+)))
2453 (define-public r-ape
2460 (uri (cran-uri "ape" version))
2463 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2464 (build-system r-build-system)
2466 `(("r-lattice" ,r-lattice)
2468 ("r-rcpp" ,r-rcpp)))
2469 (home-page "http://ape-package.ird.fr/")
2470 (synopsis "Analyses of phylogenetics and evolution")
2472 "This package provides functions for reading, writing, plotting, and
2473 manipulating phylogenetic trees, analyses of comparative data in a
2474 phylogenetic framework, ancestral character analyses, analyses of
2475 diversification and macroevolution, computing distances from DNA sequences,
2476 and several other tools.")
2477 (license license:gpl2+)))
2479 (define-public r-abbyyr
2486 (uri (cran-uri "abbyyR" version))
2489 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2490 (properties `((upstream-name . "abbyyR")))
2491 (build-system r-build-system)
2493 `(("r-curl" ,r-curl)
2496 ("r-progress" ,r-progress)
2497 ("r-readr" ,r-readr)
2499 (home-page "https://github.com/soodoku/abbyyR")
2500 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2502 "This package provides tools to get text from images of text using Abbyy
2503 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2504 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2505 passports and get the results in a variety of formats including plain text and
2506 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2507 (license license:expat)))
2509 (define-public r-colorspace
2511 (name "r-colorspace")
2516 (uri (cran-uri "colorspace" version))
2518 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2519 (build-system r-build-system)
2521 `(("r-knitr" ,r-knitr)))
2522 (home-page "https://cran.r-project.org/web/packages/colorspace")
2523 (synopsis "Color space manipulation")
2525 "This package carries out a mapping between assorted color spaces
2526 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2527 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2528 colors are provided.")
2529 (license license:bsd-3)))
2531 (define-public r-glue
2538 (uri (cran-uri "glue" version))
2541 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2542 (build-system r-build-system)
2543 ;; knitr depends on glue, so we can't add knitr here to build the
2547 `(("r-knitr" ,r-knitr)))
2548 (home-page "https://github.com/tidyverse/glue")
2549 (synopsis "Interpreted string literals")
2551 "This package provides an implementation of interpreted string literals,
2552 inspired by Python's Literal String Interpolation (PEP-0498) and
2553 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2554 (license license:expat)))
2556 (define-public r-palmerpenguins
2558 (name "r-palmerpenguins")
2563 (uri (cran-uri "palmerpenguins" version))
2566 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2568 `((upstream-name . "palmerpenguins")))
2569 (build-system r-build-system)
2570 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2571 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2573 "This package includes size measurements, clutch observations, and blood
2574 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2575 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2576 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2577 Station Long Term Ecological Research (LTER) Program.")
2578 (license license:cc0)))
2580 (define-public r-pastecs
2586 (uri (cran-uri "pastecs" version))
2589 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2590 (build-system r-build-system)
2592 `(("r-boot" ,r-boot)))
2593 (home-page "https://github.com/phgrosjean/pastecs")
2594 (synopsis "Analysis of space-time ecological series")
2596 "This package provides functions for regulation, decomposition and analysis
2597 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2598 initiative to bring PASSTEC 2000 functionalities to R.")
2599 (license license:gpl2+)))
2601 (define-public r-partykit
2607 (uri (cran-uri "partykit" version))
2610 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2611 (build-system r-build-system)
2613 `(("r-formula" ,r-formula)
2615 ("r-libcoin" ,r-libcoin)
2616 ("r-mvtnorm" ,r-mvtnorm)
2617 ("r-rpart" ,r-rpart)
2618 ("r-survival" ,r-survival)))
2619 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2620 (synopsis "Toolkit for recursive partytioning")
2622 "This package provides a toolkit with infrastructure for representing,
2623 summarizing, and visualizing tree-structured regression and classification
2625 (license license:gpl2+)))
2627 (define-public r-plogr
2634 (uri (cran-uri "plogr" version))
2637 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2638 (build-system r-build-system)
2639 (home-page "https://github.com/krlmlr/plogr")
2640 (synopsis "R bindings for the plog C++ logging library")
2642 "This package provides the header files for a stripped-down version of
2643 the plog header-only C++ logging library, and a method to log to R's standard
2645 (license license:expat)))
2647 (define-public r-pls
2654 (uri (cran-uri "pls" version))
2656 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2657 (build-system r-build-system)
2658 (home-page "https://mevik.net/work/software/pls.html")
2659 (synopsis "Partial Least Squares and Principal Component Regression")
2661 "The pls package implements multivariate regression methods: Partial Least
2662 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2663 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2666 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2667 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2668 @item multi-response models (or @dfn{PLS2})
2669 @item flexible cross-validation
2670 @item Jackknife variance estimates of regression coefficients
2671 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2672 (R)MSEP, R², and correlation loadings
2673 @item formula interface, modelled after @code{lm()}, with methods for predict,
2674 print, summary, plot, update, etc.
2675 @item extraction functions for coefficients, scores, and loadings
2676 @item MSEP, RMSEP, and R² estimates
2677 @item multiplicative scatter correction (@dfn{MSC})
2679 (license license:gpl2)))
2688 (uri (cran-uri "ps" version))
2690 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2691 (build-system r-build-system)
2692 (home-page "https://ps.r-lib.org")
2693 (synopsis "List, query, and manipulate system processes")
2695 "The ps package implements an API to list, query, and manipulate system
2696 processes. Most of its code is based on the @code{psutil} Python package.")
2697 (license license:bsd-3)))
2699 (define-public r-pkgbuild
2706 (uri (cran-uri "pkgbuild" version))
2708 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2709 (build-system r-build-system)
2711 `(("r-callr" ,r-callr)
2713 ("r-crayon" ,r-crayon)
2715 ("r-prettyunits" ,r-prettyunits)
2717 ("r-rprojroot" ,r-rprojroot)
2718 ("r-withr" ,r-withr)))
2719 (home-page "https://github.com/r-pkgs/pkgbuild")
2720 (synopsis "Find tools needed to build R packages")
2722 "This package provides functions used to build R packages. It locates
2723 compilers needed to build R packages on various platforms and ensures the PATH
2724 is configured appropriately so R can use them.")
2725 (license license:gpl3)))
2727 (define-public r-pkgload
2734 (uri (cran-uri "pkgload" version))
2737 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2738 (build-system r-build-system)
2741 ("r-crayon" ,r-crayon)
2743 ("r-pkgbuild" ,r-pkgbuild)
2744 ("r-rlang" ,r-rlang)
2745 ("r-rprojroot" ,r-rprojroot)
2746 ("r-rstudioapi" ,r-rstudioapi)
2747 ("r-withr" ,r-withr)))
2748 (home-page "https://github.com/r-lib/pkgload")
2749 (synopsis "Simulate package installation and attach")
2751 "This package simulates the process of installing a package and then
2752 attaching it. This is a key part of the @code{devtools} package as it allows
2753 you to rapidly iterate while developing a package.")
2754 (license license:gpl3)))
2756 (define-public r-rcpp
2763 (uri (cran-uri "Rcpp" version))
2765 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2766 (build-system r-build-system)
2767 (home-page "http://www.rcpp.org")
2768 (synopsis "Seamless R and C++ integration")
2770 "The Rcpp package provides R functions as well as C++ classes which offer
2771 a seamless integration of R and C++. Many R data types and objects can be
2772 mapped back and forth to C++ equivalents which facilitates both writing of new
2773 code as well as easier integration of third-party libraries. Documentation
2774 about Rcpp is provided by several vignettes included in this package, via the
2775 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2776 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2777 @code{citation(\"Rcpp\")} for details on these last two.")
2778 (license license:gpl2+)))
2780 (define-public r-rcppthread
2782 (name "r-rcppthread")
2787 (uri (cran-uri "RcppThread" version))
2790 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2791 (properties `((upstream-name . "RcppThread")))
2792 (build-system r-build-system)
2794 "https://github.com/tnagler/RcppThread")
2795 (synopsis "R threading in C++")
2797 "This package provides a C++11-style thread class and thread pool that can
2798 safely be interrupted from R.")
2799 (license license:expat)))
2801 (define-public r-bindr
2808 (uri (cran-uri "bindr" version))
2811 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2812 (build-system r-build-system)
2813 (home-page "https://github.com/krlmlr/bindr")
2814 (synopsis "Parametrized active bindings")
2816 "This package provides a simple interface for creating active bindings
2817 where the bound function accepts additional arguments.")
2818 (license license:expat)))
2820 (define-public r-bindrcpp
2827 (uri (cran-uri "bindrcpp" version))
2830 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2831 (build-system r-build-system)
2833 `(("r-bindr" ,r-bindr)
2834 ("r-plogr" ,r-plogr)
2835 ("r-rcpp" ,r-rcpp)))
2836 (home-page "https://github.com/krlmlr/bindrcpp")
2837 (synopsis "Rcpp interface to active bindings")
2839 "This package provides an easy way to fill an environment with active
2840 bindings that call a C++ function.")
2841 (license license:expat)))
2843 (define-public r-auc
2850 (uri (cran-uri "AUC" version))
2853 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2854 (properties `((upstream-name . "AUC")))
2855 (build-system r-build-system)
2856 (home-page "https://cran.r-project.org/web/packages/AUC")
2857 (synopsis "Compute the area under the curve of selected measures")
2859 "This package includes functions to compute the area under the curve of
2860 selected measures: the area under the sensitivity curve (AUSEC), the area
2861 under the specificity curve (AUSPC), the area under the accuracy
2862 curve (AUACC), and the area under the receiver operating characteristic
2863 curve (AUROC). The curves can also be visualized. Support for partial areas
2865 (license license:gpl2+)))
2867 (define-public r-calibrate
2869 (name "r-calibrate")
2874 (uri (cran-uri "calibrate" version))
2876 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2877 (build-system r-build-system)
2879 `(("r-mass" ,r-mass)))
2880 (home-page "https://cran.r-project.org/web/packages/calibrate")
2881 (synopsis "Calibration of scatterplot and biplot axes")
2883 "This is a package for drawing calibrated scales with tick marks
2884 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2885 (license license:gpl2)))
2887 (define-public r-shape
2894 (uri (cran-uri "shape" version))
2897 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2898 (build-system r-build-system)
2899 (home-page "https://cran.r-project.org/web/packages/shape")
2900 (synopsis "Functions for plotting graphical shapes")
2902 "This package provides functions for plotting graphical shapes such as
2903 ellipses, circles, cylinders, arrows, ...")
2904 (license license:gpl3+)))
2906 (define-public r-globaloptions
2908 (name "r-globaloptions")
2913 (uri (cran-uri "GlobalOptions" version))
2915 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2916 (properties `((upstream-name . "GlobalOptions")))
2917 (build-system r-build-system)
2919 `(("r-knitr" ,r-knitr)))
2920 (home-page "https://github.com/jokergoo/GlobalOptions")
2921 (synopsis "Generate functions to get or set global options")
2923 "This package provides more controls on the option values such as
2924 validation and filtering on the values, making options invisible or private.")
2925 (license license:gpl2+)))
2927 (define-public r-circlize
2934 (uri (cran-uri "circlize" version))
2937 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2938 (build-system r-build-system)
2940 `(("r-colorspace" ,r-colorspace)
2941 ("r-globaloptions" ,r-globaloptions)
2942 ("r-shape" ,r-shape)))
2944 `(("r-knitr" ,r-knitr)))
2945 (home-page "https://github.com/jokergoo/circlize")
2946 (synopsis "Circular visualization")
2948 "Circular layout is an efficient way to visualise huge amounts of
2949 information. This package provides an implementation of circular layout
2950 generation in R as well as an enhancement of available software. Its
2951 flexibility is based on the usage of low-level graphics functions such that
2952 self-defined high-level graphics can be easily implemented by users for
2953 specific purposes. Together with the seamless connection between the powerful
2954 computational and visual environment in R, it gives users more convenience and
2955 freedom to design figures for better understanding complex patterns behind
2956 multi-dimensional data.")
2957 (license license:gpl2+)))
2959 (define-public r-powerlaw
2966 (uri (cran-uri "poweRlaw" version))
2968 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2969 (properties `((upstream-name . "poweRlaw")))
2970 (build-system r-build-system)
2972 `(("r-pracma" ,r-pracma)))
2974 `(("r-knitr" ,r-knitr)))
2975 (home-page "https://github.com/csgillespie/poweRlaw")
2976 (synopsis "Tools for the analysis of heavy tailed distributions")
2978 "This package provides an implementation of maximum likelihood estimators
2979 for a variety of heavy tailed distributions, including both the discrete and
2980 continuous power law distributions. Additionally, a goodness-of-fit based
2981 approach is used to estimate the lower cut-off for the scaling region.")
2982 ;; Any of these GPL versions.
2983 (license (list license:gpl2 license:gpl3))))
2985 (define-public r-compare
2992 (uri (cran-uri "compare" version))
2995 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2996 (build-system r-build-system)
2997 (home-page "https://cran.r-project.org/web/packages/compare")
2998 (synopsis "Comparing objects for differences")
3000 "This package provides functions to compare a model object to a
3001 comparison object. If the objects are not identical, the functions can be
3002 instructed to explore various modifications of the objects (e.g., sorting
3003 rows, dropping names) to see if the modified versions are identical.")
3004 (license license:gpl2+)))
3006 (define-public r-dendextend
3008 (name "r-dendextend")
3013 (uri (cran-uri "dendextend" version))
3016 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3017 (build-system r-build-system)
3019 `(("r-ggplot2" ,r-ggplot2)
3020 ("r-magrittr" ,r-magrittr)
3021 ("r-viridis" ,r-viridis)))
3023 `(("r-knitr" ,r-knitr)))
3024 (home-page "https://cran.r-project.org/web/packages/dendextend")
3025 (synopsis "Extending 'dendrogram' functionality in R")
3027 "This package offers a set of functions for extending @code{dendrogram}
3028 objects in R, letting you visualize and compare trees of hierarchical
3029 clusterings. You can adjust a tree's graphical parameters (the color, size,
3030 type, etc of its branches, nodes and labels) and visually and statistically
3031 compare different dendrograms to one another.")
3032 ;; Any of these versions
3033 (license (list license:gpl2 license:gpl3))))
3035 (define-public r-getoptlong
3037 (name "r-getoptlong")
3042 (uri (cran-uri "GetoptLong" version))
3045 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3046 (properties `((upstream-name . "GetoptLong")))
3047 (build-system r-build-system)
3051 `(("r-crayon" ,r-crayon)
3052 ("r-globaloptions" ,r-globaloptions)
3053 ("r-rjson" ,r-rjson)))
3055 `(("r-knitr" ,r-knitr)))
3056 (home-page "https://github.com/jokergoo/GetoptLong")
3057 (synopsis "Parsing command-line arguments and variable interpolation")
3059 "This is yet another command-line argument parser which wraps the
3060 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3061 use in R. It also provides a simple way for variable interpolation in R.")
3062 (license license:gpl2+)))
3064 (define-public r-fastmatch
3066 (name "r-fastmatch")
3071 (uri (cran-uri "fastmatch" version))
3074 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3075 (build-system r-build-system)
3076 (home-page "https://www.rforge.net/fastmatch")
3077 (synopsis "Fast match function")
3079 "This package provides a fast @code{match} replacement for cases that
3080 require repeated look-ups. It is slightly faster that R's built-in
3081 @code{match} function on first match against a table, but extremely fast on
3082 any subsequent lookup as it keeps the hash table in memory.")
3083 (license license:gpl2)))
3092 (uri (cran-uri "ff" version))
3095 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3096 (build-system r-build-system)
3097 (propagated-inputs `(("r-bit" ,r-bit)))
3098 (home-page "http://ff.r-forge.r-project.org/")
3099 (synopsis "Memory-efficient storage of large data on disk and access functions")
3101 "This package provides data structures that are stored on disk but
3102 behave (almost) as if they were in RAM by transparently mapping only a section
3104 ;; error Architecture not supported.
3105 (supported-systems (delete "aarch64-linux" %supported-systems))
3106 (license license:gpl2)))
3108 (define-public r-ffbase
3115 (uri (cran-uri "ffbase" version))
3118 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3119 (build-system r-build-system)
3122 ("r-fastmatch" ,r-fastmatch)
3124 (home-page "https://github.com/edwindj/ffbase")
3125 (synopsis "Basic statistical functions for package 'ff'")
3127 "This package extends the out of memory vectors of @code{ff} with
3128 statistical functions and other utilities to ease their usage.")
3129 (license license:gpl3)))
3131 (define-public r-prettyunits
3133 (name "r-prettyunits")
3138 (uri (cran-uri "prettyunits" version))
3141 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3142 (build-system r-build-system)
3143 (home-page "https://github.com/gaborcsardi/prettyunits")
3144 (synopsis "Pretty, human readable formatting of quantities")
3146 "This package provides tools for pretty, human readable formatting of
3148 (license license:expat)))
3150 (define-public r-reshape
3157 (uri (cran-uri "reshape" version))
3160 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3161 (build-system r-build-system)
3163 `(("r-plyr" ,r-plyr)
3164 ("r-rcpp" ,r-rcpp)))
3165 (home-page "http://had.co.nz/reshape")
3166 (synopsis "Flexibly reshape data")
3168 "Flexibly restructure and aggregate data using just two functions:
3169 @code{melt} and @code{cast}. This package provides them.")
3170 (license license:expat)))
3172 (define-public r-restrserve
3174 (name "r-restrserve")
3179 (uri (cran-uri "RestRserve" version))
3181 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3182 (build-system r-build-system)
3184 `(("r-checkmate" ,r-checkmate)
3185 ("r-jsonlite" ,r-jsonlite)
3189 ("r-rserve" ,r-rserve)
3190 ("r-uuid" ,r-uuid)))
3192 `(("r-knitr" ,r-knitr)))
3193 (home-page "https://restrserve.org")
3194 (synopsis "R web API framework")
3196 "RestRserve is an R web API framework for building high-performance AND
3197 robust microservices and app backends. With Rserve backend on UNIX-like
3198 systems it is parallel by design. It will handle incoming requests in
3199 parallel - each request in a separate fork.")
3200 (license license:gpl2+)))
3202 (define-public r-progress
3209 (uri (cran-uri "progress" version))
3212 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3213 (build-system r-build-system)
3215 `(("r-crayon" ,r-crayon)
3217 ("r-prettyunits" ,r-prettyunits)
3219 (home-page "https://github.com/gaborcsardi/progress")
3220 (synopsis "Terminal progress bars")
3222 "This package provides configurable progress bars. They may include
3223 percentage, elapsed time, and/or the estimated completion time. They work in
3224 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3225 package also provides a C++ API, that works with or without Rcpp.")
3226 (license license:expat)))
3228 (define-public r-ggally
3235 (uri (cran-uri "GGally" version))
3238 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3239 (properties `((upstream-name . "GGally")))
3240 (build-system r-build-system)
3242 `(("openssl" ,openssl)))
3244 `(("r-dplyr" ,r-dplyr)
3245 ("r-forcats" ,r-forcats)
3246 ("r-ggplot2" ,r-ggplot2)
3247 ("r-gtable" ,r-gtable)
3248 ("r-lifecycle" ,r-lifecycle)
3250 ("r-progress" ,r-progress)
3251 ("r-rcolorbrewer" ,r-rcolorbrewer)
3252 ("r-reshape" ,r-reshape)
3253 ("r-rlang" ,r-rlang)
3254 ("r-scales" ,r-scales)
3255 ("r-tidyr" ,r-tidyr)))
3256 (home-page "https://ggobi.github.io/ggally")
3257 (synopsis "Extension to ggplot2")
3259 "The R package ggplot2 is a plotting system based on the grammar of
3260 graphics. GGally extends ggplot2 by adding several functions to reduce the
3261 complexity of combining geometric objects with transformed data. Some of
3262 these functions include a pairwise plot matrix, a two group pairwise plot
3263 matrix, a parallel coordinates plot, a survival plot, and several functions to
3265 (license license:gpl2+)))
3267 (define-public r-proxy
3274 (uri (cran-uri "proxy" version))
3277 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3278 (build-system r-build-system)
3279 (home-page "https://cran.r-project.org/web/packages/proxy")
3280 (synopsis "Distance and similarity measures")
3282 "This package provides an extensible framework for the efficient
3283 calculation of auto- and cross-proximities, along with implementations of the
3284 most popular ones.")
3285 (license license:gpl2)))
3294 (uri (cran-uri "sp" version))
3296 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3297 (build-system r-build-system)
3299 `(("r-lattice" ,r-lattice)))
3300 (home-page "https://cran.r-project.org/web/packages/sp")
3301 (synopsis "Classes and methods for spatial data")
3303 "This package provides classes and methods for spatial data; the classes
3304 document where the spatial location information resides, for 2D or 3D data.
3305 Utility functions are provided, e.g. for plotting data as maps, spatial
3306 selection, as well as methods for retrieving coordinates, for subsetting,
3307 print, summary, etc.")
3308 (license license:gpl2+)))
3310 (define-public r-laplacesdemon
3312 (name "r-laplacesdemon")
3317 (uri (cran-uri "LaplacesDemon" version))
3319 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3320 (properties `((upstream-name . "LaplacesDemon")))
3321 (build-system r-build-system)
3322 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3323 (synopsis "Complete environment for Bayesian inference")
3325 "This package provides a complete environment for Bayesian inference using
3326 a variety of different samplers.")
3327 (license license:expat)))
3329 (define-public r-rmtstat
3336 (uri (cran-uri "RMTstat" version))
3339 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3340 (properties `((upstream-name . "RMTstat")))
3341 (build-system r-build-system)
3342 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3343 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3345 "This package provides functions for working with the Tracy-Widom laws
3346 and other distributions related to the eigenvalues of large Wishart
3348 (license license:bsd-3)))
3350 (define-public r-rmpi
3356 (uri (cran-uri "Rmpi" version))
3359 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3360 (properties `((upstream-name . "Rmpi")))
3361 (build-system r-build-system)
3363 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3364 #:phases (modify-phases %standard-phases
3365 (add-before 'install 'mpi-setup
3368 `(("openmpi" ,openmpi)))
3370 `(("pkg-config" ,pkg-config)))
3371 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3372 (synopsis "R interface to message-passing interface (MPI)")
3374 "This package provides an interface (wrapper) to MPI APIs. It also
3375 provides an interactive R manager and worker environment.")
3376 (license license:gpl2+)))
3378 (define-public r-lmoments
3385 (uri (cran-uri "Lmoments" version))
3388 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3389 (properties `((upstream-name . "Lmoments")))
3390 (build-system r-build-system)
3392 `(("r-rcpp" ,r-rcpp)
3393 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3394 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3395 (synopsis "L-moments and quantile mixtures")
3397 "This package contains functions to estimate L-moments and trimmed
3398 L-moments from the data. It also contains functions to estimate the
3399 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3400 quantile mixture from L-moments and trimmed L-moments.")
3401 (license license:gpl2)))
3403 (define-public r-distillery
3405 (name "r-distillery")
3410 (uri (cran-uri "distillery" version))
3413 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3414 (build-system r-build-system)
3415 (home-page "https://ral.ucar.edu/staff/ericg/")
3416 (synopsis "Functions for confidence intervals and object information")
3418 "This package provides some very simple method functions for confidence
3419 interval calculation and to distill pertinent information from a potentially
3420 complex object; primarily used in common with the packages extRemes and
3422 (license license:gpl2+)))
3424 (define-public r-etrunct
3430 (uri (cran-uri "etrunct" version))
3433 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3434 (properties `((upstream-name . "etrunct")))
3435 (build-system r-build-system)
3436 (home-page "https://cran.r-project.org/web/packages/etrunct")
3437 (synopsis "Computes moments of univariate truncated T distribution")
3438 (description "This package computes moments of univariate truncated
3439 T distribution. There is only one exported function, @code{e_trunct},
3440 which should be seen for details.")
3441 (license license:expat)))
3443 (define-public r-extremes
3450 (uri (cran-uri "extRemes" version))
3453 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3454 (properties `((upstream-name . "extRemes")))
3455 (build-system r-build-system)
3457 `(("r-distillery" ,r-distillery)
3458 ("r-lmoments" ,r-lmoments)))
3459 (home-page "https://www.assessment.ucar.edu/toolkit/")
3460 (synopsis "Extreme value analysis")
3462 "ExtRemes is a suite of functions for carrying out analyses on the
3463 extreme values of a process of interest; be they block maxima over long blocks
3464 or excesses over a high threshold.")
3465 (license license:gpl2+)))
3467 (define-public r-lmtest
3474 (uri (cran-uri "lmtest" version))
3477 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3478 (build-system r-build-system)
3480 `(("r-zoo" ,r-zoo)))
3482 `(("gfortran" ,gfortran)))
3483 (home-page "https://cran.r-project.org/web/packages/lmtest")
3484 (synopsis "Testing linear regression models")
3486 "This package provides a collection of tests, data sets, and examples for
3487 diagnostic checking in linear regression models. Furthermore, some generic
3488 tools for inference in parametric models are provided.")
3489 ;; Either version is okay
3490 (license (list license:gpl2 license:gpl3))))
3492 (define-public r-idr
3498 (uri (cran-uri "idr" version))
3501 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3502 (build-system r-build-system)
3503 (home-page "https://cran.r-project.org/web/packages/idr/")
3504 (synopsis "Irreproducible discovery rate")
3506 "This is a package for estimating the copula mixture model and plotting
3507 correspondence curves in \"Measuring reproducibility of high-throughput
3508 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3509 by Li, Brown, Huang, and Bickel")
3510 (license license:gpl2+)))
3512 (define-public r-inline
3518 (uri (cran-uri "inline" version))
3521 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3522 (build-system r-build-system)
3523 (home-page "https://cran.r-project.org/web/packages/inline")
3524 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3526 "This package provides functionality to dynamically define R functions
3527 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3528 @code{.Call} calling conventions.")
3529 ;; Any version of the LGPL.
3530 (license license:lgpl3+)))
3532 (define-public r-inum
3538 (uri (cran-uri "inum" version))
3541 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3542 (build-system r-build-system)
3544 `(("r-libcoin" ,r-libcoin)))
3545 (home-page "https://cran.r-project.org/web/packages/inum/")
3546 (synopsis "Interval and enum-type representation of vectors")
3548 "This package provides an enum-type representation of vectors and
3549 representation of intervals, including a method of coercing variables
3551 (license license:gpl2)))
3552 (define-public r-invgamma
3558 (uri (cran-uri "invgamma" version))
3561 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3562 (properties `((upstream-name . "invgamma")))
3563 (build-system r-build-system)
3564 (home-page "https://github.com/dkahle/invgamma")
3565 (synopsis "Inverse gamma distribution")
3566 (description "This package provides a light weight implementation of the
3567 standard distribution functions for the inverse gamma distribution, wrapping
3568 those for the gamma distribution in the @code{stats} package.")
3569 (license license:gpl2)))
3571 (define-public r-bdsmatrix
3573 (name "r-bdsmatrix")
3578 (uri (cran-uri "bdsmatrix" version))
3581 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3582 (properties `((upstream-name . "bdsmatrix")))
3583 (build-system r-build-system)
3584 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3585 (synopsis "Routines for block diagonal symmetric matrices")
3587 "This package provides procedures to work with block diagonal symmetric
3588 matrices, a special case of sparse matrices.")
3589 (license license:lgpl2.0)))
3591 (define-public r-bbmle
3594 (version "1.0.23.1")
3598 (uri (cran-uri "bbmle" version))
3601 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3602 (build-system r-build-system)
3604 `(("r-bdsmatrix" ,r-bdsmatrix)
3605 ("r-lattice" ,r-lattice)
3607 ("r-matrix" ,r-matrix)
3608 ("r-mvtnorm" ,r-mvtnorm)
3609 ("r-numderiv" ,r-numderiv)))
3610 (home-page "https://cran.r-project.org/web/packages/bbmle")
3611 (synopsis "Tools for General Maximum Likelihood Estimation")
3613 "This package provides methods and functions for fitting maximum
3614 likelihood models in R. This package modifies and extends the @code{mle}
3615 classes in the @code{stats4} package.")
3616 ;; Any version of the GPL
3617 (license license:gpl2+)))
3619 (define-public r-emdbook
3626 (uri (cran-uri "emdbook" version))
3629 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3630 (build-system r-build-system)
3632 `(("r-bbmle" ,r-bbmle)
3634 ("r-lattice" ,r-lattice)
3636 ("r-plyr" ,r-plyr)))
3637 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3638 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3640 "This package provides auxiliary functions and data sets for \"Ecological
3641 Models and Data\", a book presenting maximum likelihood estimation and related
3642 topics for ecologists (ISBN 978-0-691-12522-0).")
3644 (license (list license:gpl2 license:gpl3))))
3646 (define-public r-lpsolve
3653 (uri (cran-uri "lpSolve" version))
3656 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3657 (properties `((upstream-name . "lpSolve")))
3658 (build-system r-build-system)
3659 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3660 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3662 "Lp_solve is software for solving linear, integer and mixed integer
3663 programs. This implementation supplies a \"wrapper\" function in C and some R
3664 functions that solve general linear/integer problems, assignment problems, and
3665 transportation problems.")
3666 (license license:lgpl2.0)))
3668 (define-public r-limsolve
3675 (uri (cran-uri "limSolve" version))
3678 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3679 (properties `((upstream-name . "limSolve")))
3680 (build-system r-build-system)
3682 `(("r-lpsolve" ,r-lpsolve)
3684 ("r-quadprog" ,r-quadprog)))
3685 (native-inputs `(("gfortran" ,gfortran)))
3686 (home-page "https://cran.r-project.org/web/packages/limSolve")
3687 (synopsis "Solving linear inverse models")
3689 "This package provides functions that:
3692 @item find the minimum/maximum of a linear or quadratic function,
3693 @item sample an underdetermined or overdetermined system,
3694 @item solve a linear system Ax=B for the unknown x.
3697 It includes banded and tridiagonal linear systems. The package calls Fortran
3698 functions from LINPACK.")
3700 (license (list license:gpl2+ license:gpl3+))))
3702 (define-public r-fitdistrplus
3704 (name "r-fitdistrplus")
3709 (uri (cran-uri "fitdistrplus" version))
3712 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3713 (build-system r-build-system)
3715 `(("r-mass" ,r-mass)
3716 ("r-survival" ,r-survival)))
3718 `(("r-knitr" ,r-knitr)))
3719 (home-page "http://riskassessment.r-forge.r-project.org")
3720 (synopsis "Fitting a parametric distribution from data")
3722 "This package extends the @code{fitdistr} function of the MASS package
3723 with several functions to help the fit of a parametric distribution to
3724 non-censored or censored data. Censored data may contain left-censored,
3725 right-censored and interval-censored values, with several lower and upper
3726 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3727 provides moment matching (MME), quantile matching (QME) and maximum
3728 goodness-of-fit estimation (MGE) methods (available only for non-censored
3729 data). Weighted versions of MLE, MME and QME are available.")
3730 (license license:gpl2+)))
3732 (define-public r-energy
3739 (uri (cran-uri "energy" version))
3742 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3743 (build-system r-build-system)
3745 `(("r-boot" ,r-boot)
3747 ("r-rcpp" ,r-rcpp)))
3748 (home-page "https://cran.r-project.org/web/packages/energy")
3749 (synopsis "Multivariate inference via the energy of data")
3751 "This package provides e-statistics (energy) tests and statistics for
3752 multivariate and univariate inference, including distance correlation,
3753 one-sample, two-sample, and multi-sample tests for comparing multivariate
3754 distributions, are implemented. Measuring and testing multivariate
3755 independence based on distance correlation, partial distance correlation,
3756 multivariate goodness-of-fit tests, clustering based on energy distance,
3757 testing for multivariate normality, distance components (disco) for
3758 non-parametric analysis of structured data, and other energy
3759 statistics/methods are implemented.")
3760 (license license:gpl2+)))
3762 (define-public r-suppdists
3764 (name "r-suppdists")
3769 (uri (cran-uri "SuppDists" version))
3772 "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8"))))
3773 (properties `((upstream-name . "SuppDists")))
3774 (build-system r-build-system)
3775 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3776 (synopsis "Supplementary distributions")
3778 "This package provides ten distributions supplementing those built into
3779 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3780 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3781 coefficient, Johnson distributions, normal scores and generalized
3782 hypergeometric distributions. In addition two random number generators of
3783 George Marsaglia are included.")
3784 (license license:gpl2+)))
3786 (define-public r-ksamples
3793 (uri (cran-uri "kSamples" version))
3796 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3797 (properties `((upstream-name . "kSamples")))
3798 (build-system r-build-system)
3800 `(("r-suppdists" ,r-suppdists)))
3801 (home-page "https://cran.r-project.org/web/packages/kSamples")
3802 (synopsis "K-Sample rank tests and their combinations")
3804 "This package provides tools to compares k samples using the
3805 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3806 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3807 test. It computes asymptotic, simulated or (limited) exact P-values, all
3808 valid under randomization, with or without ties, or conditionally under random
3809 sampling from populations, given the observed tie pattern. Except for Steel's
3810 test and the JT test it also combines these tests across several blocks of
3812 (license license:gpl2+)))
3814 (define-public r-cvst
3821 (uri (cran-uri "CVST" version))
3824 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3825 (properties `((upstream-name . "CVST")))
3826 (build-system r-build-system)
3828 `(("r-kernlab" ,r-kernlab)
3829 ("r-matrix" ,r-matrix)))
3830 (home-page "https://cran.r-project.org/web/packages/CVST")
3831 (synopsis "Fast cross-validation via sequential testing")
3833 "This package implements the fast cross-validation via sequential
3834 testing (CVST) procedure. CVST is an improved cross-validation procedure
3835 which uses non-parametric testing coupled with sequential analysis to
3836 determine the best parameter set on linearly increasing subsets of the data.
3837 Additionally to the CVST the package contains an implementation of the
3838 ordinary k-fold cross-validation with a flexible and powerful set of helper
3839 objects and methods to handle the overall model selection process. The
3840 implementations of the Cochran's Q test with permutations and the sequential
3841 testing framework of Wald are generic and can therefore also be used in other
3843 (license license:gpl2+)))
3845 (define-public r-squarem
3852 (uri (cran-uri "SQUAREM" version))
3855 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3856 (properties `((upstream-name . "SQUAREM")))
3857 (build-system r-build-system)
3858 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3859 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3861 "This package provides algorithms for accelerating the convergence of
3862 slow, monotone sequences from smooth, contraction mapping such as the EM
3863 algorithm. It can be used to accelerate any smooth, linearly convergent
3864 acceleration scheme. A tutorial style introduction to this package is
3865 available in a vignette.")
3866 (license license:gpl2+)))
3868 (define-public r-lava
3875 (uri (cran-uri "lava" version))
3878 "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83"))))
3879 (build-system r-build-system)
3881 `(("r-numderiv" ,r-numderiv)
3882 ("r-squarem" ,r-squarem)
3883 ("r-survival" ,r-survival)))
3885 `(("r-knitr" ,r-knitr)))
3886 (home-page "https://github.com/kkholst/lava")
3887 (synopsis "Latent variable models")
3889 "This package provides tools for the estimation and simulation of latent
3891 (license license:gpl3)))
3893 (define-public r-drr
3900 (uri (cran-uri "DRR" version))
3903 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3904 (properties `((upstream-name . "DRR")))
3905 (build-system r-build-system)
3907 `(("r-cvst" ,r-cvst)
3908 ("r-kernlab" ,r-kernlab)
3909 ("r-matrix" ,r-matrix)))
3910 (home-page "https://cran.r-project.org/web/packages/DRR")
3911 (synopsis "Dimensionality reduction via regression")
3913 "This package provides an implementation of dimensionality reduction via
3914 regression using Kernel Ridge Regression.")
3915 (license license:gpl3)))
3917 (define-public r-prodlim
3920 (version "2019.11.13")
3924 (uri (cran-uri "prodlim" version))
3927 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3928 (build-system r-build-system)
3930 `(("r-kernsmooth" ,r-kernsmooth)
3933 ("r-survival" ,r-survival)))
3934 (home-page "https://cran.r-project.org/web/packages/prodlim")
3935 (synopsis "Product-limit estimation for censored event history analysis")
3937 "This package provides a fast and user-friendly implementation of
3938 nonparametric estimators for censored event history (survival) analysis with
3939 the Kaplan-Meier and Aalen-Johansen methods.")
3940 (license license:gpl2+)))
3942 (define-public r-dimred
3949 (uri (cran-uri "dimRed" version))
3952 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3953 (properties `((upstream-name . "dimRed")))
3954 (build-system r-build-system)
3957 ("r-magrittr" ,r-magrittr)))
3958 (home-page "https://github.com/gdkrmr/dimRed")
3959 (synopsis "Framework for dimensionality reduction")
3961 "This package provides a collection of dimensionality reduction
3962 techniques from R packages and provides a common interface for calling the
3964 (license license:gpl3)))
3966 (define-public r-timedate
3969 (version "3043.102")
3973 (uri (cran-uri "timeDate" version))
3976 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3977 (properties `((upstream-name . "timeDate")))
3978 (build-system r-build-system)
3979 (home-page "https://www.rmetrics.org")
3980 (synopsis "Chronological and calendar objects")
3982 "This package provides an environment for teaching \"Financial
3983 Engineering and Computational Finance\" and for managing chronological and
3985 (license license:gpl2+)))
3987 (define-public r-magic
3994 (uri (cran-uri "magic" version))
3997 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3998 (build-system r-build-system)
4000 `(("r-abind" ,r-abind)))
4001 (home-page "https://github.com/RobinHankin/magic.git")
4002 (synopsis "Create and investigate magic squares")
4004 "This package provides a collection of efficient, vectorized algorithms
4005 for the creation and investigation of magic squares and hypercubes, including
4006 a variety of functions for the manipulation and analysis of arbitrarily
4007 dimensioned arrays.")
4008 (license license:gpl2)))
4010 (define-public r-rmysql
4017 (uri (cran-uri "RMySQL" version))
4020 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4021 (properties `((upstream-name . "RMySQL")))
4022 (build-system r-build-system)
4024 `(("mariadb-dev" ,mariadb "dev")
4027 `(("r-dbi" ,r-dbi)))
4028 (home-page "https://github.com/r-dbi/RMySQL")
4029 (synopsis "Database interface and MySQL driver for R")
4031 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4032 package contains an old implementation based on legacy code from S-PLUS which
4033 is being phased out. A modern MySQL client based on Rcpp is available from
4034 the RMariaDB package.")
4035 (license license:gpl2)))
4037 (define-public r-rpostgresql
4039 (name "r-rpostgresql")
4044 (uri (cran-uri "RPostgreSQL" version))
4047 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4048 (properties `((upstream-name . "RPostgreSQL")))
4049 (build-system r-build-system)
4051 `(("postgresql" ,postgresql)))
4053 `(("r-dbi" ,r-dbi)))
4054 (home-page "https://github.com/tomoakin/RPostgreSQL")
4055 (synopsis "R interface to the PostgreSQL database system")
4057 "This package provides a Database Interface (DBI) compliant driver for R
4058 to access PostgreSQL database systems.")
4059 ;; The whole package is released under GPL version 2. It includes code
4060 ;; under the PostgreSQL license.
4061 (license license:gpl2)))
4063 (define-public r-linprog
4070 (uri (cran-uri "linprog" version))
4073 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4074 (build-system r-build-system)
4075 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4076 (home-page "http://linprog.r-forge.r-project.org/")
4077 (synopsis "Linear programming and optimization")
4079 "This package can be used to solve Linear Programming / Linear
4080 Optimization problems by using the simplex algorithm.")
4081 (license license:gpl2+)))
4083 (define-public r-geometry
4090 (uri (cran-uri "geometry" version))
4093 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4094 (build-system r-build-system)
4096 `(("r-magic" ,r-magic)
4097 ("r-linprog" ,r-linprog)
4098 ("r-lpsolve" ,r-lpsolve)
4100 ("r-rcppprogress" ,r-rcppprogress)))
4101 (home-page "http://geometry.r-forge.r-project.org/")
4102 (synopsis "Mesh generator and surface tessellator")
4104 "This package makes the qhull library available in R, in a similar manner
4105 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4106 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4107 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4108 and higher dimensions. It implements the Quickhull algorithm for computing
4109 the convex hull. Qhull does not support constrained Delaunay triangulations,
4110 or mesh generation of non-convex objects, but the package does include some R
4111 functions that allow for this. Currently the package only gives access to
4112 Delaunay triangulation and convex hull computation.")
4113 ;; The Qhull sources are included and are distributed under a custom
4114 ;; non-copyleft license. The R sources are released under GPL version 2.
4115 (license (list license:gpl2
4116 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4118 (define-public r-ddalpha
4125 (uri (cran-uri "ddalpha" version))
4128 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4129 (build-system r-build-system)
4132 ("r-class" ,r-class)
4133 ("r-geometry" ,r-geometry)
4136 ("r-robustbase" ,r-robustbase)
4137 ("r-sfsmisc" ,r-sfsmisc)))
4139 `(("gfortran" ,gfortran)))
4140 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4141 (synopsis "Depth-Based classification and calculation of data depth")
4143 "This package contains procedures for depth-based supervised learning,
4144 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4145 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4146 statistical depth function to a compact low-dimensional space, where the final
4147 classification is done. It also offers an extension to functional data and
4148 routines for calculating certain notions of statistical depth functions. 50
4149 multivariate and 5 functional classification problems are included.")
4150 (license license:gpl2)))
4152 (define-public r-gower
4159 (uri (cran-uri "gower" version))
4162 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4163 (build-system r-build-system)
4164 (home-page "https://github.com/markvanderloo/gower")
4165 (synopsis "Gower's distance")
4167 "This package provides tools to compute Gower's distance (or similarity)
4168 coefficient between records, and to compute the top-n matches between records.
4169 Core algorithms are executed in parallel on systems supporting OpenMP.")
4170 (license license:gpl3)))
4172 (define-public r-rcpproll
4179 (uri (cran-uri "RcppRoll" version))
4182 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4183 (properties `((upstream-name . "RcppRoll")))
4184 (build-system r-build-system)
4186 `(("r-rcpp" ,r-rcpp)))
4187 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4188 (synopsis "Efficient rolling and windowed operations")
4190 "This package provides fast and efficient routines for common rolling /
4191 windowed operations. Routines for the efficient computation of windowed mean,
4192 median, sum, product, minimum, maximum, standard deviation and variance are
4194 (license license:gpl2+)))
4196 (define-public r-ipred
4203 (uri (cran-uri "ipred" version))
4206 "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp"))))
4207 (build-system r-build-system)
4209 `(("r-class" ,r-class)
4212 ("r-prodlim" ,r-prodlim)
4213 ("r-rpart" ,r-rpart)
4214 ("r-survival" ,r-survival)))
4215 (home-page "https://cran.r-project.org/web/packages/ipred")
4216 (synopsis "Improved predictors")
4218 "This package provides improved predictive models by indirect
4219 classification and bagging for classification, regression and survival
4220 problems as well as resampling based estimators of prediction error.")
4221 (license license:gpl2+)))
4223 (define-public r-psych
4230 (uri (cran-uri "psych" version))
4233 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
4234 (build-system r-build-system)
4236 `(("r-lattice" ,r-lattice)
4237 ("r-mnormt" ,r-mnormt)
4238 ("r-nlme" ,r-nlme)))
4239 (home-page "https://cran.r-project.org/web/packages/psych/")
4240 (synopsis "Procedures for psychological, psychometric, and personality research")
4242 "This package provides a general purpose toolbox for personality,
4243 psychometric theory and experimental psychology. Functions are primarily for
4244 multivariate analysis and scale construction using factor analysis, principal
4245 component analysis, cluster analysis and reliability analysis, although others
4246 provide basic descriptive statistics. Item Response Theory is done using
4247 factor analysis of tetrachoric and polychoric correlations. Functions for
4248 analyzing data at multiple levels include within and between group statistics,
4249 including correlations and factor analysis. Functions for simulating and
4250 testing particular item and test structures are included. Several functions
4251 serve as a useful front end for structural equation modeling. Graphical
4252 displays of path diagrams, factor analysis and structural equation models are
4253 created using basic graphics.")
4254 (license license:gpl2+)))
4256 (define-public r-generics
4263 (uri (cran-uri "generics" version))
4266 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4267 (build-system r-build-system)
4268 (home-page "https://github.com/r-lib/generics")
4269 (synopsis "Common S3 generics not provided by base R methods")
4271 "In order to reduce potential package dependencies and conflicts,
4272 generics provides a number of commonly used S3 generics that are not provided
4273 by base R methods related to model fitting.")
4274 (license license:gpl2)))
4276 (define-public r-broom
4283 (uri (cran-uri "broom" version))
4286 "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw"))))
4287 (build-system r-build-system)
4289 `(("r-backports" ,r-backports)
4290 ("r-dplyr" ,r-dplyr)
4291 ("r-ellipsis" ,r-ellipsis)
4292 ("r-generics" ,r-generics)
4294 ("r-purrr" ,r-purrr)
4295 ("r-rlang" ,r-rlang)
4296 ("r-stringr" ,r-stringr)
4297 ("r-tibble" ,r-tibble)
4298 ("r-tidyr" ,r-tidyr)))
4300 `(("r-knitr" ,r-knitr)))
4301 (home-page "https://github.com/tidyverse/broom")
4302 (synopsis "Convert statistical analysis objects into tidy data frames")
4304 "This package provides tools to convert statistical analysis objects from
4305 R into tidy data frames, so that they can more easily be combined, reshaped
4306 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4307 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4308 summarizes a model's statistical findings such as coefficients of a
4309 regression; @code{augment}, which adds columns to the original data such as
4310 predictions, residuals and cluster assignments; and @code{glance}, which
4311 provides a one-row summary of model-level statistics.")
4312 (license license:expat)))
4314 (define-public r-recipes
4321 (uri (cran-uri "recipes" version))
4324 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4325 (build-system r-build-system)
4327 `(("r-dplyr" ,r-dplyr)
4328 ("r-generics" ,r-generics)
4330 ("r-gower" ,r-gower)
4331 ("r-ipred" ,r-ipred)
4332 ("r-lifecycle" ,r-lifecycle)
4333 ("r-lubridate" ,r-lubridate)
4334 ("r-magrittr" ,r-magrittr)
4335 ("r-matrix" ,r-matrix)
4336 ("r-purrr" ,r-purrr)
4337 ("r-rlang" ,r-rlang)
4338 ("r-tibble" ,r-tibble)
4339 ("r-tidyr" ,r-tidyr)
4340 ("r-tidyselect" ,r-tidyselect)
4341 ("r-timedate" ,r-timedate)
4342 ("r-withr" ,r-withr)))
4344 `(("r-knitr" ,r-knitr)))
4345 (home-page "https://github.com/topepo/recipes")
4346 (synopsis "Preprocessing tools to create design matrices")
4348 "Recipes is an extensible framework to create and preprocess design
4349 matrices. Recipes consist of one or more data manipulation and analysis
4350 \"steps\". Statistical parameters for the steps can be estimated from an
4351 initial data set and then applied to other data sets. The resulting design
4352 matrices can then be used as inputs into statistical or machine learning
4354 (license license:gpl2)))
4356 (define-public r-pdist
4363 (uri (cran-uri "pdist" version))
4366 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4367 (build-system r-build-system)
4368 (home-page "https://github.com/jeffwong/pdist")
4369 (synopsis "Partitioned distance function")
4371 "Pdist computes the euclidean distance between rows of a matrix X and
4372 rows of another matrix Y. Previously, this could be done by binding the two
4373 matrices together and calling @code{dist}, but this creates unnecessary
4374 computation by computing the distances between a row of X and another row of
4375 X, and likewise for Y. Pdist strictly computes distances across the two
4376 matrices, not within the same matrix, making computations significantly faster
4377 for certain use cases.")
4378 (license license:gpl3+)))
4380 (define-public r-ggrepel
4387 (uri (cran-uri "ggrepel" version))
4390 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4391 (build-system r-build-system)
4393 `(("r-ggplot2" ,r-ggplot2)
4395 ("r-rlang" ,r-rlang)
4396 ("r-scales" ,r-scales)))
4398 `(("r-knitr" ,r-knitr))) ; for vignettes
4399 (home-page "https://github.com/slowkow/ggrepel")
4400 (synopsis "Repulsive text and label geometries for ggplot2")
4402 "This package provides text and label geometries for ggplot2 that help to
4403 avoid overlapping text labels. Labels repel away from each other and away
4404 from the data points.")
4405 (license license:gpl3)))
4407 (define-public r-corrplot
4414 (uri (cran-uri "corrplot" version))
4417 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4418 (build-system r-build-system)
4419 (home-page "https://github.com/taiyun/corrplot")
4420 (synopsis "Visualization of a correlation matrix")
4422 "This package provides a graphical display of a correlation matrix or
4423 general matrix. It also contains some algorithms to do matrix reordering. In
4424 addition, corrplot is good at details, including choosing color, text labels,
4425 color labels, layout, etc.")
4426 ;; Any version of the GPL
4427 (license license:gpl2+)))
4429 (define-public r-stringdist
4431 (name "r-stringdist")
4436 (uri (cran-uri "stringdist" version))
4438 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4439 (build-system r-build-system)
4440 (home-page "https://github.com/markvanderloo/stringdist")
4441 (synopsis "Approximate string matching and string distance functions")
4443 "This package implements an approximate string matching version of R's
4444 native @code{match} function. It can calculate various string distances based
4445 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4446 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4447 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4448 can be computed between character vectors while taking proper care of encoding
4449 or between integer vectors representing generic sequences.")
4450 (license license:gpl3+)))
4452 (define-public r-ucminf
4459 (uri (cran-uri "ucminf" version))
4462 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4463 (build-system r-build-system)
4464 (native-inputs `(("gfortran" ,gfortran)))
4465 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4466 (synopsis "General-purpose unconstrained non-linear optimization")
4468 "This package provides an implementation of an algorithm for
4469 general-purpose unconstrained non-linear optimization. The algorithm is of
4470 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4471 search with a trust region type monitoring of the input to the line search
4472 algorithm. The interface of @code{ucminf} is designed for easy interchange
4473 with the package @code{optim}.")
4474 (license license:gpl2+)))
4476 (define-public r-useful
4482 (uri (cran-uri "useful" version))
4485 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4486 (properties `((upstream-name . "useful")))
4487 (build-system r-build-system)
4489 `(("r-assertthat" ,r-assertthat)
4490 ("r-dplyr" ,r-dplyr)
4491 ("r-ggplot2" ,r-ggplot2)
4492 ("r-magrittr" ,r-magrittr)
4493 ("r-matrix" ,r-matrix)
4495 ("r-purrr" ,r-purrr)
4496 ("r-scales" ,r-scales)))
4497 (home-page "https://github.com/jaredlander/useful")
4498 (synopsis "Collection of handy, useful functions")
4499 (description "This package provides a set of little functions that have been
4500 found useful to do little odds and ends such as plotting the results of K-means
4501 clustering, substituting special text characters, viewing parts of a
4502 @code{data.frame}, constructing formulas from text and building design and
4503 response matrices.")
4504 (license license:bsd-3)))
4506 (define-public r-ordinal
4509 (version "2019.12-10")
4513 (uri (cran-uri "ordinal" version))
4516 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4517 (build-system r-build-system)
4519 `(("r-mass" ,r-mass)
4520 ("r-matrix" ,r-matrix)
4521 ("r-numderiv" ,r-numderiv)
4522 ("r-ucminf" ,r-ucminf)))
4523 (home-page "https://github.com/runehaubo/ordinal")
4524 (synopsis "Regression models for ordinal data")
4526 "This package provides an implementation of cumulative link (mixed)
4527 models also known as ordered regression models, proportional odds models,
4528 proportional hazards models for grouped survival times and ordered models.
4529 Estimation is via maximum likelihood and mixed models are fitted with the
4530 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4531 (license license:gpl2+)))
4533 (define-public r-jomo
4540 (uri (cran-uri "jomo" version))
4543 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4544 (build-system r-build-system)
4546 `(("r-lme4" ,r-lme4)
4548 ("r-ordinal" ,r-ordinal)
4549 ("r-survival" ,r-survival)))
4550 (home-page "https://cran.r-project.org/web/packages/jomo/")
4551 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4553 "Similarly to Schafer's package pan, jomo is a package for multilevel
4554 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4555 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4556 possibility of handling binary and categorical data through latent normal
4557 variables, the option to use cluster-specific covariance matrices and to
4558 impute compatibly with the substantive model.")
4559 (license license:gpl2)))
4561 (define-public r-pan
4568 (uri (cran-uri "pan" version))
4571 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4572 (build-system r-build-system)
4573 (native-inputs `(("gfortran" ,gfortran)))
4574 (home-page "https://cran.r-project.org/web/packages/pan/")
4575 (synopsis "Multiple imputation for multivariate panel or clustered data")
4577 "This package implements multiple imputation for multivariate panel or
4579 (license license:gpl3)))
4581 (define-public r-mitml
4588 (uri (cran-uri "mitml" version))
4591 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4592 (build-system r-build-system)
4594 `(("r-haven" ,r-haven)
4598 `(("r-knitr" ,r-knitr)))
4599 (home-page "https://cran.r-project.org/web/packages/mitml/")
4600 (synopsis "Tools for multiple imputation in multilevel modeling")
4602 "This package provides tools for multiple imputation of missing data in
4603 multilevel modeling. It includes a user-friendly interface to the packages
4604 pan and jomo, and several functions for visualization, data management and the
4605 analysis of multiply imputed data sets.")
4606 (license license:gpl2+)))
4608 (define-public r-mice
4615 (uri (cran-uri "mice" version))
4618 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4619 (build-system r-build-system)
4621 `(("r-broom" ,r-broom)
4622 ("r-cpp11" ,r-cpp11)
4623 ("r-dplyr" ,r-dplyr)
4624 ("r-generics" ,r-generics)
4625 ("r-lattice" ,r-lattice)
4627 ("r-rlang" ,r-rlang)
4628 ("r-tidyr" ,r-tidyr)))
4629 (home-page "https://cran.r-project.org/web/packages/mice/")
4630 (synopsis "Multivariate imputation by chained equations")
4632 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4633 implemented by the MICE algorithm as described in @url{Van Buuren and
4634 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4635 variable has its own imputation model. Built-in imputation models are
4636 provided for continuous data (predictive mean matching, normal), binary
4637 data (logistic regression), unordered categorical data (polytomous logistic
4638 regression) and ordered categorical data (proportional odds). MICE can also
4639 impute continuous two-level data (normal model, pan, second-level variables).
4640 Passive imputation can be used to maintain consistency between variables.
4641 Various diagnostic plots are available to inspect the quality of the
4643 ;; Any of these two versions.
4644 (license (list license:gpl2 license:gpl3))))
4646 (define-public r-truncnorm
4648 (name "r-truncnorm")
4653 (uri (cran-uri "truncnorm" version))
4656 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4657 (build-system r-build-system)
4658 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4659 (synopsis "Truncated normal distribution")
4660 (description "This package provides functions for the truncated normal
4661 distribution with mean equal to @code{mean} and standard deviation equal to
4662 @code{sd}. It includes density, distribution, quantile, and expected value
4663 functions, as well as a random generation function.")
4664 (license license:gpl2)))
4666 (define-public r-rsolnp
4673 (uri (cran-uri "Rsolnp" version))
4676 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4677 (properties `((upstream-name . "Rsolnp")))
4678 (build-system r-build-system)
4680 `(("r-truncnorm" ,r-truncnorm)))
4681 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4682 (synopsis "General non-linear optimization")
4683 (description "The Rsolnp package implements a general non-linear augmented
4684 Lagrange multiplier method solver, a @dfn{sequential quadratic
4685 programming} (SQP) based solver).")
4686 ;; Any version of the GPL.
4687 (license license:gpl2+)))
4689 (define-public r-hardyweinberg
4691 (name "r-hardyweinberg")
4696 (uri (cran-uri "HardyWeinberg" version))
4699 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4700 (properties `((upstream-name . "HardyWeinberg")))
4701 (build-system r-build-system)
4703 `(("r-mice" ,r-mice)
4705 ("r-rsolnp" ,r-rsolnp)))
4706 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4707 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4709 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4710 diallelic genetic marker data. All classical tests (chi-square, exact,
4711 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4712 included in the package, as well as functions for power computation and for
4713 the simulation of marker data under equilibrium and disequilibrium. Routines
4714 for dealing with markers on the X-chromosome are included. Functions for
4715 testing equilibrium in the presence of missing data by using multiple
4716 imputation are also provided. Implements several graphics for exploring the
4717 equilibrium status of a large set of diallelic markers: ternary plots with
4718 acceptance regions, log-ratio plots and Q-Q plots.")
4719 (license license:gpl2+)))
4728 (uri (cran-uri "sm" version))
4731 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4732 (build-system r-build-system)
4733 (native-inputs `(("gfortran" ,gfortran)))
4734 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4735 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4737 "This is software accompanying the book 'Applied Smoothing Techniques for
4738 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4739 University Press. It provides smoothing methods for nonparametric regression
4740 and density estimation")
4741 (license license:gpl2+)))
4743 (define-public r-venndiagram
4745 (name "r-venndiagram")
4749 (uri (cran-uri "VennDiagram" version))
4752 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4753 (properties `((upstream-name . "VennDiagram")))
4754 (build-system r-build-system)
4756 `(("r-futile-logger" ,r-futile-logger)))
4757 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4758 (synopsis "Generate High-Resolution Venn and Euler Plots")
4760 "This package provides a set of functions to generate high-resolution
4761 Venn and Euler plots. It includes handling for several special cases,
4762 including two-case scaling, and extensive customization of plot shape and
4764 (license license:gpl2+)))
4766 (define-public r-vioplot
4773 (uri (cran-uri "vioplot" version))
4776 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4777 (build-system r-build-system)
4782 `(("r-knitr" ,r-knitr)))
4783 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4784 (synopsis "Violin plot")
4786 "This package provides a violin plot, which is a combination of a box
4787 plot and a kernel density plot.")
4788 (license license:bsd-3)))
4790 (define-public r-rsofia
4796 ;; This package has been removed from CRAN, so we can
4797 ;; only fetch it from the archives.
4798 (uri (string-append "https://cran.r-project.org/src/"
4799 "contrib/Archive/RSofia/RSofia_"
4803 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4804 (properties `((upstream-name . "RSofia")))
4805 (build-system r-build-system)
4807 `(("r-rcpp" ,r-rcpp)))
4808 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4809 (synopsis "Port of sofia-ml to R")
4810 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4811 suite of fast incremental algorithms for machine learning that can be used for
4812 training models for classification or ranking.")
4813 (license license:asl2.0)))
4815 (define-public r-xts
4822 (uri (cran-uri "xts" version))
4825 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4826 (build-system r-build-system)
4827 (propagated-inputs `(("r-zoo" ,r-zoo)))
4828 (home-page "https://github.com/joshuaulrich/xts")
4829 (synopsis "Extensible time series")
4831 "This package provides for uniform handling of R's different time-based
4832 data classes by extending @code{zoo}, maximizing native format information
4833 preservation and allowing for user-level customization and extension, while
4834 simplifying cross-class interoperability.")
4835 (license license:gpl2+)))
4837 (define-public r-performanceanalytics
4839 (name "r-performanceanalytics")
4844 (uri (cran-uri "PerformanceAnalytics" version))
4847 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4849 `((upstream-name . "PerformanceAnalytics")))
4850 (build-system r-build-system)
4852 `(("r-quadprog" ,r-quadprog)
4855 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4856 (synopsis "Econometric tools for performance and risk analysis")
4857 (description "This is a collection of econometric functions for
4858 performance and risk analysis. This package aims to aid practitioners and
4859 researchers in utilizing the latest research in analysis of non-normal return
4860 streams. In general, it is most tested on return (rather than price) data on
4861 a regular scale, but most functions will work with irregular return data as
4862 well, and increasing numbers of functions will work with P&L or price data
4864 ;; Either version may be picked.
4865 (license (list license:gpl2 license:gpl3))))
4867 (define-public r-laeken
4874 (uri (cran-uri "laeken" version))
4877 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4878 (build-system r-build-system)
4880 `(("r-boot" ,r-boot)
4881 ("r-mass" ,r-mass)))
4882 (home-page "https://cran.r-project.org/web/packages/laeken/")
4883 (synopsis "Estimation of indicators on social exclusion and poverty")
4884 (description "This package provides tools for the estimation of indicators
4885 on social exclusion and poverty, as well as an implementation of Pareto tail
4886 modeling for empirical income distributions.")
4887 (license license:gpl2+)))
4889 (define-public r-vcd
4896 (uri (cran-uri "vcd" version))
4899 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4900 (build-system r-build-system)
4902 `(("r-colorspace" ,r-colorspace)
4903 ("r-lmtest" ,r-lmtest)
4904 ("r-mass" ,r-mass)))
4905 (home-page "https://cran.r-project.org/web/packages/vcd/")
4906 (synopsis "Visualizing categorical data")
4907 (description "This package provides visualization techniques, data sets,
4908 summary and inference procedures aimed particularly at categorical data.
4909 Special emphasis is given to highly extensible grid graphics. The package was
4910 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4911 Friendly and is now the main support package for a new book, \"Discrete Data
4912 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4913 (license license:gpl2)))
4915 (define-public r-ica
4922 (uri (cran-uri "ica" version))
4925 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4926 (build-system r-build-system)
4927 (home-page "https://cran.r-project.org/web/packages/ica/")
4928 (synopsis "Independent component analysis")
4929 (description "This package provides tools for @dfn{Independent Component
4930 Analysis} (ICA) using various algorithms: FastICA,
4931 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4932 of Eigenmatrices} (JADE).")
4933 (license license:gpl2+)))
4935 (define-public r-dtw
4942 (uri (cran-uri "dtw" version))
4945 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4946 (build-system r-build-system)
4947 (propagated-inputs `(("r-proxy" ,r-proxy)))
4948 (home-page "http://dtw.r-forge.r-project.org/")
4949 (synopsis "Dynamic Time Warping Algorithms")
4950 (description "This package provides a comprehensive implementation of
4951 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4952 optimal (least cumulative distance) alignment between points of two time
4953 series. Common DTW variants covered include local (slope) and global (window)
4954 constraints, subsequence matches, arbitrary distance definitions,
4955 normalizations, minimum variance matching, and so on.")
4956 (license license:gpl2+)))
4958 (define-public r-sdmtools
4961 (version "1.1-221.2")
4965 (uri (cran-uri "SDMTools" version))
4968 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4969 (properties `((upstream-name . "SDMTools")))
4970 (build-system r-build-system)
4971 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4972 (home-page "https://www.rforge.net/SDMTools/")
4973 (synopsis "Species distribution modelling tools")
4974 (description "This package provides a set of tools for post processing
4975 the outcomes of species distribution modeling exercises. It includes novel
4976 methods for comparing models and tracking changes in distributions through
4977 time. It further includes methods for visualizing outcomes, selecting
4978 thresholds, calculating measures of accuracy and landscape fragmentation
4980 (license license:gpl3+)))
4982 (define-public r-scatterplot3d
4984 (name "r-scatterplot3d")
4989 (uri (cran-uri "scatterplot3d" version))
4992 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4993 (build-system r-build-system)
4994 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4995 (synopsis "3D scatter plot")
4996 (description "This package provides an implementation of scatter plots for
4997 plotting. a three dimensional point cloud.")
4998 (license license:gpl2)))
5000 (define-public r-ggridges
5007 (uri (cran-uri "ggridges" version))
5010 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5011 (build-system r-build-system)
5013 `(("r-ggplot2" ,r-ggplot2)
5015 ("r-scales" ,r-scales)
5016 ("r-withr" ,r-withr)))
5018 `(("r-knitr" ,r-knitr)))
5019 (home-page "https://github.com/clauswilke/ggridges")
5020 (synopsis "Ridgeline plots in ggplot2")
5022 "Ridgeline plots provide a convenient way of visualizing changes in
5023 distributions over time or space. This package enables the creation of such
5024 plots in @code{ggplot2}.")
5025 (license license:gpl2)))
5027 (define-public r-ggjoy
5034 (uri (cran-uri "ggjoy" version))
5037 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5038 (build-system r-build-system)
5040 `(("r-ggplot2" ,r-ggplot2)
5041 ("r-ggridges" ,r-ggridges)))
5042 (home-page "https://github.com/clauswilke/ggjoy")
5043 (synopsis "Joyplots in ggplot2")
5044 (description "Joyplots provide a convenient way of visualizing changes in
5045 distributions over time or space. This package enables the creation of such
5046 plots in @code{ggplot2}.")
5047 (license license:gpl2)))
5049 (define-public r-cli
5056 (uri (cran-uri "cli" version))
5059 "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i"))))
5060 (build-system r-build-system)
5062 `(("r-assertthat" ,r-assertthat)
5063 ("r-glue" ,r-glue)))
5064 (home-page "https://github.com/r-lib/cli#readme")
5065 (synopsis "Helpers for developing command line interfaces")
5066 (description "This package provides a suite of tools designed to build
5067 attractive command line interfaces (CLIs). It includes tools for drawing
5068 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5069 (license license:expat)))
5071 (define-public r-argparser
5073 (name "r-argparser")
5078 (uri (cran-uri "argparser" version))
5081 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5082 (build-system r-build-system)
5083 (home-page "https://bitbucket.org/djhshih/argparser")
5084 (synopsis "Command-line argument parser")
5086 "This package provides a cross-platform command-line argument parser
5087 written purely in R with no external dependencies. It is useful with the
5088 Rscript front-end and facilitates turning an R script into an executable
5090 (license license:gpl3+)))
5092 (define-public r-debugme
5099 (uri (cran-uri "debugme" version))
5102 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5103 (build-system r-build-system)
5104 (propagated-inputs `(("r-crayon" ,r-crayon)))
5105 (home-page "https://github.com/r-lib/debugme#readme")
5106 (synopsis "Debug R packages")
5108 "This package allows the user to specify debug messages as special string
5109 constants, and control debugging of packages via environment variables.")
5110 (license license:expat)))
5112 (define-public r-processx
5119 (uri (cran-uri "processx" version))
5121 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
5122 (build-system r-build-system)
5126 (home-page "https://github.com/r-lib/processx3")
5127 (synopsis "Execute and control system processes")
5129 "This package provides portable tools to run system processes in the
5130 background. It can check if a background process is running; wait on a
5131 background process to finish; get the exit status of finished processes; kill
5132 background processes and their children; restart processes. It can read the
5133 standard output and error of the processes, using non-blocking connections.
5134 @code{processx} can poll a process for standard output or error, with a
5135 timeout. It can also poll several processes at once.")
5136 (license license:expat)))
5138 (define-public r-tsp
5145 (uri (cran-uri "TSP" version))
5148 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5149 (properties `((upstream-name . "TSP")))
5150 (build-system r-build-system)
5151 (propagated-inputs `(("r-foreach" ,r-foreach)))
5152 (home-page "https://cran.r-project.org/web/packages/TSP/")
5153 (synopsis "Traveling salesperson problem (TSP)")
5154 (description "This package provides basic infrastructure and some
5155 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5156 traveling salesman problem).")
5157 (license license:gpl3)))
5159 (define-public r-qap
5166 (uri (cran-uri "qap" version))
5169 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5170 (build-system r-build-system)
5171 (native-inputs `(("gfortran" ,gfortran)))
5172 (home-page "https://cran.r-project.org/web/packages/qap/")
5173 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5174 (description "This package implements heuristics for the @dfn{quadratic
5175 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5177 (license license:gpl3)))
5179 (define-public r-gclus
5186 (uri (cran-uri "gclus" version))
5189 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5190 (build-system r-build-system)
5191 (propagated-inputs `(("r-cluster" ,r-cluster)))
5192 (home-page "https://cran.r-project.org/web/packages/gclus/")
5193 (synopsis "Clustering graphics")
5194 (description "This package orders panels in scatterplot matrices and
5195 parallel coordinate displays by some merit index. It contains various indices
5196 of merit, ordering functions, and enhanced versions of @code{pairs} and
5197 @code{parcoord} which color panels according to their merit level.")
5198 (license license:gpl2+)))
5200 (define-public r-webshot
5207 (uri (cran-uri "webshot" version))
5210 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5211 (build-system r-build-system)
5213 `(("r-callr" ,r-callr)
5214 ("r-jsonlite" ,r-jsonlite)
5215 ("r-magrittr" ,r-magrittr)))
5216 (home-page "https://github.com/wch/webshot/")
5217 (synopsis "Take screenshots of web pages")
5219 "Webshot makes it easy to take screenshots of web pages from within R.
5220 It can also run Shiny applications locally and take screenshots of the
5221 application; and it can render and screenshot static as well as interactive R
5222 Markdown documents.")
5223 (license license:gpl2)))
5225 (define-public r-seriation
5227 (name "r-seriation")
5232 (uri (cran-uri "seriation" version))
5235 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5236 (build-system r-build-system)
5238 `(("r-cluster" ,r-cluster)
5239 ("r-colorspace" ,r-colorspace)
5240 ("r-dendextend" ,r-dendextend)
5241 ("r-gclus" ,r-gclus)
5242 ("r-gplots" ,r-gplots)
5245 ("r-registry" ,r-registry)
5247 (native-inputs `(("gfortran" ,gfortran)))
5248 (home-page "https://s2.smu.edu/IDA/seriation/")
5249 (synopsis "Infrastructure for ordering objects using seriation")
5251 "This package provides infrastructure for seriation with an
5252 implementation of several seriation/sequencing techniques to reorder matrices,
5253 dissimilarity matrices, and dendrograms. It also provides (optimally)
5254 reordered heatmaps, color images and clustering visualizations like
5255 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5257 (license license:gpl3)))
5259 (define-public r-xfun
5266 (uri (cran-uri "xfun" version))
5268 (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y"))))
5269 (build-system r-build-system)
5270 ;; knitr itself depends on xfun
5273 `(("r-knitr" ,r-knitr)))
5274 (home-page "https://github.com/yihui/xfun")
5275 (synopsis "Miscellaneous functions")
5277 "This package provides miscellaneous functions commonly used in other
5278 packages maintained by Yihui Xie.")
5279 (license license:expat)))
5281 (define-public r-utf8
5288 (uri (cran-uri "utf8" version))
5291 "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk"))))
5292 (build-system r-build-system)
5294 `(("r-knitr" ,r-knitr)))
5295 (home-page "https://github.com/patperry/r-utf8")
5296 (synopsis "Unicode text processing")
5298 "This package provides tools to process and print UTF-8 encoded
5299 international text (Unicode). Input, validate, normalize, encode, format, and
5301 (license license:asl2.0)))
5303 (define-public r-zeallot
5310 (uri (cran-uri "zeallot" version))
5313 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5314 (build-system r-build-system)
5315 (home-page "https://github.com/nteetor/zeallot")
5316 (synopsis "Multiple, unpacking, and destructuring assignment")
5318 "This package provides a @code{%<-%} operator to perform multiple,
5319 unpacking, and destructuring assignment in R. The operator unpacks the
5320 right-hand side of an assignment into multiple values and assigns these values
5321 to variables on the left-hand side of the assignment.")
5322 (license license:expat)))
5324 (define-public r-vctrs
5331 (uri (cran-uri "vctrs" version))
5334 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5335 (build-system r-build-system)
5337 `(("r-digest" ,r-digest)
5338 ("r-ellipsis" ,r-ellipsis)
5340 ("r-rlang" ,r-rlang)))
5342 `(("r-knitr" ,r-knitr)))
5343 (home-page "https://github.com/r-lib/vctrs")
5344 (synopsis "Vector helpers")
5346 "There are three main goals to the @code{vctrs} package:
5349 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5350 @code{length()} and @code{class()}. These definitions are paired with a
5351 framework for type-coercion and size-recycling.
5352 @item To define type- and size-stability as desirable function properties, use
5353 them to analyse existing base function, and to propose better alternatives.
5354 This work has been particularly motivated by thinking about the ideal
5355 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5356 @item To provide a new @code{vctr} base class that makes it easy to create new
5357 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5358 a few new @code{vctrs} generics, making implementation considerably simpler
5361 (license license:gpl3)))
5363 (define-public r-pillar
5370 (uri (cran-uri "pillar" version))
5373 "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c"))))
5374 (build-system r-build-system)
5377 ("r-crayon" ,r-crayon)
5378 ("r-ellipsis" ,r-ellipsis)
5379 ("r-fansi" ,r-fansi)
5380 ("r-lifecycle" ,r-lifecycle)
5381 ("r-rlang" ,r-rlang)
5383 ("r-vctrs" ,r-vctrs)))
5385 `(("r-knitr" ,r-knitr)))
5386 (home-page "https://github.com/r-lib/pillar")
5387 (synopsis "Coloured formatting for columns")
5389 "This package provides a @code{pillar} generic designed for formatting
5390 columns of data using the full range of colours provided by modern
5392 (license license:gpl3)))
5394 (define-public r-uuid
5401 (uri (cran-uri "uuid" version))
5404 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5405 (build-system r-build-system)
5406 (home-page "https://www.rforge.net/uuid")
5407 (synopsis "Tools for generating and handling of UUIDs")
5409 "This package provides tools for generating and handling of
5410 @dfn{Universally Unique Identifiers} (UUIDs).")
5411 (license license:expat)))
5413 (define-public r-tinytex
5420 (uri (cran-uri "tinytex" version))
5423 "0dk6mpszwh1m65b0wfwjlcvpzywmasf6p31niqiq53wnd92my0gw"))))
5424 (build-system r-build-system)
5426 `(("r-xfun" ,r-xfun)))
5427 (home-page "https://github.com/yihui/tinytex")
5428 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5430 "This package provides helper functions to install and maintain the LaTeX
5431 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5432 easy-to-maintain version of TeX Live. This package also contains helper
5433 functions to compile LaTeX documents, and install missing LaTeX packages
5435 (license license:expat)))
5437 (define-public r-tinytest
5444 (uri (cran-uri "tinytest" version))
5447 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5448 (properties `((upstream-name . "tinytest")))
5449 (build-system r-build-system)
5450 (home-page "https://github.com/markvanderloo/tinytest")
5451 (synopsis "Lightweight unit testing framework")
5453 "This package provides a lightweight unit testing framework. Main
5457 @item install tests with the package;
5458 @item test results are treated as data that can be stored and manipulated;
5459 @item test files are R scripts interspersed with test commands, that can be
5461 @item fully automated build-install-test sequence for packages;
5462 @item skip tests when not run locally (e.g. on CRAN);
5463 @item flexible and configurable output printing;
5464 @item compare computed output with output stored with the package;
5465 @item run tests in parallel;
5466 @item extensible by other packages;
5467 @item report side effects.
5470 (license license:gpl3)))
5472 (define-public r-network
5479 (uri (cran-uri "network" version))
5482 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5483 (build-system r-build-system)
5485 `(("r-magrittr" ,r-magrittr)
5486 ("r-tibble" ,r-tibble)))
5487 (home-page "https://statnet.org/")
5488 (synopsis "Classes for relational data")
5490 "This package provides tools to create and modify network objects. The
5491 @code{network} class can represent a range of relational data types, and
5492 supports arbitrary vertex/edge/graph attributes.")
5493 (license license:gpl2+)))
5495 (define-public r-stabs
5502 (uri (cran-uri "stabs" version))
5505 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5506 (build-system r-build-system)
5508 `(("r-knitr" ,r-knitr)))
5509 (home-page "https://github.com/hofnerb/stabs")
5510 (synopsis "Stability selection with error control")
5512 "This package provides resampling procedures to assess the stability of
5513 selected variables with additional finite sample error control for
5514 high-dimensional variable selection procedures such as Lasso or boosting.
5515 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5516 complementary pairs stability selection with improved error bounds
5517 (Shah & Samworth, 2013) are implemented. The package can be combined with
5518 arbitrary user specified variable selection approaches.")
5519 (license license:gpl2)))
5521 (define-public r-rle
5528 (uri (cran-uri "rle" version))
5531 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5532 (properties `((upstream-name . "rle")))
5533 (build-system r-build-system)
5534 (home-page "https://cran.r-project.org/web/packages/rle/")
5535 (synopsis "Common functions for run-length encoded vectors")
5537 "This package provides common @code{base} and @code{stats} methods for
5538 @code{rle} objects, aiming to make it possible to treat them transparently as
5540 (license license:gpl3)))
5542 (define-public r-statnet-common
5544 (name "r-statnet-common")
5549 (uri (cran-uri "statnet.common" version))
5552 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5554 `((upstream-name . "statnet.common")))
5555 (build-system r-build-system)
5557 `(("r-coda" ,r-coda)
5559 (home-page "https://statnet.org")
5560 (synopsis "R scripts and utilities used by the Statnet software")
5561 (description "This package provides non-statistical utilities used by the
5562 software developed by the Statnet Project.")
5563 (license license:gpl3)))
5565 (define-public r-statcheck
5567 (name "r-statcheck")
5572 (uri (cran-uri "statcheck" version))
5575 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5576 (build-system r-build-system)
5578 `(("r-ggplot2" ,r-ggplot2)
5580 ("r-rmarkdown" ,r-rmarkdown)))
5581 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5582 (synopsis "Extract statistics from articles and recompute p-values")
5583 (description "This package can automatically extract statistical
5584 null-hypothesis significant testing (NHST) results from articles and recompute
5585 the p-values based on the reported test statistic and degrees of freedom to
5586 detect possible inconsistencies.")
5587 (license license:gpl2)))
5589 (define-public r-sna
5596 (uri (cran-uri "sna" version))
5599 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5600 (build-system r-build-system)
5602 `(("r-network" ,r-network)
5603 ("r-statnet-common" ,r-statnet-common)))
5604 (home-page "https://statnet.org")
5605 (synopsis "Tools for social network analysis")
5607 "This package provides a range of tools for social network analysis,
5608 including node and graph-level indices, structural distance and covariance
5609 methods, structural equivalence detection, network regression, random graph
5610 generation, and 2D/3D network visualization.")
5611 (license license:gpl2+)))
5613 (define-public r-tfisher
5620 (uri (cran-uri "TFisher" version))
5623 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5624 (properties `((upstream-name . "TFisher")))
5625 (build-system r-build-system)
5627 `(("r-matrix" ,r-matrix)
5628 ("r-mvtnorm" ,r-mvtnorm)
5630 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5631 (synopsis "Optimal thresholding Fisher's p-value combination method")
5633 "This package provides the @dfn{cumulative distribution function} (CDF),
5634 quantile, and statistical power calculator for a collection of thresholding
5635 Fisher's p-value combination methods, including Fisher's p-value combination
5636 method, truncated product method and, in particular, soft-thresholding
5637 Fisher's p-value combination method which is proven to be optimal in some
5638 context of signal detection. The p-value calculator for the omnibus version
5639 of these tests are also included.")
5640 (license license:gpl2)))
5642 (define-public r-ttr
5649 (uri (cran-uri "TTR" version))
5652 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5653 (properties `((upstream-name . "TTR")))
5654 (build-system r-build-system)
5656 `(("r-curl" ,r-curl)
5659 (home-page "https://github.com/joshuaulrich/TTR")
5660 (synopsis "Technical trading rules")
5662 "This package provides functions and data to construct technical trading
5664 (license license:gpl2)))
5666 (define-public r-leaps
5673 (uri (cran-uri "leaps" version))
5676 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5677 (build-system r-build-system)
5678 (native-inputs `(("gfortran" ,gfortran)))
5679 (home-page "https://cran.r-project.org/web/packages/leaps/")
5680 (synopsis "Regression subset selection")
5682 "This package provides tools for regression subset selection, including
5683 exhaustive search.")
5684 (license license:gpl2+)))
5686 (define-public r-splus2r
5693 (uri (cran-uri "splus2R" version))
5696 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5697 (properties `((upstream-name . "splus2R")))
5698 (build-system r-build-system)
5699 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5700 (synopsis "Supplemental S-PLUS functionality in R")
5702 "Currently there are many functions in S-PLUS that are missing in R. To
5703 facilitate the conversion of S-PLUS packages to R packages, this package
5704 provides some missing S-PLUS functionality in R.")
5705 (license license:gpl2)))
5707 (define-public r-ifultools
5709 (name "r-ifultools")
5714 (uri (cran-uri "ifultools" version))
5717 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5718 (build-system r-build-system)
5720 `(("r-mass" ,r-mass)
5721 ("r-splus2r" ,r-splus2r)))
5722 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5723 (synopsis "Insightful research tools")
5724 (description "This package provides C code used by the wmtsa, fractal, and
5726 (license license:gpl2)))
5728 (define-public r-sapa
5735 (uri (cran-uri "sapa" version))
5738 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5739 (build-system r-build-system)
5741 `(("r-ifultools" ,r-ifultools)
5742 ("r-splus2r" ,r-splus2r)))
5743 (home-page "https://cran.r-project.org/web/packages/sapa/")
5744 (synopsis "Spectral analysis for physical applications")
5745 (description "This package provides software for the book Spectral
5746 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5747 Cambridge University Press, 1993.")
5748 (license license:gpl2)))
5750 (define-public r-aggregation
5752 (name "r-aggregation")
5757 (uri (cran-uri "aggregation" version))
5760 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5761 (build-system r-build-system)
5762 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5763 (synopsis "Methods for p-value aggregation")
5765 "This package contains functionality for performing the following methods
5766 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5767 Fisher's method), and Sidak correction.")
5768 (license license:gpl3)))
5770 (define-public r-quantmod
5777 (uri (cran-uri "quantmod" version))
5780 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5781 (build-system r-build-system)
5783 `(("r-curl" ,r-curl)
5787 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5788 (synopsis "Quantitative financial modelling framework")
5789 (description "This package provides a quantitative financial modelling
5790 framework to allow users to specify, build, trade, and analyse quantitative
5791 financial trading strategies.")
5792 (license license:gpl3)))
5794 (define-public r-tseries
5801 (uri (cran-uri "tseries" version))
5804 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5805 (build-system r-build-system)
5807 `(("r-quadprog" ,r-quadprog)
5808 ("r-quantmod" ,r-quantmod)
5811 `(("gfortran" ,gfortran)))
5812 (home-page "https://cran.r-project.org/web/packages/tseries/")
5813 (synopsis "Time series analysis and computational finance")
5815 "This package provides functions relating to time series analysis and
5816 computational finance.")
5817 (license license:gpl2)))
5819 (define-public r-wmtsa
5826 (uri (cran-uri "wmtsa" version))
5829 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5830 (build-system r-build-system)
5832 `(("r-ifultools" ,r-ifultools)
5834 ("r-splus2r" ,r-splus2r)))
5835 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5836 (synopsis "Wavelet methods for time series analysis")
5838 "This package provides software to accompany the book \"Wavelet Methods
5839 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5840 University Press, 2000.")
5841 (license license:gpl2)))
5843 (define-public r-tsa
5850 (uri (cran-uri "TSA" version))
5853 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5854 (properties `((upstream-name . "TSA")))
5855 (build-system r-build-system)
5857 `(("r-leaps" ,r-leaps)
5858 ("r-locfit" ,r-locfit)
5860 ("r-tseries" ,r-tseries)))
5861 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5862 (synopsis "Time series analysis")
5864 "This package contains R functions and datasets detailed in the book
5865 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5866 Cryer and Kung-Sik Chan.")
