1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
21 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
22 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
23 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
24 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
26 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
28 ;;; This file is part of GNU Guix.
30 ;;; GNU Guix is free software; you can redistribute it and/or modify it
31 ;;; under the terms of the GNU General Public License as published by
32 ;;; the Free Software Foundation; either version 3 of the License, or (at
33 ;;; your option) any later version.
35 ;;; GNU Guix is distributed in the hope that it will be useful, but
36 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
37 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
38 ;;; GNU General Public License for more details.
40 ;;; You should have received a copy of the GNU General Public License
41 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
43 (define-module (gnu packages cran)
44 #:use-module ((guix licenses) #:prefix license:)
45 #:use-module (guix packages)
46 #:use-module (guix download)
47 #:use-module (guix git-download)
48 #:use-module (guix utils)
49 #:use-module (guix build-system r)
50 #:use-module (gnu packages algebra)
51 #:use-module (gnu packages autotools)
52 #:use-module (gnu packages base)
53 #:use-module (gnu packages bioinformatics)
54 #:use-module (gnu packages c)
55 #:use-module (gnu packages compression)
56 #:use-module (gnu packages curl)
57 #:use-module (gnu packages databases)
58 #:use-module (gnu packages fontutils)
59 #:use-module (gnu packages gcc)
60 #:use-module (gnu packages geo)
61 #:use-module (gnu packages ghostscript)
62 #:use-module (gnu packages gl)
63 #:use-module (gnu packages gnome)
64 #:use-module (gnu packages graph)
65 #:use-module (gnu packages gtk)
66 #:use-module (gnu packages haskell-xyz)
67 #:use-module (gnu packages icu4c)
68 #:use-module (gnu packages image)
69 #:use-module (gnu packages imagemagick)
70 #:use-module (gnu packages java)
71 #:use-module (gnu packages javascript)
72 #:use-module (gnu packages lisp-xyz)
73 #:use-module (gnu packages machine-learning)
74 #:use-module (gnu packages maths)
75 #:use-module (gnu packages mpi)
76 #:use-module (gnu packages multiprecision)
77 #:use-module (gnu packages networking)
78 #:use-module (gnu packages node)
79 #:use-module (gnu packages pcre)
80 #:use-module (gnu packages perl)
81 #:use-module (gnu packages pkg-config)
82 #:use-module (gnu packages pulseaudio) ;libsndfile
83 #:use-module (gnu packages python)
84 #:use-module (gnu packages python-xyz)
85 #:use-module (gnu packages statistics)
86 #:use-module (gnu packages tcl)
87 #:use-module (gnu packages tls)
88 #:use-module (gnu packages web)
89 #:use-module (gnu packages xorg))
91 (define-public r-rticles
98 (uri (cran-uri "rticles" version))
101 "1377fib4asazhhki4aajvld0wa35vd3zjvyl3lf2hjm2qk3vyak7"))))
102 (properties `((upstream-name . "rticles")))
103 (build-system r-build-system)
105 `(("r-knitr" ,r-knitr)
106 ("r-rmarkdown" ,r-rmarkdown)
107 ("r-tinytex" ,r-tinytex)
110 (home-page "https://github.com/rstudio/rticles")
111 (synopsis "Article formats for R Markdown")
113 "This package provides a suite of custom R Markdown formats and templates
114 for authoring journal articles and conference submissions.")
115 (license license:gpl3)))
117 (define-public r-bezier
123 (uri (cran-uri "bezier" version))
126 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
127 (build-system r-build-system)
128 (home-page "https://cran.r-project.org/web/packages/bezier/")
129 (synopsis "Bezier curve and spline toolkit")
131 "This package is a toolkit for working with Bezier curves and splines.
132 The package provides functions for point generation, arc length estimation,
133 degree elevation and curve fitting.")
134 (license license:gpl2+)))
143 (uri (cran-uri "V8" version))
146 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
147 (properties `((upstream-name . "V8")))
148 (build-system r-build-system)
151 (modify-phases %standard-phases
152 (add-after 'unpack 'find-v8
153 (lambda* (#:key inputs #:allow-other-keys)
154 (substitute* "configure"
156 (string-append "PKG_LIBS="
157 (assoc-ref inputs "node")
158 "/lib/libnode.so.64\n")))
159 (setenv "INCLUDE_DIR"
161 (assoc-ref inputs "node")
165 (assoc-ref inputs "node") "/lib"))
168 `(("node" ,libnode)))
171 ("r-jsonlite" ,r-jsonlite)
174 `(("r-knitr" ,r-knitr)))
175 (home-page "https://jeroen.cran.dev/V8")
176 (synopsis "Embedded JavaScript and WebAssembly engine for R")
178 "This package provides an R interface to V8: Google's JavaScript and
179 WebAssembly engine.")
180 (license license:expat)))
189 (uri (cran-uri "DOT" version))
192 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
193 (properties `((upstream-name . "DOT")))
194 (build-system r-build-system)
197 (home-page "http://haghish.com/dot")
198 (synopsis "Render and Export DOT Graphs in R")
200 "This package provides tools to render DOT diagram markup language in R
201 and also provides the possibility to export the graphs in PostScript and
202 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
203 programming packages such as @code{knitr} and @code{rmarkdown}.")
204 (license license:expat)))
206 (define-public r-clipr
213 (uri (cran-uri "clipr" version))
216 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
217 (build-system r-build-system)
218 (home-page "https://github.com/mdlincoln/clipr")
219 (synopsis "Read and write from the system clipboard")
221 "This package provides simple utility functions to read from and write to
222 the system clipboards.")
223 (license license:gpl3)))
231 (uri (cran-uri "zoo" version))
234 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
235 (build-system r-build-system)
237 `(("r-lattice" ,r-lattice)))
238 (home-page "http://zoo.R-Forge.R-project.org/")
239 (synopsis "S3 infrastructure for regular and irregular time series")
240 (description "This package contains an S3 class with methods for totally
241 ordered indexed observations. It is particularly aimed at irregular time
242 series of numeric vectors/matrices and factors.")
243 (license license:gpl2+)))
245 (define-public r-ggpmisc
251 (uri (cran-uri "ggpmisc" version))
254 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
255 (build-system r-build-system)
257 `(("r-broom" ,r-broom)
259 ("r-ggplot2" ,r-ggplot2)
260 ("r-gridextra" ,r-gridextra)
261 ("r-lubridate" ,r-lubridate)
262 ("r-magrittr" ,r-magrittr)
265 ("r-polynom" ,r-polynom)
267 ("r-scales" ,r-scales)
268 ("r-splus2r" ,r-splus2r)
269 ("r-stringr" ,r-stringr)
270 ("r-tibble" ,r-tibble)
274 `(("r-knitr" ,r-knitr)))
275 (home-page "https://www.r4photobiology.info/")
276 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
277 (description "This package provides extensions to @code{ggplot2},
278 respecting the grammar of its graphics paradigm.")
279 (license license:gpl2+)))
281 (define-public r-gprofiler
288 (uri (cran-uri "gProfileR" version))
291 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
292 (properties `((upstream-name . "gProfileR")))
293 (build-system r-build-system)
296 ("r-rcurl" ,r-rcurl)))
297 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
298 (synopsis "Interface to the g:Profiler toolkit")
300 "This package provides tools for functional enrichment analysis,
301 gene identifier conversion and mapping homologous genes across related
302 organisms via the @code{g:Profiler} toolkit.")
303 (license license:gpl2+)))
305 (define-public r-gprofiler2
307 (name "r-gprofiler2")
312 (uri (cran-uri "gprofiler2" version))
315 "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
316 (properties `((upstream-name . "gprofiler2")))
317 (build-system r-build-system)
319 `(("r-crosstalk" ,r-crosstalk)
321 ("r-ggplot2" ,r-ggplot2)
322 ("r-gridextra" ,r-gridextra)
323 ("r-jsonlite" ,r-jsonlite)
324 ("r-plotly" ,r-plotly)
327 ("r-viridislite" ,r-viridislite)))
328 (native-inputs `(("r-knitr" ,r-knitr)))
329 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
330 (synopsis "Interface to the g:Profiler toolset")
332 "This package provides a toolset for functional enrichment analysis and
333 visualization, gene/protein/SNP identifier conversion and mapping orthologous
334 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
338 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
340 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
342 @item @code{g:Orth}, orthology search across species;
343 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
344 genes and variant effects.
347 This package is an R interface corresponding to the 2019 update of
348 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
350 (license license:gpl2+)))
352 (define-public r-oenb
359 (uri (cran-uri "oenb" version))
362 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
363 (properties `((upstream-name . "oenb")))
364 (build-system r-build-system)
366 `(("r-dplyr" ,r-dplyr)
368 (native-inputs `(("r-knitr" ,r-knitr)))
369 (home-page "https://github.com/franzmohr/oenb")
370 (synopsis "Tools for the OeNB Data Web Service")
372 "Tools to access data from the data web service of the
373 @acronym{OeNB, Oesterreichische Nationalbank},
374 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
375 (license license:gpl2+)))
377 (define-public r-scales
384 (uri (cran-uri "scales" version))
386 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
387 (build-system r-build-system)
389 `(("r-farver" ,r-farver)
390 ("r-labeling" ,r-labeling)
391 ("r-lifecycle" ,r-lifecycle)
392 ("r-munsell" ,r-munsell)
393 ("r-rcolorbrewer" ,r-rcolorbrewer)
395 ("r-viridislite" ,r-viridislite)))
396 (home-page "https://github.com/hadley/scales")
397 (synopsis "Scale functions for visualization")
399 "This package provides graphical scales that map data to aesthetics, and
400 provides methods for automatically determining breaks and labels for axes and
402 (license license:expat)))
404 (define-public r-pheatmap
411 (uri (cran-uri "pheatmap" version))
414 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
415 (build-system r-build-system)
417 `(("r-gtable" ,r-gtable)
418 ("r-rcolorbrewer" ,r-rcolorbrewer)
419 ("r-scales" ,r-scales)))
420 (home-page "https://cran.r-project.org/web/packages/pheatmap")
421 (synopsis "Pretty heatmaps")
423 "This package provides an implementation of heatmaps that offers more
424 control over dimensions and appearance.")
425 (license license:gpl2+)))
433 (uri (cran-uri "ecp" version))
436 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
437 (build-system r-build-system)
439 `(("r-rcpp" ,r-rcpp)))
440 (home-page "https://cran.r-project.org/web/packages/ecp/")
441 (synopsis "Multiple change-point analysis of multivariate data")
443 "This package implements various procedures for finding multiple
444 change-points. Two methods make use of dynamic programming and pruning, with
445 no distributional assumptions other than the existence of certain absolute
446 moments in one method. Hierarchical and exact search methods are included.
447 All methods return the set of estimated change-points as well as other summary
449 (license license:gpl2+)))
451 (define-public r-ellipsis
458 (uri (cran-uri "ellipsis" version))
461 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
462 (build-system r-build-system)
464 `(("r-rlang" ,r-rlang)))
465 (home-page "https://github.com/hadley/ellipsis")
466 (synopsis "Tools for working with additional arguments")
468 "In S3 generics, it's useful to take @code{...} so that methods can have
469 additional arguments. But this flexibility comes at a cost: misspelled
470 arguments will be silently ignored. The @code{ellipsis} package is an
471 experiment that allows a generic to warn if any arguments passed in @code{...}
473 (license license:gpl3)))
482 (uri (cran-uri "grr" version))
485 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
486 (build-system r-build-system)
487 (home-page "https://cran.r-project.org/web/packages/grr")
488 (synopsis "Alternative implementations of base R functions")
490 "This package provides alternative implementations of some base R
491 functions, including @code{sort}, @code{order}, and @code{match}. The
492 functions are simplified but can be faster or have other advantages.")
493 (license license:gpl3)))
495 (define-public r-matrix-utils
497 (name "r-matrix-utils")
502 (uri (cran-uri "Matrix.utils" version))
505 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
506 (properties `((upstream-name . "Matrix.utils")))
507 (build-system r-build-system)
510 ("r-matrix" ,r-matrix)))
511 (home-page "https://github.com/cvarrichio/Matrix.utils")
513 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
515 "This package implements data manipulation methods such as @code{cast},
516 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
518 (license license:gpl3)))
527 (uri (cran-uri "sys" version))
530 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
531 (build-system r-build-system)
532 (home-page "https://github.com/jeroen/sys")
533 (synopsis "Powerful and reliable tools for running system commands in R")
535 "This package provides drop-in replacements for the base @code{system2()}
536 function with fine control and consistent behavior across platforms. It
537 supports clean interruption, timeout, background tasks, and streaming STDIN /
538 STDOUT / STDERR over binary or text connections. The package also provides
539 functions for evaluating expressions inside a temporary fork. Such
540 evaluations have no side effects on the main R process, and support reliable
541 interrupts and timeouts. This provides the basis for a sandboxing
543 (license license:expat)))
545 (define-public r-askpass
552 (uri (cran-uri "askpass" version))
555 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
556 (build-system r-build-system)
557 (propagated-inputs `(("r-sys" ,r-sys)))
558 (home-page "https://github.com/jeroen/askpass")
559 (synopsis "Safe password entry for R")
561 "This package provides cross-platform utilities for prompting the user
562 for credentials or a passphrase, for example to authenticate with a server or
563 read a protected key.")
564 (license license:expat)))
566 (define-public r-vegan
573 (uri (cran-uri "vegan" version))
576 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
577 (build-system r-build-system)
579 `(("gfortran" ,gfortran)))
581 `(("r-cluster" ,r-cluster)
582 ("r-knitr" ,r-knitr) ; needed for vignettes
583 ("r-lattice" ,r-lattice)
586 ("r-permute" ,r-permute)))
587 (home-page "https://cran.r-project.org/web/packages/vegan")
588 (synopsis "Functions for community ecology")
590 "The vegan package provides tools for descriptive community ecology. It
591 has most basic functions of diversity analysis, community ordination and
592 dissimilarity analysis. Most of its multivariate tools can be used for other
593 data types as well.")
594 (license license:gpl2+)))
596 (define-public r-tidyverse
603 (uri (cran-uri "tidyverse" version))
606 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
607 (build-system r-build-system)
609 `(("r-broom" ,r-broom)
611 ("r-crayon" ,r-crayon)
612 ("r-dbplyr" ,r-dbplyr)
614 ("r-forcats" ,r-forcats)
615 ("r-ggplot2" ,r-ggplot2)
619 ("r-jsonlite" ,r-jsonlite)
620 ("r-lubridate" ,r-lubridate)
621 ("r-magrittr" ,r-magrittr)
622 ("r-modelr" ,r-modelr)
623 ("r-pillar" ,r-pillar)
626 ("r-readxl" ,r-readxl)
627 ("r-reprex" ,r-reprex)
629 ("r-rstudioapi" ,r-rstudioapi)
631 ("r-stringr" ,r-stringr)
632 ("r-tibble" ,r-tibble)
635 (home-page "https://tidyverse.tidyverse.org")
636 (synopsis "Install and load packages from the \"Tidyverse\"")
638 "The @code{tidyverse} is a set of packages that work in harmony because
639 they share common data representations and API design. This package is
640 designed to make it easy to install and load multiple tidyverse packages in a
642 (license license:gpl3)))
644 (define-public r-rvest
651 (uri (cran-uri "rvest" version))
653 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
654 (build-system r-build-system)
657 ("r-magrittr" ,r-magrittr)
658 ("r-selectr" ,r-selectr)
661 `(("r-knitr" ,r-knitr)))
662 (home-page "https://github.com/hadley/rvest")
663 (synopsis "Simple web scraping for R")
665 "@code{r-rvest} helps you scrape information from web pages. It is
666 designed to work with @code{magrittr} to make it easy to express common web
667 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
668 (license license:gpl3)))
670 (define-public r-selectr
677 (uri (cran-uri "selectr" version))
679 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
680 (build-system r-build-system)
682 `(("r-stringr" ,r-stringr)
684 (home-page "https://sjp.co.nz/projects/selectr/")
685 (synopsis "Translate CSS selectors to XPath expressions")
687 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
688 expression. This allows you to use CSS selectors when working with the XML
689 package as it can only evaluate XPath expressions. Also provided are
690 convenience functions useful for using CSS selectors on XML nodes. This
691 package is a port of the Python package @code{cssselect}.")
692 (license license:bsd-3)))
694 (define-public r-reprex
701 (uri (cran-uri "reprex" version))
704 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
705 (build-system r-build-system)
707 `(("r-callr" ,r-callr)
711 ("r-rmarkdown" ,r-rmarkdown)
712 ("r-whisker" ,r-whisker)
713 ("r-withr" ,r-withr)))
714 (home-page "https://github.com/tidyverse/reprex")
715 (synopsis "Prepare reproducible R code examples for sharing")
717 "This package provides a convenience wrapper that uses the
718 @code{rmarkdown} package to render small snippets of code to target formats
719 that include both code and output. The goal is to encourage the sharing of
720 small, reproducible, and runnable examples on code-oriented websites or email.
721 @code{reprex} also extracts clean, runnable R code from various common formats,
722 such as copy/paste from an R session.")
723 (license license:expat)))
725 (define-public r-reordercluster
727 (name "r-reordercluster")
731 (uri (cran-uri "ReorderCluster" version))
734 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
735 (build-system r-build-system)
737 `(("r-gplots" ,r-gplots)
739 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
740 (synopsis "Reordering the dendrogram according to the class labels")
741 (description "This package provides tools for performing the leaf reordering
742 for the dendrogram that preserves the hierarchical clustering result and at the
743 same time tries to group instances from the same class together.")
744 (license license:gpl3+)))
746 (define-public r-callr
753 (uri (cran-uri "callr" version))
756 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
757 (build-system r-build-system)
760 ("r-processx" ,r-processx)))
761 (home-page "https://github.com/r-lib/callr#readme")
762 (synopsis "Call R from R")
764 "It is sometimes useful to perform a computation in a separate R process,
765 without affecting the current R process at all. This package does exactly
767 (license license:expat)))
769 (define-public r-readxl
776 (uri (cran-uri "readxl" version))
779 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
780 (build-system r-build-system)
782 `(("r-cellranger" ,r-cellranger)
783 ("r-progress" ,r-progress)
785 ("r-tibble" ,r-tibble)))
786 (home-page "https://readxl.tidyverse.org")
787 (synopsis "Read Excel files")
789 "This package lets you import Excel files into R. It supports
790 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
791 the embedded @code{RapidXML} C++ library.")
792 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
793 ;; 'rapidxml' which is Boost.
794 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
796 (define-public r-modelr
803 (uri (cran-uri "modelr" version))
806 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
807 (build-system r-build-system)
809 `(("r-broom" ,r-broom)
810 ("r-magrittr" ,r-magrittr)
813 ("r-tibble" ,r-tibble)
815 ("r-tidyselect" ,r-tidyselect)
816 ("r-vctrs" ,r-vctrs)))
817 (home-page "https://github.com/tidyverse/modelr")
818 (synopsis "Helper functions for modelling in pipelines")
820 "Functions for modelling that help you seamlessly integrate modelling
821 into a pipeline of data manipulation and visualisation.")
822 (license license:gpl3)))
824 (define-public r-httpuv
830 (uri (cran-uri "httpuv" version))
833 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
834 (build-system r-build-system)
838 ("r-promises" ,r-promises)
841 (home-page "https://github.com/rstudio/httpuv")
842 (synopsis "HTTP and WebSocket server library for R")
844 "The httpuv package provides low-level socket and protocol support for
845 handling HTTP and WebSocket requests directly from within R. It is primarily
846 intended as a building block for other packages, rather than making it
847 particularly easy to create complete web applications using httpuv alone.")
848 ;; This package includes third-party code that was originally released
849 ;; under various non-copyleft licenses. Full licensing information can be
850 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
851 (license license:gpl3+)))
853 (define-public r-jsonlite
859 (uri (cran-uri "jsonlite" version))
862 "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
863 (build-system r-build-system)
865 `(("r-knitr" ,r-knitr)))
866 (home-page "https://arxiv.org/abs/1403.2805")
867 (synopsis "Robust, high performance JSON parser and generator for R")
869 "The jsonlite package provides a fast JSON parser and generator optimized
870 for statistical data and the web. It offers flexible, robust, high
871 performance tools for working with JSON in R and is particularly powerful for
872 building pipelines and interacting with a web API. In addition to converting
873 JSON data from/to R objects, jsonlite contains functions to stream, validate,
874 and prettify JSON data. The unit tests included with the package verify that
875 all edge cases are encoded and decoded consistently for use with dynamic data
876 in systems and applications.")
877 (license license:expat)))
879 (define-public r-servr
885 (uri (cran-uri "servr" version))
888 "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja"))))
889 (build-system r-build-system)
891 `(("r-httpuv" ,r-httpuv)
892 ("r-jsonlite" ,r-jsonlite)
895 (home-page "https://github.com/yihui/servr")
896 (synopsis "Simple HTTP server to serve static files or dynamic documents")
898 "Servr provides an HTTP server in R to serve static files, or dynamic
899 documents that can be converted to HTML files (e.g., R Markdown) under a given
901 (license license:expat)))
903 (define-public r-htmltools
909 (uri (cran-uri "htmltools" version))
912 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
913 (build-system r-build-system)
915 `(("r-base64enc" ,r-base64enc)
916 ("r-digest" ,r-digest)
917 ("r-rlang" ,r-rlang)))
918 (home-page "https://cran.r-project.org/web/packages/htmltools")
919 (synopsis "R tools for HTML")
921 "This package provides tools for HTML generation and output in R.")
922 (license license:expat)))
924 (define-public r-htmlwidgets
926 (name "r-htmlwidgets")
930 (uri (cran-uri "htmlwidgets" version))
933 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
934 (build-system r-build-system)
936 `(("r-htmltools" ,r-htmltools)
937 ("r-jsonlite" ,r-jsonlite)
939 (home-page "https://github.com/ramnathv/htmlwidgets")
940 (synopsis "HTML Widgets for R")
942 "HTML widgets is a framework for creating HTML widgets that render in
943 various contexts including the R console, R Markdown documents, and Shiny web
945 (license license:expat)))
947 (define-public r-htmltable
954 (uri (cran-uri "htmlTable" version))
956 (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
957 (properties `((upstream-name . "htmlTable")))
958 (build-system r-build-system)
960 `(("r-checkmate" ,r-checkmate)
961 ("r-htmltools" ,r-htmltools)
962 ("r-htmlwidgets" ,r-htmlwidgets)
964 ("r-magrittr" ,r-magrittr)
965 ("r-rstudioapi" ,r-rstudioapi)
966 ("r-stringr" ,r-stringr)))
968 `(("r-knitr" ,r-knitr)))
969 (home-page "http://gforge.se/packages/")
970 (synopsis "Advanced tables for Markdown/HTML")
972 "This package provides functions to build tables with advanced layout
973 elements such as row spanners, column spanners, table spanners, zebra
974 striping, and more. While allowing advanced layout, the underlying
975 CSS-structure is simple in order to maximize compatibility with word
976 processors such as LibreOffice. The package also contains a few text
977 formatting functions that help outputting text compatible with HTML or
979 (license license:gpl3+)))
981 (define-public r-curl
987 (uri (cran-uri "curl" version))
990 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
991 (build-system r-build-system)
994 (modify-phases %standard-phases
995 ;; The environment variable CURL_CA_BUNDLE is only respected when
996 ;; running Windows, so we disable the platform checks.
997 ;; This can be removed once the libcurl has been patched.
998 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1000 (substitute* "R/onload.R"
1001 (("if \\(!grepl\\(\"mingw\".*")
1003 (substitute* "src/handle.c"
1004 (("/\\* Only set" m)
1006 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1007 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1014 `(("pkg-config" ,pkg-config)))
1015 (home-page "https://github.com/jeroenooms/curl")
1016 (synopsis "HTTP client for R")
1018 "The @code{curl()} and @code{curl_download()} functions provide highly
1019 configurable drop-in replacements for base @code{url()} and
1020 @code{download.file()} with better performance, support for encryption, gzip
1021 compression, authentication, and other @code{libcurl} goodies. The core of
1022 the package implements a framework for performing fully customized requests
1023 where data can be processed either in memory, on disk, or streaming via the
1024 callback or connection interfaces.")
1025 (license license:expat)))
1027 (define-public r-hwriter
1034 (uri (cran-uri "hwriter" version))
1037 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1038 (build-system r-build-system)
1039 (home-page "https://cran.r-project.org/web/packages/hwriter")
1040 (synopsis "Output R objects in HTML format")
1042 "This package provides easy-to-use and versatile functions to output R
1043 objects in HTML format.")
1044 (license license:lgpl2.1+)))
1046 (define-public r-rjson
1053 (uri (cran-uri "rjson" version))
1056 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1057 (build-system r-build-system)
1058 (home-page "https://cran.r-project.org/web/packages/rjson")
1059 (synopsis "JSON library for R")
1061 "This package provides functions to convert R objects into JSON objects
1063 (license license:gpl2+)))
1065 (define-public r-fastmap
1072 (uri (cran-uri "fastmap" version))
1075 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1076 (properties `((upstream-name . "fastmap")))
1077 (build-system r-build-system)
1078 (home-page "https://r-lib.github.io/fastmap/")
1079 (synopsis "Fast implementation of a key-value store")
1081 "This package provides a fast implementation of a key-value store.
1082 Environments are commonly used as key-value stores, but every time a new key
1083 is used, it is added to R's global symbol table, causing a small amount of
1084 memory leakage. This can be problematic in cases where many different keys
1085 are used. Fastmap avoids this memory leak issue by implementing the map using
1086 data structures in C++.")
1087 (license license:expat)))
1089 (define-public r-shiny
1097 (url "https://github.com/rstudio/shiny")
1098 (commit (string-append "v" version))))
1099 (file-name (git-file-name name version))
1102 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1103 (build-system r-build-system)
1105 `(#:modules ((guix build r-build-system)
1106 (guix build minify-build-system)
1109 #:imported-modules (,@%r-build-system-modules
1110 (guix build minify-build-system))
1112 (modify-phases (@ (guix build r-build-system) %standard-phases)
1113 (add-after 'unpack 'replace-bundled-minified-JavaScript
1114 (lambda* (#:key inputs #:allow-other-keys)
1115 (let ((replace-file (lambda (old new)
1116 (format #t "replacing ~a with ~a\n" old new)
1118 (symlink new old))))
1119 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1120 ;; contain just data. They are not minified code, so we don't
1122 (with-directory-excursion "inst/www/shared"
1123 (replace-file "bootstrap/shim/respond.min.js"
1124 (string-append (assoc-ref inputs "js-respond")
1125 "/share/javascript/respond.min.js"))
1126 (replace-file "bootstrap/shim/html5shiv.min.js"
1127 (string-append (assoc-ref inputs "js-html5shiv")
1128 "/share/javascript/html5shiv.min.js"))
1129 (replace-file "json2-min.js"
1130 (string-append (assoc-ref inputs "js-json2")
1131 "/share/javascript/json2-min.js"))
1132 (replace-file "strftime/strftime-min.js"
1133 (string-append (assoc-ref inputs "js-strftime")
1134 "/share/javascript/strftime.min.js"))
1135 (replace-file "highlight/highlight.pack.js"
1136 (string-append (assoc-ref inputs "js-highlight")
1137 "/share/javascript/highlight.min.js"))
1138 (replace-file "datatables/js/jquery.dataTables.min.js"
1139 (string-append (assoc-ref inputs "js-datatables")
1140 "/share/javascript/jquery.dataTables.min.js"))
1141 (replace-file "selectize/js/selectize.min.js"
1142 (string-append (assoc-ref inputs "js-selectize")
1143 "/share/javascript/selectize.min.js"))
1144 (replace-file "selectize/js/es5-shim.min.js"
1145 (string-append (assoc-ref inputs "js-es5-shim")
1146 "/share/javascript/es5-shim.min.js"))
1147 (for-each (match-lambda
1149 (delete-file target)
1150 (minify source #:target target)))
1151 '(("jqueryui/jquery-ui.js" .
1152 "jqueryui/jquery-ui.min.js")
1153 ("datepicker/js/bootstrap-datepicker.js" .
1154 "datepicker/js/bootstrap-datepicker.min.js")
1155 ("ionrangeslider/js/ion.rangeSlider.js" .
1156 "ionrangeslider/js/ion.rangeSlider.min.js")
1157 ("bootstrap/js/bootstrap.js" .
1158 "bootstrap/js/bootstrap.min.js")
1163 ("legacy/jquery.js" .
1164 "legacy/jquery.min.js")
1165 ("showdown/src/showdown.js" .
1166 "showdown/compressed/showdown.js")))))
1169 `(("r-crayon" ,r-crayon)
1170 ("r-digest" ,r-digest)
1171 ("r-fastmap" ,r-fastmap)
1172 ("r-htmltools" ,r-htmltools)
1173 ("r-httpuv" ,r-httpuv)
1174 ("r-jsonlite" ,r-jsonlite)
1175 ("r-later" ,r-later)
1177 ("r-promises" ,r-promises)
1179 ("r-rlang" ,r-rlang)
1180 ("r-sourcetools" ,r-sourcetools)
1181 ("r-withr" ,r-withr)
1182 ("r-xtable" ,r-xtable)))
1184 `(("js-datatables" ,js-datatables)
1185 ("js-html5shiv" ,js-html5shiv)
1186 ("js-json2" ,js-json2)
1187 ("js-respond" ,js-respond)
1188 ("js-selectize" ,js-selectize)
1189 ("js-strftime" ,js-strftime)
1190 ("js-highlight" ,js-highlight)
1191 ("js-es5-shim" ,js-es5-shim)))
1193 `(("uglify-js" ,uglify-js)
1194 ("gfortran" ,gfortran)))
1195 (home-page "http://shiny.rstudio.com")
1196 (synopsis "Easy interactive web applications with R")
1198 "Makes it incredibly easy to build interactive web applications
1199 with R. Automatic \"reactive\" binding between inputs and outputs and
1200 extensive prebuilt widgets make it possible to build beautiful,
1201 responsive, and powerful applications with minimal effort.")
1202 (license license:artistic2.0)))
1204 ;; This package includes minified JavaScript files. When upgrading please
1205 ;; check that there are no new minified JavaScript files.
1206 (define-public r-shinytree
1208 (name "r-shinytree")
1213 (uri (cran-uri "shinyTree" version))
1216 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1217 (modules '((guix build utils)))
1220 ;; Delete minified JavaScript
1221 (for-each delete-file
1222 '("inst/www/jsTree-3.3.7/libs/require.js"
1223 "inst/www/jsTree-3.3.7/libs/jquery.js"
1224 "inst/www/jsTree-3.3.7/jstree.min.js"))
1226 (properties `((upstream-name . "shinyTree")))
1227 (build-system r-build-system)
1229 `(#:modules ((guix build utils)
1230 (guix build r-build-system)
1234 (modify-phases %standard-phases
1235 (add-after 'unpack 'replace-minified-javascript
1236 (lambda* (#:key inputs #:allow-other-keys)
1237 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1238 (symlink (string-append (assoc-ref inputs "js-requirejs")
1239 "/share/javascript/require.min.js")
1244 `((,(assoc-ref inputs "js-jquery")
1248 (lambda (sources targets)
1249 (for-each (lambda (source target)
1250 (format #t "Processing ~a --> ~a~%"
1252 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1253 (call-with-output-file target
1255 (dump-port minified port)))))
1259 `(("r-htmlwidgets" ,r-htmlwidgets)
1260 ("r-jsonlite" ,r-jsonlite)
1261 ("r-promises" ,r-promises)
1262 ("r-shiny" ,r-shiny)
1263 ("r-stringr" ,r-stringr)))
1265 `(("js-requirejs" ,js-requirejs)))
1267 `(("uglify-js" ,uglify-js)
1271 (uri "https://code.jquery.com/jquery-3.3.1.js")
1274 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1275 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1276 (synopsis "jsTree bindings for Shiny")
1278 "This package exposes R bindings to jsTree, a JavaScript library that
1279 supports interactive trees, to enable rich, editable trees in Shiny.")
1280 (license license:expat)))
1282 (define-public r-shinydashboard
1284 (name "r-shinydashboard")
1288 (uri (cran-uri "shinydashboard" version))
1291 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1292 (build-system r-build-system)
1293 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1294 ;; Regenerate it from the included sources.
1296 `(#:modules ((guix build utils)
1297 (guix build r-build-system)
1300 (modify-phases %standard-phases
1301 (add-after 'unpack 'generate-minified-javascript
1303 (with-directory-excursion "inst/AdminLTE"
1304 (delete-file "app.min.js")
1305 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1306 (call-with-output-file "app.min.js"
1308 (dump-port minified port))))))))))
1310 `(("r-htmltools" ,r-htmltools)
1311 ("r-promises" ,r-promises)
1312 ("r-shiny" ,r-shiny)))
1314 `(("uglify-js" ,uglify-js)))
1315 (home-page "https://rstudio.github.io/shinydashboard/")
1316 (synopsis "Create dashboards with shiny")
1317 (description "This package provides an extension to the Shiny web
1318 application framework for R, making it easy to create attractive dashboards.")
1319 ;; This package includes software that was released under the Expat
1320 ;; license, but the whole package is released under GPL version 2 or
1322 (license license:gpl2+)))
1324 (define-public r-shinyfiles
1326 (name "r-shinyfiles")
1331 (uri (cran-uri "shinyFiles" version))
1333 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1334 (properties `((upstream-name . "shinyFiles")))
1335 (build-system r-build-system)
1338 ("r-htmltools" ,r-htmltools)
1339 ("r-jsonlite" ,r-jsonlite)
1340 ("r-shiny" ,r-shiny)
1341 ("r-tibble" ,r-tibble)))
1342 (home-page "https://github.com/thomasp85/shinyFiles")
1343 (synopsis "Server-side file system viewer for Shiny")
1345 "This package provides functionality for client-side navigation of the
1346 server side file system in shiny apps. In case the app is running locally
1347 this gives the user direct access to the file system without the need to
1348 \"download\" files to a temporary location. Both file and folder selection as
1349 well as file saving is available.")
1350 (license license:gpl2+)))
1352 (define-public r-shinythemes
1354 (name "r-shinythemes")
1359 (uri (cran-uri "shinythemes" version))
1362 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1363 (properties `((upstream-name . "shinythemes")))
1364 (build-system r-build-system)
1365 (propagated-inputs `(("r-shiny" ,r-shiny)))
1366 (home-page "https://rstudio.github.io/shinythemes/")
1367 (synopsis "Themes for Shiny")
1369 "This package provides themes for use with Shiny. It includes several
1370 Bootstrap themes, which are packaged for use with Shiny applications.")
1371 ;; The package is released under version 3 of the GPL, but it includes
1372 ;; source files that are covered by the Expat license. It also includes
1373 ;; fonts under SIL or the ASL.
1374 (license (list license:gpl3 license:expat
1375 license:silofl1.1 license:asl2.0))))
1377 ;; The package sources include minified variants of d3.js and non-minified
1378 ;; source code of d3-jetpack.
1379 (define-public r-d3r
1386 (uri (cran-uri "d3r" version))
1389 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1390 (build-system r-build-system)
1392 `(#:modules ((guix build utils)
1393 (guix build r-build-system)
1397 (modify-phases %standard-phases
1398 (add-after 'unpack 'process-javascript
1399 (lambda* (#:key inputs #:allow-other-keys)
1400 (with-directory-excursion "inst/www/d3/"
1404 `((,(assoc-ref inputs "d3.v3.js")
1405 "v3/dist/d3.min.js")
1406 (,(assoc-ref inputs "d3.v4.js")
1407 "v4/dist/d3.min.js")
1408 (,(assoc-ref inputs "d3.v5.js")
1409 "v5/dist/d3.min.js"))))
1410 (lambda (sources targets)
1411 (for-each (lambda (source target)
1412 (format #t "Processing ~a --> ~a~%"
1414 (delete-file target)
1415 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1416 (call-with-output-file target
1418 (dump-port minified port)))))
1422 `(("r-dplyr" ,r-dplyr)
1423 ("r-htmltools" ,r-htmltools)
1424 ("r-rlang" ,r-rlang)
1425 ("r-tidyr" ,r-tidyr)))
1427 `(("uglify-js" ,uglify-js)
1431 (uri "https://d3js.org/d3.v3.js")
1434 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1438 (uri "https://d3js.org/d3.v4.js")
1441 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1445 (uri "https://d3js.org/d3.v5.js")
1448 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1449 (home-page "https://github.com/timelyportfolio/d3r")
1450 (synopsis "d3.js utilities for R")
1452 "This package provides a suite of functions to help ease the use of the
1453 d3.js visualization library in R. These helpers include
1454 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1455 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1456 R objects into the JSON format that the d3.js library expects.")
1457 (license license:bsd-3)))
1459 ;; We use the latest commit here because the last release was in 2016 while
1460 ;; the latest commit was in 2018.
1461 (define-public r-sankeyd3
1462 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1466 (version (git-version "0.3.2" revision commit))
1471 (url "https://github.com/fbreitwieser/sankeyD3")
1473 (file-name (git-file-name name version))
1476 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1477 (build-system r-build-system)
1480 ("r-htmlwidgets" ,r-htmlwidgets)
1481 ("r-shiny" ,r-shiny)
1482 ("r-magrittr" ,r-magrittr)))
1483 (home-page "https://github.com/fbreitwieser/sankeyD3")
1484 (synopsis "Sankey network graphs from R")
1486 "This package provides an R library to generate Sankey network graphs
1487 in R and Shiny via the D3 visualization library.")
1488 ;; The R code is licensed under GPLv3+. It includes the non-minified
1489 ;; JavaScript source code of d3-sankey, which is released under the
1490 ;; 3-clause BSD license.
1491 (license (list license:gpl3+ license:bsd-3)))))
1493 (define-public r-crosstalk
1495 (name "r-crosstalk")
1500 (uri (cran-uri "crosstalk" version))
1503 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1504 (build-system r-build-system)
1506 `(("r-htmltools" ,r-htmltools)
1507 ("r-jsonlite" ,r-jsonlite)
1508 ("r-lazyeval" ,r-lazyeval)
1510 (home-page "https://rstudio.github.io/crosstalk/")
1511 (synopsis "Inter-widget interactivity for HTML widgets")
1513 "This package provides building blocks for allowing HTML widgets to
1514 communicate with each other, with Shiny or without (i.e. static @code{.html}
1515 files). It currently supports linked brushing and filtering.")
1516 (license license:expat)))
1518 (define-public r-rook
1525 (uri (cran-uri "Rook" version))
1528 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1529 (properties `((upstream-name . "Rook")))
1530 (build-system r-build-system)
1531 (propagated-inputs `(("r-brew" ,r-brew)))
1532 (home-page "https://cran.r-project.org/web/packages/Rook")
1533 (synopsis "Web server interface for R")
1535 "This package contains the Rook specification and convenience software
1536 for building and running Rook applications. A Rook application is an R
1537 reference class object that implements a @code{call} method or an R closure
1538 that takes exactly one argument, an environment, and returns a list with three
1539 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1540 (license license:gpl2)))
1542 (define-public r-miniui
1549 (uri (cran-uri "miniUI" version))
1552 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1553 (properties `((upstream-name . "miniUI")))
1554 (build-system r-build-system)
1556 `(("r-htmltools" ,r-htmltools)
1557 ("r-shiny" ,r-shiny)))
1558 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1559 (synopsis "Shiny UI widgets for small screens")
1561 "This package provides UI widget and layout functions for writing Shiny apps that
1562 work well on small screens.")
1563 (license license:gpl3)))
1565 (define-public r-feather
1572 (uri (cran-uri "feather" version))
1575 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1576 (build-system r-build-system)
1580 ("r-tibble" ,r-tibble)))
1581 (home-page "https://github.com/wesm/feather")
1582 (synopsis "R Bindings to the Feather API")
1583 (description "Read and write feather files, a lightweight binary columnar
1584 data store designed for maximum speed.")
1585 (license license:asl2.0)))
1587 (define-public r-maps
1594 (uri (cran-uri "maps" version))
1597 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1598 (build-system r-build-system)
1599 (home-page "https://cran.r-project.org/web/packages/maps")
1600 (synopsis "Draw geographical maps")
1601 (description "This package provides an R module for display of maps.
1602 Projection code and larger maps are in separate packages (@code{mapproj} and
1604 (license license:gpl2)))
1606 (define-public r-mapproj
1613 (uri (cran-uri "mapproj" version))
1616 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1617 (build-system r-build-system)
1618 (propagated-inputs `(("r-maps" ,r-maps)))
1619 (home-page "https://cran.r-project.org/web/packages/mapproj")
1620 (synopsis "Map projection in R")
1621 (description "This package converts latitude/longitude into projected
1623 (license (list license:gpl2 ; The R interface
1624 (license:non-copyleft ; The C code
1625 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1626 "Lucent Public License Version 1.02")))))
1628 (define-public r-rgooglemaps
1630 (name "r-rgooglemaps")
1635 (uri (cran-uri "RgoogleMaps" version))
1638 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1639 (properties `((upstream-name . "RgoogleMaps")))
1640 (build-system r-build-system)
1644 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1645 (synopsis "Use Google Maps in R")
1646 (description "This package serves two purposes:
1648 @item Provide a comfortable R interface to query the Google server for static
1650 @item Use the map as a background image to overlay plots within R. This
1651 requires proper coordinate scaling.
1653 (license license:gpl2+)))
1655 (define-public r-geosphere
1657 (name "r-geosphere")
1662 (uri (cran-uri "geosphere" version))
1665 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1666 (build-system r-build-system)
1667 (propagated-inputs `(("r-sp" ,r-sp)))
1668 (home-page "https://cran.r-project.org/web/packages/geosphere")
1669 (synopsis "Spherical trigonometry")
1670 (description "This package computes spherical trigonometry for geographic
1671 applications. That is, compute distances and related measures for angular
1672 (longitude/latitude) locations.")
1673 (license license:gpl3+)))
1675 (define-public r-jpeg
1682 (uri (cran-uri "jpeg" version))
1685 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1686 (build-system r-build-system)
1687 (inputs `(("libjpeg" ,libjpeg-turbo)))
1688 (home-page "https://www.rforge.net/jpeg/")
1689 (synopsis "Read and write JPEG images with R")
1690 (description "This package provides a way to read, write and display
1691 bitmap images stored in the JPEG format with R. It can read and write both
1692 files and in-memory raw vectors.")
1693 (license license:gpl2+)))
1695 (define-public r-ggmap
1702 (uri (cran-uri "ggmap" version))
1705 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1706 (build-system r-build-system)
1708 `(("r-bitops" ,r-bitops)
1709 ("r-digest" ,r-digest)
1710 ("r-dplyr" ,r-dplyr)
1711 ("r-ggplot2" ,r-ggplot2)
1715 ("r-magrittr" ,r-magrittr)
1718 ("r-purrr" ,r-purrr)
1719 ("r-rgooglemaps" ,r-rgooglemaps)
1720 ("r-rjson" ,r-rjson)
1721 ("r-scales" ,r-scales)
1722 ("r-stringr" ,r-stringr)
1723 ("r-tibble" ,r-tibble)
1724 ("r-tidyr" ,r-tidyr)))
1725 (home-page "https://github.com/dkahle/ggmap")
1726 (synopsis "Spatial visualization with ggplot2")
1727 (description "This package provides a collection of functions to visualize
1728 spatial data and models on top of static maps from various online sources (e.g
1729 Google Maps and Stamen Maps). It includes tools common to those tasks,
1730 including functions for geolocation and routing.")
1731 (license license:gpl2)))
1733 (define-public r-haven
1740 (uri (cran-uri "haven" version))
1743 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1744 (build-system r-build-system)
1748 `(("r-knitr" ,r-knitr)))
1750 `(("r-forcats" ,r-forcats)
1753 ("r-rlang" ,r-rlang)
1754 ("r-readr" ,r-readr)
1755 ("r-tibble" ,r-tibble)
1756 ("r-tidyselect" ,r-tidyselect)
1757 ("r-vctrs" ,r-vctrs)))
1758 (home-page "https://haven.tidyverse.org")
1759 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1761 "This package lets you mport foreign statistical formats into R via the
1762 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1763 (license license:expat)))
1765 (define-public r-amap
1771 (uri (cran-uri "amap" version))
1774 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1775 (build-system r-build-system)
1777 `(("gfortran" ,gfortran)))
1778 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1779 (synopsis "Another multidimensional analysis package")
1780 (description "This package provides tools for clustering and principal
1781 component analysis (with robust methods, and parallelized functions).")
1782 (license license:gpl2+)))
1784 (define-public r-ape
1791 (uri (cran-uri "ape" version))
1794 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
1795 (build-system r-build-system)
1797 `(("r-lattice" ,r-lattice)
1799 ("r-rcpp" ,r-rcpp)))
1800 (home-page "http://ape-package.ird.fr/")
1801 (synopsis "Analyses of phylogenetics and evolution")
1803 "This package provides functions for reading, writing, plotting, and
1804 manipulating phylogenetic trees, analyses of comparative data in a
1805 phylogenetic framework, ancestral character analyses, analyses of
1806 diversification and macroevolution, computing distances from DNA sequences,
1807 and several other tools.")
1808 (license license:gpl2+)))
1810 (define-public r-abbyyr
1817 (uri (cran-uri "abbyyR" version))
1820 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1821 (properties `((upstream-name . "abbyyR")))
1822 (build-system r-build-system)
1824 `(("r-curl" ,r-curl)
1827 ("r-progress" ,r-progress)
1828 ("r-readr" ,r-readr)
1830 (home-page "https://github.com/soodoku/abbyyR")
1831 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1833 "This package provides tools to get text from images of text using Abbyy
1834 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1835 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1836 passports and get the results in a variety of formats including plain text and
1837 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1838 (license license:expat)))
1840 (define-public r-colorspace
1842 (name "r-colorspace")
1847 (uri (cran-uri "colorspace" version))
1849 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1850 (build-system r-build-system)
1851 (home-page "https://cran.r-project.org/web/packages/colorspace")
1852 (synopsis "Color space manipulation")
1854 "This package carries out a mapping between assorted color spaces
1855 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1856 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1857 colors are provided.")
1858 (license license:bsd-3)))
1860 (define-public r-glue
1867 (uri (cran-uri "glue" version))
1870 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1871 (build-system r-build-system)
1872 ;; knitr depends on glue, so we can't add knitr here to build the
1876 `(("r-knitr" ,r-knitr)))
1877 (home-page "https://github.com/tidyverse/glue")
1878 (synopsis "Interpreted string literals")
1880 "This package provides an implementation of interpreted string literals,
1881 inspired by Python's Literal String Interpolation (PEP-0498) and
1882 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1883 (license license:expat)))
1885 (define-public r-pastecs
1891 (uri (cran-uri "pastecs" version))
1894 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1895 (build-system r-build-system)
1897 `(("r-boot" ,r-boot)))
1898 (home-page "http://www.sciviews.org/pastecs")
1899 (synopsis "Analysis of space-time ecological series")
1901 "This package provides functions for regulation, decomposition and analysis
1902 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1903 initiative to bring PASSTEC 2000 functionalities to R.")
1904 (license license:gpl2+)))
1906 (define-public r-plogr
1913 (uri (cran-uri "plogr" version))
1916 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1917 (build-system r-build-system)
1918 (home-page "https://github.com/krlmlr/plogr")
1919 (synopsis "R bindings for the plog C++ logging library")
1921 "This package provides the header files for a stripped-down version of
1922 the plog header-only C++ logging library, and a method to log to R's standard
1924 (license license:expat)))
1926 (define-public r-pls
1933 (uri (cran-uri "pls" version))
1935 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
1936 (build-system r-build-system)
1937 (home-page "https://mevik.net/work/software/pls.html")
1938 (synopsis "Partial Least Squares and Principal Component Regression")
1940 "The pls package implements multivariate regression methods: Partial Least
1941 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1942 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1945 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1946 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1947 @item multi-response models (or @dfn{PLS2})
1948 @item flexible cross-validation
1949 @item Jackknife variance estimates of regression coefficients
1950 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1951 (R)MSEP, R², and correlation loadings
1952 @item formula interface, modelled after @code{lm()}, with methods for predict,
1953 print, summary, plot, update, etc.
1954 @item extraction functions for coefficients, scores, and loadings
1955 @item MSEP, RMSEP, and R² estimates
1956 @item multiplicative scatter correction (@dfn{MSC})
1958 (license license:gpl2)))
1967 (uri (cran-uri "ps" version))
1969 (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44"))))
1970 (build-system r-build-system)
1971 (home-page "https://ps.r-lib.org")
1972 (synopsis "List, query, and manipulate system processes")
1974 "The ps package implements an API to list, query, and manipulate system
1975 processes. Most of its code is based on the @code{psutil} Python package.")
1976 (license license:bsd-3)))
1978 (define-public r-pkgbuild
1985 (uri (cran-uri "pkgbuild" version))
1987 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
1988 (build-system r-build-system)
1990 `(("r-callr" ,r-callr)
1992 ("r-crayon" ,r-crayon)
1994 ("r-prettyunits" ,r-prettyunits)
1996 ("r-rprojroot" ,r-rprojroot)
1997 ("r-withr" ,r-withr)))
1998 (home-page "https://github.com/r-pkgs/pkgbuild")
1999 (synopsis "Find tools needed to build R packages")
2001 "This package provides functions used to build R packages. It locates
2002 compilers needed to build R packages on various platforms and ensures the PATH
2003 is configured appropriately so R can use them.")
2004 (license license:gpl3)))
2006 (define-public r-pkgload
2013 (uri (cran-uri "pkgload" version))
2016 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2017 (build-system r-build-system)
2020 ("r-crayon" ,r-crayon)
2022 ("r-pkgbuild" ,r-pkgbuild)
2023 ("r-rlang" ,r-rlang)
2024 ("r-rprojroot" ,r-rprojroot)
2025 ("r-rstudioapi" ,r-rstudioapi)
2026 ("r-withr" ,r-withr)))
2027 (home-page "https://github.com/r-lib/pkgload")
2028 (synopsis "Simulate package installation and attach")
2030 "This package simulates the process of installing a package and then
2031 attaching it. This is a key part of the @code{devtools} package as it allows
2032 you to rapidly iterate while developing a package.")
2033 (license license:gpl3)))
2035 (define-public r-rcpp
2042 (uri (cran-uri "Rcpp" version))
2044 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2045 (build-system r-build-system)
2046 (home-page "http://www.rcpp.org")
2047 (synopsis "Seamless R and C++ integration")
2049 "The Rcpp package provides R functions as well as C++ classes which offer
2050 a seamless integration of R and C++. Many R data types and objects can be
2051 mapped back and forth to C++ equivalents which facilitates both writing of new
2052 code as well as easier integration of third-party libraries. Documentation
2053 about Rcpp is provided by several vignettes included in this package, via the
2054 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2055 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2056 @code{citation(\"Rcpp\")} for details on these last two.")
2057 (license license:gpl2+)))
2059 (define-public r-bindr
2066 (uri (cran-uri "bindr" version))
2069 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2070 (build-system r-build-system)
2071 (home-page "https://github.com/krlmlr/bindr")
2072 (synopsis "Parametrized active bindings")
2074 "This package provides a simple interface for creating active bindings
2075 where the bound function accepts additional arguments.")
2076 (license license:expat)))
2078 (define-public r-bindrcpp
2085 (uri (cran-uri "bindrcpp" version))
2088 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2089 (build-system r-build-system)
2091 `(("r-bindr" ,r-bindr)
2092 ("r-plogr" ,r-plogr)
2093 ("r-rcpp" ,r-rcpp)))
2094 (home-page "https://github.com/krlmlr/bindrcpp")
2095 (synopsis "Rcpp interface to active bindings")
2097 "This package provides an easy way to fill an environment with active
2098 bindings that call a C++ function.")
2099 (license license:expat)))
2101 (define-public r-auc
2108 (uri (cran-uri "AUC" version))
2111 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2112 (properties `((upstream-name . "AUC")))
2113 (build-system r-build-system)
2114 (home-page "https://cran.r-project.org/web/packages/AUC")
2115 (synopsis "Compute the area under the curve of selected measures")
2117 "This package includes functions to compute the area under the curve of
2118 selected measures: the area under the sensitivity curve (AUSEC), the area
2119 under the specificity curve (AUSPC), the area under the accuracy
2120 curve (AUACC), and the area under the receiver operating characteristic
2121 curve (AUROC). The curves can also be visualized. Support for partial areas
2123 (license license:gpl2+)))
2125 (define-public r-calibrate
2127 (name "r-calibrate")
2132 (uri (cran-uri "calibrate" version))
2134 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2135 (build-system r-build-system)
2137 `(("r-mass" ,r-mass)))
2138 (home-page "https://cran.r-project.org/web/packages/calibrate")
2139 (synopsis "Calibration of scatterplot and biplot axes")
2141 "This is a package for drawing calibrated scales with tick marks
2142 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2143 (license license:gpl2)))
2145 (define-public r-shape
2152 (uri (cran-uri "shape" version))
2155 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2156 (build-system r-build-system)
2157 (home-page "https://cran.r-project.org/web/packages/shape")
2158 (synopsis "Functions for plotting graphical shapes")
2160 "This package provides functions for plotting graphical shapes such as
2161 ellipses, circles, cylinders, arrows, ...")
2162 (license license:gpl3+)))
2164 (define-public r-globaloptions
2166 (name "r-globaloptions")
2171 (uri (cran-uri "GlobalOptions" version))
2173 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2174 (properties `((upstream-name . "GlobalOptions")))
2175 (build-system r-build-system)
2177 `(("r-knitr" ,r-knitr)))
2178 (home-page "https://github.com/jokergoo/GlobalOptions")
2179 (synopsis "Generate functions to get or set global options")
2181 "This package provides more controls on the option values such as
2182 validation and filtering on the values, making options invisible or private.")
2183 (license license:gpl2+)))
2185 (define-public r-circlize
2192 (uri (cran-uri "circlize" version))
2195 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2196 (build-system r-build-system)
2198 `(("r-colorspace" ,r-colorspace)
2199 ("r-globaloptions" ,r-globaloptions)
2200 ("r-shape" ,r-shape)))
2202 `(("r-knitr" ,r-knitr)))
2203 (home-page "https://github.com/jokergoo/circlize")
2204 (synopsis "Circular visualization")
2206 "Circular layout is an efficient way to visualise huge amounts of
2207 information. This package provides an implementation of circular layout
2208 generation in R as well as an enhancement of available software. Its
2209 flexibility is based on the usage of low-level graphics functions such that
2210 self-defined high-level graphics can be easily implemented by users for
2211 specific purposes. Together with the seamless connection between the powerful
2212 computational and visual environment in R, it gives users more convenience and
2213 freedom to design figures for better understanding complex patterns behind
2214 multi-dimensional data.")
2215 (license license:gpl2+)))
2217 (define-public r-powerlaw
2224 (uri (cran-uri "poweRlaw" version))
2226 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2227 (properties `((upstream-name . "poweRlaw")))
2228 (build-system r-build-system)
2230 `(("r-pracma" ,r-pracma)))
2232 `(("r-knitr" ,r-knitr)))
2233 (home-page "https://github.com/csgillespie/poweRlaw")
2234 (synopsis "Tools for the analysis of heavy tailed distributions")
2236 "This package provides an implementation of maximum likelihood estimators
2237 for a variety of heavy tailed distributions, including both the discrete and
2238 continuous power law distributions. Additionally, a goodness-of-fit based
2239 approach is used to estimate the lower cut-off for the scaling region.")
2240 ;; Any of these GPL versions.
2241 (license (list license:gpl2 license:gpl3))))
2243 (define-public r-compare
2250 (uri (cran-uri "compare" version))
2253 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2254 (build-system r-build-system)
2255 (home-page "https://cran.r-project.org/web/packages/compare")
2256 (synopsis "Comparing objects for differences")
2258 "This package provides functions to compare a model object to a
2259 comparison object. If the objects are not identical, the functions can be
2260 instructed to explore various modifications of the objects (e.g., sorting
2261 rows, dropping names) to see if the modified versions are identical.")
2262 (license license:gpl2+)))
2264 (define-public r-dendextend
2266 (name "r-dendextend")
2271 (uri (cran-uri "dendextend" version))
2274 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2275 (build-system r-build-system)
2277 `(("r-ggplot2" ,r-ggplot2)
2278 ("r-magrittr" ,r-magrittr)
2279 ("r-viridis" ,r-viridis)))
2280 (home-page "https://cran.r-project.org/web/packages/dendextend")
2281 (synopsis "Extending 'dendrogram' functionality in R")
2283 "This package offers a set of functions for extending @code{dendrogram}
2284 objects in R, letting you visualize and compare trees of hierarchical
2285 clusterings. You can adjust a tree's graphical parameters (the color, size,
2286 type, etc of its branches, nodes and labels) and visually and statistically
2287 compare different dendrograms to one another.")
2288 ;; Any of these versions
2289 (license (list license:gpl2 license:gpl3))))
2291 (define-public r-getoptlong
2293 (name "r-getoptlong")
2298 (uri (cran-uri "GetoptLong" version))
2301 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2302 (properties `((upstream-name . "GetoptLong")))
2303 (build-system r-build-system)
2307 `(("r-crayon" ,r-crayon)
2308 ("r-globaloptions" ,r-globaloptions)
2309 ("r-rjson" ,r-rjson)))
2311 `(("r-knitr" ,r-knitr)))
2312 (home-page "https://github.com/jokergoo/GetoptLong")
2313 (synopsis "Parsing command-line arguments and variable interpolation")
2315 "This is yet another command-line argument parser which wraps the
2316 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2317 use in R. It also provides a simple way for variable interpolation in R.")
2318 (license license:gpl2+)))
2320 (define-public r-fastmatch
2322 (name "r-fastmatch")
2327 (uri (cran-uri "fastmatch" version))
2330 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2331 (build-system r-build-system)
2332 (home-page "https://www.rforge.net/fastmatch")
2333 (synopsis "Fast match function")
2335 "This package provides a fast @code{match} replacement for cases that
2336 require repeated look-ups. It is slightly faster that R's built-in
2337 @code{match} function on first match against a table, but extremely fast on
2338 any subsequent lookup as it keeps the hash table in memory.")
2339 (license license:gpl2)))
2348 (uri (cran-uri "ff" version))
2351 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0"))))
2352 (build-system r-build-system)
2353 (propagated-inputs `(("r-bit" ,r-bit)))
2354 (home-page "http://ff.r-forge.r-project.org/")
2355 (synopsis "Memory-efficient storage of large data on disk and access functions")
2357 "This package provides data structures that are stored on disk but
2358 behave (almost) as if they were in RAM by transparently mapping only a section
2360 ;; error Architecture not supported.
2361 (supported-systems (delete "aarch64-linux" %supported-systems))
2362 (license license:gpl2)))
2364 (define-public r-ffbase
2371 (uri (cran-uri "ffbase" version))
2374 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2375 (build-system r-build-system)
2378 ("r-fastmatch" ,r-fastmatch)
2380 (home-page "https://github.com/edwindj/ffbase")
2381 (synopsis "Basic statistical functions for package 'ff'")
2383 "This package extends the out of memory vectors of @code{ff} with
2384 statistical functions and other utilities to ease their usage.")
2385 (license license:gpl3)))
2387 (define-public r-prettyunits
2389 (name "r-prettyunits")
2394 (uri (cran-uri "prettyunits" version))
2397 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2398 (build-system r-build-system)
2399 (home-page "https://github.com/gaborcsardi/prettyunits")
2400 (synopsis "Pretty, human readable formatting of quantities")
2402 "This package provides tools for pretty, human readable formatting of
2404 (license license:expat)))
2406 (define-public r-reshape
2413 (uri (cran-uri "reshape" version))
2416 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2417 (build-system r-build-system)
2419 `(("r-plyr" ,r-plyr)
2420 ("r-rcpp" ,r-rcpp)))
2421 (home-page "http://had.co.nz/reshape")
2422 (synopsis "Flexibly reshape data")
2424 "Flexibly restructure and aggregate data using just two functions:
2425 @code{melt} and @code{cast}. This package provides them.")
2426 (license license:expat)))
2428 (define-public r-progress
2435 (uri (cran-uri "progress" version))
2438 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2439 (build-system r-build-system)
2441 `(("r-crayon" ,r-crayon)
2443 ("r-prettyunits" ,r-prettyunits)
2445 (home-page "https://github.com/gaborcsardi/progress")
2446 (synopsis "Terminal progress bars")
2448 "This package provides configurable progress bars. They may include
2449 percentage, elapsed time, and/or the estimated completion time. They work in
2450 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2451 package also provides a C++ API, that works with or without Rcpp.")
2452 (license license:expat)))
2454 (define-public r-ggally
2461 (uri (cran-uri "GGally" version))
2464 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2465 (properties `((upstream-name . "GGally")))
2466 (build-system r-build-system)
2468 `(("libressl" ,libressl)))
2470 `(("r-ggplot2" ,r-ggplot2)
2471 ("r-gtable" ,r-gtable)
2472 ("r-lifecycle" ,r-lifecycle)
2474 ("r-progress" ,r-progress)
2475 ("r-rcolorbrewer" ,r-rcolorbrewer)
2476 ("r-reshape" ,r-reshape)
2477 ("r-rlang" ,r-rlang)
2478 ("r-scales" ,r-scales)))
2479 (home-page "https://ggobi.github.io/ggally")
2480 (synopsis "Extension to ggplot2")
2482 "The R package ggplot2 is a plotting system based on the grammar of
2483 graphics. GGally extends ggplot2 by adding several functions to reduce the
2484 complexity of combining geometric objects with transformed data. Some of
2485 these functions include a pairwise plot matrix, a two group pairwise plot
2486 matrix, a parallel coordinates plot, a survival plot, and several functions to
2488 (license license:gpl2+)))
2490 (define-public r-proxy
2497 (uri (cran-uri "proxy" version))
2500 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2501 (build-system r-build-system)
2502 (home-page "https://cran.r-project.org/web/packages/proxy")
2503 (synopsis "Distance and similarity measures")
2505 "This package provides an extensible framework for the efficient
2506 calculation of auto- and cross-proximities, along with implementations of the
2507 most popular ones.")
2508 (license license:gpl2)))
2517 (uri (cran-uri "sp" version))
2519 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2520 (build-system r-build-system)
2522 `(("r-lattice" ,r-lattice)))
2523 (home-page "https://cran.r-project.org/web/packages/sp")
2524 (synopsis "Classes and methods for spatial data")
2526 "This package provides classes and methods for spatial data; the classes
2527 document where the spatial location information resides, for 2D or 3D data.
2528 Utility functions are provided, e.g. for plotting data as maps, spatial
2529 selection, as well as methods for retrieving coordinates, for subsetting,
2530 print, summary, etc.")
2531 (license license:gpl2+)))
2533 (define-public r-rmtstat
2540 (uri (cran-uri "RMTstat" version))
2543 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2544 (properties `((upstream-name . "RMTstat")))
2545 (build-system r-build-system)
2546 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2547 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2549 "This package provides functions for working with the Tracy-Widom laws
2550 and other distributions related to the eigenvalues of large Wishart
2552 (license license:bsd-3)))
2554 (define-public r-rmpi
2560 (uri (cran-uri "Rmpi" version))
2563 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2564 (properties `((upstream-name . "Rmpi")))
2565 (build-system r-build-system)
2567 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2568 #:phases (modify-phases %standard-phases
2569 (add-before 'install 'mpi-setup
2572 `(("openmpi" ,openmpi)))
2574 `(("pkg-config" ,pkg-config)))
2575 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2576 (synopsis "R interface to message-passing interface (MPI)")
2578 "This package provides an interface (wrapper) to MPI APIs. It also
2579 provides an interactive R manager and worker environment.")
2580 (license license:gpl2+)))
2582 (define-public r-lmoments
2589 (uri (cran-uri "Lmoments" version))
2592 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2593 (properties `((upstream-name . "Lmoments")))
2594 (build-system r-build-system)
2596 `(("r-rcpp" ,r-rcpp)
2597 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2598 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2599 (synopsis "L-moments and quantile mixtures")
2601 "This package contains functions to estimate L-moments and trimmed
2602 L-moments from the data. It also contains functions to estimate the
2603 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2604 quantile mixture from L-moments and trimmed L-moments.")
2605 (license license:gpl2)))
2607 (define-public r-distillery
2609 (name "r-distillery")
2614 (uri (cran-uri "distillery" version))
2617 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2618 (build-system r-build-system)
2619 (home-page "https://ral.ucar.edu/staff/ericg/")
2620 (synopsis "Functions for confidence intervals and object information")
2622 "This package provides some very simple method functions for confidence
2623 interval calculation and to distill pertinent information from a potentially
2624 complex object; primarily used in common with the packages extRemes and
2626 (license license:gpl2+)))
2628 (define-public r-extremes
2635 (uri (cran-uri "extRemes" version))
2638 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2639 (properties `((upstream-name . "extRemes")))
2640 (build-system r-build-system)
2642 `(("r-distillery" ,r-distillery)
2643 ("r-lmoments" ,r-lmoments)))
2644 (home-page "https://www.assessment.ucar.edu/toolkit/")
2645 (synopsis "Extreme value analysis")
2647 "ExtRemes is a suite of functions for carrying out analyses on the
2648 extreme values of a process of interest; be they block maxima over long blocks
2649 or excesses over a high threshold.")
2650 (license license:gpl2+)))
2652 (define-public r-lmtest
2659 (uri (cran-uri "lmtest" version))
2662 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2663 (build-system r-build-system)
2665 `(("r-zoo" ,r-zoo)))
2667 `(("gfortran" ,gfortran)))
2668 (home-page "https://cran.r-project.org/web/packages/lmtest")
2669 (synopsis "Testing linear regression models")
2671 "This package provides a collection of tests, data sets, and examples for
2672 diagnostic checking in linear regression models. Furthermore, some generic
2673 tools for inference in parametric models are provided.")
2674 ;; Either version is okay
2675 (license (list license:gpl2 license:gpl3))))
2677 (define-public r-idr
2683 (uri (cran-uri "idr" version))
2686 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2687 (build-system r-build-system)
2688 (home-page "https://cran.r-project.org/web/packages/idr/")
2689 (synopsis "Irreproducible discovery rate")
2691 "This is a package for estimating the copula mixture model and plotting
2692 correspondence curves in \"Measuring reproducibility of high-throughput
2693 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2694 by Li, Brown, Huang, and Bickel")
2695 (license license:gpl2+)))
2697 (define-public r-inline
2703 (uri (cran-uri "inline" version))
2706 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2707 (build-system r-build-system)
2708 (home-page "https://cran.r-project.org/web/packages/inline")
2709 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2711 "This package provides functionality to dynamically define R functions
2712 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2713 @code{.Call} calling conventions.")
2714 ;; Any version of the LGPL.
2715 (license license:lgpl3+)))
2717 (define-public r-inum
2723 (uri (cran-uri "inum" version))
2726 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2727 (build-system r-build-system)
2729 `(("r-libcoin" ,r-libcoin)))
2730 (home-page "https://cran.r-project.org/web/packages/inum/")
2731 (synopsis "Interval and enum-type representation of vectors")
2733 "This package provides an enum-type representation of vectors and
2734 representation of intervals, including a method of coercing variables
2736 (license license:gpl2)))
2738 (define-public r-bdsmatrix
2740 (name "r-bdsmatrix")
2745 (uri (cran-uri "bdsmatrix" version))
2748 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2749 (properties `((upstream-name . "bdsmatrix")))
2750 (build-system r-build-system)
2751 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2752 (synopsis "Routines for block diagonal symmetric matrices")
2754 "This package provides procedures to work with block diagonal symmetric
2755 matrices, a special case of sparse matrices.")
2756 (license license:lgpl2.0)))
2758 (define-public r-bbmle
2761 (version "1.0.23.1")
2765 (uri (cran-uri "bbmle" version))
2768 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2769 (build-system r-build-system)
2771 `(("r-bdsmatrix" ,r-bdsmatrix)
2772 ("r-lattice" ,r-lattice)
2774 ("r-matrix" ,r-matrix)
2775 ("r-mvtnorm" ,r-mvtnorm)
2776 ("r-numderiv" ,r-numderiv)))
2777 (home-page "https://cran.r-project.org/web/packages/bbmle")
2778 (synopsis "Tools for General Maximum Likelihood Estimation")
2780 "This package provides methods and functions for fitting maximum
2781 likelihood models in R. This package modifies and extends the @code{mle}
2782 classes in the @code{stats4} package.")
2783 ;; Any version of the GPL
2784 (license license:gpl2+)))
2786 (define-public r-emdbook
2793 (uri (cran-uri "emdbook" version))
2796 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2797 (build-system r-build-system)
2799 `(("r-bbmle" ,r-bbmle)
2801 ("r-lattice" ,r-lattice)
2803 ("r-plyr" ,r-plyr)))
2804 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2805 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2807 "This package provides auxiliary functions and data sets for \"Ecological
2808 Models and Data\", a book presenting maximum likelihood estimation and related
2809 topics for ecologists (ISBN 978-0-691-12522-0).")
2811 (license (list license:gpl2 license:gpl3))))
2813 (define-public r-lpsolve
2820 (uri (cran-uri "lpSolve" version))
2823 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2824 (properties `((upstream-name . "lpSolve")))
2825 (build-system r-build-system)
2826 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2827 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2829 "Lp_solve is software for solving linear, integer and mixed integer
2830 programs. This implementation supplies a \"wrapper\" function in C and some R
2831 functions that solve general linear/integer problems, assignment problems, and
2832 transportation problems.")
2833 (license license:lgpl2.0)))
2835 (define-public r-limsolve
2842 (uri (cran-uri "limSolve" version))
2845 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2846 (properties `((upstream-name . "limSolve")))
2847 (build-system r-build-system)
2849 `(("r-lpsolve" ,r-lpsolve)
2851 ("r-quadprog" ,r-quadprog)))
2852 (native-inputs `(("gfortran" ,gfortran)))
2853 (home-page "https://cran.r-project.org/web/packages/limSolve")
2854 (synopsis "Solving linear inverse models")
2856 "This package provides functions that:
2859 @item find the minimum/maximum of a linear or quadratic function,
2860 @item sample an underdetermined or overdetermined system,
2861 @item solve a linear system Ax=B for the unknown x.
2864 It includes banded and tridiagonal linear systems. The package calls Fortran
2865 functions from LINPACK.")
2867 (license (list license:gpl2+ license:gpl3+))))
2869 (define-public r-fitdistrplus
2871 (name "r-fitdistrplus")
2876 (uri (cran-uri "fitdistrplus" version))
2879 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2880 (build-system r-build-system)
2882 `(("r-mass" ,r-mass)
2883 ("r-survival" ,r-survival)))
2885 `(("r-knitr" ,r-knitr)))
2886 (home-page "http://riskassessment.r-forge.r-project.org")
2887 (synopsis "Fitting a parametric distribution from data")
2889 "This package extends the @code{fitdistr} function of the MASS package
2890 with several functions to help the fit of a parametric distribution to
2891 non-censored or censored data. Censored data may contain left-censored,
2892 right-censored and interval-censored values, with several lower and upper
2893 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2894 provides moment matching (MME), quantile matching (QME) and maximum
2895 goodness-of-fit estimation (MGE) methods (available only for non-censored
2896 data). Weighted versions of MLE, MME and QME are available.")
2897 (license license:gpl2+)))
2899 (define-public r-energy
2906 (uri (cran-uri "energy" version))
2909 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2910 (build-system r-build-system)
2912 `(("r-boot" ,r-boot)
2913 ("r-rcpp" ,r-rcpp)))
2914 (home-page "https://cran.r-project.org/web/packages/energy")
2915 (synopsis "Multivariate inference via the energy of data")
2917 "This package provides e-statistics (energy) tests and statistics for
2918 multivariate and univariate inference, including distance correlation,
2919 one-sample, two-sample, and multi-sample tests for comparing multivariate
2920 distributions, are implemented. Measuring and testing multivariate
2921 independence based on distance correlation, partial distance correlation,
2922 multivariate goodness-of-fit tests, clustering based on energy distance,
2923 testing for multivariate normality, distance components (disco) for
2924 non-parametric analysis of structured data, and other energy
2925 statistics/methods are implemented.")
2926 (license license:gpl2+)))
2928 (define-public r-suppdists
2930 (name "r-suppdists")
2935 (uri (cran-uri "SuppDists" version))
2938 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2939 (properties `((upstream-name . "SuppDists")))
2940 (build-system r-build-system)
2941 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2942 (synopsis "Supplementary distributions")
2944 "This package provides ten distributions supplementing those built into
2945 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2946 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2947 coefficient, Johnson distributions, normal scores and generalized
2948 hypergeometric distributions. In addition two random number generators of
2949 George Marsaglia are included.")
2950 (license license:gpl2+)))
2952 (define-public r-ksamples
2959 (uri (cran-uri "kSamples" version))
2962 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2963 (properties `((upstream-name . "kSamples")))
2964 (build-system r-build-system)
2966 `(("r-suppdists" ,r-suppdists)))
2967 (home-page "https://cran.r-project.org/web/packages/kSamples")
2968 (synopsis "K-Sample rank tests and their combinations")
2970 "This package provides tools to compares k samples using the
2971 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2972 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2973 test. It computes asymptotic, simulated or (limited) exact P-values, all
2974 valid under randomization, with or without ties, or conditionally under random
2975 sampling from populations, given the observed tie pattern. Except for Steel's
2976 test and the JT test it also combines these tests across several blocks of
2978 (license license:gpl2+)))
2980 (define-public r-cvst
2987 (uri (cran-uri "CVST" version))
2990 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2991 (properties `((upstream-name . "CVST")))
2992 (build-system r-build-system)
2994 `(("r-kernlab" ,r-kernlab)
2995 ("r-matrix" ,r-matrix)))
2996 (home-page "https://cran.r-project.org/web/packages/CVST")
2997 (synopsis "Fast cross-validation via sequential testing")
2999 "This package implements the fast cross-validation via sequential
3000 testing (CVST) procedure. CVST is an improved cross-validation procedure
3001 which uses non-parametric testing coupled with sequential analysis to
3002 determine the best parameter set on linearly increasing subsets of the data.
