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 "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l"))))
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 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
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 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
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 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2275 (build-system r-build-system)
2277 `(("r-ggplot2" ,r-ggplot2)
2278 ("r-magrittr" ,r-magrittr)
2279 ("r-viridis" ,r-viridis)))
2281 `(("r-knitr" ,r-knitr)))
2282 (home-page "https://cran.r-project.org/web/packages/dendextend")
2283 (synopsis "Extending 'dendrogram' functionality in R")
2285 "This package offers a set of functions for extending @code{dendrogram}
2286 objects in R, letting you visualize and compare trees of hierarchical
2287 clusterings. You can adjust a tree's graphical parameters (the color, size,
2288 type, etc of its branches, nodes and labels) and visually and statistically
2289 compare different dendrograms to one another.")
2290 ;; Any of these versions
2291 (license (list license:gpl2 license:gpl3))))
2293 (define-public r-getoptlong
2295 (name "r-getoptlong")
2300 (uri (cran-uri "GetoptLong" version))
2303 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2304 (properties `((upstream-name . "GetoptLong")))
2305 (build-system r-build-system)
2309 `(("r-crayon" ,r-crayon)
2310 ("r-globaloptions" ,r-globaloptions)
2311 ("r-rjson" ,r-rjson)))
2313 `(("r-knitr" ,r-knitr)))
2314 (home-page "https://github.com/jokergoo/GetoptLong")
2315 (synopsis "Parsing command-line arguments and variable interpolation")
2317 "This is yet another command-line argument parser which wraps the
2318 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2319 use in R. It also provides a simple way for variable interpolation in R.")
2320 (license license:gpl2+)))
2322 (define-public r-fastmatch
2324 (name "r-fastmatch")
2329 (uri (cran-uri "fastmatch" version))
2332 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2333 (build-system r-build-system)
2334 (home-page "https://www.rforge.net/fastmatch")
2335 (synopsis "Fast match function")
2337 "This package provides a fast @code{match} replacement for cases that
2338 require repeated look-ups. It is slightly faster that R's built-in
2339 @code{match} function on first match against a table, but extremely fast on
2340 any subsequent lookup as it keeps the hash table in memory.")
2341 (license license:gpl2)))
2350 (uri (cran-uri "ff" version))
2353 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0"))))
2354 (build-system r-build-system)
2355 (propagated-inputs `(("r-bit" ,r-bit)))
2356 (home-page "http://ff.r-forge.r-project.org/")
2357 (synopsis "Memory-efficient storage of large data on disk and access functions")
2359 "This package provides data structures that are stored on disk but
2360 behave (almost) as if they were in RAM by transparently mapping only a section
2362 ;; error Architecture not supported.
2363 (supported-systems (delete "aarch64-linux" %supported-systems))
2364 (license license:gpl2)))
2366 (define-public r-ffbase
2373 (uri (cran-uri "ffbase" version))
2376 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2377 (build-system r-build-system)
2380 ("r-fastmatch" ,r-fastmatch)
2382 (home-page "https://github.com/edwindj/ffbase")
2383 (synopsis "Basic statistical functions for package 'ff'")
2385 "This package extends the out of memory vectors of @code{ff} with
2386 statistical functions and other utilities to ease their usage.")
2387 (license license:gpl3)))
2389 (define-public r-prettyunits
2391 (name "r-prettyunits")
2396 (uri (cran-uri "prettyunits" version))
2399 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2400 (build-system r-build-system)
2401 (home-page "https://github.com/gaborcsardi/prettyunits")
2402 (synopsis "Pretty, human readable formatting of quantities")
2404 "This package provides tools for pretty, human readable formatting of
2406 (license license:expat)))
2408 (define-public r-reshape
2415 (uri (cran-uri "reshape" version))
2418 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2419 (build-system r-build-system)
2421 `(("r-plyr" ,r-plyr)
2422 ("r-rcpp" ,r-rcpp)))
2423 (home-page "http://had.co.nz/reshape")
2424 (synopsis "Flexibly reshape data")
2426 "Flexibly restructure and aggregate data using just two functions:
2427 @code{melt} and @code{cast}. This package provides them.")
2428 (license license:expat)))
2430 (define-public r-progress
2437 (uri (cran-uri "progress" version))
2440 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2441 (build-system r-build-system)
2443 `(("r-crayon" ,r-crayon)
2445 ("r-prettyunits" ,r-prettyunits)
2447 (home-page "https://github.com/gaborcsardi/progress")
2448 (synopsis "Terminal progress bars")
2450 "This package provides configurable progress bars. They may include
2451 percentage, elapsed time, and/or the estimated completion time. They work in
2452 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2453 package also provides a C++ API, that works with or without Rcpp.")
2454 (license license:expat)))
2456 (define-public r-ggally
2463 (uri (cran-uri "GGally" version))
2466 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2467 (properties `((upstream-name . "GGally")))
2468 (build-system r-build-system)
2470 `(("libressl" ,libressl)))
2472 `(("r-ggplot2" ,r-ggplot2)
2473 ("r-gtable" ,r-gtable)
2474 ("r-lifecycle" ,r-lifecycle)
2476 ("r-progress" ,r-progress)
2477 ("r-rcolorbrewer" ,r-rcolorbrewer)
2478 ("r-reshape" ,r-reshape)
2479 ("r-rlang" ,r-rlang)
2480 ("r-scales" ,r-scales)))
2481 (home-page "https://ggobi.github.io/ggally")
2482 (synopsis "Extension to ggplot2")
2484 "The R package ggplot2 is a plotting system based on the grammar of
2485 graphics. GGally extends ggplot2 by adding several functions to reduce the
2486 complexity of combining geometric objects with transformed data. Some of
2487 these functions include a pairwise plot matrix, a two group pairwise plot
2488 matrix, a parallel coordinates plot, a survival plot, and several functions to
2490 (license license:gpl2+)))
2492 (define-public r-proxy
2499 (uri (cran-uri "proxy" version))
2502 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2503 (build-system r-build-system)
2504 (home-page "https://cran.r-project.org/web/packages/proxy")
2505 (synopsis "Distance and similarity measures")
2507 "This package provides an extensible framework for the efficient
2508 calculation of auto- and cross-proximities, along with implementations of the
2509 most popular ones.")
2510 (license license:gpl2)))
2519 (uri (cran-uri "sp" version))
2521 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2522 (build-system r-build-system)
2524 `(("r-lattice" ,r-lattice)))
2525 (home-page "https://cran.r-project.org/web/packages/sp")
2526 (synopsis "Classes and methods for spatial data")
2528 "This package provides classes and methods for spatial data; the classes
2529 document where the spatial location information resides, for 2D or 3D data.
2530 Utility functions are provided, e.g. for plotting data as maps, spatial
2531 selection, as well as methods for retrieving coordinates, for subsetting,
2532 print, summary, etc.")
2533 (license license:gpl2+)))
2535 (define-public r-rmtstat
2542 (uri (cran-uri "RMTstat" version))
2545 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2546 (properties `((upstream-name . "RMTstat")))
2547 (build-system r-build-system)
2548 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2549 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2551 "This package provides functions for working with the Tracy-Widom laws
2552 and other distributions related to the eigenvalues of large Wishart
2554 (license license:bsd-3)))
2556 (define-public r-rmpi
2562 (uri (cran-uri "Rmpi" version))
2565 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2566 (properties `((upstream-name . "Rmpi")))
2567 (build-system r-build-system)
2569 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2570 #:phases (modify-phases %standard-phases
2571 (add-before 'install 'mpi-setup
2574 `(("openmpi" ,openmpi)))
2576 `(("pkg-config" ,pkg-config)))
2577 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2578 (synopsis "R interface to message-passing interface (MPI)")
2580 "This package provides an interface (wrapper) to MPI APIs. It also
2581 provides an interactive R manager and worker environment.")
2582 (license license:gpl2+)))
2584 (define-public r-lmoments
2591 (uri (cran-uri "Lmoments" version))
2594 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2595 (properties `((upstream-name . "Lmoments")))
2596 (build-system r-build-system)
2598 `(("r-rcpp" ,r-rcpp)
2599 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2600 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2601 (synopsis "L-moments and quantile mixtures")
2603 "This package contains functions to estimate L-moments and trimmed
2604 L-moments from the data. It also contains functions to estimate the
2605 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2606 quantile mixture from L-moments and trimmed L-moments.")
2607 (license license:gpl2)))
2609 (define-public r-distillery
2611 (name "r-distillery")
2616 (uri (cran-uri "distillery" version))
2619 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2620 (build-system r-build-system)
2621 (home-page "https://ral.ucar.edu/staff/ericg/")
2622 (synopsis "Functions for confidence intervals and object information")
2624 "This package provides some very simple method functions for confidence
2625 interval calculation and to distill pertinent information from a potentially
2626 complex object; primarily used in common with the packages extRemes and
2628 (license license:gpl2+)))
2630 (define-public r-extremes
2637 (uri (cran-uri "extRemes" version))
2640 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2641 (properties `((upstream-name . "extRemes")))
2642 (build-system r-build-system)
2644 `(("r-distillery" ,r-distillery)
2645 ("r-lmoments" ,r-lmoments)))
2646 (home-page "https://www.assessment.ucar.edu/toolkit/")
2647 (synopsis "Extreme value analysis")
2649 "ExtRemes is a suite of functions for carrying out analyses on the
2650 extreme values of a process of interest; be they block maxima over long blocks
2651 or excesses over a high threshold.")
2652 (license license:gpl2+)))
2654 (define-public r-lmtest
2661 (uri (cran-uri "lmtest" version))
2664 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2665 (build-system r-build-system)
2667 `(("r-zoo" ,r-zoo)))
2669 `(("gfortran" ,gfortran)))
2670 (home-page "https://cran.r-project.org/web/packages/lmtest")
2671 (synopsis "Testing linear regression models")
2673 "This package provides a collection of tests, data sets, and examples for
2674 diagnostic checking in linear regression models. Furthermore, some generic
2675 tools for inference in parametric models are provided.")
2676 ;; Either version is okay
2677 (license (list license:gpl2 license:gpl3))))
2679 (define-public r-idr
2685 (uri (cran-uri "idr" version))
2688 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2689 (build-system r-build-system)
2690 (home-page "https://cran.r-project.org/web/packages/idr/")
2691 (synopsis "Irreproducible discovery rate")
2693 "This is a package for estimating the copula mixture model and plotting
2694 correspondence curves in \"Measuring reproducibility of high-throughput
2695 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2696 by Li, Brown, Huang, and Bickel")
2697 (license license:gpl2+)))
2699 (define-public r-inline
2705 (uri (cran-uri "inline" version))
2708 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2709 (build-system r-build-system)
2710 (home-page "https://cran.r-project.org/web/packages/inline")
2711 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2713 "This package provides functionality to dynamically define R functions
2714 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2715 @code{.Call} calling conventions.")
2716 ;; Any version of the LGPL.
2717 (license license:lgpl3+)))
2719 (define-public r-inum
2725 (uri (cran-uri "inum" version))
2728 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2729 (build-system r-build-system)
2731 `(("r-libcoin" ,r-libcoin)))
2732 (home-page "https://cran.r-project.org/web/packages/inum/")
2733 (synopsis "Interval and enum-type representation of vectors")
2735 "This package provides an enum-type representation of vectors and
2736 representation of intervals, including a method of coercing variables
2738 (license license:gpl2)))
2740 (define-public r-bdsmatrix
2742 (name "r-bdsmatrix")
2747 (uri (cran-uri "bdsmatrix" version))
2750 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2751 (properties `((upstream-name . "bdsmatrix")))
2752 (build-system r-build-system)
2753 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2754 (synopsis "Routines for block diagonal symmetric matrices")
2756 "This package provides procedures to work with block diagonal symmetric
2757 matrices, a special case of sparse matrices.")
2758 (license license:lgpl2.0)))
2760 (define-public r-bbmle
2763 (version "1.0.23.1")
2767 (uri (cran-uri "bbmle" version))
2770 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2771 (build-system r-build-system)
2773 `(("r-bdsmatrix" ,r-bdsmatrix)
2774 ("r-lattice" ,r-lattice)
2776 ("r-matrix" ,r-matrix)
2777 ("r-mvtnorm" ,r-mvtnorm)
2778 ("r-numderiv" ,r-numderiv)))
2779 (home-page "https://cran.r-project.org/web/packages/bbmle")
2780 (synopsis "Tools for General Maximum Likelihood Estimation")
2782 "This package provides methods and functions for fitting maximum
2783 likelihood models in R. This package modifies and extends the @code{mle}
2784 classes in the @code{stats4} package.")
2785 ;; Any version of the GPL
2786 (license license:gpl2+)))
2788 (define-public r-emdbook
2795 (uri (cran-uri "emdbook" version))
2798 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2799 (build-system r-build-system)
2801 `(("r-bbmle" ,r-bbmle)
2803 ("r-lattice" ,r-lattice)
2805 ("r-plyr" ,r-plyr)))
2806 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2807 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2809 "This package provides auxiliary functions and data sets for \"Ecological
2810 Models and Data\", a book presenting maximum likelihood estimation and related
2811 topics for ecologists (ISBN 978-0-691-12522-0).")
2813 (license (list license:gpl2 license:gpl3))))
2815 (define-public r-lpsolve
2822 (uri (cran-uri "lpSolve" version))
2825 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2826 (properties `((upstream-name . "lpSolve")))
2827 (build-system r-build-system)
2828 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2829 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2831 "Lp_solve is software for solving linear, integer and mixed integer
2832 programs. This implementation supplies a \"wrapper\" function in C and some R
2833 functions that solve general linear/integer problems, assignment problems, and
2834 transportation problems.")
2835 (license license:lgpl2.0)))
2837 (define-public r-limsolve
2844 (uri (cran-uri "limSolve" version))
2847 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2848 (properties `((upstream-name . "limSolve")))
2849 (build-system r-build-system)
2851 `(("r-lpsolve" ,r-lpsolve)
2853 ("r-quadprog" ,r-quadprog)))
2854 (native-inputs `(("gfortran" ,gfortran)))
2855 (home-page "https://cran.r-project.org/web/packages/limSolve")
2856 (synopsis "Solving linear inverse models")
2858 "This package provides functions that:
2861 @item find the minimum/maximum of a linear or quadratic function,
2862 @item sample an underdetermined or overdetermined system,
2863 @item solve a linear system Ax=B for the unknown x.
2866 It includes banded and tridiagonal linear systems. The package calls Fortran
2867 functions from LINPACK.")
2869 (license (list license:gpl2+ license:gpl3+))))
2871 (define-public r-fitdistrplus
2873 (name "r-fitdistrplus")
2878 (uri (cran-uri "fitdistrplus" version))
2881 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2882 (build-system r-build-system)
2884 `(("r-mass" ,r-mass)
2885 ("r-survival" ,r-survival)))
2887 `(("r-knitr" ,r-knitr)))
2888 (home-page "http://riskassessment.r-forge.r-project.org")
2889 (synopsis "Fitting a parametric distribution from data")
2891 "This package extends the @code{fitdistr} function of the MASS package
2892 with several functions to help the fit of a parametric distribution to
2893 non-censored or censored data. Censored data may contain left-censored,
2894 right-censored and interval-censored values, with several lower and upper
2895 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2896 provides moment matching (MME), quantile matching (QME) and maximum
2897 goodness-of-fit estimation (MGE) methods (available only for non-censored
2898 data). Weighted versions of MLE, MME and QME are available.")
2899 (license license:gpl2+)))
2901 (define-public r-energy
2908 (uri (cran-uri "energy" version))
2911 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2912 (build-system r-build-system)
2914 `(("r-boot" ,r-boot)
2915 ("r-rcpp" ,r-rcpp)))
2916 (home-page "https://cran.r-project.org/web/packages/energy")
2917 (synopsis "Multivariate inference via the energy of data")
2919 "This package provides e-statistics (energy) tests and statistics for
2920 multivariate and univariate inference, including distance correlation,
2921 one-sample, two-sample, and multi-sample tests for comparing multivariate
2922 distributions, are implemented. Measuring and testing multivariate
2923 independence based on distance correlation, partial distance correlation,
2924 multivariate goodness-of-fit tests, clustering based on energy distance,
2925 testing for multivariate normality, distance components (disco) for
2926 non-parametric analysis of structured data, and other energy
2927 statistics/methods are implemented.")
2928 (license license:gpl2+)))
2930 (define-public r-suppdists
2932 (name "r-suppdists")
2937 (uri (cran-uri "SuppDists" version))
2940 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2941 (properties `((upstream-name . "SuppDists")))
2942 (build-system r-build-system)
2943 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2944 (synopsis "Supplementary distributions")
2946 "This package provides ten distributions supplementing those built into
2947 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2948 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2949 coefficient, Johnson distributions, normal scores and generalized
2950 hypergeometric distributions. In addition two random number generators of
2951 George Marsaglia are included.")
2952 (license license:gpl2+)))
2954 (define-public r-ksamples
2961 (uri (cran-uri "kSamples" version))
2964 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2965 (properties `((upstream-name . "kSamples")))
2966 (build-system r-build-system)
2968 `(("r-suppdists" ,r-suppdists)))
2969 (home-page "https://cran.r-project.org/web/packages/kSamples")
2970 (synopsis "K-Sample rank tests and their combinations")
2972 "This package provides tools to compares k samples using the
2973 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2974 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2975 test. It computes asymptotic, simulated or (limited) exact P-values, all
2976 valid under randomization, with or without ties, or conditionally under random
2977 sampling from populations, given the observed tie pattern. Except for Steel's
2978 test and the JT test it also combines these tests across several blocks of
2980 (license license:gpl2+)))
2982 (define-public r-cvst
2989 (uri (cran-uri "CVST" version))
2992 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2993 (properties `((upstream-name . "CVST")))
2994 (build-system r-build-system)
2996 `(("r-kernlab" ,r-kernlab)
2997 ("r-matrix" ,r-matrix)))
2998 (home-page "https://cran.r-project.org/web/packages/CVST")
2999 (synopsis "Fast cross-validation via sequential testing")
3001 "This package implements the fast cross-validation via sequential
3002 testing (CVST) procedure. CVST is an improved cross-validation procedure
3003 which uses non-parametric testing coupled with sequential analysis to
3004 determine the best parameter set on linearly increasing subsets of the data.
3005 Additionally to the CVST the package contains an implementation of the
3006 ordinary k-fold cross-validation with a flexible and powerful set of helper
3007 objects and methods to handle the overall model selection process. The
3008 implementations of the Cochran's Q test with permutations and the sequential
3009 testing framework of Wald are generic and can therefore also be used in other
3011 (license license:gpl2+)))
3013 (define-public r-squarem
3020 (uri (cran-uri "SQUAREM" version))
3023 "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb"))))
3024 (properties `((upstream-name . "SQUAREM")))
3025 (build-system r-build-system)
3026 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3027 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3029 "This package provides algorithms for accelerating the convergence of
3030 slow, monotone sequences from smooth, contraction mapping such as the EM
3031 algorithm. It can be used to accelerate any smooth, linearly convergent
3032 acceleration scheme. A tutorial style introduction to this package is
3033 available in a vignette.")
3034 (license license:gpl2+)))
3036 (define-public r-lava
3043 (uri (cran-uri "lava" version))
3046 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3047 (build-system r-build-system)
3049 `(("r-numderiv" ,r-numderiv)
3050 ("r-squarem" ,r-squarem)
3051 ("r-survival" ,r-survival)))
3052 (home-page "https://github.com/kkholst/lava")
3053 (synopsis "Latent variable models")
3055 "This package provides tools for the estimation and simulation of latent
3057 (license license:gpl3)))
3059 (define-public r-drr
3066 (uri (cran-uri "DRR" version))
3069 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3070 (properties `((upstream-name . "DRR")))
3071 (build-system r-build-system)
3073 `(("r-cvst" ,r-cvst)
3074 ("r-kernlab" ,r-kernlab)
3075 ("r-matrix" ,r-matrix)))
3076 (home-page "https://cran.r-project.org/web/packages/DRR")
3077 (synopsis "Dimensionality reduction via regression")
3079 "This package provides an implementation of dimensionality reduction via
3080 regression using Kernel Ridge Regression.")
3081 (license license:gpl3)))
3083 (define-public r-prodlim
3086 (version "2019.11.13")
3090 (uri (cran-uri "prodlim" version))
3093 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3094 (build-system r-build-system)
3096 `(("r-kernsmooth" ,r-kernsmooth)
3099 ("r-survival" ,r-survival)))
3100 (home-page "https://cran.r-project.org/web/packages/prodlim")
3101 (synopsis "Product-limit estimation for censored event history analysis")
3103 "This package provides a fast and user-friendly implementation of
3104 nonparametric estimators for censored event history (survival) analysis with
3105 the Kaplan-Meier and Aalen-Johansen methods.")
3106 (license license:gpl2+)))
3108 (define-public r-dimred
3115 (uri (cran-uri "dimRed" version))
3118 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3119 (properties `((upstream-name . "dimRed")))
3120 (build-system r-build-system)
3123 ("r-magrittr" ,r-magrittr)))
3124 (home-page "https://github.com/gdkrmr/dimRed")
3125 (synopsis "Framework for dimensionality reduction")
3127 "This package provides a collection of dimensionality reduction
3128 techniques from R packages and provides a common interface for calling the
3130 (license license:gpl3)))
3132 (define-public r-timedate
3135 (version "3043.102")
3139 (uri (cran-uri "timeDate" version))
3142 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3143 (properties `((upstream-name . "timeDate")))
3144 (build-system r-build-system)
3145 (home-page "https://www.rmetrics.org")
3146 (synopsis "Chronological and calendar objects")
3148 "This package provides an environment for teaching \"Financial
3149 Engineering and Computational Finance\" and for managing chronological and
3151 (license license:gpl2+)))
3153 (define-public r-magic
3160 (uri (cran-uri "magic" version))
3163 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3164 (build-system r-build-system)
3166 `(("r-abind" ,r-abind)))
3167 (home-page "https://github.com/RobinHankin/magic.git")
3168 (synopsis "Create and investigate magic squares")
3170 "This package provides a collection of efficient, vectorized algorithms
3171 for the creation and investigation of magic squares and hypercubes, including
3172 a variety of functions for the manipulation and analysis of arbitrarily
3173 dimensioned arrays.")
3174 (license license:gpl2)))
3176 (define-public r-rmysql
3183 (uri (cran-uri "RMySQL" version))
3186 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3187 (properties `((upstream-name . "RMySQL")))
3188 (build-system r-build-system)
3190 `(("mariadb" ,mariadb "lib")
3191 ("mariadb-dev" ,mariadb "dev")
3194 `(("r-dbi" ,r-dbi)))
3195 (home-page "https://github.com/r-dbi/RMySQL")
3196 (synopsis "Database interface and MySQL driver for R")
3198 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3199 package contains an old implementation based on legacy code from S-PLUS which
3200 is being phased out. A modern MySQL client based on Rcpp is available from
3201 the RMariaDB package.")
3202 (license license:gpl2)))
3204 (define-public r-rpostgresql
3206 (name "r-rpostgresql")
3211 (uri (cran-uri "RPostgreSQL" version))
3214 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3215 (properties `((upstream-name . "RPostgreSQL")))
3216 (build-system r-build-system)
3218 `(("postgresql" ,postgresql)))
3220 `(("r-dbi" ,r-dbi)))
3221 (home-page "https://github.com/tomoakin/RPostgreSQL")
3222 (synopsis "R interface to the PostgreSQL database system")
3224 "This package provides a Database Interface (DBI) compliant driver for R
3225 to access PostgreSQL database systems.")
3226 ;; The whole package is released under GPL version 2. It includes code
3227 ;; under the PostgreSQL license.
3228 (license license:gpl2)))
3230 (define-public r-linprog
3237 (uri (cran-uri "linprog" version))
3240 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3241 (build-system r-build-system)
3242 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3243 (home-page "http://linprog.r-forge.r-project.org/")
3244 (synopsis "Linear programming and optimization")
3246 "This package can be used to solve Linear Programming / Linear
3247 Optimization problems by using the simplex algorithm.")
3248 (license license:gpl2+)))
3250 (define-public r-geometry
3257 (uri (cran-uri "geometry" version))
3260 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3261 (build-system r-build-system)
3263 `(("r-magic" ,r-magic)
3264 ("r-linprog" ,r-linprog)
3265 ("r-lpsolve" ,r-lpsolve)
3267 ("r-rcppprogress" ,r-rcppprogress)))
3268 (home-page "http://geometry.r-forge.r-project.org/")
3269 (synopsis "Mesh generation and surface tesselation")
3271 "This package makes the qhull library available in R, in a similar manner
3272 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3273 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3274 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3275 and higher dimensions. It implements the Quickhull algorithm for computing
3276 the convex hull. Qhull does not support constrained Delaunay triangulations,
3277 or mesh generation of non-convex objects, but the package does include some R
3278 functions that allow for this. Currently the package only gives access to
3279 Delaunay triangulation and convex hull computation.")
3280 ;; The Qhull sources are included and are distributed under a custom
3281 ;; non-copyleft license. The R sources are released under GPL version 2.
3282 (license (list license:gpl2
3283 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3285 (define-public r-ddalpha
3292 (uri (cran-uri "ddalpha" version))
3295 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3296 (build-system r-build-system)
3299 ("r-class" ,r-class)
3300 ("r-geometry" ,r-geometry)
3303 ("r-robustbase" ,r-robustbase)
3304 ("r-sfsmisc" ,r-sfsmisc)))
3306 `(("gfortran" ,gfortran)))
3307 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3308 (synopsis "Depth-Based classification and calculation of data depth")
3310 "This package contains procedures for depth-based supervised learning,
3311 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3312 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3313 statistical depth function to a compact low-dimensional space, where the final
3314 classification is done. It also offers an extension to functional data and
3315 routines for calculating certain notions of statistical depth functions. 50
3316 multivariate and 5 functional classification problems are included.")
3317 (license license:gpl2)))
3319 (define-public r-gower
3326 (uri (cran-uri "gower" version))
3329 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3330 (build-system r-build-system)
3331 (home-page "https://github.com/markvanderloo/gower")
3332 (synopsis "Gower's distance")
3334 "This package provides tools to compute Gower's distance (or similarity)
3335 coefficient between records, and to compute the top-n matches between records.
3336 Core algorithms are executed in parallel on systems supporting OpenMP.")
3337 (license license:gpl3)))
3339 (define-public r-rcpproll
3346 (uri (cran-uri "RcppRoll" version))
3349 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3350 (properties `((upstream-name . "RcppRoll")))
3351 (build-system r-build-system)
3353 `(("r-rcpp" ,r-rcpp)))
3354 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3355 (synopsis "Efficient rolling and windowed operations")
3357 "This package provides fast and efficient routines for common rolling /
3358 windowed operations. Routines for the efficient computation of windowed mean,
3359 median, sum, product, minimum, maximum, standard deviation and variance are
3361 (license license:gpl2+)))
3363 (define-public r-ipred
3370 (uri (cran-uri "ipred" version))
3373 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3374 (build-system r-build-system)
3376 `(("r-class" ,r-class)
3379 ("r-prodlim" ,r-prodlim)
3380 ("r-rpart" ,r-rpart)
3381 ("r-survival" ,r-survival)))
3382 (home-page "https://cran.r-project.org/web/packages/ipred")
3383 (synopsis "Improved predictors")
3385 "This package provides improved predictive models by indirect
3386 classification and bagging for classification, regression and survival
3387 problems as well as resampling based estimators of prediction error.")
3388 (license license:gpl2+)))
3390 (define-public r-psych
3397 (uri (cran-uri "psych" version))
3400 "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
3401 (build-system r-build-system)
3403 `(("r-lattice" ,r-lattice)
3404 ("r-mnormt" ,r-mnormt)
3405 ("r-nlme" ,r-nlme)))
3406 (home-page "https://cran.r-project.org/web/packages/psych/")
3407 (synopsis "Procedures for psychological, psychometric, and personality research")
3409 "This package provides a general purpose toolbox for personality,
3410 psychometric theory and experimental psychology. Functions are primarily for
3411 multivariate analysis and scale construction using factor analysis, principal
3412 component analysis, cluster analysis and reliability analysis, although others
3413 provide basic descriptive statistics. Item Response Theory is done using
3414 factor analysis of tetrachoric and polychoric correlations. Functions for
3415 analyzing data at multiple levels include within and between group statistics,
3416 including correlations and factor analysis. Functions for simulating and
3417 testing particular item and test structures are included. Several functions
3418 serve as a useful front end for structural equation modeling. Graphical
3419 displays of path diagrams, factor analysis and structural equation models are
3420 created using basic graphics.")
3421 (license license:gpl2+)))
3423 (define-public r-generics
3430 (uri (cran-uri "generics" version))
3433 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3434 (build-system r-build-system)
3435 (home-page "https://github.com/r-lib/generics")
3436 (synopsis "Common S3 generics not provided by base R methods")
3438 "In order to reduce potential package dependencies and conflicts,
3439 generics provides a number of commonly used S3 generics that are not provided
3440 by base R methods related to model fitting.")
3441 (license license:gpl2)))
3443 (define-public r-broom
3450 (uri (cran-uri "broom" version))
3453 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3454 (build-system r-build-system)
3456 `(("r-backports" ,r-backports)
3457 ("r-dplyr" ,r-dplyr)
3458 ("r-ellipsis" ,r-ellipsis)
3459 ("r-generics" ,r-generics)
3461 ("r-purrr" ,r-purrr)
3462 ("r-rlang" ,r-rlang)
3463 ("r-stringr" ,r-stringr)
3464 ("r-tibble" ,r-tibble)
3465 ("r-tidyr" ,r-tidyr)))
3467 `(("r-knitr" ,r-knitr)))
3468 (home-page "https://github.com/tidyverse/broom")
3469 (synopsis "Convert statistical analysis objects into tidy data frames")
3471 "This package provides tools to convert statistical analysis objects from
3472 R into tidy data frames, so that they can more easily be combined, reshaped
3473 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3474 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3475 summarizes a model's statistical findings such as coefficients of a
3476 regression; @code{augment}, which adds columns to the original data such as
3477 predictions, residuals and cluster assignments; and @code{glance}, which
3478 provides a one-row summary of model-level statistics.")
3479 (license license:expat)))
3481 (define-public r-recipes
3488 (uri (cran-uri "recipes" version))
3491 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3492 (build-system r-build-system)
3494 `(("r-dplyr" ,r-dplyr)
3495 ("r-generics" ,r-generics)
3497 ("r-gower" ,r-gower)
3498 ("r-ipred" ,r-ipred)
3499 ("r-lifecycle" ,r-lifecycle)
3500 ("r-lubridate" ,r-lubridate)
3501 ("r-magrittr" ,r-magrittr)
3502 ("r-matrix" ,r-matrix)
3503 ("r-purrr" ,r-purrr)
3504 ("r-rlang" ,r-rlang)
3505 ("r-tibble" ,r-tibble)
3506 ("r-tidyr" ,r-tidyr)
3507 ("r-tidyselect" ,r-tidyselect)
3508 ("r-timedate" ,r-timedate)
3509 ("r-withr" ,r-withr)))
3511 `(("r-knitr" ,r-knitr)))
3512 (home-page "https://github.com/topepo/recipes")
3513 (synopsis "Preprocessing tools to create design matrices")
3515 "Recipes is an extensible framework to create and preprocess design
3516 matrices. Recipes consist of one or more data manipulation and analysis
3517 \"steps\". Statistical parameters for the steps can be estimated from an
3518 initial data set and then applied to other data sets. The resulting design
3519 matrices can then be used as inputs into statistical or machine learning
3521 (license license:gpl2)))
3523 (define-public r-pdist
3530 (uri (cran-uri "pdist" version))
3533 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3534 (build-system r-build-system)
3535 (home-page "https://github.com/jeffwong/pdist")
3536 (synopsis "Partitioned distance function")
3538 "Pdist computes the euclidean distance between rows of a matrix X and
3539 rows of another matrix Y. Previously, this could be done by binding the two
3540 matrices together and calling @code{dist}, but this creates unnecessary
3541 computation by computing the distances between a row of X and another row of
3542 X, and likewise for Y. Pdist strictly computes distances across the two
3543 matrices, not within the same matrix, making computations significantly faster
3544 for certain use cases.")
3545 (license license:gpl3+)))
3547 (define-public r-ggrepel
3554 (uri (cran-uri "ggrepel" version))
3557 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3558 (build-system r-build-system)
3560 `(("r-ggplot2" ,r-ggplot2)
3562 ("r-scales" ,r-scales)))
3564 `(("r-knitr" ,r-knitr))) ; for vignettes
3565 (home-page "https://github.com/slowkow/ggrepel")
3566 (synopsis "Repulsive text and label geometries for ggplot2")
3568 "This package provides text and label geometries for ggplot2 that help to
3569 avoid overlapping text labels. Labels repel away from each other and away
3570 from the data points.")
3571 (license license:gpl3)))
3573 (define-public r-corrplot
3580 (uri (cran-uri "corrplot" version))
3583 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3584 (build-system r-build-system)
3585 (home-page "https://github.com/taiyun/corrplot")
3586 (synopsis "Visualization of a correlation matrix")
3588 "This package provides a graphical display of a correlation matrix or
3589 general matrix. It also contains some algorithms to do matrix reordering. In
3590 addition, corrplot is good at details, including choosing color, text labels,
3591 color labels, layout, etc.")
3592 ;; Any version of the GPL
3593 (license license:gpl2+)))
3595 (define-public r-stringdist
3597 (name "r-stringdist")
3602 (uri (cran-uri "stringdist" version))
3604 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb"))))
3605 (build-system r-build-system)
3606 (home-page "https://github.com/markvanderloo/stringdist")
3607 (synopsis "Approximate string matching and string distance functions")
3609 "This package implements an approximate string matching version of R's
3610 native @code{match} function. It can calculate various string distances based
3611 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3612 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3613 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3614 can be computed between character vectors while taking proper care of encoding
3615 or between integer vectors representing generic sequences.")
3616 (license license:gpl3+)))
3618 (define-public r-ucminf
3625 (uri (cran-uri "ucminf" version))
3628 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3629 (build-system r-build-system)
3630 (native-inputs `(("gfortran" ,gfortran)))
3631 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3632 (synopsis "General-purpose unconstrained non-linear optimization")
3634 "This package provides an implementation of an algorithm for
3635 general-purpose unconstrained non-linear optimization. The algorithm is of
3636 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3637 search with a trust region type monitoring of the input to the line search
3638 algorithm. The interface of @code{ucminf} is designed for easy interchange
3639 with the package @code{optim}.")
3640 (license license:gpl2+)))
3642 (define-public r-ordinal
3645 (version "2019.12-10")
3649 (uri (cran-uri "ordinal" version))
3652 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3653 (build-system r-build-system)
3655 `(("r-mass" ,r-mass)
3656 ("r-matrix" ,r-matrix)
3657 ("r-numderiv" ,r-numderiv)
3658 ("r-ucminf" ,r-ucminf)))
3659 (home-page "https://github.com/runehaubo/ordinal")
3660 (synopsis "Regression models for ordinal data")
3662 "This package provides an implementation of cumulative link (mixed)
3663 models also known as ordered regression models, proportional odds models,
3664 proportional hazards models for grouped survival times and ordered models.
3665 Estimation is via maximum likelihood and mixed models are fitted with the
3666 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3667 (license license:gpl2+)))
3669 (define-public r-jomo
3676 (uri (cran-uri "jomo" version))
3679 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3680 (build-system r-build-system)
3682 `(("r-lme4" ,r-lme4)
3684 ("r-ordinal" ,r-ordinal)
3685 ("r-survival" ,r-survival)))
3686 (home-page "https://cran.r-project.org/web/packages/jomo/")
3687 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3689 "Similarly to Schafer's package pan, jomo is a package for multilevel
3690 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3691 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3692 possibility of handling binary and categorical data through latent normal
3693 variables, the option to use cluster-specific covariance matrices and to
3694 impute compatibly with the substantive model.")
3695 (license license:gpl2)))
3697 (define-public r-pan
3704 (uri (cran-uri "pan" version))
3707 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3708 (build-system r-build-system)
3709 (native-inputs `(("gfortran" ,gfortran)))
3710 (home-page "https://cran.r-project.org/web/packages/pan/")
3711 (synopsis "Multiple imputation for multivariate panel or clustered data")
3713 "This package implements multiple imputation for multivariate panel or
3715 (license license:gpl3)))
3717 (define-public r-mitml
3724 (uri (cran-uri "mitml" version))
3727 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3728 (build-system r-build-system)
3730 `(("r-haven" ,r-haven)
3733 (home-page "https://cran.r-project.org/web/packages/mitml/")
3734 (synopsis "Tools for multiple imputation in multilevel modeling")
3736 "This package provides tools for multiple imputation of missing data in
3737 multilevel modeling. It includes a user-friendly interface to the packages
3738 pan and jomo, and several functions for visualization, data management and the
3739 analysis of multiply imputed data sets.")
3740 (license license:gpl2+)))
3742 (define-public r-mice
3749 (uri (cran-uri "mice" version))
3752 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3753 (build-system r-build-system)
3755 `(("r-broom" ,r-broom)
3756 ("r-dplyr" ,r-dplyr)
3757 ("r-generics" ,r-generics)
3758 ("r-lattice" ,r-lattice)
3760 ("r-tidyr" ,r-tidyr)))
3761 (home-page "https://cran.r-project.org/web/packages/mice/")
3762 (synopsis "Multivariate imputation by chained equations")
3764 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3765 implemented by the MICE algorithm as described in @url{Van Buuren and
3766 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3767 variable has its own imputation model. Built-in imputation models are
3768 provided for continuous data (predictive mean matching, normal), binary
3769 data (logistic regression), unordered categorical data (polytomous logistic
3770 regression) and ordered categorical data (proportional odds). MICE can also
3771 impute continuous two-level data (normal model, pan, second-level variables).
3772 Passive imputation can be used to maintain consistency between variables.
3773 Various diagnostic plots are available to inspect the quality of the
3775 ;; Any of these two versions.
3776 (license (list license:gpl2 license:gpl3))))
3778 (define-public r-truncnorm
3780 (name "r-truncnorm")
3785 (uri (cran-uri "truncnorm" version))
3788 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3789 (build-system r-build-system)
3790 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3791 (synopsis "Truncated normal distribution")
3792 (description "This package provides functions for the truncated normal
3793 distribution with mean equal to @code{mean} and standard deviation equal to
3794 @code{sd}. It includes density, distribution, quantile, and expected value
3795 functions, as well as a random generation function.")
3796 (license license:gpl2)))
3798 (define-public r-rsolnp
3805 (uri (cran-uri "Rsolnp" version))
3808 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3809 (properties `((upstream-name . "Rsolnp")))
3810 (build-system r-build-system)
3812 `(("r-truncnorm" ,r-truncnorm)))
3813 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3814 (synopsis "General non-linear optimization")
3815 (description "The Rsolnp package implements a general non-linear augmented
3816 Lagrange multiplier method solver, a @dfn{sequential quadratic
3817 programming} (SQP) based solver).")
3818 ;; Any version of the GPL.
3819 (license license:gpl2+)))
3821 (define-public r-hardyweinberg
3823 (name "r-hardyweinberg")
3828 (uri (cran-uri "HardyWeinberg" version))
3831 "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh"))))
3832 (properties `((upstream-name . "HardyWeinberg")))
3833 (build-system r-build-system)
3835 `(("r-mice" ,r-mice)
3837 ("r-rsolnp" ,r-rsolnp)))
3838 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3839 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3841 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3842 diallelic genetic marker data. All classical tests (chi-square, exact,
3843 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3844 included in the package, as well as functions for power computation and for
3845 the simulation of marker data under equilibrium and disequilibrium. Routines
3846 for dealing with markers on the X-chromosome are included. Functions for
3847 testing equilibrium in the presence of missing data by using multiple
3848 imputation are also provided. Implements several graphics for exploring the
3849 equilibrium status of a large set of diallelic markers: ternary plots with
3850 acceptance regions, log-ratio plots and Q-Q plots.")
3851 (license license:gpl2+)))
3860 (uri (cran-uri "sm" version))
3863 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3864 (build-system r-build-system)
3865 (native-inputs `(("gfortran" ,gfortran)))
3866 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3867 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3869 "This is software accompanying the book 'Applied Smoothing Techniques for
3870 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3871 University Press. It provides smoothing methods for nonparametric regression
3872 and density estimation")
3873 (license license:gpl2+)))
3875 (define-public r-venndiagram
3877 (name "r-venndiagram")
3881 (uri (cran-uri "VennDiagram" version))
3884 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3885 (properties `((upstream-name . "VennDiagram")))
3886 (build-system r-build-system)
3888 `(("r-futile-logger" ,r-futile-logger)))
3889 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3890 (synopsis "Generate High-Resolution Venn and Euler Plots")
3892 "This package provides a set of functions to generate high-resolution
3893 Venn and Euler plots. It includes handling for several special cases,
3894 including two-case scaling, and extensive customization of plot shape and
3896 (license license:gpl2+)))
3898 (define-public r-vioplot
3905 (uri (cran-uri "vioplot" version))
3908 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3909 (build-system r-build-system)
3914 `(("r-knitr" ,r-knitr)))
3915 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3916 (synopsis "Violin plot")
3918 "This package provides a violin plot, which is a combination of a box
3919 plot and a kernel density plot.")
3920 (license license:bsd-3)))
3922 (define-public r-rsofia
3928 ;; This package has been removed from CRAN, so we can
3929 ;; only fetch it from the archives.
3930 (uri (string-append "https://cran.r-project.org/src/"
3931 "contrib/Archive/RSofia/RSofia_"
3935 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3936 (properties `((upstream-name . "RSofia")))
3937 (build-system r-build-system)
3939 `(("r-rcpp" ,r-rcpp)))
3940 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3941 (synopsis "Port of sofia-ml to R")
3942 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3943 suite of fast incremental algorithms for machine learning that can be used for
3944 training models for classification or ranking.")
3945 (license license:asl2.0)))
3947 (define-public r-xts
3954 (uri (cran-uri "xts" version))
3957 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3958 (build-system r-build-system)
3959 (propagated-inputs `(("r-zoo" ,r-zoo)))
3960 (home-page "https://github.com/joshuaulrich/xts")
3961 (synopsis "Extensible time series")
3963 "This package provides for uniform handling of R's different time-based
3964 data classes by extending @code{zoo}, maximizing native format information
3965 preservation and allowing for user-level customization and extension, while
3966 simplifying cross-class interoperability.")
3967 (license license:gpl2+)))
3969 (define-public r-performanceanalytics
3971 (name "r-performanceanalytics")
3976 (uri (cran-uri "PerformanceAnalytics" version))
3979 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3981 `((upstream-name . "PerformanceAnalytics")))
3982 (build-system r-build-system)
3984 `(("r-quadprog" ,r-quadprog)
3987 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3988 (synopsis "Econometric tools for performance and risk analysis")
3989 (description "This is a collection of econometric functions for
3990 performance and risk analysis. This package aims to aid practitioners and
3991 researchers in utilizing the latest research in analysis of non-normal return
3992 streams. In general, it is most tested on return (rather than price) data on
3993 a regular scale, but most functions will work with irregular return data as
3994 well, and increasing numbers of functions will work with P&L or price data
3996 ;; Either version may be picked.
3997 (license (list license:gpl2 license:gpl3))))
3999 (define-public r-laeken
4006 (uri (cran-uri "laeken" version))
4009 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4010 (build-system r-build-system)
4012 `(("r-boot" ,r-boot)
4013 ("r-mass" ,r-mass)))
4014 (home-page "https://cran.r-project.org/web/packages/laeken/")
4015 (synopsis "Estimation of indicators on social exclusion and poverty")
4016 (description "This package provides tools for the estimation of indicators
4017 on social exclusion and poverty, as well as an implementation of Pareto tail
4018 modeling for empirical income distributions.")
4019 (license license:gpl2+)))
4021 (define-public r-vcd
4028 (uri (cran-uri "vcd" version))
4031 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4032 (build-system r-build-system)
4034 `(("r-colorspace" ,r-colorspace)
4035 ("r-lmtest" ,r-lmtest)
4036 ("r-mass" ,r-mass)))
4037 (home-page "https://cran.r-project.org/web/packages/vcd/")
4038 (synopsis "Visualizing categorical data")
4039 (description "This package provides visualization techniques, data sets,
4040 summary and inference procedures aimed particularly at categorical data.
4041 Special emphasis is given to highly extensible grid graphics. The package was
4042 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4043 Friendly and is now the main support package for a new book, \"Discrete Data
4044 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4045 (license license:gpl2)))
4047 (define-public r-ica
4054 (uri (cran-uri "ica" version))
4057 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4058 (build-system r-build-system)
4059 (home-page "https://cran.r-project.org/web/packages/ica/")
4060 (synopsis "Independent component analysis")
4061 (description "This package provides tools for @dfn{Independent Component
4062 Analysis} (ICA) using various algorithms: FastICA,
4063 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4064 of Eigenmatrices} (JADE).")
4065 (license license:gpl2+)))
4067 (define-public r-dtw
4074 (uri (cran-uri "dtw" version))
4077 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4078 (build-system r-build-system)
4079 (propagated-inputs `(("r-proxy" ,r-proxy)))
4080 (home-page "http://dtw.r-forge.r-project.org/")
4081 (synopsis "Dynamic Time Warping Algorithms")
4082 (description "This package provides a comprehensive implementation of
4083 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4084 optimal (least cumulative distance) alignment between points of two time
4085 series. Common DTW variants covered include local (slope) and global (window)
4086 constraints, subsequence matches, arbitrary distance definitions,
4087 normalizations, minimum variance matching, and so on.")