5867 (license license:gpl2+)))
5869 (define-public r-extradistr
5871 (name "r-extradistr")
5876 (uri (cran-uri "extraDistr" version))
5879 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5880 (properties `((upstream-name . "extraDistr")))
5881 (build-system r-build-system)
5883 `(("r-rcpp" ,r-rcpp)))
5884 (home-page "https://github.com/twolodzko/extraDistr")
5885 (synopsis "Additional univariate and multivariate distributions")
5887 "This package implements density, distribution functions, quantile
5888 functions and random generation functions for a large number of univariate and
5889 multivariate distributions.")
5890 (license license:gpl2)))
5892 (define-public r-fractal
5899 (uri (cran-uri "fractal" version))
5902 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5903 (build-system r-build-system)
5905 `(("r-ifultools" ,r-ifultools)
5908 ("r-scatterplot3d" ,r-scatterplot3d)
5909 ("r-splus2r" ,r-splus2r)
5910 ("r-wmtsa" ,r-wmtsa)))
5911 (home-page "https://cran.r-project.org/web/packages/fractal/")
5912 (synopsis "Fractal time series modeling and analysis")
5914 "This package provides tools for stochastic fractal and deterministic
5915 chaotic time series analysis.")
5916 (license license:gpl2)))
5918 (define-public r-urca
5925 (uri (cran-uri "urca" version))
5928 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5929 (build-system r-build-system)
5930 (propagated-inputs `(("r-nlme" ,r-nlme)))
5931 (native-inputs `(("gfortran" ,gfortran)))
5932 (home-page "https://cran.r-project.org/web/packages/urca/")
5933 (synopsis "Unit root and cointegration tests for time series data")
5935 "This package provides unit root and cointegration tests encountered in
5936 applied econometric analysis.")
5937 (license license:gpl2+)))
5939 (define-public r-cubature
5946 (uri (cran-uri "cubature" version))
5949 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5950 (build-system r-build-system)
5952 `(("r-rcpp" ,r-rcpp)))
5954 `(("r-knitr" ,r-knitr)))
5955 (home-page "https://github.com/bnaras/cubature")
5956 (synopsis "Adaptive multivariate integration over hypercubes")
5958 "This package is an R wrapper around the cubature C library for adaptive
5959 multivariate integration over hypercubes. This version provides both
5960 @code{hcubature} and @code{pcubature} routines in addition to a vector
5962 ;; The included cubature C library is released under GPLv2+, but the
5963 ;; wrapper declares the license to be GPLv3+.
5964 (license (list license:gpl2+ license:gpl3+))))
5966 (define-public r-trend
5973 (uri (cran-uri "trend" version))
5976 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5977 (build-system r-build-system)
5979 `(("r-extradistr" ,r-extradistr)))
5981 `(("gfortran" ,gfortran)))
5982 (home-page "https://cran.r-project.org/web/packages/trend/")
5983 (synopsis "Non-parametric trend tests and change-point detection")
5985 "The analysis of environmental data often requires the detection of
5986 trends and change-points. This package includes tests for trend
5987 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5988 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5989 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5990 correlation trend test), change-point detection (Lanzante's test procedures,
5991 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5992 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5993 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5994 sample Robust Rank-Order Distributional Test.")
5995 (license license:gpl3)))
5997 (define-public r-expm
6004 (uri (cran-uri "expm" version))
6007 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6008 (build-system r-build-system)
6009 (propagated-inputs `(("r-matrix" ,r-matrix)))
6010 (native-inputs `(("gfortran" ,gfortran)))
6011 (home-page "https://r-forge.r-project.org/projects/expm/")
6012 (synopsis "Tools for matrix exponentials and related quantities")
6014 "This package provides tools for the computation of the matrix
6015 exponential, logarithm, square root, and related quantities.")
6016 (license license:gpl2+)))
6018 (define-public r-complexplus
6020 (name "r-complexplus")
6025 (uri (cran-uri "complexplus" version))
6028 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6029 (build-system r-build-system)
6031 `(("r-expm" ,r-expm)
6032 ("r-matrix" ,r-matrix)))
6033 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6034 (synopsis "Functions of complex or real variables")
6036 "This package extends several functions to the complex domain, including
6037 the matrix exponential and logarithm, and the determinant.")
6038 (license license:gpl2)))
6040 (define-public r-phontools
6042 (name "r-phontools")
6047 (uri (cran-uri "phonTools" version))
6050 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6051 (properties `((upstream-name . "phonTools")))
6052 (build-system r-build-system)
6053 (home-page "http://www.santiagobarreda.com/rscripts.html")
6054 (synopsis "Tools for phonetic and acoustic analyses")
6056 "This package contains tools for the organization, display, and analysis
6057 of the sorts of data frequently encountered in phonetics research and
6058 experimentation, including the easy creation of IPA vowel plots, and the
6059 creation and manipulation of WAVE audio files.")
6060 (license license:bsd-2)))
6069 (uri (cran-uri "np" version))
6072 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6073 (build-system r-build-system)
6075 `(("r-boot" ,r-boot)
6076 ("r-cubature" ,r-cubature)
6077 ("r-quadprog" ,r-quadprog)
6078 ("r-quantreg" ,r-quantreg)))
6079 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6080 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6081 (description "This package provides non-parametric (and semi-parametric)
6082 kernel methods that seamlessly handle a mix of continuous, unordered, and
6083 ordered factor data types.")
6084 ;; Any version of the GPL.
6085 (license license:gpl3+)))
6087 (define-public r-powerplus
6089 (name "r-powerplus")
6094 (uri (cran-uri "powerplus" version))
6097 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6098 (build-system r-build-system)
6100 `(("r-complexplus" ,r-complexplus)
6103 ("r-matrix" ,r-matrix)
6104 ("r-phontools" ,r-phontools)))
6105 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6106 (synopsis "Exponentiation operations")
6108 "This package provides tools for the computation of matrix and scalar
6110 (license license:gpl2)))
6112 (define-public r-egg
6119 (uri (cran-uri "egg" version))
6122 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6123 (properties `((upstream-name . "egg")))
6124 (build-system r-build-system)
6126 `(("r-ggplot2" ,r-ggplot2)
6127 ("r-gridextra" ,r-gridextra)
6128 ("r-gtable" ,r-gtable)))
6129 (home-page "https://cran.r-project.org/web/packages/egg")
6130 (synopsis "Extensions for ggplot2")
6132 "This package provides miscellaneous functions to help customize ggplot2
6133 objects. High-level functions are provided to post-process ggplot2 layouts
6134 and allow alignment between plot panels, as well as setting panel sizes to
6135 fixed values. Other functions include a custom @code{geom}, and helper
6136 functions to enforce symmetric scales or add tags to facetted plots.")
6137 (license license:gpl3)))
6139 (define-public r-heatmaply
6141 (name "r-heatmaply")
6146 (uri (cran-uri "heatmaply" version))
6149 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6150 (build-system r-build-system)
6152 `(("r-assertthat" ,r-assertthat)
6153 ("r-colorspace" ,r-colorspace)
6154 ("r-dendextend" ,r-dendextend)
6156 ("r-ggplot2" ,r-ggplot2)
6157 ("r-htmlwidgets" ,r-htmlwidgets)
6158 ("r-magrittr" ,r-magrittr)
6159 ("r-plotly" ,r-plotly)
6160 ("r-rcolorbrewer" ,r-rcolorbrewer)
6161 ("r-reshape2" ,r-reshape2)
6162 ("r-scales" ,r-scales)
6163 ("r-seriation" ,r-seriation)
6164 ("r-viridis" ,r-viridis)
6165 ("r-webshot" ,r-webshot)))
6167 `(("r-knitr" ,r-knitr)))
6168 (home-page "https://cran.r-project.org/package=heatmaply")
6169 (synopsis "Interactive cluster heat maps using plotly")
6171 "This package enables you to create interactive cluster heatmaps that can
6172 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6173 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6174 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6175 a popular graphical method for visualizing high-dimensional data, in which a
6176 table of numbers is encoded as a grid of colored cells. The rows and columns
6177 of the matrix are ordered to highlight patterns and are often accompanied by
6179 ;; Either version of the license.
6180 (license (list license:gpl2 license:gpl3))))
6189 (uri (cran-uri "h5" version))
6192 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6193 (build-system r-build-system)
6198 `(("which" ,which)))
6200 `(("r-rcpp" ,r-rcpp)))
6201 (home-page "https://github.com/mannau/h5")
6202 (synopsis "Interface to the HDF5 Library")
6204 "This package provides an S4 interface to the HDF5 library supporting
6205 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6206 binary files in a language independent format. The HDF5 format can therefore
6207 be used as an alternative to R's save/load mechanism. Since h5 is able to
6208 access only subsets of stored data it can also handle data sets which do not
6210 (license license:bsd-2)))
6212 (define-public r-cgdsr
6219 (uri (cran-uri "cgdsr" version))
6222 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6223 (build-system r-build-system)
6225 `(("r-httr" ,r-httr)
6226 ("r-r-methodss3" ,r-r-methodss3)
6227 ("r-r-oo" ,r-r-oo)))
6228 (home-page "https://github.com/cBioPortal/cgdsr")
6229 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6231 "This package provides a basic set of R functions for querying the Cancer
6232 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6233 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6234 (license license:lgpl3)))
6236 (define-public r-import
6243 (uri (cran-uri "import" version))
6246 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6247 (build-system r-build-system)
6249 `(("r-knitr" ,r-knitr)))
6250 (home-page "https://github.com/smbache/import")
6251 (synopsis "Import mechanism for R")
6253 "This is an alternative mechanism for importing objects from packages.
6254 The syntax allows for importing multiple objects from a package with a single
6255 command in an expressive way. The import package bridges some of the gap
6256 between using @code{library} (or @code{require}) and direct (single-object)
6257 imports. Furthermore the imported objects are not placed in the current
6258 environment. It is also possible to import objects from stand-alone @code{.R}
6260 (license license:expat)))
6262 (define-public r-shinyace
6269 (uri (cran-uri "shinyAce" version))
6272 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6273 (properties `((upstream-name . "shinyAce")))
6274 (build-system r-build-system)
6276 `(("r-shiny" ,r-shiny)
6277 ("r-jsonlite" ,r-jsonlite)))
6278 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6279 (synopsis "Ace editor bindings for Shiny")
6281 "This package provides Ace editor bindings to enable a rich text editing
6282 environment within Shiny.")
6283 (license license:expat)))
6285 (define-public r-randomizr
6287 (name "r-randomizr")
6292 (uri (cran-uri "randomizr" version))
6295 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6296 (properties `((upstream-name . "randomizr")))
6297 (build-system r-build-system)
6299 `(("r-knitr" ,r-knitr)))
6300 (home-page "https://declaredesign.org/r/randomizr/")
6301 (synopsis "Tools for common forms of random assignment and sampling")
6303 "This package provides tools for generating random assignments for common
6304 experimental designs and random samples for common sampling designs.")
6305 (license license:expat)))
6307 (define-public r-base64url
6309 (name "r-base64url")
6314 (uri (cran-uri "base64url" version))
6317 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6318 (build-system r-build-system)
6320 `(("r-backports" ,r-backports)))
6321 (home-page "https://github.com/mllg/base64url")
6322 (synopsis "Fast and URL-safe base64 encoder and decoder")
6324 "This package provides a URL-safe base64 encoder and decoder. In
6325 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6326 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6327 encoder does not fill the string with trailing @code{=}. The resulting
6328 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6329 and thus are safe to use in URLs or for file names. The package also comes
6330 with a simple base32 encoder/decoder suited for case insensitive file
6332 (license license:gpl3)))
6334 (define-public r-radiant-data
6336 (name "r-radiant-data")
6341 (uri (cran-uri "radiant.data" version))
6344 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6345 (modules '((guix build utils)))
6348 ;; Delete files that are under CC-NC-SA.
6349 (delete-file-recursively "inst/app/tools/help")
6351 (properties `((upstream-name . "radiant.data")))
6352 (build-system r-build-system)
6354 `(("r-base64enc" ,r-base64enc)
6355 ("r-broom" ,r-broom)
6358 ("r-dplyr" ,r-dplyr)
6361 ("r-ggplot2" ,r-ggplot2)
6362 ("r-import" ,r-import)
6363 ("r-jsonlite" ,r-jsonlite)
6364 ("r-knitr" ,r-knitr)
6365 ("r-lubridate" ,r-lubridate)
6366 ("r-magrittr" ,r-magrittr)
6367 ("r-markdown" ,r-markdown)
6369 ("r-patchwork" ,r-patchwork)
6370 ("r-plotly" ,r-plotly)
6371 ("r-psych" ,r-psych)
6372 ("r-randomizr" ,r-randomizr)
6373 ("r-readr" ,r-readr)
6374 ("r-readxl" ,r-readxl)
6375 ("r-rlang" ,r-rlang)
6376 ("r-rmarkdown" ,r-rmarkdown)
6377 ("r-rstudioapi" ,r-rstudioapi)
6378 ("r-scales" ,r-scales)
6379 ("r-shiny" ,r-shiny)
6380 ("r-shinyfiles" ,r-shinyfiles)
6381 ("r-shinyace" ,r-shinyace)
6382 ("r-stringi" ,r-stringi)
6383 ("r-tibble" ,r-tibble)
6384 ("r-tidyr" ,r-tidyr)
6385 ("r-writexl" ,r-writexl)))
6386 (home-page "https://github.com/radiant-rstats/radiant.data")
6387 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6389 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6390 visualizing, summarizing, transforming, and combining data. It also contains
6391 functionality to generate reproducible reports of the analyses conducted in
6393 (license license:agpl3)))
6395 (define-public r-algdesign
6397 (name "r-algdesign")
6402 (uri (cran-uri "AlgDesign" version))
6404 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6405 (properties `((upstream-name . "AlgDesign")))
6406 (build-system r-build-system)
6407 (home-page "https://github.com/jvbraun/AlgDesign")
6408 (synopsis "Algorithmic experimental design")
6410 "This package provides tools to calculate exact and approximate theory
6411 experimental designs for D, A, and I criteria. Very large designs may be
6412 created. Experimental designs may be blocked or blocked designs created from
6413 a candidate list, using several criteria. The blocking can be done when whole
6414 and within plot factors interact.")
6415 (license license:gpl2+)))
6417 (define-public r-signal
6424 (uri (cran-uri "signal" version))
6427 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6428 (build-system r-build-system)
6429 (propagated-inputs `(("r-mass" ,r-mass)))
6430 (native-inputs `(("gfortran" ,gfortran)))
6431 (home-page "https://cran.r-project.org/web/packages/signal/")
6432 (synopsis "Signal processing")
6434 "This package provides a set of signal processing functions originally
6435 written for Matlab and GNU Octave. It includes filter generation utilities,
6436 filtering functions, resampling routines, and visualization of filter models.
6437 It also includes interpolation functions.")
6438 (license license:gpl2)))
6440 (define-public r-gsubfn
6447 (uri (cran-uri "gsubfn" version))
6450 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6451 (build-system r-build-system)
6452 (propagated-inputs `(("r-proto" ,r-proto)))
6453 (home-page "https://code.google.com/archive/p/gsubfn/")
6454 (synopsis "Utilities for strings and function arguments.")
6456 "This package provides @code{gsubfn} which is like @code{gsub} but can
6457 take a replacement function or certain other objects instead of the
6458 replacement string. Matches and back references are input to the replacement
6459 function and replaced by the function output. @code{gsubfn} can be used to
6460 split strings based on content rather than delimiters and for quasi-perl-style
6461 string interpolation. The package also has facilities for translating
6462 formulas to functions and allowing such formulas in function calls instead of
6464 (license license:gpl2+)))
6466 (define-public r-sqldf
6473 (uri (cran-uri "sqldf" version))
6476 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6477 (build-system r-build-system)
6479 `(("r-chron" ,r-chron)
6481 ("r-gsubfn" ,r-gsubfn)
6482 ("r-proto" ,r-proto)
6483 ("r-rsqlite" ,r-rsqlite)))
6484 (home-page "https://github.com/ggrothendieck/sqldf")
6485 (synopsis "Manipulate R data frames using SQL")
6487 "The @code{sqldf} function is typically passed a single argument which is
6488 an SQL select statement where the table names are ordinary R data frame names.
6489 @code{sqldf} transparently sets up a database, imports the data frames into
6490 that database, performs the SQL statement and returns the result using a
6491 heuristic to determine which class to assign to each column of the returned
6492 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6493 used to read filtered files into R even if the original files are larger than
6494 R itself can handle.")
6495 (license license:gpl2)))
6497 (define-public r-abind
6504 (uri (cran-uri "abind" version))
6507 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6508 (build-system r-build-system)
6509 (home-page "https://cran.r-project.org/web/packages/abind/")
6510 (synopsis "Combine multidimensional arrays")
6512 "This package provides tools to combine multidimensional arrays into a
6513 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6514 works with vectors, matrices, and higher-dimensional arrays. It also provides
6515 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6516 extracting and replacing data in arrays.")
6517 (license license:lgpl2.0+)))
6519 (define-public r-prroc
6526 (uri (cran-uri "PRROC" version))
6529 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6530 (properties `((upstream-name . "PRROC")))
6531 (build-system r-build-system)
6532 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6533 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6535 "This package computes the areas under the @dfn{precision-recall} (PR)
6536 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6537 contrast to other implementations, the interpolation between points of the PR
6538 curve is done by a non-linear piecewise function. In addition to the areas
6539 under the curves, the curves themselves can also be computed and plotted by a
6540 specific S3-method.")
6541 (license license:gpl3)))
6543 (define-public r-vim
6550 (uri (cran-uri "VIM" version))
6553 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6554 (properties `((upstream-name . "VIM")))
6555 (build-system r-build-system)
6558 ("r-colorspace" ,r-colorspace)
6559 ("r-data-table" ,r-data-table)
6560 ("r-e1071" ,r-e1071)
6561 ("r-laeken" ,r-laeken)
6562 ("r-magrittr" ,r-magrittr)
6565 ("r-ranger" ,r-ranger)
6567 ("r-robustbase" ,r-robustbase)
6571 `(("r-knitr" ,r-knitr)))
6572 (home-page "https://github.com/alexkowa/VIM")
6573 (synopsis "Visualization and imputation of missing values")
6575 "This package provides tools for the visualization of missing and/or
6576 imputed values are introduced, which can be used for exploring the data and
6577 the structure of the missing and/or imputed values. Depending on this
6578 structure of the missing values, the corresponding methods may help to
6579 identify the mechanism generating the missing values and explore the
6580 data including missing values. In addition, the quality of imputation can be
6581 visually explored using various univariate, bivariate, multiple and
6582 multivariate plot methods.")
6583 (license license:gpl2+)))
6585 (define-public r-fnn
6592 (uri (cran-uri "FNN" version))
6595 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6596 (properties `((upstream-name . "FNN")))
6597 (build-system r-build-system)
6598 (home-page "https://cran.r-project.org/web/packages/FNN")
6599 (synopsis "Fast nearest neighbor search algorithms and applications")
6601 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6602 search algorithms. Related applications including KNN classification,
6603 regression and information measures are implemented.")
6604 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6605 ;; later can be used.
6606 (license license:gpl2+)))
6608 (define-public r-smoother
6615 (uri (cran-uri "smoother" version))
6618 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6619 (build-system r-build-system)
6621 `(("r-ttr" ,r-ttr)))
6622 (home-page "https://cran.r-project.org/web/packages/smoother")
6623 (synopsis "Functions relating to the smoothing of numerical data")
6625 "This package provides a collection of methods for smoothing numerical
6626 data, commencing with a port of the Matlab gaussian window smoothing function.
6627 In addition, several functions typically used in smoothing of financial data
6629 (license license:gpl2)))
6631 (define-public r-riverplot
6633 (name "r-riverplot")
6638 (uri (cran-uri "riverplot" version))
6641 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6642 (build-system r-build-system)
6644 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6646 `(("r-knitr" ,r-knitr)))
6647 (home-page "https://logfc.wordpress.com")
6648 (synopsis "Sankey or ribbon plots")
6650 "Sankey plots are a type of diagram that is convenient to illustrate how
6651 flow of information, resources etc. separates and joins, much like observing
6652 how rivers split and merge. For example, they can be used to compare
6653 different clusterings. This package provides an implementation of Sankey
6655 (license license:gpl2+)))
6657 (define-public r-dyn
6664 (uri (cran-uri "dyn" version))
6667 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6668 (build-system r-build-system)
6670 `(("r-zoo" ,r-zoo)))
6671 (home-page "https://cran.r-project.org/web/packages/dyn")
6672 (synopsis "Time series regression")
6674 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6675 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6676 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6677 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6678 @code{randomForest::randomForest()} and other regression functions, allowing
6679 those functions to be used with time series including specifications that may
6680 contain lags, diffs and missing values.")
6682 (license license:gpl2+)))
6684 (define-public r-catdap
6691 (uri (cran-uri "catdap" version))
6694 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6695 (build-system r-build-system)
6697 `(("gfortran" ,gfortran)))
6698 (home-page "https://cran.r-project.org/web/packages/catdap/")
6699 (synopsis "Tools for categorical data analysis")
6701 "This package provides functions for analyzing multivariate data.
6702 Dependencies of the distribution of the specified variable (response
6703 variable) to other variables (explanatory variables) are derived and
6704 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6705 (license license:gpl2+)))
6707 (define-public r-arules
6714 (uri (cran-uri "arules" version))
6717 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6718 (build-system r-build-system)
6720 `(("r-matrix" ,r-matrix)))
6721 (home-page "https://github.com/mhahsler/arules")
6722 (synopsis "Mining association rules and frequent itemsets")
6724 "This package provides an infrastructure for representing, manipulating
6725 and analyzing transaction data and patterns (frequent itemsets and association rules).
6726 It also provides C implementations of the association mining algorithms Apriori
6728 (license license:gpl3)))
6730 (define-public r-parsedate
6732 (name "r-parsedate")
6737 (uri (cran-uri "parsedate" version))
6740 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6741 (build-system r-build-system)
6743 `(("r-rematch2" ,r-rematch2)))
6744 (home-page "https://github.com/gaborcsardi/parsedate")
6746 "Recognize and parse dates in various formats")
6748 "This package provides three functions for dealing with dates:
6749 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6750 time formats, @code{parse_date} parses dates in unspecified formats,
6751 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6752 (license license:gpl2)))
6754 (define-public r-abc-data
6761 (uri (cran-uri "abc.data" version))
6764 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6765 (properties `((upstream-name . "abc.data")))
6766 (build-system r-build-system)
6767 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6768 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6770 "This package contains data which are used by functions of the abc
6771 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6772 algorithms for performing parameter estimation, model selection, and
6774 (license license:gpl3+)))
6776 (define-public r-abc
6783 (uri (cran-uri "abc" version))
6786 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6787 (build-system r-build-system)
6789 `(("r-abc-data" ,r-abc-data)
6790 ("r-locfit" ,r-locfit)
6793 ("r-quantreg" ,r-quantreg)))
6794 (home-page "https://cran.r-project.org/web/packages/abc/")
6795 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6797 "This package implements several @dfn{Approximate Bayesian
6798 Computation} (ABC) algorithms for performing parameter estimation, model
6799 selection, and goodness-of-fit. Cross-validation tools are also available for
6800 measuring the accuracy of ABC estimates, and to calculate the
6801 misclassification probabilities of different models.")
6802 (license license:gpl3+)))
6804 (define-public r-zip
6811 (uri (cran-uri "zip" version))
6814 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6815 (build-system r-build-system)
6816 (home-page "https://github.com/gaborcsardi/zip")
6817 (synopsis "Cross-platform Zip compression")
6819 "This package provides a cross-platform Zip compression library for R.
6820 It is a replacement for the @code{zip} function, that does not require any
6821 additional external tools on any platform.")
6822 (license license:cc0)))
6824 (define-public r-openxlsx
6831 (uri (cran-uri "openxlsx" version))
6834 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6835 (build-system r-build-system)
6837 `(("r-rcpp" ,r-rcpp)
6838 ("r-stringi" ,r-stringi)
6841 `(("r-knitr" ,r-knitr)))
6842 (home-page "https://github.com/awalker89/openxlsx")
6843 (synopsis "Read, write and edit XLSX files")
6845 "This package simplifies the creation of Excel @code{.xlsx} files by
6846 providing a high level interface to writing, styling and editing worksheets.
6847 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6848 and @code{XLConnect} packages with the added benefit of removing the
6849 dependency on Java.")
6850 (license license:gpl3)))
6852 (define-public r-rio
6859 (uri (cran-uri "rio" version))
6862 "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d"))))
6863 (build-system r-build-system)
6865 `(("r-curl" ,r-curl)
6866 ("r-data-table" ,r-data-table)
6867 ("r-foreign" ,r-foreign)
6868 ("r-haven" ,r-haven)
6869 ("r-openxlsx" ,r-openxlsx)
6870 ("r-readxl" ,r-readxl)
6871 ("r-tibble" ,r-tibble)))
6873 `(("r-knitr" ,r-knitr)))
6874 (home-page "https://github.com/leeper/rio")
6875 (synopsis "Swiss-army knife for data I/O")
6877 "This package provides streamlined data import and export infrastructure
6878 by making assumptions that the user is probably willing to make: @code{import}
6879 and @code{export} determine the data structure from the file extension,
6880 reasonable defaults are used for data import and export (e.g.,
6881 @code{stringsAsFactors=FALSE}), web-based import is natively
6882 supported (including from SSL/HTTPS), compressed files can be read directly
6883 without explicit decompression, and fast import packages are used where
6884 appropriate. An additional convenience function, @code{convert}, provides a
6885 simple method for converting between file types.")
6886 (license license:gpl2)))
6888 (define-public r-maptools
6895 (uri (cran-uri "maptools" version))
6898 "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l"))))
6899 (build-system r-build-system)
6901 `(("r-foreign" ,r-foreign)
6902 ("r-lattice" ,r-lattice)
6904 (home-page "https://r-forge.r-project.org/projects/maptools/")
6905 (synopsis "Tools for reading and handling spatial objects")
6907 "This package provides a set of tools for manipulating and reading
6908 geographic data, in particular ESRI Shapefiles. It includes binary access to
6909 GSHHG shoreline files. The package also provides interface wrappers for
6910 exchanging spatial objects with other R packages.")
6911 ;; The C source files from shapelib are released under the Expat license.
6912 ;; The R code is released under GPL version 2 or later.
6913 (license (list license:gpl2+
6916 (define-public r-later
6923 (uri (cran-uri "later" version))
6926 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6927 (build-system r-build-system)
6931 ("r-rlang" ,r-rlang)))
6933 `(("r-knitr" ,r-knitr)))
6934 (home-page "https://github.com/r-lib/later")
6935 (synopsis "Utilities for delaying function execution")
6937 "This package provides tools to execute arbitrary R or C functions some
6938 time after the current time, after the R execution stack has emptied.")
6939 (license license:gpl2+)))
6941 (define-public r-promises
6948 (uri (cran-uri "promises" version))
6951 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
6952 (build-system r-build-system)
6954 `(("r-later" ,r-later)
6955 ("r-magrittr" ,r-magrittr)
6958 ("r-rlang" ,r-rlang)))
6960 `(("r-knitr" ,r-knitr)))
6961 (home-page "https://rstudio.github.io/promises")
6962 (synopsis "Abstractions for promise-based asynchronous programming")
6964 "This package provides fundamental abstractions for doing asynchronous
6965 programming in R using promises. Asynchronous programming is useful for
6966 allowing a single R process to orchestrate multiple tasks in the background
6967 while also attending to something else. Semantics are similar to JavaScript
6968 promises, but with a syntax that is idiomatic R.")
6969 (license license:expat)))
6971 (define-public r-dosnow
6978 (uri (cran-uri "doSNOW" version))
6981 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6982 (properties `((upstream-name . "doSNOW")))
6983 (build-system r-build-system)
6985 `(("r-foreach" ,r-foreach)
6986 ("r-iterators" ,r-iterators)
6987 ("r-snow" ,r-snow)))
6988 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6989 (synopsis "Foreach parallel adaptor for the snow package")
6991 "This package provides a parallel backend for the @code{%dopar%} function
6992 using the @code{snow} package.")
6993 (license license:gpl2)))
6995 (define-public r-fst
7002 (uri (cran-uri "fst" version))
7005 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7006 (properties `((upstream-name . "fst")))
7007 (build-system r-build-system)
7008 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7009 (home-page "http://www.fstpackage.org")
7010 (synopsis "Fast serialization of data frames")
7012 "The fst package for R provides a fast, easy and flexible way to
7013 serialize data frames. With access speeds of multiple GB/s, fst is
7014 specifically designed to unlock the potential of high speed solid state disks.
7015 Data frames stored in the fst format have full random access, both in column
7016 and rows. The fst format allows for random access of stored data and
7017 compression with the LZ4 and ZSTD compressors.")
7018 (license license:agpl3)))
7020 (define-public r-snowfall
7023 (version "1.84-6.1")
7026 (uri (cran-uri "snowfall" version))
7028 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7029 (build-system r-build-system)
7031 `(("r-snow" ,r-snow)))
7032 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7033 (synopsis "Easier cluster computing")
7034 (description "This package is a usability wrapper around snow for easier
7035 development of parallel R programs. This package offers e.g. extended error
7036 checks, and additional functions. All functions work in sequential mode, too,
7037 if no cluster is present or wished. The package is also designed as connector
7038 to the cluster management tool @code{sfCluster}, but can also used without
7040 (license license:gpl2+)))
7042 (define-public r-rgexf
7049 (uri (cran-uri "rgexf" version))
7052 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7055 ;; Delete minified JavaScript files
7056 (for-each delete-file
7057 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7058 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7059 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7061 (properties `((upstream-name . "rgexf")))
7062 (build-system r-build-system)
7064 `(#:modules ((guix build utils)
7065 (guix build r-build-system)
7069 (modify-phases %standard-phases
7070 (add-after 'unpack 'process-javascript
7071 (lambda* (#:key inputs #:allow-other-keys)
7072 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7073 (with-directory-excursion "inst/gexf-js/js/"
7077 `((,(assoc-ref inputs "js-jquery")
7078 "jquery-2.0.2.min.js")
7079 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7080 "jquery-ui-1.10.3.custom.min.js")
7081 (,(assoc-ref inputs "js-jquery-mousewheel")
7082 "jquery.mousewheel.min.js"))))
7083 (lambda (sources targets)
7084 (for-each (lambda (source target)
7085 (format #true "Processing ~a --> ~a~%"
7087 (invoke "esbuild" source "--minify"
7088 (string-append "--outfile=" target)))
7092 `(("r-igraph" ,r-igraph)
7093 ("r-servr" ,r-servr)
7096 `(("r-knitr" ,r-knitr)
7097 ("esbuild" ,esbuild)
7102 (uri "https://code.jquery.com/jquery-2.0.2.js")
7105 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7109 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7112 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7113 ("js-jquery-mousewheel"
7116 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7117 3.0.6/jquery.mousewheel.js")
7120 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7121 (home-page "https://gvegayon.github.io/rgexf")
7122 (synopsis "Build, import and export GEXF graph files")
7124 "Create, read and write GEXF (Graph Exchange XML Format) graph
7125 files (used in Gephi and others). It allows the user to easily build/read
7126 graph files including attributes, GEXF visual attributes (such as color, size,
7127 and position), network dynamics (for both edges and nodes) and edge weighting.
7128 Users can build/handle graphs element-by-element or massively through
7129 data-frames, visualize the graph on a web browser through gexf-js (a
7130 JavaScript library) and interact with the igraph package.")
7131 (license license:expat)))
7133 (define-public r-data-tree
7135 (name "r-data-tree")
7140 (uri (cran-uri "data.tree" version))
7143 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7144 (properties `((upstream-name . "data.tree")))
7145 (build-system r-build-system)
7148 ("r-stringi" ,r-stringi)))
7150 `(("r-knitr" ,r-knitr)))
7151 (home-page "https://github.com/gluc/data.tree")
7152 (synopsis "General purpose hierarchical data structure")
7154 "Create tree structures from hierarchical data, and traverse the tree in
7155 various orders. Aggregate, cumulate, print, plot, convert to and from
7156 data.frame and more. This is useful for decision trees, machine learning,
7157 finance, conversion from and to JSON, and many other applications.")
7158 (license license:gpl2+)))
7160 (define-public r-collapsibletree
7162 (name "r-collapsibletree")
7167 (uri (cran-uri "collapsibleTree" version))
7170 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7173 ;; Delete minified JavaScript file
7174 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7177 `((upstream-name . "collapsibleTree")))
7178 (build-system r-build-system)
7181 (modify-phases %standard-phases
7182 (add-after 'unpack 'process-javascript
7183 (lambda* (#:key inputs #:allow-other-keys)
7184 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7185 (let ((source (assoc-ref inputs "d3.v4.js"))
7186 (target "d3.min.js"))
7187 (format #t "Processing ~a --> ~a~%"
7189 (invoke "esbuild" source "--minify"
7190 (string-append "--outfile=" target)))))))))
7192 `(("r-data-tree" ,r-data-tree)
7193 ("r-htmlwidgets" ,r-htmlwidgets)))
7195 `(("esbuild" ,esbuild)
7199 (uri "https://d3js.org/d3.v4.js")
7202 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7203 (home-page "https://github.com/AdeelK93/collapsibleTree")
7204 (synopsis "Interactive collapsible tree diagrams using D3.js")
7206 "This is a package for interactive Reingold-Tilford tree diagrams created
7207 using D3.js, where every node can be expanded and collapsed by clicking on it.
7208 Tooltips and color gradients can be mapped to nodes using a numeric column in
7209 the source data frame.")
7210 (license license:gpl3+)))
7212 (define-public r-rappdirs
7219 (uri (cran-uri "rappdirs" version))
7222 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7223 (build-system r-build-system)
7224 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7225 (synopsis "Determine where to save data, caches, and logs")
7227 "This package provides an easy way to determine which directories on the
7228 user's computer should be used to save data, caches and logs. It is a port of
7229 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7230 (license license:expat)))
7232 (define-public r-rastervis
7234 (name "r-rastervis")
7239 (uri (cran-uri "rasterVis" version))
7242 "0m7fjd53apxim0d0rjnyzc28vmfcg4spcrn0zbnk8llillxji1hi"))))
7243 (properties `((upstream-name . "rasterVis")))
7244 (build-system r-build-system)
7246 `(("r-hexbin" ,r-hexbin)
7247 ("r-lattice" ,r-lattice)
7248 ("r-latticeextra" ,r-latticeextra)
7249 ("r-raster" ,r-raster)
7250 ("r-rcolorbrewer" ,r-rcolorbrewer)
7252 ("r-terra" ,r-terra)
7253 ("r-viridislite" ,r-viridislite)
7255 (home-page "https://oscarperpinan.github.io/rastervis/")
7256 (synopsis "Visualization methods for raster data")
7258 "This package provides methods for enhanced visualization and interaction
7259 with raster data. It implements visualization methods for quantitative data
7260 and categorical data, both for univariate and multivariate rasters. It also
7261 provides methods to display spatiotemporal rasters, and vector fields.")
7262 (license license:gpl3)))
7264 (define-public r-rentrez
7271 (uri (cran-uri "rentrez" version))
7274 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7275 (properties `((upstream-name . "rentrez")))
7276 (build-system r-build-system)
7278 `(("r-httr" ,r-httr)
7279 ("r-jsonlite" ,r-jsonlite)
7282 `(("r-knitr" ,r-knitr)))
7283 (home-page "https://docs.ropensci.org/rentrez/")
7284 (synopsis "Entrez in R")
7286 "This package provides an R interface to the NCBI's EUtils API,
7287 allowing users to search databases like GenBank PubMed, process the results of
7288 those searches and pull data into their R sessions.")
7289 (license license:expat)))
7291 (define-public r-renv
7298 (uri (cran-uri "renv" version))
7301 "16n2dz9jibc03f7q1wrzxss6l5jmaks7m2lnli9dz9anvcmxbdia"))))
7302 (properties `((upstream-name . "renv")))
7303 (build-system r-build-system)
7305 `(("r-knitr" ,r-knitr)))
7306 (home-page "https://rstudio.github.io/renv")
7307 (synopsis "Project environments")
7309 "This package provides a dependency management toolkit for R. Using
7310 renv, you can create and manage project-local R libraries, save the state of
7311 these libraries to a lockfile, and later restore your library as required.
7312 Together, these tools can help make your projects more isolated, portable, and
7314 (license license:expat)))
7316 (define-public r-learnr
7323 (uri (cran-uri "learnr" version))
7326 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7327 (build-system r-build-system)
7329 `(("r-checkmate" ,r-checkmate)
7330 ("r-ellipsis" ,r-ellipsis)
7331 ("r-evaluate" ,r-evaluate)
7332 ("r-htmltools" ,r-htmltools)
7333 ("r-htmlwidgets" ,r-htmlwidgets)
7334 ("r-jsonlite" ,r-jsonlite)
7335 ("r-knitr" ,r-knitr)
7336 ("r-markdown" ,r-markdown)
7337 ("r-rappdirs" ,r-rappdirs)
7339 ("r-rmarkdown" ,r-rmarkdown)
7340 ("r-rprojroot" ,r-rprojroot)
7341 ("r-shiny" ,r-shiny)
7342 ("r-withr" ,r-withr)))
7343 (home-page "https://rstudio.github.io/learnr/")
7344 (synopsis "Interactive tutorials for R")
7346 "This package provides tools to create interactive tutorials using R
7347 Markdown. Use a combination of narrative, figures, videos, exercises, and
7348 quizzes to create self-paced tutorials for learning about R and R packages.")
7349 (license license:asl2.0)))
7351 (define-public r-analytics
7353 (name "r-analytics")
7358 (uri (cran-uri "analytics" version))
7361 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7362 (build-system r-build-system)
7365 ("r-cluster" ,r-cluster)
7366 ("r-fractal" ,r-fractal)
7367 ("r-lmtest" ,r-lmtest)
7370 ("r-powerplus" ,r-powerplus)
7371 ("r-robust" ,r-robust)
7372 ("r-trend" ,r-trend)
7376 (home-page "https://cran.r-project.org/web/packages/analytics/")
7377 (synopsis "Collection of data analysis tools")
7379 "This package is a collection of data analysis tools. It includes tools
7380 for regression outlier detection in a fitted linear model, stationary
7381 bootstrap using a truncated geometric distribution, a comprehensive test for
7382 weak stationarity, column means by group, weighted biplots, and a heuristic to
7383 obtain a better initial configuration in non-metric MDS.")
7384 (license license:gpl2)))
7386 (define-public r-reticulate
7388 (name "r-reticulate")
7393 (uri (cran-uri "reticulate" version))
7396 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7397 (build-system r-build-system)
7398 (inputs `(("python" ,python)))
7400 `(("r-rappdirs" ,r-rappdirs)
7401 ("r-jsonlite" ,r-jsonlite)
7402 ("r-matrix" ,r-matrix)
7403 ("r-rcpp" ,r-rcpp)))
7405 `(("r-knitr" ,r-knitr)))
7406 (home-page "https://github.com/rstudio/reticulate")
7407 (synopsis "R interface to Python")
7409 "This package provides an interface from R to Python modules, classes,
7410 and functions. When calling into Python, R data types are automatically
7411 converted to their equivalent Python types. When values are returned from
7412 Python to R they are converted back to R types.")
7413 (license license:asl2.0)))
7415 (define-public r-bibtex
7422 (uri (cran-uri "bibtex" version))
7425 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7426 (build-system r-build-system)
7427 (propagated-inputs `(("r-stringr" ,r-stringr)))
7428 (home-page "https://github.com/romainfrancois/bibtex")
7429 (synopsis "Bibtex parser")
7430 (description "This package provides a utility for R to parse a bibtex
7432 (license license:gpl2+)))
7434 (define-public r-ggseqlogo
7436 (name "r-ggseqlogo")
7441 (uri (cran-uri "ggseqlogo" version))
7444 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7445 (build-system r-build-system)
7446 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7447 (home-page "https://github.com/omarwagih/ggseqlogo")
7448 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7450 "The range of functions provided by this package makes it possible to
7451 draw highly versatile genomic sequence logos. Features include, but are not
7452 limited to, modifying colour schemes and fonts used to draw the logo,
7453 generating multiple logo plots, and aiding the visualisation with annotations.
7454 Sequence logos can easily be combined with other ggplot2 plots.")
7455 ;; Unspecified version of the LGPL.
7456 (license license:lgpl3+)))
7458 (define-public r-ggsci
7465 (uri (cran-uri "ggsci" version))
7468 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7469 (build-system r-build-system)
7471 `(("r-ggplot2" ,r-ggplot2)
7472 ("r-scales" ,r-scales)))
7473 (home-page "https://nanx.me/ggsci/")
7474 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7476 "This package provides a collection of ggplot2 color palettes inspired by
7477 plots in scientific journals, data visualization libraries, science fiction
7478 movies, and TV shows.")
7479 (license license:gpl3)))
7481 (define-public r-ggsignif
7488 (uri (cran-uri "ggsignif" version))
7491 "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh"))))
7492 (build-system r-build-system)
7494 `(("r-knitr" ,r-knitr)))
7496 `(("r-ggplot2" ,r-ggplot2)))
7497 (home-page "https://github.com/const-ae/ggsignif")
7498 (synopsis "Significance brackets for ggplot2")
7500 "Enrich your ggplots with group-wise comparisons. This package provides
7501 an easy way to indicate if two groups are significantly different. Commonly
7502 this is shown by a bracket on top connecting the groups of interest which
7503 itself is annotated with the level of significance. The package provides a
7504 single layer that takes the groups for comparison and the test as arguments
7505 and adds the annotation to the plot.")
7506 (license license:gpl3)))
7508 (define-public r-rstatix
7515 (uri (cran-uri "rstatix" version))
7518 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
7519 (properties `((upstream-name . "rstatix")))
7520 (build-system r-build-system)
7522 `(("r-broom" ,r-broom)
7524 ("r-corrplot" ,r-corrplot)
7525 ("r-dplyr" ,r-dplyr)
7526 ("r-generics" ,r-generics)
7527 ("r-magrittr" ,r-magrittr)
7528 ("r-purrr" ,r-purrr)
7529 ("r-rlang" ,r-rlang)
7530 ("r-tibble" ,r-tibble)
7531 ("r-tidyr" ,r-tidyr)
7532 ("r-tidyselect" ,r-tidyselect)))
7533 (home-page "https://rpkgs.datanovia.com/rstatix/")
7534 (synopsis "Pipe-friendly framework for basic statistical tests")
7536 "This package provides a simple and intuitive pipe-friendly framework,
7537 coherent with the @code{tidyverse} design philosophy, for performing basic
7538 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7539 correlation analyses. The output of each test is automatically transformed
7540 into a tidy data frame to facilitate visualization. Additional functions are
7541 available for reshaping, reordering, manipulating and visualizing correlation
7543 (license license:gpl2)))
7545 (define-public r-ggpubr
7552 (uri (cran-uri "ggpubr" version))
7555 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7556 (build-system r-build-system)
7558 `(("r-cowplot" ,r-cowplot)
7559 ("r-dplyr" ,r-dplyr)
7560 ("r-ggplot2" ,r-ggplot2)
7561 ("r-ggrepel" ,r-ggrepel)
7562 ("r-ggsci" ,r-ggsci)
7563 ("r-ggsignif" ,r-ggsignif)
7565 ("r-gridextra" ,r-gridextra)
7566 ("r-magrittr" ,r-magrittr)
7567 ("r-polynom" ,r-polynom)
7568 ("r-purrr" ,r-purrr)
7569 ("r-rlang" ,r-rlang)
7570 ("r-scales" ,r-scales)
7571 ("r-rstatix" ,r-rstatix)
7572 ("r-tibble" ,r-tibble)
7573 ("r-tidyr" ,r-tidyr)))
7574 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7575 (synopsis "ggplot2-based publication-ready plots")
7577 "The ggplot2 package is an excellent and flexible package for elegant
7578 data visualization in R. However the default generated plots require some
7579 formatting before we can send them for publication. The ggpubr package
7580 provides some easy-to-use functions for creating and customizing ggplot2-based
7581 publication-ready plots.")
7582 (license license:gpl2)))
7584 (define-public r-ellipse
7591 (uri (cran-uri "ellipse" version))
7594 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7595 (build-system r-build-system)
7596 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7597 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7599 "This package contains various routines for drawing ellipses and
7600 ellipse-like confidence regions, implementing the plots described in Murdoch
7601 and Chow (1996), A graphical display of large correlation matrices, The
7602 American Statistician 50, 178-180. There are also routines implementing the
7603 profile plots described in Bates and Watts (1988), Nonlinear Regression
7604 Analysis and its Applications.")
7605 (license license:gpl2+)))
7607 (define-public r-flashclust
7609 (name "r-flashclust")
7614 (uri (cran-uri "flashClust" version))
7617 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7618 (properties `((upstream-name . "flashClust")))
7619 (build-system r-build-system)
7620 (native-inputs `(("gfortran" ,gfortran)))
7621 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7622 (synopsis "Implementation of optimal hierarchical clustering")
7624 "This package provides a fast implementation of hierarchical
7626 (license license:gpl2+)))
7628 (define-public r-factominer
7630 (name "r-factominer")
7635 (uri (cran-uri "FactoMineR" version))
7638 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7639 (properties `((upstream-name . "FactoMineR")))
7640 (build-system r-build-system)
7643 ("r-cluster" ,r-cluster)
7645 ("r-ellipse" ,r-ellipse)
7646 ("r-flashclust" ,r-flashclust)
7647 ("r-ggplot2" ,r-ggplot2)
7648 ("r-ggrepel" ,r-ggrepel)
7649 ("r-lattice" ,r-lattice)
7650 ("r-leaps" ,r-leaps)
7652 ("r-scatterplot3d" ,r-scatterplot3d)))
7654 `(("r-knitr" ,r-knitr)))
7655 (home-page "http://factominer.free.fr")
7656 (synopsis "Multivariate exploratory data analysis and data mining")
7658 "This package provides exploratory data analysis methods to summarize,
7659 visualize and describe datasets. The main principal component methods are
7660 available, those with the largest potential in terms of applications:
7661 principal component analysis (PCA) when variables are quantitative,
7662 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7663 variables are categorical, Multiple Factor Analysis when variables are
7664 structured in groups, etc. and hierarchical cluster analysis.")
7665 (license license:gpl2+)))
7667 (define-public r-factoextra
7669 (name "r-factoextra")
7674 (uri (cran-uri "factoextra" version))
7677 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7678 (build-system r-build-system)
7680 `(("r-abind" ,r-abind)
7681 ("r-cluster" ,r-cluster)
7682 ("r-dendextend" ,r-dendextend)
7683 ("r-factominer" ,r-factominer)
7684 ("r-ggplot2" ,r-ggplot2)
7685 ("r-ggpubr" ,r-ggpubr)
7686 ("r-ggrepel" ,r-ggrepel)
7687 ("r-reshape2" ,r-reshape2)
7688 ("r-tidyr" ,r-tidyr)))
7689 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7690 (synopsis "Extract and visualize the results of multivariate data analyses")
7692 "This package provides some easy-to-use functions to extract and
7693 visualize the output of multivariate data analyses, including
7694 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7695 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7696 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7697 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7698 packages. It contains also functions for simplifying some clustering analysis
7699 steps and provides ggplot2-based elegant data visualization.")
7700 (license license:gpl2)))
7702 (define-public r-fansi
7709 (uri (cran-uri "fansi" version))
7712 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7713 (build-system r-build-system)
7715 `(("r-knitr" ,r-knitr))) ; for vignettes
7716 (home-page "https://github.com/brodieG/fansi")
7717 (synopsis "ANSI control sequence aware string functions")
7719 "This package provides counterparts to R string manipulation functions
7720 that account for the effects of ANSI text formatting control sequences.")
7721 (license license:gpl2+)))
7723 (define-public r-nbclust
7730 (uri (cran-uri "NbClust" version))
7733 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7734 (properties `((upstream-name . "NbClust")))
7735 (build-system r-build-system)
7736 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7737 (synopsis "Determine the best number of clusters in a data set")
7739 "NbClust provides 30 indexes for determining the optimal number of
7740 clusters in a data set and offers the best clustering scheme from different
7741 results to the user.")
7742 (license license:gpl2)))
7744 (define-public r-hdf5r
7751 (uri (cran-uri "hdf5r" version))
7754 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7755 (build-system r-build-system)
7760 `(("r-bit64" ,r-bit64)
7763 `(("r-knitr" ,r-knitr)))
7764 (home-page "https://hhoeflin.github.io/hdf5r")
7765 (synopsis "Interface to the HDF5 binary data format")
7767 "HDF5 is a data model, library and file format for storing and managing
7768 large amounts of data. This package provides a nearly feature complete,
7769 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7770 functionality is added so that HDF5 objects behave very similar to their
7771 corresponding R counterparts.")
7772 (license license:asl2.0)))
7774 (define-public r-itertools
7776 (name "r-itertools")
7781 (uri (cran-uri "itertools" version))
7784 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7785 (build-system r-build-system)
7787 `(("r-iterators" ,r-iterators)))
7788 (home-page "https://cran.r-project.org/web/packages/itertools/")
7789 (synopsis "Iterator tools")
7791 "This package provides various tools for creating iterators, many
7792 patterned after functions in the Python @code{itertools} module, and others
7793 patterned after functions in the snow package.")
7794 (license license:gpl2)))
7796 (define-public r-polynom
7803 (uri (cran-uri "polynom" version))
7806 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7807 (build-system r-build-system)
7808 (home-page "https://cran.r-project.org/web/packages/polynom/")
7809 (synopsis "Functions for univariate polynomial manipulations")
7811 "This package provides a collection of functions to implement a class for
7812 univariate polynomial manipulations.")
7813 (license license:gpl2)))
7815 (define-public r-gbrd
7822 (uri (cran-uri "gbRd" version))
7825 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7826 (properties `((upstream-name . "gbRd")))
7827 (build-system r-build-system)
7828 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7829 (synopsis "Utilities for processing Rd objects and files")
7831 "This package provides utilities for processing Rd objects and files.
7832 Extract argument descriptions and other parts of the help pages of
7834 (license license:gpl2+)))
7836 (define-public r-rjags
7843 (uri (cran-uri "rjags" version))
7846 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7847 (build-system r-build-system)
7849 `(("r-coda" ,r-coda)))
7853 `(("pkg-config" ,pkg-config)))
7854 (home-page "http://mcmc-jags.sourceforge.net")
7855 (synopsis "Bayesian graphical models using MCMC")
7857 "This package provides an R interface to the JAGS MCMC library. JAGS is
7858 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7859 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7860 (license license:gpl2)))
7862 (define-public r-rbibutils
7864 (name "r-rbibutils")
7869 (uri (cran-uri "rbibutils" version))
7872 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7873 (properties `((upstream-name . "rbibutils")))
7874 (build-system r-build-system)
7875 (home-page "https://geobosh.github.io/rbibutils/")
7876 (synopsis "Convert between bibliography formats")
7878 "This package converts between a number of bibliography formats,
7879 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7880 utilities and supports all bibliography formats and character encodings
7881 implemented in bibutils.")
7882 (license license:gpl2)))
7884 (define-public r-rdpack
7891 (uri (cran-uri "Rdpack" version))
7894 "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
7895 (properties `((upstream-name . "Rdpack")))
7896 (build-system r-build-system)
7898 `(("r-rbibutils" ,r-rbibutils)))
7899 (home-page "https://github.com/GeoBosh/Rdpack")
7900 (synopsis "Update and manipulate Rd documentation objects")
7902 "This package provides functions for manipulation of R documentation
7903 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7904 updating Rd documentation for functions, methods and classes; it also includes
7905 Rd macros for citations and import of references from bibtex files for use in
7906 Rd files and roxygen2 comments, as well as many functions for manipulation of
7907 references and Rd files.")
7908 (license license:gpl2+)))
7910 (define-public r-officer
7917 (uri (cran-uri "officer" version))
7920 "1apg0dh1zfhrqcbbmm8318l40gyjbqc2l9sdvwxx7qi8mzc1mqvw"))))
7921 (build-system r-build-system)
7928 `(("r-knitr" ,r-knitr)))
7929 (home-page "https://davidgohel.github.io/officer")
7930 (synopsis "Manipulation of Word and PowerPoint documents")
7932 "This package provides tools to access and manipulate Word and PowerPoint
7933 documents from R. The package focuses on tabular and graphical reporting from
7934 R; it also provides two functions that let users get document content into
7935 data objects. A set of functions lets add and remove images, tables and
7936 paragraphs of text in new or existing documents. When working with PowerPoint
7937 presentations, slides can be added or removed; shapes inside slides can also
7938 be added or removed. When working with Word documents, a cursor can be used
7939 to help insert or delete content at a specific location in the document.")
7940 (license license:gpl3)))
7942 (define-public r-profilemodel
7944 (name "r-profilemodel")
7949 (uri (cran-uri "profileModel" version))
7952 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7953 (properties `((upstream-name . "profileModel")))
7954 (build-system r-build-system)
7955 (home-page "https://github.com/ikosmidis/profileModel")
7956 (synopsis "Profiling inference functions for various model classes")
7958 "This package provides tools that can be used to calculate, evaluate,
7959 plot and use for inference the profiles of *arbitrary* inference functions for
7960 arbitrary @code{glm}-like fitted models with linear predictors. More information
7961 on the methods that are implemented can be found in Kosmidis (2008)
7962 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7963 (license license:gpl2+)))
7965 (define-public r-brglm
7972 (uri (cran-uri "brglm" version))
7975 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7976 (properties `((upstream-name . "brglm")))
7977 (build-system r-build-system)
7979 `(("r-profilemodel" ,r-profilemodel)))
7980 (home-page "https://github.com/ikosmidis/brglm")
7981 (synopsis "Bias reduction in binomial-response generalized linear models")
7983 "Fit generalized linear models with binomial responses using either an
7984 adjusted-score approach to bias reduction or maximum penalized likelihood
7985 where penalization is by Jeffreys invariant prior. These procedures return
7986 estimates with improved frequentist properties (bias, mean squared error) that
7987 are always finite even in cases where the maximum likelihood estimates are
7988 infinite (data separation). Fitting takes place by fitting generalized linear
7989 models on iteratively updated pseudo-data. The interface is essentially the
7990 same as @code{glm}. More flexibility is provided by the fact that custom
7991 pseudo-data representations can be specified and used for model fitting.
7992 Functions are provided for the construction of confidence intervals for the
7993 reduced-bias estimates.")
7994 (license license:gpl2+)))
7996 (define-public r-entropy
8003 (uri (cran-uri "entropy" version))
8006 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8007 (properties `((upstream-name . "entropy")))
8008 (build-system r-build-system)
8009 (home-page "https://www.strimmerlab.org/software/entropy/")
8010 (synopsis "Estimation of entropy, mutual information and related quantities")
8012 "This package implements various estimators of entropy, such as the
8013 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8014 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8015 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8016 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8017 mutual information, and chi-squared statistic of independence. In addition
8018 there are functions for discretizing continuous random variables.")
8019 (license license:gpl3+)))
8021 (define-public r-abn
8028 (uri (cran-uri "abn" version))
8031 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8032 (build-system r-build-system)
8036 `(("r-lme4" ,r-lme4)
8039 ("r-rcpparmadillo" ,r-rcpparmadillo)
8040 ("r-rjags" ,r-rjags)))
8041 (home-page "https://r-bayesian-networks.org/")
8042 (synopsis "Modelling multivariate data with additive bayesian networks")
8044 "Bayesian network analysis is a form of probabilistic graphical models
8045 which derives from empirical data a directed acyclic graph, DAG, describing
8046 the dependency structure between random variables. An additive Bayesian
8047 network model consists of a form of a DAG where each node comprises a
8048 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8049 equivalent to Bayesian multivariate regression using graphical modelling, they
8050 generalises the usual multivariable regression, GLM, to multiple dependent
8051 variables. This package provides routines to help determine optimal Bayesian
8052 network models for a given data set, where these models are used to identify
8053 statistical dependencies in messy, complex data.")
8054 (license license:gpl2+)))
8056 (define-public r-acd
8063 (uri (cran-uri "ACD" version))
8066 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8067 (properties `((upstream-name . "ACD")))
8068 (build-system r-build-system)
8069 (home-page "https://cran.r-project.org/web/packages/ACD/")
8070 (synopsis "Categorical data analysis with complete or missing responses")
8072 "This package provides tools for categorical data analysis with complete
8073 or missing responses.")
8074 (license license:gpl2+)))
8076 (define-public r-acdm
8083 (uri (cran-uri "ACDm" version))
8086 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8087 (properties `((upstream-name . "ACDm")))
8088 (build-system r-build-system)
8090 `(("r-dplyr" ,r-dplyr)
8091 ("r-ggplot2" ,r-ggplot2)
8093 ("r-rsolnp" ,r-rsolnp)
8095 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8096 (synopsis "Tools for Autoregressive Conditional Duration Models")
8098 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8099 and Russell, 1998) models. It creates trade, price or volume durations from
8100 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8102 (license license:gpl2+)))
8104 (define-public r-overlap
8111 (uri (cran-uri "overlap" version))
8114 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8115 (build-system r-build-system)
8116 (home-page "https://cran.r-project.org/web/packages/overlap/")
8117 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8119 "This package provides functions to fit kernel density functions to data
8120 on temporal activity patterns of animals; estimate coefficients of overlapping
8121 of densities for two species; and calculate bootstrap estimates of confidence
8123 (license license:gpl3+)))
8125 (define-public r-snakecase
8127 (name "r-snakecase")
8132 (uri (cran-uri "snakecase" version))
8135 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8136 (build-system r-build-system)
8138 `(("r-stringi" ,r-stringi)
8139 ("r-stringr" ,r-stringr)))
8140 (home-page "https://github.com/Tazinho/snakecase")
8141 (synopsis "Convert strings into any case")
8143 "This package provides a consistent, flexible and easy to use tool to
8144 parse and convert strings into cases like snake or camel among others.")
8145 (license license:gpl3)))
8147 (define-public r-prediction
8149 (name "r-prediction")
8154 (uri (cran-uri "prediction" version))
8157 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8158 (build-system r-build-system)
8160 `(("r-data-table" ,r-data-table)))
8161 (home-page "https://github.com/leeper/prediction")
8162 (synopsis "Tidy, type-safe prediction methods")
8164 "This package provides the @code{prediction()} function, a type-safe
8165 alternative to @code{predict()} that always returns a data frame. The package
8166 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8167 from the @code{stats} package, as well as numerous other model classes from
8168 other add-on packages.")
8169 (license license:expat)))
8171 (define-public r-insight
8178 (uri (cran-uri "insight" version))
8181 "1la4yxzfl9fnknamnaziil6gvpdzl78z16lfzis9jgzg8r9q0y5l"))))
8182 (build-system r-build-system)
8184 `(("r-knitr" ,r-knitr)))
8185 (home-page "https://easystats.github.io/insight/")
8186 (synopsis "Easy access to model information for various model objects")
8188 "This package provides a tool to provide an easy, intuitive and
8189 consistent access to information contained in various R models, like model
8190 formulas, model terms, information about random effects, data that was used to
8191 fit the model or data from response variables. The package mainly revolves
8192 around two types of functions: Functions that find (the names of) information,
8193 starting with @code{find_}, and functions that get the underlying data,
8194 starting with @code{get_}. The package has a consistent syntax and works with
8195 many different model objects, where otherwise functions to access these
8196 information are missing.")
8197 (license license:gpl3)))
8199 (define-public r-sjlabelled
8201 (name "r-sjlabelled")
8206 (uri (cran-uri "sjlabelled" version))
8209 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8210 (build-system r-build-system)
8212 `(("r-insight" ,r-insight)))
8214 `(("r-knitr" ,r-knitr)))
8215 (home-page "https://github.com/strengejacke/sjlabelled")
8216 (synopsis "Labelled data utility functions")
8218 "This package provides a collection of functions dealing with labelled
8219 data, like reading and writing data between R and other statistical software
8220 packages. This includes easy ways to get, set or change value and variable
8221 label attributes, to convert labelled vectors into factors or numeric (and
8222 vice versa), or to deal with multiple declared missing values.")
8223 (license license:gpl3)))
8225 (define-public r-sjmisc
8232 (uri (cran-uri "sjmisc" version))
8235 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8236 (build-system r-build-system)
8238 `(("r-dplyr" ,r-dplyr)
8239 ("r-insight" ,r-insight)
8240 ("r-magrittr" ,r-magrittr)
8241 ("r-purrr" ,r-purrr)
8242 ("r-rlang" ,r-rlang)
8243 ("r-sjlabelled" ,r-sjlabelled)
8244 ("r-tidyselect" ,r-tidyselect)))
8246 `(("r-knitr" ,r-knitr)))
8247 (home-page "https://github.com/strengejacke/sjmisc")
8248 (synopsis "Data and variable transformation functions")
8250 "This package is a collection of miscellaneous utility functions,
8251 supporting data transformation tasks like recoding, dichotomizing or grouping
8252 variables, setting and replacing missing values. The data transformation
8253 functions also support labelled data, and all integrate seamlessly into a
8254 tidyverse workflow.")
8255 (license license:gpl3)))
8257 (define-public r-nortest
8264 (uri (cran-uri "nortest" version))
8267 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8268 (build-system r-build-system)
8269 (home-page "https://cran.r-project.org/web/packages/nortest/")
8270 (synopsis "Tests for normality")
8272 "This package provides five omnibus tests for testing the composite
8273 hypothesis of normality.")
8274 (license license:gpl2+)))
8276 (define-public r-moonbook
8283 (uri (cran-uri "moonBook" version))
8286 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8287 (properties `((upstream-name . "moonBook")))
8288 (build-system r-build-system)
8290 `(("r-magrittr" ,r-magrittr)
8291 ("r-nortest" ,r-nortest)
8292 ("r-sjmisc" ,r-sjmisc)
8293 ("r-stringr" ,r-stringr)
8294 ("r-survival" ,r-survival)
8295 ("r-ztable" ,r-ztable)))
8297 `(("r-knitr" ,r-knitr)))
8298 (home-page "https://github.com/cardiomoon/moonBook")
8299 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8301 "This package provides several analysis-related functions for the book
8302 entitled \"R statistics and graph for medical articles\" (written in Korean),
8303 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8305 (license license:gpl2)))
8307 (define-public r-flextable
8309 (name "r-flextable")
8314 (uri (cran-uri "flextable" version))
8317 "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma"))))
8318 (build-system r-build-system)
8320 `(("r-base64enc" ,r-base64enc)
8321 ("r-data-table" ,r-data-table)
8322 ("r-gdtools" ,r-gdtools)
8323 ("r-htmltools" ,r-htmltools)
8324 ("r-knitr" ,r-knitr)
8325 ("r-officer" ,r-officer)
8326 ("r-rlang" ,r-rlang)
8327 ("r-rmarkdown" ,r-rmarkdown)
8329 ("r-xml2" ,r-xml2)))
8331 `(("r-knitr" ,r-knitr)))
8332 (home-page "https://davidgohel.github.io/flextable")
8333 (synopsis "Functions for tabular reporting")
8335 "This package provides tools to create pretty tables for HTML documents
8336 and other formats. Functions are provided to let users create tables, modify
8337 and format their content. It extends the @code{officer} package and can be
8338 used within R markdown documents when rendering to HTML and to Word
8340 (license license:gpl3)))
8342 (define-public r-writexl
8349 (uri (cran-uri "writexl" version))
8352 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8353 (build-system r-build-system)
8354 (inputs `(("zlib" ,zlib)))
8355 (home-page "https://github.com/ropensci/writexl")
8356 (synopsis "Export data frames to xlsx format")
8358 "This package provides a data frame to xlsx exporter based on
8360 (license license:bsd-2)))
8362 (define-public r-biasedurn
8364 (name "r-biasedurn")
8369 (uri (cran-uri "BiasedUrn" version))
8372 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8373 (properties `((upstream-name . "BiasedUrn")))
8374 (build-system r-build-system)
8375 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8376 (synopsis "Biased Urn model distributions")
8378 "This package provides statistical models of biased sampling in the form
8379 of univariate and multivariate noncentral hypergeometric distributions,
8380 including Wallenius' noncentral hypergeometric distribution and Fisher's
8381 noncentral hypergeometric distribution (also called extended hypergeometric
8383 (license license:gpl3)))
8385 (define-public r-goplot
8392 (uri (cran-uri "GOplot" version))
8395 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8396 (properties `((upstream-name . "GOplot")))
8397 (build-system r-build-system)
8399 `(("r-ggdendro" ,r-ggdendro)
8400 ("r-ggplot2" ,r-ggplot2)
8401 ("r-gridextra" ,r-gridextra)
8402 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8403 (home-page "https://github.com/wencke/wencke.github.io")
8404 (synopsis "Visualization of functional analysis data")
8406 "This package provides an implementation of multilayered visualizations
8407 for enhanced graphical representation of functional analysis data. It
8408 combines and integrates omics data derived from expression and functional
8409 annotation enrichment analyses. Its plotting functions have been developed
8410 with an hierarchical structure in mind: starting from a general overview to
8411 identify the most enriched categories (modified bar plot, bubble plot) to a
8412 more detailed one displaying different types of relevant information for the
8413 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8414 Venn diagram, heatmap).")
8415 (license license:gpl2)))
8417 (define-public r-getopt
8424 (uri (cran-uri "getopt" version))
8427 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8428 (build-system r-build-system)
8429 (home-page "https://github.com/trevorld/getopt")
8430 (synopsis "Command-line option processor for R")
8432 "This package is designed to be used with Rscript to write shebang
8433 scripts that accept short and long options. Many users will prefer to
8434 use the packages @code{optparse} or @code{argparse} which add extra
8435 features like automatically generated help options and usage texts,
8436 support for default values, positional argument support, etc.")
8437 (license license:gpl2+)))
8439 (define-public r-findpython
8441 (name "r-findpython")
8446 (uri (cran-uri "findpython" version))
8449 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8450 (build-system r-build-system)
8451 (home-page "https://github.com/trevorld/findpython")
8452 (synopsis "Functions to find an acceptable Python binary")
8454 "This package was designed to find an acceptable Python binary that
8455 matches version and feature constraints.")
8456 (license license:expat)))
8458 ;; This in not the same as "r-argparser"
8459 (define-public r-argparse
8466 (uri (cran-uri "argparse" version))
8469 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8470 (build-system r-build-system)
8471 (inputs `(("python" ,python)))
8473 `(("r-findpython" ,r-findpython)
8474 ("r-jsonlite" ,r-jsonlite)
8477 `(("r-knitr" ,r-knitr)))
8478 (home-page "https://github.com/trevorld/argparse")
8479 (synopsis "Command line optional and positional argument parser")
8481 "This package provides a command line parser to be used with Rscript to
8482 write shebang scripts that gracefully accept positional and optional arguments
8483 and automatically generate usage notices.")
8484 (license license:gpl2+)))
8486 (define-public r-hash
8493 (uri (cran-uri "hash" version))
8496 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8497 (build-system r-build-system)
8498 (home-page "https://cran.r-project.org/web/packages/hash/")
8499 (synopsis "Implementation of hash/associated arrays/dictionaries")
8501 "This package implements a data structure similar to hashes in Perl and
8502 dictionaries in Python but with a purposefully R flavor. For objects of
8503 appreciable size, access using hashes outperforms native named lists and
8505 (license license:gpl2+)))
8507 (define-public r-orddom
8514 (uri (cran-uri "orddom" version))
8517 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8518 (build-system r-build-system)
8519 (propagated-inputs `(("r-psych" ,r-psych)))
8520 (home-page "https://cran.r-project.org/web/packages/orddom/")
8521 (synopsis "Ordinal dominance statistics")
8523 "This package provides tools to compute ordinal, statistics and effect
8524 sizes as an alternative to mean comparison: Cliff's delta or success rate
8525 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8526 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8527 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8528 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8529 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8530 Group (Non-)Overlap considerations.")
8531 (license license:gpl2)))
8533 (define-public r-deriv
8540 (uri (cran-uri "Deriv" version))
8543 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
8544 (properties `((upstream-name . "Deriv")))
8545 (build-system r-build-system)
8546 (home-page "https://cran.r-project.org/web/packages/Deriv")
8547 (synopsis "Symbolic differentiation")
8549 "This package provides an R-based solution for symbolic differentiation.
8550 It admits user-defined functions as well as function substitution in arguments
8551 of functions to be differentiated. Some symbolic simplification is part of
8553 (license license:gpl3+)))
8555 (define-public r-doby
8562 (uri (cran-uri "doBy" version))
8565 "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00"))))
8566 (properties `((upstream-name . "doBy")))
8567 (build-system r-build-system)
8569 `(("r-broom" ,r-broom)
8570 ("r-deriv" ,r-deriv)
8571 ("r-dplyr" ,r-dplyr)
8572 ("r-ggplot2" ,r-ggplot2)
8573 ("r-magrittr" ,r-magrittr)
8575 ("r-matrix" ,r-matrix)
8576 ("r-pbkrtest" ,r-pbkrtest)
8577 ("r-tibble" ,r-tibble)))
8579 `(("r-knitr" ,r-knitr)))
8580 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8581 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8583 "This package contains:
8586 @item facilities for working with grouped data: @code{do}
8587 something to data stratified @code{by} some variables.
8588 @item implementations of least-squares means, general linear contrasts, and
8589 @item miscellaneous other utilities.
8591 (license license:gpl2+)))
8593 (define-public r-refgenome
8595 (name "r-refgenome")
8600 (uri (cran-uri "refGenome" version))
8603 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8604 (properties `((upstream-name . "refGenome")))
8605 (build-system r-build-system)
8609 ("r-rsqlite" ,r-rsqlite)))
8610 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8612 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8614 "This package contains functionality for importing and managing of
8615 downloaded genome annotation data from the Ensembl genome browser (European
8616 Bioinformatics Institute) and from the UCSC genome browser (University of
8617 California, Santa Cruz) and annotation routines for genomic positions and
8618 splice site positions.")
8619 (license license:gpl2)))
8621 (define-public r-basix
8628 (uri (cran-uri "BASIX" version))
8631 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8632 (properties `((upstream-name . "BASIX")))
8633 (build-system r-build-system)
8634 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8635 (synopsis "Efficient C/C++ toolset for R")
8637 "BASIX provides some efficient C/C++ implementations of native R
8638 procedures to speed up calculations in R.")
8639 (license license:gpl2)))
8641 (define-public r-blockfest
8643 (name "r-blockfest")
8648 (uri (cran-uri "BlockFeST" version))
8651 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
8652 (properties `((upstream-name . "BlockFeST")))
8653 (build-system r-build-system)
8654 (propagated-inputs `(("r-basix" ,r-basix)))
8655 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8656 (synopsis "Bayesian calculation of region-specific fixation index")
8658 "This package provides an R implementation of an extension of the
8659 BayeScan software for codominant markers, adding the option to group
8660 individual SNPs into pre-defined blocks. A typical application of this new
8661 approach is the identification of genomic regions, genes, or gene sets
8662 containing one or more SNPs that evolved under directional selection.")
8663 (license license:gpl2)))
8665 (define-public r-proc
8668 (version "1.17.0.1")
8672 (uri (cran-uri "pROC" version))
8675 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8676 (properties `((upstream-name . "pROC")))
8677 (build-system r-build-system)
8679 `(("r-plyr" ,r-plyr)
8680 ("r-rcpp" ,r-rcpp)))
8681 (home-page "https://web.expasy.org/pROC/")
8682 (synopsis "Display and analyze ROC curves")
8684 "This package provides tools for visualizing, smoothing and comparing
8685 receiver operating characteristic (ROC curves). The area under the
8686 curve (AUC) can be compared with statistical tests based on U-statistics or
8687 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8688 (license license:gpl3+)))
8690 (define-public r-rootsolve
8692 (name "r-rootsolve")
8697 (uri (cran-uri "rootSolve" version))
8700 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8701 (properties `((upstream-name . "rootSolve")))
8702 (build-system r-build-system)
8703 (native-inputs `(("gfortran" ,gfortran)))
8704 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8705 (synopsis "Tools for the analysis of ordinary differential equations")
8707 "This package provides routines to find the root of nonlinear functions,
8708 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8709 differential equations} (ODE). It includes routines that:
8712 @item generate gradient and jacobian matrices (full and banded),
8713 @item find roots of non-linear equations by the Newton-Raphson method,
8714 @item estimate steady-state conditions of a system of (differential) equations
8715 in full, banded or sparse form, using the Newton-Raphson method, or by
8716 dynamically running,
8717 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8718 and 3-D partial differential equations, that have been converted to ordinary
8719 differential equations by numerical differencing (using the method-of-lines
8722 (license license:gpl2+)))
8724 (define-public r-abcanalysis
8726 (name "r-abcanalysis")
8731 (uri (cran-uri "ABCanalysis" version))
8733 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8734 (properties `((upstream-name . "ABCanalysis")))
8735 (build-system r-build-system)
8736 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8737 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8738 (synopsis "Computed ABC Analysis")
8740 "Multivariate data sets often differ in several factors or derived statistical
8741 parameters, which have to be selected for a valid interpretation. Basing this
8742 selection on traditional statistical limits leads occasionally to the perception
8743 of losing information from a data set. This package provides tools to calculate
8744 these limits on the basis of the mathematical properties of the distribution of
8745 the analyzed items.")
8746 (license license:gpl3)))
8748 (define-public r-slam
8755 (uri (cran-uri "slam" version))
8757 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8758 (build-system r-build-system)
8759 (home-page "https://cran.r-project.org/web/packages/slam/")
8760 (synopsis "Sparse lightweight arrays and matrices")
8762 "This package contains data structures and algorithms for sparse arrays and matrices,
8763 based on index arrays and simple triplet representations, respectively.")
8764 (license license:gpl2)))
8766 (define-public r-manipulatewidget
8768 (name "r-manipulatewidget")
8773 (uri (cran-uri "manipulateWidget" version))
8775 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8777 `((upstream-name . "manipulateWidget")))
8778 (build-system r-build-system)
8780 `(("r-base64enc" ,r-base64enc)
8781 ("r-codetools" ,r-codetools)
8782 ("r-htmltools" ,r-htmltools)
8783 ("r-htmlwidgets" ,r-htmlwidgets)
8784 ("r-knitr" ,r-knitr)
8785 ("r-miniui" ,r-miniui)
8786 ("r-shiny" ,r-shiny)
8787 ("r-webshot" ,r-webshot)))
8788 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8789 (synopsis "Add even more interactivity to interactive charts")
8791 "This package lets you create in just a few lines of R code a nice user interface to
8792 modify the data or the graphical parameters of one or multiple interactive
8793 charts. It is useful to quickly explore visually some data or for package
8794 developers to generate user interfaces easy to maintain.")
8795 (license license:gpl2+)))
8804 (uri (cran-uri "A3" version))
8806 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8807 (properties `((upstream-name . "A3")))
8808 (build-system r-build-system)
8810 `(("r-pbapply" ,r-pbapply)
8811 ("r-xtable" ,r-xtable)))
8812 (home-page "https://cran.r-project.org/web/packages/A3/")
8813 (synopsis "Error metrics for predictive models")
8815 "This package supplies tools for tabulating and analyzing the results of predictive
8816 models. The methods employed are applicable to virtually any predictive model
8817 and make comparisons between different methodologies straightforward.")
8818 (license license:gpl2+)))
8820 (define-public r-infotheo
8827 (uri (cran-uri "infotheo" version))
8830 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8831 (build-system r-build-system)
8832 (home-page "http://homepage.meyerp.com/software")
8833 (synopsis "Information-theoretic measures")
8835 "This package implements various measures of information theory based on
8836 several entropy estimators.")
8837 (license license:gpl3+)))
8839 (define-public r-abcoptim
8846 (uri (cran-uri "ABCoptim" version))
8848 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8849 (properties `((upstream-name . "ABCoptim")))
8850 (build-system r-build-system)
8851 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8852 (home-page "https://github.com/gvegayon/ABCoptim/")
8853 (synopsis "Optimization of Artificial Bee Colony algorithm")
8855 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8856 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8857 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8858 algorithms, and uses only common control parameters such as colony size and
8859 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8860 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8861 This version is a work-in-progress and is written in R code.")
8862 (license license:expat)))
8864 (define-public r-abcp2
8871 (uri (cran-uri "ABCp2" version))
8873 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8874 (properties `((upstream-name . "ABCp2")))
8875 (build-system r-build-system)
8876 (propagated-inputs `(("r-mass" ,r-mass)))
8877 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8878 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8880 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8881 Poisson, and Gamma distribution and estimates the proportional paternity of the
8882 second male (P2) based on the best fit distribution.")
8883 (license license:gpl2)))
8885 (define-public r-abcrf
8892 (uri (cran-uri "abcrf" version))
8894 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8895 (build-system r-build-system)
8897 `(("r-doparallel" ,r-doparallel)
8898 ("r-foreach" ,r-foreach)
8900 ("r-matrixstats" ,r-matrixstats)
8901 ("r-ranger" ,r-ranger)
8903 ("r-rcpparmadillo" ,r-rcpparmadillo)
8904 ("r-readr" ,r-readr)
8905 ("r-stringr" ,r-stringr)))
8906 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8907 (synopsis "Approximate bayesian computation via random forests")
8909 "This package performs approximate bayesian computation (ABC) model choice and
8910 parameter inference via random forests. This machine learning tool named random
8911 forests (RF) can conduct selection among the highly complex models covered by
8913 (license license:gpl2+)))
8915 (define-public r-abctools
8922 (uri (cran-uri "abctools" version))
8924 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8925 (build-system r-build-system)
8928 ("r-abind" ,r-abind)
8929 ("r-hmisc" ,r-hmisc)
8930 ("r-plyr" ,r-plyr)))
8931 (home-page "https://github.com/dennisprangle/abctools/")
8932 (synopsis "Tools for ABC analyses")
8934 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8935 including summary statistic selection and assessing coverage. This includes
8936 recent dimension reduction algorithms to tune the choice of summary statistics,
8937 and coverage methods to tune the choice of threshold.")
8938 (license license:gpl2+)))
8940 (define-public r-ggstance
8947 (uri (cran-uri "ggstance" version))
8949 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8950 (build-system r-build-system)
8952 `(("r-ggplot2" ,r-ggplot2)
8954 ("r-rlang" ,r-rlang)
8955 ("r-withr" ,r-withr)))
8956 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8957 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8959 "This package is a @code{r-ggplot2} extension that provides flipped components:
8961 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8962 @item vertical versions of @code{r-ggplot2} positions.
8964 (license license:gpl3)))
8966 (define-public r-mosaiccore
8968 (name "r-mosaiccore")
8973 (uri (cran-uri "mosaicCore" version))
8975 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8976 (properties `((upstream-name . "mosaicCore")))
8977 (build-system r-build-system)
8979 `(("r-dplyr" ,r-dplyr)
8981 ("r-rlang" ,r-rlang)
8982 ("r-tidyr" ,r-tidyr)))
8983 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8984 (synopsis "Common utilities for mosaic family packages")
8986 "Common utilities used in other Mosaic family packages are collected here.")
8987 (license license:gpl2+)))
8989 (define-public r-labelled
8996 (uri (cran-uri "labelled" version))
8999 "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg"))))
9000 (properties `((upstream-name . "labelled")))
9001 (build-system r-build-system)
9003 `(("r-dplyr" ,r-dplyr)
9004 ("r-haven" ,r-haven)
9005 ("r-lifecycle" ,r-lifecycle)
9006 ("r-rlang" ,r-rlang)
9007 ("r-stringr" ,r-stringr)
9008 ("r-tidyr" ,r-tidyr)
9009 ("r-vctrs" ,r-vctrs)))
9011 `(("r-knitr" ,r-knitr)))
9012 (home-page "http://larmarange.github.io/labelled/")
9013 (synopsis "Manipulating labelled data")
9015 "This package provides useful functions to deal with the
9016 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9018 (license license:gpl3)))
9020 (define-public r-ggformula
9022 (name "r-ggformula")
9027 (uri (cran-uri "ggformula" version))
9029 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9030 (build-system r-build-system)
9032 `(("r-ggforce" ,r-ggforce)
9033 ("r-ggplot2" ,r-ggplot2)
9034 ("r-ggridges" ,r-ggridges)
9035 ("r-ggstance" ,r-ggstance)
9036 ("r-labelled" ,r-labelled)
9037 ("r-magrittr" ,r-magrittr)
9038 ("r-mosaiccore" ,r-mosaiccore)
9039 ("r-rlang" ,r-rlang)
9040 ("r-scales" ,r-scales)
9041 ("r-stringr" ,r-stringr)
9042 ("r-tibble" ,r-tibble)))
9044 `(("r-knitr" ,r-knitr)))
9045 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9046 (synopsis "Formula interface for the @code{r-ggplot2}")
9048 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9049 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9050 and extends the excellent simplicity of the lattice-graphics formula interface,
9051 while providing the intuitive capabilities of @code{r-ggplot2}.")
9052 (license license:expat)))
9054 (define-public r-mosaicdata
9056 (name "r-mosaicdata")
9061 (uri (cran-uri "mosaicData" version))
9063 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9064 (properties `((upstream-name . "mosaicData")))
9065 (build-system r-build-system)
9066 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9067 (synopsis "Data sets for project Mosaic")
9069 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9070 used to teach mathematics, statistics, computation and modeling.")
9071 (license license:gpl2+)))
9073 (define-public r-raster
9080 (uri (cran-uri "raster" version))
9083 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9084 (build-system r-build-system)
9086 `(("r-rcpp" ,r-rcpp)
9088 (home-page "https://www.rspatial.org/")
9089 (synopsis "Geographic data analysis and modeling")
9091 "The package implements basic and high-level functions for reading,
9092 writing, manipulating, analyzing and modeling of gridded spatial data.
9093 Processing of very large files is supported.")
9094 (license license:gpl3+)))
9096 (define-public r-mosaic
9103 (uri (cran-uri "mosaic" version))
9105 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9106 (build-system r-build-system)
9108 `(("r-broom" ,r-broom)
9109 ("r-dplyr" ,r-dplyr)
9110 ("r-ggdendro" ,r-ggdendro)
9111 ("r-ggformula" ,r-ggformula)
9112 ("r-ggplot2" ,r-ggplot2)
9113 ("r-ggrepel" ,r-ggrepel)
9115 ("r-gridextra" ,r-gridextra)
9116 ("r-lattice" ,r-lattice)
9117 ("r-latticeextra" ,r-latticeextra)
9118 ("r-lazyeval" ,r-lazyeval)
9120 ("r-matrix" ,r-matrix)
9121 ("r-mosaiccore" ,r-mosaiccore)
9122 ("r-mosaicdata" ,r-mosaicdata)
9123 ("r-readr" ,r-readr)
9124 ("r-tidyr" ,r-tidyr)))
9126 `(("r-knitr" ,r-knitr)))
9127 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9128 (synopsis "Mathematics, statistics, and computation teaching utilities")
9130 "This package contain data sets and utilities from
9131 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9132 statistics, computation and modeling. Project MOSAIC is a community of
9133 educators working to tie together aspects of quantitative work that students
9134 in science, technology, engineering and mathematics will need in their
9135 professional lives, but which are usually taught in isolation, if at all.")