3003 Additionally to the CVST the package contains an implementation of the
3004 ordinary k-fold cross-validation with a flexible and powerful set of helper
3005 objects and methods to handle the overall model selection process. The
3006 implementations of the Cochran's Q test with permutations and the sequential
3007 testing framework of Wald are generic and can therefore also be used in other
3009 (license license:gpl2+)))
3011 (define-public r-squarem
3018 (uri (cran-uri "SQUAREM" version))
3021 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
3022 (properties `((upstream-name . "SQUAREM")))
3023 (build-system r-build-system)
3024 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3025 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3027 "This package provides algorithms for accelerating the convergence of
3028 slow, monotone sequences from smooth, contraction mapping such as the EM
3029 algorithm. It can be used to accelerate any smooth, linearly convergent
3030 acceleration scheme. A tutorial style introduction to this package is
3031 available in a vignette.")
3032 (license license:gpl2+)))
3034 (define-public r-lava
3041 (uri (cran-uri "lava" version))
3044 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3045 (build-system r-build-system)
3047 `(("r-numderiv" ,r-numderiv)
3048 ("r-squarem" ,r-squarem)
3049 ("r-survival" ,r-survival)))
3050 (home-page "https://github.com/kkholst/lava")
3051 (synopsis "Latent variable models")
3053 "This package provides tools for the estimation and simulation of latent
3055 (license license:gpl3)))
3057 (define-public r-drr
3064 (uri (cran-uri "DRR" version))
3067 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3068 (properties `((upstream-name . "DRR")))
3069 (build-system r-build-system)
3071 `(("r-cvst" ,r-cvst)
3072 ("r-kernlab" ,r-kernlab)
3073 ("r-matrix" ,r-matrix)))
3074 (home-page "https://cran.r-project.org/web/packages/DRR")
3075 (synopsis "Dimensionality reduction via regression")
3077 "This package provides an implementation of dimensionality reduction via
3078 regression using Kernel Ridge Regression.")
3079 (license license:gpl3)))
3081 (define-public r-prodlim
3084 (version "2019.11.13")
3088 (uri (cran-uri "prodlim" version))
3091 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3092 (build-system r-build-system)
3094 `(("r-kernsmooth" ,r-kernsmooth)
3097 ("r-survival" ,r-survival)))
3098 (home-page "https://cran.r-project.org/web/packages/prodlim")
3099 (synopsis "Product-limit estimation for censored event history analysis")
3101 "This package provides a fast and user-friendly implementation of
3102 nonparametric estimators for censored event history (survival) analysis with
3103 the Kaplan-Meier and Aalen-Johansen methods.")
3104 (license license:gpl2+)))
3106 (define-public r-dimred
3113 (uri (cran-uri "dimRed" version))
3116 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3117 (properties `((upstream-name . "dimRed")))
3118 (build-system r-build-system)
3121 ("r-magrittr" ,r-magrittr)))
3122 (home-page "https://github.com/gdkrmr/dimRed")
3123 (synopsis "Framework for dimensionality reduction")
3125 "This package provides a collection of dimensionality reduction
3126 techniques from R packages and provides a common interface for calling the
3128 (license license:gpl3)))
3130 (define-public r-timedate
3133 (version "3043.102")
3137 (uri (cran-uri "timeDate" version))
3140 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3141 (properties `((upstream-name . "timeDate")))
3142 (build-system r-build-system)
3143 (home-page "https://www.rmetrics.org")
3144 (synopsis "Chronological and calendar objects")
3146 "This package provides an environment for teaching \"Financial
3147 Engineering and Computational Finance\" and for managing chronological and
3149 (license license:gpl2+)))
3151 (define-public r-magic
3158 (uri (cran-uri "magic" version))
3161 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3162 (build-system r-build-system)
3164 `(("r-abind" ,r-abind)))
3165 (home-page "https://github.com/RobinHankin/magic.git")
3166 (synopsis "Create and investigate magic squares")
3168 "This package provides a collection of efficient, vectorized algorithms
3169 for the creation and investigation of magic squares and hypercubes, including
3170 a variety of functions for the manipulation and analysis of arbitrarily
3171 dimensioned arrays.")
3172 (license license:gpl2)))
3174 (define-public r-rmysql
3181 (uri (cran-uri "RMySQL" version))
3184 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3185 (properties `((upstream-name . "RMySQL")))
3186 (build-system r-build-system)
3188 `(("mariadb" ,mariadb "lib")
3189 ("mariadb-dev" ,mariadb "dev")
3192 `(("r-dbi" ,r-dbi)))
3193 (home-page "https://github.com/r-dbi/RMySQL")
3194 (synopsis "Database interface and MySQL driver for R")
3196 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3197 package contains an old implementation based on legacy code from S-PLUS which
3198 is being phased out. A modern MySQL client based on Rcpp is available from
3199 the RMariaDB package.")
3200 (license license:gpl2)))
3202 (define-public r-rpostgresql
3204 (name "r-rpostgresql")
3209 (uri (cran-uri "RPostgreSQL" version))
3212 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3213 (properties `((upstream-name . "RPostgreSQL")))
3214 (build-system r-build-system)
3216 `(("postgresql" ,postgresql)))
3218 `(("r-dbi" ,r-dbi)))
3219 (home-page "https://github.com/tomoakin/RPostgreSQL")
3220 (synopsis "R interface to the PostgreSQL database system")
3222 "This package provides a Database Interface (DBI) compliant driver for R
3223 to access PostgreSQL database systems.")
3224 ;; The whole package is released under GPL version 2. It includes code
3225 ;; under the PostgreSQL license.
3226 (license license:gpl2)))
3228 (define-public r-linprog
3235 (uri (cran-uri "linprog" version))
3238 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3239 (build-system r-build-system)
3240 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3241 (home-page "http://linprog.r-forge.r-project.org/")
3242 (synopsis "Linear programming and optimization")
3244 "This package can be used to solve Linear Programming / Linear
3245 Optimization problems by using the simplex algorithm.")
3246 (license license:gpl2+)))
3248 (define-public r-geometry
3255 (uri (cran-uri "geometry" version))
3258 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3259 (build-system r-build-system)
3261 `(("r-magic" ,r-magic)
3262 ("r-linprog" ,r-linprog)
3263 ("r-lpsolve" ,r-lpsolve)
3265 ("r-rcppprogress" ,r-rcppprogress)))
3266 (home-page "http://geometry.r-forge.r-project.org/")
3267 (synopsis "Mesh generation and surface tesselation")
3269 "This package makes the qhull library available in R, in a similar manner
3270 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3271 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3272 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3273 and higher dimensions. It implements the Quickhull algorithm for computing
3274 the convex hull. Qhull does not support constrained Delaunay triangulations,
3275 or mesh generation of non-convex objects, but the package does include some R
3276 functions that allow for this. Currently the package only gives access to
3277 Delaunay triangulation and convex hull computation.")
3278 ;; The Qhull sources are included and are distributed under a custom
3279 ;; non-copyleft license. The R sources are released under GPL version 2.
3280 (license (list license:gpl2
3281 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3283 (define-public r-ddalpha
3290 (uri (cran-uri "ddalpha" version))
3293 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3294 (build-system r-build-system)
3297 ("r-class" ,r-class)
3298 ("r-geometry" ,r-geometry)
3301 ("r-robustbase" ,r-robustbase)
3302 ("r-sfsmisc" ,r-sfsmisc)))
3304 `(("gfortran" ,gfortran)))
3305 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3306 (synopsis "Depth-Based classification and calculation of data depth")
3308 "This package contains procedures for depth-based supervised learning,
3309 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3310 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3311 statistical depth function to a compact low-dimensional space, where the final
3312 classification is done. It also offers an extension to functional data and
3313 routines for calculating certain notions of statistical depth functions. 50
3314 multivariate and 5 functional classification problems are included.")
3315 (license license:gpl2)))
3317 (define-public r-gower
3324 (uri (cran-uri "gower" version))
3327 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3328 (build-system r-build-system)
3329 (home-page "https://github.com/markvanderloo/gower")
3330 (synopsis "Gower's distance")
3332 "This package provides tools to compute Gower's distance (or similarity)
3333 coefficient between records, and to compute the top-n matches between records.
3334 Core algorithms are executed in parallel on systems supporting OpenMP.")
3335 (license license:gpl3)))
3337 (define-public r-rcpproll
3344 (uri (cran-uri "RcppRoll" version))
3347 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3348 (properties `((upstream-name . "RcppRoll")))
3349 (build-system r-build-system)
3351 `(("r-rcpp" ,r-rcpp)))
3352 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3353 (synopsis "Efficient rolling and windowed operations")
3355 "This package provides fast and efficient routines for common rolling /
3356 windowed operations. Routines for the efficient computation of windowed mean,
3357 median, sum, product, minimum, maximum, standard deviation and variance are
3359 (license license:gpl2+)))
3361 (define-public r-ipred
3368 (uri (cran-uri "ipred" version))
3371 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3372 (build-system r-build-system)
3374 `(("r-class" ,r-class)
3377 ("r-prodlim" ,r-prodlim)
3378 ("r-rpart" ,r-rpart)
3379 ("r-survival" ,r-survival)))
3380 (home-page "https://cran.r-project.org/web/packages/ipred")
3381 (synopsis "Improved predictors")
3383 "This package provides improved predictive models by indirect
3384 classification and bagging for classification, regression and survival
3385 problems as well as resampling based estimators of prediction error.")
3386 (license license:gpl2+)))
3388 (define-public r-psych
3395 (uri (cran-uri "psych" version))
3398 "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
3399 (build-system r-build-system)
3401 `(("r-lattice" ,r-lattice)
3402 ("r-mnormt" ,r-mnormt)
3403 ("r-nlme" ,r-nlme)))
3404 (home-page "https://cran.r-project.org/web/packages/psych/")
3405 (synopsis "Procedures for psychological, psychometric, and personality research")
3407 "This package provides a general purpose toolbox for personality,
3408 psychometric theory and experimental psychology. Functions are primarily for
3409 multivariate analysis and scale construction using factor analysis, principal
3410 component analysis, cluster analysis and reliability analysis, although others
3411 provide basic descriptive statistics. Item Response Theory is done using
3412 factor analysis of tetrachoric and polychoric correlations. Functions for
3413 analyzing data at multiple levels include within and between group statistics,
3414 including correlations and factor analysis. Functions for simulating and
3415 testing particular item and test structures are included. Several functions
3416 serve as a useful front end for structural equation modeling. Graphical
3417 displays of path diagrams, factor analysis and structural equation models are
3418 created using basic graphics.")
3419 (license license:gpl2+)))
3421 (define-public r-generics
3428 (uri (cran-uri "generics" version))
3431 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3432 (build-system r-build-system)
3433 (home-page "https://github.com/r-lib/generics")
3434 (synopsis "Common S3 generics not provided by base R methods")
3436 "In order to reduce potential package dependencies and conflicts,
3437 generics provides a number of commonly used S3 generics that are not provided
3438 by base R methods related to model fitting.")
3439 (license license:gpl2)))
3441 (define-public r-broom
3448 (uri (cran-uri "broom" version))
3451 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3452 (build-system r-build-system)
3454 `(("r-backports" ,r-backports)
3455 ("r-dplyr" ,r-dplyr)
3456 ("r-ellipsis" ,r-ellipsis)
3457 ("r-generics" ,r-generics)
3459 ("r-purrr" ,r-purrr)
3460 ("r-rlang" ,r-rlang)
3461 ("r-stringr" ,r-stringr)
3462 ("r-tibble" ,r-tibble)
3463 ("r-tidyr" ,r-tidyr)))
3465 `(("r-knitr" ,r-knitr)))
3466 (home-page "https://github.com/tidyverse/broom")
3467 (synopsis "Convert statistical analysis objects into tidy data frames")
3469 "This package provides tools to convert statistical analysis objects from
3470 R into tidy data frames, so that they can more easily be combined, reshaped
3471 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3472 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3473 summarizes a model's statistical findings such as coefficients of a
3474 regression; @code{augment}, which adds columns to the original data such as
3475 predictions, residuals and cluster assignments; and @code{glance}, which
3476 provides a one-row summary of model-level statistics.")
3477 (license license:expat)))
3479 (define-public r-recipes
3486 (uri (cran-uri "recipes" version))
3489 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3490 (build-system r-build-system)
3492 `(("r-dplyr" ,r-dplyr)
3493 ("r-generics" ,r-generics)
3495 ("r-gower" ,r-gower)
3496 ("r-ipred" ,r-ipred)
3497 ("r-lifecycle" ,r-lifecycle)
3498 ("r-lubridate" ,r-lubridate)
3499 ("r-magrittr" ,r-magrittr)
3500 ("r-matrix" ,r-matrix)
3501 ("r-purrr" ,r-purrr)
3502 ("r-rlang" ,r-rlang)
3503 ("r-tibble" ,r-tibble)
3504 ("r-tidyr" ,r-tidyr)
3505 ("r-tidyselect" ,r-tidyselect)
3506 ("r-timedate" ,r-timedate)
3507 ("r-withr" ,r-withr)))
3509 `(("r-knitr" ,r-knitr)))
3510 (home-page "https://github.com/topepo/recipes")
3511 (synopsis "Preprocessing tools to create design matrices")
3513 "Recipes is an extensible framework to create and preprocess design
3514 matrices. Recipes consist of one or more data manipulation and analysis
3515 \"steps\". Statistical parameters for the steps can be estimated from an
3516 initial data set and then applied to other data sets. The resulting design
3517 matrices can then be used as inputs into statistical or machine learning
3519 (license license:gpl2)))
3521 (define-public r-pdist
3528 (uri (cran-uri "pdist" version))
3531 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3532 (build-system r-build-system)
3533 (home-page "https://github.com/jeffwong/pdist")
3534 (synopsis "Partitioned distance function")
3536 "Pdist computes the euclidean distance between rows of a matrix X and
3537 rows of another matrix Y. Previously, this could be done by binding the two
3538 matrices together and calling @code{dist}, but this creates unnecessary
3539 computation by computing the distances between a row of X and another row of
3540 X, and likewise for Y. Pdist strictly computes distances across the two
3541 matrices, not within the same matrix, making computations significantly faster
3542 for certain use cases.")
3543 (license license:gpl3+)))
3545 (define-public r-ggrepel
3552 (uri (cran-uri "ggrepel" version))
3555 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3556 (build-system r-build-system)
3558 `(("r-ggplot2" ,r-ggplot2)
3560 ("r-scales" ,r-scales)))
3562 `(("r-knitr" ,r-knitr))) ; for vignettes
3563 (home-page "https://github.com/slowkow/ggrepel")
3564 (synopsis "Repulsive text and label geometries for ggplot2")
3566 "This package provides text and label geometries for ggplot2 that help to
3567 avoid overlapping text labels. Labels repel away from each other and away
3568 from the data points.")
3569 (license license:gpl3)))
3571 (define-public r-corrplot
3578 (uri (cran-uri "corrplot" version))
3581 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3582 (build-system r-build-system)
3583 (home-page "https://github.com/taiyun/corrplot")
3584 (synopsis "Visualization of a correlation matrix")
3586 "This package provides a graphical display of a correlation matrix or
3587 general matrix. It also contains some algorithms to do matrix reordering. In
3588 addition, corrplot is good at details, including choosing color, text labels,
3589 color labels, layout, etc.")
3590 ;; Any version of the GPL
3591 (license license:gpl2+)))
3593 (define-public r-stringdist
3595 (name "r-stringdist")
3600 (uri (cran-uri "stringdist" version))
3602 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb"))))
3603 (build-system r-build-system)
3604 (home-page "https://github.com/markvanderloo/stringdist")
3605 (synopsis "Approximate string matching and string distance functions")
3607 "This package implements an approximate string matching version of R's
3608 native @code{match} function. It can calculate various string distances based
3609 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3610 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3611 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3612 can be computed between character vectors while taking proper care of encoding
3613 or between integer vectors representing generic sequences.")
3614 (license license:gpl3+)))
3616 (define-public r-ucminf
3623 (uri (cran-uri "ucminf" version))
3626 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3627 (build-system r-build-system)
3628 (native-inputs `(("gfortran" ,gfortran)))
3629 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3630 (synopsis "General-purpose unconstrained non-linear optimization")
3632 "This package provides an implementation of an algorithm for
3633 general-purpose unconstrained non-linear optimization. The algorithm is of
3634 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3635 search with a trust region type monitoring of the input to the line search
3636 algorithm. The interface of @code{ucminf} is designed for easy interchange
3637 with the package @code{optim}.")
3638 (license license:gpl2+)))
3640 (define-public r-ordinal
3643 (version "2019.12-10")
3647 (uri (cran-uri "ordinal" version))
3650 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3651 (build-system r-build-system)
3653 `(("r-mass" ,r-mass)
3654 ("r-matrix" ,r-matrix)
3655 ("r-numderiv" ,r-numderiv)
3656 ("r-ucminf" ,r-ucminf)))
3657 (home-page "https://github.com/runehaubo/ordinal")
3658 (synopsis "Regression models for ordinal data")
3660 "This package provides an implementation of cumulative link (mixed)
3661 models also known as ordered regression models, proportional odds models,
3662 proportional hazards models for grouped survival times and ordered models.
3663 Estimation is via maximum likelihood and mixed models are fitted with the
3664 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3665 (license license:gpl2+)))
3667 (define-public r-jomo
3674 (uri (cran-uri "jomo" version))
3677 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3678 (build-system r-build-system)
3680 `(("r-lme4" ,r-lme4)
3682 ("r-ordinal" ,r-ordinal)
3683 ("r-survival" ,r-survival)))
3684 (home-page "https://cran.r-project.org/web/packages/jomo/")
3685 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3687 "Similarly to Schafer's package pan, jomo is a package for multilevel
3688 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3689 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3690 possibility of handling binary and categorical data through latent normal
3691 variables, the option to use cluster-specific covariance matrices and to
3692 impute compatibly with the substantive model.")
3693 (license license:gpl2)))
3695 (define-public r-pan
3702 (uri (cran-uri "pan" version))
3705 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3706 (build-system r-build-system)
3707 (native-inputs `(("gfortran" ,gfortran)))
3708 (home-page "https://cran.r-project.org/web/packages/pan/")
3709 (synopsis "Multiple imputation for multivariate panel or clustered data")
3711 "This package implements multiple imputation for multivariate panel or
3713 (license license:gpl3)))
3715 (define-public r-mitml
3722 (uri (cran-uri "mitml" version))
3725 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3726 (build-system r-build-system)
3728 `(("r-haven" ,r-haven)
3731 (home-page "https://cran.r-project.org/web/packages/mitml/")
3732 (synopsis "Tools for multiple imputation in multilevel modeling")
3734 "This package provides tools for multiple imputation of missing data in
3735 multilevel modeling. It includes a user-friendly interface to the packages
3736 pan and jomo, and several functions for visualization, data management and the
3737 analysis of multiply imputed data sets.")
3738 (license license:gpl2+)))
3740 (define-public r-mice
3747 (uri (cran-uri "mice" version))
3750 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3751 (build-system r-build-system)
3753 `(("r-broom" ,r-broom)
3754 ("r-dplyr" ,r-dplyr)
3755 ("r-generics" ,r-generics)
3756 ("r-lattice" ,r-lattice)
3758 ("r-tidyr" ,r-tidyr)))
3759 (home-page "https://cran.r-project.org/web/packages/mice/")
3760 (synopsis "Multivariate imputation by chained equations")
3762 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3763 implemented by the MICE algorithm as described in @url{Van Buuren and
3764 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3765 variable has its own imputation model. Built-in imputation models are
3766 provided for continuous data (predictive mean matching, normal), binary
3767 data (logistic regression), unordered categorical data (polytomous logistic
3768 regression) and ordered categorical data (proportional odds). MICE can also
3769 impute continuous two-level data (normal model, pan, second-level variables).
3770 Passive imputation can be used to maintain consistency between variables.
3771 Various diagnostic plots are available to inspect the quality of the
3773 ;; Any of these two versions.
3774 (license (list license:gpl2 license:gpl3))))
3776 (define-public r-truncnorm
3778 (name "r-truncnorm")
3783 (uri (cran-uri "truncnorm" version))
3786 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3787 (build-system r-build-system)
3788 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3789 (synopsis "Truncated normal distribution")
3790 (description "This package provides functions for the truncated normal
3791 distribution with mean equal to @code{mean} and standard deviation equal to
3792 @code{sd}. It includes density, distribution, quantile, and expected value
3793 functions, as well as a random generation function.")
3794 (license license:gpl2)))
3796 (define-public r-rsolnp
3803 (uri (cran-uri "Rsolnp" version))
3806 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3807 (properties `((upstream-name . "Rsolnp")))
3808 (build-system r-build-system)
3810 `(("r-truncnorm" ,r-truncnorm)))
3811 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3812 (synopsis "General non-linear optimization")
3813 (description "The Rsolnp package implements a general non-linear augmented
3814 Lagrange multiplier method solver, a @dfn{sequential quadratic
3815 programming} (SQP) based solver).")
3816 ;; Any version of the GPL.
3817 (license license:gpl2+)))
3819 (define-public r-hardyweinberg
3821 (name "r-hardyweinberg")
3826 (uri (cran-uri "HardyWeinberg" version))
3829 "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh"))))
3830 (properties `((upstream-name . "HardyWeinberg")))
3831 (build-system r-build-system)
3833 `(("r-mice" ,r-mice)
3835 ("r-rsolnp" ,r-rsolnp)))
3836 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3837 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3839 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3840 diallelic genetic marker data. All classical tests (chi-square, exact,
3841 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3842 included in the package, as well as functions for power computation and for
3843 the simulation of marker data under equilibrium and disequilibrium. Routines
3844 for dealing with markers on the X-chromosome are included. Functions for
3845 testing equilibrium in the presence of missing data by using multiple
3846 imputation are also provided. Implements several graphics for exploring the
3847 equilibrium status of a large set of diallelic markers: ternary plots with
3848 acceptance regions, log-ratio plots and Q-Q plots.")
3849 (license license:gpl2+)))
3858 (uri (cran-uri "sm" version))
3861 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3862 (build-system r-build-system)
3863 (native-inputs `(("gfortran" ,gfortran)))
3864 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3865 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3867 "This is software accompanying the book 'Applied Smoothing Techniques for
3868 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3869 University Press. It provides smoothing methods for nonparametric regression
3870 and density estimation")
3871 (license license:gpl2+)))
3873 (define-public r-venndiagram
3875 (name "r-venndiagram")
3879 (uri (cran-uri "VennDiagram" version))
3882 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3883 (properties `((upstream-name . "VennDiagram")))
3884 (build-system r-build-system)
3886 `(("r-futile-logger" ,r-futile-logger)))
3887 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3888 (synopsis "Generate High-Resolution Venn and Euler Plots")
3890 "This package provides a set of functions to generate high-resolution
3891 Venn and Euler plots. It includes handling for several special cases,
3892 including two-case scaling, and extensive customization of plot shape and
3894 (license license:gpl2+)))
3896 (define-public r-vioplot
3903 (uri (cran-uri "vioplot" version))
3906 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3907 (build-system r-build-system)
3912 `(("r-knitr" ,r-knitr)))
3913 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3914 (synopsis "Violin plot")
3916 "This package provides a violin plot, which is a combination of a box
3917 plot and a kernel density plot.")
3918 (license license:bsd-3)))
3920 (define-public r-rsofia
3926 ;; This package has been removed from CRAN, so we can
3927 ;; only fetch it from the archives.
3928 (uri (string-append "https://cran.r-project.org/src/"
3929 "contrib/Archive/RSofia/RSofia_"
3933 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3934 (properties `((upstream-name . "RSofia")))
3935 (build-system r-build-system)
3937 `(("r-rcpp" ,r-rcpp)))
3938 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3939 (synopsis "Port of sofia-ml to R")
3940 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3941 suite of fast incremental algorithms for machine learning that can be used for
3942 training models for classification or ranking.")
3943 (license license:asl2.0)))
3945 (define-public r-xts
3952 (uri (cran-uri "xts" version))
3955 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3956 (build-system r-build-system)
3957 (propagated-inputs `(("r-zoo" ,r-zoo)))
3958 (home-page "https://github.com/joshuaulrich/xts")
3959 (synopsis "Extensible time series")
3961 "This package provides for uniform handling of R's different time-based
3962 data classes by extending @code{zoo}, maximizing native format information
3963 preservation and allowing for user-level customization and extension, while
3964 simplifying cross-class interoperability.")
3965 (license license:gpl2+)))
3967 (define-public r-performanceanalytics
3969 (name "r-performanceanalytics")
3974 (uri (cran-uri "PerformanceAnalytics" version))
3977 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3979 `((upstream-name . "PerformanceAnalytics")))
3980 (build-system r-build-system)
3982 `(("r-quadprog" ,r-quadprog)
3985 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3986 (synopsis "Econometric tools for performance and risk analysis")
3987 (description "This is a collection of econometric functions for
3988 performance and risk analysis. This package aims to aid practitioners and
3989 researchers in utilizing the latest research in analysis of non-normal return
3990 streams. In general, it is most tested on return (rather than price) data on
3991 a regular scale, but most functions will work with irregular return data as
3992 well, and increasing numbers of functions will work with P&L or price data
3994 ;; Either version may be picked.
3995 (license (list license:gpl2 license:gpl3))))
3997 (define-public r-laeken
4004 (uri (cran-uri "laeken" version))
4007 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4008 (build-system r-build-system)
4010 `(("r-boot" ,r-boot)
4011 ("r-mass" ,r-mass)))
4012 (home-page "https://cran.r-project.org/web/packages/laeken/")
4013 (synopsis "Estimation of indicators on social exclusion and poverty")
4014 (description "This package provides tools for the estimation of indicators
4015 on social exclusion and poverty, as well as an implementation of Pareto tail
4016 modeling for empirical income distributions.")
4017 (license license:gpl2+)))
4019 (define-public r-vcd
4026 (uri (cran-uri "vcd" version))
4029 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4030 (build-system r-build-system)
4032 `(("r-colorspace" ,r-colorspace)
4033 ("r-lmtest" ,r-lmtest)
4034 ("r-mass" ,r-mass)))
4035 (home-page "https://cran.r-project.org/web/packages/vcd/")
4036 (synopsis "Visualizing categorical data")
4037 (description "This package provides visualization techniques, data sets,
4038 summary and inference procedures aimed particularly at categorical data.
4039 Special emphasis is given to highly extensible grid graphics. The package was
4040 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4041 Friendly and is now the main support package for a new book, \"Discrete Data
4042 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4043 (license license:gpl2)))
4045 (define-public r-ica
4052 (uri (cran-uri "ica" version))
4055 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4056 (build-system r-build-system)
4057 (home-page "https://cran.r-project.org/web/packages/ica/")
4058 (synopsis "Independent component analysis")
4059 (description "This package provides tools for @dfn{Independent Component
4060 Analysis} (ICA) using various algorithms: FastICA,
4061 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4062 of Eigenmatrices} (JADE).")
4063 (license license:gpl2+)))
4065 (define-public r-dtw
4072 (uri (cran-uri "dtw" version))
4075 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4076 (build-system r-build-system)
4077 (propagated-inputs `(("r-proxy" ,r-proxy)))
4078 (home-page "http://dtw.r-forge.r-project.org/")
4079 (synopsis "Dynamic Time Warping Algorithms")
4080 (description "This package provides a comprehensive implementation of
4081 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4082 optimal (least cumulative distance) alignment between points of two time
4083 series. Common DTW variants covered include local (slope) and global (window)
4084 constraints, subsequence matches, arbitrary distance definitions,
4085 normalizations, minimum variance matching, and so on.")
4086 (license license:gpl2+)))
4088 (define-public r-sdmtools
4091 (version "1.1-221.2")
4095 (uri (cran-uri "SDMTools" version))
4098 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4099 (properties `((upstream-name . "SDMTools")))
4100 (build-system r-build-system)
4101 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4102 (home-page "https://www.rforge.net/SDMTools/")
4103 (synopsis "Species distribution modelling tools")
4104 (description "This package provides a set of tools for post processing
4105 the outcomes of species distribution modeling exercises. It includes novel
4106 methods for comparing models and tracking changes in distributions through
4107 time. It further includes methods for visualizing outcomes, selecting
4108 thresholds, calculating measures of accuracy and landscape fragmentation
4110 (license license:gpl3+)))
4112 (define-public r-scatterplot3d
4114 (name "r-scatterplot3d")
4119 (uri (cran-uri "scatterplot3d" version))
4122 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4123 (build-system r-build-system)
4124 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4125 (synopsis "3D scatter plot")
4126 (description "This package provides an implementation of scatter plots for
4127 plotting. a three dimensional point cloud.")
4128 (license license:gpl2)))
4130 (define-public r-ggridges
4137 (uri (cran-uri "ggridges" version))
4140 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4141 (build-system r-build-system)
4143 `(("r-ggplot2" ,r-ggplot2)
4145 ("r-scales" ,r-scales)
4146 ("r-withr" ,r-withr)))
4147 (home-page "https://github.com/clauswilke/ggridges")
4148 (synopsis "Ridgeline plots in ggplot2")
4150 "Ridgeline plots provide a convenient way of visualizing changes in
4151 distributions over time or space. This package enables the creation of such
4152 plots in @code{ggplot2}.")
4153 (license license:gpl2)))
4155 (define-public r-ggjoy
4162 (uri (cran-uri "ggjoy" version))
4165 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4166 (build-system r-build-system)
4168 `(("r-ggplot2" ,r-ggplot2)
4169 ("r-ggridges" ,r-ggridges)))
4170 (home-page "https://github.com/clauswilke/ggjoy")
4171 (synopsis "Joyplots in ggplot2")
4172 (description "Joyplots provide a convenient way of visualizing changes in
4173 distributions over time or space. This package enables the creation of such
4174 plots in @code{ggplot2}.")
4175 (license license:gpl2)))
4177 (define-public r-cli
4184 (uri (cran-uri "cli" version))
4187 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4188 (build-system r-build-system)
4190 `(("r-assertthat" ,r-assertthat)
4191 ("r-crayon" ,r-crayon)
4192 ("r-fansi" ,r-fansi)
4193 ("r-glue" ,r-glue)))
4194 (home-page "https://github.com/r-lib/cli#readme")
4195 (synopsis "Helpers for developing command line interfaces")
4196 (description "This package provides a suite of tools designed to build
4197 attractive command line interfaces (CLIs). It includes tools for drawing
4198 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4199 (license license:expat)))
4201 (define-public r-argparser
4203 (name "r-argparser")
4208 (uri (cran-uri "argparser" version))
4211 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4212 (build-system r-build-system)
4213 (home-page "https://bitbucket.org/djhshih/argparser")
4214 (synopsis "Command-line argument parser")
4216 "This package provides a cross-platform command-line argument parser
4217 written purely in R with no external dependencies. It is useful with the
4218 Rscript front-end and facilitates turning an R script into an executable
4220 (license license:gpl3+)))
4222 (define-public r-debugme
4229 (uri (cran-uri "debugme" version))
4232 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4233 (build-system r-build-system)
4234 (propagated-inputs `(("r-crayon" ,r-crayon)))
4235 (home-page "https://github.com/r-lib/debugme#readme")
4236 (synopsis "Debug R packages")
4238 "This package allows the user to specify debug messages as special string
4239 constants, and control debugging of packages via environment variables.")
4240 (license license:expat)))
4242 (define-public r-processx
4249 (uri (cran-uri "processx" version))
4251 (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
4252 (build-system r-build-system)
4256 (home-page "https://github.com/r-lib/processx3")
4257 (synopsis "Execute and control system processes")
4259 "This package provides portable tools to run system processes in the
4260 background. It can check if a background process is running; wait on a
4261 background process to finish; get the exit status of finished processes; kill
4262 background processes and their children; restart processes. It can read the
4263 standard output and error of the processes, using non-blocking connections.
4264 @code{processx} can poll a process for standard output or error, with a
4265 timeout. It can also poll several processes at once.")
4266 (license license:expat)))
4268 (define-public r-tsp
4275 (uri (cran-uri "TSP" version))
4278 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4279 (properties `((upstream-name . "TSP")))
4280 (build-system r-build-system)
4281 (propagated-inputs `(("r-foreach" ,r-foreach)))
4282 (home-page "https://cran.r-project.org/web/packages/TSP/")
4283 (synopsis "Traveling salesperson problem (TSP)")
4284 (description "This package provides basic infrastructure and some
4285 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4286 traveling salesman problem).")
4287 (license license:gpl3)))
4289 (define-public r-qap
4296 (uri (cran-uri "qap" version))
4299 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4300 (build-system r-build-system)
4301 (native-inputs `(("gfortran" ,gfortran)))
4302 (home-page "https://cran.r-project.org/web/packages/qap/")
4303 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4304 (description "This package implements heuristics for the @dfn{quadratic
4305 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4307 (license license:gpl3)))
4309 (define-public r-gclus
4316 (uri (cran-uri "gclus" version))
4319 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4320 (build-system r-build-system)
4321 (propagated-inputs `(("r-cluster" ,r-cluster)))
4322 (home-page "https://cran.r-project.org/web/packages/gclus/")
4323 (synopsis "Clustering graphics")
4324 (description "This package orders panels in scatterplot matrices and
4325 parallel coordinate displays by some merit index. It contains various indices
4326 of merit, ordering functions, and enhanced versions of @code{pairs} and
4327 @code{parcoord} which color panels according to their merit level.")
4328 (license license:gpl2+)))
4330 (define-public r-webshot
4337 (uri (cran-uri "webshot" version))
4340 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4341 (build-system r-build-system)
4343 `(("r-callr" ,r-callr)
4344 ("r-jsonlite" ,r-jsonlite)
4345 ("r-magrittr" ,r-magrittr)))
4346 (home-page "https://github.com/wch/webshot/")
4347 (synopsis "Take screenshots of web pages")
4349 "Webshot makes it easy to take screenshots of web pages from within R.
4350 It can also run Shiny applications locally and take screenshots of the
4351 application; and it can render and screenshot static as well as interactive R
4352 Markdown documents.")
4353 (license license:gpl2)))
4355 (define-public r-seriation
4357 (name "r-seriation")
4362 (uri (cran-uri "seriation" version))
4365 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4366 (build-system r-build-system)
4368 `(("r-cluster" ,r-cluster)
4369 ("r-colorspace" ,r-colorspace)
4370 ("r-dendextend" ,r-dendextend)
4371 ("r-gclus" ,r-gclus)
4372 ("r-gplots" ,r-gplots)
4375 ("r-registry" ,r-registry)
4377 (native-inputs `(("gfortran" ,gfortran)))
4378 (home-page "https://s2.smu.edu/IDA/seriation/")
4379 (synopsis "Infrastructure for ordering objects using seriation")
4381 "This package provides infrastructure for seriation with an
4382 implementation of several seriation/sequencing techniques to reorder matrices,
4383 dissimilarity matrices, and dendrograms. It also provides (optimally)
4384 reordered heatmaps, color images and clustering visualizations like
4385 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4387 (license license:gpl3)))
4389 (define-public r-xfun
4396 (uri (cran-uri "xfun" version))
4398 (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
4399 (build-system r-build-system)
4400 ;; knitr itself depends on xfun
4403 `(("r-knitr" ,r-knitr)))
4404 (home-page "https://github.com/yihui/xfun")
4405 (synopsis "Miscellaneous functions")
4407 "This package provides miscellaneous functions commonly used in other
4408 packages maintained by Yihui Xie.")
4409 (license license:expat)))
4411 (define-public r-utf8
4418 (uri (cran-uri "utf8" version))
4421 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4422 (build-system r-build-system)
4423 (home-page "https://github.com/patperry/r-utf8")
4424 (synopsis "Unicode text processing")
4426 "This package provides tools to process and print UTF-8 encoded
4427 international text (Unicode). Input, validate, normalize, encode, format, and
4429 (license license:asl2.0)))
4431 (define-public r-zeallot
4438 (uri (cran-uri "zeallot" version))
4441 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4442 (build-system r-build-system)
4443 (home-page "https://github.com/nteetor/zeallot")
4444 (synopsis "Multiple, unpacking, and destructuring assignment")
4446 "This package provides a @code{%<-%} operator to perform multiple,
4447 unpacking, and destructuring assignment in R. The operator unpacks the
4448 right-hand side of an assignment into multiple values and assigns these values
4449 to variables on the left-hand side of the assignment.")
4450 (license license:expat)))
4452 (define-public r-vctrs
4459 (uri (cran-uri "vctrs" version))
4462 "05s8v3ms4jaim44c7m4y0dnv8mysj9b26cdfyrfgcjpllayrjib2"))))
4463 (build-system r-build-system)
4465 `(("r-digest" ,r-digest)
4466 ("r-ellipsis" ,r-ellipsis)
4468 ("r-rlang" ,r-rlang)))
4470 `(("r-knitr" ,r-knitr)))
4471 (home-page "https://github.com/r-lib/vctrs")
4472 (synopsis "Vector helpers")
4474 "There are three main goals to the @code{vctrs} package:
4477 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4478 @code{length()} and @code{class()}. These definitions are paired with a
4479 framework for type-coercion and size-recycling.
4480 @item To define type- and size-stability as desirable function properties, use
4481 them to analyse existing base function, and to propose better alternatives.
4482 This work has been particularly motivated by thinking about the ideal
4483 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4484 @item To provide a new @code{vctr} base class that makes it easy to create new
4485 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4486 a few new @code{vctrs} generics, making implementation considerably simpler
4489 (license license:gpl3)))
4491 (define-public r-pillar
4498 (uri (cran-uri "pillar" version))
4501 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4502 (build-system r-build-system)
4505 ("r-crayon" ,r-crayon)
4506 ("r-ellipsis" ,r-ellipsis)
4507 ("r-fansi" ,r-fansi)
4508 ("r-lifecycle" ,r-lifecycle)
4509 ("r-rlang" ,r-rlang)
4511 ("r-vctrs" ,r-vctrs)))
4512 (home-page "https://github.com/r-lib/pillar")
4513 (synopsis "Coloured formatting for columns")
4515 "This package provides a @code{pillar} generic designed for formatting
4516 columns of data using the full range of colours provided by modern
4518 (license license:gpl3)))
4520 (define-public r-uuid
4527 (uri (cran-uri "uuid" version))
4530 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4531 (build-system r-build-system)
4532 (home-page "https://www.rforge.net/uuid")
4533 (synopsis "Tools for generating and handling of UUIDs")
4535 "This package provides tools for generating and handling of
4536 @dfn{Universally Unique Identifiers} (UUIDs).")
4537 (license license:expat)))
4539 (define-public r-tinytex
4546 (uri (cran-uri "tinytex" version))
4549 "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza"))))
4550 (build-system r-build-system)
4552 `(("r-xfun" ,r-xfun)))
4553 (home-page "https://github.com/yihui/tinytex")
4554 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4556 "This package provides helper functions to install and maintain the LaTeX
4557 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4558 easy-to-maintain version of TeX Live. This package also contains helper
4559 functions to compile LaTeX documents, and install missing LaTeX packages
4561 (license license:expat)))
4563 (define-public r-network
4570 (uri (cran-uri "network" version))
4573 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4574 (build-system r-build-system)
4576 `(("r-magrittr" ,r-magrittr)
4577 ("r-tibble" ,r-tibble)))
4578 (home-page "https://statnet.org/")
4579 (synopsis "Classes for relational data")
4581 "This package provides tools to create and modify network objects. The
4582 @code{network} class can represent a range of relational data types, and
4583 supports arbitrary vertex/edge/graph attributes.")
4584 (license license:gpl2+)))
4586 (define-public r-statnet-common
4588 (name "r-statnet-common")
4593 (uri (cran-uri "statnet.common" version))
4596 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4598 `((upstream-name . "statnet.common")))
4599 (build-system r-build-system)
4601 `(("r-coda" ,r-coda)))
4602 (home-page "https://statnet.org")
4603 (synopsis "R scripts and utilities used by the Statnet software")
4604 (description "This package provides non-statistical utilities used by the
4605 software developed by the Statnet Project.")
4606 (license license:gpl3)))
4608 (define-public r-statcheck
4610 (name "r-statcheck")
4615 (uri (cran-uri "statcheck" version))
4618 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4619 (build-system r-build-system)
4621 `(("r-ggplot2" ,r-ggplot2)
4623 ("r-rmarkdown" ,r-rmarkdown)))
4624 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4625 (synopsis "Extract statistics from articles and recompute p-values")
4626 (description "This package can automatically extract statistical
4627 null-hypothesis significant testing (NHST) results from articles and recompute
4628 the p-values based on the reported test statistic and degrees of freedom to
4629 detect possible inconsistencies.")
4630 (license license:gpl2)))
4632 (define-public r-sna
4639 (uri (cran-uri "sna" version))
4642 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4643 (build-system r-build-system)
4645 `(("r-network" ,r-network)
4646 ("r-statnet-common" ,r-statnet-common)))
4647 (home-page "https://statnet.org")
4648 (synopsis "Tools for social network analysis")
4650 "This package provides a range of tools for social network analysis,
4651 including node and graph-level indices, structural distance and covariance
4652 methods, structural equivalence detection, network regression, random graph
4653 generation, and 2D/3D network visualization.")
4654 (license license:gpl2+)))
4656 (define-public r-tfisher
4663 (uri (cran-uri "TFisher" version))
4666 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4667 (properties `((upstream-name . "TFisher")))
4668 (build-system r-build-system)
4670 `(("r-matrix" ,r-matrix)
4671 ("r-mvtnorm" ,r-mvtnorm)
4673 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4674 (synopsis "Optimal thresholding Fisher's p-value combination method")
4676 "This package provides the @dfn{cumulative distribution function} (CDF),
4677 quantile, and statistical power calculator for a collection of thresholding
4678 Fisher's p-value combination methods, including Fisher's p-value combination
4679 method, truncated product method and, in particular, soft-thresholding
4680 Fisher's p-value combination method which is proven to be optimal in some
4681 context of signal detection. The p-value calculator for the omnibus version
4682 of these tests are also included.")
4683 (license license:gpl2)))
4685 (define-public r-ttr
4692 (uri (cran-uri "TTR" version))
4695 "0dcmfr98bxhdhszsdr1yjhvy4kplnfm88fh8sdzrkjank1qsxia2"))))
4696 (properties `((upstream-name . "TTR")))
4697 (build-system r-build-system)
4699 `(("r-curl" ,r-curl)
4702 (home-page "https://github.com/joshuaulrich/TTR")
4703 (synopsis "Technical trading rules")
4705 "This package provides functions and data to construct technical trading
4707 (license license:gpl2)))
4709 (define-public r-leaps
4716 (uri (cran-uri "leaps" version))
4719 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4720 (build-system r-build-system)
4721 (native-inputs `(("gfortran" ,gfortran)))
4722 (home-page "https://cran.r-project.org/web/packages/leaps/")
4723 (synopsis "Regression subset selection")
4725 "This package provides tools for regression subset selection, including
4726 exhaustive search.")
4727 (license license:gpl2+)))
4729 (define-public r-splus2r
4736 (uri (cran-uri "splus2R" version))
4739 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4740 (properties `((upstream-name . "splus2R")))
4741 (build-system r-build-system)
4742 (native-inputs `(("gfortran" ,gfortran)))
4743 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4744 (synopsis "Supplemental S-PLUS functionality in R")
4746 "Currently there are many functions in S-PLUS that are missing in R. To
4747 facilitate the conversion of S-PLUS packages to R packages, this package
4748 provides some missing S-PLUS functionality in R.")
4749 (license license:gpl2)))
4751 (define-public r-ifultools
4753 (name "r-ifultools")
4758 (uri (cran-uri "ifultools" version))
4761 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4762 (build-system r-build-system)
4764 `(("r-mass" ,r-mass)
4765 ("r-splus2r" ,r-splus2r)))
4766 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4767 (synopsis "Insightful research tools")
4768 (description "This package provides C code used by the wmtsa, fractal, and
4770 (license license:gpl2)))
4772 (define-public r-sapa
4779 (uri (cran-uri "sapa" version))
4782 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4783 (build-system r-build-system)
4785 `(("r-ifultools" ,r-ifultools)
4786 ("r-splus2r" ,r-splus2r)))
4787 (home-page "https://cran.r-project.org/web/packages/sapa/")
4788 (synopsis "Spectral analysis for physical applications")
4789 (description "This package provides software for the book Spectral
4790 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4791 Cambridge University Press, 1993.")
4792 (license license:gpl2)))
4794 (define-public r-aggregation
4796 (name "r-aggregation")
4801 (uri (cran-uri "aggregation" version))
4804 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4805 (build-system r-build-system)
4806 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4807 (synopsis "Methods for p-value aggregation")
4809 "This package contains functionality for performing the following methods
4810 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4811 Fisher's method), and Sidak correction.")
4812 (license license:gpl3)))
4814 (define-public r-quantmod
4821 (uri (cran-uri "quantmod" version))
4824 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4825 (build-system r-build-system)
4827 `(("r-curl" ,r-curl)
4831 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4832 (synopsis "Quantitative financial modelling framework")
4833 (description "This package provides a quantitative financial modelling
4834 framework to allow users to specify, build, trade, and analyse quantitative
4835 financial trading strategies.")
4836 (license license:gpl3)))
4838 (define-public r-tseries
4845 (uri (cran-uri "tseries" version))
4848 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4849 (build-system r-build-system)
4851 `(("r-quadprog" ,r-quadprog)
4852 ("r-quantmod" ,r-quantmod)
4855 `(("gfortran" ,gfortran)))
4856 (home-page "https://cran.r-project.org/web/packages/tseries/")
4857 (synopsis "Time series analysis and computational finance")
4859 "This package provides functions relating to time series analysis and
4860 computational finance.")
4861 (license license:gpl2)))
4863 (define-public r-wmtsa
4870 (uri (cran-uri "wmtsa" version))
4873 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4874 (build-system r-build-system)
4876 `(("r-ifultools" ,r-ifultools)
4878 ("r-splus2r" ,r-splus2r)))
4879 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4880 (synopsis "Wavelet methods for time series analysis")
4882 "This package provides software to accompany the book \"Wavelet Methods
4883 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4884 University Press, 2000.")
4885 (license license:gpl2)))
4887 (define-public r-tsa
4894 (uri (cran-uri "TSA" version))
4897 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4898 (properties `((upstream-name . "TSA")))
4899 (build-system r-build-system)
4901 `(("r-leaps" ,r-leaps)
4902 ("r-locfit" ,r-locfit)
4903 ("r-mgcv" ,r-mgcv)))
4904 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4905 (synopsis "Time series analysis")
4907 "This package contains R functions and datasets detailed in the book
4908 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4909 Cryer and Kung-Sik Chan.")
4910 (license license:gpl2+)))
4912 (define-public r-extradistr
4914 (name "r-extradistr")
4919 (uri (cran-uri "extraDistr" version))
4922 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4923 (properties `((upstream-name . "extraDistr")))
4924 (build-system r-build-system)
4926 `(("r-rcpp" ,r-rcpp)))
4927 (home-page "https://github.com/twolodzko/extraDistr")
4928 (synopsis "Additional univariate and multivariate distributions")
4930 "This package implements density, distribution functions, quantile
4931 functions and random generation functions for a large number of univariate and
4932 multivariate distributions.")
4933 (license license:gpl2)))
4935 (define-public r-fractal
4942 (uri (cran-uri "fractal" version))
4945 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4946 (build-system r-build-system)
4948 `(("r-ifultools" ,r-ifultools)
4951 ("r-scatterplot3d" ,r-scatterplot3d)
4952 ("r-splus2r" ,r-splus2r)
4953 ("r-wmtsa" ,r-wmtsa)))
4954 (home-page "https://cran.r-project.org/web/packages/fractal/")
4955 (synopsis "Fractal time series modeling and analysis")
4957 "This package provides tools for stochastic fractal and deterministic
4958 chaotic time series analysis.")
4959 (license license:gpl2)))
4961 (define-public r-urca
4968 (uri (cran-uri "urca" version))
4971 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4972 (build-system r-build-system)
4973 (propagated-inputs `(("r-nlme" ,r-nlme)))
4974 (native-inputs `(("gfortran" ,gfortran)))
4975 (home-page "https://cran.r-project.org/web/packages/urca/")
4976 (synopsis "Unit root and cointegration tests for time series data")
4978 "This package provides unit root and cointegration tests encountered in
4979 applied econometric analysis.")
4980 (license license:gpl2+)))
4982 (define-public r-cubature
4989 (uri (cran-uri "cubature" version))
4992 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
4993 (build-system r-build-system)
4995 `(("r-rcpp" ,r-rcpp)))
4997 `(("r-knitr" ,r-knitr)))
4998 (home-page "https://github.com/bnaras/cubature")
4999 (synopsis "Adaptive multivariate integration over hypercubes")
5001 "This package is an R wrapper around the cubature C library for adaptive
5002 multivariate integration over hypercubes. This version provides both
5003 @code{hcubature} and @code{pcubature} routines in addition to a vector
5005 ;; The included cubature C library is released under GPLv2+, but the
5006 ;; wrapper declares the license to be GPLv3+.
5007 (license (list license:gpl2+ license:gpl3+))))
5009 (define-public r-trend
5016 (uri (cran-uri "trend" version))
5019 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
5020 (build-system r-build-system)
5022 `(("r-extradistr" ,r-extradistr)))
5024 `(("gfortran" ,gfortran)))
5025 (home-page "https://cran.r-project.org/web/packages/trend/")
5026 (synopsis "Non-parametric trend tests and change-point detection")
5028 "The analysis of environmental data often requires the detection of
5029 trends and change-points. This package includes tests for trend
5030 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5031 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5032 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5033 correlation trend test), change-point detection (Lanzante's test procedures,
5034 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5035 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5036 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5037 sample Robust Rank-Order Distributional Test.")
5038 (license license:gpl3)))
5040 (define-public r-expm
5047 (uri (cran-uri "expm" version))
5050 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5051 (build-system r-build-system)
5052 (propagated-inputs `(("r-matrix" ,r-matrix)))
5053 (native-inputs `(("gfortran" ,gfortran)))
5054 (home-page "https://r-forge.r-project.org/projects/expm/")
5055 (synopsis "Tools for matrix exponentials and related quantities")
5057 "This package provides tools for the computation of the matrix
5058 exponential, logarithm, square root, and related quantities.")
5059 (license license:gpl2+)))
5061 (define-public r-complexplus
5063 (name "r-complexplus")
5068 (uri (cran-uri "complexplus" version))
5071 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5072 (build-system r-build-system)
5074 `(("r-expm" ,r-expm)
5075 ("r-matrix" ,r-matrix)))
5076 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5077 (synopsis "Functions of complex or real variables")
5079 "This package extends several functions to the complex domain, including
5080 the matrix exponential and logarithm, and the determinant.")
5081 (license license:gpl2)))
5083 (define-public r-phontools
5085 (name "r-phontools")
5090 (uri (cran-uri "phonTools" version))
5093 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5094 (properties `((upstream-name . "phonTools")))
5095 (build-system r-build-system)
5096 (home-page "http://www.santiagobarreda.com/rscripts.html")
5097 (synopsis "Tools for phonetic and acoustic analyses")
5099 "This package contains tools for the organization, display, and analysis
5100 of the sorts of data frequently encountered in phonetics research and
5101 experimentation, including the easy creation of IPA vowel plots, and the
5102 creation and manipulation of WAVE audio files.")
5103 (license license:bsd-2)))
5112 (uri (cran-uri "np" version))
5115 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5116 (build-system r-build-system)
5118 `(("r-boot" ,r-boot)
5119 ("r-cubature" ,r-cubature)
5120 ("r-quadprog" ,r-quadprog)
5121 ("r-quantreg" ,r-quantreg)))
5122 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5123 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5124 (description "This package provides non-parametric (and semi-parametric)
5125 kernel methods that seamlessly handle a mix of continuous, unordered, and
5126 ordered factor data types.")
5127 ;; Any version of the GPL.
5128 (license license:gpl3+)))
5130 (define-public r-powerplus
5132 (name "r-powerplus")
5137 (uri (cran-uri "powerplus" version))
5140 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5141 (build-system r-build-system)
5143 `(("r-complexplus" ,r-complexplus)
5146 ("r-matrix" ,r-matrix)
5147 ("r-phontools" ,r-phontools)))
5148 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5149 (synopsis "Exponentiation operations")
5151 "This package provides tools for the computation of matrix and scalar
5153 (license license:gpl2)))
5155 (define-public r-egg
5162 (uri (cran-uri "egg" version))
5165 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5166 (properties `((upstream-name . "egg")))
5167 (build-system r-build-system)
5169 `(("r-ggplot2" ,r-ggplot2)
5170 ("r-gridextra" ,r-gridextra)
5171 ("r-gtable" ,r-gtable)))
5172 (home-page "https://cran.r-project.org/web/packages/egg")
5173 (synopsis "Extensions for ggplot2")
5175 "This package provides miscellaneous functions to help customize ggplot2
5176 objects. High-level functions are provided to post-process ggplot2 layouts
5177 and allow alignment between plot panels, as well as setting panel sizes to
5178 fixed values. Other functions include a custom @code{geom}, and helper
5179 functions to enforce symmetric scales or add tags to facetted plots.")
5180 (license license:gpl3)))
5182 (define-public r-heatmaply
5184 (name "r-heatmaply")
5189 (uri (cran-uri "heatmaply" version))
5192 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5193 (build-system r-build-system)
5195 `(("r-assertthat" ,r-assertthat)
5196 ("r-colorspace" ,r-colorspace)
5197 ("r-dendextend" ,r-dendextend)
5199 ("r-ggplot2" ,r-ggplot2)
5200 ("r-htmlwidgets" ,r-htmlwidgets)
5201 ("r-magrittr" ,r-magrittr)
5202 ("r-plotly" ,r-plotly)
5203 ("r-rcolorbrewer" ,r-rcolorbrewer)
5204 ("r-reshape2" ,r-reshape2)
5205 ("r-scales" ,r-scales)
5206 ("r-seriation" ,r-seriation)
5207 ("r-viridis" ,r-viridis)
5208 ("r-webshot" ,r-webshot)))
5210 `(("r-knitr" ,r-knitr)))
5211 (home-page "https://cran.r-project.org/package=heatmaply")
5212 (synopsis "Interactive cluster heat maps using plotly")
5214 "This package enables you to create interactive cluster heatmaps that can
5215 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5216 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5217 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5218 a popular graphical method for visualizing high-dimensional data, in which a
5219 table of numbers is encoded as a grid of colored cells. The rows and columns
5220 of the matrix are ordered to highlight patterns and are often accompanied by
5222 ;; Either version of the license.
5223 (license (list license:gpl2 license:gpl3))))
5232 (uri (cran-uri "h5" version))
5235 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5236 (build-system r-build-system)
5241 `(("which" ,which)))
5243 `(("r-rcpp" ,r-rcpp)))
5244 (home-page "https://github.com/mannau/h5")
5245 (synopsis "Interface to the HDF5 Library")
5247 "This package provides an S4 interface to the HDF5 library supporting
5248 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5249 binary files in a language independent format. The HDF5 format can therefore
5250 be used as an alternative to R's save/load mechanism. Since h5 is able to
5251 access only subsets of stored data it can also handle data sets which do not
5253 (license license:bsd-2)))
5255 (define-public r-cgdsr
5262 (uri (cran-uri "cgdsr" version))
5265 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5266 (build-system r-build-system)
5268 `(("r-httr" ,r-httr)
5269 ("r-r-methodss3" ,r-r-methodss3)
5270 ("r-r-oo" ,r-r-oo)))
5271 (home-page "https://github.com/cBioPortal/cgdsr")
5272 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5274 "This package provides a basic set of R functions for querying the Cancer
5275 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5276 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5277 (license license:lgpl3)))
5279 (define-public r-import
5286 (uri (cran-uri "import" version))
5289 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5290 (build-system r-build-system)
5291 (home-page "https://github.com/smbache/import")
5292 (synopsis "Import mechanism for R")
5294 "This is an alternative mechanism for importing objects from packages.
5295 The syntax allows for importing multiple objects from a package with a single
5296 command in an expressive way. The import package bridges some of the gap
5297 between using @code{library} (or @code{require}) and direct (single-object)
5298 imports. Furthermore the imported objects are not placed in the current
5299 environment. It is also possible to import objects from stand-alone @code{.R}
5301 (license license:expat)))
5303 (define-public r-shinyace
5310 (uri (cran-uri "shinyAce" version))
5313 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5314 (properties `((upstream-name . "shinyAce")))
5315 (build-system r-build-system)
5317 `(("r-shiny" ,r-shiny)
5318 ("r-jsonlite" ,r-jsonlite)))
5319 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5320 (synopsis "Ace editor bindings for Shiny")
5322 "This package provides Ace editor bindings to enable a rich text editing
5323 environment within Shiny.")
5324 (license license:expat)))
5326 (define-public r-randomizr
5328 (name "r-randomizr")
5333 (uri (cran-uri "randomizr" version))
5336 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5337 (properties `((upstream-name . "randomizr")))
5338 (build-system r-build-system)
5340 `(("r-knitr" ,r-knitr)))
5341 (home-page "https://declaredesign.org/r/randomizr/")
5342 (synopsis "Tools for common forms of random assignment and sampling")
5344 "This package provides tools for generating random assignments for common
5345 experimental designs and random samples for common sampling designs.")
5346 (license license:expat)))
5348 (define-public r-base64url
5350 (name "r-base64url")
5355 (uri (cran-uri "base64url" version))
5358 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5359 (build-system r-build-system)
5361 `(("r-backports" ,r-backports)))
5362 (home-page "https://github.com/mllg/base64url")
5363 (synopsis "Fast and URL-safe base64 encoder and decoder")
5365 "This package provides a URL-safe base64 encoder and decoder. In
5366 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5367 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5368 encoder does not fill the string with trailing @code{=}. The resulting
5369 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5370 and thus are safe to use in URLs or for file names. The package also comes
5371 with a simple base32 encoder/decoder suited for case insensitive file
5373 (license license:gpl3)))
5375 (define-public r-radiant-data
5377 (name "r-radiant-data")
5382 (uri (cran-uri "radiant.data" version))
5385 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5386 (modules '((guix build utils)))
5389 ;; Delete files that are under CC-NC-SA.
5390 (delete-file-recursively "inst/app/tools/help")
5392 (properties `((upstream-name . "radiant.data")))
5393 (build-system r-build-system)
5395 `(("r-base64enc" ,r-base64enc)
5396 ("r-broom" ,r-broom)
5399 ("r-dplyr" ,r-dplyr)
5402 ("r-ggplot2" ,r-ggplot2)
5403 ("r-import" ,r-import)
5404 ("r-jsonlite" ,r-jsonlite)
5405 ("r-knitr" ,r-knitr)
5406 ("r-lubridate" ,r-lubridate)
5407 ("r-magrittr" ,r-magrittr)
5408 ("r-markdown" ,r-markdown)
5410 ("r-patchwork" ,r-patchwork)
5411 ("r-plotly" ,r-plotly)
5412 ("r-psych" ,r-psych)
5413 ("r-randomizr" ,r-randomizr)
5414 ("r-readr" ,r-readr)
5415 ("r-readxl" ,r-readxl)
5416 ("r-rlang" ,r-rlang)
5417 ("r-rmarkdown" ,r-rmarkdown)
5418 ("r-rstudioapi" ,r-rstudioapi)
5419 ("r-scales" ,r-scales)
5420 ("r-shiny" ,r-shiny)
5421 ("r-shinyfiles" ,r-shinyfiles)
5422 ("r-shinyace" ,r-shinyace)
5423 ("r-stringi" ,r-stringi)
5424 ("r-tibble" ,r-tibble)
5425 ("r-tidyr" ,r-tidyr)
5426 ("r-writexl" ,r-writexl)))
5427 (home-page "https://github.com/radiant-rstats/radiant.data")
5428 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5430 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5431 visualizing, summarizing, transforming, and combining data. It also contains
5432 functionality to generate reproducible reports of the analyses conducted in
5434 (license license:agpl3)))
5436 (define-public r-algdesign
5438 (name "r-algdesign")
5443 (uri (cran-uri "AlgDesign" version))
5445 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5446 (properties `((upstream-name . "AlgDesign")))
5447 (build-system r-build-system)
5448 (home-page "https://github.com/jvbraun/AlgDesign")
5449 (synopsis "Algorithmic experimental design")
5451 "This package provides tools to calculate exact and approximate theory
5452 experimental designs for D, A, and I criteria. Very large designs may be
5453 created. Experimental designs may be blocked or blocked designs created from
5454 a candidate list, using several criteria. The blocking can be done when whole
5455 and within plot factors interact.")
5456 (license license:gpl2+)))
5458 (define-public r-signal
5465 (uri (cran-uri "signal" version))
5468 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5469 (build-system r-build-system)
5470 (propagated-inputs `(("r-mass" ,r-mass)))
5471 (native-inputs `(("gfortran" ,gfortran)))
5472 (home-page "https://cran.r-project.org/web/packages/signal/")
5473 (synopsis "Signal processing")
5475 "This package provides a set of signal processing functions originally
5476 written for Matlab and GNU Octave. It includes filter generation utilities,
5477 filtering functions, resampling routines, and visualization of filter models.
5478 It also includes interpolation functions.")
5479 (license license:gpl2)))
5481 (define-public r-gsubfn
5488 (uri (cran-uri "gsubfn" version))
5491 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5492 (build-system r-build-system)
5493 (propagated-inputs `(("r-proto" ,r-proto)))
5494 (home-page "https://code.google.com/archive/p/gsubfn/")
5495 (synopsis "Utilities for strings and function arguments.")
5497 "This package provides @code{gsubfn} which is like @code{gsub} but can
5498 take a replacement function or certain other objects instead of the
5499 replacement string. Matches and back references are input to the replacement
5500 function and replaced by the function output. @code{gsubfn} can be used to
5501 split strings based on content rather than delimiters and for quasi-perl-style
5502 string interpolation. The package also has facilities for translating
5503 formulas to functions and allowing such formulas in function calls instead of
5505 (license license:gpl2+)))
5507 (define-public r-sqldf
5514 (uri (cran-uri "sqldf" version))
5517 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5518 (build-system r-build-system)
5520 `(("r-chron" ,r-chron)
5522 ("r-gsubfn" ,r-gsubfn)
5523 ("r-proto" ,r-proto)
5524 ("r-rsqlite" ,r-rsqlite)))
5525 (home-page "https://github.com/ggrothendieck/sqldf")
5526 (synopsis "Manipulate R data frames using SQL")
5528 "The @code{sqldf} function is typically passed a single argument which is
5529 an SQL select statement where the table names are ordinary R data frame names.
5530 @code{sqldf} transparently sets up a database, imports the data frames into
5531 that database, performs the SQL statement and returns the result using a
5532 heuristic to determine which class to assign to each column of the returned
5533 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5534 used to read filtered files into R even if the original files are larger than
5535 R itself can handle.")
5536 (license license:gpl2)))
5538 (define-public r-abind
5545 (uri (cran-uri "abind" version))
5548 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5549 (build-system r-build-system)
5550 (home-page "https://cran.r-project.org/web/packages/abind/")
5551 (synopsis "Combine multidimensional arrays")
5553 "This package provides tools to combine multidimensional arrays into a
5554 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5555 works with vectors, matrices, and higher-dimensional arrays. It also provides
5556 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5557 extracting and replacing data in arrays.")
5558 (license license:lgpl2.0+)))
5560 (define-public r-prroc
5567 (uri (cran-uri "PRROC" version))
5570 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5571 (properties `((upstream-name . "PRROC")))
5572 (build-system r-build-system)
5573 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5574 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5576 "This package computes the areas under the @dfn{precision-recall} (PR)
5577 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5578 contrast to other implementations, the interpolation between points of the PR
5579 curve is done by a non-linear piecewise function. In addition to the areas
5580 under the curves, the curves themselves can also be computed and plotted by a
5581 specific S3-method.")
5582 (license license:gpl3)))
5584 (define-public r-vim
5591 (uri (cran-uri "VIM" version))
5594 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5595 (properties `((upstream-name . "VIM")))
5596 (build-system r-build-system)
5599 ("r-colorspace" ,r-colorspace)
5600 ("r-data-table" ,r-data-table)
5601 ("r-e1071" ,r-e1071)
5602 ("r-laeken" ,r-laeken)
5603 ("r-magrittr" ,r-magrittr)
5606 ("r-ranger" ,r-ranger)
5608 ("r-robustbase" ,r-robustbase)
5612 `(("r-knitr" ,r-knitr)))
5613 (home-page "https://github.com/alexkowa/VIM")
5614 (synopsis "Visualization and imputation of missing values")
5616 "This package provides tools for the visualization of missing and/or
5617 imputed values are introduced, which can be used for exploring the data and
5618 the structure of the missing and/or imputed values. Depending on this
5619 structure of the missing values, the corresponding methods may help to
5620 identify the mechanism generating the missing values and allows to explore the
5621 data including missing values. In addition, the quality of imputation can be
5622 visually explored using various univariate, bivariate, multiple and
5623 multivariate plot methods.")
5624 (license license:gpl2+)))
5626 (define-public r-fnn
5633 (uri (cran-uri "FNN" version))
5636 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5637 (properties `((upstream-name . "FNN")))
5638 (build-system r-build-system)
5639 (home-page "https://cran.r-project.org/web/packages/FNN")
5640 (synopsis "Fast nearest neighbor search algorithms and applications")
5642 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5643 search algorithms. Related applications including KNN classification,
5644 regression and information measures are implemented.")
5645 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5646 ;; later can be used.
5647 (license license:gpl2+)))
5649 (define-public r-smoother
5656 (uri (cran-uri "smoother" version))
5659 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5660 (build-system r-build-system)
5662 `(("r-ttr" ,r-ttr)))
5663 (home-page "https://cran.r-project.org/web/packages/smoother")
5664 (synopsis "Functions relating to the smoothing of numerical data")
5666 "This package provides a collection of methods for smoothing numerical
5667 data, commencing with a port of the Matlab gaussian window smoothing function.
5668 In addition, several functions typically used in smoothing of financial data
5670 (license license:gpl2)))
5672 (define-public r-riverplot
5674 (name "r-riverplot")
5679 (uri (cran-uri "riverplot" version))
5682 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5683 (build-system r-build-system)
5684 (home-page "https://logfc.wordpress.com")
5685 (synopsis "Sankey or ribbon plots")
5687 "Sankey plots are a type of diagram that is convenient to illustrate how
5688 flow of information, resources etc. separates and joins, much like observing
5689 how rivers split and merge. For example, they can be used to compare
5690 different clusterings. This package provides an implementation of Sankey
5692 (license license:gpl2+)))
5694 (define-public r-dyn
5701 (uri (cran-uri "dyn" version))
5704 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5705 (build-system r-build-system)
5707 `(("r-zoo" ,r-zoo)))
5708 (home-page "https://cran.r-project.org/web/packages/dyn")
5709 (synopsis "Time series regression")
5711 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5712 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5713 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5714 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5715 @code{randomForest::randomForest()} and other regression functions, allowing
5716 those functions to be used with time series including specifications that may
5717 contain lags, diffs and missing values.")
5719 (license license:gpl2+)))
5721 (define-public r-catdap
5728 (uri (cran-uri "catdap" version))
5731 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5732 (build-system r-build-system)
5734 `(("gfortran" ,gfortran)))
5735 (home-page "https://cran.r-project.org/web/packages/catdap/")
5736 (synopsis "Tools for categorical data analysis")
5738 "This package provides functions for analyzing multivariate data.
5739 Dependencies of the distribution of the specified variable (response
5740 variable) to other variables (explanatory variables) are derived and
5741 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5742 (license license:gpl2+)))
5744 (define-public r-arules
5751 (uri (cran-uri "arules" version))
5754 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5755 (build-system r-build-system)
5757 `(("r-matrix" ,r-matrix)))
5758 (home-page "https://github.com/mhahsler/arules")
5759 (synopsis "Mining association rules and frequent itemsets")
5761 "This package provides an infrastructure for representing, manipulating
5762 and analyzing transaction data and patterns (frequent itemsets and association rules).
5763 It also provides C implementations of the association mining algorithms Apriori
5765 (license license:gpl3)))
5767 (define-public r-parsedate
5769 (name "r-parsedate")
5774 (uri (cran-uri "parsedate" version))
5777 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5778 (build-system r-build-system)
5780 `(("r-rematch2" ,r-rematch2)))
5781 (home-page "https://github.com/gaborcsardi/parsedate")
5783 "Recognize and parse dates in various formats")
5785 "This package provides three functions for dealing with dates:
5786 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5787 time formats, @code{parse_date} parses dates in unspecified formats,
5788 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5789 (license license:gpl2)))
5791 (define-public r-abc-data
5798 (uri (cran-uri "abc.data" version))
5801 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5802 (properties `((upstream-name . "abc.data")))
5803 (build-system r-build-system)
5804 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5805 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5807 "This package contains data which are used by functions of the abc
5808 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5809 algorithms for performing parameter estimation, model selection, and
5811 (license license:gpl3+)))
5813 (define-public r-abc
5820 (uri (cran-uri "abc" version))
5823 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5824 (build-system r-build-system)
5826 `(("r-abc-data" ,r-abc-data)
5827 ("r-locfit" ,r-locfit)
5830 ("r-quantreg" ,r-quantreg)))
5831 (home-page "https://cran.r-project.org/web/packages/abc/")
5832 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5834 "This package implements several @dfn{Approximate Bayesian
5835 Computation} (ABC) algorithms for performing parameter estimation, model
5836 selection, and goodness-of-fit. Cross-validation tools are also available for
5837 measuring the accuracy of ABC estimates, and to calculate the
5838 misclassification probabilities of different models.")
5839 (license license:gpl3+)))
5841 (define-public r-zip
5848 (uri (cran-uri "zip" version))
5851 "1dfsagb7bx35x4zx6f5xk2sk057fbyhskkpw3w72b805cjw920da"))))
5852 (build-system r-build-system)
5853 (home-page "https://github.com/gaborcsardi/zip")
5854 (synopsis "Cross-platform Zip compression")
5856 "This package provides a cross-platform Zip compression library for R.
5857 It is a replacement for the @code{zip} function, that does not require any
5858 additional external tools on any platform.")
5859 (license license:cc0)))
5861 (define-public r-openxlsx
5868 (uri (cran-uri "openxlsx" version))
5871 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5872 (build-system r-build-system)
5874 `(("r-rcpp" ,r-rcpp)
5875 ("r-stringi" ,r-stringi)
5878 `(("r-knitr" ,r-knitr)))
5879 (home-page "https://github.com/awalker89/openxlsx")
5880 (synopsis "Read, write and edit XLSX files")
5882 "This package simplifies the creation of Excel @code{.xlsx} files by
5883 providing a high level interface to writing, styling and editing worksheets.
5884 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5885 and @code{XLConnect} packages with the added benefit of removing the
5886 dependency on Java.")
5887 (license license:gpl3)))
5889 (define-public r-rio
5896 (uri (cran-uri "rio" version))
5899 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5900 (build-system r-build-system)
5902 `(("r-curl" ,r-curl)
5903 ("r-data-table" ,r-data-table)
5904 ("r-foreign" ,r-foreign)
5905 ("r-haven" ,r-haven)
5906 ("r-openxlsx" ,r-openxlsx)
5907 ("r-readxl" ,r-readxl)
5908 ("r-tibble" ,r-tibble)))
5909 (home-page "https://github.com/leeper/rio")
5910 (synopsis "Swiss-army knife for data I/O")
5912 "This package provides streamlined data import and export infrastructure
5913 by making assumptions that the user is probably willing to make: @code{import}
5914 and @code{export} determine the data structure from the file extension,
5915 reasonable defaults are used for data import and export (e.g.,
5916 @code{stringsAsFactors=FALSE}), web-based import is natively
5917 supported (including from SSL/HTTPS), compressed files can be read directly
5918 without explicit decompression, and fast import packages are used where
5919 appropriate. An additional convenience function, @code{convert}, provides a
5920 simple method for converting between file types.")
5921 (license license:gpl2)))
5923 (define-public r-maptools
5930 (uri (cran-uri "maptools" version))
5933 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5934 (build-system r-build-system)
5936 `(("r-foreign" ,r-foreign)
5937 ("r-lattice" ,r-lattice)
5939 (home-page "https://r-forge.r-project.org/projects/maptools/")
5940 (synopsis "Tools for reading and handling spatial objects")
5942 "This package provides a set of tools for manipulating and reading
5943 geographic data, in particular ESRI Shapefiles. It includes binary access to
5944 GSHHG shoreline files. The package also provides interface wrappers for
5945 exchanging spatial objects with other R packages.")