4088 (license license:gpl2+)))
4090 (define-public r-sdmtools
4093 (version "1.1-221.2")
4097 (uri (cran-uri "SDMTools" version))
4100 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4101 (properties `((upstream-name . "SDMTools")))
4102 (build-system r-build-system)
4103 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4104 (home-page "https://www.rforge.net/SDMTools/")
4105 (synopsis "Species distribution modelling tools")
4106 (description "This package provides a set of tools for post processing
4107 the outcomes of species distribution modeling exercises. It includes novel
4108 methods for comparing models and tracking changes in distributions through
4109 time. It further includes methods for visualizing outcomes, selecting
4110 thresholds, calculating measures of accuracy and landscape fragmentation
4112 (license license:gpl3+)))
4114 (define-public r-scatterplot3d
4116 (name "r-scatterplot3d")
4121 (uri (cran-uri "scatterplot3d" version))
4124 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4125 (build-system r-build-system)
4126 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4127 (synopsis "3D scatter plot")
4128 (description "This package provides an implementation of scatter plots for
4129 plotting. a three dimensional point cloud.")
4130 (license license:gpl2)))
4132 (define-public r-ggridges
4139 (uri (cran-uri "ggridges" version))
4142 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4143 (build-system r-build-system)
4145 `(("r-ggplot2" ,r-ggplot2)
4147 ("r-scales" ,r-scales)
4148 ("r-withr" ,r-withr)))
4149 (home-page "https://github.com/clauswilke/ggridges")
4150 (synopsis "Ridgeline plots in ggplot2")
4152 "Ridgeline plots provide a convenient way of visualizing changes in
4153 distributions over time or space. This package enables the creation of such
4154 plots in @code{ggplot2}.")
4155 (license license:gpl2)))
4157 (define-public r-ggjoy
4164 (uri (cran-uri "ggjoy" version))
4167 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4168 (build-system r-build-system)
4170 `(("r-ggplot2" ,r-ggplot2)
4171 ("r-ggridges" ,r-ggridges)))
4172 (home-page "https://github.com/clauswilke/ggjoy")
4173 (synopsis "Joyplots in ggplot2")
4174 (description "Joyplots provide a convenient way of visualizing changes in
4175 distributions over time or space. This package enables the creation of such
4176 plots in @code{ggplot2}.")
4177 (license license:gpl2)))
4179 (define-public r-cli
4186 (uri (cran-uri "cli" version))
4189 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4190 (build-system r-build-system)
4192 `(("r-assertthat" ,r-assertthat)
4193 ("r-crayon" ,r-crayon)
4194 ("r-fansi" ,r-fansi)
4195 ("r-glue" ,r-glue)))
4196 (home-page "https://github.com/r-lib/cli#readme")
4197 (synopsis "Helpers for developing command line interfaces")
4198 (description "This package provides a suite of tools designed to build
4199 attractive command line interfaces (CLIs). It includes tools for drawing
4200 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4201 (license license:expat)))
4203 (define-public r-argparser
4205 (name "r-argparser")
4210 (uri (cran-uri "argparser" version))
4213 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4214 (build-system r-build-system)
4215 (home-page "https://bitbucket.org/djhshih/argparser")
4216 (synopsis "Command-line argument parser")
4218 "This package provides a cross-platform command-line argument parser
4219 written purely in R with no external dependencies. It is useful with the
4220 Rscript front-end and facilitates turning an R script into an executable
4222 (license license:gpl3+)))
4224 (define-public r-debugme
4231 (uri (cran-uri "debugme" version))
4234 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4235 (build-system r-build-system)
4236 (propagated-inputs `(("r-crayon" ,r-crayon)))
4237 (home-page "https://github.com/r-lib/debugme#readme")
4238 (synopsis "Debug R packages")
4240 "This package allows the user to specify debug messages as special string
4241 constants, and control debugging of packages via environment variables.")
4242 (license license:expat)))
4244 (define-public r-processx
4251 (uri (cran-uri "processx" version))
4253 (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
4254 (build-system r-build-system)
4258 (home-page "https://github.com/r-lib/processx3")
4259 (synopsis "Execute and control system processes")
4261 "This package provides portable tools to run system processes in the
4262 background. It can check if a background process is running; wait on a
4263 background process to finish; get the exit status of finished processes; kill
4264 background processes and their children; restart processes. It can read the
4265 standard output and error of the processes, using non-blocking connections.
4266 @code{processx} can poll a process for standard output or error, with a
4267 timeout. It can also poll several processes at once.")
4268 (license license:expat)))
4270 (define-public r-tsp
4277 (uri (cran-uri "TSP" version))
4280 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4281 (properties `((upstream-name . "TSP")))
4282 (build-system r-build-system)
4283 (propagated-inputs `(("r-foreach" ,r-foreach)))
4284 (home-page "https://cran.r-project.org/web/packages/TSP/")
4285 (synopsis "Traveling salesperson problem (TSP)")
4286 (description "This package provides basic infrastructure and some
4287 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4288 traveling salesman problem).")
4289 (license license:gpl3)))
4291 (define-public r-qap
4298 (uri (cran-uri "qap" version))
4301 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4302 (build-system r-build-system)
4303 (native-inputs `(("gfortran" ,gfortran)))
4304 (home-page "https://cran.r-project.org/web/packages/qap/")
4305 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4306 (description "This package implements heuristics for the @dfn{quadratic
4307 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4309 (license license:gpl3)))
4311 (define-public r-gclus
4318 (uri (cran-uri "gclus" version))
4321 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4322 (build-system r-build-system)
4323 (propagated-inputs `(("r-cluster" ,r-cluster)))
4324 (home-page "https://cran.r-project.org/web/packages/gclus/")
4325 (synopsis "Clustering graphics")
4326 (description "This package orders panels in scatterplot matrices and
4327 parallel coordinate displays by some merit index. It contains various indices
4328 of merit, ordering functions, and enhanced versions of @code{pairs} and
4329 @code{parcoord} which color panels according to their merit level.")
4330 (license license:gpl2+)))
4332 (define-public r-webshot
4339 (uri (cran-uri "webshot" version))
4342 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4343 (build-system r-build-system)
4345 `(("r-callr" ,r-callr)
4346 ("r-jsonlite" ,r-jsonlite)
4347 ("r-magrittr" ,r-magrittr)))
4348 (home-page "https://github.com/wch/webshot/")
4349 (synopsis "Take screenshots of web pages")
4351 "Webshot makes it easy to take screenshots of web pages from within R.
4352 It can also run Shiny applications locally and take screenshots of the
4353 application; and it can render and screenshot static as well as interactive R
4354 Markdown documents.")
4355 (license license:gpl2)))
4357 (define-public r-seriation
4359 (name "r-seriation")
4364 (uri (cran-uri "seriation" version))
4367 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4368 (build-system r-build-system)
4370 `(("r-cluster" ,r-cluster)
4371 ("r-colorspace" ,r-colorspace)
4372 ("r-dendextend" ,r-dendextend)
4373 ("r-gclus" ,r-gclus)
4374 ("r-gplots" ,r-gplots)
4377 ("r-registry" ,r-registry)
4379 (native-inputs `(("gfortran" ,gfortran)))
4380 (home-page "https://s2.smu.edu/IDA/seriation/")
4381 (synopsis "Infrastructure for ordering objects using seriation")
4383 "This package provides infrastructure for seriation with an
4384 implementation of several seriation/sequencing techniques to reorder matrices,
4385 dissimilarity matrices, and dendrograms. It also provides (optimally)
4386 reordered heatmaps, color images and clustering visualizations like
4387 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4389 (license license:gpl3)))
4391 (define-public r-xfun
4398 (uri (cran-uri "xfun" version))
4400 (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
4401 (build-system r-build-system)
4402 ;; knitr itself depends on xfun
4405 `(("r-knitr" ,r-knitr)))
4406 (home-page "https://github.com/yihui/xfun")
4407 (synopsis "Miscellaneous functions")
4409 "This package provides miscellaneous functions commonly used in other
4410 packages maintained by Yihui Xie.")
4411 (license license:expat)))
4413 (define-public r-utf8
4420 (uri (cran-uri "utf8" version))
4423 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4424 (build-system r-build-system)
4425 (home-page "https://github.com/patperry/r-utf8")
4426 (synopsis "Unicode text processing")
4428 "This package provides tools to process and print UTF-8 encoded
4429 international text (Unicode). Input, validate, normalize, encode, format, and
4431 (license license:asl2.0)))
4433 (define-public r-zeallot
4440 (uri (cran-uri "zeallot" version))
4443 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4444 (build-system r-build-system)
4445 (home-page "https://github.com/nteetor/zeallot")
4446 (synopsis "Multiple, unpacking, and destructuring assignment")
4448 "This package provides a @code{%<-%} operator to perform multiple,
4449 unpacking, and destructuring assignment in R. The operator unpacks the
4450 right-hand side of an assignment into multiple values and assigns these values
4451 to variables on the left-hand side of the assignment.")
4452 (license license:expat)))
4454 (define-public r-vctrs
4461 (uri (cran-uri "vctrs" version))
4464 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
4465 (build-system r-build-system)
4467 `(("r-digest" ,r-digest)
4468 ("r-ellipsis" ,r-ellipsis)
4470 ("r-rlang" ,r-rlang)))
4472 `(("r-knitr" ,r-knitr)))
4473 (home-page "https://github.com/r-lib/vctrs")
4474 (synopsis "Vector helpers")
4476 "There are three main goals to the @code{vctrs} package:
4479 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4480 @code{length()} and @code{class()}. These definitions are paired with a
4481 framework for type-coercion and size-recycling.
4482 @item To define type- and size-stability as desirable function properties, use
4483 them to analyse existing base function, and to propose better alternatives.
4484 This work has been particularly motivated by thinking about the ideal
4485 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4486 @item To provide a new @code{vctr} base class that makes it easy to create new
4487 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4488 a few new @code{vctrs} generics, making implementation considerably simpler
4491 (license license:gpl3)))
4493 (define-public r-pillar
4500 (uri (cran-uri "pillar" version))
4503 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4504 (build-system r-build-system)
4507 ("r-crayon" ,r-crayon)
4508 ("r-ellipsis" ,r-ellipsis)
4509 ("r-fansi" ,r-fansi)
4510 ("r-lifecycle" ,r-lifecycle)
4511 ("r-rlang" ,r-rlang)
4513 ("r-vctrs" ,r-vctrs)))
4514 (home-page "https://github.com/r-lib/pillar")
4515 (synopsis "Coloured formatting for columns")
4517 "This package provides a @code{pillar} generic designed for formatting
4518 columns of data using the full range of colours provided by modern
4520 (license license:gpl3)))
4522 (define-public r-uuid
4529 (uri (cran-uri "uuid" version))
4532 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4533 (build-system r-build-system)
4534 (home-page "https://www.rforge.net/uuid")
4535 (synopsis "Tools for generating and handling of UUIDs")
4537 "This package provides tools for generating and handling of
4538 @dfn{Universally Unique Identifiers} (UUIDs).")
4539 (license license:expat)))
4541 (define-public r-tinytex
4548 (uri (cran-uri "tinytex" version))
4551 "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza"))))
4552 (build-system r-build-system)
4554 `(("r-xfun" ,r-xfun)))
4555 (home-page "https://github.com/yihui/tinytex")
4556 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4558 "This package provides helper functions to install and maintain the LaTeX
4559 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4560 easy-to-maintain version of TeX Live. This package also contains helper
4561 functions to compile LaTeX documents, and install missing LaTeX packages
4563 (license license:expat)))
4565 (define-public r-network
4572 (uri (cran-uri "network" version))
4575 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4576 (build-system r-build-system)
4578 `(("r-magrittr" ,r-magrittr)
4579 ("r-tibble" ,r-tibble)))
4580 (home-page "https://statnet.org/")
4581 (synopsis "Classes for relational data")
4583 "This package provides tools to create and modify network objects. The
4584 @code{network} class can represent a range of relational data types, and
4585 supports arbitrary vertex/edge/graph attributes.")
4586 (license license:gpl2+)))
4588 (define-public r-statnet-common
4590 (name "r-statnet-common")
4595 (uri (cran-uri "statnet.common" version))
4598 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4600 `((upstream-name . "statnet.common")))
4601 (build-system r-build-system)
4603 `(("r-coda" ,r-coda)))
4604 (home-page "https://statnet.org")
4605 (synopsis "R scripts and utilities used by the Statnet software")
4606 (description "This package provides non-statistical utilities used by the
4607 software developed by the Statnet Project.")
4608 (license license:gpl3)))
4610 (define-public r-statcheck
4612 (name "r-statcheck")
4617 (uri (cran-uri "statcheck" version))
4620 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4621 (build-system r-build-system)
4623 `(("r-ggplot2" ,r-ggplot2)
4625 ("r-rmarkdown" ,r-rmarkdown)))
4626 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4627 (synopsis "Extract statistics from articles and recompute p-values")
4628 (description "This package can automatically extract statistical
4629 null-hypothesis significant testing (NHST) results from articles and recompute
4630 the p-values based on the reported test statistic and degrees of freedom to
4631 detect possible inconsistencies.")
4632 (license license:gpl2)))
4634 (define-public r-sna
4641 (uri (cran-uri "sna" version))
4644 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4645 (build-system r-build-system)
4647 `(("r-network" ,r-network)
4648 ("r-statnet-common" ,r-statnet-common)))
4649 (home-page "https://statnet.org")
4650 (synopsis "Tools for social network analysis")
4652 "This package provides a range of tools for social network analysis,
4653 including node and graph-level indices, structural distance and covariance
4654 methods, structural equivalence detection, network regression, random graph
4655 generation, and 2D/3D network visualization.")
4656 (license license:gpl2+)))
4658 (define-public r-tfisher
4665 (uri (cran-uri "TFisher" version))
4668 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4669 (properties `((upstream-name . "TFisher")))
4670 (build-system r-build-system)
4672 `(("r-matrix" ,r-matrix)
4673 ("r-mvtnorm" ,r-mvtnorm)
4675 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4676 (synopsis "Optimal thresholding Fisher's p-value combination method")
4678 "This package provides the @dfn{cumulative distribution function} (CDF),
4679 quantile, and statistical power calculator for a collection of thresholding
4680 Fisher's p-value combination methods, including Fisher's p-value combination
4681 method, truncated product method and, in particular, soft-thresholding
4682 Fisher's p-value combination method which is proven to be optimal in some
4683 context of signal detection. The p-value calculator for the omnibus version
4684 of these tests are also included.")
4685 (license license:gpl2)))
4687 (define-public r-ttr
4694 (uri (cran-uri "TTR" version))
4697 "12g187pljnxjjx0s0rsq9lzvwvxyvymi6l9ykkkzg1j48mi1dm56"))))
4698 (properties `((upstream-name . "TTR")))
4699 (build-system r-build-system)
4701 `(("r-curl" ,r-curl)
4704 (home-page "https://github.com/joshuaulrich/TTR")
4705 (synopsis "Technical trading rules")
4707 "This package provides functions and data to construct technical trading
4709 (license license:gpl2)))
4711 (define-public r-leaps
4718 (uri (cran-uri "leaps" version))
4721 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4722 (build-system r-build-system)
4723 (native-inputs `(("gfortran" ,gfortran)))
4724 (home-page "https://cran.r-project.org/web/packages/leaps/")
4725 (synopsis "Regression subset selection")
4727 "This package provides tools for regression subset selection, including
4728 exhaustive search.")
4729 (license license:gpl2+)))
4731 (define-public r-splus2r
4738 (uri (cran-uri "splus2R" version))
4741 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4742 (properties `((upstream-name . "splus2R")))
4743 (build-system r-build-system)
4744 (native-inputs `(("gfortran" ,gfortran)))
4745 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4746 (synopsis "Supplemental S-PLUS functionality in R")
4748 "Currently there are many functions in S-PLUS that are missing in R. To
4749 facilitate the conversion of S-PLUS packages to R packages, this package
4750 provides some missing S-PLUS functionality in R.")
4751 (license license:gpl2)))
4753 (define-public r-ifultools
4755 (name "r-ifultools")
4760 (uri (cran-uri "ifultools" version))
4763 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4764 (build-system r-build-system)
4766 `(("r-mass" ,r-mass)
4767 ("r-splus2r" ,r-splus2r)))
4768 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4769 (synopsis "Insightful research tools")
4770 (description "This package provides C code used by the wmtsa, fractal, and
4772 (license license:gpl2)))
4774 (define-public r-sapa
4781 (uri (cran-uri "sapa" version))
4784 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4785 (build-system r-build-system)
4787 `(("r-ifultools" ,r-ifultools)
4788 ("r-splus2r" ,r-splus2r)))
4789 (home-page "https://cran.r-project.org/web/packages/sapa/")
4790 (synopsis "Spectral analysis for physical applications")
4791 (description "This package provides software for the book Spectral
4792 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4793 Cambridge University Press, 1993.")
4794 (license license:gpl2)))
4796 (define-public r-aggregation
4798 (name "r-aggregation")
4803 (uri (cran-uri "aggregation" version))
4806 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4807 (build-system r-build-system)
4808 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4809 (synopsis "Methods for p-value aggregation")
4811 "This package contains functionality for performing the following methods
4812 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4813 Fisher's method), and Sidak correction.")
4814 (license license:gpl3)))
4816 (define-public r-quantmod
4823 (uri (cran-uri "quantmod" version))
4826 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4827 (build-system r-build-system)
4829 `(("r-curl" ,r-curl)
4833 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4834 (synopsis "Quantitative financial modelling framework")
4835 (description "This package provides a quantitative financial modelling
4836 framework to allow users to specify, build, trade, and analyse quantitative
4837 financial trading strategies.")
4838 (license license:gpl3)))
4840 (define-public r-tseries
4847 (uri (cran-uri "tseries" version))
4850 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4851 (build-system r-build-system)
4853 `(("r-quadprog" ,r-quadprog)
4854 ("r-quantmod" ,r-quantmod)
4857 `(("gfortran" ,gfortran)))
4858 (home-page "https://cran.r-project.org/web/packages/tseries/")
4859 (synopsis "Time series analysis and computational finance")
4861 "This package provides functions relating to time series analysis and
4862 computational finance.")
4863 (license license:gpl2)))
4865 (define-public r-wmtsa
4872 (uri (cran-uri "wmtsa" version))
4875 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4876 (build-system r-build-system)
4878 `(("r-ifultools" ,r-ifultools)
4880 ("r-splus2r" ,r-splus2r)))
4881 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4882 (synopsis "Wavelet methods for time series analysis")
4884 "This package provides software to accompany the book \"Wavelet Methods
4885 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4886 University Press, 2000.")
4887 (license license:gpl2)))
4889 (define-public r-tsa
4896 (uri (cran-uri "TSA" version))
4899 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4900 (properties `((upstream-name . "TSA")))
4901 (build-system r-build-system)
4903 `(("r-leaps" ,r-leaps)
4904 ("r-locfit" ,r-locfit)
4905 ("r-mgcv" ,r-mgcv)))
4906 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4907 (synopsis "Time series analysis")
4909 "This package contains R functions and datasets detailed in the book
4910 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4911 Cryer and Kung-Sik Chan.")
4912 (license license:gpl2+)))
4914 (define-public r-extradistr
4916 (name "r-extradistr")
4921 (uri (cran-uri "extraDistr" version))
4924 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4925 (properties `((upstream-name . "extraDistr")))
4926 (build-system r-build-system)
4928 `(("r-rcpp" ,r-rcpp)))
4929 (home-page "https://github.com/twolodzko/extraDistr")
4930 (synopsis "Additional univariate and multivariate distributions")
4932 "This package implements density, distribution functions, quantile
4933 functions and random generation functions for a large number of univariate and
4934 multivariate distributions.")
4935 (license license:gpl2)))
4937 (define-public r-fractal
4944 (uri (cran-uri "fractal" version))
4947 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4948 (build-system r-build-system)
4950 `(("r-ifultools" ,r-ifultools)
4953 ("r-scatterplot3d" ,r-scatterplot3d)
4954 ("r-splus2r" ,r-splus2r)
4955 ("r-wmtsa" ,r-wmtsa)))
4956 (home-page "https://cran.r-project.org/web/packages/fractal/")
4957 (synopsis "Fractal time series modeling and analysis")
4959 "This package provides tools for stochastic fractal and deterministic
4960 chaotic time series analysis.")
4961 (license license:gpl2)))
4963 (define-public r-urca
4970 (uri (cran-uri "urca" version))
4973 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4974 (build-system r-build-system)
4975 (propagated-inputs `(("r-nlme" ,r-nlme)))
4976 (native-inputs `(("gfortran" ,gfortran)))
4977 (home-page "https://cran.r-project.org/web/packages/urca/")
4978 (synopsis "Unit root and cointegration tests for time series data")
4980 "This package provides unit root and cointegration tests encountered in
4981 applied econometric analysis.")
4982 (license license:gpl2+)))
4984 (define-public r-cubature
4991 (uri (cran-uri "cubature" version))
4994 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
4995 (build-system r-build-system)
4997 `(("r-rcpp" ,r-rcpp)))
4999 `(("r-knitr" ,r-knitr)))
5000 (home-page "https://github.com/bnaras/cubature")
5001 (synopsis "Adaptive multivariate integration over hypercubes")
5003 "This package is an R wrapper around the cubature C library for adaptive
5004 multivariate integration over hypercubes. This version provides both
5005 @code{hcubature} and @code{pcubature} routines in addition to a vector
5007 ;; The included cubature C library is released under GPLv2+, but the
5008 ;; wrapper declares the license to be GPLv3+.
5009 (license (list license:gpl2+ license:gpl3+))))
5011 (define-public r-trend
5018 (uri (cran-uri "trend" version))
5021 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
5022 (build-system r-build-system)
5024 `(("r-extradistr" ,r-extradistr)))
5026 `(("gfortran" ,gfortran)))
5027 (home-page "https://cran.r-project.org/web/packages/trend/")
5028 (synopsis "Non-parametric trend tests and change-point detection")
5030 "The analysis of environmental data often requires the detection of
5031 trends and change-points. This package includes tests for trend
5032 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5033 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5034 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5035 correlation trend test), change-point detection (Lanzante's test procedures,
5036 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5037 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5038 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5039 sample Robust Rank-Order Distributional Test.")
5040 (license license:gpl3)))
5042 (define-public r-expm
5049 (uri (cran-uri "expm" version))
5052 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5053 (build-system r-build-system)
5054 (propagated-inputs `(("r-matrix" ,r-matrix)))
5055 (native-inputs `(("gfortran" ,gfortran)))
5056 (home-page "https://r-forge.r-project.org/projects/expm/")
5057 (synopsis "Tools for matrix exponentials and related quantities")
5059 "This package provides tools for the computation of the matrix
5060 exponential, logarithm, square root, and related quantities.")
5061 (license license:gpl2+)))
5063 (define-public r-complexplus
5065 (name "r-complexplus")
5070 (uri (cran-uri "complexplus" version))
5073 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5074 (build-system r-build-system)
5076 `(("r-expm" ,r-expm)
5077 ("r-matrix" ,r-matrix)))
5078 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5079 (synopsis "Functions of complex or real variables")
5081 "This package extends several functions to the complex domain, including
5082 the matrix exponential and logarithm, and the determinant.")
5083 (license license:gpl2)))
5085 (define-public r-phontools
5087 (name "r-phontools")
5092 (uri (cran-uri "phonTools" version))
5095 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5096 (properties `((upstream-name . "phonTools")))
5097 (build-system r-build-system)
5098 (home-page "http://www.santiagobarreda.com/rscripts.html")
5099 (synopsis "Tools for phonetic and acoustic analyses")
5101 "This package contains tools for the organization, display, and analysis
5102 of the sorts of data frequently encountered in phonetics research and
5103 experimentation, including the easy creation of IPA vowel plots, and the
5104 creation and manipulation of WAVE audio files.")
5105 (license license:bsd-2)))
5114 (uri (cran-uri "np" version))
5117 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5118 (build-system r-build-system)
5120 `(("r-boot" ,r-boot)
5121 ("r-cubature" ,r-cubature)
5122 ("r-quadprog" ,r-quadprog)
5123 ("r-quantreg" ,r-quantreg)))
5124 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5125 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5126 (description "This package provides non-parametric (and semi-parametric)
5127 kernel methods that seamlessly handle a mix of continuous, unordered, and
5128 ordered factor data types.")
5129 ;; Any version of the GPL.
5130 (license license:gpl3+)))
5132 (define-public r-powerplus
5134 (name "r-powerplus")
5139 (uri (cran-uri "powerplus" version))
5142 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5143 (build-system r-build-system)
5145 `(("r-complexplus" ,r-complexplus)
5148 ("r-matrix" ,r-matrix)
5149 ("r-phontools" ,r-phontools)))
5150 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5151 (synopsis "Exponentiation operations")
5153 "This package provides tools for the computation of matrix and scalar
5155 (license license:gpl2)))
5157 (define-public r-egg
5164 (uri (cran-uri "egg" version))
5167 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5168 (properties `((upstream-name . "egg")))
5169 (build-system r-build-system)
5171 `(("r-ggplot2" ,r-ggplot2)
5172 ("r-gridextra" ,r-gridextra)
5173 ("r-gtable" ,r-gtable)))
5174 (home-page "https://cran.r-project.org/web/packages/egg")
5175 (synopsis "Extensions for ggplot2")
5177 "This package provides miscellaneous functions to help customize ggplot2
5178 objects. High-level functions are provided to post-process ggplot2 layouts
5179 and allow alignment between plot panels, as well as setting panel sizes to
5180 fixed values. Other functions include a custom @code{geom}, and helper
5181 functions to enforce symmetric scales or add tags to facetted plots.")
5182 (license license:gpl3)))
5184 (define-public r-heatmaply
5186 (name "r-heatmaply")
5191 (uri (cran-uri "heatmaply" version))
5194 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5195 (build-system r-build-system)
5197 `(("r-assertthat" ,r-assertthat)
5198 ("r-colorspace" ,r-colorspace)
5199 ("r-dendextend" ,r-dendextend)
5201 ("r-ggplot2" ,r-ggplot2)
5202 ("r-htmlwidgets" ,r-htmlwidgets)
5203 ("r-magrittr" ,r-magrittr)
5204 ("r-plotly" ,r-plotly)
5205 ("r-rcolorbrewer" ,r-rcolorbrewer)
5206 ("r-reshape2" ,r-reshape2)
5207 ("r-scales" ,r-scales)
5208 ("r-seriation" ,r-seriation)
5209 ("r-viridis" ,r-viridis)
5210 ("r-webshot" ,r-webshot)))
5212 `(("r-knitr" ,r-knitr)))
5213 (home-page "https://cran.r-project.org/package=heatmaply")
5214 (synopsis "Interactive cluster heat maps using plotly")
5216 "This package enables you to create interactive cluster heatmaps that can
5217 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5218 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5219 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5220 a popular graphical method for visualizing high-dimensional data, in which a
5221 table of numbers is encoded as a grid of colored cells. The rows and columns
5222 of the matrix are ordered to highlight patterns and are often accompanied by
5224 ;; Either version of the license.
5225 (license (list license:gpl2 license:gpl3))))
5234 (uri (cran-uri "h5" version))
5237 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5238 (build-system r-build-system)
5243 `(("which" ,which)))
5245 `(("r-rcpp" ,r-rcpp)))
5246 (home-page "https://github.com/mannau/h5")
5247 (synopsis "Interface to the HDF5 Library")
5249 "This package provides an S4 interface to the HDF5 library supporting
5250 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5251 binary files in a language independent format. The HDF5 format can therefore
5252 be used as an alternative to R's save/load mechanism. Since h5 is able to
5253 access only subsets of stored data it can also handle data sets which do not
5255 (license license:bsd-2)))
5257 (define-public r-cgdsr
5264 (uri (cran-uri "cgdsr" version))
5267 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5268 (build-system r-build-system)
5270 `(("r-httr" ,r-httr)
5271 ("r-r-methodss3" ,r-r-methodss3)
5272 ("r-r-oo" ,r-r-oo)))
5273 (home-page "https://github.com/cBioPortal/cgdsr")
5274 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5276 "This package provides a basic set of R functions for querying the Cancer
5277 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5278 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5279 (license license:lgpl3)))
5281 (define-public r-import
5288 (uri (cran-uri "import" version))
5291 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5292 (build-system r-build-system)
5293 (home-page "https://github.com/smbache/import")
5294 (synopsis "Import mechanism for R")
5296 "This is an alternative mechanism for importing objects from packages.
5297 The syntax allows for importing multiple objects from a package with a single
5298 command in an expressive way. The import package bridges some of the gap
5299 between using @code{library} (or @code{require}) and direct (single-object)
5300 imports. Furthermore the imported objects are not placed in the current
5301 environment. It is also possible to import objects from stand-alone @code{.R}
5303 (license license:expat)))
5305 (define-public r-shinyace
5312 (uri (cran-uri "shinyAce" version))
5315 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5316 (properties `((upstream-name . "shinyAce")))
5317 (build-system r-build-system)
5319 `(("r-shiny" ,r-shiny)
5320 ("r-jsonlite" ,r-jsonlite)))
5321 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5322 (synopsis "Ace editor bindings for Shiny")
5324 "This package provides Ace editor bindings to enable a rich text editing
5325 environment within Shiny.")
5326 (license license:expat)))
5328 (define-public r-randomizr
5330 (name "r-randomizr")
5335 (uri (cran-uri "randomizr" version))
5338 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5339 (properties `((upstream-name . "randomizr")))
5340 (build-system r-build-system)
5342 `(("r-knitr" ,r-knitr)))
5343 (home-page "https://declaredesign.org/r/randomizr/")
5344 (synopsis "Tools for common forms of random assignment and sampling")
5346 "This package provides tools for generating random assignments for common
5347 experimental designs and random samples for common sampling designs.")
5348 (license license:expat)))
5350 (define-public r-base64url
5352 (name "r-base64url")
5357 (uri (cran-uri "base64url" version))
5360 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5361 (build-system r-build-system)
5363 `(("r-backports" ,r-backports)))
5364 (home-page "https://github.com/mllg/base64url")
5365 (synopsis "Fast and URL-safe base64 encoder and decoder")
5367 "This package provides a URL-safe base64 encoder and decoder. In
5368 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5369 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5370 encoder does not fill the string with trailing @code{=}. The resulting
5371 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5372 and thus are safe to use in URLs or for file names. The package also comes
5373 with a simple base32 encoder/decoder suited for case insensitive file
5375 (license license:gpl3)))
5377 (define-public r-radiant-data
5379 (name "r-radiant-data")
5384 (uri (cran-uri "radiant.data" version))
5387 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5388 (modules '((guix build utils)))
5391 ;; Delete files that are under CC-NC-SA.
5392 (delete-file-recursively "inst/app/tools/help")
5394 (properties `((upstream-name . "radiant.data")))
5395 (build-system r-build-system)
5397 `(("r-base64enc" ,r-base64enc)
5398 ("r-broom" ,r-broom)
5401 ("r-dplyr" ,r-dplyr)
5404 ("r-ggplot2" ,r-ggplot2)
5405 ("r-import" ,r-import)
5406 ("r-jsonlite" ,r-jsonlite)
5407 ("r-knitr" ,r-knitr)
5408 ("r-lubridate" ,r-lubridate)
5409 ("r-magrittr" ,r-magrittr)
5410 ("r-markdown" ,r-markdown)
5412 ("r-patchwork" ,r-patchwork)
5413 ("r-plotly" ,r-plotly)
5414 ("r-psych" ,r-psych)
5415 ("r-randomizr" ,r-randomizr)
5416 ("r-readr" ,r-readr)
5417 ("r-readxl" ,r-readxl)
5418 ("r-rlang" ,r-rlang)
5419 ("r-rmarkdown" ,r-rmarkdown)
5420 ("r-rstudioapi" ,r-rstudioapi)
5421 ("r-scales" ,r-scales)
5422 ("r-shiny" ,r-shiny)
5423 ("r-shinyfiles" ,r-shinyfiles)
5424 ("r-shinyace" ,r-shinyace)
5425 ("r-stringi" ,r-stringi)
5426 ("r-tibble" ,r-tibble)
5427 ("r-tidyr" ,r-tidyr)
5428 ("r-writexl" ,r-writexl)))
5429 (home-page "https://github.com/radiant-rstats/radiant.data")
5430 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5432 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5433 visualizing, summarizing, transforming, and combining data. It also contains
5434 functionality to generate reproducible reports of the analyses conducted in
5436 (license license:agpl3)))
5438 (define-public r-algdesign
5440 (name "r-algdesign")
5445 (uri (cran-uri "AlgDesign" version))
5447 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5448 (properties `((upstream-name . "AlgDesign")))
5449 (build-system r-build-system)
5450 (home-page "https://github.com/jvbraun/AlgDesign")
5451 (synopsis "Algorithmic experimental design")
5453 "This package provides tools to calculate exact and approximate theory
5454 experimental designs for D, A, and I criteria. Very large designs may be
5455 created. Experimental designs may be blocked or blocked designs created from
5456 a candidate list, using several criteria. The blocking can be done when whole
5457 and within plot factors interact.")
5458 (license license:gpl2+)))
5460 (define-public r-signal
5467 (uri (cran-uri "signal" version))
5470 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5471 (build-system r-build-system)
5472 (propagated-inputs `(("r-mass" ,r-mass)))
5473 (native-inputs `(("gfortran" ,gfortran)))
5474 (home-page "https://cran.r-project.org/web/packages/signal/")
5475 (synopsis "Signal processing")
5477 "This package provides a set of signal processing functions originally
5478 written for Matlab and GNU Octave. It includes filter generation utilities,
5479 filtering functions, resampling routines, and visualization of filter models.
5480 It also includes interpolation functions.")
5481 (license license:gpl2)))
5483 (define-public r-gsubfn
5490 (uri (cran-uri "gsubfn" version))
5493 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5494 (build-system r-build-system)
5495 (propagated-inputs `(("r-proto" ,r-proto)))
5496 (home-page "https://code.google.com/archive/p/gsubfn/")
5497 (synopsis "Utilities for strings and function arguments.")
5499 "This package provides @code{gsubfn} which is like @code{gsub} but can
5500 take a replacement function or certain other objects instead of the
5501 replacement string. Matches and back references are input to the replacement
5502 function and replaced by the function output. @code{gsubfn} can be used to
5503 split strings based on content rather than delimiters and for quasi-perl-style
5504 string interpolation. The package also has facilities for translating
5505 formulas to functions and allowing such formulas in function calls instead of
5507 (license license:gpl2+)))
5509 (define-public r-sqldf
5516 (uri (cran-uri "sqldf" version))
5519 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5520 (build-system r-build-system)
5522 `(("r-chron" ,r-chron)
5524 ("r-gsubfn" ,r-gsubfn)
5525 ("r-proto" ,r-proto)
5526 ("r-rsqlite" ,r-rsqlite)))
5527 (home-page "https://github.com/ggrothendieck/sqldf")
5528 (synopsis "Manipulate R data frames using SQL")
5530 "The @code{sqldf} function is typically passed a single argument which is
5531 an SQL select statement where the table names are ordinary R data frame names.
5532 @code{sqldf} transparently sets up a database, imports the data frames into
5533 that database, performs the SQL statement and returns the result using a
5534 heuristic to determine which class to assign to each column of the returned
5535 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5536 used to read filtered files into R even if the original files are larger than
5537 R itself can handle.")
5538 (license license:gpl2)))
5540 (define-public r-abind
5547 (uri (cran-uri "abind" version))
5550 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5551 (build-system r-build-system)
5552 (home-page "https://cran.r-project.org/web/packages/abind/")
5553 (synopsis "Combine multidimensional arrays")
5555 "This package provides tools to combine multidimensional arrays into a
5556 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5557 works with vectors, matrices, and higher-dimensional arrays. It also provides
5558 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5559 extracting and replacing data in arrays.")
5560 (license license:lgpl2.0+)))
5562 (define-public r-prroc
5569 (uri (cran-uri "PRROC" version))
5572 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5573 (properties `((upstream-name . "PRROC")))
5574 (build-system r-build-system)
5575 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5576 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5578 "This package computes the areas under the @dfn{precision-recall} (PR)
5579 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5580 contrast to other implementations, the interpolation between points of the PR
5581 curve is done by a non-linear piecewise function. In addition to the areas
5582 under the curves, the curves themselves can also be computed and plotted by a
5583 specific S3-method.")
5584 (license license:gpl3)))
5586 (define-public r-vim
5593 (uri (cran-uri "VIM" version))
5596 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5597 (properties `((upstream-name . "VIM")))
5598 (build-system r-build-system)
5601 ("r-colorspace" ,r-colorspace)
5602 ("r-data-table" ,r-data-table)
5603 ("r-e1071" ,r-e1071)
5604 ("r-laeken" ,r-laeken)
5605 ("r-magrittr" ,r-magrittr)
5608 ("r-ranger" ,r-ranger)
5610 ("r-robustbase" ,r-robustbase)
5614 `(("r-knitr" ,r-knitr)))
5615 (home-page "https://github.com/alexkowa/VIM")
5616 (synopsis "Visualization and imputation of missing values")
5618 "This package provides tools for the visualization of missing and/or
5619 imputed values are introduced, which can be used for exploring the data and
5620 the structure of the missing and/or imputed values. Depending on this
5621 structure of the missing values, the corresponding methods may help to
5622 identify the mechanism generating the missing values and allows to explore the
5623 data including missing values. In addition, the quality of imputation can be
5624 visually explored using various univariate, bivariate, multiple and
5625 multivariate plot methods.")
5626 (license license:gpl2+)))
5628 (define-public r-fnn
5635 (uri (cran-uri "FNN" version))
5638 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5639 (properties `((upstream-name . "FNN")))
5640 (build-system r-build-system)
5641 (home-page "https://cran.r-project.org/web/packages/FNN")
5642 (synopsis "Fast nearest neighbor search algorithms and applications")
5644 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5645 search algorithms. Related applications including KNN classification,
5646 regression and information measures are implemented.")
5647 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5648 ;; later can be used.
5649 (license license:gpl2+)))
5651 (define-public r-smoother
5658 (uri (cran-uri "smoother" version))
5661 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5662 (build-system r-build-system)
5664 `(("r-ttr" ,r-ttr)))
5665 (home-page "https://cran.r-project.org/web/packages/smoother")
5666 (synopsis "Functions relating to the smoothing of numerical data")
5668 "This package provides a collection of methods for smoothing numerical
5669 data, commencing with a port of the Matlab gaussian window smoothing function.
5670 In addition, several functions typically used in smoothing of financial data
5672 (license license:gpl2)))
5674 (define-public r-riverplot
5676 (name "r-riverplot")
5681 (uri (cran-uri "riverplot" version))
5684 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5685 (build-system r-build-system)
5686 (home-page "https://logfc.wordpress.com")
5687 (synopsis "Sankey or ribbon plots")
5689 "Sankey plots are a type of diagram that is convenient to illustrate how
5690 flow of information, resources etc. separates and joins, much like observing
5691 how rivers split and merge. For example, they can be used to compare
5692 different clusterings. This package provides an implementation of Sankey
5694 (license license:gpl2+)))
5696 (define-public r-dyn
5703 (uri (cran-uri "dyn" version))
5706 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5707 (build-system r-build-system)
5709 `(("r-zoo" ,r-zoo)))
5710 (home-page "https://cran.r-project.org/web/packages/dyn")
5711 (synopsis "Time series regression")
5713 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5714 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5715 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5716 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5717 @code{randomForest::randomForest()} and other regression functions, allowing
5718 those functions to be used with time series including specifications that may
5719 contain lags, diffs and missing values.")
5721 (license license:gpl2+)))
5723 (define-public r-catdap
5730 (uri (cran-uri "catdap" version))
5733 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5734 (build-system r-build-system)
5736 `(("gfortran" ,gfortran)))
5737 (home-page "https://cran.r-project.org/web/packages/catdap/")
5738 (synopsis "Tools for categorical data analysis")
5740 "This package provides functions for analyzing multivariate data.
5741 Dependencies of the distribution of the specified variable (response
5742 variable) to other variables (explanatory variables) are derived and
5743 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5744 (license license:gpl2+)))
5746 (define-public r-arules
5753 (uri (cran-uri "arules" version))
5756 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5757 (build-system r-build-system)
5759 `(("r-matrix" ,r-matrix)))
5760 (home-page "https://github.com/mhahsler/arules")
5761 (synopsis "Mining association rules and frequent itemsets")
5763 "This package provides an infrastructure for representing, manipulating
5764 and analyzing transaction data and patterns (frequent itemsets and association rules).
5765 It also provides C implementations of the association mining algorithms Apriori
5767 (license license:gpl3)))
5769 (define-public r-parsedate
5771 (name "r-parsedate")
5776 (uri (cran-uri "parsedate" version))
5779 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5780 (build-system r-build-system)
5782 `(("r-rematch2" ,r-rematch2)))
5783 (home-page "https://github.com/gaborcsardi/parsedate")
5785 "Recognize and parse dates in various formats")
5787 "This package provides three functions for dealing with dates:
5788 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5789 time formats, @code{parse_date} parses dates in unspecified formats,
5790 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5791 (license license:gpl2)))
5793 (define-public r-abc-data
5800 (uri (cran-uri "abc.data" version))
5803 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5804 (properties `((upstream-name . "abc.data")))
5805 (build-system r-build-system)
5806 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5807 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5809 "This package contains data which are used by functions of the abc
5810 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5811 algorithms for performing parameter estimation, model selection, and
5813 (license license:gpl3+)))
5815 (define-public r-abc
5822 (uri (cran-uri "abc" version))
5825 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5826 (build-system r-build-system)
5828 `(("r-abc-data" ,r-abc-data)
5829 ("r-locfit" ,r-locfit)
5832 ("r-quantreg" ,r-quantreg)))
5833 (home-page "https://cran.r-project.org/web/packages/abc/")
5834 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5836 "This package implements several @dfn{Approximate Bayesian
5837 Computation} (ABC) algorithms for performing parameter estimation, model
5838 selection, and goodness-of-fit. Cross-validation tools are also available for
5839 measuring the accuracy of ABC estimates, and to calculate the
5840 misclassification probabilities of different models.")
5841 (license license:gpl3+)))
5843 (define-public r-zip
5850 (uri (cran-uri "zip" version))
5853 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
5854 (build-system r-build-system)
5855 (home-page "https://github.com/gaborcsardi/zip")
5856 (synopsis "Cross-platform Zip compression")
5858 "This package provides a cross-platform Zip compression library for R.
5859 It is a replacement for the @code{zip} function, that does not require any
5860 additional external tools on any platform.")
5861 (license license:cc0)))
5863 (define-public r-openxlsx
5870 (uri (cran-uri "openxlsx" version))
5873 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5874 (build-system r-build-system)
5876 `(("r-rcpp" ,r-rcpp)
5877 ("r-stringi" ,r-stringi)
5880 `(("r-knitr" ,r-knitr)))
5881 (home-page "https://github.com/awalker89/openxlsx")
5882 (synopsis "Read, write and edit XLSX files")
5884 "This package simplifies the creation of Excel @code{.xlsx} files by
5885 providing a high level interface to writing, styling and editing worksheets.
5886 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5887 and @code{XLConnect} packages with the added benefit of removing the
5888 dependency on Java.")
5889 (license license:gpl3)))
5891 (define-public r-rio
5898 (uri (cran-uri "rio" version))
5901 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5902 (build-system r-build-system)
5904 `(("r-curl" ,r-curl)
5905 ("r-data-table" ,r-data-table)
5906 ("r-foreign" ,r-foreign)
5907 ("r-haven" ,r-haven)
5908 ("r-openxlsx" ,r-openxlsx)
5909 ("r-readxl" ,r-readxl)
5910 ("r-tibble" ,r-tibble)))
5911 (home-page "https://github.com/leeper/rio")
5912 (synopsis "Swiss-army knife for data I/O")
5914 "This package provides streamlined data import and export infrastructure
5915 by making assumptions that the user is probably willing to make: @code{import}
5916 and @code{export} determine the data structure from the file extension,
5917 reasonable defaults are used for data import and export (e.g.,
5918 @code{stringsAsFactors=FALSE}), web-based import is natively
5919 supported (including from SSL/HTTPS), compressed files can be read directly
5920 without explicit decompression, and fast import packages are used where
5921 appropriate. An additional convenience function, @code{convert}, provides a
5922 simple method for converting between file types.")
5923 (license license:gpl2)))
5925 (define-public r-maptools
5932 (uri (cran-uri "maptools" version))
5935 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
5936 (build-system r-build-system)
5938 `(("r-foreign" ,r-foreign)
5939 ("r-lattice" ,r-lattice)
5941 (home-page "https://r-forge.r-project.org/projects/maptools/")
5942 (synopsis "Tools for reading and handling spatial objects")
5944 "This package provides a set of tools for manipulating and reading
5945 geographic data, in particular ESRI Shapefiles. It includes binary access to
5946 GSHHG shoreline files. The package also provides interface wrappers for
5947 exchanging spatial objects with other R packages.")
5948 ;; The C source files from shapelib are released under the Expat license.
5949 ;; The R code is released under GPL version 2 or later.
5950 (license (list license:gpl2+
5953 (define-public r-later
5960 (uri (cran-uri "later" version))
5963 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5964 (build-system r-build-system)
5968 ("r-rlang" ,r-rlang)))
5970 `(("r-knitr" ,r-knitr)))
5971 (home-page "https://github.com/r-lib/later")
5972 (synopsis "Utilities for delaying function execution")
5974 "This package provides tools to execute arbitrary R or C functions some
5975 time after the current time, after the R execution stack has emptied.")
5976 (license license:gpl2+)))
5978 (define-public r-promises
5985 (uri (cran-uri "promises" version))
5988 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5989 (build-system r-build-system)
5991 `(("r-later" ,r-later)
5992 ("r-magrittr" ,r-magrittr)
5995 ("r-rlang" ,r-rlang)))
5997 `(("r-knitr" ,r-knitr)))
5998 (home-page "https://rstudio.github.io/promises")
5999 (synopsis "Abstractions for promise-based asynchronous programming")
6001 "This package provides fundamental abstractions for doing asynchronous
6002 programming in R using promises. Asynchronous programming is useful for
6003 allowing a single R process to orchestrate multiple tasks in the background
6004 while also attending to something else. Semantics are similar to JavaScript
6005 promises, but with a syntax that is idiomatic R.")