9136 (license license:gpl2+)))
9138 (define-public r-abd
9145 (uri (cran-uri "abd" version))
9147 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9148 (build-system r-build-system)
9150 `(("r-lattice" ,r-lattice)
9151 ("r-mosaic" ,r-mosaic)
9152 ("r-nlme" ,r-nlme)))
9153 (home-page "https://cran.r-project.org/web/packages/abd/")
9154 (synopsis "Analysis of biological data")
9156 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9157 biological data by Michael Whitlock and Dolph Schluter.")
9158 (license license:gpl2)))
9160 (define-public r-svgui
9167 (uri (cran-uri "svGUI" version))
9169 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9170 (properties `((upstream-name . "svGUI")))
9171 (build-system r-build-system)
9172 (home-page "https://github.com/SciViews/svGUI/")
9173 (synopsis "Functions for managing GUI clients in R")
9175 "The SciViews @code{svGUI} package eases the management of Graphical User
9176 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9177 centralizes info about GUI elements currently used, and it dispatches GUI
9178 calls to the particular toolkits in use in function of the context.")
9179 (license license:gpl2)))
9181 (define-public r-svdialogs
9183 (name "r-svdialogs")
9188 (uri (cran-uri "svDialogs" version))
9190 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9191 (properties `((upstream-name . "svDialogs")))
9192 (build-system r-build-system)
9195 ("zenity" ,zenity)))
9197 `(("r-rstudioapi" ,r-rstudioapi)
9198 ("r-svgui" ,r-svgui)))
9199 (home-page "https://github.com/SciViews/svDialogs/")
9200 (synopsis "Portable dialog boxes")
9202 "This package helps to construct standard dialog boxes for your GUI, including
9203 message boxes, input boxes, list, file or directory selection, and others. In
9204 case R cannot display GUI dialog boxes, a simpler command line version of these
9205 interactive elements is also provided as a fallback solution.")
9206 (license license:gpl2)))
9208 (define-public r-abe
9215 (uri (cran-uri "abe" version))
9218 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9219 (build-system r-build-system)
9220 (home-page "https://cran.r-project.org/web/packages/abe/")
9221 (synopsis "Augmented backward elimination")
9223 "This package performs augmented backward elimination and checks the
9224 stability of the obtained model. Augmented backward elimination combines
9225 significance or information based criteria with the change in estimate to
9226 either select the optimal model for prediction purposes or to serve as a tool
9227 to obtain a practically sound, highly interpretable model.")
9228 (license license:gpl2+)))
9230 (define-public r-abf2
9237 (uri (cran-uri "abf2" version))
9239 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9240 (build-system r-build-system)
9241 (home-page "https://cran.r-project.org/web/packages/abf2/")
9242 (synopsis "Load gap-free axon @code{r-abf2} files")
9244 "This package loads electrophysiology data from ABF2 files, as created by
9245 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9246 mode are currently supported.")
9247 (license license:artistic2.0)))
9249 (define-public r-abhgenotyper
9251 (name "r-abhgenotyper")
9256 (uri (cran-uri "ABHgenotypeR" version))
9258 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9259 (properties `((upstream-name . "ABHgenotypeR")))
9260 (build-system r-build-system)
9262 `(("r-ggplot2" ,r-ggplot2)
9263 ("r-reshape2" ,r-reshape2)))
9264 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9265 (synopsis "Visualize and manipulate ABH genotypes")
9267 "The @code{r-abhgenotyper} package provides simple imputation,
9268 error-correction and plotting capacities for genotype data. The package is
9269 supposed to serve as an intermediate but independent analysis tool between the
9270 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9271 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9272 genotypes as \"graphical genotypes\".")
9273 (license license:gpl3)))
9275 (define-public r-furrr
9282 (uri (cran-uri "furrr" version))
9285 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9286 (build-system r-build-system)
9288 `(("r-ellipsis" ,r-ellipsis)
9289 ("r-future" ,r-future)
9290 ("r-globals" ,r-globals)
9291 ("r-lifecycle" ,r-lifecycle)
9292 ("r-purrr" ,r-purrr)
9293 ("r-rlang" ,r-rlang)
9294 ("r-vctrs" ,r-vctrs)))
9295 (home-page "https://github.com/DavisVaughan/furrr")
9296 (synopsis "Apply mapping functions in parallel using futures")
9298 "This package provides implementations of the family of @code{map()}
9299 functions from the @code{purrr} package that can be resolved using any
9300 @code{future}-supported backend, e.g. parallel on the local machine or
9301 distributed on a compute cluster.")
9302 (license license:lgpl2.1+)))
9304 (define-public r-abjutils
9311 (uri (cran-uri "abjutils" version))
9313 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9314 (build-system r-build-system)
9316 `(("r-dplyr" ,r-dplyr)
9317 ("r-magrittr" ,r-magrittr)
9318 ("r-purrr" ,r-purrr)
9319 ("r-rlang" ,r-rlang)
9320 ("r-rstudioapi" ,r-rstudioapi)
9321 ("r-stringi" ,r-stringi)
9322 ("r-stringr" ,r-stringr)
9323 ("r-tidyr" ,r-tidyr)))
9324 (home-page "https://github.com/abjur/abjutils/")
9325 (synopsis "Collection of tools for jurimetrical analysis")
9327 "This package implements general purpose tools, such as functions for
9328 sampling and basic manipulation of Brazilian lawsuits identification number.
9329 It also implements functions for text cleaning, such as accentuation
9331 (license license:expat)))
9333 (define-public r-abnormality
9335 (name "r-abnormality")
9340 (uri (cran-uri "abnormality" version))
9342 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9343 (build-system r-build-system)
9345 `(("r-mass" ,r-mass)
9346 ("r-matrix" ,r-matrix)))
9347 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9348 (synopsis "Measure a subject's abnormality with respect to a reference population")
9350 "This package contains functions to implement the methodology and
9351 considerations laid out by Marks et al. in the article \"Measuring abnormality
9352 in high dimensional spaces: applications in biomechanical gait analysis\".
9353 Using high-dimensional datasets to measure a subject's overall level of
9354 abnormality as compared to a reference population is often needed in outcomes
9356 (license license:expat)))
9358 (define-public r-abodoutlier
9360 (name "r-abodoutlier")
9365 (uri (cran-uri "abodOutlier" version))
9367 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9368 (properties `((upstream-name . "abodOutlier")))
9369 (build-system r-build-system)
9371 `(("r-cluster" ,r-cluster)))
9372 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9373 (synopsis "Angle-based outlier detection")
9375 "This package performs angle-based outlier detection on a given data
9376 frame. It offers three methods to process data:
9378 @item full but slow implementation using all the data that has cubic
9380 @item a fully randomized method;
9381 @item a method using k-nearest neighbours.
9383 These algorithms are well suited for high dimensional data outlier
9385 (license license:expat)))
9387 (define-public r-abps
9394 (uri (cran-uri "ABPS" version))
9396 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9397 (properties `((upstream-name . "ABPS")))
9398 (build-system r-build-system)
9399 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9400 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9401 (synopsis "Abnormal blood profile score to detect blood doping")
9403 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9404 The ABPS is a part of the Athlete biological passport program of the World
9405 anti-doping agency, which combines several blood parameters into a single
9406 score in order to detect blood doping. The package also contains functions to
9407 calculate other scores used in anti-doping programs, such as the ratio of
9408 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9409 (license license:gpl2+)))
9411 (define-public r-parmigene
9413 (name "r-parmigene")
9418 (uri (cran-uri "parmigene" version))
9421 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9422 (build-system r-build-system)
9423 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9424 (synopsis "Mutual information estimation for gene network reconstruction")
9426 "This package provides a parallel estimation of the mutual information
9427 based on entropy estimates from k-nearest neighbors distances and algorithms
9428 for the reconstruction of gene regulatory networks.")
9429 (license license:agpl3+)))
9431 (define-public r-pscl
9438 (uri (cran-uri "pscl" version))
9440 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9441 (build-system r-build-system)
9443 `(("r-mass" ,r-mass)))
9444 (home-page "https://github.com/atahk/pscl/")
9445 (synopsis "Political science computational laboratory")
9447 "The @code{pscl} is an R package providing classes and methods for:
9449 @item Bayesian analysis of roll call data (item-response models);
9450 @item elementary Bayesian statistics;
9451 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9453 @item utility functions.
9455 (license license:gpl2)))
9457 (define-public r-accelmissing
9459 (name "r-accelmissing")
9464 (uri (cran-uri "accelmissing" version))
9466 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9467 (build-system r-build-system)
9469 `(("r-mice" ,r-mice)
9470 ("r-pscl" ,r-pscl)))
9471 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9472 (synopsis "Missing value imputation for accelerometer data")
9474 "This package provides a statistical method to impute the missing values in
9475 accelerometer data. The methodology includes both parametric and
9476 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9477 model. It also provides multiple functions to preprocess the accelerometer data
9478 previous to the missing data imputation. These include detecting the wearing
9479 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9480 (license license:gpl2+)))
9482 (define-public r-mhsmm
9489 (uri (cran-uri "mhsmm" version))
9491 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9492 (build-system r-build-system)
9493 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9494 (home-page "https://github.com/jaredo/mhsmm/")
9495 (synopsis "Inference for hidden Markov and semi-Markov models")
9497 "The @code{r-mhsmm} package implements estimation and prediction methods for
9498 hidden Markov and semi-Markov models for multiple observation sequences. Such
9499 techniques are of interest when observed data is thought to be dependent on some
9500 unobserved (or hidden) state. Also, this package is suitable for equidistant
9501 time series data, with multivariate and/or missing data. Allows user defined
9502 emission distributions.")
9503 (license license:gpl2+)))
9505 (define-public r-nleqslv
9512 (uri (cran-uri "nleqslv" version))
9514 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9515 (build-system r-build-system)
9516 (native-inputs `(("gfortran" ,gfortran)))
9517 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9518 (synopsis "Solve systems of nonlinear equations")
9520 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9521 Broyden or a Newton method with a choice of global strategies such as line
9522 search and trust region. There are options for using a numerical or user
9523 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9524 singular or ill-conditioned Jacobian.")
9525 (license license:gpl2+)))
9527 (define-public r-physicalactivity
9529 (name "r-physicalactivity")
9534 (uri (cran-uri "PhysicalActivity" version))
9536 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9538 `((upstream-name . "PhysicalActivity")))
9539 (build-system r-build-system)
9540 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9541 (synopsis "Procesing accelerometer data for physical activity measurement")
9543 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9544 for classification of monitor wear and nonwear time intervals in accelerometer
9545 data collected to assess physical activity. The package also contains functions
9546 for making plots of accelerometer data and obtaining the summary of various
9547 information including daily monitor wear time and the mean monitor wear time
9548 during valid days. The revised package version 0.2-1 improved the functions
9549 regarding speed, robustness and add better support for time zones and daylight
9550 saving. In addition, several functions were added:
9552 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9553 @item the @code{markPAI} can categorize physical activity intensity level based
9554 on user-defined cut-points of accelerometer counts.
9556 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9557 @code{queryActigraph} functions.")
9558 (license license:gpl3+)))
9560 (define-public r-acc
9567 (uri (cran-uri "acc" version))
9569 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9570 (build-system r-build-system)
9572 `(("r-circlize" ,r-circlize)
9574 ("r-ggplot2" ,r-ggplot2)
9575 ("r-iterators" ,r-iterators)
9576 ("r-mhsmm" ,r-mhsmm)
9577 ("r-nleqslv" ,r-nleqslv)
9578 ("r-physicalactivity" ,r-physicalactivity)
9580 ("r-r-utils" ,r-r-utils)
9582 ("r-rcpparmadillo" ,r-rcpparmadillo)
9583 ("r-rsqlite" ,r-rsqlite)
9585 (home-page "https://cran.r-project.org/web/packages/acc/")
9586 (synopsis "Exploring accelerometer data")
9588 "This package processes accelerometer data from uni-axial and tri-axial devices
9589 and generates data summaries. Also, includes functions to plot, analyze, and
9590 simulate accelerometer data.")
9591 (license license:gpl2+)))
9593 (define-public r-rbenchmark
9595 (name "r-rbenchmark")
9600 (uri (cran-uri "rbenchmark" version))
9602 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9603 (build-system r-build-system)
9604 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9605 (synopsis "Benchmarking routine for R")
9607 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9608 and is intended to facilitate benchmarking of arbitrary R code. The library
9609 consists of just one function, benchmark, which is a simple wrapper around
9610 system.time. Given a specification of the benchmarking process (counts of
9611 replications, evaluation environment) and an arbitrary number of expressions,
9612 benchmark evaluates each of the expressions in the specified environment,
9613 replicating the evaluation as many times as specified, and returning the results
9614 conveniently wrapped into a data frame.")
9615 (license license:gpl2+)))
9617 (define-public r-mitools
9624 (uri (cran-uri "mitools" version))
9627 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9628 (build-system r-build-system)
9629 (propagated-inputs `(("r-dbi" ,r-dbi)))
9630 (home-page "https://cran.r-project.org/web/packages/mitools/")
9631 (synopsis "Tools for multiple imputation of missing data")
9633 "This package provides tools to perform analyses and combine results from
9634 multiple-imputation datasets.")
9635 (license license:gpl2)))
9637 (define-public r-mixsqp
9643 (uri (cran-uri "mixsqp" version))
9646 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9647 (properties `((upstream-name . "mixsqp")))
9648 (build-system r-build-system)
9650 `(("r-irlba" ,r-irlba)
9652 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9654 `(("r-knitr" ,r-knitr)))
9655 (home-page "https://github.com/stephenslab/mixsqp")
9657 "Sequential quadratic programming for maximum-likelihood estimation")
9659 "This package provides an optimization method based on sequential
9660 quadratic programming for maximum likelihood estimation of the mixture
9661 proportions in a finite mixture model where the component densities are
9662 known. The algorithm is expected to obtain solutions that are at least
9663 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9664 are expected to arrive at solutions more quickly when the number of
9665 samples is large and the number of mixture components is not too large.")
9666 (license license:expat)))
9668 (define-public r-magick
9675 (uri (cran-uri "magick" version))
9678 "0m1kij6pp7dmsrhl80h60iyccjqmbbb3zdnqdc9sgy1kj1x3pscp"))))
9679 (build-system r-build-system)
9681 `(("imagemagick" ,imagemagick)
9684 `(("r-curl" ,r-curl)
9685 ("r-magrittr" ,r-magrittr)
9686 ("r-rcpp" ,r-rcpp)))
9688 `(("pkg-config" ,pkg-config)
9689 ("r-knitr" ,r-knitr)))
9690 (home-page "https://github.com/ropensci/magick")
9691 (synopsis "Advanced graphics and image-processing in R")
9693 "This package provides bindings to ImageMagick, a comprehensive image
9694 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9695 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9696 operations are vectorized via the Magick++ STL meaning they operate either on
9697 a single frame or a series of frames for working with layers, collages, or
9698 animation. In RStudio, images are automatically previewed when printed to the
9699 console, resulting in an interactive editing environment.")
9700 (license license:expat)))
9702 (define-public r-survey
9709 (uri (cran-uri "survey" version))
9712 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9713 (build-system r-build-system)
9715 `(("r-lattice" ,r-lattice)
9716 ("r-matrix" ,r-matrix)
9717 ("r-minqa" ,r-minqa)
9718 ("r-mitools" ,r-mitools)
9719 ("r-numderiv" ,r-numderiv)
9720 ("r-survival" ,r-survival)))
9721 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9722 (synopsis "Analysis of complex survey samples")
9724 "This package provides tools for the analysis of complex survey samples.
9725 The provided features include: summary statistics, two-sample tests, rank
9726 tests, generalised linear models, cumulative link models, Cox models,
9727 loglinear models, and general maximum pseudolikelihood estimation for
9728 multistage stratified, cluster-sampled, unequally weighted survey samples;
9729 variances by Taylor series linearisation or replicate weights;
9730 post-stratification, calibration, and raking; two-phase subsampling designs;
9731 graphics; PPS sampling without replacement; principal components, and factor
9733 ;; Either version of the GPL.
9734 (license (list license:gpl2 license:gpl3))))
9736 (define-public r-gee
9743 (uri (cran-uri "gee" version))
9746 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9747 (properties `((upstream-name . "gee")))
9748 (build-system r-build-system)
9750 `(("gfortran" ,gfortran)))
9751 (home-page "https://cran.r-project.org/web/packages/gee/")
9752 (synopsis "Generalized estimation equation solver")
9754 "This package provides a solver for generalized estimation equations.")
9755 (license license:gpl2)))
9757 (define-public r-tab
9764 (uri (cran-uri "tab" version))
9767 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9768 (properties `((upstream-name . "tab")))
9769 (build-system r-build-system)
9771 `(("r-dplyr" ,r-dplyr)
9773 ("r-knitr" ,r-knitr)
9775 ("r-survey" ,r-survey)
9776 ("r-survival" ,r-survival)
9777 ("r-xtable" ,r-xtable)))
9778 (home-page "https://cran.r-project.org/web/packages/tab/")
9779 (synopsis "Create summary tables for statistical reports")
9781 "This package contains functions for creating various types of summary
9782 tables, e.g. comparing characteristics across levels of a categorical variable
9783 and summarizing fitted generalized linear models, generalized estimating
9784 equations, and Cox proportional hazards models. Functions are available to
9785 handle data from simple random samples as well as complex surveys.")
9786 (license license:gpl3+)))
9788 (define-public r-dvmisc
9795 (uri (cran-uri "dvmisc" version))
9797 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9798 (build-system r-build-system)
9800 `(("r-cubature" ,r-cubature)
9801 ("r-data-table" ,r-data-table)
9802 ("r-dplyr" ,r-dplyr)
9803 ("r-ggplot2" ,r-ggplot2)
9805 ("r-mvtnorm" ,r-mvtnorm)
9806 ("r-pracma" ,r-pracma)
9807 ("r-rbenchmark" ,r-rbenchmark)
9809 ("r-survey" ,r-survey)
9811 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9812 (synopsis "Faster computation of common statistics and miscellaneous functions")
9814 "This package implements faster versions of base R functions (e.g. mean, standard
9815 deviation, covariance, weighted mean), mostly written in C++, along with
9816 miscellaneous functions for various purposes (e.g. create the histogram with
9817 fitted probability density function or probability mass function curve, create
9818 the body mass index groups, assess the linearity assumption in logistic
9820 (license license:gpl2)))
9822 (define-public r-accelerometry
9824 (name "r-accelerometry")
9829 (uri (cran-uri "accelerometry" version))
9831 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9832 (build-system r-build-system)
9834 `(("r-dvmisc" ,r-dvmisc)
9835 ("r-rcpp" ,r-rcpp)))
9836 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9837 (synopsis "Functions for processing accelerometer data")
9839 "This package provides a collection of functions that perform operations on
9840 time-series accelerometer data, such as identify the non-wear time, flag minutes
9841 that are part of an activity bout, and find the maximum 10-minute average count
9842 value. The functions are generally very flexible, allowing for a variety of
9843 algorithms to be implemented.")
9844 (license license:gpl3)))
9846 (define-public r-absim
9853 (uri (cran-uri "AbSim" version))
9855 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9856 (properties `((upstream-name . "AbSim")))
9857 (build-system r-build-system)
9860 ("r-powerlaw" ,r-powerlaw)))
9861 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9862 (synopsis "Time resolved simulations of antibody repertoires")
9864 "This package provides simulation methods for the evolution of antibody repertoires.
9865 The heavy and light chain variable region of both human and C57BL/6 mice can
9866 be simulated in a time-dependent fashion. Both single lineages using one set of
9867 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9868 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9869 Upon completion, the main loop of the algorithm begins, with each iteration
9870 representing one simulated time step. Various mutation events are possible at
9871 each time step, contributing to a diverse final repertoire.")
9872 (license license:gpl2)))
9874 (define-public r-quic
9881 (uri (cran-uri "QUIC" version))
9883 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9884 (properties `((upstream-name . "QUIC")))
9885 (build-system r-build-system)
9886 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9887 (synopsis "Regularized sparse inverse covariance matrix estimation")
9889 "This package implements the regularized Gaussian maximum likelihood
9890 estimation of the inverse of a covariance matrix. It uses Newton's method and
9891 coordinate descent to solve the regularized inverse covariance matrix
9892 estimation problem.")
9893 ;; The project home page states that the release is under GPLv3 or later.
9894 ;; The CRAN page only says GPL-3.
9895 (license license:gpl3+)))
9897 (define-public r-abundant
9904 (uri (cran-uri "abundant" version))
9906 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9907 (build-system r-build-system)
9909 `(("r-quic" ,r-quic)))
9910 (home-page "https://cran.r-project.org/web/packages/abundant/")
9911 (synopsis "Abundant regression and high-dimensional principal fitted components")
9913 "This package provides tools to fit and predict with the high-dimensional
9914 principal fitted components model. This model is described by Cook, Forzani,
9915 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9916 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9917 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9918 (license license:gpl2+)))
9920 (define-public r-ac3net
9927 (uri (cran-uri "Ac3net" version))
9929 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9930 (properties `((upstream-name . "Ac3net")))
9931 (build-system r-build-system)
9933 `(("r-data-table" ,r-data-table)))
9934 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9935 (synopsis "Inferring directional conservative causal core gene networks")
9936 (description "This package infers directional Conservative causal core
9937 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9938 directional network.")
9939 (license license:gpl3+)))
9941 (define-public r-aca
9948 (uri (cran-uri "ACA" version))
9950 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9951 (properties `((upstream-name . "ACA")))
9952 (build-system r-build-system)
9953 (home-page "https://cran.r-project.org/web/packages/ACA/")
9954 (synopsis "Abrupt change-point or aberration detection in point series")
9956 "This package offers an interactive function for the detection of breakpoints in
9958 ;; Any version of the GPL
9959 (license (list license:gpl2+ license:gpl3+))))
9961 (define-public r-acceptancesampling
9963 (name "r-acceptancesampling")
9968 (uri (cran-uri "AcceptanceSampling" version))
9970 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9972 `((upstream-name . "AcceptanceSampling")))
9973 (build-system r-build-system)
9974 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9975 (synopsis "Creation and evaluation of acceptance sampling plans")
9977 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9978 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9979 in quality control and improvement. International standards of acceptance
9980 sampling provide sampling plans for specific circumstances. The aim of this
9981 package is to provide an easy-to-use interface to visualize single, double or
9982 multiple sampling plans. In addition, methods have been provided to enable the
9983 user to assess sampling plans against pre-specified levels of performance, as
9984 measured by the probability of acceptance for a given level of quality in the
9986 (license license:gpl3+)))
9988 (define-public r-acclma
9995 (uri (cran-uri "ACCLMA" version))
9997 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
9998 (properties `((upstream-name . "ACCLMA")))
9999 (build-system r-build-system)
10000 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10001 (synopsis "ACC & LMA graph plotting")
10003 "This package contains a function that imports data from a @acronym{CSV,
10004 Comma-Separated Values} file, or uses manually entered data from the format (x,
10005 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10006 Curve} vs @acronym{LOI, Line of Independence} graph and
10007 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10008 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10009 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10010 string) was passed, a manual data entry window is opened. The header parameter
10011 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10012 a header row or not. The dataset should contain only one independent variable
10013 (x) and one dependent variable (y) and can contain a weight for each
10015 (license license:gpl2)))
10017 (define-public r-aspi
10024 (uri (cran-uri "aspi" version))
10026 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10027 (build-system r-build-system)
10029 "https://cran.r-project.org/web/packages/aspi/")
10031 "Analysis of symmetry of parasitic infections")
10033 "This package provides tools for the analysis and visualization of bilateral
10034 asymmetry in parasitic infections.")
10035 (license license:gpl3+)))
10037 (define-public r-sandwich
10039 (name "r-sandwich")
10044 (uri (cran-uri "sandwich" version))
10047 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10048 (build-system r-build-system)
10050 `(("r-zoo" ,r-zoo)))
10051 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10052 (synopsis "Robust Covariance Matrix Estimators")
10054 "This package provides model-robust standard error estimators for
10055 cross-sectional, time series, clustered, panel, and longitudinal data.")
10056 ;; Either version of the license.
10057 (license (list license:gpl2 license:gpl3))))
10059 (define-public r-th-data
10066 (uri (cran-uri "TH.data" version))
10069 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10070 (properties `((upstream-name . "TH.data")))
10071 (build-system r-build-system)
10073 `(("r-mass" ,r-mass)
10074 ("r-survival" ,r-survival)))
10075 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10076 (synopsis "Shared data sets")
10078 "This package contains supporting data sets that are used in other
10079 packages maintained by Torsten Hothorn.")
10080 (license license:gpl3)))
10082 (define-public r-multcomp
10084 (name "r-multcomp")
10089 (uri (cran-uri "multcomp" version))
10092 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10093 (build-system r-build-system)
10095 `(("r-codetools" ,r-codetools)
10096 ("r-mvtnorm" ,r-mvtnorm)
10097 ("r-sandwich" ,r-sandwich)
10098 ("r-survival" ,r-survival)
10099 ("r-th-data" ,r-th-data)))
10100 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10101 (synopsis "Simultaneous inference in general parametric models")
10103 "Simultaneous tests and confidence intervals for general linear
10104 hypotheses in parametric models, including linear, generalized linear, linear
10105 mixed effects, and survival models. The package includes demos reproducing
10106 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10107 Hothorn, Westfall, 2010, CRC Press).")
10108 (license license:gpl2)))
10110 (define-public r-emmeans
10117 (uri (cran-uri "emmeans" version))
10120 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
10121 (build-system r-build-system)
10123 `(("r-estimability" ,r-estimability)
10124 ("r-mvtnorm" ,r-mvtnorm)
10125 ("r-numderiv" ,r-numderiv)
10127 ("r-xtable" ,r-xtable)))
10129 `(("r-knitr" ,r-knitr)))
10130 (home-page "https://github.com/rvlenth/emmeans")
10131 (synopsis "Estimated marginal means, aka least-squares means")
10133 "This package provides tools to obtain @dfn{estimated marginal
10134 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10135 be used to compute contrasts or linear functions of EMMs, trends, and
10136 comparisons of slopes.")
10137 ;; Either version of the license.
10138 (license (list license:gpl2 license:gpl3))))
10140 (define-public r-pwr
10147 (uri (cran-uri "pwr" version))
10150 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10151 (build-system r-build-system)
10153 `(("r-knitr" ,r-knitr)))
10154 (home-page "https://github.com/heliosdrm/pwr")
10155 (synopsis "Basic functions for power analysis")
10157 "This package provides power analysis functions along the lines of
10159 (license license:gpl3+)))
10161 (define-public r-libcoin
10168 (uri (cran-uri "libcoin" version))
10170 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10171 (build-system r-build-system)
10172 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10173 (home-page "https://cran.r-project.org/web/packages/libcoin")
10174 (synopsis "Linear test statistics for permutation inference")
10176 "This package provides basic infrastructure for linear test statistics
10177 and permutation inference in the framework of Strasser and Weber (1999).")
10178 (license license:gpl2)))
10180 (define-public r-coin
10187 (uri (cran-uri "coin" version))
10190 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10191 (build-system r-build-system)
10193 `(("r-libcoin" ,r-libcoin)
10194 ("r-matrixstats" ,r-matrixstats)
10195 ("r-modeltools" ,r-modeltools)
10196 ("r-multcomp" ,r-multcomp)
10197 ("r-mvtnorm" ,r-mvtnorm)
10198 ("r-survival" ,r-survival)))
10199 (home-page "http://coin.r-forge.r-project.org")
10200 (synopsis "Conditional inference procedures in a permutation test framework")
10202 "This package provides conditional inference procedures for the general
10203 independence problem including two-sample, K-sample (non-parametric ANOVA),
10204 correlation, censored, ordered and multivariate problems.")
10205 (license license:gpl2)))
10207 (define-public r-bayesplot
10209 (name "r-bayesplot")
10214 (uri (cran-uri "bayesplot" version))
10217 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10218 (build-system r-build-system)
10220 `(("pandoc" ,pandoc)
10221 ("pandoc-citeproc" ,pandoc-citeproc)))
10223 `(("r-knitr" ,r-knitr)))
10225 `(("r-dplyr" ,r-dplyr)
10226 ("r-ggplot2" ,r-ggplot2)
10227 ("r-ggridges" ,r-ggridges)
10229 ("r-reshape2" ,r-reshape2)
10230 ("r-rlang" ,r-rlang)
10231 ("r-tibble" ,r-tibble)
10232 ("r-tidyselect" ,r-tidyselect)))
10233 (home-page "https://mc-stan.org/bayesplot")
10234 (synopsis "Plotting for Bayesian models")
10236 "This package provides plotting functions for posterior analysis, model
10237 checking, and MCMC diagnostics. The package is designed not only to provide
10238 convenient functionality for users, but also a common set of functions that
10239 can be easily used by developers working on a variety of R packages for
10240 Bayesian modeling.")
10241 (license license:gpl3+)))
10243 (define-public r-tmb
10250 (uri (cran-uri "TMB" version))
10253 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10254 (properties `((upstream-name . "TMB")))
10255 (build-system r-build-system)
10257 `(("r-matrix" ,r-matrix)
10258 ("r-rcppeigen" ,r-rcppeigen)))
10259 (home-page "http://tmb-project.org")
10260 (synopsis "Template model builder: a general random effect tool")
10262 "With this tool, a user should be able to quickly implement complex
10263 random effect models through simple C++ templates. The package combines
10264 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10265 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10266 from R) to obtain an efficient implementation of the applied Laplace
10267 approximation with exact derivatives. Key features are: Automatic sparseness
10268 detection, parallelism through BLAS and parallel user templates.")
10269 (license license:gpl2)))
10271 (define-public r-sjstats
10278 (uri (cran-uri "sjstats" version))
10280 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10281 (build-system r-build-system)
10283 `(("r-bayestestr" ,r-bayestestr)
10284 ("r-broom" ,r-broom)
10285 ("r-dplyr" ,r-dplyr)
10286 ("r-effectsize" ,r-effectsize)
10287 ("r-emmeans" ,r-emmeans)
10288 ("r-insight" ,r-insight)
10290 ("r-magrittr" ,r-magrittr)
10292 ("r-modelr" ,r-modelr)
10293 ("r-parameters" ,r-parameters)
10294 ("r-performance" ,r-performance)
10295 ("r-purrr" ,r-purrr)
10296 ("r-rlang" ,r-rlang)
10297 ("r-sjlabelled" ,r-sjlabelled)
10298 ("r-sjmisc" ,r-sjmisc)
10299 ("r-tidyr" ,r-tidyr)))
10300 (home-page "https://github.com/strengejacke/sjstats")
10301 (synopsis "Functions for common statistical computations")
10303 "This package provides a collection of convenient functions for common
10304 statistical computations, which are not directly provided by R's @code{base}
10305 or @code{stats} packages. This package aims at providing, first, shortcuts
10306 for statistical measures, which otherwise could only be calculated with
10307 additional effort. Second, these shortcut functions are generic, and can be
10308 applied not only to vectors, but also to other objects as well. The focus of
10309 most functions lies on summary statistics or fit measures for regression
10310 models, including generalized linear models, mixed effects models and Bayesian
10312 (license license:gpl3)))
10314 (define-public r-glmmtmb
10317 (version "1.0.2.1")
10321 (uri (cran-uri "glmmTMB" version))
10324 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10325 (properties `((upstream-name . "glmmTMB")))
10326 (build-system r-build-system)
10328 `(("r-lme4" ,r-lme4)
10329 ("r-matrix" ,r-matrix)
10331 ("r-rcppeigen" ,r-rcppeigen)
10334 `(("r-knitr" ,r-knitr))) ; for vignettes
10335 (home-page "https://github.com/glmmTMB")
10336 (synopsis "Generalized linear mixed models")
10338 "Fit linear and generalized linear mixed models with various extensions,
10339 including zero-inflation. The models are fitted using maximum likelihood
10340 estimation via the Template Model Builder. Random effects are assumed to be
10341 Gaussian on the scale of the linear predictor and are integrated out using the
10342 Laplace approximation. Gradients are calculated using automatic
10344 (license license:agpl3+)))
10346 (define-public r-bayestestr
10348 (name "r-bayestestr")
10353 (uri (cran-uri "bayestestR" version))
10356 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10357 (properties `((upstream-name . "bayestestR")))
10358 (build-system r-build-system)
10360 `(("r-insight" ,r-insight)))
10362 `(("r-knitr" ,r-knitr)))
10363 (home-page "https://github.com/easystats/bayestestR")
10364 (synopsis "Describe Bayesian models and posterior distributions")
10366 "This package provides utilities to understand and describe posterior
10367 distributions and Bayesian models. It includes point-estimates such as
10368 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10369 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10370 ROPE percentage and pd).")
10371 (license license:gpl3)))
10373 (define-public r-performance
10375 (name "r-performance")
10380 (uri (cran-uri "performance" version))
10383 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10384 (build-system r-build-system)
10386 `(("r-bayestestr" ,r-bayestestr)
10387 ("r-insight" ,r-insight)))
10388 (home-page "https://easystats.github.io/performance/")
10389 (synopsis "Assessment of regression models performance")
10391 "This package provides utilities for computing measures to assess model
10392 quality, which are not directly provided by R's @code{base} or @code{stats}
10393 packages. These include e.g. measures like r-squared, intraclass correlation
10394 coefficient, root mean squared error or functions to check models for
10395 overdispersion, singularity or zero-inflation and more. Functions apply to a
10396 large variety of regression models, including generalized linear models, mixed
10397 effects models and Bayesian models.")
10398 (license license:gpl3)))
10400 (define-public r-ggeffects
10402 (name "r-ggeffects")
10407 (uri (cran-uri "ggeffects" version))
10410 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10411 (build-system r-build-system)
10413 `(("r-insight" ,r-insight)
10415 ("r-sjlabelled" ,r-sjlabelled)))
10417 `(("r-knitr" ,r-knitr)))
10418 (home-page "https://github.com/strengejacke/ggeffects")
10419 (synopsis "Create tidy data frames of marginal effects for ggplot")
10421 "This package provides tools to compute marginal effects from statistical
10422 models and return the result as tidy data frames. These data frames are ready
10423 to use with the @code{ggplot2} package. Marginal effects can be calculated
10424 for many different models. Interaction terms, splines and polynomial terms
10425 are also supported. The two main functions are @code{ggpredict()} and
10426 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10427 results using @code{ggplot2}.")
10428 (license license:gpl3)))
10430 (define-public r-effectsize
10432 (name "r-effectsize")
10437 (uri (cran-uri "effectsize" version))
10440 "0mgkq12ym72ncakkjpkzkjglhksyhj3iw8v4a8fjgpf7prvn191g"))))
10441 (properties `((upstream-name . "effectsize")))
10442 (build-system r-build-system)
10444 `(("r-bayestestr" ,r-bayestestr)
10445 ("r-insight" ,r-insight)
10446 ("r-parameters" ,r-parameters)))
10448 `(("r-knitr" ,r-knitr)))
10449 (home-page "https://github.com/easystats/effectsize")
10450 (synopsis "Indices of effect size and standardized parameters")
10452 "This package provides utilities to work with indices of effect size and
10453 standardized parameters for a wide variety of models, allowing computation and
10454 conversion of indices such as Cohen's d, r, odds, etc.")
10455 (license license:gpl3)))
10457 (define-public r-sjplot
10464 (uri (cran-uri "sjPlot" version))
10466 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10467 (properties `((upstream-name . "sjPlot")))
10468 (build-system r-build-system)
10470 `(("r-bayestestr" ,r-bayestestr)
10471 ("r-dplyr" ,r-dplyr)
10472 ("r-effectsize" ,r-effectsize)
10473 ("r-ggeffects" ,r-ggeffects)
10474 ("r-ggplot2" ,r-ggplot2)
10475 ("r-insight" ,r-insight)
10476 ("r-knitr" ,r-knitr)
10478 ("r-parameters" ,r-parameters)
10479 ("r-performance" ,r-performance)
10480 ("r-purrr" ,r-purrr)
10481 ("r-rlang" ,r-rlang)
10482 ("r-scales" ,r-scales)
10483 ("r-sjlabelled" ,r-sjlabelled)
10484 ("r-sjmisc" ,r-sjmisc)
10485 ("r-sjstats" ,r-sjstats)
10486 ("r-tidyr" ,r-tidyr)))
10488 `(("r-knitr" ,r-knitr)))
10489 (home-page "https://strengejacke.github.io/sjPlot/")
10490 (synopsis "Data visualization for statistics in social science")
10492 "This package represents a collection of plotting and table output
10493 functions for data visualization. Results of various statistical
10494 analyses (that are commonly used in social sciences) can be visualized using
10495 this package, including simple and cross tabulated frequencies, histograms,
10496 box plots, (generalized) linear models, mixed effects models, principal
10497 component analysis and correlation matrices, cluster analyses, scatter plots,
10498 stacked scales, effects plots of regression models (including interaction
10499 terms) and much more. This package supports labelled data.")
10500 (license license:gpl3)))
10502 (define-public r-ini
10509 (uri (cran-uri "ini" version))
10512 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10513 (build-system r-build-system)
10514 (home-page "https://github.com/dvdscripter/ini")
10515 (synopsis "Read and write configuration files")
10517 "This package provides tools to parse simple @code{.ini} configuration
10518 files to an structured list. Users can manipulate this resulting list with
10519 @code{lapply()} functions. This same structured list can be used to write
10520 back to file after modifications.")
10521 (license license:gpl3)))
10523 (define-public r-gitcreds
10525 (name "r-gitcreds")
10530 (uri (cran-uri "gitcreds" version))
10533 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10534 (properties `((upstream-name . "gitcreds")))
10535 (build-system r-build-system)
10536 (inputs `(("git" ,git-minimal)))
10537 (native-inputs `(("r-knitr" ,r-knitr)))
10538 (home-page "https://github.com/r-lib/gitcreds")
10539 (synopsis "Query git credentials from R")
10541 "Query, set, and delete credentials from the git credential store.
10542 Manage GitHub tokens and other git credentials. This package is to be used by
10543 other packages that need to authenticate to GitHub and/or other git
10545 (license license:expat)))
10547 (define-public r-gh
10554 (uri (cran-uri "gh" version))
10557 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10558 (build-system r-build-system)
10561 ("r-gitcreds" ,r-gitcreds)
10564 ("r-jsonlite" ,r-jsonlite)))
10566 `(("r-knitr" ,r-knitr)))
10567 (home-page "https://github.com/r-lib/gh#readme")
10568 (synopsis "Access the GitHub API via R")
10570 "This package provides a minimal R client to access the GitHub API.")
10571 (license license:expat)))
10573 (define-public r-fs
10580 (uri (cran-uri "fs" version))
10583 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10584 (build-system r-build-system)
10586 `(("r-knitr" ,r-knitr)))
10587 (home-page "https://fs.r-lib.org")
10588 (synopsis "Cross-platform file system operations based on libuv")
10590 "This package provides a cross-platform interface to file system
10591 operations, built on top of the libuv C library.")
10592 (license license:gpl3)))
10594 (define-public r-clisymbols
10596 (name "r-clisymbols")
10601 (uri (cran-uri "clisymbols" version))
10604 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10605 (build-system r-build-system)
10606 (home-page "https://github.com/gaborcsardi/clisymbols")
10607 (synopsis "Unicode symbols at the R prompt")
10609 "This package provides a small subset of Unicode symbols, that are useful
10610 when building command line applications. They fall back to alternatives on
10611 terminals that do not support Unicode.")
10612 (license license:expat)))
10614 (define-public r-credentials
10616 (name "r-credentials")
10621 (uri (cran-uri "credentials" version))
10624 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10625 (properties `((upstream-name . "credentials")))
10626 (build-system r-build-system)
10629 (modify-phases %standard-phases
10630 (add-after 'unpack 'setenv-HOME
10632 ;; This is necessary because git looks for $HOME/.gitconfig
10633 (setenv "HOME" "/tmp")
10636 `(("git" ,git-minimal)))
10638 `(("r-askpass" ,r-askpass)
10640 ("r-jsonlite" ,r-jsonlite)
10641 ("r-openssl" ,r-openssl)
10644 `(("r-knitr" ,r-knitr)))
10645 (home-page "https://docs.ropensci.org/credentials/")
10646 (synopsis "Tools for managing SSH and Git credentials")
10648 "This package assists you in setting up and retrieving of HTTPS and SSH
10649 credentials for use with git and other services. For HTTPS remotes the
10650 package interfaces the @command{git-credential} utility which @command{git}
10651 uses to store HTTP usernames and passwords. For SSH remotes this package
10652 provides convenient functions to find or generate appropriate SSH keys. The
10653 package both helps the user to setup a local git installation, and also
10654 provides a back-end for git/ssh client libraries to authenticate with existing
10655 user credentials.")
10656 (license license:expat)))
10658 (define-public r-gert
10665 (uri (cran-uri "gert" version))
10668 "0ag2ia6cfb5drf3517lg5nhik1w0nv09a75wdy5jdciws1qra3d6"))))
10669 (properties `((upstream-name . "gert")))
10670 (build-system r-build-system)
10672 `(("libgit2" ,libgit2)
10675 `(("r-askpass" ,r-askpass)
10676 ("r-credentials" ,r-credentials)
10677 ("r-openssl" ,r-openssl)
10678 ("r-rstudioapi" ,r-rstudioapi)
10682 `(("pkg-config" ,pkg-config)
10683 ("r-knitr" ,r-knitr)))
10684 (home-page "https://docs.ropensci.org/gert/")
10685 (synopsis "Simple Git client for R")
10687 "This package provides a simple git client for R based on libgit2 with
10688 support for SSH and HTTPS remotes. All functions in gert use basic R data
10689 types (such as vectors and data-frames) for their arguments and return values.
10690 User credentials are shared with command line git through the
10691 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10692 (license license:expat)))
10694 (define-public r-usethis
10701 (uri (cran-uri "usethis" version))
10704 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10705 (build-system r-build-system)
10708 ("r-clipr" ,r-clipr)
10709 ("r-crayon" ,r-crayon)
10716 ("r-jsonlite" ,r-jsonlite)
10717 ("r-lifecycle" ,r-lifecycle)
10718 ("r-purrr" ,r-purrr)
10719 ("r-rappdirs" ,r-rappdirs)
10720 ("r-rlang" ,r-rlang)
10721 ("r-rprojroot" ,r-rprojroot)
10722 ("r-rstudioapi" ,r-rstudioapi)
10723 ("r-whisker" ,r-whisker)
10724 ("r-withr" ,r-withr)
10725 ("r-yaml" ,r-yaml)))
10726 (home-page "https://github.com/r-lib/usethis")
10727 (synopsis "Automate R package and project setup")
10729 "This package helps you to automate R package and project setup tasks
10730 that are otherwise performed manually. This includes setting up unit testing,
10731 test coverage, continuous integration, Git, GitHub integration, licenses,
10732 Rcpp, RStudio projects, and more.")
10733 (license license:gpl3)))
10735 (define-public r-sessioninfo
10737 (name "r-sessioninfo")
10742 (uri (cran-uri "sessioninfo" version))
10745 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10746 (build-system r-build-system)
10749 ("r-withr" ,r-withr)))
10750 (home-page "https://github.com/r-lib/sessioninfo#readme")
10751 (synopsis "R session information")
10753 "This package provides tools to query and print information about the
10754 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10755 more information about packages, and where they were installed from.")
10756 (license license:gpl2)))
10758 (define-public r-remotes
10765 (uri (cran-uri "remotes" version))
10768 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10769 (build-system r-build-system)
10771 `(("r-knitr" ,r-knitr)))
10772 (home-page "https://github.com/r-lib/remotes#readme")
10773 (synopsis "R package installation from remote repositories")
10775 "Download and install R packages stored in GitHub, BitBucket, or plain
10776 subversion or git repositories. This package is a lightweight replacement of
10777 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10778 the code was copied over from @code{devtools}.")
10779 (license license:gpl2+)))
10781 (define-public r-xopen
10788 (uri (cran-uri "xopen" version))
10791 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10792 (build-system r-build-system)
10794 `(("r-processx" ,r-processx)))
10795 (home-page "https://github.com/r-lib/xopen#readme")
10796 (synopsis "Open system files, URLs, anything")
10798 "This package provides a cross-platform solution to open files,
10799 directories or URLs with their associated programs.")
10800 (license license:expat)))
10802 (define-public r-rcmdcheck
10804 (name "r-rcmdcheck")
10809 (uri (cran-uri "rcmdcheck" version))
10812 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10813 (build-system r-build-system)
10815 `(("r-callr" ,r-callr)
10817 ("r-crayon" ,r-crayon)
10819 ("r-digest" ,r-digest)
10820 ("r-pkgbuild" ,r-pkgbuild)
10821 ("r-prettyunits" ,r-prettyunits)
10823 ("r-rprojroot" ,r-rprojroot)
10824 ("r-sessioninfo" ,r-sessioninfo)
10825 ("r-withr" ,r-withr)
10826 ("r-xopen" ,r-xopen)))
10827 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10828 (synopsis "Run R CMD check from R and capture results")
10830 "Run @code{R CMD check} from R programmatically, and capture the results
10831 of the individual checks.")
10832 (license license:expat)))
10834 (define-public r-rapportools
10836 (name "r-rapportools")
10841 (uri (cran-uri "rapportools" version))
10844 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10845 (build-system r-build-system)
10847 `(("r-pander" ,r-pander)
10849 ("r-reshape" ,r-reshape)))
10850 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10851 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10853 "This package provides helper functions that act as wrappers to more
10854 advanced statistical methods with the advantage of having sane defaults for
10856 (license license:agpl3+)))
10858 (define-public r-pander
10865 (uri (cran-uri "pander" version))
10868 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10869 (build-system r-build-system)
10871 `(("r-digest" ,r-digest)
10872 ("r-rcpp" ,r-rcpp)))
10873 (home-page "https://rapporter.github.io/pander")
10874 (synopsis "Render R objects into Pandoc's markdown")
10876 "The main aim of the pander R package is to provide a minimal and easy
10877 tool for rendering R objects into Pandoc's markdown. The package is also
10878 capable of exporting/converting complex Pandoc documents (reports) in various
10880 ;; This package is licensed under either the AGPLv3+ or the very rarely
10882 (license license:agpl3+)))
10884 (define-public r-summarytools
10886 (name "r-summarytools")
10891 (uri (cran-uri "summarytools" version))
10894 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10895 (build-system r-build-system)
10897 `(("r-base64enc" ,r-base64enc)
10898 ("r-checkmate" ,r-checkmate)
10899 ("r-dplyr" ,r-dplyr)
10900 ("r-htmltools" ,r-htmltools)
10901 ("r-lubridate" ,r-lubridate)
10902 ("r-magick" ,r-magick)
10903 ("r-matrixstats" ,r-matrixstats)
10904 ("r-pander" ,r-pander)
10906 ("r-rapportools" ,r-rapportools)
10907 ("r-tibble" ,r-tibble)
10908 ("r-tidyr" ,r-tidyr)))
10910 `(("r-knitr" ,r-knitr)))
10911 (home-page "https://github.com/dcomtois/summarytools")
10912 (synopsis "Tools to quickly and neatly summarize data")
10914 "This package provides tools for data frame summaries, cross-tabulations,
10915 weight-enabled frequency tables and common univariate statistics in concise
10916 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10917 good point-of-entry for exploring data, both for experienced and new R
10919 (license license:gpl2)))
10921 (define-public r-lsei
10928 (uri (cran-uri "lsei" version))
10931 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10932 (build-system r-build-system)
10934 `(("gfortran" ,gfortran)))
10935 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10936 (synopsis "Solve regression problems under equality/inequality constraints")
10938 "It contains functions that solve least squares linear regression
10939 problems under linear equality/inequality constraints. Functions for solving
10940 quadratic programming problems are also available, which transform such
10941 problems into least squares ones first.")
10942 (license license:gpl2+)))
10944 (define-public r-npsurv
10951 (uri (cran-uri "npsurv" version))
10954 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10955 (build-system r-build-system)
10957 `(("r-lsei" ,r-lsei)))
10958 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10959 (synopsis "Nonparametric survival analysis")
10961 "This package contains functions for non-parametric survival analysis of
10962 exact and interval-censored observations.")
10963 (license license:gpl2+)))
10965 (define-public r-clusteval
10967 (name "r-clusteval")
10972 (uri (cran-uri "clusteval" version))
10975 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10976 (build-system r-build-system)
10978 `(("r-mvtnorm" ,r-mvtnorm)
10979 ("r-rcpp" ,r-rcpp)))
10980 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10981 (synopsis "Evaluation of clustering algorithms")
10983 "This R package provides a suite of tools to evaluate clustering
10984 algorithms, clusterings, and individual clusters.")
10985 (license license:expat)))
10987 (define-public r-tweedie
10994 (uri (cran-uri "tweedie" version))
10997 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
10998 (build-system r-build-system)
10999 (native-inputs `(("gfortran" ,gfortran)))
11000 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11001 (synopsis "Evaluation of Tweedie exponential family models")
11003 "Maximum likelihood computations for Tweedie families, including the
11004 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11005 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11006 and related methods.")
11007 (license license:gpl2+)))
11009 (define-public r-rcppgsl
11016 (uri (cran-uri "RcppGSL" version))
11018 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11019 (properties `((upstream-name . "RcppGSL")))
11020 (build-system r-build-system)
11022 `(("r-rcpp" ,r-rcpp)
11024 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11025 (synopsis "Rcpp integration for GSL vectors and matrices")
11027 "The GNU Scientific Library (or GSL) is a collection of numerical
11028 routines for scientific computing. It is particularly useful for C and C++
11029 programs as it provides a standard C interface to a wide range of mathematical
11030 routines. There are over 1000 functions in total with an extensive test
11031 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11032 structures and R using concepts from Rcpp which is itself a package that eases
11033 the interfaces between R and C++.")
11034 (license license:gpl2+)))
11036 (define-public r-mvabund
11043 (uri (cran-uri "mvabund" version))
11046 "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
11047 (build-system r-build-system)
11049 `(("r-mass" ,r-mass)
11051 ("r-rcppgsl" ,r-rcppgsl)
11052 ("r-statmod" ,r-statmod)
11053 ("r-tweedie" ,r-tweedie)))
11054 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11055 (synopsis "Statistical methods for analysing multivariate abundance data")
11057 "This package provides a set of tools for displaying, modeling and
11058 analysing multivariate abundance data in community ecology.")
11059 (license license:lgpl2.1+)))
11061 (define-public r-afex
11068 (uri (cran-uri "afex" version))
11071 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11072 (build-system r-build-system)
11076 ("r-lmertest" ,r-lmertest)
11077 ("r-pbkrtest" ,r-pbkrtest)
11078 ("r-reshape2" ,r-reshape2)))
11080 `(("r-knitr" ,r-knitr)))
11081 (home-page "https://afex.singmann.science/")
11082 (synopsis "Analysis of factorial experiments")
11084 "This package provides convenience functions for analyzing factorial
11085 experiments using ANOVA or mixed models.")
11086 (license license:gpl2+)))
11088 (define-public r-lmertest
11090 (name "r-lmertest")
11095 (uri (cran-uri "lmerTest" version))
11098 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11099 (properties `((upstream-name . "lmerTest")))
11100 (build-system r-build-system)
11102 `(("r-ggplot2" ,r-ggplot2)
11105 ("r-numderiv" ,r-numderiv)))
11106 (home-page "https://github.com/runehaubo/lmerTestR")
11107 (synopsis "Tests in linear mixed effects models")
11109 "This package provides p-values in type I, II or III anova and summary
11110 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11111 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11112 package. Model selection methods include step, drop1 and anova-like tables
11113 for random effects (ranova). Methods for Least-Square means (LS-means) and
11114 tests of linear contrasts of fixed effects are also available.")
11115 (license license:gpl2+)))
11117 (define-public r-r2glmm
11124 (uri (cran-uri "r2glmm" version))
11127 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11128 (build-system r-build-system)
11130 `(("r-afex" ,r-afex)
11131 ("r-data-table" ,r-data-table)
11132 ("r-dplyr" ,r-dplyr)
11133 ("r-ggplot2" ,r-ggplot2)
11134 ("r-gridextra" ,r-gridextra)
11135 ("r-lmertest" ,r-lmertest)
11137 ("r-matrix" ,r-matrix)
11139 ("r-pbkrtest" ,r-pbkrtest)))
11140 (home-page "https://github.com/bcjaeger/r2glmm")
11141 (synopsis "Compute R squared for mixed (multilevel) models")
11143 "This package computes model and semi partial R squared with confidence
11144 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11145 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11146 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11148 (license license:gpl2)))
11150 (define-public r-weights
11157 (uri (cran-uri "weights" version))
11160 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11161 (build-system r-build-system)
11163 `(("r-gdata" ,r-gdata)
11164 ("r-hmisc" ,r-hmisc)
11165 ("r-mice" ,r-mice)))
11167 "https://cran.r-project.org/web/packages/weights/")
11168 (synopsis "Weighting and weighted statistics")
11169 (description "This package Provides a variety of functions for producing
11170 simple weighted statistics, such as weighted Pearson's correlations, partial
11171 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11172 includes some software for quickly recoding survey data and plotting point
11173 estimates from interaction terms in regressions (and multiply imputed
11174 regressions). NOTE: Weighted partial correlation calculations pulled to
11176 (license license:gpl2+)))
11178 (define-public r-rcppannoy
11180 (name "r-rcppannoy")
11185 (uri (cran-uri "RcppAnnoy" version))
11188 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11189 (properties `((upstream-name . "RcppAnnoy")))
11190 (build-system r-build-system)
11192 `(("r-rcpp" ,r-rcpp)))
11193 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11194 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11196 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11197 for efficient memory usage as well an ability to load from and save to disk.
11198 This package provides an R interface.")
11199 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11201 (license (list license:gpl2+ license:asl2.0))))
11203 (define-public r-rcpphnsw
11205 (name "r-rcpphnsw")
11210 (uri (cran-uri "RcppHNSW" version))
11213 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11214 (properties `((upstream-name . "RcppHNSW")))
11215 (build-system r-build-system)
11216 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11217 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11218 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11220 "Hnswlib is a C++ library for approximate nearest neighbors. This
11221 package provides a minimal R interface by relying on the Rcpp package.")
11222 ;; hnswlib is released under Version 2.0 of the Apache License.
11223 (license (list license:gpl3 license:asl2.0))))
11225 (define-public r-rcppparallel
11227 (name "r-rcppparallel")
11232 (uri (cran-uri "RcppParallel" version))
11235 "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki"))))
11236 (properties `((upstream-name . "RcppParallel")))
11237 (build-system r-build-system)
11238 (home-page "https://rcppcore.github.io/RcppParallel/")
11239 (synopsis "Parallel programming tools for Rcpp")
11241 "This package provides high level functions for parallel programming with
11242 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11243 the work of a standard serial @code{for} loop into a parallel one and the
11244 @code{parallelReduce()} function can be used for accumulating aggregates or
11246 (license license:gpl2)))
11248 (define-public r-ncdf4
11255 (uri (cran-uri "ncdf4" version))
11258 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11259 (build-system r-build-system)
11261 `(("netcdf" ,netcdf)
11263 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11264 (synopsis "R interface to Unidata netCDF format data files")
11266 "This package provides a high-level R interface to data files written
11267 using Unidata's netCDF library (version 4 or earlier), which are binary data
11268 files that are portable across platforms and include metadata information in
11269 addition to the data sets. Using this package, netCDF files can be opened and
11270 data sets read in easily. It is also easy to create new netCDF dimensions,
11271 variables, and files, in either version 3 or 4 format, and manipulate existing
11273 (license license:gpl3+)))
11275 (define-public r-biocmanager
11277 (name "r-biocmanager")
11278 (version "1.30.10")
11282 (uri (cran-uri "BiocManager" version))
11284 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
11285 (properties `((upstream-name . "BiocManager")))
11286 (build-system r-build-system)
11287 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11288 (synopsis "Access the Bioconductor project package repository")
11290 "This package provides a convenient tool to install and update
11291 Bioconductor packages.")
11292 (license license:artistic2.0)))
11294 (define-public r-rgl
11297 (version "0.105.22")
11301 (uri (cran-uri "rgl" version))
11304 "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz"))))
11305 (build-system r-build-system)
11307 `(("pkg-config" ,pkg-config)
11308 ("r-knitr" ,r-knitr)))
11310 `(("freetype" ,freetype)
11317 `(("r-crosstalk" ,r-crosstalk)
11318 ("r-htmltools" ,r-htmltools)
11319 ("r-htmlwidgets" ,r-htmlwidgets)
11320 ("r-jsonlite" ,r-jsonlite)
11321 ("r-knitr" ,r-knitr)
11322 ("r-magrittr" ,r-magrittr)
11323 ("r-manipulatewidget" ,r-manipulatewidget)
11324 ("r-shiny" ,r-shiny)))
11325 (home-page "https://r-forge.r-project.org/projects/rgl/")
11326 (synopsis "3D visualization using OpenGL")
11328 "This package provides medium to high level functions for 3D interactive graphics,
11329 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11330 as functions for constructing representations of geometric
11331 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11332 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11333 image formats, including PNG, Postscript, SVG, PGF.")
11334 ;; Any version of the GPL.
11335 (license (list license:gpl2+ license:gpl3+))))
11337 (define-public r-multicool
11339 (name "r-multicool")
11344 (uri (cran-uri "multicool" version))
11347 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11348 (build-system r-build-system)
11349 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11350 (home-page "https://cran.r-project.org/web/packages/multicool/")
11351 (synopsis "Permutations of multisets in cool-lex order")
11353 "This package provides a set of tools to permute multisets without loops
11354 or hash tables and to generate integer partitions. Cool-lex order is similar
11355 to colexicographical order.")
11356 (license license:gpl2)))
11358 (define-public r-misc3d
11365 (uri (cran-uri "misc3d" version))
11368 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11369 (build-system r-build-system)
11370 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11371 (synopsis "Miscellaneous 3D Plots")
11373 "This package provides a collection of miscellaneous 3d plots, including
11375 ;; Any version of the GPL.
11376 (license (list license:gpl2+ license:gpl3+))))
11378 (define-public r-ks
11385 (uri (cran-uri "ks" version))
11387 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11388 (build-system r-build-system)
11391 ("r-kernlab" ,r-kernlab)
11392 ("r-kernsmooth" ,r-kernsmooth)
11393 ("r-matrix" ,r-matrix)
11394 ("r-mclust" ,r-mclust)
11396 ("r-multicool" ,r-multicool)
11397 ("r-mvtnorm" ,r-mvtnorm)
11398 ("r-plot3d" ,r-plot3d)))
11399 (home-page "https://www.mvstat.net/tduong/")
11400 (synopsis "Kernel smoothing")
11402 "This package provides kernel smoothers for univariate and multivariate
11403 data, including density functions, density derivatives, cumulative
11404 distributions, modal clustering, discriminant analysis, and two-sample
11405 hypothesis testing.")
11406 ;; Either version of the GPL.
11407 (license (list license:gpl2 license:gpl3))))
11409 (define-public r-feature
11416 (uri (cran-uri "feature" version))
11419 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11420 (build-system r-build-system)
11423 ("r-plot3d" ,r-plot3d)))
11425 `(("r-knitr" ,r-knitr)))
11426 (home-page "https://www.mvstat.net/tduong/")
11427 (synopsis "Inferential feature significance for kernel density estimation")
11429 "The feature package contains functions to display and compute kernel
11430 density estimates, significant gradient and significant curvature regions.
11431 Significant gradient and/or curvature regions often correspond to significant
11432 features (e.g. local modes).")
11433 ;; Either version of the GPL.
11434 (license (list license:gpl2 license:gpl3))))
11436 (define-public r-arm
11443 (uri (cran-uri "arm" version))
11446 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11447 (build-system r-build-system)
11449 `(("r-abind" ,r-abind)
11451 ("r-hmisc" ,r-hmisc)
11454 ("r-matrix" ,r-matrix)
11455 ("r-nlme" ,r-nlme)))
11456 (home-page "https://cran.r-project.org/web/packages/arm/")
11457 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11459 "This package provides functions to accompany A. Gelman and J. Hill,
11460 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11461 University Press, 2007.")
11462 (license license:gpl3+)))
11464 (define-public r-circular
11466 (name "r-circular")
11471 (uri (cran-uri "circular" version))
11474 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11475 (build-system r-build-system)
11477 `(("r-boot" ,r-boot)
11478 ("r-mvtnorm" ,r-mvtnorm)))
11480 `(("gfortran" ,gfortran)))
11481 (home-page "https://cran.r-project.org/web/packages/circular/")
11482 (synopsis "Circular statistics")
11484 "This package provides tools for circular statistics, from \"Topics in
11485 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11487 (license license:gpl2+)))
11489 (define-public r-activity
11491 (name "r-activity")
11496 (uri (cran-uri "activity" version))
11499 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
11500 (build-system r-build-system)
11502 `(("r-circular" ,r-circular)
11503 ("r-insol" ,r-insol)
11504 ("r-pbapply" ,r-pbapply)))
11505 (home-page "https://cran.r-project.org/web/packages/activity/")
11506 (synopsis "Animal activity statistics")
11508 "This package provides functions to fit kernel density functions to
11509 animal activity time data; plot activity distributions; quantify overall
11510 levels of activity; statistically compare activity metrics through
11511 bootstrapping; and evaluate variation in linear variables with time (or other
11512 circular variables).")
11513 (license license:gpl3)))
11515 (define-public r-ouch
11522 (uri (cran-uri "ouch" version))
11525 "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q"))))
11526 (build-system r-build-system)
11527 (propagated-inputs `(("r-subplex" ,r-subplex)))
11528 (home-page "https://kingaa.github.io/ouch/")
11529 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11531 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11532 for evolution along a phylogenetic tree.")
11533 (license license:gpl2+)))
11535 (define-public r-fmsb
11542 (uri (cran-uri "fmsb" version))
11545 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11546 (build-system r-build-system)
11547 (home-page "http://minato.sip21c.org/msb/")
11548 (synopsis "Functions for medical statistics book with demographic data")
11550 "This package provides several utility functions for the book entitled
11551 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11552 Japan, 2007) with Japanese demographic data and some demographic analysis
11553 related functions.")
11554 (license license:gpl2+)))
11556 (define-public r-stabledist
11558 (name "r-stabledist")
11563 (uri (cran-uri "stabledist" version))
11566 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11567 (build-system r-build-system)
11568 (home-page "https://www.rmetrics.org")
11569 (synopsis "Stable distribution functions")
11571 "This package provides density, probability and quantile functions, and
11572 random number generation for (skew) stable distributions, using the
11573 parametrizations of Nolan.")
11574 (license license:gpl2+)))
11576 (define-public r-gsl
11583 (uri (cran-uri "gsl" version))
11586 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11587 (build-system r-build-system)
11590 (home-page "https://cran.r-project.org/web/packages/gsl")
11591 (synopsis "Wrapper for the GNU Scientific Library")
11593 "This package provides an R wrapper for the special functions and quasi
11594 random number generators of the GNU Scientific Library.")
11595 (license license:gpl2+)))
11597 (define-public r-adgoftest
11599 (name "r-adgoftest")
11604 (uri (cran-uri "ADGofTest" version))
11607 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11608 (properties `((upstream-name . "ADGofTest")))
11609 (build-system r-build-system)
11610 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11611 (synopsis "Anderson-Darling GoF test")
11613 "This package provides an implementation of the Anderson-Darling GoF test
11614 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11615 Anderson-Darling Distribution\".")
11616 ;; Any version of the GPL.
11617 (license license:gpl3+)))
11619 (define-public r-sodium
11626 (uri (cran-uri "sodium" version))
11629 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11630 (properties `((upstream-name . "sodium")))
11631 (build-system r-build-system)
11633 `(("libsodium" ,libsodium)))
11635 `(("pkg-config" ,pkg-config)
11636 ("r-knitr" ,r-knitr)))
11637 (home-page "https://github.com/jeroen/sodium")
11638 (synopsis "R bindings to the libsodium crypto library")
11640 "This package provides bindings to libsodium: a library for encryption,
11641 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11642 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11643 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11644 (license license:expat)))
11646 (define-public r-softimpute
11648 (name "r-softimpute")
11653 (uri (cran-uri "softImpute" version))
11656 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11657 (properties `((upstream-name . "softImpute")))
11658 (build-system r-build-system)
11660 `(("r-matrix" ,r-matrix)))
11662 `(("gfortran" ,gfortran)))
11663 (home-page "https://cran.r-project.org/web/packages/softImpute")
11664 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11666 "This package provides iterative methods for matrix completion that use
11667 nuclear-norm regularization. The package includes procedures for centering
11668 and scaling rows, columns or both, and for computing low-rank @dfn{single
11669 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11671 (license license:gpl2)))
11673 (define-public r-fftwtools
11675 (name "r-fftwtools")
11680 (uri (cran-uri "fftwtools" version))
11683 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
11684 (build-system r-build-system)
11685 (inputs `(("fftw" ,fftw)))
11687 `(("pkg-config" ,pkg-config)))
11688 (home-page "https://github.com/krahim/fftwtools")
11689 (synopsis "Wrapper for FFTW3")
11691 "This package provides a wrapper for several FFTW functions. It provides
11692 access to the two-dimensional FFT, the multivariate FFT, and the
11693 one-dimensional real to complex FFT using the FFTW3 library. The package
11694 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11695 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11696 The FFT functions have a parameter that allows them to not return the
11697 redundant complex conjugate when the input is real data.")
11698 (license license:gpl2+)))
11700 (define-public r-tiff
11707 (uri (cran-uri "tiff" version))
11710 "101n6x70fr1dhcwx53g3s8q1j4wh93y0388v1s1316f8558rxqxh"))))
11711 (build-system r-build-system)
11713 `(("libtiff" ,libtiff)
11714 ("libjpeg" ,libjpeg-turbo)
11716 (home-page "https://www.rforge.net/tiff/")
11717 (synopsis "Read and write TIFF images")
11719 "This package provides an easy and simple way to read, write and display
11720 bitmap images stored in the TIFF format. It can read and write both files and
11721 in-memory raw vectors.")
11722 ;; Either of these two license versions.
11723 (license (list license:gpl2 license:gpl3))))
11725 (define-public r-nlp
11732 (uri (cran-uri "NLP" version))
11735 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11736 (properties `((upstream-name . "NLP")))
11737 (build-system r-build-system)
11738 (home-page "https://cran.r-project.org/web/packages/NLP/")
11739 (synopsis "Natural language processing infrastructure")
11741 "This package provides basic classes and methods for Natural Language
11743 (license license:gpl3)))
11745 (define-public r-tm
11752 (uri (cran-uri "tm" version))
11755 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11756 (properties `((upstream-name . "tm")))
11757 (build-system r-build-system)
11763 ("r-xml2" ,r-xml2)))
11764 (home-page "http://tm.r-forge.r-project.org/")
11765 (synopsis "Text mining package")
11767 "This package provides a framework for text mining applications within R.")
11768 (license license:gpl3)))
11770 (define-public r-waveslim
11772 (name "r-waveslim")
11777 (uri (cran-uri "waveslim" version))
11780 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11781 (build-system r-build-system)
11783 `(("gfortran" ,gfortran)))
11784 (home-page "http://waveslim.blogspot.com")
11785 (synopsis "Basic wavelet routines for signal processing")
11787 "This package provides basic wavelet routines for time series (1D),
11788 image (2D) and array (3D) analysis. The code provided here is based on
11789 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11790 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11791 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11792 pairs (Selesnick 2001, 2002).")
11793 (license license:bsd-3)))
11795 (define-public r-wordcloud
11797 (name "r-wordcloud")
11802 (uri (cran-uri "wordcloud" version))
11805 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11806 (build-system r-build-system)
11808 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11810 ;; The "tm" package is only "suggested" according to CRAN, but the
11811 ;; wordcloud package cannot be loaded without it.
11813 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11814 (synopsis "Word clouds")
11816 "This package provides functionality to create pretty word clouds,
11817 visualize differences and similarity between documents, and avoid
11818 over-plotting in scatter plots with text.")
11819 (license license:lgpl2.1)))
11821 (define-public r-colorramps
11823 (name "r-colorramps")
11828 (uri (cran-uri "colorRamps" version))
11831 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11832 (properties `((upstream-name . "colorRamps")))
11833 (build-system r-build-system)
11834 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11835 (synopsis "Build color tables")
11836 (description "This package provides features to build gradient color
11838 ;; Any version of the GPL
11839 (license license:gpl3+)))
11841 (define-public r-tidytree
11843 (name "r-tidytree")
11848 (uri (cran-uri "tidytree" version))
11850 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11851 (build-system r-build-system)
11854 ("r-dplyr" ,r-dplyr)
11855 ("r-lazyeval" ,r-lazyeval)
11856 ("r-magrittr" ,r-magrittr)
11857 ("r-rlang" ,r-rlang)
11858 ("r-tibble" ,r-tibble)))
11860 `(("r-knitr" ,r-knitr)))
11861 (home-page "https://github.com/GuangchuangYu/tidytree")
11862 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11864 "Phylogenetic trees generally contain multiple components including nodes,
11865 edges, branches and associated data. This package provides an approach to
11866 convert tree objects to tidy data frames. It also provides tidy interfaces to
11867 manipulate tree data.")
11868 (license license:artistic2.0)))
11870 (define-public r-rvcheck
11877 (uri (cran-uri "rvcheck" version))
11879 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11880 (build-system r-build-system)
11882 `(("r-biocmanager" ,r-biocmanager)
11883 ("r-rlang" ,r-rlang)))
11884 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11885 (synopsis "R package version check")
11887 "This package provides tools to check the latest release version of R and
11888 R packages (on CRAN, Bioconductor or Github).")
11889 (license license:artistic2.0)))
11891 (define-public r-docopt
11898 (uri (cran-uri "docopt" version))
11901 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11902 (build-system r-build-system)
11903 (home-page "https://github.com/docopt/docopt.R")
11904 (synopsis "Command-line interface specification language")
11906 "This package enables you to define a command-line interface by just
11907 giving it a description in the specific format.")
11908 (license license:expat)))
11910 (define-public r-sparsesvd
11912 (name "r-sparsesvd")
11917 (uri (cran-uri "sparsesvd" version))
11920 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11921 (build-system r-build-system)
11922 (propagated-inputs `(("r-matrix" ,r-matrix)))
11923 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11924 (synopsis "Sparse truncated singular value decomposition")
11926 "This package provides a Wrapper around the SVDLIBC library
11927 for (truncated) singular value decomposition of a sparse matrix. Currently,
11928 only sparse real matrices in Matrix package format are supported.")
11929 ;; SVDLIBC is released under BSD-2. The R interface is released under
11931 (license (list license:bsd-3 license:bsd-2))))
11933 (define-public r-speedglm
11935 (name "r-speedglm")
11940 (uri (cran-uri "speedglm" version))
11943 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11944 (build-system r-build-system)
11946 `(("r-mass" ,r-mass)
11947 ("r-matrix" ,r-matrix)))
11948 (home-page "https://cran.r-project.org/web/packages/speedglm")
11949 (synopsis "Fit linear and generalized linear models to large data sets")
11951 "This package provides tools for fitting linear models and generalized
11952 linear models to large data sets by updating algorithms.")
11953 ;; Any version of the GPL
11954 (license license:gpl2+)))
11956 (define-public r-densityclust
11958 (name "r-densityclust")
11963 (uri (cran-uri "densityClust" version))
11966 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11967 (properties `((upstream-name . "densityClust")))
11968 (build-system r-build-system)
11971 ("r-ggplot2" ,r-ggplot2)
11972 ("r-ggrepel" ,r-ggrepel)
11973 ("r-gridextra" ,r-gridextra)
11974 ("r-rcolorbrewer" ,r-rcolorbrewer)
11976 ("r-rtsne" ,r-rtsne)))
11977 (home-page "https://cran.r-project.org/web/packages/densityClust")
11978 (synopsis "Clustering by fast search and find of density peaks")
11980 "This package provides an improved implementation (based on k-nearest
11981 neighbors) of the density peak clustering algorithm, originally described by
11982 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11983 large datasets (> 100,000 samples) very efficiently.")
11984 (license license:gpl2+)))
11986 (define-public r-combinat
11988 (name "r-combinat")
11993 (uri (cran-uri "combinat" version))
11996 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
11997 (build-system r-build-system)
11998 (home-page "https://cran.r-project.org/web/packages/combinat")
11999 (synopsis "Combinatorics utilities")
12000 (description "This package provides assorted routines for combinatorics.")
12001 (license license:gpl2)))
12003 (define-public r-qlcmatrix
12005 (name "r-qlcmatrix")
12010 (uri (cran-uri "qlcMatrix" version))
12013 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12014 (properties `((upstream-name . "qlcMatrix")))
12015 (build-system r-build-system)
12017 `(("r-docopt" ,r-docopt)
12018 ("r-matrix" ,r-matrix)
12020 ("r-sparsesvd" ,r-sparsesvd)))
12021 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12022 (synopsis "Sparse matrix functions for quantitative language comparison")
12024 "This package provides an extension of the functionality of the Matrix
12025 package for using sparse matrices. Some of the functions are very general,
12026 while other are highly specific for the special data format used for
12027 @dfn{quantitative language comparison} (QLC).")
12028 (license license:gpl3)))
12030 (define-public r-ddrtree
12037 (uri (cran-uri "DDRTree" version))
12040 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12041 (properties `((upstream-name . "DDRTree")))
12042 (build-system r-build-system)
12045 ("r-irlba" ,r-irlba)
12047 ("r-rcppeigen" ,r-rcppeigen)))
12048 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12049 (synopsis "Learning principal graphs with DDRTree")
12051 "This package provides an implementation of the framework of
12052 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12053 dimensional space while constructs a principal tree which passes through the
12054 middle of the data simultaneously. DDRTree shows superiority to
12055 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12056 intrinsic structure of single cell genomics data. In general, it could be
12057 used to reconstruct the temporal progression as well as the bifurcation
12058 structure of any data type.")
12059 (license license:asl2.0)))
12061 (define-public r-corpcor
12068 (uri (cran-uri "corpcor" version))
12071 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12072 (build-system r-build-system)
12073 (home-page "http://strimmerlab.org/software/corpcor/")
12074 (synopsis "Efficient estimation of covariance and (partial) correlation")
12076 "This package implements a James-Stein-type shrinkage estimator for the
12077 covariance matrix, with separate shrinkage for variances and correlations.
12078 Furthermore, functions are available for fast singular value decomposition,
12079 for computing the pseudoinverse, and for checking the rank and positive
12080 definiteness of a matrix.")
12081 (license license:gpl3+)))
12083 (define-public r-rspectra
12085 (name "r-rspectra")
12090 (uri (cran-uri "RSpectra" version))
12093 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12094 (properties `((upstream-name . "RSpectra")))
12095 (build-system r-build-system)
12097 `(("r-matrix" ,r-matrix)
12099 ("r-rcppeigen" ,r-rcppeigen)))
12100 (home-page "https://github.com/yixuan/RSpectra")
12101 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12103 "This package provides an R interface to the Spectra library for
12104 large-scale eigenvalue and SVD problems. It is typically used to compute a
12105 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12106 which is usually more efficient than @code{eigen()} if k << n.")
12108 (license license:mpl2.0)))
12110 (define-public r-vbsr
12117 (uri (cran-uri "vbsr" version))
12120 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12121 (build-system r-build-system)
12122 (home-page "https://cran.r-project.org/web/packages/vbsr")
12123 (synopsis "Variational Bayes spike regression regularized linear models")
12125 "This package provides an efficient algorithm for solving ultra-sparse
12126 regularized regression models using a variational Bayes algorithm with a spike
12127 prior. The algorithm is solved on a path, with coordinate updates, and is
12128 capable of generating very sparse models. Very general model
12129 diagnostics for controlling type-1 errors are also provided.")
12130 (license license:gpl2)))
12132 (define-public r-flare
12139 (uri (cran-uri "flare" version))
12142 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12143 (build-system r-build-system)
12145 `(("r-igraph" ,r-igraph)
12146 ("r-lattice" ,r-lattice)
12148 ("r-matrix" ,r-matrix)))
12149 (home-page "https://cran.r-project.org/web/packages/flare")
12150 (synopsis "Family of Lasso regression implementations")
12152 "This package provides implementations of a family of Lasso variants
12153 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12154 high dimensional sparse linear models.")
12155 (license license:gpl2)))
12157 (define-public r-lassopv
12164 (uri (cran-uri "lassopv" version))
12167 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12168 (build-system r-build-system)
12169 (propagated-inputs `(("r-lars" ,r-lars)))
12170 (home-page "https://github.com/lingfeiwang/lassopv")
12171 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12173 "This package enables you to estimate the p-values for predictors x
12174 against target variable y in Lasso regression, using the regularization
12175 strength when each predictor enters the active set of regularization path for
12176 the first time as the statistic.")
12177 (license license:gpl3)))
12179 (define-public r-splitstackshape
12181 (name "r-splitstackshape")
12186 (uri (cran-uri "splitstackshape" version))
12189 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12190 (build-system r-build-system)
12192 `(("r-data-table" ,r-data-table)))
12193 (home-page "https://github.com/mrdwab/splitstackshape")
12194 (synopsis "Stack and reshape datasets after splitting concatenated values")
12196 "Online data collection tools like Google Forms often export
12197 multiple-response questions with data concatenated in cells. The
12198 @code{concat.split} (cSplit) family of functions provided by this package
12199 splits such data into separate cells. This package also includes functions to
12200 stack groups of columns and to reshape wide data, even when the data are
12201 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12202 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12204 (license license:gpl3)))
12206 (define-public r-tfmpvalue
12208 (name "r-tfmpvalue")
12213 (uri (cran-uri "TFMPvalue" version))
12216 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12217 (properties `((upstream-name . "TFMPvalue")))
12218 (build-system r-build-system)
12219 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12220 (home-page "https://github.com/ge11232002/TFMPvalue")
12221 (synopsis "P-value computation for position weight matrices")
12223 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12224 identification from sequence/alignments, we are interested in the significance
12225 of certain match scores. TFMPvalue provides the accurate calculation of a
12226 p-value with a score threshold for position weight matrices, or the score with
12227 a given p-value. It is an interface to code originally made available by
12228 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12229 Touzet and Varre (2007).")
12230 (license license:gpl2)))
12232 (define-public r-rnifti
12239 (uri (cran-uri "RNifti" version))
12242 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12243 (properties `((upstream-name . "RNifti")))
12244 (build-system r-build-system)
12245 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12246 (home-page "https://github.com/jonclayden/RNifti")
12247 (synopsis "Fast R and C++ access to NIfTI images")
12249 "This package provides very fast read and write access to images stored
12250 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12251 compiled C and interpreted R code. It also provides a C/C++ API that can be
12252 used by other packages.")
12253 (license license:gpl2)))
12255 (define-public r-shades
12262 (uri (cran-uri "shades" version))
12265 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12266 (build-system r-build-system)
12267 (home-page "https://github.com/jonclayden/shades")
12268 (synopsis "Simple color manipulation")
12270 "This package provides functions for easily manipulating colors,
12271 creating color scales and calculating color distances.")
12272 (license license:bsd-3)))
12274 (define-public r-ore
12281 (uri (cran-uri "ore" version))
12283 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12284 (build-system r-build-system)
12285 (home-page "https://github.com/jonclayden/ore")
12286 (synopsis "R interface to the Onigmo regular expression library")
12288 "This package provides an alternative to R's built-in functionality for
12289 handling regular expressions, based on the Onigmo library. It offers
12290 first-class compiled regex objects, partial matching and function-based
12291 substitutions, amongst other features.")
12292 (license license:bsd-3)))
12294 (define-public r-reportr
12301 (uri (cran-uri "reportr" version))
12304 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12305 (build-system r-build-system)
12306 (propagated-inputs `(("r-ore" ,r-ore)))
12307 (home-page "https://github.com/jonclayden/reportr")
12308 (synopsis "General message and error reporting system")
12310 "This package provides a system for reporting messages, which offers
12311 certain useful features over the standard R system, such as the incorporation
12312 of output consolidation, message filtering, assertions, expression
12313 substitution, automatic generation of stack traces for debugging, and
12314 conditional reporting based on the current \"output level\".")
12315 (license license:gpl2)))
12317 (define-public r-tractor-base
12319 (name "r-tractor-base")
12320 (version "3.3.3.1")
12324 (uri (cran-uri "tractor.base" version))
12327 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12328 (properties `((upstream-name . "tractor.base")))
12329 (build-system r-build-system)
12332 ("r-reportr" ,r-reportr)
12333 ("r-rnifti" ,r-rnifti)
12334 ("r-shades" ,r-shades)))
12335 (home-page "https://www.tractor-mri.org.uk")
12336 (synopsis "Read, manipulate and visualize magnetic resonance images")
12338 "This package provides functions for working with magnetic resonance
12339 images. It supports reading and writing of popular file formats (DICOM,
12340 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12341 visualization; flexible image manipulation; metadata and sparse image
12343 (license license:gpl2)))
12345 (define-public r-grimport
12347 (name "r-grimport")
12352 (uri (cran-uri "grImport" version))
12355 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12356 (properties `((upstream-name . "grImport")))
12357 (build-system r-build-system)
12359 `(("ghostscript" ,ghostscript)))
12361 `(("r-xml" ,r-xml)))
12362 (home-page "https://cran.r-project.org/web/packages/grImport")
12363 (synopsis "Convert, import, and draw PostScript pictures")
12365 "This package provides functions for converting, importing, and drawing
12366 PostScript pictures in R plots.")
12367 (license license:gpl2+)))
12369 (define-public r-grimport2
12371 (name "r-grimport2")
12376 (uri (cran-uri "grImport2" version))
12379 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12380 (properties `((upstream-name . "grImport2")))
12381 (build-system r-build-system)
12383 `(("r-base64enc" ,r-base64enc)
12387 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12388 (synopsis "Import SVG graphics")
12390 "This package provides functions for importing external vector images and
12391 drawing them as part of R plots. This package is different from the
12392 @code{grImport} package because, where that package imports PostScript format
12393 images, this package imports SVG format images. Furthermore, this package
12394 imports a specific subset of SVG, so external images must be preprocessed
12395 using a package like @code{rsvg} to produce SVG that this package can import.
12396 SVG features that are not supported by R graphics, such as gradient fills, can
12397 be imported and then exported via the @code{gridSVG} package.")