5946 ;; The C source files from shapelib are released under the Expat license.
5947 ;; The R code is released under GPL version 2 or later.
5948 (license (list license:gpl2+
5951 (define-public r-later
5958 (uri (cran-uri "later" version))
5961 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5962 (build-system r-build-system)
5966 ("r-rlang" ,r-rlang)))
5968 `(("r-knitr" ,r-knitr)))
5969 (home-page "https://github.com/r-lib/later")
5970 (synopsis "Utilities for delaying function execution")
5972 "This package provides tools to execute arbitrary R or C functions some
5973 time after the current time, after the R execution stack has emptied.")
5974 (license license:gpl2+)))
5976 (define-public r-promises
5983 (uri (cran-uri "promises" version))
5986 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5987 (build-system r-build-system)
5989 `(("r-later" ,r-later)
5990 ("r-magrittr" ,r-magrittr)
5993 ("r-rlang" ,r-rlang)))
5995 `(("r-knitr" ,r-knitr)))
5996 (home-page "https://rstudio.github.io/promises")
5997 (synopsis "Abstractions for promise-based asynchronous programming")
5999 "This package provides fundamental abstractions for doing asynchronous
6000 programming in R using promises. Asynchronous programming is useful for
6001 allowing a single R process to orchestrate multiple tasks in the background
6002 while also attending to something else. Semantics are similar to JavaScript
6003 promises, but with a syntax that is idiomatic R.")
6004 (license license:expat)))
6006 (define-public r-dosnow
6013 (uri (cran-uri "doSNOW" version))
6016 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6017 (properties `((upstream-name . "doSNOW")))
6018 (build-system r-build-system)
6020 `(("r-foreach" ,r-foreach)
6021 ("r-iterators" ,r-iterators)
6022 ("r-snow" ,r-snow)))
6023 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6024 (synopsis "Foreach parallel adaptor for the snow package")
6026 "This package provides a parallel backend for the @code{%dopar%} function
6027 using the @code{snow} package.")
6028 (license license:gpl2)))
6030 (define-public r-snowfall
6033 (version "1.84-6.1")
6036 (uri (cran-uri "snowfall" version))
6038 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6039 (build-system r-build-system)
6041 `(("r-snow" ,r-snow)))
6042 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6043 (synopsis "Easier cluster computing")
6044 (description "This package is a usability wrapper around snow for easier
6045 development of parallel R programs. This package offers e.g. extended error
6046 checks, and additional functions. All functions work in sequential mode, too,
6047 if no cluster is present or wished. The package is also designed as connector
6048 to the cluster management tool @code{sfCluster}, but can also used without
6050 (license license:gpl2+)))
6052 (define-public r-rappdirs
6059 (uri (cran-uri "rappdirs" version))
6062 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6063 (build-system r-build-system)
6064 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6065 (synopsis "Determine where to save data, caches, and logs")
6067 "This package provides an easy way to determine which directories on the
6068 user's computer should be used to save data, caches and logs. It is a port of
6069 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6070 (license license:expat)))
6072 (define-public r-renv
6079 (uri (cran-uri "renv" version))
6082 "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3"))))
6083 (properties `((upstream-name . "renv")))
6084 (build-system r-build-system)
6086 `(("r-knitr" ,r-knitr)))
6087 (home-page "https://rstudio.github.io/renv")
6088 (synopsis "Project environments")
6090 "This package provides a dependency management toolkit for R. Using
6091 renv, you can create and manage project-local R libraries, save the state of
6092 these libraries to a lockfile, and later restore your library as required.
6093 Together, these tools can help make your projects more isolated, portable, and
6095 (license license:expat)))
6097 (define-public r-learnr
6104 (uri (cran-uri "learnr" version))
6107 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6108 (build-system r-build-system)
6110 `(("r-checkmate" ,r-checkmate)
6111 ("r-ellipsis" ,r-ellipsis)
6112 ("r-evaluate" ,r-evaluate)
6113 ("r-htmltools" ,r-htmltools)
6114 ("r-htmlwidgets" ,r-htmlwidgets)
6115 ("r-jsonlite" ,r-jsonlite)
6116 ("r-knitr" ,r-knitr)
6117 ("r-markdown" ,r-markdown)
6118 ("r-rappdirs" ,r-rappdirs)
6120 ("r-rmarkdown" ,r-rmarkdown)
6121 ("r-rprojroot" ,r-rprojroot)
6122 ("r-shiny" ,r-shiny)
6123 ("r-withr" ,r-withr)))
6124 (home-page "https://rstudio.github.io/learnr/")
6125 (synopsis "Interactive tutorials for R")
6127 "This package provides tools to create interactive tutorials using R
6128 Markdown. Use a combination of narrative, figures, videos, exercises, and
6129 quizzes to create self-paced tutorials for learning about R and R packages.")
6130 (license license:asl2.0)))
6132 (define-public r-analytics
6134 (name "r-analytics")
6139 (uri (cran-uri "analytics" version))
6142 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6143 (build-system r-build-system)
6146 ("r-cluster" ,r-cluster)
6147 ("r-fractal" ,r-fractal)
6148 ("r-lmtest" ,r-lmtest)
6151 ("r-powerplus" ,r-powerplus)
6152 ("r-robust" ,r-robust)
6153 ("r-trend" ,r-trend)
6157 (home-page "https://cran.r-project.org/web/packages/analytics/")
6158 (synopsis "Collection of data analysis tools")
6160 "This package is a collection of data analysis tools. It includes tools
6161 for regression outlier detection in a fitted linear model, stationary
6162 bootstrap using a truncated geometric distribution, a comprehensive test for
6163 weak stationarity, column means by group, weighted biplots, and a heuristic to
6164 obtain a better initial configuration in non-metric MDS.")
6165 (license license:gpl2)))
6167 (define-public r-reticulate
6169 (name "r-reticulate")
6174 (uri (cran-uri "reticulate" version))
6177 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6178 (build-system r-build-system)
6179 (inputs `(("python" ,python)))
6181 `(("r-rappdirs" ,r-rappdirs)
6182 ("r-jsonlite" ,r-jsonlite)
6183 ("r-matrix" ,r-matrix)
6184 ("r-rcpp" ,r-rcpp)))
6186 `(("r-knitr" ,r-knitr)))
6187 (home-page "https://github.com/rstudio/reticulate")
6188 (synopsis "R interface to Python")
6190 "This package provides an interface from R to Python modules, classes,
6191 and functions. When calling into Python, R data types are automatically
6192 converted to their equivalent Python types. When values are returned from
6193 Python to R they are converted back to R types.")
6194 (license license:asl2.0)))
6196 (define-public r-bibtex
6203 (uri (cran-uri "bibtex" version))
6206 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6207 (build-system r-build-system)
6208 (propagated-inputs `(("r-stringr" ,r-stringr)))
6209 (home-page "https://github.com/romainfrancois/bibtex")
6210 (synopsis "Bibtex parser")
6211 (description "This package provides a utility for R to parse a bibtex
6213 (license license:gpl2+)))
6215 (define-public r-ggseqlogo
6217 (name "r-ggseqlogo")
6222 (uri (cran-uri "ggseqlogo" version))
6225 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6226 (build-system r-build-system)
6227 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6228 (home-page "https://github.com/omarwagih/ggseqlogo")
6229 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6231 "The range of functions provided by this package makes it possible to
6232 draw highly versatile genomic sequence logos. Features include, but are not
6233 limited to, modifying colour schemes and fonts used to draw the logo,
6234 generating multiple logo plots, and aiding the visualisation with annotations.
6235 Sequence logos can easily be combined with other ggplot2 plots.")
6236 ;; Unspecified version of the LGPL.
6237 (license license:lgpl3+)))
6239 (define-public r-ggsci
6246 (uri (cran-uri "ggsci" version))
6249 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6250 (build-system r-build-system)
6252 `(("r-ggplot2" ,r-ggplot2)
6253 ("r-scales" ,r-scales)))
6254 (home-page "https://nanx.me/ggsci/")
6255 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6257 "This package provides a collection of ggplot2 color palettes inspired by
6258 plots in scientific journals, data visualization libraries, science fiction
6259 movies, and TV shows.")
6260 (license license:gpl3)))
6262 (define-public r-ggsignif
6269 (uri (cran-uri "ggsignif" version))
6272 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6273 (build-system r-build-system)
6275 `(("r-knitr" ,r-knitr)))
6277 `(("r-ggplot2" ,r-ggplot2)))
6278 (home-page "https://github.com/const-ae/ggsignif")
6279 (synopsis "Significance brackets for ggplot2")
6281 "Enrich your ggplots with group-wise comparisons. This package provides
6282 an easy way to indicate if two groups are significantly different. Commonly
6283 this is shown by a bracket on top connecting the groups of interest which
6284 itself is annotated with the level of significance. The package provides a
6285 single layer that takes the groups for comparison and the test as arguments
6286 and adds the annotation to the plot.")
6287 (license license:gpl3)))
6289 (define-public r-rstatix
6296 (uri (cran-uri "rstatix" version))
6299 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6300 (properties `((upstream-name . "rstatix")))
6301 (build-system r-build-system)
6303 `(("r-broom" ,r-broom)
6305 ("r-corrplot" ,r-corrplot)
6306 ("r-dplyr" ,r-dplyr)
6307 ("r-generics" ,r-generics)
6308 ("r-magrittr" ,r-magrittr)
6309 ("r-purrr" ,r-purrr)
6310 ("r-rlang" ,r-rlang)
6311 ("r-tibble" ,r-tibble)
6312 ("r-tidyr" ,r-tidyr)
6313 ("r-tidyselect" ,r-tidyselect)))
6314 (home-page "https://rpkgs.datanovia.com/rstatix/")
6315 (synopsis "Pipe-friendly framework for basic statistical tests")
6317 "This package provides a simple and intuitive pipe-friendly framework,
6318 coherent with the @code{tidyverse} design philosophy, for performing basic
6319 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6320 correlation analyses. The output of each test is automatically transformed
6321 into a tidy data frame to facilitate visualization. Additional functions are
6322 available for reshaping, reordering, manipulating and visualizing correlation
6324 (license license:gpl2)))
6326 (define-public r-ggpubr
6333 (uri (cran-uri "ggpubr" version))
6336 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6337 (build-system r-build-system)
6339 `(("r-cowplot" ,r-cowplot)
6340 ("r-dplyr" ,r-dplyr)
6341 ("r-ggplot2" ,r-ggplot2)
6342 ("r-ggrepel" ,r-ggrepel)
6343 ("r-ggsci" ,r-ggsci)
6344 ("r-ggsignif" ,r-ggsignif)
6346 ("r-gridextra" ,r-gridextra)
6347 ("r-magrittr" ,r-magrittr)
6348 ("r-polynom" ,r-polynom)
6349 ("r-purrr" ,r-purrr)
6350 ("r-rlang" ,r-rlang)
6351 ("r-scales" ,r-scales)
6352 ("r-rstatix" ,r-rstatix)
6353 ("r-tibble" ,r-tibble)
6354 ("r-tidyr" ,r-tidyr)))
6355 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6356 (synopsis "ggplot2-based publication-ready plots")
6358 "The ggplot2 package is an excellent and flexible package for elegant
6359 data visualization in R. However the default generated plots require some
6360 formatting before we can send them for publication. The ggpubr package
6361 provides some easy-to-use functions for creating and customizing ggplot2-based
6362 publication-ready plots.")
6363 (license license:gpl2)))
6365 (define-public r-ellipse
6372 (uri (cran-uri "ellipse" version))
6375 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6376 (build-system r-build-system)
6377 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6378 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6380 "This package contains various routines for drawing ellipses and
6381 ellipse-like confidence regions, implementing the plots described in Murdoch
6382 and Chow (1996), A graphical display of large correlation matrices, The
6383 American Statistician 50, 178-180. There are also routines implementing the
6384 profile plots described in Bates and Watts (1988), Nonlinear Regression
6385 Analysis and its Applications.")
6386 (license license:gpl2+)))
6388 (define-public r-flashclust
6390 (name "r-flashclust")
6395 (uri (cran-uri "flashClust" version))
6398 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6399 (properties `((upstream-name . "flashClust")))
6400 (build-system r-build-system)
6401 (native-inputs `(("gfortran" ,gfortran)))
6402 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6403 (synopsis "Implementation of optimal hierarchical clustering")
6405 "This package provides a fast implementation of hierarchical
6407 (license license:gpl2+)))
6409 (define-public r-factominer
6411 (name "r-factominer")
6416 (uri (cran-uri "FactoMineR" version))
6419 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6420 (properties `((upstream-name . "FactoMineR")))
6421 (build-system r-build-system)
6424 ("r-cluster" ,r-cluster)
6425 ("r-ellipse" ,r-ellipse)
6426 ("r-flashclust" ,r-flashclust)
6427 ("r-ggplot2" ,r-ggplot2)
6428 ("r-ggrepel" ,r-ggrepel)
6429 ("r-lattice" ,r-lattice)
6430 ("r-leaps" ,r-leaps)
6432 ("r-scatterplot3d" ,r-scatterplot3d)))
6433 (home-page "http://factominer.free.fr")
6434 (synopsis "Multivariate exploratory data analysis and data mining")
6436 "This package provides exploratory data analysis methods to summarize,
6437 visualize and describe datasets. The main principal component methods are
6438 available, those with the largest potential in terms of applications:
6439 principal component analysis (PCA) when variables are quantitative,
6440 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6441 variables are categorical, Multiple Factor Analysis when variables are
6442 structured in groups, etc. and hierarchical cluster analysis.")
6443 (license license:gpl2+)))
6445 (define-public r-factoextra
6447 (name "r-factoextra")
6452 (uri (cran-uri "factoextra" version))
6455 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6456 (build-system r-build-system)
6458 `(("r-abind" ,r-abind)
6459 ("r-cluster" ,r-cluster)
6460 ("r-dendextend" ,r-dendextend)
6461 ("r-factominer" ,r-factominer)
6462 ("r-ggplot2" ,r-ggplot2)
6463 ("r-ggpubr" ,r-ggpubr)
6464 ("r-ggrepel" ,r-ggrepel)
6465 ("r-reshape2" ,r-reshape2)
6466 ("r-tidyr" ,r-tidyr)))
6467 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6468 (synopsis "Extract and visualize the results of multivariate data analyses")
6470 "This package provides some easy-to-use functions to extract and
6471 visualize the output of multivariate data analyses, including
6472 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6473 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6474 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6475 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6476 packages. It contains also functions for simplifying some clustering analysis
6477 steps and provides ggplot2-based elegant data visualization.")
6478 (license license:gpl2)))
6480 (define-public r-fansi
6487 (uri (cran-uri "fansi" version))
6490 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6491 (build-system r-build-system)
6493 `(("r-knitr" ,r-knitr))) ; for vignettes
6494 (home-page "https://github.com/brodieG/fansi")
6495 (synopsis "ANSI control sequence aware string functions")
6497 "This package provides counterparts to R string manipulation functions
6498 that account for the effects of ANSI text formatting control sequences.")
6499 (license license:gpl2+)))
6501 (define-public r-nbclust
6508 (uri (cran-uri "NbClust" version))
6511 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6512 (properties `((upstream-name . "NbClust")))
6513 (build-system r-build-system)
6514 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6515 (synopsis "Determine the best number of clusters in a data set")
6517 "NbClust provides 30 indexes for determining the optimal number of
6518 clusters in a data set and offers the best clustering scheme from different
6519 results to the user.")
6520 (license license:gpl2)))
6522 (define-public r-hdf5r
6529 (uri (cran-uri "hdf5r" version))
6532 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6533 (build-system r-build-system)
6538 `(("r-bit64" ,r-bit64)
6541 `(("r-knitr" ,r-knitr)))
6542 (home-page "https://hhoeflin.github.io/hdf5r")
6543 (synopsis "Interface to the HDF5 binary data format")
6545 "HDF5 is a data model, library and file format for storing and managing
6546 large amounts of data. This package provides a nearly feature complete,
6547 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6548 functionality is added so that HDF5 objects behave very similar to their
6549 corresponding R counterparts.")
6550 (license license:asl2.0)))
6552 (define-public r-itertools
6554 (name "r-itertools")
6559 (uri (cran-uri "itertools" version))
6562 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6563 (build-system r-build-system)
6565 `(("r-iterators" ,r-iterators)))
6566 (home-page "https://cran.r-project.org/web/packages/itertools/")
6567 (synopsis "Iterator tools")
6569 "This package provides various tools for creating iterators, many
6570 patterned after functions in the Python @code{itertools} module, and others
6571 patterned after functions in the snow package.")
6572 (license license:gpl2)))
6574 (define-public r-polynom
6581 (uri (cran-uri "polynom" version))
6584 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6585 (build-system r-build-system)
6586 (home-page "https://cran.r-project.org/web/packages/polynom/")
6587 (synopsis "Functions for univariate polynomial manipulations")
6589 "This package provides a collection of functions to implement a class for
6590 univariate polynomial manipulations.")
6591 (license license:gpl2)))
6593 (define-public r-gbrd
6600 (uri (cran-uri "gbRd" version))
6603 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6604 (properties `((upstream-name . "gbRd")))
6605 (build-system r-build-system)
6606 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6607 (synopsis "Utilities for processing Rd objects and files")
6609 "This package provides utilities for processing Rd objects and files.
6610 Extract argument descriptions and other parts of the help pages of
6612 (license license:gpl2+)))
6614 (define-public r-rjags
6621 (uri (cran-uri "rjags" version))
6624 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6625 (build-system r-build-system)
6627 `(("r-coda" ,r-coda)))
6631 `(("pkg-config" ,pkg-config)))
6632 (home-page "http://mcmc-jags.sourceforge.net")
6633 (synopsis "Bayesian graphical models using MCMC")
6635 "This package provides an R interface to the JAGS MCMC library. JAGS is
6636 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6637 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6638 (license license:gpl2)))
6640 (define-public r-rdpack
6647 (uri (cran-uri "Rdpack" version))
6650 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6651 (properties `((upstream-name . "Rdpack")))
6652 (build-system r-build-system)
6654 `(("r-bibtex" ,r-bibtex)
6655 ("r-gbrd" ,r-gbrd)))
6656 (home-page "https://github.com/GeoBosh/Rdpack")
6657 (synopsis "Update and manipulate Rd documentation objects")
6659 "This package provides functions for manipulation of R documentation
6660 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6661 updating Rd documentation for functions, methods and classes; it also includes
6662 Rd macros for citations and import of references from bibtex files for use in
6663 Rd files and roxygen2 comments, as well as many functions for manipulation of
6664 references and Rd files.")
6665 (license license:gpl2+)))
6667 (define-public r-officer
6674 (uri (cran-uri "officer" version))
6677 "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x"))))
6678 (build-system r-build-system)
6680 `(("r-magrittr" ,r-magrittr)
6686 `(("r-knitr" ,r-knitr)))
6687 (home-page "https://davidgohel.github.io/officer")
6688 (synopsis "Manipulation of Word and PowerPoint documents")
6690 "This package provides tools to access and manipulate Word and PowerPoint
6691 documents from R. The package focuses on tabular and graphical reporting from
6692 R; it also provides two functions that let users get document content into
6693 data objects. A set of functions lets add and remove images, tables and
6694 paragraphs of text in new or existing documents. When working with PowerPoint
6695 presentations, slides can be added or removed; shapes inside slides can also
6696 be added or removed. When working with Word documents, a cursor can be used
6697 to help insert or delete content at a specific location in the document.")
6698 (license license:gpl3)))
6700 (define-public r-profilemodel
6702 (name "r-profilemodel")
6707 (uri (cran-uri "profileModel" version))
6710 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6711 (properties `((upstream-name . "profileModel")))
6712 (build-system r-build-system)
6713 (home-page "https://github.com/ikosmidis/profileModel")
6714 (synopsis "Profiling inference functions for various model classes")
6716 "This package provides tools that can be used to calculate, evaluate,
6717 plot and use for inference the profiles of *arbitrary* inference functions for
6718 arbitrary @code{glm}-like fitted models with linear predictors. More information
6719 on the methods that are implemented can be found in Kosmidis (2008)
6720 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6721 (license license:gpl2+)))
6723 (define-public r-brglm
6730 (uri (cran-uri "brglm" version))
6733 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6734 (properties `((upstream-name . "brglm")))
6735 (build-system r-build-system)
6737 `(("r-profilemodel" ,r-profilemodel)))
6738 (home-page "https://github.com/ikosmidis/brglm")
6739 (synopsis "Bias reduction in binomial-response generalized linear models")
6741 "Fit generalized linear models with binomial responses using either an
6742 adjusted-score approach to bias reduction or maximum penalized likelihood
6743 where penalization is by Jeffreys invariant prior. These procedures return
6744 estimates with improved frequentist properties (bias, mean squared error) that
6745 are always finite even in cases where the maximum likelihood estimates are
6746 infinite (data separation). Fitting takes place by fitting generalized linear
6747 models on iteratively updated pseudo-data. The interface is essentially the
6748 same as @code{glm}. More flexibility is provided by the fact that custom
6749 pseudo-data representations can be specified and used for model fitting.
6750 Functions are provided for the construction of confidence intervals for the
6751 reduced-bias estimates.")
6752 (license license:gpl2+)))
6754 (define-public r-entropy
6761 (uri (cran-uri "entropy" version))
6764 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6765 (properties `((upstream-name . "entropy")))
6766 (build-system r-build-system)
6767 (home-page "https://www.strimmerlab.org/software/entropy/")
6768 (synopsis "Estimation of entropy, mutual information and related quantities")
6770 "This package implements various estimators of entropy, such as the
6771 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6772 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6773 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6774 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6775 mutual information, and chi-squared statistic of independence. In addition
6776 there are functions for discretizing continuous random variables.")
6777 (license license:gpl3+)))
6779 (define-public r-abn
6786 (uri (cran-uri "abn" version))
6789 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6790 (build-system r-build-system)
6794 `(("r-boot" ,r-boot)
6795 ("r-brglm" ,r-brglm)
6796 ("r-entropy" ,r-entropy)
6799 ("r-moments" ,r-moments)
6802 ("r-rcpparmadillo" ,r-rcpparmadillo)
6803 ("r-rjags" ,r-rjags)))
6804 (home-page "https://r-bayesian-networks.org/")
6805 (synopsis "Modelling multivariate data with additive bayesian networks")
6807 "Bayesian network analysis is a form of probabilistic graphical models
6808 which derives from empirical data a directed acyclic graph, DAG, describing
6809 the dependency structure between random variables. An additive Bayesian
6810 network model consists of a form of a DAG where each node comprises a
6811 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6812 equivalent to Bayesian multivariate regression using graphical modelling, they
6813 generalises the usual multivariable regression, GLM, to multiple dependent
6814 variables. This package provides routines to help determine optimal Bayesian
6815 network models for a given data set, where these models are used to identify
6816 statistical dependencies in messy, complex data.")
6817 (license license:gpl2+)))
6819 (define-public r-acd
6826 (uri (cran-uri "ACD" version))
6829 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6830 (properties `((upstream-name . "ACD")))
6831 (build-system r-build-system)
6832 (home-page "https://cran.r-project.org/web/packages/ACD/")
6833 (synopsis "Categorical data analysis with complete or missing responses")
6835 "This package provides tools for categorical data analysis with complete
6836 or missing responses.")
6837 (license license:gpl2+)))
6839 (define-public r-acdm
6846 (uri (cran-uri "ACDm" version))
6849 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6850 (properties `((upstream-name . "ACDm")))
6851 (build-system r-build-system)
6853 `(("r-dplyr" ,r-dplyr)
6854 ("r-ggplot2" ,r-ggplot2)
6856 ("r-rsolnp" ,r-rsolnp)
6858 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6859 (synopsis "Tools for Autoregressive Conditional Duration Models")
6861 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6862 and Russell, 1998) models. It creates trade, price or volume durations from
6863 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6865 (license license:gpl2+)))
6867 (define-public r-overlap
6874 (uri (cran-uri "overlap" version))
6877 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6878 (build-system r-build-system)
6879 (home-page "https://cran.r-project.org/web/packages/overlap/")
6880 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6882 "This package provides functions to fit kernel density functions to data
6883 on temporal activity patterns of animals; estimate coefficients of overlapping
6884 of densities for two species; and calculate bootstrap estimates of confidence
6886 (license license:gpl3+)))
6888 (define-public r-snakecase
6890 (name "r-snakecase")
6895 (uri (cran-uri "snakecase" version))
6898 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6899 (build-system r-build-system)
6901 `(("r-stringi" ,r-stringi)
6902 ("r-stringr" ,r-stringr)))
6903 (home-page "https://github.com/Tazinho/snakecase")
6904 (synopsis "Convert strings into any case")
6906 "This package provides a consistent, flexible and easy to use tool to
6907 parse and convert strings into cases like snake or camel among others.")
6908 (license license:gpl3)))
6910 (define-public r-prediction
6912 (name "r-prediction")
6917 (uri (cran-uri "prediction" version))
6920 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6921 (build-system r-build-system)
6923 `(("r-data-table" ,r-data-table)))
6924 (home-page "https://github.com/leeper/prediction")
6925 (synopsis "Tidy, type-safe prediction methods")
6927 "This package provides the @code{prediction()} function, a type-safe
6928 alternative to @code{predict()} that always returns a data frame. The package
6929 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6930 from the @code{stats} package, as well as numerous other model classes from
6931 other add-on packages.")
6932 (license license:expat)))
6934 (define-public r-insight
6941 (uri (cran-uri "insight" version))
6944 "1ajc8c5mi3ma5411lmlqp2ihkk5n0h8a1c0r3j07wk33p31c1qvl"))))
6945 (build-system r-build-system)
6947 `(("r-knitr" ,r-knitr)))
6948 (home-page "https://easystats.github.io/insight/")
6949 (synopsis "Easy access to model information for various model objects")
6951 "This package provides a tool to provide an easy, intuitive and
6952 consistent access to information contained in various R models, like model
6953 formulas, model terms, information about random effects, data that was used to
6954 fit the model or data from response variables. The package mainly revolves
6955 around two types of functions: Functions that find (the names of) information,
6956 starting with @code{find_}, and functions that get the underlying data,
6957 starting with @code{get_}. The package has a consistent syntax and works with
6958 many different model objects, where otherwise functions to access these
6959 information are missing.")
6960 (license license:gpl3)))
6962 (define-public r-sjlabelled
6964 (name "r-sjlabelled")
6969 (uri (cran-uri "sjlabelled" version))
6972 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
6973 (build-system r-build-system)
6975 `(("r-insight" ,r-insight)))
6977 `(("r-knitr" ,r-knitr)))
6978 (home-page "https://github.com/strengejacke/sjlabelled")
6979 (synopsis "Labelled data utility functions")
6981 "This package provides a collection of functions dealing with labelled
6982 data, like reading and writing data between R and other statistical software
6983 packages. This includes easy ways to get, set or change value and variable
6984 label attributes, to convert labelled vectors into factors or numeric (and
6985 vice versa), or to deal with multiple declared missing values.")
6986 (license license:gpl3)))
6988 (define-public r-sjmisc
6995 (uri (cran-uri "sjmisc" version))
6998 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6999 (build-system r-build-system)
7001 `(("r-dplyr" ,r-dplyr)
7002 ("r-insight" ,r-insight)
7003 ("r-magrittr" ,r-magrittr)
7004 ("r-purrr" ,r-purrr)
7005 ("r-rlang" ,r-rlang)
7006 ("r-sjlabelled" ,r-sjlabelled)
7007 ("r-tidyselect" ,r-tidyselect)))
7009 `(("r-knitr" ,r-knitr)))
7010 (home-page "https://github.com/strengejacke/sjmisc")
7011 (synopsis "Data and variable transformation functions")
7013 "This package is a collection of miscellaneous utility functions,
7014 supporting data transformation tasks like recoding, dichotomizing or grouping
7015 variables, setting and replacing missing values. The data transformation
7016 functions also support labelled data, and all integrate seamlessly into a
7017 tidyverse workflow.")
7018 (license license:gpl3)))
7020 (define-public r-nortest
7027 (uri (cran-uri "nortest" version))
7030 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7031 (build-system r-build-system)
7032 (home-page "https://cran.r-project.org/web/packages/nortest/")
7033 (synopsis "Tests for normality")
7035 "This package provides five omnibus tests for testing the composite
7036 hypothesis of normality.")
7037 (license license:gpl2+)))
7039 (define-public r-moonbook
7046 (uri (cran-uri "moonBook" version))
7049 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7050 (properties `((upstream-name . "moonBook")))
7051 (build-system r-build-system)
7053 `(("r-magrittr" ,r-magrittr)
7054 ("r-nortest" ,r-nortest)
7055 ("r-purrr" ,r-purrr)
7056 ("r-sjmisc" ,r-sjmisc)
7057 ("r-stringr" ,r-stringr)
7058 ("r-survival" ,r-survival)))
7059 (home-page "https://github.com/cardiomoon/moonBook")
7060 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7062 "This package provides several analysis-related functions for the book
7063 entitled \"R statistics and graph for medical articles\" (written in Korean),
7064 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7066 (license license:gpl2)))
7068 (define-public r-flextable
7070 (name "r-flextable")
7075 (uri (cran-uri "flextable" version))
7078 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7079 (build-system r-build-system)
7081 `(("r-base64enc" ,r-base64enc)
7082 ("r-data-table" ,r-data-table)
7083 ("r-gdtools" ,r-gdtools)
7084 ("r-htmltools" ,r-htmltools)
7085 ("r-knitr" ,r-knitr)
7086 ("r-officer" ,r-officer)
7087 ("r-rlang" ,r-rlang)
7088 ("r-rmarkdown" ,r-rmarkdown)
7090 ("r-xml2" ,r-xml2)))
7091 (home-page "https://davidgohel.github.io/flextable")
7092 (synopsis "Functions for tabular reporting")
7094 "This package provides tools to create pretty tables for HTML documents
7095 and other formats. Functions are provided to let users create tables, modify
7096 and format their content. It extends the @code{officer} package and can be
7097 used within R markdown documents when rendering to HTML and to Word
7099 (license license:gpl3)))
7101 (define-public r-writexl
7108 (uri (cran-uri "writexl" version))
7111 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7112 (build-system r-build-system)
7113 (inputs `(("zlib" ,zlib)))
7114 (home-page "https://github.com/ropensci/writexl")
7115 (synopsis "Export data frames to xlsx format")
7117 "This package provides a data frame to xlsx exporter based on
7119 (license license:bsd-2)))
7121 (define-public r-biasedurn
7123 (name "r-biasedurn")
7128 (uri (cran-uri "BiasedUrn" version))
7131 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7132 (properties `((upstream-name . "BiasedUrn")))
7133 (build-system r-build-system)
7134 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7135 (synopsis "Biased Urn model distributions")
7137 "This package provides statistical models of biased sampling in the form
7138 of univariate and multivariate noncentral hypergeometric distributions,
7139 including Wallenius' noncentral hypergeometric distribution and Fisher's
7140 noncentral hypergeometric distribution (also called extended hypergeometric
7142 (license license:gpl3)))
7144 (define-public r-goplot
7151 (uri (cran-uri "GOplot" version))
7154 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7155 (properties `((upstream-name . "GOplot")))
7156 (build-system r-build-system)
7158 `(("r-ggdendro" ,r-ggdendro)
7159 ("r-ggplot2" ,r-ggplot2)
7160 ("r-gridextra" ,r-gridextra)
7161 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7162 (home-page "https://github.com/wencke/wencke.github.io")
7163 (synopsis "Visualization of functional analysis data")
7165 "This package provides an implementation of multilayered visualizations
7166 for enhanced graphical representation of functional analysis data. It
7167 combines and integrates omics data derived from expression and functional
7168 annotation enrichment analyses. Its plotting functions have been developed
7169 with an hierarchical structure in mind: starting from a general overview to
7170 identify the most enriched categories (modified bar plot, bubble plot) to a
7171 more detailed one displaying different types of relevant information for the
7172 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7173 Venn diagram, heatmap).")
7174 (license license:gpl2)))
7176 (define-public r-getopt
7183 (uri (cran-uri "getopt" version))
7186 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7187 (build-system r-build-system)
7188 (home-page "https://github.com/trevorld/getopt")
7189 (synopsis "Command-line option processor for R")
7191 "This package is designed to be used with Rscript to write shebang
7192 scripts that accept short and long options. Many users will prefer to
7193 use the packages @code{optparse} or @code{argparse} which add extra
7194 features like automatically generated help options and usage texts,
7195 support for default values, positional argument support, etc.")
7196 (license license:gpl2+)))
7198 (define-public r-findpython
7200 (name "r-findpython")
7205 (uri (cran-uri "findpython" version))
7208 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7209 (build-system r-build-system)
7210 (home-page "https://github.com/trevorld/findpython")
7211 (synopsis "Functions to find an acceptable Python binary")
7213 "This package was designed to find an acceptable Python binary that
7214 matches version and feature constraints.")
7215 (license license:expat)))
7217 ;; This in not the same as "r-argparser"
7218 (define-public r-argparse
7225 (uri (cran-uri "argparse" version))
7228 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7229 (build-system r-build-system)
7230 (inputs `(("python" ,python)))
7232 `(("r-findpython" ,r-findpython)
7233 ("r-jsonlite" ,r-jsonlite)
7235 (home-page "https://github.com/trevorld/argparse")
7236 (synopsis "Command line optional and positional argument parser")
7238 "This package provides a command line parser to be used with Rscript to
7239 write shebang scripts that gracefully accept positional and optional arguments
7240 and automatically generate usage notices.")
7241 (license license:gpl2+)))
7243 (define-public r-hash
7250 (uri (cran-uri "hash" version))
7253 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7254 (build-system r-build-system)
7255 (home-page "https://cran.r-project.org/web/packages/hash/")
7256 (synopsis "Implementation of hash/associated arrays/dictionaries")
7258 "This package implements a data structure similar to hashes in Perl and
7259 dictionaries in Python but with a purposefully R flavor. For objects of
7260 appreciable size, access using hashes outperforms native named lists and
7262 (license license:gpl2+)))
7264 (define-public r-orddom
7271 (uri (cran-uri "orddom" version))
7274 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7275 (build-system r-build-system)
7276 (propagated-inputs `(("r-psych" ,r-psych)))
7277 (home-page "https://cran.r-project.org/web/packages/orddom/")
7278 (synopsis "Ordinal dominance statistics")
7280 "This package provides tools to compute ordinal, statistics and effect
7281 sizes as an alternative to mean comparison: Cliff's delta or success rate
7282 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7283 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7284 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7285 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7286 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7287 Group (Non-)Overlap considerations.")
7288 (license license:gpl2)))
7290 (define-public r-deriv
7297 (uri (cran-uri "Deriv" version))
7300 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7301 (properties `((upstream-name . "Deriv")))
7302 (build-system r-build-system)
7303 (home-page "https://cran.r-project.org/web/packages/Deriv")
7304 (synopsis "Symbolic differentiation")
7306 "This package provides an R-based solution for symbolic differentiation.
7307 It admits user-defined functions as well as function substitution in arguments
7308 of functions to be differentiated. Some symbolic simplification is part of
7310 (license license:gpl3+)))
7312 (define-public r-doby
7319 (uri (cran-uri "doBy" version))
7322 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7323 (properties `((upstream-name . "doBy")))
7324 (build-system r-build-system)
7326 `(("r-broom" ,r-broom)
7327 ("r-deriv" ,r-deriv)
7328 ("r-dplyr" ,r-dplyr)
7329 ("r-ggplot2" ,r-ggplot2)
7330 ("r-magrittr" ,r-magrittr)
7332 ("r-matrix" ,r-matrix)
7333 ("r-pbkrtest" ,r-pbkrtest)
7334 ("r-tibble" ,r-tibble)))
7336 `(("r-knitr" ,r-knitr)))
7337 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7338 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7340 "This package contains:
7343 @item facilities for working with grouped data: @code{do}
7344 something to data stratified @code{by} some variables.
7345 @item implementations of least-squares means, general linear contrasts, and
7346 @item miscellaneous other utilities.
7348 (license license:gpl2+)))
7350 (define-public r-refgenome
7352 (name "r-refgenome")
7357 (uri (cran-uri "refGenome" version))
7360 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7361 (properties `((upstream-name . "refGenome")))
7362 (build-system r-build-system)
7366 ("r-rsqlite" ,r-rsqlite)))
7367 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7369 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7371 "This package contains functionality for importing and managing of
7372 downloaded genome annotation data from the Ensembl genome browser (European
7373 Bioinformatics Institute) and from the UCSC genome browser (University of
7374 California, Santa Cruz) and annotation routines for genomic positions and
7375 splice site positions.")
7376 (license license:gpl2)))
7378 (define-public r-basix
7385 (uri (cran-uri "BASIX" version))
7388 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7389 (properties `((upstream-name . "BASIX")))
7390 (build-system r-build-system)
7391 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7392 (synopsis "Efficient C/C++ toolset for R")
7394 "BASIX provides some efficient C/C++ implementations of native R
7395 procedures to speed up calculations in R.")
7396 (license license:gpl2)))
7398 (define-public r-blockfest
7400 (name "r-blockfest")
7405 (uri (cran-uri "BlockFeST" version))
7408 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7409 (properties `((upstream-name . "BlockFeST")))
7410 (build-system r-build-system)
7411 (propagated-inputs `(("r-basix" ,r-basix)))
7412 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7413 (synopsis "Bayesian calculation of region-specific fixation index")
7415 "This package provides an R implementation of an extension of the
7416 BayeScan software for codominant markers, adding the option to group
7417 individual SNPs into pre-defined blocks. A typical application of this new
7418 approach is the identification of genomic regions, genes, or gene sets
7419 containing one or more SNPs that evolved under directional selection.")
7420 (license license:gpl2)))
7422 (define-public r-proc
7429 (uri (cran-uri "pROC" version))
7432 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7433 (properties `((upstream-name . "pROC")))
7434 (build-system r-build-system)
7436 `(("r-plyr" ,r-plyr)
7437 ("r-rcpp" ,r-rcpp)))
7438 (home-page "https://web.expasy.org/pROC/")
7439 (synopsis "Display and analyze ROC curves")
7441 "This package provides tools for visualizing, smoothing and comparing
7442 receiver operating characteristic (ROC curves). The area under the
7443 curve (AUC) can be compared with statistical tests based on U-statistics or
7444 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7445 (license license:gpl3+)))
7447 (define-public r-rootsolve
7449 (name "r-rootsolve")
7454 (uri (cran-uri "rootSolve" version))
7457 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7458 (properties `((upstream-name . "rootSolve")))
7459 (build-system r-build-system)
7460 (native-inputs `(("gfortran" ,gfortran)))
7461 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7462 (synopsis "Tools for the analysis of ordinary differential equations")
7464 "This package provides routines to find the root of nonlinear functions,
7465 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7466 differential equations} (ODE). It includes routines that:
7469 @item generate gradient and jacobian matrices (full and banded),
7470 @item find roots of non-linear equations by the Newton-Raphson method,
7471 @item estimate steady-state conditions of a system of (differential) equations
7472 in full, banded or sparse form, using the Newton-Raphson method, or by
7473 dynamically running,
7474 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7475 and 3-D partial differential equations, that have been converted to ordinary
7476 differential equations by numerical differencing (using the method-of-lines
7479 (license license:gpl2+)))
7481 (define-public r-abcanalysis
7483 (name "r-abcanalysis")
7488 (uri (cran-uri "ABCanalysis" version))
7490 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7491 (properties `((upstream-name . "ABCanalysis")))
7492 (build-system r-build-system)
7493 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7494 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7495 (synopsis "Computed ABC Analysis")
7497 "Multivariate data sets often differ in several factors or derived statistical
7498 parameters, which have to be selected for a valid interpretation. Basing this
7499 selection on traditional statistical limits leads occasionally to the perception
7500 of losing information from a data set. This package provides tools to calculate
7501 these limits on the basis of the mathematical properties of the distribution of
7502 the analyzed items.")
7503 (license license:gpl3)))
7505 (define-public r-slam
7512 (uri (cran-uri "slam" version))
7514 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7515 (build-system r-build-system)
7516 (home-page "https://cran.r-project.org/web/packages/slam/")
7517 (synopsis "Sparse lightweight arrays and matrices")
7519 "This package contains data structures and algorithms for sparse arrays and matrices,
7520 based on index arrays and simple triplet representations, respectively.")
7521 (license license:gpl2)))
7523 (define-public r-manipulatewidget
7525 (name "r-manipulatewidget")
7530 (uri (cran-uri "manipulateWidget" version))
7532 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7534 `((upstream-name . "manipulateWidget")))
7535 (build-system r-build-system)
7537 `(("r-base64enc" ,r-base64enc)
7538 ("r-codetools" ,r-codetools)
7539 ("r-htmltools" ,r-htmltools)
7540 ("r-htmlwidgets" ,r-htmlwidgets)
7541 ("r-knitr" ,r-knitr)
7542 ("r-miniui" ,r-miniui)
7543 ("r-shiny" ,r-shiny)
7544 ("r-webshot" ,r-webshot)))
7545 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7546 (synopsis "Add even more interactivity to interactive charts")
7548 "This package lets you create in just a few lines of R code a nice user interface to
7549 modify the data or the graphical parameters of one or multiple interactive
7550 charts. It is useful to quickly explore visually some data or for package
7551 developers to generate user interfaces easy to maintain.")
7552 (license license:gpl2+)))
7561 (uri (cran-uri "A3" version))
7563 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7564 (properties `((upstream-name . "A3")))
7565 (build-system r-build-system)
7567 `(("r-pbapply" ,r-pbapply)
7568 ("r-xtable" ,r-xtable)))
7569 (home-page "https://cran.r-project.org/web/packages/A3/")
7570 (synopsis "Error metrics for predictive models")
7572 "This package supplies tools for tabulating and analyzing the results of predictive
7573 models. The methods employed are applicable to virtually any predictive model
7574 and make comparisons between different methodologies straightforward.")
7575 (license license:gpl2+)))
7577 (define-public r-infotheo
7584 (uri (cran-uri "infotheo" version))
7587 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7588 (build-system r-build-system)
7589 (home-page "http://homepage.meyerp.com/software")
7590 (synopsis "Information-theoretic measures")
7592 "This package implements various measures of information theory based on
7593 several entropy estimators.")
7594 (license license:gpl3+)))
7596 (define-public r-abcoptim
7603 (uri (cran-uri "ABCoptim" version))
7605 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7606 (properties `((upstream-name . "ABCoptim")))
7607 (build-system r-build-system)
7608 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7609 (home-page "https://github.com/gvegayon/ABCoptim/")
7610 (synopsis "Optimization of Artificial Bee Colony algorithm")
7612 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7613 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7614 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7615 algorithms, and uses only common control parameters such as colony size and
7616 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7617 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7618 This version is a work-in-progress and is written in R code.")
7619 (license license:expat)))
7621 (define-public r-abcp2
7628 (uri (cran-uri "ABCp2" version))
7630 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7631 (properties `((upstream-name . "ABCp2")))
7632 (build-system r-build-system)
7633 (propagated-inputs `(("r-mass" ,r-mass)))
7634 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7635 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7637 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7638 Poisson, and Gamma distribution and estimates the proportional paternity of the
7639 second male (P2) based on the best fit distribution.")
7640 (license license:gpl2)))
7642 (define-public r-abcrf
7649 (uri (cran-uri "abcrf" version))
7651 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7652 (build-system r-build-system)
7654 `(("r-doparallel" ,r-doparallel)
7655 ("r-foreach" ,r-foreach)
7657 ("r-matrixstats" ,r-matrixstats)
7658 ("r-ranger" ,r-ranger)
7660 ("r-rcpparmadillo" ,r-rcpparmadillo)
7661 ("r-readr" ,r-readr)
7662 ("r-stringr" ,r-stringr)))
7663 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7664 (synopsis "Approximate bayesian computation via random forests")
7666 "This package performs approximate bayesian computation (ABC) model choice and
7667 parameter inference via random forests. This machine learning tool named random
7668 forests (RF) can conduct selection among the highly complex models covered by
7670 (license license:gpl2+)))
7672 (define-public r-abctools
7679 (uri (cran-uri "abctools" version))
7681 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7682 (build-system r-build-system)
7685 ("r-abind" ,r-abind)
7686 ("r-hmisc" ,r-hmisc)
7687 ("r-plyr" ,r-plyr)))
7688 (home-page "https://github.com/dennisprangle/abctools/")
7689 (synopsis "Tools for ABC analyses")
7691 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7692 including summary statistic selection and assessing coverage. This includes
7693 recent dimension reduction algorithms to tune the choice of summary statistics,
7694 and coverage methods to tune the choice of threshold.")
7695 (license license:gpl2+)))
7697 (define-public r-ggstance
7704 (uri (cran-uri "ggstance" version))
7706 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7707 (build-system r-build-system)
7709 `(("r-ggplot2" ,r-ggplot2)
7711 ("r-rlang" ,r-rlang)
7712 ("r-withr" ,r-withr)))
7713 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7714 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7716 "This package is a @code{r-ggplot2} extension that provides flipped components:
7718 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7719 @item vertical versions of @code{r-ggplot2} positions.
7721 (license license:gpl3)))
7723 (define-public r-mosaiccore
7725 (name "r-mosaiccore")
7730 (uri (cran-uri "mosaicCore" version))
7732 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7733 (properties `((upstream-name . "mosaicCore")))
7734 (build-system r-build-system)
7736 `(("r-dplyr" ,r-dplyr)
7737 ("r-lazyeval" ,r-lazyeval)
7739 ("r-rlang" ,r-rlang)
7740 ("r-tidyr" ,r-tidyr)))
7741 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7742 (synopsis "Common utilities for mosaic family packages")
7744 "Common utilities used in other Mosaic family packages are collected here.")
7745 (license license:gpl2+)))
7747 (define-public r-ggformula
7749 (name "r-ggformula")
7754 (uri (cran-uri "ggformula" version))
7756 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7757 (build-system r-build-system)
7759 `(("r-ggforce" ,r-ggforce)
7760 ("r-ggplot2" ,r-ggplot2)
7761 ("r-ggstance" ,r-ggstance)
7762 ("r-magrittr" ,r-magrittr)
7763 ("r-mosaiccore" ,r-mosaiccore)
7764 ("r-rlang" ,r-rlang)
7765 ("r-stringr" ,r-stringr)
7766 ("r-tibble" ,r-tibble)))
7767 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7768 (synopsis "Formula interface for the @code{r-ggplot2}")
7770 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7771 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7772 and extends the excellent simplicity of the lattice-graphics formula interface,
7773 while providing the intuitive capabilities of @code{r-ggplot2}.")
7774 (license license:expat)))
7776 (define-public r-mosaicdata
7778 (name "r-mosaicdata")
7783 (uri (cran-uri "mosaicData" version))
7785 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7786 (properties `((upstream-name . "mosaicData")))
7787 (build-system r-build-system)
7788 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7789 (synopsis "Data sets for project Mosaic")
7791 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7792 used to teach mathematics, statistics, computation and modeling.")
7793 (license license:gpl2+)))
7795 (define-public r-raster
7802 (uri (cran-uri "raster" version))
7805 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7806 (build-system r-build-system)
7808 `(("r-rcpp" ,r-rcpp)
7810 (home-page "https://www.rspatial.org/")
7811 (synopsis "Geographic data analysis and modeling")
7813 "The package implements basic and high-level functions for reading,
7814 writing, manipulating, analyzing and modeling of gridded spatial data.
7815 Processing of very large files is supported.")
7816 (license license:gpl3+)))
7818 (define-public r-mosaic
7825 (uri (cran-uri "mosaic" version))
7827 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7828 (build-system r-build-system)
7830 `(("r-broom" ,r-broom)
7831 ("r-dplyr" ,r-dplyr)
7832 ("r-ggdendro" ,r-ggdendro)
7833 ("r-ggformula" ,r-ggformula)
7834 ("r-ggplot2" ,r-ggplot2)
7835 ("r-ggrepel" ,r-ggrepel)
7837 ("r-gridextra" ,r-gridextra)
7838 ("r-lattice" ,r-lattice)
7839 ("r-latticeextra" ,r-latticeextra)
7840 ("r-lazyeval" ,r-lazyeval)
7842 ("r-matrix" ,r-matrix)
7843 ("r-mosaiccore" ,r-mosaiccore)
7844 ("r-mosaicdata" ,r-mosaicdata)
7845 ("r-readr" ,r-readr)
7846 ("r-tidyr" ,r-tidyr)))
7848 `(("r-knitr" ,r-knitr)))
7849 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7850 (synopsis "Mathematics, statistics, and computation teaching utilities")
7852 "This package contain data sets and utilities from
7853 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7854 statistics, computation and modeling. Project MOSAIC is a community of
7855 educators working to tie together aspects of quantitative work that students
7856 in science, technology, engineering and mathematics will need in their
7857 professional lives, but which are usually taught in isolation, if at all.")
7858 (license license:gpl2+)))
7860 (define-public r-abd
7867 (uri (cran-uri "abd" version))
7869 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7870 (build-system r-build-system)
7872 `(("r-lattice" ,r-lattice)
7873 ("r-mosaic" ,r-mosaic)
7874 ("r-nlme" ,r-nlme)))
7875 (home-page "https://cran.r-project.org/web/packages/abd/")
7876 (synopsis "Analysis of biological data")
7878 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7879 biological data by Michael Whitlock and Dolph Schluter.")
7880 (license license:gpl2)))
7882 (define-public r-svgui
7889 (uri (cran-uri "svGUI" version))
7891 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7892 (properties `((upstream-name . "svGUI")))
7893 (build-system r-build-system)
7894 (home-page "https://github.com/SciViews/svGUI/")
7895 (synopsis "Functions for managing GUI clients in R")
7897 "The SciViews @code{svGUI} package eases the management of Graphical User
7898 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7899 centralizes info about GUI elements currently used, and it dispatches GUI
7900 calls to the particular toolkits in use in function of the context.")
7901 (license license:gpl2)))
7903 (define-public r-svdialogs
7905 (name "r-svdialogs")
7910 (uri (cran-uri "svDialogs" version))
7912 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7913 (properties `((upstream-name . "svDialogs")))
7914 (build-system r-build-system)
7917 ("zenity" ,zenity)))
7919 `(("r-rstudioapi" ,r-rstudioapi)
7920 ("r-svgui" ,r-svgui)))
7921 (home-page "https://github.com/SciViews/svDialogs/")
7922 (synopsis "Portable dialog boxes")
7924 "This package helps to construct standard dialog boxes for your GUI, including
7925 message boxes, input boxes, list, file or directory selection, and others. In
7926 case R cannot display GUI dialog boxes, a simpler command line version of these
7927 interactive elements is also provided as a fallback solution.")
7928 (license license:gpl2)))
7930 (define-public r-abe
7937 (uri (cran-uri "abe" version))
7940 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7941 (build-system r-build-system)
7942 (home-page "https://cran.r-project.org/web/packages/abe/")
7943 (synopsis "Augmented backward elimination")
7945 "This package performs augmented backward elimination and checks the
7946 stability of the obtained model. Augmented backward elimination combines
7947 significance or information based criteria with the change in estimate to
7948 either select the optimal model for prediction purposes or to serve as a tool
7949 to obtain a practically sound, highly interpretable model.")
7950 (license license:gpl2+)))
7952 (define-public r-abf2
7959 (uri (cran-uri "abf2" version))
7961 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7962 (build-system r-build-system)
7963 (home-page "https://cran.r-project.org/web/packages/abf2/")
7964 (synopsis "Load gap-free axon @code{r-abf2} files")
7966 "This package loads electrophysiology data from ABF2 files, as created by
7967 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7968 mode are currently supported.")
7969 (license license:artistic2.0)))
7971 (define-public r-abhgenotyper
7973 (name "r-abhgenotyper")
7978 (uri (cran-uri "ABHgenotypeR" version))
7980 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7981 (properties `((upstream-name . "ABHgenotypeR")))
7982 (build-system r-build-system)
7984 `(("r-ggplot2" ,r-ggplot2)
7985 ("r-reshape2" ,r-reshape2)))
7986 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7987 (synopsis "Visualize and manipulate ABH genotypes")
7989 "The @code{r-abhgenotyper} package provides simple imputation,
7990 error-correction and plotting capacities for genotype data. The package is
7991 supposed to serve as an intermediate but independent analysis tool between the
7992 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7993 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7994 genotypes as \"graphical genotypes\".")
7995 (license license:gpl3)))
7997 (define-public r-furrr
8004 (uri (cran-uri "furrr" version))
8007 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8008 (build-system r-build-system)
8010 `(("r-future" ,r-future)
8011 ("r-globals" ,r-globals)
8012 ("r-purrr" ,r-purrr)
8013 ("r-rlang" ,r-rlang)))
8014 (home-page "https://github.com/DavisVaughan/furrr")
8015 (synopsis "Apply mapping functions in parallel using futures")
8017 "This package provides implementations of the family of @code{map()}
8018 functions from the @code{purrr} package that can be resolved using any
8019 @code{future}-supported backend, e.g. parallel on the local machine or
8020 distributed on a compute cluster.")
8021 (license license:lgpl2.1+)))
8023 (define-public r-abjutils
8030 (uri (cran-uri "abjutils" version))
8032 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8033 (build-system r-build-system)
8035 `(("r-dplyr" ,r-dplyr)
8036 ("r-magrittr" ,r-magrittr)
8037 ("r-purrr" ,r-purrr)
8038 ("r-rlang" ,r-rlang)
8039 ("r-rstudioapi" ,r-rstudioapi)
8040 ("r-stringi" ,r-stringi)
8041 ("r-stringr" ,r-stringr)
8042 ("r-tidyr" ,r-tidyr)))
8043 (home-page "https://github.com/abjur/abjutils/")
8044 (synopsis "Collection of tools for jurimetrical analysis")
8046 "This package implements general purpose tools, such as functions for
8047 sampling and basic manipulation of Brazilian lawsuits identification number.
8048 It also implements functions for text cleaning, such as accentuation
8050 (license license:expat)))
8052 (define-public r-abnormality
8054 (name "r-abnormality")
8059 (uri (cran-uri "abnormality" version))
8061 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8062 (build-system r-build-system)
8064 `(("r-mass" ,r-mass)
8065 ("r-matrix" ,r-matrix)))
8066 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8067 (synopsis "Measure a subject's abnormality with respect to a reference population")
8069 "This package contains functions to implement the methodology and
8070 considerations laid out by Marks et al. in the article \"Measuring abnormality
8071 in high dimensional spaces: applications in biomechanical gait analysis\".
8072 Using high-dimensional datasets to measure a subject's overall level of
8073 abnormality as compared to a reference population is often needed in outcomes
8075 (license license:expat)))
8077 (define-public r-abodoutlier
8079 (name "r-abodoutlier")
8084 (uri (cran-uri "abodOutlier" version))
8086 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8087 (properties `((upstream-name . "abodOutlier")))
8088 (build-system r-build-system)
8090 `(("r-cluster" ,r-cluster)))
8091 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8092 (synopsis "Angle-based outlier detection")
8094 "This package performs angle-based outlier detection on a given data
8095 frame. It offers three methods to process data:
8097 @item full but slow implementation using all the data that has cubic
8099 @item a fully randomized method;
8100 @item a method using k-nearest neighbours.
8102 These algorithms are well suited for high dimensional data outlier
8104 (license license:expat)))
8106 (define-public r-abps
8113 (uri (cran-uri "ABPS" version))
8115 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8116 (properties `((upstream-name . "ABPS")))
8117 (build-system r-build-system)
8118 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8119 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8120 (synopsis "Abnormal blood profile score to detect blood doping")
8122 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8123 The ABPS is a part of the Athlete biological passport program of the World
8124 anti-doping agency, which combines several blood parameters into a single
8125 score in order to detect blood doping. The package also contains functions to
8126 calculate other scores used in anti-doping programs, such as the ratio of
8127 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8128 (license license:gpl2+)))
8130 (define-public r-parmigene
8132 (name "r-parmigene")
8137 (uri (cran-uri "parmigene" version))
8140 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8141 (build-system r-build-system)
8142 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8143 (synopsis "Mutual information estimation for gene network reconstruction")
8145 "This package provides a parallel estimation of the mutual information
8146 based on entropy estimates from k-nearest neighbors distances and algorithms
8147 for the reconstruction of gene regulatory networks.")
8148 (license license:agpl3+)))
8150 (define-public r-pscl
8157 (uri (cran-uri "pscl" version))
8159 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8160 (build-system r-build-system)
8162 `(("r-mass" ,r-mass)))
8163 (home-page "https://github.com/atahk/pscl/")
8164 (synopsis "Political science computational laboratory")
8166 "The @code{pscl} is an R package providing classes and methods for:
8168 @item Bayesian analysis of roll call data (item-response models);
8169 @item elementary Bayesian statistics;
8170 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8172 @item utility functions.
8174 (license license:gpl2)))
8176 (define-public r-accelmissing
8178 (name "r-accelmissing")
8183 (uri (cran-uri "accelmissing" version))
8185 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8186 (build-system r-build-system)
8188 `(("r-mice" ,r-mice)
8189 ("r-pscl" ,r-pscl)))
8190 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8191 (synopsis "Missing value imputation for accelerometer data")
8193 "This package provides a statistical method to impute the missing values in
8194 accelerometer data. The methodology includes both parametric and
8195 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8196 model. It also provides multiple functions to preprocess the accelerometer data
8197 previous to the missing data imputation. These include detecting the wearing
8198 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8199 (license license:gpl2+)))
8201 (define-public r-mhsmm
8208 (uri (cran-uri "mhsmm" version))
8210 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8211 (build-system r-build-system)
8212 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8213 (home-page "https://github.com/jaredo/mhsmm/")
8214 (synopsis "Inference for hidden Markov and semi-Markov models")
8216 "The @code{r-mhsmm} package implements estimation and prediction methods for
8217 hidden Markov and semi-Markov models for multiple observation sequences. Such
8218 techniques are of interest when observed data is thought to be dependent on some
8219 unobserved (or hidden) state. Also, this package is suitable for equidistant
8220 time series data, with multivariate and/or missing data. Allows user defined
8221 emission distributions.")
8222 (license license:gpl2+)))
8224 (define-public r-nleqslv
8231 (uri (cran-uri "nleqslv" version))
8233 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8234 (build-system r-build-system)
8235 (native-inputs `(("gfortran" ,gfortran)))
8236 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8237 (synopsis "Solve systems of nonlinear equations")
8239 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8240 Broyden or a Newton method with a choice of global strategies such as line
8241 search and trust region. There are options for using a numerical or user
8242 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8243 singular or ill-conditioned Jacobian.")
8244 (license license:gpl2+)))
8246 (define-public r-physicalactivity
8248 (name "r-physicalactivity")
8253 (uri (cran-uri "PhysicalActivity" version))
8255 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8257 `((upstream-name . "PhysicalActivity")))
8258 (build-system r-build-system)
8259 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8260 (synopsis "Procesing accelerometer data for physical activity measurement")
8262 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8263 for classification of monitor wear and nonwear time intervals in accelerometer
8264 data collected to assess physical activity. The package also contains functions
8265 for making plots of accelerometer data and obtaining the summary of various
8266 information including daily monitor wear time and the mean monitor wear time
8267 during valid days. The revised package version 0.2-1 improved the functions
8268 regarding speed, robustness and add better support for time zones and daylight
8269 saving. In addition, several functions were added:
8271 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8272 @item the @code{markPAI} can categorize physical activity intensity level based
8273 on user-defined cut-points of accelerometer counts.
8275 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8276 @code{queryActigraph} functions.")
8277 (license license:gpl3+)))
8279 (define-public r-acc
8286 (uri (cran-uri "acc" version))
8288 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8289 (build-system r-build-system)
8291 `(("r-circlize" ,r-circlize)
8293 ("r-ggplot2" ,r-ggplot2)
8294 ("r-iterators" ,r-iterators)
8295 ("r-mhsmm" ,r-mhsmm)
8296 ("r-nleqslv" ,r-nleqslv)
8297 ("r-physicalactivity" ,r-physicalactivity)
8299 ("r-r-utils" ,r-r-utils)
8301 ("r-rcpparmadillo" ,r-rcpparmadillo)
8302 ("r-rsqlite" ,r-rsqlite)
8304 (home-page "https://cran.r-project.org/web/packages/acc/")
8305 (synopsis "Exploring accelerometer data")
8307 "This package processes accelerometer data from uni-axial and tri-axial devices
8308 and generates data summaries. Also, includes functions to plot, analyze, and
8309 simulate accelerometer data.")
8310 (license license:gpl2+)))
8312 (define-public r-rbenchmark
8314 (name "r-rbenchmark")
8319 (uri (cran-uri "rbenchmark" version))
8321 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8322 (build-system r-build-system)
8323 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8324 (synopsis "Benchmarking routine for R")
8326 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8327 and is intended to facilitate benchmarking of arbitrary R code. The library
8328 consists of just one function, benchmark, which is a simple wrapper around
8329 system.time. Given a specification of the benchmarking process (counts of
8330 replications, evaluation environment) and an arbitrary number of expressions,
8331 benchmark evaluates each of the expressions in the specified environment,
8332 replicating the evaluation as many times as specified, and returning the results
8333 conveniently wrapped into a data frame.")
8334 (license license:gpl2+)))
8336 (define-public r-mitools
8343 (uri (cran-uri "mitools" version))
8346 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8347 (build-system r-build-system)
8348 (propagated-inputs `(("r-dbi" ,r-dbi)))
8349 (home-page "https://cran.r-project.org/web/packages/mitools/")
8350 (synopsis "Tools for multiple imputation of missing data")
8352 "This package provides tools to perform analyses and combine results from
8353 multiple-imputation datasets.")
8354 (license license:gpl2)))
8356 (define-public r-magick
8363 (uri (cran-uri "magick" version))
8366 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8367 (build-system r-build-system)
8369 `(("imagemagick" ,imagemagick)
8372 `(("r-curl" ,r-curl)
8373 ("r-magrittr" ,r-magrittr)
8374 ("r-rcpp" ,r-rcpp)))
8376 `(("pkg-config" ,pkg-config)
8377 ("r-knitr" ,r-knitr)))
8378 (home-page "https://github.com/ropensci/magick")
8379 (synopsis "Advanced graphics and image-processing in R")
8381 "This package provides bindings to ImageMagick, a comprehensive image
8382 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8383 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8384 operations are vectorized via the Magick++ STL meaning they operate either on
8385 a single frame or a series of frames for working with layers, collages, or
8386 animation. In RStudio, images are automatically previewed when printed to the
8387 console, resulting in an interactive editing environment.")
8388 (license license:expat)))
8390 (define-public r-survey
8397 (uri (cran-uri "survey" version))
8400 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8401 (build-system r-build-system)
8403 `(("r-lattice" ,r-lattice)
8404 ("r-matrix" ,r-matrix)
8405 ("r-minqa" ,r-minqa)
8406 ("r-mitools" ,r-mitools)
8407 ("r-numderiv" ,r-numderiv)
8408 ("r-survival" ,r-survival)))
8409 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8410 (synopsis "Analysis of complex survey samples")
8412 "This package provides tools for the analysis of complex survey samples.
8413 The provided features include: summary statistics, two-sample tests, rank
8414 tests, generalised linear models, cumulative link models, Cox models,
8415 loglinear models, and general maximum pseudolikelihood estimation for
8416 multistage stratified, cluster-sampled, unequally weighted survey samples;
8417 variances by Taylor series linearisation or replicate weights;
8418 post-stratification, calibration, and raking; two-phase subsampling designs;
8419 graphics; PPS sampling without replacement; principal components, and factor
8421 ;; Either version of the GPL.
8422 (license (list license:gpl2 license:gpl3))))
8424 (define-public r-gee
8431 (uri (cran-uri "gee" version))
8434 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8435 (properties `((upstream-name . "gee")))
8436 (build-system r-build-system)
8438 `(("gfortran" ,gfortran)))
8439 (home-page "https://cran.r-project.org/web/packages/gee/")
8440 (synopsis "Generalized estimation equation solver")
8442 "This package provides a solver for generalized estimation equations.")
8443 (license license:gpl2)))
8445 (define-public r-tab
8452 (uri (cran-uri "tab" version))
8455 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8456 (properties `((upstream-name . "tab")))
8457 (build-system r-build-system)
8459 `(("r-dplyr" ,r-dplyr)
8461 ("r-knitr" ,r-knitr)
8463 ("r-survey" ,r-survey)
8464 ("r-survival" ,r-survival)
8465 ("r-xtable" ,r-xtable)))
8466 (home-page "https://cran.r-project.org/web/packages/tab/")
8467 (synopsis "Create summary tables for statistical reports")
8469 "This package contains functions for creating various types of summary
8470 tables, e.g. comparing characteristics across levels of a categorical variable
8471 and summarizing fitted generalized linear models, generalized estimating
8472 equations, and Cox proportional hazards models. Functions are available to
8473 handle data from simple random samples as well as complex surveys.")
8474 (license license:gpl3+)))
8476 (define-public r-dvmisc
8483 (uri (cran-uri "dvmisc" version))
8485 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8486 (build-system r-build-system)
8488 `(("r-cubature" ,r-cubature)
8489 ("r-data-table" ,r-data-table)
8490 ("r-dplyr" ,r-dplyr)
8491 ("r-ggplot2" ,r-ggplot2)
8493 ("r-mvtnorm" ,r-mvtnorm)
8494 ("r-pracma" ,r-pracma)
8495 ("r-rbenchmark" ,r-rbenchmark)
8497 ("r-survey" ,r-survey)
8499 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8500 (synopsis "Faster computation of common statistics and miscellaneous functions")
8502 "This package implements faster versions of base R functions (e.g. mean, standard
8503 deviation, covariance, weighted mean), mostly written in C++, along with
8504 miscellaneous functions for various purposes (e.g. create the histogram with
8505 fitted probability density function or probability mass function curve, create
8506 the body mass index groups, assess the linearity assumption in logistic
8508 (license license:gpl2)))
8510 (define-public r-accelerometry
8512 (name "r-accelerometry")
8517 (uri (cran-uri "accelerometry" version))
8519 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8520 (build-system r-build-system)
8522 `(("r-dvmisc" ,r-dvmisc)
8523 ("r-rcpp" ,r-rcpp)))
8524 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8525 (synopsis "Functions for processing accelerometer data")
8527 "This package provides a collection of functions that perform operations on
8528 time-series accelerometer data, such as identify the non-wear time, flag minutes
8529 that are part of an activity bout, and find the maximum 10-minute average count
8530 value. The functions are generally very flexible, allowing for a variety of
8531 algorithms to be implemented.")
8532 (license license:gpl3)))
8534 (define-public r-absim
8541 (uri (cran-uri "AbSim" version))
8543 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8544 (properties `((upstream-name . "AbSim")))
8545 (build-system r-build-system)
8548 ("r-powerlaw" ,r-powerlaw)))
8549 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8550 (synopsis "Time resolved simulations of antibody repertoires")
8552 "This package provides simulation methods for the evolution of antibody repertoires.
8553 The heavy and light chain variable region of both human and C57BL/6 mice can
8554 be simulated in a time-dependent fashion. Both single lineages using one set of
8555 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8556 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8557 Upon completion, the main loop of the algorithm begins, with each iteration
8558 representing one simulated time step. Various mutation events are possible at
8559 each time step, contributing to a diverse final repertoire.")
8560 (license license:gpl2)))
8562 (define-public r-quic
8569 (uri (cran-uri "QUIC" version))
8571 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8572 (properties `((upstream-name . "QUIC")))
8573 (build-system r-build-system)
8574 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8575 (synopsis "Regularized sparse inverse covariance matrix estimation")
8577 "This package implements the regularized Gaussian maximum likelihood
8578 estimation of the inverse of a covariance matrix. It uses Newton's method and
8579 coordinate descent to solve the regularized inverse covariance matrix
8580 estimation problem.")
8581 ;; The project home page states that the release is under GPLv3 or later.
8582 ;; The CRAN page only says GPL-3.
8583 (license license:gpl3+)))
8585 (define-public r-abundant
8592 (uri (cran-uri "abundant" version))
8594 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8595 (build-system r-build-system)
8597 `(("r-quic" ,r-quic)))
8598 (home-page "https://cran.r-project.org/web/packages/abundant/")
8599 (synopsis "Abundant regression and high-dimensional principal fitted components")
8601 "This package provides tools to fit and predict with the high-dimensional
8602 principal fitted components model. This model is described by Cook, Forzani,
8603 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8604 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8605 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8606 (license license:gpl2+)))
8608 (define-public r-ac3net
8615 (uri (cran-uri "Ac3net" version))
8617 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8618 (properties `((upstream-name . "Ac3net")))
8619 (build-system r-build-system)
8621 `(("r-data-table" ,r-data-table)))
8622 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8623 (synopsis "Inferring directional conservative causal core gene networks")
8624 (description "This package infers directional Conservative causal core
8625 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8626 directional network.")
8627 (license license:gpl3+)))
8629 (define-public r-aca
8636 (uri (cran-uri "ACA" version))
8638 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8639 (properties `((upstream-name . "ACA")))
8640 (build-system r-build-system)
8641 (home-page "https://cran.r-project.org/web/packages/ACA/")
8642 (synopsis "Abrupt change-point or aberration detection in point series")
8644 "This package offers an interactive function for the detection of breakpoints in
8646 ;; Any version of the GPL
8647 (license (list license:gpl2+ license:gpl3+))))
8649 (define-public r-acceptancesampling
8651 (name "r-acceptancesampling")
8656 (uri (cran-uri "AcceptanceSampling" version))
8658 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8660 `((upstream-name . "AcceptanceSampling")))
8661 (build-system r-build-system)
8662 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8663 (synopsis "Creation and evaluation of acceptance sampling plans")
8665 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8666 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8667 in quality control and improvement. International standards of acceptance
8668 sampling provide sampling plans for specific circumstances. The aim of this
8669 package is to provide an easy-to-use interface to visualize single, double or
8670 multiple sampling plans. In addition, methods have been provided to enable the
8671 user to assess sampling plans against pre-specified levels of performance, as
8672 measured by the probability of acceptance for a given level of quality in the
8674 (license license:gpl3+)))
8676 (define-public r-acclma
8683 (uri (cran-uri "ACCLMA" version))
8685 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8686 (properties `((upstream-name . "ACCLMA")))
8687 (build-system r-build-system)
8688 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8689 (synopsis "ACC & LMA graph plotting")
8691 "This package contains a function that imports data from a @acronym{CSV,
8692 Comma-Separated Values} file, or uses manually entered data from the format (x,
8693 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8694 Curve} vs @acronym{LOI, Line of Independence} graph and
8695 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8696 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8697 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8698 string) was passed, a manual data entry window is opened. The header parameter
8699 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8700 a header row or not. The dataset should contain only one independent variable
8701 (x) and one dependent variable (y) and can contain a weight for each
8703 (license license:gpl2)))
8705 (define-public r-aspi
8712 (uri (cran-uri "aspi" version))
8714 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8715 (build-system r-build-system)
8717 "https://cran.r-project.org/web/packages/aspi/")
8719 "Analysis of symmetry of parasitic infections")
8721 "This package provides tools for the analysis and visualization of bilateral
8722 asymmetry in parasitic infections.")
8723 (license license:gpl3+)))
8725 (define-public r-sandwich
8732 (uri (cran-uri "sandwich" version))
8735 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8736 (build-system r-build-system)
8738 `(("r-zoo" ,r-zoo)))
8739 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8740 (synopsis "Robust Covariance Matrix Estimators")
8742 "This package provides model-robust standard error estimators for
8743 cross-sectional, time series, clustered, panel, and longitudinal data.")
8744 ;; Either version of the license.
8745 (license (list license:gpl2 license:gpl3))))
8747 (define-public r-th-data
8754 (uri (cran-uri "TH.data" version))
8757 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8758 (properties `((upstream-name . "TH.data")))
8759 (build-system r-build-system)
8761 `(("r-mass" ,r-mass)
8762 ("r-survival" ,r-survival)))
8763 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8764 (synopsis "Shared data sets")
8766 "This package contains supporting data sets that are used in other
8767 packages maintained by Torsten Hothorn.")
8768 (license license:gpl3)))
8770 (define-public r-multcomp
8777 (uri (cran-uri "multcomp" version))
8780 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8781 (build-system r-build-system)
8783 `(("r-codetools" ,r-codetools)
8784 ("r-mvtnorm" ,r-mvtnorm)
8785 ("r-sandwich" ,r-sandwich)
8786 ("r-survival" ,r-survival)
8787 ("r-th-data" ,r-th-data)))
8788 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8789 (synopsis "Simultaneous inference in general parametric models")
8791 "Simultaneous tests and confidence intervals for general linear
8792 hypotheses in parametric models, including linear, generalized linear, linear
8793 mixed effects, and survival models. The package includes demos reproducing
8794 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8795 Hothorn, Westfall, 2010, CRC Press).")
8796 (license license:gpl2)))
8798 (define-public r-emmeans
8805 (uri (cran-uri "emmeans" version))
8808 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
8809 (build-system r-build-system)
8811 `(("r-estimability" ,r-estimability)
8812 ("r-mvtnorm" ,r-mvtnorm)
8813 ("r-numderiv" ,r-numderiv)
8815 ("r-xtable" ,r-xtable)))
8817 `(("r-knitr" ,r-knitr)))
8818 (home-page "https://github.com/rvlenth/emmeans")
8819 (synopsis "Estimated marginal means, aka least-squares means")
8821 "This package provides tools to obtain @dfn{estimated marginal
8822 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8823 be used to compute contrasts or linear functions of EMMs, trends, and
8824 comparisons of slopes.")