6006 (license license:expat)))
6008 (define-public r-dosnow
6015 (uri (cran-uri "doSNOW" version))
6018 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6019 (properties `((upstream-name . "doSNOW")))
6020 (build-system r-build-system)
6022 `(("r-foreach" ,r-foreach)
6023 ("r-iterators" ,r-iterators)
6024 ("r-snow" ,r-snow)))
6025 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6026 (synopsis "Foreach parallel adaptor for the snow package")
6028 "This package provides a parallel backend for the @code{%dopar%} function
6029 using the @code{snow} package.")
6030 (license license:gpl2)))
6032 (define-public r-snowfall
6035 (version "1.84-6.1")
6038 (uri (cran-uri "snowfall" version))
6040 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6041 (build-system r-build-system)
6043 `(("r-snow" ,r-snow)))
6044 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6045 (synopsis "Easier cluster computing")
6046 (description "This package is a usability wrapper around snow for easier
6047 development of parallel R programs. This package offers e.g. extended error
6048 checks, and additional functions. All functions work in sequential mode, too,
6049 if no cluster is present or wished. The package is also designed as connector
6050 to the cluster management tool @code{sfCluster}, but can also used without
6052 (license license:gpl2+)))
6054 (define-public r-rappdirs
6061 (uri (cran-uri "rappdirs" version))
6064 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6065 (build-system r-build-system)
6066 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6067 (synopsis "Determine where to save data, caches, and logs")
6069 "This package provides an easy way to determine which directories on the
6070 user's computer should be used to save data, caches and logs. It is a port of
6071 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6072 (license license:expat)))
6074 (define-public r-renv
6081 (uri (cran-uri "renv" version))
6084 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
6085 (properties `((upstream-name . "renv")))
6086 (build-system r-build-system)
6088 `(("r-knitr" ,r-knitr)))
6089 (home-page "https://rstudio.github.io/renv")
6090 (synopsis "Project environments")
6092 "This package provides a dependency management toolkit for R. Using
6093 renv, you can create and manage project-local R libraries, save the state of
6094 these libraries to a lockfile, and later restore your library as required.
6095 Together, these tools can help make your projects more isolated, portable, and
6097 (license license:expat)))
6099 (define-public r-learnr
6106 (uri (cran-uri "learnr" version))
6109 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6110 (build-system r-build-system)
6112 `(("r-checkmate" ,r-checkmate)
6113 ("r-ellipsis" ,r-ellipsis)
6114 ("r-evaluate" ,r-evaluate)
6115 ("r-htmltools" ,r-htmltools)
6116 ("r-htmlwidgets" ,r-htmlwidgets)
6117 ("r-jsonlite" ,r-jsonlite)
6118 ("r-knitr" ,r-knitr)
6119 ("r-markdown" ,r-markdown)
6120 ("r-rappdirs" ,r-rappdirs)
6122 ("r-rmarkdown" ,r-rmarkdown)
6123 ("r-rprojroot" ,r-rprojroot)
6124 ("r-shiny" ,r-shiny)
6125 ("r-withr" ,r-withr)))
6126 (home-page "https://rstudio.github.io/learnr/")
6127 (synopsis "Interactive tutorials for R")
6129 "This package provides tools to create interactive tutorials using R
6130 Markdown. Use a combination of narrative, figures, videos, exercises, and
6131 quizzes to create self-paced tutorials for learning about R and R packages.")
6132 (license license:asl2.0)))
6134 (define-public r-analytics
6136 (name "r-analytics")
6141 (uri (cran-uri "analytics" version))
6144 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6145 (build-system r-build-system)
6148 ("r-cluster" ,r-cluster)
6149 ("r-fractal" ,r-fractal)
6150 ("r-lmtest" ,r-lmtest)
6153 ("r-powerplus" ,r-powerplus)
6154 ("r-robust" ,r-robust)
6155 ("r-trend" ,r-trend)
6159 (home-page "https://cran.r-project.org/web/packages/analytics/")
6160 (synopsis "Collection of data analysis tools")
6162 "This package is a collection of data analysis tools. It includes tools
6163 for regression outlier detection in a fitted linear model, stationary
6164 bootstrap using a truncated geometric distribution, a comprehensive test for
6165 weak stationarity, column means by group, weighted biplots, and a heuristic to
6166 obtain a better initial configuration in non-metric MDS.")
6167 (license license:gpl2)))
6169 (define-public r-reticulate
6171 (name "r-reticulate")
6176 (uri (cran-uri "reticulate" version))
6179 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6180 (build-system r-build-system)
6181 (inputs `(("python" ,python)))
6183 `(("r-rappdirs" ,r-rappdirs)
6184 ("r-jsonlite" ,r-jsonlite)
6185 ("r-matrix" ,r-matrix)
6186 ("r-rcpp" ,r-rcpp)))
6188 `(("r-knitr" ,r-knitr)))
6189 (home-page "https://github.com/rstudio/reticulate")
6190 (synopsis "R interface to Python")
6192 "This package provides an interface from R to Python modules, classes,
6193 and functions. When calling into Python, R data types are automatically
6194 converted to their equivalent Python types. When values are returned from
6195 Python to R they are converted back to R types.")
6196 (license license:asl2.0)))
6198 (define-public r-bibtex
6205 (uri (cran-uri "bibtex" version))
6208 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6209 (build-system r-build-system)
6210 (propagated-inputs `(("r-stringr" ,r-stringr)))
6211 (home-page "https://github.com/romainfrancois/bibtex")
6212 (synopsis "Bibtex parser")
6213 (description "This package provides a utility for R to parse a bibtex
6215 (license license:gpl2+)))
6217 (define-public r-ggseqlogo
6219 (name "r-ggseqlogo")
6224 (uri (cran-uri "ggseqlogo" version))
6227 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6228 (build-system r-build-system)
6229 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6230 (home-page "https://github.com/omarwagih/ggseqlogo")
6231 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6233 "The range of functions provided by this package makes it possible to
6234 draw highly versatile genomic sequence logos. Features include, but are not
6235 limited to, modifying colour schemes and fonts used to draw the logo,
6236 generating multiple logo plots, and aiding the visualisation with annotations.
6237 Sequence logos can easily be combined with other ggplot2 plots.")
6238 ;; Unspecified version of the LGPL.
6239 (license license:lgpl3+)))
6241 (define-public r-ggsci
6248 (uri (cran-uri "ggsci" version))
6251 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6252 (build-system r-build-system)
6254 `(("r-ggplot2" ,r-ggplot2)
6255 ("r-scales" ,r-scales)))
6256 (home-page "https://nanx.me/ggsci/")
6257 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6259 "This package provides a collection of ggplot2 color palettes inspired by
6260 plots in scientific journals, data visualization libraries, science fiction
6261 movies, and TV shows.")
6262 (license license:gpl3)))
6264 (define-public r-ggsignif
6271 (uri (cran-uri "ggsignif" version))
6274 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6275 (build-system r-build-system)
6277 `(("r-knitr" ,r-knitr)))
6279 `(("r-ggplot2" ,r-ggplot2)))
6280 (home-page "https://github.com/const-ae/ggsignif")
6281 (synopsis "Significance brackets for ggplot2")
6283 "Enrich your ggplots with group-wise comparisons. This package provides
6284 an easy way to indicate if two groups are significantly different. Commonly
6285 this is shown by a bracket on top connecting the groups of interest which
6286 itself is annotated with the level of significance. The package provides a
6287 single layer that takes the groups for comparison and the test as arguments
6288 and adds the annotation to the plot.")
6289 (license license:gpl3)))
6291 (define-public r-rstatix
6298 (uri (cran-uri "rstatix" version))
6301 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6302 (properties `((upstream-name . "rstatix")))
6303 (build-system r-build-system)
6305 `(("r-broom" ,r-broom)
6307 ("r-corrplot" ,r-corrplot)
6308 ("r-dplyr" ,r-dplyr)
6309 ("r-generics" ,r-generics)
6310 ("r-magrittr" ,r-magrittr)
6311 ("r-purrr" ,r-purrr)
6312 ("r-rlang" ,r-rlang)
6313 ("r-tibble" ,r-tibble)
6314 ("r-tidyr" ,r-tidyr)
6315 ("r-tidyselect" ,r-tidyselect)))
6316 (home-page "https://rpkgs.datanovia.com/rstatix/")
6317 (synopsis "Pipe-friendly framework for basic statistical tests")
6319 "This package provides a simple and intuitive pipe-friendly framework,
6320 coherent with the @code{tidyverse} design philosophy, for performing basic
6321 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6322 correlation analyses. The output of each test is automatically transformed
6323 into a tidy data frame to facilitate visualization. Additional functions are
6324 available for reshaping, reordering, manipulating and visualizing correlation
6326 (license license:gpl2)))
6328 (define-public r-ggpubr
6335 (uri (cran-uri "ggpubr" version))
6338 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6339 (build-system r-build-system)
6341 `(("r-cowplot" ,r-cowplot)
6342 ("r-dplyr" ,r-dplyr)
6343 ("r-ggplot2" ,r-ggplot2)
6344 ("r-ggrepel" ,r-ggrepel)
6345 ("r-ggsci" ,r-ggsci)
6346 ("r-ggsignif" ,r-ggsignif)
6348 ("r-gridextra" ,r-gridextra)
6349 ("r-magrittr" ,r-magrittr)
6350 ("r-polynom" ,r-polynom)
6351 ("r-purrr" ,r-purrr)
6352 ("r-rlang" ,r-rlang)
6353 ("r-scales" ,r-scales)
6354 ("r-rstatix" ,r-rstatix)
6355 ("r-tibble" ,r-tibble)
6356 ("r-tidyr" ,r-tidyr)))
6357 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6358 (synopsis "ggplot2-based publication-ready plots")
6360 "The ggplot2 package is an excellent and flexible package for elegant
6361 data visualization in R. However the default generated plots require some
6362 formatting before we can send them for publication. The ggpubr package
6363 provides some easy-to-use functions for creating and customizing ggplot2-based
6364 publication-ready plots.")
6365 (license license:gpl2)))
6367 (define-public r-ellipse
6374 (uri (cran-uri "ellipse" version))
6377 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6378 (build-system r-build-system)
6379 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6380 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6382 "This package contains various routines for drawing ellipses and
6383 ellipse-like confidence regions, implementing the plots described in Murdoch
6384 and Chow (1996), A graphical display of large correlation matrices, The
6385 American Statistician 50, 178-180. There are also routines implementing the
6386 profile plots described in Bates and Watts (1988), Nonlinear Regression
6387 Analysis and its Applications.")
6388 (license license:gpl2+)))
6390 (define-public r-flashclust
6392 (name "r-flashclust")
6397 (uri (cran-uri "flashClust" version))
6400 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6401 (properties `((upstream-name . "flashClust")))
6402 (build-system r-build-system)
6403 (native-inputs `(("gfortran" ,gfortran)))
6404 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6405 (synopsis "Implementation of optimal hierarchical clustering")
6407 "This package provides a fast implementation of hierarchical
6409 (license license:gpl2+)))
6411 (define-public r-factominer
6413 (name "r-factominer")
6418 (uri (cran-uri "FactoMineR" version))
6421 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6422 (properties `((upstream-name . "FactoMineR")))
6423 (build-system r-build-system)
6426 ("r-cluster" ,r-cluster)
6427 ("r-ellipse" ,r-ellipse)
6428 ("r-flashclust" ,r-flashclust)
6429 ("r-ggplot2" ,r-ggplot2)
6430 ("r-ggrepel" ,r-ggrepel)
6431 ("r-lattice" ,r-lattice)
6432 ("r-leaps" ,r-leaps)
6434 ("r-scatterplot3d" ,r-scatterplot3d)))
6435 (home-page "http://factominer.free.fr")
6436 (synopsis "Multivariate exploratory data analysis and data mining")
6438 "This package provides exploratory data analysis methods to summarize,
6439 visualize and describe datasets. The main principal component methods are
6440 available, those with the largest potential in terms of applications:
6441 principal component analysis (PCA) when variables are quantitative,
6442 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6443 variables are categorical, Multiple Factor Analysis when variables are
6444 structured in groups, etc. and hierarchical cluster analysis.")
6445 (license license:gpl2+)))
6447 (define-public r-factoextra
6449 (name "r-factoextra")
6454 (uri (cran-uri "factoextra" version))
6457 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6458 (build-system r-build-system)
6460 `(("r-abind" ,r-abind)
6461 ("r-cluster" ,r-cluster)
6462 ("r-dendextend" ,r-dendextend)
6463 ("r-factominer" ,r-factominer)
6464 ("r-ggplot2" ,r-ggplot2)
6465 ("r-ggpubr" ,r-ggpubr)
6466 ("r-ggrepel" ,r-ggrepel)
6467 ("r-reshape2" ,r-reshape2)
6468 ("r-tidyr" ,r-tidyr)))
6469 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6470 (synopsis "Extract and visualize the results of multivariate data analyses")
6472 "This package provides some easy-to-use functions to extract and
6473 visualize the output of multivariate data analyses, including
6474 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6475 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6476 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6477 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6478 packages. It contains also functions for simplifying some clustering analysis
6479 steps and provides ggplot2-based elegant data visualization.")
6480 (license license:gpl2)))
6482 (define-public r-fansi
6489 (uri (cran-uri "fansi" version))
6492 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6493 (build-system r-build-system)
6495 `(("r-knitr" ,r-knitr))) ; for vignettes
6496 (home-page "https://github.com/brodieG/fansi")
6497 (synopsis "ANSI control sequence aware string functions")
6499 "This package provides counterparts to R string manipulation functions
6500 that account for the effects of ANSI text formatting control sequences.")
6501 (license license:gpl2+)))
6503 (define-public r-nbclust
6510 (uri (cran-uri "NbClust" version))
6513 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6514 (properties `((upstream-name . "NbClust")))
6515 (build-system r-build-system)
6516 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6517 (synopsis "Determine the best number of clusters in a data set")
6519 "NbClust provides 30 indexes for determining the optimal number of
6520 clusters in a data set and offers the best clustering scheme from different
6521 results to the user.")
6522 (license license:gpl2)))
6524 (define-public r-hdf5r
6531 (uri (cran-uri "hdf5r" version))
6534 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6535 (build-system r-build-system)
6540 `(("r-bit64" ,r-bit64)
6543 `(("r-knitr" ,r-knitr)))
6544 (home-page "https://hhoeflin.github.io/hdf5r")
6545 (synopsis "Interface to the HDF5 binary data format")
6547 "HDF5 is a data model, library and file format for storing and managing
6548 large amounts of data. This package provides a nearly feature complete,
6549 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6550 functionality is added so that HDF5 objects behave very similar to their
6551 corresponding R counterparts.")
6552 (license license:asl2.0)))
6554 (define-public r-itertools
6556 (name "r-itertools")
6561 (uri (cran-uri "itertools" version))
6564 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6565 (build-system r-build-system)
6567 `(("r-iterators" ,r-iterators)))
6568 (home-page "https://cran.r-project.org/web/packages/itertools/")
6569 (synopsis "Iterator tools")
6571 "This package provides various tools for creating iterators, many
6572 patterned after functions in the Python @code{itertools} module, and others
6573 patterned after functions in the snow package.")
6574 (license license:gpl2)))
6576 (define-public r-polynom
6583 (uri (cran-uri "polynom" version))
6586 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6587 (build-system r-build-system)
6588 (home-page "https://cran.r-project.org/web/packages/polynom/")
6589 (synopsis "Functions for univariate polynomial manipulations")
6591 "This package provides a collection of functions to implement a class for
6592 univariate polynomial manipulations.")
6593 (license license:gpl2)))
6595 (define-public r-gbrd
6602 (uri (cran-uri "gbRd" version))
6605 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6606 (properties `((upstream-name . "gbRd")))
6607 (build-system r-build-system)
6608 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6609 (synopsis "Utilities for processing Rd objects and files")
6611 "This package provides utilities for processing Rd objects and files.
6612 Extract argument descriptions and other parts of the help pages of
6614 (license license:gpl2+)))
6616 (define-public r-rjags
6623 (uri (cran-uri "rjags" version))
6626 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6627 (build-system r-build-system)
6629 `(("r-coda" ,r-coda)))
6633 `(("pkg-config" ,pkg-config)))
6634 (home-page "http://mcmc-jags.sourceforge.net")
6635 (synopsis "Bayesian graphical models using MCMC")
6637 "This package provides an R interface to the JAGS MCMC library. JAGS is
6638 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6639 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6640 (license license:gpl2)))
6642 (define-public r-rdpack
6649 (uri (cran-uri "Rdpack" version))
6652 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6653 (properties `((upstream-name . "Rdpack")))
6654 (build-system r-build-system)
6656 `(("r-bibtex" ,r-bibtex)
6657 ("r-gbrd" ,r-gbrd)))
6658 (home-page "https://github.com/GeoBosh/Rdpack")
6659 (synopsis "Update and manipulate Rd documentation objects")
6661 "This package provides functions for manipulation of R documentation
6662 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6663 updating Rd documentation for functions, methods and classes; it also includes
6664 Rd macros for citations and import of references from bibtex files for use in
6665 Rd files and roxygen2 comments, as well as many functions for manipulation of
6666 references and Rd files.")
6667 (license license:gpl2+)))
6669 (define-public r-officer
6676 (uri (cran-uri "officer" version))
6679 "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
6680 (build-system r-build-system)
6682 `(("r-magrittr" ,r-magrittr)
6688 `(("r-knitr" ,r-knitr)))
6689 (home-page "https://davidgohel.github.io/officer")
6690 (synopsis "Manipulation of Word and PowerPoint documents")
6692 "This package provides tools to access and manipulate Word and PowerPoint
6693 documents from R. The package focuses on tabular and graphical reporting from
6694 R; it also provides two functions that let users get document content into
6695 data objects. A set of functions lets add and remove images, tables and
6696 paragraphs of text in new or existing documents. When working with PowerPoint
6697 presentations, slides can be added or removed; shapes inside slides can also
6698 be added or removed. When working with Word documents, a cursor can be used
6699 to help insert or delete content at a specific location in the document.")
6700 (license license:gpl3)))
6702 (define-public r-profilemodel
6704 (name "r-profilemodel")
6709 (uri (cran-uri "profileModel" version))
6712 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6713 (properties `((upstream-name . "profileModel")))
6714 (build-system r-build-system)
6715 (home-page "https://github.com/ikosmidis/profileModel")
6716 (synopsis "Profiling inference functions for various model classes")
6718 "This package provides tools that can be used to calculate, evaluate,
6719 plot and use for inference the profiles of *arbitrary* inference functions for
6720 arbitrary @code{glm}-like fitted models with linear predictors. More information
6721 on the methods that are implemented can be found in Kosmidis (2008)
6722 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6723 (license license:gpl2+)))
6725 (define-public r-brglm
6732 (uri (cran-uri "brglm" version))
6735 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6736 (properties `((upstream-name . "brglm")))
6737 (build-system r-build-system)
6739 `(("r-profilemodel" ,r-profilemodel)))
6740 (home-page "https://github.com/ikosmidis/brglm")
6741 (synopsis "Bias reduction in binomial-response generalized linear models")
6743 "Fit generalized linear models with binomial responses using either an
6744 adjusted-score approach to bias reduction or maximum penalized likelihood
6745 where penalization is by Jeffreys invariant prior. These procedures return
6746 estimates with improved frequentist properties (bias, mean squared error) that
6747 are always finite even in cases where the maximum likelihood estimates are
6748 infinite (data separation). Fitting takes place by fitting generalized linear
6749 models on iteratively updated pseudo-data. The interface is essentially the
6750 same as @code{glm}. More flexibility is provided by the fact that custom
6751 pseudo-data representations can be specified and used for model fitting.
6752 Functions are provided for the construction of confidence intervals for the
6753 reduced-bias estimates.")
6754 (license license:gpl2+)))
6756 (define-public r-entropy
6763 (uri (cran-uri "entropy" version))
6766 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6767 (properties `((upstream-name . "entropy")))
6768 (build-system r-build-system)
6769 (home-page "https://www.strimmerlab.org/software/entropy/")
6770 (synopsis "Estimation of entropy, mutual information and related quantities")
6772 "This package implements various estimators of entropy, such as the
6773 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6774 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6775 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6776 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6777 mutual information, and chi-squared statistic of independence. In addition
6778 there are functions for discretizing continuous random variables.")
6779 (license license:gpl3+)))
6781 (define-public r-abn
6788 (uri (cran-uri "abn" version))
6791 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6792 (build-system r-build-system)
6796 `(("r-boot" ,r-boot)
6797 ("r-brglm" ,r-brglm)
6798 ("r-entropy" ,r-entropy)
6801 ("r-moments" ,r-moments)
6804 ("r-rcpparmadillo" ,r-rcpparmadillo)
6805 ("r-rjags" ,r-rjags)))
6806 (home-page "https://r-bayesian-networks.org/")
6807 (synopsis "Modelling multivariate data with additive bayesian networks")
6809 "Bayesian network analysis is a form of probabilistic graphical models
6810 which derives from empirical data a directed acyclic graph, DAG, describing
6811 the dependency structure between random variables. An additive Bayesian
6812 network model consists of a form of a DAG where each node comprises a
6813 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6814 equivalent to Bayesian multivariate regression using graphical modelling, they
6815 generalises the usual multivariable regression, GLM, to multiple dependent
6816 variables. This package provides routines to help determine optimal Bayesian
6817 network models for a given data set, where these models are used to identify
6818 statistical dependencies in messy, complex data.")
6819 (license license:gpl2+)))
6821 (define-public r-acd
6828 (uri (cran-uri "ACD" version))
6831 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6832 (properties `((upstream-name . "ACD")))
6833 (build-system r-build-system)
6834 (home-page "https://cran.r-project.org/web/packages/ACD/")
6835 (synopsis "Categorical data analysis with complete or missing responses")
6837 "This package provides tools for categorical data analysis with complete
6838 or missing responses.")
6839 (license license:gpl2+)))
6841 (define-public r-acdm
6848 (uri (cran-uri "ACDm" version))
6851 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6852 (properties `((upstream-name . "ACDm")))
6853 (build-system r-build-system)
6855 `(("r-dplyr" ,r-dplyr)
6856 ("r-ggplot2" ,r-ggplot2)
6858 ("r-rsolnp" ,r-rsolnp)
6860 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6861 (synopsis "Tools for Autoregressive Conditional Duration Models")
6863 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6864 and Russell, 1998) models. It creates trade, price or volume durations from
6865 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6867 (license license:gpl2+)))
6869 (define-public r-overlap
6876 (uri (cran-uri "overlap" version))
6879 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6880 (build-system r-build-system)
6881 (home-page "https://cran.r-project.org/web/packages/overlap/")
6882 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6884 "This package provides functions to fit kernel density functions to data
6885 on temporal activity patterns of animals; estimate coefficients of overlapping
6886 of densities for two species; and calculate bootstrap estimates of confidence
6888 (license license:gpl3+)))
6890 (define-public r-snakecase
6892 (name "r-snakecase")
6897 (uri (cran-uri "snakecase" version))
6900 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6901 (build-system r-build-system)
6903 `(("r-stringi" ,r-stringi)
6904 ("r-stringr" ,r-stringr)))
6905 (home-page "https://github.com/Tazinho/snakecase")
6906 (synopsis "Convert strings into any case")
6908 "This package provides a consistent, flexible and easy to use tool to
6909 parse and convert strings into cases like snake or camel among others.")
6910 (license license:gpl3)))
6912 (define-public r-prediction
6914 (name "r-prediction")
6919 (uri (cran-uri "prediction" version))
6922 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6923 (build-system r-build-system)
6925 `(("r-data-table" ,r-data-table)))
6926 (home-page "https://github.com/leeper/prediction")
6927 (synopsis "Tidy, type-safe prediction methods")
6929 "This package provides the @code{prediction()} function, a type-safe
6930 alternative to @code{predict()} that always returns a data frame. The package
6931 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6932 from the @code{stats} package, as well as numerous other model classes from
6933 other add-on packages.")
6934 (license license:expat)))
6936 (define-public r-insight
6943 (uri (cran-uri "insight" version))
6946 "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
6947 (build-system r-build-system)
6949 `(("r-knitr" ,r-knitr)))
6950 (home-page "https://easystats.github.io/insight/")
6951 (synopsis "Easy access to model information for various model objects")
6953 "This package provides a tool to provide an easy, intuitive and
6954 consistent access to information contained in various R models, like model
6955 formulas, model terms, information about random effects, data that was used to
6956 fit the model or data from response variables. The package mainly revolves
6957 around two types of functions: Functions that find (the names of) information,
6958 starting with @code{find_}, and functions that get the underlying data,
6959 starting with @code{get_}. The package has a consistent syntax and works with
6960 many different model objects, where otherwise functions to access these
6961 information are missing.")
6962 (license license:gpl3)))
6964 (define-public r-sjlabelled
6966 (name "r-sjlabelled")
6971 (uri (cran-uri "sjlabelled" version))
6974 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
6975 (build-system r-build-system)
6977 `(("r-insight" ,r-insight)))
6979 `(("r-knitr" ,r-knitr)))
6980 (home-page "https://github.com/strengejacke/sjlabelled")
6981 (synopsis "Labelled data utility functions")
6983 "This package provides a collection of functions dealing with labelled
6984 data, like reading and writing data between R and other statistical software
6985 packages. This includes easy ways to get, set or change value and variable
6986 label attributes, to convert labelled vectors into factors or numeric (and
6987 vice versa), or to deal with multiple declared missing values.")
6988 (license license:gpl3)))
6990 (define-public r-sjmisc
6997 (uri (cran-uri "sjmisc" version))
7000 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7001 (build-system r-build-system)
7003 `(("r-dplyr" ,r-dplyr)
7004 ("r-insight" ,r-insight)
7005 ("r-magrittr" ,r-magrittr)
7006 ("r-purrr" ,r-purrr)
7007 ("r-rlang" ,r-rlang)
7008 ("r-sjlabelled" ,r-sjlabelled)
7009 ("r-tidyselect" ,r-tidyselect)))
7011 `(("r-knitr" ,r-knitr)))
7012 (home-page "https://github.com/strengejacke/sjmisc")
7013 (synopsis "Data and variable transformation functions")
7015 "This package is a collection of miscellaneous utility functions,
7016 supporting data transformation tasks like recoding, dichotomizing or grouping
7017 variables, setting and replacing missing values. The data transformation
7018 functions also support labelled data, and all integrate seamlessly into a
7019 tidyverse workflow.")
7020 (license license:gpl3)))
7022 (define-public r-nortest
7029 (uri (cran-uri "nortest" version))
7032 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7033 (build-system r-build-system)
7034 (home-page "https://cran.r-project.org/web/packages/nortest/")
7035 (synopsis "Tests for normality")
7037 "This package provides five omnibus tests for testing the composite
7038 hypothesis of normality.")
7039 (license license:gpl2+)))
7041 (define-public r-moonbook
7048 (uri (cran-uri "moonBook" version))
7051 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7052 (properties `((upstream-name . "moonBook")))
7053 (build-system r-build-system)
7055 `(("r-magrittr" ,r-magrittr)
7056 ("r-nortest" ,r-nortest)
7057 ("r-purrr" ,r-purrr)
7058 ("r-sjmisc" ,r-sjmisc)
7059 ("r-stringr" ,r-stringr)
7060 ("r-survival" ,r-survival)))
7061 (home-page "https://github.com/cardiomoon/moonBook")
7062 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7064 "This package provides several analysis-related functions for the book
7065 entitled \"R statistics and graph for medical articles\" (written in Korean),
7066 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7068 (license license:gpl2)))
7070 (define-public r-flextable
7072 (name "r-flextable")
7077 (uri (cran-uri "flextable" version))
7080 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7081 (build-system r-build-system)
7083 `(("r-base64enc" ,r-base64enc)
7084 ("r-data-table" ,r-data-table)
7085 ("r-gdtools" ,r-gdtools)
7086 ("r-htmltools" ,r-htmltools)
7087 ("r-knitr" ,r-knitr)
7088 ("r-officer" ,r-officer)
7089 ("r-rlang" ,r-rlang)
7090 ("r-rmarkdown" ,r-rmarkdown)
7092 ("r-xml2" ,r-xml2)))
7093 (home-page "https://davidgohel.github.io/flextable")
7094 (synopsis "Functions for tabular reporting")
7096 "This package provides tools to create pretty tables for HTML documents
7097 and other formats. Functions are provided to let users create tables, modify
7098 and format their content. It extends the @code{officer} package and can be
7099 used within R markdown documents when rendering to HTML and to Word
7101 (license license:gpl3)))
7103 (define-public r-writexl
7110 (uri (cran-uri "writexl" version))
7113 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7114 (build-system r-build-system)
7115 (inputs `(("zlib" ,zlib)))
7116 (home-page "https://github.com/ropensci/writexl")
7117 (synopsis "Export data frames to xlsx format")
7119 "This package provides a data frame to xlsx exporter based on
7121 (license license:bsd-2)))
7123 (define-public r-biasedurn
7125 (name "r-biasedurn")
7130 (uri (cran-uri "BiasedUrn" version))
7133 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7134 (properties `((upstream-name . "BiasedUrn")))
7135 (build-system r-build-system)
7136 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7137 (synopsis "Biased Urn model distributions")
7139 "This package provides statistical models of biased sampling in the form
7140 of univariate and multivariate noncentral hypergeometric distributions,
7141 including Wallenius' noncentral hypergeometric distribution and Fisher's
7142 noncentral hypergeometric distribution (also called extended hypergeometric
7144 (license license:gpl3)))
7146 (define-public r-goplot
7153 (uri (cran-uri "GOplot" version))
7156 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7157 (properties `((upstream-name . "GOplot")))
7158 (build-system r-build-system)
7160 `(("r-ggdendro" ,r-ggdendro)
7161 ("r-ggplot2" ,r-ggplot2)
7162 ("r-gridextra" ,r-gridextra)
7163 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7164 (home-page "https://github.com/wencke/wencke.github.io")
7165 (synopsis "Visualization of functional analysis data")
7167 "This package provides an implementation of multilayered visualizations
7168 for enhanced graphical representation of functional analysis data. It
7169 combines and integrates omics data derived from expression and functional
7170 annotation enrichment analyses. Its plotting functions have been developed
7171 with an hierarchical structure in mind: starting from a general overview to
7172 identify the most enriched categories (modified bar plot, bubble plot) to a
7173 more detailed one displaying different types of relevant information for the
7174 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7175 Venn diagram, heatmap).")
7176 (license license:gpl2)))
7178 (define-public r-getopt
7185 (uri (cran-uri "getopt" version))
7188 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7189 (build-system r-build-system)
7190 (home-page "https://github.com/trevorld/getopt")
7191 (synopsis "Command-line option processor for R")
7193 "This package is designed to be used with Rscript to write shebang
7194 scripts that accept short and long options. Many users will prefer to
7195 use the packages @code{optparse} or @code{argparse} which add extra
7196 features like automatically generated help options and usage texts,
7197 support for default values, positional argument support, etc.")
7198 (license license:gpl2+)))
7200 (define-public r-findpython
7202 (name "r-findpython")
7207 (uri (cran-uri "findpython" version))
7210 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7211 (build-system r-build-system)
7212 (home-page "https://github.com/trevorld/findpython")
7213 (synopsis "Functions to find an acceptable Python binary")
7215 "This package was designed to find an acceptable Python binary that
7216 matches version and feature constraints.")
7217 (license license:expat)))
7219 ;; This in not the same as "r-argparser"
7220 (define-public r-argparse
7227 (uri (cran-uri "argparse" version))
7230 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7231 (build-system r-build-system)
7232 (inputs `(("python" ,python)))
7234 `(("r-findpython" ,r-findpython)
7235 ("r-jsonlite" ,r-jsonlite)
7237 (home-page "https://github.com/trevorld/argparse")
7238 (synopsis "Command line optional and positional argument parser")
7240 "This package provides a command line parser to be used with Rscript to
7241 write shebang scripts that gracefully accept positional and optional arguments
7242 and automatically generate usage notices.")
7243 (license license:gpl2+)))
7245 (define-public r-hash
7252 (uri (cran-uri "hash" version))
7255 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7256 (build-system r-build-system)
7257 (home-page "https://cran.r-project.org/web/packages/hash/")
7258 (synopsis "Implementation of hash/associated arrays/dictionaries")
7260 "This package implements a data structure similar to hashes in Perl and
7261 dictionaries in Python but with a purposefully R flavor. For objects of
7262 appreciable size, access using hashes outperforms native named lists and
7264 (license license:gpl2+)))
7266 (define-public r-orddom
7273 (uri (cran-uri "orddom" version))
7276 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7277 (build-system r-build-system)
7278 (propagated-inputs `(("r-psych" ,r-psych)))
7279 (home-page "https://cran.r-project.org/web/packages/orddom/")
7280 (synopsis "Ordinal dominance statistics")
7282 "This package provides tools to compute ordinal, statistics and effect
7283 sizes as an alternative to mean comparison: Cliff's delta or success rate
7284 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7285 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7286 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7287 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7288 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7289 Group (Non-)Overlap considerations.")
7290 (license license:gpl2)))
7292 (define-public r-deriv
7299 (uri (cran-uri "Deriv" version))
7302 "16rq65x1xhxvqwn4p427divay3b9fgam2lxccxb8529adnrxmw6p"))))
7303 (properties `((upstream-name . "Deriv")))
7304 (build-system r-build-system)
7305 (home-page "https://cran.r-project.org/web/packages/Deriv")
7306 (synopsis "Symbolic differentiation")
7308 "This package provides an R-based solution for symbolic differentiation.
7309 It admits user-defined functions as well as function substitution in arguments
7310 of functions to be differentiated. Some symbolic simplification is part of
7312 (license license:gpl3+)))
7314 (define-public r-doby
7321 (uri (cran-uri "doBy" version))
7324 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7325 (properties `((upstream-name . "doBy")))
7326 (build-system r-build-system)
7328 `(("r-broom" ,r-broom)
7329 ("r-deriv" ,r-deriv)
7330 ("r-dplyr" ,r-dplyr)
7331 ("r-ggplot2" ,r-ggplot2)
7332 ("r-magrittr" ,r-magrittr)
7334 ("r-matrix" ,r-matrix)
7335 ("r-pbkrtest" ,r-pbkrtest)
7336 ("r-tibble" ,r-tibble)))
7338 `(("r-knitr" ,r-knitr)))
7339 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7340 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7342 "This package contains:
7345 @item facilities for working with grouped data: @code{do}
7346 something to data stratified @code{by} some variables.
7347 @item implementations of least-squares means, general linear contrasts, and
7348 @item miscellaneous other utilities.
7350 (license license:gpl2+)))
7352 (define-public r-refgenome
7354 (name "r-refgenome")
7359 (uri (cran-uri "refGenome" version))
7362 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7363 (properties `((upstream-name . "refGenome")))
7364 (build-system r-build-system)
7368 ("r-rsqlite" ,r-rsqlite)))
7369 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7371 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7373 "This package contains functionality for importing and managing of
7374 downloaded genome annotation data from the Ensembl genome browser (European
7375 Bioinformatics Institute) and from the UCSC genome browser (University of
7376 California, Santa Cruz) and annotation routines for genomic positions and
7377 splice site positions.")
7378 (license license:gpl2)))
7380 (define-public r-basix
7387 (uri (cran-uri "BASIX" version))
7390 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7391 (properties `((upstream-name . "BASIX")))
7392 (build-system r-build-system)
7393 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7394 (synopsis "Efficient C/C++ toolset for R")
7396 "BASIX provides some efficient C/C++ implementations of native R
7397 procedures to speed up calculations in R.")
7398 (license license:gpl2)))
7400 (define-public r-blockfest
7402 (name "r-blockfest")
7407 (uri (cran-uri "BlockFeST" version))
7410 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7411 (properties `((upstream-name . "BlockFeST")))
7412 (build-system r-build-system)
7413 (propagated-inputs `(("r-basix" ,r-basix)))
7414 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7415 (synopsis "Bayesian calculation of region-specific fixation index")
7417 "This package provides an R implementation of an extension of the
7418 BayeScan software for codominant markers, adding the option to group
7419 individual SNPs into pre-defined blocks. A typical application of this new
7420 approach is the identification of genomic regions, genes, or gene sets
7421 containing one or more SNPs that evolved under directional selection.")
7422 (license license:gpl2)))
7424 (define-public r-proc
7431 (uri (cran-uri "pROC" version))
7434 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7435 (properties `((upstream-name . "pROC")))
7436 (build-system r-build-system)
7438 `(("r-plyr" ,r-plyr)
7439 ("r-rcpp" ,r-rcpp)))
7440 (home-page "https://web.expasy.org/pROC/")
7441 (synopsis "Display and analyze ROC curves")
7443 "This package provides tools for visualizing, smoothing and comparing
7444 receiver operating characteristic (ROC curves). The area under the
7445 curve (AUC) can be compared with statistical tests based on U-statistics or
7446 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7447 (license license:gpl3+)))
7449 (define-public r-rootsolve
7451 (name "r-rootsolve")
7456 (uri (cran-uri "rootSolve" version))
7459 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7460 (properties `((upstream-name . "rootSolve")))
7461 (build-system r-build-system)
7462 (native-inputs `(("gfortran" ,gfortran)))
7463 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7464 (synopsis "Tools for the analysis of ordinary differential equations")
7466 "This package provides routines to find the root of nonlinear functions,
7467 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7468 differential equations} (ODE). It includes routines that:
7471 @item generate gradient and jacobian matrices (full and banded),
7472 @item find roots of non-linear equations by the Newton-Raphson method,
7473 @item estimate steady-state conditions of a system of (differential) equations
7474 in full, banded or sparse form, using the Newton-Raphson method, or by
7475 dynamically running,
7476 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7477 and 3-D partial differential equations, that have been converted to ordinary
7478 differential equations by numerical differencing (using the method-of-lines
7481 (license license:gpl2+)))
7483 (define-public r-abcanalysis
7485 (name "r-abcanalysis")
7490 (uri (cran-uri "ABCanalysis" version))
7492 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7493 (properties `((upstream-name . "ABCanalysis")))
7494 (build-system r-build-system)
7495 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7496 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7497 (synopsis "Computed ABC Analysis")
7499 "Multivariate data sets often differ in several factors or derived statistical
7500 parameters, which have to be selected for a valid interpretation. Basing this
7501 selection on traditional statistical limits leads occasionally to the perception
7502 of losing information from a data set. This package provides tools to calculate
7503 these limits on the basis of the mathematical properties of the distribution of
7504 the analyzed items.")
7505 (license license:gpl3)))
7507 (define-public r-slam
7514 (uri (cran-uri "slam" version))
7516 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7517 (build-system r-build-system)
7518 (home-page "https://cran.r-project.org/web/packages/slam/")
7519 (synopsis "Sparse lightweight arrays and matrices")
7521 "This package contains data structures and algorithms for sparse arrays and matrices,
7522 based on index arrays and simple triplet representations, respectively.")
7523 (license license:gpl2)))
7525 (define-public r-manipulatewidget
7527 (name "r-manipulatewidget")
7532 (uri (cran-uri "manipulateWidget" version))
7534 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7536 `((upstream-name . "manipulateWidget")))
7537 (build-system r-build-system)
7539 `(("r-base64enc" ,r-base64enc)
7540 ("r-codetools" ,r-codetools)
7541 ("r-htmltools" ,r-htmltools)
7542 ("r-htmlwidgets" ,r-htmlwidgets)
7543 ("r-knitr" ,r-knitr)
7544 ("r-miniui" ,r-miniui)
7545 ("r-shiny" ,r-shiny)
7546 ("r-webshot" ,r-webshot)))
7547 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7548 (synopsis "Add even more interactivity to interactive charts")
7550 "This package lets you create in just a few lines of R code a nice user interface to
7551 modify the data or the graphical parameters of one or multiple interactive
7552 charts. It is useful to quickly explore visually some data or for package
7553 developers to generate user interfaces easy to maintain.")
7554 (license license:gpl2+)))
7563 (uri (cran-uri "A3" version))
7565 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7566 (properties `((upstream-name . "A3")))
7567 (build-system r-build-system)
7569 `(("r-pbapply" ,r-pbapply)
7570 ("r-xtable" ,r-xtable)))
7571 (home-page "https://cran.r-project.org/web/packages/A3/")
7572 (synopsis "Error metrics for predictive models")
7574 "This package supplies tools for tabulating and analyzing the results of predictive
7575 models. The methods employed are applicable to virtually any predictive model
7576 and make comparisons between different methodologies straightforward.")
7577 (license license:gpl2+)))
7579 (define-public r-infotheo
7586 (uri (cran-uri "infotheo" version))
7589 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7590 (build-system r-build-system)
7591 (home-page "http://homepage.meyerp.com/software")
7592 (synopsis "Information-theoretic measures")
7594 "This package implements various measures of information theory based on
7595 several entropy estimators.")
7596 (license license:gpl3+)))
7598 (define-public r-abcoptim
7605 (uri (cran-uri "ABCoptim" version))
7607 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7608 (properties `((upstream-name . "ABCoptim")))
7609 (build-system r-build-system)
7610 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7611 (home-page "https://github.com/gvegayon/ABCoptim/")
7612 (synopsis "Optimization of Artificial Bee Colony algorithm")
7614 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7615 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7616 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7617 algorithms, and uses only common control parameters such as colony size and
7618 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7619 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7620 This version is a work-in-progress and is written in R code.")
7621 (license license:expat)))
7623 (define-public r-abcp2
7630 (uri (cran-uri "ABCp2" version))
7632 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7633 (properties `((upstream-name . "ABCp2")))
7634 (build-system r-build-system)
7635 (propagated-inputs `(("r-mass" ,r-mass)))
7636 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7637 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7639 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7640 Poisson, and Gamma distribution and estimates the proportional paternity of the
7641 second male (P2) based on the best fit distribution.")
7642 (license license:gpl2)))
7644 (define-public r-abcrf
7651 (uri (cran-uri "abcrf" version))
7653 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7654 (build-system r-build-system)
7656 `(("r-doparallel" ,r-doparallel)
7657 ("r-foreach" ,r-foreach)
7659 ("r-matrixstats" ,r-matrixstats)
7660 ("r-ranger" ,r-ranger)
7662 ("r-rcpparmadillo" ,r-rcpparmadillo)
7663 ("r-readr" ,r-readr)
7664 ("r-stringr" ,r-stringr)))
7665 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7666 (synopsis "Approximate bayesian computation via random forests")
7668 "This package performs approximate bayesian computation (ABC) model choice and
7669 parameter inference via random forests. This machine learning tool named random
7670 forests (RF) can conduct selection among the highly complex models covered by
7672 (license license:gpl2+)))
7674 (define-public r-abctools
7681 (uri (cran-uri "abctools" version))
7683 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7684 (build-system r-build-system)
7687 ("r-abind" ,r-abind)
7688 ("r-hmisc" ,r-hmisc)
7689 ("r-plyr" ,r-plyr)))
7690 (home-page "https://github.com/dennisprangle/abctools/")
7691 (synopsis "Tools for ABC analyses")
7693 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7694 including summary statistic selection and assessing coverage. This includes
7695 recent dimension reduction algorithms to tune the choice of summary statistics,
7696 and coverage methods to tune the choice of threshold.")
7697 (license license:gpl2+)))
7699 (define-public r-ggstance
7706 (uri (cran-uri "ggstance" version))
7708 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7709 (build-system r-build-system)
7711 `(("r-ggplot2" ,r-ggplot2)
7713 ("r-rlang" ,r-rlang)
7714 ("r-withr" ,r-withr)))
7715 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7716 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7718 "This package is a @code{r-ggplot2} extension that provides flipped components:
7720 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7721 @item vertical versions of @code{r-ggplot2} positions.
7723 (license license:gpl3)))
7725 (define-public r-mosaiccore
7727 (name "r-mosaiccore")
7732 (uri (cran-uri "mosaicCore" version))
7734 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7735 (properties `((upstream-name . "mosaicCore")))
7736 (build-system r-build-system)
7738 `(("r-dplyr" ,r-dplyr)
7739 ("r-lazyeval" ,r-lazyeval)
7741 ("r-rlang" ,r-rlang)
7742 ("r-tidyr" ,r-tidyr)))
7743 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7744 (synopsis "Common utilities for mosaic family packages")
7746 "Common utilities used in other Mosaic family packages are collected here.")
7747 (license license:gpl2+)))
7749 (define-public r-ggformula
7751 (name "r-ggformula")
7756 (uri (cran-uri "ggformula" version))
7758 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7759 (build-system r-build-system)
7761 `(("r-ggforce" ,r-ggforce)
7762 ("r-ggplot2" ,r-ggplot2)
7763 ("r-ggstance" ,r-ggstance)
7764 ("r-magrittr" ,r-magrittr)
7765 ("r-mosaiccore" ,r-mosaiccore)
7766 ("r-rlang" ,r-rlang)
7767 ("r-stringr" ,r-stringr)
7768 ("r-tibble" ,r-tibble)))
7769 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7770 (synopsis "Formula interface for the @code{r-ggplot2}")
7772 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7773 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7774 and extends the excellent simplicity of the lattice-graphics formula interface,
7775 while providing the intuitive capabilities of @code{r-ggplot2}.")
7776 (license license:expat)))
7778 (define-public r-mosaicdata
7780 (name "r-mosaicdata")
7785 (uri (cran-uri "mosaicData" version))
7787 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7788 (properties `((upstream-name . "mosaicData")))
7789 (build-system r-build-system)
7790 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7791 (synopsis "Data sets for project Mosaic")
7793 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7794 used to teach mathematics, statistics, computation and modeling.")
7795 (license license:gpl2+)))
7797 (define-public r-raster
7804 (uri (cran-uri "raster" version))
7807 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7808 (build-system r-build-system)
7810 `(("r-rcpp" ,r-rcpp)
7812 (home-page "https://www.rspatial.org/")
7813 (synopsis "Geographic data analysis and modeling")
7815 "The package implements basic and high-level functions for reading,
7816 writing, manipulating, analyzing and modeling of gridded spatial data.