12398 (license license:gpl2+)))
12400 (define-public r-kohonen
12407 (uri (cran-uri "kohonen" version))
12410 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12411 (build-system r-build-system)
12413 `(("r-rcpp" ,r-rcpp)))
12414 (home-page "https://cran.r-project.org/web/packages/kohonen")
12415 (synopsis "Supervised and unsupervised self-organising maps")
12417 "This package provides functions to train @dfn{self-organising
12418 maps} (SOMs). Also interrogation of the maps and prediction using trained
12419 maps are supported. The name of the package refers to Teuvo Kohonen, the
12420 inventor of the SOM.")
12421 (license license:gpl2+)))
12423 (define-public r-nnls
12430 (uri (cran-uri "nnls" version))
12433 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12434 (build-system r-build-system)
12435 (native-inputs `(("gfortran" ,gfortran)))
12436 (home-page "https://cran.r-project.org/web/packages/nnls")
12437 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12439 "This package provides an R interface to the Lawson-Hanson implementation
12440 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12441 the combination of non-negative and non-positive constraints.")
12442 (license license:gpl2+)))
12444 (define-public r-iso
12447 (version "0.0-18.1")
12451 (uri (cran-uri "Iso" version))
12454 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12455 (properties `((upstream-name . "Iso")))
12456 (build-system r-build-system)
12457 (native-inputs `(("gfortran" ,gfortran)))
12458 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12459 (synopsis "Functions to perform isotonic regression")
12461 "This package provides support for linear order and unimodal
12462 order (univariate) isotonic regression and bivariate isotonic regression with
12463 linear order on both variables.")
12464 (license license:gpl2+)))
12466 (define-public r-chemometricswithr
12468 (name "r-chemometricswithr")
12473 (uri (cran-uri "ChemometricsWithR" version))
12476 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12478 `((upstream-name . "ChemometricsWithR")))
12479 (build-system r-build-system)
12481 `(("r-devtools" ,r-devtools)
12482 ("r-kohonen" ,r-kohonen)
12485 (home-page "https://github.com/rwehrens/CWR")
12486 (synopsis "Chemometrics with R")
12488 "This package provides functions and scripts used in the book
12489 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12490 Life Sciences\" by Ron Wehrens, Springer (2011).")
12491 (license license:gpl2+)))
12493 (define-public r-als
12500 (uri (cran-uri "ALS" version))
12503 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12504 (properties `((upstream-name . "ALS")))
12505 (build-system r-build-system)
12508 ("r-nnls" ,r-nnls)))
12509 (home-page "https://cran.r-project.org/web/packages/ALS")
12510 (synopsis "Multivariate curve resolution alternating least squares")
12512 "Alternating least squares is often used to resolve components
12513 contributing to data with a bilinear structure; the basic technique may be
12514 extended to alternating constrained least squares. This package provides an
12515 implementation of @dfn{multivariate curve resolution alternating least
12516 squares} (MCR-ALS).
12518 Commonly applied constraints include unimodality, non-negativity, and
12519 normalization of components. Several data matrices may be decomposed
12520 simultaneously by assuming that one of the two matrices in the bilinear
12521 decomposition is shared between datasets.")
12522 (license license:gpl2+)))
12524 (define-public r-strucchange
12526 (name "r-strucchange")
12531 (uri (cran-uri "strucchange" version))
12534 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12535 (build-system r-build-system)
12537 `(("r-sandwich" ,r-sandwich)
12539 (home-page "https://cran.r-project.org/web/packages/strucchange")
12540 (synopsis "Testing, monitoring, and dating structural changes")
12542 "This package provides tools for testing, monitoring and dating
12543 structural changes in (linear) regression models. It features tests/methods
12544 from the generalized fluctuation test framework as well as from the F
12545 test (Chow test) framework. This includes methods to fit, plot and test
12546 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12547 statistics, respectively. It is possible to monitor incoming data online
12548 using fluctuation processes. Finally, the breakpoints in regression models
12549 with structural changes can be estimated together with confidence intervals.
12550 Emphasis is always given to methods for visualizing the data.")
12551 ;; Either of these two GPL versions
12552 (license (list license:gpl2 license:gpl3))))
12554 (define-public r-pixmap
12561 (uri (cran-uri "pixmap" version))
12564 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12565 (build-system r-build-system)
12566 (home-page "https://cran.r-project.org/web/packages/pixmap")
12567 (synopsis "Tools for bitmap images")
12569 "This package provides functions for importing, exporting, plotting and
12570 other manipulations of bitmapped images.")
12571 (license license:gpl2)))
12573 (define-public r-rapidjsonr
12575 (name "r-rapidjsonr")
12580 (uri (cran-uri "rapidjsonr" version))
12583 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12584 (build-system r-build-system)
12585 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12586 (synopsis "JSON parser")
12588 "This package provides JSON parsing capability through the Rapidjson
12590 (license license:expat)))
12592 (define-public r-ontologyindex
12594 (name "r-ontologyindex")
12599 (uri (cran-uri "ontologyIndex" version))
12602 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12603 (properties `((upstream-name . "ontologyIndex")))
12604 (build-system r-build-system)
12606 `(("r-knitr" ,r-knitr)))
12607 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12608 (synopsis "Functions for processing ontologies in R")
12610 "This package provides functions for reading ontologies into R as lists
12611 and manipulating sets of ontological terms.")
12612 (license license:gpl2+)))
12614 (define-public r-gargle
12621 (uri (cran-uri "gargle" version))
12624 "0hsqn4hf935wn6vk2pwym7la4sdvy271y4cashp38pg4hkpg9zph"))))
12625 (build-system r-build-system)
12630 ("r-jsonlite" ,r-jsonlite)
12631 ("r-rlang" ,r-rlang)
12632 ("r-withr" ,r-withr)))
12634 `(("r-knitr" ,r-knitr)))
12635 (home-page "https://gargle.r-lib.org")
12636 (synopsis "Utilities for working with Google APIs")
12638 "This package provides utilities for working with Google APIs. This
12639 includes functions and classes for handling common credential types and for
12640 preparing, executing, and processing HTTP requests.")
12641 (license license:expat)))
12643 (define-public r-bigrquery
12645 (name "r-bigrquery")
12650 (uri (cran-uri "bigrquery" version))
12653 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12654 (build-system r-build-system)
12656 `(("r-assertthat" ,r-assertthat)
12657 ("r-bit64" ,r-bit64)
12660 ("r-gargle" ,r-gargle)
12663 ("r-jsonlite" ,r-jsonlite)
12664 ("r-prettyunits" ,r-prettyunits)
12665 ("r-progress" ,r-progress)
12666 ("r-rapidjsonr" ,r-rapidjsonr)
12668 ("r-rlang" ,r-rlang)
12669 ("r-tibble" ,r-tibble)))
12670 (home-page "https://github.com/rstats-db/bigrquery")
12671 (synopsis "R interface to Google's BigQuery API")
12673 "This package provides an R interface to Google's BigQuery database.")
12674 (license license:gpl3)))
12676 (define-public r-gmp
12683 (uri (cran-uri "gmp" version))
12686 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12687 (build-system r-build-system)
12690 (modify-phases %standard-phases
12691 (add-after 'unpack 'set-CC
12692 (lambda _ (setenv "CC" "gcc") #t)))))
12693 (inputs `(("gmp" ,gmp)))
12694 (home-page "https://cran.r-project.org/web/packages/gmp")
12695 (synopsis "Multiple precision arithmetic")
12697 "This package supports multiple precision arithmetic (big integers and
12698 rationals, prime number tests, matrix computation), \"arithmetic without
12699 limitations\" using the GNU Multiple Precision library.")
12700 ;; Any version of the GPL.
12701 (license license:gpl3+)))
12703 (define-public r-rmpfr
12710 (uri (cran-uri "Rmpfr" version))
12713 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12714 (properties `((upstream-name . "Rmpfr")))
12715 (build-system r-build-system)
12720 `(("r-gmp" ,r-gmp)))
12722 `(("pkg-config" ,pkg-config)))
12723 (home-page "http://rmpfr.r-forge.r-project.org/")
12724 (synopsis "R bindings to the MPFR library")
12726 "This package supports arithmetic (via S4 classes and methods) for
12727 arbitrary precision floating point numbers, including transcendental
12728 functions. To this end, the package interfaces with the @dfn{Multiple
12729 Precision Floating-Point Reliable} (MPFR) library.")
12730 (license license:gpl2+)))
12732 (define-public r-assertive-base
12734 (name "r-assertive-base")
12739 (uri (cran-uri "assertive.base" version))
12742 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12744 `((upstream-name . "assertive.base")))
12745 (build-system r-build-system)
12746 (home-page "https://bitbucket.org/richierocks/assertive.base")
12747 (synopsis "Core of the assertive package")
12749 "This package provides a minimal set of predicates and assertions used by
12750 the assertive package. This is mainly for use by other package developers who
12751 want to include run-time testing features in their own packages.")
12752 (license license:gpl3+)))
12754 (define-public r-assertive-properties
12756 (name "r-assertive-properties")
12761 (uri (cran-uri "assertive.properties" version))
12764 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12766 `((upstream-name . "assertive.properties")))
12767 (build-system r-build-system)
12769 `(("r-assertive-base" ,r-assertive-base)))
12770 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12771 (synopsis "Assertions to check properties of variables")
12773 "This package provides a set of predicates and assertions for checking
12774 the properties of variables, such as length, names and attributes. This is
12775 mainly for use by other package developers who want to include run-time
12776 testing features in their own packages.")
12777 (license license:gpl3+)))
12779 (define-public r-assertive-numbers
12781 (name "r-assertive-numbers")
12786 (uri (cran-uri "assertive.numbers" version))
12789 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12791 `((upstream-name . "assertive.numbers")))
12792 (build-system r-build-system)
12794 `(("r-assertive-base" ,r-assertive-base)))
12795 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12796 (synopsis "Assertions to check properties of numbers")
12798 "This package provides a set of predicates and assertions for checking
12799 the properties of numbers. This is mainly for use by other package developers
12800 who want to include run-time testing features in their own packages.")
12801 (license license:gpl3+)))
12803 (define-public r-assertive-sets
12805 (name "r-assertive-sets")
12810 (uri (cran-uri "assertive.sets" version))
12813 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12815 `((upstream-name . "assertive.sets")))
12816 (build-system r-build-system)
12818 `(("r-assertive-base" ,r-assertive-base)))
12819 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12820 (synopsis "Assertions to check properties of sets")
12822 "This package provides a set of predicates and assertions for checking
12823 the properties of sets. This is mainly for use by other package developers
12824 who want to include run-time testing features in their own packages.")
12825 (license license:gpl3+)))
12827 (define-public r-assertive-matrices
12829 (name "r-assertive-matrices")
12834 (uri (cran-uri "assertive.matrices" version))
12837 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12839 `((upstream-name . "assertive.matrices")))
12840 (build-system r-build-system)
12842 `(("r-assertive-base" ,r-assertive-base)))
12843 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12844 (synopsis "Assertions to check properties of matrices")
12846 "This package provides a set of predicates and assertions for checking
12847 the properties of matrices. This is mainly for use by other package
12848 developers who want to include run-time testing features in their own
12850 (license license:gpl3+)))
12852 (define-public r-assertive-models
12854 (name "r-assertive-models")
12859 (uri (cran-uri "assertive.models" version))
12862 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12864 `((upstream-name . "assertive.models")))
12865 (build-system r-build-system)
12867 `(("r-assertive-base" ,r-assertive-base)))
12868 (home-page "https://bitbucket.org/richierocks/assertive.models")
12869 (synopsis "Assertions to check properties of models")
12871 "This package provides a set of predicates and assertions for checking
12872 the properties of models. This is mainly for use by other package developers
12873 who want to include run-time testing features in their own packages.")
12874 (license license:gpl3+)))
12876 (define-public r-assertive-reflection
12878 (name "r-assertive-reflection")
12883 (uri (cran-uri "assertive.reflection" version))
12886 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12888 `((upstream-name . "assertive.reflection")))
12889 (build-system r-build-system)
12891 `(("r-assertive-base" ,r-assertive-base)))
12892 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12893 (synopsis "Assertions for checking the state of R")
12895 "This package provides a set of predicates and assertions for checking
12896 the state and capabilities of R, the operating system it is running on, and
12897 the IDE being used. This is mainly for use by other package developers who
12898 want to include run-time testing features in their own packages.")
12899 (license license:gpl3+)))
12901 (define-public r-assertive-types
12903 (name "r-assertive-types")
12908 (uri (cran-uri "assertive.types" version))
12911 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12913 `((upstream-name . "assertive.types")))
12914 (build-system r-build-system)
12916 `(("r-assertive-base" ,r-assertive-base)
12917 ("r-assertive-properties" ,r-assertive-properties)
12918 ("r-codetools" ,r-codetools)))
12919 (home-page "https://bitbucket.org/richierocks/assertive.types")
12920 (synopsis "Assertions to check types of variables")
12922 "This package provides a set of predicates and assertions for checking
12923 the types of variables. This is mainly for use by other package developers
12924 who want to include run-time testing features in their own packages.")
12925 (license license:gpl3+)))
12927 (define-public r-assertive-files
12929 (name "r-assertive-files")
12934 (uri (cran-uri "assertive.files" version))
12937 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12939 `((upstream-name . "assertive.files")))
12940 (build-system r-build-system)
12942 `(("r-assertive-base" ,r-assertive-base)
12943 ("r-assertive-numbers" ,r-assertive-numbers)))
12944 (home-page "https://bitbucket.org/richierocks/assertive.files")
12945 (synopsis "Assertions to check properties of files")
12947 "This package provides a set of predicates and assertions for checking
12948 the properties of files and connections. This is mainly for use by other
12949 package developers who want to include run-time testing features in their own
12951 (license license:gpl3+)))
12953 (define-public r-assertive-code
12955 (name "r-assertive-code")
12960 (uri (cran-uri "assertive.code" version))
12963 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12965 `((upstream-name . "assertive.code")))
12966 (build-system r-build-system)
12968 `(("r-assertive-base" ,r-assertive-base)
12969 ("r-assertive-properties" ,r-assertive-properties)
12970 ("r-assertive-types" ,r-assertive-types)))
12971 (home-page "https://bitbucket.org/richierocks/assertive.code")
12972 (synopsis "Assertions to check properties of code")
12974 "This package provides a set of predicates and assertions for checking
12975 the properties of code. This is mainly for use by other package developers
12976 who want to include run-time testing features in their own packages.")
12977 (license license:gpl3+)))
12979 (define-public r-assertive-datetimes
12981 (name "r-assertive-datetimes")
12986 (uri (cran-uri "assertive.datetimes" version))
12989 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
12991 `((upstream-name . "assertive.datetimes")))
12992 (build-system r-build-system)
12994 `(("r-assertive-base" ,r-assertive-base)
12995 ("r-assertive-types" ,r-assertive-types)))
12996 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
12997 (synopsis "Assertions to check properties of dates and times")
12999 "This package provides a set of predicates and assertions for checking
13000 the properties of dates and times. This is mainly for use by other package
13001 developers who want to include run-time testing features in their own
13003 (license license:gpl3+)))
13005 (define-public r-assertive-strings
13007 (name "r-assertive-strings")
13012 (uri (cran-uri "assertive.strings" version))
13015 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13017 `((upstream-name . "assertive.strings")))
13018 (build-system r-build-system)
13020 `(("r-assertive-base" ,r-assertive-base)
13021 ("r-assertive-types" ,r-assertive-types)
13022 ("r-stringi" ,r-stringi)))
13023 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13024 (synopsis "Assertions to check properties of strings")
13026 "This package provides a set of predicates and assertions for checking
13027 the properties of strings. This is mainly for use by other package developers
13028 who want to include run-time testing features in their own packages.")
13029 (license license:gpl3+)))
13031 (define-public r-assertive-data-us
13033 (name "r-assertive-data-us")
13038 (uri (cran-uri "assertive.data.us" version))
13041 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13043 `((upstream-name . "assertive.data.us")))
13044 (build-system r-build-system)
13046 `(("r-assertive-base" ,r-assertive-base)
13047 ("r-assertive-strings" ,r-assertive-strings)))
13048 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13049 (synopsis "Assertions to check properties of strings")
13051 "This package provides a set of predicates and assertions for checking
13052 the properties of US-specific complex data types. This is mainly for use by
13053 other package developers who want to include run-time testing features in
13054 their own packages.")
13055 (license license:gpl3+)))
13057 (define-public r-assertive-data-uk
13059 (name "r-assertive-data-uk")
13064 (uri (cran-uri "assertive.data.uk" version))
13067 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13069 `((upstream-name . "assertive.data.uk")))
13070 (build-system r-build-system)
13072 `(("r-assertive-base" ,r-assertive-base)
13073 ("r-assertive-strings" ,r-assertive-strings)))
13074 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13075 (synopsis "Assertions to check properties of strings")
13077 "This package provides a set of predicates and assertions for checking
13078 the properties of UK-specific complex data types. This is mainly for use by
13079 other package developers who want to include run-time testing features in
13080 their own packages.")
13081 (license license:gpl3+)))
13083 (define-public r-assertive-data
13085 (name "r-assertive-data")
13090 (uri (cran-uri "assertive.data" version))
13093 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13095 `((upstream-name . "assertive.data")))
13096 (build-system r-build-system)
13098 `(("r-assertive-base" ,r-assertive-base)
13099 ("r-assertive-strings" ,r-assertive-strings)))
13100 (home-page "https://bitbucket.org/richierocks/assertive.data")
13101 (synopsis "Assertions to check properties of data")
13103 "This package provides a set of predicates and assertions for checking
13104 the properties of (country independent) complex data types. This is mainly
13105 for use by other package developers who want to include run-time testing
13106 features in their own packages.")
13107 (license license:gpl3+)))
13109 (define-public r-assertive
13111 (name "r-assertive")
13116 (uri (cran-uri "assertive" version))
13119 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13120 (build-system r-build-system)
13122 `(("r-assertive-base" ,r-assertive-base)
13123 ("r-assertive-code" ,r-assertive-code)
13124 ("r-assertive-data" ,r-assertive-data)
13125 ("r-assertive-data-uk" ,r-assertive-data-uk)
13126 ("r-assertive-data-us" ,r-assertive-data-us)
13127 ("r-assertive-datetimes" ,r-assertive-datetimes)
13128 ("r-assertive-files" ,r-assertive-files)
13129 ("r-assertive-matrices" ,r-assertive-matrices)
13130 ("r-assertive-models" ,r-assertive-models)
13131 ("r-assertive-numbers" ,r-assertive-numbers)
13132 ("r-assertive-properties" ,r-assertive-properties)
13133 ("r-assertive-reflection" ,r-assertive-reflection)
13134 ("r-assertive-sets" ,r-assertive-sets)
13135 ("r-assertive-strings" ,r-assertive-strings)
13136 ("r-assertive-types" ,r-assertive-types)
13137 ("r-knitr" ,r-knitr)))
13139 `(("r-knitr" ,r-knitr)))
13140 (home-page "https://bitbucket.org/richierocks/assertive")
13141 (synopsis "Readable check functions to ensure code integrity")
13143 "This package provides lots of predicates (@code{is_*} functions) to
13144 check the state of your variables, and assertions (@code{assert_*} functions)
13145 to throw errors if they aren't in the right form.")
13146 (license license:gpl3+)))
13148 (define-public r-dotcall64
13150 (name "r-dotcall64")
13155 (uri (cran-uri "dotCall64" version))
13158 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
13159 (properties `((upstream-name . "dotCall64")))
13160 (build-system r-build-system)
13161 (native-inputs `(("gfortran" ,gfortran)))
13162 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13163 (synopsis "Enhanced foreign function interface supporting long vectors")
13165 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13166 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13167 supports long vectors, arguments of type 64-bit integer, and provides a
13168 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13169 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13170 (license license:gpl2+)))
13172 (define-public r-spam
13179 (uri (cran-uri "spam" version))
13181 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13182 (build-system r-build-system)
13184 `(("r-dotcall64" ,r-dotcall64)))
13186 `(("gfortran" ,gfortran)
13187 ("r-knitr" ,r-knitr)))
13188 (home-page "https://www.math.uzh.ch/pages/spam/")
13189 (synopsis "Sparse matrix algebra")
13191 "This package provides a set of functions for sparse matrix algebra.
13192 Differences with other sparse matrix packages are:
13195 @item it only supports (essentially) one sparse matrix format;
13196 @item it is based on transparent and simple structure(s);
13197 @item it is tailored for MCMC calculations within G(M)RF;
13198 @item and it is fast and scalable (with the extension package @code{spam64}).
13200 ;; Either of these licenses
13201 (license (list license:bsd-3 license:lgpl2.0))))
13203 (define-public r-fields
13210 (uri (cran-uri "fields" version))
13212 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13213 (build-system r-build-system)
13215 `(("r-maps" ,r-maps)
13216 ("r-spam" ,r-spam)))
13218 `(("gfortran" ,gfortran)))
13219 (home-page "https://www.image.ucar.edu/fields")
13220 (synopsis "Tools for spatial data")
13222 "This is a package for curve, surface and function fitting with an
13223 emphasis on splines, spatial data and spatial statistics. The major methods
13224 include cubic, and thin plate splines, Kriging, and compactly supported
13225 covariance functions for large data sets.")
13226 (license license:gpl2+)))
13228 (define-public r-spatialextremes
13230 (name "r-spatialextremes")
13235 (uri (cran-uri "SpatialExtremes" version))
13238 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13240 `((upstream-name . "SpatialExtremes")))
13241 (build-system r-build-system)
13243 `(("r-fields" ,r-fields)
13244 ("r-maps" ,r-maps)))
13245 (home-page "http://spatialextremes.r-forge.r-project.org/")
13246 (synopsis "Modelling spatial extremes")
13248 "This package provides tools for the statistical modelling of spatial
13249 extremes using max-stable processes, copula or Bayesian hierarchical models.
13250 More precisely, this package allows (conditional) simulations from various
13251 parametric max-stable models, analysis of the extremal spatial dependence, the
13252 fitting of such processes using composite likelihoods or least square (simple
13253 max-stable processes only), model checking and selection and prediction.")
13254 (license license:gpl2+)))
13256 (define-public r-drc
13263 (uri (cran-uri "drc" version))
13266 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13267 (build-system r-build-system)
13270 ("r-gtools" ,r-gtools)
13272 ("r-multcomp" ,r-multcomp)
13273 ("r-plotrix" ,r-plotrix)
13274 ("r-scales" ,r-scales)))
13275 (home-page "https://cran.r-project.org/web/packages/drc")
13276 (synopsis "Analysis of dose-response curves")
13278 "This package provides a suite of flexible and versatile model fitting
13279 and after-fitting functions for the analysis of dose-response data.")
13280 (license license:gpl2+)))
13282 (define-public r-rmeta
13289 (uri (cran-uri "rmeta" version))
13292 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13293 (build-system r-build-system)
13294 (home-page "https://cran.r-project.org/web/packages/rmeta")
13295 (synopsis "Tools for meta-analysis")
13297 "This package provides functions for simple fixed and random effects
13298 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13299 draws standard summary plots, funnel plots, and computes summaries and tests
13300 for association and heterogeneity.")
13301 (license license:gpl2)))
13303 (define-public r-bootstrap
13305 (name "r-bootstrap")
13310 (uri (cran-uri "bootstrap" version))
13313 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13314 (build-system r-build-system)
13315 (native-inputs `(("gfortran" ,gfortran)))
13316 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13317 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13319 "This package provides software and data for the book \"An Introduction
13320 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13321 This package is primarily provided for projects already based on it, and for
13322 support of the book. New projects should preferentially use the recommended
13323 package \"boot\".")
13324 (license license:bsd-3)))
13326 (define-public r-survivalroc
13328 (name "r-survivalroc")
13333 (uri (cran-uri "survivalROC" version))
13336 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13337 (properties `((upstream-name . "survivalROC")))
13338 (build-system r-build-system)
13339 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13340 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13342 "Compute time-dependent ROC curve from censored survival data using
13343 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13344 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13345 (license license:gpl2+)))
13347 (define-public r-longitudinal
13349 (name "r-longitudinal")
13354 (uri (cran-uri "longitudinal" version))
13357 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13358 (build-system r-build-system)
13359 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13360 (home-page "http://strimmerlab.org/software/longitudinal/")
13361 (synopsis "Analysis of multiple time course data")
13363 "This package contains general data structures and functions for
13364 longitudinal data with multiple variables, repeated measurements, and
13365 irregularly spaced time points. It also implements a shrinkage estimator of
13366 dynamical correlation and dynamical covariance.")
13367 (license license:gpl3+)))
13369 (define-public r-genenet
13376 (uri (cran-uri "GeneNet" version))
13379 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13380 (properties `((upstream-name . "GeneNet")))
13381 (build-system r-build-system)
13383 `(("r-corpcor" ,r-corpcor)
13384 ("r-fdrtool" ,r-fdrtool)
13385 ("r-longitudinal" ,r-longitudinal)))
13386 (home-page "http://strimmerlab.org/software/genenet/")
13387 (synopsis "Modeling and inferring gene networks")
13389 "This package analyzes gene expression (time series) data with focus on
13390 the inference of gene networks. In particular, GeneNet implements the methods
13391 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13392 for learning large-scale gene association networks (including assignment of
13393 putative directions).")
13394 (license license:gpl3+)))
13396 (define-public r-rbamtools
13398 (name "r-rbamtools")
13399 (version "2.16.17")
13403 (uri (cran-uri "rbamtools" version))
13406 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13407 (build-system r-build-system)
13408 (inputs `(("zlib" ,zlib)))
13410 `(("r-refgenome" ,r-refgenome)))
13411 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13412 (synopsis "Read and write BAM (binary alignment) files")
13414 "This package provides an R interface to functions of the SAMtools
13416 (license license:artistic2.0)))
13418 (define-public r-protviz
13425 (uri (cran-uri "protViz" version))
13428 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13429 (properties `((upstream-name . "protViz")))
13430 (build-system r-build-system)
13431 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13432 (home-page "https://github.com/protViz/protViz/")
13433 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13435 "This package helps with quality checks, visualizations and analysis of
13436 mass spectrometry data, coming from proteomics experiments. The package is
13437 developed, tested and used at the Functional Genomics Center Zurich, where it
13438 is used mainly for prototyping, teaching, and having fun with proteomics data.
13439 But it can also be used to do data analysis for small scale data sets.")
13440 (license license:gpl3)))
13442 (define-public r-cmprsk
13449 (uri (cran-uri "cmprsk" version))
13451 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13452 (build-system r-build-system)
13454 `(("r-survival" ,r-survival)))
13456 `(("gfortran" ,gfortran)))
13457 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13458 (synopsis "Subdistribution analysis of competing risks")
13460 "This package provides tool for estimation, testing and regression
13461 modeling of subdistribution functions in competing risks, as described in
13462 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13463 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13464 A proportional hazards model for the subdistribution of a competing risk,
13465 JASA, 94:496-509.")
13466 (license license:gpl2+)))
13468 (define-public r-etm
13475 (uri (cran-uri "etm" version))
13478 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13479 (build-system r-build-system)
13481 `(("r-data-table" ,r-data-table)
13482 ("r-lattice" ,r-lattice)
13484 ("r-rcpparmadillo" ,r-rcpparmadillo)
13485 ("r-survival" ,r-survival)))
13486 (home-page "https://cran.r-project.org/web/packages/etm")
13487 (synopsis "Empirical transition matrix")
13489 "The @dfn{empirical transition matrix} (etm) package estimates
13490 the matrix of transition probabilities for any time-inhomogeneous multistate
13491 model with finite state space using the Aalen-Johansen estimator.")
13492 (license license:expat)))
13494 (define-public r-epi
13501 (uri (cran-uri "Epi" version))
13504 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
13505 (properties `((upstream-name . "Epi")))
13506 (build-system r-build-system)
13508 `(("r-cmprsk" ,r-cmprsk)
13509 ("r-data-table" ,r-data-table)
13510 ("r-dplyr" ,r-dplyr)
13513 ("r-matrix" ,r-matrix)
13515 ("r-numderiv" ,r-numderiv)
13517 ("r-purrr" ,r-purrr)
13518 ("r-survival" ,r-survival)
13520 (home-page "https://BendixCarstensen.com/Epi/")
13521 (synopsis "Statistical analysis in epidemiology")
13523 "This package provides functions for demographic and epidemiological
13524 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13525 particular representation, manipulation and simulation of multistate data -
13526 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13527 @code{etm} and @code{cmprsk} packages. It also contains functions for
13528 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13529 data and some useful functions for tabulation and plotting, as well as a
13530 number of epidemiological data sets.")
13531 (license license:gpl2)))
13533 (define-public r-ppls
13536 (version "1.6-1.1")
13540 (uri (cran-uri "ppls" version))
13543 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13544 (build-system r-build-system)
13545 (propagated-inputs `(("r-mass" ,r-mass)))
13546 (home-page "https://cran.r-project.org/web/packages/ppls")
13547 (synopsis "Penalized partial least squares")
13549 "This package contains linear and nonlinear regression methods based on
13550 partial least squares and penalization techniques. Model parameters are
13551 selected via cross-validation, and confidence intervals ans tests for the
13552 regression coefficients can be conducted via jackknifing.")
13553 (license license:gpl2+)))
13555 (define-public r-huge
13558 (version "1.3.4.1")
13562 (uri (cran-uri "huge" version))
13564 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13565 (build-system r-build-system)
13567 `(("r-igraph" ,r-igraph)
13569 ("r-matrix" ,r-matrix)
13571 ("r-rcppeigen" ,r-rcppeigen)))
13572 (home-page "https://cran.r-project.org/web/packages/huge")
13573 (synopsis "High-dimensional undirected graph estimation")
13575 "This package provides a general framework for high-dimensional
13576 undirected graph estimation. It integrates data preprocessing, neighborhood
13577 screening, graph estimation, and model selection techniques into a pipeline.")
13578 (license license:gpl2)))
13580 (define-public r-parcor
13587 (uri (cran-uri "parcor" version))
13590 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13591 (build-system r-build-system)
13594 ("r-genenet" ,r-genenet)
13595 ("r-glmnet" ,r-glmnet)
13597 ("r-ppls" ,r-ppls)))
13598 (home-page "https://cran.r-project.org/web/packages/parcor")
13599 (synopsis "Regularized estimation of partial correlation matrices")
13601 "This package estimates the matrix of partial correlations based on
13602 different regularized regression methods: lasso, adaptive lasso, PLS, and
13603 Ridge Regression. In addition, the package provides model selection for
13604 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13605 (license license:gpl2+)))
13607 (define-public r-mcmc
13614 (uri (cran-uri "mcmc" version))
13617 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13618 (build-system r-build-system)
13619 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13620 (synopsis "Markov chain Monte Carlo")
13622 "This package simulates continuous distributions of random vectors using
13623 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13624 function that evaluates the log unnormalized density. Algorithms are random
13625 walk Metropolis algorithm (function @code{metrop}), simulated
13626 tempering (function @code{temper}), and morphometric random walk
13627 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13628 by change of variable.")
13629 (license license:expat)))
13631 (define-public r-listenv
13638 (uri (cran-uri "listenv" version))
13641 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13642 (build-system r-build-system)
13644 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13645 (home-page "https://github.com/HenrikBengtsson/listenv")
13646 (synopsis "Environments behaving (almost) as lists")
13648 "This package implements list environments. List environments are
13649 environments that have list-like properties. For instance, the elements of a
13650 list environment are ordered and can be accessed and iterated over using index
13652 (license license:lgpl2.1+)))
13654 (define-public r-globals
13661 (uri (cran-uri "globals" version))
13664 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13665 (build-system r-build-system)
13667 `(("r-codetools" ,r-codetools)))
13668 (home-page "https://github.com/HenrikBengtsson/globals")
13669 (synopsis "Identify global objects in R expressions")
13671 "This package provides tools to identify global (\"unknown\" or \"free\")
13672 objects in R expressions by code inspection using various strategies, e.g.
13673 conservative or liberal. The objective of this package is to make it as
13674 simple as possible to identify global objects for the purpose of exporting
13675 them in distributed compute environments.")
13676 (license license:lgpl2.1+)))
13678 (define-public r-parallelly
13680 (name "r-parallelly")
13685 (uri (cran-uri "parallelly" version))
13688 "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6"))))
13689 (properties `((upstream-name . "parallelly")))
13690 (build-system r-build-system)
13691 (home-page "https://github.com/HenrikBengtsson/parallelly")
13692 (synopsis "Enhancements of the parallel package")
13694 "This package provides utility functions that enhance the @code{parallel}
13695 package and support the built-in parallel backends of the @code{future}
13696 package. For example, @code{availableCores} gives the number of CPU cores
13697 available to your R process as given by R options and environment variables,
13698 including those set by job schedulers on high-performance compute clusters.
13699 If none is set, it will fall back to @code{parallel::detectCores}. Another
13700 example is @code{makeClusterPSOCK}, which is backward compatible with
13701 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13702 remote cluster workers without the need for configuring the firewall to do
13703 port-forwarding to your local computer.")
13704 (license license:lgpl2.1+)))
13706 (define-public r-future
13713 (uri (cran-uri "future" version))
13716 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13717 (build-system r-build-system)
13719 `(("r-digest" ,r-digest)
13720 ("r-globals" ,r-globals)
13721 ("r-listenv" ,r-listenv)
13722 ("r-parallelly" ,r-parallelly)))
13724 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13725 (home-page "https://github.com/HenrikBengtsson/future")
13726 (synopsis "Unified parallel and distributed processing in R")
13728 "The purpose of this package is to provide a lightweight and unified
13729 Future API for sequential and parallel processing of R expression via futures.
13730 This package implements sequential, multicore, multisession, and cluster
13731 futures. With these, R expressions can be evaluated on the local machine, in
13732 parallel a set of local machines, or distributed on a mix of local and remote
13733 machines. Extensions to this package implement additional backends for
13734 processing futures via compute cluster schedulers etc. Because of its unified
13735 API, there is no need to modify any code in order to switch from sequential on
13736 the local machine to, say, distributed processing on a remote compute cluster.")
13737 (license license:lgpl2.1+)))
13739 (define-public r-future-apply
13741 (name "r-future-apply")
13746 (uri (cran-uri "future.apply" version))
13749 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13750 (properties `((upstream-name . "future.apply")))
13751 (build-system r-build-system)
13753 `(("r-future" ,r-future)
13754 ("r-globals" ,r-globals)))
13756 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13757 (home-page "https://github.com/HenrikBengtsson/future.apply")
13758 (synopsis "Apply function to elements in parallel using futures")
13760 "This package provides implementations of @code{apply()},
13761 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13762 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13763 can be resolved using any future-supported backend, e.g. parallel on the local
13764 machine or distributed on a compute cluster.")
13765 (license license:gpl2+)))
13767 (define-public r-rsvd
13774 (uri (cran-uri "rsvd" version))
13777 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13778 (build-system r-build-system)
13780 `(("r-matrix" ,r-matrix)))
13781 (home-page "https://github.com/erichson/rSVD")
13782 (synopsis "Randomized singular value decomposition")
13784 "Low-rank matrix decompositions are fundamental tools and widely used for
13785 data analysis, dimension reduction, and data compression. Classically, highly
13786 accurate deterministic matrix algorithms are used for this task. However, the
13787 emergence of large-scale data has severely challenged our computational
13788 ability to analyze big data. The concept of randomness has been demonstrated
13789 as an effective strategy to quickly produce approximate answers to familiar
13790 problems such as the @dfn{singular value decomposition} (SVD). This package
13791 provides several randomized matrix algorithms such as the randomized singular
13792 value decomposition (@code{rsvd}), randomized principal component
13793 analysis (@code{rpca}), randomized robust principal component
13794 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13795 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13796 functions are provided.")
13797 (license license:gpl3+)))
13799 (define-public r-sloop
13806 (uri (cran-uri "sloop" version))
13809 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13810 (build-system r-build-system)
13812 `(("r-codetools" ,r-codetools)
13813 ("r-crayon" ,r-crayon)
13814 ("r-purrr" ,r-purrr)
13815 ("r-rlang" ,r-rlang)
13816 ("r-tibble" ,r-tibble)))
13817 (home-page "https://github.com/r-lib/sloop")
13818 (synopsis "Helpers for object-oriented programming in R")
13820 "This package provides a collection of helper functions designed to
13821 help you to better understand object oriented programming in R, particularly
13823 (license license:gpl3)))
13825 (define-public r-capushe
13832 (uri (cran-uri "capushe" version))
13835 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13836 (build-system r-build-system)
13837 (propagated-inputs `(("r-mass" ,r-mass)))
13838 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13839 (synopsis "Calibrating penalties using slope heuristics")
13841 "This package provides tools for the calibration of penalized criteria
13842 for model selection. The calibration methods available are based on the slope
13844 (license license:gpl2+)))
13846 (define-public r-dorng
13853 (uri (cran-uri "doRNG" version))
13856 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13857 (properties `((upstream-name . "doRNG")))
13858 (build-system r-build-system)
13860 `(("r-foreach" ,r-foreach)
13861 ("r-iterators" ,r-iterators)
13862 ("r-rngtools" ,r-rngtools)))
13863 (home-page "https://renozao.github.io/doRNG/")
13864 (synopsis "Generic reproducible parallel backend for foreach loops")
13866 "This package provides functions to perform reproducible parallel
13867 @code{foreach} loops, using independent random streams as generated by
13868 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13869 convert standard @code{%dopar%} loops into fully reproducible loops,
13870 independently of the number of workers, the task scheduling strategy, or the
13871 chosen parallel environment and associated foreach backend.")
13872 (license license:gpl2+)))
13874 (define-public r-blockmodeling
13876 (name "r-blockmodeling")
13881 (uri (cran-uri "blockmodeling" version))
13884 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13885 (build-system r-build-system)
13887 `(("r-matrix" ,r-matrix)))
13888 (native-inputs `(("gfortran" ,gfortran)))
13889 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13890 (synopsis "Generalized and classical blockmodeling of valued networks")
13892 "This package is primarily meant as an implementation of generalized
13893 blockmodeling for valued networks. In addition, measures of similarity or
13894 dissimilarity based on structural equivalence and regular equivalence (REGE
13895 algorithms) can be computed and partitioned matrices can be plotted.")
13896 (license license:gpl2+)))
13898 (define-public r-upsetr
13905 (uri (cran-uri "UpSetR" version))
13908 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13909 (properties `((upstream-name . "UpSetR")))
13910 (build-system r-build-system)
13912 `(("r-ggplot2" ,r-ggplot2)
13913 ("r-gridextra" ,r-gridextra)
13915 ("r-scales" ,r-scales)))
13916 (home-page "https://github.com/hms-dbmi/UpSetR")
13917 (synopsis "Visualize intersecting sets")
13919 "This package provides a more scalable alternative to Venn and Euler
13920 diagrams for visualizing intersecting sets. Create visualizations of
13921 intersecting sets using a novel matrix design, along with visualizations of
13922 several common set, element and attribute related tasks.")
13923 (license license:expat)))
13925 ;; This package includes a JavaScript file, which is not minified. When
13926 ;; upgrading please check that there are no new minified JavaScript files.
13927 (define-public r-shinybs
13934 (uri (cran-uri "shinyBS" version))
13937 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13938 (properties `((upstream-name . "shinyBS")))
13939 (build-system r-build-system)
13940 ;; The tests spawn Shiny browser apps. They cannot be run
13941 ;; non-interactively.
13942 (arguments '(#:tests? #f))
13944 `(("r-htmltools" ,r-htmltools)
13945 ("r-shiny" ,r-shiny)))
13946 (home-page "https://ebailey78.github.io/shinyBS/")
13947 (synopsis "Twitter Bootstrap components for Shiny")
13949 "This package adds additional Twitter Bootstrap components to Shiny.")
13950 (license license:gpl3)))
13952 (define-public r-shinyjqui
13954 (name "r-shinyjqui")
13959 (uri (cran-uri "shinyjqui" version))
13962 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
13965 (delete-file "inst/www/shinyjqui.min.js")))))
13966 (properties `((upstream-name . "shinyjqui")))
13967 (build-system r-build-system)
13970 (modify-phases %standard-phases
13971 (add-after 'unpack 'process-javascript
13972 (lambda* (#:key inputs #:allow-other-keys)
13973 (with-directory-excursion "inst/www/"
13974 (let ((source "shinyjqui.js")
13975 (target "shinyjqui.min.js"))
13976 (format #true "Processing ~a --> ~a~%"
13978 (invoke "esbuild" source "--minify"
13979 (string-append "--outfile=" target)))))))))
13981 `(("r-htmltools" ,r-htmltools)
13982 ("r-htmlwidgets" ,r-htmlwidgets)
13983 ("r-jsonlite" ,r-jsonlite)
13984 ("r-shiny" ,r-shiny)))
13986 `(("r-knitr" ,r-knitr)
13987 ("esbuild" ,esbuild)))
13988 (home-page "https://github.com/yang-tang/shinyjqui")
13989 (synopsis "jQuery UI interactions and effects for Shiny")
13991 "This is an extension to Shiny that brings interactions and animation
13992 effects from the jQuery UI library.")
13993 (license license:expat)))
13995 (define-public r-outliers
13997 (name "r-outliers")
14002 (uri (cran-uri "outliers" version))
14005 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14006 (build-system r-build-system)
14007 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14008 (synopsis "Tests for outliers")
14010 "This package provides a collection of some tests commonly used for
14011 identifying outliers.")
14012 (license license:gpl2+)))
14014 (define-public r-bayesm
14021 (uri (cran-uri "bayesm" version))
14023 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14024 (build-system r-build-system)
14026 `(("r-rcpp" ,r-rcpp)
14027 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14028 (home-page "http://www.perossi.org/home/bsm-1")
14029 (synopsis "Bayesian inference for marketing/micro-econometrics")
14031 "This package covers many important models used in marketing and
14032 micro-econometrics applications, including Bayes Regression (univariate or
14033 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14034 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14035 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14036 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14037 Estimation with normal base, Hierarchical Linear Models with normal prior and
14038 covariates, Hierarchical Linear Models with a mixture of normals prior and
14039 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14040 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14041 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14042 analysis of choice-based conjoint data, Bayesian treatment of linear
14043 instrumental variables models, Analysis of Multivariate Ordinal survey data
14044 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14045 Coefficient Logit Models.")
14046 (license license:gpl2+)))
14048 (define-public r-tensora
14055 (uri (cran-uri "tensorA" version))
14058 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14059 (properties `((upstream-name . "tensorA")))
14060 (build-system r-build-system)
14061 (home-page "http://www.stat.boogaart.de/tensorA")
14062 (synopsis "Advanced tensor arithmetic with named indices")
14064 "This package provides convenience functions for advanced linear algebra
14065 with tensors and computation with datasets of tensors on a higher level
14066 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14067 co- and contravariate indices, and parallel computations on sequences of
14069 (license license:gpl2+)))
14071 (define-public r-rarpack
14078 (uri (cran-uri "rARPACK" version))
14081 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14082 (properties `((upstream-name . "rARPACK")))
14083 (build-system r-build-system)
14084 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14085 (home-page "https://github.com/yixuan/rARPACK")
14086 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14088 "This package was previously an R wrapper of the ARPACK library, and now
14089 a shell of the R package RSpectra, an R interface to the Spectra library for
14090 solving large scale eigenvalue/vector problems. The current version of
14091 rARPACK simply imports and exports the functions provided by RSpectra. New
14092 users of rARPACK are advised to switch to the RSpectra package.")
14093 (license license:bsd-3)))
14095 (define-public r-compositions
14097 (name "r-compositions")
14102 (uri (cran-uri "compositions" version))
14105 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14106 (build-system r-build-system)
14108 `(("r-bayesm" ,r-bayesm)
14110 ("r-robustbase" ,r-robustbase)
14111 ("r-tensora" ,r-tensora)))
14113 `(("r-knitr" ,r-knitr)))
14114 (home-page "http://www.stat.boogaart.de/compositions")
14115 (synopsis "Compositional data analysis")
14117 "This package provides functions for the consistent analysis of
14118 compositional data (e.g. portions of substances) and positive
14119 numbers (e.g. concentrations).")
14120 (license license:gpl2+)))
14122 (define-public r-cobs
14129 (uri (cran-uri "cobs" version))
14132 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14133 (build-system r-build-system)
14135 `(("r-quantreg" ,r-quantreg)
14136 ("r-sparsem" ,r-sparsem)))
14137 (home-page "https://cran.r-project.org/web/packages/cobs")
14138 (synopsis "Constrained B-Splines (sparse matrix based)")
14140 "This package provides qualitatively constrained (regression) smoothing
14141 splines via linear programming and sparse matrices.")
14142 (license license:gpl2+)))
14144 (define-public r-drimpute
14146 (name "r-drimpute")
14151 (uri (cran-uri "DrImpute" version))
14154 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14155 (properties `((upstream-name . "DrImpute")))
14156 (build-system r-build-system)
14158 `(("r-rcpp" ,r-rcpp)
14159 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14160 (home-page "https://github.com/ikwak2/DrImpute")
14161 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14163 "This is an R package for imputing dropout events. Many statistical
14164 methods in cell type identification, visualization and lineage reconstruction
14165 do not account for dropout events. DrImpute can improve the performance of
14166 such software by imputing dropout events.")
14167 (license license:gpl3)))
14169 (define-public r-gamlss-dist
14171 (name "r-gamlss-dist")
14176 (uri (cran-uri "gamlss.dist" version))
14178 (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc"))))
14179 (properties `((upstream-name . "gamlss.dist")))
14180 (build-system r-build-system)
14181 (propagated-inputs `(("r-mass" ,r-mass)))
14182 (home-page "http://www.gamlss.org/")
14183 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14185 "This package provides a set of distributions which can be used for
14186 modelling the response variables in Generalized Additive Models for Location
14187 Scale and Shape. The distributions can be continuous, discrete or mixed
14188 distributions. Extra distributions can be created, by transforming, any
14189 continuous distribution defined on the real line, to a distribution defined on
14190 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14191 transformation, respectively.")
14192 ;; Either version of the GPL.
14193 (license (list license:gpl2 license:gpl3))))
14195 ;; This package includes JavaScript files, which are not minified. When
14196 ;; upgrading please check that there are no new minified JavaScript files.
14197 (define-public r-shinyjs
14204 (uri (cran-uri "shinyjs" version))
14207 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14208 (build-system r-build-system)
14210 `(("r-digest" ,r-digest)
14211 ("r-htmltools" ,r-htmltools)
14212 ("r-jsonlite" ,r-jsonlite)
14213 ("r-shiny" ,r-shiny)))
14215 `(("r-knitr" ,r-knitr)))
14216 (home-page "https://deanattali.com/shinyjs")
14217 (synopsis "Improve the user experience of your Shiny apps")
14219 "Perform common useful JavaScript operations in Shiny apps that will
14220 greatly improve your apps without having to know any JavaScript. Examples
14221 include: hiding an element, disabling an input, resetting an input back to its
14222 original value, delaying code execution by a few seconds, and many more useful
14223 functions for both the end user and the developer. Shinyjs can also be used
14224 to easily call your own custom JavaScript functions from R.")
14225 (license license:agpl3+)))
14227 ;; This package includes minified JavaScript files. When upgrading please
14228 ;; check that there are no new minified JavaScript files.
14229 (define-public r-colourpicker
14231 (name "r-colourpicker")
14236 (uri (cran-uri "colourpicker" version))
14239 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14240 (build-system r-build-system)
14242 `(#:modules ((guix build utils)
14243 (guix build r-build-system)
14247 (modify-phases %standard-phases
14248 (add-after 'unpack 'process-javascript
14249 (lambda* (#:key inputs #:allow-other-keys)
14250 (with-directory-excursion "inst"
14254 `((,(assoc-ref inputs "js-salvattore")
14255 "examples/colourInput/www/salvattore.min.js")
14256 (,(assoc-ref inputs "js-jquery")
14257 "htmlwidgets/lib/jquery/jquery.min.js")
14258 ("www/shared/colourpicker/js/colourpicker.js"
14259 "www/shared/colourpicker/js/colourpicker.min.js"))))
14260 (lambda (sources targets)
14261 (for-each (lambda (source target)
14262 (format #t "Processing ~a --> ~a~%"
14264 (delete-file target)
14265 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14266 (call-with-output-file target
14268 (dump-port minified port)))))
14269 sources targets))))
14272 `(("r-ggplot2" ,r-ggplot2)
14273 ("r-htmltools" ,r-htmltools)
14274 ("r-htmlwidgets" ,r-htmlwidgets)
14275 ("r-jsonlite" ,r-jsonlite)
14276 ("r-miniui" ,r-miniui)
14277 ("r-shiny" ,r-shiny)
14278 ("r-shinyjs" ,r-shinyjs)))
14280 `(("r-knitr" ,r-knitr)
14281 ("uglify-js" ,uglify-js)
14285 (uri "https://code.jquery.com/jquery-3.3.1.js")
14288 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14292 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14295 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14296 (home-page "https://github.com/daattali/colourpicker")
14297 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14299 "This package provides a color picker that can be used as an input in
14300 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14301 custom color palettes, and many more options. A plot color helper tool is
14302 available as an RStudio Addin, which helps you pick colors to use in your
14303 plots. A more generic color picker RStudio Addin is also provided to let you
14304 select colors to use in your R code.")
14305 (license license:expat)))
14307 (define-public r-ggextra
14314 (uri (cran-uri "ggExtra" version))
14317 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14318 (properties `((upstream-name . "ggExtra")))
14319 (build-system r-build-system)
14321 `(("r-colourpicker" ,r-colourpicker)
14322 ("r-ggplot2" ,r-ggplot2)
14323 ("r-gtable" ,r-gtable)
14324 ("r-miniui" ,r-miniui)
14326 ("r-scales" ,r-scales)
14327 ("r-shiny" ,r-shiny)
14328 ("r-shinyjs" ,r-shinyjs)))
14330 `(("r-knitr" ,r-knitr)))
14331 (home-page "https://github.com/daattali/ggExtra")
14332 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14334 "This package is a collection of functions and layers to enhance ggplot2.
14335 The flagship function is @code{ggMarginal()}, which can be used to add
14336 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14337 (license license:expat)))
14339 (define-public r-minpack-lm
14341 (name "r-minpack-lm")
14346 (uri (cran-uri "minpack.lm" version))
14349 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14350 (properties `((upstream-name . "minpack.lm")))
14351 (build-system r-build-system)
14352 (native-inputs `(("gfortran" ,gfortran)))
14353 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14354 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14356 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14357 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14358 problems by a modification of the Levenberg-Marquardt algorithm, with support
14359 for lower and upper parameter bounds. The implementation can be used via
14360 @code{nls}-like calls using the @code{nlsLM} function.")
14361 (license license:gpl3)))
14363 (define-public r-moments
14370 (uri (cran-uri "moments" version))
14373 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14374 (build-system r-build-system)
14375 (home-page "https://cran.r-project.org/web/packages/moments")
14376 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14378 "This package provides functions to calculate: moments, Pearson's
14379 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14380 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14381 (license license:gpl2+)))
14383 (define-public r-msir
14390 (uri (cran-uri "msir" version))
14393 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14394 (build-system r-build-system)
14396 `(("r-mclust" ,r-mclust)))
14398 `(("r-knitr" ,r-knitr)))
14399 (home-page "https://cran.r-project.org/web/packages/msir")
14400 (synopsis "Model-based sliced inverse regression")
14402 "This is an R package for dimension reduction based on finite Gaussian
14403 mixture modeling of inverse regression.")
14404 (license license:gpl2+)))
14406 (define-public r-pbivnorm
14408 (name "r-pbivnorm")
14413 (uri (cran-uri "pbivnorm" version))
14416 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14417 (build-system r-build-system)
14418 (native-inputs `(("gfortran" ,gfortran)))
14419 (home-page "https://github.com/brentonk/pbivnorm")
14420 (synopsis "Vectorized bivariate normal CDF")
14422 "This package provides a vectorized R function for calculating
14423 probabilities from a standard bivariate normal CDF.")
14424 (license license:gpl2+)))
14426 (define-public r-lavaan
14433 (uri (cran-uri "lavaan" version))
14436 "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0"))))
14437 (build-system r-build-system)
14439 `(("r-mass" ,r-mass)
14440 ("r-mnormt" ,r-mnormt)
14441 ("r-numderiv" ,r-numderiv)
14442 ("r-pbivnorm" ,r-pbivnorm)))
14443 (home-page "https://lavaan.ugent.be")
14444 (synopsis "Latent variable analysis")
14446 "This package provides tools to fit a variety of latent variable models,
14447 including confirmatory factor analysis, structural equation modeling and
14448 latent growth curve models.")
14449 (license license:gpl2+)))
14451 (define-public r-nonnest2
14453 (name "r-nonnest2")
14458 (uri (cran-uri "nonnest2" version))
14461 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14462 (build-system r-build-system)
14464 `(("r-compquadform" ,r-compquadform)
14465 ("r-lavaan" ,r-lavaan)
14466 ("r-mvtnorm" ,r-mvtnorm)
14467 ("r-sandwich" ,r-sandwich)))
14469 `(("r-knitr" ,r-knitr)))
14470 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14471 (synopsis "Tests of non-nested models")
14473 "This package allows for testing of non-nested models. It includes tests
14474 of model distinguishability and of model fit that can be applied to both
14475 nested and non-nested models. The package also includes functionality to
14476 obtain confidence intervals associated with AIC and BIC.")
14477 ;; Either version of the GPL.
14478 (license (list license:gpl2 license:gpl3))))
14480 (define-public r-penalized
14482 (name "r-penalized")
14487 (uri (cran-uri "penalized" version))
14490 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14491 (build-system r-build-system)
14493 `(("r-rcpp" ,r-rcpp)
14494 ("r-rcpparmadillo" ,r-rcpparmadillo)
14495 ("r-survival" ,r-survival)))
14496 (home-page "https://cran.r-project.org/web/packages/penalized/")
14497 (synopsis "Penalized estimation in GLMs and in the Cox model")
14499 "This package provides tools for fitting possibly high dimensional
14500 penalized regression models. The penalty structure can be any combination of
14501 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14502 constraint on the regression coefficients. The supported regression models
14503 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14504 model. Cross-validation routines allow optimization of the tuning
14506 (license license:gpl2+)))
14508 (define-public r-zim
14515 (uri (cran-uri "ZIM" version))
14518 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14519 (properties `((upstream-name . "ZIM")))
14520 (build-system r-build-system)
14521 (propagated-inputs `(("r-mass" ,r-mass)))
14522 (home-page "https://github.com/biostatstudio/ZIM")
14523 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14525 "Analyze count time series with excess zeros. Two types of statistical
14526 models are supported: Markov regression and state-space models. They are also
14527 known as observation-driven and parameter-driven models respectively in the
14528 time series literature. The functions used for Markov regression or
14529 observation-driven models can also be used to fit ordinary regression models
14530 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14531 negative binomial (ZINB) assumption. The package also contains miscellaneous
14532 functions to compute density, distribution, quantile, and generate random
14533 numbers from ZIP and ZINB distributions.")
14534 (license license:gpl3)))
14536 (define-public r-nor1mix
14543 (uri (cran-uri "nor1mix" version))
14546 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14547 (build-system r-build-system)
14548 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14549 (synopsis "Normal (1-d) mixture models")
14551 "This package provides S3 classes and methods for one-dimensional normal
14552 mixture models, for, e.g., density estimation or clustering algorithms
14553 research and teaching; it provides the widely used Marron-Wand densities. It
14554 also provides tools for efficient random number generation and graphics.")
14555 (license license:gpl2+)))
14557 (define-public r-beanplot
14559 (name "r-beanplot")
14564 (uri (cran-uri "beanplot" version))
14567 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14568 (build-system r-build-system)
14569 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14570 (synopsis "Visualization via beanplots")
14572 "This package provides beanplots, an alternative to
14573 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14575 (license license:gpl2)))
14577 (define-public r-pbdzmq
14584 (uri (cran-uri "pbdZMQ" version))
14587 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14588 (properties `((upstream-name . "pbdZMQ")))
14589 (build-system r-build-system)
14591 `(("zeromq" ,zeromq)
14594 `(("pkg-config" ,pkg-config)))
14595 (home-page "https://pbdr.org/")
14596 (synopsis "R interface to ZeroMQ")
14598 "ZeroMQ is a well-known library for high-performance asynchronous
14599 messaging in scalable, distributed applications. This package provides high
14600 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14601 interactive client/server programming frameworks. A few wrapper functions
14602 compatible with @code{rzmq} are also provided.")
14603 (license license:gpl3)))
14605 (define-public r-repr
14612 (uri (cran-uri "repr" version))
14615 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14616 (build-system r-build-system)
14618 `(("r-base64enc" ,r-base64enc)
14619 ("r-htmltools" ,r-htmltools)
14620 ("r-jsonlite" ,r-jsonlite)
14621 ("r-pillar" ,r-pillar)))
14622 (home-page "https://cran.r-project.org/web/packages/repr/")
14623 (synopsis "Serializable representations")
14625 "This package provides string and binary representations of objects for
14626 several formats and MIME types.")
14627 (license license:gpl3)))
14629 (define-public r-irdisplay
14631 (name "r-irdisplay")
14636 (uri (cran-uri "IRdisplay" version))
14639 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14640 (properties `((upstream-name . "IRdisplay")))
14641 (build-system r-build-system)
14643 `(("r-repr" ,r-repr)))
14644 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14645 (synopsis "Jupyter display machinery")
14647 "This package provides an interface to the rich display capabilities of
14648 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14649 running IRkernel session.")
14650 (license license:expat)))
14652 (define-public r-irkernel
14654 (name "r-irkernel")
14659 (uri (cran-uri "IRkernel" version))
14662 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14663 (properties `((upstream-name . "IRkernel")))
14664 (build-system r-build-system)
14667 (modify-phases %standard-phases
14668 (add-after 'install 'install-kernelspec
14669 (lambda* (#:key outputs #:allow-other-keys)
14670 (let ((out (assoc-ref outputs "out")))
14671 (setenv "HOME" "/tmp")
14672 (invoke "jupyter" "kernelspec" "install"
14675 (string-append out "/site-library/IRkernel/kernelspec"))
14676 ;; Record the absolute file name of the 'R' executable in
14678 (substitute* (string-append out "/share/jupyter"
14679 "/kernels/ir/kernel.json")
14681 (string-append "[\"" (which "R") "\",")))
14684 `(("jupyter" ,jupyter)))
14686 `(("r-crayon" ,r-crayon)
14687 ("r-digest" ,r-digest)
14688 ("r-evaluate" ,r-evaluate)
14689 ("r-irdisplay" ,r-irdisplay)
14690 ("r-jsonlite" ,r-jsonlite)
14691 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14692 ("r-minimal" ,r-minimal)
14693 ("r-pbdzmq" ,r-pbdzmq)
14695 ("r-uuid" ,r-uuid)))
14696 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14697 (synopsis "Native R kernel for Jupyter")
14699 "The R kernel for the Jupyter environment executes R code which the
14700 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14702 (license license:expat)))
14704 (define-public r-gmodels
14711 (uri (cran-uri "gmodels" version))
14714 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14715 (build-system r-build-system)
14717 `(("r-gdata" ,r-gdata)
14718 ("r-mass" ,r-mass)))
14719 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14720 (synopsis "Various R programming tools for model fitting")
14722 "This package provides various R programming tools for model fitting.")
14723 (license license:gpl2)))
14725 (define-public r-apcluster
14727 (name "r-apcluster")
14732 (uri (cran-uri "apcluster" version))
14735 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14736 (build-system r-build-system)
14738 `(("r-matrix" ,r-matrix)
14739 ("r-rcpp" ,r-rcpp)))
14740 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14741 (synopsis "Affinity propagation clustering")
14743 "This package implements affinity propagation clustering introduced by
14744 Frey and Dueck (2007). The package further provides leveraged affinity
14745 propagation and an algorithm for exemplar-based agglomerative clustering that
14746 can also be used to join clusters obtained from affinity propagation. Various
14747 plotting functions are available for analyzing clustering results.")
14748 (license license:gpl2+)))
14750 (define-public r-valr
14757 (uri (cran-uri "valr" version))
14760 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14761 (build-system r-build-system)
14763 `(("r-broom" ,r-broom)
14764 ("r-dplyr" ,r-dplyr)
14765 ("r-ggplot2" ,r-ggplot2)
14767 ("r-readr" ,r-readr)
14768 ("r-rlang" ,r-rlang)
14769 ("r-stringr" ,r-stringr)
14770 ("r-tibble" ,r-tibble)))
14772 `(("r-knitr" ,r-knitr)))
14773 (home-page "https://github.com/rnabioco/valr")
14774 (synopsis "Genome interval arithmetic in R")
14776 "This package enables you to read and manipulate genome intervals and
14777 signals. It provides functionality similar to command-line tool suites within
14778 R, enabling interactive analysis and visualization of genome-scale data.")
14779 (license license:expat)))
14781 (define-public r-rematch2
14783 (name "r-rematch2")
14788 (uri (cran-uri "rematch2" version))
14791 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14792 (build-system r-build-system)
14794 `(("r-tibble" ,r-tibble)))
14795 (home-page "https://github.com/r-lib/rematch2")
14796 (synopsis "Tidy output from regular expression matching")
14798 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14799 return the match results in tidy data frames.")
14800 (license license:expat)))
14802 (define-public r-picante
14809 (uri (cran-uri "picante" version))
14812 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14813 (build-system r-build-system)
14817 ("r-vegan" ,r-vegan)))
14818 (home-page "https://cran.r-project.org/web/packages/picante/")
14819 (synopsis "Integrating phylogenies and ecology")
14821 "This package provides functions for phylocom integration, community
14822 analyses, null-models, traits and evolution. It implements numerous
14823 ecophylogenetic approaches including measures of community phylogenetic and
14824 trait diversity, phylogenetic signal, estimation of trait values for
14825 unobserved taxa, null models for community and phylogeny randomizations, and
14826 utility functions for data input/output and phylogeny plotting. A full
14827 description of package functionality and methods are provided by Kembel et
14829 (license license:gpl2)))
14831 (define-public r-reinforcelearn
14833 (name "r-reinforcelearn")
14838 (uri (cran-uri "reinforcelearn" version))
14841 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14842 (build-system r-build-system)
14844 `(("r-checkmate" ,r-checkmate)
14846 ("r-purrr" ,r-purrr)
14848 (home-page "https://markusdumke.github.io/reinforcelearn")
14849 (synopsis "Reinforcement learning")
14851 "This package implements reinforcement learning environments and
14852 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14853 can be used with function approximation, eligibility traces (Singh & Sutton,
14854 1996) and experience replay (Mnih et al., 2013).")
14855 (license license:expat)))
14857 (define-public r-lemon
14864 (uri (cran-uri "lemon" version))
14867 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14868 (build-system r-build-system)
14870 `(("r-ggplot2" ,r-ggplot2)
14871 ("r-gridextra" ,r-gridextra)
14872 ("r-gtable" ,r-gtable)
14873 ("r-knitr" ,r-knitr)
14874 ("r-lattice" ,r-lattice)
14876 ("r-rlang" ,r-rlang)
14877 ("r-scales" ,r-scales)))
14879 `(("r-knitr" ,r-knitr)))
14880 (home-page "https://github.com/stefanedwards/lemon")
14881 (synopsis "Freshen up your ggplot2 plots")
14883 "This package provides functions for working with legends and axis lines
14884 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14886 (license license:gpl3)))
14888 (define-public r-wgaim
14895 (uri (cran-uri "wgaim" version))
14897 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14898 (build-system r-build-system)
14900 `(("r-ggplot2" ,r-ggplot2)
14902 (home-page "https://cran.r-project.org/web/packages/wgaim")
14903 (synopsis "Whole genome average interval mapping for QTL detection")
14905 "This package integrates sophisticated mixed modelling methods with a
14906 whole genome approach to detecting significant QTL in linkage maps.")
14907 (license license:gpl2+)))
14909 (define-public r-bedr
14916 (uri (cran-uri "bedr" version))
14919 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14920 (build-system r-build-system)
14922 `(("r-data-table" ,r-data-table)
14923 ("r-r-utils" ,r-r-utils)
14924 ("r-testthat" ,r-testthat)
14925 ("r-venndiagram" ,r-venndiagram)
14928 ("bedtools" ,bedtools)
14929 ("htslib" ,htslib))) ; for tabix
14931 `(("r-knitr" ,r-knitr))) ; for vignettes
14932 (home-page "https://cran.r-project.org/web/packages/bedr")
14933 (synopsis "Genomic region processing")
14935 "This package is for genomic regions processing using command line tools
14936 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14937 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14938 The bedr package's API enhances access to these tools as well as offers
14939 additional utilities for genomic regions processing.")
14940 (license license:gpl2)))
14942 (define-public r-sets
14949 (uri (cran-uri "sets" version))
14952 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14953 (properties `((upstream-name . "sets")))
14954 (build-system r-build-system)
14955 (home-page "https://cran.r-project.org/web/packages/sets")
14956 (synopsis "Sets, generalized sets, customizable sets and intervals")
14958 "This package provides data structures and basic operations for ordinary
14959 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14960 customizable sets, and intervals.")
14961 (license license:gpl2)))
14963 (define-public r-partitions
14965 (name "r-partitions")
14970 (uri (cran-uri "partitions" version))
14973 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14974 (build-system r-build-system)
14977 ("r-polynom" ,r-polynom)
14978 ("r-sets" ,r-sets)))
14979 (home-page "https://cran.r-project.org/web/packages/partitions")
14980 (synopsis "Additive partitions of integers")
14982 "This package provides tools to enumerates the partitions, unequal
14983 partitions, and restricted partitions of an integer; the three corresponding
14984 partition functions are also given.")
14985 ;; Any version of the GPL
14986 (license license:gpl2+)))
14988 (define-public r-brobdingnag
14990 (name "r-brobdingnag")
14995 (uri (cran-uri "Brobdingnag" version))
14998 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
14999 (properties `((upstream-name . "Brobdingnag")))
15000 (build-system r-build-system)
15001 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15002 (synopsis "Very large numbers in R")
15004 "This package handles very large numbers in R. Real numbers are held
15005 using their natural logarithms, plus a logical flag indicating sign. The
15006 package includes a vignette that gives a step-by-step introduction to using S4
15008 ;; Any version of the GPL
15009 (license license:gpl2+)))
15011 (define-public r-untb
15018 (uri (cran-uri "untb" version))
15021 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15022 (build-system r-build-system)
15024 `(("r-brobdingnag" ,r-brobdingnag)
15025 ("r-partitions" ,r-partitions)
15026 ("r-polynom" ,r-polynom)))
15027 (home-page "https://github.com/RobinHankin/untb.git")
15028 (synopsis "Ecological drift under the UNTB")
15030 "This package provides numerical simulations, and visualizations, of
15031 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15032 (license license:gpl2+)))
15034 (define-public r-stepwise
15036 (name "r-stepwise")
15041 (uri (cran-uri "stepwise" version))
15044 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15045 (build-system r-build-system)
15046 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15047 (synopsis "Stepwise detection of recombination breakpoints")
15049 "This package provides a stepwise approach to identifying recombination
15050 breakpoints in a genomic sequence alignment.")
15051 (license license:gpl2+)))
15053 (define-public r-snpmaxsel
15055 (name "r-snpmaxsel")
15060 (uri (cran-uri "SNPmaxsel" version))
15063 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15064 (properties `((upstream-name . "SNPmaxsel")))
15065 (build-system r-build-system)
15067 `(("r-combinat" ,r-combinat)
15068 ("r-mvtnorm" ,r-mvtnorm)))
15069 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15070 (synopsis "Maximally selected statistics for SNP data")
15072 "This package implements asymptotic methods related to maximally selected
15073 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15075 (license license:gpl2+)))
15077 (define-public r-acsnminer
15079 (name "r-acsnminer")
15080 (version "0.16.8.25")
15083 (uri (cran-uri "ACSNMineR" version))
15086 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15087 (properties `((upstream-name . "ACSNMineR")))
15088 (build-system r-build-system)
15090 `(("r-ggplot2" ,r-ggplot2)
15091 ("r-gridextra" ,r-gridextra)))
15092 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15093 (synopsis "Gene enrichment analysis")
15095 "This package provides tools to compute and represent gene set enrichment
15096 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15097 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15098 enrichment can be run with hypergeometric test or Fisher exact test, and can
15099 use multiple corrections. Visualization of data can be done either by
15100 barplots or heatmaps.")
15101 (license license:gpl2+)))
15103 (define-public r-seqinr
15110 (uri (cran-uri "seqinr" version))
15113 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15114 (build-system r-build-system)
15116 `(("r-ade4" ,r-ade4)
15117 ("r-segmented" ,r-segmented)))
15120 (home-page "http://seqinr.r-forge.r-project.org/")
15121 (synopsis "Biological sequences retrieval and analysis")
15123 "This package provides tools for exploratory data analysis and data
15124 visualization of biological sequence (DNA and protein) data. It also includes
15125 utilities for sequence data management under the ACNUC system.")
15126 (license license:gpl2+)))
15128 (define-public r-units
15135 (uri (cran-uri "units" version))
15138 "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js"))))
15139 (build-system r-build-system)
15141 `(("udunits" ,udunits)))
15143 `(("r-rcpp" ,r-rcpp)))
15145 `(("r-knitr" ,r-knitr)))
15146 (home-page "https://github.com/r-quantities/units/")
15147 (synopsis "Measurement Units for R Vectors")
15149 "This package provides support for measurement units in R vectors,
15150 matrices and arrays: automatic propagation, conversion, derivation and
15151 simplification of units; raising errors in case of unit incompatibility. It
15152 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15154 (license license:gpl2)))
15156 (define-public r-udunits2
15158 (name "r-udunits2")
15163 (uri (cran-uri "udunits2" version))
15166 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15167 (properties `((upstream-name . "udunits2")))
15168 (build-system r-build-system)
15170 `(("udunits" ,udunits)))
15171 (home-page "https://cran.r-project.org/package=udunits2")
15172 (synopsis "Udunits-2 bindings for R")
15174 "This package provides simple bindings to Unidata's udunits library.")
15175 (license license:gpl2)))
15177 (define-public r-classint
15179 (name "r-classint")
15184 (uri (cran-uri "classInt" version))
15187 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15188 (properties `((upstream-name . "classInt")))
15189 (build-system r-build-system)
15191 `(("r-class" ,r-class)
15192 ("r-e1071" ,r-e1071)
15193 ("r-kernsmooth" ,r-kernsmooth)))
15195 `(("gfortran" ,gfortran)
15196 ("r-knitr" ,r-knitr)))
15197 (home-page "https://github.com/r-spatial/classInt/")
15198 (synopsis "Choose univariate class intervals")
15200 "This package provides selected commonly used methods for choosing
15201 univariate class intervals for mapping or other graphics purposes.")
15202 (license license:gpl2+)))
15204 (define-public r-spdata
15211 (uri (cran-uri "spData" version))
15214 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15215 (properties `((upstream-name . "spData")))
15216 (build-system r-build-system)
15218 `(("r-raster" ,r-raster)
15220 (home-page "https://github.com/Nowosad/spData")
15221 (synopsis "Datasets for spatial analysis")
15223 "This a package containing diverse spatial datasets for demonstrating,
15224 benchmarking and teaching spatial data analysis. It includes R data of class
15225 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15226 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15227 of the datasets are designed to illustrate specific analysis techniques.
15228 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15229 illustrate point pattern analysis techniques.")
15230 (license license:cc0)))
15232 (define-public r-learnbayes
15234 (name "r-learnbayes")
15239 (uri (cran-uri "LearnBayes" version))
15242 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15243 (properties `((upstream-name . "LearnBayes")))
15244 (build-system r-build-system)
15245 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15246 (synopsis "Functions for learning Bayesian inference")
15248 "This package provides a collection of functions helpful in learning the
15249 basic tenets of Bayesian statistical inference. It contains functions for
15250 summarizing basic one and two parameter posterior distributions and predictive
15251 distributions. It contains MCMC algorithms for summarizing posterior
15252 distributions defined by the user. It also contains functions for regression
15253 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15255 (license license:gpl2+)))
15257 (define-public r-deldir
15264 (uri (cran-uri "deldir" version))
15267 "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
15268 (build-system r-build-system)
15269 (native-inputs `(("gfortran" ,gfortran)))
15270 (home-page "https://cran.r-project.org/web/packages/deldir")
15271 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15273 "This package provides tools for calculating the Delaunay triangulation
15274 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15275 of a planar point set. It plots triangulations and tessellations in various
15276 ways, clips tessellations to sub-windows, calculates perimeters of
15277 tessellations, and summarizes information about the tiles of the
15279 (license license:gpl2+)))
15281 (define-public r-sf
15288 (uri (cran-uri "sf" version))
15291 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15292 (build-system r-build-system)
15300 `(("r-classint" ,r-classint)
15302 ("r-magrittr" ,r-magrittr)
15304 ("r-units" ,r-units)))
15306 `(("pkg-config" ,pkg-config)
15307 ("r-knitr" ,r-knitr)))
15308 (home-page "https://github.com/r-spatial/sf/")
15309 (synopsis "Simple features for R")
15311 "This package provides support for simple features, a standardized way to
15312 encode spatial vector data. It binds to GDAL for reading and writing data, to
15313 GEOS for geometrical operations, and to PROJ for projection conversions and
15314 datum transformations.")
15315 ;; Either of these licenses
15316 (license (list license:gpl2 license:expat))))
15318 (define-public r-spdep
15325 (uri (cran-uri "spdep" version))
15328 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15329 (build-system r-build-system)
15331 `(("r-boot" ,r-boot)
15333 ("r-deldir" ,r-deldir)
15335 ("r-gmodels" ,r-gmodels)
15336 ("r-learnbayes" ,r-learnbayes)
15338 ("r-matrix" ,r-matrix)
15342 ("r-spdata" ,r-spdata)))
15344 `(("r-knitr" ,r-knitr)))
15345 (home-page "https://github.com/r-spatial/spdep/")
15346 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15348 "This package provides a collection of functions to create spatial
15349 weights matrix objects from polygon contiguities, from point patterns by
15350 distance and tessellations, for summarizing these objects, and for permitting
15351 their use in spatial data analysis, including regional aggregation by minimum
15353 (license license:gpl2+)))
15355 (define-public r-adegenet
15357 (name "r-adegenet")
15362 (uri (cran-uri "adegenet" version))
15365 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15366 (build-system r-build-system)
15368 `(("r-ade4" ,r-ade4)
15371 ("r-dplyr" ,r-dplyr)
15372 ("r-ggplot2" ,r-ggplot2)
15373 ("r-igraph" ,r-igraph)
15375 ("r-reshape2" ,r-reshape2)
15376 ("r-seqinr" ,r-seqinr)
15377 ("r-shiny" ,r-shiny)
15378 ("r-spdep" ,r-spdep)
15379 ("r-vegan" ,r-vegan)))
15380 (home-page "https://github.com/thibautjombart/adegenet")
15381 (synopsis "Exploratory analysis of genetic and genomic data")
15383 "This package provides a toolset for the exploration of genetic and
15384 genomic data. Adegenet provides formal (S4) classes for storing and handling
15385 various genetic data, including genetic markers with varying ploidy and
15386 hierarchical population structure (@code{genind} class), alleles counts by
15387 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15388 also implements original multivariate methods (DAPC, sPCA), graphics,
15389 statistical tests, simulation tools, distance and similarity measures, and
15390 several spatial methods. A range of both empirical and simulated datasets is
15391 also provided to illustrate various methods.")
15392 (license license:gpl2+)))
15394 (define-public r-pegas
15401 (uri (cran-uri "pegas" version))
15403 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15404 (build-system r-build-system)
15406 `(("r-adegenet" ,r-adegenet)
15408 (home-page "http://ape-package.ird.fr/pegas.html")
15409 (synopsis "Population and evolutionary genetics analysis system")
15411 "This package provides functions for reading, writing, plotting,
15412 analysing, and manipulating allelic and haplotypic data, including from VCF
15413 files, and for the analysis of population nucleotide sequences and
15414 micro-satellites including coalescent analyses, linkage disequilibrium,
15415 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15416 minimum spanning tree and network, and median-joining networks.")
15417 (license license:gpl2+)))
15419 (define-public r-rmetasim
15421 (name "r-rmetasim")
15426 (uri (cran-uri "rmetasim" version))
15429 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15430 (build-system r-build-system)
15432 `(("r-ade4" ,r-ade4)
15433 ("r-adegenet" ,r-adegenet)
15434 ("r-gtools" ,r-gtools)
15435 ("r-pegas" ,r-pegas)))
15436 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15437 (synopsis "Individual-based population genetic simulation environment")
15439 "This package provides an interface between R and the metasim simulation
15440 engine. The simulation environment is documented in: Strand, A.(2002),
15441 Metasim 1.0: an individual-based environment for simulating population
15442 genetics of complex population dynamics.")
15444 (license license:gpl2+)))
15446 (define-public r-genetics
15448 (name "r-genetics")
15449 (version "1.3.8.1.3")
15453 (uri (cran-uri "genetics" version))
15456 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
15457 (build-system r-build-system)
15459 `(("r-combinat" ,r-combinat)
15460 ("r-gdata" ,r-gdata)
15461 ("r-gtools" ,r-gtools)
15463 ("r-mvtnorm" ,r-mvtnorm)))
15464 (home-page "https://cran.r-project.org/web/packages/genetics/")
15465 (synopsis "Population genetics")
15467 "This package provides classes and methods for handling genetic data.
15468 It includes classes to represent genotypes and haplotypes at single markers up
15469 to multiple markers on multiple chromosomes. Function include allele
15470 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15471 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15472 and testing for linkage disequilibrium, ...")
15473 ;; Any GPL version.
15474 (license license:gpl2+)))
15476 (define-public r-snp-plotter
15478 (name "r-snp-plotter")
15483 (uri (cran-uri "snp.plotter" version))
15486 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15487 (properties `((upstream-name . "snp.plotter")))
15488 (build-system r-build-system)
15489 (propagated-inputs `(("r-genetics" ,r-genetics)))
15490 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15491 (synopsis "Plot p-values using single SNP and/or haplotype data")
15493 "This package helps you create plots of p-values using single SNP and/or
15494 haplotype data. Main features of the package include options to display a
15495 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15496 datasets simultaneously. Plots can be created using global and/or individual
15497 haplotype p-values along with single SNP p-values. Images are created as
15498 either PDF/EPS files.")
15499 (license license:gpl2+)))
15501 (define-public r-polspline
15503 (name "r-polspline")
15508 (uri (cran-uri "polspline" version))
15510 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15511 (build-system r-build-system)
15512 (native-inputs `(("gfortran" ,gfortran)))
15513 (home-page "https://cran.r-project.org/web/packages/polspline/")
15514 (synopsis "Polynomial spline routines")
15516 "This package provides routines for the polynomial spline fitting
15517 routines hazard regression, hazard estimation with flexible tails, logspline,
15518 lspec, polyclass, and polymars.")
15519 (license license:gpl2+)))
15521 (define-public r-rms
15528 (uri (cran-uri "rms" version))
15530 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15531 (build-system r-build-system)
15533 `(("r-cluster" ,r-cluster)
15534 ("r-digest" ,r-digest)
15535 ("r-ggplot2" ,r-ggplot2)
15536 ("r-hmisc" ,r-hmisc)
15537 ("r-htmltable" ,r-htmltable)
15538 ("r-htmltools" ,r-htmltools)
15539 ("r-lattice" ,r-lattice)
15541 ("r-multcomp" ,r-multcomp)
15543 ("r-polspline" ,r-polspline)
15544 ("r-quantreg" ,r-quantreg)
15545 ("r-rpart" ,r-rpart)
15546 ("r-sparsem" ,r-sparsem)
15547 ("r-survival" ,r-survival)))
15548 (native-inputs `(("gfortran" ,gfortran)))
15549 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15550 (synopsis "Regression modeling strategies")
15552 "This is a package for regression modeling, testing, estimation,
15553 validation, graphics, prediction, and typesetting by storing enhanced model
15554 design attributes in the fit. The rms package is a collection of functions
15555 that assist with and streamline modeling. It also contains functions for
15556 binary and ordinal logistic regression models, ordinal models for continuous Y
15557 with a variety of distribution families, and the Buckley-James multiple
15558 regression model for right-censored responses, and implements penalized
15559 maximum likelihood estimation for logistic and ordinary linear models. The
15560 package works with almost any regression model, but it was especially written
15561 to work with binary or ordinal regression models, Cox regression, accelerated
15562 failure time models, ordinary linear models, the Buckley-James model,
15563 generalized least squares for serially or spatially correlated observations,
15564 generalized linear models, and quantile regression.")
15565 (license license:gpl2+)))
15567 (define-public r-arsenal
15574 (uri (cran-uri "arsenal" version))
15577 "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn"))))
15578 (properties `((upstream-name . "arsenal")))
15579 (build-system r-build-system)
15580 (propagated-inputs `(("r-knitr" ,r-knitr)))
15581 (native-inputs `(("r-knitr" ,r-knitr)))
15582 (home-page "https://github.com/mayoverse/arsenal")
15583 (synopsis "Functions for large-scale statistical summaries")
15585 "This package provides an arsenal of R functions for large-scale
15586 statistical summaries, which are streamlined to work within the latest
15587 reporting tools in R and RStudio and which use formulas and versatile
15588 summary statistics for summary tables and models. The primary functions
15592 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15593 levels of one or more categorical variables;
15594 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15595 across two time points;
15596 @item @code{modelsum}, which performs simple model fits on one or more
15597 endpoints for many variables (univariate or adjusted for covariates);
15598 @item @code{freqlist}, a powerful frequency table across many categorical
15600 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15601 @item @code{write2}, a function to output tables to a document.
15604 (license license:gpl2+)))
15606 (define-public r-haplo-stats
15608 (name "r-haplo-stats")
15613 (uri (cran-uri "haplo.stats" version))
15616 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15617 (properties `((upstream-name . "haplo.stats")))
15618 (build-system r-build-system)
15620 `(("r-arsenal" ,r-arsenal)
15623 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15624 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15625 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15627 "This package provides routines for the analysis of indirectly measured
15628 haplotypes. The statistical methods assume that all subjects are unrelated
15629 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15630 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15631 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15632 examples in the vignette.")
15633 (license license:gpl2+)))
15635 (define-public r-bqtl
15642 (uri (cran-uri "bqtl" version))
15645 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15646 (build-system r-build-system)
15647 (native-inputs `(("gfortran" ,gfortran)))
15648 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15649 (synopsis "Bayesian QTL mapping toolkit")
15651 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15652 lines. It includes maximum likelihood and Bayesian tools.")
15653 (license license:gpl2+)))
15655 (define-public r-ibdreg
15662 (uri (cran-uri "ibdreg" version))
15665 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15666 (build-system r-build-system)
15667 (home-page "https://www.mayo.edu/research/labs/\
15668 statistical-genetics-genetic-epidemiology/software")
15669 (synopsis "Regression methods for IBD linkage with covariates")
15671 "This package provides a method to test genetic linkage with covariates
15672 by regression methods with response IBD sharing for relative pairs. Account
15673 for correlations of IBD statistics and covariates for relative pairs within
15674 the same pedigree.")