8825 ;; Either version of the license.
8826 (license (list license:gpl2 license:gpl3))))
8828 (define-public r-pwr
8835 (uri (cran-uri "pwr" version))
8838 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8839 (build-system r-build-system)
8841 `(("r-knitr" ,r-knitr)))
8842 (home-page "https://github.com/heliosdrm/pwr")
8843 (synopsis "Basic functions for power analysis")
8845 "This package provides power analysis functions along the lines of
8847 (license license:gpl3+)))
8849 (define-public r-libcoin
8856 (uri (cran-uri "libcoin" version))
8858 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
8859 (build-system r-build-system)
8860 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8861 (home-page "https://cran.r-project.org/web/packages/libcoin")
8862 (synopsis "Linear test statistics for permutation inference")
8864 "This package provides basic infrastructure for linear test statistics
8865 and permutation inference in the framework of Strasser and Weber (1999).")
8866 (license license:gpl2)))
8868 (define-public r-coin
8875 (uri (cran-uri "coin" version))
8878 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8879 (build-system r-build-system)
8881 `(("r-libcoin" ,r-libcoin)
8882 ("r-matrixstats" ,r-matrixstats)
8883 ("r-modeltools" ,r-modeltools)
8884 ("r-multcomp" ,r-multcomp)
8885 ("r-mvtnorm" ,r-mvtnorm)
8886 ("r-survival" ,r-survival)))
8887 (home-page "http://coin.r-forge.r-project.org")
8888 (synopsis "Conditional inference procedures in a permutation test framework")
8890 "This package provides conditional inference procedures for the general
8891 independence problem including two-sample, K-sample (non-parametric ANOVA),
8892 correlation, censored, ordered and multivariate problems.")
8893 (license license:gpl2)))
8895 (define-public r-bayesplot
8897 (name "r-bayesplot")
8902 (uri (cran-uri "bayesplot" version))
8905 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8906 (build-system r-build-system)
8908 `(("pandoc" ,pandoc)
8909 ("pandoc-citeproc" ,pandoc-citeproc)))
8911 `(("r-knitr" ,r-knitr)))
8913 `(("r-dplyr" ,r-dplyr)
8914 ("r-ggplot2" ,r-ggplot2)
8915 ("r-ggridges" ,r-ggridges)
8917 ("r-reshape2" ,r-reshape2)
8918 ("r-rlang" ,r-rlang)
8919 ("r-tibble" ,r-tibble)
8920 ("r-tidyselect" ,r-tidyselect)))
8921 (home-page "https://mc-stan.org/bayesplot")
8922 (synopsis "Plotting for Bayesian models")
8924 "This package provides plotting functions for posterior analysis, model
8925 checking, and MCMC diagnostics. The package is designed not only to provide
8926 convenient functionality for users, but also a common set of functions that
8927 can be easily used by developers working on a variety of R packages for
8928 Bayesian modeling.")
8929 (license license:gpl3+)))
8931 (define-public r-tmb
8938 (uri (cran-uri "TMB" version))
8941 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
8942 (properties `((upstream-name . "TMB")))
8943 (build-system r-build-system)
8945 `(("r-matrix" ,r-matrix)
8946 ("r-rcppeigen" ,r-rcppeigen)))
8947 (home-page "http://tmb-project.org")
8948 (synopsis "Template model builder: a general random effect tool")
8950 "With this tool, a user should be able to quickly implement complex
8951 random effect models through simple C++ templates. The package combines
8952 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8953 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8954 from R) to obtain an efficient implementation of the applied Laplace
8955 approximation with exact derivatives. Key features are: Automatic sparseness
8956 detection, parallelism through BLAS and parallel user templates.")
8957 (license license:gpl2)))
8959 (define-public r-sjstats
8966 (uri (cran-uri "sjstats" version))
8968 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8969 (build-system r-build-system)
8971 `(("r-bayestestr" ,r-bayestestr)
8972 ("r-broom" ,r-broom)
8973 ("r-dplyr" ,r-dplyr)
8974 ("r-effectsize" ,r-effectsize)
8975 ("r-emmeans" ,r-emmeans)
8976 ("r-insight" ,r-insight)
8978 ("r-magrittr" ,r-magrittr)
8980 ("r-modelr" ,r-modelr)
8981 ("r-parameters" ,r-parameters)
8982 ("r-performance" ,r-performance)
8983 ("r-purrr" ,r-purrr)
8984 ("r-rlang" ,r-rlang)
8985 ("r-sjlabelled" ,r-sjlabelled)
8986 ("r-sjmisc" ,r-sjmisc)
8987 ("r-tidyr" ,r-tidyr)))
8988 (home-page "https://github.com/strengejacke/sjstats")
8989 (synopsis "Functions for common statistical computations")
8991 "This package provides a collection of convenient functions for common
8992 statistical computations, which are not directly provided by R's @code{base}
8993 or @code{stats} packages. This package aims at providing, first, shortcuts
8994 for statistical measures, which otherwise could only be calculated with
8995 additional effort. Second, these shortcut functions are generic, and can be
8996 applied not only to vectors, but also to other objects as well. The focus of
8997 most functions lies on summary statistics or fit measures for regression
8998 models, including generalized linear models, mixed effects models and Bayesian
9000 (license license:gpl3)))
9002 (define-public r-glmmtmb
9009 (uri (cran-uri "glmmTMB" version))
9012 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9013 (properties `((upstream-name . "glmmTMB")))
9014 (build-system r-build-system)
9016 `(("r-lme4" ,r-lme4)
9017 ("r-matrix" ,r-matrix)
9019 ("r-rcppeigen" ,r-rcppeigen)
9022 `(("r-knitr" ,r-knitr))) ; for vignettes
9023 (home-page "https://github.com/glmmTMB")
9024 (synopsis "Generalized linear mixed models")
9026 "Fit linear and generalized linear mixed models with various extensions,
9027 including zero-inflation. The models are fitted using maximum likelihood
9028 estimation via the Template Model Builder. Random effects are assumed to be
9029 Gaussian on the scale of the linear predictor and are integrated out using the
9030 Laplace approximation. Gradients are calculated using automatic
9032 (license license:agpl3+)))
9034 (define-public r-bayestestr
9036 (name "r-bayestestr")
9041 (uri (cran-uri "bayestestR" version))
9044 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9045 (properties `((upstream-name . "bayestestR")))
9046 (build-system r-build-system)
9048 `(("r-insight" ,r-insight)))
9050 `(("r-knitr" ,r-knitr)))
9051 (home-page "https://github.com/easystats/bayestestR")
9052 (synopsis "Describe Bayesian models and posterior distributions")
9054 "This package provides utilities to understand and describe posterior
9055 distributions and Bayesian models. It includes point-estimates such as
9056 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9057 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9058 ROPE percentage and pd).")
9059 (license license:gpl3)))
9061 (define-public r-performance
9063 (name "r-performance")
9068 (uri (cran-uri "performance" version))
9071 "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
9072 (build-system r-build-system)
9074 `(("r-bayestestr" ,r-bayestestr)
9075 ("r-insight" ,r-insight)))
9076 (home-page "https://easystats.github.io/performance/")
9077 (synopsis "Assessment of regression models performance")
9079 "This package provides utilities for computing measures to assess model
9080 quality, which are not directly provided by R's @code{base} or @code{stats}
9081 packages. These include e.g. measures like r-squared, intraclass correlation
9082 coefficient, root mean squared error or functions to check models for
9083 overdispersion, singularity or zero-inflation and more. Functions apply to a
9084 large variety of regression models, including generalized linear models, mixed
9085 effects models and Bayesian models.")
9086 (license license:gpl3)))
9088 (define-public r-ggeffects
9090 (name "r-ggeffects")
9095 (uri (cran-uri "ggeffects" version))
9098 "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
9099 (build-system r-build-system)
9101 `(("r-insight" ,r-insight)
9103 ("r-sjlabelled" ,r-sjlabelled)))
9105 `(("r-knitr" ,r-knitr)))
9106 (home-page "https://github.com/strengejacke/ggeffects")
9107 (synopsis "Create tidy data frames of marginal effects for ggplot")
9109 "This package provides tools to compute marginal effects from statistical
9110 models and return the result as tidy data frames. These data frames are ready
9111 to use with the @code{ggplot2} package. Marginal effects can be calculated
9112 for many different models. Interaction terms, splines and polynomial terms
9113 are also supported. The two main functions are @code{ggpredict()} and
9114 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9115 results using @code{ggplot2}.")
9116 (license license:gpl3)))
9118 (define-public r-effectsize
9120 (name "r-effectsize")
9125 (uri (cran-uri "effectsize" version))
9128 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9129 (properties `((upstream-name . "effectsize")))
9130 (build-system r-build-system)
9132 `(("r-bayestestr" ,r-bayestestr)
9133 ("r-insight" ,r-insight)
9134 ("r-parameters" ,r-parameters)))
9136 `(("r-knitr" ,r-knitr)))
9137 (home-page "https://github.com/easystats/effectsize")
9138 (synopsis "Indices of effect size and standardized parameters")
9140 "This package provides utilities to work with indices of effect size and
9141 standardized parameters for a wide variety of models, allowing computation and
9142 conversion of indices such as Cohen's d, r, odds, etc.")
9143 (license license:gpl3)))
9145 (define-public r-sjplot
9152 (uri (cran-uri "sjPlot" version))
9154 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9155 (properties `((upstream-name . "sjPlot")))
9156 (build-system r-build-system)
9158 `(("r-bayestestr" ,r-bayestestr)
9159 ("r-dplyr" ,r-dplyr)
9160 ("r-effectsize" ,r-effectsize)
9161 ("r-ggeffects" ,r-ggeffects)
9162 ("r-ggplot2" ,r-ggplot2)
9163 ("r-insight" ,r-insight)
9164 ("r-knitr" ,r-knitr)
9166 ("r-parameters" ,r-parameters)
9167 ("r-performance" ,r-performance)
9168 ("r-purrr" ,r-purrr)
9169 ("r-rlang" ,r-rlang)
9170 ("r-scales" ,r-scales)
9171 ("r-sjlabelled" ,r-sjlabelled)
9172 ("r-sjmisc" ,r-sjmisc)
9173 ("r-sjstats" ,r-sjstats)
9174 ("r-tidyr" ,r-tidyr)))
9176 `(("r-knitr" ,r-knitr)))
9177 (home-page "https://strengejacke.github.io/sjPlot/")
9178 (synopsis "Data visualization for statistics in social science")
9180 "This package represents a collection of plotting and table output
9181 functions for data visualization. Results of various statistical
9182 analyses (that are commonly used in social sciences) can be visualized using
9183 this package, including simple and cross tabulated frequencies, histograms,
9184 box plots, (generalized) linear models, mixed effects models, principal
9185 component analysis and correlation matrices, cluster analyses, scatter plots,
9186 stacked scales, effects plots of regression models (including interaction
9187 terms) and much more. This package supports labelled data.")
9188 (license license:gpl3)))
9190 (define-public r-ini
9197 (uri (cran-uri "ini" version))
9200 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9201 (build-system r-build-system)
9202 (home-page "https://github.com/dvdscripter/ini")
9203 (synopsis "Read and write configuration files")
9205 "This package provides tools to parse simple @code{.ini} configuration
9206 files to an structured list. Users can manipulate this resulting list with
9207 @code{lapply()} functions. This same structured list can be used to write
9208 back to file after modifications.")
9209 (license license:gpl3)))
9218 (uri (cran-uri "gh" version))
9221 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9222 (build-system r-build-system)
9227 ("r-jsonlite" ,r-jsonlite)))
9228 (home-page "https://github.com/r-lib/gh#readme")
9229 (synopsis "Access the GitHub API via R")
9231 "This package provides a minimal R client to access the GitHub API.")
9232 (license license:expat)))
9241 (uri (cran-uri "fs" version))
9244 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9245 (build-system r-build-system)
9247 `(("r-knitr" ,r-knitr)))
9248 (home-page "https://fs.r-lib.org")
9249 (synopsis "Cross-platform file system operations based on libuv")
9251 "This package provides a cross-platform interface to file system
9252 operations, built on top of the libuv C library.")
9253 (license license:gpl3)))
9255 (define-public r-clisymbols
9257 (name "r-clisymbols")
9262 (uri (cran-uri "clisymbols" version))
9265 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9266 (build-system r-build-system)
9267 (home-page "https://github.com/gaborcsardi/clisymbols")
9268 (synopsis "Unicode symbols at the R prompt")
9270 "This package provides a small subset of Unicode symbols, that are useful
9271 when building command line applications. They fall back to alternatives on
9272 terminals that do not support Unicode.")
9273 (license license:expat)))
9275 (define-public r-usethis
9282 (uri (cran-uri "usethis" version))
9285 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9286 (build-system r-build-system)
9289 ("r-clipr" ,r-clipr)
9290 ("r-crayon" ,r-crayon)
9295 ("r-git2r" ,r-git2r)
9297 ("r-purrr" ,r-purrr)
9298 ("r-rematch2" ,r-rematch2)
9299 ("r-rlang" ,r-rlang)
9300 ("r-rprojroot" ,r-rprojroot)
9301 ("r-rstudioapi" ,r-rstudioapi)
9302 ("r-whisker" ,r-whisker)
9303 ("r-withr" ,r-withr)
9304 ("r-yaml" ,r-yaml)))
9305 (home-page "https://github.com/r-lib/usethis")
9306 (synopsis "Automate R package and project setup")
9308 "This package helps you to automate R package and project setup tasks
9309 that are otherwise performed manually. This includes setting up unit testing,
9310 test coverage, continuous integration, Git, GitHub integration, licenses,
9311 Rcpp, RStudio projects, and more.")
9312 (license license:gpl3)))
9314 (define-public r-sessioninfo
9316 (name "r-sessioninfo")
9321 (uri (cran-uri "sessioninfo" version))
9324 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9325 (build-system r-build-system)
9328 ("r-withr" ,r-withr)))
9329 (home-page "https://github.com/r-lib/sessioninfo#readme")
9330 (synopsis "R session information")
9332 "This package provides tools to query and print information about the
9333 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9334 more information about packages, and where they were installed from.")
9335 (license license:gpl2)))
9337 (define-public r-remotes
9344 (uri (cran-uri "remotes" version))
9347 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9348 (build-system r-build-system)
9350 `(("r-knitr" ,r-knitr)))
9351 (home-page "https://github.com/r-lib/remotes#readme")
9352 (synopsis "R package installation from remote repositories")
9354 "Download and install R packages stored in GitHub, BitBucket, or plain
9355 subversion or git repositories. This package is a lightweight replacement of
9356 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9357 the code was copied over from @code{devtools}.")
9358 (license license:gpl2+)))
9360 (define-public r-xopen
9367 (uri (cran-uri "xopen" version))
9370 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9371 (build-system r-build-system)
9373 `(("r-processx" ,r-processx)))
9374 (home-page "https://github.com/r-lib/xopen#readme")
9375 (synopsis "Open system files, URLs, anything")
9377 "This package provides a cross-platform solution to open files,
9378 directories or URLs with their associated programs.")
9379 (license license:expat)))
9381 (define-public r-rcmdcheck
9383 (name "r-rcmdcheck")
9388 (uri (cran-uri "rcmdcheck" version))
9391 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9392 (build-system r-build-system)
9394 `(("r-callr" ,r-callr)
9396 ("r-crayon" ,r-crayon)
9398 ("r-digest" ,r-digest)
9399 ("r-pkgbuild" ,r-pkgbuild)
9400 ("r-prettyunits" ,r-prettyunits)
9402 ("r-rprojroot" ,r-rprojroot)
9403 ("r-sessioninfo" ,r-sessioninfo)
9404 ("r-withr" ,r-withr)
9405 ("r-xopen" ,r-xopen)))
9406 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9407 (synopsis "Run R CMD check from R and capture results")
9409 "Run @code{R CMD check} from R programmatically, and capture the results
9410 of the individual checks.")
9411 (license license:expat)))
9413 (define-public r-rapportools
9415 (name "r-rapportools")
9420 (uri (cran-uri "rapportools" version))
9423 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9424 (build-system r-build-system)
9426 `(("r-pander" ,r-pander)
9428 ("r-reshape" ,r-reshape)))
9429 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9430 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9432 "This package provides helper functions that act as wrappers to more
9433 advanced statistical methods with the advantage of having sane defaults for
9435 (license license:agpl3+)))
9437 (define-public r-pander
9444 (uri (cran-uri "pander" version))
9447 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9448 (build-system r-build-system)
9450 `(("r-digest" ,r-digest)
9451 ("r-rcpp" ,r-rcpp)))
9452 (home-page "https://rapporter.github.io/pander")
9453 (synopsis "Render R objects into Pandoc's markdown")
9455 "The main aim of the pander R package is to provide a minimal and easy
9456 tool for rendering R objects into Pandoc's markdown. The package is also
9457 capable of exporting/converting complex Pandoc documents (reports) in various
9459 ;; This package is licensed under either the AGPLv3+ or the very rarely
9461 (license license:agpl3+)))
9463 (define-public r-summarytools
9465 (name "r-summarytools")
9470 (uri (cran-uri "summarytools" version))
9473 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9474 (build-system r-build-system)
9476 `(("r-base64enc" ,r-base64enc)
9477 ("r-checkmate" ,r-checkmate)
9478 ("r-dplyr" ,r-dplyr)
9479 ("r-htmltools" ,r-htmltools)
9480 ("r-lubridate" ,r-lubridate)
9481 ("r-magick" ,r-magick)
9482 ("r-matrixstats" ,r-matrixstats)
9483 ("r-pander" ,r-pander)
9485 ("r-rapportools" ,r-rapportools)
9486 ("r-tibble" ,r-tibble)
9487 ("r-tidyr" ,r-tidyr)))
9488 (home-page "https://github.com/dcomtois/summarytools")
9489 (synopsis "Tools to quickly and neatly summarize data")
9491 "This package provides tools for data frame summaries, cross-tabulations,
9492 weight-enabled frequency tables and common univariate statistics in concise
9493 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9494 good point-of-entry for exploring data, both for experienced and new R
9496 (license license:gpl2)))
9498 (define-public r-lsei
9505 (uri (cran-uri "lsei" version))
9508 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9509 (build-system r-build-system)
9511 `(("gfortran" ,gfortran)))
9512 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9513 (synopsis "Solve regression problems under equality/inequality constraints")
9515 "It contains functions that solve least squares linear regression
9516 problems under linear equality/inequality constraints. Functions for solving
9517 quadratic programming problems are also available, which transform such
9518 problems into least squares ones first.")
9519 (license license:gpl2+)))
9521 (define-public r-npsurv
9528 (uri (cran-uri "npsurv" version))
9531 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9532 (build-system r-build-system)
9534 `(("r-lsei" ,r-lsei)))
9535 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9536 (synopsis "Nonparametric survival analysis")
9538 "This package contains functions for non-parametric survival analysis of
9539 exact and interval-censored observations.")
9540 (license license:gpl2+)))
9542 (define-public r-clusteval
9544 (name "r-clusteval")
9549 (uri (cran-uri "clusteval" version))
9552 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9553 (build-system r-build-system)
9555 `(("r-mvtnorm" ,r-mvtnorm)
9556 ("r-rcpp" ,r-rcpp)))
9557 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9558 (synopsis "Evaluation of clustering algorithms")
9560 "This R package provides a suite of tools to evaluate clustering
9561 algorithms, clusterings, and individual clusters.")
9562 (license license:expat)))
9564 (define-public r-tweedie
9571 (uri (cran-uri "tweedie" version))
9574 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9575 (build-system r-build-system)
9576 (native-inputs `(("gfortran" ,gfortran)))
9577 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9578 (synopsis "Evaluation of Tweedie exponential family models")
9580 "Maximum likelihood computations for Tweedie families, including the
9581 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9582 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9583 and related methods.")
9584 (license license:gpl2+)))
9586 (define-public r-rcppgsl
9593 (uri (cran-uri "RcppGSL" version))
9595 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9596 (properties `((upstream-name . "RcppGSL")))
9597 (build-system r-build-system)
9599 `(("r-rcpp" ,r-rcpp)
9601 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9602 (synopsis "Rcpp integration for GSL vectors and matrices")
9604 "The GNU Scientific Library (or GSL) is a collection of numerical
9605 routines for scientific computing. It is particularly useful for C and C++
9606 programs as it provides a standard C interface to a wide range of mathematical
9607 routines. There are over 1000 functions in total with an extensive test
9608 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9609 structures and R using concepts from Rcpp which is itself a package that eases
9610 the interfaces between R and C++.")
9611 (license license:gpl2+)))
9613 (define-public r-mvabund
9620 (uri (cran-uri "mvabund" version))
9623 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9624 (build-system r-build-system)
9626 `(("r-mass" ,r-mass)
9628 ("r-rcppgsl" ,r-rcppgsl)
9629 ("r-statmod" ,r-statmod)
9630 ("r-tweedie" ,r-tweedie)))
9631 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9632 (synopsis "Statistical methods for analysing multivariate abundance data")
9634 "This package provides a set of tools for displaying, modeling and
9635 analysing multivariate abundance data in community ecology.")
9636 (license license:lgpl2.1+)))
9638 (define-public r-afex
9645 (uri (cran-uri "afex" version))
9648 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9649 (build-system r-build-system)
9653 ("r-lmertest" ,r-lmertest)
9654 ("r-pbkrtest" ,r-pbkrtest)
9655 ("r-reshape2" ,r-reshape2)))
9657 `(("r-knitr" ,r-knitr)))
9658 (home-page "https://afex.singmann.science/")
9659 (synopsis "Analysis of factorial experiments")
9661 "This package provides convenience functions for analyzing factorial
9662 experiments using ANOVA or mixed models.")
9663 (license license:gpl2+)))
9665 (define-public r-lmertest
9672 (uri (cran-uri "lmerTest" version))
9675 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9676 (properties `((upstream-name . "lmerTest")))
9677 (build-system r-build-system)
9679 `(("r-ggplot2" ,r-ggplot2)
9682 ("r-numderiv" ,r-numderiv)))
9683 (home-page "https://github.com/runehaubo/lmerTestR")
9684 (synopsis "Tests in linear mixed effects models")
9686 "This package provides p-values in type I, II or III anova and summary
9687 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9688 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9689 package. Model selection methods include step, drop1 and anova-like tables
9690 for random effects (ranova). Methods for Least-Square means (LS-means) and
9691 tests of linear contrasts of fixed effects are also available.")
9692 (license license:gpl2+)))
9694 (define-public r-r2glmm
9701 (uri (cran-uri "r2glmm" version))
9704 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9705 (build-system r-build-system)
9707 `(("r-afex" ,r-afex)
9708 ("r-data-table" ,r-data-table)
9709 ("r-dplyr" ,r-dplyr)
9710 ("r-ggplot2" ,r-ggplot2)
9711 ("r-gridextra" ,r-gridextra)
9712 ("r-lmertest" ,r-lmertest)
9714 ("r-matrix" ,r-matrix)
9716 ("r-pbkrtest" ,r-pbkrtest)))
9717 (home-page "https://github.com/bcjaeger/r2glmm")
9718 (synopsis "Compute R squared for mixed (multilevel) models")
9720 "This package computes model and semi partial R squared with confidence
9721 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9722 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9723 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9725 (license license:gpl2)))
9727 (define-public r-weights
9734 (uri (cran-uri "weights" version))
9737 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9738 (build-system r-build-system)
9740 `(("r-gdata" ,r-gdata)
9741 ("r-hmisc" ,r-hmisc)
9742 ("r-mice" ,r-mice)))
9744 "https://cran.r-project.org/web/packages/weights/")
9745 (synopsis "Weighting and weighted statistics")
9746 (description "This package Provides a variety of functions for producing
9747 simple weighted statistics, such as weighted Pearson's correlations, partial
9748 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9749 includes some software for quickly recoding survey data and plotting point
9750 estimates from interaction terms in regressions (and multiply imputed
9751 regressions). NOTE: Weighted partial correlation calculations pulled to
9753 (license license:gpl2+)))
9755 (define-public r-rcppannoy
9757 (name "r-rcppannoy")
9762 (uri (cran-uri "RcppAnnoy" version))
9765 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9766 (properties `((upstream-name . "RcppAnnoy")))
9767 (build-system r-build-system)
9769 `(("r-rcpp" ,r-rcpp)))
9770 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9771 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9773 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9774 for efficient memory usage as well an ability to load from and save to disk.
9775 This package provides an R interface.")
9776 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9778 (license (list license:gpl2+ license:asl2.0))))
9780 (define-public r-rcpphnsw
9787 (uri (cran-uri "RcppHNSW" version))
9790 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9791 (properties `((upstream-name . "RcppHNSW")))
9792 (build-system r-build-system)
9793 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9794 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9795 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9797 "Hnswlib is a C++ library for approximate nearest neighbors. This
9798 package provides a minimal R interface by relying on the Rcpp package.")
9799 ;; hnswlib is released under Version 2.0 of the Apache License.
9800 (license (list license:gpl3 license:asl2.0))))
9802 (define-public r-rcppparallel
9804 (name "r-rcppparallel")
9809 (uri (cran-uri "RcppParallel" version))
9812 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
9813 (properties `((upstream-name . "RcppParallel")))
9814 (build-system r-build-system)
9815 (home-page "https://rcppcore.github.io/RcppParallel/")
9816 (synopsis "Parallel programming tools for Rcpp")
9818 "This package provides high level functions for parallel programming with
9819 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9820 the work of a standard serial @code{for} loop into a parallel one and the
9821 @code{parallelReduce()} function can be used for accumulating aggregates or
9823 (license license:gpl2)))
9825 (define-public r-ncdf4
9832 (uri (cran-uri "ncdf4" version))
9835 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9836 (build-system r-build-system)
9838 `(("netcdf" ,netcdf)
9840 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9841 (synopsis "R interface to Unidata netCDF format data files")
9843 "This package provides a high-level R interface to data files written
9844 using Unidata's netCDF library (version 4 or earlier), which are binary data
9845 files that are portable across platforms and include metadata information in
9846 addition to the data sets. Using this package, netCDF files can be opened and
9847 data sets read in easily. It is also easy to create new netCDF dimensions,
9848 variables, and files, in either version 3 or 4 format, and manipulate existing
9850 (license license:gpl3+)))
9852 (define-public r-biocmanager
9854 (name "r-biocmanager")
9859 (uri (cran-uri "BiocManager" version))
9861 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9862 (properties `((upstream-name . "BiocManager")))
9863 (build-system r-build-system)
9864 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9865 (synopsis "Access the Bioconductor project package repository")
9867 "This package provides a convenient tool to install and update
9868 Bioconductor packages.")
9869 (license license:artistic2.0)))
9871 (define-public r-rgl
9874 (version "0.100.54")
9878 (uri (cran-uri "rgl" version))
9881 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9882 (build-system r-build-system)
9884 `(("pkg-config" ,pkg-config)))
9886 `(("freetype" ,freetype)
9893 `(("r-crosstalk" ,r-crosstalk)
9894 ("r-htmltools" ,r-htmltools)
9895 ("r-htmlwidgets" ,r-htmlwidgets)
9896 ("r-jsonlite" ,r-jsonlite)
9897 ("r-knitr" ,r-knitr)
9898 ("r-magrittr" ,r-magrittr)
9899 ("r-manipulatewidget" ,r-manipulatewidget)
9900 ("r-shiny" ,r-shiny)))
9901 (home-page "https://r-forge.r-project.org/projects/rgl/")
9902 (synopsis "3D visualization using OpenGL")
9904 "This package provides medium to high level functions for 3D interactive graphics,
9905 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9906 as functions for constructing representations of geometric
9907 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9908 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9909 image formats, including PNG, Postscript, SVG, PGF.")
9910 ;; Any version of the GPL.
9911 (license (list license:gpl2+ license:gpl3+))))
9913 (define-public r-multicool
9915 (name "r-multicool")
9920 (uri (cran-uri "multicool" version))
9923 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9924 (build-system r-build-system)
9925 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9926 (home-page "https://cran.r-project.org/web/packages/multicool/")
9927 (synopsis "Permutations of multisets in cool-lex order")
9929 "This package provides a set of tools to permute multisets without loops
9930 or hash tables and to generate integer partitions. Cool-lex order is similar
9931 to colexicographical order.")
9932 (license license:gpl2)))
9934 (define-public r-misc3d
9941 (uri (cran-uri "misc3d" version))
9944 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9945 (build-system r-build-system)
9946 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9947 (synopsis "Miscellaneous 3D Plots")
9949 "This package provides a collection of miscellaneous 3d plots, including
9951 ;; Any version of the GPL.
9952 (license (list license:gpl2+ license:gpl3+))))
9961 (uri (cran-uri "ks" version))
9963 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9964 (build-system r-build-system)
9967 ("r-kernlab" ,r-kernlab)
9968 ("r-kernsmooth" ,r-kernsmooth)
9969 ("r-matrix" ,r-matrix)
9970 ("r-mclust" ,r-mclust)
9972 ("r-multicool" ,r-multicool)
9973 ("r-mvtnorm" ,r-mvtnorm)))
9974 (home-page "http://www.mvstat.net/tduong/")
9975 (synopsis "Kernel smoothing")
9977 "This package provides kernel smoothers for univariate and multivariate
9978 data, including density functions, density derivatives, cumulative
9979 distributions, modal clustering, discriminant analysis, and two-sample
9980 hypothesis testing.")
9981 ;; Either version of the GPL.
9982 (license (list license:gpl2 license:gpl3))))
9984 (define-public r-feature
9991 (uri (cran-uri "feature" version))
9994 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9995 (build-system r-build-system)
9998 ("r-misc3d" ,r-misc3d)
10000 (home-page "http://www.mvstat.net/tduong/")
10001 (synopsis "Inferential feature significance for kernel density estimation")
10003 "The feature package contains functions to display and compute kernel
10004 density estimates, significant gradient and significant curvature regions.
10005 Significant gradient and/or curvature regions often correspond to significant
10006 features (e.g. local modes).")
10007 ;; Either version of the GPL.
10008 (license (list license:gpl2 license:gpl3))))
10010 (define-public r-arm
10017 (uri (cran-uri "arm" version))
10020 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10021 (build-system r-build-system)
10023 `(("r-abind" ,r-abind)
10025 ("r-hmisc" ,r-hmisc)
10028 ("r-matrix" ,r-matrix)
10029 ("r-nlme" ,r-nlme)))
10030 (home-page "https://cran.r-project.org/web/packages/arm/")
10031 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10033 "This package provides functions to accompany A. Gelman and J. Hill,
10034 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10035 University Press, 2007.")
10036 (license license:gpl3+)))
10038 (define-public r-circular
10040 (name "r-circular")
10045 (uri (cran-uri "circular" version))
10048 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10049 (build-system r-build-system)
10051 `(("r-boot" ,r-boot)
10052 ("r-mvtnorm" ,r-mvtnorm)))
10054 `(("gfortran" ,gfortran)))
10055 (home-page "https://cran.r-project.org/web/packages/circular/")
10056 (synopsis "Circular statistics")
10058 "This package provides tools for circular statistics, from \"Topics in
10059 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10061 (license license:gpl2+)))
10063 (define-public r-activity
10065 (name "r-activity")
10070 (uri (cran-uri "activity" version))
10073 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10074 (build-system r-build-system)
10076 `(("r-circular" ,r-circular)
10077 ("r-insol" ,r-insol)
10078 ("r-pbapply" ,r-pbapply)))
10079 (home-page "https://cran.r-project.org/web/packages/activity/")
10080 (synopsis "Animal activity statistics")
10082 "This package provides functions to fit kernel density functions to
10083 animal activity time data; plot activity distributions; quantify overall
10084 levels of activity; statistically compare activity metrics through
10085 bootstrapping; and evaluate variation in linear variables with time (or other
10086 circular variables).")
10087 (license license:gpl3)))
10089 (define-public r-ouch
10096 (uri (cran-uri "ouch" version))
10099 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10100 (build-system r-build-system)
10101 (propagated-inputs `(("r-subplex" ,r-subplex)))
10102 (home-page "https://kingaa.github.io/ouch/")
10103 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10105 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10106 for evolution along a phylogenetic tree.")
10107 (license license:gpl2+)))
10109 (define-public r-fmsb
10116 (uri (cran-uri "fmsb" version))
10119 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10120 (build-system r-build-system)
10121 (home-page "http://minato.sip21c.org/msb/")
10122 (synopsis "Functions for medical statistics book with demographic data")
10124 "This package provides several utility functions for the book entitled
10125 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10126 Japan, 2007) with Japanese demographic data and some demographic analysis
10127 related functions.")
10128 (license license:gpl2+)))
10130 (define-public r-stabledist
10132 (name "r-stabledist")
10137 (uri (cran-uri "stabledist" version))
10140 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10141 (build-system r-build-system)
10142 (home-page "https://www.rmetrics.org")
10143 (synopsis "Stable distribution functions")
10145 "This package provides density, probability and quantile functions, and
10146 random number generation for (skew) stable distributions, using the
10147 parametrizations of Nolan.")
10148 (license license:gpl2+)))
10150 (define-public r-gsl
10157 (uri (cran-uri "gsl" version))
10160 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10161 (build-system r-build-system)
10164 (home-page "https://cran.r-project.org/web/packages/gsl")
10165 (synopsis "Wrapper for the GNU Scientific Library")
10167 "This package provides an R wrapper for the special functions and quasi
10168 random number generators of the GNU Scientific Library.")
10169 (license license:gpl2+)))
10171 (define-public r-adgoftest
10173 (name "r-adgoftest")
10178 (uri (cran-uri "ADGofTest" version))
10181 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10182 (properties `((upstream-name . "ADGofTest")))
10183 (build-system r-build-system)
10184 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10185 (synopsis "Anderson-Darling GoF test")
10187 "This package provides an implementation of the Anderson-Darling GoF test
10188 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10189 Anderson-Darling Distribution\".")
10190 ;; Any version of the GPL.
10191 (license license:gpl3+)))
10193 (define-public r-softimpute
10195 (name "r-softimpute")
10200 (uri (cran-uri "softImpute" version))
10203 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10204 (properties `((upstream-name . "softImpute")))
10205 (build-system r-build-system)
10207 `(("r-matrix" ,r-matrix)))
10209 `(("gfortran" ,gfortran)))
10210 (home-page "https://cran.r-project.org/web/packages/softImpute")
10211 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10213 "This package provides iterative methods for matrix completion that use
10214 nuclear-norm regularization. The package includes procedures for centering
10215 and scaling rows, columns or both, and for computing low-rank @dfn{single
10216 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10218 (license license:gpl2)))
10220 (define-public r-fftwtools
10222 (name "r-fftwtools")
10227 (uri (cran-uri "fftwtools" version))
10230 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10231 (build-system r-build-system)
10232 (inputs `(("fftw" ,fftw)))
10233 (home-page "https://github.com/krahim/fftwtools")
10234 (synopsis "Wrapper for FFTW3")
10236 "This package provides a wrapper for several FFTW functions. It provides
10237 access to the two-dimensional FFT, the multivariate FFT, and the
10238 one-dimensional real to complex FFT using the FFTW3 library. The package
10239 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10240 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10241 The FFT functions have a parameter that allows them to not return the
10242 redundant complex conjugate when the input is real data.")
10243 (license license:gpl2+)))
10245 (define-public r-tiff
10252 (uri (cran-uri "tiff" version))
10255 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10256 (build-system r-build-system)
10258 `(("libtiff" ,libtiff)
10259 ("libjpeg" ,libjpeg-turbo)
10261 (home-page "https://www.rforge.net/tiff/")
10262 (synopsis "Read and write TIFF images")
10264 "This package provides an easy and simple way to read, write and display
10265 bitmap images stored in the TIFF format. It can read and write both files and
10266 in-memory raw vectors.")
10267 ;; Either of these two license versions.
10268 (license (list license:gpl2 license:gpl3))))
10270 (define-public r-nlp
10277 (uri (cran-uri "NLP" version))
10280 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10281 (properties `((upstream-name . "NLP")))
10282 (build-system r-build-system)
10283 (home-page "https://cran.r-project.org/web/packages/NLP/")
10284 (synopsis "Natural language processing infrastructure")
10286 "This package provides basic classes and methods for Natural Language
10288 (license license:gpl3)))
10290 (define-public r-tm
10297 (uri (cran-uri "tm" version))
10300 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10301 (properties `((upstream-name . "tm")))
10302 (build-system r-build-system)
10308 ("r-xml2" ,r-xml2)))
10309 (home-page "http://tm.r-forge.r-project.org/")
10310 (synopsis "Text mining package")
10312 "This package provides a framework for text mining applications within R.")
10313 (license license:gpl3)))
10315 (define-public r-waveslim
10317 (name "r-waveslim")
10322 (uri (cran-uri "waveslim" version))
10325 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10326 (build-system r-build-system)
10328 `(("gfortran" ,gfortran)))
10329 (home-page "http://waveslim.blogspot.com")
10330 (synopsis "Basic wavelet routines for signal processing")
10332 "This package provides basic wavelet routines for time series (1D),
10333 image (2D) and array (3D) analysis. The code provided here is based on
10334 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10335 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10336 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10337 pairs (Selesnick 2001, 2002).")
10338 (license license:bsd-3)))
10340 (define-public r-wordcloud
10342 (name "r-wordcloud")
10347 (uri (cran-uri "wordcloud" version))
10350 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10351 (build-system r-build-system)
10353 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10355 ;; The "tm" package is only "suggested" according to CRAN, but the
10356 ;; wordcloud package cannot be loaded without it.
10358 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10359 (synopsis "Word clouds")
10361 "This package provides functionality to create pretty word clouds,
10362 visualize differences and similarity between documents, and avoid
10363 over-plotting in scatter plots with text.")
10364 (license license:lgpl2.1)))
10366 (define-public r-colorramps
10368 (name "r-colorramps")
10373 (uri (cran-uri "colorRamps" version))
10376 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10377 (properties `((upstream-name . "colorRamps")))
10378 (build-system r-build-system)
10379 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10380 (synopsis "Build color tables")
10381 (description "This package provides features to build gradient color
10383 ;; Any version of the GPL
10384 (license license:gpl3+)))
10386 (define-public r-tidytree
10388 (name "r-tidytree")
10393 (uri (cran-uri "tidytree" version))
10395 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10396 (build-system r-build-system)
10399 ("r-dplyr" ,r-dplyr)
10400 ("r-lazyeval" ,r-lazyeval)
10401 ("r-magrittr" ,r-magrittr)
10402 ("r-rlang" ,r-rlang)
10403 ("r-tibble" ,r-tibble)))
10405 `(("r-knitr" ,r-knitr)))
10406 (home-page "https://github.com/GuangchuangYu/tidytree")
10407 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10409 "Phylogenetic trees generally contain multiple components including nodes,
10410 edges, branches and associated data. This package provides an approach to
10411 convert tree objects to tidy data frames. It also provides tidy interfaces to
10412 manipulate tree data.")
10413 (license license:artistic2.0)))
10415 (define-public r-rvcheck
10422 (uri (cran-uri "rvcheck" version))
10424 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10425 (build-system r-build-system)
10427 `(("r-biocmanager" ,r-biocmanager)
10428 ("r-rlang" ,r-rlang)))
10429 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10430 (synopsis "R package version check")
10432 "This package provides tools to check the latest release version of R and
10433 R packages (on CRAN, Bioconductor or Github).")
10434 (license license:artistic2.0)))
10436 (define-public r-docopt
10443 (uri (cran-uri "docopt" version))
10446 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10447 (build-system r-build-system)
10448 (home-page "https://github.com/docopt/docopt.R")
10449 (synopsis "Command-line interface specification language")
10451 "This package enables you to define a command-line interface by just
10452 giving it a description in the specific format.")
10453 (license license:expat)))
10455 (define-public r-sparsesvd
10457 (name "r-sparsesvd")
10462 (uri (cran-uri "sparsesvd" version))
10465 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10466 (build-system r-build-system)
10467 (propagated-inputs `(("r-matrix" ,r-matrix)))
10468 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10469 (synopsis "Sparse truncated singular value decomposition")
10471 "This package provides a Wrapper around the SVDLIBC library
10472 for (truncated) singular value decomposition of a sparse matrix. Currently,
10473 only sparse real matrices in Matrix package format are supported.")
10474 ;; SVDLIBC is released under BSD-2. The R interface is released under
10476 (license (list license:bsd-3 license:bsd-2))))
10478 (define-public r-speedglm
10480 (name "r-speedglm")
10485 (uri (cran-uri "speedglm" version))
10488 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10489 (build-system r-build-system)
10491 `(("r-mass" ,r-mass)
10492 ("r-matrix" ,r-matrix)))
10493 (home-page "https://cran.r-project.org/web/packages/speedglm")
10494 (synopsis "Fit linear and generalized linear models to large data sets")
10496 "This package provides tools for fitting linear models and generalized
10497 linear models to large data sets by updating algorithms.")
10498 ;; Any version of the GPL
10499 (license license:gpl2+)))
10501 (define-public r-densityclust
10503 (name "r-densityclust")
10508 (uri (cran-uri "densityClust" version))
10511 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10512 (properties `((upstream-name . "densityClust")))
10513 (build-system r-build-system)
10516 ("r-ggplot2" ,r-ggplot2)
10517 ("r-ggrepel" ,r-ggrepel)
10518 ("r-gridextra" ,r-gridextra)
10519 ("r-rcolorbrewer" ,r-rcolorbrewer)
10521 ("r-rtsne" ,r-rtsne)))
10522 (home-page "https://cran.r-project.org/web/packages/densityClust")
10523 (synopsis "Clustering by fast search and find of density peaks")
10525 "This package provides an improved implementation (based on k-nearest
10526 neighbors) of the density peak clustering algorithm, originally described by
10527 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10528 large datasets (> 100,000 samples) very efficiently.")
10529 (license license:gpl2+)))
10531 (define-public r-combinat
10533 (name "r-combinat")
10538 (uri (cran-uri "combinat" version))
10541 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10542 (build-system r-build-system)
10543 (home-page "https://cran.r-project.org/web/packages/combinat")
10544 (synopsis "Combinatorics utilities")
10545 (description "This package provides assorted routines for combinatorics.")
10546 (license license:gpl2)))
10548 (define-public r-qlcmatrix
10550 (name "r-qlcmatrix")
10555 (uri (cran-uri "qlcMatrix" version))
10558 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10559 (properties `((upstream-name . "qlcMatrix")))
10560 (build-system r-build-system)
10562 `(("r-docopt" ,r-docopt)
10563 ("r-matrix" ,r-matrix)
10565 ("r-sparsesvd" ,r-sparsesvd)))
10566 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10567 (synopsis "Sparse matrix functions for quantitative language comparison")
10569 "This package provides an extension of the functionality of the Matrix
10570 package for using sparse matrices. Some of the functions are very general,
10571 while other are highly specific for the special data format used for
10572 @dfn{quantitative language comparison} (QLC).")
10573 (license license:gpl3)))
10575 (define-public r-ddrtree
10582 (uri (cran-uri "DDRTree" version))
10585 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10586 (properties `((upstream-name . "DDRTree")))
10587 (build-system r-build-system)
10590 ("r-irlba" ,r-irlba)
10592 ("r-rcppeigen" ,r-rcppeigen)))
10593 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10594 (synopsis "Learning principal graphs with DDRTree")
10596 "This package provides an implementation of the framework of
10597 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10598 dimensional space while constructs a principal tree which passes through the
10599 middle of the data simultaneously. DDRTree shows superiority to
10600 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10601 intrinsic structure of single cell genomics data. In general, it could be
10602 used to reconstruct the temporal progression as well as the bifurcation
10603 structure of any data type.")
10604 (license license:asl2.0)))
10606 (define-public r-corpcor
10613 (uri (cran-uri "corpcor" version))
10616 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10617 (build-system r-build-system)
10618 (home-page "http://strimmerlab.org/software/corpcor/")
10619 (synopsis "Efficient estimation of covariance and (partial) correlation")
10621 "This package implements a James-Stein-type shrinkage estimator for the
10622 covariance matrix, with separate shrinkage for variances and correlations.
10623 Furthermore, functions are available for fast singular value decomposition,
10624 for computing the pseudoinverse, and for checking the rank and positive
10625 definiteness of a matrix.")
10626 (license license:gpl3+)))
10628 (define-public r-rspectra
10630 (name "r-rspectra")
10635 (uri (cran-uri "RSpectra" version))
10638 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10639 (properties `((upstream-name . "RSpectra")))
10640 (build-system r-build-system)
10642 `(("r-matrix" ,r-matrix)
10644 ("r-rcppeigen" ,r-rcppeigen)))
10645 (home-page "https://github.com/yixuan/RSpectra")
10646 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10648 "This package provides an R interface to the Spectra library for
10649 large-scale eigenvalue and SVD problems. It is typically used to compute a
10650 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10651 which is usually more efficient than @code{eigen()} if k << n.")
10653 (license license:mpl2.0)))
10655 (define-public r-vbsr
10662 (uri (cran-uri "vbsr" version))
10665 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10666 (build-system r-build-system)
10667 (home-page "https://cran.r-project.org/web/packages/vbsr")
10668 (synopsis "Variational Bayes spike regression regularized linear models")
10670 "This package provides an efficient algorithm for solving ultra-sparse
10671 regularized regression models using a variational Bayes algorithm with a spike
10672 prior. The algorithm is solved on a path, with coordinate updates, and is
10673 capable of generating very sparse models. Very general model
10674 diagnostics for controlling type-1 errors are also provided.")
10675 (license license:gpl2)))
10677 (define-public r-flare
10680 (version "1.6.0.2")
10684 (uri (cran-uri "flare" version))
10687 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10688 (build-system r-build-system)
10690 `(("r-igraph" ,r-igraph)
10691 ("r-lattice" ,r-lattice)
10693 ("r-matrix" ,r-matrix)))
10694 (home-page "https://cran.r-project.org/web/packages/flare")
10695 (synopsis "Family of Lasso regression implementations")
10697 "This package provides implementations of a family of Lasso variants
10698 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10699 high dimensional sparse linear models.")
10700 (license license:gpl2)))
10702 (define-public r-lassopv
10709 (uri (cran-uri "lassopv" version))
10712 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10713 (build-system r-build-system)
10714 (propagated-inputs `(("r-lars" ,r-lars)))
10715 (home-page "https://github.com/lingfeiwang/lassopv")
10716 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10718 "This package enables you to estimate the p-values for predictors x
10719 against target variable y in Lasso regression, using the regularization
10720 strength when each predictor enters the active set of regularization path for
10721 the first time as the statistic.")
10722 (license license:gpl3)))
10724 (define-public r-splitstackshape
10726 (name "r-splitstackshape")
10731 (uri (cran-uri "splitstackshape" version))
10734 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10735 (build-system r-build-system)
10737 `(("r-data-table" ,r-data-table)))
10738 (home-page "https://github.com/mrdwab/splitstackshape")
10739 (synopsis "Stack and reshape datasets after splitting concatenated values")
10741 "Online data collection tools like Google Forms often export
10742 multiple-response questions with data concatenated in cells. The
10743 @code{concat.split} (cSplit) family of functions provided by this package
10744 splits such data into separate cells. This package also includes functions to
10745 stack groups of columns and to reshape wide data, even when the data are
10746 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10747 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10749 (license license:gpl3)))
10751 (define-public r-tfmpvalue
10753 (name "r-tfmpvalue")
10758 (uri (cran-uri "TFMPvalue" version))
10761 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10762 (properties `((upstream-name . "TFMPvalue")))
10763 (build-system r-build-system)
10764 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10765 (home-page "https://github.com/ge11232002/TFMPvalue")
10766 (synopsis "P-value computation for position weight matrices")
10768 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10769 identification from sequence/alignments, we are interested in the significance
10770 of certain match scores. TFMPvalue provides the accurate calculation of a
10771 p-value with a score threshold for position weight matrices, or the score with
10772 a given p-value. It is an interface to code originally made available by
10773 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10774 Touzet and Varre (2007).")
10775 (license license:gpl2)))
10777 (define-public r-rnifti
10784 (uri (cran-uri "RNifti" version))
10787 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10788 (properties `((upstream-name . "RNifti")))
10789 (build-system r-build-system)
10790 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10791 (home-page "https://github.com/jonclayden/RNifti")
10792 (synopsis "Fast R and C++ access to NIfTI images")
10794 "This package provides very fast read and write access to images stored
10795 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10796 compiled C and interpreted R code. It also provides a C/C++ API that can be
10797 used by other packages.")
10798 (license license:gpl2)))
10800 (define-public r-shades
10807 (uri (cran-uri "shades" version))
10810 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10811 (build-system r-build-system)
10812 (home-page "https://github.com/jonclayden/shades")
10813 (synopsis "Simple color manipulation")
10815 "This package provides functions for easily manipulating colors,
10816 creating color scales and calculating color distances.")
10817 (license license:bsd-3)))
10819 (define-public r-ore
10826 (uri (cran-uri "ore" version))
10828 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10829 (build-system r-build-system)
10830 (home-page "https://github.com/jonclayden/ore")
10831 (synopsis "R interface to the Onigmo regular expression library")
10833 "This package provides an alternative to R's built-in functionality for
10834 handling regular expressions, based on the Onigmo library. It offers
10835 first-class compiled regex objects, partial matching and function-based
10836 substitutions, amongst other features.")
10837 (license license:bsd-3)))
10839 (define-public r-reportr
10846 (uri (cran-uri "reportr" version))
10849 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10850 (build-system r-build-system)
10851 (propagated-inputs `(("r-ore" ,r-ore)))
10852 (home-page "https://github.com/jonclayden/reportr")
10853 (synopsis "General message and error reporting system")
10855 "This package provides a system for reporting messages, which offers
10856 certain useful features over the standard R system, such as the incorporation
10857 of output consolidation, message filtering, assertions, expression
10858 substitution, automatic generation of stack traces for debugging, and
10859 conditional reporting based on the current \"output level\".")
10860 (license license:gpl2)))
10862 (define-public r-tractor-base
10864 (name "r-tractor-base")
10869 (uri (cran-uri "tractor.base" version))
10872 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10873 (properties `((upstream-name . "tractor.base")))
10874 (build-system r-build-system)
10877 ("r-reportr" ,r-reportr)
10878 ("r-rnifti" ,r-rnifti)
10879 ("r-shades" ,r-shades)))
10880 (home-page "https://www.tractor-mri.org.uk")
10881 (synopsis "Read, manipulate and visualize magnetic resonance images")
10883 "This package provides functions for working with magnetic resonance
10884 images. It supports reading and writing of popular file formats (DICOM,
10885 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10886 visualization; flexible image manipulation; metadata and sparse image
10888 (license license:gpl2)))
10890 (define-public r-grimport
10892 (name "r-grimport")
10897 (uri (cran-uri "grImport" version))
10900 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10901 (properties `((upstream-name . "grImport")))
10902 (build-system r-build-system)
10904 `(("ghostscript" ,ghostscript)))
10906 `(("r-xml" ,r-xml)))
10907 (home-page "https://cran.r-project.org/web/packages/grImport")
10908 (synopsis "Convert, import, and draw PostScript pictures")
10910 "This package provides functions for converting, importing, and drawing
10911 PostScript pictures in R plots.")
10912 (license license:gpl2+)))
10914 (define-public r-grimport2
10916 (name "r-grimport2")
10921 (uri (cran-uri "grImport2" version))
10924 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10925 (properties `((upstream-name . "grImport2")))
10926 (build-system r-build-system)
10928 `(("r-base64enc" ,r-base64enc)
10932 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10933 (synopsis "Import SVG graphics")
10935 "This package provides functions for importing external vector images and
10936 drawing them as part of R plots. This package is different from the
10937 @code{grImport} package because, where that package imports PostScript format
10938 images, this package imports SVG format images. Furthermore, this package
10939 imports a specific subset of SVG, so external images must be preprocessed
10940 using a package like @code{rsvg} to produce SVG that this package can import.
10941 SVG features that are not supported by R graphics, such as gradient fills, can
10942 be imported and then exported via the @code{gridSVG} package.")
10943 (license license:gpl2+)))
10945 (define-public r-kohonen
10952 (uri (cran-uri "kohonen" version))
10955 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10956 (build-system r-build-system)
10958 `(("r-rcpp" ,r-rcpp)))
10959 (home-page "https://cran.r-project.org/web/packages/kohonen")
10960 (synopsis "Supervised and unsupervised self-organising maps")
10962 "This package provides functions to train @dfn{self-organising
10963 maps} (SOMs). Also interrogation of the maps and prediction using trained
10964 maps are supported. The name of the package refers to Teuvo Kohonen, the
10965 inventor of the SOM.")
10966 (license license:gpl2+)))
10968 (define-public r-nnls
10975 (uri (cran-uri "nnls" version))
10978 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10979 (build-system r-build-system)
10980 (native-inputs `(("gfortran" ,gfortran)))
10981 (home-page "https://cran.r-project.org/web/packages/nnls")
10982 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10984 "This package provides an R interface to the Lawson-Hanson implementation
10985 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10986 the combination of non-negative and non-positive constraints.")
10987 (license license:gpl2+)))
10989 (define-public r-iso
10992 (version "0.0-18.1")
10996 (uri (cran-uri "Iso" version))
10999 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11000 (properties `((upstream-name . "Iso")))
11001 (build-system r-build-system)
11002 (native-inputs `(("gfortran" ,gfortran)))
11003 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11004 (synopsis "Functions to perform isotonic regression")
11006 "This package provides support for linear order and unimodal
11007 order (univariate) isotonic regression and bivariate isotonic regression with
11008 linear order on both variables.")
11009 (license license:gpl2+)))
11011 (define-public r-chemometricswithr
11013 (name "r-chemometricswithr")
11018 (uri (cran-uri "ChemometricsWithR" version))
11021 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11023 `((upstream-name . "ChemometricsWithR")))
11024 (build-system r-build-system)
11026 `(("r-devtools" ,r-devtools)
11027 ("r-kohonen" ,r-kohonen)
11030 (home-page "https://github.com/rwehrens/CWR")
11031 (synopsis "Chemometrics with R")
11033 "This package provides functions and scripts used in the book
11034 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11035 Life Sciences\" by Ron Wehrens, Springer (2011).")
11036 (license license:gpl2+)))
11038 (define-public r-als
11045 (uri (cran-uri "ALS" version))
11048 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11049 (properties `((upstream-name . "ALS")))
11050 (build-system r-build-system)
11053 ("r-nnls" ,r-nnls)))
11054 (home-page "https://cran.r-project.org/web/packages/ALS")
11055 (synopsis "Multivariate curve resolution alternating least squares")
11057 "Alternating least squares is often used to resolve components
11058 contributing to data with a bilinear structure; the basic technique may be
11059 extended to alternating constrained least squares. This package provides an
11060 implementation of @dfn{multivariate curve resolution alternating least
11061 squares} (MCR-ALS).
11063 Commonly applied constraints include unimodality, non-negativity, and
11064 normalization of components. Several data matrices may be decomposed
11065 simultaneously by assuming that one of the two matrices in the bilinear
11066 decomposition is shared between datasets.")
11067 (license license:gpl2+)))
11069 (define-public r-strucchange
11071 (name "r-strucchange")
11076 (uri (cran-uri "strucchange" version))
11079 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11080 (build-system r-build-system)
11082 `(("r-sandwich" ,r-sandwich)
11084 (home-page "https://cran.r-project.org/web/packages/strucchange")
11085 (synopsis "Testing, monitoring, and dating structural changes")
11087 "This package provides tools for testing, monitoring and dating
11088 structural changes in (linear) regression models. It features tests/methods
11089 from the generalized fluctuation test framework as well as from the F
11090 test (Chow test) framework. This includes methods to fit, plot and test
11091 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11092 statistics, respectively. It is possible to monitor incoming data online
11093 using fluctuation processes. Finally, the breakpoints in regression models
11094 with structural changes can be estimated together with confidence intervals.
11095 Emphasis is always given to methods for visualizing the data.")
11096 ;; Either of these two GPL versions
11097 (license (list license:gpl2 license:gpl3))))
11099 (define-public r-pixmap
11106 (uri (cran-uri "pixmap" version))
11109 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11110 (build-system r-build-system)
11111 (home-page "https://cran.r-project.org/web/packages/pixmap")
11112 (synopsis "Tools for bitmap images")
11114 "This package provides functions for importing, exporting, plotting and
11115 other manipulations of bitmapped images.")
11116 (license license:gpl2)))
11118 (define-public r-rapidjsonr
11120 (name "r-rapidjsonr")
11125 (uri (cran-uri "rapidjsonr" version))
11128 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11129 (build-system r-build-system)
11130 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11131 (synopsis "JSON parser")
11133 "This package provides JSON parsing capability through the Rapidjson
11135 (license license:expat)))
11137 (define-public r-ontologyindex
11139 (name "r-ontologyindex")
11144 (uri (cran-uri "ontologyIndex" version))
11147 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11148 (properties `((upstream-name . "ontologyIndex")))
11149 (build-system r-build-system)
11150 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11151 (synopsis "Functions for processing ontologies in R")
11153 "This package provides functions for reading ontologies into R as lists
11154 and manipulating sets of ontological terms.")
11155 (license license:gpl2+)))
11157 (define-public r-gargle
11164 (uri (cran-uri "gargle" version))
11167 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11168 (build-system r-build-system)
11173 ("r-jsonlite" ,r-jsonlite)
11174 ("r-rlang" ,r-rlang)
11175 ("r-withr" ,r-withr)))
11177 `(("r-knitr" ,r-knitr)))
11178 (home-page "https://gargle.r-lib.org")
11179 (synopsis "Utilities for working with Google APIs")
11181 "This package provides utilities for working with Google APIs. This
11182 includes functions and classes for handling common credential types and for
11183 preparing, executing, and processing HTTP requests.")
11184 (license license:expat)))
11186 (define-public r-bigrquery
11188 (name "r-bigrquery")
11193 (uri (cran-uri "bigrquery" version))
11196 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11197 (build-system r-build-system)
11199 `(("r-assertthat" ,r-assertthat)
11200 ("r-bit64" ,r-bit64)
11203 ("r-gargle" ,r-gargle)
11206 ("r-jsonlite" ,r-jsonlite)
11207 ("r-prettyunits" ,r-prettyunits)
11208 ("r-progress" ,r-progress)
11209 ("r-rapidjsonr" ,r-rapidjsonr)
11211 ("r-rlang" ,r-rlang)
11212 ("r-tibble" ,r-tibble)))
11213 (home-page "https://github.com/rstats-db/bigrquery")
11214 (synopsis "R interface to Google's BigQuery API")
11216 "This package provides an R interface to Google's BigQuery database.")
11217 (license license:gpl3)))
11219 (define-public r-gmp
11226 (uri (cran-uri "gmp" version))
11229 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11230 (build-system r-build-system)
11233 (modify-phases %standard-phases
11234 (add-after 'unpack 'set-CC
11235 (lambda _ (setenv "CC" "gcc") #t)))))
11236 (inputs `(("gmp" ,gmp)))
11237 (home-page "https://cran.r-project.org/web/packages/gmp")
11238 (synopsis "Multiple precision arithmetic")
11240 "This package supports multiple precision arithmetic (big integers and
11241 rationals, prime number tests, matrix computation), \"arithmetic without
11242 limitations\" using the GNU Multiple Precision library.")
11243 ;; Any version of the GPL.
11244 (license license:gpl3+)))
11246 (define-public r-rmpfr
11253 (uri (cran-uri "Rmpfr" version))
11256 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11257 (properties `((upstream-name . "Rmpfr")))
11258 (build-system r-build-system)
11263 `(("r-gmp" ,r-gmp)))
11265 `(("pkg-config" ,pkg-config)))
11266 (home-page "http://rmpfr.r-forge.r-project.org/")
11267 (synopsis "R bindings to the MPFR library")
11269 "This package supports arithmetic (via S4 classes and methods) for
11270 arbitrary precision floating point numbers, including transcendental
11271 functions. To this end, the package interfaces with the @dfn{Multiple
11272 Precision Floating-Point Reliable} (MPFR) library.")
11273 (license license:gpl2+)))
11275 (define-public r-assertive-base
11277 (name "r-assertive-base")
11282 (uri (cran-uri "assertive.base" version))
11285 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11287 `((upstream-name . "assertive.base")))
11288 (build-system r-build-system)
11289 (home-page "https://bitbucket.org/richierocks/assertive.base")
11290 (synopsis "Core of the assertive package")
11292 "This package provides a minimal set of predicates and assertions used by
11293 the assertive package. This is mainly for use by other package developers who
11294 want to include run-time testing features in their own packages.")
11295 (license license:gpl3+)))
11297 (define-public r-assertive-properties
11299 (name "r-assertive-properties")
11304 (uri (cran-uri "assertive.properties" version))
11307 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11309 `((upstream-name . "assertive.properties")))
11310 (build-system r-build-system)
11312 `(("r-assertive-base" ,r-assertive-base)))
11313 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11314 (synopsis "Assertions to check properties of variables")
11316 "This package provides a set of predicates and assertions for checking
11317 the properties of variables, such as length, names and attributes. This is
11318 mainly for use by other package developers who want to include run-time
11319 testing features in their own packages.")
11320 (license license:gpl3+)))
11322 (define-public r-assertive-numbers
11324 (name "r-assertive-numbers")
11329 (uri (cran-uri "assertive.numbers" version))
11332 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11334 `((upstream-name . "assertive.numbers")))
11335 (build-system r-build-system)
11337 `(("r-assertive-base" ,r-assertive-base)))
11338 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11339 (synopsis "Assertions to check properties of numbers")
11341 "This package provides a set of predicates and assertions for checking
11342 the properties of numbers. This is mainly for use by other package developers
11343 who want to include run-time testing features in their own packages.")
11344 (license license:gpl3+)))
11346 (define-public r-assertive-sets
11348 (name "r-assertive-sets")
11353 (uri (cran-uri "assertive.sets" version))
11356 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11358 `((upstream-name . "assertive.sets")))
11359 (build-system r-build-system)
11361 `(("r-assertive-base" ,r-assertive-base)))
11362 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11363 (synopsis "Assertions to check properties of sets")
11365 "This package provides a set of predicates and assertions for checking
11366 the properties of sets. This is mainly for use by other package developers
11367 who want to include run-time testing features in their own packages.")
11368 (license license:gpl3+)))
11370 (define-public r-assertive-matrices
11372 (name "r-assertive-matrices")
11377 (uri (cran-uri "assertive.matrices" version))
11380 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11382 `((upstream-name . "assertive.matrices")))
11383 (build-system r-build-system)
11385 `(("r-assertive-base" ,r-assertive-base)))
11386 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11387 (synopsis "Assertions to check properties of matrices")
11389 "This package provides a set of predicates and assertions for checking
11390 the properties of matrices. This is mainly for use by other package
11391 developers who want to include run-time testing features in their own
11393 (license license:gpl3+)))
11395 (define-public r-assertive-models
11397 (name "r-assertive-models")
11402 (uri (cran-uri "assertive.models" version))
11405 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11407 `((upstream-name . "assertive.models")))
11408 (build-system r-build-system)
11410 `(("r-assertive-base" ,r-assertive-base)))
11411 (home-page "https://bitbucket.org/richierocks/assertive.models")
11412 (synopsis "Assertions to check properties of models")
11414 "This package provides a set of predicates and assertions for checking
11415 the properties of models. This is mainly for use by other package developers
11416 who want to include run-time testing features in their own packages.")
11417 (license license:gpl3+)))
11419 (define-public r-assertive-reflection
11421 (name "r-assertive-reflection")
11426 (uri (cran-uri "assertive.reflection" version))
11429 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11431 `((upstream-name . "assertive.reflection")))
11432 (build-system r-build-system)
11434 `(("r-assertive-base" ,r-assertive-base)))
11435 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11436 (synopsis "Assertions for checking the state of R")
11438 "This package provides a set of predicates and assertions for checking
11439 the state and capabilities of R, the operating system it is running on, and
11440 the IDE being used. This is mainly for use by other package developers who
11441 want to include run-time testing features in their own packages.")
11442 (license license:gpl3+)))
11444 (define-public r-assertive-types
11446 (name "r-assertive-types")
11451 (uri (cran-uri "assertive.types" version))
11454 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11456 `((upstream-name . "assertive.types")))
11457 (build-system r-build-system)
11459 `(("r-assertive-base" ,r-assertive-base)
11460 ("r-assertive-properties" ,r-assertive-properties)
11461 ("r-codetools" ,r-codetools)))
11462 (home-page "https://bitbucket.org/richierocks/assertive.types")
11463 (synopsis "Assertions to check types of variables")
11465 "This package provides a set of predicates and assertions for checking
11466 the types of variables. This is mainly for use by other package developers
11467 who want to include run-time testing features in their own packages.")
11468 (license license:gpl3+)))
11470 (define-public r-assertive-files
11472 (name "r-assertive-files")
11477 (uri (cran-uri "assertive.files" version))
11480 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11482 `((upstream-name . "assertive.files")))
11483 (build-system r-build-system)
11485 `(("r-assertive-base" ,r-assertive-base)
11486 ("r-assertive-numbers" ,r-assertive-numbers)))
11487 (home-page "https://bitbucket.org/richierocks/assertive.files")
11488 (synopsis "Assertions to check properties of files")
11490 "This package provides a set of predicates and assertions for checking
11491 the properties of files and connections. This is mainly for use by other
11492 package developers who want to include run-time testing features in their own
11494 (license license:gpl3+)))
11496 (define-public r-assertive-code
11498 (name "r-assertive-code")
11503 (uri (cran-uri "assertive.code" version))
11506 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11508 `((upstream-name . "assertive.code")))
11509 (build-system r-build-system)
11511 `(("r-assertive-base" ,r-assertive-base)
11512 ("r-assertive-properties" ,r-assertive-properties)
11513 ("r-assertive-types" ,r-assertive-types)))
11514 (home-page "https://bitbucket.org/richierocks/assertive.code")
11515 (synopsis "Assertions to check properties of code")
11517 "This package provides a set of predicates and assertions for checking
11518 the properties of code. This is mainly for use by other package developers
11519 who want to include run-time testing features in their own packages.")
11520 (license license:gpl3+)))
11522 (define-public r-assertive-datetimes
11524 (name "r-assertive-datetimes")
11529 (uri (cran-uri "assertive.datetimes" version))
11532 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11534 `((upstream-name . "assertive.datetimes")))
11535 (build-system r-build-system)
11537 `(("r-assertive-base" ,r-assertive-base)
11538 ("r-assertive-types" ,r-assertive-types)))
11539 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11540 (synopsis "Assertions to check properties of dates and times")
11542 "This package provides a set of predicates and assertions for checking
11543 the properties of dates and times. This is mainly for use by other package
11544 developers who want to include run-time testing features in their own
11546 (license license:gpl3+)))
11548 (define-public r-assertive-strings
11550 (name "r-assertive-strings")
11555 (uri (cran-uri "assertive.strings" version))
11558 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11560 `((upstream-name . "assertive.strings")))
11561 (build-system r-build-system)
11563 `(("r-assertive-base" ,r-assertive-base)
11564 ("r-assertive-types" ,r-assertive-types)
11565 ("r-stringi" ,r-stringi)))
11566 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11567 (synopsis "Assertions to check properties of strings")
11569 "This package provides a set of predicates and assertions for checking
11570 the properties of strings. This is mainly for use by other package developers
11571 who want to include run-time testing features in their own packages.")
11572 (license license:gpl3+)))
11574 (define-public r-assertive-data-us
11576 (name "r-assertive-data-us")
11581 (uri (cran-uri "assertive.data.us" version))
11584 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11586 `((upstream-name . "assertive.data.us")))
11587 (build-system r-build-system)
11589 `(("r-assertive-base" ,r-assertive-base)
11590 ("r-assertive-strings" ,r-assertive-strings)))
11591 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11592 (synopsis "Assertions to check properties of strings")
11594 "This package provides a set of predicates and assertions for checking
11595 the properties of US-specific complex data types. This is mainly for use by
11596 other package developers who want to include run-time testing features in
11597 their own packages.")
11598 (license license:gpl3+)))
11600 (define-public r-assertive-data-uk
11602 (name "r-assertive-data-uk")
11607 (uri (cran-uri "assertive.data.uk" version))
11610 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11612 `((upstream-name . "assertive.data.uk")))
11613 (build-system r-build-system)
11615 `(("r-assertive-base" ,r-assertive-base)
11616 ("r-assertive-strings" ,r-assertive-strings)))
11617 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11618 (synopsis "Assertions to check properties of strings")
11620 "This package provides a set of predicates and assertions for checking
11621 the properties of UK-specific complex data types. This is mainly for use by
11622 other package developers who want to include run-time testing features in
11623 their own packages.")
11624 (license license:gpl3+)))
11626 (define-public r-assertive-data
11628 (name "r-assertive-data")
11633 (uri (cran-uri "assertive.data" version))
11636 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11638 `((upstream-name . "assertive.data")))
11639 (build-system r-build-system)
11641 `(("r-assertive-base" ,r-assertive-base)
11642 ("r-assertive-strings" ,r-assertive-strings)))
11643 (home-page "https://bitbucket.org/richierocks/assertive.data")
11644 (synopsis "Assertions to check properties of data")
11646 "This package provides a set of predicates and assertions for checking
11647 the properties of (country independent) complex data types. This is mainly
11648 for use by other package developers who want to include run-time testing
11649 features in their own packages.")
11650 (license license:gpl3+)))
11652 (define-public r-assertive
11654 (name "r-assertive")
11659 (uri (cran-uri "assertive" version))
11662 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11663 (build-system r-build-system)
11665 `(("r-assertive-base" ,r-assertive-base)
11666 ("r-assertive-code" ,r-assertive-code)
11667 ("r-assertive-data" ,r-assertive-data)
11668 ("r-assertive-data-uk" ,r-assertive-data-uk)
11669 ("r-assertive-data-us" ,r-assertive-data-us)
11670 ("r-assertive-datetimes" ,r-assertive-datetimes)
11671 ("r-assertive-files" ,r-assertive-files)
11672 ("r-assertive-matrices" ,r-assertive-matrices)
11673 ("r-assertive-models" ,r-assertive-models)
11674 ("r-assertive-numbers" ,r-assertive-numbers)
11675 ("r-assertive-properties" ,r-assertive-properties)
11676 ("r-assertive-reflection" ,r-assertive-reflection)
11677 ("r-assertive-sets" ,r-assertive-sets)
11678 ("r-assertive-strings" ,r-assertive-strings)
11679 ("r-assertive-types" ,r-assertive-types)
11680 ("r-knitr" ,r-knitr)))
11682 `(("r-knitr" ,r-knitr)))
11683 (home-page "https://bitbucket.org/richierocks/assertive")
11684 (synopsis "Readable check functions to ensure code integrity")
11686 "This package provides lots of predicates (@code{is_*} functions) to
11687 check the state of your variables, and assertions (@code{assert_*} functions)
11688 to throw errors if they aren't in the right form.")
11689 (license license:gpl3+)))
11691 (define-public r-dotcall64
11693 (name "r-dotcall64")
11698 (uri (cran-uri "dotCall64" version))
11701 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11702 (properties `((upstream-name . "dotCall64")))
11703 (build-system r-build-system)
11704 (native-inputs `(("gfortran" ,gfortran)))
11705 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11706 (synopsis "Enhanced foreign function interface supporting long vectors")
11708 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11709 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11710 supports long vectors, arguments of type 64-bit integer, and provides a
11711 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11712 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11713 (license license:gpl2+)))
11715 (define-public r-spam
11722 (uri (cran-uri "spam" version))
11724 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11725 (build-system r-build-system)
11727 `(("r-dotcall64" ,r-dotcall64)))
11728 (native-inputs `(("gfortran" ,gfortran)))
11729 (home-page "https://www.math.uzh.ch/pages/spam/")
11730 (synopsis "Sparse matrix algebra")
11732 "This package provides a set of functions for sparse matrix algebra.
11733 Differences with other sparse matrix packages are:
11736 @item it only supports (essentially) one sparse matrix format;
11737 @item it is based on transparent and simple structure(s);
11738 @item it is tailored for MCMC calculations within G(M)RF;
11739 @item and it is fast and scalable (with the extension package @code{spam64}).
11741 ;; Either of these licenses
11742 (license (list license:bsd-3 license:lgpl2.0))))
11744 (define-public r-fields
11751 (uri (cran-uri "fields" version))
11753 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11754 (build-system r-build-system)
11756 `(("r-maps" ,r-maps)
11757 ("r-spam" ,r-spam)))
11759 `(("gfortran" ,gfortran)))
11760 (home-page "https://www.image.ucar.edu/fields")
11761 (synopsis "Tools for spatial data")
11763 "This is a package for curve, surface and function fitting with an
11764 emphasis on splines, spatial data and spatial statistics. The major methods
11765 include cubic, and thin plate splines, Kriging, and compactly supported
11766 covariance functions for large data sets.")