7817 Processing of very large files is supported.")
7818 (license license:gpl3+)))
7820 (define-public r-mosaic
7827 (uri (cran-uri "mosaic" version))
7829 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7830 (build-system r-build-system)
7832 `(("r-broom" ,r-broom)
7833 ("r-dplyr" ,r-dplyr)
7834 ("r-ggdendro" ,r-ggdendro)
7835 ("r-ggformula" ,r-ggformula)
7836 ("r-ggplot2" ,r-ggplot2)
7837 ("r-ggrepel" ,r-ggrepel)
7839 ("r-gridextra" ,r-gridextra)
7840 ("r-lattice" ,r-lattice)
7841 ("r-latticeextra" ,r-latticeextra)
7842 ("r-lazyeval" ,r-lazyeval)
7844 ("r-matrix" ,r-matrix)
7845 ("r-mosaiccore" ,r-mosaiccore)
7846 ("r-mosaicdata" ,r-mosaicdata)
7847 ("r-readr" ,r-readr)
7848 ("r-tidyr" ,r-tidyr)))
7850 `(("r-knitr" ,r-knitr)))
7851 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7852 (synopsis "Mathematics, statistics, and computation teaching utilities")
7854 "This package contain data sets and utilities from
7855 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7856 statistics, computation and modeling. Project MOSAIC is a community of
7857 educators working to tie together aspects of quantitative work that students
7858 in science, technology, engineering and mathematics will need in their
7859 professional lives, but which are usually taught in isolation, if at all.")
7860 (license license:gpl2+)))
7862 (define-public r-abd
7869 (uri (cran-uri "abd" version))
7871 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7872 (build-system r-build-system)
7874 `(("r-lattice" ,r-lattice)
7875 ("r-mosaic" ,r-mosaic)
7876 ("r-nlme" ,r-nlme)))
7877 (home-page "https://cran.r-project.org/web/packages/abd/")
7878 (synopsis "Analysis of biological data")
7880 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7881 biological data by Michael Whitlock and Dolph Schluter.")
7882 (license license:gpl2)))
7884 (define-public r-svgui
7891 (uri (cran-uri "svGUI" version))
7893 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7894 (properties `((upstream-name . "svGUI")))
7895 (build-system r-build-system)
7896 (home-page "https://github.com/SciViews/svGUI/")
7897 (synopsis "Functions for managing GUI clients in R")
7899 "The SciViews @code{svGUI} package eases the management of Graphical User
7900 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7901 centralizes info about GUI elements currently used, and it dispatches GUI
7902 calls to the particular toolkits in use in function of the context.")
7903 (license license:gpl2)))
7905 (define-public r-svdialogs
7907 (name "r-svdialogs")
7912 (uri (cran-uri "svDialogs" version))
7914 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7915 (properties `((upstream-name . "svDialogs")))
7916 (build-system r-build-system)
7919 ("zenity" ,zenity)))
7921 `(("r-rstudioapi" ,r-rstudioapi)
7922 ("r-svgui" ,r-svgui)))
7923 (home-page "https://github.com/SciViews/svDialogs/")
7924 (synopsis "Portable dialog boxes")
7926 "This package helps to construct standard dialog boxes for your GUI, including
7927 message boxes, input boxes, list, file or directory selection, and others. In
7928 case R cannot display GUI dialog boxes, a simpler command line version of these
7929 interactive elements is also provided as a fallback solution.")
7930 (license license:gpl2)))
7932 (define-public r-abe
7939 (uri (cran-uri "abe" version))
7942 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7943 (build-system r-build-system)
7944 (home-page "https://cran.r-project.org/web/packages/abe/")
7945 (synopsis "Augmented backward elimination")
7947 "This package performs augmented backward elimination and checks the
7948 stability of the obtained model. Augmented backward elimination combines
7949 significance or information based criteria with the change in estimate to
7950 either select the optimal model for prediction purposes or to serve as a tool
7951 to obtain a practically sound, highly interpretable model.")
7952 (license license:gpl2+)))
7954 (define-public r-abf2
7961 (uri (cran-uri "abf2" version))
7963 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7964 (build-system r-build-system)
7965 (home-page "https://cran.r-project.org/web/packages/abf2/")
7966 (synopsis "Load gap-free axon @code{r-abf2} files")
7968 "This package loads electrophysiology data from ABF2 files, as created by
7969 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7970 mode are currently supported.")
7971 (license license:artistic2.0)))
7973 (define-public r-abhgenotyper
7975 (name "r-abhgenotyper")
7980 (uri (cran-uri "ABHgenotypeR" version))
7982 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7983 (properties `((upstream-name . "ABHgenotypeR")))
7984 (build-system r-build-system)
7986 `(("r-ggplot2" ,r-ggplot2)
7987 ("r-reshape2" ,r-reshape2)))
7988 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7989 (synopsis "Visualize and manipulate ABH genotypes")
7991 "The @code{r-abhgenotyper} package provides simple imputation,
7992 error-correction and plotting capacities for genotype data. The package is
7993 supposed to serve as an intermediate but independent analysis tool between the
7994 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7995 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7996 genotypes as \"graphical genotypes\".")
7997 (license license:gpl3)))
7999 (define-public r-furrr
8006 (uri (cran-uri "furrr" version))
8009 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8010 (build-system r-build-system)
8012 `(("r-future" ,r-future)
8013 ("r-globals" ,r-globals)
8014 ("r-purrr" ,r-purrr)
8015 ("r-rlang" ,r-rlang)))
8016 (home-page "https://github.com/DavisVaughan/furrr")
8017 (synopsis "Apply mapping functions in parallel using futures")
8019 "This package provides implementations of the family of @code{map()}
8020 functions from the @code{purrr} package that can be resolved using any
8021 @code{future}-supported backend, e.g. parallel on the local machine or
8022 distributed on a compute cluster.")
8023 (license license:lgpl2.1+)))
8025 (define-public r-abjutils
8032 (uri (cran-uri "abjutils" version))
8034 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8035 (build-system r-build-system)
8037 `(("r-dplyr" ,r-dplyr)
8038 ("r-magrittr" ,r-magrittr)
8039 ("r-purrr" ,r-purrr)
8040 ("r-rlang" ,r-rlang)
8041 ("r-rstudioapi" ,r-rstudioapi)
8042 ("r-stringi" ,r-stringi)
8043 ("r-stringr" ,r-stringr)
8044 ("r-tidyr" ,r-tidyr)))
8045 (home-page "https://github.com/abjur/abjutils/")
8046 (synopsis "Collection of tools for jurimetrical analysis")
8048 "This package implements general purpose tools, such as functions for
8049 sampling and basic manipulation of Brazilian lawsuits identification number.
8050 It also implements functions for text cleaning, such as accentuation
8052 (license license:expat)))
8054 (define-public r-abnormality
8056 (name "r-abnormality")
8061 (uri (cran-uri "abnormality" version))
8063 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8064 (build-system r-build-system)
8066 `(("r-mass" ,r-mass)
8067 ("r-matrix" ,r-matrix)))
8068 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8069 (synopsis "Measure a subject's abnormality with respect to a reference population")
8071 "This package contains functions to implement the methodology and
8072 considerations laid out by Marks et al. in the article \"Measuring abnormality
8073 in high dimensional spaces: applications in biomechanical gait analysis\".
8074 Using high-dimensional datasets to measure a subject's overall level of
8075 abnormality as compared to a reference population is often needed in outcomes
8077 (license license:expat)))
8079 (define-public r-abodoutlier
8081 (name "r-abodoutlier")
8086 (uri (cran-uri "abodOutlier" version))
8088 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8089 (properties `((upstream-name . "abodOutlier")))
8090 (build-system r-build-system)
8092 `(("r-cluster" ,r-cluster)))
8093 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8094 (synopsis "Angle-based outlier detection")
8096 "This package performs angle-based outlier detection on a given data
8097 frame. It offers three methods to process data:
8099 @item full but slow implementation using all the data that has cubic
8101 @item a fully randomized method;
8102 @item a method using k-nearest neighbours.
8104 These algorithms are well suited for high dimensional data outlier
8106 (license license:expat)))
8108 (define-public r-abps
8115 (uri (cran-uri "ABPS" version))
8117 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8118 (properties `((upstream-name . "ABPS")))
8119 (build-system r-build-system)
8120 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8121 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8122 (synopsis "Abnormal blood profile score to detect blood doping")
8124 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8125 The ABPS is a part of the Athlete biological passport program of the World
8126 anti-doping agency, which combines several blood parameters into a single
8127 score in order to detect blood doping. The package also contains functions to
8128 calculate other scores used in anti-doping programs, such as the ratio of
8129 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8130 (license license:gpl2+)))
8132 (define-public r-parmigene
8134 (name "r-parmigene")
8139 (uri (cran-uri "parmigene" version))
8142 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8143 (build-system r-build-system)
8144 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8145 (synopsis "Mutual information estimation for gene network reconstruction")
8147 "This package provides a parallel estimation of the mutual information
8148 based on entropy estimates from k-nearest neighbors distances and algorithms
8149 for the reconstruction of gene regulatory networks.")
8150 (license license:agpl3+)))
8152 (define-public r-pscl
8159 (uri (cran-uri "pscl" version))
8161 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8162 (build-system r-build-system)
8164 `(("r-mass" ,r-mass)))
8165 (home-page "https://github.com/atahk/pscl/")
8166 (synopsis "Political science computational laboratory")
8168 "The @code{pscl} is an R package providing classes and methods for:
8170 @item Bayesian analysis of roll call data (item-response models);
8171 @item elementary Bayesian statistics;
8172 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8174 @item utility functions.
8176 (license license:gpl2)))
8178 (define-public r-accelmissing
8180 (name "r-accelmissing")
8185 (uri (cran-uri "accelmissing" version))
8187 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8188 (build-system r-build-system)
8190 `(("r-mice" ,r-mice)
8191 ("r-pscl" ,r-pscl)))
8192 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8193 (synopsis "Missing value imputation for accelerometer data")
8195 "This package provides a statistical method to impute the missing values in
8196 accelerometer data. The methodology includes both parametric and
8197 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8198 model. It also provides multiple functions to preprocess the accelerometer data
8199 previous to the missing data imputation. These include detecting the wearing
8200 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8201 (license license:gpl2+)))
8203 (define-public r-mhsmm
8210 (uri (cran-uri "mhsmm" version))
8212 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8213 (build-system r-build-system)
8214 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8215 (home-page "https://github.com/jaredo/mhsmm/")
8216 (synopsis "Inference for hidden Markov and semi-Markov models")
8218 "The @code{r-mhsmm} package implements estimation and prediction methods for
8219 hidden Markov and semi-Markov models for multiple observation sequences. Such
8220 techniques are of interest when observed data is thought to be dependent on some
8221 unobserved (or hidden) state. Also, this package is suitable for equidistant
8222 time series data, with multivariate and/or missing data. Allows user defined
8223 emission distributions.")
8224 (license license:gpl2+)))
8226 (define-public r-nleqslv
8233 (uri (cran-uri "nleqslv" version))
8235 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8236 (build-system r-build-system)
8237 (native-inputs `(("gfortran" ,gfortran)))
8238 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8239 (synopsis "Solve systems of nonlinear equations")
8241 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8242 Broyden or a Newton method with a choice of global strategies such as line
8243 search and trust region. There are options for using a numerical or user
8244 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8245 singular or ill-conditioned Jacobian.")
8246 (license license:gpl2+)))
8248 (define-public r-physicalactivity
8250 (name "r-physicalactivity")
8255 (uri (cran-uri "PhysicalActivity" version))
8257 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8259 `((upstream-name . "PhysicalActivity")))
8260 (build-system r-build-system)
8261 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8262 (synopsis "Procesing accelerometer data for physical activity measurement")
8264 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8265 for classification of monitor wear and nonwear time intervals in accelerometer
8266 data collected to assess physical activity. The package also contains functions
8267 for making plots of accelerometer data and obtaining the summary of various
8268 information including daily monitor wear time and the mean monitor wear time
8269 during valid days. The revised package version 0.2-1 improved the functions
8270 regarding speed, robustness and add better support for time zones and daylight
8271 saving. In addition, several functions were added:
8273 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8274 @item the @code{markPAI} can categorize physical activity intensity level based
8275 on user-defined cut-points of accelerometer counts.
8277 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8278 @code{queryActigraph} functions.")
8279 (license license:gpl3+)))
8281 (define-public r-acc
8288 (uri (cran-uri "acc" version))
8290 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8291 (build-system r-build-system)
8293 `(("r-circlize" ,r-circlize)
8295 ("r-ggplot2" ,r-ggplot2)
8296 ("r-iterators" ,r-iterators)
8297 ("r-mhsmm" ,r-mhsmm)
8298 ("r-nleqslv" ,r-nleqslv)
8299 ("r-physicalactivity" ,r-physicalactivity)
8301 ("r-r-utils" ,r-r-utils)
8303 ("r-rcpparmadillo" ,r-rcpparmadillo)
8304 ("r-rsqlite" ,r-rsqlite)
8306 (home-page "https://cran.r-project.org/web/packages/acc/")
8307 (synopsis "Exploring accelerometer data")
8309 "This package processes accelerometer data from uni-axial and tri-axial devices
8310 and generates data summaries. Also, includes functions to plot, analyze, and
8311 simulate accelerometer data.")
8312 (license license:gpl2+)))
8314 (define-public r-rbenchmark
8316 (name "r-rbenchmark")
8321 (uri (cran-uri "rbenchmark" version))
8323 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8324 (build-system r-build-system)
8325 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8326 (synopsis "Benchmarking routine for R")
8328 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8329 and is intended to facilitate benchmarking of arbitrary R code. The library
8330 consists of just one function, benchmark, which is a simple wrapper around
8331 system.time. Given a specification of the benchmarking process (counts of
8332 replications, evaluation environment) and an arbitrary number of expressions,
8333 benchmark evaluates each of the expressions in the specified environment,
8334 replicating the evaluation as many times as specified, and returning the results
8335 conveniently wrapped into a data frame.")
8336 (license license:gpl2+)))
8338 (define-public r-mitools
8345 (uri (cran-uri "mitools" version))
8348 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8349 (build-system r-build-system)
8350 (propagated-inputs `(("r-dbi" ,r-dbi)))
8351 (home-page "https://cran.r-project.org/web/packages/mitools/")
8352 (synopsis "Tools for multiple imputation of missing data")
8354 "This package provides tools to perform analyses and combine results from
8355 multiple-imputation datasets.")
8356 (license license:gpl2)))
8358 (define-public r-magick
8365 (uri (cran-uri "magick" version))
8368 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8369 (build-system r-build-system)
8371 `(("imagemagick" ,imagemagick)
8374 `(("r-curl" ,r-curl)
8375 ("r-magrittr" ,r-magrittr)
8376 ("r-rcpp" ,r-rcpp)))
8378 `(("pkg-config" ,pkg-config)
8379 ("r-knitr" ,r-knitr)))
8380 (home-page "https://github.com/ropensci/magick")
8381 (synopsis "Advanced graphics and image-processing in R")
8383 "This package provides bindings to ImageMagick, a comprehensive image
8384 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8385 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8386 operations are vectorized via the Magick++ STL meaning they operate either on
8387 a single frame or a series of frames for working with layers, collages, or
8388 animation. In RStudio, images are automatically previewed when printed to the
8389 console, resulting in an interactive editing environment.")
8390 (license license:expat)))
8392 (define-public r-survey
8399 (uri (cran-uri "survey" version))
8402 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8403 (build-system r-build-system)
8405 `(("r-lattice" ,r-lattice)
8406 ("r-matrix" ,r-matrix)
8407 ("r-minqa" ,r-minqa)
8408 ("r-mitools" ,r-mitools)
8409 ("r-numderiv" ,r-numderiv)
8410 ("r-survival" ,r-survival)))
8411 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8412 (synopsis "Analysis of complex survey samples")
8414 "This package provides tools for the analysis of complex survey samples.
8415 The provided features include: summary statistics, two-sample tests, rank
8416 tests, generalised linear models, cumulative link models, Cox models,
8417 loglinear models, and general maximum pseudolikelihood estimation for
8418 multistage stratified, cluster-sampled, unequally weighted survey samples;
8419 variances by Taylor series linearisation or replicate weights;
8420 post-stratification, calibration, and raking; two-phase subsampling designs;
8421 graphics; PPS sampling without replacement; principal components, and factor
8423 ;; Either version of the GPL.
8424 (license (list license:gpl2 license:gpl3))))
8426 (define-public r-gee
8433 (uri (cran-uri "gee" version))
8436 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8437 (properties `((upstream-name . "gee")))
8438 (build-system r-build-system)
8440 `(("gfortran" ,gfortran)))
8441 (home-page "https://cran.r-project.org/web/packages/gee/")
8442 (synopsis "Generalized estimation equation solver")
8444 "This package provides a solver for generalized estimation equations.")
8445 (license license:gpl2)))
8447 (define-public r-tab
8454 (uri (cran-uri "tab" version))
8457 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8458 (properties `((upstream-name . "tab")))
8459 (build-system r-build-system)
8461 `(("r-dplyr" ,r-dplyr)
8463 ("r-knitr" ,r-knitr)
8465 ("r-survey" ,r-survey)
8466 ("r-survival" ,r-survival)
8467 ("r-xtable" ,r-xtable)))
8468 (home-page "https://cran.r-project.org/web/packages/tab/")
8469 (synopsis "Create summary tables for statistical reports")
8471 "This package contains functions for creating various types of summary
8472 tables, e.g. comparing characteristics across levels of a categorical variable
8473 and summarizing fitted generalized linear models, generalized estimating
8474 equations, and Cox proportional hazards models. Functions are available to
8475 handle data from simple random samples as well as complex surveys.")
8476 (license license:gpl3+)))
8478 (define-public r-dvmisc
8485 (uri (cran-uri "dvmisc" version))
8487 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8488 (build-system r-build-system)
8490 `(("r-cubature" ,r-cubature)
8491 ("r-data-table" ,r-data-table)
8492 ("r-dplyr" ,r-dplyr)
8493 ("r-ggplot2" ,r-ggplot2)
8495 ("r-mvtnorm" ,r-mvtnorm)
8496 ("r-pracma" ,r-pracma)
8497 ("r-rbenchmark" ,r-rbenchmark)
8499 ("r-survey" ,r-survey)
8501 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8502 (synopsis "Faster computation of common statistics and miscellaneous functions")
8504 "This package implements faster versions of base R functions (e.g. mean, standard
8505 deviation, covariance, weighted mean), mostly written in C++, along with
8506 miscellaneous functions for various purposes (e.g. create the histogram with
8507 fitted probability density function or probability mass function curve, create
8508 the body mass index groups, assess the linearity assumption in logistic
8510 (license license:gpl2)))
8512 (define-public r-accelerometry
8514 (name "r-accelerometry")
8519 (uri (cran-uri "accelerometry" version))
8521 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8522 (build-system r-build-system)
8524 `(("r-dvmisc" ,r-dvmisc)
8525 ("r-rcpp" ,r-rcpp)))
8526 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8527 (synopsis "Functions for processing accelerometer data")
8529 "This package provides a collection of functions that perform operations on
8530 time-series accelerometer data, such as identify the non-wear time, flag minutes
8531 that are part of an activity bout, and find the maximum 10-minute average count
8532 value. The functions are generally very flexible, allowing for a variety of
8533 algorithms to be implemented.")
8534 (license license:gpl3)))
8536 (define-public r-absim
8543 (uri (cran-uri "AbSim" version))
8545 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8546 (properties `((upstream-name . "AbSim")))
8547 (build-system r-build-system)
8550 ("r-powerlaw" ,r-powerlaw)))
8551 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8552 (synopsis "Time resolved simulations of antibody repertoires")
8554 "This package provides simulation methods for the evolution of antibody repertoires.
8555 The heavy and light chain variable region of both human and C57BL/6 mice can
8556 be simulated in a time-dependent fashion. Both single lineages using one set of
8557 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8558 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8559 Upon completion, the main loop of the algorithm begins, with each iteration
8560 representing one simulated time step. Various mutation events are possible at
8561 each time step, contributing to a diverse final repertoire.")
8562 (license license:gpl2)))
8564 (define-public r-quic
8571 (uri (cran-uri "QUIC" version))
8573 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8574 (properties `((upstream-name . "QUIC")))
8575 (build-system r-build-system)
8576 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8577 (synopsis "Regularized sparse inverse covariance matrix estimation")
8579 "This package implements the regularized Gaussian maximum likelihood
8580 estimation of the inverse of a covariance matrix. It uses Newton's method and
8581 coordinate descent to solve the regularized inverse covariance matrix
8582 estimation problem.")
8583 ;; The project home page states that the release is under GPLv3 or later.
8584 ;; The CRAN page only says GPL-3.
8585 (license license:gpl3+)))
8587 (define-public r-abundant
8594 (uri (cran-uri "abundant" version))
8596 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8597 (build-system r-build-system)
8599 `(("r-quic" ,r-quic)))
8600 (home-page "https://cran.r-project.org/web/packages/abundant/")
8601 (synopsis "Abundant regression and high-dimensional principal fitted components")
8603 "This package provides tools to fit and predict with the high-dimensional
8604 principal fitted components model. This model is described by Cook, Forzani,
8605 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8606 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8607 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8608 (license license:gpl2+)))
8610 (define-public r-ac3net
8617 (uri (cran-uri "Ac3net" version))
8619 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8620 (properties `((upstream-name . "Ac3net")))
8621 (build-system r-build-system)
8623 `(("r-data-table" ,r-data-table)))
8624 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8625 (synopsis "Inferring directional conservative causal core gene networks")
8626 (description "This package infers directional Conservative causal core
8627 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8628 directional network.")
8629 (license license:gpl3+)))
8631 (define-public r-aca
8638 (uri (cran-uri "ACA" version))
8640 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8641 (properties `((upstream-name . "ACA")))
8642 (build-system r-build-system)
8643 (home-page "https://cran.r-project.org/web/packages/ACA/")
8644 (synopsis "Abrupt change-point or aberration detection in point series")
8646 "This package offers an interactive function for the detection of breakpoints in
8648 ;; Any version of the GPL
8649 (license (list license:gpl2+ license:gpl3+))))
8651 (define-public r-acceptancesampling
8653 (name "r-acceptancesampling")
8658 (uri (cran-uri "AcceptanceSampling" version))
8660 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8662 `((upstream-name . "AcceptanceSampling")))
8663 (build-system r-build-system)
8664 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8665 (synopsis "Creation and evaluation of acceptance sampling plans")
8667 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8668 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8669 in quality control and improvement. International standards of acceptance
8670 sampling provide sampling plans for specific circumstances. The aim of this
8671 package is to provide an easy-to-use interface to visualize single, double or
8672 multiple sampling plans. In addition, methods have been provided to enable the
8673 user to assess sampling plans against pre-specified levels of performance, as
8674 measured by the probability of acceptance for a given level of quality in the
8676 (license license:gpl3+)))
8678 (define-public r-acclma
8685 (uri (cran-uri "ACCLMA" version))
8687 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8688 (properties `((upstream-name . "ACCLMA")))
8689 (build-system r-build-system)
8690 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8691 (synopsis "ACC & LMA graph plotting")
8693 "This package contains a function that imports data from a @acronym{CSV,
8694 Comma-Separated Values} file, or uses manually entered data from the format (x,
8695 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8696 Curve} vs @acronym{LOI, Line of Independence} graph and
8697 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8698 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8699 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8700 string) was passed, a manual data entry window is opened. The header parameter
8701 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8702 a header row or not. The dataset should contain only one independent variable
8703 (x) and one dependent variable (y) and can contain a weight for each
8705 (license license:gpl2)))
8707 (define-public r-aspi
8714 (uri (cran-uri "aspi" version))
8716 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8717 (build-system r-build-system)
8719 "https://cran.r-project.org/web/packages/aspi/")
8721 "Analysis of symmetry of parasitic infections")
8723 "This package provides tools for the analysis and visualization of bilateral
8724 asymmetry in parasitic infections.")
8725 (license license:gpl3+)))
8727 (define-public r-sandwich
8734 (uri (cran-uri "sandwich" version))
8737 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8738 (build-system r-build-system)
8740 `(("r-zoo" ,r-zoo)))
8741 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8742 (synopsis "Robust Covariance Matrix Estimators")
8744 "This package provides model-robust standard error estimators for
8745 cross-sectional, time series, clustered, panel, and longitudinal data.")
8746 ;; Either version of the license.
8747 (license (list license:gpl2 license:gpl3))))
8749 (define-public r-th-data
8756 (uri (cran-uri "TH.data" version))
8759 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8760 (properties `((upstream-name . "TH.data")))
8761 (build-system r-build-system)
8763 `(("r-mass" ,r-mass)
8764 ("r-survival" ,r-survival)))
8765 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8766 (synopsis "Shared data sets")
8768 "This package contains supporting data sets that are used in other
8769 packages maintained by Torsten Hothorn.")
8770 (license license:gpl3)))
8772 (define-public r-multcomp
8779 (uri (cran-uri "multcomp" version))
8782 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8783 (build-system r-build-system)
8785 `(("r-codetools" ,r-codetools)
8786 ("r-mvtnorm" ,r-mvtnorm)
8787 ("r-sandwich" ,r-sandwich)
8788 ("r-survival" ,r-survival)
8789 ("r-th-data" ,r-th-data)))
8790 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8791 (synopsis "Simultaneous inference in general parametric models")
8793 "Simultaneous tests and confidence intervals for general linear
8794 hypotheses in parametric models, including linear, generalized linear, linear
8795 mixed effects, and survival models. The package includes demos reproducing
8796 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8797 Hothorn, Westfall, 2010, CRC Press).")
8798 (license license:gpl2)))
8800 (define-public r-emmeans
8807 (uri (cran-uri "emmeans" version))
8810 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
8811 (build-system r-build-system)
8813 `(("r-estimability" ,r-estimability)
8814 ("r-mvtnorm" ,r-mvtnorm)
8815 ("r-numderiv" ,r-numderiv)
8817 ("r-xtable" ,r-xtable)))
8819 `(("r-knitr" ,r-knitr)))
8820 (home-page "https://github.com/rvlenth/emmeans")
8821 (synopsis "Estimated marginal means, aka least-squares means")
8823 "This package provides tools to obtain @dfn{estimated marginal
8824 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8825 be used to compute contrasts or linear functions of EMMs, trends, and
8826 comparisons of slopes.")
8827 ;; Either version of the license.
8828 (license (list license:gpl2 license:gpl3))))
8830 (define-public r-pwr
8837 (uri (cran-uri "pwr" version))
8840 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8841 (build-system r-build-system)
8843 `(("r-knitr" ,r-knitr)))
8844 (home-page "https://github.com/heliosdrm/pwr")
8845 (synopsis "Basic functions for power analysis")
8847 "This package provides power analysis functions along the lines of
8849 (license license:gpl3+)))
8851 (define-public r-libcoin
8858 (uri (cran-uri "libcoin" version))
8860 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
8861 (build-system r-build-system)
8862 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8863 (home-page "https://cran.r-project.org/web/packages/libcoin")
8864 (synopsis "Linear test statistics for permutation inference")
8866 "This package provides basic infrastructure for linear test statistics
8867 and permutation inference in the framework of Strasser and Weber (1999).")
8868 (license license:gpl2)))
8870 (define-public r-coin
8877 (uri (cran-uri "coin" version))
8880 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8881 (build-system r-build-system)
8883 `(("r-libcoin" ,r-libcoin)
8884 ("r-matrixstats" ,r-matrixstats)
8885 ("r-modeltools" ,r-modeltools)
8886 ("r-multcomp" ,r-multcomp)
8887 ("r-mvtnorm" ,r-mvtnorm)
8888 ("r-survival" ,r-survival)))
8889 (home-page "http://coin.r-forge.r-project.org")
8890 (synopsis "Conditional inference procedures in a permutation test framework")
8892 "This package provides conditional inference procedures for the general
8893 independence problem including two-sample, K-sample (non-parametric ANOVA),
8894 correlation, censored, ordered and multivariate problems.")
8895 (license license:gpl2)))
8897 (define-public r-bayesplot
8899 (name "r-bayesplot")
8904 (uri (cran-uri "bayesplot" version))
8907 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8908 (build-system r-build-system)
8910 `(("pandoc" ,pandoc)
8911 ("pandoc-citeproc" ,pandoc-citeproc)))
8913 `(("r-knitr" ,r-knitr)))
8915 `(("r-dplyr" ,r-dplyr)
8916 ("r-ggplot2" ,r-ggplot2)
8917 ("r-ggridges" ,r-ggridges)
8919 ("r-reshape2" ,r-reshape2)
8920 ("r-rlang" ,r-rlang)
8921 ("r-tibble" ,r-tibble)
8922 ("r-tidyselect" ,r-tidyselect)))
8923 (home-page "https://mc-stan.org/bayesplot")
8924 (synopsis "Plotting for Bayesian models")
8926 "This package provides plotting functions for posterior analysis, model
8927 checking, and MCMC diagnostics. The package is designed not only to provide
8928 convenient functionality for users, but also a common set of functions that
8929 can be easily used by developers working on a variety of R packages for
8930 Bayesian modeling.")
8931 (license license:gpl3+)))
8933 (define-public r-tmb
8940 (uri (cran-uri "TMB" version))
8943 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
8944 (properties `((upstream-name . "TMB")))
8945 (build-system r-build-system)
8947 `(("r-matrix" ,r-matrix)
8948 ("r-rcppeigen" ,r-rcppeigen)))
8949 (home-page "http://tmb-project.org")
8950 (synopsis "Template model builder: a general random effect tool")
8952 "With this tool, a user should be able to quickly implement complex
8953 random effect models through simple C++ templates. The package combines
8954 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8955 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8956 from R) to obtain an efficient implementation of the applied Laplace
8957 approximation with exact derivatives. Key features are: Automatic sparseness
8958 detection, parallelism through BLAS and parallel user templates.")
8959 (license license:gpl2)))
8961 (define-public r-sjstats
8968 (uri (cran-uri "sjstats" version))
8970 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8971 (build-system r-build-system)
8973 `(("r-bayestestr" ,r-bayestestr)
8974 ("r-broom" ,r-broom)
8975 ("r-dplyr" ,r-dplyr)
8976 ("r-effectsize" ,r-effectsize)
8977 ("r-emmeans" ,r-emmeans)
8978 ("r-insight" ,r-insight)
8980 ("r-magrittr" ,r-magrittr)
8982 ("r-modelr" ,r-modelr)
8983 ("r-parameters" ,r-parameters)
8984 ("r-performance" ,r-performance)
8985 ("r-purrr" ,r-purrr)
8986 ("r-rlang" ,r-rlang)
8987 ("r-sjlabelled" ,r-sjlabelled)
8988 ("r-sjmisc" ,r-sjmisc)
8989 ("r-tidyr" ,r-tidyr)))
8990 (home-page "https://github.com/strengejacke/sjstats")
8991 (synopsis "Functions for common statistical computations")
8993 "This package provides a collection of convenient functions for common
8994 statistical computations, which are not directly provided by R's @code{base}
8995 or @code{stats} packages. This package aims at providing, first, shortcuts
8996 for statistical measures, which otherwise could only be calculated with
8997 additional effort. Second, these shortcut functions are generic, and can be
8998 applied not only to vectors, but also to other objects as well. The focus of
8999 most functions lies on summary statistics or fit measures for regression
9000 models, including generalized linear models, mixed effects models and Bayesian
9002 (license license:gpl3)))
9004 (define-public r-glmmtmb
9011 (uri (cran-uri "glmmTMB" version))
9014 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9015 (properties `((upstream-name . "glmmTMB")))
9016 (build-system r-build-system)
9018 `(("r-lme4" ,r-lme4)
9019 ("r-matrix" ,r-matrix)
9021 ("r-rcppeigen" ,r-rcppeigen)
9024 `(("r-knitr" ,r-knitr))) ; for vignettes
9025 (home-page "https://github.com/glmmTMB")
9026 (synopsis "Generalized linear mixed models")
9028 "Fit linear and generalized linear mixed models with various extensions,
9029 including zero-inflation. The models are fitted using maximum likelihood
9030 estimation via the Template Model Builder. Random effects are assumed to be
9031 Gaussian on the scale of the linear predictor and are integrated out using the
9032 Laplace approximation. Gradients are calculated using automatic
9034 (license license:agpl3+)))
9036 (define-public r-bayestestr
9038 (name "r-bayestestr")
9043 (uri (cran-uri "bayestestR" version))
9046 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9047 (properties `((upstream-name . "bayestestR")))
9048 (build-system r-build-system)
9050 `(("r-insight" ,r-insight)))
9052 `(("r-knitr" ,r-knitr)))
9053 (home-page "https://github.com/easystats/bayestestR")
9054 (synopsis "Describe Bayesian models and posterior distributions")
9056 "This package provides utilities to understand and describe posterior
9057 distributions and Bayesian models. It includes point-estimates such as
9058 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9059 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9060 ROPE percentage and pd).")
9061 (license license:gpl3)))
9063 (define-public r-performance
9065 (name "r-performance")
9070 (uri (cran-uri "performance" version))
9073 "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
9074 (build-system r-build-system)
9076 `(("r-bayestestr" ,r-bayestestr)
9077 ("r-insight" ,r-insight)))
9078 (home-page "https://easystats.github.io/performance/")
9079 (synopsis "Assessment of regression models performance")
9081 "This package provides utilities for computing measures to assess model
9082 quality, which are not directly provided by R's @code{base} or @code{stats}
9083 packages. These include e.g. measures like r-squared, intraclass correlation
9084 coefficient, root mean squared error or functions to check models for
9085 overdispersion, singularity or zero-inflation and more. Functions apply to a
9086 large variety of regression models, including generalized linear models, mixed
9087 effects models and Bayesian models.")
9088 (license license:gpl3)))
9090 (define-public r-ggeffects
9092 (name "r-ggeffects")
9097 (uri (cran-uri "ggeffects" version))
9100 "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
9101 (build-system r-build-system)
9103 `(("r-insight" ,r-insight)
9105 ("r-sjlabelled" ,r-sjlabelled)))
9107 `(("r-knitr" ,r-knitr)))
9108 (home-page "https://github.com/strengejacke/ggeffects")
9109 (synopsis "Create tidy data frames of marginal effects for ggplot")
9111 "This package provides tools to compute marginal effects from statistical
9112 models and return the result as tidy data frames. These data frames are ready
9113 to use with the @code{ggplot2} package. Marginal effects can be calculated
9114 for many different models. Interaction terms, splines and polynomial terms
9115 are also supported. The two main functions are @code{ggpredict()} and
9116 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9117 results using @code{ggplot2}.")
9118 (license license:gpl3)))
9120 (define-public r-effectsize
9122 (name "r-effectsize")
9127 (uri (cran-uri "effectsize" version))
9130 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9131 (properties `((upstream-name . "effectsize")))
9132 (build-system r-build-system)
9134 `(("r-bayestestr" ,r-bayestestr)
9135 ("r-insight" ,r-insight)
9136 ("r-parameters" ,r-parameters)))
9138 `(("r-knitr" ,r-knitr)))
9139 (home-page "https://github.com/easystats/effectsize")
9140 (synopsis "Indices of effect size and standardized parameters")
9142 "This package provides utilities to work with indices of effect size and
9143 standardized parameters for a wide variety of models, allowing computation and
9144 conversion of indices such as Cohen's d, r, odds, etc.")
9145 (license license:gpl3)))
9147 (define-public r-sjplot
9154 (uri (cran-uri "sjPlot" version))
9156 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9157 (properties `((upstream-name . "sjPlot")))
9158 (build-system r-build-system)
9160 `(("r-bayestestr" ,r-bayestestr)
9161 ("r-dplyr" ,r-dplyr)
9162 ("r-effectsize" ,r-effectsize)
9163 ("r-ggeffects" ,r-ggeffects)
9164 ("r-ggplot2" ,r-ggplot2)
9165 ("r-insight" ,r-insight)
9166 ("r-knitr" ,r-knitr)
9168 ("r-parameters" ,r-parameters)
9169 ("r-performance" ,r-performance)
9170 ("r-purrr" ,r-purrr)
9171 ("r-rlang" ,r-rlang)
9172 ("r-scales" ,r-scales)
9173 ("r-sjlabelled" ,r-sjlabelled)
9174 ("r-sjmisc" ,r-sjmisc)
9175 ("r-sjstats" ,r-sjstats)
9176 ("r-tidyr" ,r-tidyr)))
9178 `(("r-knitr" ,r-knitr)))
9179 (home-page "https://strengejacke.github.io/sjPlot/")
9180 (synopsis "Data visualization for statistics in social science")
9182 "This package represents a collection of plotting and table output
9183 functions for data visualization. Results of various statistical
9184 analyses (that are commonly used in social sciences) can be visualized using
9185 this package, including simple and cross tabulated frequencies, histograms,
9186 box plots, (generalized) linear models, mixed effects models, principal
9187 component analysis and correlation matrices, cluster analyses, scatter plots,
9188 stacked scales, effects plots of regression models (including interaction
9189 terms) and much more. This package supports labelled data.")
9190 (license license:gpl3)))
9192 (define-public r-ini
9199 (uri (cran-uri "ini" version))
9202 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9203 (build-system r-build-system)
9204 (home-page "https://github.com/dvdscripter/ini")
9205 (synopsis "Read and write configuration files")
9207 "This package provides tools to parse simple @code{.ini} configuration
9208 files to an structured list. Users can manipulate this resulting list with
9209 @code{lapply()} functions. This same structured list can be used to write
9210 back to file after modifications.")
9211 (license license:gpl3)))
9220 (uri (cran-uri "gh" version))
9223 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9224 (build-system r-build-system)
9229 ("r-jsonlite" ,r-jsonlite)))
9230 (home-page "https://github.com/r-lib/gh#readme")
9231 (synopsis "Access the GitHub API via R")
9233 "This package provides a minimal R client to access the GitHub API.")
9234 (license license:expat)))
9243 (uri (cran-uri "fs" version))
9246 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9247 (build-system r-build-system)
9249 `(("r-knitr" ,r-knitr)))
9250 (home-page "https://fs.r-lib.org")
9251 (synopsis "Cross-platform file system operations based on libuv")
9253 "This package provides a cross-platform interface to file system
9254 operations, built on top of the libuv C library.")
9255 (license license:gpl3)))
9257 (define-public r-clisymbols
9259 (name "r-clisymbols")
9264 (uri (cran-uri "clisymbols" version))
9267 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9268 (build-system r-build-system)
9269 (home-page "https://github.com/gaborcsardi/clisymbols")
9270 (synopsis "Unicode symbols at the R prompt")
9272 "This package provides a small subset of Unicode symbols, that are useful
9273 when building command line applications. They fall back to alternatives on
9274 terminals that do not support Unicode.")
9275 (license license:expat)))
9277 (define-public r-usethis
9284 (uri (cran-uri "usethis" version))
9287 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9288 (build-system r-build-system)
9291 ("r-clipr" ,r-clipr)
9292 ("r-crayon" ,r-crayon)
9297 ("r-git2r" ,r-git2r)
9299 ("r-purrr" ,r-purrr)
9300 ("r-rematch2" ,r-rematch2)
9301 ("r-rlang" ,r-rlang)
9302 ("r-rprojroot" ,r-rprojroot)
9303 ("r-rstudioapi" ,r-rstudioapi)
9304 ("r-whisker" ,r-whisker)
9305 ("r-withr" ,r-withr)
9306 ("r-yaml" ,r-yaml)))
9307 (home-page "https://github.com/r-lib/usethis")
9308 (synopsis "Automate R package and project setup")
9310 "This package helps you to automate R package and project setup tasks
9311 that are otherwise performed manually. This includes setting up unit testing,
9312 test coverage, continuous integration, Git, GitHub integration, licenses,
9313 Rcpp, RStudio projects, and more.")
9314 (license license:gpl3)))
9316 (define-public r-sessioninfo
9318 (name "r-sessioninfo")
9323 (uri (cran-uri "sessioninfo" version))
9326 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9327 (build-system r-build-system)
9330 ("r-withr" ,r-withr)))
9331 (home-page "https://github.com/r-lib/sessioninfo#readme")
9332 (synopsis "R session information")
9334 "This package provides tools to query and print information about the
9335 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9336 more information about packages, and where they were installed from.")
9337 (license license:gpl2)))
9339 (define-public r-remotes
9346 (uri (cran-uri "remotes" version))
9349 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9350 (build-system r-build-system)
9352 `(("r-knitr" ,r-knitr)))
9353 (home-page "https://github.com/r-lib/remotes#readme")
9354 (synopsis "R package installation from remote repositories")
9356 "Download and install R packages stored in GitHub, BitBucket, or plain
9357 subversion or git repositories. This package is a lightweight replacement of
9358 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9359 the code was copied over from @code{devtools}.")
9360 (license license:gpl2+)))
9362 (define-public r-xopen
9369 (uri (cran-uri "xopen" version))
9372 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9373 (build-system r-build-system)
9375 `(("r-processx" ,r-processx)))
9376 (home-page "https://github.com/r-lib/xopen#readme")
9377 (synopsis "Open system files, URLs, anything")
9379 "This package provides a cross-platform solution to open files,
9380 directories or URLs with their associated programs.")
9381 (license license:expat)))
9383 (define-public r-rcmdcheck
9385 (name "r-rcmdcheck")
9390 (uri (cran-uri "rcmdcheck" version))
9393 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9394 (build-system r-build-system)
9396 `(("r-callr" ,r-callr)
9398 ("r-crayon" ,r-crayon)
9400 ("r-digest" ,r-digest)
9401 ("r-pkgbuild" ,r-pkgbuild)
9402 ("r-prettyunits" ,r-prettyunits)
9404 ("r-rprojroot" ,r-rprojroot)
9405 ("r-sessioninfo" ,r-sessioninfo)
9406 ("r-withr" ,r-withr)
9407 ("r-xopen" ,r-xopen)))
9408 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9409 (synopsis "Run R CMD check from R and capture results")
9411 "Run @code{R CMD check} from R programmatically, and capture the results
9412 of the individual checks.")
9413 (license license:expat)))
9415 (define-public r-rapportools
9417 (name "r-rapportools")
9422 (uri (cran-uri "rapportools" version))
9425 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9426 (build-system r-build-system)
9428 `(("r-pander" ,r-pander)
9430 ("r-reshape" ,r-reshape)))
9431 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9432 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9434 "This package provides helper functions that act as wrappers to more
9435 advanced statistical methods with the advantage of having sane defaults for
9437 (license license:agpl3+)))
9439 (define-public r-pander
9446 (uri (cran-uri "pander" version))
9449 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9450 (build-system r-build-system)
9452 `(("r-digest" ,r-digest)
9453 ("r-rcpp" ,r-rcpp)))
9454 (home-page "https://rapporter.github.io/pander")
9455 (synopsis "Render R objects into Pandoc's markdown")
9457 "The main aim of the pander R package is to provide a minimal and easy
9458 tool for rendering R objects into Pandoc's markdown. The package is also
9459 capable of exporting/converting complex Pandoc documents (reports) in various
9461 ;; This package is licensed under either the AGPLv3+ or the very rarely
9463 (license license:agpl3+)))
9465 (define-public r-summarytools
9467 (name "r-summarytools")
9472 (uri (cran-uri "summarytools" version))
9475 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9476 (build-system r-build-system)
9478 `(("r-base64enc" ,r-base64enc)
9479 ("r-checkmate" ,r-checkmate)
9480 ("r-dplyr" ,r-dplyr)
9481 ("r-htmltools" ,r-htmltools)
9482 ("r-lubridate" ,r-lubridate)
9483 ("r-magick" ,r-magick)
9484 ("r-matrixstats" ,r-matrixstats)
9485 ("r-pander" ,r-pander)
9487 ("r-rapportools" ,r-rapportools)
9488 ("r-tibble" ,r-tibble)
9489 ("r-tidyr" ,r-tidyr)))
9490 (home-page "https://github.com/dcomtois/summarytools")
9491 (synopsis "Tools to quickly and neatly summarize data")
9493 "This package provides tools for data frame summaries, cross-tabulations,
9494 weight-enabled frequency tables and common univariate statistics in concise
9495 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9496 good point-of-entry for exploring data, both for experienced and new R
9498 (license license:gpl2)))
9500 (define-public r-lsei
9507 (uri (cran-uri "lsei" version))
9510 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9511 (build-system r-build-system)
9513 `(("gfortran" ,gfortran)))
9514 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9515 (synopsis "Solve regression problems under equality/inequality constraints")
9517 "It contains functions that solve least squares linear regression
9518 problems under linear equality/inequality constraints. Functions for solving
9519 quadratic programming problems are also available, which transform such
9520 problems into least squares ones first.")
9521 (license license:gpl2+)))
9523 (define-public r-npsurv
9530 (uri (cran-uri "npsurv" version))
9533 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9534 (build-system r-build-system)
9536 `(("r-lsei" ,r-lsei)))
9537 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9538 (synopsis "Nonparametric survival analysis")
9540 "This package contains functions for non-parametric survival analysis of
9541 exact and interval-censored observations.")
9542 (license license:gpl2+)))
9544 (define-public r-clusteval
9546 (name "r-clusteval")
9551 (uri (cran-uri "clusteval" version))
9554 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9555 (build-system r-build-system)
9557 `(("r-mvtnorm" ,r-mvtnorm)
9558 ("r-rcpp" ,r-rcpp)))
9559 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9560 (synopsis "Evaluation of clustering algorithms")
9562 "This R package provides a suite of tools to evaluate clustering
9563 algorithms, clusterings, and individual clusters.")
9564 (license license:expat)))
9566 (define-public r-tweedie
9573 (uri (cran-uri "tweedie" version))
9576 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9577 (build-system r-build-system)
9578 (native-inputs `(("gfortran" ,gfortran)))
9579 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9580 (synopsis "Evaluation of Tweedie exponential family models")
9582 "Maximum likelihood computations for Tweedie families, including the
9583 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9584 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9585 and related methods.")