15675 (license license:gpl2+)))
15677 (define-public r-dlmap
15684 (uri (cran-uri "dlmap" version))
15687 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15688 (build-system r-build-system)
15690 `(("r-ibdreg" ,r-ibdreg)
15694 ("r-wgaim" ,r-wgaim)))
15695 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15696 (synopsis "Detection localization mapping for QTL")
15698 "This is package for QTL mapping in a mixed model framework with separate
15699 detection and localization stages. The first stage detects the number of QTL
15700 on each chromosome based on the genetic variation due to grouped markers on
15701 the chromosome; the second stage uses this information to determine the most
15702 likely QTL positions. The mixed model can accommodate general fixed and
15703 random effects, including spatial effects in field trials and pedigree
15704 effects. It is applicable to backcrosses, doubled haploids, recombinant
15705 inbred lines, F2 intercrosses, and association mapping populations.")
15706 (license license:gpl2)))
15708 (define-public r-hwde
15715 (uri (cran-uri "hwde" version))
15718 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15719 (build-system r-build-system)
15720 (home-page "https://cran.r-project.org/web/packages/hwde/")
15721 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15723 "This package fits models for genotypic disequilibria, as described in
15724 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15725 terms are available that account for first order interactions between loci.
15726 It also implements, for a single locus in a single population, a conditional
15727 exact test for Hardy-Weinberg equilibrium.")
15728 (license license:gpl2+)))
15730 (define-public r-tdthap
15737 (uri (cran-uri "tdthap" version))
15740 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15741 (build-system r-build-system)
15742 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15743 (synopsis "TDT tests for extended haplotypes")
15745 "Functions and examples are provided for transmission/disequilibrium
15746 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15747 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15748 (license license:artistic2.0)))
15750 (define-public r-sparql
15756 (uri (cran-uri "SPARQL" version))
15759 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15760 (properties `((upstream-name . "SPARQL")))
15761 (build-system r-build-system)
15763 `(("r-rcurl" ,r-rcurl)
15765 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15766 (synopsis "SPARQL client for R")
15767 (description "This package provides an interface to use SPARQL to pose
15768 SELECT or UPDATE queries to an end-point.")
15769 ;; The only license indication is found in the DESCRIPTION file,
15770 ;; which states GPL-3. So we cannot assume GPLv3+.
15771 (license license:gpl3)))
15773 (define-public r-bookdown
15775 (name "r-bookdown")
15779 (uri (cran-uri "bookdown" version))
15782 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15783 (build-system r-build-system)
15785 `(("r-htmltools" ,r-htmltools)
15786 ("r-knitr" ,r-knitr)
15787 ("r-rmarkdown" ,r-rmarkdown)
15788 ("r-tinytex" ,r-tinytex)
15791 ("pandoc" ,pandoc)))
15792 (home-page "https://github.com/rstudio/bookdown")
15793 (synopsis "Authoring books and technical documents with R markdown")
15794 (description "This package provides output formats and utilities for
15795 authoring books and technical documents with R Markdown.")
15796 (license license:gpl3)))
15798 (define-public r-optparse
15800 (name "r-optparse")
15805 (uri (cran-uri "optparse" version))
15808 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15809 (build-system r-build-system)
15811 `(("r-getopt" ,r-getopt)))
15813 `(("r-knitr" ,r-knitr)))
15814 (home-page "https://github.com/trevorld/optparse")
15815 (synopsis "Command line option parser")
15817 "This package provides a command line parser inspired by Python's
15818 @code{optparse} library to be used with Rscript to write shebang scripts
15819 that accept short and long options.")
15820 (license license:gpl2+)))
15822 (define-public r-kernlab
15829 (uri (cran-uri "kernlab" version))
15831 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15832 (build-system r-build-system)
15833 (home-page "https://cran.r-project.org/web/packages/kernlab")
15834 (synopsis "Kernel-based machine learning tools")
15836 "This package provides kernel-based machine learning methods for
15837 classification, regression, clustering, novelty detection, quantile regression
15838 and dimensionality reduction. Among other methods @code{kernlab} includes
15839 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15841 (license license:gpl2)))
15843 (define-public r-hierfstat
15845 (name "r-hierfstat")
15850 (uri (cran-uri "hierfstat" version))
15853 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15854 (build-system r-build-system)
15856 `(("r-ade4" ,r-ade4)
15857 ("r-adegenet" ,r-adegenet)
15858 ("r-gaston" ,r-gaston)
15859 ("r-gtools" ,r-gtools)))
15861 `(("r-knitr" ,r-knitr)))
15862 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15863 (synopsis "Estimation and tests of hierarchical F-statistics")
15865 "This package allows the estimation of hierarchical F-statistics from
15866 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15867 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15868 are also given to test via randomisations the significance of each F and
15869 variance components, using the likelihood-ratio statistics G.")
15870 (license license:gpl2+)))
15872 (define-public r-hapassoc
15874 (name "r-hapassoc")
15879 (uri (cran-uri "hapassoc" version))
15882 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15883 (build-system r-build-system)
15884 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15885 (synopsis "Inference of trait associations with SNP haplotypes")
15887 "Hapassoc performs likelihood inference of trait associations with
15888 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15889 functions are developed primarily for data collected in cohort or
15890 cross-sectional studies. They can accommodate uncertain haplotype phase and
15891 handle missing genotypes at some SNPs.")
15892 (license license:gpl2)))
15894 (define-public r-sampling
15896 (name "r-sampling")
15901 (uri (cran-uri "sampling" version))
15904 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15905 (build-system r-build-system)
15907 `(("r-lpsolve" ,r-lpsolve)
15908 ("r-mass" ,r-mass)))
15909 (home-page "https://cran.r-project.org/web/packages/sampling/")
15910 (synopsis "Survey sampling")
15912 "This package provides functions for drawing and calibrating samples.")
15913 (license license:gpl2+)))
15915 (define-public r-r2html
15922 (uri (cran-uri "R2HTML" version))
15925 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15926 (properties `((upstream-name . "R2HTML")))
15927 (build-system r-build-system)
15928 (home-page "https://github.com/nalimilan/R2HTML")
15929 (synopsis "HTML export for R objects")
15931 "This package includes HTML functions and methods to write in an HTML
15932 file. Thus, making HTML reports is easy. It includes a function that allows
15933 redirection on the fly, which appears to be very useful for teaching purposes,
15934 as the student can keep a copy of the produced output to keep all that they
15935 did during the course. The package comes with a vignette describing how to
15936 write HTML reports for statistical analysis. Finally, a driver for Sweave
15937 parses HTML flat files containing R code and to automatically write
15938 the corresponding outputs (tables and graphs).")
15939 (license license:gpl2+)))
15941 (define-public r-rjava
15948 (uri (cran-uri "rJava" version))
15951 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15952 (properties `((upstream-name . "rJava")))
15953 (build-system r-build-system)
15955 `(#:modules ((guix build utils)
15956 (guix build r-build-system)
15959 (modify-phases %standard-phases
15960 (add-after 'unpack 'set-JAVA_HOME
15961 (lambda* (#:key inputs #:allow-other-keys)
15962 (let ((jdk (assoc-ref inputs "jdk")))
15963 (setenv "JAVA_HOME" jdk)
15964 (setenv "JAVA" (which "java"))
15965 (setenv "JAR" (which "jar"))
15966 (setenv "JAVAC" (which "javac"))
15967 (setenv "JAVAH" (which "javah"))
15968 (setenv "JAVA_CPPFLAGS"
15969 (string-append "-I" jdk "/include "
15970 "-I" jdk "/include/linux"))
15971 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15972 ((lib) (setenv "JAVA_LIBS" lib))
15973 (_ (error "Could not find libjvm.so"))))
15977 ("jdk" ,icedtea-8 "jdk")
15980 (home-page "https://www.rforge.net/rJava/")
15981 (synopsis "Low-Level R to Java interface")
15983 "This package provides a low-level interface to the Java VM very much
15984 like .C/.Call and friends. It allows the creation of objects, calling methods
15985 and accessing fields.")
15986 (license license:gpl2)))
15988 (define-public r-svmisc
15995 (uri (cran-uri "svMisc" version))
15998 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
15999 (properties `((upstream-name . "svMisc")))
16000 (build-system r-build-system)
16001 (home-page "https://github.com/SciViews/svMisc")
16002 (synopsis "Miscellaneous functions for SciViews")
16004 "This package provides miscellaneous functions for SciViews or general
16005 use, including tools to manage a temporary environment attached to the search
16006 path for temporary variables you do not want to @code{save()} or
16007 @code{load()}; test the current platform; showing progress bars, etc.")
16008 (license license:gpl2)))
16010 (define-public r-xyz
16017 (uri (cran-uri "xyz" version))
16020 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16021 (build-system r-build-system)
16023 `(("r-rcpp" ,r-rcpp)))
16024 (home-page "https://cran.r-project.org/web/packages/xyz/")
16025 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16027 "High dimensional interaction search by brute force requires a quadratic
16028 computational cost in the number of variables. The xyz algorithm provably
16029 finds strong interactions in almost linear time. For details of the algorithm
16030 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16031 interaction search in high-dimensional data.")
16032 ;; Any version of the GPL.
16033 (license license:gpl2+)))
16035 (define-public r-rttf2pt1
16037 (name "r-rttf2pt1")
16042 (uri (cran-uri "Rttf2pt1" version))
16045 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16046 (properties `((upstream-name . "Rttf2pt1")))
16047 (build-system r-build-system)
16048 (home-page "https://github.com/wch/Rttf2pt1")
16049 (synopsis "Font conversion utility")
16051 "This package contains the program @code{ttf2pt1}, for use with the
16052 @code{extrafont} package.")
16053 ;; Most of the files are covered under the Expat license. Some files are
16054 ;; covered under BSD-3. Deviations for individual files are recorded in
16055 ;; the LICENSE file.
16056 (license (list license:bsd-3 license:expat
16057 (license:non-copyleft "file://LICENSE")))))
16059 (define-public r-extrafontdb
16061 (name "r-extrafontdb")
16066 (uri (cran-uri "extrafontdb" version))
16069 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16070 (build-system r-build-system)
16071 (home-page "https://github.com/wch/extrafontdb")
16072 (synopsis "Database for the extrafont package")
16074 "This package holds the database for the @code{extrafont} package.")
16075 (license license:gpl2)))
16077 (define-public r-extrafont
16079 (name "r-extrafont")
16084 (uri (cran-uri "extrafont" version))
16087 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16088 (build-system r-build-system)
16090 `(("r-extrafontdb" ,r-extrafontdb)
16091 ("r-rttf2pt1" ,r-rttf2pt1)))
16092 (home-page "https://github.com/wch/extrafont")
16093 (synopsis "Tools for using fonts in R")
16095 "The extrafont package makes it easier to use fonts other than the basic
16096 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16097 used with PDF or PostScript output files. There are two hurdles for using
16098 fonts in PDF (or Postscript) output files:
16101 @item Making R aware of the font and the dimensions of the characters.
16102 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16103 properly on a device that doesn't have the font. This is usually needed if
16104 you want to print the PDF file or share it with others.
16107 The extrafont package makes both of these things easier.")
16108 (license license:gpl2)))
16110 (define-public r-xkcd
16117 (uri (cran-uri "xkcd" version))
16120 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16121 (build-system r-build-system)
16123 `(("r-extrafont" ,r-extrafont)
16124 ("r-ggplot2" ,r-ggplot2)
16125 ("r-hmisc" ,r-hmisc)))
16126 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16127 (synopsis "Plot ggplot2 graphics in the XKCD style")
16129 "This package provides the means to plot ggplot2 graphs in the style of
16130 the XKCD web comic.")
16131 (license license:gpl3)))
16133 (define-public r-msigdbr
16140 (uri (cran-uri "msigdbr" version))
16143 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16144 (build-system r-build-system)
16146 `(("r-dplyr" ,r-dplyr)
16147 ("r-magrittr" ,r-magrittr)
16148 ("r-rlang" ,r-rlang)
16149 ("r-tibble" ,r-tibble)
16150 ("r-tidyselect" ,r-tidyselect)))
16152 `(("r-knitr" ,r-knitr)))
16153 (home-page "https://github.com/igordot/msigdbr")
16154 (synopsis "MSigDB gene sets for multiple organisms")
16156 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16157 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16158 software in a standard R data frame with key-value pairs. Included are the
16159 original human gene symbols and Entrez IDs as well as the equivalents for
16160 various frequently studied model organisms such as mouse, rat, pig, fly, and
16162 ;; The package is covered under the Expat license, but the upstream MSigDB
16163 ;; files are made available under the Creative Commons Attribution 4.0
16164 ;; International license.
16165 (license (list license:expat license:cc-by4.0))))
16167 (define-public r-gridgraphics
16169 (name "r-gridgraphics")
16174 (uri (cran-uri "gridGraphics" version))
16177 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16178 (properties `((upstream-name . "gridGraphics")))
16179 (build-system r-build-system)
16180 (home-page "https://github.com/pmur002/gridgraphics")
16181 (synopsis "Redraw base graphics using @code{grid} graphics")
16183 "This package provides functions to convert a page of plots drawn with
16184 the @code{graphics} package into identical output drawn with the @code{grid}
16185 package. The result looks like the original @code{graphics}-based plot, but
16186 consists of @code{grid} grobs and viewports that can then be manipulated with
16187 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16188 (license license:gpl2+)))
16190 (define-public r-farver
16197 (uri (cran-uri "farver" version))
16200 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
16201 (build-system r-build-system)
16202 (home-page "https://github.com/thomasp85/farver")
16203 (synopsis "Vectorized color conversion and comparison")
16205 "The encoding of color can be handled in many different ways, using
16206 different color spaces. As different color spaces have different uses,
16207 efficient conversion between these representations are important. This
16208 package provides a set of functions that gives access to very fast color space
16209 conversion and comparisons implemented in C++, and offers 100-fold speed
16210 improvements over the @code{convertColor} function in the @code{grDevices}
16212 (license license:expat)))
16214 (define-public r-ggplotify
16216 (name "r-ggplotify")
16221 (uri (cran-uri "ggplotify" version))
16224 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16225 (build-system r-build-system)
16227 `(("r-ggplot2" ,r-ggplot2)
16228 ("r-gridgraphics" ,r-gridgraphics)
16229 ("r-rvcheck" ,r-rvcheck)))
16231 `(("r-knitr" ,r-knitr)))
16232 (home-page "https://github.com/GuangchuangYu/ggplotify")
16233 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16235 "This package provides tools to convert plot function calls (using
16236 expression or formula) to @code{grob} or @code{ggplot} objects that are
16237 compatible with the @code{grid} and @code{ggplot2} environment. With this
16238 package, we are able to e.g. use @code{cowplot} to align plots produced by
16239 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16240 converting them to @code{ggplot} objects.")
16241 (license license:artistic2.0)))
16243 (define-public r-triebeard
16245 (name "r-triebeard")
16250 (uri (cran-uri "triebeard" version))
16253 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16254 (build-system r-build-system)
16255 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16256 (home-page "https://github.com/Ironholds/triebeard/")
16257 (synopsis "Radix trees in Rcpp")
16259 "Radix trees, or tries, are key-value data structures optimized for
16260 efficient lookups, similar in purpose to hash tables. This package provides
16261 an implementation of radix trees for use in R programming and in developing
16262 packages with Rcpp.")
16263 (license license:expat)))
16265 (define-public r-tweenr
16272 (uri (cran-uri "tweenr" version))
16275 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16276 (build-system r-build-system)
16278 `(("r-farver" ,r-farver)
16279 ("r-magrittr" ,r-magrittr)
16281 ("r-rlang" ,r-rlang)))
16282 (home-page "https://github.com/thomasp85/tweenr")
16283 (synopsis "Interpolate data for smooth animations")
16285 "In order to create smooth animation between states of data, tweening is
16286 necessary. This package provides a range of functions for creating tweened
16287 data that can be used as basis for animation. Furthermore it adds a number of
16288 vectorized interpolaters for common R data types such as numeric, date and
16290 (license license:expat)))
16292 (define-public r-polyclip
16294 (name "r-polyclip")
16299 (uri (cran-uri "polyclip" version))
16302 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16303 (build-system r-build-system)
16304 (native-inputs `(("pkg-config" ,pkg-config)))
16305 (home-page "http://www.angusj.com/delphi/clipper.php")
16306 (synopsis "Polygon clipping")
16308 "This package provides an R port of the library Clipper. It performs
16309 polygon clipping operations (intersection, union, set minus, set difference)
16310 for polygonal regions of arbitrary complexity, including holes. It computes
16311 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16312 dilations) for polygonal regions and polygonal lines. It computes the
16313 Minkowski Sum of general polygons. There is a function for removing
16314 self-intersections from polygon data.")
16315 (license license:boost1.0)))
16317 (define-public r-urltools
16319 (name "r-urltools")
16324 (uri (cran-uri "urltools" version))
16327 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16328 (build-system r-build-system)
16330 `(("r-rcpp" ,r-rcpp)
16331 ("r-triebeard" ,r-triebeard)))
16332 (home-page "https://github.com/Ironholds/urltools/")
16333 (synopsis "Vectorized tools for URL handling and parsing")
16335 "This package provides a toolkit for all URL-handling needs, including
16336 encoding and decoding, parsing, parameter extraction and modification. All
16337 functions are designed to be both fast and entirely vectorized. It is
16338 intended to be useful for people dealing with web-related datasets, such as
16339 server-side logs, although may be useful for other situations involving large
16341 (license license:expat)))
16343 (define-public r-ggforce
16350 (uri (cran-uri "ggforce" version))
16353 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
16354 (build-system r-build-system)
16356 `(("r-ggplot2" ,r-ggplot2)
16357 ("r-gtable" ,r-gtable)
16359 ("r-polyclip" ,r-polyclip)
16361 ("r-rcppeigen" ,r-rcppeigen)
16362 ("r-rlang" ,r-rlang)
16363 ("r-scales" ,r-scales)
16364 ("r-tidyselect" ,r-tidyselect)
16365 ("r-tweenr" ,r-tweenr)
16366 ("r-withr" ,r-withr)))
16367 (home-page "https://ggforce.data-imaginist.com")
16368 (synopsis "Accelerating ggplot2")
16370 "The aim of the ggplot2 package is to aid in visual data investigations.
16371 This focus has led to a lack of facilities for composing specialized plots.
16372 Thi package aims to be a collection of mainly new statistics and geometries
16373 that fills this gap.")
16374 (license license:expat)))
16376 (define-public r-europepmc
16378 (name "r-europepmc")
16383 (uri (cran-uri "europepmc" version))
16386 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16387 (build-system r-build-system)
16389 `(("r-dplyr" ,r-dplyr)
16391 ("r-jsonlite" ,r-jsonlite)
16393 ("r-progress" ,r-progress)
16394 ("r-purrr" ,r-purrr)
16395 ("r-rlang" ,r-rlang)
16396 ("r-tibble" ,r-tibble)
16397 ("r-tidyr" ,r-tidyr)
16398 ("r-urltools" ,r-urltools)
16399 ("r-xml2" ,r-xml2)))
16401 `(("r-knitr" ,r-knitr)))
16402 (home-page "https://github.com/ropensci/europepmc/")
16403 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16405 "This package provides an R Client for the
16406 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16407 Service}. It gives access to both metadata on life science literature and
16408 open access full texts. Europe PMC indexes all PubMed content and other
16409 literature sources including Agricola, a bibliographic database of citations
16410 to the agricultural literature, or Biological Patents. In addition to
16411 bibliographic metadata, the client allows users to fetch citations and
16412 reference lists. Links between life-science literature and other EBI
16413 databases, including ENA, PDB or ChEMBL are also accessible.")
16414 (license license:gpl3)))
16416 (define-public r-ggraph
16423 (uri (cran-uri "ggraph" version))
16426 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
16427 (build-system r-build-system)
16429 `(("r-digest" ,r-digest)
16430 ("r-dplyr" ,r-dplyr)
16431 ("r-ggforce" ,r-ggforce)
16432 ("r-ggplot2" ,r-ggplot2)
16433 ("r-ggrepel" ,r-ggrepel)
16434 ("r-graphlayouts" ,r-graphlayouts)
16435 ("r-gtable" ,r-gtable)
16436 ("r-igraph" ,r-igraph)
16439 ("r-rlang" ,r-rlang)
16440 ("r-scales" ,r-scales)
16441 ("r-tidygraph" ,r-tidygraph)
16442 ("r-viridis" ,r-viridis)
16443 ("r-withr" ,r-withr)))
16445 `(("r-knitr" ,r-knitr)))
16446 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16447 (synopsis "Implementation of grammar of graphics for graphs and networks")
16449 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16450 graph and network visualizations due to its reliance on tabular data input.
16451 The ggraph package is an extension of the ggplot2 API tailored to graph
16452 visualizations and provides the same flexible approach to building up plots
16454 (license license:gpl3)))
16456 (define-public r-gkmsvm
16463 (uri (cran-uri "gkmSVM" version))
16466 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
16467 (properties `((upstream-name . "gkmSVM")))
16468 (build-system r-build-system)
16470 `(("r-kernlab" ,r-kernlab)
16473 ("r-seqinr" ,r-seqinr)))
16474 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
16475 (synopsis "Gapped-kmer support vector machine")
16477 "This R package provides tools for training gapped-kmer SVM classifiers
16478 for DNA and protein sequences. This package supports several sequence
16479 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
16480 (license license:gpl2+)))
16482 (define-public r-varselrf
16484 (name "r-varselrf")
16489 (uri (cran-uri "varSelRF" version))
16492 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16493 (properties `((upstream-name . "varSelRF")))
16494 (build-system r-build-system)
16496 `(("r-randomforest" ,r-randomforest)))
16497 (home-page "https://www.ligarto.org/rdiaz/software/software")
16498 (synopsis "Variable selection using random forests")
16500 "This package provides tools for the variable selection from random
16501 forests using both backwards variable elimination (for the selection of small
16502 sets of non-redundant variables) and selection based on the importance
16503 spectrum (somewhat similar to scree plots; for the selection of large,
16504 potentially highly-correlated variables). The main applications are in
16505 high-dimensional data (e.g., microarray data, and other genomics and
16506 proteomics applications).")
16507 (license license:gpl2+)))
16509 (define-public r-pamr
16516 (uri (cran-uri "pamr" version))
16519 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16520 (build-system r-build-system)
16522 `(("r-cluster" ,r-cluster)
16523 ("r-survival" ,r-survival)))
16524 (native-inputs `(("gfortran" ,gfortran)))
16525 (home-page "https://cran.r-project.org/web/packages/pamr/")
16526 (synopsis "Prediction Analysis for Microarrays")
16528 "This package provides some functions for sample classification in
16530 (license license:gpl2)))
16532 (define-public r-rda
16535 (version "1.0.2-2.1")
16539 (uri (cran-uri "rda" version))
16542 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16543 (build-system r-build-system)
16544 (home-page "https://cran.r-project.org/web/packages/rda/")
16545 (synopsis "Shrunken centroids regularized discriminant analysis")
16547 "This package provides tools for shrunken centroids regularized
16548 discriminant analysis for the purpose of classifying high dimensional data.")
16549 (license license:gpl2+)))
16551 (define-public r-ggvis
16558 (uri (cran-uri "ggvis" version))
16561 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16562 (build-system r-build-system)
16564 `(("r-assertthat" ,r-assertthat)
16565 ("r-dplyr" ,r-dplyr)
16566 ("r-htmltools" ,r-htmltools)
16567 ("r-jsonlite" ,r-jsonlite)
16568 ("r-magrittr" ,r-magrittr)
16569 ("r-rlang" ,r-rlang)
16570 ("r-shiny" ,r-shiny)))
16571 (home-page "https://ggvis.rstudio.com/")
16572 (synopsis "Interactive grammar of graphics")
16574 "This package is a data visualization package for R providing an
16575 implementation of an interactive grammar of graphics, taking the best parts of
16576 ggplot2, combining them with the reactive framework of Shiny and drawing web
16577 graphics using Vega.")
16578 (license license:gpl2)))
16580 (define-public r-gbm
16587 (uri (cran-uri "gbm" version))
16590 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16591 (build-system r-build-system)
16593 `(("r-lattice" ,r-lattice)
16594 ("r-survival" ,r-survival)))
16596 `(("r-knitr" ,r-knitr)))
16597 (home-page "https://github.com/gbm-developers/gbm")
16598 (synopsis "Generalized boosted regression models")
16600 "This package is an implementation of extensions to Freund and Schapire's
16601 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16602 regression methods for least squares, absolute loss, t-distribution loss,
16603 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16604 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16605 and Learning to Rank measures (LambdaMart).")
16606 (license license:gpl2+)))
16608 (define-public r-threejs
16615 (uri (cran-uri "threejs" version))
16618 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16619 (build-system r-build-system)
16621 `(#:modules ((guix build utils)
16622 (guix build r-build-system)
16626 (modify-phases %standard-phases
16627 (add-after 'unpack 'process-javascript
16628 (lambda* (#:key inputs #:allow-other-keys)
16629 (with-directory-excursion "inst"
16633 `((,(assoc-ref inputs "js-jquery")
16634 "htmlwidgets/lib/jquery/jquery.min.js")
16635 (,(assoc-ref inputs "js-threejs-111")
16636 "htmlwidgets/lib/threejs-111/three.min.js"))))
16637 (lambda (sources targets)
16638 (for-each (lambda (source target)
16639 (format #t "Processing ~a --> ~a~%"
16641 (delete-file target)
16642 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16643 (call-with-output-file target
16645 (dump-port minified port)))))
16646 sources targets))))
16649 `(("r-base64enc" ,r-base64enc)
16650 ("r-crosstalk" ,r-crosstalk)
16651 ("r-htmlwidgets" ,r-htmlwidgets)
16652 ("r-igraph" ,r-igraph)))
16654 `(("uglify-js" ,uglify-js)
16658 (uri "https://code.jquery.com/jquery-1.12.4.js")
16661 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16665 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16668 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16669 (home-page "https://bwlewis.github.io/rthreejs")
16670 (synopsis "Interactive 3D scatter plots, networks and globes")
16672 "Create interactive 3D scatter plots, network plots, and globes in R
16673 using the three.js visualization library.")
16674 (license license:expat)))
16676 (define-public r-mlbench
16683 (uri (cran-uri "mlbench" version))
16686 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16687 (build-system r-build-system)
16688 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16689 (synopsis "Machine learning benchmark problems")
16691 "This package provides a collection of artificial and real-world machine
16692 learning benchmark problems, including, e.g., several data sets from the UCI
16694 (license license:gpl2)))
16696 (define-public r-mpm
16703 (uri (cran-uri "mpm" version))
16706 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16707 (build-system r-build-system)
16709 `(("r-kernsmooth" ,r-kernsmooth)
16710 ("r-mass" ,r-mass)))
16711 (home-page "http://mpm.r-forge.r-project.org")
16712 (synopsis "Multivariate projection methods")
16714 "This is a package for exploratory graphical analysis of multivariate
16715 data, specifically gene expression data with different projection methods:
16716 principal component analysis, correspondence analysis, spectral map
16718 (license license:gpl2+)))
16720 (define-public r-png
16726 (uri (cran-uri "png" version))
16729 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16730 (build-system r-build-system)
16732 `(("libpng" ,libpng)
16734 (home-page "https://www.rforge.net/png/")
16735 (synopsis "Read and write PNG images")
16737 "This package provides an easy and simple way to read, write and display
16738 bitmap images stored in the PNG format. It can read and write both files and
16739 in-memory raw vectors.")
16740 ;; Any of these GPL versions.
16741 (license (list license:gpl2 license:gpl3))))
16743 (define-public r-ggcorrplot
16745 (name "r-ggcorrplot")
16750 (uri (cran-uri "ggcorrplot" version))
16753 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16754 (build-system r-build-system)
16756 `(("r-ggplot2" ,r-ggplot2)
16757 ("r-reshape2" ,r-reshape2)))
16758 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16759 (synopsis "Visualization of a correlation matrix using ggplot2")
16761 "The ggcorrplot package can be used to visualize easily a correlation
16762 matrix using ggplot2. It provides a solution for reordering the correlation
16763 matrix and displays the significance level on the plot. It also includes a
16764 function for computing a matrix of correlation p-values.")
16765 (license license:gpl2)))
16767 (define-public r-gridtext
16769 (name "r-gridtext")
16774 (uri (cran-uri "gridtext" version))
16777 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16778 (properties `((upstream-name . "gridtext")))
16779 (build-system r-build-system)
16781 `(("r-jpeg" ,r-jpeg)
16782 ("r-markdown" ,r-markdown)
16785 ("r-rcurl" ,r-rcurl)
16786 ("r-rlang" ,r-rlang)
16787 ("r-stringr" ,r-stringr)
16788 ("r-xml2" ,r-xml2)))
16789 (home-page "https://wilkelab.org/gridtext/")
16790 (synopsis "Improved text rendering support for Grid graphics")
16792 "This package provides support for rendering of formatted text using Grid
16793 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16794 inline CSS directives, and it can be rendered both with and without word
16796 (license license:expat)))
16798 (define-public r-ggtext
16805 (uri (cran-uri "ggtext" version))
16808 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16809 (properties `((upstream-name . "ggtext")))
16810 (build-system r-build-system)
16812 `(("r-ggplot2" ,r-ggplot2)
16813 ("r-gridtext" ,r-gridtext)
16814 ("r-rlang" ,r-rlang)
16815 ("r-scales" ,r-scales)))
16816 (native-inputs `(("r-knitr" ,r-knitr)))
16817 (home-page "https://wilkelab.org/ggtext/")
16818 (synopsis "Improved text rendering support for ggplot2")
16820 "This package provides a ggplot2 extension that enables the rendering of
16821 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16822 etc.). Text boxes with automatic word wrap are also supported.")
16823 (license license:gpl2)))
16825 ;; This package includes minified JavaScript files. When upgrading please
16826 ;; check that there are no new minified JavaScript files.
16827 (define-public r-flexdashboard
16829 (name "r-flexdashboard")
16834 (uri (cran-uri "flexdashboard" version))
16837 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16838 (modules '((guix build utils)))
16841 ;; Delete bundled minified JavaScript files
16842 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16843 (delete-file "inst/www/sly/sly.min.js")
16844 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16845 (delete-file "inst/www/prism/prism.js")
16847 (build-system r-build-system)
16849 `(#:modules ((guix build utils)
16850 (guix build r-build-system)
16854 (ice-9 textual-ports))
16856 (modify-phases %standard-phases
16857 (add-after 'unpack 'process-javascript
16858 (lambda* (#:key inputs #:allow-other-keys)
16859 (with-directory-excursion "inst"
16860 ;; Concatenate all components of prism.js
16861 (let ((contents (string-join
16862 (map (lambda (name)
16863 (call-with-input-file
16864 (assoc-ref inputs name)
16868 "js-prism-line-numbers"))
16870 (call-with-output-file "prism-src.js"
16871 (cut display contents <>)))
16875 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16876 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16878 "www/sly/sly.min.js")
16880 "www/prism/prism.js")
16881 (,(assoc-ref inputs "js-raphael")
16882 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16883 (,(assoc-ref inputs "js-featherlight")
16884 "www/featherlight/featherlight.min.js"))))
16885 (lambda (sources targets)
16886 (for-each (lambda (source target)
16887 (format #t "Processing ~a --> ~a~%"
16889 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16890 (call-with-output-file target
16892 (dump-port minified port)))))
16893 sources targets))))
16896 `(("r-htmltools" ,r-htmltools)
16897 ("r-htmlwidgets" ,r-htmlwidgets)
16898 ("r-jsonlite" ,r-jsonlite)
16899 ("r-knitr" ,r-knitr)
16900 ("r-rmarkdown" ,r-rmarkdown)
16901 ("r-shiny" ,r-shiny)))
16903 `(("uglify-js" ,uglify-js)
16907 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16910 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16914 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16917 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16921 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16924 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16925 ("js-prism-line-numbers"
16928 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16931 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16935 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16938 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16939 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16940 (synopsis "R Markdown format for flexible dashboards")
16942 "This package provides an R Markdown format for converting an R Markdown
16943 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16944 of its components to the containing web page.")
16945 (license license:expat)))
16947 (define-public r-preseqr
16954 (uri (cran-uri "preseqR" version))
16957 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16958 (properties `((upstream-name . "preseqR")))
16959 (build-system r-build-system)
16961 `(("r-polynom" ,r-polynom)))
16962 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16963 (synopsis "Predicting species accumulation curves")
16965 "This package can be used to predict the r-species accumulation
16966 curve (r-SAC), which is the number of species represented at least r times as
16967 a function of the sampling effort. When r = 1, the curve is known as the
16968 species accumulation curve, or the library complexity curve in high-throughput
16969 genomic sequencing. The package includes both parametric and nonparametric
16970 methods, as described by Deng C, et al. (2018).")
16971 (license license:gpl3)))
16973 (define-public r-mapplots
16975 (name "r-mapplots")
16980 (uri (cran-uri "mapplots" version))
16983 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16984 (build-system r-build-system)
16985 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16986 (synopsis "Data visualization on maps")
16988 "This package helps you create simple maps; add sub-plots like pie plots
16989 to a map or any other plot; format, plot and export gridded data. The package
16990 was developed for displaying fisheries data but most functions can be used for
16991 more generic data visualisation.")
16992 (license license:gpl2+)))
16994 (define-public r-pmcmr
17001 (uri (cran-uri "PMCMR" version))
17004 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
17005 (properties `((upstream-name . "PMCMR")))
17006 (build-system r-build-system)
17007 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
17008 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
17010 "This is a deprecated package for calculating pairwise multiple
17011 comparisons of mean rank sums. This package is superseded by the novel
17012 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
17013 compatibility of dependent packages for some time.")
17014 (license license:gpl3+)))
17016 (define-public r-downloader
17018 (name "r-downloader")
17023 (uri (cran-uri "downloader" version))
17026 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17027 (build-system r-build-system)
17029 `(("r-digest" ,r-digest)))
17030 (home-page "https://github.com/wch/downloader")
17031 (synopsis "Download files over HTTP and HTTPS")
17033 "This package provides a wrapper for the @code{download.file} function,
17034 making it possible to download files over HTTPS across platforms. The
17035 @code{RCurl} package provides this functionality (and much more) but has
17036 external dependencies. This package has is implemented purely in R.")
17037 (license license:gpl2)))
17039 (define-public r-rex
17046 (uri (cran-uri "rex" version))
17049 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17050 (build-system r-build-system)
17052 `(("r-lazyeval" ,r-lazyeval)))
17054 `(("r-knitr" ,r-knitr)))
17055 (home-page "https://github.com/kevinushey/rex")
17056 (synopsis "Friendly regular expressions")
17058 "This package provides a friendly interface for the construction of
17059 regular expressions. Regular expressions are a very powerful feature, however
17060 they are often difficult to interpret. Rex allows you to build complex
17061 regular expressions from human readable expressions")
17062 (license license:expat)))
17064 (define-public r-xmlparsedata
17066 (name "r-xmlparsedata")
17071 (uri (cran-uri "xmlparsedata" version))
17074 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
17075 (properties `((upstream-name . "xmlparsedata")))
17076 (build-system r-build-system)
17077 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17078 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17080 "This package provides tools to convert the output of
17081 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17082 @code{XPath}, and is easier to manipulate in general.")
17083 (license license:expat)))
17085 (define-public r-cyclocomp
17087 (name "r-cyclocomp")
17092 (uri (cran-uri "cyclocomp" version))
17095 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17096 (properties `((upstream-name . "cyclocomp")))
17097 (build-system r-build-system)
17099 `(("r-callr" ,r-callr)
17100 ("r-crayon" ,r-crayon)
17102 ("r-remotes" ,r-remotes)
17103 ("r-withr" ,r-withr)))
17104 (home-page "https://github.com/MangoTheCat/cyclocomp")
17105 (synopsis "Cyclomatic complexity of R code")
17107 "Cyclomatic complexity is a software metric, used to indicate the
17108 complexity of a program. It is a quantitative measure of the number of
17109 linearly independent paths through a program's source code. This package
17110 provides tools to compute this metric.")
17111 (license license:expat)))
17113 (define-public r-lintr
17120 (uri (cran-uri "lintr" version))
17123 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17124 (properties `((upstream-name . "lintr")))
17125 (build-system r-build-system)
17127 `(("r-codetools" ,r-codetools)
17128 ("r-crayon" ,r-crayon)
17129 ("r-cyclocomp" ,r-cyclocomp)
17130 ("r-digest" ,r-digest)
17132 ("r-jsonlite" ,r-jsonlite)
17133 ("r-knitr" ,r-knitr)
17135 ("r-rstudioapi" ,r-rstudioapi)
17136 ("r-testthat" ,r-testthat)
17138 ("r-xmlparsedata" ,r-xmlparsedata)))
17139 (home-page "https://github.com/jimhester/lintr")
17140 (synopsis "Linter for R code")
17141 (description "This package checks adherence to a given style, syntax
17142 errors and possible semantic issues. It supports on the fly checking of R
17143 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17144 (license license:expat)))
17146 (define-public r-sctransform
17148 (name "r-sctransform")
17153 (uri (cran-uri "sctransform" version))
17156 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17157 (build-system r-build-system)
17159 `(("r-future" ,r-future)
17160 ("r-future-apply" ,r-future-apply)
17161 ("r-ggplot2" ,r-ggplot2)
17162 ("r-gridextra" ,r-gridextra)
17164 ("r-matrix" ,r-matrix)
17165 ("r-matrixstats" ,r-matrixstats)
17167 ("r-rcpparmadillo" ,r-rcpparmadillo)
17168 ("r-reshape2" ,r-reshape2)))
17169 (home-page "https://github.com/ChristophH/sctransform")
17170 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17172 "This package provides a normalization method for single-cell UMI count
17173 data using a variance stabilizing transformation. The transformation is based
17174 on a negative binomial regression model with regularized parameters. As part
17175 of the same regression framework, this package also provides functions for
17176 batch correction, and data correction.")
17177 (license license:gpl3)))
17179 (define-public r-styler
17186 (uri (cran-uri "styler" version))
17189 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17190 (build-system r-build-system)
17192 `(("r-backports" ,r-backports)
17194 ("r-magrittr" ,r-magrittr)
17195 ("r-purrr" ,r-purrr)
17196 ("r-r-cache" ,r-r-cache)
17197 ("r-rematch2" ,r-rematch2)
17198 ("r-rlang" ,r-rlang)
17199 ("r-rprojroot" ,r-rprojroot)
17200 ("r-tibble" ,r-tibble)
17201 ("r-withr" ,r-withr)
17202 ("r-xfun" ,r-xfun)))
17203 (home-page "https://github.com/r-lib/styler")
17204 (synopsis "Non-invasive pretty printing of R code")
17206 "This is a package for pretty-printing R code without changing the user's
17207 formatting intent.")
17208 (license license:gpl3)))
17210 (define-public r-scrime
17217 (uri (cran-uri "scrime" version))
17220 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17221 (build-system r-build-system)
17222 (home-page "https://cran.r-project.org/web/packages/scrime/")
17223 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17225 "This package provides tools for the analysis of high-dimensional data
17226 developed/implemented at the group \"Statistical Complexity Reduction In
17227 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17228 the functions can also be applied to other types of categorical data.")
17229 (license license:gpl2)))
17231 (define-public r-pbmcapply
17233 (name "r-pbmcapply")
17238 (uri (cran-uri "pbmcapply" version))
17241 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17242 (build-system r-build-system)
17243 (home-page "https://github.com/kvnkuang/pbmcapply")
17244 (synopsis "Track the progress of apply procedures with a progress bar")
17246 "This light-weight package helps you track and visualize the progress of
17247 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17248 (license license:expat)))
17250 (define-public r-blme
17257 (uri (cran-uri "blme" version))
17260 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17261 (build-system r-build-system)
17262 (propagated-inputs `(("r-lme4" ,r-lme4)))
17263 (home-page "https://github.com/vdorie/blme")
17264 (synopsis "Bayesian linear mixed-effects models")
17266 "This package provides tools for maximum a posteriori estimation for
17267 linear and generalized linear mixed-effects models in a Bayesian setting. It
17268 extends the lme4 package.")
17269 (license license:gpl2+)))
17271 (define-public r-batchtools
17273 (name "r-batchtools")
17278 (uri (cran-uri "batchtools" version))
17281 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17282 (build-system r-build-system)
17284 `(("r-backports" ,r-backports)
17285 ("r-base64url" ,r-base64url)
17287 ("r-checkmate" ,r-checkmate)
17288 ("r-data-table" ,r-data-table)
17289 ("r-digest" ,r-digest)
17291 ("r-progress" ,r-progress)
17293 ("r-rappdirs" ,r-rappdirs)
17294 ("r-stringi" ,r-stringi)
17295 ("r-withr" ,r-withr)))
17297 `(("r-knitr" ,r-knitr)))
17298 (home-page "https://github.com/mllg/batchtools")
17299 (synopsis "Tools for computation on batch systems")
17301 "As a successor of the packages BatchJobs and BatchExperiments, this
17302 package provides a parallel implementation of the Map function for high
17303 performance computing systems managed by various schedulers. A multicore and
17304 socket mode allow the parallelization on a local machines, and multiple
17305 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17306 the package provides an abstraction mechanism to define large-scale computer
17307 experiments in a well-organized and reproducible way.")
17308 (license license:lgpl3)))
17310 (define-public r-clue
17317 (uri (cran-uri "clue" version))
17320 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17321 (build-system r-build-system)
17322 (propagated-inputs `(("r-cluster" ,r-cluster)))
17323 (home-page "https://cran.r-project.org/web/packages/clue/")
17324 (synopsis "Tools for analyzing cluster ensembles")
17325 (description "Cluster ensembles are collections of individual solutions to
17326 a given clustering problem which are useful or necessary to consider in a wide
17327 range of applications. This R package provides an extensible computational
17328 environment for creating and analyzing cluster ensembles, with basic data
17329 structures for representing partitions and hierarchies, and facilities for
17330 computing on them, including methods for measuring proximity and obtaining
17331 consensus and secondary clusterings.")
17332 (license license:gpl2)))
17334 (define-public r-sitmo
17341 (uri (cran-uri "sitmo" version))
17344 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17345 (build-system r-build-system)
17346 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17347 (home-page "https://github.com/coatless/sitmo/")
17348 (synopsis "Parallel pseudo random number generator header files")
17350 "This package provides two high quality and fast PPRNGs that may be used
17351 in an OpenMP parallel environment. In addition, there is a generator for one
17352 dimensional low-discrepancy sequence.")
17353 (license license:expat)))
17355 (define-public r-dqrng
17362 (uri (cran-uri "dqrng" version))
17365 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17366 (build-system r-build-system)
17370 ("r-sitmo" ,r-sitmo)))
17371 (home-page "https://www.daqana.org/dqrng")
17372 (synopsis "Fast pseudo random number generators")
17374 "Several fast random number generators are provided as C++ header-only
17375 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17376 Additionally, fast functions for generating random numbers according to a
17377 uniform, normal and exponential distribution are included. The latter two use
17378 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17379 functions are exported to R and as a C++ interface and are enabled for use
17380 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17381 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17382 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17383 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17384 ;; whole is distributed under the terms of the AGPL 3.
17385 (license license:agpl3)))
17387 (define-public r-ingredients
17389 (name "r-ingredients")
17394 (uri (cran-uri "ingredients" version))
17397 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17398 (properties `((upstream-name . "ingredients")))
17399 (build-system r-build-system)
17401 `(("r-ggplot2" ,r-ggplot2)
17402 ("r-gridextra" ,r-gridextra)
17403 ("r-scales" ,r-scales)))
17404 (native-inputs `(("r-knitr" ,r-knitr)))
17405 (home-page "https://ModelOriented.github.io/ingredients/")
17406 (synopsis "Effects and importances of model ingredients")
17408 "This is a collection of tools for assessment of feature importance and
17409 feature effects. Key functions are:
17412 @item @code{feature_importance()} for assessment of global level feature
17414 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17415 @item @code{partial_dependence()} for partial dependence plots,
17416 @item @code{conditional_dependence()} for conditional dependence plots,
17417 @item @code{accumulated_dependence()} for accumulated local effects plots,
17418 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17419 aggregation of ceteris paribus profiles,
17420 @item generic @code{print()} and @code{plot()} for better usability of
17421 selected explainers,
17422 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17423 @item generic @code{describe()} for explanations in natural language.
17425 (license license:gpl3)))
17427 (define-public r-ibreakdown
17429 (name "r-ibreakdown")
17434 (uri (cran-uri "iBreakDown" version))
17437 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17438 (properties `((upstream-name . "iBreakDown")))
17439 (build-system r-build-system)
17440 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17441 (native-inputs `(("r-knitr" ,r-knitr)))
17442 (home-page "https://ModelOriented.github.io/iBreakDown/")
17443 (synopsis "Model agnostic instance level variable attributions")
17445 "This package provides a model agnostic tool for decomposition of
17446 predictions from black boxes. It supports additive attributions and
17447 attributions with interactions. The Break Down Table shows contributions of
17448 every variable to a final prediction. The Break Down Plot presents variable
17449 contributions in a concise graphical way. This package works for
17450 classification and regression models.")
17451 (license license:gpl3)))
17453 (define-public r-dae
17460 (uri (cran-uri "dae" version))
17463 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17464 (build-system r-build-system)
17466 `(("r-ggplot2" ,r-ggplot2)
17467 ("r-plyr" ,r-plyr)))
17469 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17470 (home-page "http://chris.brien.name")
17471 (synopsis "Functions useful in the design and ANOVA of experiments")
17473 "This package provides functions useful in the design and ANOVA of
17474 experiments. The content falls into the following groupings:
17478 @item factor manipulation functions,
17479 @item design functions,
17480 @item ANOVA functions,
17481 @item matrix functions,
17482 @item projector and canonical efficiency functions, and
17483 @item miscellaneous functions.
17486 There is a vignette called @code{DesignNotes} describing how to use the design
17487 functions for randomizing and assessing designs. The ANOVA functions
17488 facilitate the extraction of information when the @code{Error} function has
17489 been used in the call to @code{aov}.")
17490 (license license:gpl2)))
17492 (define-public r-dalex
17499 (uri (cran-uri "DALEX" version))
17502 "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz"))))
17503 (properties `((upstream-name . "DALEX")))
17504 (build-system r-build-system)
17506 `(("r-ggplot2" ,r-ggplot2)
17507 ("r-ibreakdown" ,r-ibreakdown)
17508 ("r-ingredients" ,r-ingredients)))
17509 (home-page "https://pbiecek.github.io/DALEX/")
17510 (synopsis "Descriptive machine learning explanations")
17512 "Machine Learning models are widely used and have various applications in
17513 classification or regression. Models created with boosting, bagging, stacking
17514 or similar techniques are often used due to their high performance, but such
17515 black-box models usually lack interpretability. The DALEX package contains
17516 various explainers that help to understand the link between input variables
17517 and model output.")
17518 ;; Any version of the GPL
17519 (license license:gpl3+)))
17521 (define-public r-enrichr
17528 (uri (cran-uri "enrichR" version))
17531 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17532 (properties `((upstream-name . "enrichR")))
17533 (build-system r-build-system)
17535 `(("r-ggplot2" ,r-ggplot2)
17537 ("r-rjson" ,r-rjson)))
17539 `(("r-knitr" ,r-knitr)))
17540 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17541 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17543 "This package provides an R interface to all Enrichr databases, a
17544 web-based tool for analyzing gene sets and returns any enrichment of common
17545 annotated biological functions.")
17546 (license license:gpl2+)))
17548 (define-public r-plot3d
17555 (uri (cran-uri "plot3D" version))
17558 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17559 (properties `((upstream-name . "plot3D")))
17560 (build-system r-build-system)
17561 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17562 (home-page "https://cran.r-project.org/web/packages/plot3D")
17563 (synopsis "Plot multi-dimensional data")
17565 "This package provides functions for viewing 2D and 3D data, including
17566 perspective plots, slice plots, surface plots, scatter plots, etc. It
17567 includes data sets from oceanography.")
17568 (license license:gpl3+)))
17570 (define-public r-ggfortify
17572 (name "r-ggfortify")
17577 (uri (cran-uri "ggfortify" version))
17580 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17581 (build-system r-build-system)
17583 `(("r-dplyr" ,r-dplyr)
17584 ("r-ggplot2" ,r-ggplot2)
17585 ("r-gridextra" ,r-gridextra)
17586 ("r-scales" ,r-scales)
17587 ("r-stringr" ,r-stringr)
17588 ("r-tibble" ,r-tibble)
17589 ("r-tidyr" ,r-tidyr)))
17591 `(("r-knitr" ,r-knitr)))
17592 (home-page "https://github.com/sinhrks/ggfortify")
17593 (synopsis "Data visualization tools for statistical analysis results")
17595 "This package provides unified plotting tools for statistics commonly
17596 used, such as GLM, time series, PCA families, clustering and survival
17597 analysis. The package offers a single plotting interface for these analysis
17598 results and plots in a unified style using the @code{ggplot2} package.")
17599 (license license:gpl2)))
17601 (define-public r-refmanager
17603 (name "r-refmanager")
17608 (uri (cran-uri "RefManageR" version))
17611 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17612 (properties `((upstream-name . "RefManageR")))
17613 (build-system r-build-system)
17615 `(("r-httr" ,r-httr)
17616 ("r-jsonlite" ,r-jsonlite)
17617 ("r-lubridate" ,r-lubridate)
17619 ("r-stringr" ,r-stringr)
17620 ("r-xml2" ,r-xml2)))
17622 `(("r-knitr" ,r-knitr)))
17623 (home-page "https://github.com/ropensci/RefManageR/")
17624 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17626 "This package provides tools for importing and working with bibliographic
17627 references. It greatly enhances the @code{bibentry} class by providing a
17628 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17629 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17630 by various formats for name lists (author by last names, translator by full
17631 names, etc.). Entries can be updated, combined, sorted, printed in a number
17632 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17633 into R and converted to @code{BibEntry} objects.")
17634 ;; Any of these licenses may be picked.
17635 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17637 (define-public r-citr
17644 (uri (cran-uri "citr" version))
17647 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17648 (build-system r-build-system)
17650 `(("r-assertthat" ,r-assertthat)
17653 ("r-miniui" ,r-miniui)
17654 ("r-refmanager" ,r-refmanager)
17655 ("r-rstudioapi" ,r-rstudioapi)
17656 ("r-shiny" ,r-shiny)
17657 ("r-shinyjs" ,r-shinyjs)
17658 ("r-yaml" ,r-yaml)))
17659 (home-page "https://github.com/crsh/citr")
17660 (synopsis "RStudio add-in to insert Markdown citations")
17662 "This package provides functions and an RStudio add-in that search a
17663 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17664 the current document.")
17665 (license license:expat)))
17667 (define-public r-xgboost
17670 (version "1.3.2.1")
17674 (uri (cran-uri "xgboost" version))
17677 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17678 (build-system r-build-system)
17680 `(("r-data-table" ,r-data-table)
17681 ("r-magrittr" ,r-magrittr)
17682 ("r-matrix" ,r-matrix)))
17684 `(("r-knitr" ,r-knitr)))
17685 (home-page "https://github.com/dmlc/xgboost")
17686 (synopsis "Extreme gradient boosting")
17688 "This package provides an R interface to Extreme Gradient Boosting, which
17689 is an efficient implementation of the gradient boosting framework from Chen
17690 and Guestrin (2016). The package includes efficient linear model solver and
17691 tree learning algorithms. The package can automatically do parallel
17692 computation on a single machine. It supports various objective functions,
17693 including regression, classification and ranking. The package is made to be
17694 extensible, so that users are also allowed to define their own objectives
17696 (license license:asl2.0)))
17698 (define-public r-umap
17701 (version "0.2.7.0")
17705 (uri (cran-uri "umap" version))
17708 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17709 (build-system r-build-system)
17711 `(("r-openssl" ,r-openssl)
17713 ("r-reticulate" ,r-reticulate)
17714 ("r-rspectra" ,r-rspectra)))
17716 `(("r-knitr" ,r-knitr)))
17717 (home-page "https://github.com/tkonopka/umap")
17718 (synopsis "Uniform manifold approximation and projection")
17720 "Uniform manifold approximation and projection is a technique for
17721 dimension reduction. This package provides an interface to the UMAP algorithm
17722 in R, including a translation of the original algorithm into R.")
17723 (license license:expat)))
17725 (define-public r-uwot
17732 (uri (cran-uri "uwot" version))
17735 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17736 (build-system r-build-system)
17738 `(("r-dqrng" ,r-dqrng)
17740 ("r-irlba" ,r-irlba)
17741 ("r-matrix" ,r-matrix)
17743 ("r-rcppannoy" ,r-rcppannoy)
17744 ("r-rcppprogress" ,r-rcppprogress)
17745 ("r-rspectra" ,r-rspectra)))
17746 (home-page "https://github.com/jlmelville/uwot")
17747 (synopsis "Uniform manifold approximation and projection")
17749 "This package provides an implementation of the Uniform Manifold
17750 Approximation and Projection dimensionality reduction by McInnes et
17751 al. (2018). It also provides means to transform new data and to carry out
17752 supervised dimensionality reduction. An implementation of the related
17753 LargeVis method of Tang et al. (2016) is also provided.")
17754 (license license:gpl3)))
17756 (define-public r-kableextra
17758 (name "r-kableextra")
17763 (uri (cran-uri "kableExtra" version))
17766 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
17767 (properties `((upstream-name . "kableExtra")))
17768 (build-system r-build-system)
17770 `(("r-digest" ,r-digest)
17772 ("r-htmltools" ,r-htmltools)
17773 ("r-knitr" ,r-knitr)
17774 ("r-magrittr" ,r-magrittr)
17775 ("r-rmarkdown" ,r-rmarkdown)
17776 ("r-rstudioapi" ,r-rstudioapi)
17777 ("r-rvest" ,r-rvest)
17778 ("r-scales" ,r-scales)
17779 ("r-stringr" ,r-stringr)
17780 ("r-svglite" ,r-svglite)
17781 ("r-viridislite" ,r-viridislite)
17782 ("r-webshot" ,r-webshot)
17783 ("r-xml2" ,r-xml2)))
17785 `(("r-knitr" ,r-knitr)))
17786 (home-page "https://haozhu233.github.io/kableExtra/")
17787 (synopsis "Construct complex tables with pipe syntax")
17789 "Build complex HTML or LaTeX tables using @code{kable()} from
17790 @code{knitr} and the piping syntax from @code{magrittr}. The function
17791 @code{kable()} is a light weight table generator coming from @code{knitr}.
17792 This package simplifies the way to manipulate the HTML or LaTeX codes
17793 generated by @code{kable()} and allows users to construct complex tables and
17794 customize styles using a readable syntax.")
17795 (license license:expat)))
17797 (define-public r-glasso
17804 (uri (cran-uri "glasso" version))
17806 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17807 (build-system r-build-system)
17808 (native-inputs `(("gfortran" ,gfortran)))
17809 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17810 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17812 "This is a package for estimation of a sparse inverse covariance matrix
17813 using a lasso (L1) penalty. Facilities are provided for estimates along a
17814 path of values for the regularization parameter.")
17815 (license license:gpl2)))
17817 (define-public r-rhpcblasctl
17819 (name "r-rhpcblasctl")
17820 (version "0.20-137")
17824 (uri (cran-uri "RhpcBLASctl" version))
17827 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17828 (properties `((upstream-name . "RhpcBLASctl")))
17829 (build-system r-build-system)
17830 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17831 (synopsis "Control the number of threads on BLAS")
17833 "This package allows you to control the number of threads the BLAS
17834 library uses. It is also possible to control the number of threads in
17836 (license license:agpl3+)))
17838 (define-public r-lda
17845 (uri (cran-uri "lda" version))
17848 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17849 (build-system r-build-system)
17850 (home-page "https://cran.r-project.org/web/packages/lda/")
17851 (synopsis "Collapsed Gibbs sampling methods for topic models")
17853 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17854 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17855 mixed-membership stochastic blockmodel. Inference for all of these models is
17856 implemented via a fast collapsed Gibbs sampler written in C. Utility
17857 functions for reading/writing data typically used in topic models, as well as
17858 tools for examining posterior distributions are also included.")
17859 ;; Any version of the LGPL
17860 (license license:lgpl3+)))
17862 (define-public r-rann-l1
17869 (uri (cran-uri "RANN.L1" version))
17872 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17873 (properties `((upstream-name . "RANN.L1")))
17874 (build-system r-build-system)
17875 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17876 (synopsis "Fast nearest neighbour search using L1 metric")
17878 "This package provides tools to find the k nearest neighbours for every
17879 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17880 library. There is support for approximate as well as exact searches, fixed
17881 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17882 computed using the L1 (Manhattan, taxicab) metric.")
17883 (license license:gpl3+)))
17885 (define-public r-leiden
17892 (uri (cran-uri "leiden" version))
17895 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17896 (properties `((upstream-name . "leiden")))
17897 (build-system r-build-system)
17899 `(("r-igraph" ,r-igraph)
17900 ("r-matrix" ,r-matrix)
17901 ("r-reticulate" ,r-reticulate)))
17903 `(("r-knitr" ,r-knitr)))
17904 (home-page "https://github.com/TomKellyGenetics/leiden")
17905 (synopsis "R implementation of Leiden clustering algorithm")
17907 "This package implements the Python @code{leidenalg} module to be called
17908 in R. It enables clustering using the Leiden algorithm for partitioning a
17909 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17910 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17911 (license license:gpl3)))
17913 (define-public r-patchwork
17915 (name "r-patchwork")
17920 (uri (cran-uri "patchwork" version))
17923 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17924 (build-system r-build-system)
17926 `(("r-ggplot2" ,r-ggplot2)
17927 ("r-gtable" ,r-gtable)))
17929 `(("r-knitr" ,r-knitr)))
17930 (home-page "https://github.com/thomasp85/patchwork")
17931 (synopsis "Compose ggplot2 plots")
17933 "The @code{ggplot2} package provides a strong API for sequentially
17934 building up a plot, but does not concern itself with composition of multiple
17935 plots. Patchwork is a package that expands the API to allow for arbitrarily
17936 complex composition of plots by providing mathematical operators for combining
17938 (license license:expat)))
17940 (define-public r-liger
17947 (uri (git-reference
17948 (url "https://github.com/MacoskoLab/liger")
17949 (commit (string-append "v" version))))
17950 (file-name (git-file-name name version))
17953 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17954 (modules '((guix build utils)))
17957 (delete-file "inst/java/ModularityOptimizer.jar")
17959 (build-system r-build-system)
17962 (modify-phases %standard-phases
17963 (add-after 'unpack 'build-java-part
17964 (lambda* (#:key inputs #:allow-other-keys)
17965 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17966 (for-each (lambda (file) (invoke "javac" file))
17967 (find-files "." "\\.java$"))
17968 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17969 (find-files "." "\\.class$"))
17972 `(("r-cowplot" ,r-cowplot)
17973 ("r-dosnow" ,r-dosnow)
17974 ("r-dplyr" ,r-dplyr)
17976 ("r-foreach" ,r-foreach)
17977 ("r-ggplot2" ,r-ggplot2)
17978 ("r-ggrepel" ,r-ggrepel)
17979 ("r-hmisc" ,r-hmisc)
17981 ("r-irlba" ,r-irlba)
17982 ("r-matrix" ,r-matrix)
17983 ("r-mclust" ,r-mclust)
17984 ("r-patchwork" ,r-patchwork)
17986 ("r-rann-l1" ,r-rann-l1)
17988 ("r-rcpparmadillo" ,r-rcpparmadillo)
17989 ("r-riverplot" ,r-riverplot)
17990 ("r-rtsne" ,r-rtsne)
17991 ("r-snow" ,r-snow)))
17993 `(("jdk" ,icedtea "jdk")
17994 ;; See https://github.com/MacoskoLab/liger/issues/96
17995 ;; The optimizer is released under the Expat license.
17999 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
18002 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
18004 ("r-knitr" ,r-knitr))) ; for vignettes
18005 (home-page "https://github.com/MacoskoLab/liger")
18006 (synopsis "Integrate and analyze multiple single-cell datasets")
18008 "LIGER is a package for integrating and analyzing multiple single-cell
18009 datasets, developed and maintained by the Macosko lab. It relies on
18010 integrative non-negative matrix factorization to identify shared and
18011 dataset-specific factors.")
18012 (license license:gpl3)))
18014 (define-public r-harmony
18021 (uri (git-reference
18022 (url "https://github.com/immunogenomics/harmony")
18024 (file-name (git-file-name name version))
18027 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18028 (modules '((guix build utils)))
18031 (for-each delete-file '("config.status" "configure"))
18033 (build-system r-build-system)
18035 `(("r-cowplot" ,r-cowplot)
18036 ("r-dplyr" ,r-dplyr)
18037 ("r-ggplot2" ,r-ggplot2)
18038 ("r-irlba" ,r-irlba)
18039 ("r-matrix" ,r-matrix)
18041 ("r-rcpparmadillo" ,r-rcpparmadillo)
18042 ("r-rcppprogress" ,r-rcppprogress)
18043 ("r-rlang" ,r-rlang)
18044 ("r-tibble" ,r-tibble)
18045 ("r-tidyr" ,r-tidyr)))
18047 `(("autoconf" ,autoconf)))
18048 (home-page "https://github.com/immunogenomics/harmony")
18049 (synopsis "Integration of single cell sequencing data")
18051 "This package provides an implementation of the Harmony algorithm for
18052 single cell integration, described in Korsunsky et al
18053 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18054 function and interfaces to external frameworks.")
18055 (license license:gpl3)))
18057 (define-public r-covr
18064 (uri (cran-uri "covr" version))
18066 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18067 (properties `((upstream-name . "covr")))
18068 (build-system r-build-system)
18070 `(("r-crayon" ,r-crayon)
18071 ("r-digest" ,r-digest)
18073 ("r-jsonlite" ,r-jsonlite)
18075 ("r-withr" ,r-withr)
18076 ("r-yaml" ,r-yaml)))
18078 `(("r-knitr" ,r-knitr))) ; for vignettes
18079 (home-page "https://github.com/r-lib/covr")
18080 (synopsis "Test coverage for R packages")
18082 "Thisp package enables you to track and report code coverage for your
18083 package and (optionally) upload the results to a coverage service. Code
18084 coverage is a measure of the amount of code being exercised by a set of tests.
18085 It is an indirect measure of test quality and completeness. This package is
18086 compatible with any testing methodology or framework and tracks coverage of
18087 both R code and compiled C/C++/FORTRAN code.")
18088 (license license:gpl3)))
18090 (define-public r-systemfonts
18092 (name "r-systemfonts")
18097 (uri (cran-uri "systemfonts" version))
18100 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18101 (properties `((upstream-name . "systemfonts")))
18102 (build-system r-build-system)
18104 `(("r-cpp11" ,r-cpp11)))
18106 `(("fontconfig" ,fontconfig)
18109 `(("pkg-config" ,pkg-config)
18110 ("r-knitr" ,r-knitr)))
18111 (home-page "https://github.com/r-lib/systemfonts")
18112 (synopsis "System native font finding")
18114 "This package provides system native access to the font catalogue. As
18115 font handling varies between systems it is difficult to correctly locate
18116 installed fonts across different operating systems. The 'systemfonts' package
18117 provides bindings to the native libraries for finding font files that can then
18118 be used further by e.g. graphic devices.")
18119 (license license:expat)))
18121 (define-public r-graphlayouts
18123 (name "r-graphlayouts")
18128 (uri (cran-uri "graphlayouts" version))
18131 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18132 (properties `((upstream-name . "graphlayouts")))
18133 (build-system r-build-system)
18135 `(("r-igraph" ,r-igraph)
18137 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18138 (home-page "https://github.com/schochastics/graphlayouts")
18139 (synopsis "Additional layout algorithms for network visualizations")
18141 "This package provides several layout algorithms to visualize networks
18142 which are not part of the igraph library. Most are based on the concept of
18143 stress majorization by Gansner et al. (2004)
18144 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18145 emphasize hidden group structures in networks or focus on specific nodes.")
18146 (license license:expat)))
18148 (define-public r-terra
18155 (uri (cran-uri "terra" version))
18158 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18159 (properties `((upstream-name . "terra")))
18160 (build-system r-build-system)
18165 ("sqlite" ,sqlite) ; needed for proj
18168 `(("r-raster" ,r-raster)
18169 ("r-rcpp" ,r-rcpp)))
18171 `(("pkg-config" ,pkg-config)))
18172 (home-page "https://rspatial.org/terra")
18173 (synopsis "Spatial data analysis")
18175 "This package provides methods for spatial data analysis, especially
18176 raster data. The included methods allow for low-level data manipulation as
18177 well as high-level global, local, zonal, and focal computation. The predict
18178 and interpolate methods facilitate the use of regression type (interpolation,
18179 machine learning) models for spatial prediction. Processing of very large
18180 files is supported.")
18181 (license license:gpl3+)))
18183 (define-public r-tidygraph
18185 (name "r-tidygraph")
18190 (uri (cran-uri "tidygraph" version))
18193 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18194 (properties `((upstream-name . "tidygraph")))
18195 (build-system r-build-system)
18197 `(("r-dplyr" ,r-dplyr)
18198 ("r-igraph" ,r-igraph)
18199 ("r-magrittr" ,r-magrittr)
18200 ("r-pillar" ,r-pillar)
18203 ("r-rlang" ,r-rlang)
18204 ("r-tibble" ,r-tibble)
18205 ("r-tidyr" ,r-tidyr)))
18206 (home-page "https://github.com/thomasp85/tidygraph")
18207 (synopsis "Tidy API for graph manipulation")
18209 "This package provides a graph implementation that can be thought of as
18210 two tidy data frames describing node and edge data respectively. It provides
18211 an approach to manipulate these two virtual data frames using the API defined
18212 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18213 common graph algorithms.")
18214 (license license:expat)))
18216 (define-public r-soupx
18217 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18221 (version (git-version "0.3.1" revision commit))
18225 (uri (git-reference
18226 (url "https://github.com/constantAmateur/SoupX")
18228 (file-name (git-file-name name version))
18231 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18232 (properties `((upstream-name . "SoupX")))
18233 (build-system r-build-system)
18235 `(("r-ggplot2" ,r-ggplot2)
18236 ("r-matrix" ,r-matrix)
18237 ("r-seurat" ,r-seurat)))
18238 (home-page "https://github.com/constantAmateur/SoupX")
18239 (synopsis "Single cell mRNA Soup eXterminator")
18241 "This package provides a package for quantifying, profiling and
18242 removing cell free mRNA contamination (the \"soup\") from droplet based single
18243 cell RNA-seq experiments.")
18244 (license license:gpl2))))
18246 (define-public r-assertr
18253 (uri (cran-uri "assertr" version))
18256 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18257 (build-system r-build-system)
18259 `(("r-dplyr" ,r-dplyr)
18261 ("r-rlang" ,r-rlang)))
18263 `(("r-knitr" ,r-knitr))) ; needed for vignette
18264 (home-page "https://github.com/ropensci/assertr")
18265 (synopsis "Assertive programming for R analysis pipelines")
18267 "This package provides functionality to assert conditions that have to be
18268 met so that errors in data used in analysis pipelines can fail quickly. It is
18269 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18271 (license license:expat)))
18273 (define-public r-parameters
18275 (name "r-parameters")
18280 (uri (cran-uri "parameters" version))
18283 "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm"))))
18284 (properties `((upstream-name . "parameters")))
18285 (build-system r-build-system)
18287 `(("r-bayestestr" ,r-bayestestr)
18288 ("r-insight" ,r-insight)))
18290 `(("r-knitr" ,r-knitr)))
18291 (home-page "https://cran.r-project.org/web/packages/parameters")
18292 (synopsis "Processing of model parameters")
18294 "This package provides utilities for processing the parameters of various
18295 statistical models. Beyond computing p values, CIs, and other indices for a
18296 wide variety of models, this package implements features like standardization
18297 or bootstrapping of parameters and models, feature reduction (feature
18298 extraction and variable selection) as well as conversion between indices of
18300 (license license:gpl3)))
18302 (define-public r-rgdal
18309 (uri (cran-uri "rgdal" version))
18311 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18312 (properties `((upstream-name . "rgdal")))
18313 (build-system r-build-system)
18321 `(("pkg-config" ,pkg-config)
18322 ("r-knitr" ,r-knitr)))
18323 (home-page "http://rgdal.r-forge.r-project.org")
18324 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18326 "This package provides bindings to the Geospatial Data Abstraction
18327 Library (GDAL) and access to projection/transformation operations from the
18329 (license license:gpl2+)))
18331 (define-public r-insol
18338 (uri (cran-uri "insol" version))
18341 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18342 (properties `((upstream-name . "insol")))
18343 (build-system r-build-system)
18345 `(("r-raster" ,r-raster)))
18347 `(("gfortran" ,gfortran)))
18348 (home-page "https://meteoexploration.com/R/insol/index.html")
18349 (synopsis "Tools for calculating solar radiation")
18351 "This package provides functions to compute insolation on tilted
18352 surfaces, computes atmospheric transmittance and related parameters such as:
18353 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18354 time, vector in the direction of the sun, vector normal to surface, and some
18355 atmospheric physics.")
18356 (license license:gpl2+)))
18358 (define-public r-lifecycle
18360 (name "r-lifecycle")
18365 (uri (cran-uri "lifecycle" version))
18368 "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3"))))
18369 (properties `((upstream-name . "lifecycle")))
18370 (build-system r-build-system)
18372 `(("r-glue" ,r-glue)
18373 ("r-rlang" ,r-rlang)))
18375 `(("r-knitr" ,r-knitr))) ; for vignettes
18376 (home-page "https://github.com/r-lib/lifecycle")
18377 (synopsis "Manage the life cycle of your package functions")
18379 "Manage the life cycle of your exported functions with shared
18380 conventions, documentation badges, and non-invasive deprecation warnings. The
18381 lifecycle package defines four development stages (experimental, maturing,
18382 stable, and questioning) and three deprecation stages (soft-deprecated,
18383 deprecated, and defunct). It makes it easy to insert badges corresponding to
18384 these stages in your documentation. Usage of deprecated functions are
18385 signalled with increasing levels of non-invasive verbosity.")
18386 (license license:gpl3)))
18388 (define-public r-assertable
18390 (name "r-assertable")
18395 (uri (cran-uri "assertable" version))
18398 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18399 (build-system r-build-system)
18401 `(("r-data-table" ,r-data-table)))
18403 `(("r-knitr" ,r-knitr)))
18404 (home-page "https://cran.r-project.org/web/packages/assertable/")
18405 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18406 (description "This package provides simple, flexible assertions on
18407 data.frame or data.table objects with verbose output for vetting. While other
18408 assertion packages apply towards more general use-cases, @code{assertable} is
18409 tailored towards tabular data. It includes functions to check variable names
18410 and values, whether the dataset contains all combinations of a given set of
18411 unique identifiers, and whether it is a certain length. In addition,
18412 @code{assertable} includes utility functions to check the existence of target
18413 files and to efficiently import multiple tabular data files into one
18415 (license license:gpl3)))
18417 (define-public r-quadprog
18419 (name "r-quadprog")
18424 (uri (cran-uri "quadprog" version))
18426 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18427 (build-system r-build-system)
18429 `(("gfortran" ,gfortran)))
18430 (home-page "https://cran.r-project.org/web/packages/quadprog")
18431 (synopsis "Functions to solve quadratic programming problems")
18433 "This package contains routines and documentation for solving quadratic
18434 programming problems.")
18435 (license license:gpl3+)))
18437 (define-public r-desolve
18444 (uri (cran-uri "deSolve" version))
18446 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18447 (properties `((upstream-name . "deSolve")))
18448 (build-system r-build-system)
18450 `(("gfortran" ,gfortran)))
18451 (home-page "https://desolve.r-forge.r-project.org/")
18452 (synopsis "Solvers for initial value problems of differential equations")
18453 (description "This package provides functions that solve initial value
18454 problems of a system of first-order @dfn{ordinary differential
18455 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18456 @dfn{differential algebraic equations} (DAE), and of delay differential
18457 equations. The functions provide an interface to the FORTRAN functions
18458 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18459 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18460 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18461 time steps. The package contains routines designed for solving ODEs resulting
18462 from 1-D, 2-D and 3-D partial differential equations that have been converted
18463 to ODEs by numerical differencing.")
18464 (license license:gpl2+)))
18466 (define-public r-pracma
18472 (uri (cran-uri "pracma" version))
18474 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18475 (build-system r-build-system)
18476 (home-page "https://cran.r-project.org/web/packages/pracma/")
18477 (synopsis "Practical numerical math functions")
18478 (description "This package provides functions for numerical analysis and
18479 linear algebra, numerical optimization, differential equations, plus some
18480 special functions. It uses Matlab function names where appropriate to simplify
18482 (license license:gpl3+)))
18484 (define-public r-subplex
18491 (uri (cran-uri "subplex" version))
18494 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18495 (build-system r-build-system)
18497 `(("gfortran" ,gfortran)))
18498 (home-page "https://cran.r-project.org/web/packages/subplex")
18499 (synopsis "Unconstrained optimization using the subplex algorithm")
18501 "This package implements the Subplex optimization algorithm.
18502 It solves unconstrained optimization problems using a simplex method on
18503 subspaces. The method is well suited for optimizing objective functions that
18504 are noisy or are discontinuous at the solution.")
18505 (license license:gpl3+)))
18507 (define-public r-txtplot
18514 (uri (cran-uri "txtplot" version))
18517 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18518 (build-system r-build-system)
18519 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18520 (synopsis "Text-based plotting")
18521 (description "This package provides functions to produce rudimentary ASCII
18522 graphics directly in the terminal window. This package provides a basic
18523 plotting function (and equivalents of curve, density, acf and barplot) as well
18524 as a boxplot function.")
18525 (license license:lgpl3+)))
18527 (define-public r-bio3d
18534 (uri (cran-uri "bio3d" version))
18537 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18538 (properties `((upstream-name . "bio3d")))
18539 (build-system r-build-system)
18540 (inputs `(("zlib" ,zlib)))
18541 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18542 (home-page "http://thegrantlab.org/bio3d/")
18543 (synopsis "Biological structure analysis")
18545 "This package provides utilities to process, organize and explore protein
18546 structure, sequence and dynamics data. Features include the ability to read
18547 and write structure, sequence and dynamic trajectory data, perform sequence
18548 and structure database searches, data summaries, atom selection, alignment,
18549 superposition, rigid core identification, clustering, torsion analysis,
18550 distance matrix analysis, structure and sequence conservation analysis, normal
18551 mode analysis, principal component analysis of heterogeneous structure data,
18552 and correlation network analysis from normal mode and molecular dynamics data.
18553 In addition, various utility functions are provided to enable the statistical
18554 and graphical power of the R environment to work with biological sequence and
18556 (license license:gpl2+)))
18558 (define-public r-bios2cor
18560 (name "r-bios2cor")
18565 (uri (cran-uri "Bios2cor" version))
18568 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18569 (properties `((upstream-name . "Bios2cor")))
18570 (build-system r-build-system)
18572 `(("r-bigmemory" ,r-bigmemory)
18573 ("r-bio3d" ,r-bio3d)
18574 ("r-circular" ,r-circular)
18575 ("r-igraph" ,r-igraph)))
18576 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18577 (synopsis "From biological sequences and simulations to correlation analysis")
18579 "This package provides utilities for computation and analysis of
18580 correlation/covariation in multiple sequence alignments and in side chain
18581 motions during molecular dynamics simulations. Features include the
18582 computation of correlation/covariation scores using a variety of scoring
18583 functions between either sequence positions in alignments or side chain
18584 dihedral angles in molecular dynamics simulations and utilities to analyze the
18585 correlation/covariation matrix through a variety of tools including network
18586 representation and principal components analysis. In addition, several
18587 utility functions are based on the R graphical environment to provide friendly
18588 tools for help in data interpretation.")
18589 (license license:gpl2+)))
18591 ;; This package includes minified JavaScript files. When upgrading please
18592 ;; check that there are no new minified JavaScript files.
18593 (define-public r-networkd3
18595 (name "r-networkd3")
18600 (uri (cran-uri "networkD3" version))
18603 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18606 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18608 (properties `((upstream-name . "networkD3")))
18609 (build-system r-build-system)
18611 `(#:modules ((guix build utils)
18612 (guix build r-build-system)
18616 (modify-phases %standard-phases
18617 (add-after 'unpack 'process-javascript
18618 (lambda* (#:key inputs #:allow-other-keys)
18619 (with-directory-excursion "inst/htmlwidgets/lib/"
18623 `((,(assoc-ref inputs "d3.v4.js")
18624 "d3-4.5.0/d3.min.js"))))
18625 (lambda (sources targets)
18626 (for-each (lambda (source target)
18627 (format #t "Processing ~a --> ~a~%"
18629 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18630 (call-with-output-file target
18632 (dump-port minified port)))))
18633 sources targets))))
18636 `(("uglify-js" ,uglify-js)
18637 ;; NOTE: Make sure that this version of d3 is still valid when
18638 ;; upgrading the package.
18642 (uri "https://d3js.org/d3.v4.js")
18645 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18647 `(("r-htmlwidgets" ,r-htmlwidgets)
18648 ("r-igraph" ,r-igraph)
18649 ("r-magrittr" ,r-magrittr)))
18650 (home-page "https://cran.r-project.org/package=networkD3")
18651 (synopsis "D3 JavaScript network graphs from R")
18653 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18655 (license license:gpl3+)))
18657 (define-public r-aasea
18664 (uri (cran-uri "aaSEA" version))
18667 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18668 (properties `((upstream-name . "aaSEA")))
18669 (build-system r-build-system)
18671 `(("r-bios2cor" ,r-bios2cor)
18673 ("r-hmisc" ,r-hmisc)
18674 ("r-magrittr" ,r-magrittr)
18675 ("r-networkd3" ,r-networkd3)
18676 ("r-plotly" ,r-plotly)
18677 ("r-seqinr" ,r-seqinr)
18678 ("r-shiny" ,r-shiny)
18679 ("r-shinydashboard" ,r-shinydashboard)))
18680 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18681 (synopsis "Amino acid substitution effect analyzer")
18683 "Given a protein multiple sequence alignment, it is a daunting task to
18684 assess the effects of substitutions along sequence length. The aaSEA package
18685 is intended to help researchers to rapidly analyze property changes caused by
18686 single, multiple and correlated amino acid substitutions in proteins.")
18687 (license license:gpl3)))
18689 (define-public r-abacus
18696 (uri (cran-uri "ABACUS" version))
18699 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18700 (properties `((upstream-name . "ABACUS")))
18701 (build-system r-build-system)
18703 `(("r-ggplot2" ,r-ggplot2)
18704 ("r-shiny" ,r-shiny)))
18705 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18706 (synopsis "Apps-based activities for communicating and understanding statistics")
18708 "This package provides a set of Shiny apps for effective communication
18709 and understanding in statistics. The current version includes properties of
18710 normal distribution, properties of sampling distribution, one-sample z and t
18711 tests, two samples independent (unpaired) t test and analysis of variance.")
18712 (license license:gpl3)))
18714 (define-public r-abc-rap
18721 (uri (cran-uri "ABC.RAP" version))
18724 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18725 (properties `((upstream-name . "ABC.RAP")))
18726 (build-system r-build-system)
18727 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18728 (synopsis "Array-based CpG region analysis pipeline")
18730 "This package aims to identify candidate genes that are differentially
18731 methylated between cases and controls. It applies Student's t-test and delta
18732 beta analysis to identify candidate genes containing multiple CpG sites.")
18733 (license license:gpl3)))
18735 (define-public r-abcadm
18742 (uri (cran-uri "abcADM" version))
18745 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18746 (properties `((upstream-name . "abcADM")))
18747 (build-system r-build-system)
18750 ("r-rcpp" ,r-rcpp)))
18751 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18752 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18754 "This package provides tools to estimate parameters of accumulated
18755 damage (load duration) models based on failure time data under a Bayesian
18756 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18757 long-term reliability under stochastic load profiles.")
18758 (license license:gpl3)))
18760 (define-public r-rglpk
18767 (uri (cran-uri "Rglpk" version))
18770 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18771 (properties `((upstream-name . "Rglpk")))
18772 (build-system r-build-system)
18774 `(("r-slam" ,r-slam)))
18777 (home-page "https://r-forge.r-project.org/projects/rglp/")
18778 (synopsis "R interface to the GNU Linear Programming Kit")
18780 "This package provides an R interface to the GNU Linear Programming Kit,
18781 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18782 integer linear programming} (MILP) and other related problems.")
18784 (license (list license:gpl2 license:gpl3))))
18786 (define-public r-abcdefba
18788 (name "r-abcdefba")
18793 (uri (cran-uri "abcdeFBA" version))
18796 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18797 (properties `((upstream-name . "abcdeFBA")))
18798 (build-system r-build-system)
18800 `(("r-corrplot" ,r-corrplot)
18801 ("r-lattice" ,r-lattice)
18803 ("r-rglpk" ,r-rglpk)))
18804 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18805 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18807 "This package provides functions for Constraint Based Simulation using
18808 Flux Balance Analysis and informative analysis of the data generated during
18810 (license license:gpl2)))
18812 (define-public r-abcrlda
18819 (uri (cran-uri "abcrlda" version))
18822 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18823 (properties `((upstream-name . "abcrlda")))
18824 (build-system r-build-system)
18825 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18826 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18828 "This package offers methods to perform @dfn{asymptotically
18829 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18830 cost-sensitive binary classification. The bias-correction is an estimate of
18831 the bias term added to regularized discriminant analysis that minimizes the
18833 (license license:gpl3)))
18835 (define-public r-abemus
18842 (uri (cran-uri "abemus" version))
18845 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18846 (properties `((upstream-name . "abemus")))
18847 (build-system r-build-system)
18849 `(("r-data-table" ,r-data-table)))
18850 (home-page "https://cran.r-project.org/web/packages/abemus/")
18851 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18853 "This package provides an implementation of @dfn{Adaptive Base Error
18854 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18855 platform-specific genetic knowledge and empirical signal to readily detect and
18856 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18857 cell free DNA} (cfDNA).")
18858 (license license:gpl3)))
18860 ;; This package includes minified JavaScript files. When upgrading please
18861 ;; check that there are no new minified JavaScript files.