11767 (license license:gpl2+)))
11769 (define-public r-spatialextremes
11771 (name "r-spatialextremes")
11776 (uri (cran-uri "SpatialExtremes" version))
11779 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11781 `((upstream-name . "SpatialExtremes")))
11782 (build-system r-build-system)
11784 `(("r-fields" ,r-fields)
11785 ("r-maps" ,r-maps)))
11786 (home-page "http://spatialextremes.r-forge.r-project.org/")
11787 (synopsis "Modelling spatial extremes")
11789 "This package provides tools for the statistical modelling of spatial
11790 extremes using max-stable processes, copula or Bayesian hierarchical models.
11791 More precisely, this package allows (conditional) simulations from various
11792 parametric max-stable models, analysis of the extremal spatial dependence, the
11793 fitting of such processes using composite likelihoods or least square (simple
11794 max-stable processes only), model checking and selection and prediction.")
11795 (license license:gpl2+)))
11797 (define-public r-drc
11804 (uri (cran-uri "drc" version))
11807 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11808 (build-system r-build-system)
11811 ("r-gtools" ,r-gtools)
11813 ("r-multcomp" ,r-multcomp)
11814 ("r-plotrix" ,r-plotrix)
11815 ("r-scales" ,r-scales)))
11816 (home-page "https://cran.r-project.org/web/packages/drc")
11817 (synopsis "Analysis of dose-response curves")
11819 "This package provides a suite of flexible and versatile model fitting
11820 and after-fitting functions for the analysis of dose-response data.")
11821 (license license:gpl2+)))
11823 (define-public r-rmeta
11830 (uri (cran-uri "rmeta" version))
11833 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11834 (build-system r-build-system)
11835 (home-page "https://cran.r-project.org/web/packages/rmeta")
11836 (synopsis "Tools for meta-analysis")
11838 "This package provides functions for simple fixed and random effects
11839 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11840 draws standard summary plots, funnel plots, and computes summaries and tests
11841 for association and heterogeneity.")
11842 (license license:gpl2)))
11844 (define-public r-bootstrap
11846 (name "r-bootstrap")
11851 (uri (cran-uri "bootstrap" version))
11854 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11855 (build-system r-build-system)
11856 (native-inputs `(("gfortran" ,gfortran)))
11857 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11858 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11860 "This package provides software and data for the book \"An Introduction
11861 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11862 This package is primarily provided for projects already based on it, and for
11863 support of the book. New projects should preferentially use the recommended
11864 package \"boot\".")
11865 (license license:bsd-3)))
11867 (define-public r-survivalroc
11869 (name "r-survivalroc")
11874 (uri (cran-uri "survivalROC" version))
11877 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11878 (properties `((upstream-name . "survivalROC")))
11879 (build-system r-build-system)
11880 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11881 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11883 "Compute time-dependent ROC curve from censored survival data using
11884 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11885 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11886 (license license:gpl2+)))
11888 (define-public r-longitudinal
11890 (name "r-longitudinal")
11895 (uri (cran-uri "longitudinal" version))
11898 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11899 (build-system r-build-system)
11900 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11901 (home-page "http://strimmerlab.org/software/longitudinal/")
11902 (synopsis "Analysis of multiple time course data")
11904 "This package contains general data structures and functions for
11905 longitudinal data with multiple variables, repeated measurements, and
11906 irregularly spaced time points. It also implements a shrinkage estimator of
11907 dynamical correlation and dynamical covariance.")
11908 (license license:gpl3+)))
11910 (define-public r-genenet
11917 (uri (cran-uri "GeneNet" version))
11920 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11921 (properties `((upstream-name . "GeneNet")))
11922 (build-system r-build-system)
11924 `(("r-corpcor" ,r-corpcor)
11925 ("r-fdrtool" ,r-fdrtool)
11926 ("r-longitudinal" ,r-longitudinal)))
11927 (home-page "http://strimmerlab.org/software/genenet/")
11928 (synopsis "Modeling and inferring gene networks")
11930 "This package analyzes gene expression (time series) data with focus on
11931 the inference of gene networks. In particular, GeneNet implements the methods
11932 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11933 for learning large-scale gene association networks (including assignment of
11934 putative directions).")
11935 (license license:gpl3+)))
11937 (define-public r-rbamtools
11939 (name "r-rbamtools")
11940 (version "2.16.17")
11944 (uri (cran-uri "rbamtools" version))
11947 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11948 (build-system r-build-system)
11949 (inputs `(("zlib" ,zlib)))
11951 `(("r-refgenome" ,r-refgenome)))
11952 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11953 (synopsis "Read and write BAM (binary alignment) files")
11955 "This package provides an R interface to functions of the SAMtools
11957 (license license:artistic2.0)))
11959 (define-public r-protviz
11966 (uri (cran-uri "protViz" version))
11969 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11970 (properties `((upstream-name . "protViz")))
11971 (build-system r-build-system)
11972 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11973 (home-page "https://github.com/protViz/protViz/")
11974 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11976 "This package helps with quality checks, visualizations and analysis of
11977 mass spectrometry data, coming from proteomics experiments. The package is
11978 developed, tested and used at the Functional Genomics Center Zurich, where it
11979 is used mainly for prototyping, teaching, and having fun with proteomics data.
11980 But it can also be used to do data analysis for small scale data sets.")
11981 (license license:gpl3)))
11983 (define-public r-cmprsk
11990 (uri (cran-uri "cmprsk" version))
11992 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11993 (build-system r-build-system)
11995 `(("r-survival" ,r-survival)))
11997 `(("gfortran" ,gfortran)))
11998 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11999 (synopsis "Subdistribution analysis of competing risks")
12001 "This package provides tool for estimation, testing and regression
12002 modeling of subdistribution functions in competing risks, as described in
12003 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12004 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12005 A proportional hazards model for the subdistribution of a competing risk,
12006 JASA, 94:496-509.")
12007 (license license:gpl2+)))
12009 (define-public r-etm
12016 (uri (cran-uri "etm" version))
12019 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12020 (build-system r-build-system)
12022 `(("r-data-table" ,r-data-table)
12023 ("r-lattice" ,r-lattice)
12025 ("r-rcpparmadillo" ,r-rcpparmadillo)
12026 ("r-survival" ,r-survival)))
12027 (home-page "https://cran.r-project.org/web/packages/etm")
12028 (synopsis "Empirical transition matrix")
12030 "The @dfn{empirical transition matrix} (etm) package estimates
12031 the matrix of transition probabilities for any time-inhomogeneous multistate
12032 model with finite state space using the Aalen-Johansen estimator.")
12033 (license license:expat)))
12035 (define-public r-epi
12042 (uri (cran-uri "Epi" version))
12045 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12046 (properties `((upstream-name . "Epi")))
12047 (build-system r-build-system)
12049 `(("r-cmprsk" ,r-cmprsk)
12050 ("r-data-table" ,r-data-table)
12053 ("r-matrix" ,r-matrix)
12055 ("r-numderiv" ,r-numderiv)
12057 ("r-survival" ,r-survival)
12059 (home-page "https://BendixCarstensen.com/Epi/")
12060 (synopsis "Statistical analysis in epidemiology")
12062 "This package provides functions for demographic and epidemiological
12063 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12064 particular representation, manipulation and simulation of multistate data -
12065 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12066 @code{etm} and @code{cmprsk} packages. It also contains functions for
12067 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12068 data and some useful functions for tabulation and plotting, as well as a
12069 number of epidemiological data sets.")
12070 (license license:gpl2)))
12072 (define-public r-ppls
12075 (version "1.6-1.1")
12079 (uri (cran-uri "ppls" version))
12082 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12083 (build-system r-build-system)
12084 (propagated-inputs `(("r-mass" ,r-mass)))
12085 (home-page "https://cran.r-project.org/web/packages/ppls")
12086 (synopsis "Penalized partial least squares")
12088 "This package contains linear and nonlinear regression methods based on
12089 partial least squares and penalization techniques. Model parameters are
12090 selected via cross-validation, and confidence intervals ans tests for the
12091 regression coefficients can be conducted via jackknifing.")
12092 (license license:gpl2+)))
12094 (define-public r-huge
12097 (version "1.3.4.1")
12101 (uri (cran-uri "huge" version))
12103 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12104 (build-system r-build-system)
12106 `(("r-igraph" ,r-igraph)
12108 ("r-matrix" ,r-matrix)
12110 ("r-rcppeigen" ,r-rcppeigen)))
12111 (home-page "https://cran.r-project.org/web/packages/huge")
12112 (synopsis "High-dimensional undirected graph estimation")
12114 "This package provides a general framework for high-dimensional
12115 undirected graph estimation. It integrates data preprocessing, neighborhood
12116 screening, graph estimation, and model selection techniques into a pipeline.")
12117 (license license:gpl2)))
12119 (define-public r-parcor
12126 (uri (cran-uri "parcor" version))
12129 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12130 (build-system r-build-system)
12133 ("r-genenet" ,r-genenet)
12134 ("r-glmnet" ,r-glmnet)
12136 ("r-ppls" ,r-ppls)))
12137 (home-page "https://cran.r-project.org/web/packages/parcor")
12138 (synopsis "Regularized estimation of partial correlation matrices")
12140 "This package estimates the matrix of partial correlations based on
12141 different regularized regression methods: lasso, adaptive lasso, PLS, and
12142 Ridge Regression. In addition, the package provides model selection for
12143 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12144 (license license:gpl2+)))
12146 (define-public r-mcmc
12153 (uri (cran-uri "mcmc" version))
12156 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12157 (build-system r-build-system)
12158 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12159 (synopsis "Markov chain Monte Carlo")
12161 "This package simulates continuous distributions of random vectors using
12162 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12163 function that evaluates the log unnormalized density. Algorithms are random
12164 walk Metropolis algorithm (function @code{metrop}), simulated
12165 tempering (function @code{temper}), and morphometric random walk
12166 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12167 by change of variable.")
12168 (license license:expat)))
12170 (define-public r-listenv
12177 (uri (cran-uri "listenv" version))
12180 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12181 (build-system r-build-system)
12183 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12184 (home-page "https://github.com/HenrikBengtsson/listenv")
12185 (synopsis "Environments behaving (almost) as lists")
12187 "This package implements list environments. List environments are
12188 environments that have list-like properties. For instance, the elements of a
12189 list environment are ordered and can be accessed and iterated over using index
12191 (license license:lgpl2.1+)))
12193 (define-public r-globals
12200 (uri (cran-uri "globals" version))
12203 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12204 (build-system r-build-system)
12206 `(("r-codetools" ,r-codetools)))
12207 (home-page "https://github.com/HenrikBengtsson/globals")
12208 (synopsis "Identify global objects in R expressions")
12210 "This package provides tools to identify global (\"unknown\" or \"free\")
12211 objects in R expressions by code inspection using various strategies, e.g.
12212 conservative or liberal. The objective of this package is to make it as
12213 simple as possible to identify global objects for the purpose of exporting
12214 them in distributed compute environments.")
12215 (license license:lgpl2.1+)))
12217 (define-public r-future
12224 (uri (cran-uri "future" version))
12227 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12228 (build-system r-build-system)
12230 `(("r-digest" ,r-digest)
12231 ("r-globals" ,r-globals)
12232 ("r-listenv" ,r-listenv)))
12234 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12235 (home-page "https://github.com/HenrikBengtsson/future")
12236 (synopsis "Unified parallel and distributed processing in R")
12238 "The purpose of this package is to provide a lightweight and unified
12239 Future API for sequential and parallel processing of R expression via futures.
12240 This package implements sequential, multicore, multisession, and cluster
12241 futures. With these, R expressions can be evaluated on the local machine, in
12242 parallel a set of local machines, or distributed on a mix of local and remote
12243 machines. Extensions to this package implement additional backends for
12244 processing futures via compute cluster schedulers etc. Because of its unified
12245 API, there is no need to modify any code in order to switch from sequential on
12246 the local machine to, say, distributed processing on a remote compute cluster.")
12247 (license license:lgpl2.1+)))
12249 (define-public r-future-apply
12251 (name "r-future-apply")
12256 (uri (cran-uri "future.apply" version))
12259 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12260 (properties `((upstream-name . "future.apply")))
12261 (build-system r-build-system)
12263 `(("r-future" ,r-future)
12264 ("r-globals" ,r-globals)))
12266 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12267 (home-page "https://github.com/HenrikBengtsson/future.apply")
12268 (synopsis "Apply function to elements in parallel using futures")
12270 "This package provides implementations of @code{apply()},
12271 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12272 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12273 can be resolved using any future-supported backend, e.g. parallel on the local
12274 machine or distributed on a compute cluster.")
12275 (license license:gpl2+)))
12277 (define-public r-rsvd
12284 (uri (cran-uri "rsvd" version))
12287 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12288 (build-system r-build-system)
12290 `(("r-matrix" ,r-matrix)))
12291 (home-page "https://github.com/erichson/rSVD")
12292 (synopsis "Randomized singular value decomposition")
12294 "Low-rank matrix decompositions are fundamental tools and widely used for
12295 data analysis, dimension reduction, and data compression. Classically, highly
12296 accurate deterministic matrix algorithms are used for this task. However, the
12297 emergence of large-scale data has severely challenged our computational
12298 ability to analyze big data. The concept of randomness has been demonstrated
12299 as an effective strategy to quickly produce approximate answers to familiar
12300 problems such as the @dfn{singular value decomposition} (SVD). This package
12301 provides several randomized matrix algorithms such as the randomized singular
12302 value decomposition (@code{rsvd}), randomized principal component
12303 analysis (@code{rpca}), randomized robust principal component
12304 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12305 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12306 functions are provided.")
12307 (license license:gpl3+)))
12309 (define-public r-sloop
12316 (uri (cran-uri "sloop" version))
12319 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12320 (build-system r-build-system)
12322 `(("r-codetools" ,r-codetools)
12323 ("r-crayon" ,r-crayon)
12324 ("r-purrr" ,r-purrr)
12325 ("r-rlang" ,r-rlang)
12326 ("r-tibble" ,r-tibble)))
12327 (home-page "https://github.com/r-lib/sloop")
12328 (synopsis "Helpers for object-oriented programming in R")
12330 "This package provides a collection of helper functions designed to
12331 help you to better understand object oriented programming in R, particularly
12333 (license license:gpl3)))
12335 (define-public r-capushe
12342 (uri (cran-uri "capushe" version))
12345 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12346 (build-system r-build-system)
12347 (propagated-inputs `(("r-mass" ,r-mass)))
12348 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12349 (synopsis "Calibrating penalties using slope heuristics")
12351 "This package provides tools for the calibration of penalized criteria
12352 for model selection. The calibration methods available are based on the slope
12354 (license license:gpl2+)))
12356 (define-public r-dorng
12363 (uri (cran-uri "doRNG" version))
12366 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12367 (properties `((upstream-name . "doRNG")))
12368 (build-system r-build-system)
12370 `(("r-foreach" ,r-foreach)
12371 ("r-iterators" ,r-iterators)
12372 ("r-rngtools" ,r-rngtools)))
12373 (home-page "https://renozao.github.io/doRNG/")
12374 (synopsis "Generic reproducible parallel backend for foreach loops")
12376 "This package provides functions to perform reproducible parallel
12377 @code{foreach} loops, using independent random streams as generated by
12378 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12379 convert standard @code{%dopar%} loops into fully reproducible loops,
12380 independently of the number of workers, the task scheduling strategy, or the
12381 chosen parallel environment and associated foreach backend.")
12382 (license license:gpl2+)))
12384 (define-public r-blockmodeling
12386 (name "r-blockmodeling")
12391 (uri (cran-uri "blockmodeling" version))
12394 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12395 (build-system r-build-system)
12397 `(("r-matrix" ,r-matrix)))
12398 (native-inputs `(("gfortran" ,gfortran)))
12399 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12400 (synopsis "Generalized and classical blockmodeling of valued networks")
12402 "This package is primarily meant as an implementation of generalized
12403 blockmodeling for valued networks. In addition, measures of similarity or
12404 dissimilarity based on structural equivalence and regular equivalence (REGE
12405 algorithms) can be computed and partitioned matrices can be plotted.")
12406 (license license:gpl2+)))
12408 (define-public r-upsetr
12415 (uri (cran-uri "UpSetR" version))
12418 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12419 (properties `((upstream-name . "UpSetR")))
12420 (build-system r-build-system)
12422 `(("r-ggplot2" ,r-ggplot2)
12423 ("r-gridextra" ,r-gridextra)
12425 ("r-scales" ,r-scales)))
12426 (home-page "https://github.com/hms-dbmi/UpSetR")
12427 (synopsis "Visualize intersecting sets")
12429 "This package provides a more scalable alternative to Venn and Euler
12430 diagrams for visualizing intersecting sets. Create visualizations of
12431 intersecting sets using a novel matrix design, along with visualizations of
12432 several common set, element and attribute related tasks.")
12433 (license license:expat)))
12435 ;; This package includes a JavaScript file, which is not minified. When
12436 ;; upgrading please check that there are no new minified JavaScript files.
12437 (define-public r-shinybs
12444 (uri (cran-uri "shinyBS" version))
12447 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12448 (properties `((upstream-name . "shinyBS")))
12449 (build-system r-build-system)
12450 ;; The tests spawn Shiny browser apps. They cannot be run
12451 ;; non-interactively.
12452 (arguments '(#:tests? #f))
12454 `(("r-htmltools" ,r-htmltools)
12455 ("r-shiny" ,r-shiny)))
12456 (home-page "https://ebailey78.github.io/shinyBS/")
12457 (synopsis "Twitter Bootstrap components for Shiny")
12459 "This package adds additional Twitter Bootstrap components to Shiny.")
12460 (license license:gpl3)))
12462 (define-public r-outliers
12464 (name "r-outliers")
12469 (uri (cran-uri "outliers" version))
12472 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12473 (build-system r-build-system)
12474 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12475 (synopsis "Tests for outliers")
12477 "This package provides a collection of some tests commonly used for
12478 identifying outliers.")
12479 (license license:gpl2+)))
12481 (define-public r-bayesm
12488 (uri (cran-uri "bayesm" version))
12490 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12491 (build-system r-build-system)
12493 `(("r-rcpp" ,r-rcpp)
12494 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12495 (home-page "http://www.perossi.org/home/bsm-1")
12496 (synopsis "Bayesian inference for marketing/micro-econometrics")
12498 "This package covers many important models used in marketing and
12499 micro-econometrics applications, including Bayes Regression (univariate or
12500 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12501 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12502 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12503 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12504 Estimation with normal base, Hierarchical Linear Models with normal prior and
12505 covariates, Hierarchical Linear Models with a mixture of normals prior and
12506 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12507 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12508 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12509 analysis of choice-based conjoint data, Bayesian treatment of linear
12510 instrumental variables models, Analysis of Multivariate Ordinal survey data
12511 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12512 Coefficient Logit Models.")
12513 (license license:gpl2+)))
12515 (define-public r-tensora
12522 (uri (cran-uri "tensorA" version))
12525 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12526 (properties `((upstream-name . "tensorA")))
12527 (build-system r-build-system)
12528 (home-page "http://www.stat.boogaart.de/tensorA")
12529 (synopsis "Advanced tensor arithmetic with named indices")
12531 "This package provides convenience functions for advanced linear algebra
12532 with tensors and computation with datasets of tensors on a higher level
12533 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12534 co- and contravariate indices, and parallel computations on sequences of
12536 (license license:gpl2+)))
12538 (define-public r-rarpack
12545 (uri (cran-uri "rARPACK" version))
12548 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12549 (properties `((upstream-name . "rARPACK")))
12550 (build-system r-build-system)
12551 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12552 (home-page "https://github.com/yixuan/rARPACK")
12553 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12555 "This package was previously an R wrapper of the ARPACK library, and now
12556 a shell of the R package RSpectra, an R interface to the Spectra library for
12557 solving large scale eigenvalue/vector problems. The current version of
12558 rARPACK simply imports and exports the functions provided by RSpectra. New
12559 users of rARPACK are advised to switch to the RSpectra package.")
12560 (license license:bsd-3)))
12562 (define-public r-compositions
12564 (name "r-compositions")
12569 (uri (cran-uri "compositions" version))
12572 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12573 (build-system r-build-system)
12575 `(("r-bayesm" ,r-bayesm)
12577 ("r-robustbase" ,r-robustbase)
12578 ("r-tensora" ,r-tensora)))
12580 `(("r-knitr" ,r-knitr)))
12581 (home-page "http://www.stat.boogaart.de/compositions")
12582 (synopsis "Compositional data analysis")
12584 "This package provides functions for the consistent analysis of
12585 compositional data (e.g. portions of substances) and positive
12586 numbers (e.g. concentrations).")
12587 (license license:gpl2+)))
12589 (define-public r-cobs
12596 (uri (cran-uri "cobs" version))
12599 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12600 (build-system r-build-system)
12602 `(("r-quantreg" ,r-quantreg)
12603 ("r-sparsem" ,r-sparsem)))
12604 (home-page "https://cran.r-project.org/web/packages/cobs")
12605 (synopsis "Constrained B-Splines (sparse matrix based)")
12607 "This package provides qualitatively constrained (regression) smoothing
12608 splines via linear programming and sparse matrices.")
12609 (license license:gpl2+)))
12611 (define-public r-drimpute
12613 (name "r-drimpute")
12618 (uri (cran-uri "DrImpute" version))
12621 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12622 (properties `((upstream-name . "DrImpute")))
12623 (build-system r-build-system)
12625 `(("r-rcpp" ,r-rcpp)
12626 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12627 (home-page "https://github.com/ikwak2/DrImpute")
12628 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12630 "This is an R package for imputing dropout events. Many statistical
12631 methods in cell type identification, visualization and lineage reconstruction
12632 do not account for dropout events. DrImpute can improve the performance of
12633 such software by imputing dropout events.")
12634 (license license:gpl3)))
12636 (define-public r-gamlss-dist
12638 (name "r-gamlss-dist")
12643 (uri (cran-uri "gamlss.dist" version))
12645 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12646 (properties `((upstream-name . "gamlss.dist")))
12647 (build-system r-build-system)
12648 (propagated-inputs `(("r-mass" ,r-mass)))
12649 (home-page "http://www.gamlss.org/")
12650 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12652 "This package provides a set of distributions which can be used for
12653 modelling the response variables in Generalized Additive Models for Location
12654 Scale and Shape. The distributions can be continuous, discrete or mixed
12655 distributions. Extra distributions can be created, by transforming, any
12656 continuous distribution defined on the real line, to a distribution defined on
12657 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12658 transformation, respectively.")
12659 ;; Either version of the GPL.
12660 (license (list license:gpl2 license:gpl3))))
12662 ;; This package includes JavaScript files, which are not minified. When
12663 ;; upgrading please check that there are no new minified JavaScript files.
12664 (define-public r-shinyjs
12671 (uri (cran-uri "shinyjs" version))
12674 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12675 (build-system r-build-system)
12677 `(("r-digest" ,r-digest)
12678 ("r-htmltools" ,r-htmltools)
12679 ("r-jsonlite" ,r-jsonlite)
12680 ("r-shiny" ,r-shiny)))
12681 (home-page "https://deanattali.com/shinyjs")
12682 (synopsis "Improve the user experience of your Shiny apps")
12684 "Perform common useful JavaScript operations in Shiny apps that will
12685 greatly improve your apps without having to know any JavaScript. Examples
12686 include: hiding an element, disabling an input, resetting an input back to its
12687 original value, delaying code execution by a few seconds, and many more useful
12688 functions for both the end user and the developer. Shinyjs can also be used
12689 to easily call your own custom JavaScript functions from R.")
12690 (license license:agpl3+)))
12692 ;; This package includes minified JavaScript files. When upgrading please
12693 ;; check that there are no new minified JavaScript files.
12694 (define-public r-colourpicker
12696 (name "r-colourpicker")
12701 (uri (cran-uri "colourpicker" version))
12704 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12705 (build-system r-build-system)
12707 `(#:modules ((guix build utils)
12708 (guix build r-build-system)
12712 (modify-phases %standard-phases
12713 (add-after 'unpack 'process-javascript
12714 (lambda* (#:key inputs #:allow-other-keys)
12715 (with-directory-excursion "inst"
12719 `((,(assoc-ref inputs "js-salvattore")
12720 "examples/colourInput/www/salvattore.min.js")
12721 (,(assoc-ref inputs "js-jquery")
12722 "htmlwidgets/lib/jquery/jquery.min.js")
12723 ("www/shared/colourpicker/js/colourpicker.js"
12724 "www/shared/colourpicker/js/colourpicker.min.js"))))
12725 (lambda (sources targets)
12726 (for-each (lambda (source target)
12727 (format #t "Processing ~a --> ~a~%"
12729 (delete-file target)
12730 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12731 (call-with-output-file target
12733 (dump-port minified port)))))
12734 sources targets))))
12737 `(("r-ggplot2" ,r-ggplot2)
12738 ("r-htmltools" ,r-htmltools)
12739 ("r-htmlwidgets" ,r-htmlwidgets)
12740 ("r-jsonlite" ,r-jsonlite)
12741 ("r-miniui" ,r-miniui)
12742 ("r-shiny" ,r-shiny)
12743 ("r-shinyjs" ,r-shinyjs)))
12745 `(("uglify-js" ,uglify-js)
12749 (uri "https://code.jquery.com/jquery-3.3.1.js")
12752 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12756 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12759 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12760 (home-page "https://github.com/daattali/colourpicker")
12761 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12763 "This package provides a color picker that can be used as an input in
12764 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12765 custom color palettes, and many more options. A plot color helper tool is
12766 available as an RStudio Addin, which helps you pick colors to use in your
12767 plots. A more generic color picker RStudio Addin is also provided to let you
12768 select colors to use in your R code.")
12769 (license license:expat)))
12771 (define-public r-ggextra
12778 (uri (cran-uri "ggExtra" version))
12781 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12782 (properties `((upstream-name . "ggExtra")))
12783 (build-system r-build-system)
12785 `(("r-colourpicker" ,r-colourpicker)
12786 ("r-ggplot2" ,r-ggplot2)
12787 ("r-gtable" ,r-gtable)
12788 ("r-miniui" ,r-miniui)
12790 ("r-scales" ,r-scales)
12791 ("r-shiny" ,r-shiny)
12792 ("r-shinyjs" ,r-shinyjs)))
12794 `(("r-knitr" ,r-knitr)))
12795 (home-page "https://github.com/daattali/ggExtra")
12796 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12798 "This package is a collection of functions and layers to enhance ggplot2.
12799 The flagship function is @code{ggMarginal()}, which can be used to add
12800 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12801 (license license:expat)))
12803 (define-public r-minpack-lm
12805 (name "r-minpack-lm")
12810 (uri (cran-uri "minpack.lm" version))
12813 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12814 (properties `((upstream-name . "minpack.lm")))
12815 (build-system r-build-system)
12816 (native-inputs `(("gfortran" ,gfortran)))
12817 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12818 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12820 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12821 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12822 problems by a modification of the Levenberg-Marquardt algorithm, with support
12823 for lower and upper parameter bounds. The implementation can be used via
12824 @code{nls}-like calls using the @code{nlsLM} function.")
12825 (license license:gpl3)))
12827 (define-public r-moments
12834 (uri (cran-uri "moments" version))
12837 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12838 (build-system r-build-system)
12839 (home-page "https://cran.r-project.org/web/packages/moments")
12840 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12842 "This package provides functions to calculate: moments, Pearson's
12843 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12844 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12845 (license license:gpl2+)))
12847 (define-public r-msir
12854 (uri (cran-uri "msir" version))
12857 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12858 (build-system r-build-system)
12860 `(("r-mclust" ,r-mclust)))
12861 (home-page "https://cran.r-project.org/web/packages/msir")
12862 (synopsis "Model-based sliced inverse regression")
12864 "This is an R package for dimension reduction based on finite Gaussian
12865 mixture modeling of inverse regression.")
12866 (license license:gpl2+)))
12868 (define-public r-pbivnorm
12870 (name "r-pbivnorm")
12875 (uri (cran-uri "pbivnorm" version))
12878 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12879 (build-system r-build-system)
12880 (native-inputs `(("gfortran" ,gfortran)))
12881 (home-page "https://github.com/brentonk/pbivnorm")
12882 (synopsis "Vectorized bivariate normal CDF")
12884 "This package provides a vectorized R function for calculating
12885 probabilities from a standard bivariate normal CDF.")
12886 (license license:gpl2+)))
12888 (define-public r-lavaan
12895 (uri (cran-uri "lavaan" version))
12898 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
12899 (build-system r-build-system)
12901 `(("r-mass" ,r-mass)
12902 ("r-mnormt" ,r-mnormt)
12903 ("r-numderiv" ,r-numderiv)
12904 ("r-pbivnorm" ,r-pbivnorm)))
12905 (home-page "http://lavaan.ugent.be")
12906 (synopsis "Latent variable analysis")
12908 "This package provides tools to fit a variety of latent variable models,
12909 including confirmatory factor analysis, structural equation modeling and
12910 latent growth curve models.")
12911 (license license:gpl2+)))
12913 (define-public r-nonnest2
12915 (name "r-nonnest2")
12920 (uri (cran-uri "nonnest2" version))
12923 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
12924 (build-system r-build-system)
12926 `(("r-compquadform" ,r-compquadform)
12927 ("r-lavaan" ,r-lavaan)
12928 ("r-mvtnorm" ,r-mvtnorm)
12929 ("r-sandwich" ,r-sandwich)))
12931 `(("r-knitr" ,r-knitr)))
12932 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12933 (synopsis "Tests of non-nested models")
12935 "This package allows for testing of non-nested models. It includes tests
12936 of model distinguishability and of model fit that can be applied to both
12937 nested and non-nested models. The package also includes functionality to
12938 obtain confidence intervals associated with AIC and BIC.")
12939 ;; Either version of the GPL.
12940 (license (list license:gpl2 license:gpl3))))
12942 (define-public r-penalized
12944 (name "r-penalized")
12949 (uri (cran-uri "penalized" version))
12952 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12953 (build-system r-build-system)
12955 `(("r-rcpp" ,r-rcpp)
12956 ("r-rcpparmadillo" ,r-rcpparmadillo)
12957 ("r-survival" ,r-survival)))
12958 (home-page "https://cran.r-project.org/web/packages/penalized/")
12959 (synopsis "Penalized estimation in GLMs and in the Cox model")
12961 "This package provides tools for fitting possibly high dimensional
12962 penalized regression models. The penalty structure can be any combination of
12963 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12964 constraint on the regression coefficients. The supported regression models
12965 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12966 model. Cross-validation routines allow optimization of the tuning
12968 (license license:gpl2+)))
12970 (define-public r-zim
12977 (uri (cran-uri "ZIM" version))
12980 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12981 (properties `((upstream-name . "ZIM")))
12982 (build-system r-build-system)
12983 (propagated-inputs `(("r-mass" ,r-mass)))
12984 (home-page "https://github.com/biostatstudio/ZIM")
12985 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12987 "Analyze count time series with excess zeros. Two types of statistical
12988 models are supported: Markov regression and state-space models. They are also
12989 known as observation-driven and parameter-driven models respectively in the
12990 time series literature. The functions used for Markov regression or
12991 observation-driven models can also be used to fit ordinary regression models
12992 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12993 negative binomial (ZINB) assumption. The package also contains miscellaneous
12994 functions to compute density, distribution, quantile, and generate random
12995 numbers from ZIP and ZINB distributions.")
12996 (license license:gpl3)))
12998 (define-public r-nor1mix
13005 (uri (cran-uri "nor1mix" version))
13008 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13009 (build-system r-build-system)
13010 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13011 (synopsis "Normal (1-d) mixture models")
13013 "This package provides S3 classes and methods for one-dimensional normal
13014 mixture models, for, e.g., density estimation or clustering algorithms
13015 research and teaching; it provides the widely used Marron-Wand densities. It
13016 also provides tools for efficient random number generation and graphics.")
13017 (license license:gpl2+)))
13019 (define-public r-beanplot
13021 (name "r-beanplot")
13026 (uri (cran-uri "beanplot" version))
13029 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13030 (build-system r-build-system)
13031 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13032 (synopsis "Visualization via beanplots")
13034 "This package provides beanplots, an alternative to
13035 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13037 (license license:gpl2)))
13039 (define-public r-pbdzmq
13046 (uri (cran-uri "pbdZMQ" version))
13049 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13050 (properties `((upstream-name . "pbdZMQ")))
13051 (build-system r-build-system)
13053 `(("zeromq" ,zeromq)
13056 `(("pkg-config" ,pkg-config)))
13057 (home-page "https://pbdr.org/")
13058 (synopsis "R interface to ZeroMQ")
13060 "ZeroMQ is a well-known library for high-performance asynchronous
13061 messaging in scalable, distributed applications. This package provides high
13062 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13063 interactive client/server programming frameworks. A few wrapper functions
13064 compatible with @code{rzmq} are also provided.")
13065 (license license:gpl3)))
13067 (define-public r-repr
13074 (uri (cran-uri "repr" version))
13077 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13078 (build-system r-build-system)
13080 `(("r-base64enc" ,r-base64enc)
13081 ("r-htmltools" ,r-htmltools)
13082 ("r-jsonlite" ,r-jsonlite)
13083 ("r-pillar" ,r-pillar)))
13084 (home-page "https://cran.r-project.org/web/packages/repr/")
13085 (synopsis "Serializable representations")
13087 "This package provides string and binary representations of objects for
13088 several formats and MIME types.")
13089 (license license:gpl3)))
13091 (define-public r-irdisplay
13093 (name "r-irdisplay")
13098 (uri (cran-uri "IRdisplay" version))
13101 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13102 (properties `((upstream-name . "IRdisplay")))
13103 (build-system r-build-system)
13105 `(("r-repr" ,r-repr)))
13106 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13107 (synopsis "Jupyter display machinery")
13109 "This package provides an interface to the rich display capabilities of
13110 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13111 running IRkernel session.")
13112 (license license:expat)))
13114 (define-public r-irkernel
13116 (name "r-irkernel")
13121 (uri (cran-uri "IRkernel" version))
13124 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13125 (properties `((upstream-name . "IRkernel")))
13126 (build-system r-build-system)
13129 (modify-phases %standard-phases
13130 (add-after 'install 'install-kernelspec
13131 (lambda* (#:key outputs #:allow-other-keys)
13132 (let ((out (assoc-ref outputs "out")))
13133 (setenv "HOME" "/tmp")
13134 (invoke "jupyter" "kernelspec" "install"
13137 (string-append out "/site-library/IRkernel/kernelspec"))
13138 ;; Record the absolute file name of the 'R' executable in
13140 (substitute* (string-append out "/share/jupyter"
13141 "/kernels/ir/kernel.json")
13143 (string-append "[\"" (which "R") "\",")))
13146 `(("jupyter" ,jupyter)))
13148 `(("r-crayon" ,r-crayon)
13149 ("r-digest" ,r-digest)
13150 ("r-evaluate" ,r-evaluate)
13151 ("r-irdisplay" ,r-irdisplay)
13152 ("r-jsonlite" ,r-jsonlite)
13153 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13154 ("r-minimal" ,r-minimal)
13155 ("r-pbdzmq" ,r-pbdzmq)
13157 ("r-uuid" ,r-uuid)))
13158 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13159 (synopsis "Native R kernel for Jupyter")
13161 "The R kernel for the Jupyter environment executes R code which the
13162 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13164 (license license:expat)))
13166 (define-public r-gmodels
13173 (uri (cran-uri "gmodels" version))
13176 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13177 (build-system r-build-system)
13179 `(("r-gdata" ,r-gdata)
13180 ("r-mass" ,r-mass)))
13181 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13182 (synopsis "Various R programming tools for model fitting")
13184 "This package provides various R programming tools for model fitting.")
13185 (license license:gpl2)))
13187 (define-public r-apcluster
13189 (name "r-apcluster")
13194 (uri (cran-uri "apcluster" version))
13197 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13198 (build-system r-build-system)
13200 `(("r-matrix" ,r-matrix)
13201 ("r-rcpp" ,r-rcpp)))
13202 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13203 (synopsis "Affinity propagation clustering")
13205 "This package implements affinity propagation clustering introduced by
13206 Frey and Dueck (2007). The package further provides leveraged affinity
13207 propagation and an algorithm for exemplar-based agglomerative clustering that
13208 can also be used to join clusters obtained from affinity propagation. Various
13209 plotting functions are available for analyzing clustering results.")
13210 (license license:gpl2+)))
13212 (define-public r-valr
13219 (uri (cran-uri "valr" version))
13222 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13223 (build-system r-build-system)
13225 `(("r-broom" ,r-broom)
13226 ("r-dplyr" ,r-dplyr)
13227 ("r-ggplot2" ,r-ggplot2)
13229 ("r-readr" ,r-readr)
13230 ("r-rlang" ,r-rlang)
13231 ("r-stringr" ,r-stringr)
13232 ("r-tibble" ,r-tibble)))
13234 `(("r-knitr" ,r-knitr)))
13235 (home-page "https://github.com/rnabioco/valr")
13236 (synopsis "Genome interval arithmetic in R")
13238 "This package enables you to read and manipulate genome intervals and
13239 signals. It provides functionality similar to command-line tool suites within
13240 R, enabling interactive analysis and visualization of genome-scale data.")
13241 (license license:expat)))
13243 (define-public r-rematch2
13245 (name "r-rematch2")
13250 (uri (cran-uri "rematch2" version))
13253 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13254 (build-system r-build-system)
13256 `(("r-tibble" ,r-tibble)))
13257 (home-page "https://github.com/r-lib/rematch2")
13258 (synopsis "Tidy output from regular expression matching")
13260 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13261 return the match results in tidy data frames.")
13262 (license license:expat)))
13264 (define-public r-picante
13271 (uri (cran-uri "picante" version))
13274 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13275 (build-system r-build-system)
13279 ("r-vegan" ,r-vegan)))
13280 (home-page "https://cran.r-project.org/web/packages/picante/")
13281 (synopsis "Integrating phylogenies and ecology")
13283 "This package provides functions for phylocom integration, community
13284 analyses, null-models, traits and evolution. It implements numerous
13285 ecophylogenetic approaches including measures of community phylogenetic and
13286 trait diversity, phylogenetic signal, estimation of trait values for
13287 unobserved taxa, null models for community and phylogeny randomizations, and
13288 utility functions for data input/output and phylogeny plotting. A full
13289 description of package functionality and methods are provided by Kembel et
13291 (license license:gpl2)))
13293 (define-public r-reinforcelearn
13295 (name "r-reinforcelearn")
13300 (uri (cran-uri "reinforcelearn" version))
13303 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13304 (build-system r-build-system)
13306 `(("r-checkmate" ,r-checkmate)
13308 ("r-purrr" ,r-purrr)
13310 (home-page "https://markusdumke.github.io/reinforcelearn")
13311 (synopsis "Reinforcement learning")
13313 "This package implements reinforcement learning environments and
13314 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13315 can be used with function approximation, eligibility traces (Singh & Sutton,
13316 1996) and experience replay (Mnih et al., 2013).")
13317 (license license:expat)))
13319 (define-public r-lemon
13326 (uri (cran-uri "lemon" version))
13329 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13330 (build-system r-build-system)
13332 `(("r-ggplot2" ,r-ggplot2)
13333 ("r-gridextra" ,r-gridextra)
13334 ("r-gtable" ,r-gtable)
13335 ("r-knitr" ,r-knitr)
13336 ("r-lattice" ,r-lattice)
13338 ("r-rlang" ,r-rlang)
13339 ("r-scales" ,r-scales)))
13341 `(("r-knitr" ,r-knitr)))
13342 (home-page "https://github.com/stefanedwards/lemon")
13343 (synopsis "Freshen up your ggplot2 plots")
13345 "This package provides functions for working with legends and axis lines
13346 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13348 (license license:gpl3)))
13350 (define-public r-wgaim
13357 (uri (cran-uri "wgaim" version))
13359 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13360 (build-system r-build-system)
13362 `(("r-ggplot2" ,r-ggplot2)
13364 (home-page "https://cran.r-project.org/web/packages/wgaim")
13365 (synopsis "Whole genome average interval mapping for QTL detection")
13367 "This package integrates sophisticated mixed modelling methods with a
13368 whole genome approach to detecting significant QTL in linkage maps.")
13369 (license license:gpl2+)))
13371 (define-public r-bedr
13378 (uri (cran-uri "bedr" version))
13381 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13382 (build-system r-build-system)
13384 `(("r-data-table" ,r-data-table)
13385 ("r-r-utils" ,r-r-utils)
13386 ("r-testthat" ,r-testthat)
13387 ("r-venndiagram" ,r-venndiagram)
13390 ("bedtools" ,bedtools)
13391 ("htslib" ,htslib))) ; for tabix
13393 `(("r-knitr" ,r-knitr))) ; for vignettes
13394 (home-page "https://cran.r-project.org/web/packages/bedr")
13395 (synopsis "Genomic region processing")
13397 "This package is for genomic regions processing using command line tools
13398 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13399 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13400 The bedr package's API enhances access to these tools as well as offers
13401 additional utilities for genomic regions processing.")
13402 (license license:gpl2)))
13404 (define-public r-sets
13411 (uri (cran-uri "sets" version))
13414 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13415 (properties `((upstream-name . "sets")))
13416 (build-system r-build-system)
13417 (home-page "https://cran.r-project.org/web/packages/sets")
13418 (synopsis "Sets, generalized sets, customizable sets and intervals")
13420 "This package provides data structures and basic operations for ordinary
13421 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13422 customizable sets, and intervals.")
13423 (license license:gpl2)))
13425 (define-public r-partitions
13427 (name "r-partitions")
13432 (uri (cran-uri "partitions" version))
13435 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13436 (build-system r-build-system)
13439 ("r-polynom" ,r-polynom)
13440 ("r-sets" ,r-sets)))
13441 (home-page "https://cran.r-project.org/web/packages/partitions")
13442 (synopsis "Additive partitions of integers")
13444 "This package provides tools to enumerates the partitions, unequal
13445 partitions, and restricted partitions of an integer; the three corresponding
13446 partition functions are also given.")
13447 ;; Any version of the GPL
13448 (license license:gpl2+)))
13450 (define-public r-brobdingnag
13452 (name "r-brobdingnag")
13457 (uri (cran-uri "Brobdingnag" version))
13460 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13461 (properties `((upstream-name . "Brobdingnag")))
13462 (build-system r-build-system)
13463 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13464 (synopsis "Very large numbers in R")
13466 "This package handles very large numbers in R. Real numbers are held
13467 using their natural logarithms, plus a logical flag indicating sign. The
13468 package includes a vignette that gives a step-by-step introduction to using S4
13470 ;; Any version of the GPL
13471 (license license:gpl2+)))
13473 (define-public r-untb
13480 (uri (cran-uri "untb" version))
13483 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13484 (build-system r-build-system)
13486 `(("r-brobdingnag" ,r-brobdingnag)
13487 ("r-partitions" ,r-partitions)
13488 ("r-polynom" ,r-polynom)))
13489 (home-page "https://github.com/RobinHankin/untb.git")
13490 (synopsis "Ecological drift under the UNTB")
13492 "This package provides numerical simulations, and visualizations, of
13493 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13494 (license license:gpl2+)))
13496 (define-public r-stepwise
13498 (name "r-stepwise")
13503 (uri (cran-uri "stepwise" version))
13506 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13507 (build-system r-build-system)
13508 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13509 (synopsis "Stepwise detection of recombination breakpoints")
13511 "This package provides a stepwise approach to identifying recombination
13512 breakpoints in a genomic sequence alignment.")
13513 (license license:gpl2+)))
13515 (define-public r-snpmaxsel
13517 (name "r-snpmaxsel")
13522 (uri (cran-uri "SNPmaxsel" version))
13525 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13526 (properties `((upstream-name . "SNPmaxsel")))
13527 (build-system r-build-system)
13529 `(("r-combinat" ,r-combinat)
13530 ("r-mvtnorm" ,r-mvtnorm)))
13531 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13532 (synopsis "Maximally selected statistics for SNP data")
13534 "This package implements asymptotic methods related to maximally selected
13535 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13537 (license license:gpl2+)))
13539 (define-public r-acsnminer
13541 (name "r-acsnminer")
13542 (version "0.16.8.25")
13545 (uri (cran-uri "ACSNMineR" version))
13548 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13549 (properties `((upstream-name . "ACSNMineR")))
13550 (build-system r-build-system)
13552 `(("r-ggplot2" ,r-ggplot2)
13553 ("r-gridextra" ,r-gridextra)))
13554 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13555 (synopsis "Gene enrichment analysis")
13557 "This package provides tools to compute and represent gene set enrichment
13558 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13559 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13560 enrichment can be run with hypergeometric test or Fisher exact test, and can
13561 use multiple corrections. Visualization of data can be done either by
13562 barplots or heatmaps.")
13563 (license license:gpl2+)))
13565 (define-public r-seqinr
13572 (uri (cran-uri "seqinr" version))
13575 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13576 (build-system r-build-system)
13578 `(("r-ade4" ,r-ade4)
13579 ("r-segmented" ,r-segmented)))
13582 (home-page "http://seqinr.r-forge.r-project.org/")
13583 (synopsis "Biological sequences retrieval and analysis")
13585 "This package provides tools for exploratory data analysis and data
13586 visualization of biological sequence (DNA and protein) data. It also includes
13587 utilities for sequence data management under the ACNUC system.")
13588 (license license:gpl2+)))
13590 (define-public r-units
13597 (uri (cran-uri "units" version))
13600 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13601 (build-system r-build-system)
13603 `(("udunits" ,udunits)))
13605 `(("r-rcpp" ,r-rcpp)))
13607 `(("r-knitr" ,r-knitr)))
13608 (home-page "https://github.com/r-quantities/units/")
13609 (synopsis "Measurement Units for R Vectors")
13611 "This package provides support for measurement units in R vectors,
13612 matrices and arrays: automatic propagation, conversion, derivation and
13613 simplification of units; raising errors in case of unit incompatibility. It
13614 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13616 (license license:gpl2)))
13618 (define-public r-classint
13620 (name "r-classint")
13625 (uri (cran-uri "classInt" version))
13628 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13629 (properties `((upstream-name . "classInt")))
13630 (build-system r-build-system)
13632 `(("r-class" ,r-class)
13633 ("r-e1071" ,r-e1071)
13634 ("r-kernsmooth" ,r-kernsmooth)))
13636 `(("gfortran" ,gfortran)
13637 ("r-knitr" ,r-knitr)))
13638 (home-page "https://github.com/r-spatial/classInt/")
13639 (synopsis "Choose univariate class intervals")
13641 "This package provides selected commonly used methods for choosing
13642 univariate class intervals for mapping or other graphics purposes.")
13643 (license license:gpl2+)))
13645 (define-public r-spdata
13652 (uri (cran-uri "spData" version))
13655 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13656 (properties `((upstream-name . "spData")))
13657 (build-system r-build-system)
13659 `(("r-raster" ,r-raster)
13661 (home-page "https://github.com/Nowosad/spData")
13662 (synopsis "Datasets for spatial analysis")
13664 "This a package containing diverse spatial datasets for demonstrating,
13665 benchmarking and teaching spatial data analysis. It includes R data of class
13666 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13667 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13668 of the datasets are designed to illustrate specific analysis techniques.
13669 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13670 illustrate point pattern analysis techniques.")
13671 (license license:cc0)))
13673 (define-public r-learnbayes
13675 (name "r-learnbayes")
13680 (uri (cran-uri "LearnBayes" version))
13683 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13684 (properties `((upstream-name . "LearnBayes")))
13685 (build-system r-build-system)
13686 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13687 (synopsis "Functions for learning Bayesian inference")
13689 "This package provides a collection of functions helpful in learning the
13690 basic tenets of Bayesian statistical inference. It contains functions for
13691 summarizing basic one and two parameter posterior distributions and predictive
13692 distributions. It contains MCMC algorithms for summarizing posterior
13693 distributions defined by the user. It also contains functions for regression
13694 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13696 (license license:gpl2+)))
13698 (define-public r-deldir
13705 (uri (cran-uri "deldir" version))
13708 "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
13709 (build-system r-build-system)
13710 (native-inputs `(("gfortran" ,gfortran)))
13711 (home-page "https://cran.r-project.org/web/packages/deldir")
13712 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13714 "This package provides tools for calculating the Delaunay triangulation
13715 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13716 of a planar point set. It plots triangulations and tessellations in various
13717 ways, clips tessellations to sub-windows, calculates perimeters of
13718 tessellations, and summarizes information about the tiles of the
13720 (license license:gpl2+)))
13722 (define-public r-sf
13729 (uri (cran-uri "sf" version))
13732 "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
13733 (build-system r-build-system)
13740 `(("r-classint" ,r-classint)
13742 ("r-magrittr" ,r-magrittr)
13744 ("r-units" ,r-units)))
13746 `(("pkg-config" ,pkg-config)
13747 ("r-knitr" ,r-knitr)))
13748 (home-page "https://github.com/r-spatial/sf/")
13749 (synopsis "Simple features for R")
13751 "This package provides support for simple features, a standardized way to
13752 encode spatial vector data. It binds to GDAL for reading and writing data, to
13753 GEOS for geometrical operations, and to PROJ for projection conversions and
13754 datum transformations.")
13755 ;; Either of these licenses
13756 (license (list license:gpl2 license:expat))))
13758 (define-public r-spdep
13765 (uri (cran-uri "spdep" version))
13768 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13769 (build-system r-build-system)
13771 `(("r-boot" ,r-boot)
13773 ("r-deldir" ,r-deldir)
13775 ("r-gmodels" ,r-gmodels)
13776 ("r-learnbayes" ,r-learnbayes)
13778 ("r-matrix" ,r-matrix)
13782 ("r-spdata" ,r-spdata)))
13784 `(("r-knitr" ,r-knitr)))
13785 (home-page "https://github.com/r-spatial/spdep/")
13786 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13788 "This package provides a collection of functions to create spatial
13789 weights matrix objects from polygon contiguities, from point patterns by
13790 distance and tessellations, for summarizing these objects, and for permitting
13791 their use in spatial data analysis, including regional aggregation by minimum
13793 (license license:gpl2+)))
13795 (define-public r-adegenet
13797 (name "r-adegenet")
13802 (uri (cran-uri "adegenet" version))
13805 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13806 (build-system r-build-system)
13808 `(("r-ade4" ,r-ade4)
13811 ("r-dplyr" ,r-dplyr)
13812 ("r-ggplot2" ,r-ggplot2)
13813 ("r-igraph" ,r-igraph)
13815 ("r-reshape2" ,r-reshape2)
13816 ("r-seqinr" ,r-seqinr)
13817 ("r-shiny" ,r-shiny)
13818 ("r-spdep" ,r-spdep)
13819 ("r-vegan" ,r-vegan)))
13820 (home-page "https://github.com/thibautjombart/adegenet")
13821 (synopsis "Exploratory analysis of genetic and genomic data")
13823 "This package provides a toolset for the exploration of genetic and
13824 genomic data. Adegenet provides formal (S4) classes for storing and handling
13825 various genetic data, including genetic markers with varying ploidy and
13826 hierarchical population structure (@code{genind} class), alleles counts by
13827 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13828 also implements original multivariate methods (DAPC, sPCA), graphics,
13829 statistical tests, simulation tools, distance and similarity measures, and
13830 several spatial methods. A range of both empirical and simulated datasets is
13831 also provided to illustrate various methods.")
13832 (license license:gpl2+)))
13834 (define-public r-pegas
13841 (uri (cran-uri "pegas" version))
13843 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13844 (build-system r-build-system)
13846 `(("r-adegenet" ,r-adegenet)
13848 (home-page "http://ape-package.ird.fr/pegas.html")
13849 (synopsis "Population and evolutionary genetics analysis system")
13851 "This package provides functions for reading, writing, plotting,
13852 analysing, and manipulating allelic and haplotypic data, including from VCF
13853 files, and for the analysis of population nucleotide sequences and
13854 micro-satellites including coalescent analyses, linkage disequilibrium,
13855 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13856 minimum spanning tree and network, and median-joining networks.")
13857 (license license:gpl2+)))
13859 (define-public r-rmetasim
13861 (name "r-rmetasim")
13866 (uri (cran-uri "rmetasim" version))
13869 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13870 (build-system r-build-system)
13872 `(("r-ade4" ,r-ade4)
13873 ("r-adegenet" ,r-adegenet)
13874 ("r-gtools" ,r-gtools)
13875 ("r-pegas" ,r-pegas)))
13876 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13877 (synopsis "Individual-based population genetic simulation environment")
13879 "This package provides an interface between R and the metasim simulation
13880 engine. The simulation environment is documented in: Strand, A.(2002),
13881 Metasim 1.0: an individual-based environment for simulating population
13882 genetics of complex population dynamics.")
13884 (license license:gpl2+)))
13886 (define-public r-genetics
13888 (name "r-genetics")
13889 (version "1.3.8.1.2")
13893 (uri (cran-uri "genetics" version))
13896 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13897 (build-system r-build-system)
13899 `(("r-combinat" ,r-combinat)
13900 ("r-gdata" ,r-gdata)
13901 ("r-gtools" ,r-gtools)
13903 ("r-mvtnorm" ,r-mvtnorm)))
13904 (home-page "https://cran.r-project.org/web/packages/genetics/")
13905 (synopsis "Population genetics")
13907 "This package provides classes and methods for handling genetic data.
13908 It includes classes to represent genotypes and haplotypes at single markers up
13909 to multiple markers on multiple chromosomes. Function include allele
13910 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13911 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13912 and testing for linkage disequilibrium, ...")
13913 ;; Any GPL version.
13914 (license license:gpl2+)))
13916 (define-public r-snp-plotter
13918 (name "r-snp-plotter")
13923 (uri (cran-uri "snp.plotter" version))
13926 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13927 (properties `((upstream-name . "snp.plotter")))
13928 (build-system r-build-system)
13929 (propagated-inputs `(("r-genetics" ,r-genetics)))
13930 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13931 (synopsis "Plot p-values using single SNP and/or haplotype data")
13933 "This package helps you create plots of p-values using single SNP and/or
13934 haplotype data. Main features of the package include options to display a
13935 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13936 datasets simultaneously. Plots can be created using global and/or individual
13937 haplotype p-values along with single SNP p-values. Images are created as
13938 either PDF/EPS files.")
13939 (license license:gpl2+)))
13941 (define-public r-polspline
13943 (name "r-polspline")
13948 (uri (cran-uri "polspline" version))
13950 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13951 (build-system r-build-system)
13952 (native-inputs `(("gfortran" ,gfortran)))
13953 (home-page "https://cran.r-project.org/web/packages/polspline/")
13954 (synopsis "Polynomial spline routines")
13956 "This package provides routines for the polynomial spline fitting
13957 routines hazard regression, hazard estimation with flexible tails, logspline,
13958 lspec, polyclass, and polymars.")
13959 (license license:gpl2+)))
13961 (define-public r-rms
13968 (uri (cran-uri "rms" version))
13970 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
13971 (build-system r-build-system)
13973 `(("r-cluster" ,r-cluster)
13974 ("r-digest" ,r-digest)
13975 ("r-ggplot2" ,r-ggplot2)
13976 ("r-hmisc" ,r-hmisc)
13977 ("r-htmltable" ,r-htmltable)
13978 ("r-htmltools" ,r-htmltools)
13979 ("r-lattice" ,r-lattice)
13981 ("r-multcomp" ,r-multcomp)
13983 ("r-polspline" ,r-polspline)
13984 ("r-quantreg" ,r-quantreg)
13985 ("r-rpart" ,r-rpart)
13986 ("r-sparsem" ,r-sparsem)
13987 ("r-survival" ,r-survival)))
13988 (native-inputs `(("gfortran" ,gfortran)))
13989 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13990 (synopsis "Regression modeling strategies")
13992 "This is a package for regression modeling, testing, estimation,
13993 validation, graphics, prediction, and typesetting by storing enhanced model
13994 design attributes in the fit. The rms package is a collection of functions
13995 that assist with and streamline modeling. It also contains functions for
13996 binary and ordinal logistic regression models, ordinal models for continuous Y
13997 with a variety of distribution families, and the Buckley-James multiple
13998 regression model for right-censored responses, and implements penalized
13999 maximum likelihood estimation for logistic and ordinary linear models. The
14000 package works with almost any regression model, but it was especially written
14001 to work with binary or ordinal regression models, Cox regression, accelerated
14002 failure time models, ordinary linear models, the Buckley-James model,
14003 generalized least squares for serially or spatially correlated observations,
14004 generalized linear models, and quantile regression.")
14005 (license license:gpl2+)))
14007 (define-public r-arsenal
14014 (uri (cran-uri "arsenal" version))
14017 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14018 (properties `((upstream-name . "arsenal")))
14019 (build-system r-build-system)
14020 (propagated-inputs `(("r-knitr" ,r-knitr)))
14021 (native-inputs `(("r-knitr" ,r-knitr)))
14022 (home-page "https://github.com/mayoverse/arsenal")
14023 (synopsis "Functions for large-scale statistical summaries")
14025 "This package provides an arsenal of R functions for large-scale
14026 statistical summaries, which are streamlined to work within the latest
14027 reporting tools in R and RStudio and which use formulas and versatile
14028 summary statistics for summary tables and models. The primary functions
14032 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14033 levels of one or more categorical variables;
14034 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14035 across two time points;
14036 @item @code{modelsum}, which performs simple model fits on one or more
14037 endpoints for many variables (univariate or adjusted for covariates);
14038 @item @code{freqlist}, a powerful frequency table across many categorical
14040 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14041 @item @code{write2}, a function to output tables to a document.
14044 (license license:gpl2+)))
14046 (define-public r-haplo-stats
14048 (name "r-haplo-stats")
14053 (uri (cran-uri "haplo.stats" version))
14056 "13gc980jk1pas7mz9b4nmwqd64qhh2c0xhq1z06z67jgv7k8n7dc"))))
14057 (properties `((upstream-name . "haplo.stats")))
14058 (build-system r-build-system)
14060 `(("r-arsenal" ,r-arsenal)
14063 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14064 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14065 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14067 "This package provides routines for the analysis of indirectly measured
14068 haplotypes. The statistical methods assume that all subjects are unrelated
14069 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14070 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14071 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14072 examples in the vignette.")
14073 (license license:gpl2+)))
14075 (define-public r-bqtl
14082 (uri (cran-uri "bqtl" version))
14085 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14086 (build-system r-build-system)
14087 (native-inputs `(("gfortran" ,gfortran)))
14088 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14089 (synopsis "Bayesian QTL mapping toolkit")
14091 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14092 lines. It includes maximum likelihood and Bayesian tools.")
14093 (license license:gpl2+)))
14095 (define-public r-ibdreg
14102 (uri (cran-uri "ibdreg" version))
14105 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14106 (build-system r-build-system)
14107 (home-page "https://www.mayo.edu/research/labs/\
14108 statistical-genetics-genetic-epidemiology/software")
14109 (synopsis "Regression methods for IBD linkage with covariates")
14111 "This package provides a method to test genetic linkage with covariates
14112 by regression methods with response IBD sharing for relative pairs. Account
14113 for correlations of IBD statistics and covariates for relative pairs within
14114 the same pedigree.")
14115 (license license:gpl2+)))
14117 (define-public r-dlmap
14124 (uri (cran-uri "dlmap" version))
14127 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14128 (build-system r-build-system)
14130 `(("r-ibdreg" ,r-ibdreg)
14134 ("r-wgaim" ,r-wgaim)))
14135 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14136 (synopsis "Detection localization mapping for QTL")
14138 "This is package for QTL mapping in a mixed model framework with separate
14139 detection and localization stages. The first stage detects the number of QTL
14140 on each chromosome based on the genetic variation due to grouped markers on
14141 the chromosome; the second stage uses this information to determine the most
14142 likely QTL positions. The mixed model can accommodate general fixed and
14143 random effects, including spatial effects in field trials and pedigree
14144 effects. It is applicable to backcrosses, doubled haploids, recombinant
14145 inbred lines, F2 intercrosses, and association mapping populations.")
14146 (license license:gpl2)))
14148 (define-public r-ldheatmap
14150 (name "r-ldheatmap")
14155 (uri (cran-uri "LDheatmap" version))
14158 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14159 (properties `((upstream-name . "LDheatmap")))
14160 (build-system r-build-system)
14162 `(("r-genetics" ,r-genetics)
14164 ("r-snpstats" ,r-snpstats)))
14165 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14166 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14168 "This package provides tools to produce a graphical display, as a heat
14169 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14170 optionally include the physical locations or genetic map distances of each SNP
14172 (license license:gpl3)))
14174 (define-public r-hwde
14181 (uri (cran-uri "hwde" version))
14184 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14185 (build-system r-build-system)
14186 (home-page "https://cran.r-project.org/web/packages/hwde/")
14187 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14189 "This package fits models for genotypic disequilibria, as described in
14190 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14191 terms are available that account for first order interactions between loci.
14192 It also implements, for a single locus in a single population, a conditional
14193 exact test for Hardy-Weinberg equilibrium.")
14194 (license license:gpl2+)))
14196 (define-public r-tdthap
14203 (uri (cran-uri "tdthap" version))
14206 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14207 (build-system r-build-system)
14208 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14209 (synopsis "TDT tests for extended haplotypes")
14211 "Functions and examples are provided for transmission/disequilibrium
14212 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14213 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14214 (license license:artistic2.0)))
14216 (define-public r-sparql
14222 (uri (cran-uri "SPARQL" version))
14225 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14226 (properties `((upstream-name . "SPARQL")))
14227 (build-system r-build-system)
14229 `(("r-rcurl" ,r-rcurl)
14231 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14232 (synopsis "SPARQL client for R")
14233 (description "This package provides an interface to use SPARQL to pose
14234 SELECT or UPDATE queries to an end-point.")
14235 ;; The only license indication is found in the DESCRIPTION file,
14236 ;; which states GPL-3. So we cannot assume GPLv3+.
14237 (license license:gpl3)))
14239 (define-public r-bookdown
14241 (name "r-bookdown")
14245 (uri (cran-uri "bookdown" version))
14248 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14249 (build-system r-build-system)
14251 `(("r-htmltools" ,r-htmltools)
14252 ("r-knitr" ,r-knitr)
14253 ("r-rmarkdown" ,r-rmarkdown)
14254 ("r-tinytex" ,r-tinytex)
14256 ("pandoc" ,pandoc)))
14257 (home-page "https://github.com/rstudio/bookdown")
14258 (synopsis "Authoring books and technical documents with R markdown")
14259 (description "This package provides output formats and utilities for
14260 authoring books and technical documents with R Markdown.")
14261 (license license:gpl3)))
14263 (define-public r-optparse
14265 (name "r-optparse")
14270 (uri (cran-uri "optparse" version))
14273 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14274 (build-system r-build-system)
14276 `(("r-getopt" ,r-getopt)))
14278 `(("r-knitr" ,r-knitr)))
14279 (home-page "https://github.com/trevorld/optparse")
14280 (synopsis "Command line option parser")
14282 "This package provides a command line parser inspired by Python's
14283 @code{optparse} library to be used with Rscript to write shebang scripts
14284 that accept short and long options.")
14285 (license license:gpl2+)))
14287 (define-public r-wgcna
14294 (uri (cran-uri "WGCNA" version))
14297 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14298 (properties `((upstream-name . "WGCNA")))
14299 (build-system r-build-system)
14301 `(("r-annotationdbi" ,r-annotationdbi)
14302 ("r-doparallel" ,r-doparallel)
14303 ("r-dynamictreecut" ,r-dynamictreecut)
14304 ("r-fastcluster" ,r-fastcluster)
14305 ("r-foreach" ,r-foreach)
14306 ("r-go-db" ,r-go-db)
14307 ("r-hmisc" ,r-hmisc)
14308 ("r-impute" ,r-impute)
14310 ("r-survival" ,r-survival)
14311 ("r-matrixstats" ,r-matrixstats)
14312 ("r-preprocesscore" ,r-preprocesscore)))
14314 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14315 (synopsis "Weighted correlation network analysis")
14317 "This package provides functions necessary to perform Weighted
14318 Correlation Network Analysis on high-dimensional data. It includes functions
14319 for rudimentary data cleaning, construction and summarization of correlation
14320 networks, module identification and functions for relating both variables and
14321 modules to sample traits. It also includes a number of utility functions for
14322 data manipulation and visualization.")
14323 (license license:gpl2+)))
14325 (define-public r-kernlab
14332 (uri (cran-uri "kernlab" version))
14334 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14335 (build-system r-build-system)
14336 (home-page "https://cran.r-project.org/web/packages/kernlab")
14337 (synopsis "Kernel-based machine learning tools")
14339 "This package provides kernel-based machine learning methods for
14340 classification, regression, clustering, novelty detection, quantile regression
14341 and dimensionality reduction. Among other methods @code{kernlab} includes
14342 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14344 (license license:gpl2)))
14346 (define-public r-hierfstat
14348 (name "r-hierfstat")
14353 (uri (cran-uri "hierfstat" version))
14356 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14357 (build-system r-build-system)
14359 `(("r-ade4" ,r-ade4)
14360 ("r-adegenet" ,r-adegenet)
14361 ("r-gaston" ,r-gaston)
14362 ("r-gtools" ,r-gtools)))
14364 `(("r-knitr" ,r-knitr)))
14365 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14366 (synopsis "Estimation and tests of hierarchical F-statistics")
14368 "This package allows the estimation of hierarchical F-statistics from
14369 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14370 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14371 are also given to test via randomisations the significance of each F and
14372 variance components, using the likelihood-ratio statistics G.")
14373 (license license:gpl2+)))
14375 (define-public r-hapassoc
14377 (name "r-hapassoc")
14382 (uri (cran-uri "hapassoc" version))
14385 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14386 (build-system r-build-system)
14387 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14388 (synopsis "Inference of trait associations with SNP haplotypes")
14390 "Hapassoc performs likelihood inference of trait associations with
14391 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14392 functions are developed primarily for data collected in cohort or
14393 cross-sectional studies. They can accommodate uncertain haplotype phase and
14394 handle missing genotypes at some SNPs.")
14395 (license license:gpl2)))
14397 (define-public r-sampling
14399 (name "r-sampling")
14404 (uri (cran-uri "sampling" version))
14407 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14408 (build-system r-build-system)
14410 `(("r-lpsolve" ,r-lpsolve)
14411 ("r-mass" ,r-mass)))
14412 (home-page "https://cran.r-project.org/web/packages/sampling/")
14413 (synopsis "Survey sampling")
14415 "This package provides functions for drawing and calibrating samples.")
14416 (license license:gpl2+)))
14418 (define-public r-r2html
14425 (uri (cran-uri "R2HTML" version))
14428 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14429 (properties `((upstream-name . "R2HTML")))
14430 (build-system r-build-system)
14431 (home-page "https://github.com/nalimilan/R2HTML")
14432 (synopsis "HTML export for R objects")
14434 "This package includes HTML functions and methods to write in an HTML
14435 file. Thus, making HTML reports is easy. It includes a function that allows
14436 redirection on the fly, which appears to be very useful for teaching purposes,
14437 as the student can keep a copy of the produced output to keep all that they
14438 did during the course. The package comes with a vignette describing how to
14439 write HTML reports for statistical analysis. Finally, a driver for Sweave
14440 parses HTML flat files containing R code and to automatically write
14441 the corresponding outputs (tables and graphs).")
14442 (license license:gpl2+)))
14444 (define-public r-rjava
14451 (uri (cran-uri "rJava" version))
14454 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14455 (properties `((upstream-name . "rJava")))
14456 (build-system r-build-system)
14458 `(#:modules ((guix build utils)
14459 (guix build r-build-system)
14462 (modify-phases %standard-phases
14463 (add-after 'unpack 'set-JAVA_HOME
14464 (lambda* (#:key inputs #:allow-other-keys)
14465 (let ((jdk (assoc-ref inputs "jdk")))
14466 (setenv "JAVA_HOME" jdk)
14467 (setenv "JAVA" (which "java"))
14468 (setenv "JAR" (which "jar"))
14469 (setenv "JAVAC" (which "javac"))
14470 (setenv "JAVAH" (which "javah"))
14471 (setenv "JAVA_CPPFLAGS"
14472 (string-append "-I" jdk "/include "
14473 "-I" jdk "/include/linux"))
14474 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14475 ((lib) (setenv "JAVA_LIBS" lib))
14476 (_ (error "Could not find libjvm.so"))))
14480 ("jdk" ,icedtea-8 "jdk")
14483 (home-page "https://www.rforge.net/rJava/")
14484 (synopsis "Low-Level R to Java interface")
14486 "This package provides a low-level interface to the Java VM very much
14487 like .C/.Call and friends. It allows the creation of objects, calling methods
14488 and accessing fields.")
14489 (license license:gpl2)))
14491 (define-public r-svmisc
14498 (uri (cran-uri "svMisc" version))
14501 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14502 (properties `((upstream-name . "svMisc")))
14503 (build-system r-build-system)
14504 (home-page "https://github.com/SciViews/svMisc")
14505 (synopsis "Miscellaneous functions for SciViews")
14507 "This package provides miscellaneous functions for SciViews or general
14508 use, including tools to manage a temporary environment attached to the search
14509 path for temporary variables you do not want to @code{save()} or
14510 @code{load()}; test the current platform; showing progress bars, etc.")
14511 (license license:gpl2)))
14513 (define-public r-xyz
14520 (uri (cran-uri "xyz" version))
14523 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14524 (build-system r-build-system)
14526 `(("r-rcpp" ,r-rcpp)))
14527 (home-page "https://cran.r-project.org/web/packages/xyz/")
14528 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14530 "High dimensional interaction search by brute force requires a quadratic
14531 computational cost in the number of variables. The xyz algorithm provably
14532 finds strong interactions in almost linear time. For details of the algorithm
14533 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14534 interaction search in high-dimensional data.")
14535 ;; Any version of the GPL.
14536 (license license:gpl2+)))
14538 (define-public r-rttf2pt1
14540 (name "r-rttf2pt1")
14545 (uri (cran-uri "Rttf2pt1" version))
14548 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14549 (properties `((upstream-name . "Rttf2pt1")))
14550 (build-system r-build-system)
14551 (home-page "https://github.com/wch/Rttf2pt1")
14552 (synopsis "Font conversion utility")
14554 "This package contains the program @code{ttf2pt1}, for use with the
14555 @code{extrafont} package.")
14556 ;; Most of the files are covered under the Expat license. Some files are
14557 ;; covered under BSD-3. Deviations for individual files are recorded in
14558 ;; the LICENSE file.
14559 (license (list license:bsd-3 license:expat
14560 (license:non-copyleft "file://LICENSE")))))
14562 (define-public r-extrafontdb
14564 (name "r-extrafontdb")
14569 (uri (cran-uri "extrafontdb" version))
14572 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14573 (build-system r-build-system)
14574 (home-page "https://github.com/wch/extrafontdb")
14575 (synopsis "Database for the extrafont package")
14577 "This package holds the database for the @code{extrafont} package.")
14578 (license license:gpl2)))
14580 (define-public r-extrafont
14582 (name "r-extrafont")
14587 (uri (cran-uri "extrafont" version))
14590 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14591 (build-system r-build-system)
14593 `(("r-extrafontdb" ,r-extrafontdb)
14594 ("r-rttf2pt1" ,r-rttf2pt1)))
14595 (home-page "https://github.com/wch/extrafont")
14596 (synopsis "Tools for using fonts in R")
14598 "The extrafont package makes it easier to use fonts other than the basic
14599 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14600 used with PDF or PostScript output files. There are two hurdles for using
14601 fonts in PDF (or Postscript) output files:
14604 @item Making R aware of the font and the dimensions of the characters.
14605 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14606 properly on a device that doesn't have the font. This is usually needed if
14607 you want to print the PDF file or share it with others.
14610 The extrafont package makes both of these things easier.")
14611 (license license:gpl2)))
14613 (define-public r-xkcd
14620 (uri (cran-uri "xkcd" version))
14623 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14624 (build-system r-build-system)
14626 `(("r-extrafont" ,r-extrafont)
14627 ("r-ggplot2" ,r-ggplot2)
14628 ("r-hmisc" ,r-hmisc)))
14629 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14630 (synopsis "Plot ggplot2 graphics in the XKCD style")
14632 "This package provides the means to plot ggplot2 graphs in the style of
14633 the XKCD web comic.")
14634 (license license:gpl3)))
14636 (define-public r-msigdbr
14643 (uri (cran-uri "msigdbr" version))
14646 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14647 (build-system r-build-system)
14649 `(("r-dplyr" ,r-dplyr)
14650 ("r-magrittr" ,r-magrittr)
14651 ("r-rlang" ,r-rlang)
14652 ("r-tibble" ,r-tibble)))
14654 `(("r-knitr" ,r-knitr)))
14655 (home-page "https://github.com/igordot/msigdbr")
14656 (synopsis "MSigDB gene sets for multiple organisms")
14658 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14659 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14660 software in a standard R data frame with key-value pairs. Included are the
14661 original human gene symbols and Entrez IDs as well as the equivalents for
14662 various frequently studied model organisms such as mouse, rat, pig, fly, and
14664 ;; The package is covered under the Expat license, but the upstream MSigDB
14665 ;; files are made available under the Creative Commons Attribution 4.0
14666 ;; International license.