9586 (license license:gpl2+)))
9588 (define-public r-rcppgsl
9595 (uri (cran-uri "RcppGSL" version))
9597 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9598 (properties `((upstream-name . "RcppGSL")))
9599 (build-system r-build-system)
9601 `(("r-rcpp" ,r-rcpp)
9603 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9604 (synopsis "Rcpp integration for GSL vectors and matrices")
9606 "The GNU Scientific Library (or GSL) is a collection of numerical
9607 routines for scientific computing. It is particularly useful for C and C++
9608 programs as it provides a standard C interface to a wide range of mathematical
9609 routines. There are over 1000 functions in total with an extensive test
9610 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9611 structures and R using concepts from Rcpp which is itself a package that eases
9612 the interfaces between R and C++.")
9613 (license license:gpl2+)))
9615 (define-public r-mvabund
9622 (uri (cran-uri "mvabund" version))
9625 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9626 (build-system r-build-system)
9628 `(("r-mass" ,r-mass)
9630 ("r-rcppgsl" ,r-rcppgsl)
9631 ("r-statmod" ,r-statmod)
9632 ("r-tweedie" ,r-tweedie)))
9633 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9634 (synopsis "Statistical methods for analysing multivariate abundance data")
9636 "This package provides a set of tools for displaying, modeling and
9637 analysing multivariate abundance data in community ecology.")
9638 (license license:lgpl2.1+)))
9640 (define-public r-afex
9647 (uri (cran-uri "afex" version))
9650 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9651 (build-system r-build-system)
9655 ("r-lmertest" ,r-lmertest)
9656 ("r-pbkrtest" ,r-pbkrtest)
9657 ("r-reshape2" ,r-reshape2)))
9659 `(("r-knitr" ,r-knitr)))
9660 (home-page "https://afex.singmann.science/")
9661 (synopsis "Analysis of factorial experiments")
9663 "This package provides convenience functions for analyzing factorial
9664 experiments using ANOVA or mixed models.")
9665 (license license:gpl2+)))
9667 (define-public r-lmertest
9674 (uri (cran-uri "lmerTest" version))
9677 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9678 (properties `((upstream-name . "lmerTest")))
9679 (build-system r-build-system)
9681 `(("r-ggplot2" ,r-ggplot2)
9684 ("r-numderiv" ,r-numderiv)))
9685 (home-page "https://github.com/runehaubo/lmerTestR")
9686 (synopsis "Tests in linear mixed effects models")
9688 "This package provides p-values in type I, II or III anova and summary
9689 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9690 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9691 package. Model selection methods include step, drop1 and anova-like tables
9692 for random effects (ranova). Methods for Least-Square means (LS-means) and
9693 tests of linear contrasts of fixed effects are also available.")
9694 (license license:gpl2+)))
9696 (define-public r-r2glmm
9703 (uri (cran-uri "r2glmm" version))
9706 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9707 (build-system r-build-system)
9709 `(("r-afex" ,r-afex)
9710 ("r-data-table" ,r-data-table)
9711 ("r-dplyr" ,r-dplyr)
9712 ("r-ggplot2" ,r-ggplot2)
9713 ("r-gridextra" ,r-gridextra)
9714 ("r-lmertest" ,r-lmertest)
9716 ("r-matrix" ,r-matrix)
9718 ("r-pbkrtest" ,r-pbkrtest)))
9719 (home-page "https://github.com/bcjaeger/r2glmm")
9720 (synopsis "Compute R squared for mixed (multilevel) models")
9722 "This package computes model and semi partial R squared with confidence
9723 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9724 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9725 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9727 (license license:gpl2)))
9729 (define-public r-weights
9736 (uri (cran-uri "weights" version))
9739 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9740 (build-system r-build-system)
9742 `(("r-gdata" ,r-gdata)
9743 ("r-hmisc" ,r-hmisc)
9744 ("r-mice" ,r-mice)))
9746 "https://cran.r-project.org/web/packages/weights/")
9747 (synopsis "Weighting and weighted statistics")
9748 (description "This package Provides a variety of functions for producing
9749 simple weighted statistics, such as weighted Pearson's correlations, partial
9750 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9751 includes some software for quickly recoding survey data and plotting point
9752 estimates from interaction terms in regressions (and multiply imputed
9753 regressions). NOTE: Weighted partial correlation calculations pulled to
9755 (license license:gpl2+)))
9757 (define-public r-rcppannoy
9759 (name "r-rcppannoy")
9764 (uri (cran-uri "RcppAnnoy" version))
9767 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9768 (properties `((upstream-name . "RcppAnnoy")))
9769 (build-system r-build-system)
9771 `(("r-rcpp" ,r-rcpp)))
9772 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9773 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9775 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9776 for efficient memory usage as well an ability to load from and save to disk.
9777 This package provides an R interface.")
9778 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9780 (license (list license:gpl2+ license:asl2.0))))
9782 (define-public r-rcpphnsw
9789 (uri (cran-uri "RcppHNSW" version))
9792 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9793 (properties `((upstream-name . "RcppHNSW")))
9794 (build-system r-build-system)
9795 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9796 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9797 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9799 "Hnswlib is a C++ library for approximate nearest neighbors. This
9800 package provides a minimal R interface by relying on the Rcpp package.")
9801 ;; hnswlib is released under Version 2.0 of the Apache License.
9802 (license (list license:gpl3 license:asl2.0))))
9804 (define-public r-rcppparallel
9806 (name "r-rcppparallel")
9811 (uri (cran-uri "RcppParallel" version))
9814 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
9815 (properties `((upstream-name . "RcppParallel")))
9816 (build-system r-build-system)
9817 (home-page "https://rcppcore.github.io/RcppParallel/")
9818 (synopsis "Parallel programming tools for Rcpp")
9820 "This package provides high level functions for parallel programming with
9821 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9822 the work of a standard serial @code{for} loop into a parallel one and the
9823 @code{parallelReduce()} function can be used for accumulating aggregates or
9825 (license license:gpl2)))
9827 (define-public r-ncdf4
9834 (uri (cran-uri "ncdf4" version))
9837 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9838 (build-system r-build-system)
9840 `(("netcdf" ,netcdf)
9842 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9843 (synopsis "R interface to Unidata netCDF format data files")
9845 "This package provides a high-level R interface to data files written
9846 using Unidata's netCDF library (version 4 or earlier), which are binary data
9847 files that are portable across platforms and include metadata information in
9848 addition to the data sets. Using this package, netCDF files can be opened and
9849 data sets read in easily. It is also easy to create new netCDF dimensions,
9850 variables, and files, in either version 3 or 4 format, and manipulate existing
9852 (license license:gpl3+)))
9854 (define-public r-biocmanager
9856 (name "r-biocmanager")
9861 (uri (cran-uri "BiocManager" version))
9863 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9864 (properties `((upstream-name . "BiocManager")))
9865 (build-system r-build-system)
9866 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9867 (synopsis "Access the Bioconductor project package repository")
9869 "This package provides a convenient tool to install and update
9870 Bioconductor packages.")
9871 (license license:artistic2.0)))
9873 (define-public r-rgl
9876 (version "0.100.54")
9880 (uri (cran-uri "rgl" version))
9883 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9884 (build-system r-build-system)
9886 `(("pkg-config" ,pkg-config)))
9888 `(("freetype" ,freetype)
9895 `(("r-crosstalk" ,r-crosstalk)
9896 ("r-htmltools" ,r-htmltools)
9897 ("r-htmlwidgets" ,r-htmlwidgets)
9898 ("r-jsonlite" ,r-jsonlite)
9899 ("r-knitr" ,r-knitr)
9900 ("r-magrittr" ,r-magrittr)
9901 ("r-manipulatewidget" ,r-manipulatewidget)
9902 ("r-shiny" ,r-shiny)))
9903 (home-page "https://r-forge.r-project.org/projects/rgl/")
9904 (synopsis "3D visualization using OpenGL")
9906 "This package provides medium to high level functions for 3D interactive graphics,
9907 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9908 as functions for constructing representations of geometric
9909 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9910 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9911 image formats, including PNG, Postscript, SVG, PGF.")
9912 ;; Any version of the GPL.
9913 (license (list license:gpl2+ license:gpl3+))))
9915 (define-public r-multicool
9917 (name "r-multicool")
9922 (uri (cran-uri "multicool" version))
9925 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9926 (build-system r-build-system)
9927 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9928 (home-page "https://cran.r-project.org/web/packages/multicool/")
9929 (synopsis "Permutations of multisets in cool-lex order")
9931 "This package provides a set of tools to permute multisets without loops
9932 or hash tables and to generate integer partitions. Cool-lex order is similar
9933 to colexicographical order.")
9934 (license license:gpl2)))
9936 (define-public r-misc3d
9943 (uri (cran-uri "misc3d" version))
9946 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9947 (build-system r-build-system)
9948 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9949 (synopsis "Miscellaneous 3D Plots")
9951 "This package provides a collection of miscellaneous 3d plots, including
9953 ;; Any version of the GPL.
9954 (license (list license:gpl2+ license:gpl3+))))
9963 (uri (cran-uri "ks" version))
9965 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9966 (build-system r-build-system)
9969 ("r-kernlab" ,r-kernlab)
9970 ("r-kernsmooth" ,r-kernsmooth)
9971 ("r-matrix" ,r-matrix)
9972 ("r-mclust" ,r-mclust)
9974 ("r-multicool" ,r-multicool)
9975 ("r-mvtnorm" ,r-mvtnorm)))
9976 (home-page "http://www.mvstat.net/tduong/")
9977 (synopsis "Kernel smoothing")
9979 "This package provides kernel smoothers for univariate and multivariate
9980 data, including density functions, density derivatives, cumulative
9981 distributions, modal clustering, discriminant analysis, and two-sample
9982 hypothesis testing.")
9983 ;; Either version of the GPL.
9984 (license (list license:gpl2 license:gpl3))))
9986 (define-public r-feature
9993 (uri (cran-uri "feature" version))
9996 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9997 (build-system r-build-system)
10000 ("r-misc3d" ,r-misc3d)
10002 (home-page "http://www.mvstat.net/tduong/")
10003 (synopsis "Inferential feature significance for kernel density estimation")
10005 "The feature package contains functions to display and compute kernel
10006 density estimates, significant gradient and significant curvature regions.
10007 Significant gradient and/or curvature regions often correspond to significant
10008 features (e.g. local modes).")
10009 ;; Either version of the GPL.
10010 (license (list license:gpl2 license:gpl3))))
10012 (define-public r-arm
10019 (uri (cran-uri "arm" version))
10022 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10023 (build-system r-build-system)
10025 `(("r-abind" ,r-abind)
10027 ("r-hmisc" ,r-hmisc)
10030 ("r-matrix" ,r-matrix)
10031 ("r-nlme" ,r-nlme)))
10032 (home-page "https://cran.r-project.org/web/packages/arm/")
10033 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10035 "This package provides functions to accompany A. Gelman and J. Hill,
10036 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10037 University Press, 2007.")
10038 (license license:gpl3+)))
10040 (define-public r-circular
10042 (name "r-circular")
10047 (uri (cran-uri "circular" version))
10050 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10051 (build-system r-build-system)
10053 `(("r-boot" ,r-boot)
10054 ("r-mvtnorm" ,r-mvtnorm)))
10056 `(("gfortran" ,gfortran)))
10057 (home-page "https://cran.r-project.org/web/packages/circular/")
10058 (synopsis "Circular statistics")
10060 "This package provides tools for circular statistics, from \"Topics in
10061 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10063 (license license:gpl2+)))
10065 (define-public r-activity
10067 (name "r-activity")
10072 (uri (cran-uri "activity" version))
10075 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10076 (build-system r-build-system)
10078 `(("r-circular" ,r-circular)
10079 ("r-insol" ,r-insol)
10080 ("r-pbapply" ,r-pbapply)))
10081 (home-page "https://cran.r-project.org/web/packages/activity/")
10082 (synopsis "Animal activity statistics")
10084 "This package provides functions to fit kernel density functions to
10085 animal activity time data; plot activity distributions; quantify overall
10086 levels of activity; statistically compare activity metrics through
10087 bootstrapping; and evaluate variation in linear variables with time (or other
10088 circular variables).")
10089 (license license:gpl3)))
10091 (define-public r-ouch
10098 (uri (cran-uri "ouch" version))
10101 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10102 (build-system r-build-system)
10103 (propagated-inputs `(("r-subplex" ,r-subplex)))
10104 (home-page "https://kingaa.github.io/ouch/")
10105 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10107 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10108 for evolution along a phylogenetic tree.")
10109 (license license:gpl2+)))
10111 (define-public r-fmsb
10118 (uri (cran-uri "fmsb" version))
10121 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10122 (build-system r-build-system)
10123 (home-page "http://minato.sip21c.org/msb/")
10124 (synopsis "Functions for medical statistics book with demographic data")
10126 "This package provides several utility functions for the book entitled
10127 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10128 Japan, 2007) with Japanese demographic data and some demographic analysis
10129 related functions.")
10130 (license license:gpl2+)))
10132 (define-public r-stabledist
10134 (name "r-stabledist")
10139 (uri (cran-uri "stabledist" version))
10142 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10143 (build-system r-build-system)
10144 (home-page "https://www.rmetrics.org")
10145 (synopsis "Stable distribution functions")
10147 "This package provides density, probability and quantile functions, and
10148 random number generation for (skew) stable distributions, using the
10149 parametrizations of Nolan.")
10150 (license license:gpl2+)))
10152 (define-public r-gsl
10159 (uri (cran-uri "gsl" version))
10162 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10163 (build-system r-build-system)
10166 (home-page "https://cran.r-project.org/web/packages/gsl")
10167 (synopsis "Wrapper for the GNU Scientific Library")
10169 "This package provides an R wrapper for the special functions and quasi
10170 random number generators of the GNU Scientific Library.")
10171 (license license:gpl2+)))
10173 (define-public r-adgoftest
10175 (name "r-adgoftest")
10180 (uri (cran-uri "ADGofTest" version))
10183 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10184 (properties `((upstream-name . "ADGofTest")))
10185 (build-system r-build-system)
10186 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10187 (synopsis "Anderson-Darling GoF test")
10189 "This package provides an implementation of the Anderson-Darling GoF test
10190 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10191 Anderson-Darling Distribution\".")
10192 ;; Any version of the GPL.
10193 (license license:gpl3+)))
10195 (define-public r-softimpute
10197 (name "r-softimpute")
10202 (uri (cran-uri "softImpute" version))
10205 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10206 (properties `((upstream-name . "softImpute")))
10207 (build-system r-build-system)
10209 `(("r-matrix" ,r-matrix)))
10211 `(("gfortran" ,gfortran)))
10212 (home-page "https://cran.r-project.org/web/packages/softImpute")
10213 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10215 "This package provides iterative methods for matrix completion that use
10216 nuclear-norm regularization. The package includes procedures for centering
10217 and scaling rows, columns or both, and for computing low-rank @dfn{single
10218 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10220 (license license:gpl2)))
10222 (define-public r-fftwtools
10224 (name "r-fftwtools")
10229 (uri (cran-uri "fftwtools" version))
10232 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10233 (build-system r-build-system)
10234 (inputs `(("fftw" ,fftw)))
10235 (home-page "https://github.com/krahim/fftwtools")
10236 (synopsis "Wrapper for FFTW3")
10238 "This package provides a wrapper for several FFTW functions. It provides
10239 access to the two-dimensional FFT, the multivariate FFT, and the
10240 one-dimensional real to complex FFT using the FFTW3 library. The package
10241 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10242 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10243 The FFT functions have a parameter that allows them to not return the
10244 redundant complex conjugate when the input is real data.")
10245 (license license:gpl2+)))
10247 (define-public r-tiff
10254 (uri (cran-uri "tiff" version))
10257 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10258 (build-system r-build-system)
10260 `(("libtiff" ,libtiff)
10261 ("libjpeg" ,libjpeg-turbo)
10263 (home-page "https://www.rforge.net/tiff/")
10264 (synopsis "Read and write TIFF images")
10266 "This package provides an easy and simple way to read, write and display
10267 bitmap images stored in the TIFF format. It can read and write both files and
10268 in-memory raw vectors.")
10269 ;; Either of these two license versions.
10270 (license (list license:gpl2 license:gpl3))))
10272 (define-public r-nlp
10279 (uri (cran-uri "NLP" version))
10282 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10283 (properties `((upstream-name . "NLP")))
10284 (build-system r-build-system)
10285 (home-page "https://cran.r-project.org/web/packages/NLP/")
10286 (synopsis "Natural language processing infrastructure")
10288 "This package provides basic classes and methods for Natural Language
10290 (license license:gpl3)))
10292 (define-public r-tm
10299 (uri (cran-uri "tm" version))
10302 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10303 (properties `((upstream-name . "tm")))
10304 (build-system r-build-system)
10310 ("r-xml2" ,r-xml2)))
10311 (home-page "http://tm.r-forge.r-project.org/")
10312 (synopsis "Text mining package")
10314 "This package provides a framework for text mining applications within R.")
10315 (license license:gpl3)))
10317 (define-public r-waveslim
10319 (name "r-waveslim")
10324 (uri (cran-uri "waveslim" version))
10327 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10328 (build-system r-build-system)
10330 `(("gfortran" ,gfortran)))
10331 (home-page "http://waveslim.blogspot.com")
10332 (synopsis "Basic wavelet routines for signal processing")
10334 "This package provides basic wavelet routines for time series (1D),
10335 image (2D) and array (3D) analysis. The code provided here is based on
10336 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10337 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10338 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10339 pairs (Selesnick 2001, 2002).")
10340 (license license:bsd-3)))
10342 (define-public r-wordcloud
10344 (name "r-wordcloud")
10349 (uri (cran-uri "wordcloud" version))
10352 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10353 (build-system r-build-system)
10355 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10357 ;; The "tm" package is only "suggested" according to CRAN, but the
10358 ;; wordcloud package cannot be loaded without it.
10360 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10361 (synopsis "Word clouds")
10363 "This package provides functionality to create pretty word clouds,
10364 visualize differences and similarity between documents, and avoid
10365 over-plotting in scatter plots with text.")
10366 (license license:lgpl2.1)))
10368 (define-public r-colorramps
10370 (name "r-colorramps")
10375 (uri (cran-uri "colorRamps" version))
10378 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10379 (properties `((upstream-name . "colorRamps")))
10380 (build-system r-build-system)
10381 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10382 (synopsis "Build color tables")
10383 (description "This package provides features to build gradient color
10385 ;; Any version of the GPL
10386 (license license:gpl3+)))
10388 (define-public r-tidytree
10390 (name "r-tidytree")
10395 (uri (cran-uri "tidytree" version))
10397 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10398 (build-system r-build-system)
10401 ("r-dplyr" ,r-dplyr)
10402 ("r-lazyeval" ,r-lazyeval)
10403 ("r-magrittr" ,r-magrittr)
10404 ("r-rlang" ,r-rlang)
10405 ("r-tibble" ,r-tibble)))
10407 `(("r-knitr" ,r-knitr)))
10408 (home-page "https://github.com/GuangchuangYu/tidytree")
10409 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10411 "Phylogenetic trees generally contain multiple components including nodes,
10412 edges, branches and associated data. This package provides an approach to
10413 convert tree objects to tidy data frames. It also provides tidy interfaces to
10414 manipulate tree data.")
10415 (license license:artistic2.0)))
10417 (define-public r-rvcheck
10424 (uri (cran-uri "rvcheck" version))
10426 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10427 (build-system r-build-system)
10429 `(("r-biocmanager" ,r-biocmanager)
10430 ("r-rlang" ,r-rlang)))
10431 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10432 (synopsis "R package version check")
10434 "This package provides tools to check the latest release version of R and
10435 R packages (on CRAN, Bioconductor or Github).")
10436 (license license:artistic2.0)))
10438 (define-public r-docopt
10445 (uri (cran-uri "docopt" version))
10448 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10449 (build-system r-build-system)
10450 (home-page "https://github.com/docopt/docopt.R")
10451 (synopsis "Command-line interface specification language")
10453 "This package enables you to define a command-line interface by just
10454 giving it a description in the specific format.")
10455 (license license:expat)))
10457 (define-public r-sparsesvd
10459 (name "r-sparsesvd")
10464 (uri (cran-uri "sparsesvd" version))
10467 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10468 (build-system r-build-system)
10469 (propagated-inputs `(("r-matrix" ,r-matrix)))
10470 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10471 (synopsis "Sparse truncated singular value decomposition")
10473 "This package provides a Wrapper around the SVDLIBC library
10474 for (truncated) singular value decomposition of a sparse matrix. Currently,
10475 only sparse real matrices in Matrix package format are supported.")
10476 ;; SVDLIBC is released under BSD-2. The R interface is released under
10478 (license (list license:bsd-3 license:bsd-2))))
10480 (define-public r-speedglm
10482 (name "r-speedglm")
10487 (uri (cran-uri "speedglm" version))
10490 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10491 (build-system r-build-system)
10493 `(("r-mass" ,r-mass)
10494 ("r-matrix" ,r-matrix)))
10495 (home-page "https://cran.r-project.org/web/packages/speedglm")
10496 (synopsis "Fit linear and generalized linear models to large data sets")
10498 "This package provides tools for fitting linear models and generalized
10499 linear models to large data sets by updating algorithms.")
10500 ;; Any version of the GPL
10501 (license license:gpl2+)))
10503 (define-public r-densityclust
10505 (name "r-densityclust")
10510 (uri (cran-uri "densityClust" version))
10513 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10514 (properties `((upstream-name . "densityClust")))
10515 (build-system r-build-system)
10518 ("r-ggplot2" ,r-ggplot2)
10519 ("r-ggrepel" ,r-ggrepel)
10520 ("r-gridextra" ,r-gridextra)
10521 ("r-rcolorbrewer" ,r-rcolorbrewer)
10523 ("r-rtsne" ,r-rtsne)))
10524 (home-page "https://cran.r-project.org/web/packages/densityClust")
10525 (synopsis "Clustering by fast search and find of density peaks")
10527 "This package provides an improved implementation (based on k-nearest
10528 neighbors) of the density peak clustering algorithm, originally described by
10529 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10530 large datasets (> 100,000 samples) very efficiently.")
10531 (license license:gpl2+)))
10533 (define-public r-combinat
10535 (name "r-combinat")
10540 (uri (cran-uri "combinat" version))
10543 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10544 (build-system r-build-system)
10545 (home-page "https://cran.r-project.org/web/packages/combinat")
10546 (synopsis "Combinatorics utilities")
10547 (description "This package provides assorted routines for combinatorics.")
10548 (license license:gpl2)))
10550 (define-public r-qlcmatrix
10552 (name "r-qlcmatrix")
10557 (uri (cran-uri "qlcMatrix" version))
10560 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10561 (properties `((upstream-name . "qlcMatrix")))
10562 (build-system r-build-system)
10564 `(("r-docopt" ,r-docopt)
10565 ("r-matrix" ,r-matrix)
10567 ("r-sparsesvd" ,r-sparsesvd)))
10568 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10569 (synopsis "Sparse matrix functions for quantitative language comparison")
10571 "This package provides an extension of the functionality of the Matrix
10572 package for using sparse matrices. Some of the functions are very general,
10573 while other are highly specific for the special data format used for
10574 @dfn{quantitative language comparison} (QLC).")
10575 (license license:gpl3)))
10577 (define-public r-ddrtree
10584 (uri (cran-uri "DDRTree" version))
10587 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10588 (properties `((upstream-name . "DDRTree")))
10589 (build-system r-build-system)
10592 ("r-irlba" ,r-irlba)
10594 ("r-rcppeigen" ,r-rcppeigen)))
10595 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10596 (synopsis "Learning principal graphs with DDRTree")
10598 "This package provides an implementation of the framework of
10599 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10600 dimensional space while constructs a principal tree which passes through the
10601 middle of the data simultaneously. DDRTree shows superiority to
10602 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10603 intrinsic structure of single cell genomics data. In general, it could be
10604 used to reconstruct the temporal progression as well as the bifurcation
10605 structure of any data type.")
10606 (license license:asl2.0)))
10608 (define-public r-corpcor
10615 (uri (cran-uri "corpcor" version))
10618 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10619 (build-system r-build-system)
10620 (home-page "http://strimmerlab.org/software/corpcor/")
10621 (synopsis "Efficient estimation of covariance and (partial) correlation")
10623 "This package implements a James-Stein-type shrinkage estimator for the
10624 covariance matrix, with separate shrinkage for variances and correlations.
10625 Furthermore, functions are available for fast singular value decomposition,
10626 for computing the pseudoinverse, and for checking the rank and positive
10627 definiteness of a matrix.")
10628 (license license:gpl3+)))
10630 (define-public r-rspectra
10632 (name "r-rspectra")
10637 (uri (cran-uri "RSpectra" version))
10640 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10641 (properties `((upstream-name . "RSpectra")))
10642 (build-system r-build-system)
10644 `(("r-matrix" ,r-matrix)
10646 ("r-rcppeigen" ,r-rcppeigen)))
10647 (home-page "https://github.com/yixuan/RSpectra")
10648 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10650 "This package provides an R interface to the Spectra library for
10651 large-scale eigenvalue and SVD problems. It is typically used to compute a
10652 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10653 which is usually more efficient than @code{eigen()} if k << n.")
10655 (license license:mpl2.0)))
10657 (define-public r-vbsr
10664 (uri (cran-uri "vbsr" version))
10667 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10668 (build-system r-build-system)
10669 (home-page "https://cran.r-project.org/web/packages/vbsr")
10670 (synopsis "Variational Bayes spike regression regularized linear models")
10672 "This package provides an efficient algorithm for solving ultra-sparse
10673 regularized regression models using a variational Bayes algorithm with a spike
10674 prior. The algorithm is solved on a path, with coordinate updates, and is
10675 capable of generating very sparse models. Very general model
10676 diagnostics for controlling type-1 errors are also provided.")
10677 (license license:gpl2)))
10679 (define-public r-flare
10682 (version "1.6.0.2")
10686 (uri (cran-uri "flare" version))
10689 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10690 (build-system r-build-system)
10692 `(("r-igraph" ,r-igraph)
10693 ("r-lattice" ,r-lattice)
10695 ("r-matrix" ,r-matrix)))
10696 (home-page "https://cran.r-project.org/web/packages/flare")
10697 (synopsis "Family of Lasso regression implementations")
10699 "This package provides implementations of a family of Lasso variants
10700 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10701 high dimensional sparse linear models.")
10702 (license license:gpl2)))
10704 (define-public r-lassopv
10711 (uri (cran-uri "lassopv" version))
10714 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10715 (build-system r-build-system)
10716 (propagated-inputs `(("r-lars" ,r-lars)))
10717 (home-page "https://github.com/lingfeiwang/lassopv")
10718 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10720 "This package enables you to estimate the p-values for predictors x
10721 against target variable y in Lasso regression, using the regularization
10722 strength when each predictor enters the active set of regularization path for
10723 the first time as the statistic.")
10724 (license license:gpl3)))
10726 (define-public r-splitstackshape
10728 (name "r-splitstackshape")
10733 (uri (cran-uri "splitstackshape" version))
10736 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10737 (build-system r-build-system)
10739 `(("r-data-table" ,r-data-table)))
10740 (home-page "https://github.com/mrdwab/splitstackshape")
10741 (synopsis "Stack and reshape datasets after splitting concatenated values")
10743 "Online data collection tools like Google Forms often export
10744 multiple-response questions with data concatenated in cells. The
10745 @code{concat.split} (cSplit) family of functions provided by this package
10746 splits such data into separate cells. This package also includes functions to
10747 stack groups of columns and to reshape wide data, even when the data are
10748 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10749 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10751 (license license:gpl3)))
10753 (define-public r-tfmpvalue
10755 (name "r-tfmpvalue")
10760 (uri (cran-uri "TFMPvalue" version))
10763 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10764 (properties `((upstream-name . "TFMPvalue")))
10765 (build-system r-build-system)
10766 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10767 (home-page "https://github.com/ge11232002/TFMPvalue")
10768 (synopsis "P-value computation for position weight matrices")
10770 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10771 identification from sequence/alignments, we are interested in the significance
10772 of certain match scores. TFMPvalue provides the accurate calculation of a
10773 p-value with a score threshold for position weight matrices, or the score with
10774 a given p-value. It is an interface to code originally made available by
10775 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10776 Touzet and Varre (2007).")
10777 (license license:gpl2)))
10779 (define-public r-rnifti
10786 (uri (cran-uri "RNifti" version))
10789 "0gh80n9lcpdhwmi9q78yfvbkb0kffamv7ncsna68401y9mfvn7ag"))))
10790 (properties `((upstream-name . "RNifti")))
10791 (build-system r-build-system)
10792 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10793 (home-page "https://github.com/jonclayden/RNifti")
10794 (synopsis "Fast R and C++ access to NIfTI images")
10796 "This package provides very fast read and write access to images stored
10797 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10798 compiled C and interpreted R code. It also provides a C/C++ API that can be
10799 used by other packages.")
10800 (license license:gpl2)))
10802 (define-public r-shades
10809 (uri (cran-uri "shades" version))
10812 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10813 (build-system r-build-system)
10814 (home-page "https://github.com/jonclayden/shades")
10815 (synopsis "Simple color manipulation")
10817 "This package provides functions for easily manipulating colors,
10818 creating color scales and calculating color distances.")
10819 (license license:bsd-3)))
10821 (define-public r-ore
10828 (uri (cran-uri "ore" version))
10830 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10831 (build-system r-build-system)
10832 (home-page "https://github.com/jonclayden/ore")
10833 (synopsis "R interface to the Onigmo regular expression library")
10835 "This package provides an alternative to R's built-in functionality for
10836 handling regular expressions, based on the Onigmo library. It offers
10837 first-class compiled regex objects, partial matching and function-based
10838 substitutions, amongst other features.")
10839 (license license:bsd-3)))
10841 (define-public r-reportr
10848 (uri (cran-uri "reportr" version))
10851 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10852 (build-system r-build-system)
10853 (propagated-inputs `(("r-ore" ,r-ore)))
10854 (home-page "https://github.com/jonclayden/reportr")
10855 (synopsis "General message and error reporting system")
10857 "This package provides a system for reporting messages, which offers
10858 certain useful features over the standard R system, such as the incorporation
10859 of output consolidation, message filtering, assertions, expression
10860 substitution, automatic generation of stack traces for debugging, and
10861 conditional reporting based on the current \"output level\".")
10862 (license license:gpl2)))
10864 (define-public r-tractor-base
10866 (name "r-tractor-base")
10871 (uri (cran-uri "tractor.base" version))
10874 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10875 (properties `((upstream-name . "tractor.base")))
10876 (build-system r-build-system)
10879 ("r-reportr" ,r-reportr)
10880 ("r-rnifti" ,r-rnifti)
10881 ("r-shades" ,r-shades)))
10882 (home-page "https://www.tractor-mri.org.uk")
10883 (synopsis "Read, manipulate and visualize magnetic resonance images")
10885 "This package provides functions for working with magnetic resonance
10886 images. It supports reading and writing of popular file formats (DICOM,
10887 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10888 visualization; flexible image manipulation; metadata and sparse image
10890 (license license:gpl2)))
10892 (define-public r-grimport
10894 (name "r-grimport")
10899 (uri (cran-uri "grImport" version))
10902 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10903 (properties `((upstream-name . "grImport")))
10904 (build-system r-build-system)
10906 `(("ghostscript" ,ghostscript)))
10908 `(("r-xml" ,r-xml)))
10909 (home-page "https://cran.r-project.org/web/packages/grImport")
10910 (synopsis "Convert, import, and draw PostScript pictures")
10912 "This package provides functions for converting, importing, and drawing
10913 PostScript pictures in R plots.")
10914 (license license:gpl2+)))
10916 (define-public r-grimport2
10918 (name "r-grimport2")
10923 (uri (cran-uri "grImport2" version))
10926 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10927 (properties `((upstream-name . "grImport2")))
10928 (build-system r-build-system)
10930 `(("r-base64enc" ,r-base64enc)
10934 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10935 (synopsis "Import SVG graphics")
10937 "This package provides functions for importing external vector images and
10938 drawing them as part of R plots. This package is different from the
10939 @code{grImport} package because, where that package imports PostScript format
10940 images, this package imports SVG format images. Furthermore, this package
10941 imports a specific subset of SVG, so external images must be preprocessed
10942 using a package like @code{rsvg} to produce SVG that this package can import.
10943 SVG features that are not supported by R graphics, such as gradient fills, can
10944 be imported and then exported via the @code{gridSVG} package.")
10945 (license license:gpl2+)))
10947 (define-public r-kohonen
10954 (uri (cran-uri "kohonen" version))
10957 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10958 (build-system r-build-system)
10960 `(("r-rcpp" ,r-rcpp)))
10961 (home-page "https://cran.r-project.org/web/packages/kohonen")
10962 (synopsis "Supervised and unsupervised self-organising maps")
10964 "This package provides functions to train @dfn{self-organising
10965 maps} (SOMs). Also interrogation of the maps and prediction using trained
10966 maps are supported. The name of the package refers to Teuvo Kohonen, the
10967 inventor of the SOM.")
10968 (license license:gpl2+)))
10970 (define-public r-nnls
10977 (uri (cran-uri "nnls" version))
10980 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10981 (build-system r-build-system)
10982 (native-inputs `(("gfortran" ,gfortran)))
10983 (home-page "https://cran.r-project.org/web/packages/nnls")
10984 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10986 "This package provides an R interface to the Lawson-Hanson implementation
10987 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10988 the combination of non-negative and non-positive constraints.")
10989 (license license:gpl2+)))
10991 (define-public r-iso
10994 (version "0.0-18.1")
10998 (uri (cran-uri "Iso" version))
11001 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11002 (properties `((upstream-name . "Iso")))
11003 (build-system r-build-system)
11004 (native-inputs `(("gfortran" ,gfortran)))
11005 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11006 (synopsis "Functions to perform isotonic regression")
11008 "This package provides support for linear order and unimodal
11009 order (univariate) isotonic regression and bivariate isotonic regression with
11010 linear order on both variables.")
11011 (license license:gpl2+)))
11013 (define-public r-chemometricswithr
11015 (name "r-chemometricswithr")
11020 (uri (cran-uri "ChemometricsWithR" version))
11023 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11025 `((upstream-name . "ChemometricsWithR")))
11026 (build-system r-build-system)
11028 `(("r-devtools" ,r-devtools)
11029 ("r-kohonen" ,r-kohonen)
11032 (home-page "https://github.com/rwehrens/CWR")
11033 (synopsis "Chemometrics with R")
11035 "This package provides functions and scripts used in the book
11036 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11037 Life Sciences\" by Ron Wehrens, Springer (2011).")
11038 (license license:gpl2+)))
11040 (define-public r-als
11047 (uri (cran-uri "ALS" version))
11050 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11051 (properties `((upstream-name . "ALS")))
11052 (build-system r-build-system)
11055 ("r-nnls" ,r-nnls)))
11056 (home-page "https://cran.r-project.org/web/packages/ALS")
11057 (synopsis "Multivariate curve resolution alternating least squares")
11059 "Alternating least squares is often used to resolve components
11060 contributing to data with a bilinear structure; the basic technique may be
11061 extended to alternating constrained least squares. This package provides an
11062 implementation of @dfn{multivariate curve resolution alternating least
11063 squares} (MCR-ALS).
11065 Commonly applied constraints include unimodality, non-negativity, and
11066 normalization of components. Several data matrices may be decomposed
11067 simultaneously by assuming that one of the two matrices in the bilinear
11068 decomposition is shared between datasets.")
11069 (license license:gpl2+)))
11071 (define-public r-strucchange
11073 (name "r-strucchange")
11078 (uri (cran-uri "strucchange" version))
11081 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11082 (build-system r-build-system)
11084 `(("r-sandwich" ,r-sandwich)
11086 (home-page "https://cran.r-project.org/web/packages/strucchange")
11087 (synopsis "Testing, monitoring, and dating structural changes")
11089 "This package provides tools for testing, monitoring and dating
11090 structural changes in (linear) regression models. It features tests/methods
11091 from the generalized fluctuation test framework as well as from the F
11092 test (Chow test) framework. This includes methods to fit, plot and test
11093 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11094 statistics, respectively. It is possible to monitor incoming data online
11095 using fluctuation processes. Finally, the breakpoints in regression models
11096 with structural changes can be estimated together with confidence intervals.
11097 Emphasis is always given to methods for visualizing the data.")
11098 ;; Either of these two GPL versions
11099 (license (list license:gpl2 license:gpl3))))
11101 (define-public r-pixmap
11108 (uri (cran-uri "pixmap" version))
11111 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11112 (build-system r-build-system)
11113 (home-page "https://cran.r-project.org/web/packages/pixmap")
11114 (synopsis "Tools for bitmap images")
11116 "This package provides functions for importing, exporting, plotting and
11117 other manipulations of bitmapped images.")
11118 (license license:gpl2)))
11120 (define-public r-rapidjsonr
11122 (name "r-rapidjsonr")
11127 (uri (cran-uri "rapidjsonr" version))
11130 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11131 (build-system r-build-system)
11132 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11133 (synopsis "JSON parser")
11135 "This package provides JSON parsing capability through the Rapidjson
11137 (license license:expat)))
11139 (define-public r-ontologyindex
11141 (name "r-ontologyindex")
11146 (uri (cran-uri "ontologyIndex" version))
11149 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11150 (properties `((upstream-name . "ontologyIndex")))
11151 (build-system r-build-system)
11152 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11153 (synopsis "Functions for processing ontologies in R")
11155 "This package provides functions for reading ontologies into R as lists
11156 and manipulating sets of ontological terms.")
11157 (license license:gpl2+)))
11159 (define-public r-gargle
11166 (uri (cran-uri "gargle" version))
11169 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11170 (build-system r-build-system)
11175 ("r-jsonlite" ,r-jsonlite)
11176 ("r-rlang" ,r-rlang)
11177 ("r-withr" ,r-withr)))
11179 `(("r-knitr" ,r-knitr)))
11180 (home-page "https://gargle.r-lib.org")
11181 (synopsis "Utilities for working with Google APIs")
11183 "This package provides utilities for working with Google APIs. This
11184 includes functions and classes for handling common credential types and for
11185 preparing, executing, and processing HTTP requests.")
11186 (license license:expat)))
11188 (define-public r-bigrquery
11190 (name "r-bigrquery")
11195 (uri (cran-uri "bigrquery" version))
11198 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11199 (build-system r-build-system)
11201 `(("r-assertthat" ,r-assertthat)
11202 ("r-bit64" ,r-bit64)
11205 ("r-gargle" ,r-gargle)
11208 ("r-jsonlite" ,r-jsonlite)
11209 ("r-prettyunits" ,r-prettyunits)
11210 ("r-progress" ,r-progress)
11211 ("r-rapidjsonr" ,r-rapidjsonr)
11213 ("r-rlang" ,r-rlang)
11214 ("r-tibble" ,r-tibble)))
11215 (home-page "https://github.com/rstats-db/bigrquery")
11216 (synopsis "R interface to Google's BigQuery API")
11218 "This package provides an R interface to Google's BigQuery database.")
11219 (license license:gpl3)))
11221 (define-public r-gmp
11228 (uri (cran-uri "gmp" version))
11231 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11232 (build-system r-build-system)
11235 (modify-phases %standard-phases
11236 (add-after 'unpack 'set-CC
11237 (lambda _ (setenv "CC" "gcc") #t)))))
11238 (inputs `(("gmp" ,gmp)))
11239 (home-page "https://cran.r-project.org/web/packages/gmp")
11240 (synopsis "Multiple precision arithmetic")
11242 "This package supports multiple precision arithmetic (big integers and
11243 rationals, prime number tests, matrix computation), \"arithmetic without
11244 limitations\" using the GNU Multiple Precision library.")
11245 ;; Any version of the GPL.
11246 (license license:gpl3+)))
11248 (define-public r-rmpfr
11255 (uri (cran-uri "Rmpfr" version))
11258 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11259 (properties `((upstream-name . "Rmpfr")))
11260 (build-system r-build-system)
11265 `(("r-gmp" ,r-gmp)))
11267 `(("pkg-config" ,pkg-config)))
11268 (home-page "http://rmpfr.r-forge.r-project.org/")
11269 (synopsis "R bindings to the MPFR library")
11271 "This package supports arithmetic (via S4 classes and methods) for
11272 arbitrary precision floating point numbers, including transcendental
11273 functions. To this end, the package interfaces with the @dfn{Multiple
11274 Precision Floating-Point Reliable} (MPFR) library.")
11275 (license license:gpl2+)))
11277 (define-public r-assertive-base
11279 (name "r-assertive-base")
11284 (uri (cran-uri "assertive.base" version))
11287 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11289 `((upstream-name . "assertive.base")))
11290 (build-system r-build-system)
11291 (home-page "https://bitbucket.org/richierocks/assertive.base")
11292 (synopsis "Core of the assertive package")
11294 "This package provides a minimal set of predicates and assertions used by
11295 the assertive package. This is mainly for use by other package developers who
11296 want to include run-time testing features in their own packages.")
11297 (license license:gpl3+)))
11299 (define-public r-assertive-properties
11301 (name "r-assertive-properties")
11306 (uri (cran-uri "assertive.properties" version))
11309 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11311 `((upstream-name . "assertive.properties")))
11312 (build-system r-build-system)
11314 `(("r-assertive-base" ,r-assertive-base)))
11315 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11316 (synopsis "Assertions to check properties of variables")
11318 "This package provides a set of predicates and assertions for checking
11319 the properties of variables, such as length, names and attributes. This is
11320 mainly for use by other package developers who want to include run-time
11321 testing features in their own packages.")
11322 (license license:gpl3+)))
11324 (define-public r-assertive-numbers
11326 (name "r-assertive-numbers")
11331 (uri (cran-uri "assertive.numbers" version))
11334 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11336 `((upstream-name . "assertive.numbers")))
11337 (build-system r-build-system)
11339 `(("r-assertive-base" ,r-assertive-base)))
11340 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11341 (synopsis "Assertions to check properties of numbers")
11343 "This package provides a set of predicates and assertions for checking
11344 the properties of numbers. This is mainly for use by other package developers
11345 who want to include run-time testing features in their own packages.")
11346 (license license:gpl3+)))
11348 (define-public r-assertive-sets
11350 (name "r-assertive-sets")
11355 (uri (cran-uri "assertive.sets" version))
11358 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11360 `((upstream-name . "assertive.sets")))
11361 (build-system r-build-system)
11363 `(("r-assertive-base" ,r-assertive-base)))
11364 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11365 (synopsis "Assertions to check properties of sets")
11367 "This package provides a set of predicates and assertions for checking
11368 the properties of sets. This is mainly for use by other package developers
11369 who want to include run-time testing features in their own packages.")
11370 (license license:gpl3+)))
11372 (define-public r-assertive-matrices
11374 (name "r-assertive-matrices")
11379 (uri (cran-uri "assertive.matrices" version))
11382 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11384 `((upstream-name . "assertive.matrices")))
11385 (build-system r-build-system)
11387 `(("r-assertive-base" ,r-assertive-base)))
11388 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11389 (synopsis "Assertions to check properties of matrices")
11391 "This package provides a set of predicates and assertions for checking
11392 the properties of matrices. This is mainly for use by other package
11393 developers who want to include run-time testing features in their own
11395 (license license:gpl3+)))
11397 (define-public r-assertive-models
11399 (name "r-assertive-models")
11404 (uri (cran-uri "assertive.models" version))
11407 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11409 `((upstream-name . "assertive.models")))
11410 (build-system r-build-system)
11412 `(("r-assertive-base" ,r-assertive-base)))
11413 (home-page "https://bitbucket.org/richierocks/assertive.models")
11414 (synopsis "Assertions to check properties of models")
11416 "This package provides a set of predicates and assertions for checking
11417 the properties of models. This is mainly for use by other package developers
11418 who want to include run-time testing features in their own packages.")
11419 (license license:gpl3+)))
11421 (define-public r-assertive-reflection
11423 (name "r-assertive-reflection")
11428 (uri (cran-uri "assertive.reflection" version))
11431 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11433 `((upstream-name . "assertive.reflection")))
11434 (build-system r-build-system)
11436 `(("r-assertive-base" ,r-assertive-base)))
11437 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11438 (synopsis "Assertions for checking the state of R")
11440 "This package provides a set of predicates and assertions for checking
11441 the state and capabilities of R, the operating system it is running on, and
11442 the IDE being used. This is mainly for use by other package developers who
11443 want to include run-time testing features in their own packages.")
11444 (license license:gpl3+)))
11446 (define-public r-assertive-types
11448 (name "r-assertive-types")
11453 (uri (cran-uri "assertive.types" version))
11456 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11458 `((upstream-name . "assertive.types")))
11459 (build-system r-build-system)
11461 `(("r-assertive-base" ,r-assertive-base)
11462 ("r-assertive-properties" ,r-assertive-properties)
11463 ("r-codetools" ,r-codetools)))
11464 (home-page "https://bitbucket.org/richierocks/assertive.types")
11465 (synopsis "Assertions to check types of variables")
11467 "This package provides a set of predicates and assertions for checking
11468 the types of variables. This is mainly for use by other package developers
11469 who want to include run-time testing features in their own packages.")
11470 (license license:gpl3+)))
11472 (define-public r-assertive-files
11474 (name "r-assertive-files")
11479 (uri (cran-uri "assertive.files" version))
11482 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11484 `((upstream-name . "assertive.files")))
11485 (build-system r-build-system)
11487 `(("r-assertive-base" ,r-assertive-base)
11488 ("r-assertive-numbers" ,r-assertive-numbers)))
11489 (home-page "https://bitbucket.org/richierocks/assertive.files")
11490 (synopsis "Assertions to check properties of files")
11492 "This package provides a set of predicates and assertions for checking
11493 the properties of files and connections. This is mainly for use by other
11494 package developers who want to include run-time testing features in their own
11496 (license license:gpl3+)))
11498 (define-public r-assertive-code
11500 (name "r-assertive-code")
11505 (uri (cran-uri "assertive.code" version))
11508 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11510 `((upstream-name . "assertive.code")))
11511 (build-system r-build-system)
11513 `(("r-assertive-base" ,r-assertive-base)
11514 ("r-assertive-properties" ,r-assertive-properties)
11515 ("r-assertive-types" ,r-assertive-types)))
11516 (home-page "https://bitbucket.org/richierocks/assertive.code")
11517 (synopsis "Assertions to check properties of code")
11519 "This package provides a set of predicates and assertions for checking
11520 the properties of code. This is mainly for use by other package developers
11521 who want to include run-time testing features in their own packages.")