18862 (define-public r-rintrojs
18864 (name "r-rintrojs")
18869 (uri (cran-uri "rintrojs" version))
18872 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18873 (properties `((upstream-name . "rintrojs")))
18874 (build-system r-build-system)
18876 `(#:modules ((guix build utils)
18877 (guix build r-build-system)
18881 (modify-phases %standard-phases
18882 (add-after 'unpack 'process-javascript
18883 (lambda* (#:key inputs #:allow-other-keys)
18884 (with-directory-excursion "inst/javascript/introjs/"
18888 `((,(assoc-ref inputs "intro.js")
18890 (lambda (sources targets)
18891 (for-each (lambda (source target)
18892 (format #t "Processing ~a --> ~a~%"
18894 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18895 (call-with-output-file target
18897 (dump-port minified port)))))
18898 sources targets))))
18901 `(("uglify-js" ,uglify-js)
18905 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18908 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18910 `(("r-jsonlite" ,r-jsonlite)
18911 ("r-shiny" ,r-shiny)))
18912 (home-page "https://github.com/carlganz/rintrojs")
18913 (synopsis "Wrapper for the Intro.js library")
18915 "This package provides a wrapper for the @url{http://www.introjs.com,
18916 Intro.js} library. This package makes it easy to include step-by-step
18917 introductions, and clickable hints in a Shiny application. It supports both
18918 static introductions in the UI, and programmatic introductions from the
18920 (license license:agpl3+)))
18922 (define-public r-sysfonts
18924 (name "r-sysfonts")
18929 (uri (cran-uri "sysfonts" version))
18932 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18933 (properties `((upstream-name . "sysfonts")))
18934 (build-system r-build-system)
18936 `(("freetype" ,freetype)
18940 `(("pkg-config" ,pkg-config)))
18941 (home-page "https://github.com/yixuan/sysfonts")
18942 (synopsis "Loading fonts into R")
18944 "This is a package to simplify loading of system fonts and Google Fonts
18945 into R, in order to support other packages.")
18946 (license license:gpl2)))
18948 (define-public r-showtextdb
18950 (name "r-showtextdb")
18955 (uri (cran-uri "showtextdb" version))
18958 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18959 (properties `((upstream-name . "showtextdb")))
18960 (build-system r-build-system)
18962 `(("r-sysfonts" ,r-sysfonts)))
18963 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18964 (synopsis "Font files for the 'showtext' package")
18966 "This package provides font files that can be used by the @code{showtext}
18968 (license license:asl2.0)))
18970 (define-public r-showtext
18972 (name "r-showtext")
18977 (uri (cran-uri "showtext" version))
18980 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18981 (properties `((upstream-name . "showtext")))
18982 (build-system r-build-system)
18984 `(("freetype" ,freetype)
18988 `(("r-showtextdb" ,r-showtextdb)
18989 ("r-sysfonts" ,r-sysfonts)))
18991 `(("pkg-config" ,pkg-config)
18992 ("r-knitr" ,r-knitr)))
18993 (home-page "https://github.com/yixuan/showtext")
18994 (synopsis "Using fonts more easily in R graphs")
18996 "This package aims to make it easy to use various types of
18997 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
18998 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
18999 will be converted into polygons or raster images, hence after the plot has
19000 been created, it no longer relies on the font files. No external software
19001 such as Ghostscript is needed to use this package.")
19002 (license license:asl2.0)))
19004 (define-public r-emojifont
19006 (name "r-emojifont")
19011 (uri (cran-uri "emojifont" version))
19014 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
19015 (properties `((upstream-name . "emojifont")))
19016 (build-system r-build-system)
19018 `(("r-ggplot2" ,r-ggplot2)
19019 ("r-proto" ,r-proto)
19020 ("r-showtext" ,r-showtext)
19021 ("r-sysfonts" ,r-sysfonts)))
19022 (home-page "https://guangchuangyu.github.io/emojifont")
19023 (synopsis "Emoji and Font Awesome in R graphics")
19025 "This package enables the use of emoji and the Font Awesome glyphs in
19026 both base and ggplot2 graphics.")
19027 (license license:artistic2.0)))
19029 (define-public r-abstractr
19031 (name "r-abstractr")
19036 (uri (cran-uri "abstractr" version))
19039 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19040 (properties `((upstream-name . "abstractr")))
19041 (build-system r-build-system)
19043 `(("r-colourpicker" ,r-colourpicker)
19044 ("r-emojifont" ,r-emojifont)
19045 ("r-ggplot2" ,r-ggplot2)
19046 ("r-gridextra" ,r-gridextra)
19047 ("r-rintrojs" ,r-rintrojs)
19048 ("r-shiny" ,r-shiny)
19049 ("r-shinythemes" ,r-shinythemes)))
19050 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19051 (synopsis "R-Shiny application for creating visual abstracts")
19053 "This package provides an R Shiny application to create visual abstracts
19054 for original research. A variety of user defined options and formatting are
19056 (license license:gpl3)))
19058 (define-public r-qgam
19065 (uri (cran-uri "qgam" version))
19068 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19069 (properties `((upstream-name . "qgam")))
19070 (build-system r-build-system)
19072 `(("r-doparallel" ,r-doparallel)
19075 ("r-shiny" ,r-shiny)))
19076 (native-inputs `(("r-knitr" ,r-knitr)))
19077 (home-page "https://cran.r-project.org/web/packages/qgam/")
19078 (synopsis "Smooth additive quantile regression models")
19080 "This package provides smooth additive quantile regression models, fitted
19081 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19082 the smoothing parameters are estimated automatically by marginal loss
19083 minimization, while the regression coefficients are estimated using either
19084 PIRLS or Newton algorithm. The learning rate is determined so that the
19085 Bayesian credible intervals of the estimated effects have approximately the
19086 correct coverage. The main function is @code{qgam()} which is similar to
19087 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19088 regression models.")
19089 (license license:gpl2+)))
19091 (define-public r-abtest
19098 (uri (cran-uri "abtest" version))
19101 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19102 (properties `((upstream-name . "abtest")))
19103 (build-system r-build-system)
19105 `(("r-matrix" ,r-matrix)
19106 ("r-mvtnorm" ,r-mvtnorm)
19107 ("r-plotrix" ,r-plotrix)
19109 ("r-rcolorbrewer" ,r-rcolorbrewer)
19112 ("r-truncnorm" ,r-truncnorm)))
19113 (home-page "https://cran.r-project.org/web/packages/abtest/")
19114 (synopsis "Bayesian A/B testing")
19116 "This package provides functions for Bayesian A/B testing including prior
19117 elicitation options based on Kass and Vaidyanathan (1992)
19118 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19119 (license license:gpl2+)))
19121 (define-public r-accept
19128 (uri (cran-uri "accept" version))
19131 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19132 (properties `((upstream-name . "accept")))
19133 (build-system r-build-system)
19135 `(("r-dplyr" ,r-dplyr)
19136 ("r-extrafont" ,r-extrafont)
19138 ("r-plotly" ,r-plotly)
19139 ("r-stringr" ,r-stringr)
19140 ("r-viridis" ,r-viridis)))
19141 (home-page "https://cran.r-project.org/web/packages/accept/")
19142 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19144 "This package allows clinicians to predict the rate and severity of
19145 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19146 Disease} (COPD) patients, based on the clinical prediction model published in
19147 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19148 (license license:gpl3)))
19150 (define-public r-smpracticals
19152 (name "r-smpracticals")
19157 (uri (cran-uri "SMPracticals" version))
19160 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19161 (properties `((upstream-name . "SMPracticals")))
19162 (build-system r-build-system)
19164 `(("r-ellipse" ,r-ellipse)
19167 ("r-survival" ,r-survival)))
19168 (home-page "http://statwww.epfl.ch/davison/SM/")
19169 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19171 "This package contains the datasets and a few functions for use with the
19172 practicals outlined in Appendix A of the book Statistical Models (Davison,
19173 2003, Cambridge University Press). The practicals themselves can be found at
19174 @url{http://statwww.epfl.ch/davison/SM/}.")
19175 (license license:gpl2+)))
19177 (define-public r-fgui
19184 (uri (cran-uri "fgui" version))
19187 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19188 (properties `((upstream-name . "fgui")))
19189 (build-system r-build-system)
19191 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19192 (synopsis "Create GUI for R functions")
19194 "Rapidly create a GUI for a function you created by automatically
19195 creating widgets for arguments of the function. This package automatically
19196 parses help routines for context-sensitive help to these arguments. The
19197 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19198 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19199 incorporated into the interface for greater customization for the more
19201 ;; Any version of the GPL.
19202 (license (list license:gpl2+ license:gpl3+))))
19204 (define-public r-tcltk2
19211 (uri (cran-uri "tcltk2" version))
19214 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19215 (properties `((upstream-name . "tcltk2")))
19216 (build-system r-build-system)
19220 (home-page "https://www.sciviews.org/SciViews-R")
19221 (synopsis "Tcl/Tk additions")
19223 "This package provides a series of additional Tcl commands and Tk widgets
19224 with style and various functions to supplement the tcltk package")
19225 (license license:lgpl3)))
19227 (define-public r-accrual
19234 (uri (cran-uri "accrual" version))
19237 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19238 (properties `((upstream-name . "accrual")))
19239 (build-system r-build-system)
19241 `(("r-fgui" ,r-fgui)
19242 ("r-smpracticals" ,r-smpracticals)
19243 ("r-tcltk2" ,r-tcltk2)))
19244 (home-page "https://cran.r-project.org/web/packages/accrual/")
19245 (synopsis "Bayesian accrual prediction")
19247 "Subject recruitment for medical research is challenging. Slow patient
19248 accrual leads to delay in research. Accrual monitoring during the process of
19249 recruitment is critical. Researchers need reliable tools to manage the
19250 accrual rate. This package provides an implementation of a Bayesian method
19251 that integrates researcher's experience on previous trials and data from the
19252 current study, providing reliable prediction on accrual rate for clinical
19253 studies. It provides functions for Bayesian accrual prediction which can be
19254 easily used by statisticians and clinical researchers.")
19255 (license license:gpl2)))
19257 (define-public r-accrued
19264 (uri (cran-uri "accrued" version))
19267 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19268 (properties `((upstream-name . "accrued")))
19269 (build-system r-build-system)
19270 (home-page "https://cran.r-project.org/web/packages/accrued/")
19271 (synopsis "Data quality visualization tools for partially accruing data")
19273 "This is a package for visualizing data quality of partially accruing
19275 (license license:gpl3)))
19277 (define-public r-mda
19284 (uri (cran-uri "mda" version))
19287 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19288 (properties `((upstream-name . "mda")))
19289 (build-system r-build-system)
19290 (propagated-inputs `(("r-class" ,r-class)))
19291 (native-inputs `(("gfortran" ,gfortran)))
19292 (home-page "https://cran.r-project.org/web/packages/mda/")
19293 (synopsis "Mixture and flexible discriminant analysis")
19295 "This is a package for mixture and flexible discriminant analysis,
19296 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19297 (license license:gpl2)))
19299 (define-public r-elasticnet
19301 (name "r-elasticnet")
19306 (uri (cran-uri "elasticnet" version))
19309 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19310 (properties `((upstream-name . "elasticnet")))
19311 (build-system r-build-system)
19313 `(("r-lars" ,r-lars)))
19314 (home-page "http://users.stat.umn.edu/~zouxx019/")
19315 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19317 "This package provides functions for fitting the entire solution path of
19318 the Elastic-Net and also provides functions for estimating sparse Principal
19319 Components. The Lasso solution paths can be computed by the same function.")
19320 (license license:gpl2+)))
19322 (define-public r-sparselda
19324 (name "r-sparselda")
19329 (uri (cran-uri "sparseLDA" version))
19332 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19333 (properties `((upstream-name . "sparseLDA")))
19334 (build-system r-build-system)
19336 `(("r-elasticnet" ,r-elasticnet)
19339 (home-page "https://www.imm.dtu.dk/~lkhc/")
19340 (synopsis "Sparse discriminant analysis")
19342 "This package performs sparse linear discriminant analysis for Gaussians
19343 and mixture of Gaussian models.")
19344 (license license:gpl2+)))
19346 (define-public r-accsda
19353 (uri (cran-uri "accSDA" version))
19356 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19357 (properties `((upstream-name . "accSDA")))
19358 (build-system r-build-system)
19360 `(("r-ggplot2" ,r-ggplot2)
19361 ("r-ggthemes" ,r-ggthemes)
19362 ("r-gridextra" ,r-gridextra)
19364 ("r-rarpack" ,r-rarpack)
19365 ("r-sparselda" ,r-sparselda)))
19366 (home-page "https://github.com/gumeo/accSDA/wiki")
19367 (synopsis "Accelerated sparse discriminant analysis")
19369 "This package provides an implementation of sparse linear discriminant
19370 analysis, which is a supervised classification method for multiple classes.
19371 Various novel optimization approaches to this problem are implemented
19372 including @dfn{alternating direction method of multipliers} (ADMM),
19373 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19374 Functions for performing cross validation are also supplied along with basic
19375 prediction and plotting functions. @dfn{Sparse zero variance
19376 discriminant} (SZVD) analysis is also included in the package.")
19377 (license license:gpl2+)))
19379 (define-public r-ace2fastq
19381 (name "r-ace2fastq")
19386 (uri (cran-uri "ace2fastq" version))
19389 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19390 (properties `((upstream-name . "ace2fastq")))
19391 (build-system r-build-system)
19393 `(("r-stringr" ,r-stringr)))
19394 (home-page "https://github.com/c5sire/ace2fastq")
19395 (synopsis "ACE file to FASTQ converter")
19397 "The ACE file format is used in genomics to store contigs from sequencing
19398 machines. This tools converts it into FASTQ format. Both formats contain the
19399 sequence characters and their corresponding quality information. Unlike the
19400 FASTQ file, the ACE file stores the quality values numerically. The
19401 conversion algorithm uses the standard Sanger formula. The package
19402 facilitates insertion into pipelines, and content inspection.")
19403 (license license:gpl3)))
19405 (define-public r-rngwell
19412 (uri (cran-uri "rngWELL" version))
19415 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19416 (properties `((upstream-name . "rngWELL")))
19417 (build-system r-build-system)
19418 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19419 (synopsis "Toolbox for WELL random number generators")
19421 "This is a dedicated package to WELL pseudo random generators, which were
19422 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19423 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19424 (license license:bsd-3)))
19426 (define-public r-randtoolbox
19428 (name "r-randtoolbox")
19433 (uri (cran-uri "randtoolbox" version))
19436 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19437 (properties `((upstream-name . "randtoolbox")))
19438 (build-system r-build-system)
19440 `(("r-rngwell" ,r-rngwell)))
19442 `(("gfortran" ,gfortran)))
19443 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19444 (synopsis "Toolbox for pseudo and quasi random number generation")
19446 "This package provides
19449 @item pseudo random generators, such as general linear
19450 congruential generators, multiple recursive generators and generalized
19451 feedback shift register (SF-Mersenne Twister algorithm and WELL
19454 @item quasi random generators, such as the Torus algorithm, the Sobol
19455 sequence, the Halton sequence (including the Van der Corput sequence), and
19457 @item some generator tests: the gap test, the serial test, the poker test.
19460 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19461 (license license:bsd-3)))
19463 (define-public r-lhs
19470 (uri (cran-uri "lhs" version))
19473 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19474 (properties `((upstream-name . "lhs")))
19475 (build-system r-build-system)
19476 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19478 `(("r-knitr" ,r-knitr)))
19479 (home-page "https://github.com/bertcarnell/lhs")
19480 (synopsis "Latin Hypercube Samples")
19482 "This package provides a number of methods for creating and augmenting
19483 Latin Hypercube Samples.")
19484 (license license:gpl3)))
19486 (define-public r-acebayes
19488 (name "r-acebayes")
19493 (uri (cran-uri "acebayes" version))
19496 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19497 (properties `((upstream-name . "acebayes")))
19498 (build-system r-build-system)
19500 `(("r-compare" ,r-compare)
19502 ("r-randtoolbox" ,r-randtoolbox)
19504 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19505 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19506 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19508 "Finding an optimal Bayesian experimental design involves maximizing an
19509 objective function given by the expectation of some appropriately chosen
19510 utility function with respect to the joint distribution of unknown
19511 quantities (including responses). This objective function is usually not
19512 available in closed form and the design space can be continuous and of high
19513 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19514 to maximise an approximation to the expectation of the utility function.")
19515 (license license:gpl2)))
19517 (define-public r-acet
19524 (uri (cran-uri "ACEt" version))
19527 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19528 (properties `((upstream-name . "ACEt")))
19529 (build-system r-build-system)
19534 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19535 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19536 (synopsis "Estimating dynamic heritability and twin model comparison")
19538 "This package supports twin models that are able to estimate the dynamic
19539 behaviour of the variance components in the classical twin models with respect
19540 to age using B-splines and P-splines.")
19541 (license license:gpl2+)))
19543 (define-public r-acfmperiod
19545 (name "r-acfmperiod")
19550 (uri (cran-uri "acfMPeriod" version))
19553 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19554 (properties `((upstream-name . "acfMPeriod")))
19555 (build-system r-build-system)
19557 `(("r-mass" ,r-mass)))
19558 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19559 (synopsis "Estimation of the ACF from the M-periodogram")
19561 "This package support non-robust and robust computations of the sample
19562 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19563 univariate and multivariate processes. The methodology consists in reversing
19564 the diagonalization procedure involving the periodogram or the
19565 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19566 ACOVF or the ACF as discussed in Fuller (1995)
19567 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19568 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19569 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19570 (license license:gpl2+)))
19572 (define-public r-gamlss-data
19574 (name "r-gamlss-data")
19579 (uri (cran-uri "gamlss.data" version))
19582 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19583 (properties `((upstream-name . "gamlss.data")))
19584 (build-system r-build-system)
19585 (home-page "http://www.gamlss.org/")
19586 (synopsis "GAMLSS data")
19588 "This package provides data used as examples to demonstrate GAMLSS
19590 ;; Either version of the license
19591 (license (list license:gpl2 license:gpl3))))
19593 (define-public r-gamlss
19600 (uri (cran-uri "gamlss" version))
19603 "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr"))))
19604 (properties `((upstream-name . "gamlss")))
19605 (build-system r-build-system)
19607 `(("r-gamlss-data" ,r-gamlss-data)
19608 ("r-gamlss-dist" ,r-gamlss-dist)
19611 ("r-survival" ,r-survival)))
19612 (home-page "http://www.gamlss.org/")
19613 (synopsis "Generalized additive models for location scale and shape")
19615 "This package provides functions for fitting the generalized additive
19616 models for location scale and shape introduced by Rigby and
19617 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19618 use a distributional regression approach where all the parameters of the
19619 conditional distribution of the response variable are modelled using
19620 explanatory variables.")
19621 ;; Either version of the license
19622 (license (list license:gpl2 license:gpl3))))
19624 (define-public r-acid
19631 (uri (cran-uri "acid" version))
19634 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19635 (properties `((upstream-name . "acid")))
19636 (build-system r-build-system)
19638 `(("r-gamlss" ,r-gamlss)
19639 ("r-gamlss-dist" ,r-gamlss-dist)
19640 ("r-hmisc" ,r-hmisc)))
19641 (home-page "https://cran.r-project.org/web/packages/acid/")
19642 (synopsis "Analysing conditional income distributions")
19644 "This package provides functions for the analysis of income distributions
19645 for subgroups of the population as defined by a set of variables like age,
19646 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19647 distribution as well as functions for moments, inequality measures, entropy
19648 measures and polarisation measures of income distributions. This package thus
19649 aides the analysis of income inequality by offering tools for the exploratory
19650 analysis of income distributions at the disaggregated level.")
19651 (license license:gpl3)))
19653 (define-public r-acm4r
19660 (uri (cran-uri "acm4r" version))
19663 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19664 (properties `((upstream-name . "acm4r")))
19665 (build-system r-build-system)
19666 (propagated-inputs `(("r-mass" ,r-mass)))
19667 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19668 (synopsis "Align-and-count method comparisons of RFLP data")
19670 "This is a package to compare sequence fragment lengths or molecular
19671 weights from pairs of lanes. The number of matching bands in the
19672 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19673 the align-and-count method.")
19674 ;; Any version of the GPL
19675 (license (list license:gpl2+ license:gpl3+))))
19677 (define-public r-filelock
19679 (name "r-filelock")
19684 (uri (cran-uri "filelock" version))
19687 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19688 (properties `((upstream-name . "filelock")))
19689 (build-system r-build-system)
19690 (home-page "https://github.com/r-lib/filelock")
19691 (synopsis "Portable file locking")
19693 "This library lets you place an exclusive or shared lock on a file using
19694 the appropriate system call provided by the underlying operating system.")
19695 (license license:expat)))
19697 (define-public r-filematrix
19699 (name "r-filematrix")
19704 (uri (cran-uri "filematrix" version))
19707 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19708 (properties `((upstream-name . "filematrix")))
19709 (build-system r-build-system)
19710 ;; These inputs are needed for vignettes
19712 `(("r-knitr" ,r-knitr)
19713 ("r-rmarkdown" ,r-rmarkdown)
19714 ("pandoc-citeproc" ,pandoc-citeproc)))
19715 (home-page "https://github.com/andreyshabalin/filematrix")
19716 (synopsis "File-backed matrix class with convenient read and write access")
19718 "This package provides an interface for working with large matrices
19719 stored in files, not in computer memory. It supports multiple non-character
19720 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19721 byte real values). Access to parts of the matrix is done by indexing, exactly
19722 as with usual R matrices. It supports very large matrices; the package has
19723 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19724 columns, ad allows for quick addition of extra columns to a filematrix.")
19725 (license license:lgpl3)))
19727 (define-public r-acmeeqtl
19729 (name "r-acmeeqtl")
19734 (uri (cran-uri "ACMEeqtl" version))
19737 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19738 (properties `((upstream-name . "ACMEeqtl")))
19739 (build-system r-build-system)
19741 `(("r-filematrix" ,r-filematrix)))
19742 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19743 (synopsis "Estimation of interpretable eQTL effect sizes")
19745 "This package provides a non-linear model, termed ACME, that reflects a
19746 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19747 With non-linear least-squares algorithm the maximum likelihood parameters can
19748 be estimated. The ACME model provides interpretable effect size estimates and
19749 p-values with well controlled Type-I error.")
19750 (license license:lgpl3)))
19752 (define-public r-acmer
19759 (uri (cran-uri "acmeR" version))
19762 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19763 (properties `((upstream-name . "acmeR")))
19764 (build-system r-build-system)
19765 (propagated-inputs `(("r-foreign" ,r-foreign)))
19766 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19767 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19769 "This package provides an implementation of the ACME estimator, described
19770 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19771 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19772 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19773 as carcasses age; variable bleed-through at successive searches; and interval
19774 mortality estimates. The package provides, based on search data, functions
19775 for estimating the mortality inflation factor in Frequentist and Bayesian
19777 (license license:expat)))
19779 (define-public r-r-huge
19786 (uri (cran-uri "R.huge" version))
19789 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19790 (properties `((upstream-name . "R.huge")))
19791 (build-system r-build-system)
19793 `(("r-r-methodss3" ,r-r-methodss3)
19795 ("r-r-utils" ,r-r-utils)))
19796 (home-page "https://github.com/HenrikBengtsson/R.huge")
19797 (synopsis "Methods for accessing huge amounts of data")
19799 "This is a deprecated package for accessing huge amounts of data.
19800 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19801 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19802 the @code{aroma.affymetrix} package.")
19803 (license license:lgpl2.1+)))
19805 (define-public r-r-filesets
19807 (name "r-r-filesets")
19812 (uri (cran-uri "R.filesets" version))
19815 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19816 (properties `((upstream-name . "R.filesets")))
19817 (build-system r-build-system)
19819 `(("r-digest" ,r-digest)
19820 ("r-r-cache" ,r-r-cache)
19821 ("r-r-methodss3" ,r-r-methodss3)
19823 ("r-r-utils" ,r-r-utils)))
19824 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19825 (synopsis "Easy handling of and access to files")
19827 "This package provides classes and methods to locate, setup, subset,
19828 navigate and iterate file sets, i.e. sets of files located in one or more
19829 directories on the file system. The API is designed such that these classes
19830 can be extended via inheritance to provide a richer API for special file
19831 formats. Moreover, a specific name format is defined such that filenames and
19832 directories can be considered to have full names which consists of a name
19833 followed by comma-separated tags. This adds additional flexibility to
19834 identify file sets and individual files.")
19835 (license license:lgpl2.1+)))
19837 (define-public r-r-devices
19839 (name "r-r-devices")
19844 (uri (cran-uri "R.devices" version))
19847 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19848 (properties `((upstream-name . "R.devices")))
19849 (build-system r-build-system)
19851 `(("r-base64enc" ,r-base64enc)
19852 ("r-r-methodss3" ,r-r-methodss3)
19854 ("r-r-utils" ,r-r-utils)))
19855 (home-page "https://github.com/HenrikBengtsson/R.devices")
19856 (synopsis "Unified handling of graphics devices")
19858 "This package provides functions for creating plots and image files in a
19859 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19860 Default device options as well as scales and aspect ratios are controlled in a
19861 uniform way across all device types. Switching output format requires minimal
19862 changes in code. This package is ideal for large-scale batch processing,
19863 because it will never leave open graphics devices or incomplete image files
19864 behind, even on errors or user interrupts.")
19865 (license license:lgpl2.1+)))
19867 (define-public r-acnr
19874 (uri (cran-uri "acnr" version))
19877 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19878 (properties `((upstream-name . "acnr")))
19879 (build-system r-build-system)
19880 (home-page "https://github.com/mpierrejean/acnr")
19881 (synopsis "Annotated copy-number regions")
19883 "This package provides SNP array data from different types of copy-number
19884 regions. These regions were identified manually by the authors of the package
19885 and may be used to generate realistic data sets with known truth.")
19886 (license license:lgpl2.1+)))
19888 (define-public r-acopula
19895 (uri (cran-uri "acopula" version))
19898 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19899 (properties `((upstream-name . "acopula")))
19900 (build-system r-build-system)
19901 (home-page "https://cran.r-project.org/web/packages/acopula/")
19902 (synopsis "Modelling dependence with multivariate Archimax copulas")
19904 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19905 package provides definitions of several parametric families of generator and
19906 dependence function, computes CDF and PDF, estimates parameters, tests for
19907 goodness of fit, generates random sample and checks copula properties for
19908 custom constructs. In the 2-dimensional case explicit formulas for density
19909 are used, contrary to higher dimensions when all derivatives are linearly
19910 approximated. Several non-archimax families (normal, FGM, Plackett) are
19911 provided as well.")
19912 (license license:gpl2)))
19914 (define-public r-tuner
19921 (uri (cran-uri "tuneR" version))
19924 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19925 (properties `((upstream-name . "tuneR")))
19926 (build-system r-build-system)
19927 (propagated-inputs `(("r-signal" ,r-signal)))
19928 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19929 (synopsis "Analysis of music and speech")
19931 "This is a package for the analysis of music and speech. Analyze music
19932 and speech, extract features like MFCCs, handle wave files and their
19933 representation in various ways, read MP3, read MIDI, perform steps of a
19934 transcription, ...")
19935 ;; Either of these versions.
19936 (license (list license:gpl2 license:gpl3))))
19938 (define-public r-seewave
19945 (uri (cran-uri "seewave" version))
19948 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19949 (properties `((upstream-name . "seewave")))
19950 (build-system r-build-system)
19952 `(("libsndfile" ,libsndfile)))
19954 `(("r-tuner" ,r-tuner)))
19955 (home-page "http://rug.mnhn.fr/seewave")
19956 (synopsis "Sound analysis and synthesis")
19958 "This package provides functions for analysing, manipulating, displaying,
19959 editing and synthesizing time waves (particularly sound). This package
19960 processes time analysis (oscillograms and envelopes), spectral content,
19961 resonance quality factor, entropy, cross correlation and autocorrelation,
19962 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19963 and 3D spectrograms and many other analyses.")
19964 (license license:gpl2+)))
19966 (define-public r-acousticndlcoder
19968 (name "r-acousticndlcoder")
19973 (uri (cran-uri "AcousticNDLCodeR" version))
19976 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19978 `((upstream-name . "AcousticNDLCodeR")))
19979 (build-system r-build-system)
19981 `(("r-seewave" ,r-seewave)
19982 ("r-tuner" ,r-tuner)
19984 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19985 (synopsis "Coding sound files for use with NDL")
19987 "Make acoustic cues to use with the R package @code{ndl}.
19988 The package implements functions used in the PLoS ONE paper \"Words from
19989 spontaneous conversational speech can be recognized with human-like accuracy
19990 by an error-driven learning algorithm that discriminates between meanings
19991 straight from smart acoustic features, bypassing the phoneme as recognition
19992 unit.\" @url{doi:10.1371/journal.pone.0174623}")
19993 (license license:gpl2+)))
19995 (define-public r-acp
20002 (uri (cran-uri "acp" version))
20005 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
20006 (properties `((upstream-name . "acp")))
20007 (build-system r-build-system)
20009 `(("r-quantmod" ,r-quantmod)
20010 ("r-tseries" ,r-tseries)))
20011 (home-page "https://cran.r-project.org/web/packages/acp/")
20012 (synopsis "Autoregressive conditional Poisson")
20014 "This package supports the analysis of count data exhibiting
20015 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
20016 model (ACP(p,q)) proposed by Heinen (2003).")
20017 (license license:gpl2)))
20019 (define-public r-ada
20026 (uri (cran-uri "ada" version))
20029 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20030 (properties `((upstream-name . "ada")))
20031 (build-system r-build-system)
20032 (propagated-inputs `(("r-rpart" ,r-rpart)))
20033 (home-page "https://cran.r-project.org/web/packages/ada/")
20034 (synopsis "Stochastic boosting")
20036 "This package provides a straightforward, well-documented, and broad
20037 boosting routine for classification, ideally suited for small to
20038 moderate-sized data sets. It performs discrete, real, and gentle boost under
20039 both exponential and logistic loss on a given data set.")
20040 ;; Any version of the GPL.
20041 (license (list license:gpl2+ license:gpl3+))))
20043 (define-public r-genalg
20050 (uri (cran-uri "genalg" version))
20053 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20054 (properties `((upstream-name . "genalg")))
20055 (build-system r-build-system)
20056 (home-page "https://github.com/egonw/genalg")
20057 (synopsis "R based genetic algorithm")
20059 "This package provides an R based genetic algorithm for binary and
20060 floating point chromosomes.")
20061 (license license:gpl2)))
20063 (define-public r-kernelfactory
20065 (name "r-kernelfactory")
20070 (uri (cran-uri "kernelFactory" version))
20073 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20074 (properties `((upstream-name . "kernelFactory")))
20075 (build-system r-build-system)
20078 ("r-genalg" ,r-genalg)
20079 ("r-kernlab" ,r-kernlab)
20080 ("r-randomforest" ,r-randomforest)))
20081 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20082 (synopsis "Ensemble of kernel machines")
20084 "Kernel factory is an ensemble method where each base classifier (random
20085 forest) is fit on the kernel matrix of a subset of the training data.")
20086 (license license:gpl2+)))
20088 (define-public r-dummies
20095 (uri (cran-uri "dummies" version))
20098 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20099 (properties `((upstream-name . "dummies")))
20100 (build-system r-build-system)
20101 (home-page "https://decisionpatterns.com")
20102 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20104 "This package lets you expand factors, characters and other eligible
20105 classes into dummy/indicator variables.")
20106 (license license:gpl2+)))
20108 (define-public r-acrm
20115 (uri (cran-uri "aCRM" version))
20118 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20119 (properties `((upstream-name . "aCRM")))
20120 (build-system r-build-system)
20123 ("r-dummies" ,r-dummies)
20124 ("r-kernelfactory" ,r-kernelfactory)
20125 ("r-randomforest" ,r-randomforest)))
20126 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20127 (synopsis "Convenience functions for analytical customer relationship management")
20129 "This package provides convenience functions for data preparation and
20130 modeling often used in @dfn{analytical customer relationship
20131 management} (aCRM).")
20132 (license license:gpl2+)))
20134 (define-public r-treeclust
20136 (name "r-treeclust")
20141 (uri (cran-uri "treeClust" version))
20144 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20145 (properties `((upstream-name . "treeClust")))
20146 (build-system r-build-system)
20148 `(("r-cluster" ,r-cluster)
20149 ("r-rpart" ,r-rpart)))
20150 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20151 (synopsis "Cluster distances through trees")
20153 "This package provides tools to create a measure of inter-point
20154 dissimilarity useful for clustering mixed data, and, optionally, perform the
20156 (license license:gpl2+)))
20158 (define-public r-acrosstic
20160 (name "r-acrosstic")
20165 (uri (cran-uri "AcrossTic" version))
20168 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20169 (properties `((upstream-name . "AcrossTic")))
20170 (build-system r-build-system)
20172 `(("r-lpsolve" ,r-lpsolve)
20173 ("r-treeclust" ,r-treeclust)))
20174 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20175 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20177 "This is a package for constructing minimum-cost regular spanning
20178 subgraph as part of a non-parametric two-sample test for equality of
20180 (license license:gpl2+)))
20182 (define-public r-acrt
20189 (uri (cran-uri "acrt" version))
20192 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20193 (properties `((upstream-name . "acrt")))
20194 (build-system r-build-system)
20196 `(("r-rcpp" ,r-rcpp)
20197 ("r-rcppeigen" ,r-rcppeigen)
20198 ("r-sandwich" ,r-sandwich)))
20199 (home-page "https://cran.r-project.org/web/packages/acrt/")
20200 (synopsis "Autocorrelation robust testing")
20202 "This package provides functions for testing affine hypotheses on the
20203 regression coefficient vector in regression models with autocorrelated
20205 (license license:gpl2)))
20207 (define-public r-acs
20214 (uri (cran-uri "acs" version))
20217 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20218 (properties `((upstream-name . "acs")))
20219 (build-system r-build-system)
20221 `(("r-httr" ,r-httr)
20224 ("r-stringr" ,r-stringr)
20226 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20227 (synopsis "Work with data from the US Census")
20229 "This package provides a general toolkit for downloading, managing,
20230 analyzing, and presenting data from the
20231 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20232 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20233 American Community Survey (ACS). Confidence intervals provided with ACS data
20234 are converted to standard errors to be bundled with estimates in complex
20235 @code{acs} objects. The package provides new methods to conduct standard
20236 operations on @code{acs} objects and present/plot data in statistically
20237 appropriate ways.")
20238 (license license:gpl3)))
20240 (define-public r-acss-data
20242 (name "r-acss-data")
20247 (uri (cran-uri "acss.data" version))
20250 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20251 (properties `((upstream-name . "acss.data")))
20252 (build-system r-build-system)
20253 (home-page "http://complexitycalculator.com/methodology.html")
20254 (synopsis "Data for algorithmic complexity of short strings")
20256 "This is a data only package providing the algorithmic complexity of
20257 short strings, computed using the coding theorem method. For a given set of
20258 symbols in a string, all possible or a large number of random samples of
20259 Turing machines with a given number of states (e.g., 5) and number of symbols
20260 corresponding to the number of symbols in the strings were simulated until
20261 they reached a halting state or failed to end. This package contains data on
20262 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20263 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20264 distribution of the halting states.")
20265 (license license:gpl2+)))
20267 (define-public r-acss
20274 (uri (cran-uri "acss" version))
20277 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20278 (properties `((upstream-name . "acss")))
20279 (build-system r-build-system)
20281 `(("r-acss-data" ,r-acss-data)
20283 (home-page "http://complexitycalculator.com/methodology.html")
20284 (synopsis "Algorithmic complexity for short strings")
20286 "The main purpose of this package is to provide the algorithmic
20287 complexity for short strings, an approximation of the Kolmogorov Complexity of
20288 a short string using the coding theorem method. While the database containing
20289 the complexity is provided in the data only package @code{acss.data}, this
20290 package provides functions accessing the data such as @code{prob_random}
20291 returning the posterior probability that a given string was produced by a
20292 random process. In addition, two traditional (but problematic) measures of
20293 complexity are also provided: entropy and change complexity.")
20294 (license license:gpl2+)))
20296 (define-public r-acswr
20303 (uri (cran-uri "ACSWR" version))
20306 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20307 (properties `((upstream-name . "ACSWR")))
20308 (build-system r-build-system)
20310 `(("r-mass" ,r-mass)))
20311 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20312 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20314 "This is a companion package for the book \"A Course in Statistics with
20315 R\" (ISBN 978-1-119-15272-9.)")
20316 (license license:gpl2)))
20318 (define-public r-alabama
20321 (version "2015.3-1")
20325 (uri (cran-uri "alabama" version))
20328 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20329 (properties `((upstream-name . "alabama")))
20330 (build-system r-build-system)
20331 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20332 (home-page "https://cran.r-project.org/web/packages/alabama/")
20333 (synopsis "Constrained nonlinear optimization")
20335 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20336 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20337 constraints. Linear or nonlinear equality and inequality constraints are
20339 (license license:gpl2+)))
20341 (define-public r-gdina
20348 (uri (cran-uri "GDINA" version))
20351 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20352 (properties `((upstream-name . "GDINA")))
20353 (build-system r-build-system)
20355 `(("r-alabama" ,r-alabama)
20356 ("r-ggplot2" ,r-ggplot2)
20358 ("r-nloptr" ,r-nloptr)
20359 ("r-numderiv" ,r-numderiv)
20361 ("r-rcpparmadillo" ,r-rcpparmadillo)
20362 ("r-rsolnp" ,r-rsolnp)
20363 ("r-shiny" ,r-shiny)
20364 ("r-shinydashboard" ,r-shinydashboard)))
20366 `(("r-knitr" ,r-knitr)))
20367 (home-page "https://github.com/Wenchao-Ma/GDINA")
20368 (synopsis "Generalized DINA model framework")
20370 "This package provides a set of psychometric tools for cognitive
20371 diagnosis modeling based on the generalized deterministic inputs, noisy and
20372 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20373 and its extensions, including the sequential G-DINA model by Ma and de la
20374 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20375 polytomous G-DINA model by Chen and de la Torre
20376 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20377 distribution can be independent, saturated, higher-order, loglinear smoothed
20378 or structured. Q-matrix validation, item and model fit statistics, model
20379 comparison at test and item level and differential item functioning can also
20380 be conducted. A graphical user interface is also provided.")
20381 (license license:gpl3)))
20383 (define-public r-actcd
20390 (uri (cran-uri "ACTCD" version))
20393 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20394 (properties `((upstream-name . "ACTCD")))
20395 (build-system r-build-system)
20397 `(("r-gdina" ,r-gdina)
20398 ("r-r-methodss3" ,r-r-methodss3)))
20400 `(("gfortran" ,gfortran)))
20401 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20402 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20404 "This is a package supporting cluster analysis for cognitive diagnosis
20405 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20406 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20407 sum-scores, cluster analysis techniques can be used to classify examinees into
20408 latent classes based on their attribute patterns. In addition to the
20409 algorithms used to classify data, three labeling approaches are proposed to
20410 label clusters so that examinees' attribute profiles can be obtained.")
20411 (license license:gpl2+)))
20413 (define-public r-ineq
20420 (uri (cran-uri "ineq" version))
20423 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20424 (properties `((upstream-name . "ineq")))
20425 (build-system r-build-system)
20426 (home-page "https://cran.r-project.org/web/packages/ineq/")
20427 (synopsis "Measuring inequality, concentration, and poverty")
20429 "This package provides tools for measuring inequality, concentration, and
20430 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20431 ;; Either of these two versions.
20432 (license (list license:gpl2 license:gpl3))))
20434 (define-public r-actfrag
20441 (uri (cran-uri "ActFrag" version))
20444 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20445 (properties `((upstream-name . "ActFrag")))
20446 (build-system r-build-system)
20448 `(("r-accelerometry" ,r-accelerometry)
20449 ("r-dplyr" ,r-dplyr)
20451 ("r-survival" ,r-survival)
20452 ("r-tidyr" ,r-tidyr)))
20453 (home-page "https://github.com/junruidi/ActFrag")
20454 (synopsis "Activity fragmentation metrics extraction")
20456 "This package provides functions to extract commonly used fragmentation
20457 metrics to quantify time accumulation strategies based on minute level
20458 actigraphy-measured activity counts data.")
20459 (license license:gpl3)))
20461 (define-public r-ash
20468 (uri (cran-uri "ash" version))
20471 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20472 (properties `((upstream-name . "ash")))
20473 (build-system r-build-system)
20474 (native-inputs `(("gfortran" ,gfortran)))
20475 (home-page "https://cran.r-project.org/web/packages/ash/")
20476 (synopsis "David Scott's ASH routines")
20478 "This package provides David Scott's ASH routines ported from S-PLUS to
20480 (license license:gpl2+)))
20482 (define-public r-hdrcde
20489 (uri (cran-uri "hdrcde" version))
20492 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20493 (properties `((upstream-name . "hdrcde")))
20494 (build-system r-build-system)
20497 ("r-ggplot2" ,r-ggplot2)
20498 ("r-kernsmooth" ,r-kernsmooth)
20500 ("r-locfit" ,r-locfit)
20501 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20502 (native-inputs `(("gfortran" ,gfortran)))
20503 (home-page "http://pkg.robjhyndman.com/hdrcde")
20504 (synopsis "Highest density regions and conditional density estimation")
20506 "This is a package for the computation of highest density regions in one
20507 and two dimensions, kernel estimation of univariate density functions
20508 conditional on one covariate, and multimodal regression.")
20509 (license license:gpl3)))
20511 (define-public r-rainbow
20518 (uri (cran-uri "rainbow" version))
20521 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20522 (properties `((upstream-name . "rainbow")))
20523 (build-system r-build-system)
20525 `(("r-cluster" ,r-cluster)
20526 ("r-colorspace" ,r-colorspace)
20527 ("r-hdrcde" ,r-hdrcde)
20530 ("r-pcapp" ,r-pcapp)))
20531 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20532 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20534 "This is a package for visualizing functional data and identifying
20535 functional outliers with bagplots, boxplots and rainbow plots.")
20536 (license license:gpl3)))
20538 (define-public r-fds
20545 (uri (cran-uri "fds" version))
20548 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20549 (properties `((upstream-name . "fds")))
20550 (build-system r-build-system)
20552 `(("r-rainbow" ,r-rainbow)
20553 ("r-rcurl" ,r-rcurl)))
20554 (home-page "https://cran.r-project.org/web/packages/fds/")
20555 (synopsis "Functional data sets")
20556 (description "This package contains a list of functional time series,
20557 sliced functional time series, and functional data sets. Functional time
20558 series is a special type of functional data observed over time. Sliced
20559 functional time series is a special type of functional time series with a time
20560 variable observed over time.")
20561 (license license:gpl2+)))
20563 (define-public r-fda
20570 (uri (cran-uri "fda" version))
20573 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20574 (properties `((upstream-name . "fda")))
20575 (build-system r-build-system)
20578 ("r-matrix" ,r-matrix)))
20579 (home-page "https://www.functionaldata.org")
20580 (synopsis "Functional data analysis")
20582 "These functions were developed to support functional data analysis as
20583 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20584 Analysis. The package includes data sets and script files working many
20586 (license license:gpl2+)))
20588 (define-public r-actigraphy
20590 (name "r-actigraphy")
20595 (uri (cran-uri "Actigraphy" version))
20598 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20599 (properties `((upstream-name . "Actigraphy")))
20600 (build-system r-build-system)
20602 `(("r-fda" ,r-fda)))
20603 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20604 (synopsis "Actigraphy data analysis")
20606 "This package provides tools for functional linear modeling and analysis
20607 of actigraphy data.")
20608 (license license:asl2.0)))
20610 (define-public r-activedriver
20612 (name "r-activedriver")
20617 (uri (cran-uri "ActiveDriver" version))
20620 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20621 (properties `((upstream-name . "ActiveDriver")))
20622 (build-system r-build-system)
20624 `(("r-mass" ,r-mass)))
20625 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20626 (synopsis "Tools for finding cancer driver proteins")
20628 "This package provides a mutation analysis tool that discovers cancer
20629 driver genes with frequent mutations in protein signalling sites such as
20630 post-translational modifications (phosphorylation, ubiquitination, etc). The
20631 Poisson generalized linear regression model identifies genes where cancer
20632 mutations in signalling sites are more frequent than expected from the
20633 sequence of the entire gene. Integration of mutations with signalling
20634 information helps find new driver genes and propose candidate mechanisms to
20636 (license license:gpl2+)))
20638 (define-public r-activitycounts
20640 (name "r-activitycounts")
20645 (uri (cran-uri "activityCounts" version))
20648 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20650 `((upstream-name . "activityCounts")))
20651 (build-system r-build-system)
20653 `(("r-lubridate" ,r-lubridate)
20654 ("r-magrittr" ,r-magrittr)
20655 ("r-seewave" ,r-seewave)
20656 ("r-signal" ,r-signal)
20657 ("r-tibble" ,r-tibble)))
20658 (home-page "https://github.com/walkabillylab/activityCounts")
20659 (synopsis "Generate ActiLife counts")
20661 "ActiLife generates activity counts from data collected by Actigraph
20662 accelerometers. Actigraph is one of the most common research-grade
20663 accelerometers. There is considerable research validating and developing
20664 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20665 counts are proprietary and difficult to implement if researchers use different
20666 accelerometer brands. The code creates ActiLife counts from raw acceleration
20667 data for different accelerometer brands.")
20668 (license license:gpl3)))
20670 (define-public r-activityindex
20672 (name "r-activityindex")
20677 (uri (cran-uri "ActivityIndex" version))
20680 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20681 (properties `((upstream-name . "ActivityIndex")))
20682 (build-system r-build-system)
20684 `(("r-data-table" ,r-data-table)
20685 ("r-matrixstats" ,r-matrixstats)
20686 ("r-r-utils" ,r-r-utils)))
20688 `(("r-knitr" ,r-knitr)))
20689 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20690 (synopsis "Activity Index calculation using raw accelerometry data")
20692 "This is a package to read raw accelerometry from GT3X+ accelerometry
20693 data and plain table data to calculate the Activity Index from Bai et
20694 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20695 (license license:gpl3)))
20697 (define-public r-activpal
20699 (name "r-activpal")
20704 (uri (cran-uri "activPAL" version))
20707 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20708 (properties `((upstream-name . "activPAL")))
20709 (build-system r-build-system)
20711 `(("r-devtools" ,r-devtools)
20712 ("r-dplyr" ,r-dplyr)
20713 ("r-ggplot2" ,r-ggplot2)
20714 ("r-lubridate" ,r-lubridate)
20715 ("r-magrittr" ,r-magrittr)
20716 ("r-tidyr" ,r-tidyr)))
20717 (home-page "https://cran.r-project.org/web/packages/activPAL")
20718 (synopsis "Processing and chart generation from activPAL events files")
20720 "This package contains functions to generate pre-defined summary
20721 statistics from activPAL events files. The package also contains functions to
20722 produce informative graphics that visualize physical activity behaviour and
20723 trends. This includes generating graphs that align physical activity
20724 behaviour with additional time based observations described by other data
20725 sets, such as sleep diaries and continuous glucose monitoring data.")
20726 (license license:gpl3)))
20728 (define-public r-activpalprocessing
20730 (name "r-activpalprocessing")
20735 (uri (cran-uri "activpalProcessing" version))
20738 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20740 `((upstream-name . "activpalProcessing")))
20741 (build-system r-build-system)
20743 `(("r-chron" ,r-chron)))
20744 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20745 (synopsis "Process activPAL events files")
20747 "This package performs estimation of physical activity and sedentary
20748 behavior variables from activPAL events files.")
20749 ;; Either version of the GPL.
20750 (license (list license:gpl2 license:gpl3))))
20752 (define-public r-actogrammr
20754 (name "r-actogrammr")
20759 (uri (cran-uri "actogrammr" version))
20762 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20763 (properties `((upstream-name . "actogrammr")))
20764 (build-system r-build-system)
20766 `(("r-dplyr" ,r-dplyr)
20767 ("r-ggplot2" ,r-ggplot2)
20768 ("r-lubridate" ,r-lubridate)
20769 ("r-readr" ,r-readr)
20770 ("r-tidyr" ,r-tidyr)))
20771 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20772 (synopsis "Read in activity data and plot actograms")
20774 "Read in activity measurements from standard file formats used by
20775 circadian rhythm researchers, currently only ClockLab format, and process and
20776 plot the data. The central type of plot is the actogram, as first described
20777 in \"Activity and distribution of certain wild mice in relation to biotic
20778 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20779 (license license:gpl3)))
20781 (define-public r-expint
20788 (uri (cran-uri "expint" version))
20791 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20792 (properties `((upstream-name . "expint")))
20793 (build-system r-build-system)
20794 (home-page "https://gitlab.com/vigou3/expint")
20795 (synopsis "Exponential integral and incomplete Gamma function")
20797 "This package provides the exponential integrals @code{E_1(x)},
20798 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20799 function @code{G(a, x)} defined for negative values of its first argument.
20800 The package also gives easy access to the underlying C routines through an
20801 API; see the package vignette for details.")
20802 (license license:gpl2+)))
20804 (define-public r-actuar
20811 (uri (cran-uri "actuar" version))
20814 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20815 (properties `((upstream-name . "actuar")))
20816 (build-system r-build-system)
20817 (propagated-inputs `(("r-expint" ,r-expint)))
20818 (home-page "https://gitlab.com/vigou3/actuar")
20819 (synopsis "Actuarial functions and heavy tailed distributions")
20821 "This package provides functions and data sets for actuarial science:
20822 modeling of loss distributions; risk theory and ruin theory; simulation of
20823 compound models, discrete mixtures and compound hierarchical models;
20824 credibility theory. It boasts support for many additional probability
20825 distributions to model insurance loss amounts and loss frequency: 19
20826 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20827 distribution; zero-truncated and zero-modified extensions of the standard
20828 discrete distributions. It also supports phase-type distributions commonly
20829 used to compute ruin probabilities.")
20830 (license license:gpl2+)))
20832 (define-public r-bmp
20839 (uri (cran-uri "bmp" version))
20842 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20843 (properties `((upstream-name . "bmp")))
20844 (build-system r-build-system)
20845 (home-page "https://cran.r-project.org/web/packages/bmp/")
20846 (synopsis "Read Bitmap (BMP) images")
20848 "This package provides pure R tools to read BMP format images. It is
20849 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20850 (license license:gpl2+)))
20852 (define-public r-readbitmap
20854 (name "r-readbitmap")
20859 (uri (cran-uri "readbitmap" version))
20862 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20863 (properties `((upstream-name . "readbitmap")))
20864 (build-system r-build-system)
20866 `(("libjpeg" ,libjpeg-turbo)
20867 ("libpng" ,libpng)))
20872 ("r-tiff" ,r-tiff)))
20873 (home-page "https://github.com/jefferis/readbitmap")
20874 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20876 "This package provides tools to identify and read BMP, JPEG, PNG, and
20877 TIFF format bitmap images. Identification defaults to the use of the magic
20878 number embedded in the file rather than the file extension.")
20879 (license license:gpl2+)))
20881 (define-public r-imager
20888 (uri (cran-uri "imager" version))
20891 "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd"))))
20892 (properties `((upstream-name . "imager")))
20893 (build-system r-build-system)
20896 ("libtiff" ,libtiff)
20900 `(("r-downloader" ,r-downloader)
20901 ("r-igraph" ,r-igraph)
20903 ("r-magrittr" ,r-magrittr)
20905 ("r-purrr" ,r-purrr)
20907 ("r-readbitmap" ,r-readbitmap)
20908 ("r-stringr" ,r-stringr)))
20910 `(("pkg-config" ,pkg-config)
20911 ("r-knitr" ,r-knitr)))
20912 (home-page "https://dahtah.github.io/imager/")
20913 (synopsis "Image processing library")
20915 "This is a package for fast image processing for images in up to 4
20916 dimensions (two spatial dimensions, one time/depth dimension, one color
20917 dimension). It provides most traditional image processing tools (filtering,
20918 morphology, transformations, etc.) as well as various functions for easily
20919 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20920 simple, modern C++ library for image processing.")
20921 (license license:lgpl3)))
20923 (define-public r-acuityview
20925 (name "r-acuityview")
20930 (uri (cran-uri "AcuityView" version))
20933 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20934 (properties `((upstream-name . "AcuityView")))
20935 (build-system r-build-system)
20937 `(("r-fftwtools" ,r-fftwtools)
20938 ("r-imager" ,r-imager)
20939 ("r-plotrix" ,r-plotrix)))
20940 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20941 (synopsis "Display scenes as seen by an animal with less acute vision")
20943 "This package provides a simple method for representing a visual scene as
20944 it may be seen by an animal with less acute vision.")
20945 (license license:gpl2+)))
20947 (define-public r-caret
20954 (uri (cran-uri "caret" version))
20957 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20958 (build-system r-build-system)
20960 `(("r-foreach" ,r-foreach)
20961 ("r-ggplot2" ,r-ggplot2)
20962 ("r-lattice" ,r-lattice)
20963 ("r-modelmetrics" ,r-modelmetrics)
20967 ("r-recipes" ,r-recipes)
20968 ("r-reshape2" ,r-reshape2)
20969 ("r-withr" ,r-withr)))
20971 `(("r-knitr" ,r-knitr)))
20972 (home-page "https://github.com/topepo/caret")
20973 (synopsis "Classification and regression training")
20975 "This package provides miscellaneous functions for training and plotting
20976 classification and regression models.")
20977 (license license:gpl2+)))
20979 (define-public r-adabag
20986 (uri (cran-uri "adabag" version))
20989 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20990 (properties `((upstream-name . "adabag")))
20991 (build-system r-build-system)
20993 `(("r-caret" ,r-caret)
20994 ("r-doparallel" ,r-doparallel)
20995 ("r-foreach" ,r-foreach)
20996 ("r-rpart" ,r-rpart)))
20997 (home-page "https://cran.r-project.org/web/packages/adabag/")
20998 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
21000 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
21001 Breiman's Bagging algorithm using classification trees as individual
21002 classifiers. Once these classifiers have been trained, they can be used to
21003 predict on new data. Also, cross validation estimation of the error can be
21005 (license license:gpl2+)))
21007 (define-public r-adagio
21014 (uri (cran-uri "adagio" version))
21017 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21018 (properties `((upstream-name . "adagio")))
21019 (build-system r-build-system)
21020 (native-inputs `(("gfortran" ,gfortran)))
21021 (home-page "https://cran.r-project.org/web/packages/adagio/")
21022 (synopsis "Discrete and global optimization routines")
21024 "This package provides methods and algorithms for discrete optimization,
21025 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21026 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21028 (license license:gpl3+)))
21030 (define-public r-univoutl
21032 (name "r-univoutl")
21037 (uri (cran-uri "univOutl" version))
21040 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21041 (properties `((upstream-name . "univOutl")))
21042 (build-system r-build-system)
21044 `(("r-hmisc" ,r-hmisc)
21045 ("r-robustbase" ,r-robustbase)))
21046 (home-page "https://github.com/marcellodo/univOutl")
21047 (synopsis "Detection of univariate outliers")
21049 "This package provides well-known outlier detection techniques in the
21050 univariate case. Methods to deal with skewed distribution are included too.
21051 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21052 historical data is implemented as well. When available, survey weights can be
21053 used in outliers detection.")
21054 (license license:gpl2+)))
21056 (define-public r-tolerance
21058 (name "r-tolerance")
21063 (uri (cran-uri "tolerance" version))
21066 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21067 (properties `((upstream-name . "tolerance")))
21068 (build-system r-build-system)
21070 `(("r-mass" ,r-mass)
21072 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21073 (synopsis "Statistical tolerance intervals and regions")
21075 "This package provides functions for estimating tolerance
21076 limits (intervals) for various univariate distributions (binomial, Cauchy,
21077 discrete Pareto, exponential, two-parameter exponential, extreme value,
21078 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21079 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21080 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21081 nonparametric tolerance intervals, tolerance bands for regression
21082 settings (linear regression, nonlinear regression, nonparametric regression,
21083 and multivariate regression), and analysis of variance tolerance intervals.
21084 Visualizations are also available for most of these settings.")
21085 (license license:gpl2+)))
21087 (define-public r-additivitytests
21089 (name "r-additivitytests")
21094 (uri (cran-uri "additivityTests" version))
21097 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21099 `((upstream-name . "additivityTests")))
21100 (build-system r-build-system)
21101 (home-page "https://github.com/simecek/additivityTests")
21102 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21104 "This package provides an implementation of the Tukey, Mandel,
21105 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21106 (license license:gpl3)))
21108 (define-public r-flexclust
21110 (name "r-flexclust")
21115 (uri (cran-uri "flexclust" version))
21118 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21119 (properties `((upstream-name . "flexclust")))
21120 (build-system r-build-system)
21122 `(("r-class" ,r-class)
21123 ("r-lattice" ,r-lattice)
21124 ("r-modeltools" ,r-modeltools)))
21125 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21126 (synopsis "Flexible cluster algorithms")
21128 "The main function @code{kcca} implements a general framework for
21129 k-centroids cluster analysis supporting arbitrary distance measures and
21130 centroid computation. Further cluster methods include hard competitive
21131 learning, neural gas, and QT clustering. There are numerous visualization
21132 methods for cluster results (neighborhood graphs, convex cluster hulls,
21133 barcharts of centroids, ...), and bootstrap methods for the analysis of
21134 cluster stability.")
21135 (license license:gpl2)))
21137 (define-public r-biclust
21144 (uri (cran-uri "biclust" version))
21147 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21148 (properties `((upstream-name . "biclust")))
21149 (build-system r-build-system)
21151 `(("r-additivitytests" ,r-additivitytests)
21152 ("r-colorspace" ,r-colorspace)
21153 ("r-flexclust" ,r-flexclust)
21154 ("r-ggplot2" ,r-ggplot2)
21155 ("r-lattice" ,r-lattice)
21157 ("r-tidyr" ,r-tidyr)))
21158 (home-page "https://cran.r-project.org/web/packages/biclust/")
21159 (synopsis "BiCluster algorithms")
21161 "The main function @code{biclust()} provides several algorithms to find
21162 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21163 In addition, the package provides methods for data
21164 preprocessing (normalization and discretization), visualization, and
21165 validation of bicluster solutions.")
21166 (license license:gpl3)))
21168 (define-public r-icge
21175 (uri (cran-uri "ICGE" version))
21178 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21179 (properties `((upstream-name . "ICGE")))
21180 (build-system r-build-system)
21182 `(("r-cluster" ,r-cluster)
21183 ("r-mass" ,r-mass)))
21184 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21185 (synopsis "Cluster estimation and identification of atypical units")
21187 "ICGE is a package that helps to estimate the number of real clusters in
21188 data as well as to identify atypical units. The underlying methods are based
21189 on distances rather than on unit x variables.")
21190 (license license:gpl2+)))
21192 (define-public r-depth
21195 (version "2.1-1.1")
21199 (uri (cran-uri "depth" version))
21202 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21203 (properties `((upstream-name . "depth")))
21204 (build-system r-build-system)
21206 `(("r-abind" ,r-abind)
21207 ("r-circular" ,r-circular)
21210 `(("gfortran" ,gfortran)))
21211 (home-page "https://cran.r-project.org/web/packages/depth/")
21212 (synopsis "Nonparametric depth functions for multivariate analysis")
21214 "This package provides tools for depth functions methodology applied to
21215 multivariate analysis. Besides allowing calculation of depth values and
21216 depth-based location estimators, the package includes functions or drawing
21217 contour plots and perspective plots of depth functions. Euclidean and
21218 spherical depths are supported.")
21219 (license license:gpl2)))
21221 (define-public r-archetypes
21223 (name "r-archetypes")
21224 (version "2.2-0.1")
21228 (uri (cran-uri "archetypes" version))
21231 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21232 (properties `((upstream-name . "archetypes")))
21233 (build-system r-build-system)
21235 `(("r-modeltools" ,r-modeltools)
21236 ("r-nnls" ,r-nnls)))
21237 (home-page "https://cran.r-project.org/web/packages/archetypes")
21238 (synopsis "Archetypal analysis")
21240 "The main function @code{archetypes} implements a framework for
21241 archetypal analysis supporting arbitrary problem solving mechanisms for the
21242 different conceptual parts of the algorithm.")
21243 (license license:gpl2+)))
21245 (define-public r-shapes
21252 (uri (cran-uri "shapes" version))
21255 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21256 (properties `((upstream-name . "shapes")))
21257 (build-system r-build-system)
21259 `(("r-mass" ,r-mass)
21260 ("r-minpack-lm" ,r-minpack-lm)
21262 ("r-scatterplot3d" ,r-scatterplot3d)))
21263 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21264 (synopsis "Statistical shape analysis")
21266 "This package provides routines for the statistical analysis of landmark
21267 shapes, including Procrustes analysis, graphical displays, principal
21268 components analysis, permutation and bootstrap tests, thin-plate spline
21269 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21270 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21271 Edition), John Wiley and Sons.")
21272 (license license:gpl2)))
21274 (define-public r-anthropometry
21276 (name "r-anthropometry")
21281 (uri (cran-uri "Anthropometry" version))
21284 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21285 (properties `((upstream-name . "Anthropometry")))
21286 (build-system r-build-system)
21288 `(("r-archetypes" ,r-archetypes)
21289 ("r-biclust" ,r-biclust)
21290 ("r-cluster" ,r-cluster)
21291 ("r-depth" ,r-depth)
21296 ("r-shapes" ,r-shapes)))
21298 `(("r-knitr" ,r-knitr)))
21299 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21300 (synopsis "Statistical methods for anthropometric data")
21302 "This package provides statistical methods especially developed to
21303 analyze anthropometric data. These methods are aimed at providing effective
21304 solutions to some commons problems related to Ergonomics and Anthropometry.
21305 They are based on clustering, the statistical concept of data depth,
21306 statistical shape analysis and archetypal analysis.")
21307 (license license:gpl2+)))
21309 (define-public r-adamethods
21311 (name "r-adamethods")
21316 (uri (cran-uri "adamethods" version))
21319 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21320 (properties `((upstream-name . "adamethods")))
21321 (build-system r-build-system)
21323 `(("r-anthropometry" ,r-anthropometry)
21324 ("r-archetypes" ,r-archetypes)
21326 ("r-foreach" ,r-foreach)
21328 ("r-tolerance" ,r-tolerance)
21329 ("r-univoutl" ,r-univoutl)))
21330 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21331 (synopsis "Archetypoid algorithms and anomaly detection")
21333 "This package is a collection of several algorithms to obtain
21334 archetypoids with small and large databases and with both classical
21335 multivariate data and functional data (univariate and multivariate). Some of
21336 these algorithms also detect anomalies (outliers).")
21337 (license license:gpl2+)))
21339 (define-public r-idpmisc
21346 (uri (cran-uri "IDPmisc" version))
21349 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21350 (properties `((upstream-name . "IDPmisc")))
21351 (build-system r-build-system)
21353 `(("r-lattice" ,r-lattice)))
21354 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21355 (synopsis "Functions for data analyses and visualization")
21357 "This package provides different high-level graphics functions for
21358 displaying large datasets, displaying circular data in a very flexible way,
21359 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21360 2D-plots, creating figures with differently colored margin and plot region.
21361 In addition, the package contains auxiliary functions for data manipulation
21362 like omitting observations with irregular values or selecting data by logical
21363 vectors, which include NAs. Other functions are especially useful in
21364 spectroscopy and analyses of environmental data: robust baseline fitting,
21365 finding peaks in spectra, converting humidity measures.")
21366 (license license:gpl3+)))
21368 (define-public r-qqman
21375 (uri (cran-uri "qqman" version))
21378 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21379 (properties `((upstream-name . "qqman")))
21380 (build-system r-build-system)
21382 `(("r-calibrate" ,r-calibrate)))
21383 (home-page "https://cran.r-project.org/web/packages/qqman/")
21384 (synopsis "Q-Q and Manhattan plots for GWAS data")
21386 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21387 from PLINK results.")
21388 (license license:gpl3)))
21390 (define-public r-ggplot-multistats
21392 (name "r-ggplot-multistats")
21397 (uri (cran-uri "ggplot.multistats" version))
21400 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21402 `((upstream-name . "ggplot.multistats")))
21403 (build-system r-build-system)
21405 `(("r-ggplot2" ,r-ggplot2)
21406 ("r-hexbin" ,r-hexbin)
21407 ("r-rlang" ,r-rlang)
21408 ("r-scales" ,r-scales)))
21409 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21410 (synopsis "Multiple summary statistics for binned stats/geometries")
21412 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21413 which functions similar to its singular form, but allows the use of multiple
21414 statistics per bin. Those statistics can be mapped to multiple bin
21416 (license license:gpl3)))
21418 (define-public r-knn-covertree
21420 (name "r-knn-covertree")
21425 (uri (cran-uri "knn.covertree" version))
21428 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21429 (properties `((upstream-name . "knn.covertree")))
21430 (build-system r-build-system)
21432 `(("r-matrix" ,r-matrix)
21434 ("r-rcppeigen" ,r-rcppeigen)))
21435 (home-page "https://github.com/flying-sheep/knn.covertree")
21436 (synopsis "Accurate kNN Implementation with multiple distance measures")
21438 "Similarly to the FNN package, this package allows calculation of the k
21439 nearest neighbors (kNN) of a data matrix. The implementation is based on
21440 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21441 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21442 (license license:agpl3+)))
21444 (define-public r-poibin
21451 (uri (cran-uri "poibin" version))
21454 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21455 (properties `((upstream-name . "poibin")))
21456 (build-system r-build-system)
21457 (home-page "https://cran.r-project.org/web/packages/poibin/")
21458 (synopsis "Poisson binomial distribution")
21460 "This package provides an implementation of both the exact and
21461 approximation methods for computing the @dfn{cumulative distribution
21462 function} (CDF) of the Poisson binomial distribution. It also provides the
21463 @dfn{probability mass function} (PMF), quantile function, and random number
21464 generation for the Poisson binomial distribution.")
21465 (license license:gpl2)))
21467 (define-public r-diagram
21474 (uri (cran-uri "diagram" version))
21477 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21478 (properties `((upstream-name . "diagram")))
21479 (build-system r-build-system)
21481 `(("r-shape" ,r-shape)))
21482 (home-page "https://cran.r-project.org/web/packages/diagram/")
21483 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21485 "This package provides tools to visualize simple graphs (networks) based
21486 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21487 electrical networks, etc. It also includes supporting material for the book
21488 \"A practical guide to ecological modelling - using R as a simulation
21489 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21490 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21491 Francesca Mazzia (2012).")
21492 (license license:gpl2+)))
21494 (define-public r-lim
21501 (uri (cran-uri "LIM" version))
21504 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21505 (properties `((upstream-name . "LIM")))
21506 (build-system r-build-system)
21508 `(("r-diagram" ,r-diagram)
21509 ("r-limsolve" ,r-limsolve)))
21510 (home-page "https://cran.r-project.org/web/packages/LIM/")
21511 (synopsis "Linear inverse model examples and solution methods")
21513 "This package provides functions that read and solve linear inverse
21514 problems (food web problems, linear programming problems).")
21515 (license license:gpl2+)))
21517 (define-public r-shinycssloaders
21519 (name "r-shinycssloaders")
21524 (uri (cran-uri "shinycssloaders" version))
21527 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21529 `((upstream-name . "shinycssloaders")))
21530 (build-system r-build-system)
21532 `(("r-digest" ,r-digest)
21534 ("r-shiny" ,r-shiny)))
21535 (home-page "https://github.com/andrewsali/shinycssloaders")
21536 (synopsis "Add CSS loading animations to Shiny outputs")
21538 "This package provides tools to create a lightweight Shiny wrapper for
21539 the css-loaders created by Luke Hass
21540 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21541 automatically show a loader when the output is (re)calculating.")
21542 (license license:gpl3)))
21544 (define-public r-rsvg
21551 (uri (cran-uri "rsvg" version))
21554 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21555 (properties `((upstream-name . "rsvg")))
21556 (build-system r-build-system)
21558 `(("librsvg" ,librsvg)
21561 `(("pkg-config" ,pkg-config)
21562 ("r-knitr" ,r-knitr)))
21563 (home-page "https://github.com/jeroen/rsvg#readme")
21564 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21566 "This package allows you to render vector-based SVG images into
21567 high-quality custom-size bitmap arrays using the librsvg2 library. The
21568 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21569 addition, the package can convert images directly to various formats such as
21570 PDF or PostScript.")
21571 (license license:expat)))
21573 (define-public r-influencer
21575 (name "r-influencer")
21580 (uri (cran-uri "influenceR" version))
21583 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21584 (properties `((upstream-name . "influenceR")))
21585 (build-system r-build-system)
21587 `(("r-igraph" ,r-igraph)
21588 ("r-matrix" ,r-matrix)))
21589 (home-page "https://github.com/rcc-uchicago/influenceR")
21590 (synopsis "Tools to quantify structural importance of nodes in a network")
21592 "This package provides functionality to compute various node centrality
21593 measures on networks. Included are functions to compute betweenness
21594 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21595 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21596 algorithm to identify key players, and Valente's bridging metric. The
21597 betweenness, Key Players, and bridging implementations are parallelized with
21599 (license license:gpl2)))
21601 (define-public r-emplik
21608 (uri (cran-uri "emplik" version))
21611 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21612 (properties `((upstream-name . "emplik")))
21613 (build-system r-build-system)
21615 `(("r-quantreg" ,r-quantreg)))
21616 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21617 (synopsis "Empirical likelihood ratio for censored/truncated data")
21619 "This package provides empirical likelihood ratio tests for
21620 means/quantiles/hazards from possibly censored and/or truncated data. It also
21622 (license license:gpl2+)))
21624 (define-public r-imputeyn
21626 (name "r-imputeyn")
21631 (uri (cran-uri "imputeYn" version))
21634 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21635 (properties `((upstream-name . "imputeYn")))
21636 (build-system r-build-system)
21638 `(("r-boot" ,r-boot)
21639 ("r-emplik" ,r-emplik)
21640 ("r-mvtnorm" ,r-mvtnorm)
21641 ("r-quadprog" ,r-quadprog)
21642 ("r-survival" ,r-survival)))
21643 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21644 (synopsis "Impute last largest censored observation under weighted least squares")
21646 "This package allows for the imputation of the last largest censored
21647 observantions. This method brings less bias and more efficient estimates for
21649 (license license:gpl2)))
21651 (define-public r-adapenetclass
21653 (name "r-adapenetclass")
21658 (uri (cran-uri "AdapEnetClass" version))
21661 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21662 (properties `((upstream-name . "AdapEnetClass")))
21663 (build-system r-build-system)
21665 `(("r-glmnet" ,r-glmnet)
21666 ("r-imputeyn" ,r-imputeyn)
21668 ("r-quadprog" ,r-quadprog)))
21669 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21670 (synopsis "Class of adaptive elastic net methods for censored data")
21672 "This package provides methods for variable selection for AFT models.")
21673 (license license:gpl2)))
21675 (define-public r-flock
21682 (uri (cran-uri "flock" version))
21685 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21686 (properties `((upstream-name . "flock")))
21687 (build-system r-build-system)
21688 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21689 (home-page "https://cran.r-project.org/web/packages/flock/")
21690 (synopsis "Process synchronization using file locks")
21692 "This package implements synchronization between R processes (spawned by
21693 using the @code{parallel} package for instance) using file locks. It supports
21694 both exclusive and shared locking.")
21695 (license license:asl2.0)))
21697 (define-public r-archivist
21699 (name "r-archivist")
21704 (uri (cran-uri "archivist" version))
21707 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21708 (properties `((upstream-name . "archivist")))
21709 (build-system r-build-system)
21712 ("r-digest" ,r-digest)
21713 ("r-flock" ,r-flock)
21715 ("r-lubridate" ,r-lubridate)
21716 ("r-magrittr" ,r-magrittr)
21717 ("r-rcurl" ,r-rcurl)
21718 ("r-rsqlite" ,r-rsqlite)))
21720 `(("r-knitr" ,r-knitr)))
21721 (home-page "https://pbiecek.github.io/archivist/")
21722 (synopsis "Tools for storing, restoring and searching for R objects")
21724 "Data exploration and modelling is a process in which a lot of data
21725 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21726 statistical models, different versions of data sets and different versions of
21727 results. Archivist helps to store and manage artifacts created in R. It
21728 allows you to store selected artifacts as binary files together with their
21729 metadata and relations. Archivist allows sharing artifacts with others. It
21730 can look for already created artifacts by using its class, name, date of the
21731 creation or other properties. It also makes it easy to restore such
21733 (license license:gpl2)))
21735 (define-public r-versions
21737 (name "r-versions")
21742 (uri (cran-uri "versions" version))
21745 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21746 (properties `((upstream-name . "versions")))
21747 (build-system r-build-system)
21748 (home-page "https://cran.r-project.org/web/packages/versions/")
21749 (synopsis "Query and install specific versions of CRAN packages")
21751 "This package allows you to install specified versions of R packages
21752 hosted on CRAN and provides functions to list available versions and the
21753 versions of currently installed packages.")
21754 (license license:bsd-3)))
21756 (define-public r-adapr
21763 (uri (cran-uri "adapr" version))
21766 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21767 (properties `((upstream-name . "adapr")))
21768 (build-system r-build-system)
21770 `(("r-archivist" ,r-archivist)
21771 ("r-devtools" ,r-devtools)
21772 ("r-digest" ,r-digest)
21773 ("r-doparallel" ,r-doparallel)
21774 ("r-gdata" ,r-gdata)
21775 ("r-ggplot2" ,r-ggplot2)
21776 ("r-git2r" ,r-git2r)
21777 ("r-igraph" ,r-igraph)
21778 ("r-knitr" ,r-knitr)
21779 ("r-plotly" ,r-plotly)
21781 ("r-rmarkdown" ,r-rmarkdown)
21782 ("r-shiny" ,r-shiny)
21783 ("r-shinydashboard" ,r-shinydashboard)
21784 ("r-versions" ,r-versions)))
21785 (home-page "https://cran.r-project.org/web/packages/adapr/")
21786 (synopsis "Implementation of an accountable data analysis process")
21788 "This package tracks reading and writing within R scripts that are
21789 organized into a directed acyclic graph. It contains an interactive Shiny
21790 application @code{adaprApp()}. It uses Git and file hashes to track version
21791 histories of inputs and outputs.")
21792 (license license:lgpl2.0)))
21794 (define-public r-adapsamp
21796 (name "r-adapsamp")
21801 (uri (cran-uri "AdapSamp" version))
21804 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21805 (properties `((upstream-name . "AdapSamp")))
21806 (build-system r-build-system)
21807 (propagated-inputs `(("r-pracma" ,r-pracma)))
21808 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21809 (synopsis "Adaptive sampling algorithms")
21811 "For distributions whose probability density functions are log-concave,
21812 the adaptive rejection sampling algorithm can be used to build envelope
21813 functions for sampling. For others, the modified adaptive rejection sampling
21814 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21815 adaptive slice sampling algorithm can be used. This R package mainly includes
21816 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21817 @code{rASS()}. These functions can realize sampling based on the algorithms
21819 (license license:gpl2)))
21821 (define-public r-adaptalint
21823 (name "r-adaptalint")
21828 (uri (cran-uri "adaptalint" version))
21831 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21832 (properties `((upstream-name . "adaptalint")))
21833 (build-system r-build-system)
21835 `(("r-dplyr" ,r-dplyr)
21836 ("r-lintr" ,r-lintr)
21837 ("r-purrr" ,r-purrr)))
21838 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21839 (synopsis "Check R code style")
21841 "This package provides tools to infer the code style (which style rules
21842 are followed and which ones are not) from one package and use it to check
21843 another. This makes it easier to find and correct the most important problems
21845 (license license:gpl3)))
21847 (define-public r-fracdiff
21849 (name "r-fracdiff")
21854 (uri (cran-uri "fracdiff" version))
21857 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21858 (properties `((upstream-name . "fracdiff")))
21859 (build-system r-build-system)
21860 (home-page "https://github.com/mmaechler/fracdiff")
21862 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21864 "This package provides tools for the maximum likelihood estimation of the
21865 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21866 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21867 (license license:gpl2+)))
21869 (define-public r-forecast
21871 (name "r-forecast")
21876 (uri (cran-uri "forecast" version))
21879 "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
21880 (properties `((upstream-name . "forecast")))
21881 (build-system r-build-system)
21883 `(("r-colorspace" ,r-colorspace)
21884 ("r-fracdiff" ,r-fracdiff)
21885 ("r-ggplot2" ,r-ggplot2)
21886 ("r-lmtest" ,r-lmtest)
21887 ("r-magrittr" ,r-magrittr)
21890 ("r-rcpparmadillo" ,r-rcpparmadillo)
21891 ("r-timedate" ,r-timedate)
21892 ("r-tseries" ,r-tseries)
21896 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21897 (home-page "https://pkg.robjhyndman.com/forecast/")
21898 (synopsis "Forecasting functions for time series and linear models")
21900 "This package provides methods and tools for displaying and analysing
21901 univariate time series forecasts including exponential smoothing via state
21902 space models and automatic ARIMA modelling.")
21903 (license license:gpl3)))
21905 (define-public r-xmisc
21912 (uri (cran-uri "Xmisc" version))
21915 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21916 (properties `((upstream-name . "Xmisc")))
21917 (build-system r-build-system)
21918 (home-page "https://cran.r-project.org/package=Xmisc")
21920 "Xiaobei's miscellaneous classes and functions")
21922 "This package provides Xiaobei's miscellaneous classes and functions,
21923 which are useful when developing R packages for @dfn{object oriented
21924 programming} (OOP) using R Reference Class.")
21925 (license license:gpl2+)))
21927 (define-public r-proxyc
21934 (uri (cran-uri "proxyC" version))
21937 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21938 (properties `((upstream-name . "proxyC")))
21939 (build-system r-build-system)
21941 `(("r-matrix" ,r-matrix)
21943 ("r-rcpparmadillo" ,r-rcpparmadillo)
21944 ("r-rcppparallel" ,r-rcppparallel)))
21945 (home-page "https://cran.r-project.org/package=proxyC")
21946 (synopsis "Compute proximity in large sparse matrices")
21948 "This package provides efficient tools to compute the proximity between
21949 rows or columns of large matrices. Functions are optimised for large sparse
21950 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21951 similarity/distance measures, computation of correlation, cosine similarity
21952 and Euclidean distance is particularly fast.")
21953 (license license:gpl3)))
21955 (define-public r-isocodes
21957 (name "r-isocodes")
21958 (version "2021.02.24")
21962 (uri (cran-uri "ISOcodes" version))
21965 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
21966 (properties `((upstream-name . "ISOcodes")))
21967 (build-system r-build-system)
21968 (home-page "https://cran.r-project.org/package=ISOcodes")
21969 (synopsis "Selected ISO codes")
21971 "This package provides ISO language, territory, currency, script and
21972 character codes. It provides ISO 639 language codes, ISO 3166 territory
21973 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21974 character codes as well as the UN M.49 area codes.")
21975 (license license:gpl2)))
21977 (define-public r-stopwords
21979 (name "r-stopwords")
21984 (uri (cran-uri "stopwords" version))
21987 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
21988 (properties `((upstream-name . "stopwords")))
21989 (build-system r-build-system)
21991 `(("r-isocodes" ,r-isocodes)))
21992 (home-page "https://github.com/quanteda/stopwords")
21993 (synopsis "Multilingual stopword lists")
21995 "This package provides multiple sources of stopwords, for use in text
21996 analysis and natural language processing.")
21997 (license license:expat)))
21999 (define-public r-spacyr
22006 (uri (cran-uri "spacyr" version))
22009 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
22010 (properties `((upstream-name . "spacyr")))
22011 (build-system r-build-system)
22013 `(("r-data-table" ,r-data-table)
22014 ("r-reticulate" ,r-reticulate)))
22015 (home-page "https://spacyr.quanteda.io")
22016 (synopsis "R wrapper for the spaCy NLP library")
22018 "This package provides an R wrapper to the Python @dfn{natural language
22019 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22020 (license license:gpl3)))
22022 (define-public r-snowballc
22024 (name "r-snowballc")
22029 (uri (cran-uri "SnowballC" version))
22032 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22033 (properties `((upstream-name . "SnowballC")))
22034 (build-system r-build-system)
22035 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22036 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22038 "This package provides an R interface to the C @code{libstemmer} library
22039 that implements Porter's word stemming algorithm for collapsing words to a
22040 common root to aid comparison of vocabulary. Currently supported languages
22041 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22042 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22043 (license license:bsd-3)))
22045 (define-public r-quanteda
22047 (name "r-quanteda")
22052 (uri (cran-uri "quanteda" version))
22055 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22056 (properties `((upstream-name . "quanteda")))
22057 (build-system r-build-system)
22059 `(("r-data-table" ,r-data-table)
22060 ("r-digest" ,r-digest)
22061 ("r-extrafont" ,r-extrafont)
22062 ("r-fastmatch" ,r-fastmatch)
22063 ("r-ggplot2" ,r-ggplot2)
22064 ("r-ggrepel" ,r-ggrepel)
22065 ("r-jsonlite" ,r-jsonlite)
22066 ("r-magrittr" ,r-magrittr)
22067 ("r-matrix" ,r-matrix)
22068 ("r-network" ,r-network)
22069 ("r-proxyc" ,r-proxyc)
22071 ("r-rcpparmadillo" ,r-rcpparmadillo)
22072 ("r-rcppparallel" ,r-rcppparallel)
22074 ("r-snowballc" ,r-snowballc)
22075 ("r-stopwords" ,r-stopwords)
22076 ("r-stringi" ,r-stringi)
22078 ("r-yaml" ,r-yaml)))
22080 `(("r-knitr" ,r-knitr)))
22081 (home-page "https://quanteda.io")
22082 (synopsis "Quantitative analysis of textual data")
22084 "This package provides a fast, flexible, and comprehensive framework for
22085 quantitative text analysis in R. It provides functionality for corpus
22086 management, creating and manipulating tokens and ngrams, exploring keywords in
22087 context, forming and manipulating sparse matrices of documents by features and
22088 feature co-occurrences, analyzing keywords, computing feature similarities and
22089 distances, applying content dictionaries, applying supervised and unsupervised
22090 machine learning, visually representing text and text analyses, and more.")
22091 (license license:gpl3)))
22093 (define-public r-topicmodels
22095 (name "r-topicmodels")
22100 (uri (cran-uri "topicmodels" version))
22103 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22104 (properties `((upstream-name . "topicmodels")))
22105 (build-system r-build-system)
22109 `(("r-modeltools" ,r-modeltools)
22112 (home-page "https://cran.r-project.org/package=topicmodels")
22113 (synopsis "Topic models")
22115 "This package provides an interface to the C code for @dfn{Latent
22116 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22117 David M. Blei and co-authors and the C++ code for fitting LDA models using
22118 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22119 (license license:gpl2)))
22121 (define-public r-stm
22128 (uri (cran-uri "stm" version))
22131 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22132 (properties `((upstream-name . "stm")))
22133 (build-system r-build-system)
22135 `(("r-data-table" ,r-data-table)
22136 ("r-glmnet" ,r-glmnet)
22138 ("r-matrix" ,r-matrix)
22139 ("r-matrixstats" ,r-matrixstats)
22140 ("r-quadprog" ,r-quadprog)
22141 ("r-quanteda" ,r-quanteda)
22143 ("r-rcpparmadillo" ,r-rcpparmadillo)
22145 ("r-stringr" ,r-stringr)))
22146 (home-page "http://www.structuraltopicmodel.com/")
22147 (synopsis "Estimation of the Structural Topic Model")
22149 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22150 topic models with document-level covariates. The package also includes tools
22151 for model selection, visualization, and estimation of topic-covariate
22153 (license license:expat)))
22155 (define-public r-polycor
22162 (uri (cran-uri "polycor" version))
22165 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22166 (properties `((upstream-name . "polycor")))
22167 (build-system r-build-system)
22169 `(("r-matrix" ,r-matrix)
22170 ("r-mvtnorm" ,r-mvtnorm)))
22171 (home-page "https://r-forge.r-project.org/projects/polycor/")
22172 (synopsis "Polychoric and polyserial correlations")
22174 "This package provides tools to compute polychoric and polyserial
22175 correlations by quick \"two-step\" methods or ML, optionally with standard
22176 errors; tetrachoric and biserial correlations are special cases.")