14667 (license (list license:expat license:cc-by4.0))))
14669 (define-public r-gridgraphics
14671 (name "r-gridgraphics")
14676 (uri (cran-uri "gridGraphics" version))
14679 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14680 (properties `((upstream-name . "gridGraphics")))
14681 (build-system r-build-system)
14682 (home-page "https://github.com/pmur002/gridgraphics")
14683 (synopsis "Redraw base graphics using @code{grid} graphics")
14685 "This package provides functions to convert a page of plots drawn with
14686 the @code{graphics} package into identical output drawn with the @code{grid}
14687 package. The result looks like the original @code{graphics}-based plot, but
14688 consists of @code{grid} grobs and viewports that can then be manipulated with
14689 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14690 (license license:gpl2+)))
14692 (define-public r-farver
14699 (uri (cran-uri "farver" version))
14702 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14703 (build-system r-build-system)
14704 (home-page "https://github.com/thomasp85/farver")
14705 (synopsis "Vectorized color conversion and comparison")
14707 "The encoding of color can be handled in many different ways, using
14708 different color spaces. As different color spaces have different uses,
14709 efficient conversion between these representations are important. This
14710 package provides a set of functions that gives access to very fast color space
14711 conversion and comparisons implemented in C++, and offers 100-fold speed
14712 improvements over the @code{convertColor} function in the @code{grDevices}
14714 (license license:expat)))
14716 (define-public r-ggplotify
14718 (name "r-ggplotify")
14723 (uri (cran-uri "ggplotify" version))
14726 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14727 (build-system r-build-system)
14729 `(("r-ggplot2" ,r-ggplot2)
14730 ("r-gridgraphics" ,r-gridgraphics)
14731 ("r-rvcheck" ,r-rvcheck)))
14733 `(("r-knitr" ,r-knitr)))
14734 (home-page "https://github.com/GuangchuangYu/ggplotify")
14735 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14737 "This package provides tools to convert plot function calls (using
14738 expression or formula) to @code{grob} or @code{ggplot} objects that are
14739 compatible with the @code{grid} and @code{ggplot2} environment. With this
14740 package, we are able to e.g. use @code{cowplot} to align plots produced by
14741 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14742 converting them to @code{ggplot} objects.")
14743 (license license:artistic2.0)))
14745 (define-public r-triebeard
14747 (name "r-triebeard")
14752 (uri (cran-uri "triebeard" version))
14755 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14756 (build-system r-build-system)
14757 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14758 (home-page "https://github.com/Ironholds/triebeard/")
14759 (synopsis "Radix trees in Rcpp")
14761 "Radix trees, or tries, are key-value data structures optimized for
14762 efficient lookups, similar in purpose to hash tables. This package provides
14763 an implementation of radix trees for use in R programming and in developing
14764 packages with Rcpp.")
14765 (license license:expat)))
14767 (define-public r-tweenr
14774 (uri (cran-uri "tweenr" version))
14777 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14778 (build-system r-build-system)
14780 `(("r-farver" ,r-farver)
14781 ("r-magrittr" ,r-magrittr)
14783 ("r-rlang" ,r-rlang)))
14784 (home-page "https://github.com/thomasp85/tweenr")
14785 (synopsis "Interpolate data for smooth animations")
14787 "In order to create smooth animation between states of data, tweening is
14788 necessary. This package provides a range of functions for creating tweened
14789 data that can be used as basis for animation. Furthermore it adds a number of
14790 vectorized interpolaters for common R data types such as numeric, date and
14792 (license license:expat)))
14794 (define-public r-polyclip
14796 (name "r-polyclip")
14801 (uri (cran-uri "polyclip" version))
14804 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14805 (build-system r-build-system)
14806 (native-inputs `(("pkg-config" ,pkg-config)))
14807 (home-page "http://www.angusj.com/delphi/clipper.php")
14808 (synopsis "Polygon clipping")
14810 "This package provides an R port of the library Clipper. It performs
14811 polygon clipping operations (intersection, union, set minus, set difference)
14812 for polygonal regions of arbitrary complexity, including holes. It computes
14813 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14814 dilations) for polygonal regions and polygonal lines. It computes the
14815 Minkowski Sum of general polygons. There is a function for removing
14816 self-intersections from polygon data.")
14817 (license license:boost1.0)))
14819 (define-public r-urltools
14821 (name "r-urltools")
14826 (uri (cran-uri "urltools" version))
14829 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14830 (build-system r-build-system)
14832 `(("r-rcpp" ,r-rcpp)
14833 ("r-triebeard" ,r-triebeard)))
14834 (home-page "https://github.com/Ironholds/urltools/")
14835 (synopsis "Vectorized tools for URL handling and parsing")
14837 "This package provides a toolkit for all URL-handling needs, including
14838 encoding and decoding, parsing, parameter extraction and modification. All
14839 functions are designed to be both fast and entirely vectorized. It is
14840 intended to be useful for people dealing with web-related datasets, such as
14841 server-side logs, although may be useful for other situations involving large
14843 (license license:expat)))
14845 (define-public r-ggforce
14852 (uri (cran-uri "ggforce" version))
14855 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
14856 (build-system r-build-system)
14858 `(("r-ggplot2" ,r-ggplot2)
14859 ("r-gtable" ,r-gtable)
14861 ("r-polyclip" ,r-polyclip)
14863 ("r-rcppeigen" ,r-rcppeigen)
14864 ("r-rlang" ,r-rlang)
14865 ("r-scales" ,r-scales)
14866 ("r-tidyselect" ,r-tidyselect)
14867 ("r-tweenr" ,r-tweenr)
14868 ("r-withr" ,r-withr)))
14869 (home-page "https://ggforce.data-imaginist.com")
14870 (synopsis "Accelerating ggplot2")
14872 "The aim of the ggplot2 package is to aid in visual data investigations.
14873 This focus has led to a lack of facilities for composing specialized plots.
14874 Thi package aims to be a collection of mainly new statistics and geometries
14875 that fills this gap.")
14876 (license license:expat)))
14878 (define-public r-europepmc
14880 (name "r-europepmc")
14885 (uri (cran-uri "europepmc" version))
14888 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14889 (build-system r-build-system)
14891 `(("r-dplyr" ,r-dplyr)
14893 ("r-jsonlite" ,r-jsonlite)
14895 ("r-progress" ,r-progress)
14896 ("r-purrr" ,r-purrr)
14897 ("r-rlang" ,r-rlang)
14898 ("r-tibble" ,r-tibble)
14899 ("r-tidyr" ,r-tidyr)
14900 ("r-urltools" ,r-urltools)
14901 ("r-xml2" ,r-xml2)))
14903 `(("r-knitr" ,r-knitr)))
14904 (home-page "https://github.com/ropensci/europepmc/")
14905 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14907 "This package provides an R Client for the
14908 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14909 Service}. It gives access to both metadata on life science literature and
14910 open access full texts. Europe PMC indexes all PubMed content and other
14911 literature sources including Agricola, a bibliographic database of citations
14912 to the agricultural literature, or Biological Patents. In addition to
14913 bibliographic metadata, the client allows users to fetch citations and
14914 reference lists. Links between life-science literature and other EBI
14915 databases, including ENA, PDB or ChEMBL are also accessible.")
14916 (license license:gpl3)))
14918 (define-public r-ggraph
14925 (uri (cran-uri "ggraph" version))
14928 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14929 (build-system r-build-system)
14931 `(("r-digest" ,r-digest)
14932 ("r-dplyr" ,r-dplyr)
14933 ("r-ggforce" ,r-ggforce)
14934 ("r-ggplot2" ,r-ggplot2)
14935 ("r-ggrepel" ,r-ggrepel)
14936 ("r-graphlayouts" ,r-graphlayouts)
14937 ("r-gtable" ,r-gtable)
14938 ("r-igraph" ,r-igraph)
14941 ("r-rlang" ,r-rlang)
14942 ("r-scales" ,r-scales)
14943 ("r-tidygraph" ,r-tidygraph)
14944 ("r-viridis" ,r-viridis)))
14946 `(("r-knitr" ,r-knitr)))
14947 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14948 (synopsis "Implementation of grammar of graphics for graphs and networks")
14950 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14951 graph and network visualizations due to its reliance on tabular data input.
14952 The ggraph package is an extension of the ggplot2 API tailored to graph
14953 visualizations and provides the same flexible approach to building up plots
14955 (license license:gpl3)))
14957 (define-public r-varselrf
14959 (name "r-varselrf")
14964 (uri (cran-uri "varSelRF" version))
14967 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14968 (properties `((upstream-name . "varSelRF")))
14969 (build-system r-build-system)
14971 `(("r-randomforest" ,r-randomforest)))
14972 (home-page "https://www.ligarto.org/rdiaz/software/software")
14973 (synopsis "Variable selection using random forests")
14975 "This package provides tools for the variable selection from random
14976 forests using both backwards variable elimination (for the selection of small
14977 sets of non-redundant variables) and selection based on the importance
14978 spectrum (somewhat similar to scree plots; for the selection of large,
14979 potentially highly-correlated variables). The main applications are in
14980 high-dimensional data (e.g., microarray data, and other genomics and
14981 proteomics applications).")
14982 (license license:gpl2+)))
14984 (define-public r-pamr
14991 (uri (cran-uri "pamr" version))
14994 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14995 (build-system r-build-system)
14997 `(("r-cluster" ,r-cluster)
14998 ("r-survival" ,r-survival)))
14999 (native-inputs `(("gfortran" ,gfortran)))
15000 (home-page "https://cran.r-project.org/web/packages/pamr/")
15001 (synopsis "Prediction Analysis for Microarrays")
15003 "This package provides some functions for sample classification in
15005 (license license:gpl2)))
15007 (define-public r-rda
15010 (version "1.0.2-2.1")
15014 (uri (cran-uri "rda" version))
15017 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15018 (build-system r-build-system)
15019 (home-page "https://cran.r-project.org/web/packages/rda/")
15020 (synopsis "Shrunken centroids regularized discriminant analysis")
15022 "This package provides tools for shrunken centroids regularized
15023 discriminant analysis for the purpose of classifying high dimensional data.")
15024 (license license:gpl2+)))
15026 (define-public r-ggvis
15033 (uri (cran-uri "ggvis" version))
15036 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15037 (build-system r-build-system)
15039 `(("r-assertthat" ,r-assertthat)
15040 ("r-dplyr" ,r-dplyr)
15041 ("r-htmltools" ,r-htmltools)
15042 ("r-jsonlite" ,r-jsonlite)
15043 ("r-lazyeval" ,r-lazyeval)
15044 ("r-magrittr" ,r-magrittr)
15045 ("r-shiny" ,r-shiny)))
15046 (home-page "https://ggvis.rstudio.com/")
15047 (synopsis "Interactive grammar of graphics")
15049 "This package is a data visualization package for R providing an
15050 implementation of an interactive grammar of graphics, taking the best parts of
15051 ggplot2, combining them with the reactive framework of Shiny and drawing web
15052 graphics using Vega.")
15053 (license license:gpl2)))
15055 (define-public r-gbm
15062 (uri (cran-uri "gbm" version))
15065 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15066 (build-system r-build-system)
15068 `(("r-lattice" ,r-lattice)
15069 ("r-survival" ,r-survival)))
15071 `(("r-knitr" ,r-knitr)))
15072 (home-page "https://github.com/gbm-developers/gbm")
15073 (synopsis "Generalized boosted regression models")
15075 "This package is an implementation of extensions to Freund and Schapire's
15076 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15077 regression methods for least squares, absolute loss, t-distribution loss,
15078 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15079 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15080 and Learning to Rank measures (LambdaMart).")
15081 (license license:gpl2+)))
15083 (define-public r-threejs
15090 (uri (cran-uri "threejs" version))
15093 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15094 (build-system r-build-system)
15096 `(#:modules ((guix build utils)
15097 (guix build r-build-system)
15101 (modify-phases %standard-phases
15102 (add-after 'unpack 'process-javascript
15103 (lambda* (#:key inputs #:allow-other-keys)
15104 (with-directory-excursion "inst"
15108 `((,(assoc-ref inputs "js-jquery")
15109 "htmlwidgets/lib/jquery/jquery.min.js")
15110 (,(assoc-ref inputs "js-threejs-111")
15111 "htmlwidgets/lib/threejs-111/three.min.js"))))
15112 (lambda (sources targets)
15113 (for-each (lambda (source target)
15114 (format #t "Processing ~a --> ~a~%"
15116 (delete-file target)
15117 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15118 (call-with-output-file target
15120 (dump-port minified port)))))
15121 sources targets))))
15124 `(("r-base64enc" ,r-base64enc)
15125 ("r-crosstalk" ,r-crosstalk)
15126 ("r-htmlwidgets" ,r-htmlwidgets)
15127 ("r-igraph" ,r-igraph)))
15129 `(("uglify-js" ,uglify-js)
15133 (uri "https://code.jquery.com/jquery-1.12.4.js")
15136 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15140 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15143 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15144 (home-page "https://bwlewis.github.io/rthreejs")
15145 (synopsis "Interactive 3D scatter plots, networks and globes")
15147 "Create interactive 3D scatter plots, network plots, and globes in R
15148 using the three.js visualization library.")
15149 (license license:expat)))
15151 (define-public r-mlbench
15158 (uri (cran-uri "mlbench" version))
15161 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15162 (build-system r-build-system)
15163 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15164 (synopsis "Machine learning benchmark problems")
15166 "This package provides a collection of artificial and real-world machine
15167 learning benchmark problems, including, e.g., several data sets from the UCI
15169 (license license:gpl2)))
15171 (define-public r-mpm
15178 (uri (cran-uri "mpm" version))
15181 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15182 (build-system r-build-system)
15184 `(("r-kernsmooth" ,r-kernsmooth)
15185 ("r-mass" ,r-mass)))
15186 (home-page "http://mpm.r-forge.r-project.org")
15187 (synopsis "Multivariate projection methods")
15189 "This is a package for exploratory graphical analysis of multivariate
15190 data, specifically gene expression data with different projection methods:
15191 principal component analysis, correspondence analysis, spectral map
15193 (license license:gpl2+)))
15195 (define-public r-png
15201 (uri (cran-uri "png" version))
15204 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15205 (build-system r-build-system)
15207 `(("libpng" ,libpng)
15209 (home-page "https://www.rforge.net/png/")
15210 (synopsis "Read and write PNG images")
15212 "This package provides an easy and simple way to read, write and display
15213 bitmap images stored in the PNG format. It can read and write both files and
15214 in-memory raw vectors.")
15215 ;; Any of these GPL versions.
15216 (license (list license:gpl2 license:gpl3))))
15218 (define-public r-ggcorrplot
15220 (name "r-ggcorrplot")
15225 (uri (cran-uri "ggcorrplot" version))
15228 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15229 (build-system r-build-system)
15231 `(("r-ggplot2" ,r-ggplot2)
15232 ("r-reshape2" ,r-reshape2)))
15233 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15234 (synopsis "Visualization of a correlation matrix using ggplot2")
15236 "The ggcorrplot package can be used to visualize easily a correlation
15237 matrix using ggplot2. It provides a solution for reordering the correlation
15238 matrix and displays the significance level on the plot. It also includes a
15239 function for computing a matrix of correlation p-values.")
15240 (license license:gpl2)))
15242 ;; This package includes minified JavaScript files. When upgrading please
15243 ;; check that there are no new minified JavaScript files.
15244 (define-public r-flexdashboard
15246 (name "r-flexdashboard")
15251 (uri (cran-uri "flexdashboard" version))
15254 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15255 (modules '((guix build utils)))
15258 ;; Delete bundled minified JavaScript files
15259 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15260 (delete-file "inst/www/sly/sly.min.js")
15261 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15262 (delete-file "inst/www/prism/prism.js")
15264 (build-system r-build-system)
15266 `(#:modules ((guix build utils)
15267 (guix build r-build-system)
15271 (ice-9 textual-ports))
15273 (modify-phases %standard-phases
15274 (add-after 'unpack 'process-javascript
15275 (lambda* (#:key inputs #:allow-other-keys)
15276 (with-directory-excursion "inst"
15277 ;; Concatenate all components of prism.js
15278 (let ((contents (string-join
15279 (map (lambda (name)
15280 (call-with-input-file
15281 (assoc-ref inputs name)
15285 "js-prism-line-numbers"))
15287 (call-with-output-file "prism-src.js"
15288 (cut display contents <>)))
15292 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15293 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15295 "www/sly/sly.min.js")
15297 "www/prism/prism.js")
15298 (,(assoc-ref inputs "js-raphael")
15299 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15300 (,(assoc-ref inputs "js-featherlight")
15301 "www/featherlight/featherlight.min.js"))))
15302 (lambda (sources targets)
15303 (for-each (lambda (source target)
15304 (format #t "Processing ~a --> ~a~%"
15306 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15307 (call-with-output-file target
15309 (dump-port minified port)))))
15310 sources targets))))
15313 `(("r-htmltools" ,r-htmltools)
15314 ("r-htmlwidgets" ,r-htmlwidgets)
15315 ("r-jsonlite" ,r-jsonlite)
15316 ("r-knitr" ,r-knitr)
15317 ("r-rmarkdown" ,r-rmarkdown)
15318 ("r-shiny" ,r-shiny)))
15320 `(("uglify-js" ,uglify-js)
15324 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15327 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15331 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15334 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15338 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15341 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15342 ("js-prism-line-numbers"
15345 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15348 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15352 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15355 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15356 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15357 (synopsis "R Markdown format for flexible dashboards")
15359 "This package provides an R Markdown format for converting an R Markdown
15360 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15361 of its components to the containing web page.")
15362 (license license:expat)))
15364 (define-public r-preseqr
15371 (uri (cran-uri "preseqR" version))
15374 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15375 (properties `((upstream-name . "preseqR")))
15376 (build-system r-build-system)
15378 `(("r-polynom" ,r-polynom)))
15379 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15380 (synopsis "Predicting species accumulation curves")
15382 "This package can be used to predict the r-species accumulation
15383 curve (r-SAC), which is the number of species represented at least r times as
15384 a function of the sampling effort. When r = 1, the curve is known as the
15385 species accumulation curve, or the library complexity curve in high-throughput
15386 genomic sequencing. The package includes both parametric and nonparametric
15387 methods, as described by Deng C, et al. (2018).")
15388 (license license:gpl3)))
15390 (define-public r-mapplots
15392 (name "r-mapplots")
15397 (uri (cran-uri "mapplots" version))
15400 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15401 (build-system r-build-system)
15402 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15403 (synopsis "Data visualization on maps")
15405 "This package helps you create simple maps; add sub-plots like pie plots
15406 to a map or any other plot; format, plot and export gridded data. The package
15407 was developed for displaying fisheries data but most functions can be used for
15408 more generic data visualisation.")
15409 (license license:gpl2+)))
15411 (define-public r-pmcmr
15418 (uri (cran-uri "PMCMR" version))
15421 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15422 (properties `((upstream-name . "PMCMR")))
15423 (build-system r-build-system)
15424 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15425 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15427 "This is a deprecated package for calculating pairwise multiple
15428 comparisons of mean rank sums. This package is superseded by the novel
15429 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15430 compatibility of dependent packages for some time.")
15431 (license license:gpl3+)))
15433 (define-public r-downloader
15435 (name "r-downloader")
15440 (uri (cran-uri "downloader" version))
15443 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15444 (build-system r-build-system)
15446 `(("r-digest" ,r-digest)))
15447 (home-page "https://github.com/wch/downloader")
15448 (synopsis "Download files over HTTP and HTTPS")
15450 "This package provides a wrapper for the @code{download.file} function,
15451 making it possible to download files over HTTPS across platforms. The
15452 @code{RCurl} package provides this functionality (and much more) but has
15453 external dependencies. This package has is implemented purely in R.")
15454 (license license:gpl2)))
15456 (define-public r-rex
15463 (uri (cran-uri "rex" version))
15466 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15467 (build-system r-build-system)
15469 `(("r-lazyeval" ,r-lazyeval)))
15471 `(("r-knitr" ,r-knitr)))
15472 (home-page "https://github.com/kevinushey/rex")
15473 (synopsis "Friendly regular expressions")
15475 "This package provides a friendly interface for the construction of
15476 regular expressions. Regular expressions are a very powerful feature, however
15477 they are often difficult to interpret. Rex allows you to build complex
15478 regular expressions from human readable expressions")
15479 (license license:expat)))
15481 (define-public r-xmlparsedata
15483 (name "r-xmlparsedata")
15488 (uri (cran-uri "xmlparsedata" version))
15491 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15492 (properties `((upstream-name . "xmlparsedata")))
15493 (build-system r-build-system)
15494 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15495 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15497 "This package provides tools to convert the output of
15498 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15499 @code{XPath}, and is easier to manipulate in general.")
15500 (license license:expat)))
15502 (define-public r-cyclocomp
15504 (name "r-cyclocomp")
15509 (uri (cran-uri "cyclocomp" version))
15512 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15513 (properties `((upstream-name . "cyclocomp")))
15514 (build-system r-build-system)
15516 `(("r-callr" ,r-callr)
15517 ("r-crayon" ,r-crayon)
15519 ("r-remotes" ,r-remotes)
15520 ("r-withr" ,r-withr)))
15521 (home-page "https://github.com/MangoTheCat/cyclocomp")
15522 (synopsis "Cyclomatic complexity of R code")
15524 "Cyclomatic complexity is a software metric, used to indicate the
15525 complexity of a program. It is a quantitative measure of the number of
15526 linearly independent paths through a program's source code. This package
15527 provides tools to compute this metric.")
15528 (license license:expat)))
15530 (define-public r-lintr
15537 (uri (cran-uri "lintr" version))
15540 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15541 (properties `((upstream-name . "lintr")))
15542 (build-system r-build-system)
15544 `(("r-codetools" ,r-codetools)
15545 ("r-crayon" ,r-crayon)
15546 ("r-cyclocomp" ,r-cyclocomp)
15547 ("r-digest" ,r-digest)
15549 ("r-jsonlite" ,r-jsonlite)
15550 ("r-knitr" ,r-knitr)
15552 ("r-rstudioapi" ,r-rstudioapi)
15553 ("r-testthat" ,r-testthat)
15555 ("r-xmlparsedata" ,r-xmlparsedata)))
15556 (home-page "https://github.com/jimhester/lintr")
15557 (synopsis "Linter for R code")
15558 (description "This package checks adherence to a given style, syntax
15559 errors and possible semantic issues. It supports on the fly checking of R
15560 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15561 (license license:expat)))
15563 (define-public r-sctransform
15565 (name "r-sctransform")
15570 (uri (cran-uri "sctransform" version))
15573 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15574 (build-system r-build-system)
15576 `(("r-future-apply" ,r-future-apply)
15577 ("r-ggplot2" ,r-ggplot2)
15578 ("r-gridextra" ,r-gridextra)
15580 ("r-matrix" ,r-matrix)
15582 ("r-rcppeigen" ,r-rcppeigen)
15583 ("r-reshape2" ,r-reshape2)))
15584 (home-page "https://github.com/ChristophH/sctransform")
15585 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15587 "This package provides a normalization method for single-cell UMI count
15588 data using a variance stabilizing transformation. The transformation is based
15589 on a negative binomial regression model with regularized parameters. As part
15590 of the same regression framework, this package also provides functions for
15591 batch correction, and data correction.")
15592 (license license:gpl3)))
15594 (define-public r-styler
15601 (uri (cran-uri "styler" version))
15604 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15605 (build-system r-build-system)
15607 `(("r-backports" ,r-backports)
15609 ("r-magrittr" ,r-magrittr)
15610 ("r-purrr" ,r-purrr)
15611 ("r-r-cache" ,r-r-cache)
15612 ("r-rematch2" ,r-rematch2)
15613 ("r-rlang" ,r-rlang)
15614 ("r-rprojroot" ,r-rprojroot)
15615 ("r-tibble" ,r-tibble)
15616 ("r-withr" ,r-withr)
15617 ("r-xfun" ,r-xfun)))
15618 (home-page "https://github.com/r-lib/styler")
15619 (synopsis "Non-invasive pretty printing of R code")
15621 "This is a package for pretty-printing R code without changing the user's
15622 formatting intent.")
15623 (license license:gpl3)))
15625 (define-public r-scrime
15632 (uri (cran-uri "scrime" version))
15635 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15636 (build-system r-build-system)
15637 (home-page "https://cran.r-project.org/web/packages/scrime/")
15638 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15640 "This package provides tools for the analysis of high-dimensional data
15641 developed/implemented at the group \"Statistical Complexity Reduction In
15642 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15643 the functions can also be applied to other types of categorical data.")
15644 (license license:gpl2)))
15646 (define-public r-pbmcapply
15648 (name "r-pbmcapply")
15653 (uri (cran-uri "pbmcapply" version))
15656 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15657 (build-system r-build-system)
15658 (home-page "https://github.com/kvnkuang/pbmcapply")
15659 (synopsis "Track the progress of apply procedures with a progress bar")
15661 "This light-weight package helps you track and visualize the progress of
15662 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15663 (license license:expat)))
15665 (define-public r-blme
15672 (uri (cran-uri "blme" version))
15675 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15676 (build-system r-build-system)
15677 (propagated-inputs `(("r-lme4" ,r-lme4)))
15678 (home-page "https://github.com/vdorie/blme")
15679 (synopsis "Bayesian linear mixed-effects models")
15681 "This package provides tools for maximum a posteriori estimation for
15682 linear and generalized linear mixed-effects models in a Bayesian setting. It
15683 extends the lme4 package.")
15684 (license license:gpl2+)))
15686 (define-public r-batchtools
15688 (name "r-batchtools")
15693 (uri (cran-uri "batchtools" version))
15696 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15697 (build-system r-build-system)
15699 `(("r-backports" ,r-backports)
15700 ("r-base64url" ,r-base64url)
15702 ("r-checkmate" ,r-checkmate)
15703 ("r-data-table" ,r-data-table)
15704 ("r-digest" ,r-digest)
15706 ("r-progress" ,r-progress)
15708 ("r-rappdirs" ,r-rappdirs)
15709 ("r-stringi" ,r-stringi)
15710 ("r-withr" ,r-withr)))
15712 `(("r-knitr" ,r-knitr)))
15713 (home-page "https://github.com/mllg/batchtools")
15714 (synopsis "Tools for computation on batch systems")
15716 "As a successor of the packages BatchJobs and BatchExperiments, this
15717 package provides a parallel implementation of the Map function for high
15718 performance computing systems managed by various schedulers. A multicore and
15719 socket mode allow the parallelization on a local machines, and multiple
15720 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15721 the package provides an abstraction mechanism to define large-scale computer
15722 experiments in a well-organized and reproducible way.")
15723 (license license:lgpl3)))
15725 (define-public r-clue
15732 (uri (cran-uri "clue" version))
15735 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15736 (build-system r-build-system)
15737 (propagated-inputs `(("r-cluster" ,r-cluster)))
15738 (home-page "https://cran.r-project.org/web/packages/clue/")
15739 (synopsis "Tools for analyzing cluster ensembles")
15740 (description "Cluster ensembles are collections of individual solutions to
15741 a given clustering problem which are useful or necessary to consider in a wide
15742 range of applications. This R package provides an extensible computational
15743 environment for creating and analyzing cluster ensembles, with basic data
15744 structures for representing partitions and hierarchies, and facilities for
15745 computing on them, including methods for measuring proximity and obtaining
15746 consensus and secondary clusterings.")
15747 (license license:gpl2)))
15749 (define-public r-sitmo
15756 (uri (cran-uri "sitmo" version))
15759 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15760 (build-system r-build-system)
15761 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15762 (home-page "https://github.com/coatless/sitmo/")
15763 (synopsis "Parallel pseudo random number generator header files")
15765 "This package provides two high quality and fast PPRNGs that may be used
15766 in an OpenMP parallel environment. In addition, there is a generator for one
15767 dimensional low-discrepancy sequence.")
15768 (license license:expat)))
15770 (define-public r-dqrng
15777 (uri (cran-uri "dqrng" version))
15780 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15781 (build-system r-build-system)
15785 ("r-sitmo" ,r-sitmo)))
15786 (home-page "https://www.daqana.org/dqrng")
15787 (synopsis "Fast pseudo random number generators")
15789 "Several fast random number generators are provided as C++ header-only
15790 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15791 Additionally, fast functions for generating random numbers according to a
15792 uniform, normal and exponential distribution are included. The latter two use
15793 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15794 functions are exported to R and as a C++ interface and are enabled for use
15795 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15796 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15797 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15798 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15799 ;; whole is distributed under the terms of the AGPL 3.
15800 (license license:agpl3)))
15802 (define-public r-ingredients
15804 (name "r-ingredients")
15809 (uri (cran-uri "ingredients" version))
15812 "0l0dqrm9am6wk8jcf8cdhc6xnrna9cqr5wz6lsnczq2gf6ybhjg1"))))
15813 (properties `((upstream-name . "ingredients")))
15814 (build-system r-build-system)
15816 `(("r-ggplot2" ,r-ggplot2)
15817 ("r-gridextra" ,r-gridextra)
15818 ("r-scales" ,r-scales)))
15819 (native-inputs `(("r-knitr" ,r-knitr)))
15820 (home-page "https://ModelOriented.github.io/ingredients/")
15821 (synopsis "Effects and importances of model ingredients")
15823 "This is a collection of tools for assessment of feature importance and
15824 feature effects. Key functions are:
15827 @item @code{feature_importance()} for assessment of global level feature
15829 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15830 @item @code{partial_dependence()} for partial dependence plots,
15831 @item @code{conditional_dependence()} for conditional dependence plots,
15832 @item @code{accumulated_dependence()} for accumulated local effects plots,
15833 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15834 aggregation of ceteris paribus profiles,
15835 @item generic @code{print()} and @code{plot()} for better usability of
15836 selected explainers,
15837 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15838 @item generic @code{describe()} for explanations in natural language.
15840 (license license:gpl3)))
15842 (define-public r-ibreakdown
15844 (name "r-ibreakdown")
15849 (uri (cran-uri "iBreakDown" version))
15852 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
15853 (properties `((upstream-name . "iBreakDown")))
15854 (build-system r-build-system)
15855 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15856 (native-inputs `(("r-knitr" ,r-knitr)))
15857 (home-page "https://ModelOriented.github.io/iBreakDown/")
15858 (synopsis "Model agnostic instance level variable attributions")
15860 "This package provides a model agnostic tool for decomposition of
15861 predictions from black boxes. It supports additive attributions and
15862 attributions with interactions. The Break Down Table shows contributions of
15863 every variable to a final prediction. The Break Down Plot presents variable
15864 contributions in a concise graphical way. This package works for
15865 classification and regression models.")
15866 (license license:gpl3)))
15868 (define-public r-dae
15875 (uri (cran-uri "dae" version))
15878 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
15879 (build-system r-build-system)
15881 `(("r-ggplot2" ,r-ggplot2)
15882 ("r-plyr" ,r-plyr)))
15884 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
15885 (home-page "http://chris.brien.name")
15886 (synopsis "Functions useful in the design and ANOVA of experiments")
15888 "This package provides functions useful in the design and ANOVA of
15889 experiments. The content falls into the following groupings:
15893 @item factor manipulation functions,
15894 @item design functions,
15895 @item ANOVA functions,
15896 @item matrix functions,
15897 @item projector and canonical efficiency functions, and
15898 @item miscellaneous functions.
15901 There is a vignette called @code{DesignNotes} describing how to use the design
15902 functions for randomizing and assessing designs. The ANOVA functions
15903 facilitate the extraction of information when the @code{Error} function has
15904 been used in the call to @code{aov}.")
15905 (license license:gpl2)))
15907 (define-public r-dalex
15910 (version "1.3.1.1")
15914 (uri (cran-uri "DALEX" version))
15917 "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
15918 (properties `((upstream-name . "DALEX")))
15919 (build-system r-build-system)
15921 `(("r-ggplot2" ,r-ggplot2)
15922 ("r-ibreakdown" ,r-ibreakdown)
15923 ("r-ingredients" ,r-ingredients)))
15924 (home-page "https://pbiecek.github.io/DALEX/")
15925 (synopsis "Descriptive machine learning explanations")
15927 "Machine Learning models are widely used and have various applications in
15928 classification or regression. Models created with boosting, bagging, stacking
15929 or similar techniques are often used due to their high performance, but such
15930 black-box models usually lack interpretability. The DALEX package contains
15931 various explainers that help to understand the link between input variables
15932 and model output.")
15933 ;; Any version of the GPL
15934 (license license:gpl3+)))
15936 (define-public r-enrichr
15943 (uri (cran-uri "enrichR" version))
15946 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15947 (properties `((upstream-name . "enrichR")))
15948 (build-system r-build-system)
15950 `(("r-httr" ,r-httr)
15951 ("r-rjson" ,r-rjson)))
15952 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15953 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15955 "This package provides an R interface to all Enrichr databases, a
15956 web-based tool for analyzing gene sets and returns any enrichment of common
15957 annotated biological functions.")
15958 (license license:gpl2+)))
15960 (define-public r-plot3d
15967 (uri (cran-uri "plot3D" version))
15970 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15971 (properties `((upstream-name . "plot3D")))
15972 (build-system r-build-system)
15973 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15974 (home-page "https://cran.r-project.org/web/packages/plot3D")
15975 (synopsis "Plot multi-dimensional data")
15977 "This package provides functions for viewing 2D and 3D data, including
15978 perspective plots, slice plots, surface plots, scatter plots, etc. It
15979 includes data sets from oceanography.")
15980 (license license:gpl3+)))
15982 (define-public r-ggfortify
15984 (name "r-ggfortify")
15989 (uri (cran-uri "ggfortify" version))
15992 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15993 (build-system r-build-system)
15995 `(("r-dplyr" ,r-dplyr)
15996 ("r-ggplot2" ,r-ggplot2)
15997 ("r-gridextra" ,r-gridextra)
15998 ("r-scales" ,r-scales)
15999 ("r-stringr" ,r-stringr)
16000 ("r-tibble" ,r-tibble)
16001 ("r-tidyr" ,r-tidyr)))
16003 `(("r-knitr" ,r-knitr)))
16004 (home-page "https://github.com/sinhrks/ggfortify")
16005 (synopsis "Data visualization tools for statistical analysis results")
16007 "This package provides unified plotting tools for statistics commonly
16008 used, such as GLM, time series, PCA families, clustering and survival
16009 analysis. The package offers a single plotting interface for these analysis
16010 results and plots in a unified style using the @code{ggplot2} package.")
16011 (license license:gpl2)))
16013 (define-public r-refmanager
16015 (name "r-refmanager")
16020 (uri (cran-uri "RefManageR" version))
16023 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16024 (properties `((upstream-name . "RefManageR")))
16025 (build-system r-build-system)
16027 `(("r-bibtex" ,r-bibtex)
16029 ("r-jsonlite" ,r-jsonlite)
16030 ("r-lubridate" ,r-lubridate)
16032 ("r-stringr" ,r-stringr)
16033 ("r-xml2" ,r-xml2)))
16034 (home-page "https://github.com/ropensci/RefManageR/")
16035 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16037 "This package provides tools for importing and working with bibliographic
16038 references. It greatly enhances the @code{bibentry} class by providing a
16039 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16040 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16041 by various formats for name lists (author by last names, translator by full
16042 names, etc.). Entries can be updated, combined, sorted, printed in a number
16043 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16044 into R and converted to @code{BibEntry} objects.")
16045 ;; Any of these licenses may be picked.
16046 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16048 (define-public r-citr
16055 (uri (cran-uri "citr" version))
16058 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16059 (build-system r-build-system)
16061 `(("r-assertthat" ,r-assertthat)
16064 ("r-miniui" ,r-miniui)
16065 ("r-refmanager" ,r-refmanager)
16066 ("r-rstudioapi" ,r-rstudioapi)
16067 ("r-shiny" ,r-shiny)
16068 ("r-shinyjs" ,r-shinyjs)
16069 ("r-yaml" ,r-yaml)))
16070 (home-page "https://github.com/crsh/citr")
16071 (synopsis "RStudio add-in to insert Markdown citations")
16073 "This package provides functions and an RStudio add-in that search a
16074 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16075 the current document.")
16076 (license license:expat)))
16078 (define-public r-xgboost
16081 (version "1.1.1.1")
16085 (uri (cran-uri "xgboost" version))
16088 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
16089 (build-system r-build-system)
16091 `(("r-data-table" ,r-data-table)
16092 ("r-magrittr" ,r-magrittr)
16093 ("r-matrix" ,r-matrix)
16094 ("r-stringi" ,r-stringi)))
16096 `(("r-knitr" ,r-knitr)))
16097 (home-page "https://github.com/dmlc/xgboost")
16098 (synopsis "Extreme gradient boosting")
16100 "This package provides an R interface to Extreme Gradient Boosting, which
16101 is an efficient implementation of the gradient boosting framework from Chen
16102 and Guestrin (2016). The package includes efficient linear model solver and
16103 tree learning algorithms. The package can automatically do parallel
16104 computation on a single machine. It supports various objective functions,
16105 including regression, classification and ranking. The package is made to be
16106 extensible, so that users are also allowed to define their own objectives
16108 (license license:asl2.0)))
16110 (define-public r-umap
16113 (version "0.2.6.0")
16117 (uri (cran-uri "umap" version))
16120 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16121 (build-system r-build-system)
16123 `(("r-openssl" ,r-openssl)
16125 ("r-reticulate" ,r-reticulate)
16126 ("r-rspectra" ,r-rspectra)))
16128 `(("r-knitr" ,r-knitr)))
16129 (home-page "https://github.com/tkonopka/umap")
16130 (synopsis "Uniform manifold approximation and projection")
16132 "Uniform manifold approximation and projection is a technique for
16133 dimension reduction. This package provides an interface to the UMAP algorithm
16134 in R, including a translation of the original algorithm into R.")
16135 (license license:expat)))
16137 (define-public r-uwot
16144 (uri (cran-uri "uwot" version))
16147 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16148 (build-system r-build-system)
16150 `(("r-dqrng" ,r-dqrng)
16152 ("r-irlba" ,r-irlba)
16153 ("r-matrix" ,r-matrix)
16155 ("r-rcppannoy" ,r-rcppannoy)
16156 ("r-rcppprogress" ,r-rcppprogress)
16157 ("r-rspectra" ,r-rspectra)))
16158 (home-page "https://github.com/jlmelville/uwot")
16159 (synopsis "Uniform manifold approximation and projection")
16161 "This package provides an implementation of the Uniform Manifold
16162 Approximation and Projection dimensionality reduction by McInnes et
16163 al. (2018). It also provides means to transform new data and to carry out
16164 supervised dimensionality reduction. An implementation of the related
16165 LargeVis method of Tang et al. (2016) is also provided.")
16166 (license license:gpl3)))
16168 (define-public r-kableextra
16170 (name "r-kableextra")
16175 (uri (cran-uri "kableExtra" version))
16178 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16179 (properties `((upstream-name . "kableExtra")))
16180 (build-system r-build-system)
16182 `(("r-digest" ,r-digest)
16184 ("r-htmltools" ,r-htmltools)
16185 ("r-knitr" ,r-knitr)
16186 ("r-magrittr" ,r-magrittr)
16187 ("r-readr" ,r-readr)
16188 ("r-rmarkdown" ,r-rmarkdown)
16189 ("r-rstudioapi" ,r-rstudioapi)
16190 ("r-rvest" ,r-rvest)
16191 ("r-scales" ,r-scales)
16192 ("r-stringr" ,r-stringr)
16193 ("r-viridislite" ,r-viridislite)
16194 ("r-webshot" ,r-webshot)
16195 ("r-xml2" ,r-xml2)))
16196 (home-page "https://haozhu233.github.io/kableExtra/")
16197 (synopsis "Construct complex tables with pipe syntax")
16199 "Build complex HTML or LaTeX tables using @code{kable()} from
16200 @code{knitr} and the piping syntax from @code{magrittr}. The function
16201 @code{kable()} is a light weight table generator coming from @code{knitr}.
16202 This package simplifies the way to manipulate the HTML or LaTeX codes
16203 generated by @code{kable()} and allows users to construct complex tables and
16204 customize styles using a readable syntax.")
16205 (license license:expat)))
16207 (define-public r-glasso
16214 (uri (cran-uri "glasso" version))
16216 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16217 (build-system r-build-system)
16218 (native-inputs `(("gfortran" ,gfortran)))
16219 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16220 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16222 "This is a package for estimation of a sparse inverse covariance matrix
16223 using a lasso (L1) penalty. Facilities are provided for estimates along a
16224 path of values for the regularization parameter.")
16225 (license license:gpl2)))
16227 (define-public r-rhpcblasctl
16229 (name "r-rhpcblasctl")
16230 (version "0.20-137")
16234 (uri (cran-uri "RhpcBLASctl" version))
16237 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16238 (properties `((upstream-name . "RhpcBLASctl")))
16239 (build-system r-build-system)
16240 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16241 (synopsis "Control the number of threads on BLAS")
16243 "This package allows you to control the number of threads the BLAS
16244 library uses. It is also possible to control the number of threads in
16246 (license license:agpl3+)))
16248 (define-public r-lda
16255 (uri (cran-uri "lda" version))
16258 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16259 (build-system r-build-system)
16260 (home-page "https://cran.r-project.org/web/packages/lda/")
16261 (synopsis "Collapsed Gibbs sampling methods for topic models")
16263 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16264 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16265 mixed-membership stochastic blockmodel. Inference for all of these models is
16266 implemented via a fast collapsed Gibbs sampler written in C. Utility
16267 functions for reading/writing data typically used in topic models, as well as
16268 tools for examining posterior distributions are also included.")
16269 ;; Any version of the LGPL
16270 (license license:lgpl3+)))
16272 (define-public r-rann-l1
16279 (uri (cran-uri "RANN.L1" version))
16282 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16283 (properties `((upstream-name . "RANN.L1")))
16284 (build-system r-build-system)
16285 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16286 (synopsis "Fast nearest neighbour search using L1 metric")
16288 "This package provides tools to find the k nearest neighbours for every
16289 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16290 library. There is support for approximate as well as exact searches, fixed
16291 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16292 computed using the L1 (Manhattan, taxicab) metric.")
16293 (license license:gpl3+)))
16295 (define-public r-leiden
16302 (uri (cran-uri "leiden" version))
16305 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16306 (properties `((upstream-name . "leiden")))
16307 (build-system r-build-system)
16309 `(("r-igraph" ,r-igraph)
16310 ("r-matrix" ,r-matrix)
16311 ("r-reticulate" ,r-reticulate)))
16312 (home-page "https://github.com/TomKellyGenetics/leiden")
16313 (synopsis "R implementation of Leiden clustering algorithm")
16315 "This package implements the Python @code{leidenalg} module to be called
16316 in R. It enables clustering using the Leiden algorithm for partitioning a
16317 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16318 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16319 (license license:gpl3)))
16321 (define-public r-patchwork
16323 (name "r-patchwork")
16328 (uri (cran-uri "patchwork" version))
16331 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16332 (build-system r-build-system)
16334 `(("r-ggplot2" ,r-ggplot2)
16335 ("r-gtable" ,r-gtable)))
16337 `(("r-knitr" ,r-knitr)))
16338 (home-page "https://github.com/thomasp85/patchwork")
16339 (synopsis "Compose ggplot2 plots")
16341 "The @code{ggplot2} package provides a strong API for sequentially
16342 building up a plot, but does not concern itself with composition of multiple
16343 plots. Patchwork is a package that expands the API to allow for arbitrarily
16344 complex composition of plots by providing mathmatical operators for combining
16346 (license license:expat)))
16348 (define-public r-liger
16355 (uri (git-reference
16356 (url "https://github.com/MacoskoLab/liger")
16357 (commit (string-append "v" version))))
16358 (file-name (git-file-name name version))
16361 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16362 (modules '((guix build utils)))
16365 (delete-file "inst/java/ModularityOptimizer.jar")
16367 (build-system r-build-system)
16370 (modify-phases %standard-phases
16371 (add-after 'unpack 'build-java-part
16372 (lambda* (#:key inputs #:allow-other-keys)
16373 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16374 (for-each (lambda (file) (invoke "javac" file))
16375 (find-files "." "\\.java$"))
16376 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16377 (find-files "." "\\.class$"))
16380 `(("r-cowplot" ,r-cowplot)
16381 ("r-dosnow" ,r-dosnow)
16382 ("r-dplyr" ,r-dplyr)
16384 ("r-foreach" ,r-foreach)
16385 ("r-ggplot2" ,r-ggplot2)
16386 ("r-ggrepel" ,r-ggrepel)
16387 ("r-hmisc" ,r-hmisc)
16389 ("r-irlba" ,r-irlba)
16390 ("r-matrix" ,r-matrix)
16391 ("r-mclust" ,r-mclust)
16392 ("r-patchwork" ,r-patchwork)
16394 ("r-rann-l1" ,r-rann-l1)
16396 ("r-rcpparmadillo" ,r-rcpparmadillo)
16397 ("r-riverplot" ,r-riverplot)
16398 ("r-rtsne" ,r-rtsne)
16399 ("r-snow" ,r-snow)))
16401 `(("jdk" ,icedtea "jdk")
16402 ;; See https://github.com/MacoskoLab/liger/issues/96
16403 ;; The optimizer is released under the Expat license.
16407 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16410 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16412 ("r-knitr" ,r-knitr))) ; for vignettes
16413 (home-page "https://github.com/MacoskoLab/liger")
16414 (synopsis "Integrate and analyze multiple single-cell datasets")
16416 "LIGER is a package for integrating and analyzing multiple single-cell
16417 datasets, developed and maintained by the Macosko lab. It relies on
16418 integrative non-negative matrix factorization to identify shared and
16419 dataset-specific factors.")
16420 (license license:gpl3)))
16422 (define-public r-harmony
16429 (uri (git-reference
16430 (url "https://github.com/immunogenomics/harmony")
16432 (file-name (git-file-name name version))
16435 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16436 (modules '((guix build utils)))
16439 (for-each delete-file '("config.status" "configure"))
16441 (build-system r-build-system)
16443 `(("r-cowplot" ,r-cowplot)
16444 ("r-dplyr" ,r-dplyr)
16445 ("r-ggplot2" ,r-ggplot2)
16446 ("r-irlba" ,r-irlba)
16447 ("r-matrix" ,r-matrix)
16449 ("r-rcpparmadillo" ,r-rcpparmadillo)
16450 ("r-rcppprogress" ,r-rcppprogress)
16451 ("r-rlang" ,r-rlang)
16452 ("r-tibble" ,r-tibble)
16453 ("r-tidyr" ,r-tidyr)))
16455 `(("autoconf" ,autoconf)))
16456 (home-page "https://github.com/immunogenomics/harmony")
16457 (synopsis "Integration of single cell sequencing data")
16459 "This package provides an implementation of the Harmony algorithm for
16460 single cell integration, described in Korsunsky et al
16461 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16462 function and interfaces to external frameworks.")
16463 (license license:gpl3)))
16465 (define-public r-covr
16472 (uri (cran-uri "covr" version))
16474 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16475 (properties `((upstream-name . "covr")))
16476 (build-system r-build-system)
16478 `(("r-crayon" ,r-crayon)
16479 ("r-digest" ,r-digest)
16481 ("r-jsonlite" ,r-jsonlite)
16483 ("r-withr" ,r-withr)
16484 ("r-yaml" ,r-yaml)))
16486 `(("r-knitr" ,r-knitr))) ; for vignettes
16487 (home-page "https://github.com/r-lib/covr")
16488 (synopsis "Test coverage for R packages")
16490 "Thisp package enables you to track and report code coverage for your
16491 package and (optionally) upload the results to a coverage service. Code
16492 coverage is a measure of the amount of code being exercised by a set of tests.
16493 It is an indirect measure of test quality and completeness. This package is
16494 compatible with any testing methodology or framework and tracks coverage of
16495 both R code and compiled C/C++/FORTRAN code.")
16496 (license license:gpl3)))
16498 (define-public r-systemfonts
16500 (name "r-systemfonts")
16505 (uri (cran-uri "systemfonts" version))
16508 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16509 (properties `((upstream-name . "systemfonts")))
16510 (build-system r-build-system)
16512 `(("fontconfig" ,fontconfig)
16515 `(("pkg-config" ,pkg-config)
16516 ("r-knitr" ,r-knitr)))
16517 (home-page "https://github.com/r-lib/systemfonts")
16518 (synopsis "System native font finding")
16520 "This package provides system native access to the font catalogue. As
16521 font handling varies between systems it is difficult to correctly locate
16522 installed fonts across different operating systems. The 'systemfonts' package
16523 provides bindings to the native libraries for finding font files that can then
16524 be used further by e.g. graphic devices.")
16525 (license license:expat)))
16527 (define-public r-graphlayouts
16529 (name "r-graphlayouts")
16534 (uri (cran-uri "graphlayouts" version))
16537 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16538 (properties `((upstream-name . "graphlayouts")))
16539 (build-system r-build-system)
16541 `(("r-igraph" ,r-igraph)
16543 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16544 (home-page "https://github.com/schochastics/graphlayouts")
16545 (synopsis "Additional layout algorithms for network visualizations")
16547 "This package provides several layout algorithms to visualize networks
16548 which are not part of the igraph library. Most are based on the concept of
16549 stress majorization by Gansner et al. (2004)
16550 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16551 emphasize hidden group structures in networks or focus on specific nodes.")
16552 (license license:expat)))
16554 (define-public r-tidygraph
16556 (name "r-tidygraph")
16561 (uri (cran-uri "tidygraph" version))
16564 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16565 (properties `((upstream-name . "tidygraph")))
16566 (build-system r-build-system)
16568 `(("r-dplyr" ,r-dplyr)
16569 ("r-igraph" ,r-igraph)
16570 ("r-magrittr" ,r-magrittr)
16571 ("r-pillar" ,r-pillar)
16574 ("r-rlang" ,r-rlang)
16575 ("r-tibble" ,r-tibble)
16576 ("r-tidyr" ,r-tidyr)))
16577 (home-page "https://github.com/thomasp85/tidygraph")
16578 (synopsis "Tidy API for graph manipulation")
16580 "This package provides a graph implementation that can be thought of as
16581 two tidy data frames describing node and edge data respectively. It provides
16582 an approach to manipulate these two virtual data frames using the API defined
16583 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16584 common graph algorithms.")
16585 (license license:expat)))
16587 (define-public r-soupx
16588 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16592 (version (git-version "0.3.1" revision commit))
16596 (uri (git-reference
16597 (url "https://github.com/constantAmateur/SoupX")
16599 (file-name (git-file-name name version))
16602 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16603 (properties `((upstream-name . "SoupX")))
16604 (build-system r-build-system)
16606 `(("r-ggplot2" ,r-ggplot2)
16607 ("r-matrix" ,r-matrix)
16608 ("r-seurat" ,r-seurat)))
16609 (home-page "https://github.com/constantAmateur/SoupX")
16610 (synopsis "Single cell mRNA Soup eXterminator")
16612 "This package provides a package for quantifying, profiling and
16613 removing cell free mRNA contamination (the \"soup\") from droplet based single
16614 cell RNA-seq experiments.")
16615 (license license:gpl2))))
16617 (define-public r-assertr
16624 (uri (cran-uri "assertr" version))
16627 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16628 (build-system r-build-system)
16630 `(("r-dplyr" ,r-dplyr)
16632 ("r-rlang" ,r-rlang)))
16634 `(("r-knitr" ,r-knitr))) ; needed for vignette
16635 (home-page "https://github.com/ropensci/assertr")
16636 (synopsis "Assertive programming for R analysis pipelines")
16638 "This package provides functionality to assert conditions that have to be
16639 met so that errors in data used in analysis pipelines can fail quickly. It is
16640 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16642 (license license:expat)))
16644 (define-public r-parameters
16646 (name "r-parameters")
16651 (uri (cran-uri "parameters" version))
16654 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16655 (properties `((upstream-name . "parameters")))
16656 (build-system r-build-system)
16658 `(("r-bayestestr" ,r-bayestestr)
16659 ("r-insight" ,r-insight)))
16661 `(("r-knitr" ,r-knitr)))
16662 (home-page "https://cran.r-project.org/web/packages/parameters")
16663 (synopsis "Processing of model parameters")
16665 "This package provides utilities for processing the parameters of various
16666 statistical models. Beyond computing p values, CIs, and other indices for a
16667 wide variety of models, this package implements features like standardization
16668 or bootstrapping of parameters and models, feature reduction (feature
16669 extraction and variable selection) as well as conversion between indices of
16671 (license license:gpl3)))
16673 (define-public r-rgdal
16680 (uri (cran-uri "rgdal" version))
16682 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16683 (properties `((upstream-name . "rgdal")))
16684 (build-system r-build-system)
16692 `(("pkg-config" ,pkg-config)
16693 ("r-knitr" ,r-knitr)))
16694 (home-page "http://rgdal.r-forge.r-project.org")
16695 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16697 "This package provides bindings to the Geospatial Data Abstraction
16698 Library (GDAL) and access to projection/transformation operations from the
16700 (license license:gpl2+)))
16702 (define-public r-insol
16709 (uri (cran-uri "insol" version))
16712 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16713 (properties `((upstream-name . "insol")))
16714 (build-system r-build-system)
16716 `(("r-raster" ,r-raster)))
16718 `(("gfortran" ,gfortran)))
16719 (home-page "https://meteoexploration.com/R/insol/index.html")
16720 (synopsis "Tools for calculating solar radiation")
16722 "This package provides functions to compute insolation on tilted
16723 surfaces, computes atmospheric transmittance and related parameters such as:
16724 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16725 time, vector in the direction of the sun, vector normal to surface, and some
16726 atmospheric physics.")
16727 (license license:gpl2+)))
16729 (define-public r-lifecycle
16731 (name "r-lifecycle")
16736 (uri (cran-uri "lifecycle" version))
16739 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16740 (properties `((upstream-name . "lifecycle")))
16741 (build-system r-build-system)
16743 `(("r-glue" ,r-glue)
16744 ("r-rlang" ,r-rlang)))
16746 `(("r-knitr" ,r-knitr))) ; for vignettes
16747 (home-page "https://github.com/r-lib/lifecycle")
16748 (synopsis "Manage the life cycle of your package functions")
16750 "Manage the life cycle of your exported functions with shared
16751 conventions, documentation badges, and non-invasive deprecation warnings. The
16752 lifecycle package defines four development stages (experimental, maturing,
16753 stable, and questioning) and three deprecation stages (soft-deprecated,
16754 deprecated, and defunct). It makes it easy to insert badges corresponding to
16755 these stages in your documentation. Usage of deprecated functions are
16756 signalled with increasing levels of non-invasive verbosity.")
16757 (license license:gpl3)))
16759 (define-public r-assertable
16761 (name "r-assertable")
16766 (uri (cran-uri "assertable" version))
16769 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16770 (build-system r-build-system)
16772 `(("r-data-table" ,r-data-table)))
16773 (home-page "https://cran.r-project.org/web/packages/assertable/")
16774 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16775 (description "This package provides simple, flexible assertions on
16776 data.frame or data.table objects with verbose output for vetting. While other
16777 assertion packages apply towards more general use-cases, @code{assertable} is
16778 tailored towards tabular data. It includes functions to check variable names
16779 and values, whether the dataset contains all combinations of a given set of
16780 unique identifiers, and whether it is a certain length. In addition,
16781 @code{assertable} includes utility functions to check the existence of target
16782 files and to efficiently import multiple tabular data files into one
16784 (license license:gpl3)))
16786 (define-public r-quadprog
16788 (name "r-quadprog")
16793 (uri (cran-uri "quadprog" version))
16795 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16796 (build-system r-build-system)
16798 `(("gfortran" ,gfortran)))
16799 (home-page "https://cran.r-project.org/web/packages/quadprog")
16800 (synopsis "Functions to solve quadratic programming problems")
16802 "This package contains routines and documentation for solving quadratic
16803 programming problems.")
16804 (license license:gpl3+)))
16806 (define-public r-desolve
16813 (uri (cran-uri "deSolve" version))
16815 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16816 (properties `((upstream-name . "deSolve")))
16817 (build-system r-build-system)
16819 `(("gfortran" ,gfortran)))
16820 (home-page "https://desolve.r-forge.r-project.org/")
16821 (synopsis "Solvers for initial value problems of differential equations")
16822 (description "This package provides functions that solve initial value
16823 problems of a system of first-order @dfn{ordinary differential
16824 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16825 @dfn{differential algebraic equations} (DAE), and of delay differential
16826 equations. The functions provide an interface to the FORTRAN functions
16827 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16828 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16829 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16830 time steps. The package contains routines designed for solving ODEs resulting
16831 from 1-D, 2-D and 3-D partial differential equations that have been converted
16832 to ODEs by numerical differencing.")
16833 (license license:gpl2+)))
16835 (define-public r-pracma
16841 (uri (cran-uri "pracma" version))
16843 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16844 (build-system r-build-system)
16845 (home-page "https://cran.r-project.org/web/packages/pracma/")
16846 (synopsis "Practical numerical math functions")
16847 (description "This package provides functions for numerical analysis and
16848 linear algebra, numerical optimization, differential equations, plus some
16849 special functions. It uses Matlab function names where appropriate to simplify
16851 (license license:gpl3+)))
16853 (define-public r-subplex
16860 (uri (cran-uri "subplex" version))
16863 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16864 (build-system r-build-system)
16866 `(("gfortran" ,gfortran)))
16867 (home-page "https://cran.r-project.org/web/packages/subplex")
16868 (synopsis "Unconstrained optimization using the subplex algorithm")
16870 "This package implements the Subplex optimization algorithm.
16871 It solves unconstrained optimization problems using a simplex method on
16872 subspaces. The method is well suited for optimizing objective functions that
16873 are noisy or are discontinuous at the solution.")
16874 (license license:gpl3+)))
16876 (define-public r-txtplot
16883 (uri (cran-uri "txtplot" version))
16886 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16887 (build-system r-build-system)
16888 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16889 (synopsis "Text-based plotting")
16890 (description "This package provides functions to produce rudimentary ASCII
16891 graphics directly in the terminal window. This package provides a basic
16892 plotting function (and equivalents of curve, density, acf and barplot) as well
16893 as a boxplot function.")
16894 (license license:lgpl3+)))
16896 (define-public r-bio3d
16903 (uri (cran-uri "bio3d" version))
16906 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16907 (properties `((upstream-name . "bio3d")))
16908 (build-system r-build-system)
16909 (inputs `(("zlib" ,zlib)))
16910 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16911 (home-page "http://thegrantlab.org/bio3d/")
16912 (synopsis "Biological structure analysis")
16914 "This package provides utilities to process, organize and explore protein
16915 structure, sequence and dynamics data. Features include the ability to read
16916 and write structure, sequence and dynamic trajectory data, perform sequence
16917 and structure database searches, data summaries, atom selection, alignment,
16918 superposition, rigid core identification, clustering, torsion analysis,
16919 distance matrix analysis, structure and sequence conservation analysis, normal
16920 mode analysis, principal component analysis of heterogeneous structure data,
16921 and correlation network analysis from normal mode and molecular dynamics data.
16922 In addition, various utility functions are provided to enable the statistical
16923 and graphical power of the R environment to work with biological sequence and
16925 (license license:gpl2+)))
16927 (define-public r-bios2cor
16929 (name "r-bios2cor")
16934 (uri (cran-uri "Bios2cor" version))
16937 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16938 (properties `((upstream-name . "Bios2cor")))
16939 (build-system r-build-system)
16941 `(("r-bigmemory" ,r-bigmemory)
16942 ("r-bio3d" ,r-bio3d)
16943 ("r-circular" ,r-circular)
16944 ("r-igraph" ,r-igraph)))
16945 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16946 (synopsis "From biological sequences and simulations to correlation analysis")
16948 "This package provides utilities for computation and analysis of
16949 correlation/covariation in multiple sequence alignments and in side chain
16950 motions during molecular dynamics simulations. Features include the
16951 computation of correlation/covariation scores using a variety of scoring
16952 functions between either sequence positions in alignments or side chain
16953 dihedral angles in molecular dynamics simulations and utilities to analyze the
16954 correlation/covariation matrix through a variety of tools including network
16955 representation and principal components analysis. In addition, several
16956 utility functions are based on the R graphical environment to provide friendly
16957 tools for help in data interpretation.")
16958 (license license:gpl2+)))
16960 ;; This package includes minified JavaScript files. When upgrading please
16961 ;; check that there are no new minified JavaScript files.
16962 (define-public r-networkd3
16964 (name "r-networkd3")
16969 (uri (cran-uri "networkD3" version))
16972 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16975 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16977 (properties `((upstream-name . "networkD3")))
16978 (build-system r-build-system)
16980 `(#:modules ((guix build utils)
16981 (guix build r-build-system)
16985 (modify-phases %standard-phases
16986 (add-after 'unpack 'process-javascript
16987 (lambda* (#:key inputs #:allow-other-keys)
16988 (with-directory-excursion "inst/htmlwidgets/lib/"
16992 `((,(assoc-ref inputs "d3.v4.js")
16993 "d3-4.5.0/d3.min.js"))))
16994 (lambda (sources targets)
16995 (for-each (lambda (source target)
16996 (format #t "Processing ~a --> ~a~%"
16998 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16999 (call-with-output-file target
17001 (dump-port minified port)))))
17002 sources targets))))
17005 `(("uglify-js" ,uglify-js)
17006 ;; NOTE: Make sure that this version of d3 is still valid when
17007 ;; upgrading the package.
17011 (uri "https://d3js.org/d3.v4.js")
17014 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17016 `(("r-htmlwidgets" ,r-htmlwidgets)
17017 ("r-igraph" ,r-igraph)
17018 ("r-magrittr" ,r-magrittr)))
17019 (home-page "https://cran.r-project.org/package=networkD3")
17020 (synopsis "D3 JavaScript network graphs from R")
17022 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17024 (license license:gpl3+)))
17026 (define-public r-aasea
17033 (uri (cran-uri "aaSEA" version))
17036 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17037 (properties `((upstream-name . "aaSEA")))
17038 (build-system r-build-system)
17040 `(("r-bios2cor" ,r-bios2cor)
17042 ("r-hmisc" ,r-hmisc)
17043 ("r-magrittr" ,r-magrittr)
17044 ("r-networkd3" ,r-networkd3)
17045 ("r-plotly" ,r-plotly)
17046 ("r-seqinr" ,r-seqinr)
17047 ("r-shiny" ,r-shiny)
17048 ("r-shinydashboard" ,r-shinydashboard)))
17049 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17050 (synopsis "Amino acid substitution effect analyzer")
17052 "Given a protein multiple sequence alignment, it is a daunting task to
17053 assess the effects of substitutions along sequence length. The aaSEA package
17054 is intended to help researchers to rapidly analyze property changes caused by
17055 single, multiple and correlated amino acid substitutions in proteins.")
17056 (license license:gpl3)))
17058 (define-public r-abacus
17065 (uri (cran-uri "ABACUS" version))
17068 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17069 (properties `((upstream-name . "ABACUS")))
17070 (build-system r-build-system)
17072 `(("r-ggplot2" ,r-ggplot2)
17073 ("r-shiny" ,r-shiny)))
17074 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17075 (synopsis "Apps-based activities for communicating and understanding statistics")
17077 "This package provides a set of Shiny apps for effective communication
17078 and understanding in statistics. The current version includes properties of
17079 normal distribution, properties of sampling distribution, one-sample z and t
17080 tests, two samples independent (unpaired) t test and analysis of variance.")
17081 (license license:gpl3)))
17083 (define-public r-abc-rap
17090 (uri (cran-uri "ABC.RAP" version))
17093 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17094 (properties `((upstream-name . "ABC.RAP")))
17095 (build-system r-build-system)
17096 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17097 (synopsis "Array-based CpG region analysis pipeline")
17099 "This package aims to identify candidate genes that are differentially
17100 methylated between cases and controls. It applies Student's t-test and delta
17101 beta analysis to identify candidate genes containing multiple CpG sites.")
17102 (license license:gpl3)))
17104 (define-public r-abcadm
17111 (uri (cran-uri "abcADM" version))
17114 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17115 (properties `((upstream-name . "abcADM")))
17116 (build-system r-build-system)
17119 ("r-rcpp" ,r-rcpp)))
17120 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17121 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17123 "This package provides tools to estimate parameters of accumulated
17124 damage (load duration) models based on failure time data under a Bayesian
17125 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17126 long-term reliability under stochastic load profiles.")
17127 (license license:gpl3)))
17129 (define-public r-rglpk
17136 (uri (cran-uri "Rglpk" version))
17139 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17140 (properties `((upstream-name . "Rglpk")))
17141 (build-system r-build-system)
17143 `(("r-slam" ,r-slam)))
17146 (home-page "https://r-forge.r-project.org/projects/rglp/")
17147 (synopsis "R interface to the GNU Linear Programming Kit")
17149 "This package provides an R interface to the GNU Linear Programming Kit,
17150 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17151 integer linear programming} (MILP) and other related problems.")
17153 (license (list license:gpl2 license:gpl3))))
17155 (define-public r-abcdefba
17157 (name "r-abcdefba")
17162 (uri (cran-uri "abcdeFBA" version))
17165 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17166 (properties `((upstream-name . "abcdeFBA")))
17167 (build-system r-build-system)
17169 `(("r-corrplot" ,r-corrplot)
17170 ("r-lattice" ,r-lattice)
17172 ("r-rglpk" ,r-rglpk)))
17173 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17174 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17176 "This package provides functions for Constraint Based Simulation using
17177 Flux Balance Analysis and informative analysis of the data generated during
17179 (license license:gpl2)))
17181 (define-public r-abcrlda
17188 (uri (cran-uri "abcrlda" version))
17191 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17192 (properties `((upstream-name . "abcrlda")))
17193 (build-system r-build-system)
17194 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17195 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17197 "This package offers methods to perform @dfn{asymptotically
17198 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17199 cost-sensitive binary classification. The bias-correction is an estimate of
17200 the bias term added to regularized discriminant analysis that minimizes the
17202 (license license:gpl3)))
17204 (define-public r-abemus
17211 (uri (cran-uri "abemus" version))
17214 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17215 (properties `((upstream-name . "abemus")))
17216 (build-system r-build-system)
17218 `(("r-data-table" ,r-data-table)))
17219 (home-page "https://cran.r-project.org/web/packages/abemus/")
17220 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17222 "This package provides an implementation of @dfn{Adaptive Base Error
17223 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17224 platform-specific genetic knowledge and empirical signal to readily detect and
17225 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17226 cell free DNA} (cfDNA).")
17227 (license license:gpl3)))
17229 ;; This package includes minified JavaScript files. When upgrading please
17230 ;; check that there are no new minified JavaScript files.
17231 (define-public r-rintrojs
17233 (name "r-rintrojs")
17238 (uri (cran-uri "rintrojs" version))
17241 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17242 (properties `((upstream-name . "rintrojs")))
17243 (build-system r-build-system)
17245 `(#:modules ((guix build utils)
17246 (guix build r-build-system)
17250 (modify-phases %standard-phases
17251 (add-after 'unpack 'process-javascript
17252 (lambda* (#:key inputs #:allow-other-keys)
17253 (with-directory-excursion "inst/javascript/introjs/"
17257 `((,(assoc-ref inputs "intro.js")
17259 (lambda (sources targets)
17260 (for-each (lambda (source target)
17261 (format #t "Processing ~a --> ~a~%"
17263 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17264 (call-with-output-file target
17266 (dump-port minified port)))))
17267 sources targets))))
17270 `(("uglify-js" ,uglify-js)
17274 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17277 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17279 `(("r-jsonlite" ,r-jsonlite)
17280 ("r-shiny" ,r-shiny)))
17281 (home-page "https://github.com/carlganz/rintrojs")
17282 (synopsis "Wrapper for the Intro.js library")
17284 "This package provides a wrapper for the @url{http://www.introjs.com,
17285 Intro.js} library. This package makes it easy to include step-by-step
17286 introductions, and clickable hints in a Shiny application. It supports both
17287 static introductions in the UI, and programmatic introductions from the
17289 (license license:agpl3+)))
17291 (define-public r-sysfonts
17293 (name "r-sysfonts")
17298 (uri (cran-uri "sysfonts" version))
17301 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17302 (properties `((upstream-name . "sysfonts")))
17303 (build-system r-build-system)
17305 `(("freetype" ,freetype)
17309 `(("pkg-config" ,pkg-config)))
17310 (home-page "https://github.com/yixuan/sysfonts")
17311 (synopsis "Loading fonts into R")
17313 "This is a package to simplify loading of system fonts and Google Fonts
17314 into R, in order to support other packages.")
17315 (license license:gpl2)))
17317 (define-public r-showtextdb
17319 (name "r-showtextdb")
17324 (uri (cran-uri "showtextdb" version))
17327 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17328 (properties `((upstream-name . "showtextdb")))
17329 (build-system r-build-system)
17331 `(("r-sysfonts" ,r-sysfonts)))
17332 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17333 (synopsis "Font files for the 'showtext' package")
17335 "This package provides font files that can be used by the @code{showtext}
17337 (license license:asl2.0)))
17339 (define-public r-showtext
17341 (name "r-showtext")
17346 (uri (cran-uri "showtext" version))
17349 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17350 (properties `((upstream-name . "showtext")))
17351 (build-system r-build-system)
17353 `(("freetype" ,freetype)
17357 `(("r-showtextdb" ,r-showtextdb)
17358 ("r-sysfonts" ,r-sysfonts)))
17360 `(("pkg-config" ,pkg-config)
17361 ("r-knitr" ,r-knitr)))
17362 (home-page "https://github.com/yixuan/showtext")
17363 (synopsis "Using fonts more easily in R graphs")
17365 "This package aims to make it easy to use various types of
17366 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17367 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17368 will be converted into polygons or raster images, hence after the plot has
17369 been created, it no longer relies on the font files. No external software
17370 such as Ghostscript is needed to use this package.")
17371 (license license:asl2.0)))
17373 (define-public r-emojifont
17375 (name "r-emojifont")
17380 (uri (cran-uri "emojifont" version))
17383 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17384 (properties `((upstream-name . "emojifont")))
17385 (build-system r-build-system)
17387 `(("r-ggplot2" ,r-ggplot2)
17388 ("r-proto" ,r-proto)
17389 ("r-showtext" ,r-showtext)
17390 ("r-sysfonts" ,r-sysfonts)))
17391 (home-page "https://guangchuangyu.github.io/emojifont")
17392 (synopsis "Emoji and Font Awesome in R graphics")
17394 "This package enables the use of emoji and the Font Awesome glyphs in
17395 both base and ggplot2 graphics.")
17396 (license license:artistic2.0)))
17398 (define-public r-abstractr
17400 (name "r-abstractr")
17405 (uri (cran-uri "abstractr" version))
17408 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17409 (properties `((upstream-name . "abstractr")))
17410 (build-system r-build-system)
17412 `(("r-colourpicker" ,r-colourpicker)
17413 ("r-emojifont" ,r-emojifont)
17414 ("r-ggplot2" ,r-ggplot2)
17415 ("r-gridextra" ,r-gridextra)
17416 ("r-rintrojs" ,r-rintrojs)
17417 ("r-shiny" ,r-shiny)
17418 ("r-shinythemes" ,r-shinythemes)))
17419 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17420 (synopsis "R-Shiny application for creating visual abstracts")
17422 "This package provides an R Shiny application to create visual abstracts
17423 for original research. A variety of user defined options and formatting are
17425 (license license:gpl3)))
17427 (define-public r-qgam
17434 (uri (cran-uri "qgam" version))
17437 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17438 (properties `((upstream-name . "qgam")))
17439 (build-system r-build-system)
17441 `(("r-doparallel" ,r-doparallel)
17444 ("r-shiny" ,r-shiny)))
17445 (native-inputs `(("r-knitr" ,r-knitr)))
17446 (home-page "https://cran.r-project.org/web/packages/qgam/")
17447 (synopsis "Smooth additive quantile regression models")
17449 "This package provides smooth additive quantile regression models, fitted
17450 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17451 the smoothing parameters are estimated automatically by marginal loss
17452 minimization, while the regression coefficients are estimated using either
17453 PIRLS or Newton algorithm. The learning rate is determined so that the
17454 Bayesian credible intervals of the estimated effects have approximately the
17455 correct coverage. The main function is @code{qgam()} which is similar to
17456 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17457 regression models.")
17458 (license license:gpl2+)))
17460 (define-public r-abtest
17467 (uri (cran-uri "abtest" version))
17470 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17471 (properties `((upstream-name . "abtest")))
17472 (build-system r-build-system)
17474 `(("r-matrix" ,r-matrix)
17475 ("r-mvtnorm" ,r-mvtnorm)
17476 ("r-plotrix" ,r-plotrix)
17478 ("r-rcolorbrewer" ,r-rcolorbrewer)
17481 ("r-truncnorm" ,r-truncnorm)))
17482 (home-page "https://cran.r-project.org/web/packages/abtest/")
17483 (synopsis "Bayesian A/B testing")
17485 "This package provides functions for Bayesian A/B testing including prior
17486 elicitation options based on Kass and Vaidyanathan (1992)
17487 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17488 (license license:gpl2+)))
17490 (define-public r-accept
17497 (uri (cran-uri "accept" version))
17500 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17501 (properties `((upstream-name . "accept")))
17502 (build-system r-build-system)
17504 `(("r-dplyr" ,r-dplyr)
17505 ("r-extrafont" ,r-extrafont)
17507 ("r-plotly" ,r-plotly)
17508 ("r-stringr" ,r-stringr)
17509 ("r-viridis" ,r-viridis)))
17510 (home-page "https://cran.r-project.org/web/packages/accept/")
17511 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17513 "This package allows clinicians to predict the rate and severity of
17514 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17515 Disease} (COPD) patients, based on the clinical prediction model published in
17516 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17517 (license license:gpl3)))
17519 (define-public r-smpracticals
17521 (name "r-smpracticals")
17526 (uri (cran-uri "SMPracticals" version))
17529 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17530 (properties `((upstream-name . "SMPracticals")))
17531 (build-system r-build-system)
17533 `(("r-ellipse" ,r-ellipse)
17536 ("r-survival" ,r-survival)))
17537 (home-page "http://statwww.epfl.ch/davison/SM/")
17538 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17540 "This package contains the datasets and a few functions for use with the
17541 practicals outlined in Appendix A of the book Statistical Models (Davison,
17542 2003, Cambridge University Press). The practicals themselves can be found at
17543 @url{http://statwww.epfl.ch/davison/SM/}.")