11522 (license license:gpl3+)))
11524 (define-public r-assertive-datetimes
11526 (name "r-assertive-datetimes")
11531 (uri (cran-uri "assertive.datetimes" version))
11534 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11536 `((upstream-name . "assertive.datetimes")))
11537 (build-system r-build-system)
11539 `(("r-assertive-base" ,r-assertive-base)
11540 ("r-assertive-types" ,r-assertive-types)))
11541 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11542 (synopsis "Assertions to check properties of dates and times")
11544 "This package provides a set of predicates and assertions for checking
11545 the properties of dates and times. This is mainly for use by other package
11546 developers who want to include run-time testing features in their own
11548 (license license:gpl3+)))
11550 (define-public r-assertive-strings
11552 (name "r-assertive-strings")
11557 (uri (cran-uri "assertive.strings" version))
11560 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11562 `((upstream-name . "assertive.strings")))
11563 (build-system r-build-system)
11565 `(("r-assertive-base" ,r-assertive-base)
11566 ("r-assertive-types" ,r-assertive-types)
11567 ("r-stringi" ,r-stringi)))
11568 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11569 (synopsis "Assertions to check properties of strings")
11571 "This package provides a set of predicates and assertions for checking
11572 the properties of strings. This is mainly for use by other package developers
11573 who want to include run-time testing features in their own packages.")
11574 (license license:gpl3+)))
11576 (define-public r-assertive-data-us
11578 (name "r-assertive-data-us")
11583 (uri (cran-uri "assertive.data.us" version))
11586 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11588 `((upstream-name . "assertive.data.us")))
11589 (build-system r-build-system)
11591 `(("r-assertive-base" ,r-assertive-base)
11592 ("r-assertive-strings" ,r-assertive-strings)))
11593 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11594 (synopsis "Assertions to check properties of strings")
11596 "This package provides a set of predicates and assertions for checking
11597 the properties of US-specific complex data types. This is mainly for use by
11598 other package developers who want to include run-time testing features in
11599 their own packages.")
11600 (license license:gpl3+)))
11602 (define-public r-assertive-data-uk
11604 (name "r-assertive-data-uk")
11609 (uri (cran-uri "assertive.data.uk" version))
11612 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11614 `((upstream-name . "assertive.data.uk")))
11615 (build-system r-build-system)
11617 `(("r-assertive-base" ,r-assertive-base)
11618 ("r-assertive-strings" ,r-assertive-strings)))
11619 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11620 (synopsis "Assertions to check properties of strings")
11622 "This package provides a set of predicates and assertions for checking
11623 the properties of UK-specific complex data types. This is mainly for use by
11624 other package developers who want to include run-time testing features in
11625 their own packages.")
11626 (license license:gpl3+)))
11628 (define-public r-assertive-data
11630 (name "r-assertive-data")
11635 (uri (cran-uri "assertive.data" version))
11638 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11640 `((upstream-name . "assertive.data")))
11641 (build-system r-build-system)
11643 `(("r-assertive-base" ,r-assertive-base)
11644 ("r-assertive-strings" ,r-assertive-strings)))
11645 (home-page "https://bitbucket.org/richierocks/assertive.data")
11646 (synopsis "Assertions to check properties of data")
11648 "This package provides a set of predicates and assertions for checking
11649 the properties of (country independent) complex data types. This is mainly
11650 for use by other package developers who want to include run-time testing
11651 features in their own packages.")
11652 (license license:gpl3+)))
11654 (define-public r-assertive
11656 (name "r-assertive")
11661 (uri (cran-uri "assertive" version))
11664 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11665 (build-system r-build-system)
11667 `(("r-assertive-base" ,r-assertive-base)
11668 ("r-assertive-code" ,r-assertive-code)
11669 ("r-assertive-data" ,r-assertive-data)
11670 ("r-assertive-data-uk" ,r-assertive-data-uk)
11671 ("r-assertive-data-us" ,r-assertive-data-us)
11672 ("r-assertive-datetimes" ,r-assertive-datetimes)
11673 ("r-assertive-files" ,r-assertive-files)
11674 ("r-assertive-matrices" ,r-assertive-matrices)
11675 ("r-assertive-models" ,r-assertive-models)
11676 ("r-assertive-numbers" ,r-assertive-numbers)
11677 ("r-assertive-properties" ,r-assertive-properties)
11678 ("r-assertive-reflection" ,r-assertive-reflection)
11679 ("r-assertive-sets" ,r-assertive-sets)
11680 ("r-assertive-strings" ,r-assertive-strings)
11681 ("r-assertive-types" ,r-assertive-types)
11682 ("r-knitr" ,r-knitr)))
11684 `(("r-knitr" ,r-knitr)))
11685 (home-page "https://bitbucket.org/richierocks/assertive")
11686 (synopsis "Readable check functions to ensure code integrity")
11688 "This package provides lots of predicates (@code{is_*} functions) to
11689 check the state of your variables, and assertions (@code{assert_*} functions)
11690 to throw errors if they aren't in the right form.")
11691 (license license:gpl3+)))
11693 (define-public r-dotcall64
11695 (name "r-dotcall64")
11700 (uri (cran-uri "dotCall64" version))
11703 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11704 (properties `((upstream-name . "dotCall64")))
11705 (build-system r-build-system)
11706 (native-inputs `(("gfortran" ,gfortran)))
11707 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11708 (synopsis "Enhanced foreign function interface supporting long vectors")
11710 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11711 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11712 supports long vectors, arguments of type 64-bit integer, and provides a
11713 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11714 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11715 (license license:gpl2+)))
11717 (define-public r-spam
11724 (uri (cran-uri "spam" version))
11726 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11727 (build-system r-build-system)
11729 `(("r-dotcall64" ,r-dotcall64)))
11730 (native-inputs `(("gfortran" ,gfortran)))
11731 (home-page "https://www.math.uzh.ch/pages/spam/")
11732 (synopsis "Sparse matrix algebra")
11734 "This package provides a set of functions for sparse matrix algebra.
11735 Differences with other sparse matrix packages are:
11738 @item it only supports (essentially) one sparse matrix format;
11739 @item it is based on transparent and simple structure(s);
11740 @item it is tailored for MCMC calculations within G(M)RF;
11741 @item and it is fast and scalable (with the extension package @code{spam64}).
11743 ;; Either of these licenses
11744 (license (list license:bsd-3 license:lgpl2.0))))
11746 (define-public r-fields
11753 (uri (cran-uri "fields" version))
11755 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11756 (build-system r-build-system)
11758 `(("r-maps" ,r-maps)
11759 ("r-spam" ,r-spam)))
11761 `(("gfortran" ,gfortran)))
11762 (home-page "https://www.image.ucar.edu/fields")
11763 (synopsis "Tools for spatial data")
11765 "This is a package for curve, surface and function fitting with an
11766 emphasis on splines, spatial data and spatial statistics. The major methods
11767 include cubic, and thin plate splines, Kriging, and compactly supported
11768 covariance functions for large data sets.")
11769 (license license:gpl2+)))
11771 (define-public r-spatialextremes
11773 (name "r-spatialextremes")
11778 (uri (cran-uri "SpatialExtremes" version))
11781 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11783 `((upstream-name . "SpatialExtremes")))
11784 (build-system r-build-system)
11786 `(("r-fields" ,r-fields)
11787 ("r-maps" ,r-maps)))
11788 (home-page "http://spatialextremes.r-forge.r-project.org/")
11789 (synopsis "Modelling spatial extremes")
11791 "This package provides tools for the statistical modelling of spatial
11792 extremes using max-stable processes, copula or Bayesian hierarchical models.
11793 More precisely, this package allows (conditional) simulations from various
11794 parametric max-stable models, analysis of the extremal spatial dependence, the
11795 fitting of such processes using composite likelihoods or least square (simple
11796 max-stable processes only), model checking and selection and prediction.")
11797 (license license:gpl2+)))
11799 (define-public r-drc
11806 (uri (cran-uri "drc" version))
11809 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11810 (build-system r-build-system)
11813 ("r-gtools" ,r-gtools)
11815 ("r-multcomp" ,r-multcomp)
11816 ("r-plotrix" ,r-plotrix)
11817 ("r-scales" ,r-scales)))
11818 (home-page "https://cran.r-project.org/web/packages/drc")
11819 (synopsis "Analysis of dose-response curves")
11821 "This package provides a suite of flexible and versatile model fitting
11822 and after-fitting functions for the analysis of dose-response data.")
11823 (license license:gpl2+)))
11825 (define-public r-rmeta
11832 (uri (cran-uri "rmeta" version))
11835 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11836 (build-system r-build-system)
11837 (home-page "https://cran.r-project.org/web/packages/rmeta")
11838 (synopsis "Tools for meta-analysis")
11840 "This package provides functions for simple fixed and random effects
11841 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11842 draws standard summary plots, funnel plots, and computes summaries and tests
11843 for association and heterogeneity.")
11844 (license license:gpl2)))
11846 (define-public r-bootstrap
11848 (name "r-bootstrap")
11853 (uri (cran-uri "bootstrap" version))
11856 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11857 (build-system r-build-system)
11858 (native-inputs `(("gfortran" ,gfortran)))
11859 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11860 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11862 "This package provides software and data for the book \"An Introduction
11863 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11864 This package is primarily provided for projects already based on it, and for
11865 support of the book. New projects should preferentially use the recommended
11866 package \"boot\".")
11867 (license license:bsd-3)))
11869 (define-public r-survivalroc
11871 (name "r-survivalroc")
11876 (uri (cran-uri "survivalROC" version))
11879 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11880 (properties `((upstream-name . "survivalROC")))
11881 (build-system r-build-system)
11882 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11883 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11885 "Compute time-dependent ROC curve from censored survival data using
11886 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11887 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11888 (license license:gpl2+)))
11890 (define-public r-longitudinal
11892 (name "r-longitudinal")
11897 (uri (cran-uri "longitudinal" version))
11900 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11901 (build-system r-build-system)
11902 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11903 (home-page "http://strimmerlab.org/software/longitudinal/")
11904 (synopsis "Analysis of multiple time course data")
11906 "This package contains general data structures and functions for
11907 longitudinal data with multiple variables, repeated measurements, and
11908 irregularly spaced time points. It also implements a shrinkage estimator of
11909 dynamical correlation and dynamical covariance.")
11910 (license license:gpl3+)))
11912 (define-public r-genenet
11919 (uri (cran-uri "GeneNet" version))
11922 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11923 (properties `((upstream-name . "GeneNet")))
11924 (build-system r-build-system)
11926 `(("r-corpcor" ,r-corpcor)
11927 ("r-fdrtool" ,r-fdrtool)
11928 ("r-longitudinal" ,r-longitudinal)))
11929 (home-page "http://strimmerlab.org/software/genenet/")
11930 (synopsis "Modeling and inferring gene networks")
11932 "This package analyzes gene expression (time series) data with focus on
11933 the inference of gene networks. In particular, GeneNet implements the methods
11934 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11935 for learning large-scale gene association networks (including assignment of
11936 putative directions).")
11937 (license license:gpl3+)))
11939 (define-public r-rbamtools
11941 (name "r-rbamtools")
11942 (version "2.16.17")
11946 (uri (cran-uri "rbamtools" version))
11949 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11950 (build-system r-build-system)
11951 (inputs `(("zlib" ,zlib)))
11953 `(("r-refgenome" ,r-refgenome)))
11954 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11955 (synopsis "Read and write BAM (binary alignment) files")
11957 "This package provides an R interface to functions of the SAMtools
11959 (license license:artistic2.0)))
11961 (define-public r-protviz
11968 (uri (cran-uri "protViz" version))
11971 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11972 (properties `((upstream-name . "protViz")))
11973 (build-system r-build-system)
11974 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11975 (home-page "https://github.com/protViz/protViz/")
11976 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11978 "This package helps with quality checks, visualizations and analysis of
11979 mass spectrometry data, coming from proteomics experiments. The package is
11980 developed, tested and used at the Functional Genomics Center Zurich, where it
11981 is used mainly for prototyping, teaching, and having fun with proteomics data.
11982 But it can also be used to do data analysis for small scale data sets.")
11983 (license license:gpl3)))
11985 (define-public r-cmprsk
11992 (uri (cran-uri "cmprsk" version))
11994 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11995 (build-system r-build-system)
11997 `(("r-survival" ,r-survival)))
11999 `(("gfortran" ,gfortran)))
12000 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12001 (synopsis "Subdistribution analysis of competing risks")
12003 "This package provides tool for estimation, testing and regression
12004 modeling of subdistribution functions in competing risks, as described in
12005 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12006 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12007 A proportional hazards model for the subdistribution of a competing risk,
12008 JASA, 94:496-509.")
12009 (license license:gpl2+)))
12011 (define-public r-etm
12018 (uri (cran-uri "etm" version))
12021 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12022 (build-system r-build-system)
12024 `(("r-data-table" ,r-data-table)
12025 ("r-lattice" ,r-lattice)
12027 ("r-rcpparmadillo" ,r-rcpparmadillo)
12028 ("r-survival" ,r-survival)))
12029 (home-page "https://cran.r-project.org/web/packages/etm")
12030 (synopsis "Empirical transition matrix")
12032 "The @dfn{empirical transition matrix} (etm) package estimates
12033 the matrix of transition probabilities for any time-inhomogeneous multistate
12034 model with finite state space using the Aalen-Johansen estimator.")
12035 (license license:expat)))
12037 (define-public r-epi
12044 (uri (cran-uri "Epi" version))
12047 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12048 (properties `((upstream-name . "Epi")))
12049 (build-system r-build-system)
12051 `(("r-cmprsk" ,r-cmprsk)
12052 ("r-data-table" ,r-data-table)
12055 ("r-matrix" ,r-matrix)
12057 ("r-numderiv" ,r-numderiv)
12059 ("r-survival" ,r-survival)
12061 (home-page "https://BendixCarstensen.com/Epi/")
12062 (synopsis "Statistical analysis in epidemiology")
12064 "This package provides functions for demographic and epidemiological
12065 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12066 particular representation, manipulation and simulation of multistate data -
12067 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12068 @code{etm} and @code{cmprsk} packages. It also contains functions for
12069 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12070 data and some useful functions for tabulation and plotting, as well as a
12071 number of epidemiological data sets.")
12072 (license license:gpl2)))
12074 (define-public r-ppls
12077 (version "1.6-1.1")
12081 (uri (cran-uri "ppls" version))
12084 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12085 (build-system r-build-system)
12086 (propagated-inputs `(("r-mass" ,r-mass)))
12087 (home-page "https://cran.r-project.org/web/packages/ppls")
12088 (synopsis "Penalized partial least squares")
12090 "This package contains linear and nonlinear regression methods based on
12091 partial least squares and penalization techniques. Model parameters are
12092 selected via cross-validation, and confidence intervals ans tests for the
12093 regression coefficients can be conducted via jackknifing.")
12094 (license license:gpl2+)))
12096 (define-public r-huge
12099 (version "1.3.4.1")
12103 (uri (cran-uri "huge" version))
12105 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12106 (build-system r-build-system)
12108 `(("r-igraph" ,r-igraph)
12110 ("r-matrix" ,r-matrix)
12112 ("r-rcppeigen" ,r-rcppeigen)))
12113 (home-page "https://cran.r-project.org/web/packages/huge")
12114 (synopsis "High-dimensional undirected graph estimation")
12116 "This package provides a general framework for high-dimensional
12117 undirected graph estimation. It integrates data preprocessing, neighborhood
12118 screening, graph estimation, and model selection techniques into a pipeline.")
12119 (license license:gpl2)))
12121 (define-public r-parcor
12128 (uri (cran-uri "parcor" version))
12131 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12132 (build-system r-build-system)
12135 ("r-genenet" ,r-genenet)
12136 ("r-glmnet" ,r-glmnet)
12138 ("r-ppls" ,r-ppls)))
12139 (home-page "https://cran.r-project.org/web/packages/parcor")
12140 (synopsis "Regularized estimation of partial correlation matrices")
12142 "This package estimates the matrix of partial correlations based on
12143 different regularized regression methods: lasso, adaptive lasso, PLS, and
12144 Ridge Regression. In addition, the package provides model selection for
12145 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12146 (license license:gpl2+)))
12148 (define-public r-mcmc
12155 (uri (cran-uri "mcmc" version))
12158 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12159 (build-system r-build-system)
12160 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12161 (synopsis "Markov chain Monte Carlo")
12163 "This package simulates continuous distributions of random vectors using
12164 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12165 function that evaluates the log unnormalized density. Algorithms are random
12166 walk Metropolis algorithm (function @code{metrop}), simulated
12167 tempering (function @code{temper}), and morphometric random walk
12168 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12169 by change of variable.")
12170 (license license:expat)))
12172 (define-public r-listenv
12179 (uri (cran-uri "listenv" version))
12182 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12183 (build-system r-build-system)
12185 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12186 (home-page "https://github.com/HenrikBengtsson/listenv")
12187 (synopsis "Environments behaving (almost) as lists")
12189 "This package implements list environments. List environments are
12190 environments that have list-like properties. For instance, the elements of a
12191 list environment are ordered and can be accessed and iterated over using index
12193 (license license:lgpl2.1+)))
12195 (define-public r-globals
12202 (uri (cran-uri "globals" version))
12205 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12206 (build-system r-build-system)
12208 `(("r-codetools" ,r-codetools)))
12209 (home-page "https://github.com/HenrikBengtsson/globals")
12210 (synopsis "Identify global objects in R expressions")
12212 "This package provides tools to identify global (\"unknown\" or \"free\")
12213 objects in R expressions by code inspection using various strategies, e.g.
12214 conservative or liberal. The objective of this package is to make it as
12215 simple as possible to identify global objects for the purpose of exporting
12216 them in distributed compute environments.")
12217 (license license:lgpl2.1+)))
12219 (define-public r-future
12226 (uri (cran-uri "future" version))
12229 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12230 (build-system r-build-system)
12232 `(("r-digest" ,r-digest)
12233 ("r-globals" ,r-globals)
12234 ("r-listenv" ,r-listenv)))
12236 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12237 (home-page "https://github.com/HenrikBengtsson/future")
12238 (synopsis "Unified parallel and distributed processing in R")
12240 "The purpose of this package is to provide a lightweight and unified
12241 Future API for sequential and parallel processing of R expression via futures.
12242 This package implements sequential, multicore, multisession, and cluster
12243 futures. With these, R expressions can be evaluated on the local machine, in
12244 parallel a set of local machines, or distributed on a mix of local and remote
12245 machines. Extensions to this package implement additional backends for
12246 processing futures via compute cluster schedulers etc. Because of its unified
12247 API, there is no need to modify any code in order to switch from sequential on
12248 the local machine to, say, distributed processing on a remote compute cluster.")
12249 (license license:lgpl2.1+)))
12251 (define-public r-future-apply
12253 (name "r-future-apply")
12258 (uri (cran-uri "future.apply" version))
12261 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12262 (properties `((upstream-name . "future.apply")))
12263 (build-system r-build-system)
12265 `(("r-future" ,r-future)
12266 ("r-globals" ,r-globals)))
12268 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12269 (home-page "https://github.com/HenrikBengtsson/future.apply")
12270 (synopsis "Apply function to elements in parallel using futures")
12272 "This package provides implementations of @code{apply()},
12273 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12274 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12275 can be resolved using any future-supported backend, e.g. parallel on the local
12276 machine or distributed on a compute cluster.")
12277 (license license:gpl2+)))
12279 (define-public r-rsvd
12286 (uri (cran-uri "rsvd" version))
12289 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12290 (build-system r-build-system)
12292 `(("r-matrix" ,r-matrix)))
12293 (home-page "https://github.com/erichson/rSVD")
12294 (synopsis "Randomized singular value decomposition")
12296 "Low-rank matrix decompositions are fundamental tools and widely used for
12297 data analysis, dimension reduction, and data compression. Classically, highly
12298 accurate deterministic matrix algorithms are used for this task. However, the
12299 emergence of large-scale data has severely challenged our computational
12300 ability to analyze big data. The concept of randomness has been demonstrated
12301 as an effective strategy to quickly produce approximate answers to familiar
12302 problems such as the @dfn{singular value decomposition} (SVD). This package
12303 provides several randomized matrix algorithms such as the randomized singular
12304 value decomposition (@code{rsvd}), randomized principal component
12305 analysis (@code{rpca}), randomized robust principal component
12306 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12307 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12308 functions are provided.")
12309 (license license:gpl3+)))
12311 (define-public r-sloop
12318 (uri (cran-uri "sloop" version))
12321 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12322 (build-system r-build-system)
12324 `(("r-codetools" ,r-codetools)
12325 ("r-crayon" ,r-crayon)
12326 ("r-purrr" ,r-purrr)
12327 ("r-rlang" ,r-rlang)
12328 ("r-tibble" ,r-tibble)))
12329 (home-page "https://github.com/r-lib/sloop")
12330 (synopsis "Helpers for object-oriented programming in R")
12332 "This package provides a collection of helper functions designed to
12333 help you to better understand object oriented programming in R, particularly
12335 (license license:gpl3)))
12337 (define-public r-capushe
12344 (uri (cran-uri "capushe" version))
12347 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12348 (build-system r-build-system)
12349 (propagated-inputs `(("r-mass" ,r-mass)))
12350 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12351 (synopsis "Calibrating penalties using slope heuristics")
12353 "This package provides tools for the calibration of penalized criteria
12354 for model selection. The calibration methods available are based on the slope
12356 (license license:gpl2+)))
12358 (define-public r-dorng
12365 (uri (cran-uri "doRNG" version))
12368 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12369 (properties `((upstream-name . "doRNG")))
12370 (build-system r-build-system)
12372 `(("r-foreach" ,r-foreach)
12373 ("r-iterators" ,r-iterators)
12374 ("r-rngtools" ,r-rngtools)))
12375 (home-page "https://renozao.github.io/doRNG/")
12376 (synopsis "Generic reproducible parallel backend for foreach loops")
12378 "This package provides functions to perform reproducible parallel
12379 @code{foreach} loops, using independent random streams as generated by
12380 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12381 convert standard @code{%dopar%} loops into fully reproducible loops,
12382 independently of the number of workers, the task scheduling strategy, or the
12383 chosen parallel environment and associated foreach backend.")
12384 (license license:gpl2+)))
12386 (define-public r-blockmodeling
12388 (name "r-blockmodeling")
12393 (uri (cran-uri "blockmodeling" version))
12396 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12397 (build-system r-build-system)
12399 `(("r-matrix" ,r-matrix)))
12400 (native-inputs `(("gfortran" ,gfortran)))
12401 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12402 (synopsis "Generalized and classical blockmodeling of valued networks")
12404 "This package is primarily meant as an implementation of generalized
12405 blockmodeling for valued networks. In addition, measures of similarity or
12406 dissimilarity based on structural equivalence and regular equivalence (REGE
12407 algorithms) can be computed and partitioned matrices can be plotted.")
12408 (license license:gpl2+)))
12410 (define-public r-upsetr
12417 (uri (cran-uri "UpSetR" version))
12420 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12421 (properties `((upstream-name . "UpSetR")))
12422 (build-system r-build-system)
12424 `(("r-ggplot2" ,r-ggplot2)
12425 ("r-gridextra" ,r-gridextra)
12427 ("r-scales" ,r-scales)))
12428 (home-page "https://github.com/hms-dbmi/UpSetR")
12429 (synopsis "Visualize intersecting sets")
12431 "This package provides a more scalable alternative to Venn and Euler
12432 diagrams for visualizing intersecting sets. Create visualizations of
12433 intersecting sets using a novel matrix design, along with visualizations of
12434 several common set, element and attribute related tasks.")
12435 (license license:expat)))
12437 ;; This package includes a JavaScript file, which is not minified. When
12438 ;; upgrading please check that there are no new minified JavaScript files.
12439 (define-public r-shinybs
12446 (uri (cran-uri "shinyBS" version))
12449 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12450 (properties `((upstream-name . "shinyBS")))
12451 (build-system r-build-system)
12452 ;; The tests spawn Shiny browser apps. They cannot be run
12453 ;; non-interactively.
12454 (arguments '(#:tests? #f))
12456 `(("r-htmltools" ,r-htmltools)
12457 ("r-shiny" ,r-shiny)))
12458 (home-page "https://ebailey78.github.io/shinyBS/")
12459 (synopsis "Twitter Bootstrap components for Shiny")
12461 "This package adds additional Twitter Bootstrap components to Shiny.")
12462 (license license:gpl3)))
12464 (define-public r-outliers
12466 (name "r-outliers")
12471 (uri (cran-uri "outliers" version))
12474 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12475 (build-system r-build-system)
12476 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12477 (synopsis "Tests for outliers")
12479 "This package provides a collection of some tests commonly used for
12480 identifying outliers.")
12481 (license license:gpl2+)))
12483 (define-public r-bayesm
12490 (uri (cran-uri "bayesm" version))
12492 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12493 (build-system r-build-system)
12495 `(("r-rcpp" ,r-rcpp)
12496 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12497 (home-page "http://www.perossi.org/home/bsm-1")
12498 (synopsis "Bayesian inference for marketing/micro-econometrics")
12500 "This package covers many important models used in marketing and
12501 micro-econometrics applications, including Bayes Regression (univariate or
12502 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12503 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12504 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12505 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12506 Estimation with normal base, Hierarchical Linear Models with normal prior and
12507 covariates, Hierarchical Linear Models with a mixture of normals prior and
12508 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12509 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12510 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12511 analysis of choice-based conjoint data, Bayesian treatment of linear
12512 instrumental variables models, Analysis of Multivariate Ordinal survey data
12513 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12514 Coefficient Logit Models.")
12515 (license license:gpl2+)))
12517 (define-public r-tensora
12524 (uri (cran-uri "tensorA" version))
12527 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12528 (properties `((upstream-name . "tensorA")))
12529 (build-system r-build-system)
12530 (home-page "http://www.stat.boogaart.de/tensorA")
12531 (synopsis "Advanced tensor arithmetic with named indices")
12533 "This package provides convenience functions for advanced linear algebra
12534 with tensors and computation with datasets of tensors on a higher level
12535 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12536 co- and contravariate indices, and parallel computations on sequences of
12538 (license license:gpl2+)))
12540 (define-public r-rarpack
12547 (uri (cran-uri "rARPACK" version))
12550 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12551 (properties `((upstream-name . "rARPACK")))
12552 (build-system r-build-system)
12553 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12554 (home-page "https://github.com/yixuan/rARPACK")
12555 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12557 "This package was previously an R wrapper of the ARPACK library, and now
12558 a shell of the R package RSpectra, an R interface to the Spectra library for
12559 solving large scale eigenvalue/vector problems. The current version of
12560 rARPACK simply imports and exports the functions provided by RSpectra. New
12561 users of rARPACK are advised to switch to the RSpectra package.")
12562 (license license:bsd-3)))
12564 (define-public r-compositions
12566 (name "r-compositions")
12571 (uri (cran-uri "compositions" version))
12574 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12575 (build-system r-build-system)
12577 `(("r-bayesm" ,r-bayesm)
12579 ("r-robustbase" ,r-robustbase)
12580 ("r-tensora" ,r-tensora)))
12582 `(("r-knitr" ,r-knitr)))
12583 (home-page "http://www.stat.boogaart.de/compositions")
12584 (synopsis "Compositional data analysis")
12586 "This package provides functions for the consistent analysis of
12587 compositional data (e.g. portions of substances) and positive
12588 numbers (e.g. concentrations).")
12589 (license license:gpl2+)))
12591 (define-public r-cobs
12598 (uri (cran-uri "cobs" version))
12601 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12602 (build-system r-build-system)
12604 `(("r-quantreg" ,r-quantreg)
12605 ("r-sparsem" ,r-sparsem)))
12606 (home-page "https://cran.r-project.org/web/packages/cobs")
12607 (synopsis "Constrained B-Splines (sparse matrix based)")
12609 "This package provides qualitatively constrained (regression) smoothing
12610 splines via linear programming and sparse matrices.")
12611 (license license:gpl2+)))
12613 (define-public r-drimpute
12615 (name "r-drimpute")
12620 (uri (cran-uri "DrImpute" version))
12623 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12624 (properties `((upstream-name . "DrImpute")))
12625 (build-system r-build-system)
12627 `(("r-rcpp" ,r-rcpp)
12628 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12629 (home-page "https://github.com/ikwak2/DrImpute")
12630 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12632 "This is an R package for imputing dropout events. Many statistical
12633 methods in cell type identification, visualization and lineage reconstruction
12634 do not account for dropout events. DrImpute can improve the performance of
12635 such software by imputing dropout events.")
12636 (license license:gpl3)))
12638 (define-public r-gamlss-dist
12640 (name "r-gamlss-dist")
12645 (uri (cran-uri "gamlss.dist" version))
12647 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12648 (properties `((upstream-name . "gamlss.dist")))
12649 (build-system r-build-system)
12650 (propagated-inputs `(("r-mass" ,r-mass)))
12651 (home-page "http://www.gamlss.org/")
12652 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12654 "This package provides a set of distributions which can be used for
12655 modelling the response variables in Generalized Additive Models for Location
12656 Scale and Shape. The distributions can be continuous, discrete or mixed
12657 distributions. Extra distributions can be created, by transforming, any
12658 continuous distribution defined on the real line, to a distribution defined on
12659 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12660 transformation, respectively.")
12661 ;; Either version of the GPL.
12662 (license (list license:gpl2 license:gpl3))))
12664 ;; This package includes JavaScript files, which are not minified. When
12665 ;; upgrading please check that there are no new minified JavaScript files.
12666 (define-public r-shinyjs
12673 (uri (cran-uri "shinyjs" version))
12676 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12677 (build-system r-build-system)
12679 `(("r-digest" ,r-digest)
12680 ("r-htmltools" ,r-htmltools)
12681 ("r-jsonlite" ,r-jsonlite)
12682 ("r-shiny" ,r-shiny)))
12683 (home-page "https://deanattali.com/shinyjs")
12684 (synopsis "Improve the user experience of your Shiny apps")
12686 "Perform common useful JavaScript operations in Shiny apps that will
12687 greatly improve your apps without having to know any JavaScript. Examples
12688 include: hiding an element, disabling an input, resetting an input back to its
12689 original value, delaying code execution by a few seconds, and many more useful
12690 functions for both the end user and the developer. Shinyjs can also be used
12691 to easily call your own custom JavaScript functions from R.")
12692 (license license:agpl3+)))
12694 ;; This package includes minified JavaScript files. When upgrading please
12695 ;; check that there are no new minified JavaScript files.
12696 (define-public r-colourpicker
12698 (name "r-colourpicker")
12703 (uri (cran-uri "colourpicker" version))
12706 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12707 (build-system r-build-system)
12709 `(#:modules ((guix build utils)
12710 (guix build r-build-system)
12714 (modify-phases %standard-phases
12715 (add-after 'unpack 'process-javascript
12716 (lambda* (#:key inputs #:allow-other-keys)
12717 (with-directory-excursion "inst"
12721 `((,(assoc-ref inputs "js-salvattore")
12722 "examples/colourInput/www/salvattore.min.js")
12723 (,(assoc-ref inputs "js-jquery")
12724 "htmlwidgets/lib/jquery/jquery.min.js")
12725 ("www/shared/colourpicker/js/colourpicker.js"
12726 "www/shared/colourpicker/js/colourpicker.min.js"))))
12727 (lambda (sources targets)
12728 (for-each (lambda (source target)
12729 (format #t "Processing ~a --> ~a~%"
12731 (delete-file target)
12732 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12733 (call-with-output-file target
12735 (dump-port minified port)))))
12736 sources targets))))
12739 `(("r-ggplot2" ,r-ggplot2)
12740 ("r-htmltools" ,r-htmltools)
12741 ("r-htmlwidgets" ,r-htmlwidgets)
12742 ("r-jsonlite" ,r-jsonlite)
12743 ("r-miniui" ,r-miniui)
12744 ("r-shiny" ,r-shiny)
12745 ("r-shinyjs" ,r-shinyjs)))
12747 `(("uglify-js" ,uglify-js)
12751 (uri "https://code.jquery.com/jquery-3.3.1.js")
12754 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12758 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12761 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12762 (home-page "https://github.com/daattali/colourpicker")
12763 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12765 "This package provides a color picker that can be used as an input in
12766 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12767 custom color palettes, and many more options. A plot color helper tool is
12768 available as an RStudio Addin, which helps you pick colors to use in your
12769 plots. A more generic color picker RStudio Addin is also provided to let you
12770 select colors to use in your R code.")
12771 (license license:expat)))
12773 (define-public r-ggextra
12780 (uri (cran-uri "ggExtra" version))
12783 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12784 (properties `((upstream-name . "ggExtra")))
12785 (build-system r-build-system)
12787 `(("r-colourpicker" ,r-colourpicker)
12788 ("r-ggplot2" ,r-ggplot2)
12789 ("r-gtable" ,r-gtable)
12790 ("r-miniui" ,r-miniui)
12792 ("r-scales" ,r-scales)
12793 ("r-shiny" ,r-shiny)
12794 ("r-shinyjs" ,r-shinyjs)))
12796 `(("r-knitr" ,r-knitr)))
12797 (home-page "https://github.com/daattali/ggExtra")
12798 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12800 "This package is a collection of functions and layers to enhance ggplot2.
12801 The flagship function is @code{ggMarginal()}, which can be used to add
12802 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12803 (license license:expat)))
12805 (define-public r-minpack-lm
12807 (name "r-minpack-lm")
12812 (uri (cran-uri "minpack.lm" version))
12815 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12816 (properties `((upstream-name . "minpack.lm")))
12817 (build-system r-build-system)
12818 (native-inputs `(("gfortran" ,gfortran)))
12819 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12820 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12822 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12823 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12824 problems by a modification of the Levenberg-Marquardt algorithm, with support
12825 for lower and upper parameter bounds. The implementation can be used via
12826 @code{nls}-like calls using the @code{nlsLM} function.")
12827 (license license:gpl3)))
12829 (define-public r-moments
12836 (uri (cran-uri "moments" version))
12839 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12840 (build-system r-build-system)
12841 (home-page "https://cran.r-project.org/web/packages/moments")
12842 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12844 "This package provides functions to calculate: moments, Pearson's
12845 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12846 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12847 (license license:gpl2+)))
12849 (define-public r-msir
12856 (uri (cran-uri "msir" version))
12859 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12860 (build-system r-build-system)
12862 `(("r-mclust" ,r-mclust)))
12863 (home-page "https://cran.r-project.org/web/packages/msir")
12864 (synopsis "Model-based sliced inverse regression")
12866 "This is an R package for dimension reduction based on finite Gaussian
12867 mixture modeling of inverse regression.")
12868 (license license:gpl2+)))
12870 (define-public r-pbivnorm
12872 (name "r-pbivnorm")
12877 (uri (cran-uri "pbivnorm" version))
12880 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12881 (build-system r-build-system)
12882 (native-inputs `(("gfortran" ,gfortran)))
12883 (home-page "https://github.com/brentonk/pbivnorm")
12884 (synopsis "Vectorized bivariate normal CDF")
12886 "This package provides a vectorized R function for calculating
12887 probabilities from a standard bivariate normal CDF.")
12888 (license license:gpl2+)))
12890 (define-public r-lavaan
12897 (uri (cran-uri "lavaan" version))
12900 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
12901 (build-system r-build-system)
12903 `(("r-mass" ,r-mass)
12904 ("r-mnormt" ,r-mnormt)
12905 ("r-numderiv" ,r-numderiv)
12906 ("r-pbivnorm" ,r-pbivnorm)))
12907 (home-page "http://lavaan.ugent.be")
12908 (synopsis "Latent variable analysis")
12910 "This package provides tools to fit a variety of latent variable models,
12911 including confirmatory factor analysis, structural equation modeling and
12912 latent growth curve models.")
12913 (license license:gpl2+)))
12915 (define-public r-nonnest2
12917 (name "r-nonnest2")
12922 (uri (cran-uri "nonnest2" version))
12925 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
12926 (build-system r-build-system)
12928 `(("r-compquadform" ,r-compquadform)
12929 ("r-lavaan" ,r-lavaan)
12930 ("r-mvtnorm" ,r-mvtnorm)
12931 ("r-sandwich" ,r-sandwich)))
12933 `(("r-knitr" ,r-knitr)))
12934 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12935 (synopsis "Tests of non-nested models")
12937 "This package allows for testing of non-nested models. It includes tests
12938 of model distinguishability and of model fit that can be applied to both
12939 nested and non-nested models. The package also includes functionality to
12940 obtain confidence intervals associated with AIC and BIC.")
12941 ;; Either version of the GPL.
12942 (license (list license:gpl2 license:gpl3))))
12944 (define-public r-penalized
12946 (name "r-penalized")
12951 (uri (cran-uri "penalized" version))
12954 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12955 (build-system r-build-system)
12957 `(("r-rcpp" ,r-rcpp)
12958 ("r-rcpparmadillo" ,r-rcpparmadillo)
12959 ("r-survival" ,r-survival)))
12960 (home-page "https://cran.r-project.org/web/packages/penalized/")
12961 (synopsis "Penalized estimation in GLMs and in the Cox model")
12963 "This package provides tools for fitting possibly high dimensional
12964 penalized regression models. The penalty structure can be any combination of
12965 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12966 constraint on the regression coefficients. The supported regression models
12967 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12968 model. Cross-validation routines allow optimization of the tuning
12970 (license license:gpl2+)))
12972 (define-public r-zim
12979 (uri (cran-uri "ZIM" version))
12982 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12983 (properties `((upstream-name . "ZIM")))
12984 (build-system r-build-system)
12985 (propagated-inputs `(("r-mass" ,r-mass)))
12986 (home-page "https://github.com/biostatstudio/ZIM")
12987 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12989 "Analyze count time series with excess zeros. Two types of statistical
12990 models are supported: Markov regression and state-space models. They are also
12991 known as observation-driven and parameter-driven models respectively in the
12992 time series literature. The functions used for Markov regression or
12993 observation-driven models can also be used to fit ordinary regression models
12994 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12995 negative binomial (ZINB) assumption. The package also contains miscellaneous
12996 functions to compute density, distribution, quantile, and generate random
12997 numbers from ZIP and ZINB distributions.")
12998 (license license:gpl3)))
13000 (define-public r-nor1mix
13007 (uri (cran-uri "nor1mix" version))
13010 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13011 (build-system r-build-system)
13012 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13013 (synopsis "Normal (1-d) mixture models")
13015 "This package provides S3 classes and methods for one-dimensional normal
13016 mixture models, for, e.g., density estimation or clustering algorithms
13017 research and teaching; it provides the widely used Marron-Wand densities. It
13018 also provides tools for efficient random number generation and graphics.")
13019 (license license:gpl2+)))
13021 (define-public r-beanplot
13023 (name "r-beanplot")
13028 (uri (cran-uri "beanplot" version))
13031 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13032 (build-system r-build-system)
13033 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13034 (synopsis "Visualization via beanplots")
13036 "This package provides beanplots, an alternative to
13037 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13039 (license license:gpl2)))
13041 (define-public r-pbdzmq
13048 (uri (cran-uri "pbdZMQ" version))
13051 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13052 (properties `((upstream-name . "pbdZMQ")))
13053 (build-system r-build-system)
13055 `(("zeromq" ,zeromq)
13058 `(("pkg-config" ,pkg-config)))
13059 (home-page "https://pbdr.org/")
13060 (synopsis "R interface to ZeroMQ")
13062 "ZeroMQ is a well-known library for high-performance asynchronous
13063 messaging in scalable, distributed applications. This package provides high
13064 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13065 interactive client/server programming frameworks. A few wrapper functions
13066 compatible with @code{rzmq} are also provided.")
13067 (license license:gpl3)))
13069 (define-public r-repr
13076 (uri (cran-uri "repr" version))
13079 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13080 (build-system r-build-system)
13082 `(("r-base64enc" ,r-base64enc)
13083 ("r-htmltools" ,r-htmltools)
13084 ("r-jsonlite" ,r-jsonlite)
13085 ("r-pillar" ,r-pillar)))
13086 (home-page "https://cran.r-project.org/web/packages/repr/")
13087 (synopsis "Serializable representations")
13089 "This package provides string and binary representations of objects for
13090 several formats and MIME types.")
13091 (license license:gpl3)))
13093 (define-public r-irdisplay
13095 (name "r-irdisplay")
13100 (uri (cran-uri "IRdisplay" version))
13103 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13104 (properties `((upstream-name . "IRdisplay")))
13105 (build-system r-build-system)
13107 `(("r-repr" ,r-repr)))
13108 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13109 (synopsis "Jupyter display machinery")
13111 "This package provides an interface to the rich display capabilities of
13112 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13113 running IRkernel session.")
13114 (license license:expat)))
13116 (define-public r-irkernel
13118 (name "r-irkernel")
13123 (uri (cran-uri "IRkernel" version))
13126 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13127 (properties `((upstream-name . "IRkernel")))
13128 (build-system r-build-system)
13131 (modify-phases %standard-phases
13132 (add-after 'install 'install-kernelspec
13133 (lambda* (#:key outputs #:allow-other-keys)
13134 (let ((out (assoc-ref outputs "out")))
13135 (setenv "HOME" "/tmp")
13136 (invoke "jupyter" "kernelspec" "install"
13139 (string-append out "/site-library/IRkernel/kernelspec"))
13140 ;; Record the absolute file name of the 'R' executable in
13142 (substitute* (string-append out "/share/jupyter"
13143 "/kernels/ir/kernel.json")
13145 (string-append "[\"" (which "R") "\",")))
13148 `(("jupyter" ,jupyter)))
13150 `(("r-crayon" ,r-crayon)
13151 ("r-digest" ,r-digest)
13152 ("r-evaluate" ,r-evaluate)
13153 ("r-irdisplay" ,r-irdisplay)
13154 ("r-jsonlite" ,r-jsonlite)
13155 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13156 ("r-minimal" ,r-minimal)
13157 ("r-pbdzmq" ,r-pbdzmq)
13159 ("r-uuid" ,r-uuid)))
13160 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13161 (synopsis "Native R kernel for Jupyter")
13163 "The R kernel for the Jupyter environment executes R code which the
13164 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13166 (license license:expat)))
13168 (define-public r-gmodels
13175 (uri (cran-uri "gmodels" version))
13178 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13179 (build-system r-build-system)
13181 `(("r-gdata" ,r-gdata)
13182 ("r-mass" ,r-mass)))
13183 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13184 (synopsis "Various R programming tools for model fitting")
13186 "This package provides various R programming tools for model fitting.")
13187 (license license:gpl2)))
13189 (define-public r-apcluster
13191 (name "r-apcluster")
13196 (uri (cran-uri "apcluster" version))
13199 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13200 (build-system r-build-system)
13202 `(("r-matrix" ,r-matrix)
13203 ("r-rcpp" ,r-rcpp)))
13204 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13205 (synopsis "Affinity propagation clustering")
13207 "This package implements affinity propagation clustering introduced by
13208 Frey and Dueck (2007). The package further provides leveraged affinity
13209 propagation and an algorithm for exemplar-based agglomerative clustering that
13210 can also be used to join clusters obtained from affinity propagation. Various
13211 plotting functions are available for analyzing clustering results.")
13212 (license license:gpl2+)))
13214 (define-public r-valr
13221 (uri (cran-uri "valr" version))
13224 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13225 (build-system r-build-system)
13227 `(("r-broom" ,r-broom)
13228 ("r-dplyr" ,r-dplyr)
13229 ("r-ggplot2" ,r-ggplot2)
13231 ("r-readr" ,r-readr)
13232 ("r-rlang" ,r-rlang)
13233 ("r-stringr" ,r-stringr)
13234 ("r-tibble" ,r-tibble)))
13236 `(("r-knitr" ,r-knitr)))
13237 (home-page "https://github.com/rnabioco/valr")
13238 (synopsis "Genome interval arithmetic in R")
13240 "This package enables you to read and manipulate genome intervals and
13241 signals. It provides functionality similar to command-line tool suites within
13242 R, enabling interactive analysis and visualization of genome-scale data.")
13243 (license license:expat)))
13245 (define-public r-rematch2
13247 (name "r-rematch2")
13252 (uri (cran-uri "rematch2" version))
13255 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13256 (build-system r-build-system)
13258 `(("r-tibble" ,r-tibble)))
13259 (home-page "https://github.com/r-lib/rematch2")
13260 (synopsis "Tidy output from regular expression matching")
13262 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13263 return the match results in tidy data frames.")
13264 (license license:expat)))
13266 (define-public r-picante
13273 (uri (cran-uri "picante" version))
13276 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13277 (build-system r-build-system)
13281 ("r-vegan" ,r-vegan)))
13282 (home-page "https://cran.r-project.org/web/packages/picante/")
13283 (synopsis "Integrating phylogenies and ecology")
13285 "This package provides functions for phylocom integration, community
13286 analyses, null-models, traits and evolution. It implements numerous
13287 ecophylogenetic approaches including measures of community phylogenetic and
13288 trait diversity, phylogenetic signal, estimation of trait values for
13289 unobserved taxa, null models for community and phylogeny randomizations, and
13290 utility functions for data input/output and phylogeny plotting. A full
13291 description of package functionality and methods are provided by Kembel et
13293 (license license:gpl2)))
13295 (define-public r-reinforcelearn
13297 (name "r-reinforcelearn")
13302 (uri (cran-uri "reinforcelearn" version))
13305 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13306 (build-system r-build-system)
13308 `(("r-checkmate" ,r-checkmate)
13310 ("r-purrr" ,r-purrr)
13312 (home-page "https://markusdumke.github.io/reinforcelearn")
13313 (synopsis "Reinforcement learning")
13315 "This package implements reinforcement learning environments and
13316 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13317 can be used with function approximation, eligibility traces (Singh & Sutton,
13318 1996) and experience replay (Mnih et al., 2013).")