22177 (license license:gpl2+)))
22179 (define-public r-msm
22186 (uri (cran-uri "msm" version))
22189 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22190 (properties `((upstream-name . "msm")))
22191 (build-system r-build-system)
22193 `(("r-expm" ,r-expm)
22194 ("r-mvtnorm" ,r-mvtnorm)
22195 ("r-survival" ,r-survival)))
22196 (home-page "https://github.com/chjackson/msm")
22197 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22199 "This package provides functions for fitting continuous-time Markov and
22200 hidden Markov multi-state models to longitudinal data. It was designed for
22201 processes observed at arbitrary times in continuous time (panel data) but some
22202 other observation schemes are supported. Both Markov transition rates and the
22203 hidden Markov output process can be modelled in terms of covariates, which may
22204 be constant or piecewise-constant in time.")
22205 (license license:gpl2+)))
22207 (define-public r-ltm
22214 (uri (cran-uri "ltm" version))
22217 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22218 (properties `((upstream-name . "ltm")))
22219 (build-system r-build-system)
22221 `(("r-mass" ,r-mass)
22223 ("r-polycor" ,r-polycor)))
22224 (home-page "https://github.com/drizopoulos/ltm")
22225 (synopsis "Latent trait models under IRT")
22227 "This is a package supporting the analysis of multivariate dichotomous
22228 and polytomous data using latent trait models under the Item Response Theory
22229 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22230 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22232 (license license:gpl2+)))
22234 (define-public r-mi
22241 (uri (cran-uri "mi" version))
22244 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22245 (properties `((upstream-name . "mi")))
22246 (build-system r-build-system)
22249 ("r-matrix" ,r-matrix)))
22250 (home-page "http://www.stat.columbia.edu/~gelman/")
22251 (synopsis "Missing data imputation and model checking")
22253 "This package provides functions for data manipulation, imputing missing
22254 values in an approximate Bayesian framework, diagnostics of the models used to
22255 generate the imputations, confidence-building mechanisms to validate some of
22256 the assumptions of the imputation algorithm, and functions to analyze multiply
22257 imputed data sets with the appropriate degree of sampling uncertainty.")
22258 (license license:gpl2+)))
22260 (define-public r-matrixcalc
22262 (name "r-matrixcalc")
22267 (uri (cran-uri "matrixcalc" version))
22270 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22271 (properties `((upstream-name . "matrixcalc")))
22272 (build-system r-build-system)
22273 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22274 (synopsis "Collection of functions for matrix calculations")
22276 "This package provides a collection of functions to support matrix
22277 calculations for probability, econometric and numerical analysis. There are
22278 additional functions that are comparable to APL functions which are useful for
22279 actuarial models such as pension mathematics.")
22280 (license license:gpl2+)))
22282 (define-public r-sem
22289 (uri (cran-uri "sem" version))
22292 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22293 (properties `((upstream-name . "sem")))
22294 (build-system r-build-system)
22296 `(("r-boot" ,r-boot)
22298 ("r-matrixcalc" ,r-matrixcalc)
22300 (home-page "https://cran.r-project.org/package=sem")
22301 (synopsis "Structural equation models")
22303 "This package provides functions for fitting general linear structural
22304 equation models (with observed and latent variables) using the RAM approach,
22305 and for fitting structural equations in observed-variable models by two-stage
22307 (license license:gpl2+)))
22309 (define-public r-semtools
22311 (name "r-semtools")
22316 (uri (cran-uri "semTools" version))
22319 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22320 (properties `((upstream-name . "semTools")))
22321 (build-system r-build-system)
22323 `(("r-lavaan" ,r-lavaan)))
22324 (home-page "https://github.com/simsem/semTools/wiki")
22325 (synopsis "Useful tools for structural equation modeling")
22327 "This package provides useful tools for structural equation modeling.")
22328 (license license:gpl2+)))
22330 (define-public r-regsem
22337 (uri (cran-uri "regsem" version))
22340 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22341 (properties `((upstream-name . "regsem")))
22342 (build-system r-build-system)
22344 `(("r-lavaan" ,r-lavaan)
22346 ("r-rcpparmadillo" ,r-rcpparmadillo)
22347 ("r-rsolnp" ,r-rsolnp)))
22349 `(("r-knitr" ,r-knitr)))
22350 (home-page "https://cran.r-project.org/package=regsem")
22351 (synopsis "Regularized structural equation modeling")
22353 "This package uses both ridge and lasso penalties (and extensions) to
22354 penalize specific parameters in structural equation models. The package
22355 offers additional cost functions, cross validation, and other extensions
22356 beyond traditional structural equation models. It also contains a function to
22357 perform @dfn{exploratory mediation} (XMed).")
22358 (license license:gpl2+)))
22360 (define-public r-stanheaders
22362 (name "r-stanheaders")
22363 (version "2.21.0-7")
22367 (uri (cran-uri "StanHeaders" version))
22370 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22371 (properties `((upstream-name . "StanHeaders")))
22372 (build-system r-build-system)
22373 (inputs `(("pandoc" ,pandoc)))
22375 `(("r-rcppeigen" ,r-rcppeigen)
22376 ("r-rcppparallel" ,r-rcppparallel)))
22378 `(("gfortran" ,gfortran)
22379 ("r-knitr" ,r-knitr))) ; for vignettes
22380 (home-page "https://mc-stan.org/")
22381 (synopsis "C++ header files for Stan")
22383 "The C++ header files of the Stan project are provided by this package.
22384 There is a shared object containing part of the @code{CVODES} library, but it
22385 is not accessible from R. @code{r-stanheaders} is only useful for developers
22386 who want to utilize the @code{LinkingTo} directive of their package's
22387 DESCRIPTION file to build on the Stan library without incurring unnecessary
22390 The Stan project develops a probabilistic programming language that implements
22391 full or approximate Bayesian statistical inference via Markov Chain Monte
22392 Carlo or variational methods and implements (optionally penalized) maximum
22393 likelihood estimation via optimization. The Stan library includes an advanced
22394 automatic differentiation scheme, templated statistical and linear algebra
22395 functions that can handle the automatically differentiable scalar types (and
22396 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22397 package provides user-facing R functions to parse, compile, test, estimate,
22398 and analyze Stan models.")
22399 (license license:bsd-3)))
22401 (define-public r-rpf
22408 (uri (cran-uri "rpf" version))
22411 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22412 (properties `((upstream-name . "rpf")))
22413 (build-system r-build-system)
22415 `(("r-lifecycle" ,r-lifecycle)
22416 ("r-mvtnorm" ,r-mvtnorm)
22418 ("r-rcppeigen" ,r-rcppeigen)))
22420 `(("r-knitr" ,r-knitr)))
22421 (home-page "https://github.com/jpritikin/rpf")
22422 (synopsis "Response probability functions")
22424 "The purpose of this package is to factor out logic and math common to
22425 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22426 core support code suitable for more specialized IRT packages to build upon.
22427 Complete access to optimized C functions is made available with
22428 @code{R_RegisterCCallable()}.")
22429 (license license:gpl3+)))
22431 (define-public r-openmx
22438 (uri (cran-uri "OpenMx" version))
22441 "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj"))))
22442 (properties `((upstream-name . "OpenMx")))
22443 (build-system r-build-system)
22446 ("r-digest" ,r-digest)
22447 ("r-lifecycle" ,r-lifecycle)
22449 ("r-matrix" ,r-matrix)
22451 ("r-rcppeigen" ,r-rcppeigen)
22453 ("r-stanheaders" ,r-stanheaders)))
22454 (native-inputs `(("gfortran" ,gfortran)))
22455 (home-page "http://openmx.ssri.psu.edu")
22456 (synopsis "Extended structural equation modelling")
22458 "This package allows for the estimation of a wide variety of advanced
22459 multivariate statistical models. It consists of a library of functions and
22460 optimizers that allow you to quickly and flexibly define an SEM model and
22461 estimate parameters given observed data.")
22462 (license license:asl2.0)))
22464 (define-public r-kutils
22471 (uri (cran-uri "kutils" version))
22474 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22475 (properties `((upstream-name . "kutils")))
22476 (build-system r-build-system)
22478 `(("r-foreign" ,r-foreign)
22479 ("r-openxlsx" ,r-openxlsx)
22481 ("r-runit" ,r-runit)
22482 ("r-xtable" ,r-xtable)))
22483 (home-page "https://cran.r-project.org/package=kutils")
22484 (synopsis "Project management tools")
22486 "This package provides tools for data importation, recoding, and
22487 inspection. There are functions to create new project folders, R code
22488 templates, create uniquely named output directories, and to quickly obtain a
22489 visual summary for each variable in a data frame. The main feature here is
22490 the systematic implementation of the \"variable key\" framework for data
22491 importation and recoding.")
22492 (license license:gpl2)))
22494 (define-public r-rockchalk
22496 (name "r-rockchalk")
22497 (version "1.8.144")
22501 (uri (cran-uri "rockchalk" version))
22504 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22505 (properties `((upstream-name . "rockchalk")))
22506 (build-system r-build-system)
22508 `(("r-cardata" ,r-cardata)
22509 ("r-kutils" ,r-kutils)
22511 ("r-mass" ,r-mass)))
22512 (home-page "https://cran.r-project.org/package=rockchalk")
22513 (synopsis "Regression estimation and presentation")
22515 "This package provides a collection of functions for interpretation and
22516 presentation of regression analysis. These functions are used to produce the
22517 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22518 includes regression diagnostics, regression tables, and plots of interactions
22519 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22520 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22521 fairly comprehensive overview.")
22522 (license license:gpl3+)))
22524 (define-public r-lisreltor
22526 (name "r-lisreltor")
22531 (uri (cran-uri "lisrelToR" version))
22534 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22535 (properties `((upstream-name . "lisrelToR")))
22536 (build-system r-build-system)
22537 (home-page "https://cran.r-project.org/package=lisrelToR")
22538 (synopsis "Import output from LISREL into R")
22540 "This is an unofficial package aimed at automating the import of LISREL
22542 (license license:gpl2)))
22544 (define-public r-bdgraph
22551 (uri (cran-uri "BDgraph" version))
22554 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22555 (properties `((upstream-name . "BDgraph")))
22556 (build-system r-build-system)
22558 `(("r-igraph" ,r-igraph)))
22559 (home-page "https://www.uva.nl/profile/a.mohammadi")
22560 (synopsis "Bayesian structure learning in graphical models")
22562 "This package provides statistical tools for Bayesian structure learning
22563 in undirected graphical models for continuous, discrete, and mixed data. It
22564 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22565 on a continuous-time birth-death process.")
22566 (license license:gpl2+)))
22568 (define-public r-d3network
22570 (name "r-d3network")
22571 (version "0.5.2.1")
22575 (uri (cran-uri "d3Network" version))
22578 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22579 (properties `((upstream-name . "d3Network")))
22580 (build-system r-build-system)
22582 `(("r-plyr" ,r-plyr)
22583 ("r-rjson" ,r-rjson)
22584 ("r-whisker" ,r-whisker)))
22585 (home-page "http://christophergandrud.github.io/d3Network/")
22586 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22588 "This package is intended to make it easy to create D3 JavaScript
22589 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22590 (license license:gpl3+)))
22592 (define-public r-qgraph
22599 (uri (cran-uri "qgraph" version))
22602 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22603 (properties `((upstream-name . "qgraph")))
22604 (build-system r-build-system)
22606 `(("r-abind" ,r-abind)
22607 ("r-colorspace" ,r-colorspace)
22608 ("r-corpcor" ,r-corpcor)
22609 ("r-dplyr" ,r-dplyr)
22610 ("r-fdrtool" ,r-fdrtool)
22611 ("r-ggplot2" ,r-ggplot2)
22612 ("r-glasso" ,r-glasso)
22613 ("r-gtools" ,r-gtools)
22614 ("r-hmisc" ,r-hmisc)
22615 ("r-igraph" ,r-igraph)
22617 ("r-lavaan" ,r-lavaan)
22618 ("r-matrix" ,r-matrix)
22619 ("r-pbapply" ,r-pbapply)
22622 ("r-psych" ,r-psych)
22624 ("r-reshape2" ,r-reshape2)))
22625 (home-page "http://sachaepskamp.com/qgraph/")
22626 (synopsis "Weighted network visualization and analysis")
22628 "This package implements tools for weighted network visualization and
22629 analysis, as well as Gaussian graphical model computation. It contains graph
22630 plotting methods, and tools for psychometric data visualization and graphical
22631 model estimation. See Epskamp et al. (2012)
22632 @url{doi:10.18637/jss.v048.i04}.")
22633 (license license:gpl2)))
22635 (define-public r-semplot
22642 (uri (cran-uri "semPlot" version))
22645 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22646 (properties `((upstream-name . "semPlot")))
22647 (build-system r-build-system)
22649 `(("r-colorspace" ,r-colorspace)
22650 ("r-corpcor" ,r-corpcor)
22651 ("r-igraph" ,r-igraph)
22652 ("r-lavaan" ,r-lavaan)
22653 ("r-lisreltor" ,r-lisreltor)
22654 ("r-openmx" ,r-openmx)
22656 ("r-qgraph" ,r-qgraph)
22657 ("r-regsem" ,r-regsem)
22658 ("r-rockchalk" ,r-rockchalk)
22661 (home-page "https://github.com/SachaEpskamp/semPlot")
22662 (synopsis "Unified visualizations of structural equation models")
22664 "Structural equation modeling (SEM) has a long history of representing
22665 models graphically as path diagrams. The semPlot package for R fills the gap
22666 between advanced, but time-consuming, graphical software and the limited
22667 graphics produced automatically by SEM software. In addition, semPlot offers
22668 more functionality than drawing path diagrams: it can act as a common ground
22669 for importing SEM results into R. Any result usable as input to semPlot can
22670 also be represented in any of the three popular SEM frame-works, as well as
22671 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22672 (license license:gpl2)))
22674 (define-public r-cdm
22681 (uri (cran-uri "CDM" version))
22684 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22685 (properties `((upstream-name . "CDM")))
22686 (build-system r-build-system)
22688 `(("r-mvtnorm" ,r-mvtnorm)
22689 ("r-polycor" ,r-polycor)
22691 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22693 "https://github.com/alexanderrobitzsch/CDM")
22694 (synopsis "Cognitive diagnosis modeling")
22696 "This package provides functions for cognitive diagnosis modeling and
22697 multidimensional item response modeling for dichotomous and polytomous item
22698 responses. It enables the estimation of the DINA and DINO model, the multiple
22699 group (polytomous) GDINA model, the multiple choice DINA model, the general
22700 diagnostic model (GDM), the structured latent class model (SLCA), and
22701 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22702 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22703 estimation and the package structure. For tutorials on how to use the CDM
22704 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22705 well as Ravand and Robitzsch (2015).")
22706 (license license:gpl2+)))
22708 (define-public r-tam
22715 (uri (cran-uri "TAM" version))
22718 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22719 (properties `((upstream-name . "TAM")))
22720 (build-system r-build-system)
22724 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22725 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22726 (synopsis "Test analysis modules")
22728 "This package includes tools for marginal maximum likelihood estimation
22729 and joint maximum likelihood estimation for unidimensional and
22730 multidimensional item response models. The package functionality covers the
22731 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22732 multi-faceted Rasch model, nominal item response model, structured latent
22733 class model, mixture distribution IRT models, and located latent class models.
22734 Latent regression models and plausible value imputation are also supported.")
22735 (license license:gpl2+)))
22737 (define-public r-erm
22744 (uri (cran-uri "eRm" version))
22747 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
22748 (properties `((upstream-name . "eRm")))
22749 (build-system r-build-system)
22751 `(("r-colorspace" ,r-colorspace)
22752 ("r-lattice" ,r-lattice)
22754 ("r-matrix" ,r-matrix)
22755 ("r-psych" ,r-psych)))
22756 (native-inputs `(("gfortran" ,gfortran)))
22757 (home-page "https://cran.r-project.org/package=eRm")
22758 (synopsis "Extended Rasch modeling")
22760 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22761 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22762 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22763 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22764 data matrix. Additional features are the ML estimation of the person
22765 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22766 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22767 infit and outfit measures, ICC and other plots, automated stepwise item
22768 elimination, and a simulation module for various binary data matrices.")
22769 (license license:gpl3)))
22771 (define-public r-irtoys
22778 (uri (cran-uri "irtoys" version))
22781 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22782 (properties `((upstream-name . "irtoys")))
22783 (build-system r-build-system)
22787 (home-page "https://cran.r-project.org/package=irtoys")
22788 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22790 "This package provides a collection of functions useful in learning and
22791 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22792 programs. It provides basic CTT analysis, a simple common interface to the
22793 estimation of item parameters in IRT models for binary responses with three
22794 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22795 EAP, WLE, plausible values), item and person fit statistics, scaling
22796 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22797 array of parametric and non-parametric (kernel) plots. It estimates and plots
22798 Haberman's interaction model when all items are dichotomously scored.")
22799 (license license:gpl2+)))
22801 (define-public r-iheatmapr
22803 (name "r-iheatmapr")
22808 (uri (cran-uri "iheatmapr" version))
22811 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22812 (properties `((upstream-name . "iheatmapr")))
22813 (build-system r-build-system)
22815 `(("r-fastcluster" ,r-fastcluster)
22816 ("r-ggdendro" ,r-ggdendro)
22817 ("r-htmlwidgets" ,r-htmlwidgets)
22818 ("r-jsonlite" ,r-jsonlite)
22819 ("r-knitr" ,r-knitr)
22820 ("r-magrittr" ,r-magrittr)
22821 ("r-rcolorbrewer" ,r-rcolorbrewer)
22822 ("r-scales" ,r-scales)))
22824 `(("r-knitr" ,r-knitr)))
22825 (home-page "https://docs.ropensci.org/iheatmapr")
22826 (synopsis "Interactive, Complex Heatmaps")
22828 "iheatmapr is an R package for building complex, interactive heatmaps
22829 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22830 subplots along the rows or columns of the main heatmap add more information
22831 about each row or column. For example, a one column additional heatmap may
22832 indicate what group a particular row or column belongs to. Complex heatmaps
22833 may also include multiple side by side heatmaps which show different types of
22834 data for the same conditions. Interactivity can improve complex heatmaps by
22835 providing tooltips with information about each cell and enabling zooming into
22836 interesting features. iheatmapr uses the plotly library for interactivity.")
22837 (license license:expat)))
22839 (define-public r-packrat
22846 (uri (cran-uri "packrat" version))
22849 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22850 (properties `((upstream-name . "packrat")))
22851 (build-system r-build-system)
22852 (home-page "https://github.com/rstudio/packrat/")
22853 (synopsis "Dependency management R projects")
22855 "This package provides a dependency manager for R projects that allows
22856 you to manage the R packages your project depends on in an isolated, portable,
22857 and reproducible way.")
22858 (license license:gpl2)))
22860 (define-public r-rsconnect
22862 (name "r-rsconnect")
22867 (uri (cran-uri "rsconnect" version))
22870 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22871 (properties `((upstream-name . "rsconnect")))
22872 (build-system r-build-system)
22874 `(("r-curl" ,r-curl)
22875 ("r-digest" ,r-digest)
22876 ("r-jsonlite" ,r-jsonlite)
22877 ("r-openssl" ,r-openssl)
22878 ("r-packrat" ,r-packrat)
22879 ("r-rstudioapi" ,r-rstudioapi)
22880 ("r-yaml" ,r-yaml)))
22881 (home-page "https://github.com/rstudio/rsconnect")
22882 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22884 "This package provides a programmatic deployment interface for RPubs,
22885 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22886 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22887 (license license:gpl2)))
22889 ;; This package includes minified JavaScript files. When upgrading please
22890 ;; check that there are no new minified JavaScript files.
22891 (define-public r-dygraphs
22893 (name "r-dygraphs")
22894 (version "1.1.1.6")
22898 (uri (cran-uri "dygraphs" version))
22901 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22902 (properties `((upstream-name . "dygraphs")))
22903 (build-system r-build-system)
22905 `(#:modules ((guix build utils)
22906 (guix build r-build-system)
22910 (modify-phases %standard-phases
22911 (add-after 'unpack 'process-javascript
22912 (lambda* (#:key inputs #:allow-other-keys)
22913 (with-directory-excursion "inst/htmlwidgets/lib/"
22917 `(("dygraphs/dygraph-combined-dev.js"
22918 "dygraph-combined.js")
22919 (,(assoc-ref inputs "js-jquery")
22920 "jquery/jquery.min.js")
22921 (,(assoc-ref inputs "js-fquarter")
22922 "fquarter/moment-fquarter.min.js"))))
22923 (lambda (sources targets)
22924 (for-each (lambda (source target)
22925 (format #t "Processing ~a --> ~a~%"
22927 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22928 (call-with-output-file target
22930 (dump-port minified port)))))
22931 sources targets))))
22934 `(("uglify-js" ,uglify-js)
22935 ;; They actually use version 1.11.1, but this more recent version
22936 ;; should be just fine.
22940 (uri "https://code.jquery.com/jquery-1.12.4.js")
22943 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22947 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22948 "moment-fquarter/1.0.1/moment-fquarter.js"))
22951 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22953 `(("r-htmltools" ,r-htmltools)
22954 ("r-htmlwidgets" ,r-htmlwidgets)
22955 ("r-magrittr" ,r-magrittr)
22958 (home-page "https://github.com/rstudio/dygraphs")
22959 (synopsis "Interface to Dygraphs interactive time series charting library")
22961 "This package provides an R interface to the dygraphs JavaScript charting
22962 library (a copy of which is included in the package). It provides rich
22963 facilities for charting time-series data in R, including highly configurable
22964 series- and axis-display and interactive features like zoom/pan and
22965 series/point highlighting.")
22966 (license license:expat)))
22968 (define-public r-shinystan
22970 (name "r-shinystan")
22975 (uri (cran-uri "shinystan" version))
22978 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22979 (properties `((upstream-name . "shinystan")))
22980 (build-system r-build-system)
22982 `(("r-bayesplot" ,r-bayesplot)
22983 ("r-colourpicker" ,r-colourpicker)
22985 ("r-dygraphs" ,r-dygraphs)
22986 ("r-ggplot2" ,r-ggplot2)
22987 ("r-gridextra" ,r-gridextra)
22988 ("r-gtools" ,r-gtools)
22989 ("r-markdown" ,r-markdown)
22990 ("r-reshape2" ,r-reshape2)
22991 ("r-rsconnect" ,r-rsconnect)
22992 ("r-rstan" ,r-rstan)
22993 ("r-shiny" ,r-shiny)
22994 ("r-shinyjs" ,r-shinyjs)
22995 ("r-shinythemes" ,r-shinythemes)
22996 ("r-threejs" ,r-threejs)
22997 ("r-xtable" ,r-xtable)
22999 (home-page "https://mc-stan.org/")
23000 (synopsis "Interactive visual and numerical analysis for Bayesian models")
23002 "This package provides a graphical user interface for interactive
23003 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
23004 for analyzing a posterior sample. The interface is powered by the Shiny web
23005 application framework and works with the output of MCMC programs written in
23006 any programming language (and has extended functionality for Stan models fit
23007 using the @code{rstan} and @code{rstanarm} packages).")
23008 (license license:gpl3+)))
23010 (define-public r-rstantools
23012 (name "r-rstantools")
23017 (uri (cran-uri "rstantools" version))
23020 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23021 (properties `((upstream-name . "rstantools")))
23022 (build-system r-build-system)
23023 (inputs `(("pandoc" ,pandoc)))
23025 `(("r-desc" ,r-desc)
23027 ("r-rcppparallel" ,r-rcppparallel)))
23029 `(("r-knitr" ,r-knitr)))
23030 (home-page "https://mc-stan.org/rstantools/")
23031 (synopsis "Tools for developing R packages interfacing with Stan")
23033 "This package provides various tools for developers of R packages
23034 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23035 up the required package structure, S3 generics and default methods to unify
23036 function naming across Stan-based R packages, and vignettes with
23037 recommendations for developers.")
23038 (license license:gpl3+)))
23040 (define-public r-loo
23047 (uri (cran-uri "loo" version))
23049 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23050 (properties `((upstream-name . "loo")))
23051 (build-system r-build-system)
23053 `(("pandoc" ,pandoc)
23054 ("pandoc-citeproc" ,pandoc-citeproc)))
23056 `(("r-checkmate" ,r-checkmate)
23057 ("r-matrixstats" ,r-matrixstats)))
23059 `(("r-knitr" ,r-knitr)))
23060 (home-page "https://mc-stan.org/loo/")
23061 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23063 "This package provides an implementation of efficient approximate
23064 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23065 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23066 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23067 procedure for regularizing importance weights. As a byproduct of the
23068 calculations, we also obtain approximate standard errors for estimated
23069 predictive errors and for the comparison of predictive errors between models.
23070 The package also provides methods for using stacking and other model weighting
23071 techniques to average Bayesian predictive distributions.")
23072 (license license:gpl3+)))
23074 (define-public r-rstan
23081 (uri (cran-uri "rstan" version))
23084 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23085 (properties `((upstream-name . "rstan")))
23086 (build-system r-build-system)
23089 (modify-phases %standard-phases
23090 (add-before 'install 'set-timezone
23091 ;; This package is picky about timezones.
23092 (lambda* (#:key inputs #:allow-other-keys)
23093 (setenv "TZ" "UTC+1")
23095 (string-append (assoc-ref inputs "tzdata")
23096 "/share/zoneinfo"))
23099 `(("tzdata" ,tzdata-for-tests)
23101 ("r-knitr" ,r-knitr)))
23104 ("r-ggplot2" ,r-ggplot2)
23105 ("r-gridextra" ,r-gridextra)
23106 ("r-inline" ,r-inline)
23108 ("r-pkgbuild" ,r-pkgbuild)
23110 ("r-rcppeigen" ,r-rcppeigen)
23111 ("r-rcppparallel" ,r-rcppparallel)
23112 ("r-stanheaders" ,r-stanheaders)
23114 ("r-withr" ,r-withr)))
23115 (home-page "https://discourse.mc-stan.org/")
23116 (synopsis "R interface to Stan")
23118 "User-facing R functions are provided to parse, compile, test, estimate,
23119 and analyze Stan models by accessing the header-only Stan library provided by
23120 the StanHeaders package. The Stan project develops a probabilistic
23121 programming language that implements full Bayesian statistical inference via
23122 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23123 approximation, and (optionally penalized) maximum likelihood estimation via
23124 optimization. In all three cases, automatic differentiation is used to
23125 quickly and accurately evaluate gradients without burdening the user with the
23126 need to derive the partial derivatives.")
23127 (license license:gpl3+)))
23129 (define-public r-rstanarm
23131 (name "r-rstanarm")
23136 (uri (cran-uri "rstanarm" version))
23139 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23140 (properties `((upstream-name . "rstanarm")))
23141 (build-system r-build-system)
23143 `(("pandoc" ,pandoc)
23144 ("pandoc-citeproc" ,pandoc-citeproc)))
23146 `(("r-bayesplot" ,r-bayesplot)
23148 ("r-ggplot2" ,r-ggplot2)
23151 ("r-matrix" ,r-matrix)
23154 ("r-rcppeigen" ,r-rcppeigen)
23155 ("r-rcppparallel" ,r-rcppparallel)
23156 ("r-rstan" ,r-rstan)
23157 ("r-rstantools" ,r-rstantools)
23158 ("r-shinystan" ,r-shinystan)
23159 ("r-stanheaders" ,r-stanheaders)
23160 ("r-survival" ,r-survival)))
23162 `(("r-knitr" ,r-knitr)))
23163 (home-page "https://mc-stan.org/rstanarm/")
23164 (synopsis "Bayesian applied regression modeling via Stan")
23166 "This package estimates previously compiled regression models using the
23167 @code{rstan} package, which provides the R interface to the Stan C++ library
23168 for Bayesian estimation. Users specify models via the customary R syntax with
23169 a formula and @code{data.frame} plus some additional arguments for priors.")
23170 (license license:gpl3+)))
23172 (define-public r-kendall
23179 (uri (cran-uri "Kendall" version))
23182 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23183 (properties `((upstream-name . "Kendall")))
23184 (build-system r-build-system)
23186 `(("r-boot" ,r-boot)))
23188 `(("gfortran" ,gfortran)))
23189 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23190 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23192 "This package computes the Kendall rank correlation and Mann-Kendall
23194 (license license:gpl2+)))
23196 (define-public r-keyring
23203 (uri (cran-uri "keyring" version))
23206 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23207 (properties `((upstream-name . "keyring")))
23208 (build-system r-build-system)
23210 `(("r-assertthat" ,r-assertthat)
23211 ("r-filelock" ,r-filelock)
23212 ("r-getpass" ,r-getpass)
23213 ("r-openssl" ,r-openssl)
23215 ("r-rappdirs" ,r-rappdirs)
23216 ("r-sodium" ,r-sodium)
23217 ("r-yaml" ,r-yaml)))
23218 (native-inputs `(("pkg-config" ,pkg-config)))
23219 (home-page "https://github.com/r-lib/keyring")
23220 (synopsis "Access the system credential store from R")
23222 "This package provides a platform-independent API to access the operating
23223 system's credential store. It currently supports Keychain on macOS,
23224 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23225 simple, platform independent store implemented with environment variables.
23226 Additional storage back-ends can be added easily.")
23227 (license license:expat)))
23229 (define-public r-zyp
23232 (version "0.10-1.1")
23236 (uri (cran-uri "zyp" version))
23239 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23240 (properties `((upstream-name . "zyp")))
23241 (build-system r-build-system)
23243 `(("r-kendall" ,r-kendall)))
23244 (home-page "https://cran.r-project.org/web/packages/zyp/")
23245 (synopsis "Zhang + Yue-Pilon Trends Package")
23247 "This package contains an efficient implementation of Sen's slope
23248 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23249 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23251 (license license:lgpl2.1)))
23253 (define-public r-rlinsolve
23255 (name "r-rlinsolve")
23260 (uri (cran-uri "Rlinsolve" version))
23263 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23264 (properties `((upstream-name . "Rlinsolve")))
23265 (build-system r-build-system)
23267 `(("r-matrix" ,r-matrix)
23269 ("r-rcpparmadillo" ,r-rcpparmadillo)
23270 ("r-rdpack" ,r-rdpack)))
23271 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23272 (synopsis "Iterative solvers for (sparse) linear system of equations")
23274 "Solving a system of linear equations is one of the most fundamental
23275 computational problems for many fields of mathematical studies, such as
23276 regression problems from statistics or numerical partial differential
23277 equations. This package provides basic stationary iterative solvers such as
23278 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23279 Nonstationary, also known as Krylov subspace methods are also provided.
23280 Sparse matrix computation is also supported in that solving large and sparse
23281 linear systems can be manageable using the @code{Matrix} package along with
23282 @code{RcppArmadillo}.")
23283 (license license:gpl3+)))
23285 (define-public r-zvcv
23292 (uri (cran-uri "ZVCV" version))
23295 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23296 (properties `((upstream-name . "ZVCV")))
23297 (build-system r-build-system)
23299 `(("r-abind" ,r-abind)
23301 ("r-dplyr" ,r-dplyr)
23302 ("r-glmnet" ,r-glmnet)
23303 ("r-magrittr" ,r-magrittr)
23304 ("r-mvtnorm" ,r-mvtnorm)
23306 ("r-rcpparmadillo" ,r-rcpparmadillo)
23307 ("r-rlinsolve" ,r-rlinsolve)))
23308 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23309 (synopsis "Zero-Variance Control Variates")
23311 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23312 to reduce the variance of Monte Carlo estimators of expectations using the
23313 derivatives of the log target. Once the derivatives are available, the only
23314 additional computational effort is in solving a linear regression problem.
23315 This method has been extended to higher dimensions using regularisation. This
23316 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23317 samples, derivatives and function evaluations are available. Additional
23318 functions for applying ZV-CV to two estimators for the normalising constant of
23319 the posterior distribution in Bayesian statistics are also supplied.")
23320 (license license:gpl2+)))
23322 (define-public r-ztype
23329 (uri (cran-uri "ztype" version))
23332 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23333 (properties `((upstream-name . "ztype")))
23334 (build-system r-build-system)
23336 `(("r-assertthat" ,r-assertthat)
23337 ("r-dplyr" ,r-dplyr)
23338 ("r-ggplot2" ,r-ggplot2)
23339 ("r-lubridate" ,r-lubridate)
23340 ("r-magrittr" ,r-magrittr)
23341 ("r-rvest" ,r-rvest)
23342 ("r-stringr" ,r-stringr)))
23343 (home-page "https://cran.r-project.org/web/packages/ztype/")
23344 (synopsis "Run a Ztype game loaded with R functions")
23346 "How fast can you type R functions on your keyboard? Find out by running
23347 a @code{zty.pe} game: export R functions as instructions to type to destroy
23348 opponents' vessels.")
23349 (license license:gpl3)))
23351 (define-public r-zseq
23358 (uri (cran-uri "Zseq" version))
23361 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23362 (properties `((upstream-name . "Zseq")))
23363 (build-system r-build-system)
23365 `(("r-gmp" ,r-gmp)))
23366 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23367 (synopsis "Integer sequence generator")
23369 "This package generates well-known integer sequences. The @code{gmp}
23370 package is adopted for computing with arbitrarily large numbers. Every
23371 function has a hyperlink to its corresponding item in the @dfn{On-Line
23372 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23373 (license license:gpl3+)))
23375 (define-public r-isoband
23382 (uri (cran-uri "isoband" version))
23385 "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn"))))
23386 (properties `((upstream-name . "isoband")))
23387 (build-system r-build-system)
23389 `(("r-knitr" ,r-knitr)))
23390 (home-page "https://github.com/wilkelab/isoband")
23391 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23393 "This package provides a fast C++ implementation to generate contour
23394 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23395 containing elevation data.")
23396 (license license:expat)))
23398 (define-public r-ppcor
23405 (uri (cran-uri "ppcor" version))
23408 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23409 (properties `((upstream-name . "ppcor")))
23410 (build-system r-build-system)
23412 `(("r-mass" ,r-mass)))
23413 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23414 (synopsis "Partial and semi-partial correlation")
23416 "This package provides users not only with a function to readily
23417 calculate the higher-order partial and semi-partial correlations but also with
23418 statistics and p-values of the correlation coefficients.")
23419 (license license:gpl2)))
23421 (define-public r-hrbrthemes
23423 (name "r-hrbrthemes")
23428 (uri (cran-uri "hrbrthemes" version))
23430 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23431 (properties `((upstream-name . "hrbrthemes")))
23432 (build-system r-build-system)
23434 `(("r-extrafont" ,r-extrafont)
23435 ("r-gdtools" ,r-gdtools)
23436 ("r-ggplot2" ,r-ggplot2)
23437 ("r-htmltools" ,r-htmltools)
23438 ("r-knitr" ,r-knitr)
23439 ("r-magrittr" ,r-magrittr)
23440 ("r-rmarkdown" ,r-rmarkdown)
23441 ("r-scales" ,r-scales)))
23443 `(("r-knitr" ,r-knitr)))
23444 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23445 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23447 "This package provides a compilation of extra @code{ggplot2} themes,
23448 scales and utilities, including a spell check function for plot label fields
23449 and an overall emphasis on typography.")
23450 (license license:expat)))
23452 (define-public r-crochet
23459 (uri (cran-uri "crochet" version))
23462 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23463 (build-system r-build-system)
23465 `(("r-knitr" ,r-knitr)))
23466 (home-page "https://github.com/agrueneberg/crochet")
23467 (synopsis "Implementation Helper for Matrix-Like Types")
23469 "Functions to help implement the extraction / subsetting / indexing
23470 function @code{[} and replacement function @code{[<-} of custom matrix-like
23471 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23472 as possible (with tests to prove it).")
23473 (license license:expat)))
23475 (define-public r-boa
23478 (version "1.1.8-2")
23482 (uri (cran-uri "boa" version))
23485 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23486 (properties `((upstream-name . "boa")))
23487 (build-system r-build-system)
23488 (home-page "https://www.jstatsoft.org/v21/i11")
23489 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23491 "This package provides a menu-driven program and library of functions for
23492 carrying out convergence diagnostics and statistical and graphical analysis of
23493 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23494 (license license:gpl2+)))
23496 (define-public r-httpcode
23498 (name "r-httpcode")
23502 (uri (cran-uri "httpcode" version))
23505 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23506 (build-system r-build-system)
23507 (home-page "https://github.com/sckott/httpcode")
23508 (synopsis "HTTP status code helper")
23509 (description "@code{httpcode} provides functionality for finding and
23510 explaining the meaning of @code{HTTP} status codes. Functions are included for
23511 searching for codes by full or partial number, by message, and to get
23512 appropriate dog and cat images for many status codes.")
23513 (license license:expat)))
23515 (define-public r-latex2exp
23517 (name "r-latex2exp")
23521 (uri (cran-uri "latex2exp" version))
23524 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23525 (build-system r-build-system)
23527 `(("r-stringr" ,r-stringr)
23528 ("r-magrittr" ,r-magrittr)))
23529 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23530 (synopsis "Use LaTeX expressions in plots")
23531 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23532 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23533 rendered as text, axis labels, etc. throughout R's plotting system.")
23534 (license license:expat)))
23536 (define-public r-oai
23542 (uri (cran-uri "oai" version))
23545 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23546 (build-system r-build-system)
23548 `(("r-xml2" ,r-xml2)
23551 ("r-stringr" ,r-stringr)
23552 ("r-tibble" ,r-tibble)))
23553 (home-page "https://github.com/ropensci/oai/")
23554 (synopsis "General purpose OAI-PMH services client")
23555 (description "@code{oai} provides a general purpose client to work with
23556 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23557 service. Functions are provided to work with the OAI-PMH verbs:
23558 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23559 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23560 (license license:expat)))
23562 (define-public r-argon2
23569 (uri (cran-uri "argon2" version))
23572 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23573 (properties `((upstream-name . "argon2")))
23574 (build-system r-build-system)
23575 (home-page "https://github.com/wrathematics/argon2")
23576 (synopsis "Secure password hashing based on the argon2 algorithm")
23578 "This package provides utilities for secure password hashing via the
23579 argon2 algorithm.")
23580 (license license:bsd-2)))
23582 (define-public r-getpass
23589 (uri (cran-uri "getPass" version))
23592 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23593 (properties `((upstream-name . "getPass")))
23594 (build-system r-build-system)
23596 `(("r-rstudioapi" ,r-rstudioapi)))
23597 (home-page "https://github.com/wrathematics/getPass")
23598 (synopsis "Masked user input")
23600 "This package provides a micro-package for reading \"passwords\", i.e.
23601 reading user input with masking, so that the input is not displayed as it is
23602 typed. Currently, RStudio, the command line (every OS), and any platform
23603 where tcltk is present are supported.")
23604 (license license:bsd-2)))
23606 (define-public r-remoter
23613 (uri (cran-uri "remoter" version))
23616 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23617 (properties `((upstream-name . "remoter")))
23618 (build-system r-build-system)
23620 `(("r-argon2" ,r-argon2)
23621 ("r-getpass" ,r-getpass)
23622 ("r-pbdzmq" ,r-pbdzmq)
23624 (home-page "https://github.com/RBigData/remoter")
23625 (synopsis "Control a remote R session from a local one")
23627 "This package provides a set of utilities for client/server computing
23628 with R, controlling a remote R session (the server) from a local one (the
23630 (license license:bsd-2)))
23632 (define-public r-asd
23639 (uri (cran-uri "asd" version))
23642 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23643 (properties `((upstream-name . "asd")))
23644 (build-system r-build-system)
23646 `(("r-mvtnorm" ,r-mvtnorm)))
23647 (home-page "https://cran.r-project.org/web/packages/asd")
23648 (synopsis "Simulations for Adaptive Seamless Designs")
23650 "This package provdes means to run simulations for adaptive seamless
23651 designs with and without early outcomes for treatment selection and
23652 subpopulation type designs.")
23653 (license license:gpl3)))
23655 (define-public r-nbconvertr
23657 (name "r-nbconvertr")
23662 (uri (cran-uri "nbconvertR" version))
23665 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23666 (properties `((upstream-name . "nbconvertR")))
23667 (build-system r-build-system)
23669 `(("jupyter" ,python-nbconvert)
23670 ("pandoc" ,pandoc)))
23671 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23672 (synopsis "Vignette engine wrapping Jupyter notebooks")
23674 "This package calls the Jupyter script @code{nbconvert} to create
23675 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23676 containing rich text, code, and its output. Code cells can be edited and
23677 evaluated interactively.")
23678 (license license:gpl3)))
23680 (define-public r-bridgesampling
23682 (name "r-bridgesampling")
23687 (uri (cran-uri "bridgesampling" version))
23690 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23692 `((upstream-name . "bridgesampling")))
23693 (build-system r-build-system)
23695 `(("r-brobdingnag" ,r-brobdingnag)
23697 ("r-matrix" ,r-matrix)
23698 ("r-mvtnorm" ,r-mvtnorm)
23699 ("r-scales" ,r-scales)
23700 ("r-stringr" ,r-stringr)))
23702 `(("r-knitr" ,r-knitr)))
23703 (home-page "https://github.com/quentingronau/bridgesampling")
23704 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23706 "This package provides functions for estimating marginal likelihoods,
23707 Bayes factors, posterior model probabilities, and normalizing constants in
23708 general, via different versions of bridge sampling.")
23709 (license license:gpl2+)))
23711 (define-public r-tea
23718 (uri (cran-uri "tea" version))
23721 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23723 `((upstream-name . "tea")))
23724 (build-system r-build-system)
23726 `(("r-matrix" ,r-matrix)))
23727 (home-page "https://cran.r-project.org/web/packages/tea/")
23728 (synopsis "Threshold estimation approaches")
23730 "This package provides different approaches for selecting the threshold
23731 in generalized Pareto distributions. Most of them are based on minimizing the
23732 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23733 Others are heuristically motivated by searching for stable sample paths, i.e.
23734 a nearly constant region of the tail index estimator with respect to k, which
23735 is the number of data in the tail. The third class is motivated by graphical
23736 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23737 is also implemented here.")
23738 (license license:gpl3)))
23740 (define-public r-awsmethods
23742 (name "r-awsmethods")
23747 (uri (cran-uri "awsMethods" version))
23750 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23752 `((upstream-name . "awsMethods")))
23753 (build-system r-build-system)
23754 (home-page "http://www.wias-berlin.de/software/imaging/")
23755 (synopsis "Class and methods definitions")
23757 "This package defines the generic method @code{extract} and provides
23758 @code{openMP} support as needed in several packages like
23759 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23760 (license license:gpl2+)))
23762 (define-public r-aws
23769 (uri (cran-uri "aws" version))
23772 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23774 `((upstream-name . "aws")))
23775 (build-system r-build-system)
23777 `(("r-awsmethods" ,r-awsmethods)
23780 `(("gfortran" ,gfortran)))
23781 (home-page "https://cran.r-project.org/web/packages/aws/")
23782 (synopsis "Adaptive weights smoothing")
23784 "This package provides a collection of R-functions implementing adaptive
23785 smoothing procedures in 1D, 2D and 3D. This includes the
23786 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23787 Confidence Intervals} (ICI), variational approaches, and a non-local means
23789 (license license:gpl2+)))
23791 (define-public r-sgloptim
23793 (name "r-sgloptim")
23798 (uri (cran-uri "sglOptim" version))
23801 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23803 `((upstream-name . "sglOptim")))
23804 (build-system r-build-system)
23807 ("r-doparallel" ,r-doparallel)
23808 ("r-foreach" ,r-foreach)
23809 ("r-matrix" ,r-matrix)
23811 ("r-rcpparmadillo" ,r-rcpparmadillo)
23812 ("r-rcppprogress" ,r-rcppprogress)))
23814 `(("r-knitr" ,r-knitr)))
23815 (home-page "https://github.com/nielsrhansen/sglOptim")
23816 (synopsis "Generic sparse group Lasso solver")
23818 "This package provides a fast generic solver for sparse group lasso
23819 optimization problems. The loss (objective) function must be defined in a C++
23820 module. The optimization problem is solved using a coordinate gradient
23821 descent algorithm. Convergence of the algorithm is established and the
23822 algorithm is applicable to a broad class of loss functions. Use of parallel
23823 computing for cross validation and subsampling is supported through the
23824 @code{foreach} and @code{doParallel} packages.")
23825 (license license:gpl2+)))
23827 (define-public r-grouped
23834 (uri (cran-uri "grouped" version))
23837 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23839 `((upstream-name . "grouped")))
23840 (build-system r-build-system)
23842 `(("r-mass" ,r-mass)))
23843 (home-page "https://cran.r-project.org/web/packages/grouped/")
23844 (synopsis "Regression analysis of grouped and coarse data")
23846 "This package provides regression models for grouped and coarse data,
23847 under the coarsened at random assumption.")
23848 (license license:gpl2+)))
23850 (define-public r-stam
23857 (uri (cran-uri "stam" version))
23860 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23862 `((upstream-name . "stam")))
23863 (build-system r-build-system)
23867 (home-page "https://cran.r-project.org/web/packages/stam")
23868 (synopsis "Spatio-temporal analysis and modelling")
23870 "This package provides various methods to conduct Spatio-Temporal
23871 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23872 Inferred Spatio-Temporal Modelling.")
23873 (license license:gpl2+)))
23875 (define-public r-dcv
23882 (uri (cran-uri "dcv" version))
23885 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23887 `((upstream-name . "dcv")))
23888 (build-system r-build-system)
23890 `(("r-lmtest" ,r-lmtest)))
23891 (home-page "https://cran.r-project.org/web/packages/dcv/")
23892 (synopsis "Conventional cross-validation statistics for climate-growth model")
23894 "This package performs several conventional cross-validation statistical
23895 methods for climate-growth model in the climate reconstruction from tree
23896 rings, including Sign Test statistic, Reduction of Error statistic, Product
23897 Mean Test, Durbin-Watson statistic etc.")
23898 (license license:gpl2)))
23900 (define-public r-rcdd
23907 (uri (cran-uri "rcdd" version))
23910 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23912 `((upstream-name . "rcdd")))
23913 (build-system r-build-system)
23916 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23917 (synopsis "Computational geometry")
23919 "This package converts back and forth between two representations of a
23920 convex polytope: as solution of a set of linear equalities and inequalities
23921 and as convex hull of set of points and rays. Also does linear programming
23922 and redundant generator elimination. All functions can use exact
23923 infinite-precision rational arithmetic.")
23924 (license license:gpl2)))
23926 (define-public r-rxnat
23933 (uri (cran-uri "Rxnat" version))
23936 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23938 `((upstream-name . "Rxnat")))
23939 (build-system r-build-system)
23941 `(("r-dplyr" ,r-dplyr)
23943 ("r-rcurl" ,r-rcurl)
23944 ("r-tibble" ,r-tibble)))
23946 `(("r-knitr" ,r-knitr)))
23947 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23948 (synopsis "Queries and extracts images from neuroimaging datasets")
23950 "This package allows communication with the Extensible Neuroimaging
23951 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23953 (license license:gpl2)))
23955 (define-public r-rserve
23962 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23963 version ".tar.gz"))
23966 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23967 (build-system r-build-system)
23970 (modify-phases %standard-phases
23971 (add-before 'install 'install-server-binary
23972 ;; Makevars tries to install to R's store directory.
23973 (lambda* (#:key outputs #:allow-other-keys)
23974 (let* ((out (assoc-ref outputs "out"))
23975 (bin (string-append out "/bin")))
23976 (substitute* "src/Makevars.in"
23977 (("\\$\\(R_HOME\\)") out))
23978 (mkdir-p bin)))))))
23980 `(("r-checkmate" ,r-checkmate)
23982 ("r-jsonlite" ,r-jsonlite)
23983 ("r-knitr" ,r-knitr)
23986 ("r-uuid" ,r-uuid)))
23988 `(("openssl" ,openssl)
23990 (home-page "https://github.com/s-u/Rserve")
23992 "Server providing access to R from many languages and systems")
23994 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
23995 binary requests to be sent to R. Every connection has a separate workspace
23996 and working directory. Client-side implementations are available for popular
23997 languages such as C/C++ and Java, allowing any application to use facilities
23998 of R without the need of linking to R code. Rserve supports remote
23999 connection, user authentication and file transfer. A simple R client is
24000 included in this package as well.")
24001 (license license:gpl2)))
24003 (define-public r-gamm4
24010 (uri (cran-uri "gamm4" version))
24013 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
24014 (properties `((upstream-name . "gamm4")))
24015 (build-system r-build-system)
24017 `(("r-lme4" ,r-lme4)
24018 ("r-matrix" ,r-matrix)
24019 ("r-mgcv" ,r-mgcv)))
24020 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24021 (synopsis "Generalized additive mixed models using mgcv and lme4")
24023 "Estimate generalized additive mixed models via a version of function
24024 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24026 (license license:gpl2+)))
24028 (define-public r-optimx
24031 (version "2020-4.2")
24035 (uri (cran-uri "optimx" version))
24038 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24039 (properties `((upstream-name . "optimx")))
24040 (build-system r-build-system)
24041 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24042 (native-inputs `(("r-knitr" ,r-knitr)))
24043 (home-page "https://cran.r-project.org/web/packages/optimx/")
24044 (synopsis "Expanded replacement and extension of the optim function")
24046 "This package provides a replacement and extension of the @code{optim}
24047 function to call to several function minimization codes in R in a single
24048 statement. These methods handle smooth, possibly box constrained functions of
24049 several or many parameters. Note that the function @code{optimr} was prepared
24050 to simplify the incorporation of minimization codes going forward. This
24051 package also implements some utility codes and some extra solvers, including
24052 safeguarded Newton methods. Many methods previously separate are now included
24054 (license license:gpl2)))
24056 (define-public r-projpred
24058 (name "r-projpred")
24063 (uri (cran-uri "projpred" version))
24066 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24067 (properties `((upstream-name . "projpred")))
24068 (build-system r-build-system)
24070 `(("r-dplyr" ,r-dplyr)
24071 ("r-gamm4" ,r-gamm4)
24072 ("r-ggplot2" ,r-ggplot2)
24075 ("r-magrittr" ,r-magrittr)
24078 ("r-optimx" ,r-optimx)
24080 ("r-rcpparmadillo" ,r-rcpparmadillo)
24081 ("r-rngtools" ,r-rngtools)
24082 ("r-rstantools" ,r-rstantools)
24083 ("r-tidyverse" ,r-tidyverse)))
24084 (native-inputs `(("r-knitr" ,r-knitr)))
24085 (home-page "https://mc-stan.org/projpred/")
24086 (synopsis "Projection predictive feature selection")
24088 "This package performs projection predictive feature selection for
24089 generalized linear models and generalized linear and additive multilevel
24090 models. The package is compatible with the @code{rstanarm} and @code{brms}
24091 packages, but other reference models can also be used. See the package
24092 vignette for more information and examples.")
24093 (license license:gpl3)))
24095 (define-public r-brms
24102 (uri (cran-uri "brms" version))
24105 "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1"))))
24106 (properties `((upstream-name . "brms")))
24107 (build-system r-build-system)
24109 `(("r-abind" ,r-abind)
24110 ("r-backports" ,r-backports)
24111 ("r-bayesplot" ,r-bayesplot)
24112 ("r-bridgesampling" ,r-bridgesampling)
24114 ("r-future" ,r-future)
24115 ("r-ggplot2" ,r-ggplot2)
24118 ("r-matrix" ,r-matrix)
24119 ("r-matrixstats" ,r-matrixstats)
24121 ("r-nleqslv" ,r-nleqslv)
24123 ("r-projpred" ,r-projpred)
24125 ("r-rstan" ,r-rstan)
24126 ("r-rstantools" ,r-rstantools)
24127 ("r-shinystan" ,r-shinystan)))
24128 (native-inputs `(("r-knitr" ,r-knitr)))
24130 "https://github.com/paul-buerkner/brms")
24132 "Bayesian Regression Models using 'Stan'")
24134 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24135 using 'Stan' for full Bayesian inference. A wide range of distributions and
24136 link functions are supported, allowing users to fit -- among others -- linear,
24137 robust linear, count data, survival, response times, ordinal, zero-inflated,
24138 hurdle, and even self-defined mixture models all in a multilevel context.
24139 Further modeling options include non-linear and smooth terms, auto-correlation
24140 structures, censored data, meta-analytic standard errors, and quite a few
24141 more. In addition, all parameters of the response distribution can be
24142 predicted in order to perform distributional regression. Prior specifications
24143 are flexible and explicitly encourage users to apply prior distributions that
24144 actually reflect their beliefs. Model fit can easily be assessed and compared
24145 with posterior predictive checks and leave-one-out cross-validation.")
24146 (license license:gpl2)))
24148 (define-public r-mstate
24155 (uri (cran-uri "mstate" version))
24158 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24159 (properties `((upstream-name . "mstate")))
24160 (build-system r-build-system)
24162 `(("r-data-table" ,r-data-table)
24163 ("r-lattice" ,r-lattice)
24164 ("r-magrittr" ,r-magrittr)
24165 ("r-rcolorbrewer" ,r-rcolorbrewer)
24166 ("r-rlang" ,r-rlang)
24167 ("r-survival" ,r-survival)
24168 ("r-viridis" ,r-viridis)))
24170 `(("r-knitr" ,r-knitr)))
24172 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24174 "Data Preparation, Estimation and Prediction in Multi-State Models")
24176 "Contains functions for data preparation, descriptives, hazard estimation
24177 and prediction with Aalen-Johansen or simulation in competing risks and
24178 multi-state models.")
24179 (license license:gpl2+)))
24181 (define-public r-scatterpie
24183 (name "r-scatterpie")
24188 (uri (cran-uri "scatterpie" version))
24191 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24192 (properties `((upstream-name . "scatterpie")))
24193 (build-system r-build-system)
24195 `(("r-ggforce" ,r-ggforce)
24196 ("r-ggplot2" ,r-ggplot2)
24197 ("r-rlang" ,r-rlang)
24198 ("r-rvcheck" ,r-rvcheck)
24199 ("r-tidyr" ,r-tidyr)))
24201 `(("r-knitr" ,r-knitr)))
24202 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24203 (synopsis "Scatter pie plot")
24205 "This package creates scatterpie plots, especially useful for plotting
24207 (license license:artistic2.0)))
24209 (define-public r-scrypt
24216 (uri (cran-uri "scrypt" version))
24219 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24220 (properties `((upstream-name . "scrypt")))
24221 (build-system r-build-system)
24223 `(("r-rcpp" ,r-rcpp)))
24224 (home-page "https://github.com/rstudio/rscrypt")
24225 (synopsis "Key derivation functions for R based on Scrypt")
24227 "This package provides functions for working with the scrypt key
24228 derivation functions. Scrypt is a password-based key derivation function
24229 created by Colin Percival. The algorithm was specifically designed to make it
24230 costly to perform large-scale custom hardware attacks by requiring large
24231 amounts of memory.")
24232 (license license:bsd-2)))
24234 (define-public r-boruta
24241 (uri (cran-uri "Boruta" version))
24244 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24245 (properties `((upstream-name . "Boruta")))
24246 (build-system r-build-system)
24247 (propagated-inputs `(("r-ranger" ,r-ranger)))
24248 (home-page "https://gitlab.com/mbq/Boruta/")
24249 (synopsis "Wrapper algorithm for all relevant feature selection")
24251 "This package provides an all relevant feature selection wrapper
24252 algorithm. It finds relevant features by comparing original attributes'
24253 importance with importance achievable at random, estimated using their
24254 permuted copies (shadows).")
24255 (license license:gpl2+)))
24257 (define-public r-directlabels
24259 (name "r-directlabels")
24260 (version "2021.1.13")
24264 (uri (cran-uri "directlabels" version))
24267 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24268 (build-system r-build-system)
24270 `(("r-quadprog" ,r-quadprog)))
24272 `(("r-knitr" ,r-knitr)))
24273 (home-page "http://directlabels.r-forge.r-project.org/")
24274 (synopsis "Direct labels for multicolor plots")
24276 "This package provides an extensible framework for automatically placing
24277 direct labels onto multicolor plots. Label positions are described using
24278 positioning methods that can be re-used across several different plots. There
24279 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24280 inferring an appropriate positioning method.")
24281 (license license:gpl3)))
24283 (define-public r-lsd
24290 (uri (cran-uri "LSD" version))
24292 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24293 (properties `((upstream-name . "LSD")))
24294 (build-system r-build-system)
24295 (home-page "https://cran.r-project.org/web/packages/LSD/")
24296 (synopsis "Lots of superior depictions tool creates colorful plots")
24298 "This package creates lots of colorful plots in a multitude of variations.
24299 Try a demo of the LSD by running @code{demotour()}.")
24301 (license (list license:gpl2 license:gpl3))))
24303 (define-public r-phylogram
24305 (name "r-phylogram")
24310 (uri (cran-uri "phylogram" version))
24312 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24313 (properties `((upstream-name . "phylogram")))
24314 (build-system r-build-system)
24315 (propagated-inputs `(("r-ape" ,r-ape)))
24316 (home-page "https://github.com/ropensci/phylogram/")
24317 (synopsis "Dendrograms for evolutionary analysis")
24319 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24320 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24321 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24322 as well as several tools for command-line tree manipulation and import/export
24323 via Newick parenthetic text. This improves accessibility to the comprehensive
24324 range of object-specific analytical and tree-visualization functions found
24325 across a wide array of bioinformatic R packages.")
24326 (license license:gpl3)))
24328 (define-public r-kmer
24335 (uri (cran-uri "kmer" version))
24337 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24338 (properties `((upstream-name . "kmer")))
24339 (build-system r-build-system)
24341 `(("r-openssl" ,r-openssl)
24342 ("r-phylogram" ,r-phylogram)
24343 ("r-rcpp" ,r-rcpp)))
24344 (home-page "https://github.com/shaunpwilkinson/kmer/")
24345 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24347 "@code{r-kmer} is an R package for rapidly computing distance matrices
24348 and clustering large sequence datasets using fast alignment-free k-mer
24349 counting and recursive k-means partitioning.")
24350 (license license:gpl3)))
24352 (define-public r-hardhat
24359 (uri (cran-uri "hardhat" version))
24362 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24363 (properties `((upstream-name . "hardhat")))
24364 (build-system r-build-system)
24366 `(("r-glue" ,r-glue)
24367 ("r-rlang" ,r-rlang)
24368 ("r-tibble" ,r-tibble)
24369 ("r-vctrs" ,r-vctrs)))
24371 `(("r-knitr" ,r-knitr)))
24372 (home-page "https://github.com/tidymodels/hardhat")
24373 (synopsis "Construct modeling packages")
24375 "Building modeling packages is hard. A large amount of effort generally
24376 goes into providing an implementation for a new method that is efficient,
24377 fast, and correct, but often less emphasis is put on the user interface. A
24378 good interface requires specialized knowledge about S3 methods and formulas,
24379 which the average package developer might not have. The goal of
24380 @code{hardhat} is to reduce the burden around building new modeling packages
24381 by providing functionality for preprocessing, predicting, and validating
24383 (license license:expat)))
24385 (define-public r-lightgbm
24387 (name "r-lightgbm")
24392 (uri (cran-uri "lightgbm" version))
24395 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24396 (properties `((upstream-name . "lightgbm")))
24397 (build-system r-build-system)
24399 `(("r-data-table" ,r-data-table)
24400 ("r-jsonlite" ,r-jsonlite)
24401 ("r-matrix" ,r-matrix)
24403 (home-page "https://github.com/Microsoft/LightGBM")
24404 (synopsis "Light gradient boosting machine")
24406 "Tree based algorithms can be improved by introducing boosting
24407 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24408 al. (2017). This package offers an R interface to work with it. It is
24409 designed to be distributed and efficient with the following goals:
24412 @item Faster training speed and higher efficiency;
24413 @item lower memory usage;
24414 @item better accuracy;
24415 @item parallel learning supported; and
24416 @item capable of handling large-scale data.
24419 (license license:expat)))
24421 (define-public r-shapforxgboost
24423 (name "r-shapforxgboost")
24428 (uri (cran-uri "SHAPforxgboost" version))
24431 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24433 `((upstream-name . "SHAPforxgboost")))
24434 (build-system r-build-system)
24436 `(("r-bbmisc" ,r-bbmisc)
24437 ("r-data-table" ,r-data-table)
24438 ("r-ggextra" ,r-ggextra)
24439 ("r-ggforce" ,r-ggforce)
24440 ("r-ggplot2" ,r-ggplot2)
24441 ("r-ggpubr" ,r-ggpubr)
24442 ("r-lightgbm" ,r-lightgbm)
24443 ("r-rcolorbrewer" ,r-rcolorbrewer)
24444 ("r-xgboost" ,r-xgboost)))
24445 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24446 (synopsis "SHAP Plots for XGBoost")
24448 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24449 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24450 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24451 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24453 (license license:expat)))
24455 (define-public r-rismed
24462 (uri (cran-uri "RISmed" version))
24465 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24466 (properties `((upstream-name . "RISmed")))
24467 (build-system r-build-system)
24468 (home-page "https://cran.r-project.org/web/packages/RISmed")
24469 (synopsis "Download content from NCBI databases")
24471 "This package provides a set of tools to extract bibliographic
24472 content from the National Center for Biotechnology Information (NCBI)
24473 databases, including PubMed. The name RISmed is a portmanteau of
24474 RIS (for Research Information Systems, a common tag format for
24475 bibliographic data) and PubMed.")
24476 (license license:gpl2+)))
24478 (define-public r-semver
24485 (uri (cran-uri "semver" version))
24488 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24489 (properties `((upstream-name . "semver")))
24490 (build-system r-build-system)
24492 `(("r-assertthat" ,r-assertthat)
24493 ("r-rcpp" ,r-rcpp)))
24494 (native-inputs `(("r-knitr" ,r-knitr)))
24495 (home-page "https://github.com/johndharrison/semver")
24496 (synopsis "Parser for Semantic Versioning 2.0.0")
24498 "This package provides tools and functions for parsing, rendering and
24499 operating on semantic version strings. Semantic versioning is a simple set of
24500 rules and requirements that dictate how version numbers are assigned and
24501 incremented as outlined at @url{http://semver.org}.")
24502 (license license:expat)))
24504 (define-public r-binman
24511 (uri (cran-uri "binman" version))
24514 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24515 (properties `((upstream-name . "binman")))
24516 (build-system r-build-system)
24518 `(("r-assertthat" ,r-assertthat)
24520 ("r-jsonlite" ,r-jsonlite)
24521 ("r-rappdirs" ,r-rappdirs)
24522 ("r-semver" ,r-semver)
24524 ("r-yaml" ,r-yaml)))
24525 (native-inputs `(("r-knitr" ,r-knitr)))
24526 (home-page "https://github.com/ropensci/binman")
24527 (synopsis "Binary download manager")
24529 "This package provides tools and functions for managing the download of
24530 binary files. Binary repositories are defined in the YAML format. Defining
24531 new pre-download, download and post-download templates allow additional
24532 repositories to be added.")
24533 (license license:expat)))
24535 (define-public r-wdman
24542 (uri (cran-uri "wdman" version))
24545 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24546 (properties `((upstream-name . "wdman")))
24547 (build-system r-build-system)
24549 `(("r-assertthat" ,r-assertthat)
24550 ("r-binman" ,r-binman)
24551 ("r-processx" ,r-processx)
24552 ("r-semver" ,r-semver)
24553 ("r-yaml" ,r-yaml)))
24554 (native-inputs `(("r-knitr" ,r-knitr)))
24555 (home-page "https://docs.ropensci.org/wdman/")
24556 (synopsis "Webdriver/Selenium binary manager")
24558 "There are a number of binary files associated with the
24559 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24560 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24561 @url{https://github.com/mozilla/geckodriver},
24562 @url{http://phantomjs.org/download.html}, and
24563 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24564 more information). This package provides functions to download these binaries
24565 and to manage processes involving them.")
24566 (license license:expat)))
24568 (define-public r-rselenium
24570 (name "r-rselenium")
24575 (uri (cran-uri "RSelenium" version))
24578 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24579 (properties `((upstream-name . "RSelenium")))
24580 (build-system r-build-system)
24582 `(("r-binman" ,r-binman)
24583 ("r-catools" ,r-catools)
24585 ("r-openssl" ,r-openssl)
24586 ("r-wdman" ,r-wdman)
24588 (native-inputs `(("r-knitr" ,r-knitr)))
24589 (home-page "https://docs.ropensci.org/RSelenium/")
24590 (synopsis "R bindings for Selenium WebDriver")
24592 "This package provides a set of R bindings for the Selenium 2.0
24593 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24594 information) using the @code{JsonWireProtocol} (see
24595 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24596 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24597 a user would either locally or on a remote machine using the Selenium server
24598 it marks a leap forward in terms of web browser automation. Selenium
24599 automates web browsers (commonly referred to as browsers). Using RSelenium
24600 you can automate browsers locally or remotely.")
24601 (license license:agpl3+)))
24603 (define-public r-conquer
24610 (uri (cran-uri "conquer" version))
24613 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24614 (properties `((upstream-name . "conquer")))
24615 (build-system r-build-system)
24617 `(("r-matrix" ,r-matrix)
24618 ("r-matrixstats" ,r-matrixstats)
24620 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24621 (home-page "https://github.com/XiaoouPan/conquer")
24622 (synopsis "Convolution-type smoothed quantile regression")
24624 "This package provides fast and accurate convolution-type smoothed
24625 quantile regression, implemented using Barzilai-Borwein gradient descent with
24626 a Huber regression warm start. Confidence intervals for regression
24627 coefficients are constructed using multiplier bootstrap.")
24628 (license license:gpl3)))
24630 (define-public r-fastshap
24632 (name "r-fastshap")
24637 (uri (cran-uri "fastshap" version))
24640 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24641 (properties `((upstream-name . "fastshap")))
24642 (build-system r-build-system)
24644 `(("r-abind" ,r-abind)
24645 ("r-ggplot2" ,r-ggplot2)
24646 ("r-gridextra" ,r-gridextra)
24647 ("r-matrixstats" ,r-matrixstats)
24650 ("r-rcpparmadillo" ,r-rcpparmadillo)
24651 ("r-tibble" ,r-tibble)))
24652 (home-page "https://github.com/bgreenwell/fastshap")
24653 (synopsis "Fast approximate Shapley values")
24655 "This package computes fast (relative to other implementations)
24656 approximate Shapley values for any supervised learning model. Shapley values
24657 help to explain the predictions from any black box model using ideas from game
24658 theory; see @url{Strumbel and Kononenko (2014),
24659 doi.org/10.1007/s10115-013-0679-x} for details.")
24660 (license license:gpl2+)))
24662 (define-public r-metrics
24669 (uri (cran-uri "Metrics" version))
24672 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24673 (properties `((upstream-name . "Metrics")))
24674 (build-system r-build-system)
24675 (home-page "https://github.com/mfrasco/Metrics")
24676 (synopsis "Evaluation metrics for machine learning")
24678 "This package provides an implementation of evaluation metrics in R that
24679 are commonly used in supervised machine learning. It implements metrics for
24680 regression, time series, binary classification, classification, and
24681 information retrieval problems. It has zero dependencies and a consistent,
24682 simple interface for all functions.")
24683 (license license:bsd-3)))
24685 (define-public r-iml
24692 (uri (cran-uri "iml" version))
24695 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24696 (properties `((upstream-name . "iml")))
24697 (build-system r-build-system)
24699 `(("r-checkmate" ,r-checkmate)
24700 ("r-data-table" ,r-data-table)
24701 ("r-formula" ,r-formula)
24702 ("r-future" ,r-future)
24703 ("r-future-apply" ,r-future-apply)
24704 ("r-ggplot2" ,r-ggplot2)
24705 ("r-gridextra" ,r-gridextra)
24706 ("r-metrics" ,r-metrics)
24707 ("r-prediction" ,r-prediction)
24709 (native-inputs `(("r-knitr" ,r-knitr)))
24710 (home-page "https://github.com/christophM/iml")
24711 (synopsis "Interpretable machine learning")
24713 "This package provides interpretability methods to analyze the behavior
24714 and predictions of any machine learning model. Implemented methods are:
24717 @item Feature importance described by Fisher et al. (2018),
24718 @item accumulated local effects plots described by Apley (2018),
24719 @item partial dependence plots described by Friedman (2001),
24720 @item individual conditional expectation ('ice') plots described by Goldstein
24721 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24722 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24723 @item the Shapley Value described by Strumbelj et. al (2014)
24724 @url{https://doi.org/10.1007/s10115-013-0679-x},
24725 @item feature interactions described by Friedman et. al
24726 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24729 (license license:expat)))
24731 (define-public r-goftest
24738 (uri (cran-uri "goftest" version))
24741 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24742 (properties `((upstream-name . "goftest")))
24743 (build-system r-build-system)
24744 (home-page "https://github.com/baddstats/goftest")
24745 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24747 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24748 goodness-of-fit for continuous univariate distributions, using efficient
24750 (license license:gpl2+)))
24752 (define-public r-tensor
24759 (uri (cran-uri "tensor" version))
24762 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24763 (properties `((upstream-name . "tensor")))
24764 (build-system r-build-system)
24765 (home-page "https://cran.r-project.org/web/packages/tensor/")
24766 (synopsis "Tensor product of arrays")
24768 "The tensor product of two arrays is notionally an outer product of the
24769 arrays collapsed in specific extents by summing along the appropriate
24770 diagonals. This package allows you to compute the tensor product of arrays.")
24771 (license license:gpl2+)))
24773 (define-public r-spatstat-utils
24775 (name "r-spatstat-utils")
24780 (uri (cran-uri "spatstat.utils" version))
24783 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24785 `((upstream-name . "spatstat.utils")))
24786 (build-system r-build-system)
24787 (home-page "http://www.spatstat.org")
24788 (synopsis "Utility functions for spatstat")
24790 "This package contains utility functions for the @code{spatstat} package
24791 which may also be useful for other purposes.")
24792 (license license:gpl2+)))
24794 (define-public r-spatstat-sparse
24796 (name "r-spatstat-sparse")
24801 (uri (cran-uri "spatstat.sparse" version))
24804 "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2"))))
24806 `((upstream-name . "spatstat.sparse")))
24807 (build-system r-build-system)
24809 `(("r-abind" ,r-abind)
24810 ("r-matrix" ,r-matrix)
24811 ("r-spatstat-utils" ,r-spatstat-utils)
24812 ("r-tensor" ,r-tensor)))
24813 (home-page "http://spatstat.org/")
24814 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
24816 "This package defines sparse three-dimensional arrays and supports
24817 standard operations on them. The package also includes utility functions for
24818 matrix calculations that are common in statistics, such as quadratic forms.")
24819 (license license:gpl2+)))
24821 (define-public r-spatstat-data
24823 (name "r-spatstat-data")
24828 (uri (cran-uri "spatstat.data" version))
24831 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24832 (properties `((upstream-name . "spatstat.data")))
24833 (build-system r-build-system)
24835 `(("r-matrix" ,r-matrix)
24836 ("r-spatstat-utils" ,r-spatstat-utils)))
24837 (home-page "http://www.spatstat.org")
24838 (synopsis "Datasets for spatstat")
24840 "This package contains all the datasets for the @code{spatstat}
24842 (license license:gpl2+)))
24844 (define-public r-spatstat-geom
24846 (name "r-spatstat-geom")
24851 (uri (cran-uri "spatstat.geom" version))
24854 "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk"))))
24855 (properties `((upstream-name . "spatstat.geom")))
24856 (build-system r-build-system)
24858 `(("r-deldir" ,r-deldir)
24859 ("r-polyclip" ,r-polyclip)
24860 ("r-spatstat-data" ,r-spatstat-data)
24861 ("r-spatstat-sparse" ,r-spatstat-sparse)
24862 ("r-spatstat-utils" ,r-spatstat-utils)))
24863 (home-page "http://spatstat.org/")
24864 (synopsis "Geometrical functionality of the spatstat package")
24866 "This is a subset of the original spatstat package, containing the
24867 user-level code from spatstat which performs geometrical operations, except
24868 for the geometry of linear networks.")
24869 (license license:gpl2+)))
24871 (define-public r-spatstat-core
24873 (name "r-spatstat-core")
24878 (uri (cran-uri "spatstat.core" version))
24881 "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3"))))
24882 (properties `((upstream-name . "spatstat.core")))
24883 (build-system r-build-system)
24885 `(("r-abind" ,r-abind)
24886 ("r-goftest" ,r-goftest)
24887 ("r-matrix" ,r-matrix)
24890 ("r-rpart" ,r-rpart)
24891 ("r-spatstat-data" ,r-spatstat-data)
24892 ("r-spatstat-geom" ,r-spatstat-geom)
24893 ("r-spatstat-sparse" ,r-spatstat-sparse)
24894 ("r-spatstat-utils" ,r-spatstat-utils)
24895 ("r-tensor" ,r-tensor)))
24896 (home-page "http://spatstat.org/")
24897 (synopsis "Core functionality of the spatstat package")
24899 "This is a subset of the original spatstat package, containing all of the
24900 user-level code from spatstat, except for the code for linear networks.")
24901 (license license:gpl2+)))
24903 (define-public r-spatstat-linnet
24905 (name "r-spatstat-linnet")
24910 (uri (cran-uri "spatstat.linnet" version))
24913 "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv"))))
24915 `((upstream-name . "spatstat.linnet")))
24916 (build-system r-build-system)
24918 `(("r-matrix" ,r-matrix)
24919 ("r-spatstat-core" ,r-spatstat-core)
24920 ("r-spatstat-data" ,r-spatstat-data)
24921 ("r-spatstat-geom" ,r-spatstat-geom)
24922 ("r-spatstat-utils" ,r-spatstat-utils)))
24923 (home-page "http://spatstat.org/")
24924 (synopsis "Linear networks functionality of the spatstat package")
24926 "This is a subset of the spatstat package, containing its functionality
24927 for spatial data on a linear network.")
24928 (license license:gpl2+)))
24930 (define-public r-spatstat
24932 (name "r-spatstat")
24937 (uri (cran-uri "spatstat" version))
24940 "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw"))))
24941 (properties `((upstream-name . "spatstat")))
24942 (build-system r-build-system)
24944 `(("r-spatstat-core" ,r-spatstat-core)
24945 ("r-spatstat-data" ,r-spatstat-data)
24946 ("r-spatstat-geom" ,r-spatstat-geom)
24947 ("r-spatstat-linnet" ,r-spatstat-linnet)
24948 ("r-spatstat-utils" ,r-spatstat-utils)))
24949 (home-page "http://www.spatstat.org")
24950 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24952 "This package provides a comprehensive toolbox for analysing Spatial
24953 Point Patterns. It is focused mainly on two-dimensional point patterns,
24954 including multitype/marked points, in any spatial region. It also supports
24955 three-dimensional point patterns, space-time point patterns in any number of
24956 dimensions, point patterns on a linear network, and patterns of other
24957 geometrical objects. It supports spatial covariate data such as pixel images
24958 and contains over 2000 functions for plotting spatial data, exploratory data
24959 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24960 formal inference.")
24961 (license license:gpl2+)))
24963 (define-public r-gaston
24970 (uri (cran-uri "gaston" version))
24973 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24974 (properties `((upstream-name . "gaston")))
24975 (build-system r-build-system)
24976 (inputs `(("zlib" ,zlib)))
24978 `(("r-rcpp" ,r-rcpp)
24979 ("r-rcppeigen" ,r-rcppeigen)
24980 ("r-rcppparallel" ,r-rcppparallel)))
24981 (native-inputs `(("r-knitr" ,r-knitr)))
24982 (home-page "https://cran.r-project.org/web/packages/gaston/")
24983 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24985 "This is a package for the manipulation of genetic data (SNPs).
24986 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24987 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24988 for linear mixed models (AIREML).")
24989 (license license:gpl3)))
24991 (define-public r-cpp11
24998 (uri (cran-uri "cpp11" version))
25001 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
25002 (properties `((upstream-name . "cpp11")))
25003 (build-system r-build-system)
25004 (native-inputs `(("r-knitr" ,r-knitr)))
25005 (home-page "https://github.com/r-lib/cpp11")
25006 (synopsis "C++11 Interface for R's C Interface")
25008 "This package provides a header only, C++11 interface to R's C interface.
25009 Compared to other approaches @code{cpp11} strives to be safe against long
25010 jumps from the C API as well as C++ exceptions, conform to normal R function
25011 semantics and supports interaction with @code{ALTREP} vectors.")
25012 (license license:expat)))
25014 (define-public r-rcppziggurat
25016 (name "r-rcppziggurat")
25021 (uri (cran-uri "RcppZiggurat" version))
25024 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
25025 (properties `((upstream-name . "RcppZiggurat")))
25026 (build-system r-build-system)
25028 `(("r-rcpp" ,r-rcpp)
25029 ("r-rcppgsl" ,r-rcppgsl)))
25030 (native-inputs `(("r-knitr" ,r-knitr)))
25031 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
25032 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
25034 "The Ziggurat generator for normally distributed random numbers,
25035 originally proposed by Marsaglia and Tsang (2000,
25036 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
25037 times starting with Leong et al (2005,
25038 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
25039 aggregation for comparing different implementations in order to provide a
25040 'faster but good enough' alternative for use with R and C++ code.")
25041 (license license:gpl2+)))
25043 (define-public r-rfast
25050 (uri (cran-uri "Rfast" version))
25053 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
25054 (properties `((upstream-name . "Rfast")))
25055 (build-system r-build-system)
25057 `(("r-rcpp" ,r-rcpp)
25058 ("r-rcpparmadillo" ,r-rcpparmadillo)
25059 ("r-rcppziggurat" ,r-rcppziggurat)))
25060 (home-page "https://github.com/RfastOfficial/Rfast")
25061 (synopsis "Collection of efficient and fast R functions")
25063 "This package provides a collection of fast (utility) functions for data
25064 analysis. Column- and row- wise means, medians, variances, minimums,
25065 maximums, many t, F and G-square tests, many regressions (normal, logistic,
25066 Poisson), are some of the many fast functions.")
25067 (license license:gpl2+)))
25069 (define-public r-clusterr
25071 (name "r-clusterr")
25076 (uri (cran-uri "ClusterR" version))
25079 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
25080 (properties `((upstream-name . "ClusterR")))
25081 (build-system r-build-system)
25083 `(("r-ggplot2" ,r-ggplot2)
25085 ("r-gtools" ,r-gtools)
25087 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25088 (native-inputs `(("r-knitr" ,r-knitr)))
25089 (home-page "https://github.com/mlampros/ClusterR")
25090 (synopsis "Clustering")
25092 "This package provides Gaussian mixture models, k-means,
25093 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
25094 option to plot, validate, predict (new data) and estimate the optimal number
25095 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
25096 the computationally intensive parts of the functions. For more information,
25100 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
25101 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
25102 @url{https://doi.org/10.18637/jss.v001.i04};
25103 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
25104 Library, @url{https://doi.org/10.1145/1772690.1772862};
25105 @item \"Armadillo: a template-based C++ library
25106 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
25107 Software, @url{https://doi.org/10.21105/joss.00026};
25108 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
25109 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
25110 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
25113 (license license:gpl3)))
25115 (define-public r-spectrum
25117 (name "r-spectrum")
25122 (uri (cran-uri "Spectrum" version))
25125 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25126 (properties `((upstream-name . "Spectrum")))
25127 (build-system r-build-system)
25129 `(("r-clusterr" ,r-clusterr)
25130 ("r-diptest" ,r-diptest)
25131 ("r-ggplot2" ,r-ggplot2)
25132 ("r-rfast" ,r-rfast)))
25133 (native-inputs `(("r-knitr" ,r-knitr)))
25134 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25135 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25137 "This package provides a self-tuning spectral clustering method for
25138 single or multi-view data. Spectrum uses a new type of adaptive density aware
25139 kernel that strengthens connections in the graph based on common nearest
25140 neighbours. It uses a tensor product graph data integration and diffusion
25141 procedure to integrate different data sources and reduce noise. Spectrum uses
25142 either the eigengap or multimodality gap heuristics to determine the number of
25143 clusters. The method is sufficiently flexible so that a wide range of
25144 Gaussian and non-Gaussian structures can be clustered with automatic selection
25146 (license license:agpl3+)))
25148 (define-public r-nabor
25155 (uri (cran-uri "nabor" version))
25158 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25159 (properties `((upstream-name . "nabor")))
25160 (build-system r-build-system)
25164 ("r-rcppeigen" ,r-rcppeigen)))
25165 (home-page "https://cran.r-project.org/web/packages/nabor/")
25166 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25168 "This package provides an R wrapper for libnabo, an exact or approximate
25169 k nearest neighbour library which is optimised for low dimensional
25170 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25171 designed as a drop-in replacement for the RANN function @code{nn2}. In
25172 addition, objects which include the k-d tree search structure can be returned
25173 to speed up repeated queries of the same set of target points.")
25174 (license license:bsd-3)))
25176 (define-public r-muhaz
25179 (version "1.2.6.1")
25183 (uri (cran-uri "muhaz" version))
25186 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25187 (properties `((upstream-name . "muhaz")))
25188 (build-system r-build-system)
25190 `(("r-survival" ,r-survival)))
25192 `(("gfortran" ,gfortran)))
25193 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25194 (synopsis "Hazard function estimation in survival analysis")
25196 "This package produces a smooth estimate of the hazard function for
25198 ;; Any version of the GPL.
25199 (license license:gpl3+)))
25201 (define-public r-flexsurv
25203 (name "r-flexsurv")
25208 (uri (cran-uri "flexsurv" version))
25211 "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9"))))
25212 (properties `((upstream-name . "flexsurv")))
25213 (build-system r-build-system)
25215 `(("r-assertthat" ,r-assertthat)
25216 ("r-desolve" ,r-desolve)
25217 ("r-dplyr" ,r-dplyr)
25218 ("r-generics" ,r-generics)
25219 ("r-magrittr" ,r-magrittr)
25220 ("r-matrix" ,r-matrix)
25221 ("r-mstate" ,r-mstate)
25222 ("r-muhaz" ,r-muhaz)
25223 ("r-mvtnorm" ,r-mvtnorm)
25224 ("r-numderiv" ,r-numderiv)
25225 ("r-purrr" ,r-purrr)
25226 ("r-quadprog" ,r-quadprog)
25228 ("r-rlang" ,r-rlang)
25229 ("r-rstpm2" ,r-rstpm2)
25230 ("r-survival" ,r-survival)
25231 ("r-tibble" ,r-tibble)
25232 ("r-tidyr" ,r-tidyr)
25233 ("r-tidyselect" ,r-tidyselect)))
25235 `(("r-knitr" ,r-knitr)))
25236 (home-page "https://github.com/chjackson/flexsurv-dev")
25237 (synopsis "Flexible parametric survival and multi-state models")
25239 "This package provides flexible parametric models for time-to-event data,
25240 including the Royston-Parmar spline model, generalized gamma and generalized F
25241 distributions. Any user-defined parametric distribution can be fitted, given
25242 at least an R function defining the probability density or hazard. There are
25243 also tools for fitting and predicting from fully parametric multi-state
25245 (license license:gpl2+)))
25247 (define-public r-transphylo
25249 (name "r-transphylo")
25254 (uri (cran-uri "TransPhylo" version))
25257 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25258 (properties `((upstream-name . "TransPhylo")))
25259 (build-system r-build-system)
25262 ("r-rcpp" ,r-rcpp)))
25264 `(("r-knitr" ,r-knitr)))
25265 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25266 (synopsis "Inference of transmission tree from a dated phylogeny")
25268 "This is a package to infer transmission trees from a dated phylogeny.