17544 (license license:gpl2+)))
17546 (define-public r-fgui
17553 (uri (cran-uri "fgui" version))
17556 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17557 (properties `((upstream-name . "fgui")))
17558 (build-system r-build-system)
17560 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17561 (synopsis "Create GUI for R functions")
17563 "Rapidly create a GUI for a function you created by automatically
17564 creating widgets for arguments of the function. This package automatically
17565 parses help routines for context-sensitive help to these arguments. The
17566 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17567 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17568 incorporated into the interface for greater customization for the more
17570 ;; Any version of the GPL.
17571 (license (list license:gpl2+ license:gpl3+))))
17573 (define-public r-tcltk2
17580 (uri (cran-uri "tcltk2" version))
17583 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17584 (properties `((upstream-name . "tcltk2")))
17585 (build-system r-build-system)
17589 (home-page "https://www.sciviews.org/SciViews-R")
17590 (synopsis "Tcl/Tk additions")
17592 "This package provides a series of additional Tcl commands and Tk widgets
17593 with style and various functions to supplement the tcltk package")
17594 (license license:lgpl3)))
17596 (define-public r-accrual
17603 (uri (cran-uri "accrual" version))
17606 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17607 (properties `((upstream-name . "accrual")))
17608 (build-system r-build-system)
17610 `(("r-fgui" ,r-fgui)
17611 ("r-smpracticals" ,r-smpracticals)
17612 ("r-tcltk2" ,r-tcltk2)))
17613 (home-page "https://cran.r-project.org/web/packages/accrual/")
17614 (synopsis "Bayesian accrual prediction")
17616 "Subject recruitment for medical research is challenging. Slow patient
17617 accrual leads to delay in research. Accrual monitoring during the process of
17618 recruitment is critical. Researchers need reliable tools to manage the
17619 accrual rate. This package provides an implementation of a Bayesian method
17620 that integrates researcher's experience on previous trials and data from the
17621 current study, providing reliable prediction on accrual rate for clinical
17622 studies. It provides functions for Bayesian accrual prediction which can be
17623 easily used by statisticians and clinical researchers.")
17624 (license license:gpl2)))
17626 (define-public r-accrued
17633 (uri (cran-uri "accrued" version))
17636 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17637 (properties `((upstream-name . "accrued")))
17638 (build-system r-build-system)
17639 (home-page "https://cran.r-project.org/web/packages/accrued/")
17640 (synopsis "Data quality visualization tools for partially accruing data")
17642 "This is a package for visualizing data quality of partially accruing
17644 (license license:gpl3)))
17646 (define-public r-mda
17653 (uri (cran-uri "mda" version))
17656 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17657 (properties `((upstream-name . "mda")))
17658 (build-system r-build-system)
17659 (propagated-inputs `(("r-class" ,r-class)))
17660 (native-inputs `(("gfortran" ,gfortran)))
17661 (home-page "https://cran.r-project.org/web/packages/mda/")
17662 (synopsis "Mixture and flexible discriminant analysis")
17664 "This is a package for mixture and flexible discriminant analysis,
17665 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17666 (license license:gpl2)))
17668 (define-public r-elasticnet
17670 (name "r-elasticnet")
17675 (uri (cran-uri "elasticnet" version))
17678 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17679 (properties `((upstream-name . "elasticnet")))
17680 (build-system r-build-system)
17682 `(("r-lars" ,r-lars)))
17683 (home-page "http://users.stat.umn.edu/~zouxx019/")
17684 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17686 "This package provides functions for fitting the entire solution path of
17687 the Elastic-Net and also provides functions for estimating sparse Principal
17688 Components. The Lasso solution paths can be computed by the same function.")
17689 (license license:gpl2+)))
17691 (define-public r-sparselda
17693 (name "r-sparselda")
17698 (uri (cran-uri "sparseLDA" version))
17701 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17702 (properties `((upstream-name . "sparseLDA")))
17703 (build-system r-build-system)
17705 `(("r-elasticnet" ,r-elasticnet)
17708 (home-page "https://www.imm.dtu.dk/~lkhc/")
17709 (synopsis "Sparse discriminant analysis")
17711 "This package performs sparse linear discriminant analysis for Gaussians
17712 and mixture of Gaussian models.")
17713 (license license:gpl2+)))
17715 (define-public r-accsda
17722 (uri (cran-uri "accSDA" version))
17725 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17726 (properties `((upstream-name . "accSDA")))
17727 (build-system r-build-system)
17729 `(("r-ggplot2" ,r-ggplot2)
17730 ("r-ggthemes" ,r-ggthemes)
17731 ("r-gridextra" ,r-gridextra)
17733 ("r-rarpack" ,r-rarpack)
17734 ("r-sparselda" ,r-sparselda)))
17735 (home-page "https://github.com/gumeo/accSDA/wiki")
17736 (synopsis "Accelerated sparse discriminant analysis")
17738 "This package provides an implementation of sparse linear discriminant
17739 analysis, which is a supervised classification method for multiple classes.
17740 Various novel optimization approaches to this problem are implemented
17741 including @dfn{alternating direction method of multipliers} (ADMM),
17742 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17743 Functions for performing cross validation are also supplied along with basic
17744 prediction and plotting functions. @dfn{Sparse zero variance
17745 discriminant} (SZVD) analysis is also included in the package.")
17746 (license license:gpl2+)))
17748 (define-public r-ace2fastq
17750 (name "r-ace2fastq")
17755 (uri (cran-uri "ace2fastq" version))
17758 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17759 (properties `((upstream-name . "ace2fastq")))
17760 (build-system r-build-system)
17762 `(("r-stringr" ,r-stringr)))
17763 (home-page "https://github.com/c5sire/ace2fastq")
17764 (synopsis "ACE file to FASTQ converter")
17766 "The ACE file format is used in genomics to store contigs from sequencing
17767 machines. This tools converts it into FASTQ format. Both formats contain the
17768 sequence characters and their corresponding quality information. Unlike the
17769 FASTQ file, the ACE file stores the quality values numerically. The
17770 conversion algorithm uses the standard Sanger formula. The package
17771 facilitates insertion into pipelines, and content inspection.")
17772 (license license:gpl3)))
17774 (define-public r-rngwell
17781 (uri (cran-uri "rngWELL" version))
17784 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17785 (properties `((upstream-name . "rngWELL")))
17786 (build-system r-build-system)
17787 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17788 (synopsis "Toolbox for WELL random number generators")
17790 "This is a dedicated package to WELL pseudo random generators, which were
17791 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17792 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17793 (license license:bsd-3)))
17795 (define-public r-randtoolbox
17797 (name "r-randtoolbox")
17802 (uri (cran-uri "randtoolbox" version))
17805 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17806 (properties `((upstream-name . "randtoolbox")))
17807 (build-system r-build-system)
17809 `(("r-rngwell" ,r-rngwell)))
17811 `(("gfortran" ,gfortran)))
17812 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17813 (synopsis "Toolbox for pseudo and quasi random number generation")
17815 "This package provides
17818 @item pseudo random generators, such as general linear
17819 congruential generators, multiple recursive generators and generalized
17820 feedback shift register (SF-Mersenne Twister algorithm and WELL
17823 @item quasi random generators, such as the Torus algorithm, the Sobol
17824 sequence, the Halton sequence (including the Van der Corput sequence), and
17826 @item some generator tests: the gap test, the serial test, the poker test.
17829 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17830 (license license:bsd-3)))
17832 (define-public r-lhs
17839 (uri (cran-uri "lhs" version))
17842 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17843 (properties `((upstream-name . "lhs")))
17844 (build-system r-build-system)
17845 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17847 `(("r-knitr" ,r-knitr)))
17848 (home-page "https://github.com/bertcarnell/lhs")
17849 (synopsis "Latin Hypercube Samples")
17851 "This package provides a number of methods for creating and augmenting
17852 Latin Hypercube Samples.")
17853 (license license:gpl3)))
17855 (define-public r-acebayes
17857 (name "r-acebayes")
17862 (uri (cran-uri "acebayes" version))
17865 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17866 (properties `((upstream-name . "acebayes")))
17867 (build-system r-build-system)
17869 `(("r-compare" ,r-compare)
17871 ("r-randtoolbox" ,r-randtoolbox)
17873 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17874 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17875 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17877 "Finding an optimal Bayesian experimental design involves maximizing an
17878 objective function given by the expectation of some appropriately chosen
17879 utility function with respect to the joint distribution of unknown
17880 quantities (including responses). This objective function is usually not
17881 available in closed form and the design space can be continuous and of high
17882 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17883 to maximise an approximation to the expectation of the utility function.")
17884 (license license:gpl2)))
17886 (define-public r-acet
17893 (uri (cran-uri "ACEt" version))
17896 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17897 (properties `((upstream-name . "ACEt")))
17898 (build-system r-build-system)
17903 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17904 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17905 (synopsis "Estimating dynamic heritability and twin model comparison")
17907 "This package supports twin models that are able to estimate the dynamic
17908 behaviour of the variance components in the classical twin models with respect
17909 to age using B-splines and P-splines.")
17910 (license license:gpl2+)))
17912 (define-public r-acfmperiod
17914 (name "r-acfmperiod")
17919 (uri (cran-uri "acfMPeriod" version))
17922 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17923 (properties `((upstream-name . "acfMPeriod")))
17924 (build-system r-build-system)
17926 `(("r-mass" ,r-mass)))
17927 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17928 (synopsis "Estimation of the ACF from the M-periodogram")
17930 "This package support non-robust and robust computations of the sample
17931 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17932 univariate and multivariate processes. The methodology consists in reversing
17933 the diagonalization procedure involving the periodogram or the
17934 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17935 ACOVF or the ACF as discussed in Fuller (1995)
17936 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17937 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17938 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17939 (license license:gpl2+)))
17941 (define-public r-gamlss-data
17943 (name "r-gamlss-data")
17948 (uri (cran-uri "gamlss.data" version))
17951 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17952 (properties `((upstream-name . "gamlss.data")))
17953 (build-system r-build-system)
17954 (home-page "http://www.gamlss.org/")
17955 (synopsis "GAMLSS data")
17957 "This package provides data used as examples to demonstrate GAMLSS
17959 ;; Either version of the license
17960 (license (list license:gpl2 license:gpl3))))
17962 (define-public r-gamlss
17969 (uri (cran-uri "gamlss" version))
17972 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
17973 (properties `((upstream-name . "gamlss")))
17974 (build-system r-build-system)
17976 `(("r-gamlss-data" ,r-gamlss-data)
17977 ("r-gamlss-dist" ,r-gamlss-dist)
17980 ("r-survival" ,r-survival)))
17981 (home-page "http://www.gamlss.org/")
17982 (synopsis "Generalized additive models for location scale and shape")
17984 "This package provides functions for fitting the generalized additive
17985 models for location scale and shape introduced by Rigby and
17986 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17987 use a distributional regression approach where all the parameters of the
17988 conditional distribution of the response variable are modelled using
17989 explanatory variables.")
17990 ;; Either version of the license
17991 (license (list license:gpl2 license:gpl3))))
17993 (define-public r-acid
18000 (uri (cran-uri "acid" version))
18003 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18004 (properties `((upstream-name . "acid")))
18005 (build-system r-build-system)
18007 `(("r-gamlss" ,r-gamlss)
18008 ("r-gamlss-dist" ,r-gamlss-dist)
18009 ("r-hmisc" ,r-hmisc)))
18010 (home-page "https://cran.r-project.org/web/packages/acid/")
18011 (synopsis "Analysing conditional income distributions")
18013 "This package provides functions for the analysis of income distributions
18014 for subgroups of the population as defined by a set of variables like age,
18015 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18016 distribution as well as functions for moments, inequality measures, entropy
18017 measures and polarisation measures of income distributions. This package thus
18018 aides the analysis of income inequality by offering tools for the exploratory
18019 analysis of income distributions at the disaggregated level.")
18020 (license license:gpl3)))
18022 (define-public r-acm4r
18029 (uri (cran-uri "acm4r" version))
18032 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18033 (properties `((upstream-name . "acm4r")))
18034 (build-system r-build-system)
18035 (propagated-inputs `(("r-mass" ,r-mass)))
18036 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18037 (synopsis "Align-and-count method comparisons of RFLP data")
18039 "This is a package to compare sequence fragment lengths or molecular
18040 weights from pairs of lanes. The number of matching bands in the
18041 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18042 the align-and-count method.")
18043 ;; Any version of the GPL
18044 (license (list license:gpl2+ license:gpl3+))))
18046 (define-public r-filematrix
18048 (name "r-filematrix")
18053 (uri (cran-uri "filematrix" version))
18056 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18057 (properties `((upstream-name . "filematrix")))
18058 (build-system r-build-system)
18059 ;; These inputs are needed for vignettes
18061 `(("r-knitr" ,r-knitr)
18062 ("r-rmarkdown" ,r-rmarkdown)
18063 ("pandoc-citeproc" ,pandoc-citeproc)))
18064 (home-page "https://github.com/andreyshabalin/filematrix")
18065 (synopsis "File-backed matrix class with convenient read and write access")
18067 "This package provides an interface for working with large matrices
18068 stored in files, not in computer memory. It supports multiple non-character
18069 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18070 byte real values). Access to parts of the matrix is done by indexing, exactly
18071 as with usual R matrices. It supports very large matrices; the package has
18072 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18073 columns, ad allows for quick addition of extra columns to a filematrix.")
18074 (license license:lgpl3)))
18076 (define-public r-acmeeqtl
18078 (name "r-acmeeqtl")
18083 (uri (cran-uri "ACMEeqtl" version))
18086 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18087 (properties `((upstream-name . "ACMEeqtl")))
18088 (build-system r-build-system)
18090 `(("r-filematrix" ,r-filematrix)))
18091 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18092 (synopsis "Estimation of interpretable eQTL effect sizes")
18094 "This package provides a non-linear model, termed ACME, that reflects a
18095 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18096 With non-linear least-squares algorithm the maximum likelihood parameters can
18097 be estimated. The ACME model provides interpretable effect size estimates and
18098 p-values with well controlled Type-I error.")
18099 (license license:lgpl3)))
18101 (define-public r-acmer
18108 (uri (cran-uri "acmeR" version))
18111 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18112 (properties `((upstream-name . "acmeR")))
18113 (build-system r-build-system)
18114 (propagated-inputs `(("r-foreign" ,r-foreign)))
18115 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18116 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18118 "This package provides an implementation of the ACME estimator, described
18119 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18120 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18121 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18122 as carcasses age; variable bleed-through at successive searches; and interval
18123 mortality estimates. The package provides, based on search data, functions
18124 for estimating the mortality inflation factor in Frequentist and Bayesian
18126 (license license:expat)))
18128 (define-public r-r-huge
18135 (uri (cran-uri "R.huge" version))
18138 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18139 (properties `((upstream-name . "R.huge")))
18140 (build-system r-build-system)
18142 `(("r-r-methodss3" ,r-r-methodss3)
18144 ("r-r-utils" ,r-r-utils)))
18145 (home-page "https://github.com/HenrikBengtsson/R.huge")
18146 (synopsis "Methods for accessing huge amounts of data")
18148 "This is a deprecated package for accessing huge amounts of data.
18149 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18150 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18151 the @code{aroma.affymetrix} package.")
18152 (license license:lgpl2.1+)))
18154 (define-public r-r-filesets
18156 (name "r-r-filesets")
18161 (uri (cran-uri "R.filesets" version))
18164 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18165 (properties `((upstream-name . "R.filesets")))
18166 (build-system r-build-system)
18168 `(("r-digest" ,r-digest)
18169 ("r-r-cache" ,r-r-cache)
18170 ("r-r-methodss3" ,r-r-methodss3)
18172 ("r-r-utils" ,r-r-utils)))
18173 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18174 (synopsis "Easy handling of and access to files")
18176 "This package provides classes and methods to locate, setup, subset,
18177 navigate and iterate file sets, i.e. sets of files located in one or more
18178 directories on the file system. The API is designed such that these classes
18179 can be extended via inheritance to provide a richer API for special file
18180 formats. Moreover, a specific name format is defined such that filenames and
18181 directories can be considered to have full names which consists of a name
18182 followed by comma-separated tags. This adds additional flexibility to
18183 identify file sets and individual files.")
18184 (license license:lgpl2.1+)))
18186 (define-public r-r-devices
18188 (name "r-r-devices")
18193 (uri (cran-uri "R.devices" version))
18196 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18197 (properties `((upstream-name . "R.devices")))
18198 (build-system r-build-system)
18200 `(("r-base64enc" ,r-base64enc)
18201 ("r-r-methodss3" ,r-r-methodss3)
18203 ("r-r-utils" ,r-r-utils)))
18204 (home-page "https://github.com/HenrikBengtsson/R.devices")
18205 (synopsis "Unified handling of graphics devices")
18207 "This package provides functions for creating plots and image files in a
18208 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18209 Default device options as well as scales and aspect ratios are controlled in a
18210 uniform way across all device types. Switching output format requires minimal
18211 changes in code. This package is ideal for large-scale batch processing,
18212 because it will never leave open graphics devices or incomplete image files
18213 behind, even on errors or user interrupts.")
18214 (license license:lgpl2.1+)))
18216 (define-public r-acnr
18223 (uri (cran-uri "acnr" version))
18226 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18227 (properties `((upstream-name . "acnr")))
18228 (build-system r-build-system)
18229 (home-page "https://github.com/mpierrejean/acnr")
18230 (synopsis "Annotated copy-number regions")
18232 "This package provides SNP array data from different types of copy-number
18233 regions. These regions were identified manually by the authors of the package
18234 and may be used to generate realistic data sets with known truth.")
18235 (license license:lgpl2.1+)))
18237 (define-public r-acopula
18244 (uri (cran-uri "acopula" version))
18247 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18248 (properties `((upstream-name . "acopula")))
18249 (build-system r-build-system)
18250 (home-page "https://cran.r-project.org/web/packages/acopula/")
18251 (synopsis "Modelling dependence with multivariate Archimax copulas")
18253 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18254 package provides definitions of several parametric families of generator and
18255 dependence function, computes CDF and PDF, estimates parameters, tests for
18256 goodness of fit, generates random sample and checks copula properties for
18257 custom constructs. In the 2-dimensional case explicit formulas for density
18258 are used, contrary to higher dimensions when all derivatives are linearly
18259 approximated. Several non-archimax families (normal, FGM, Plackett) are
18260 provided as well.")
18261 (license license:gpl2)))
18263 (define-public r-tuner
18270 (uri (cran-uri "tuneR" version))
18273 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18274 (properties `((upstream-name . "tuneR")))
18275 (build-system r-build-system)
18276 (propagated-inputs `(("r-signal" ,r-signal)))
18277 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18278 (synopsis "Analysis of music and speech")
18280 "This is a package for the analysis of music and speech. Analyze music
18281 and speech, extract features like MFCCs, handle wave files and their
18282 representation in various ways, read MP3, read MIDI, perform steps of a
18283 transcription, ...")
18284 ;; Either of these versions.
18285 (license (list license:gpl2 license:gpl3))))
18287 (define-public r-seewave
18294 (uri (cran-uri "seewave" version))
18297 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18298 (properties `((upstream-name . "seewave")))
18299 (build-system r-build-system)
18301 `(("libsndfile" ,libsndfile)))
18303 `(("r-tuner" ,r-tuner)))
18304 (home-page "http://rug.mnhn.fr/seewave")
18305 (synopsis "Sound analysis and synthesis")
18307 "This package provides functions for analysing, manipulating, displaying,
18308 editing and synthesizing time waves (particularly sound). This package
18309 processes time analysis (oscillograms and envelopes), spectral content,
18310 resonance quality factor, entropy, cross correlation and autocorrelation,
18311 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18312 and 3D spectrograms and many other analyses.")
18313 (license license:gpl2+)))
18315 (define-public r-acousticndlcoder
18317 (name "r-acousticndlcoder")
18322 (uri (cran-uri "AcousticNDLCodeR" version))
18325 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18327 `((upstream-name . "AcousticNDLCodeR")))
18328 (build-system r-build-system)
18330 `(("r-seewave" ,r-seewave)
18331 ("r-tuner" ,r-tuner)
18333 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18334 (synopsis "Coding sound files for use with NDL")
18336 "Make acoustic cues to use with the R package @code{ndl}.
18337 The package implements functions used in the PLoS ONE paper \"Words from
18338 spontaneous conversational speech can be recognized with human-like accuracy
18339 by an error-driven learning algorithm that discriminates between meanings
18340 straight from smart acoustic features, bypassing the phoneme as recognition
18341 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18342 (license license:gpl2+)))
18344 (define-public r-acp
18351 (uri (cran-uri "acp" version))
18354 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18355 (properties `((upstream-name . "acp")))
18356 (build-system r-build-system)
18358 `(("r-quantmod" ,r-quantmod)
18359 ("r-tseries" ,r-tseries)))
18360 (home-page "https://cran.r-project.org/web/packages/acp/")
18361 (synopsis "Autoregressive conditional Poisson")
18363 "This package supports the analysis of count data exhibiting
18364 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18365 model (ACP(p,q)) proposed by Heinen (2003).")
18366 (license license:gpl2)))
18368 (define-public r-ada
18375 (uri (cran-uri "ada" version))
18378 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18379 (properties `((upstream-name . "ada")))
18380 (build-system r-build-system)
18381 (propagated-inputs `(("r-rpart" ,r-rpart)))
18382 (home-page "https://cran.r-project.org/web/packages/ada/")
18383 (synopsis "Stochastic boosting")
18385 "This package provides a straightforward, well-documented, and broad
18386 boosting routine for classification, ideally suited for small to
18387 moderate-sized data sets. It performs discrete, real, and gentle boost under
18388 both exponential and logistic loss on a given data set.")
18389 ;; Any version of the GPL.
18390 (license (list license:gpl2+ license:gpl3+))))
18392 (define-public r-genalg
18399 (uri (cran-uri "genalg" version))
18402 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18403 (properties `((upstream-name . "genalg")))
18404 (build-system r-build-system)
18405 (home-page "https://github.com/egonw/genalg")
18406 (synopsis "R based genetic algorithm")
18408 "This package provides an R based genetic algorithm for binary and
18409 floating point chromosomes.")
18410 (license license:gpl2)))
18412 (define-public r-kernelfactory
18414 (name "r-kernelfactory")
18419 (uri (cran-uri "kernelFactory" version))
18422 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18423 (properties `((upstream-name . "kernelFactory")))
18424 (build-system r-build-system)
18427 ("r-genalg" ,r-genalg)
18428 ("r-kernlab" ,r-kernlab)
18429 ("r-randomforest" ,r-randomforest)))
18430 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18431 (synopsis "Ensemble of kernel machines")
18433 "Kernel factory is an ensemble method where each base classifier (random
18434 forest) is fit on the kernel matrix of a subset of the training data.")
18435 (license license:gpl2+)))
18437 (define-public r-dummies
18444 (uri (cran-uri "dummies" version))
18447 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18448 (properties `((upstream-name . "dummies")))
18449 (build-system r-build-system)
18450 (home-page "https://decisionpatterns.com")
18451 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18453 "This package lets you expand factors, characters and other eligible
18454 classes into dummy/indicator variables.")
18455 (license license:gpl2+)))
18457 (define-public r-acrm
18464 (uri (cran-uri "aCRM" version))
18467 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18468 (properties `((upstream-name . "aCRM")))
18469 (build-system r-build-system)
18472 ("r-dummies" ,r-dummies)
18473 ("r-kernelfactory" ,r-kernelfactory)
18474 ("r-randomforest" ,r-randomforest)))
18475 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18476 (synopsis "Convenience functions for analytical customer relationship management")
18478 "This package provides convenience functions for data preparation and
18479 modeling often used in @dfn{analytical customer relationship
18480 management} (aCRM).")
18481 (license license:gpl2+)))
18483 (define-public r-treeclust
18485 (name "r-treeclust")
18490 (uri (cran-uri "treeClust" version))
18493 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18494 (properties `((upstream-name . "treeClust")))
18495 (build-system r-build-system)
18497 `(("r-cluster" ,r-cluster)
18498 ("r-rpart" ,r-rpart)))
18499 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18500 (synopsis "Cluster distances through trees")
18502 "This package provides tools to create a measure of inter-point
18503 dissimilarity useful for clustering mixed data, and, optionally, perform the
18505 (license license:gpl2+)))
18507 (define-public r-acrosstic
18509 (name "r-acrosstic")
18514 (uri (cran-uri "AcrossTic" version))
18517 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18518 (properties `((upstream-name . "AcrossTic")))
18519 (build-system r-build-system)
18521 `(("r-lpsolve" ,r-lpsolve)
18522 ("r-treeclust" ,r-treeclust)))
18523 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18524 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18526 "This is a package for constructing minimum-cost regular spanning
18527 subgraph as part of a non-parametric two-sample test for equality of
18529 (license license:gpl2+)))
18531 (define-public r-acrt
18538 (uri (cran-uri "acrt" version))
18541 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18542 (properties `((upstream-name . "acrt")))
18543 (build-system r-build-system)
18545 `(("r-rcpp" ,r-rcpp)
18546 ("r-rcppeigen" ,r-rcppeigen)
18547 ("r-sandwich" ,r-sandwich)))
18548 (home-page "https://cran.r-project.org/web/packages/acrt/")
18549 (synopsis "Autocorrelation robust testing")
18551 "This package provides functions for testing affine hypotheses on the
18552 regression coefficient vector in regression models with autocorrelated
18554 (license license:gpl2)))
18556 (define-public r-acs
18563 (uri (cran-uri "acs" version))
18566 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18567 (properties `((upstream-name . "acs")))
18568 (build-system r-build-system)
18570 `(("r-httr" ,r-httr)
18573 ("r-stringr" ,r-stringr)
18575 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18576 (synopsis "Work with data from the US Census")
18578 "This package provides a general toolkit for downloading, managing,
18579 analyzing, and presenting data from the
18580 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18581 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18582 American Community Survey (ACS). Confidence intervals provided with ACS data
18583 are converted to standard errors to be bundled with estimates in complex
18584 @code{acs} objects. The package provides new methods to conduct standard
18585 operations on @code{acs} objects and present/plot data in statistically
18586 appropriate ways.")
18587 (license license:gpl3)))
18589 (define-public r-acss-data
18591 (name "r-acss-data")
18596 (uri (cran-uri "acss.data" version))
18599 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18600 (properties `((upstream-name . "acss.data")))
18601 (build-system r-build-system)
18602 (home-page "http://complexitycalculator.com/methodology.html")
18603 (synopsis "Data for algorithmic complexity of short strings")
18605 "This is a data only package providing the algorithmic complexity of
18606 short strings, computed using the coding theorem method. For a given set of
18607 symbols in a string, all possible or a large number of random samples of
18608 Turing machines with a given number of states (e.g., 5) and number of symbols
18609 corresponding to the number of symbols in the strings were simulated until
18610 they reached a halting state or failed to end. This package contains data on
18611 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18612 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18613 distribution of the halting states.")
18614 (license license:gpl2+)))
18616 (define-public r-acss
18623 (uri (cran-uri "acss" version))
18626 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18627 (properties `((upstream-name . "acss")))
18628 (build-system r-build-system)
18630 `(("r-acss-data" ,r-acss-data)
18632 (home-page "http://complexitycalculator.com/methodology.html")
18633 (synopsis "Algorithmic complexity for short strings")
18635 "The main purpose of this package is to provide the algorithmic
18636 complexity for short strings, an approximation of the Kolmogorov Complexity of
18637 a short string using the coding theorem method. While the database containing
18638 the complexity is provided in the data only package @code{acss.data}, this
18639 package provides functions accessing the data such as @code{prob_random}
18640 returning the posterior probability that a given string was produced by a
18641 random process. In addition, two traditional (but problematic) measures of
18642 complexity are also provided: entropy and change complexity.")
18643 (license license:gpl2+)))
18645 (define-public r-acswr
18652 (uri (cran-uri "ACSWR" version))
18655 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18656 (properties `((upstream-name . "ACSWR")))
18657 (build-system r-build-system)
18659 `(("r-mass" ,r-mass)))
18660 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18661 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18663 "This is a companion package for the book \"A Course in Statistics with
18664 R\" (ISBN 978-1-119-15272-9.)")
18665 (license license:gpl2)))
18667 (define-public r-alabama
18670 (version "2015.3-1")
18674 (uri (cran-uri "alabama" version))
18677 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18678 (properties `((upstream-name . "alabama")))
18679 (build-system r-build-system)
18680 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18681 (home-page "https://cran.r-project.org/web/packages/alabama/")
18682 (synopsis "Constrained nonlinear optimization")
18684 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18685 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18686 constraints. Linear or nonlinear equality and inequality constraints are
18688 (license license:gpl2+)))
18690 (define-public r-gdina
18697 (uri (cran-uri "GDINA" version))
18700 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18701 (properties `((upstream-name . "GDINA")))
18702 (build-system r-build-system)
18704 `(("r-alabama" ,r-alabama)
18705 ("r-ggplot2" ,r-ggplot2)
18707 ("r-nloptr" ,r-nloptr)
18708 ("r-numderiv" ,r-numderiv)
18710 ("r-rcpparmadillo" ,r-rcpparmadillo)
18711 ("r-rsolnp" ,r-rsolnp)
18712 ("r-shiny" ,r-shiny)
18713 ("r-shinydashboard" ,r-shinydashboard)))
18715 `(("r-knitr" ,r-knitr)))
18716 (home-page "https://github.com/Wenchao-Ma/GDINA")
18717 (synopsis "Generalized DINA model framework")
18719 "This package provides a set of psychometric tools for cognitive
18720 diagnosis modeling based on the generalized deterministic inputs, noisy and
18721 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18722 and its extensions, including the sequential G-DINA model by Ma and de la
18723 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18724 polytomous G-DINA model by Chen and de la Torre
18725 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18726 distribution can be independent, saturated, higher-order, loglinear smoothed
18727 or structured. Q-matrix validation, item and model fit statistics, model
18728 comparison at test and item level and differential item functioning can also
18729 be conducted. A graphical user interface is also provided.")
18730 (license license:gpl3)))
18732 (define-public r-actcd
18739 (uri (cran-uri "ACTCD" version))
18742 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18743 (properties `((upstream-name . "ACTCD")))
18744 (build-system r-build-system)
18746 `(("r-gdina" ,r-gdina)
18747 ("r-r-methodss3" ,r-r-methodss3)))
18749 `(("gfortran" ,gfortran)))
18750 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18751 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18753 "This is a package supporting cluster analysis for cognitive diagnosis
18754 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18755 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18756 sum-scores, cluster analysis techniques can be used to classify examinees into
18757 latent classes based on their attribute patterns. In addition to the
18758 algorithms used to classify data, three labeling approaches are proposed to
18759 label clusters so that examinees' attribute profiles can be obtained.")
18760 (license license:gpl2+)))
18762 (define-public r-ineq
18769 (uri (cran-uri "ineq" version))
18772 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18773 (properties `((upstream-name . "ineq")))
18774 (build-system r-build-system)
18775 (home-page "https://cran.r-project.org/web/packages/ineq/")
18776 (synopsis "Measuring inequality, concentration, and poverty")
18778 "This package provides tools for measuring inequality, concentration, and
18779 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18780 ;; Either of these two versions.
18781 (license (list license:gpl2 license:gpl3))))
18783 (define-public r-actfrag
18790 (uri (cran-uri "ActFrag" version))
18793 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18794 (properties `((upstream-name . "ActFrag")))
18795 (build-system r-build-system)
18797 `(("r-accelerometry" ,r-accelerometry)
18798 ("r-dplyr" ,r-dplyr)
18800 ("r-survival" ,r-survival)
18801 ("r-tidyr" ,r-tidyr)))
18802 (home-page "https://github.com/junruidi/ActFrag")
18803 (synopsis "Activity fragmentation metrics extraction")
18805 "This package provides functions to extract commonly used fragmentation
18806 metrics to quantify time accumulation strategies based on minute level
18807 actigraphy-measured activity counts data.")
18808 (license license:gpl3)))
18810 (define-public r-fda
18813 (version "5.1.5.1")
18817 (uri (cran-uri "fda" version))
18820 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
18821 (properties `((upstream-name . "fda")))
18822 (build-system r-build-system)
18824 `(("r-matrix" ,r-matrix)))
18825 (home-page "https://www.functionaldata.org")
18826 (synopsis "Functional data analysis")
18828 "These functions were developed to support functional data analysis as
18829 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18830 Analysis. The package includes data sets and script files working many
18832 (license license:gpl2+)))
18834 (define-public r-actigraphy
18836 (name "r-actigraphy")
18841 (uri (cran-uri "Actigraphy" version))
18844 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18845 (properties `((upstream-name . "Actigraphy")))
18846 (build-system r-build-system)
18848 `(("r-fda" ,r-fda)))
18849 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18850 (synopsis "Actigraphy data analysis")
18852 "This package provides tools for functional linear modeling and analysis
18853 of actigraphy data.")
18854 (license license:asl2.0)))
18856 (define-public r-activedriver
18858 (name "r-activedriver")
18863 (uri (cran-uri "ActiveDriver" version))
18866 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18867 (properties `((upstream-name . "ActiveDriver")))
18868 (build-system r-build-system)
18870 `(("r-mass" ,r-mass)))
18871 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18872 (synopsis "Tools for finding cancer driver proteins")
18874 "This package provides a mutation analysis tool that discovers cancer
18875 driver genes with frequent mutations in protein signalling sites such as
18876 post-translational modifications (phosphorylation, ubiquitination, etc). The
18877 Poisson generalized linear regression model identifies genes where cancer
18878 mutations in signalling sites are more frequent than expected from the
18879 sequence of the entire gene. Integration of mutations with signalling
18880 information helps find new driver genes and propose candidate mechanisms to
18882 (license license:gpl2+)))
18884 (define-public r-activitycounts
18886 (name "r-activitycounts")
18891 (uri (cran-uri "activityCounts" version))
18894 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18896 `((upstream-name . "activityCounts")))
18897 (build-system r-build-system)
18899 `(("r-lubridate" ,r-lubridate)
18900 ("r-magrittr" ,r-magrittr)
18901 ("r-seewave" ,r-seewave)
18902 ("r-signal" ,r-signal)
18903 ("r-tibble" ,r-tibble)))
18904 (home-page "https://github.com/walkabillylab/activityCounts")
18905 (synopsis "Generate ActiLife counts")
18907 "ActiLife generates activity counts from data collected by Actigraph
18908 accelerometers. Actigraph is one of the most common research-grade
18909 accelerometers. There is considerable research validating and developing
18910 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18911 counts are proprietary and difficult to implement if researchers use different
18912 accelerometer brands. The code creates ActiLife counts from raw acceleration
18913 data for different accelerometer brands.")
18914 (license license:gpl3)))
18916 (define-public r-activityindex
18918 (name "r-activityindex")
18923 (uri (cran-uri "ActivityIndex" version))
18926 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18927 (properties `((upstream-name . "ActivityIndex")))
18928 (build-system r-build-system)
18930 `(("r-data-table" ,r-data-table)
18931 ("r-matrixstats" ,r-matrixstats)
18932 ("r-r-utils" ,r-r-utils)))
18933 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18934 (synopsis "Activity Index calculation using raw accelerometry data")
18936 "This is a package to read raw accelerometry from GT3X+ accelerometry
18937 data and plain table data to calculate the Activity Index from Bai et
18938 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18939 (license license:gpl3)))
18941 (define-public r-activpal
18943 (name "r-activpal")
18948 (uri (cran-uri "activPAL" version))
18951 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18952 (properties `((upstream-name . "activPAL")))
18953 (build-system r-build-system)
18955 `(("r-devtools" ,r-devtools)
18956 ("r-dplyr" ,r-dplyr)
18957 ("r-ggplot2" ,r-ggplot2)
18958 ("r-lubridate" ,r-lubridate)
18959 ("r-magrittr" ,r-magrittr)
18960 ("r-tidyr" ,r-tidyr)))
18961 (home-page "https://cran.r-project.org/web/packages/activPAL")
18962 (synopsis "Processing and chart generation from activPAL events files")
18964 "This package contains functions to generate pre-defined summary
18965 statistics from activPAL events files. The package also contains functions to
18966 produce informative graphics that visualize physical activity behaviour and
18967 trends. This includes generating graphs that align physical activity
18968 behaviour with additional time based observations described by other data
18969 sets, such as sleep diaries and continuous glucose monitoring data.")
18970 (license license:gpl3)))
18972 (define-public r-activpalprocessing
18974 (name "r-activpalprocessing")
18979 (uri (cran-uri "activpalProcessing" version))
18982 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18984 `((upstream-name . "activpalProcessing")))
18985 (build-system r-build-system)
18987 `(("r-chron" ,r-chron)))
18988 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18989 (synopsis "Process activPAL events files")
18991 "This package performs estimation of physical activity and sedentary
18992 behavior variables from activPAL events files.")
18993 ;; Either version of the GPL.
18994 (license (list license:gpl2 license:gpl3))))
18996 (define-public r-actogrammr
18998 (name "r-actogrammr")
19003 (uri (cran-uri "actogrammr" version))
19006 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19007 (properties `((upstream-name . "actogrammr")))
19008 (build-system r-build-system)
19010 `(("r-dplyr" ,r-dplyr)
19011 ("r-ggplot2" ,r-ggplot2)
19012 ("r-lubridate" ,r-lubridate)
19013 ("r-readr" ,r-readr)
19014 ("r-tidyr" ,r-tidyr)))
19015 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19016 (synopsis "Read in activity data and plot actograms")
19018 "Read in activity measurements from standard file formats used by
19019 circadian rhythm researchers, currently only ClockLab format, and process and
19020 plot the data. The central type of plot is the actogram, as first described
19021 in \"Activity and distribution of certain wild mice in relation to biotic
19022 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19023 (license license:gpl3)))
19025 (define-public r-expint
19032 (uri (cran-uri "expint" version))
19035 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19036 (properties `((upstream-name . "expint")))
19037 (build-system r-build-system)
19038 (home-page "https://gitlab.com/vigou3/expint")
19039 (synopsis "Exponential integral and incomplete Gamma function")
19041 "This package provides the exponential integrals @code{E_1(x)},
19042 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19043 function @code{G(a, x)} defined for negative values of its first argument.
19044 The package also gives easy access to the underlying C routines through an
19045 API; see the package vignette for details.")
19046 (license license:gpl2+)))
19048 (define-public r-actuar
19055 (uri (cran-uri "actuar" version))
19058 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19059 (properties `((upstream-name . "actuar")))
19060 (build-system r-build-system)
19061 (propagated-inputs `(("r-expint" ,r-expint)))
19062 (home-page "https://gitlab.com/vigou3/actuar")
19063 (synopsis "Actuarial functions and heavy tailed distributions")
19065 "This package provides functions and data sets for actuarial science:
19066 modeling of loss distributions; risk theory and ruin theory; simulation of
19067 compound models, discrete mixtures and compound hierarchical models;
19068 credibility theory. It boasts support for many additional probability
19069 distributions to model insurance loss amounts and loss frequency: 19
19070 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19071 distribution; zero-truncated and zero-modified extensions of the standard
19072 discrete distributions. It also supports phase-type distributions commonly
19073 used to compute ruin probabilities.")
19074 (license license:gpl2+)))
19076 (define-public r-bmp
19083 (uri (cran-uri "bmp" version))
19086 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19087 (properties `((upstream-name . "bmp")))
19088 (build-system r-build-system)
19089 (home-page "https://cran.r-project.org/web/packages/bmp/")
19090 (synopsis "Read Bitmap (BMP) images")
19092 "This package provides pure R tools to read BMP format images. It is
19093 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19094 (license license:gpl2+)))
19096 (define-public r-readbitmap
19098 (name "r-readbitmap")
19103 (uri (cran-uri "readbitmap" version))
19106 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19107 (properties `((upstream-name . "readbitmap")))
19108 (build-system r-build-system)
19110 `(("libjpeg" ,libjpeg-turbo)
19111 ("libpng" ,libpng)))
19116 ("r-tiff" ,r-tiff)))
19117 (home-page "https://github.com/jefferis/readbitmap")
19118 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19120 "This package provides tools to identify and read BMP, JPEG, PNG, and
19121 TIFF format bitmap images. Identification defaults to the use of the magic
19122 number embedded in the file rather than the file extension.")
19123 (license license:gpl2+)))
19125 (define-public r-imager
19132 (uri (cran-uri "imager" version))
19135 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19136 (properties `((upstream-name . "imager")))
19137 (build-system r-build-system)
19140 ("libtiff" ,libtiff)
19144 `(("r-downloader" ,r-downloader)
19145 ("r-igraph" ,r-igraph)
19147 ("r-magrittr" ,r-magrittr)
19149 ("r-purrr" ,r-purrr)
19151 ("r-readbitmap" ,r-readbitmap)
19152 ("r-stringr" ,r-stringr)))
19154 `(("pkg-config" ,pkg-config)
19155 ("r-knitr" ,r-knitr)))
19156 (home-page "https://dahtah.github.io/imager/")
19157 (synopsis "Image processing library")
19159 "This is a package for fast image processing for images in up to 4
19160 dimensions (two spatial dimensions, one time/depth dimension, one color
19161 dimension). It provides most traditional image processing tools (filtering,
19162 morphology, transformations, etc.) as well as various functions for easily
19163 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19164 simple, modern C++ library for image processing.")
19165 (license license:lgpl3)))
19167 (define-public r-acuityview
19169 (name "r-acuityview")
19174 (uri (cran-uri "AcuityView" version))
19177 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19178 (properties `((upstream-name . "AcuityView")))
19179 (build-system r-build-system)
19181 `(("r-fftwtools" ,r-fftwtools)
19182 ("r-imager" ,r-imager)
19183 ("r-plotrix" ,r-plotrix)))
19184 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19185 (synopsis "Display scenes as seen by an animal with less acute vision")
19187 "This package provides a simple method for representing a visual scene as
19188 it may be seen by an animal with less acute vision.")
19189 (license license:gpl2+)))
19191 (define-public r-caret
19198 (uri (cran-uri "caret" version))
19201 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19202 (build-system r-build-system)
19204 `(("r-foreach" ,r-foreach)
19205 ("r-ggplot2" ,r-ggplot2)
19206 ("r-lattice" ,r-lattice)
19207 ("r-modelmetrics" ,r-modelmetrics)
19211 ("r-recipes" ,r-recipes)
19212 ("r-reshape2" ,r-reshape2)
19213 ("r-withr" ,r-withr)))
19215 `(("r-knitr" ,r-knitr)))
19216 (home-page "https://github.com/topepo/caret")
19217 (synopsis "Classification and regression training")
19219 "This package provides miscellaneous functions for training and plotting
19220 classification and regression models.")
19221 (license license:gpl2+)))
19223 (define-public r-adabag
19230 (uri (cran-uri "adabag" version))
19233 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19234 (properties `((upstream-name . "adabag")))
19235 (build-system r-build-system)
19237 `(("r-caret" ,r-caret)
19238 ("r-doparallel" ,r-doparallel)
19239 ("r-foreach" ,r-foreach)
19240 ("r-rpart" ,r-rpart)))
19241 (home-page "https://cran.r-project.org/web/packages/adabag/")
19242 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19244 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19245 Breiman's Bagging algorithm using classification trees as individual
19246 classifiers. Once these classifiers have been trained, they can be used to
19247 predict on new data. Also, cross validation estimation of the error can be
19249 (license license:gpl2+)))
19251 (define-public r-adagio
19258 (uri (cran-uri "adagio" version))
19261 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19262 (properties `((upstream-name . "adagio")))
19263 (build-system r-build-system)
19264 (native-inputs `(("gfortran" ,gfortran)))
19265 (home-page "https://cran.r-project.org/web/packages/adagio/")
19266 (synopsis "Discrete and global optimization routines")
19268 "This package provides methods and algorithms for discrete optimization,
19269 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19270 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19272 (license license:gpl3+)))
19274 (define-public r-univoutl
19276 (name "r-univoutl")
19281 (uri (cran-uri "univOutl" version))
19284 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19285 (properties `((upstream-name . "univOutl")))
19286 (build-system r-build-system)
19288 `(("r-hmisc" ,r-hmisc)
19289 ("r-robustbase" ,r-robustbase)))
19290 (home-page "https://github.com/marcellodo/univOutl")
19291 (synopsis "Detection of univariate outliers")
19293 "This package provides well-known outlier detection techniques in the
19294 univariate case. Methods to deal with skewed distribution are included too.
19295 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19296 historical data is implemented as well. When available, survey weights can be
19297 used in outliers detection.")
19298 (license license:gpl2+)))
19300 (define-public r-tolerance
19302 (name "r-tolerance")
19307 (uri (cran-uri "tolerance" version))
19310 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19311 (properties `((upstream-name . "tolerance")))
19312 (build-system r-build-system)
19314 `(("r-mass" ,r-mass)
19316 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19317 (synopsis "Statistical tolerance intervals and regions")
19319 "This package provides functions for estimating tolerance
19320 limits (intervals) for various univariate distributions (binomial, Cauchy,
19321 discrete Pareto, exponential, two-parameter exponential, extreme value,
19322 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19323 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19324 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19325 nonparametric tolerance intervals, tolerance bands for regression
19326 settings (linear regression, nonlinear regression, nonparametric regression,
19327 and multivariate regression), and analysis of variance tolerance intervals.
19328 Visualizations are also available for most of these settings.")
19329 (license license:gpl2+)))
19331 (define-public r-additivitytests
19333 (name "r-additivitytests")
19338 (uri (cran-uri "additivityTests" version))
19341 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19343 `((upstream-name . "additivityTests")))
19344 (build-system r-build-system)
19345 (home-page "https://github.com/simecek/additivityTests")
19346 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19348 "This package provides an implementation of the Tukey, Mandel,
19349 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19350 (license license:gpl3)))
19352 (define-public r-flexclust
19354 (name "r-flexclust")
19359 (uri (cran-uri "flexclust" version))
19362 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19363 (properties `((upstream-name . "flexclust")))
19364 (build-system r-build-system)
19366 `(("r-class" ,r-class)
19367 ("r-lattice" ,r-lattice)
19368 ("r-modeltools" ,r-modeltools)))
19369 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19370 (synopsis "Flexible cluster algorithms")
19372 "The main function @code{kcca} implements a general framework for
19373 k-centroids cluster analysis supporting arbitrary distance measures and
19374 centroid computation. Further cluster methods include hard competitive
19375 learning, neural gas, and QT clustering. There are numerous visualization
19376 methods for cluster results (neighborhood graphs, convex cluster hulls,
19377 barcharts of centroids, ...), and bootstrap methods for the analysis of
19378 cluster stability.")
19379 (license license:gpl2)))
19381 (define-public r-biclust
19388 (uri (cran-uri "biclust" version))
19391 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19392 (properties `((upstream-name . "biclust")))
19393 (build-system r-build-system)
19395 `(("r-additivitytests" ,r-additivitytests)
19396 ("r-colorspace" ,r-colorspace)
19397 ("r-flexclust" ,r-flexclust)
19398 ("r-ggplot2" ,r-ggplot2)
19399 ("r-lattice" ,r-lattice)
19401 ("r-tidyr" ,r-tidyr)))
19402 (home-page "https://cran.r-project.org/web/packages/biclust/")
19403 (synopsis "BiCluster algorithms")
19405 "The main function @code{biclust()} provides several algorithms to find
19406 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19407 In addition, the package provides methods for data
19408 preprocessing (normalization and discretization), visualization, and
19409 validation of bicluster solutions.")
19410 (license license:gpl3)))
19412 (define-public r-icge
19419 (uri (cran-uri "ICGE" version))
19422 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19423 (properties `((upstream-name . "ICGE")))
19424 (build-system r-build-system)
19426 `(("r-cluster" ,r-cluster)
19427 ("r-mass" ,r-mass)))
19428 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19429 (synopsis "Cluster estimation and identification of atypical units")
19431 "ICGE is a package that helps to estimate the number of real clusters in
19432 data as well as to identify atypical units. The underlying methods are based
19433 on distances rather than on unit x variables.")
19434 (license license:gpl2+)))
19436 (define-public r-depth
19439 (version "2.1-1.1")
19443 (uri (cran-uri "depth" version))
19446 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19447 (properties `((upstream-name . "depth")))
19448 (build-system r-build-system)
19450 `(("r-abind" ,r-abind)
19451 ("r-circular" ,r-circular)
19454 `(("gfortran" ,gfortran)))
19455 (home-page "https://cran.r-project.org/web/packages/depth/")
19456 (synopsis "Nonparametric depth functions for multivariate analysis")
19458 "This package provides tools for depth functions methodology applied to
19459 multivariate analysis. Besides allowing calculation of depth values and
19460 depth-based location estimators, the package includes functions or drawing
19461 contour plots and perspective plots of depth functions. Euclidian and
19462 spherical depths are supported.")
19463 (license license:gpl2)))
19465 (define-public r-archetypes
19467 (name "r-archetypes")
19468 (version "2.2-0.1")
19472 (uri (cran-uri "archetypes" version))
19475 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19476 (properties `((upstream-name . "archetypes")))
19477 (build-system r-build-system)
19479 `(("r-modeltools" ,r-modeltools)
19480 ("r-nnls" ,r-nnls)))
19481 (home-page "https://cran.r-project.org/web/packages/archetypes")
19482 (synopsis "Archetypal analysis")
19484 "The main function @code{archetypes} implements a framework for
19485 archetypal analysis supporting arbitrary problem solving mechanisms for the
19486 different conceptual parts of the algorithm.")
19487 (license license:gpl2+)))
19489 (define-public r-shapes
19496 (uri (cran-uri "shapes" version))
19499 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19500 (properties `((upstream-name . "shapes")))
19501 (build-system r-build-system)
19503 `(("r-mass" ,r-mass)
19504 ("r-minpack-lm" ,r-minpack-lm)
19506 ("r-scatterplot3d" ,r-scatterplot3d)))
19507 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19508 (synopsis "Statistical shape analysis")
19510 "This package provides routines for the statistical analysis of landmark
19511 shapes, including Procrustes analysis, graphical displays, principal
19512 components analysis, permutation and bootstrap tests, thin-plate spline
19513 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19514 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19515 Edition), John Wiley and Sons.")
19516 (license license:gpl2)))
19518 (define-public r-anthropometry
19520 (name "r-anthropometry")
19525 (uri (cran-uri "Anthropometry" version))
19528 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19529 (properties `((upstream-name . "Anthropometry")))
19530 (build-system r-build-system)
19532 `(("r-archetypes" ,r-archetypes)
19533 ("r-biclust" ,r-biclust)
19534 ("r-cluster" ,r-cluster)
19535 ("r-depth" ,r-depth)
19540 ("r-shapes" ,r-shapes)))
19542 `(("r-knitr" ,r-knitr)))
19543 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19544 (synopsis "Statistical methods for anthropometric data")
19546 "This package provides statistical methods especially developed to
19547 analyze anthropometric data. These methods are aimed at providing effective
19548 solutions to some commons problems related to Ergonomics and Anthropometry.
19549 They are based on clustering, the statistical concept of data depth,
19550 statistical shape analysis and archetypal analysis.")
19551 (license license:gpl2+)))
19553 (define-public r-adamethods
19555 (name "r-adamethods")
19560 (uri (cran-uri "adamethods" version))
19563 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19564 (properties `((upstream-name . "adamethods")))
19565 (build-system r-build-system)
19567 `(("r-anthropometry" ,r-anthropometry)
19568 ("r-archetypes" ,r-archetypes)
19570 ("r-foreach" ,r-foreach)
19572 ("r-tolerance" ,r-tolerance)
19573 ("r-univoutl" ,r-univoutl)))
19574 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19575 (synopsis "Archetypoid algorithms and anomaly detection")
19577 "This package is a collection of several algorithms to obtain
19578 archetypoids with small and large databases and with both classical
19579 multivariate data and functional data (univariate and multivariate). Some of
19580 these algorithms also allow to detect anomalies (outliers).")
19581 (license license:gpl2+)))
19583 (define-public r-idpmisc
19590 (uri (cran-uri "IDPmisc" version))
19593 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19594 (properties `((upstream-name . "IDPmisc")))
19595 (build-system r-build-system)
19597 `(("r-lattice" ,r-lattice)))
19598 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19599 (synopsis "Functions for data analyses and visualization")
19601 "This package provides different high-level graphics functions for
19602 displaying large datasets, displaying circular data in a very flexible way,
19603 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19604 2D-plots, creating figures with differently colored margin and plot region.
19605 In addition, the package contains auxiliary functions for data manipulation
19606 like omitting observations with irregular values or selecting data by logical
19607 vectors, which include NAs. Other functions are especially useful in
19608 spectroscopy and analyses of environmental data: robust baseline fitting,
19609 finding peaks in spectra, converting humidity measures.")
19610 (license license:gpl3+)))
19612 (define-public r-qqman
19619 (uri (cran-uri "qqman" version))
19622 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19623 (properties `((upstream-name . "qqman")))
19624 (build-system r-build-system)
19626 `(("r-calibrate" ,r-calibrate)))
19627 (home-page "https://cran.r-project.org/web/packages/qqman/")
19628 (synopsis "Q-Q and Manhattan plots for GWAS data")
19630 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19631 from PLINK results.")
19632 (license license:gpl3)))
19634 (define-public r-ggplot-multistats
19636 (name "r-ggplot-multistats")
19641 (uri (cran-uri "ggplot.multistats" version))
19644 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19646 `((upstream-name . "ggplot.multistats")))
19647 (build-system r-build-system)
19649 `(("r-ggplot2" ,r-ggplot2)
19650 ("r-hexbin" ,r-hexbin)
19651 ("r-rlang" ,r-rlang)
19652 ("r-scales" ,r-scales)))
19653 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19654 (synopsis "Multiple summary statistics for binned stats/geometries")
19656 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19657 which functions similar to its singular form, but allows the use of multiple
19658 statistics per bin. Those statistics can be mapped to multiple bin
19660 (license license:gpl3)))
19662 (define-public r-knn-covertree
19664 (name "r-knn-covertree")
19669 (uri (cran-uri "knn.covertree" version))
19672 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19673 (properties `((upstream-name . "knn.covertree")))
19674 (build-system r-build-system)
19676 `(("r-matrix" ,r-matrix)
19678 ("r-rcppeigen" ,r-rcppeigen)))
19679 (home-page "https://github.com/flying-sheep/knn.covertree")
19680 (synopsis "Accurate kNN Implementation with multiple distance measures")
19682 "Similarly to the FNN package, this package allows calculation of the k
19683 nearest neighbors (kNN) of a data matrix. The implementation is based on
19684 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19685 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19686 (license license:agpl3+)))
19688 (define-public r-poibin
19695 (uri (cran-uri "poibin" version))
19698 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19699 (properties `((upstream-name . "poibin")))
19700 (build-system r-build-system)
19701 (home-page "https://cran.r-project.org/web/packages/poibin/")
19702 (synopsis "Poisson binomial distribution")
19704 "This package provides an implementation of both the exact and
19705 approximation methods for computing the @dfn{cumulative distribution
19706 function} (CDF) of the Poisson binomial distribution. It also provides the
19707 @dfn{probability mass function} (PMF), quantile function, and random number
19708 generation for the Poisson binomial distribution.")
19709 (license license:gpl2)))
19711 (define-public r-diagram
19718 (uri (cran-uri "diagram" version))
19721 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19722 (properties `((upstream-name . "diagram")))
19723 (build-system r-build-system)
19725 `(("r-shape" ,r-shape)))
19726 (home-page "https://cran.r-project.org/web/packages/diagram/")
19727 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19729 "This package provides tools to visualize simple graphs (networks) based
19730 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19731 electrical networks, etc. It also includes supporting material for the book
19732 \"A practical guide to ecological modelling - using R as a simulation
19733 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19734 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19735 Francesca Mazzia (2012).")
19736 (license license:gpl2+)))
19738 (define-public r-lim
19745 (uri (cran-uri "LIM" version))
19748 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19749 (properties `((upstream-name . "LIM")))
19750 (build-system r-build-system)
19752 `(("r-diagram" ,r-diagram)
19753 ("r-limsolve" ,r-limsolve)))
19754 (home-page "https://cran.r-project.org/web/packages/LIM/")
19755 (synopsis "Linear inverse model examples and solution methods")
19757 "This package provides functions that read and solve linear inverse
19758 problems (food web problems, linear programming problems).")
19759 (license license:gpl2+)))
19761 (define-public r-shinycssloaders
19763 (name "r-shinycssloaders")
19768 (uri (cran-uri "shinycssloaders" version))
19771 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19773 `((upstream-name . "shinycssloaders")))
19774 (build-system r-build-system)
19776 `(("r-digest" ,r-digest)
19778 ("r-shiny" ,r-shiny)))
19779 (home-page "https://github.com/andrewsali/shinycssloaders")
19780 (synopsis "Add CSS loading animations to Shiny outputs")
19782 "This package provides tools to create a lightweight Shiny wrapper for
19783 the css-loaders created by Luke Hass
19784 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19785 automatically show a loader when the output is (re)calculating.")
19786 (license license:gpl3)))
19788 (define-public r-rsvg
19795 (uri (cran-uri "rsvg" version))
19798 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19799 (properties `((upstream-name . "rsvg")))
19800 (build-system r-build-system)
19802 `(("librsvg" ,librsvg)
19805 `(("pkg-config" ,pkg-config)
19806 ("r-knitr" ,r-knitr)))
19807 (home-page "https://github.com/jeroen/rsvg#readme")
19808 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19810 "This package allows you to render vector-based SVG images into
19811 high-quality custom-size bitmap arrays using the librsvg2 library. The
19812 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19813 addition, the package can convert images directly to various formats such as
19814 PDF or PostScript.")
19815 (license license:expat)))
19817 (define-public r-influencer
19819 (name "r-influencer")
19824 (uri (cran-uri "influenceR" version))
19827 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19828 (properties `((upstream-name . "influenceR")))
19829 (build-system r-build-system)
19831 `(("r-igraph" ,r-igraph)
19832 ("r-matrix" ,r-matrix)))
19833 (home-page "https://github.com/rcc-uchicago/influenceR")
19834 (synopsis "Tools to quantify structural importance of nodes in a network")
19836 "This package provides functionality to compute various node centrality
19837 measures on networks. Included are functions to compute betweenness
19838 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19839 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19840 algorithm to identify key players, and Valente's bridging metric. The
19841 betweenness, Key Players, and bridging implementations are parallelized with
19843 (license license:gpl2)))
19845 (define-public r-emplik
19852 (uri (cran-uri "emplik" version))
19855 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19856 (properties `((upstream-name . "emplik")))
19857 (build-system r-build-system)
19859 `(("r-quantreg" ,r-quantreg)))
19860 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19861 (synopsis "Empirical likelihood ratio for censored/truncated data")
19863 "This package provides empirical likelihood ratio tests for
19864 means/quantiles/hazards from possibly censored and/or truncated data. It also
19866 (license license:gpl2+)))
19868 (define-public r-imputeyn
19870 (name "r-imputeyn")
19875 (uri (cran-uri "imputeYn" version))
19878 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19879 (properties `((upstream-name . "imputeYn")))
19880 (build-system r-build-system)
19882 `(("r-boot" ,r-boot)
19883 ("r-emplik" ,r-emplik)
19884 ("r-mvtnorm" ,r-mvtnorm)
19885 ("r-quadprog" ,r-quadprog)
19886 ("r-survival" ,r-survival)))
19887 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19888 (synopsis "Impute last largest censored observation under weighted least squares")
19890 "This package allows for the imputation of the last largest censored
19891 observantions. This method brings less bias and more efficient estimates for
19893 (license license:gpl2)))
19895 (define-public r-adapenetclass
19897 (name "r-adapenetclass")
19902 (uri (cran-uri "AdapEnetClass" version))
19905 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19906 (properties `((upstream-name . "AdapEnetClass")))
19907 (build-system r-build-system)
19909 `(("r-glmnet" ,r-glmnet)
19910 ("r-imputeyn" ,r-imputeyn)
19912 ("r-quadprog" ,r-quadprog)))
19913 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19914 (synopsis "Class of adaptive elastic net methods for censored data")
19916 "This package provides methods for variable selection for AFT models.")
19917 (license license:gpl2)))
19919 (define-public r-flock
19926 (uri (cran-uri "flock" version))
19929 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19930 (properties `((upstream-name . "flock")))
19931 (build-system r-build-system)
19932 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19933 (home-page "https://cran.r-project.org/web/packages/flock/")
19934 (synopsis "Process synchronization using file locks")
19936 "This package implements synchronization between R processes (spawned by
19937 using the @code{parallel} package for instance) using file locks. It supports
19938 both exclusive and shared locking.")
19939 (license license:asl2.0)))
19941 (define-public r-archivist
19943 (name "r-archivist")
19948 (uri (cran-uri "archivist" version))
19951 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19952 (properties `((upstream-name . "archivist")))
19953 (build-system r-build-system)
19956 ("r-digest" ,r-digest)
19957 ("r-flock" ,r-flock)
19959 ("r-lubridate" ,r-lubridate)
19960 ("r-magrittr" ,r-magrittr)
19961 ("r-rcurl" ,r-rcurl)
19962 ("r-rsqlite" ,r-rsqlite)))
19963 (home-page "https://pbiecek.github.io/archivist/")
19964 (synopsis "Tools for storing, restoring and searching for R objects")
19966 "Data exploration and modelling is a process in which a lot of data
19967 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19968 statistical models, different versions of data sets and different versions of
19969 results. Archivist helps to store and manage artifacts created in R. It
19970 allows you to store selected artifacts as binary files together with their
19971 metadata and relations. Archivist allows sharing artifacts with others. It
19972 can look for already created artifacts by using its class, name, date of the
19973 creation or other properties. It also makes it easy to restore such
19975 (license license:gpl2)))
19977 (define-public r-versions
19979 (name "r-versions")
19984 (uri (cran-uri "versions" version))
19987 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19988 (properties `((upstream-name . "versions")))
19989 (build-system r-build-system)
19990 (home-page "https://cran.r-project.org/web/packages/versions/")
19991 (synopsis "Query and install specific versions of CRAN packages")
19993 "This package allows you to install specified versions of R packages
19994 hosted on CRAN and provides functions to list available versions and the
19995 versions of currently installed packages.")
19996 (license license:bsd-3)))
19998 (define-public r-adapr
20005 (uri (cran-uri "adapr" version))
20008 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20009 (properties `((upstream-name . "adapr")))
20010 (build-system r-build-system)
20012 `(("r-archivist" ,r-archivist)
20013 ("r-devtools" ,r-devtools)
20014 ("r-digest" ,r-digest)
20015 ("r-doparallel" ,r-doparallel)
20016 ("r-gdata" ,r-gdata)
20017 ("r-ggplot2" ,r-ggplot2)
20018 ("r-git2r" ,r-git2r)
20019 ("r-igraph" ,r-igraph)
20020 ("r-knitr" ,r-knitr)
20021 ("r-plotly" ,r-plotly)
20023 ("r-rmarkdown" ,r-rmarkdown)
20024 ("r-shiny" ,r-shiny)
20025 ("r-shinydashboard" ,r-shinydashboard)
20026 ("r-versions" ,r-versions)))
20027 (home-page "https://cran.r-project.org/web/packages/adapr/")
20028 (synopsis "Implementation of an accountable data analysis process")
20030 "This package tracks reading and writing within R scripts that are
20031 organized into a directed acyclic graph. It contains an interactive Shiny
20032 application @code{adaprApp()}. It uses Git and file hashes to track version
20033 histories of inputs and outputs.")
20034 (license license:lgpl2.0)))
20036 (define-public r-adapsamp
20038 (name "r-adapsamp")
20043 (uri (cran-uri "AdapSamp" version))
20046 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20047 (properties `((upstream-name . "AdapSamp")))
20048 (build-system r-build-system)
20049 (propagated-inputs `(("r-pracma" ,r-pracma)))
20050 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20051 (synopsis "Adaptive sampling algorithms")
20053 "For distributions whose probability density functions are log-concave,
20054 the adaptive rejection sampling algorithm can be used to build envelope
20055 functions for sampling. For others, the modified adaptive rejection sampling
20056 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20057 adaptive slice sampling algorithm can be used. This R package mainly includes
20058 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20059 @code{rASS()}. These functions can realize sampling based on the algorithms
20061 (license license:gpl2)))
20063 (define-public r-adaptalint
20065 (name "r-adaptalint")
20070 (uri (cran-uri "adaptalint" version))
20073 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20074 (properties `((upstream-name . "adaptalint")))
20075 (build-system r-build-system)
20077 `(("r-dplyr" ,r-dplyr)
20078 ("r-lintr" ,r-lintr)
20079 ("r-purrr" ,r-purrr)))
20080 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20081 (synopsis "Check R code style")
20083 "This package provides tools to infer the code style (which style rules
20084 are followed and which ones are not) from one package and use it to check
20085 another. This makes it easier to find and correct the most important problems
20087 (license license:gpl3)))
20089 (define-public r-fracdiff
20091 (name "r-fracdiff")
20096 (uri (cran-uri "fracdiff" version))
20099 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20100 (properties `((upstream-name . "fracdiff")))
20101 (build-system r-build-system)
20102 (home-page "https://github.com/mmaechler/fracdiff")
20104 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20106 "This package provides tools for the maximum likelihood estimation of the
20107 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20108 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20109 (license license:gpl2+)))
20111 (define-public r-forecast
20113 (name "r-forecast")
20118 (uri (cran-uri "forecast" version))
20121 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20122 (properties `((upstream-name . "forecast")))
20123 (build-system r-build-system)
20125 `(("r-colorspace" ,r-colorspace)
20126 ("r-fracdiff" ,r-fracdiff)
20127 ("r-ggplot2" ,r-ggplot2)
20128 ("r-lmtest" ,r-lmtest)
20129 ("r-magrittr" ,r-magrittr)
20132 ("r-rcpparmadillo" ,r-rcpparmadillo)
20133 ("r-timedate" ,r-timedate)
20134 ("r-tseries" ,r-tseries)
20138 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20139 (home-page "https://pkg.robjhyndman.com/forecast/")
20140 (synopsis "Forecasting functions for time series and linear models")
20142 "This package provides methods and tools for displaying and analysing
20143 univariate time series forecasts including exponential smoothing via state
20144 space models and automatic ARIMA modelling.")
20145 (license license:gpl3)))
20147 (define-public r-xmisc
20154 (uri (cran-uri "Xmisc" version))
20157 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20158 (properties `((upstream-name . "Xmisc")))
20159 (build-system r-build-system)
20160 (home-page "https://cran.r-project.org/package=Xmisc")
20162 "Xiaobei's miscellaneous classes and functions")
20164 "This package provides Xiaobei's miscellaneous classes and functions,
20165 which are useful when developing R packages for @dfn{object oriented
20166 programming} (OOP) using R Reference Class.")
20167 (license license:gpl2+)))
20169 (define-public r-proxyc
20176 (uri (cran-uri "proxyC" version))
20179 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20180 (properties `((upstream-name . "proxyC")))
20181 (build-system r-build-system)
20183 `(("r-matrix" ,r-matrix)
20185 ("r-rcpparmadillo" ,r-rcpparmadillo)
20186 ("r-rcppparallel" ,r-rcppparallel)))
20187 (home-page "https://cran.r-project.org/package=proxyC")
20188 (synopsis "Compute proximity in large sparse matrices")
20190 "This package provides efficient tools to compute the proximity between
20191 rows or columns of large matrices. Functions are optimised for large sparse
20192 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20193 similarity/distance measures, computation of correlation, cosine similarity
20194 and Euclidean distance is particularly fast.")
20195 (license license:gpl3)))
20197 (define-public r-isocodes
20199 (name "r-isocodes")
20200 (version "2020.03.16")
20204 (uri (cran-uri "ISOcodes" version))
20207 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20208 (properties `((upstream-name . "ISOcodes")))
20209 (build-system r-build-system)
20210 (home-page "https://cran.r-project.org/package=ISOcodes")
20211 (synopsis "Selected ISO codes")
20213 "This package provides ISO language, territory, currency, script and
20214 character codes. It provides ISO 639 language codes, ISO 3166 territory
20215 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20216 character codes as well as the UN M.49 area codes.")
20217 (license license:gpl2)))
20219 (define-public r-stopwords
20221 (name "r-stopwords")
20226 (uri (cran-uri "stopwords" version))
20229 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20230 (properties `((upstream-name . "stopwords")))
20231 (build-system r-build-system)
20233 `(("r-desc" ,r-desc)
20234 ("r-isocodes" ,r-isocodes)
20235 ("r-usethis" ,r-usethis)))
20236 (home-page "https://github.com/quanteda/stopwords")
20237 (synopsis "Multilingual stopword lists")
20239 "This package provides multiple sources of stopwords, for use in text
20240 analysis and natural language processing.")
20241 (license license:expat)))
20243 (define-public r-spacyr
20250 (uri (cran-uri "spacyr" version))
20253 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20254 (properties `((upstream-name . "spacyr")))
20255 (build-system r-build-system)
20257 `(("r-data-table" ,r-data-table)
20258 ("r-reticulate" ,r-reticulate)))
20259 (home-page "https://spacyr.quanteda.io")
20260 (synopsis "R wrapper for the spaCy NLP library")
20262 "This package provides an R wrapper to the Python @dfn{natural language
20263 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20264 (license license:gpl3)))
20266 (define-public r-snowballc
20268 (name "r-snowballc")
20273 (uri (cran-uri "SnowballC" version))
20276 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20277 (properties `((upstream-name . "SnowballC")))
20278 (build-system r-build-system)
20279 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20280 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20282 "This package provides an R interface to the C @code{libstemmer} library
20283 that implements Porter's word stemming algorithm for collapsing words to a
20284 common root to aid comparison of vocabulary. Currently supported languages
20285 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20286 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20287 (license license:bsd-3)))
20289 (define-public r-quanteda
20291 (name "r-quanteda")
20296 (uri (cran-uri "quanteda" version))
20299 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20300 (properties `((upstream-name . "quanteda")))
20301 (build-system r-build-system)
20303 `(("r-data-table" ,r-data-table)
20304 ("r-digest" ,r-digest)
20305 ("r-extrafont" ,r-extrafont)
20306 ("r-fastmatch" ,r-fastmatch)
20307 ("r-ggplot2" ,r-ggplot2)
20308 ("r-ggrepel" ,r-ggrepel)
20309 ("r-jsonlite" ,r-jsonlite)
20310 ("r-magrittr" ,r-magrittr)
20311 ("r-matrix" ,r-matrix)
20312 ("r-network" ,r-network)
20313 ("r-proxyc" ,r-proxyc)
20315 ("r-rcpparmadillo" ,r-rcpparmadillo)
20316 ("r-rcppparallel" ,r-rcppparallel)
20318 ("r-snowballc" ,r-snowballc)
20319 ("r-stopwords" ,r-stopwords)
20320 ("r-stringi" ,r-stringi)
20322 ("r-yaml" ,r-yaml)))
20324 `(("r-knitr" ,r-knitr)))
20325 (home-page "https://quanteda.io")
20326 (synopsis "Quantitative analysis of textual data")
20328 "This package provides a fast, flexible, and comprehensive framework for
20329 quantitative text analysis in R. It provides functionality for corpus
20330 management, creating and manipulating tokens and ngrams, exploring keywords in
20331 context, forming and manipulating sparse matrices of documents by features and
20332 feature co-occurrences, analyzing keywords, computing feature similarities and
20333 distances, applying content dictionaries, applying supervised and unsupervised
20334 machine learning, visually representing text and text analyses, and more.")