13319 (license license:expat)))
13321 (define-public r-lemon
13328 (uri (cran-uri "lemon" version))
13331 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13332 (build-system r-build-system)
13334 `(("r-ggplot2" ,r-ggplot2)
13335 ("r-gridextra" ,r-gridextra)
13336 ("r-gtable" ,r-gtable)
13337 ("r-knitr" ,r-knitr)
13338 ("r-lattice" ,r-lattice)
13340 ("r-rlang" ,r-rlang)
13341 ("r-scales" ,r-scales)))
13343 `(("r-knitr" ,r-knitr)))
13344 (home-page "https://github.com/stefanedwards/lemon")
13345 (synopsis "Freshen up your ggplot2 plots")
13347 "This package provides functions for working with legends and axis lines
13348 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13350 (license license:gpl3)))
13352 (define-public r-wgaim
13359 (uri (cran-uri "wgaim" version))
13361 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13362 (build-system r-build-system)
13364 `(("r-ggplot2" ,r-ggplot2)
13366 (home-page "https://cran.r-project.org/web/packages/wgaim")
13367 (synopsis "Whole genome average interval mapping for QTL detection")
13369 "This package integrates sophisticated mixed modelling methods with a
13370 whole genome approach to detecting significant QTL in linkage maps.")
13371 (license license:gpl2+)))
13373 (define-public r-bedr
13380 (uri (cran-uri "bedr" version))
13383 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13384 (build-system r-build-system)
13386 `(("r-data-table" ,r-data-table)
13387 ("r-r-utils" ,r-r-utils)
13388 ("r-testthat" ,r-testthat)
13389 ("r-venndiagram" ,r-venndiagram)
13392 ("bedtools" ,bedtools)
13393 ("htslib" ,htslib))) ; for tabix
13395 `(("r-knitr" ,r-knitr))) ; for vignettes
13396 (home-page "https://cran.r-project.org/web/packages/bedr")
13397 (synopsis "Genomic region processing")
13399 "This package is for genomic regions processing using command line tools
13400 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13401 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13402 The bedr package's API enhances access to these tools as well as offers
13403 additional utilities for genomic regions processing.")
13404 (license license:gpl2)))
13406 (define-public r-sets
13413 (uri (cran-uri "sets" version))
13416 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13417 (properties `((upstream-name . "sets")))
13418 (build-system r-build-system)
13419 (home-page "https://cran.r-project.org/web/packages/sets")
13420 (synopsis "Sets, generalized sets, customizable sets and intervals")
13422 "This package provides data structures and basic operations for ordinary
13423 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13424 customizable sets, and intervals.")
13425 (license license:gpl2)))
13427 (define-public r-partitions
13429 (name "r-partitions")
13434 (uri (cran-uri "partitions" version))
13437 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13438 (build-system r-build-system)
13441 ("r-polynom" ,r-polynom)
13442 ("r-sets" ,r-sets)))
13443 (home-page "https://cran.r-project.org/web/packages/partitions")
13444 (synopsis "Additive partitions of integers")
13446 "This package provides tools to enumerates the partitions, unequal
13447 partitions, and restricted partitions of an integer; the three corresponding
13448 partition functions are also given.")
13449 ;; Any version of the GPL
13450 (license license:gpl2+)))
13452 (define-public r-brobdingnag
13454 (name "r-brobdingnag")
13459 (uri (cran-uri "Brobdingnag" version))
13462 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13463 (properties `((upstream-name . "Brobdingnag")))
13464 (build-system r-build-system)
13465 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13466 (synopsis "Very large numbers in R")
13468 "This package handles very large numbers in R. Real numbers are held
13469 using their natural logarithms, plus a logical flag indicating sign. The
13470 package includes a vignette that gives a step-by-step introduction to using S4
13472 ;; Any version of the GPL
13473 (license license:gpl2+)))
13475 (define-public r-untb
13482 (uri (cran-uri "untb" version))
13485 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13486 (build-system r-build-system)
13488 `(("r-brobdingnag" ,r-brobdingnag)
13489 ("r-partitions" ,r-partitions)
13490 ("r-polynom" ,r-polynom)))
13491 (home-page "https://github.com/RobinHankin/untb.git")
13492 (synopsis "Ecological drift under the UNTB")
13494 "This package provides numerical simulations, and visualizations, of
13495 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13496 (license license:gpl2+)))
13498 (define-public r-stepwise
13500 (name "r-stepwise")
13505 (uri (cran-uri "stepwise" version))
13508 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13509 (build-system r-build-system)
13510 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13511 (synopsis "Stepwise detection of recombination breakpoints")
13513 "This package provides a stepwise approach to identifying recombination
13514 breakpoints in a genomic sequence alignment.")
13515 (license license:gpl2+)))
13517 (define-public r-snpmaxsel
13519 (name "r-snpmaxsel")
13524 (uri (cran-uri "SNPmaxsel" version))
13527 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13528 (properties `((upstream-name . "SNPmaxsel")))
13529 (build-system r-build-system)
13531 `(("r-combinat" ,r-combinat)
13532 ("r-mvtnorm" ,r-mvtnorm)))
13533 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13534 (synopsis "Maximally selected statistics for SNP data")
13536 "This package implements asymptotic methods related to maximally selected
13537 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13539 (license license:gpl2+)))
13541 (define-public r-acsnminer
13543 (name "r-acsnminer")
13544 (version "0.16.8.25")
13547 (uri (cran-uri "ACSNMineR" version))
13550 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13551 (properties `((upstream-name . "ACSNMineR")))
13552 (build-system r-build-system)
13554 `(("r-ggplot2" ,r-ggplot2)
13555 ("r-gridextra" ,r-gridextra)))
13556 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13557 (synopsis "Gene enrichment analysis")
13559 "This package provides tools to compute and represent gene set enrichment
13560 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13561 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13562 enrichment can be run with hypergeometric test or Fisher exact test, and can
13563 use multiple corrections. Visualization of data can be done either by
13564 barplots or heatmaps.")
13565 (license license:gpl2+)))
13567 (define-public r-seqinr
13574 (uri (cran-uri "seqinr" version))
13577 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13578 (build-system r-build-system)
13580 `(("r-ade4" ,r-ade4)
13581 ("r-segmented" ,r-segmented)))
13584 (home-page "http://seqinr.r-forge.r-project.org/")
13585 (synopsis "Biological sequences retrieval and analysis")
13587 "This package provides tools for exploratory data analysis and data
13588 visualization of biological sequence (DNA and protein) data. It also includes
13589 utilities for sequence data management under the ACNUC system.")
13590 (license license:gpl2+)))
13592 (define-public r-units
13599 (uri (cran-uri "units" version))
13602 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13603 (build-system r-build-system)
13605 `(("udunits" ,udunits)))
13607 `(("r-rcpp" ,r-rcpp)))
13609 `(("r-knitr" ,r-knitr)))
13610 (home-page "https://github.com/r-quantities/units/")
13611 (synopsis "Measurement Units for R Vectors")
13613 "This package provides support for measurement units in R vectors,
13614 matrices and arrays: automatic propagation, conversion, derivation and
13615 simplification of units; raising errors in case of unit incompatibility. It
13616 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13618 (license license:gpl2)))
13620 (define-public r-classint
13622 (name "r-classint")
13627 (uri (cran-uri "classInt" version))
13630 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13631 (properties `((upstream-name . "classInt")))
13632 (build-system r-build-system)
13634 `(("r-class" ,r-class)
13635 ("r-e1071" ,r-e1071)
13636 ("r-kernsmooth" ,r-kernsmooth)))
13638 `(("gfortran" ,gfortran)
13639 ("r-knitr" ,r-knitr)))
13640 (home-page "https://github.com/r-spatial/classInt/")
13641 (synopsis "Choose univariate class intervals")
13643 "This package provides selected commonly used methods for choosing
13644 univariate class intervals for mapping or other graphics purposes.")
13645 (license license:gpl2+)))
13647 (define-public r-spdata
13654 (uri (cran-uri "spData" version))
13657 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13658 (properties `((upstream-name . "spData")))
13659 (build-system r-build-system)
13661 `(("r-raster" ,r-raster)
13663 (home-page "https://github.com/Nowosad/spData")
13664 (synopsis "Datasets for spatial analysis")
13666 "This a package containing diverse spatial datasets for demonstrating,
13667 benchmarking and teaching spatial data analysis. It includes R data of class
13668 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13669 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13670 of the datasets are designed to illustrate specific analysis techniques.
13671 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13672 illustrate point pattern analysis techniques.")
13673 (license license:cc0)))
13675 (define-public r-learnbayes
13677 (name "r-learnbayes")
13682 (uri (cran-uri "LearnBayes" version))
13685 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13686 (properties `((upstream-name . "LearnBayes")))
13687 (build-system r-build-system)
13688 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13689 (synopsis "Functions for learning Bayesian inference")
13691 "This package provides a collection of functions helpful in learning the
13692 basic tenets of Bayesian statistical inference. It contains functions for
13693 summarizing basic one and two parameter posterior distributions and predictive
13694 distributions. It contains MCMC algorithms for summarizing posterior
13695 distributions defined by the user. It also contains functions for regression
13696 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13698 (license license:gpl2+)))
13700 (define-public r-deldir
13707 (uri (cran-uri "deldir" version))
13710 "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
13711 (build-system r-build-system)
13712 (native-inputs `(("gfortran" ,gfortran)))
13713 (home-page "https://cran.r-project.org/web/packages/deldir")
13714 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13716 "This package provides tools for calculating the Delaunay triangulation
13717 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13718 of a planar point set. It plots triangulations and tessellations in various
13719 ways, clips tessellations to sub-windows, calculates perimeters of
13720 tessellations, and summarizes information about the tiles of the
13722 (license license:gpl2+)))
13724 (define-public r-sf
13731 (uri (cran-uri "sf" version))
13734 "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
13735 (build-system r-build-system)
13742 `(("r-classint" ,r-classint)
13744 ("r-magrittr" ,r-magrittr)
13746 ("r-units" ,r-units)))
13748 `(("pkg-config" ,pkg-config)
13749 ("r-knitr" ,r-knitr)))
13750 (home-page "https://github.com/r-spatial/sf/")
13751 (synopsis "Simple features for R")
13753 "This package provides support for simple features, a standardized way to
13754 encode spatial vector data. It binds to GDAL for reading and writing data, to
13755 GEOS for geometrical operations, and to PROJ for projection conversions and
13756 datum transformations.")
13757 ;; Either of these licenses
13758 (license (list license:gpl2 license:expat))))
13760 (define-public r-spdep
13767 (uri (cran-uri "spdep" version))
13770 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13771 (build-system r-build-system)
13773 `(("r-boot" ,r-boot)
13775 ("r-deldir" ,r-deldir)
13777 ("r-gmodels" ,r-gmodels)
13778 ("r-learnbayes" ,r-learnbayes)
13780 ("r-matrix" ,r-matrix)
13784 ("r-spdata" ,r-spdata)))
13786 `(("r-knitr" ,r-knitr)))
13787 (home-page "https://github.com/r-spatial/spdep/")
13788 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13790 "This package provides a collection of functions to create spatial
13791 weights matrix objects from polygon contiguities, from point patterns by
13792 distance and tessellations, for summarizing these objects, and for permitting
13793 their use in spatial data analysis, including regional aggregation by minimum
13795 (license license:gpl2+)))
13797 (define-public r-adegenet
13799 (name "r-adegenet")
13804 (uri (cran-uri "adegenet" version))
13807 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13808 (build-system r-build-system)
13810 `(("r-ade4" ,r-ade4)
13813 ("r-dplyr" ,r-dplyr)
13814 ("r-ggplot2" ,r-ggplot2)
13815 ("r-igraph" ,r-igraph)
13817 ("r-reshape2" ,r-reshape2)
13818 ("r-seqinr" ,r-seqinr)
13819 ("r-shiny" ,r-shiny)
13820 ("r-spdep" ,r-spdep)
13821 ("r-vegan" ,r-vegan)))
13822 (home-page "https://github.com/thibautjombart/adegenet")
13823 (synopsis "Exploratory analysis of genetic and genomic data")
13825 "This package provides a toolset for the exploration of genetic and
13826 genomic data. Adegenet provides formal (S4) classes for storing and handling
13827 various genetic data, including genetic markers with varying ploidy and
13828 hierarchical population structure (@code{genind} class), alleles counts by
13829 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13830 also implements original multivariate methods (DAPC, sPCA), graphics,
13831 statistical tests, simulation tools, distance and similarity measures, and
13832 several spatial methods. A range of both empirical and simulated datasets is
13833 also provided to illustrate various methods.")
13834 (license license:gpl2+)))
13836 (define-public r-pegas
13843 (uri (cran-uri "pegas" version))
13845 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13846 (build-system r-build-system)
13848 `(("r-adegenet" ,r-adegenet)
13850 (home-page "http://ape-package.ird.fr/pegas.html")
13851 (synopsis "Population and evolutionary genetics analysis system")
13853 "This package provides functions for reading, writing, plotting,
13854 analysing, and manipulating allelic and haplotypic data, including from VCF
13855 files, and for the analysis of population nucleotide sequences and
13856 micro-satellites including coalescent analyses, linkage disequilibrium,
13857 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13858 minimum spanning tree and network, and median-joining networks.")
13859 (license license:gpl2+)))
13861 (define-public r-rmetasim
13863 (name "r-rmetasim")
13868 (uri (cran-uri "rmetasim" version))
13871 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13872 (build-system r-build-system)
13874 `(("r-ade4" ,r-ade4)
13875 ("r-adegenet" ,r-adegenet)
13876 ("r-gtools" ,r-gtools)
13877 ("r-pegas" ,r-pegas)))
13878 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13879 (synopsis "Individual-based population genetic simulation environment")
13881 "This package provides an interface between R and the metasim simulation
13882 engine. The simulation environment is documented in: Strand, A.(2002),
13883 Metasim 1.0: an individual-based environment for simulating population
13884 genetics of complex population dynamics.")
13886 (license license:gpl2+)))
13888 (define-public r-genetics
13890 (name "r-genetics")
13891 (version "1.3.8.1.2")
13895 (uri (cran-uri "genetics" version))
13898 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13899 (build-system r-build-system)
13901 `(("r-combinat" ,r-combinat)
13902 ("r-gdata" ,r-gdata)
13903 ("r-gtools" ,r-gtools)
13905 ("r-mvtnorm" ,r-mvtnorm)))
13906 (home-page "https://cran.r-project.org/web/packages/genetics/")
13907 (synopsis "Population genetics")
13909 "This package provides classes and methods for handling genetic data.
13910 It includes classes to represent genotypes and haplotypes at single markers up
13911 to multiple markers on multiple chromosomes. Function include allele
13912 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13913 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13914 and testing for linkage disequilibrium, ...")
13915 ;; Any GPL version.
13916 (license license:gpl2+)))
13918 (define-public r-snp-plotter
13920 (name "r-snp-plotter")
13925 (uri (cran-uri "snp.plotter" version))
13928 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13929 (properties `((upstream-name . "snp.plotter")))
13930 (build-system r-build-system)
13931 (propagated-inputs `(("r-genetics" ,r-genetics)))
13932 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13933 (synopsis "Plot p-values using single SNP and/or haplotype data")
13935 "This package helps you create plots of p-values using single SNP and/or
13936 haplotype data. Main features of the package include options to display a
13937 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13938 datasets simultaneously. Plots can be created using global and/or individual
13939 haplotype p-values along with single SNP p-values. Images are created as
13940 either PDF/EPS files.")
13941 (license license:gpl2+)))
13943 (define-public r-polspline
13945 (name "r-polspline")
13950 (uri (cran-uri "polspline" version))
13952 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13953 (build-system r-build-system)
13954 (native-inputs `(("gfortran" ,gfortran)))
13955 (home-page "https://cran.r-project.org/web/packages/polspline/")
13956 (synopsis "Polynomial spline routines")
13958 "This package provides routines for the polynomial spline fitting
13959 routines hazard regression, hazard estimation with flexible tails, logspline,
13960 lspec, polyclass, and polymars.")
13961 (license license:gpl2+)))
13963 (define-public r-rms
13970 (uri (cran-uri "rms" version))
13972 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
13973 (build-system r-build-system)
13975 `(("r-cluster" ,r-cluster)
13976 ("r-digest" ,r-digest)
13977 ("r-ggplot2" ,r-ggplot2)
13978 ("r-hmisc" ,r-hmisc)
13979 ("r-htmltable" ,r-htmltable)
13980 ("r-htmltools" ,r-htmltools)
13981 ("r-lattice" ,r-lattice)
13983 ("r-multcomp" ,r-multcomp)
13985 ("r-polspline" ,r-polspline)
13986 ("r-quantreg" ,r-quantreg)
13987 ("r-rpart" ,r-rpart)
13988 ("r-sparsem" ,r-sparsem)
13989 ("r-survival" ,r-survival)))
13990 (native-inputs `(("gfortran" ,gfortran)))
13991 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13992 (synopsis "Regression modeling strategies")
13994 "This is a package for regression modeling, testing, estimation,
13995 validation, graphics, prediction, and typesetting by storing enhanced model
13996 design attributes in the fit. The rms package is a collection of functions
13997 that assist with and streamline modeling. It also contains functions for
13998 binary and ordinal logistic regression models, ordinal models for continuous Y
13999 with a variety of distribution families, and the Buckley-James multiple
14000 regression model for right-censored responses, and implements penalized
14001 maximum likelihood estimation for logistic and ordinary linear models. The
14002 package works with almost any regression model, but it was especially written
14003 to work with binary or ordinal regression models, Cox regression, accelerated
14004 failure time models, ordinary linear models, the Buckley-James model,
14005 generalized least squares for serially or spatially correlated observations,
14006 generalized linear models, and quantile regression.")
14007 (license license:gpl2+)))
14009 (define-public r-arsenal
14016 (uri (cran-uri "arsenal" version))
14019 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14020 (properties `((upstream-name . "arsenal")))
14021 (build-system r-build-system)
14022 (propagated-inputs `(("r-knitr" ,r-knitr)))
14023 (native-inputs `(("r-knitr" ,r-knitr)))
14024 (home-page "https://github.com/mayoverse/arsenal")
14025 (synopsis "Functions for large-scale statistical summaries")
14027 "This package provides an arsenal of R functions for large-scale
14028 statistical summaries, which are streamlined to work within the latest
14029 reporting tools in R and RStudio and which use formulas and versatile
14030 summary statistics for summary tables and models. The primary functions
14034 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14035 levels of one or more categorical variables;
14036 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14037 across two time points;
14038 @item @code{modelsum}, which performs simple model fits on one or more
14039 endpoints for many variables (univariate or adjusted for covariates);
14040 @item @code{freqlist}, a powerful frequency table across many categorical
14042 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14043 @item @code{write2}, a function to output tables to a document.
14046 (license license:gpl2+)))
14048 (define-public r-haplo-stats
14050 (name "r-haplo-stats")
14055 (uri (cran-uri "haplo.stats" version))
14058 "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
14059 (properties `((upstream-name . "haplo.stats")))
14060 (build-system r-build-system)
14062 `(("r-arsenal" ,r-arsenal)
14065 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14066 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14067 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14069 "This package provides routines for the analysis of indirectly measured
14070 haplotypes. The statistical methods assume that all subjects are unrelated
14071 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14072 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14073 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14074 examples in the vignette.")
14075 (license license:gpl2+)))
14077 (define-public r-bqtl
14084 (uri (cran-uri "bqtl" version))
14087 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14088 (build-system r-build-system)
14089 (native-inputs `(("gfortran" ,gfortran)))
14090 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14091 (synopsis "Bayesian QTL mapping toolkit")
14093 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14094 lines. It includes maximum likelihood and Bayesian tools.")
14095 (license license:gpl2+)))
14097 (define-public r-ibdreg
14104 (uri (cran-uri "ibdreg" version))
14107 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14108 (build-system r-build-system)
14109 (home-page "https://www.mayo.edu/research/labs/\
14110 statistical-genetics-genetic-epidemiology/software")
14111 (synopsis "Regression methods for IBD linkage with covariates")
14113 "This package provides a method to test genetic linkage with covariates
14114 by regression methods with response IBD sharing for relative pairs. Account
14115 for correlations of IBD statistics and covariates for relative pairs within
14116 the same pedigree.")
14117 (license license:gpl2+)))
14119 (define-public r-dlmap
14126 (uri (cran-uri "dlmap" version))
14129 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14130 (build-system r-build-system)
14132 `(("r-ibdreg" ,r-ibdreg)
14136 ("r-wgaim" ,r-wgaim)))
14137 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14138 (synopsis "Detection localization mapping for QTL")
14140 "This is package for QTL mapping in a mixed model framework with separate
14141 detection and localization stages. The first stage detects the number of QTL
14142 on each chromosome based on the genetic variation due to grouped markers on
14143 the chromosome; the second stage uses this information to determine the most
14144 likely QTL positions. The mixed model can accommodate general fixed and
14145 random effects, including spatial effects in field trials and pedigree
14146 effects. It is applicable to backcrosses, doubled haploids, recombinant
14147 inbred lines, F2 intercrosses, and association mapping populations.")
14148 (license license:gpl2)))
14150 (define-public r-ldheatmap
14152 (name "r-ldheatmap")
14157 (uri (cran-uri "LDheatmap" version))
14160 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14161 (properties `((upstream-name . "LDheatmap")))
14162 (build-system r-build-system)
14164 `(("r-genetics" ,r-genetics)
14166 ("r-snpstats" ,r-snpstats)))
14167 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14168 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14170 "This package provides tools to produce a graphical display, as a heat
14171 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14172 optionally include the physical locations or genetic map distances of each SNP
14174 (license license:gpl3)))
14176 (define-public r-hwde
14183 (uri (cran-uri "hwde" version))
14186 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14187 (build-system r-build-system)
14188 (home-page "https://cran.r-project.org/web/packages/hwde/")
14189 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14191 "This package fits models for genotypic disequilibria, as described in
14192 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14193 terms are available that account for first order interactions between loci.
14194 It also implements, for a single locus in a single population, a conditional
14195 exact test for Hardy-Weinberg equilibrium.")
14196 (license license:gpl2+)))
14198 (define-public r-tdthap
14205 (uri (cran-uri "tdthap" version))
14208 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14209 (build-system r-build-system)
14210 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14211 (synopsis "TDT tests for extended haplotypes")
14213 "Functions and examples are provided for transmission/disequilibrium
14214 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14215 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14216 (license license:artistic2.0)))
14218 (define-public r-sparql
14224 (uri (cran-uri "SPARQL" version))
14227 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14228 (properties `((upstream-name . "SPARQL")))
14229 (build-system r-build-system)
14231 `(("r-rcurl" ,r-rcurl)
14233 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14234 (synopsis "SPARQL client for R")
14235 (description "This package provides an interface to use SPARQL to pose
14236 SELECT or UPDATE queries to an end-point.")
14237 ;; The only license indication is found in the DESCRIPTION file,
14238 ;; which states GPL-3. So we cannot assume GPLv3+.
14239 (license license:gpl3)))
14241 (define-public r-bookdown
14243 (name "r-bookdown")
14247 (uri (cran-uri "bookdown" version))
14250 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14251 (build-system r-build-system)
14253 `(("r-htmltools" ,r-htmltools)
14254 ("r-knitr" ,r-knitr)
14255 ("r-rmarkdown" ,r-rmarkdown)
14256 ("r-tinytex" ,r-tinytex)
14258 ("pandoc" ,pandoc)))
14259 (home-page "https://github.com/rstudio/bookdown")
14260 (synopsis "Authoring books and technical documents with R markdown")
14261 (description "This package provides output formats and utilities for
14262 authoring books and technical documents with R Markdown.")
14263 (license license:gpl3)))
14265 (define-public r-optparse
14267 (name "r-optparse")
14272 (uri (cran-uri "optparse" version))
14275 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14276 (build-system r-build-system)
14278 `(("r-getopt" ,r-getopt)))
14280 `(("r-knitr" ,r-knitr)))
14281 (home-page "https://github.com/trevorld/optparse")
14282 (synopsis "Command line option parser")
14284 "This package provides a command line parser inspired by Python's
14285 @code{optparse} library to be used with Rscript to write shebang scripts
14286 that accept short and long options.")
14287 (license license:gpl2+)))
14289 (define-public r-wgcna
14296 (uri (cran-uri "WGCNA" version))
14299 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14300 (properties `((upstream-name . "WGCNA")))
14301 (build-system r-build-system)
14303 `(("r-annotationdbi" ,r-annotationdbi)
14304 ("r-doparallel" ,r-doparallel)
14305 ("r-dynamictreecut" ,r-dynamictreecut)
14306 ("r-fastcluster" ,r-fastcluster)
14307 ("r-foreach" ,r-foreach)
14308 ("r-go-db" ,r-go-db)
14309 ("r-hmisc" ,r-hmisc)
14310 ("r-impute" ,r-impute)
14312 ("r-survival" ,r-survival)
14313 ("r-matrixstats" ,r-matrixstats)
14314 ("r-preprocesscore" ,r-preprocesscore)))
14316 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14317 (synopsis "Weighted correlation network analysis")
14319 "This package provides functions necessary to perform Weighted
14320 Correlation Network Analysis on high-dimensional data. It includes functions
14321 for rudimentary data cleaning, construction and summarization of correlation
14322 networks, module identification and functions for relating both variables and
14323 modules to sample traits. It also includes a number of utility functions for
14324 data manipulation and visualization.")
14325 (license license:gpl2+)))
14327 (define-public r-kernlab
14334 (uri (cran-uri "kernlab" version))
14336 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14337 (build-system r-build-system)
14338 (home-page "https://cran.r-project.org/web/packages/kernlab")
14339 (synopsis "Kernel-based machine learning tools")
14341 "This package provides kernel-based machine learning methods for
14342 classification, regression, clustering, novelty detection, quantile regression
14343 and dimensionality reduction. Among other methods @code{kernlab} includes
14344 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14346 (license license:gpl2)))
14348 (define-public r-hierfstat
14350 (name "r-hierfstat")
14355 (uri (cran-uri "hierfstat" version))
14358 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14359 (build-system r-build-system)
14361 `(("r-ade4" ,r-ade4)
14362 ("r-adegenet" ,r-adegenet)
14363 ("r-gaston" ,r-gaston)
14364 ("r-gtools" ,r-gtools)))
14366 `(("r-knitr" ,r-knitr)))
14367 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14368 (synopsis "Estimation and tests of hierarchical F-statistics")
14370 "This package allows the estimation of hierarchical F-statistics from
14371 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14372 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14373 are also given to test via randomisations the significance of each F and
14374 variance components, using the likelihood-ratio statistics G.")
14375 (license license:gpl2+)))
14377 (define-public r-hapassoc
14379 (name "r-hapassoc")
14384 (uri (cran-uri "hapassoc" version))
14387 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14388 (build-system r-build-system)
14389 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14390 (synopsis "Inference of trait associations with SNP haplotypes")
14392 "Hapassoc performs likelihood inference of trait associations with
14393 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14394 functions are developed primarily for data collected in cohort or
14395 cross-sectional studies. They can accommodate uncertain haplotype phase and
14396 handle missing genotypes at some SNPs.")
14397 (license license:gpl2)))
14399 (define-public r-sampling
14401 (name "r-sampling")
14406 (uri (cran-uri "sampling" version))
14409 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14410 (build-system r-build-system)
14412 `(("r-lpsolve" ,r-lpsolve)
14413 ("r-mass" ,r-mass)))
14414 (home-page "https://cran.r-project.org/web/packages/sampling/")
14415 (synopsis "Survey sampling")
14417 "This package provides functions for drawing and calibrating samples.")
14418 (license license:gpl2+)))
14420 (define-public r-r2html
14427 (uri (cran-uri "R2HTML" version))
14430 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14431 (properties `((upstream-name . "R2HTML")))
14432 (build-system r-build-system)
14433 (home-page "https://github.com/nalimilan/R2HTML")
14434 (synopsis "HTML export for R objects")
14436 "This package includes HTML functions and methods to write in an HTML
14437 file. Thus, making HTML reports is easy. It includes a function that allows
14438 redirection on the fly, which appears to be very useful for teaching purposes,
14439 as the student can keep a copy of the produced output to keep all that they
14440 did during the course. The package comes with a vignette describing how to
14441 write HTML reports for statistical analysis. Finally, a driver for Sweave
14442 parses HTML flat files containing R code and to automatically write
14443 the corresponding outputs (tables and graphs).")
14444 (license license:gpl2+)))
14446 (define-public r-rjava
14453 (uri (cran-uri "rJava" version))
14456 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14457 (properties `((upstream-name . "rJava")))
14458 (build-system r-build-system)
14460 `(#:modules ((guix build utils)
14461 (guix build r-build-system)
14464 (modify-phases %standard-phases
14465 (add-after 'unpack 'set-JAVA_HOME
14466 (lambda* (#:key inputs #:allow-other-keys)
14467 (let ((jdk (assoc-ref inputs "jdk")))
14468 (setenv "JAVA_HOME" jdk)
14469 (setenv "JAVA" (which "java"))
14470 (setenv "JAR" (which "jar"))
14471 (setenv "JAVAC" (which "javac"))
14472 (setenv "JAVAH" (which "javah"))
14473 (setenv "JAVA_CPPFLAGS"
14474 (string-append "-I" jdk "/include "
14475 "-I" jdk "/include/linux"))
14476 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14477 ((lib) (setenv "JAVA_LIBS" lib))
14478 (_ (error "Could not find libjvm.so"))))
14482 ("jdk" ,icedtea-8 "jdk")
14485 (home-page "https://www.rforge.net/rJava/")
14486 (synopsis "Low-Level R to Java interface")
14488 "This package provides a low-level interface to the Java VM very much
14489 like .C/.Call and friends. It allows the creation of objects, calling methods
14490 and accessing fields.")
14491 (license license:gpl2)))
14493 (define-public r-svmisc
14500 (uri (cran-uri "svMisc" version))
14503 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14504 (properties `((upstream-name . "svMisc")))
14505 (build-system r-build-system)
14506 (home-page "https://github.com/SciViews/svMisc")
14507 (synopsis "Miscellaneous functions for SciViews")
14509 "This package provides miscellaneous functions for SciViews or general
14510 use, including tools to manage a temporary environment attached to the search
14511 path for temporary variables you do not want to @code{save()} or
14512 @code{load()}; test the current platform; showing progress bars, etc.")
14513 (license license:gpl2)))
14515 (define-public r-xyz
14522 (uri (cran-uri "xyz" version))
14525 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14526 (build-system r-build-system)
14528 `(("r-rcpp" ,r-rcpp)))
14529 (home-page "https://cran.r-project.org/web/packages/xyz/")
14530 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14532 "High dimensional interaction search by brute force requires a quadratic
14533 computational cost in the number of variables. The xyz algorithm provably
14534 finds strong interactions in almost linear time. For details of the algorithm
14535 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14536 interaction search in high-dimensional data.")
14537 ;; Any version of the GPL.
14538 (license license:gpl2+)))
14540 (define-public r-rttf2pt1
14542 (name "r-rttf2pt1")
14547 (uri (cran-uri "Rttf2pt1" version))
14550 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14551 (properties `((upstream-name . "Rttf2pt1")))
14552 (build-system r-build-system)
14553 (home-page "https://github.com/wch/Rttf2pt1")
14554 (synopsis "Font conversion utility")
14556 "This package contains the program @code{ttf2pt1}, for use with the
14557 @code{extrafont} package.")
14558 ;; Most of the files are covered under the Expat license. Some files are
14559 ;; covered under BSD-3. Deviations for individual files are recorded in
14560 ;; the LICENSE file.
14561 (license (list license:bsd-3 license:expat
14562 (license:non-copyleft "file://LICENSE")))))
14564 (define-public r-extrafontdb
14566 (name "r-extrafontdb")
14571 (uri (cran-uri "extrafontdb" version))
14574 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14575 (build-system r-build-system)
14576 (home-page "https://github.com/wch/extrafontdb")
14577 (synopsis "Database for the extrafont package")
14579 "This package holds the database for the @code{extrafont} package.")
14580 (license license:gpl2)))
14582 (define-public r-extrafont
14584 (name "r-extrafont")
14589 (uri (cran-uri "extrafont" version))
14592 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14593 (build-system r-build-system)
14595 `(("r-extrafontdb" ,r-extrafontdb)
14596 ("r-rttf2pt1" ,r-rttf2pt1)))
14597 (home-page "https://github.com/wch/extrafont")
14598 (synopsis "Tools for using fonts in R")
14600 "The extrafont package makes it easier to use fonts other than the basic
14601 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14602 used with PDF or PostScript output files. There are two hurdles for using
14603 fonts in PDF (or Postscript) output files:
14606 @item Making R aware of the font and the dimensions of the characters.
14607 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14608 properly on a device that doesn't have the font. This is usually needed if
14609 you want to print the PDF file or share it with others.
14612 The extrafont package makes both of these things easier.")
14613 (license license:gpl2)))
14615 (define-public r-xkcd
14622 (uri (cran-uri "xkcd" version))
14625 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14626 (build-system r-build-system)
14628 `(("r-extrafont" ,r-extrafont)
14629 ("r-ggplot2" ,r-ggplot2)
14630 ("r-hmisc" ,r-hmisc)))
14631 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14632 (synopsis "Plot ggplot2 graphics in the XKCD style")
14634 "This package provides the means to plot ggplot2 graphs in the style of
14635 the XKCD web comic.")
14636 (license license:gpl3)))
14638 (define-public r-msigdbr
14645 (uri (cran-uri "msigdbr" version))
14648 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14649 (build-system r-build-system)
14651 `(("r-dplyr" ,r-dplyr)
14652 ("r-magrittr" ,r-magrittr)
14653 ("r-rlang" ,r-rlang)
14654 ("r-tibble" ,r-tibble)))
14656 `(("r-knitr" ,r-knitr)))
14657 (home-page "https://github.com/igordot/msigdbr")
14658 (synopsis "MSigDB gene sets for multiple organisms")
14660 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14661 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14662 software in a standard R data frame with key-value pairs. Included are the
14663 original human gene symbols and Entrez IDs as well as the equivalents for
14664 various frequently studied model organisms such as mouse, rat, pig, fly, and
14666 ;; The package is covered under the Expat license, but the upstream MSigDB
14667 ;; files are made available under the Creative Commons Attribution 4.0
14668 ;; International license.
14669 (license (list license:expat license:cc-by4.0))))
14671 (define-public r-gridgraphics
14673 (name "r-gridgraphics")
14678 (uri (cran-uri "gridGraphics" version))
14681 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14682 (properties `((upstream-name . "gridGraphics")))
14683 (build-system r-build-system)
14684 (home-page "https://github.com/pmur002/gridgraphics")
14685 (synopsis "Redraw base graphics using @code{grid} graphics")
14687 "This package provides functions to convert a page of plots drawn with
14688 the @code{graphics} package into identical output drawn with the @code{grid}
14689 package. The result looks like the original @code{graphics}-based plot, but
14690 consists of @code{grid} grobs and viewports that can then be manipulated with
14691 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14692 (license license:gpl2+)))
14694 (define-public r-farver
14701 (uri (cran-uri "farver" version))
14704 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14705 (build-system r-build-system)
14706 (home-page "https://github.com/thomasp85/farver")
14707 (synopsis "Vectorized color conversion and comparison")
14709 "The encoding of color can be handled in many different ways, using
14710 different color spaces. As different color spaces have different uses,
14711 efficient conversion between these representations are important. This
14712 package provides a set of functions that gives access to very fast color space
14713 conversion and comparisons implemented in C++, and offers 100-fold speed
14714 improvements over the @code{convertColor} function in the @code{grDevices}
14716 (license license:expat)))
14718 (define-public r-ggplotify
14720 (name "r-ggplotify")
14725 (uri (cran-uri "ggplotify" version))
14728 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14729 (build-system r-build-system)
14731 `(("r-ggplot2" ,r-ggplot2)
14732 ("r-gridgraphics" ,r-gridgraphics)
14733 ("r-rvcheck" ,r-rvcheck)))
14735 `(("r-knitr" ,r-knitr)))
14736 (home-page "https://github.com/GuangchuangYu/ggplotify")
14737 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14739 "This package provides tools to convert plot function calls (using
14740 expression or formula) to @code{grob} or @code{ggplot} objects that are
14741 compatible with the @code{grid} and @code{ggplot2} environment. With this
14742 package, we are able to e.g. use @code{cowplot} to align plots produced by
14743 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14744 converting them to @code{ggplot} objects.")
14745 (license license:artistic2.0)))
14747 (define-public r-triebeard
14749 (name "r-triebeard")
14754 (uri (cran-uri "triebeard" version))
14757 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14758 (build-system r-build-system)
14759 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14760 (home-page "https://github.com/Ironholds/triebeard/")
14761 (synopsis "Radix trees in Rcpp")
14763 "Radix trees, or tries, are key-value data structures optimized for
14764 efficient lookups, similar in purpose to hash tables. This package provides
14765 an implementation of radix trees for use in R programming and in developing
14766 packages with Rcpp.")
14767 (license license:expat)))
14769 (define-public r-tweenr
14776 (uri (cran-uri "tweenr" version))
14779 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14780 (build-system r-build-system)
14782 `(("r-farver" ,r-farver)
14783 ("r-magrittr" ,r-magrittr)
14785 ("r-rlang" ,r-rlang)))
14786 (home-page "https://github.com/thomasp85/tweenr")
14787 (synopsis "Interpolate data for smooth animations")
14789 "In order to create smooth animation between states of data, tweening is
14790 necessary. This package provides a range of functions for creating tweened
14791 data that can be used as basis for animation. Furthermore it adds a number of
14792 vectorized interpolaters for common R data types such as numeric, date and
14794 (license license:expat)))
14796 (define-public r-polyclip
14798 (name "r-polyclip")
14803 (uri (cran-uri "polyclip" version))
14806 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14807 (build-system r-build-system)
14808 (native-inputs `(("pkg-config" ,pkg-config)))
14809 (home-page "http://www.angusj.com/delphi/clipper.php")
14810 (synopsis "Polygon clipping")
14812 "This package provides an R port of the library Clipper. It performs
14813 polygon clipping operations (intersection, union, set minus, set difference)
14814 for polygonal regions of arbitrary complexity, including holes. It computes
14815 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14816 dilations) for polygonal regions and polygonal lines. It computes the
14817 Minkowski Sum of general polygons. There is a function for removing
14818 self-intersections from polygon data.")
14819 (license license:boost1.0)))
14821 (define-public r-urltools
14823 (name "r-urltools")
14828 (uri (cran-uri "urltools" version))
14831 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14832 (build-system r-build-system)
14834 `(("r-rcpp" ,r-rcpp)
14835 ("r-triebeard" ,r-triebeard)))
14836 (home-page "https://github.com/Ironholds/urltools/")
14837 (synopsis "Vectorized tools for URL handling and parsing")
14839 "This package provides a toolkit for all URL-handling needs, including
14840 encoding and decoding, parsing, parameter extraction and modification. All
14841 functions are designed to be both fast and entirely vectorized. It is
14842 intended to be useful for people dealing with web-related datasets, such as
14843 server-side logs, although may be useful for other situations involving large
14845 (license license:expat)))
14847 (define-public r-ggforce
14854 (uri (cran-uri "ggforce" version))
14857 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
14858 (build-system r-build-system)
14860 `(("r-ggplot2" ,r-ggplot2)
14861 ("r-gtable" ,r-gtable)
14863 ("r-polyclip" ,r-polyclip)
14865 ("r-rcppeigen" ,r-rcppeigen)
14866 ("r-rlang" ,r-rlang)
14867 ("r-scales" ,r-scales)
14868 ("r-tidyselect" ,r-tidyselect)
14869 ("r-tweenr" ,r-tweenr)
14870 ("r-withr" ,r-withr)))
14871 (home-page "https://ggforce.data-imaginist.com")
14872 (synopsis "Accelerating ggplot2")
14874 "The aim of the ggplot2 package is to aid in visual data investigations.
14875 This focus has led to a lack of facilities for composing specialized plots.
14876 Thi package aims to be a collection of mainly new statistics and geometries
14877 that fills this gap.")
14878 (license license:expat)))
14880 (define-public r-europepmc
14882 (name "r-europepmc")
14887 (uri (cran-uri "europepmc" version))
14890 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14891 (build-system r-build-system)
14893 `(("r-dplyr" ,r-dplyr)
14895 ("r-jsonlite" ,r-jsonlite)
14897 ("r-progress" ,r-progress)
14898 ("r-purrr" ,r-purrr)
14899 ("r-rlang" ,r-rlang)
14900 ("r-tibble" ,r-tibble)
14901 ("r-tidyr" ,r-tidyr)
14902 ("r-urltools" ,r-urltools)
14903 ("r-xml2" ,r-xml2)))
14905 `(("r-knitr" ,r-knitr)))
14906 (home-page "https://github.com/ropensci/europepmc/")
14907 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14909 "This package provides an R Client for the
14910 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14911 Service}. It gives access to both metadata on life science literature and
14912 open access full texts. Europe PMC indexes all PubMed content and other
14913 literature sources including Agricola, a bibliographic database of citations
14914 to the agricultural literature, or Biological Patents. In addition to
14915 bibliographic metadata, the client allows users to fetch citations and
14916 reference lists. Links between life-science literature and other EBI
14917 databases, including ENA, PDB or ChEMBL are also accessible.")
14918 (license license:gpl3)))
14920 (define-public r-ggraph
14927 (uri (cran-uri "ggraph" version))
14930 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14931 (build-system r-build-system)
14933 `(("r-digest" ,r-digest)
14934 ("r-dplyr" ,r-dplyr)
14935 ("r-ggforce" ,r-ggforce)
14936 ("r-ggplot2" ,r-ggplot2)
14937 ("r-ggrepel" ,r-ggrepel)
14938 ("r-graphlayouts" ,r-graphlayouts)
14939 ("r-gtable" ,r-gtable)
14940 ("r-igraph" ,r-igraph)
14943 ("r-rlang" ,r-rlang)
14944 ("r-scales" ,r-scales)
14945 ("r-tidygraph" ,r-tidygraph)
14946 ("r-viridis" ,r-viridis)))
14948 `(("r-knitr" ,r-knitr)))
14949 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14950 (synopsis "Implementation of grammar of graphics for graphs and networks")
14952 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14953 graph and network visualizations due to its reliance on tabular data input.
14954 The ggraph package is an extension of the ggplot2 API tailored to graph
14955 visualizations and provides the same flexible approach to building up plots
14957 (license license:gpl3)))
14959 (define-public r-varselrf
14961 (name "r-varselrf")
14966 (uri (cran-uri "varSelRF" version))
14969 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14970 (properties `((upstream-name . "varSelRF")))
14971 (build-system r-build-system)
14973 `(("r-randomforest" ,r-randomforest)))
14974 (home-page "https://www.ligarto.org/rdiaz/software/software")
14975 (synopsis "Variable selection using random forests")
14977 "This package provides tools for the variable selection from random
14978 forests using both backwards variable elimination (for the selection of small
14979 sets of non-redundant variables) and selection based on the importance
14980 spectrum (somewhat similar to scree plots; for the selection of large,
14981 potentially highly-correlated variables). The main applications are in
14982 high-dimensional data (e.g., microarray data, and other genomics and
14983 proteomics applications).")
14984 (license license:gpl2+)))
14986 (define-public r-pamr
14993 (uri (cran-uri "pamr" version))
14996 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14997 (build-system r-build-system)
14999 `(("r-cluster" ,r-cluster)
15000 ("r-survival" ,r-survival)))
15001 (native-inputs `(("gfortran" ,gfortran)))
15002 (home-page "https://cran.r-project.org/web/packages/pamr/")
15003 (synopsis "Prediction Analysis for Microarrays")
15005 "This package provides some functions for sample classification in
15007 (license license:gpl2)))
15009 (define-public r-rda
15012 (version "1.0.2-2.1")
15016 (uri (cran-uri "rda" version))
15019 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15020 (build-system r-build-system)
15021 (home-page "https://cran.r-project.org/web/packages/rda/")
15022 (synopsis "Shrunken centroids regularized discriminant analysis")
15024 "This package provides tools for shrunken centroids regularized
15025 discriminant analysis for the purpose of classifying high dimensional data.")
15026 (license license:gpl2+)))
15028 (define-public r-ggvis
15035 (uri (cran-uri "ggvis" version))
15038 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15039 (build-system r-build-system)
15041 `(("r-assertthat" ,r-assertthat)
15042 ("r-dplyr" ,r-dplyr)
15043 ("r-htmltools" ,r-htmltools)
15044 ("r-jsonlite" ,r-jsonlite)
15045 ("r-lazyeval" ,r-lazyeval)
15046 ("r-magrittr" ,r-magrittr)
15047 ("r-shiny" ,r-shiny)))
15048 (home-page "https://ggvis.rstudio.com/")
15049 (synopsis "Interactive grammar of graphics")
15051 "This package is a data visualization package for R providing an
15052 implementation of an interactive grammar of graphics, taking the best parts of
15053 ggplot2, combining them with the reactive framework of Shiny and drawing web
15054 graphics using Vega.")
15055 (license license:gpl2)))
15057 (define-public r-gbm
15064 (uri (cran-uri "gbm" version))
15067 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15068 (build-system r-build-system)
15070 `(("r-lattice" ,r-lattice)
15071 ("r-survival" ,r-survival)))
15073 `(("r-knitr" ,r-knitr)))
15074 (home-page "https://github.com/gbm-developers/gbm")
15075 (synopsis "Generalized boosted regression models")
15077 "This package is an implementation of extensions to Freund and Schapire's
15078 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15079 regression methods for least squares, absolute loss, t-distribution loss,
15080 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15081 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15082 and Learning to Rank measures (LambdaMart).")