25269 It includes methods to simulate and analyze outbreaks. The methodology is
25270 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25271 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25272 (license license:gpl2+)))
25274 (define-public r-km-ci
25281 (uri (cran-uri "km.ci" version))
25284 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25285 (properties `((upstream-name . "km.ci")))
25286 (build-system r-build-system)
25288 `(("r-survival" ,r-survival)))
25289 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25290 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25292 "This package computes various @dfn{confidence intervals} (CI) for the
25293 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25294 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25295 Nair and Hall and Wellner.")
25296 (license license:gpl2+)))
25298 (define-public r-kmsurv
25305 (uri (cran-uri "KMsurv" version))
25308 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25309 (properties `((upstream-name . "KMsurv")))
25310 (build-system r-build-system)
25311 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25312 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25314 "This package provides data sets and functions for Klein and Moeschberger
25315 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25317 (license license:gpl3+)))
25319 (define-public r-survmisc
25321 (name "r-survmisc")
25326 (uri (cran-uri "survMisc" version))
25329 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25330 (properties `((upstream-name . "survMisc")))
25331 (build-system r-build-system)
25333 `(("r-data-table" ,r-data-table)
25334 ("r-ggplot2" ,r-ggplot2)
25335 ("r-gridextra" ,r-gridextra)
25336 ("r-km-ci" ,r-km-ci)
25337 ("r-kmsurv" ,r-kmsurv)
25338 ("r-knitr" ,r-knitr)
25339 ("r-survival" ,r-survival)
25340 ("r-xtable" ,r-xtable)
25343 `(("r-knitr" ,r-knitr)))
25344 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25345 (synopsis "Miscellaneous functions for survival data")
25347 "This package provides a collection of functions to help in the analysis
25348 of right-censored survival data. These extend the methods available in
25349 the @code{survival} package.")
25350 (license license:gpl2)))
25352 (define-public r-exactranktests
25354 (name "r-exactranktests")
25359 (uri (cran-uri "exactRankTests" version))
25362 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25364 `((upstream-name . "exactRankTests")))
25365 (build-system r-build-system)
25366 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25367 (synopsis "Exact distributions for rank and permutation tests")
25369 "This package computes exact conditional p-values and quantiles using an
25370 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25371 (license license:gpl2+)))
25373 (define-public r-maxstat
25380 (uri (cran-uri "maxstat" version))
25383 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25384 (properties `((upstream-name . "maxstat")))
25385 (build-system r-build-system)
25387 `(("r-exactranktests" ,r-exactranktests)
25388 ("r-mvtnorm" ,r-mvtnorm)))
25389 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25390 (synopsis "Maximally selected rank statistics")
25392 "This package provides maximally selected rank statistics with several
25393 p-value approximations.")
25394 (license license:gpl2+)))
25396 (define-public r-survminer
25398 (name "r-survminer")
25403 (uri (cran-uri "survminer" version))
25406 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
25407 (properties `((upstream-name . "survminer")))
25408 (build-system r-build-system)
25410 `(("r-broom" ,r-broom)
25411 ("r-dplyr" ,r-dplyr)
25412 ("r-ggplot2" ,r-ggplot2)
25413 ("r-ggpubr" ,r-ggpubr)
25414 ("r-ggtext" ,r-ggtext)
25415 ("r-gridextra" ,r-gridextra)
25416 ("r-magrittr" ,r-magrittr)
25417 ("r-maxstat" ,r-maxstat)
25418 ("r-purrr" ,r-purrr)
25419 ("r-rlang" ,r-rlang)
25420 ("r-scales" ,r-scales)
25421 ("r-survival" ,r-survival)
25422 ("r-survmisc" ,r-survmisc)
25423 ("r-tibble" ,r-tibble)
25424 ("r-tidyr" ,r-tidyr)))
25426 `(("r-knitr" ,r-knitr)))
25427 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25428 (synopsis "Drawing survival curves using ggplot2")
25430 "This package contains the function @code{ggsurvplot()} for easily
25431 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25432 risk' table and 'censoring count plot'. Other functions are also available to
25433 plot adjusted curves for Cox model and to visually examine Cox model
25435 (license license:gpl2)))
25437 (define-public r-forge
25444 (uri (cran-uri "forge" version))
25447 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25448 (properties `((upstream-name . "forge")))
25449 (build-system r-build-system)
25451 `(("r-magrittr" ,r-magrittr)
25452 ("r-rlang" ,r-rlang)))
25453 (home-page "https://cran.r-project.org/web/packages/forge/")
25454 (synopsis "Cast values into shape")
25456 "This package provides helper functions with a consistent interface to
25457 coerce and verify the types and shapes of values for input checking.")
25458 (license license:asl2.0)))
25460 (define-public r-config
25467 (uri (cran-uri "config" version))
25470 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25471 (properties `((upstream-name . "config")))
25472 (build-system r-build-system)
25474 `(("r-yaml" ,r-yaml)))
25476 `(("r-knitr" ,r-knitr)))
25477 (home-page "https://github.com/rstudio/config")
25478 (synopsis "Manage environment specific configuration values")
25480 "This package lets you manage configuration values across multiple
25481 environments (e.g. development, test, production). It reads values using a
25482 function that determines the current environment and returns the appropriate
25484 (license license:gpl3)))
25486 (define-public r-adaptivesparsity
25488 (name "r-adaptivesparsity")
25492 (uri (cran-uri "AdaptiveSparsity" version))
25495 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25497 `((upstream-name . "AdaptiveSparsity")))
25498 (build-system r-build-system)
25501 (modify-phases %standard-phases
25502 (add-after 'unpack 'link-against-armadillo
25504 (substitute* "src/Makevars"
25505 (("PKG_LIBS=" prefix)
25506 (string-append prefix "-larmadillo")))
25509 `(("r-mass" ,r-mass)
25510 ("r-matrix" ,r-matrix)
25512 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25514 `(("armadillo" ,armadillo)))
25515 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25516 (synopsis "Adaptive sparsity models")
25518 "This package implements the Figueiredo machine learning algorithm for
25519 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25520 geometric models.")
25521 (license license:lgpl3+)))
25523 (define-public r-diffusionmap
25525 (name "r-diffusionmap")
25530 (uri (cran-uri "diffusionMap" version))
25533 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25534 (properties `((upstream-name . "diffusionMap")))
25535 (build-system r-build-system)
25537 `(("r-igraph" ,r-igraph)
25538 ("r-matrix" ,r-matrix)
25539 ("r-scatterplot3d" ,r-scatterplot3d)))
25540 (home-page "https://www.r-project.org")
25541 (synopsis "Diffusion map")
25542 (description "This package implements the diffusion map method of data
25543 parametrization, including creation and visualization of diffusion maps,
25544 clustering with diffusion K-means and regression using the adaptive regression
25546 (license license:gpl2)))
25548 (define-public r-igraph
25555 (uri (cran-uri "igraph" version))
25558 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25559 (build-system r-build-system)
25561 `(("gfortran" ,gfortran)))
25565 ("libxml2" ,libxml2)
25568 `(("r-magrittr" ,r-magrittr)
25569 ("r-matrix" ,r-matrix)
25570 ("r-pkgconfig" ,r-pkgconfig)))
25571 (home-page "https://igraph.org")
25572 (synopsis "Network analysis and visualization")
25574 "This package provides routines for simple graphs and network analysis.
25575 It can handle large graphs very well and provides functions for generating
25576 random and regular graphs, graph visualization, centrality methods and much
25578 (license license:gpl2+)))
25580 (define-public r-workflows
25582 (name "r-workflows")
25587 (uri (cran-uri "workflows" version))
25590 "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz"))))
25591 (properties `((upstream-name . "workflows")))
25592 (build-system r-build-system)
25595 ("r-ellipsis" ,r-ellipsis)
25596 ("r-generics" ,r-generics)
25598 ("r-hardhat" ,r-hardhat)
25599 ("r-parsnip" ,r-parsnip)
25600 ("r-rlang" ,r-rlang)
25601 ("r-tidyselect" ,r-tidyselect)
25602 ("r-vctrs" ,r-vctrs)))
25604 `(("r-knitr" ,r-knitr)))
25605 (home-page "https://github.com/tidymodels/workflows")
25606 (synopsis "Modeling workflows")
25608 "A workflow is an object that can bundle together your pre-processing,
25609 modeling, and post-processing requests. For example, if you have a
25610 @code{recipe} and @code{parsnip} model, these can be combined into a
25611 workflow. The advantages are:
25614 @item You don’t have to keep track of separate objects in your workspace.
25615 @item The recipe prepping and model fitting can be executed using a single
25616 call to @code{fit()}.
25617 @item If you have custom tuning parameter settings, these can be defined using
25618 a simpler interface when combined with @code{tune}.
25619 @item In the future, workflows will be able to add post-processing operations,
25620 such as modifying the probability cutoff for two-class models.
25623 (license license:expat)))
25625 (define-public r-gpfit
25632 (uri (cran-uri "GPfit" version))
25635 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25636 (properties `((upstream-name . "GPfit")))
25637 (build-system r-build-system)
25639 `(("r-lattice" ,r-lattice)
25641 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25642 (synopsis "Gaussian Processes modeling")
25644 "This package provides a computationally stable approach of fitting a
25645 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25646 (license license:gpl2)))
25648 (define-public r-yardstick
25650 (name "r-yardstick")
25655 (uri (cran-uri "yardstick" version))
25658 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25659 (properties `((upstream-name . "yardstick")))
25660 (build-system r-build-system)
25662 `(("r-dplyr" ,r-dplyr)
25663 ("r-generics" ,r-generics)
25665 ("r-rlang" ,r-rlang)
25666 ("r-tidyselect" ,r-tidyselect)))
25668 `(("r-knitr" ,r-knitr)))
25669 (home-page "https://github.com/tidymodels/yardstick")
25670 (synopsis "Tidy characterizations of model performance")
25672 "This package provides tidy tools for quantifying how well a model fits
25673 to a data set such as confusion matrices, class probability curve summaries,
25674 and regression metrics (e.g., RMSE).")
25675 (license license:gpl2)))
25677 (define-public r-warp
25684 (uri (cran-uri "warp" version))
25687 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25688 (properties `((upstream-name . "warp")))
25689 (build-system r-build-system)
25690 (native-inputs `(("r-knitr" ,r-knitr)))
25691 (home-page "https://github.com/DavisVaughan/warp")
25692 (synopsis "Group dates")
25694 "This package provides tooling to group dates by a variety of periods
25695 including: yearly, monthly, by second, by week of the month, and more. The
25696 groups are defined in such a way that they also represent the distance between
25697 dates in terms of the period. This extracts valuable information that can be
25698 used in further calculations that rely on a specific temporal spacing between
25700 (license license:expat)))
25702 (define-public r-slider
25709 (uri (cran-uri "slider" version))
25712 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25713 (properties `((upstream-name . "slider")))
25714 (build-system r-build-system)
25716 `(("r-glue" ,r-glue)
25717 ("r-rlang" ,r-rlang)
25718 ("r-vctrs" ,r-vctrs)
25719 ("r-warp" ,r-warp)))
25720 (native-inputs `(("r-knitr" ,r-knitr)))
25721 (home-page "https://github.com/DavisVaughan/slider")
25722 (synopsis "Sliding window functions")
25724 "This package provides type-stable rolling window functions over any R
25725 data type. Cumulative and expanding windows are also supported. For more
25726 advanced usage, an index can be used as a secondary vector that defines how
25727 sliding windows are to be created.")
25728 (license license:expat)))
25730 (define-public r-rsample
25737 (uri (cran-uri "rsample" version))
25740 "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c"))))
25741 (properties `((upstream-name . "rsample")))
25742 (build-system r-build-system)
25744 `(("r-dplyr" ,r-dplyr)
25745 ("r-ellipsis" ,r-ellipsis)
25746 ("r-furrr" ,r-furrr)
25747 ("r-generics" ,r-generics)
25748 ("r-purrr" ,r-purrr)
25749 ("r-rlang" ,r-rlang)
25750 ("r-slider" ,r-slider)
25751 ("r-tibble" ,r-tibble)
25752 ("r-tidyr" ,r-tidyr)
25753 ("r-tidyselect" ,r-tidyselect)
25754 ("r-vctrs" ,r-vctrs)))
25756 `(("r-knitr" ,r-knitr)))
25757 (home-page "https://rsample.tidymodels.org")
25758 (synopsis "General resampling infrastructure")
25760 "This package provides classes and functions to create and summarize
25761 different types of resampling objects (e.g. bootstrap, cross-validation).")
25762 (license license:gpl2)))
25764 (define-public r-dicedesign
25766 (name "r-dicedesign")
25771 (uri (cran-uri "DiceDesign" version))
25774 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
25775 (properties `((upstream-name . "DiceDesign")))
25776 (build-system r-build-system)
25777 (home-page "http://dice.emse.fr/")
25778 (synopsis "Designs of computer experiments")
25780 "This package provides tools to create some specific @code{Space-Filling
25781 Design} (SFD) and to test their quality.")
25782 (license license:gpl3)))
25784 (define-public r-dials
25791 (uri (cran-uri "dials" version))
25794 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25795 (properties `((upstream-name . "dials")))
25796 (build-system r-build-system)
25798 `(("r-dicedesign" ,r-dicedesign)
25799 ("r-dplyr" ,r-dplyr)
25801 ("r-purrr" ,r-purrr)
25802 ("r-rlang" ,r-rlang)
25803 ("r-scales" ,r-scales)
25804 ("r-tibble" ,r-tibble)
25805 ("r-vctrs" ,r-vctrs)
25806 ("r-withr" ,r-withr)))
25807 (native-inputs `(("r-knitr" ,r-knitr)))
25808 (home-page "https://dials.tidymodels.org/")
25809 (synopsis "Tools for creating tuning parameter values")
25811 "Many models contain tuning parameters (i.e. parameters that cannot be
25812 directly estimated from the data). These tools can be used to define objects
25813 for creating, simulating, or validating values for such parameters.")
25814 (license license:gpl2)))
25816 (define-public r-tune
25823 (uri (cran-uri "tune" version))
25826 "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293"))))
25827 (properties `((upstream-name . "tune")))
25828 (build-system r-build-system)
25831 ("r-dials" ,r-dials)
25832 ("r-dplyr" ,r-dplyr)
25833 ("r-foreach" ,r-foreach)
25834 ("r-generics" ,r-generics)
25835 ("r-ggplot2" ,r-ggplot2)
25837 ("r-gpfit" ,r-gpfit)
25838 ("r-parsnip" ,r-parsnip)
25839 ("r-purrr" ,r-purrr)
25840 ("r-recipes" ,r-recipes)
25841 ("r-rlang" ,r-rlang)
25842 ("r-rsample" ,r-rsample)
25843 ("r-tibble" ,r-tibble)
25844 ("r-tidyr" ,r-tidyr)
25845 ("r-vctrs" ,r-vctrs)
25846 ("r-workflows" ,r-workflows)
25847 ("r-yardstick" ,r-yardstick)))
25848 (home-page "https://github.com/tidymodels/tune")
25849 (synopsis "Tidy tuning tools")
25851 "The ability to tune models is important. @code{tune} contains functions
25852 and classes to be used in conjunction with other @code{tidymodels} packages
25853 for finding reasonable values of hyper-parameters in models, pre-processing
25854 methods, and post-processing steps.")
25855 (license license:expat)))
25857 (define-public r-workflowsets
25859 (name "r-workflowsets")
25864 (uri (cran-uri "workflowsets" version))
25867 "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p"))))
25868 (properties `((upstream-name . "workflowsets")))
25869 (build-system r-build-system)
25872 ("r-dplyr" ,r-dplyr)
25873 ("r-ggplot2" ,r-ggplot2)
25874 ("r-prettyunits" ,r-prettyunits)
25875 ("r-purrr" ,r-purrr)
25876 ("r-rlang" ,r-rlang)
25877 ("r-rsample" ,r-rsample)
25878 ("r-tibble" ,r-tibble)
25879 ("r-tidyr" ,r-tidyr)
25881 ("r-vctrs" ,r-vctrs)
25882 ("r-withr" ,r-withr)
25883 ("r-workflows" ,r-workflows)))
25885 `(("r-knitr" ,r-knitr)))
25886 (home-page "https://github.com/tidymodels/workflowsets")
25887 (synopsis "Create a collection of tidymodels workflows")
25889 "A workflow is a combination of a model and preprocessors (e.g, a
25890 formula, recipe, etc.). In order to try different combinations of these, an
25891 object can be created that contains many workflows. There are functions to
25892 create workflows en masse as well as training them and visualizing the
25894 (license license:expat)))
25896 (define-public r-tidyposterior
25898 (name "r-tidyposterior")
25903 (uri (cran-uri "tidyposterior" version))
25906 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25907 (properties `((upstream-name . "tidyposterior")))
25908 (build-system r-build-system)
25910 `(("r-dplyr" ,r-dplyr)
25911 ("r-generics" ,r-generics)
25912 ("r-ggplot2" ,r-ggplot2)
25913 ("r-lifecycle" ,r-lifecycle)
25914 ("r-purrr" ,r-purrr)
25915 ("r-rlang" ,r-rlang)
25916 ("r-rsample" ,r-rsample)
25917 ("r-rstanarm" ,r-rstanarm)
25918 ("r-tibble" ,r-tibble)
25919 ("r-tidyr" ,r-tidyr)
25920 ("r-vctrs" ,r-vctrs)))
25922 `(("r-knitr" ,r-knitr)))
25923 (home-page "https://tidyposterior.tidymodels.org")
25924 (synopsis "Bayesian analysis to compare models using resampling statistics")
25926 "This package can be used to conduct post hoc analyses of resampling
25927 results generated by models. For example, if two models are evaluated with
25928 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25929 are 10 paired statistics. These can be used to make comparisons between
25930 models without involving a test set.")
25931 (license license:gpl2)))
25933 (define-public r-tidypredict
25935 (name "r-tidypredict")
25940 (uri (cran-uri "tidypredict" version))
25943 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25944 (properties `((upstream-name . "tidypredict")))
25945 (build-system r-build-system)
25947 `(("r-dplyr" ,r-dplyr)
25948 ("r-generics" ,r-generics)
25949 ("r-knitr" ,r-knitr)
25950 ("r-purrr" ,r-purrr)
25951 ("r-rlang" ,r-rlang)
25952 ("r-stringr" ,r-stringr)
25953 ("r-tibble" ,r-tibble)
25954 ("r-tidyr" ,r-tidyr)))
25956 `(("r-knitr" ,r-knitr)))
25957 (home-page "https://tidypredict.tidymodels.org")
25958 (synopsis "Run predictions inside the database")
25960 "This package parses a fitted R model object, and returns a formula in
25961 Tidy Eval code that calculates the predictions. It works with several
25962 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25963 final SQL translation of the algorithm. It currently supports @code{lm()},
25964 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25965 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25966 (license license:gpl3)))
25968 (define-public r-janeaustenr
25970 (name "r-janeaustenr")
25975 (uri (cran-uri "janeaustenr" version))
25978 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25979 (properties `((upstream-name . "janeaustenr")))
25980 (build-system r-build-system)
25981 (home-page "https://github.com/juliasilge/janeaustenr")
25982 (synopsis "Jane Austen's complete novels")
25984 "This package provides the full texts for Jane Austen's six completed
25985 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25986 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25987 and \"Persuasion\".")
25988 (license license:expat)))
25990 (define-public r-tokenizers
25992 (name "r-tokenizers")
25997 (uri (cran-uri "tokenizers" version))
26000 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
26001 (properties `((upstream-name . "tokenizers")))
26002 (build-system r-build-system)
26004 `(("r-rcpp" ,r-rcpp)
26005 ("r-snowballc" ,r-snowballc)
26006 ("r-stringi" ,r-stringi)))
26008 `(("r-knitr" ,r-knitr)))
26009 (home-page "https://lincolnmullen.com/software/tokenizers/")
26010 (synopsis "Fast, consistent tokenization of natural language text")
26012 "This is a package for converting natural language text into tokens.
26013 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
26014 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
26015 Treebank, regular expressions, as well as functions for counting characters,
26016 words, and sentences, and a function for splitting longer texts into separate
26017 documents, each with the same number of words. The tokenizers have a
26018 consistent interface, and the package is built on the @code{stringi} and
26019 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
26020 (license license:expat)))
26022 (define-public r-hunspell
26024 (name "r-hunspell")
26029 (uri (cran-uri "hunspell" version))
26032 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
26033 (properties `((upstream-name . "hunspell")))
26034 (build-system r-build-system)
26036 `(("r-digest" ,r-digest)
26037 ("r-rcpp" ,r-rcpp)))
26039 `(("r-knitr" ,r-knitr)))
26040 (home-page "https://github.com/ropensci/hunspell#readme")
26041 (synopsis "High-performance stemmer, tokenizer, and spell checker")
26043 "This package provides a low-level spell checker and morphological
26044 analyzer based on the famous @code{hunspell} library. The package can analyze
26045 or check individual words as well as parse text, LaTeX, HTML or XML documents.
26046 For a more user-friendly interface use the @code{spelling} package which
26047 builds on this package to automate checking of files, documentation and
26048 vignettes in all common formats.")
26049 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
26050 ;; MPL; in addition to these licenses the rest of the R wrapper is also
26051 ;; available under the Expat license.
26052 (license (list license:gpl2
26057 (define-public r-tidytext
26059 (name "r-tidytext")
26064 (uri (cran-uri "tidytext" version))
26067 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
26068 (properties `((upstream-name . "tidytext")))
26069 (build-system r-build-system)
26071 `(("r-dplyr" ,r-dplyr)
26072 ("r-generics" ,r-generics)
26073 ("r-hunspell" ,r-hunspell)
26074 ("r-janeaustenr" ,r-janeaustenr)
26075 ("r-lifecycle" ,r-lifecycle)
26076 ("r-matrix" ,r-matrix)
26077 ("r-purrr" ,r-purrr)
26078 ("r-rlang" ,r-rlang)
26079 ("r-stringr" ,r-stringr)
26080 ("r-tibble" ,r-tibble)
26081 ("r-tokenizers" ,r-tokenizers)
26082 ("r-vctrs" ,r-vctrs)))
26084 `(("r-knitr" ,r-knitr)))
26085 (home-page "https://github.com/juliasilge/tidytext")
26086 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
26088 "This is a package for text mining for word processing and sentiment
26089 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
26090 (license license:expat)))
26092 (define-public r-parsnip
26099 (uri (cran-uri "parsnip" version))
26102 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
26103 (properties `((upstream-name . "parsnip")))
26104 (build-system r-build-system)
26106 `(("r-dplyr" ,r-dplyr)
26107 ("r-generics" ,r-generics)
26108 ("r-globals" ,r-globals)
26110 ("r-magrittr" ,r-magrittr)
26111 ("r-prettyunits" ,r-prettyunits)
26112 ("r-purrr" ,r-purrr)
26113 ("r-rlang" ,r-rlang)
26114 ("r-tibble" ,r-tibble)
26115 ("r-tidyr" ,r-tidyr)
26116 ("r-vctrs" ,r-vctrs)))
26118 `(("r-knitr" ,r-knitr)))
26119 (home-page "https://parsnip.tidymodels.org")
26120 (synopsis "Common API to modeling and analysis functions")
26122 "This package provides a common interface to allow users to specify a
26123 model without having to remember the different argument names across different
26124 functions or computational engines (e.g. R, Spark, Stan, etc).")
26125 (license license:gpl2)))
26127 (define-public r-infer
26134 (uri (cran-uri "infer" version))
26137 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
26138 (properties `((upstream-name . "infer")))
26139 (build-system r-build-system)
26141 `(("r-dplyr" ,r-dplyr)
26142 ("r-ggplot2" ,r-ggplot2)
26144 ("r-magrittr" ,r-magrittr)
26145 ("r-purrr" ,r-purrr)
26146 ("r-rlang" ,r-rlang)
26147 ("r-tibble" ,r-tibble)))
26149 `(("r-knitr" ,r-knitr)))
26150 (home-page "https://github.com/tidymodels/infer")
26151 (synopsis "Tidy statistical inference")
26153 "The objective of this package is to perform inference using an
26154 expressive statistical grammar that coheres with the Tidy design framework.")
26155 (license license:cc0)))
26157 (define-public r-modeldata
26159 (name "r-modeldata")
26164 (uri (cran-uri "modeldata" version))
26167 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
26168 (properties `((upstream-name . "modeldata")))
26169 (build-system r-build-system)
26170 (home-page "https://modeldata.tidymodels.org")
26171 (synopsis "Data sets useful for modeling packages")
26173 "This package provides data sets used for demonstrating or testing
26174 model-related packages.")
26175 (license license:expat)))
26177 (define-public r-tidymodels
26179 (name "r-tidymodels")
26184 (uri (cran-uri "tidymodels" version))
26187 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26188 (properties `((upstream-name . "tidymodels")))
26189 (build-system r-build-system)
26191 `(("r-broom" ,r-broom)
26193 ("r-dials" ,r-dials)
26194 ("r-dplyr" ,r-dplyr)
26195 ("r-ggplot2" ,r-ggplot2)
26196 ("r-infer" ,r-infer)
26197 ("r-magrittr" ,r-magrittr)
26198 ("r-modeldata" ,r-modeldata)
26199 ("r-parsnip" ,r-parsnip)
26200 ("r-purrr" ,r-purrr)
26201 ("r-recipes" ,r-recipes)
26202 ("r-rlang" ,r-rlang)
26203 ("r-rsample" ,r-rsample)
26204 ("r-rstudioapi" ,r-rstudioapi)
26205 ("r-tibble" ,r-tibble)
26206 ("r-tidyr" ,r-tidyr)
26208 ("r-workflows" ,r-workflows)
26209 ("r-yardstick" ,r-yardstick)))
26211 `(("r-knitr" ,r-knitr)
26212 ("r-rmarkdown" ,r-rmarkdown)
26214 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26215 (home-page "https://github.com/tidymodels/tidymodels")
26216 (synopsis "Tidy collection for modeling and statistical analysis")
26218 "The tidy modeling \"verse\" is a collection of packages for modeling and
26219 statistical analysis that share the underlying design philosophy, grammar, and
26220 data structures of the tidyverse.")
26221 (license license:gpl3)))
26223 (define-public r-lsa
26230 (uri (cran-uri "lsa" version))
26233 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
26234 (properties `((upstream-name . "lsa")))
26235 (build-system r-build-system)
26237 `(("r-snowballc" ,r-snowballc)))
26238 (home-page "https://cran.r-project.org/package=lsa")
26239 (synopsis "Latent semantic analysis")
26241 "The basic idea of latent semantic analysis (LSA) is, that text do have a
26242 higher order (=latent semantic) structure which, however, is obscured by word
26243 usage (e.g. through the use of synonyms or polysemy). By using conceptual
26244 indices that are derived statistically via a truncated singular value
26245 decomposition (a two-mode factor analysis) over a given document-term matrix,
26246 this variability problem can be overcome.")
26247 (license license:gpl2+)))
26249 (define-public r-mlecens
26256 (uri (cran-uri "MLEcens" version))
26259 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26260 (properties `((upstream-name . "MLEcens")))
26261 (build-system r-build-system)
26262 (home-page "http://stat.ethz.ch/~maathuis/")
26263 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26265 "This package contains functions to compute the nonparametric
26266 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26267 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26268 To be more precise, we consider the situation where we observe a set of
26269 rectangles that are known to contain the unobservable realizations of (X,Y).
26270 We compute the MLE based on such a set of rectangles. The methods can also be
26271 used for univariate censored data (see data set @code{cosmesis}), and for
26272 censored data with competing risks (see data set @code{menopause}). The
26273 package also provides functions to visualize the observed data and the MLE.")
26274 (license license:gpl2+)))
26276 (define-public r-metafor
26283 (uri (cran-uri "metafor" version))
26286 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26287 (properties `((upstream-name . "metafor")))
26288 (build-system r-build-system)
26290 `(("r-matrix" ,r-matrix)
26291 ("r-nlme" ,r-nlme)))
26292 (home-page "https://cran.r-project.org/web/packages/metafor/")
26293 (synopsis "Meta-analysis package for R")
26295 "This package provides a comprehensive collection of functions for
26296 conducting meta-analyses in R. The package includes functions to calculate
26297 various effect sizes or outcome measures, fit fixed-, random-, and
26298 mixed-effects models to such data, carry out moderator and meta-regression
26299 analyses, and create various types of meta-analytical plots (e.g., forest,
26300 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26301 and person-time data, the package also provides functions that implement
26302 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26303 a variety of suitable generalized linear (mixed-effects) models (i.e.
26304 mixed-effects logistic and Poisson regression models). Finally, the package
26305 provides functionality for fitting meta-analytic multivariate/multilevel
26306 models that account for non-independent sampling errors and/or true
26307 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26308 endpoints, or other forms of clustering). Network meta-analyses and
26309 meta-analyses accounting for known correlation structures (e.g. due to
26310 phylogenetic relatedness) can also be conducted.")
26311 (license license:gpl2+)))
26313 (define-public r-altmeta
26320 (uri (cran-uri "altmeta" version))
26323 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26324 (properties `((upstream-name . "altmeta")))
26325 (build-system r-build-system)
26327 `(("r-coda" ,r-coda)
26329 ("r-matrix" ,r-matrix)
26330 ("r-metafor" ,r-metafor)
26331 ("r-rjags" ,r-rjags)))
26332 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26333 (synopsis "Alternative meta-analysis methods")
26335 "This package provides alternative statistical methods for meta-analysis,
26339 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26340 relative risks, and risk differences
26341 @item heterogeneity tests and measures that are robust to outliers;
26342 @item measures, tests, and visualization tools for publication bias or
26343 small-study effects;
26344 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26345 specificities, etc.;
26346 @item meta-analysis methods for synthesizing proportions;
26347 @item models for multivariate meta-analysis.
26350 (license license:gpl2+)))
26352 (define-public r-perm
26355 (version "1.0-0.0")
26359 (uri (cran-uri "perm" version))
26362 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26363 (properties `((upstream-name . "perm")))
26364 (build-system r-build-system)
26365 (home-page "https://cran.r-project.org/web/packages/perm/")
26366 (synopsis "Exact or asymptotic permutation tests")
26368 "This package provides several methods for performing permutation tests.
26369 It has three main functions, to perform linear permutation tests. These tests
26370 are tests where the test statistic is the sum of the product of a
26371 covariate (usually group indicator) and the scores.")
26372 ;; Any version of the GPL
26373 (license license:gpl2+)))
26375 (define-public r-qtl
26382 (uri (cran-uri "qtl" version))
26385 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26386 (build-system r-build-system)
26387 (home-page "https://rqtl.org/")
26388 (synopsis "R package for analyzing QTL experiments in genetics")
26389 (description "R/qtl is an extension library for the R statistics system.
26390 It is used to analyze experimental crosses for identifying genes contributing
26391 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26393 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26394 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26396 (license license:gpl3)))
26398 (define-public r-qtl2
26404 (uri (cran-uri "qtl2" version))
26406 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26407 (build-system r-build-system)
26409 `(("r-data-table" ,r-data-table)
26410 ("r-jsonlite" ,r-jsonlite)
26412 ("r-rcppeigen" ,r-rcppeigen)
26413 ("r-rsqlite" ,r-rsqlite)
26414 ("r-yaml" ,r-yaml)))
26415 (home-page "https://kbroman.org/qtl2/")
26416 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26418 "This package provides a set of tools to perform @dfn{Quantitative Trait
26419 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26420 @code{R/qtl} package to better handle high-dimensional data and complex cross
26421 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26422 (license license:gpl3)))
26424 (define-public r-seqminer
26426 (name "r-seqminer")
26431 (uri (cran-uri "seqminer" version))
26434 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26435 (build-system r-build-system)
26438 (home-page "http://seqminer.genomic.codes")
26439 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26441 "This package provides tools to integrate nucleotide sequencing
26442 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26443 ;; Any version of the GPL is acceptable
26444 (license (list license:gpl2+ license:gpl3+))))
26446 (define-public r-maldiquant
26448 (name "r-maldiquant")
26453 (uri (cran-uri "MALDIquant" version))
26456 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26457 (properties `((upstream-name . "MALDIquant")))
26458 (build-system r-build-system)
26459 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26460 (synopsis "Quantitative analysis of mass spectrometry data")
26462 "This package provides a complete analysis pipeline for matrix-assisted
26463 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26464 two-dimensional mass spectrometry data. In addition to commonly used plotting
26465 and processing methods it includes distinctive features, namely baseline
26466 subtraction methods such as morphological filters (TopHat) or the
26467 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26468 alignment using warping functions, handling of replicated measurements as well
26469 as allowing spectra with different resolutions.")
26470 (license license:gpl3+)))
26472 (define-public r-scattermore
26474 (name "r-scattermore")
26479 (uri (cran-uri "scattermore" version))
26482 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26483 (properties `((upstream-name . "scattermore")))
26484 (build-system r-build-system)
26486 `(("r-ggplot2" ,r-ggplot2)
26487 ("r-scales" ,r-scales)))
26488 (home-page "https://github.com/exaexa/scattermore")
26489 (synopsis "Scatterplots with more points")
26491 "This package provides C-based tools for converting large scatterplot
26492 data to rasters. It speeds up plotting of data with millions of points.")
26493 (license license:gpl3+)))
26495 (define-public r-seuratobject
26497 (name "r-seuratobject")
26502 (uri (cran-uri "SeuratObject" version))
26505 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26506 (properties `((upstream-name . "SeuratObject")))
26507 (build-system r-build-system)
26509 `(("r-matrix" ,r-matrix)
26511 ("r-rcppeigen" ,r-rcppeigen)
26512 ("r-rlang" ,r-rlang)
26513 ("r-sctransform" ,r-sctransform)))
26514 (home-page "https://satijalab.org/seurat")
26515 (synopsis "Data structures for single cell data")
26517 "This package defines S4 classes for single-cell genomic data and
26518 associated information, such as dimensionality reduction embeddings,
26519 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26520 access methods and R-native hooks to ensure the Seurat object is familiar to
26522 (license license:gpl3)))
26524 (define-public r-seurat
26530 (uri (cran-uri "Seurat" version))
26533 "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
26534 (properties `((upstream-name . "Seurat")))
26535 (build-system r-build-system)
26537 `(("r-cluster" ,r-cluster)
26538 ("r-cowplot" ,r-cowplot)
26539 ("r-fitdistrplus" ,r-fitdistrplus)
26540 ("r-future" ,r-future)
26541 ("r-future-apply" ,r-future-apply)
26542 ("r-ggplot2" ,r-ggplot2)
26543 ("r-ggrepel" ,r-ggrepel)
26544 ("r-ggridges" ,r-ggridges)
26547 ("r-igraph" ,r-igraph)
26548 ("r-irlba" ,r-irlba)
26549 ("r-jsonlite" ,r-jsonlite)
26550 ("r-kernsmooth" ,r-kernsmooth)
26551 ("r-leiden" ,r-leiden)
26552 ("r-lmtest" ,r-lmtest)
26554 ("r-matrix" ,r-matrix)
26555 ("r-matrixstats" ,r-matrixstats)
26556 ("r-miniui" ,r-miniui)
26557 ("r-patchwork" ,r-patchwork)
26558 ("r-pbapply" ,r-pbapply)
26559 ("r-plotly" ,r-plotly)
26562 ("r-rcolorbrewer" ,r-rcolorbrewer)
26564 ("r-rcppannoy" ,r-rcppannoy)
26565 ("r-rcppeigen" ,r-rcppeigen)
26566 ("r-rcppprogress" ,r-rcppprogress)
26567 ("r-reticulate" ,r-reticulate)
26568 ("r-rlang" ,r-rlang)
26570 ("r-rtsne" ,r-rtsne)
26571 ("r-scales" ,r-scales)
26572 ("r-scattermore" ,r-scattermore)
26573 ("r-sctransform" ,r-sctransform)
26574 ("r-seuratobject" ,r-seuratobject)
26575 ("r-shiny" ,r-shiny)
26576 ("r-spatstat-core" ,r-spatstat-core)
26577 ("r-spatstat-geom" ,r-spatstat-geom)
26578 ("r-tibble" ,r-tibble)
26579 ("r-uwot" ,r-uwot)))
26580 (home-page "http://www.satijalab.org/seurat")
26581 (synopsis "Seurat is an R toolkit for single cell genomics")
26583 "This package is an R package designed for QC, analysis, and
26584 exploration of single cell RNA-seq data. It easily enables widely-used
26585 analytical techniques, including the identification of highly variable genes,
26586 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26587 algorithms; density clustering, hierarchical clustering, k-means, and the
26588 discovery of differentially expressed genes and markers.")
26589 (license license:gpl3)))
26591 (define-public r-phangorn
26593 (name "r-phangorn")
26598 (uri (cran-uri "phangorn" version))
26601 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26602 (build-system r-build-system)
26605 ("r-fastmatch" ,r-fastmatch)
26606 ("r-igraph" ,r-igraph)
26607 ("r-magrittr" ,r-magrittr)
26608 ("r-matrix" ,r-matrix)
26609 ("r-quadprog" ,r-quadprog)
26610 ("r-rcpp" ,r-rcpp)))
26611 (home-page "https://github.com/KlausVigo/phangorn")
26612 (synopsis "Phylogenetic analysis in R")
26614 "Phangorn is a package for phylogenetic analysis in R. It supports
26615 estimation of phylogenetic trees and networks using Maximum Likelihood,
26616 Maximum Parsimony, distance methods and Hadamard conjugation.")
26617 (license license:gpl2+)))
26619 (define-public r-diversitree
26621 (name "r-diversitree")
26626 (uri (cran-uri "diversitree" version))
26629 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26630 (build-system r-build-system)
26632 `(("gfortran" ,gfortran)))
26633 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26636 ("r-desolve" ,r-desolve)
26638 ("r-subplex" ,r-subplex)))
26639 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26640 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26641 (description "This package contains a number of comparative \"phylogenetic\"
26642 methods, mostly focusing on analysing diversification and character evolution.
26643 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26644 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26645 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26646 include Markov models of discrete and continuous trait evolution and constant
26647 rate speciation and extinction.")
26648 (license license:gpl2+)))
26650 (define-public r-calculus
26652 (name "r-calculus")
26657 (uri (cran-uri "calculus" version))
26660 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26661 (properties `((upstream-name . "calculus")))
26662 (build-system r-build-system)
26664 `(("r-rcpp" ,r-rcpp)))
26666 `(("r-knitr" ,r-knitr)))
26667 (home-page "https://github.com/eguidotti/calculus")
26668 (synopsis "High dimensional numerical and symbolic calculus")
26670 "Efficient C++ optimized functions for numerical and symbolic calculus.
26671 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26672 convention, fast computation of the Levi-Civita symbol and generalized
26673 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26674 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26675 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26676 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26677 parabolic or user defined by custom scale factors.")
26678 (license license:gpl3)))
26680 (define-public r-decon
26687 (uri (cran-uri "decon" version))
26690 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26691 (properties `((upstream-name . "decon")))
26692 (build-system r-build-system)
26694 `(("gfortran" ,gfortran)))
26696 "https://cran.r-project.org/web/packages/decon/")
26697 (synopsis "Deconvolution Estimation in Measurement Error Models")
26699 "This package contains a collection of functions to deal with
26700 nonparametric measurement error problems using deconvolution
26701 kernel methods. We focus two measurement error models in the
26702 package: (1) an additive measurement error model, where the
26703 goal is to estimate the density or distribution function from
26704 contaminated data; (2) nonparametric regression model with
26705 errors-in-variables. The R functions allow the measurement errors
26706 to be either homoscedastic or heteroscedastic. To make the
26707 deconvolution estimators computationally more efficient in R,
26708 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26709 density estimation with error-free data to the deconvolution
26710 kernel estimation. Several methods for the selection of the
26711 data-driven smoothing parameter are also provided in the package.
26712 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26713 estimation in measurement error models: The R package decon.
26714 Journal of Statistical Software, 39(10), 1-24.")
26715 (license license:gpl3+)))
26717 (define-public r-locpol
26724 (uri (cran-uri "locpol" version))
26727 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26728 (properties `((upstream-name . "locpol")))
26729 (build-system r-build-system)
26731 "https://cran.r-project.org/web/packages/locpol/")
26732 (synopsis "Kernel Local Polynomial Regression")
26734 "Computes local polynomial estimators for the regression and
26735 also density. It comprises several different utilities to handle
26736 kernel estimators.")
26737 (license license:gpl2+)))
26739 (define-public r-lpme
26746 (uri (cran-uri "lpme" version))
26749 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26750 (properties `((upstream-name . "lpme")))
26751 (build-system r-build-system)
26753 `(("r-decon" ,r-decon)
26754 ("r-flexmix" ,r-flexmix)
26755 ("r-locpol" ,r-locpol)
26757 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26759 "https://cran.r-project.org/web/packages/lpme/")
26760 (synopsis "Nonparametric Estimation of Measurement Error Models")
26762 "Provide nonparametric methods for mean regression model,
26763 modal regression and conditional density estimation in the
26764 presence/absence of measurement error. Bandwidth selection is
26765 also provided for each method.")
26766 (license license:gpl2+)))
26768 (define-public r-aws-signature
26770 (name "r-aws-signature")
26775 (uri (cran-uri "aws.signature" version))
26778 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26779 (properties `((upstream-name . "aws.signature")))
26780 (build-system r-build-system)
26782 `(("r-base64enc" ,r-base64enc)
26783 ("r-digest" ,r-digest)))
26784 (home-page "https://github.com/cloudyr/aws.signature")
26785 (synopsis "Amazon Web Services Request Signatures")
26787 "This package generates version 2 and 4 request signatures for Amazon Web
26788 Services (AWS) and provides a mechanism for retrieving credentials from
26789 environment variables, AWS credentials files, and EC2 instance metadata. For
26790 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26791 (license license:gpl2+)))
26793 (define-public r-aws-s3
26800 (uri (cran-uri "aws.s3" version))
26803 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26804 (properties `((upstream-name . "aws.s3")))
26805 (build-system r-build-system)
26807 `(("r-aws-signature" ,r-aws-signature)
26808 ("r-base64enc" ,r-base64enc)
26810 ("r-digest" ,r-digest)
26812 ("r-xml2" ,r-xml2)))
26813 (home-page "https://github.com/cloudyr/aws.s3")
26814 (synopsis "AWS S3 Client Package")
26816 "This package provides a simple client package for the Amazon Web
26817 Services (AWS) Simple Storage Service (S3) REST API.")
26818 (license license:gpl2+)))
26820 (define-public r-lgr
26826 (uri (cran-uri "lgr" version))
26829 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26830 (build-system r-build-system)
26834 `(("r-knitr" ,r-knitr)))
26835 (home-page "https://s-fleck.github.io/lgr/")
26836 (synopsis "Fully featured logging framework")
26837 (description "This package offers a flexible, feature-rich yet
26838 light-weight logging framework based on @code{R6} classes. It supports
26839 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26840 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26841 well as email and push notifications.")
26842 (license license:expat)))
26844 (define-public r-mlr3measures
26846 (name "r-mlr3measures")
26850 (uri (cran-uri "mlr3measures" version))
26853 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26854 (build-system r-build-system)
26856 `(("r-checkmate" ,r-checkmate)
26857 ("r-prroc" ,r-prroc)))
26858 (home-page "https://mlr3measures.mlr-org.com/")
26859 (synopsis "Performance measures for mlr3")
26860 (description "This package implements multiple performance measures for
26861 supervised learning. It includes over 40 measures for regression and
26862 classification. Additionally, meta information about the performance measures
26863 can be queried, e.g. what the best and worst possible performances scores
26865 (license license:lgpl3)))
26867 (define-public r-mlr3misc
26869 (name "r-mlr3misc")
26873 (uri (cran-uri "mlr3misc" version))
26876 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26877 (build-system r-build-system)
26879 `(("r-backports" ,r-backports)
26880 ("r-checkmate" ,r-checkmate)
26881 ("r-data-table" ,r-data-table)
26883 (home-page "https://mlr3misc.mlr-org.com/")
26884 (synopsis "Helper functions for mlr3")
26885 (description "@code{mlr3misc} provides frequently used helper functions
26886 and assertions used in @code{mlr3} and its companion packages. It comes with
26887 helper functions for functional programming, for printing, to work with
26888 @code{data.table}, as well as some generally useful @code{R6} classes. This
26889 package also supersedes the package @code{BBmisc}.")
26890 (license license:lgpl3)))
26892 (define-public r-paradox
26898 (uri (cran-uri "paradox" version))
26901 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
26902 (build-system r-build-system)
26904 `(("r-backports" ,r-backports)
26905 ("r-checkmate" ,r-checkmate)
26906 ("r-data-table" ,r-data-table)
26907 ("r-mlr3misc" ,r-mlr3misc)
26909 (home-page "https://paradox.mlr-org.com/")
26910 (synopsis "Define and work with parameter spaces for complex algorithms")
26911 (description "With this package it is possible to define parameter spaces,
26912 constraints and dependencies for arbitrary algorithms, and to program on such
26913 spaces. It also includes statistical designs and random samplers. Objects are
26914 implemented as @code{R6} classes.")
26915 (license license:lgpl3)))
26917 (define-public r-mlr3
26923 (uri (cran-uri "mlr3" version))
26926 "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl"))))
26927 (build-system r-build-system)
26930 ("r-backports" ,r-backports)
26931 ("r-checkmate" ,r-checkmate)
26932 ("r-data-table" ,r-data-table)
26933 ("r-digest" ,r-digest)
26934 ("r-future-apply" ,r-future-apply)
26936 ("r-mlbench" ,r-mlbench)
26937 ("r-mlr3measures" ,r-mlr3measures)
26938 ("r-mlr3misc" ,r-mlr3misc)
26939 ("r-palmerpenguins" ,r-palmerpenguins)
26940 ("r-paradox" ,r-paradox)
26941 ("r-parallelly" ,r-parallelly)
26942 ("r-uuid" ,r-uuid)))
26943 (home-page "https://mlr3.mlr-org.com/")
26944 (synopsis "Machine Learning in R - Next Generation")
26945 (description "@code{mlr3} enables efficient, object-oriented programming
26946 on the building blocks of machine learning. It provides @code{R6} objects for
26947 tasks, learners, resamplings, and measures. The package is geared towards
26948 scalability and larger datasets by supporting parallelization and out-of-memory
26949 data-backends like databases. While @code{mlr3} focuses on the core
26950 computational operations, add-on packages provide additional functionality.")
26951 (license license:lgpl3)))
26953 (define-public r-mlr3learners
26955 (name "r-mlr3learners")
26959 (uri (cran-uri "mlr3learners" version))
26962 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26963 (build-system r-build-system)
26965 `(("r-data-table" ,r-data-table)
26967 ("r-mlr3misc" ,r-mlr3misc)
26968 ("r-paradox" ,r-paradox)
26970 (home-page "https://mlr3learners.mlr-org.com/")
26971 (synopsis "Recommended Learners for @code{mlr3}")
26972 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26973 with interfaces to essential machine learning packages on CRAN. This includes,
26974 but is not limited to: (penalized) linear and logistic regression, linear and
26975 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26976 vector machines, and gradient boosting.")
26977 (license license:lgpl3)))
26979 (define-public r-bbotk
26986 (uri (cran-uri "bbotk" version))
26989 "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550"))))
26990 (properties `((upstream-name . "bbotk")))
26991 (build-system r-build-system)
26993 `(("r-checkmate" ,r-checkmate)
26994 ("r-data-table" ,r-data-table)
26996 ("r-mlr3misc" ,r-mlr3misc)
26997 ("r-paradox" ,r-paradox)
27000 `(("r-knitr" ,r-knitr)))
27001 (home-page "https://bbotk.mlr-org.com")
27002 (synopsis "Black-Box Optimization Toolkit")
27003 (description "This package provides a common framework for optimization of
27004 black-box functions for other packages, e.g. @code{mlr3}. It offers various
27005 optimization methods e.g. grid search, random search and generalized simulated
27007 (license license:lgpl3)))
27009 (define-public r-mlr3tuning
27011 (name "r-mlr3tuning")
27015 (uri (cran-uri "mlr3tuning" version))
27018 "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv"))))
27019 (build-system r-build-system)
27021 `(("r-bbotk" ,r-bbotk)
27022 ("r-checkmate" ,r-checkmate)
27023 ("r-data-table" ,r-data-table)
27026 ("r-mlr3misc" ,r-mlr3misc)
27027 ("r-paradox" ,r-paradox)
27029 (home-page "https://mlr3tuning.mlr-org.com/")
27030 (synopsis "Tuning for @code{mlr3}")
27031 (description "@code{mlr3tuning} implements methods for hyperparameter
27032 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
27033 termination criteria can be set and combined. The class @code{AutoTuner} provides a
27034 convenient way to perform nested resampling in combination with @code{mlr3}.")
27035 (license license:lgpl3)))
27037 (define-public r-fontliberation
27039 (name "r-fontliberation")
27044 (uri (cran-uri "fontLiberation" version))
27047 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
27049 `((upstream-name . "fontLiberation")))
27050 (build-system r-build-system)
27051 (home-page "https://cran.r-project.org/package=fontLiberation")
27052 (synopsis "Liberation fonts")
27054 "This package provides a placeholder for the Liberation fontset intended
27055 for the fontquiver package. This fontset covers the 12 combinations of
27056 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
27057 supported in R graphics devices.")
27058 (license license:silofl1.1)))
27060 (define-public r-fontbitstreamvera
27062 (name "r-fontbitstreamvera")
27067 (uri (cran-uri "fontBitstreamVera" version))
27070 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
27072 `((upstream-name . "fontBitstreamVera")))
27073 (build-system r-build-system)
27074 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
27075 (synopsis "Fonts for fontquiver")
27077 "This package is a placeholder for the Bitstream Vera font. It is
27078 intended for the fontquiver package.")
27080 (license:fsdg-compatible
27081 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
27082 "The Font Software may be sold as part of a larger software package but
27083 no copy of one or more of the Font Software typefaces may be sold by
27086 (define-public r-fontquiver
27088 (name "r-fontquiver")
27093 (uri (cran-uri "fontquiver" version))
27096 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
27097 (properties `((upstream-name . "fontquiver")))
27098 (build-system r-build-system)
27100 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
27101 ("r-fontliberation" ,r-fontliberation)))
27102 (home-page "https://cran.r-project.org/package=fontquiver")
27103 (synopsis "Set of installed fonts")
27105 "This package provides a set of fonts. This is useful when you want to
27106 avoid system fonts to make sure your outputs are reproducible.")
27107 (license license:gpl3)))
27109 (define-public r-freetypeharfbuzz
27111 (name "r-freetypeharfbuzz")
27116 (uri (cran-uri "freetypeharfbuzz" version))
27119 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
27121 `((upstream-name . "freetypeharfbuzz")))
27122 (build-system r-build-system)
27125 (modify-phases %standard-phases
27126 (add-after 'unpack 'prepare-static-libraries
27127 (lambda* (#:key inputs #:allow-other-keys)
27128 (mkdir-p "src/target/include")
27129 (let ((freetype (assoc-ref inputs "static-freetype"))
27130 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
27131 (substitute* "src/Makevars.in"
27132 (("include @MK_FILE@") "") ; do not build static libs
27133 (("^HB_STATIC_LIB =.*")
27134 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
27135 (("^FT_STATIC_LIB =.*")
27136 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
27137 (copy-recursively (string-append freetype "/include")
27138 "src/target/include")
27139 (copy-recursively (string-append harfbuzz "/include")
27140 "src/target/include")))))))
27142 `(("r-fontquiver" ,r-fontquiver)))
27143 ;; This may defeat the purpose of this package as our versions of freetype
27144 ;; and harfbuzz obviously differ from the tarballs offered by this
27145 ;; project. On the other hand, Guix arguably does a better job at
27146 ;; "ensur[ing] deterministic computation".
27148 `(("static-freetype"
27150 (inherit (static-package freetype))
27152 `(#:configure-flags
27153 (list "--enable-static=yes"
27158 "--without-harfbuzz")))))
27161 (inherit (static-package harfbuzz))
27163 `(#:tests? #false ; fail because shared library is disabled
27165 (list "--enable-static=yes"
27166 "--enable-shared=no"
27168 "--with-freetype=yes"
27171 "--without-fontconfig"
27172 "--without-glib")))))))
27175 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27176 (synopsis "Deterministic computation of text box metrics")
27178 "Unlike other tools that dynamically link to the Cairo stack,
27179 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27180 harfbuzz libraries. This ensures deterministic computation of text box
27181 extents for situations where reproducible results are crucial (for instance
27182 unit tests of graphics).")
27183 (license license:gpl3)))
27185 (define-public r-vdiffr
27192 (uri (cran-uri "vdiffr" version))
27195 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27198 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27199 (properties `((upstream-name . "vdiffr")))
27200 (build-system r-build-system)
27203 (modify-phases %standard-phases
27204 (add-after 'unpack 'process-javascript
27205 (lambda* (#:key inputs #:allow-other-keys)
27206 (with-directory-excursion "inst/htmlwidgets/lib/"
27207 (let ((source (assoc-ref inputs "js-jquery"))
27208 (target "jquery.min.js"))
27209 (format #true "Processing ~a --> ~a~%"
27211 (invoke "esbuild" source "--minify"
27212 (string-append "--outfile=" target)))))))))
27214 `(("freetype" ,freetype)
27215 ("harfbuzz" ,harfbuzz)))
27218 ("r-devtools" ,r-devtools)
27219 ("r-diffobj" ,r-diffobj)
27220 ("r-fontquiver" ,r-fontquiver)
27221 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27222 ("r-gdtools" ,r-gdtools)
27224 ("r-htmltools" ,r-htmltools)
27225 ("r-htmlwidgets" ,r-htmlwidgets)
27226 ("r-purrr" ,r-purrr)
27229 ("r-rlang" ,r-rlang)
27230 ("r-shiny" ,r-shiny)
27231 ("r-testthat" ,r-testthat)
27232 ("r-usethis" ,r-usethis)
27233 ("r-xml2" ,r-xml2)))
27235 `(("esbuild" ,esbuild)
27239 (uri "https://code.jquery.com/jquery-1.12.4.js")
27242 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27243 (home-page "https://github.com/r-lib/vdiffr")
27244 (synopsis "Visual regression testing and graphical diffing")
27246 "This package is an extension to the testthat package that makes it easy
27247 to add graphical unit tests. It provides a Shiny application to manage the
27249 (license license:gpl3)))
27251 (define-public r-highlight
27253 (name "r-highlight")
27258 (uri (cran-uri "highlight" version))
27261 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27262 (properties `((upstream-name . "highlight")))
27263 (build-system r-build-system)
27264 (home-page "https://github.com/hadley/highlight")
27265 (synopsis "Syntax highlighter for R code")
27267 "This package provides a syntax highlighter for R code based on the
27268 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27269 includes a custom Sweave driver performing syntax highlighting of R code
27271 (license license:gpl3+)))
27273 (define-public r-clustree
27275 (name "r-clustree")
27280 (uri (cran-uri "clustree" version))
27283 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27284 (properties `((upstream-name . "clustree")))
27285 (build-system r-build-system)
27287 `(("r-checkmate" ,r-checkmate)
27288 ("r-dplyr" ,r-dplyr)
27289 ("r-ggplot2" ,r-ggplot2)
27290 ("r-ggraph" ,r-ggraph)
27291 ("r-ggrepel" ,r-ggrepel)
27292 ("r-igraph" ,r-igraph)
27293 ("r-rlang" ,r-rlang)
27294 ("r-tidygraph" ,r-tidygraph)
27295 ("r-viridis" ,r-viridis)))
27297 `(("r-knitr" ,r-knitr)))
27298 (home-page "https://github.com/lazappi/clustree")
27299 (synopsis "Visualize clusterings at different resolutions")
27301 "Deciding what resolution to use can be a difficult question when
27302 approaching a clustering analysis. One way to approach this problem is to
27303 look at how samples move as the number of clusters increases. This package
27304 allows you to produce clustering trees, a visualization for interrogating
27305 clusterings as resolution increases.")
27306 (license license:gpl3)))
27308 (define-public r-textshaping
27310 (name "r-textshaping")
27315 (uri (cran-uri "textshaping" version))
27318 "0fqh4z505b2qriqcj70g2hhdgiawd3w2rs9rqxdwizz5vk8jjygx"))))
27319 (properties `((upstream-name . "textshaping")))
27320 (build-system r-build-system)
27322 `(("freetype" ,freetype)
27323 ("fribidi" ,fribidi)
27324 ("harfbuzz" ,harfbuzz)
27327 `(("r-cpp11" ,r-cpp11)
27328 ("r-systemfonts" ,r-systemfonts)))
27330 `(("pkg-config" ,pkg-config)
27331 ("r-knitr" ,r-knitr)))
27332 (home-page "https://github.com/r-lib/textshaping")
27333 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27335 "This package provides access to the text shaping functionality in the
27336 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27337 is a low-level utility package mainly for graphic devices that expands upon
27338 the font tool-set provided by the @code{systemfonts} package.")
27339 (license license:expat)))
27341 (define-public r-ragg
27348 (uri (cran-uri "ragg" version))
27351 "0nh1xxrxgdbq9anzkc6k3n519czp9hqyiizakm3m2gl4l4w0vp0q"))))
27352 (properties `((upstream-name . "ragg")))
27353 (build-system r-build-system)
27355 `(("freetype" ,freetype)
27356 ("libjpeg" ,libjpeg-turbo)
27358 ("libtiff" ,libtiff)
27361 `(("r-systemfonts" ,r-systemfonts)
27362 ("r-textshaping" ,r-textshaping)))
27364 `(("pkg-config" ,pkg-config)))
27365 (home-page "https://ragg.r-lib.org")
27366 (synopsis "Graphic devices based on AGG")
27368 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27369 drawing library. The ragg package provides a set of graphic devices based on
27370 AGG to use as alternative to the raster devices provided through the
27371 @code{grDevices} package.")
27372 (license license:expat)))
27374 (define-public r-downlit
27381 (uri (cran-uri "downlit" version))
27384 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27385 (properties `((upstream-name . "downlit")))
27386 (build-system r-build-system)
27388 `(("r-brio" ,r-brio)
27389 ("r-digest" ,r-digest)
27390 ("r-evaluate" ,r-evaluate)
27391 ("r-fansi" ,r-fansi)
27392 ("r-rlang" ,r-rlang)
27393 ("r-vctrs" ,r-vctrs)
27394 ("r-yaml" ,r-yaml)))
27395 (home-page "https://downlit.r-lib.org/")
27396 (synopsis "Syntax highlighting and automatic linking")
27398 "This package provides syntax highlighting of R code, specifically
27399 designed for the needs of RMarkdown packages like @code{pkgdown},
27400 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27401 to their documentation on the web, and automatic translation of ANSI escapes
27402 in output to the equivalent HTML.")
27403 (license license:expat)))
27405 (define-public r-pkgdown
27412 (uri (cran-uri "pkgdown" version))
27415 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27416 (properties `((upstream-name . "pkgdown")))
27417 (build-system r-build-system)
27418 (inputs `(("pandoc" ,pandoc)))
27420 `(("r-callr" ,r-callr)
27421 ("r-crayon" ,r-crayon)
27423 ("r-digest" ,r-digest)
27424 ("r-downlit" ,r-downlit)
27427 ("r-magrittr" ,r-magrittr)
27428 ("r-memoise" ,r-memoise)
27429 ("r-openssl" ,r-openssl)
27430 ("r-purrr" ,r-purrr)
27432 ("r-rematch2" ,r-rematch2)
27433 ("r-rlang" ,r-rlang)
27434 ("r-rmarkdown" ,r-rmarkdown)
27435 ("r-tibble" ,r-tibble)
27436 ("r-whisker" ,r-whisker)
27437 ("r-withr" ,r-withr)
27439 ("r-yaml" ,r-yaml)))
27441 `(("r-knitr" ,r-knitr)))
27442 (home-page "https://pkgdown.r-lib.org")
27443 (synopsis "Make static HTML documentation for an R package")
27445 "The goal of this package is to generate an attractive and useful website
27446 from a source package. @code{pkgdown} converts your documentation, vignettes,
27447 README file, and more to HTML making it easy to share information about your
27449 (license license:expat)))
27451 (define-public r-prereg
27458 (uri (cran-uri "prereg" version))
27461 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
27462 (properties `((upstream-name . "prereg")))
27463 (build-system r-build-system)
27465 `(("r-rmarkdown" ,r-rmarkdown)))
27466 (home-page "https://github.com/crsh/prereg")
27468 "R Markdown Templates to preregister Scientific Studies")
27470 "This package provides a collection of templates to author
27471 preregistration documents for scientific studies in PDF format.")
27472 (license license:gpl3)))
27474 (define-public r-ez
27481 (uri (cran-uri "ez" version))
27484 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
27485 (properties `((upstream-name . "ez")))
27486 (build-system r-build-system)
27489 ("r-ggplot2" ,r-ggplot2)
27492 ("r-matrix" ,r-matrix)
27495 ("r-reshape2" ,r-reshape2)
27496 ("r-scales" ,r-scales)
27497 ("r-stringr" ,r-stringr)))
27498 (home-page "https://github.com/mike-lawrence/ez")
27499 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
27501 "Facilitates easy analysis of factorial experiments, including purely
27502 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
27503 and mixed within-and-between-Ss designs. The functions in this package aim to
27504 provide simple, intuitive and consistent specification of data analysis and
27505 visualization. Visualization functions also include design visualization for
27506 pre-analysis data auditing, and correlation matrix visualization. Finally,
27507 this package includes functions for non-parametric analysis, including
27508 permutation tests and bootstrap resampling. The bootstrap function obtains
27509 predictions either by cell means or by more advanced/powerful mixed effects
27510 models, yielding predictions and confidence intervals that may be easily
27511 visualized at any level of the experiment's design.")
27512 (license license:gpl2+)))
27514 (define-public r-qdapregex
27516 (name "r-qdapregex")
27521 (uri (cran-uri "qdapRegex" version))
27524 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
27525 (properties `((upstream-name . "qdapRegex")))
27526 (build-system r-build-system)
27527 (propagated-inputs `(("r-stringi" ,r-stringi)))
27529 "https://trinker.github.com/qdapRegex/")
27531 "Regular Expression Removal, Extraction, and Replacement Tools")
27533 "This package provides a collection of regular expression tools
27534 associated with the @code{qdap} package that may be useful outside of the
27535 context of discourse analysis. Tools include removal/extraction/replacement of
27536 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
27537 percentages, citations, person tags, phone numbers, times, and zip codes.")
27538 (license license:gpl2)))
27540 (define-public r-mgsub
27547 (uri (cran-uri "mgsub" version))
27550 "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr"))))
27551 (properties `((upstream-name . "mgsub")))
27552 (build-system r-build-system)
27553 (native-inputs `(("r-knitr" ,r-knitr)))
27555 "https://cran.r-project.org/package=mgsub")
27557 "Safe, Multiple, Simultaneous String Substitution")
27559 "Designed to enable simultaneous substitution in strings in a safe
27560 fashion. Safe means it does not rely on placeholders (which can cause errors
27561 in same length matches).")
27562 (license license:expat)))
27564 (define-public r-textshape
27566 (name "r-textshape")
27571 (uri (cran-uri "textshape" version))
27574 "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
27575 (properties `((upstream-name . "textshape")))
27576 (build-system r-build-system)
27578 `(("r-data-table" ,r-data-table)
27580 ("r-stringi" ,r-stringi)))
27581 (home-page "https://github.com/trinker/textshape")
27582 (synopsis "Tools for Reshaping Text")
27584 "Tools that can be used to reshape and restructure text data.")
27585 (license license:gpl2)))
27587 (define-public r-syuzhet
27594 (uri (cran-uri "syuzhet" version))
27597 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
27598 (properties `((upstream-name . "syuzhet")))
27599 (build-system r-build-system)
27601 `(("r-dplyr" ,r-dplyr)
27604 ("r-rlang" ,r-rlang)
27605 ("r-textshape" ,r-textshape)
27606 ("r-tidyr" ,r-tidyr)
27608 (native-inputs `(("r-knitr" ,r-knitr)))
27609 (home-page "https://github.com/mjockers/syuzhet")
27611 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
27613 "Extracts sentiment and sentiment-derived plot arcs from text using a
27614 variety of sentiment dictionaries conveniently packaged for consumption by R
27615 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
27616 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
27617 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
27618 M. and Turney, Peter D. Applicable references are available in
27619 @file{README.md} and in the documentation for the @code{get_sentiment}
27620 function. The package also provides a hack for implementing Stanford's coreNLP
27621 sentiment parser. The package provides several methods for plot arc
27623 (license license:gpl3)))
27625 (define-public r-lexicon
27632 (uri (cran-uri "lexicon" version))
27635 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
27636 (properties `((upstream-name . "lexicon")))
27637 (build-system r-build-system)
27639 `(("r-data-table" ,r-data-table)
27640 ("r-syuzhet" ,r-syuzhet)))
27641 (home-page "https://github.com/trinker/lexicon")
27642 (synopsis "Lexicons for Text Analysis")
27644 "This package provides a collection of lexical hash tables, dictionaries,
27646 (license license:gpl3)))
27648 (define-public r-english
27655 (uri (cran-uri "english" version))
27658 "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1"))))
27659 (properties `((upstream-name . "english")))
27660 (build-system r-build-system)
27661 (native-inputs `(("r-knitr" ,r-knitr)))
27663 "https://cran.r-project.org/package=english")
27664 (synopsis "Translate Integers into English")
27666 "Allow numbers to be presented in an English language version, one, two,
27667 three, ... Ordinals are also available, first, second, third, ... and
27668 indefinite article choice, \"a\" or \"an\".")
27669 (license license:gpl2)))
27671 (define-public r-textclean
27673 (name "r-textclean")
27678 (uri (cran-uri "textclean" version))
27681 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
27682 (properties `((upstream-name . "textclean")))
27683 (build-system r-build-system)
27685 `(("r-data-table" ,r-data-table)
27686 ("r-english" ,r-english)
27688 ("r-lexicon" ,r-lexicon)
27689 ("r-mgsub" ,r-mgsub)
27690 ("r-qdapregex" ,r-qdapregex)
27691 ("r-stringi" ,r-stringi)
27692 ("r-textshape" ,r-textshape)))
27694 "https://github.com/trinker/textclean")
27695 (synopsis "Text Cleaning Tools")
27697 "Tools to clean and process text. Tools are geared at checking for
27698 substrings that are not optimal for analysis and replacing or removing them
27699 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
27700 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
27701 extracting them into new variables. For example, emoticons are often used in
27702 text but not always easily handled by analysis algorithms. The
27703 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
27704 (license license:gpl2)))
27706 (define-public r-striprtf
27708 (name "r-striprtf")
27713 (uri (cran-uri "striprtf" version))
27716 "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd"))))
27717 (properties `((upstream-name . "striprtf")))
27718 (build-system r-build-system)
27720 `(("r-magrittr" ,r-magrittr)
27722 ("r-stringr" ,r-stringr)))
27723 (home-page "https://github.com/kota7/striprtf")
27724 (synopsis "Extract Text from RTF File")
27726 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
27727 (license license:expat)))
27729 (define-public r-ndjson
27736 (uri (cran-uri "ndjson" version))
27739 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
27740 (modules '((guix build utils)))
27743 ;; unvendor gzstream
27744 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
27746 (properties `((upstream-name . "ndjson")))
27747 (build-system r-build-system)
27750 (modify-phases %standard-phases
27751 (add-after 'unpack 'use-system-gzstream
27752 (lambda* (#:key inputs #:allow-other-keys)
27753 (substitute* "src/Makevars"
27754 (("PKG_LIBS = " all)
27755 (string-append all "-lgzstream ")))
27757 (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream)))
27759 `(("r-data-table" ,r-data-table)
27761 ("r-tibble" ,r-tibble)))
27762 (home-page "https://gitlab.com/hrbrmstr/ndjson")
27764 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
27766 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
27767 modern ndjson files contain large numbers of records. These constructs may not
27768 be columnar in nature, but it is often useful to read in these files and
27769 \"flatten\" the structure out to enable working with the data in an R
27770 @code{data.frame}-like context. Functions are provided that make it possible
27771 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
27772 validate the format of the records or create \"flat\" @code{data.table}
27773 structures from them.")
27774 (license license:expat)))
27776 (define-public r-streamr
27783 (uri (cran-uri "streamR" version))
27786 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
27787 (properties `((upstream-name . "streamR")))
27788 (build-system r-build-system)
27790 `(("r-ndjson" ,r-ndjson)
27791 ("r-rcurl" ,r-rcurl)
27792 ("r-rjson" ,r-rjson)))
27794 "https://cran.r-project.org/package=streamR")
27796 "Access to Twitter Streaming API via R")
27798 "This package provides functions to access Twitter's filter, sample, and
27799 user streams, and to parse the output into data frames.")
27800 (license license:gpl2)))
27802 (define-public r-readods
27809 (uri (cran-uri "readODS" version))
27812 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
27813 (properties `((upstream-name . "readODS")))
27814 (build-system r-build-system)
27816 `(("r-cellranger" ,r-cellranger)
27817 ("r-readr" ,r-readr)
27818 ("r-stringi" ,r-stringi)
27819 ("r-xml2" ,r-xml2)))
27820 (native-inputs `(("r-knitr" ,r-knitr)))
27822 "https://cran.r-project.org/package=readODS")
27823 (synopsis "Read and Write ODS Files")
27825 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
27826 Also support writing data frame into ODS file.")
27827 (license license:gpl3)))
27829 (define-public r-qpdf
27836 (uri (cran-uri "qpdf" version))
27839 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
27840 (modules '((guix build utils)))
27843 ;; unvendor libqpdf
27844 (delete-file-recursively "src/libqpdf")
27845 (delete-file-recursively "src/include/qpdf")
27847 (properties `((upstream-name . "qpdf")))
27848 (build-system r-build-system)
27851 (modify-phases %standard-phases
27852 (add-after 'unpack 'configure
27854 (setenv "EXTERNAL_QPDF" "1")
27860 `(("r-askpass" ,r-askpass)
27862 ("r-rcpp" ,r-rcpp)))
27863 (native-inputs `(("pkg-config" ,pkg-config)))
27864 (home-page "https://github.com/ropensci/qpdf")
27866 "Split, Combine and Compress PDF Files")
27868 "Content-preserving transformations transformations of PDF files such as
27869 split, combine, and compress. This package interfaces directly to the
27870 @code{qpdf} C++ API and does not require any command line utilities. Note that
27871 @code{qpdf} does not read actual content from PDF files: to extract text and
27872 data you need the @code{pdftools} package.")
27873 (license license:asl2.0)))
27875 (define-public r-pdftools
27877 (name "r-pdftools")
27882 (uri (cran-uri "pdftools" version))
27885 "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx"))))
27886 (properties `((upstream-name . "pdftools")))
27887 (build-system r-build-system)
27890 ("poppler" ,poppler)))
27892 `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp)))
27893 (native-inputs `(("pkg-config" ,pkg-config)))
27895 "https://docs.ropensci.org/pdftools/")
27897 "Text Extraction, Rendering and Converting of PDF Documents")
27899 "Utilities based on @code{libpoppler} for extracting text, fonts,
27900 attachments and metadata from a PDF file. Also supports high quality rendering
27901 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
27902 further processing in R.")
27903 (license license:expat)))
27905 (define-public r-antiword
27907 (name "r-antiword")
27912 (uri (cran-uri "antiword" version))
27915 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
27916 (modules '((guix build utils)))
27919 ;; unvendor libantiword
27920 (delete-file-recursively "src")
27922 (properties `((upstream-name . "antiword")))
27923 (build-system r-build-system)
27926 (modify-phases %standard-phases
27927 (add-after 'unpack 'use-system-antiword
27928 (lambda* (#:key inputs #:allow-other-keys)
27929 (substitute* "R/antiword.R"
27930 (("system.file\\(\"bin\", package = \"antiword\"\\)")
27931 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
27933 (inputs `(("antiword" ,antiword)))
27934 (propagated-inputs `(("r-sys" ,r-sys)))
27936 "https://github.com/ropensci/antiword#readme")
27938 "Extract Text from Microsoft Word Documents")
27940 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
27941 documents. The utility only supports the old @code{doc} format, not the new
27942 xml based @code{docx} format. Use the @code{xml2} package to read the
27944 (license license:gpl2)))
27946 (define-public r-readtext
27948 (name "r-readtext")
27953 (uri (cran-uri "readtext" version))
27956 "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y"))))
27957 (properties `((upstream-name . "readtext")))
27958 (build-system r-build-system)
27960 `(("r-antiword" ,r-antiword)
27961 ("r-data-table" ,r-data-table)
27962 ("r-digest" ,r-digest)
27964 ("r-jsonlite" ,r-jsonlite)
27965 ("r-pdftools" ,r-pdftools)
27966 ("r-readods" ,r-readods)
27967 ("r-readxl" ,r-readxl)
27968 ("r-streamr" ,r-streamr)
27969 ("r-stringi" ,r-stringi)
27970 ("r-striprtf" ,r-striprtf)
27971 ("r-tibble" ,r-tibble)
27972 ("r-xml2" ,r-xml2)))
27973 (native-inputs `(("r-knitr" ,r-knitr)))
27975 "https://github.com/quanteda/readtext")
27977 "Import and Handling for Plain and Formatted Text Files")
27979 "This package provides functions for importing and handling text files
27980 and formatted text files with additional meta-data, such including @code{.csv},
27981 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
27982 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
27983 (license license:gpl3)))
27985 (define-public r-packcircles
27987 (name "r-packcircles")
27992 (uri (cran-uri "packcircles" version))
27995 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
27996 (properties `((upstream-name . "packcircles")))
27997 (build-system r-build-system)
27998 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
27999 (native-inputs `(("r-knitr" ,r-knitr)))
28001 "https://github.com/mbedward/packcircles")
28002 (synopsis "Circle Packing")
28004 "Algorithms to find arrangements of non-overlapping circles.")
28005 (license license:expat)))
28007 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
28009 (define-public r-lwgeom
28016 (uri (cran-uri "lwgeom" version))
28019 "0byhjqa2acns8mznl1ngnfygxxxyszvnq66qfg0smhhhdkwr67aa"))))
28020 (properties `((upstream-name . "lwgeom")))
28021 (build-system r-build-system)
28022 (inputs `(("geos" ,geos) ("proj" ,proj) ("sqlite" ,sqlite)))
28024 `(("r-rcpp" ,r-rcpp)
28026 ("r-units" ,r-units)))
28027 (native-inputs `(("pkg-config" ,pkg-config)))
28029 "https://github.com/r-spatial/lwgeom/")
28031 "Bindings to Selected 'liblwgeom' Functions for Simple Features")
28033 "Access to selected functions found in
28034 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
28035 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
28036 (license license:gpl2)))
28038 (define-public r-stars
28045 (uri (cran-uri "stars" version))
28048 "0ybk899rc0rpf2cv5kwk78fvis5xnr255hfcy5khdxsxdqgl0m9j"))))
28049 (properties `((upstream-name . "stars")))
28050 (build-system r-build-system)
28052 `(("r-abind" ,r-abind)
28053 ("r-classint" ,r-classint)
28054 ("r-lwgeom" ,r-lwgeom)
28055 ("r-rlang" ,r-rlang)
28057 ("r-units" ,r-units)))
28058 (native-inputs `(("r-knitr" ,r-knitr)))
28059 (home-page "https://r-spatial.github.io/stars/")
28061 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
28063 "Reading, manipulating, writing and plotting spatiotemporal arrays
28064 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
28065 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
28066 (license license:asl2.0)))
28068 (define-public r-tmaptools
28070 (name "r-tmaptools")
28075 (uri (cran-uri "tmaptools" version))
28078 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
28079 (properties `((upstream-name . "tmaptools")))
28080 (build-system r-build-system)
28082 `(("r-dichromat" ,r-dichromat)
28083 ("r-lwgeom" ,r-lwgeom)
28084 ("r-magrittr" ,r-magrittr)
28085 ("r-rcolorbrewer" ,r-rcolorbrewer)
28087 ("r-stars" ,r-stars)
28088 ("r-units" ,r-units)
28089 ("r-viridislite" ,r-viridislite)
28092 "https://github.com/mtennekes/tmaptools")
28093 (synopsis "Thematic Map Tools")
28095 "Set of tools for reading and processing spatial data. The aim is to
28096 supply the workflow to create thematic maps. This package also facilitates
28097 @code{tmap}, the package for visualizing thematic maps.")
28098 (license license:gpl3)))
28100 (define-public r-rworldmap
28102 (name "r-rworldmap")
28107 (uri (cran-uri "rworldmap" version))
28110 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
28111 (properties `((upstream-name . "rworldmap")))
28112 (build-system r-build-system)
28114 `(("r-fields" ,r-fields)
28115 ("r-maptools" ,r-maptools)
28118 "https://github.com/AndySouth/rworldmap/")
28119 (synopsis "Mapping Global Data")
28121 "Enables mapping of country level and gridded user datasets.")
28122 (license license:gpl2+)))
28124 (define-public r-rtweet
28131 (uri (cran-uri "rtweet" version))
28134 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
28135 (properties `((upstream-name . "rtweet")))
28136 (build-system r-build-system)
28138 `(("r-httpuv" ,r-httpuv)
28140 ("r-jsonlite" ,r-jsonlite)
28141 ("r-magrittr" ,r-magrittr)
28142 ("r-progress" ,r-progress)
28144 ("r-tibble" ,r-tibble)))
28145 (native-inputs `(("r-knitr" ,r-knitr)))
28147 "https://docs.ropensci.org/rtweet/")
28148 (synopsis "Collecting Twitter Data")
28150 "An implementation of calls designed to collect and organize Twitter data
28151 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
28152 Application Program Interfaces (API)}.")
28153 (license license:expat)))
28155 (define-public r-intervals
28157 (name "r-intervals")
28162 (uri (cran-uri "intervals" version))
28165 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
28166 (properties `((upstream-name . "intervals")))
28167 (build-system r-build-system)
28168 (home-page "https://github.com/edzer/intervals")
28170 "Tools for Working with Points and Intervals")
28172 "Tools for working with and comparing sets of points and intervals.")
28173 (license license:artistic2.0)))
28175 (define-public r-eyelinker
28177 (name "r-eyelinker")
28182 (uri (cran-uri "eyelinker" version))
28185 "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2"))))
28186 (properties `((upstream-name . "eyelinker")))
28187 (build-system r-build-system)
28189 `(("r-intervals" ,r-intervals)
28190 ("r-readr" ,r-readr)
28191 ("r-stringi" ,r-stringi)
28192 ("r-stringr" ,r-stringr)
28193 ("r-tibble" ,r-tibble)))
28194 (native-inputs `(("r-knitr" ,r-knitr)))
28196 "https://github.com/a-hurst/eyelinker")
28198 "Import ASC Files from EyeLink Eye Trackers")
28200 "Imports plain-text ASC data files from EyeLink eye trackers into
28201 (relatively) tidy data frames for analysis and visualization.")
28202 (license license:gpl3)))
28204 (define-public r-btm
28211 (uri (cran-uri "BTM" version))
28214 "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb"))))
28215 (properties `((upstream-name . "BTM")))
28216 (build-system r-build-system)
28217 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
28218 (home-page "https://github.com/bnosac/BTM")
28219 (synopsis "Biterm Topic Models for Short Text")
28221 "Biterm Topic Models find topics in collections of short texts. It is a
28222 word co-occurrence based topic model that learns topics by modeling word-word
28223 co-occurrences patterns which are called biterms. This in contrast to
28224 traditional topic models like Latent Dirichlet Allocation and Probabilistic
28225 Latent Semantic Analysis which are word-document co-occurrence topic models. A
28226 biterm consists of two words co-occurring in the same short text window. This
28227 context window can for example be a twitter message, a short answer on a
28228 survey, a sentence of a text or a document identifier. The techniques are
28229 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
28230 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
28231 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
28233 (license license:asl2.0)))
28235 (define-public r-textplot
28237 (name "r-textplot")
28242 (uri (cran-uri "textplot" version))
28245 "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy"))))
28246 (properties `((upstream-name . "textplot")))
28247 (build-system r-build-system)
28249 `(("r-data-table" ,r-data-table)
28250 ("r-lattice" ,r-lattice)
28251 ("r-matrix" ,r-matrix)))
28252 (native-inputs `(("r-knitr" ,r-knitr)))
28253 (home-page "https://github.com/bnosac/textplot")
28254 (synopsis "Text Plots")
28256 "Visualise complex relations in texts. This is done by providing
28257 functionalities for displaying text co-occurrence networks, text correlation
28258 networks, dependency relationships as well as text clustering. Feel free to
28259 join the effort of providing interesting text visualisations.")
28260 (license license:gpl2)))
28262 (define-public r-gsa
28269 (uri (cran-uri "GSA" version))
28272 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
28273 (properties `((upstream-name . "GSA")))
28274 (build-system r-build-system)
28275 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
28276 (synopsis "Gene set analysis")
28277 (description "This package lets you determine the significance of
28278 pre-defined sets of genes with respect to an outcome variable, such as a group
28279 indicator, a quantitative variable or a survival time.")
28280 ;; Any version of the LGPL
28281 (license license:lgpl3+)))
28283 (define-public r-samr
28290 (uri (cran-uri "samr" version))
28293 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
28294 (properties `((upstream-name . "samr")))
28295 (build-system r-build-system)
28298 ("r-impute" ,r-impute)
28299 ("r-matrixstats" ,r-matrixstats)
28300 ("r-openxlsx" ,r-openxlsx)
28301 ("r-shiny" ,r-shiny)
28302 ("r-shinyfiles" ,r-shinyfiles)))
28303 (native-inputs `(("gfortran" ,gfortran)))
28304 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
28305 (synopsis "Significance analysis of Microarrays")
28307 "This is a package for significance analysis of Microarrays for
28308 differential expression analysis, RNAseq data and related problems.")
28309 ;; Any version of the LGPL
28310 (license license:lgpl3+)))