20335 (license license:gpl3)))
20337 (define-public r-topicmodels
20339 (name "r-topicmodels")
20344 (uri (cran-uri "topicmodels" version))
20347 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20348 (properties `((upstream-name . "topicmodels")))
20349 (build-system r-build-system)
20353 `(("r-modeltools" ,r-modeltools)
20356 (home-page "https://cran.r-project.org/package=topicmodels")
20357 (synopsis "Topic models")
20359 "This package provides an interface to the C code for @dfn{Latent
20360 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20361 David M. Blei and co-authors and the C++ code for fitting LDA models using
20362 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20363 (license license:gpl2)))
20365 (define-public r-stm
20372 (uri (cran-uri "stm" version))
20375 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20376 (properties `((upstream-name . "stm")))
20377 (build-system r-build-system)
20379 `(("r-data-table" ,r-data-table)
20380 ("r-glmnet" ,r-glmnet)
20382 ("r-matrix" ,r-matrix)
20383 ("r-matrixstats" ,r-matrixstats)
20384 ("r-quadprog" ,r-quadprog)
20385 ("r-quanteda" ,r-quanteda)
20387 ("r-rcpparmadillo" ,r-rcpparmadillo)
20389 ("r-stringr" ,r-stringr)))
20390 (home-page "http://www.structuraltopicmodel.com/")
20391 (synopsis "Estimation of the Structural Topic Model")
20393 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20394 topic models with document-level covariates. The package also includes tools
20395 for model selection, visualization, and estimation of topic-covariate
20397 (license license:expat)))
20399 (define-public r-polycor
20406 (uri (cran-uri "polycor" version))
20409 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20410 (properties `((upstream-name . "polycor")))
20411 (build-system r-build-system)
20413 `(("r-matrix" ,r-matrix)
20414 ("r-mvtnorm" ,r-mvtnorm)))
20415 (home-page "https://r-forge.r-project.org/projects/polycor/")
20416 (synopsis "Polychoric and polyserial correlations")
20418 "This package provides tools to compute polychoric and polyserial
20419 correlations by quick \"two-step\" methods or ML, optionally with standard
20420 errors; tetrachoric and biserial correlations are special cases.")
20421 (license license:gpl2+)))
20423 (define-public r-msm
20430 (uri (cran-uri "msm" version))
20433 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20434 (properties `((upstream-name . "msm")))
20435 (build-system r-build-system)
20437 `(("r-expm" ,r-expm)
20438 ("r-mvtnorm" ,r-mvtnorm)
20439 ("r-survival" ,r-survival)))
20440 (home-page "https://github.com/chjackson/msm")
20441 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20443 "This package provides functions for fitting continuous-time Markov and
20444 hidden Markov multi-state models to longitudinal data. It was designed for
20445 processes observed at arbitrary times in continuous time (panel data) but some
20446 other observation schemes are supported. Both Markov transition rates and the
20447 hidden Markov output process can be modelled in terms of covariates, which may
20448 be constant or piecewise-constant in time.")
20449 (license license:gpl2+)))
20451 (define-public r-ltm
20458 (uri (cran-uri "ltm" version))
20461 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20462 (properties `((upstream-name . "ltm")))
20463 (build-system r-build-system)
20465 `(("r-mass" ,r-mass)
20467 ("r-polycor" ,r-polycor)))
20468 (home-page "https://github.com/drizopoulos/ltm")
20469 (synopsis "Latent trait models under IRT")
20471 "This is a package supporting the analysis of multivariate dichotomous
20472 and polytomous data using latent trait models under the Item Response Theory
20473 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20474 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20476 (license license:gpl2+)))
20478 (define-public r-mi
20485 (uri (cran-uri "mi" version))
20488 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20489 (properties `((upstream-name . "mi")))
20490 (build-system r-build-system)
20493 ("r-matrix" ,r-matrix)))
20494 (home-page "http://www.stat.columbia.edu/~gelman/")
20495 (synopsis "Missing data imputation and model checking")
20497 "This package provides functions for data manipulation, imputing missing
20498 values in an approximate Bayesian framework, diagnostics of the models used to
20499 generate the imputations, confidence-building mechanisms to validate some of
20500 the assumptions of the imputation algorithm, and functions to analyze multiply
20501 imputed data sets with the appropriate degree of sampling uncertainty.")
20502 (license license:gpl2+)))
20504 (define-public r-matrixcalc
20506 (name "r-matrixcalc")
20511 (uri (cran-uri "matrixcalc" version))
20514 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20515 (properties `((upstream-name . "matrixcalc")))
20516 (build-system r-build-system)
20517 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20518 (synopsis "Collection of functions for matrix calculations")
20520 "This package provides a collection of functions to support matrix
20521 calculations for probability, econometric and numerical analysis. There are
20522 additional functions that are comparable to APL functions which are useful for
20523 actuarial models such as pension mathematics.")
20524 (license license:gpl2+)))
20526 (define-public r-sem
20533 (uri (cran-uri "sem" version))
20536 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20537 (properties `((upstream-name . "sem")))
20538 (build-system r-build-system)
20540 `(("r-boot" ,r-boot)
20542 ("r-matrixcalc" ,r-matrixcalc)
20544 (home-page "https://cran.r-project.org/package=sem")
20545 (synopsis "Structural equation models")
20547 "This package provides functions for fitting general linear structural
20548 equation models (with observed and latent variables) using the RAM approach,
20549 and for fitting structural equations in observed-variable models by two-stage
20551 (license license:gpl2+)))
20553 (define-public r-semtools
20555 (name "r-semtools")
20560 (uri (cran-uri "semTools" version))
20563 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20564 (properties `((upstream-name . "semTools")))
20565 (build-system r-build-system)
20567 `(("r-lavaan" ,r-lavaan)))
20568 (home-page "https://github.com/simsem/semTools/wiki")
20569 (synopsis "Useful tools for structural equation modeling")
20571 "This package provides useful tools for structural equation modeling.")
20572 (license license:gpl2+)))
20574 (define-public r-regsem
20581 (uri (cran-uri "regsem" version))
20584 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20585 (properties `((upstream-name . "regsem")))
20586 (build-system r-build-system)
20588 `(("r-lavaan" ,r-lavaan)
20590 ("r-rcpparmadillo" ,r-rcpparmadillo)
20591 ("r-rsolnp" ,r-rsolnp)))
20592 (home-page "https://cran.r-project.org/package=regsem")
20593 (synopsis "Regularized structural equation modeling")
20595 "This package uses both ridge and lasso penalties (and extensions) to
20596 penalize specific parameters in structural equation models. The package
20597 offers additional cost functions, cross validation, and other extensions
20598 beyond traditional structural equation models. It also contains a function to
20599 perform @dfn{exploratory mediation} (XMed).")
20600 (license license:gpl2+)))
20602 (define-public r-stanheaders
20604 (name "r-stanheaders")
20605 (version "2.21.0-6")
20609 (uri (cran-uri "StanHeaders" version))
20612 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20613 (properties `((upstream-name . "StanHeaders")))
20614 (build-system r-build-system)
20615 (inputs `(("pandoc" ,pandoc)))
20617 `(("r-rcppeigen" ,r-rcppeigen)
20618 ("r-rcppparallel" ,r-rcppparallel)))
20620 `(("gfortran" ,gfortran)
20621 ("r-knitr" ,r-knitr))) ; for vignettes
20622 (home-page "https://mc-stan.org/")
20623 (synopsis "C++ header files for Stan")
20625 "The C++ header files of the Stan project are provided by this package.
20626 There is a shared object containing part of the @code{CVODES} library, but it
20627 is not accessible from R. @code{r-stanheaders} is only useful for developers
20628 who want to utilize the @code{LinkingTo} directive of their package's
20629 DESCRIPTION file to build on the Stan library without incurring unnecessary
20632 The Stan project develops a probabilistic programming language that implements
20633 full or approximate Bayesian statistical inference via Markov Chain Monte
20634 Carlo or variational methods and implements (optionally penalized) maximum
20635 likelihood estimation via optimization. The Stan library includes an advanced
20636 automatic differentiation scheme, templated statistical and linear algebra
20637 functions that can handle the automatically differentiable scalar types (and
20638 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20639 package provides user-facing R functions to parse, compile, test, estimate,
20640 and analyze Stan models.")
20641 (license license:bsd-3)))
20643 (define-public r-rpf
20650 (uri (cran-uri "rpf" version))
20653 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20654 (properties `((upstream-name . "rpf")))
20655 (build-system r-build-system)
20657 `(("r-lifecycle" ,r-lifecycle)
20658 ("r-mvtnorm" ,r-mvtnorm)
20660 ("r-rcppeigen" ,r-rcppeigen)))
20662 `(("r-knitr" ,r-knitr)))
20663 (home-page "https://github.com/jpritikin/rpf")
20664 (synopsis "Response probability functions")
20666 "The purpose of this package is to factor out logic and math common to
20667 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20668 core support code suitable for more specialized IRT packages to build upon.
20669 Complete access to optimized C functions is made available with
20670 @code{R_RegisterCCallable()}.")
20671 (license license:gpl3+)))
20673 (define-public r-openmx
20680 (uri (cran-uri "OpenMx" version))
20683 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20684 (properties `((upstream-name . "OpenMx")))
20685 (build-system r-build-system)
20688 ("r-digest" ,r-digest)
20690 ("r-matrix" ,r-matrix)
20692 ("r-rcppeigen" ,r-rcppeigen)
20694 ("r-stanheaders" ,r-stanheaders)))
20695 (native-inputs `(("gfortran" ,gfortran)))
20696 (home-page "http://openmx.ssri.psu.edu")
20697 (synopsis "Extended structural equation modelling")
20699 "This package allows for the estimation of a wide variety of advanced
20700 multivariate statistical models. It consists of a library of functions and
20701 optimizers that allow you to quickly and flexibly define an SEM model and
20702 estimate parameters given observed data.")
20703 (license license:asl2.0)))
20705 (define-public r-kutils
20712 (uri (cran-uri "kutils" version))
20715 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20716 (properties `((upstream-name . "kutils")))
20717 (build-system r-build-system)
20719 `(("r-foreign" ,r-foreign)
20720 ("r-openxlsx" ,r-openxlsx)
20722 ("r-runit" ,r-runit)
20723 ("r-xtable" ,r-xtable)))
20724 (home-page "https://cran.r-project.org/package=kutils")
20725 (synopsis "Project management tools")
20727 "This package provides tools for data importation, recoding, and
20728 inspection. There are functions to create new project folders, R code
20729 templates, create uniquely named output directories, and to quickly obtain a
20730 visual summary for each variable in a data frame. The main feature here is
20731 the systematic implementation of the \"variable key\" framework for data
20732 importation and recoding.")
20733 (license license:gpl2)))
20735 (define-public r-rockchalk
20737 (name "r-rockchalk")
20738 (version "1.8.144")
20742 (uri (cran-uri "rockchalk" version))
20745 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20746 (properties `((upstream-name . "rockchalk")))
20747 (build-system r-build-system)
20749 `(("r-cardata" ,r-cardata)
20750 ("r-kutils" ,r-kutils)
20752 ("r-mass" ,r-mass)))
20753 (home-page "https://cran.r-project.org/package=rockchalk")
20754 (synopsis "Regression estimation and presentation")
20756 "This package provides a collection of functions for interpretation and
20757 presentation of regression analysis. These functions are used to produce the
20758 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20759 includes regression diagnostics, regression tables, and plots of interactions
20760 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20761 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20762 fairly comprehensive overview.")
20763 (license license:gpl3+)))
20765 (define-public r-lisreltor
20767 (name "r-lisreltor")
20772 (uri (cran-uri "lisrelToR" version))
20775 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20776 (properties `((upstream-name . "lisrelToR")))
20777 (build-system r-build-system)
20778 (home-page "https://cran.r-project.org/package=lisrelToR")
20779 (synopsis "Import output from LISREL into R")
20781 "This is an unofficial package aimed at automating the import of LISREL
20783 (license license:gpl2)))
20785 (define-public r-bdgraph
20792 (uri (cran-uri "BDgraph" version))
20795 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20796 (properties `((upstream-name . "BDgraph")))
20797 (build-system r-build-system)
20799 `(("r-igraph" ,r-igraph)))
20800 (home-page "https://www.uva.nl/profile/a.mohammadi")
20801 (synopsis "Bayesian structure learning in graphical models")
20803 "This package provides statistical tools for Bayesian structure learning
20804 in undirected graphical models for continuous, discrete, and mixed data. It
20805 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20806 on a continuous-time birth-death process.")
20807 (license license:gpl2+)))
20809 (define-public r-d3network
20811 (name "r-d3network")
20812 (version "0.5.2.1")
20816 (uri (cran-uri "d3Network" version))
20819 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20820 (properties `((upstream-name . "d3Network")))
20821 (build-system r-build-system)
20823 `(("r-plyr" ,r-plyr)
20824 ("r-rjson" ,r-rjson)
20825 ("r-whisker" ,r-whisker)))
20826 (home-page "http://christophergandrud.github.io/d3Network/")
20827 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20829 "This package is intended to make it easy to create D3 JavaScript
20830 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20831 (license license:gpl3+)))
20833 (define-public r-qgraph
20840 (uri (cran-uri "qgraph" version))
20843 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20844 (properties `((upstream-name . "qgraph")))
20845 (build-system r-build-system)
20847 `(("r-abind" ,r-abind)
20848 ("r-bdgraph" ,r-bdgraph)
20849 ("r-colorspace" ,r-colorspace)
20850 ("r-corpcor" ,r-corpcor)
20851 ("r-d3network" ,r-d3network)
20852 ("r-dplyr" ,r-dplyr)
20853 ("r-fdrtool" ,r-fdrtool)
20854 ("r-ggplot2" ,r-ggplot2)
20855 ("r-ggraph" ,r-ggraph)
20856 ("r-glasso" ,r-glasso)
20857 ("r-gtools" ,r-gtools)
20858 ("r-hmisc" ,r-hmisc)
20860 ("r-igraph" ,r-igraph)
20862 ("r-lavaan" ,r-lavaan)
20863 ("r-matrix" ,r-matrix)
20864 ("r-pbapply" ,r-pbapply)
20867 ("r-psych" ,r-psych)
20869 ("r-reshape2" ,r-reshape2)
20870 ("r-tidygraph" ,r-tidygraph)))
20871 (home-page "http://sachaepskamp.com/qgraph/")
20872 (synopsis "Weighted network visualization and analysis")
20874 "This package implements tools for weighted network visualization and
20875 analysis, as well as Gaussian graphical model computation. It contains graph
20876 plotting methods, and tools for psychometric data visualization and graphical
20877 model estimation. See Epskamp et al. (2012)
20878 @url{doi:10.18637/jss.v048.i04}.")
20879 (license license:gpl2)))
20881 (define-public r-semplot
20888 (uri (cran-uri "semPlot" version))
20891 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20892 (properties `((upstream-name . "semPlot")))
20893 (build-system r-build-system)
20895 `(("r-colorspace" ,r-colorspace)
20896 ("r-corpcor" ,r-corpcor)
20897 ("r-igraph" ,r-igraph)
20898 ("r-lavaan" ,r-lavaan)
20899 ("r-lisreltor" ,r-lisreltor)
20900 ("r-openmx" ,r-openmx)
20902 ("r-qgraph" ,r-qgraph)
20903 ("r-regsem" ,r-regsem)
20904 ("r-rockchalk" ,r-rockchalk)
20907 (home-page "https://github.com/SachaEpskamp/semPlot")
20908 (synopsis "Unified visualizations of structural equation models")
20910 "Structural equation modeling (SEM) has a long history of representing
20911 models graphically as path diagrams. The semPlot package for R fills the gap
20912 between advanced, but time-consuming, graphical software and the limited
20913 graphics produced automatically by SEM software. In addition, semPlot offers
20914 more functionality than drawing path diagrams: it can act as a common ground
20915 for importing SEM results into R. Any result usable as input to semPlot can
20916 also be represented in any of the three popular SEM frame-works, as well as
20917 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20918 (license license:gpl2)))
20920 (define-public r-cdm
20927 (uri (cran-uri "CDM" version))
20930 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20931 (properties `((upstream-name . "CDM")))
20932 (build-system r-build-system)
20934 `(("r-mvtnorm" ,r-mvtnorm)
20935 ("r-polycor" ,r-polycor)
20937 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20939 "https://github.com/alexanderrobitzsch/CDM")
20940 (synopsis "Cognitive diagnosis modeling")
20942 "This package provides functions for cognitive diagnosis modeling and
20943 multidimensional item response modeling for dichotomous and polytomous item
20944 responses. It enables the estimation of the DINA and DINO model, the multiple
20945 group (polytomous) GDINA model, the multiple choice DINA model, the general
20946 diagnostic model (GDM), the structured latent class model (SLCA), and
20947 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20948 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20949 estimation and the package structure. For tutorials on how to use the CDM
20950 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20951 well as Ravand and Robitzsch (2015).")
20952 (license license:gpl2+)))
20954 (define-public r-tam
20961 (uri (cran-uri "TAM" version))
20964 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20965 (properties `((upstream-name . "TAM")))
20966 (build-system r-build-system)
20970 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20971 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20972 (synopsis "Test analysis modules")
20974 "This package includes tools for marginal maximum likelihood estimation
20975 and joint maximum likelihood estimation for unidimensional and
20976 multidimensional item response models. The package functionality covers the
20977 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20978 multi-faceted Rasch model, nominal item response model, structured latent
20979 class model, mixture distribution IRT models, and located latent class models.
20980 Latent regression models and plausible value imputation are also supported.")
20981 (license license:gpl2+)))
20983 (define-public r-erm
20990 (uri (cran-uri "eRm" version))
20993 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20994 (properties `((upstream-name . "eRm")))
20995 (build-system r-build-system)
20997 `(("r-colorspace" ,r-colorspace)
20998 ("r-lattice" ,r-lattice)
21000 ("r-matrix" ,r-matrix)
21001 ("r-psych" ,r-psych)))
21002 (native-inputs `(("gfortran" ,gfortran)))
21003 (home-page "https://cran.r-project.org/package=eRm")
21004 (synopsis "Extended Rasch modeling")
21006 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21007 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21008 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21009 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21010 data matrix. Additional features are the ML estimation of the person
21011 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21012 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21013 infit and outfit measures, ICC and other plots, automated stepwise item
21014 elimination, and a simulation module for various binary data matrices.")
21015 (license license:gpl3)))
21017 (define-public r-irtoys
21024 (uri (cran-uri "irtoys" version))
21027 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21028 (properties `((upstream-name . "irtoys")))
21029 (build-system r-build-system)
21033 (home-page "https://cran.r-project.org/package=irtoys")
21034 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21036 "This package provides a collection of functions useful in learning and
21037 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21038 programs. It provides basic CTT analysis, a simple common interface to the
21039 estimation of item parameters in IRT models for binary responses with three
21040 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21041 EAP, WLE, plausible values), item and person fit statistics, scaling
21042 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21043 array of parametric and non-parametric (kernel) plots. It estimates and plots
21044 Haberman's interaction model when all items are dichotomously scored.")
21045 (license license:gpl2+)))
21047 (define-public r-iheatmapr
21049 (name "r-iheatmapr")
21054 (uri (cran-uri "iheatmapr" version))
21057 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21058 (properties `((upstream-name . "iheatmapr")))
21059 (build-system r-build-system)
21061 `(("r-fastcluster" ,r-fastcluster)
21062 ("r-ggdendro" ,r-ggdendro)
21063 ("r-htmlwidgets" ,r-htmlwidgets)
21064 ("r-jsonlite" ,r-jsonlite)
21065 ("r-knitr" ,r-knitr)
21066 ("r-magrittr" ,r-magrittr)
21067 ("r-rcolorbrewer" ,r-rcolorbrewer)
21068 ("r-scales" ,r-scales)))
21070 `(("r-knitr" ,r-knitr)))
21071 (home-page "https://docs.ropensci.org/iheatmapr")
21072 (synopsis "Interactive, Complex Heatmaps")
21074 "iheatmapr is an R package for building complex, interactive heatmaps
21075 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21076 subplots along the rows or columns of the main heatmap add more information
21077 about each row or column. For example, a one column additional heatmap may
21078 indicate what group a particular row or column belongs to. Complex heatmaps
21079 may also include multiple side by side heatmaps which show different types of
21080 data for the same conditions. Interactivity can improve complex heatmaps by
21081 providing tooltips with information about each cell and enabling zooming into
21082 interesting features. iheatmapr uses the plotly library for interactivity.")
21083 (license license:expat)))
21085 (define-public r-packrat
21092 (uri (cran-uri "packrat" version))
21095 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21096 (properties `((upstream-name . "packrat")))
21097 (build-system r-build-system)
21098 (home-page "https://github.com/rstudio/packrat/")
21099 (synopsis "Dependency management R projects")
21101 "This package provides a dependency manager for R projects that allows
21102 you to manage the R packages your project depends on in an isolated, portable,
21103 and reproducible way.")
21104 (license license:gpl2)))
21106 (define-public r-rsconnect
21108 (name "r-rsconnect")
21113 (uri (cran-uri "rsconnect" version))
21116 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21117 (properties `((upstream-name . "rsconnect")))
21118 (build-system r-build-system)
21120 `(("r-curl" ,r-curl)
21121 ("r-digest" ,r-digest)
21122 ("r-jsonlite" ,r-jsonlite)
21123 ("r-openssl" ,r-openssl)
21124 ("r-packrat" ,r-packrat)
21125 ("r-rstudioapi" ,r-rstudioapi)
21126 ("r-yaml" ,r-yaml)))
21127 (home-page "https://github.com/rstudio/rsconnect")
21128 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21130 "This package provides a programmatic deployment interface for RPubs,
21131 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21132 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21133 (license license:gpl2)))
21135 ;; This package includes minified JavaScript files. When upgrading please
21136 ;; check that there are no new minified JavaScript files.
21137 (define-public r-dygraphs
21139 (name "r-dygraphs")
21140 (version "1.1.1.6")
21144 (uri (cran-uri "dygraphs" version))
21147 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21148 (properties `((upstream-name . "dygraphs")))
21149 (build-system r-build-system)
21151 `(#:modules ((guix build utils)
21152 (guix build r-build-system)
21156 (modify-phases %standard-phases
21157 (add-after 'unpack 'process-javascript
21158 (lambda* (#:key inputs #:allow-other-keys)
21159 (with-directory-excursion "inst/htmlwidgets/lib/"
21163 `(("dygraphs/dygraph-combined-dev.js"
21164 "dygraph-combined.js")
21165 (,(assoc-ref inputs "js-jquery")
21166 "jquery/jquery.min.js")
21167 (,(assoc-ref inputs "js-fquarter")
21168 "fquarter/moment-fquarter.min.js"))))
21169 (lambda (sources targets)
21170 (for-each (lambda (source target)
21171 (format #t "Processing ~a --> ~a~%"
21173 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21174 (call-with-output-file target
21176 (dump-port minified port)))))
21177 sources targets))))
21180 `(("uglify-js" ,uglify-js)
21181 ;; They actually use version 1.11.1, but this more recent version
21182 ;; should be just fine.
21186 (uri "https://code.jquery.com/jquery-1.12.4.js")
21189 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21193 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21194 "moment-fquarter/1.0.1/moment-fquarter.js"))
21197 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21199 `(("r-htmltools" ,r-htmltools)
21200 ("r-htmlwidgets" ,r-htmlwidgets)
21201 ("r-magrittr" ,r-magrittr)
21204 (home-page "https://github.com/rstudio/dygraphs")
21205 (synopsis "Interface to Dygraphs interactive time series charting library")
21207 "This package provides an R interface to the dygraphs JavaScript charting
21208 library (a copy of which is included in the package). It provides rich
21209 facilities for charting time-series data in R, including highly configurable
21210 series- and axis-display and interactive features like zoom/pan and
21211 series/point highlighting.")
21212 (license license:expat)))
21214 (define-public r-shinystan
21216 (name "r-shinystan")
21221 (uri (cran-uri "shinystan" version))
21224 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21225 (properties `((upstream-name . "shinystan")))
21226 (build-system r-build-system)
21228 `(("r-bayesplot" ,r-bayesplot)
21229 ("r-colourpicker" ,r-colourpicker)
21231 ("r-dygraphs" ,r-dygraphs)
21232 ("r-ggplot2" ,r-ggplot2)
21233 ("r-gridextra" ,r-gridextra)
21234 ("r-gtools" ,r-gtools)
21235 ("r-markdown" ,r-markdown)
21236 ("r-reshape2" ,r-reshape2)
21237 ("r-rsconnect" ,r-rsconnect)
21238 ("r-rstan" ,r-rstan)
21239 ("r-shiny" ,r-shiny)
21240 ("r-shinyjs" ,r-shinyjs)
21241 ("r-shinythemes" ,r-shinythemes)
21242 ("r-threejs" ,r-threejs)
21243 ("r-xtable" ,r-xtable)
21245 (home-page "https://mc-stan.org/")
21246 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21248 "This package provides a graphical user interface for interactive
21249 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21250 for analyzing a posterior sample. The interface is powered by the Shiny web
21251 application framework and works with the output of MCMC programs written in
21252 any programming language (and has extended functionality for Stan models fit
21253 using the @code{rstan} and @code{rstanarm} packages).")
21254 (license license:gpl3+)))
21256 (define-public r-rstantools
21258 (name "r-rstantools")
21263 (uri (cran-uri "rstantools" version))
21266 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21267 (properties `((upstream-name . "rstantools")))
21268 (build-system r-build-system)
21269 (inputs `(("pandoc" ,pandoc)))
21271 `(("r-desc" ,r-desc)
21273 ("r-rcppparallel" ,r-rcppparallel)))
21275 `(("r-knitr" ,r-knitr)))
21276 (home-page "https://mc-stan.org/rstantools/")
21277 (synopsis "Tools for developing R packages interfacing with Stan")
21279 "This package provides various tools for developers of R packages
21280 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21281 up the required package structure, S3 generics and default methods to unify
21282 function naming across Stan-based R packages, and vignettes with
21283 recommendations for developers.")
21284 (license license:gpl3+)))
21286 (define-public r-loo
21293 (uri (cran-uri "loo" version))
21295 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21296 (properties `((upstream-name . "loo")))
21297 (build-system r-build-system)
21299 `(("pandoc" ,pandoc)
21300 ("pandoc-citeproc" ,pandoc-citeproc)))
21302 `(("r-checkmate" ,r-checkmate)
21303 ("r-matrixstats" ,r-matrixstats)))
21305 `(("r-knitr" ,r-knitr)))
21306 (home-page "https://mc-stan.org/loo/")
21307 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21309 "This package provides an implementation of efficient approximate
21310 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21311 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21312 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21313 procedure for regularizing importance weights. As a byproduct of the
21314 calculations, we also obtain approximate standard errors for estimated
21315 predictive errors and for the comparison of predictive errors between models.
21316 The package also provides methods for using stacking and other model weighting
21317 techniques to average Bayesian predictive distributions.")
21318 (license license:gpl3+)))
21320 (define-public r-rstan
21327 (uri (cran-uri "rstan" version))
21330 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21331 (properties `((upstream-name . "rstan")))
21332 (build-system r-build-system)
21335 (modify-phases %standard-phases
21336 (add-before 'install 'set-timezone
21337 ;; This package is picky about timezones.
21338 (lambda* (#:key inputs #:allow-other-keys)
21339 (setenv "TZ" "UTC+1")
21341 (string-append (assoc-ref inputs "tzdata")
21342 "/share/zoneinfo"))
21345 `(("tzdata" ,tzdata-for-tests)
21347 ("r-knitr" ,r-knitr)))
21350 ("r-ggplot2" ,r-ggplot2)
21351 ("r-gridextra" ,r-gridextra)
21352 ("r-inline" ,r-inline)
21354 ("r-pkgbuild" ,r-pkgbuild)
21356 ("r-rcppeigen" ,r-rcppeigen)
21357 ("r-rcppparallel" ,r-rcppparallel)
21358 ("r-stanheaders" ,r-stanheaders)
21360 ("r-withr" ,r-withr)))
21361 (home-page "https://discourse.mc-stan.org/")
21362 (synopsis "R interface to Stan")
21364 "User-facing R functions are provided to parse, compile, test, estimate,
21365 and analyze Stan models by accessing the header-only Stan library provided by
21366 the StanHeaders package. The Stan project develops a probabilistic
21367 programming language that implements full Bayesian statistical inference via
21368 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21369 approximation, and (optionally penalized) maximum likelihood estimation via
21370 optimization. In all three cases, automatic differentiation is used to
21371 quickly and accurately evaluate gradients without burdening the user with the
21372 need to derive the partial derivatives.")
21373 (license license:gpl3+)))
21375 (define-public r-rstanarm
21377 (name "r-rstanarm")
21382 (uri (cran-uri "rstanarm" version))
21385 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21386 (properties `((upstream-name . "rstanarm")))
21387 (build-system r-build-system)
21389 `(("pandoc" ,pandoc)
21390 ("pandoc-citeproc" ,pandoc-citeproc)))
21392 `(("r-bayesplot" ,r-bayesplot)
21394 ("r-ggplot2" ,r-ggplot2)
21397 ("r-matrix" ,r-matrix)
21400 ("r-rcppeigen" ,r-rcppeigen)
21401 ("r-rcppparallel" ,r-rcppparallel)
21402 ("r-rstan" ,r-rstan)
21403 ("r-rstantools" ,r-rstantools)
21404 ("r-shinystan" ,r-shinystan)
21405 ("r-stanheaders" ,r-stanheaders)
21406 ("r-survival" ,r-survival)))
21408 `(("r-knitr" ,r-knitr)))
21409 (home-page "https://mc-stan.org/rstanarm/")
21410 (synopsis "Bayesian applied regression modeling via Stan")
21412 "This package estimates previously compiled regression models using the
21413 @code{rstan} package, which provides the R interface to the Stan C++ library
21414 for Bayesian estimation. Users specify models via the customary R syntax with
21415 a formula and @code{data.frame} plus some additional arguments for priors.")
21416 (license license:gpl3+)))
21418 (define-public r-kendall
21425 (uri (cran-uri "Kendall" version))
21428 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21429 (properties `((upstream-name . "Kendall")))
21430 (build-system r-build-system)
21432 `(("r-boot" ,r-boot)))
21434 `(("gfortran" ,gfortran)))
21435 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21436 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21438 "This package computes the Kendall rank correlation and Mann-Kendall
21440 (license license:gpl2+)))
21442 (define-public r-zyp
21445 (version "0.10-1.1")
21449 (uri (cran-uri "zyp" version))
21452 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21453 (properties `((upstream-name . "zyp")))
21454 (build-system r-build-system)
21456 `(("r-kendall" ,r-kendall)))
21457 (home-page "https://cran.r-project.org/web/packages/zyp/")
21458 (synopsis "Zhang + Yue-Pilon Trends Package")
21460 "This package contains an efficient implementation of Sen's slope
21461 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21462 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21464 (license license:lgpl2.1)))
21466 (define-public r-rlinsolve
21468 (name "r-rlinsolve")
21473 (uri (cran-uri "Rlinsolve" version))
21476 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21477 (properties `((upstream-name . "Rlinsolve")))
21478 (build-system r-build-system)
21480 `(("r-matrix" ,r-matrix)
21482 ("r-rcpparmadillo" ,r-rcpparmadillo)
21483 ("r-rdpack" ,r-rdpack)))
21484 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21485 (synopsis "Iterative solvers for (sparse) linear system of equations")
21487 "Solving a system of linear equations is one of the most fundamental
21488 computational problems for many fields of mathematical studies, such as
21489 regression problems from statistics or numerical partial differential
21490 equations. This package provides basic stationary iterative solvers such as
21491 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21492 Nonstationary, also known as Krylov subspace methods are also provided.
21493 Sparse matrix computation is also supported in that solving large and sparse
21494 linear systems can be manageable using the @code{Matrix} package along with
21495 @code{RcppArmadillo}.")
21496 (license license:gpl3+)))
21498 (define-public r-zvcv
21505 (uri (cran-uri "ZVCV" version))
21508 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21509 (properties `((upstream-name . "ZVCV")))
21510 (build-system r-build-system)
21512 `(("r-abind" ,r-abind)
21514 ("r-dplyr" ,r-dplyr)
21515 ("r-glmnet" ,r-glmnet)
21516 ("r-magrittr" ,r-magrittr)
21517 ("r-mvtnorm" ,r-mvtnorm)
21519 ("r-rcpparmadillo" ,r-rcpparmadillo)
21520 ("r-rlinsolve" ,r-rlinsolve)))
21521 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21522 (synopsis "Zero-Variance Control Variates")
21524 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21525 to reduce the variance of Monte Carlo estimators of expectations using the
21526 derivatives of the log target. Once the derivatives are available, the only
21527 additional computational effort is in solving a linear regression problem.
21528 This method has been extended to higher dimensions using regularisation. This
21529 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21530 samples, derivatives and function evaluations are available. Additional
21531 functions for applying ZV-CV to two estimators for the normalising constant of
21532 the posterior distribution in Bayesian statistics are also supplied.")
21533 (license license:gpl2+)))
21535 (define-public r-ztype
21542 (uri (cran-uri "ztype" version))
21545 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21546 (properties `((upstream-name . "ztype")))
21547 (build-system r-build-system)
21549 `(("r-assertthat" ,r-assertthat)
21550 ("r-dplyr" ,r-dplyr)
21551 ("r-ggplot2" ,r-ggplot2)
21552 ("r-lubridate" ,r-lubridate)
21553 ("r-magrittr" ,r-magrittr)
21554 ("r-rvest" ,r-rvest)
21555 ("r-stringr" ,r-stringr)))
21556 (home-page "https://cran.r-project.org/web/packages/ztype/")
21557 (synopsis "Run a Ztype game loaded with R functions")
21559 "How fast can you type R functions on your keyboard? Find out by running
21560 a @code{zty.pe} game: export R functions as instructions to type to destroy
21561 opponents' vessels.")
21562 (license license:gpl3)))
21564 (define-public r-zseq
21571 (uri (cran-uri "Zseq" version))
21574 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21575 (properties `((upstream-name . "Zseq")))
21576 (build-system r-build-system)
21578 `(("r-gmp" ,r-gmp)))
21579 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21580 (synopsis "Integer sequence generator")
21582 "This package generates well-known integer sequences. The @code{gmp}
21583 package is adopted for computing with arbitrarily large numbers. Every
21584 function has a hyperlink to its corresponding item in the @dfn{On-Line
21585 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21586 (license license:gpl3+)))
21588 (define-public r-isoband
21595 (uri (cran-uri "isoband" version))
21598 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21599 (properties `((upstream-name . "isoband")))
21600 (build-system r-build-system)
21602 `(("r-testthat" ,r-testthat)))
21604 `(("r-knitr" ,r-knitr)))
21605 (home-page "https://github.com/wilkelab/isoband")
21606 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21608 "This package provides a fast C++ implementation to generate contour
21609 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21610 containing elevation data.")
21611 (license license:expat)))
21613 (define-public r-ppcor
21620 (uri (cran-uri "ppcor" version))
21623 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21624 (properties `((upstream-name . "ppcor")))
21625 (build-system r-build-system)
21627 `(("r-mass" ,r-mass)))
21628 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21629 (synopsis "Partial and semi-partial correlation")
21631 "This package provides users not only with a function to readily
21632 calculate the higher-order partial and semi-partial correlations but also with
21633 statistics and p-values of the correlation coefficients.")
21634 (license license:gpl2)))
21636 (define-public r-hrbrthemes
21638 (name "r-hrbrthemes")
21643 (uri (cran-uri "hrbrthemes" version))
21645 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21646 (properties `((upstream-name . "hrbrthemes")))
21647 (build-system r-build-system)
21649 `(("r-extrafont" ,r-extrafont)
21650 ("r-gdtools" ,r-gdtools)
21651 ("r-ggplot2" ,r-ggplot2)
21652 ("r-htmltools" ,r-htmltools)
21653 ("r-knitr" ,r-knitr)
21654 ("r-magrittr" ,r-magrittr)
21655 ("r-rmarkdown" ,r-rmarkdown)
21656 ("r-scales" ,r-scales)))
21658 `(("r-knitr" ,r-knitr)))
21659 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21660 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21662 "This package provides a compilation of extra @code{ggplot2} themes,
21663 scales and utilities, including a spell check function for plot label fields
21664 and an overall emphasis on typography.")
21665 (license license:expat)))
21667 (define-public r-crochet
21674 (uri (cran-uri "crochet" version))
21677 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21678 (build-system r-build-system)
21680 `(("r-knitr" ,r-knitr)))
21681 (home-page "https://github.com/agrueneberg/crochet")
21682 (synopsis "Implementation Helper for Matrix-Like Types")
21684 "Functions to help implement the extraction / subsetting / indexing
21685 function @code{[} and replacement function @code{[<-} of custom matrix-like
21686 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21687 as possible (with tests to prove it).")
21688 (license license:expat)))
21690 (define-public r-boa
21693 (version "1.1.8-2")
21697 (uri (cran-uri "boa" version))
21700 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21701 (properties `((upstream-name . "boa")))
21702 (build-system r-build-system)
21703 (home-page "http://www.jstatsoft.org/v21/i11")
21704 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21706 "This package provides a menu-driven program and library of functions for
21707 carrying out convergence diagnostics and statistical and graphical analysis of
21708 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21709 (license license:gpl2+)))
21711 (define-public r-httpcode
21713 (name "r-httpcode")
21717 (uri (cran-uri "httpcode" version))
21720 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21721 (build-system r-build-system)
21722 (home-page "https://github.com/sckott/httpcode")
21723 (synopsis "HTTP status code helper")
21724 (description "@code{httpcode} provides functionality for finding and
21725 explaining the meaning of @code{HTTP} status codes. Functions are included for
21726 searching for codes by full or partial number, by message, and to get
21727 appropriate dog and cat images for many status codes.")
21728 (license license:expat)))
21730 (define-public r-latex2exp
21732 (name "r-latex2exp")
21736 (uri (cran-uri "latex2exp" version))
21739 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21740 (build-system r-build-system)
21742 `(("r-stringr" ,r-stringr)
21743 ("r-magrittr", r-magrittr)))
21744 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21745 (synopsis "Use LaTeX expressions in plots")
21746 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21747 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21748 rendered as text, axis labels, etc. throughout R's plotting system.")
21749 (license license:expat)))
21751 (define-public r-oai
21757 (uri (cran-uri "oai" version))
21760 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21761 (build-system r-build-system)
21763 `(("r-xml2" ,r-xml2)
21766 ("r-stringr" ,r-stringr)
21767 ("r-tibble" ,r-tibble)))
21768 (home-page "https://github.com/ropensci/oai/")
21769 (synopsis "General purpose OAI-PMH services client")
21770 (description "@code{oai} provides a general purpose client to work with
21771 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21772 service. Functions are provided to work with the OAI-PMH verbs:
21773 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21774 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21775 (license license:expat)))
21777 (define-public r-argon2
21784 (uri (cran-uri "argon2" version))
21787 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21788 (properties `((upstream-name . "argon2")))
21789 (build-system r-build-system)
21790 (home-page "https://github.com/wrathematics/argon2")
21791 (synopsis "Secure password hashing based on the argon2 algorithm")
21793 "This package provides utilities for secure password hashing via the
21794 argon2 algorithm.")
21795 (license license:bsd-2)))
21797 (define-public r-getpass
21804 (uri (cran-uri "getPass" version))
21807 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21808 (properties `((upstream-name . "getPass")))
21809 (build-system r-build-system)
21811 `(("r-rstudioapi" ,r-rstudioapi)))
21812 (home-page "https://github.com/wrathematics/getPass")
21813 (synopsis "Masked user input")
21815 "This package provides a micro-package for reading \"passwords\", i.e.
21816 reading user input with masking, so that the input is not displayed as it is
21817 typed. Currently, RStudio, the command line (every OS), and any platform
21818 where tcltk is present are supported.")
21819 (license license:bsd-2)))
21821 (define-public r-remoter
21828 (uri (cran-uri "remoter" version))
21831 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21832 (properties `((upstream-name . "remoter")))
21833 (build-system r-build-system)
21835 `(("r-argon2" ,r-argon2)
21836 ("r-getpass" ,r-getpass)
21837 ("r-pbdzmq" ,r-pbdzmq)
21839 (home-page "https://github.com/RBigData/remoter")
21840 (synopsis "Control a remote R session from a local one")
21842 "This package provides a set of utilities for client/server computing
21843 with R, controlling a remote R session (the server) from a local one (the
21845 (license license:bsd-2)))
21847 (define-public r-asd
21854 (uri (cran-uri "asd" version))
21857 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21858 (properties `((upstream-name . "asd")))
21859 (build-system r-build-system)
21861 `(("r-mvtnorm" ,r-mvtnorm)))
21862 (home-page "https://cran.r-project.org/web/packages/asd")
21863 (synopsis "Simulations for Adaptive Seamless Designs")
21865 "This package provdes means to run simulations for adaptive seamless
21866 designs with and without early outcomes for treatment selection and
21867 subpopulation type designs.")
21868 (license license:gpl3)))
21870 (define-public r-nbconvertr
21872 (name "r-nbconvertr")
21877 (uri (cran-uri "nbconvertR" version))
21880 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21881 (properties `((upstream-name . "nbconvertR")))
21882 (build-system r-build-system)
21884 `(("jupyter" ,python-nbconvert)
21885 ("pandoc" ,pandoc)))
21886 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21887 (synopsis "Vignette engine wrapping Jupyter notebooks")
21889 "This package calls the Jupyter script @code{nbconvert} to create
21890 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21891 containing rich text, code, and its output. Code cells can be edited and
21892 evaluated interactively.")
21893 (license license:gpl3)))
21895 (define-public r-bridgesampling
21897 (name "r-bridgesampling")
21902 (uri (cran-uri "bridgesampling" version))
21905 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21907 `((upstream-name . "bridgesampling")))
21908 (build-system r-build-system)
21910 `(("r-brobdingnag" ,r-brobdingnag)
21912 ("r-matrix" ,r-matrix)
21913 ("r-mvtnorm" ,r-mvtnorm)
21914 ("r-scales" ,r-scales)
21915 ("r-stringr" ,r-stringr)))
21917 `(("r-knitr" ,r-knitr)))
21918 (home-page "https://github.com/quentingronau/bridgesampling")
21919 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21921 "This package provides functions for estimating marginal likelihoods,
21922 Bayes factors, posterior model probabilities, and normalizing constants in
21923 general, via different versions of bridge sampling.")
21924 (license license:gpl2+)))
21926 (define-public r-tea
21933 (uri (cran-uri "tea" version))
21936 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21938 `((upstream-name . "tea")))
21939 (build-system r-build-system)
21941 `(("r-matrix" ,r-matrix)))
21942 (home-page "https://cran.r-project.org/web/packages/tea/")
21943 (synopsis "Threshold estimation approaches")
21945 "This package provides different approaches for selecting the threshold
21946 in generalized Pareto distributions. Most of them are based on minimizing the
21947 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21948 Others are heuristically motivated by searching for stable sample paths, i.e.
21949 a nearly constant region of the tail index estimator with respect to k, which
21950 is the number of data in the tail. The third class is motivated by graphical
21951 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21952 is also implemented here.")
21953 (license license:gpl3)))
21955 (define-public r-awsmethods
21957 (name "r-awsmethods")
21962 (uri (cran-uri "awsMethods" version))
21965 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21967 `((upstream-name . "awsMethods")))
21968 (build-system r-build-system)
21969 (home-page "http://www.wias-berlin.de/software/imaging/")
21970 (synopsis "Class and methods definitions")
21972 "This package defines the generic method @code{extract} and provides
21973 @code{openMP} support as needed in several packages like
21974 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21975 (license license:gpl2+)))
21977 (define-public r-aws
21984 (uri (cran-uri "aws" version))
21987 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
21989 `((upstream-name . "aws")))
21990 (build-system r-build-system)
21992 `(("r-awsmethods" ,r-awsmethods)
21995 `(("gfortran" ,gfortran)))
21996 (home-page "https://cran.r-project.org/web/packages/aws/")
21997 (synopsis "Adaptive weights smoothing")
21999 "This package provides a collection of R-functions implementing adaptive
22000 smoothing procedures in 1D, 2D and 3D. This includes the
22001 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22002 Confidence Intervals} (ICI), variational approaches, and a non-local means
22004 (license license:gpl2+)))
22006 (define-public r-sgloptim
22008 (name "r-sgloptim")
22013 (uri (cran-uri "sglOptim" version))
22016 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22018 `((upstream-name . "sglOptim")))
22019 (build-system r-build-system)
22022 ("r-doparallel" ,r-doparallel)
22023 ("r-foreach" ,r-foreach)
22024 ("r-matrix" ,r-matrix)
22026 ("r-rcpparmadillo" ,r-rcpparmadillo)
22027 ("r-rcppprogress" ,r-rcppprogress)))
22029 `(("r-knitr" ,r-knitr)))
22030 (home-page "https://github.com/nielsrhansen/sglOptim")
22031 (synopsis "Generic sparse group Lasso solver")
22033 "This package provides a fast generic solver for sparse group lasso
22034 optimization problems. The loss (objective) function must be defined in a C++
22035 module. The optimization problem is solved using a coordinate gradient
22036 descent algorithm. Convergence of the algorithm is established and the
22037 algorithm is applicable to a broad class of loss functions. Use of parallel
22038 computing for cross validation and subsampling is supported through the
22039 @code{foreach} and @code{doParallel} packages.")
22040 (license license:gpl2+)))
22042 (define-public r-grouped
22049 (uri (cran-uri "grouped" version))
22052 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22054 `((upstream-name . "grouped")))
22055 (build-system r-build-system)
22057 `(("r-mass" ,r-mass)))
22058 (home-page "https://cran.r-project.org/web/packages/grouped/")
22059 (synopsis "Regression analysis of grouped and coarse data")
22061 "This package provides regression models for grouped and coarse data,
22062 under the coarsened at random assumption.")
22063 (license license:gpl2+)))
22065 (define-public r-stam
22072 (uri (cran-uri "stam" version))
22075 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22077 `((upstream-name . "stam")))
22078 (build-system r-build-system)
22082 (home-page "https://cran.r-project.org/web/packages/stam")
22083 (synopsis "Spatio-temporal analysis and modelling")
22085 "This package provides various methods to conduct Spatio-Temporal
22086 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22087 Inferred Spatio-Temporal Modelling.")
22088 (license license:gpl2+)))
22090 (define-public r-dcv
22097 (uri (cran-uri "dcv" version))
22100 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22102 `((upstream-name . "dcv")))
22103 (build-system r-build-system)
22105 `(("r-lmtest" ,r-lmtest)))
22106 (home-page "https://cran.r-project.org/web/packages/dcv/")
22107 (synopsis "Conventional cross-validation statistics for climate-growth model")
22109 "This package performs several conventional cross-validation statistical
22110 methods for climate-growth model in the climate reconstruction from tree
22111 rings, including Sign Test statistic, Reduction of Error statistic, Product
22112 Mean Test, Durbin-Watson statistic etc.")
22113 (license license:gpl2)))
22115 (define-public r-rcdd
22122 (uri (cran-uri "rcdd" version))
22125 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22127 `((upstream-name . "rcdd")))
22128 (build-system r-build-system)
22131 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22132 (synopsis "Computational geometry")
22134 "This package converts back and forth between two representations of a
22135 convex polytope: as solution of a set of linear equalities and inequalities
22136 and as convex hull of set of points and rays. Also does linear programming
22137 and redundant generator elimination. All functions can use exact
22138 infinite-precision rational arithmetic.")
22139 (license license:gpl2)))
22141 (define-public r-rxnat
22148 (uri (cran-uri "Rxnat" version))
22151 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22153 `((upstream-name . "Rxnat")))
22154 (build-system r-build-system)
22156 `(("r-dplyr" ,r-dplyr)
22158 ("r-rcurl" ,r-rcurl)))
22160 `(("r-knitr" ,r-knitr)))
22161 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22162 (synopsis "Queries and extracts images from neuroimaging datasets")
22164 "This package allows communication with the Extensible Neuroimaging
22165 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22167 (license license:gpl2)))
22169 (define-public r-rserve
22176 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22177 version ".tar.gz"))
22180 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22181 (build-system r-build-system)
22183 `(("r-checkmate" ,r-checkmate)
22185 ("r-jsonlite" ,r-jsonlite)
22186 ("r-knitr" ,r-knitr)
22189 ("r-uuid" ,r-uuid)))
22191 `(("openssl" ,openssl)
22193 (home-page "https://github.com/s-u/Rserve")
22195 "Server providing access to R from many languages and systems")
22197 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22198 binary requests to be sent to R. Every connection has a separate workspace
22199 and working directory. Client-side implementations are available for popular
22200 languages such as C/C++ and Java, allowing any application to use facilities
22201 of R without the need of linking to R code. Rserve supports remote
22202 connection, user authentication and file transfer. A simple R client is
22203 included in this package as well.")
22204 (license license:gpl2)))
22206 (define-public r-brms
22213 (uri (cran-uri "brms" version))
22216 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22217 (properties `((upstream-name . "brms")))
22218 (build-system r-build-system)
22220 `(("r-abind" ,r-abind)
22221 ("r-backports" ,r-backports)
22222 ("r-bayesplot" ,r-bayesplot)
22223 ("r-bridgesampling" ,r-bridgesampling)
22225 ("r-future" ,r-future)
22226 ("r-ggplot2" ,r-ggplot2)
22229 ("r-matrix" ,r-matrix)
22230 ("r-matrixstats" ,r-matrixstats)
22232 ("r-nleqslv" ,r-nleqslv)
22235 ("r-rstan" ,r-rstan)
22236 ("r-rstantools" ,r-rstantools)
22237 ("r-shinystan" ,r-shinystan)))
22238 (native-inputs `(("r-knitr" ,r-knitr)))
22240 "https://github.com/paul-buerkner/brms")
22242 "Bayesian Regression Models using 'Stan'")
22244 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22245 using 'Stan' for full Bayesian inference. A wide range of distributions and
22246 link functions are supported, allowing users to fit -- among others -- linear,
22247 robust linear, count data, survival, response times, ordinal, zero-inflated,
22248 hurdle, and even self-defined mixture models all in a multilevel context.
22249 Further modeling options include non-linear and smooth terms, auto-correlation
22250 structures, censored data, meta-analytic standard errors, and quite a few
22251 more. In addition, all parameters of the response distribution can be
22252 predicted in order to perform distributional regression. Prior specifications
22253 are flexible and explicitly encourage users to apply prior distributions that
22254 actually reflect their beliefs. Model fit can easily be assessed and compared
22255 with posterior predictive checks and leave-one-out cross-validation.")
22256 (license license:gpl2)))
22258 (define-public r-mstate
22265 (uri (cran-uri "mstate" version))
22268 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22269 (properties `((upstream-name . "mstate")))
22270 (build-system r-build-system)
22272 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22273 ("r-survival" ,r-survival)))
22275 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22277 "Data Preparation, Estimation and Prediction in Multi-State Models")
22279 "Contains functions for data preparation, descriptives, hazard estimation
22280 and prediction with Aalen-Johansen or simulation in competing risks and
22281 multi-state models.")
22282 (license license:gpl2+)))
22284 (define-public r-scatterpie
22286 (name "r-scatterpie")
22291 (uri (cran-uri "scatterpie" version))
22294 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22295 (properties `((upstream-name . "scatterpie")))
22296 (build-system r-build-system)
22298 `(("r-ggforce" ,r-ggforce)
22299 ("r-ggplot2" ,r-ggplot2)
22300 ("r-rlang" ,r-rlang)
22301 ("r-rvcheck" ,r-rvcheck)
22302 ("r-tidyr" ,r-tidyr)))
22304 `(("r-knitr" ,r-knitr)))
22305 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22306 (synopsis "Scatter pie plot")
22308 "This package creates scatterpie plots, especially useful for plotting
22310 (license license:artistic2.0)))
22312 (define-public r-boruta
22319 (uri (cran-uri "Boruta" version))
22322 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22323 (properties `((upstream-name . "Boruta")))
22324 (build-system r-build-system)
22325 (propagated-inputs `(("r-ranger" ,r-ranger)))
22326 (home-page "https://gitlab.com/mbq/Boruta/")
22327 (synopsis "Wrapper algorithm for all relevant feature selection")
22329 "This package provides an all relevant feature selection wrapper
22330 algorithm. It finds relevant features by comparing original attributes'
22331 importance with importance achievable at random, estimated using their
22332 permuted copies (shadows).")
22333 (license license:gpl2+)))
22335 (define-public r-directlabels
22337 (name "r-directlabels")
22338 (version "2020.6.17")
22342 (uri (cran-uri "directlabels" version))
22345 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22346 (build-system r-build-system)
22348 `(("r-quadprog" ,r-quadprog)))
22350 `(("r-knitr" ,r-knitr)))
22351 (home-page "http://directlabels.r-forge.r-project.org/")
22352 (synopsis "Direct labels for multicolor plots")
22354 "This package provides an extensible framework for automatically placing
22355 direct labels onto multicolor plots. Label positions are described using
22356 positioning methods that can be re-used across several different plots. There
22357 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22358 inferring an appropriate positioning method.")
22359 (license license:gpl3)))
22361 (define-public r-lsd
22368 (uri (cran-uri "LSD" version))
22370 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22371 (properties `((upstream-name . "LSD")))
22372 (build-system r-build-system)
22373 (home-page "https://cran.r-project.org/web/packages/LSD/")
22374 (synopsis "Lots of superior depictions tool creates colorful plots")
22376 "This package creates lots of colorful plots in a multitude of variations.
22377 Try a demo of the LSD by running @code{demotour()}.")
22379 (license (list license:gpl2 license:gpl3))))
22381 (define-public r-fourcseq
22383 (name "r-fourcseq")
22388 (uri (bioconductor-uri "FourCSeq" version))
22390 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22391 (properties `((upstream-name . "FourCSeq")))
22392 (build-system r-build-system)
22394 `(("r-biobase" ,r-biobase)
22395 ("r-biostrings" ,r-biostrings)
22396 ("r-deseq2" ,r-deseq2)
22398 ("r-genomicalignments" ,r-genomicalignments)
22399 ("r-genomicranges" ,r-genomicranges)
22400 ("r-ggbio" ,r-ggbio)
22401 ("r-ggplot2" ,r-ggplot2)
22402 ("r-gtools" ,r-gtools)
22404 ("r-matrix" ,r-matrix)
22405 ("r-reshape2" ,r-reshape2)
22406 ("r-rsamtools" ,r-rsamtools)
22407 ("r-rtracklayer" ,r-rtracklayer)
22408 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22410 `(("r-knitr" ,r-knitr)))
22412 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22413 (synopsis "Analysis of multiplexed 4C sequencing data")
22415 "This package is an R package dedicated to the analysis of (multiplexed)
22416 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22417 interactions between DNA elements and identify differential interactions
22418 between conditions. The statistical analysis in R starts with individual bam
22419 files for each sample as inputs. To obtain these files, the package contains
22420 a Python script to demultiplex libraries and trim off primer sequences. With
22421 a standard alignment software the required bam files can be then be
22423 (license license:gpl3+)))
22425 (define-public r-phylogram
22427 (name "r-phylogram")
22432 (uri (cran-uri "phylogram" version))
22434 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22435 (properties `((upstream-name . "phylogram")))
22436 (build-system r-build-system)
22437 (propagated-inputs `(("r-ape" ,r-ape)))
22438 (home-page "https://github.com/ropensci/phylogram/")
22439 (synopsis "Dendrograms for evolutionary analysis")
22441 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22442 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22443 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22444 as well as several tools for command-line tree manipulation and import/export
22445 via Newick parenthetic text. This improves accessibility to the comprehensive
22446 range of object-specific analytical and tree-visualization functions found
22447 across a wide array of bioinformatic R packages.")
22448 (license license:gpl3)))
22450 (define-public r-kmer
22457 (uri (cran-uri "kmer" version))
22459 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22460 (properties `((upstream-name . "kmer")))
22461 (build-system r-build-system)
22463 `(("r-openssl" ,r-openssl)
22464 ("r-phylogram" ,r-phylogram)
22465 ("r-rcpp" ,r-rcpp)))
22466 (home-page "https://github.com/shaunpwilkinson/kmer/")
22467 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22469 "@code{r-kmer} is an R package for rapidly computing distance matrices
22470 and clustering large sequence datasets using fast alignment-free k-mer
22471 counting and recursive k-means partitioning.")
22472 (license license:gpl3)))
22474 (define-public r-shapforxgboost
22476 (name "r-shapforxgboost")
22481 (uri (cran-uri "SHAPforxgboost" version))
22484 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22486 `((upstream-name . "SHAPforxgboost")))
22487 (build-system r-build-system)
22489 `(("r-bbmisc" ,r-bbmisc)
22490 ("r-data-table" ,r-data-table)
22491 ("r-ggextra" ,r-ggextra)
22492 ("r-ggforce" ,r-ggforce)
22493 ("r-ggplot2" ,r-ggplot2)
22494 ("r-ggpubr" ,r-ggpubr)
22495 ("r-rcolorbrewer" ,r-rcolorbrewer)
22496 ("r-xgboost" ,r-xgboost)))
22497 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22498 (synopsis "SHAP Plots for XGBoost")
22500 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22501 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22502 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22503 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22505 (license license:expat)))
22507 (define-public r-rismed
22514 (uri (cran-uri "RISmed" version))
22517 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22518 (properties `((upstream-name . "RISmed")))
22519 (build-system r-build-system)
22520 (home-page "https://cran.r-project.org/web/packages/RISmed")
22521 (synopsis "Download content from NCBI databases")
22523 "This package provides a set of tools to extract bibliographic
22524 content from the National Center for Biotechnology Information (NCBI)
22525 databases, including PubMed. The name RISmed is a portmanteau of
22526 RIS (for Research Information Systems, a common tag format for
22527 bibliographic data) and PubMed.")
22528 (license license:gpl2+)))
22530 (define-public r-semver
22537 (uri (cran-uri "semver" version))
22540 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22541 (properties `((upstream-name . "semver")))
22542 (build-system r-build-system)
22544 `(("r-assertthat" ,r-assertthat)
22545 ("r-rcpp" ,r-rcpp)))
22546 (native-inputs `(("r-knitr" ,r-knitr)))
22547 (home-page "https://github.com/johndharrison/semver")
22548 (synopsis "Parser for Semantic Versioning 2.0.0")
22550 "This package provides tools and functions for parsing, rendering and
22551 operating on semantic version strings. Semantic versioning is a simple set of
22552 rules and requirements that dictate how version numbers are assigned and
22553 incremented as outlined at @url{http://semver.org}.")
22554 (license license:expat)))
22556 (define-public r-binman
22563 (uri (cran-uri "binman" version))
22566 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22567 (properties `((upstream-name . "binman")))
22568 (build-system r-build-system)
22570 `(("r-assertthat" ,r-assertthat)
22572 ("r-jsonlite" ,r-jsonlite)
22573 ("r-rappdirs" ,r-rappdirs)
22574 ("r-semver" ,r-semver)
22576 ("r-yaml" ,r-yaml)))
22577 (native-inputs `(("r-knitr" ,r-knitr)))
22578 (home-page "https://github.com/ropensci/binman")
22579 (synopsis "Binary download manager")
22581 "This package provides tools and functions for managing the download of
22582 binary files. Binary repositories are defined in the YAML format. Defining
22583 new pre-download, download and post-download templates allow additional
22584 repositories to be added.")
22585 (license license:expat)))
22587 (define-public r-wdman
22594 (uri (cran-uri "wdman" version))
22597 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22598 (properties `((upstream-name . "wdman")))
22599 (build-system r-build-system)
22601 `(("r-assertthat" ,r-assertthat)
22602 ("r-binman" ,r-binman)
22603 ("r-processx" ,r-processx)
22604 ("r-semver" ,r-semver)
22605 ("r-yaml" ,r-yaml)))
22606 (native-inputs `(("r-knitr" ,r-knitr)))
22607 (home-page "https://docs.ropensci.org/wdman/")
22608 (synopsis "Webdriver/Selenium binary manager")
22610 "There are a number of binary files associated with the
22611 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22612 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22613 @url{https://github.com/mozilla/geckodriver},
22614 @url{http://phantomjs.org/download.html}, and
22615 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22616 more information). This package provides functions to download these binaries
22617 and to manage processes involving them.")
22618 (license license:expat)))
22620 (define-public r-rselenium
22622 (name "r-rselenium")
22627 (uri (cran-uri "RSelenium" version))
22630 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22631 (properties `((upstream-name . "RSelenium")))
22632 (build-system r-build-system)
22634 `(("r-binman" ,r-binman)
22635 ("r-catools" ,r-catools)
22637 ("r-openssl" ,r-openssl)
22638 ("r-wdman" ,r-wdman)
22640 (native-inputs `(("r-knitr" ,r-knitr)))
22641 (home-page "https://docs.ropensci.org/RSelenium/")
22642 (synopsis "R bindings for Selenium WebDriver")
22644 "This package provides a set of R bindings for the Selenium 2.0
22645 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22646 information) using the @code{JsonWireProtocol} (see
22647 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22648 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22649 a user would either locally or on a remote machine using the Selenium server
22650 it marks a leap forward in terms of web browser automation. Selenium
22651 automates web browsers (commonly referred to as browsers). Using RSelenium
22652 you can automate browsers locally or remotely.")
22653 (license license:agpl3+)))
22655 (define-public r-conquer
22662 (uri (cran-uri "conquer" version))
22665 "1c7id7wgspma5bdcirrhw7f9fp709zxpj31klivasdbvd4jgi4vb"))))
22666 (properties `((upstream-name . "conquer")))
22667 (build-system r-build-system)
22669 `(("r-matrix" ,r-matrix)
22670 ("r-matrixstats" ,r-matrixstats)
22672 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22673 (home-page "https://github.com/XiaoouPan/conquer")
22674 (synopsis "Convolution-type smoothed quantile regression")
22676 "This package provides fast and accurate convolution-type smoothed
22677 quantile regression, implemented using Barzilai-Borwein gradient descent with
22678 a Huber regression warm start. Confidence intervals for regression
22679 coefficients are constructed using multiplier bootstrap.")
22680 (license license:gpl3)))
22682 (define-public r-fastshap
22684 (name "r-fastshap")
22689 (uri (cran-uri "fastshap" version))
22692 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22693 (properties `((upstream-name . "fastshap")))
22694 (build-system r-build-system)
22696 `(("r-abind" ,r-abind)
22697 ("r-ggplot2" ,r-ggplot2)
22698 ("r-gridextra" ,r-gridextra)
22699 ("r-matrixstats" ,r-matrixstats)
22702 ("r-rcpparmadillo" ,r-rcpparmadillo)
22703 ("r-tibble" ,r-tibble)))
22704 (home-page "https://github.com/bgreenwell/fastshap")
22705 (synopsis "Fast approximate Shapley values")
22707 "This package computes fast (relative to other implementations)
22708 approximate Shapley values for any supervised learning model. Shapley values
22709 help to explain the predictions from any black box model using ideas from game
22710 theory; see @url{Strumbel and Kononenko (2014),
22711 doi.org/10.1007/s10115-013-0679-x} for details.")
22712 (license license:gpl2+)))
22714 (define-public r-metrics
22721 (uri (cran-uri "Metrics" version))
22724 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22725 (properties `((upstream-name . "Metrics")))
22726 (build-system r-build-system)
22727 (home-page "https://github.com/mfrasco/Metrics")
22728 (synopsis "Evaluation metrics for machine learning")
22730 "This package provides an implementation of evaluation metrics in R that
22731 are commonly used in supervised machine learning. It implements metrics for
22732 regression, time series, binary classification, classification, and
22733 information retrieval problems. It has zero dependencies and a consistent,
22734 simple interface for all functions.")
22735 (license license:bsd-3)))
22737 (define-public r-iml
22744 (uri (cran-uri "iml" version))
22747 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22748 (properties `((upstream-name . "iml")))
22749 (build-system r-build-system)
22751 `(("r-checkmate" ,r-checkmate)
22752 ("r-data-table" ,r-data-table)
22753 ("r-formula" ,r-formula)
22754 ("r-future" ,r-future)
22755 ("r-future-apply" ,r-future-apply)
22756 ("r-ggplot2" ,r-ggplot2)
22757 ("r-gridextra" ,r-gridextra)
22758 ("r-metrics" ,r-metrics)
22759 ("r-prediction" ,r-prediction)
22761 (native-inputs `(("r-knitr" ,r-knitr)))
22762 (home-page "https://github.com/christophM/iml")
22763 (synopsis "Interpretable machine learning")
22765 "This package provides interpretability methods to analyze the behavior
22766 and predictions of any machine learning model. Implemented methods are:
22769 @item Feature importance described by Fisher et al. (2018),
22770 @item accumulated local effects plots described by Apley (2018),
22771 @item partial dependence plots described by Friedman (2001),
22772 @item individual conditional expectation ('ice') plots described by Goldstein
22773 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
22774 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
22775 @item the Shapley Value described by Strumbelj et. al (2014)
22776 @url{https://doi.org/10.1007/s10115-013-0679-x},
22777 @item feature interactions described by Friedman et. al
22778 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
22781 (license license:expat)))
22783 (define-public r-goftest
22790 (uri (cran-uri "goftest" version))
22793 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
22794 (properties `((upstream-name . "goftest")))
22795 (build-system r-build-system)
22796 (home-page "https://github.com/baddstats/goftest")
22797 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
22799 "This package provides Cramer-Von Mises and Anderson-Darling tests of
22800 goodness-of-fit for continuous univariate distributions, using efficient
22802 (license license:gpl2+)))
22804 (define-public r-tensor
22811 (uri (cran-uri "tensor" version))
22814 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
22815 (properties `((upstream-name . "tensor")))
22816 (build-system r-build-system)
22817 (home-page "https://cran.r-project.org/web/packages/tensor/")
22818 (synopsis "Tensor product of arrays")
22820 "The tensor product of two arrays is notionally an outer product of the
22821 arrays collapsed in specific extents by summing along the appropriate
22822 diagonals. This package allows you to compute the tensor product of arrays.")
22823 (license license:gpl2+)))
22825 (define-public r-spatstat-utils
22827 (name "r-spatstat-utils")
22832 (uri (cran-uri "spatstat.utils" version))
22835 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
22837 `((upstream-name . "spatstat.utils")))
22838 (build-system r-build-system)
22839 (home-page "http://www.spatstat.org")
22840 (synopsis "Utility functions for spatstat")
22842 "This package contains utility functions for the @code{spatstat} package
22843 which may also be useful for other purposes.")
22844 (license license:gpl2+)))
22846 (define-public r-spatstat-data
22848 (name "r-spatstat-data")
22853 (uri (cran-uri "spatstat.data" version))
22856 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
22857 (properties `((upstream-name . "spatstat.data")))
22858 (build-system r-build-system)
22860 `(("r-matrix" ,r-matrix)
22861 ("r-spatstat-utils" ,r-spatstat-utils)))
22862 (home-page "http://www.spatstat.org")
22863 (synopsis "Datasets for spatstat")
22865 "This package contains all the datasets for the @code{spatstat}
22867 (license license:gpl2+)))
22869 (define-public r-spatstat
22871 (name "r-spatstat")
22876 (uri (cran-uri "spatstat" version))
22879 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
22880 (properties `((upstream-name . "spatstat")))
22881 (build-system r-build-system)
22883 `(("r-abind" ,r-abind)
22884 ("r-deldir" ,r-deldir)
22885 ("r-goftest" ,r-goftest)
22886 ("r-matrix" ,r-matrix)
22889 ("r-polyclip" ,r-polyclip)
22890 ("r-rpart" ,r-rpart)
22891 ("r-spatstat-data" ,r-spatstat-data)
22892 ("r-spatstat-utils" ,r-spatstat-utils)
22893 ("r-tensor" ,r-tensor)))
22894 (home-page "http://www.spatstat.org")
22895 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
22897 "This package provides a comprehensive toolbox for analysing Spatial
22898 Point Patterns. It is focused mainly on two-dimensional point patterns,
22899 including multitype/marked points, in any spatial region. It also supports
22900 three-dimensional point patterns, space-time point patterns in any number of
22901 dimensions, point patterns on a linear network, and patterns of other
22902 geometrical objects. It supports spatial covariate data such as pixel images
22903 and contains over 2000 functions for plotting spatial data, exploratory data
22904 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
22905 formal inference.")
22906 (license license:gpl2+)))
22908 (define-public r-gaston
22915 (uri (cran-uri "gaston" version))
22918 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
22919 (properties `((upstream-name . "gaston")))
22920 (build-system r-build-system)
22921 (inputs `(("zlib" ,zlib)))
22923 `(("r-rcpp" ,r-rcpp)
22924 ("r-rcppeigen" ,r-rcppeigen)
22925 ("r-rcppparallel" ,r-rcppparallel)))
22926 (native-inputs `(("r-knitr" ,r-knitr)))
22927 (home-page "https://cran.r-project.org/web/packages/gaston/")
22928 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
22930 "This is a package for the manipulation of genetic data (SNPs).
22931 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
22932 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
22933 for linear mixed models (AIREML).")
22934 (license license:gpl3)))
22936 (define-public r-cpp11
22943 (uri (cran-uri "cpp11" version))
22946 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
22947 (properties `((upstream-name . "cpp11")))
22948 (build-system r-build-system)
22949 (native-inputs `(("r-knitr" ,r-knitr)))
22950 (home-page "https://github.com/r-lib/cpp11")
22951 (synopsis "C++11 Interface for R's C Interface")
22953 "This package provides a header only, C++11 interface to R's C interface.
22954 Compared to other approaches @code{cpp11} strives to be safe against long
22955 jumps from the C API as well as C++ exceptions, conform to normal R function
22956 semantics and supports interaction with @code{ALTREP} vectors.")
22957 (license license:expat)))
22959 (define-public r-rcppziggurat
22961 (name "r-rcppziggurat")
22966 (uri (cran-uri "RcppZiggurat" version))
22969 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
22970 (properties `((upstream-name . "RcppZiggurat")))
22971 (build-system r-build-system)
22973 `(("r-rcpp" ,r-rcpp)
22974 ("r-rcppgsl" ,r-rcppgsl)))
22975 (native-inputs `(("r-knitr" ,r-knitr)))
22976 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
22977 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
22979 "The Ziggurat generator for normally distributed random numbers,
22980 originally proposed by Marsaglia and Tsang (2000,
22981 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
22982 times starting with Leong et al (2005,
22983 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
22984 aggregation for comparing different implementations in order to provide a
22985 'faster but good enough' alternative for use with R and C++ code.")
22986 (license license:gpl2+)))
22988 (define-public r-rfast
22995 (uri (cran-uri "Rfast" version))
22998 "18m8xhg24kygwhq7avdp1hibilicb5wppi2wdmc36fkqljc274y0"))))
22999 (properties `((upstream-name . "Rfast")))
23000 (build-system r-build-system)
23002 `(("r-rcpp" ,r-rcpp)
23003 ("r-rcpparmadillo" ,r-rcpparmadillo)
23004 ("r-rcppziggurat" ,r-rcppziggurat)))
23005 (home-page "https://github.com/RfastOfficial/Rfast")
23006 (synopsis "Collection of efficient and fast R functions")
23008 "This package provides a collection of fast (utility) functions for data
23009 analysis. Column- and row- wise means, medians, variances, minimums,
23010 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23011 Poisson), are some of the many fast functions.")
23012 (license license:gpl2+)))
23014 (define-public r-clusterr
23016 (name "r-clusterr")
23021 (uri (cran-uri "ClusterR" version))
23024 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23025 (properties `((upstream-name . "ClusterR")))
23026 (build-system r-build-system)
23028 `(("r-ggplot2" ,r-ggplot2)
23030 ("r-gtools" ,r-gtools)
23032 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23033 (native-inputs `(("r-knitr" ,r-knitr)))
23034 (home-page "https://github.com/mlampros/ClusterR")
23035 (synopsis "Clustering")
23037 "This package provides Gaussian mixture models, k-means,
23038 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23039 option to plot, validate, predict (new data) and estimate the optimal number
23040 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23041 the computationally intensive parts of the functions. For more information,
23045 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23046 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23047 @url{https://doi.org/10.18637/jss.v001.i04};
23048 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23049 Library, @url{https://doi.org/10.1145/1772690.1772862};
23050 @item \"Armadillo: a template-based C++ library
23051 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23052 Software, @url{https://doi.org/10.21105/joss.00026};
23053 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23054 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23055 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23058 (license license:gpl3)))
23060 (define-public r-spectrum
23062 (name "r-spectrum")
23067 (uri (cran-uri "Spectrum" version))
23070 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23071 (properties `((upstream-name . "Spectrum")))
23072 (build-system r-build-system)
23074 `(("r-clusterr" ,r-clusterr)
23075 ("r-diptest" ,r-diptest)
23076 ("r-ggplot2" ,r-ggplot2)
23077 ("r-rfast" ,r-rfast)))
23078 (native-inputs `(("r-knitr" ,r-knitr)))
23079 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23080 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23082 "This package provides a self-tuning spectral clustering method for
23083 single or multi-view data. Spectrum uses a new type of adaptive density aware
23084 kernel that strengthens connections in the graph based on common nearest
23085 neighbours. It uses a tensor product graph data integration and diffusion
23086 procedure to integrate different data sources and reduce noise. Spectrum uses
23087 either the eigengap or multimodality gap heuristics to determine the number of
23088 clusters. The method is sufficiently flexible so that a wide range of
23089 Gaussian and non-Gaussian structures can be clustered with automatic selection
23091 (license license:agpl3+)))
23093 (define-public r-nabor
23100 (uri (cran-uri "nabor" version))
23103 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23104 (properties `((upstream-name . "nabor")))
23105 (build-system r-build-system)
23109 ("r-rcppeigen" ,r-rcppeigen)))
23110 (home-page "https://cran.r-project.org/web/packages/nabor/")
23111 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23113 "This package provides an R wrapper for libnabo, an exact or approximate
23114 k nearest neighbour library which is optimised for low dimensional
23115 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23116 designed as a drop-in replacement for the RANN function @code{nn2}. In
23117 addition, objects which include the k-d tree search structure can be returned
23118 to speed up repeated queries of the same set of target points.")
23119 (license license:bsd-3)))