15083 (license license:gpl2+)))
15085 (define-public r-threejs
15092 (uri (cran-uri "threejs" version))
15095 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15096 (build-system r-build-system)
15098 `(#:modules ((guix build utils)
15099 (guix build r-build-system)
15103 (modify-phases %standard-phases
15104 (add-after 'unpack 'process-javascript
15105 (lambda* (#:key inputs #:allow-other-keys)
15106 (with-directory-excursion "inst"
15110 `((,(assoc-ref inputs "js-jquery")
15111 "htmlwidgets/lib/jquery/jquery.min.js")
15112 (,(assoc-ref inputs "js-threejs-111")
15113 "htmlwidgets/lib/threejs-111/three.min.js"))))
15114 (lambda (sources targets)
15115 (for-each (lambda (source target)
15116 (format #t "Processing ~a --> ~a~%"
15118 (delete-file target)
15119 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15120 (call-with-output-file target
15122 (dump-port minified port)))))
15123 sources targets))))
15126 `(("r-base64enc" ,r-base64enc)
15127 ("r-crosstalk" ,r-crosstalk)
15128 ("r-htmlwidgets" ,r-htmlwidgets)
15129 ("r-igraph" ,r-igraph)))
15131 `(("uglify-js" ,uglify-js)
15135 (uri "https://code.jquery.com/jquery-1.12.4.js")
15138 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15142 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15145 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15146 (home-page "https://bwlewis.github.io/rthreejs")
15147 (synopsis "Interactive 3D scatter plots, networks and globes")
15149 "Create interactive 3D scatter plots, network plots, and globes in R
15150 using the three.js visualization library.")
15151 (license license:expat)))
15153 (define-public r-mlbench
15160 (uri (cran-uri "mlbench" version))
15163 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15164 (build-system r-build-system)
15165 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15166 (synopsis "Machine learning benchmark problems")
15168 "This package provides a collection of artificial and real-world machine
15169 learning benchmark problems, including, e.g., several data sets from the UCI
15171 (license license:gpl2)))
15173 (define-public r-mpm
15180 (uri (cran-uri "mpm" version))
15183 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15184 (build-system r-build-system)
15186 `(("r-kernsmooth" ,r-kernsmooth)
15187 ("r-mass" ,r-mass)))
15188 (home-page "http://mpm.r-forge.r-project.org")
15189 (synopsis "Multivariate projection methods")
15191 "This is a package for exploratory graphical analysis of multivariate
15192 data, specifically gene expression data with different projection methods:
15193 principal component analysis, correspondence analysis, spectral map
15195 (license license:gpl2+)))
15197 (define-public r-png
15203 (uri (cran-uri "png" version))
15206 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15207 (build-system r-build-system)
15209 `(("libpng" ,libpng)
15211 (home-page "https://www.rforge.net/png/")
15212 (synopsis "Read and write PNG images")
15214 "This package provides an easy and simple way to read, write and display
15215 bitmap images stored in the PNG format. It can read and write both files and
15216 in-memory raw vectors.")
15217 ;; Any of these GPL versions.
15218 (license (list license:gpl2 license:gpl3))))
15220 (define-public r-ggcorrplot
15222 (name "r-ggcorrplot")
15227 (uri (cran-uri "ggcorrplot" version))
15230 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15231 (build-system r-build-system)
15233 `(("r-ggplot2" ,r-ggplot2)
15234 ("r-reshape2" ,r-reshape2)))
15235 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15236 (synopsis "Visualization of a correlation matrix using ggplot2")
15238 "The ggcorrplot package can be used to visualize easily a correlation
15239 matrix using ggplot2. It provides a solution for reordering the correlation
15240 matrix and displays the significance level on the plot. It also includes a
15241 function for computing a matrix of correlation p-values.")
15242 (license license:gpl2)))
15244 ;; This package includes minified JavaScript files. When upgrading please
15245 ;; check that there are no new minified JavaScript files.
15246 (define-public r-flexdashboard
15248 (name "r-flexdashboard")
15253 (uri (cran-uri "flexdashboard" version))
15256 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15257 (modules '((guix build utils)))
15260 ;; Delete bundled minified JavaScript files
15261 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15262 (delete-file "inst/www/sly/sly.min.js")
15263 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15264 (delete-file "inst/www/prism/prism.js")
15266 (build-system r-build-system)
15268 `(#:modules ((guix build utils)
15269 (guix build r-build-system)
15273 (ice-9 textual-ports))
15275 (modify-phases %standard-phases
15276 (add-after 'unpack 'process-javascript
15277 (lambda* (#:key inputs #:allow-other-keys)
15278 (with-directory-excursion "inst"
15279 ;; Concatenate all components of prism.js
15280 (let ((contents (string-join
15281 (map (lambda (name)
15282 (call-with-input-file
15283 (assoc-ref inputs name)
15287 "js-prism-line-numbers"))
15289 (call-with-output-file "prism-src.js"
15290 (cut display contents <>)))
15294 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15295 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15297 "www/sly/sly.min.js")
15299 "www/prism/prism.js")
15300 (,(assoc-ref inputs "js-raphael")
15301 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15302 (,(assoc-ref inputs "js-featherlight")
15303 "www/featherlight/featherlight.min.js"))))
15304 (lambda (sources targets)
15305 (for-each (lambda (source target)
15306 (format #t "Processing ~a --> ~a~%"
15308 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15309 (call-with-output-file target
15311 (dump-port minified port)))))
15312 sources targets))))
15315 `(("r-htmltools" ,r-htmltools)
15316 ("r-htmlwidgets" ,r-htmlwidgets)
15317 ("r-jsonlite" ,r-jsonlite)
15318 ("r-knitr" ,r-knitr)
15319 ("r-rmarkdown" ,r-rmarkdown)
15320 ("r-shiny" ,r-shiny)))
15322 `(("uglify-js" ,uglify-js)
15326 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15329 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15333 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15336 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15340 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15343 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15344 ("js-prism-line-numbers"
15347 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15350 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15354 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15357 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15358 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15359 (synopsis "R Markdown format for flexible dashboards")
15361 "This package provides an R Markdown format for converting an R Markdown
15362 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15363 of its components to the containing web page.")
15364 (license license:expat)))
15366 (define-public r-preseqr
15373 (uri (cran-uri "preseqR" version))
15376 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15377 (properties `((upstream-name . "preseqR")))
15378 (build-system r-build-system)
15380 `(("r-polynom" ,r-polynom)))
15381 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15382 (synopsis "Predicting species accumulation curves")
15384 "This package can be used to predict the r-species accumulation
15385 curve (r-SAC), which is the number of species represented at least r times as
15386 a function of the sampling effort. When r = 1, the curve is known as the
15387 species accumulation curve, or the library complexity curve in high-throughput
15388 genomic sequencing. The package includes both parametric and nonparametric
15389 methods, as described by Deng C, et al. (2018).")
15390 (license license:gpl3)))
15392 (define-public r-mapplots
15394 (name "r-mapplots")
15399 (uri (cran-uri "mapplots" version))
15402 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15403 (build-system r-build-system)
15404 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15405 (synopsis "Data visualization on maps")
15407 "This package helps you create simple maps; add sub-plots like pie plots
15408 to a map or any other plot; format, plot and export gridded data. The package
15409 was developed for displaying fisheries data but most functions can be used for
15410 more generic data visualisation.")
15411 (license license:gpl2+)))
15413 (define-public r-pmcmr
15420 (uri (cran-uri "PMCMR" version))
15423 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15424 (properties `((upstream-name . "PMCMR")))
15425 (build-system r-build-system)
15426 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15427 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15429 "This is a deprecated package for calculating pairwise multiple
15430 comparisons of mean rank sums. This package is superseded by the novel
15431 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15432 compatibility of dependent packages for some time.")
15433 (license license:gpl3+)))
15435 (define-public r-downloader
15437 (name "r-downloader")
15442 (uri (cran-uri "downloader" version))
15445 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15446 (build-system r-build-system)
15448 `(("r-digest" ,r-digest)))
15449 (home-page "https://github.com/wch/downloader")
15450 (synopsis "Download files over HTTP and HTTPS")
15452 "This package provides a wrapper for the @code{download.file} function,
15453 making it possible to download files over HTTPS across platforms. The
15454 @code{RCurl} package provides this functionality (and much more) but has
15455 external dependencies. This package has is implemented purely in R.")
15456 (license license:gpl2)))
15458 (define-public r-rex
15465 (uri (cran-uri "rex" version))
15468 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15469 (build-system r-build-system)
15471 `(("r-lazyeval" ,r-lazyeval)))
15473 `(("r-knitr" ,r-knitr)))
15474 (home-page "https://github.com/kevinushey/rex")
15475 (synopsis "Friendly regular expressions")
15477 "This package provides a friendly interface for the construction of
15478 regular expressions. Regular expressions are a very powerful feature, however
15479 they are often difficult to interpret. Rex allows you to build complex
15480 regular expressions from human readable expressions")
15481 (license license:expat)))
15483 (define-public r-xmlparsedata
15485 (name "r-xmlparsedata")
15490 (uri (cran-uri "xmlparsedata" version))
15493 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15494 (properties `((upstream-name . "xmlparsedata")))
15495 (build-system r-build-system)
15496 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15497 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15499 "This package provides tools to convert the output of
15500 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15501 @code{XPath}, and is easier to manipulate in general.")
15502 (license license:expat)))
15504 (define-public r-cyclocomp
15506 (name "r-cyclocomp")
15511 (uri (cran-uri "cyclocomp" version))
15514 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15515 (properties `((upstream-name . "cyclocomp")))
15516 (build-system r-build-system)
15518 `(("r-callr" ,r-callr)
15519 ("r-crayon" ,r-crayon)
15521 ("r-remotes" ,r-remotes)
15522 ("r-withr" ,r-withr)))
15523 (home-page "https://github.com/MangoTheCat/cyclocomp")
15524 (synopsis "Cyclomatic complexity of R code")
15526 "Cyclomatic complexity is a software metric, used to indicate the
15527 complexity of a program. It is a quantitative measure of the number of
15528 linearly independent paths through a program's source code. This package
15529 provides tools to compute this metric.")
15530 (license license:expat)))
15532 (define-public r-lintr
15539 (uri (cran-uri "lintr" version))
15542 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15543 (properties `((upstream-name . "lintr")))
15544 (build-system r-build-system)
15546 `(("r-codetools" ,r-codetools)
15547 ("r-crayon" ,r-crayon)
15548 ("r-cyclocomp" ,r-cyclocomp)
15549 ("r-digest" ,r-digest)
15551 ("r-jsonlite" ,r-jsonlite)
15552 ("r-knitr" ,r-knitr)
15554 ("r-rstudioapi" ,r-rstudioapi)
15555 ("r-testthat" ,r-testthat)
15557 ("r-xmlparsedata" ,r-xmlparsedata)))
15558 (home-page "https://github.com/jimhester/lintr")
15559 (synopsis "Linter for R code")
15560 (description "This package checks adherence to a given style, syntax
15561 errors and possible semantic issues. It supports on the fly checking of R
15562 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15563 (license license:expat)))
15565 (define-public r-sctransform
15567 (name "r-sctransform")
15572 (uri (cran-uri "sctransform" version))
15575 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15576 (build-system r-build-system)
15578 `(("r-future-apply" ,r-future-apply)
15579 ("r-ggplot2" ,r-ggplot2)
15580 ("r-gridextra" ,r-gridextra)
15582 ("r-matrix" ,r-matrix)
15584 ("r-rcppeigen" ,r-rcppeigen)
15585 ("r-reshape2" ,r-reshape2)))
15586 (home-page "https://github.com/ChristophH/sctransform")
15587 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15589 "This package provides a normalization method for single-cell UMI count
15590 data using a variance stabilizing transformation. The transformation is based
15591 on a negative binomial regression model with regularized parameters. As part
15592 of the same regression framework, this package also provides functions for
15593 batch correction, and data correction.")
15594 (license license:gpl3)))
15596 (define-public r-styler
15603 (uri (cran-uri "styler" version))
15606 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15607 (build-system r-build-system)
15609 `(("r-backports" ,r-backports)
15611 ("r-magrittr" ,r-magrittr)
15612 ("r-purrr" ,r-purrr)
15613 ("r-r-cache" ,r-r-cache)
15614 ("r-rematch2" ,r-rematch2)
15615 ("r-rlang" ,r-rlang)
15616 ("r-rprojroot" ,r-rprojroot)
15617 ("r-tibble" ,r-tibble)
15618 ("r-withr" ,r-withr)
15619 ("r-xfun" ,r-xfun)))
15620 (home-page "https://github.com/r-lib/styler")
15621 (synopsis "Non-invasive pretty printing of R code")
15623 "This is a package for pretty-printing R code without changing the user's
15624 formatting intent.")
15625 (license license:gpl3)))
15627 (define-public r-scrime
15634 (uri (cran-uri "scrime" version))
15637 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15638 (build-system r-build-system)
15639 (home-page "https://cran.r-project.org/web/packages/scrime/")
15640 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15642 "This package provides tools for the analysis of high-dimensional data
15643 developed/implemented at the group \"Statistical Complexity Reduction In
15644 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15645 the functions can also be applied to other types of categorical data.")
15646 (license license:gpl2)))
15648 (define-public r-pbmcapply
15650 (name "r-pbmcapply")
15655 (uri (cran-uri "pbmcapply" version))
15658 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15659 (build-system r-build-system)
15660 (home-page "https://github.com/kvnkuang/pbmcapply")
15661 (synopsis "Track the progress of apply procedures with a progress bar")
15663 "This light-weight package helps you track and visualize the progress of
15664 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15665 (license license:expat)))
15667 (define-public r-blme
15674 (uri (cran-uri "blme" version))
15677 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15678 (build-system r-build-system)
15679 (propagated-inputs `(("r-lme4" ,r-lme4)))
15680 (home-page "https://github.com/vdorie/blme")
15681 (synopsis "Bayesian linear mixed-effects models")
15683 "This package provides tools for maximum a posteriori estimation for
15684 linear and generalized linear mixed-effects models in a Bayesian setting. It
15685 extends the lme4 package.")
15686 (license license:gpl2+)))
15688 (define-public r-batchtools
15690 (name "r-batchtools")
15695 (uri (cran-uri "batchtools" version))
15698 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15699 (build-system r-build-system)
15701 `(("r-backports" ,r-backports)
15702 ("r-base64url" ,r-base64url)
15704 ("r-checkmate" ,r-checkmate)
15705 ("r-data-table" ,r-data-table)
15706 ("r-digest" ,r-digest)
15708 ("r-progress" ,r-progress)
15710 ("r-rappdirs" ,r-rappdirs)
15711 ("r-stringi" ,r-stringi)
15712 ("r-withr" ,r-withr)))
15714 `(("r-knitr" ,r-knitr)))
15715 (home-page "https://github.com/mllg/batchtools")
15716 (synopsis "Tools for computation on batch systems")
15718 "As a successor of the packages BatchJobs and BatchExperiments, this
15719 package provides a parallel implementation of the Map function for high
15720 performance computing systems managed by various schedulers. A multicore and
15721 socket mode allow the parallelization on a local machines, and multiple
15722 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15723 the package provides an abstraction mechanism to define large-scale computer
15724 experiments in a well-organized and reproducible way.")
15725 (license license:lgpl3)))
15727 (define-public r-clue
15734 (uri (cran-uri "clue" version))
15737 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15738 (build-system r-build-system)
15739 (propagated-inputs `(("r-cluster" ,r-cluster)))
15740 (home-page "https://cran.r-project.org/web/packages/clue/")
15741 (synopsis "Tools for analyzing cluster ensembles")
15742 (description "Cluster ensembles are collections of individual solutions to
15743 a given clustering problem which are useful or necessary to consider in a wide
15744 range of applications. This R package provides an extensible computational
15745 environment for creating and analyzing cluster ensembles, with basic data
15746 structures for representing partitions and hierarchies, and facilities for
15747 computing on them, including methods for measuring proximity and obtaining
15748 consensus and secondary clusterings.")
15749 (license license:gpl2)))
15751 (define-public r-sitmo
15758 (uri (cran-uri "sitmo" version))
15761 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15762 (build-system r-build-system)
15763 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15764 (home-page "https://github.com/coatless/sitmo/")
15765 (synopsis "Parallel pseudo random number generator header files")
15767 "This package provides two high quality and fast PPRNGs that may be used
15768 in an OpenMP parallel environment. In addition, there is a generator for one
15769 dimensional low-discrepancy sequence.")
15770 (license license:expat)))
15772 (define-public r-dqrng
15779 (uri (cran-uri "dqrng" version))
15782 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15783 (build-system r-build-system)
15787 ("r-sitmo" ,r-sitmo)))
15788 (home-page "https://www.daqana.org/dqrng")
15789 (synopsis "Fast pseudo random number generators")
15791 "Several fast random number generators are provided as C++ header-only
15792 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15793 Additionally, fast functions for generating random numbers according to a
15794 uniform, normal and exponential distribution are included. The latter two use
15795 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15796 functions are exported to R and as a C++ interface and are enabled for use
15797 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15798 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15799 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15800 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15801 ;; whole is distributed under the terms of the AGPL 3.
15802 (license license:agpl3)))
15804 (define-public r-ingredients
15806 (name "r-ingredients")
15811 (uri (cran-uri "ingredients" version))
15814 "0l0dqrm9am6wk8jcf8cdhc6xnrna9cqr5wz6lsnczq2gf6ybhjg1"))))
15815 (properties `((upstream-name . "ingredients")))
15816 (build-system r-build-system)
15818 `(("r-ggplot2" ,r-ggplot2)
15819 ("r-gridextra" ,r-gridextra)
15820 ("r-scales" ,r-scales)))
15821 (native-inputs `(("r-knitr" ,r-knitr)))
15822 (home-page "https://ModelOriented.github.io/ingredients/")
15823 (synopsis "Effects and importances of model ingredients")
15825 "This is a collection of tools for assessment of feature importance and
15826 feature effects. Key functions are:
15829 @item @code{feature_importance()} for assessment of global level feature
15831 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15832 @item @code{partial_dependence()} for partial dependence plots,
15833 @item @code{conditional_dependence()} for conditional dependence plots,
15834 @item @code{accumulated_dependence()} for accumulated local effects plots,
15835 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15836 aggregation of ceteris paribus profiles,
15837 @item generic @code{print()} and @code{plot()} for better usability of
15838 selected explainers,
15839 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15840 @item generic @code{describe()} for explanations in natural language.
15842 (license license:gpl3)))
15844 (define-public r-ibreakdown
15846 (name "r-ibreakdown")
15851 (uri (cran-uri "iBreakDown" version))
15854 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
15855 (properties `((upstream-name . "iBreakDown")))
15856 (build-system r-build-system)
15857 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15858 (native-inputs `(("r-knitr" ,r-knitr)))
15859 (home-page "https://ModelOriented.github.io/iBreakDown/")
15860 (synopsis "Model agnostic instance level variable attributions")
15862 "This package provides a model agnostic tool for decomposition of
15863 predictions from black boxes. It supports additive attributions and
15864 attributions with interactions. The Break Down Table shows contributions of
15865 every variable to a final prediction. The Break Down Plot presents variable
15866 contributions in a concise graphical way. This package works for
15867 classification and regression models.")
15868 (license license:gpl3)))
15870 (define-public r-dae
15877 (uri (cran-uri "dae" version))
15880 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
15881 (build-system r-build-system)
15883 `(("r-ggplot2" ,r-ggplot2)
15884 ("r-plyr" ,r-plyr)))
15886 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
15887 (home-page "http://chris.brien.name")
15888 (synopsis "Functions useful in the design and ANOVA of experiments")
15890 "This package provides functions useful in the design and ANOVA of
15891 experiments. The content falls into the following groupings:
15895 @item factor manipulation functions,
15896 @item design functions,
15897 @item ANOVA functions,
15898 @item matrix functions,
15899 @item projector and canonical efficiency functions, and
15900 @item miscellaneous functions.
15903 There is a vignette called @code{DesignNotes} describing how to use the design
15904 functions for randomizing and assessing designs. The ANOVA functions
15905 facilitate the extraction of information when the @code{Error} function has
15906 been used in the call to @code{aov}.")
15907 (license license:gpl2)))
15909 (define-public r-dalex
15912 (version "1.3.1.1")
15916 (uri (cran-uri "DALEX" version))
15919 "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
15920 (properties `((upstream-name . "DALEX")))
15921 (build-system r-build-system)
15923 `(("r-ggplot2" ,r-ggplot2)
15924 ("r-ibreakdown" ,r-ibreakdown)
15925 ("r-ingredients" ,r-ingredients)))
15926 (home-page "https://pbiecek.github.io/DALEX/")
15927 (synopsis "Descriptive machine learning explanations")
15929 "Machine Learning models are widely used and have various applications in
15930 classification or regression. Models created with boosting, bagging, stacking
15931 or similar techniques are often used due to their high performance, but such
15932 black-box models usually lack interpretability. The DALEX package contains
15933 various explainers that help to understand the link between input variables
15934 and model output.")
15935 ;; Any version of the GPL
15936 (license license:gpl3+)))
15938 (define-public r-enrichr
15945 (uri (cran-uri "enrichR" version))
15948 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15949 (properties `((upstream-name . "enrichR")))
15950 (build-system r-build-system)
15952 `(("r-httr" ,r-httr)
15953 ("r-rjson" ,r-rjson)))
15954 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15955 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15957 "This package provides an R interface to all Enrichr databases, a
15958 web-based tool for analyzing gene sets and returns any enrichment of common
15959 annotated biological functions.")
15960 (license license:gpl2+)))
15962 (define-public r-plot3d
15969 (uri (cran-uri "plot3D" version))
15972 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15973 (properties `((upstream-name . "plot3D")))
15974 (build-system r-build-system)
15975 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15976 (home-page "https://cran.r-project.org/web/packages/plot3D")
15977 (synopsis "Plot multi-dimensional data")
15979 "This package provides functions for viewing 2D and 3D data, including
15980 perspective plots, slice plots, surface plots, scatter plots, etc. It
15981 includes data sets from oceanography.")
15982 (license license:gpl3+)))
15984 (define-public r-ggfortify
15986 (name "r-ggfortify")
15991 (uri (cran-uri "ggfortify" version))
15994 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15995 (build-system r-build-system)
15997 `(("r-dplyr" ,r-dplyr)
15998 ("r-ggplot2" ,r-ggplot2)
15999 ("r-gridextra" ,r-gridextra)
16000 ("r-scales" ,r-scales)
16001 ("r-stringr" ,r-stringr)
16002 ("r-tibble" ,r-tibble)
16003 ("r-tidyr" ,r-tidyr)))
16005 `(("r-knitr" ,r-knitr)))
16006 (home-page "https://github.com/sinhrks/ggfortify")
16007 (synopsis "Data visualization tools for statistical analysis results")
16009 "This package provides unified plotting tools for statistics commonly
16010 used, such as GLM, time series, PCA families, clustering and survival
16011 analysis. The package offers a single plotting interface for these analysis
16012 results and plots in a unified style using the @code{ggplot2} package.")
16013 (license license:gpl2)))
16015 (define-public r-refmanager
16017 (name "r-refmanager")
16022 (uri (cran-uri "RefManageR" version))
16025 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16026 (properties `((upstream-name . "RefManageR")))
16027 (build-system r-build-system)
16029 `(("r-bibtex" ,r-bibtex)
16031 ("r-jsonlite" ,r-jsonlite)
16032 ("r-lubridate" ,r-lubridate)
16034 ("r-stringr" ,r-stringr)
16035 ("r-xml2" ,r-xml2)))
16036 (home-page "https://github.com/ropensci/RefManageR/")
16037 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16039 "This package provides tools for importing and working with bibliographic
16040 references. It greatly enhances the @code{bibentry} class by providing a
16041 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16042 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16043 by various formats for name lists (author by last names, translator by full
16044 names, etc.). Entries can be updated, combined, sorted, printed in a number
16045 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16046 into R and converted to @code{BibEntry} objects.")
16047 ;; Any of these licenses may be picked.
16048 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16050 (define-public r-citr
16057 (uri (cran-uri "citr" version))
16060 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16061 (build-system r-build-system)
16063 `(("r-assertthat" ,r-assertthat)
16066 ("r-miniui" ,r-miniui)
16067 ("r-refmanager" ,r-refmanager)
16068 ("r-rstudioapi" ,r-rstudioapi)
16069 ("r-shiny" ,r-shiny)
16070 ("r-shinyjs" ,r-shinyjs)
16071 ("r-yaml" ,r-yaml)))
16072 (home-page "https://github.com/crsh/citr")
16073 (synopsis "RStudio add-in to insert Markdown citations")
16075 "This package provides functions and an RStudio add-in that search a
16076 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16077 the current document.")
16078 (license license:expat)))
16080 (define-public r-xgboost
16083 (version "1.1.1.1")
16087 (uri (cran-uri "xgboost" version))
16090 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
16091 (build-system r-build-system)
16093 `(("r-data-table" ,r-data-table)
16094 ("r-magrittr" ,r-magrittr)
16095 ("r-matrix" ,r-matrix)
16096 ("r-stringi" ,r-stringi)))
16098 `(("r-knitr" ,r-knitr)))
16099 (home-page "https://github.com/dmlc/xgboost")
16100 (synopsis "Extreme gradient boosting")
16102 "This package provides an R interface to Extreme Gradient Boosting, which
16103 is an efficient implementation of the gradient boosting framework from Chen
16104 and Guestrin (2016). The package includes efficient linear model solver and
16105 tree learning algorithms. The package can automatically do parallel
16106 computation on a single machine. It supports various objective functions,
16107 including regression, classification and ranking. The package is made to be
16108 extensible, so that users are also allowed to define their own objectives
16110 (license license:asl2.0)))
16112 (define-public r-umap
16115 (version "0.2.6.0")
16119 (uri (cran-uri "umap" version))
16122 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16123 (build-system r-build-system)
16125 `(("r-openssl" ,r-openssl)
16127 ("r-reticulate" ,r-reticulate)
16128 ("r-rspectra" ,r-rspectra)))
16130 `(("r-knitr" ,r-knitr)))
16131 (home-page "https://github.com/tkonopka/umap")
16132 (synopsis "Uniform manifold approximation and projection")
16134 "Uniform manifold approximation and projection is a technique for
16135 dimension reduction. This package provides an interface to the UMAP algorithm
16136 in R, including a translation of the original algorithm into R.")
16137 (license license:expat)))
16139 (define-public r-uwot
16146 (uri (cran-uri "uwot" version))
16149 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16150 (build-system r-build-system)
16152 `(("r-dqrng" ,r-dqrng)
16154 ("r-irlba" ,r-irlba)
16155 ("r-matrix" ,r-matrix)
16157 ("r-rcppannoy" ,r-rcppannoy)
16158 ("r-rcppprogress" ,r-rcppprogress)
16159 ("r-rspectra" ,r-rspectra)))
16160 (home-page "https://github.com/jlmelville/uwot")
16161 (synopsis "Uniform manifold approximation and projection")
16163 "This package provides an implementation of the Uniform Manifold
16164 Approximation and Projection dimensionality reduction by McInnes et
16165 al. (2018). It also provides means to transform new data and to carry out
16166 supervised dimensionality reduction. An implementation of the related
16167 LargeVis method of Tang et al. (2016) is also provided.")
16168 (license license:gpl3)))
16170 (define-public r-kableextra
16172 (name "r-kableextra")
16177 (uri (cran-uri "kableExtra" version))
16180 "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
16181 (properties `((upstream-name . "kableExtra")))
16182 (build-system r-build-system)
16184 `(("r-digest" ,r-digest)
16186 ("r-htmltools" ,r-htmltools)
16187 ("r-knitr" ,r-knitr)
16188 ("r-magrittr" ,r-magrittr)
16189 ("r-rmarkdown" ,r-rmarkdown)
16190 ("r-rstudioapi" ,r-rstudioapi)
16191 ("r-rvest" ,r-rvest)
16192 ("r-scales" ,r-scales)
16193 ("r-stringr" ,r-stringr)
16194 ("r-viridislite" ,r-viridislite)
16195 ("r-webshot" ,r-webshot)
16196 ("r-xml2" ,r-xml2)))
16198 `(("r-knitr" ,r-knitr)))
16199 (home-page "https://haozhu233.github.io/kableExtra/")
16200 (synopsis "Construct complex tables with pipe syntax")
16202 "Build complex HTML or LaTeX tables using @code{kable()} from
16203 @code{knitr} and the piping syntax from @code{magrittr}. The function
16204 @code{kable()} is a light weight table generator coming from @code{knitr}.
16205 This package simplifies the way to manipulate the HTML or LaTeX codes
16206 generated by @code{kable()} and allows users to construct complex tables and
16207 customize styles using a readable syntax.")
16208 (license license:expat)))
16210 (define-public r-glasso
16217 (uri (cran-uri "glasso" version))
16219 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16220 (build-system r-build-system)
16221 (native-inputs `(("gfortran" ,gfortran)))
16222 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16223 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16225 "This is a package for estimation of a sparse inverse covariance matrix
16226 using a lasso (L1) penalty. Facilities are provided for estimates along a
16227 path of values for the regularization parameter.")
16228 (license license:gpl2)))
16230 (define-public r-rhpcblasctl
16232 (name "r-rhpcblasctl")
16233 (version "0.20-137")
16237 (uri (cran-uri "RhpcBLASctl" version))
16240 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16241 (properties `((upstream-name . "RhpcBLASctl")))
16242 (build-system r-build-system)
16243 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16244 (synopsis "Control the number of threads on BLAS")
16246 "This package allows you to control the number of threads the BLAS
16247 library uses. It is also possible to control the number of threads in
16249 (license license:agpl3+)))
16251 (define-public r-lda
16258 (uri (cran-uri "lda" version))
16261 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16262 (build-system r-build-system)
16263 (home-page "https://cran.r-project.org/web/packages/lda/")
16264 (synopsis "Collapsed Gibbs sampling methods for topic models")
16266 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16267 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16268 mixed-membership stochastic blockmodel. Inference for all of these models is
16269 implemented via a fast collapsed Gibbs sampler written in C. Utility
16270 functions for reading/writing data typically used in topic models, as well as
16271 tools for examining posterior distributions are also included.")
16272 ;; Any version of the LGPL
16273 (license license:lgpl3+)))
16275 (define-public r-rann-l1
16282 (uri (cran-uri "RANN.L1" version))
16285 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16286 (properties `((upstream-name . "RANN.L1")))
16287 (build-system r-build-system)
16288 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16289 (synopsis "Fast nearest neighbour search using L1 metric")
16291 "This package provides tools to find the k nearest neighbours for every
16292 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16293 library. There is support for approximate as well as exact searches, fixed
16294 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16295 computed using the L1 (Manhattan, taxicab) metric.")
16296 (license license:gpl3+)))
16298 (define-public r-leiden
16305 (uri (cran-uri "leiden" version))
16308 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16309 (properties `((upstream-name . "leiden")))
16310 (build-system r-build-system)
16312 `(("r-igraph" ,r-igraph)
16313 ("r-matrix" ,r-matrix)
16314 ("r-reticulate" ,r-reticulate)))
16315 (home-page "https://github.com/TomKellyGenetics/leiden")
16316 (synopsis "R implementation of Leiden clustering algorithm")
16318 "This package implements the Python @code{leidenalg} module to be called
16319 in R. It enables clustering using the Leiden algorithm for partitioning a
16320 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16321 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16322 (license license:gpl3)))
16324 (define-public r-patchwork
16326 (name "r-patchwork")
16331 (uri (cran-uri "patchwork" version))
16334 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16335 (build-system r-build-system)
16337 `(("r-ggplot2" ,r-ggplot2)
16338 ("r-gtable" ,r-gtable)))
16340 `(("r-knitr" ,r-knitr)))
16341 (home-page "https://github.com/thomasp85/patchwork")
16342 (synopsis "Compose ggplot2 plots")
16344 "The @code{ggplot2} package provides a strong API for sequentially
16345 building up a plot, but does not concern itself with composition of multiple
16346 plots. Patchwork is a package that expands the API to allow for arbitrarily
16347 complex composition of plots by providing mathmatical operators for combining
16349 (license license:expat)))
16351 (define-public r-liger
16358 (uri (git-reference
16359 (url "https://github.com/MacoskoLab/liger")
16360 (commit (string-append "v" version))))
16361 (file-name (git-file-name name version))
16364 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16365 (modules '((guix build utils)))
16368 (delete-file "inst/java/ModularityOptimizer.jar")
16370 (build-system r-build-system)
16373 (modify-phases %standard-phases
16374 (add-after 'unpack 'build-java-part
16375 (lambda* (#:key inputs #:allow-other-keys)
16376 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16377 (for-each (lambda (file) (invoke "javac" file))
16378 (find-files "." "\\.java$"))
16379 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16380 (find-files "." "\\.class$"))
16383 `(("r-cowplot" ,r-cowplot)
16384 ("r-dosnow" ,r-dosnow)
16385 ("r-dplyr" ,r-dplyr)
16387 ("r-foreach" ,r-foreach)
16388 ("r-ggplot2" ,r-ggplot2)
16389 ("r-ggrepel" ,r-ggrepel)
16390 ("r-hmisc" ,r-hmisc)
16392 ("r-irlba" ,r-irlba)
16393 ("r-matrix" ,r-matrix)
16394 ("r-mclust" ,r-mclust)
16395 ("r-patchwork" ,r-patchwork)
16397 ("r-rann-l1" ,r-rann-l1)
16399 ("r-rcpparmadillo" ,r-rcpparmadillo)
16400 ("r-riverplot" ,r-riverplot)
16401 ("r-rtsne" ,r-rtsne)
16402 ("r-snow" ,r-snow)))
16404 `(("jdk" ,icedtea "jdk")
16405 ;; See https://github.com/MacoskoLab/liger/issues/96
16406 ;; The optimizer is released under the Expat license.
16410 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16413 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16415 ("r-knitr" ,r-knitr))) ; for vignettes
16416 (home-page "https://github.com/MacoskoLab/liger")
16417 (synopsis "Integrate and analyze multiple single-cell datasets")
16419 "LIGER is a package for integrating and analyzing multiple single-cell
16420 datasets, developed and maintained by the Macosko lab. It relies on
16421 integrative non-negative matrix factorization to identify shared and
16422 dataset-specific factors.")
16423 (license license:gpl3)))
16425 (define-public r-harmony
16432 (uri (git-reference
16433 (url "https://github.com/immunogenomics/harmony")
16435 (file-name (git-file-name name version))
16438 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16439 (modules '((guix build utils)))
16442 (for-each delete-file '("config.status" "configure"))
16444 (build-system r-build-system)
16446 `(("r-cowplot" ,r-cowplot)
16447 ("r-dplyr" ,r-dplyr)
16448 ("r-ggplot2" ,r-ggplot2)
16449 ("r-irlba" ,r-irlba)
16450 ("r-matrix" ,r-matrix)
16452 ("r-rcpparmadillo" ,r-rcpparmadillo)
16453 ("r-rcppprogress" ,r-rcppprogress)
16454 ("r-rlang" ,r-rlang)
16455 ("r-tibble" ,r-tibble)
16456 ("r-tidyr" ,r-tidyr)))
16458 `(("autoconf" ,autoconf)))
16459 (home-page "https://github.com/immunogenomics/harmony")
16460 (synopsis "Integration of single cell sequencing data")
16462 "This package provides an implementation of the Harmony algorithm for
16463 single cell integration, described in Korsunsky et al
16464 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16465 function and interfaces to external frameworks.")
16466 (license license:gpl3)))
16468 (define-public r-covr
16475 (uri (cran-uri "covr" version))
16477 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16478 (properties `((upstream-name . "covr")))
16479 (build-system r-build-system)
16481 `(("r-crayon" ,r-crayon)
16482 ("r-digest" ,r-digest)
16484 ("r-jsonlite" ,r-jsonlite)
16486 ("r-withr" ,r-withr)
16487 ("r-yaml" ,r-yaml)))
16489 `(("r-knitr" ,r-knitr))) ; for vignettes
16490 (home-page "https://github.com/r-lib/covr")
16491 (synopsis "Test coverage for R packages")
16493 "Thisp package enables you to track and report code coverage for your
16494 package and (optionally) upload the results to a coverage service. Code
16495 coverage is a measure of the amount of code being exercised by a set of tests.
16496 It is an indirect measure of test quality and completeness. This package is
16497 compatible with any testing methodology or framework and tracks coverage of
16498 both R code and compiled C/C++/FORTRAN code.")
16499 (license license:gpl3)))
16501 (define-public r-systemfonts
16503 (name "r-systemfonts")
16508 (uri (cran-uri "systemfonts" version))
16511 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16512 (properties `((upstream-name . "systemfonts")))
16513 (build-system r-build-system)
16515 `(("fontconfig" ,fontconfig)
16518 `(("pkg-config" ,pkg-config)
16519 ("r-knitr" ,r-knitr)))
16520 (home-page "https://github.com/r-lib/systemfonts")
16521 (synopsis "System native font finding")
16523 "This package provides system native access to the font catalogue. As
16524 font handling varies between systems it is difficult to correctly locate
16525 installed fonts across different operating systems. The 'systemfonts' package
16526 provides bindings to the native libraries for finding font files that can then
16527 be used further by e.g. graphic devices.")
16528 (license license:expat)))
16530 (define-public r-graphlayouts
16532 (name "r-graphlayouts")
16537 (uri (cran-uri "graphlayouts" version))
16540 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16541 (properties `((upstream-name . "graphlayouts")))
16542 (build-system r-build-system)
16544 `(("r-igraph" ,r-igraph)
16546 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16547 (home-page "https://github.com/schochastics/graphlayouts")
16548 (synopsis "Additional layout algorithms for network visualizations")
16550 "This package provides several layout algorithms to visualize networks
16551 which are not part of the igraph library. Most are based on the concept of
16552 stress majorization by Gansner et al. (2004)
16553 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16554 emphasize hidden group structures in networks or focus on specific nodes.")
16555 (license license:expat)))
16557 (define-public r-tidygraph
16559 (name "r-tidygraph")
16564 (uri (cran-uri "tidygraph" version))
16567 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16568 (properties `((upstream-name . "tidygraph")))
16569 (build-system r-build-system)
16571 `(("r-dplyr" ,r-dplyr)
16572 ("r-igraph" ,r-igraph)
16573 ("r-magrittr" ,r-magrittr)
16574 ("r-pillar" ,r-pillar)
16577 ("r-rlang" ,r-rlang)
16578 ("r-tibble" ,r-tibble)
16579 ("r-tidyr" ,r-tidyr)))
16580 (home-page "https://github.com/thomasp85/tidygraph")
16581 (synopsis "Tidy API for graph manipulation")
16583 "This package provides a graph implementation that can be thought of as
16584 two tidy data frames describing node and edge data respectively. It provides
16585 an approach to manipulate these two virtual data frames using the API defined
16586 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16587 common graph algorithms.")
16588 (license license:expat)))
16590 (define-public r-soupx
16591 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16595 (version (git-version "0.3.1" revision commit))
16599 (uri (git-reference
16600 (url "https://github.com/constantAmateur/SoupX")
16602 (file-name (git-file-name name version))
16605 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16606 (properties `((upstream-name . "SoupX")))
16607 (build-system r-build-system)
16609 `(("r-ggplot2" ,r-ggplot2)
16610 ("r-matrix" ,r-matrix)
16611 ("r-seurat" ,r-seurat)))
16612 (home-page "https://github.com/constantAmateur/SoupX")
16613 (synopsis "Single cell mRNA Soup eXterminator")
16615 "This package provides a package for quantifying, profiling and
16616 removing cell free mRNA contamination (the \"soup\") from droplet based single
16617 cell RNA-seq experiments.")
16618 (license license:gpl2))))
16620 (define-public r-assertr
16627 (uri (cran-uri "assertr" version))
16630 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16631 (build-system r-build-system)
16633 `(("r-dplyr" ,r-dplyr)
16635 ("r-rlang" ,r-rlang)))
16637 `(("r-knitr" ,r-knitr))) ; needed for vignette
16638 (home-page "https://github.com/ropensci/assertr")
16639 (synopsis "Assertive programming for R analysis pipelines")
16641 "This package provides functionality to assert conditions that have to be
16642 met so that errors in data used in analysis pipelines can fail quickly. It is
16643 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16645 (license license:expat)))
16647 (define-public r-parameters
16649 (name "r-parameters")
16654 (uri (cran-uri "parameters" version))
16657 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16658 (properties `((upstream-name . "parameters")))
16659 (build-system r-build-system)
16661 `(("r-bayestestr" ,r-bayestestr)
16662 ("r-insight" ,r-insight)))
16664 `(("r-knitr" ,r-knitr)))
16665 (home-page "https://cran.r-project.org/web/packages/parameters")
16666 (synopsis "Processing of model parameters")
16668 "This package provides utilities for processing the parameters of various
16669 statistical models. Beyond computing p values, CIs, and other indices for a
16670 wide variety of models, this package implements features like standardization
16671 or bootstrapping of parameters and models, feature reduction (feature
16672 extraction and variable selection) as well as conversion between indices of
16674 (license license:gpl3)))
16676 (define-public r-rgdal
16683 (uri (cran-uri "rgdal" version))
16685 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16686 (properties `((upstream-name . "rgdal")))
16687 (build-system r-build-system)
16695 `(("pkg-config" ,pkg-config)
16696 ("r-knitr" ,r-knitr)))
16697 (home-page "http://rgdal.r-forge.r-project.org")
16698 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16700 "This package provides bindings to the Geospatial Data Abstraction
16701 Library (GDAL) and access to projection/transformation operations from the
16703 (license license:gpl2+)))
16705 (define-public r-insol
16712 (uri (cran-uri "insol" version))
16715 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16716 (properties `((upstream-name . "insol")))
16717 (build-system r-build-system)
16719 `(("r-raster" ,r-raster)))
16721 `(("gfortran" ,gfortran)))
16722 (home-page "https://meteoexploration.com/R/insol/index.html")
16723 (synopsis "Tools for calculating solar radiation")
16725 "This package provides functions to compute insolation on tilted
16726 surfaces, computes atmospheric transmittance and related parameters such as:
16727 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16728 time, vector in the direction of the sun, vector normal to surface, and some
16729 atmospheric physics.")
16730 (license license:gpl2+)))
16732 (define-public r-lifecycle
16734 (name "r-lifecycle")
16739 (uri (cran-uri "lifecycle" version))
16742 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16743 (properties `((upstream-name . "lifecycle")))
16744 (build-system r-build-system)
16746 `(("r-glue" ,r-glue)
16747 ("r-rlang" ,r-rlang)))
16749 `(("r-knitr" ,r-knitr))) ; for vignettes
16750 (home-page "https://github.com/r-lib/lifecycle")
16751 (synopsis "Manage the life cycle of your package functions")
16753 "Manage the life cycle of your exported functions with shared
16754 conventions, documentation badges, and non-invasive deprecation warnings. The
16755 lifecycle package defines four development stages (experimental, maturing,
16756 stable, and questioning) and three deprecation stages (soft-deprecated,
16757 deprecated, and defunct). It makes it easy to insert badges corresponding to
16758 these stages in your documentation. Usage of deprecated functions are
16759 signalled with increasing levels of non-invasive verbosity.")
16760 (license license:gpl3)))
16762 (define-public r-assertable
16764 (name "r-assertable")
16769 (uri (cran-uri "assertable" version))
16772 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16773 (build-system r-build-system)
16775 `(("r-data-table" ,r-data-table)))
16776 (home-page "https://cran.r-project.org/web/packages/assertable/")
16777 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16778 (description "This package provides simple, flexible assertions on
16779 data.frame or data.table objects with verbose output for vetting. While other
16780 assertion packages apply towards more general use-cases, @code{assertable} is
16781 tailored towards tabular data. It includes functions to check variable names
16782 and values, whether the dataset contains all combinations of a given set of
16783 unique identifiers, and whether it is a certain length. In addition,
16784 @code{assertable} includes utility functions to check the existence of target
16785 files and to efficiently import multiple tabular data files into one
16787 (license license:gpl3)))
16789 (define-public r-quadprog
16791 (name "r-quadprog")
16796 (uri (cran-uri "quadprog" version))
16798 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16799 (build-system r-build-system)
16801 `(("gfortran" ,gfortran)))
16802 (home-page "https://cran.r-project.org/web/packages/quadprog")
16803 (synopsis "Functions to solve quadratic programming problems")
16805 "This package contains routines and documentation for solving quadratic
16806 programming problems.")
16807 (license license:gpl3+)))
16809 (define-public r-desolve
16816 (uri (cran-uri "deSolve" version))
16818 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16819 (properties `((upstream-name . "deSolve")))
16820 (build-system r-build-system)
16822 `(("gfortran" ,gfortran)))
16823 (home-page "https://desolve.r-forge.r-project.org/")
16824 (synopsis "Solvers for initial value problems of differential equations")
16825 (description "This package provides functions that solve initial value
16826 problems of a system of first-order @dfn{ordinary differential
16827 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16828 @dfn{differential algebraic equations} (DAE), and of delay differential
16829 equations. The functions provide an interface to the FORTRAN functions
16830 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16831 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16832 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16833 time steps. The package contains routines designed for solving ODEs resulting
16834 from 1-D, 2-D and 3-D partial differential equations that have been converted
16835 to ODEs by numerical differencing.")
16836 (license license:gpl2+)))
16838 (define-public r-pracma
16844 (uri (cran-uri "pracma" version))
16846 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16847 (build-system r-build-system)
16848 (home-page "https://cran.r-project.org/web/packages/pracma/")
16849 (synopsis "Practical numerical math functions")
16850 (description "This package provides functions for numerical analysis and
16851 linear algebra, numerical optimization, differential equations, plus some
16852 special functions. It uses Matlab function names where appropriate to simplify
16854 (license license:gpl3+)))
16856 (define-public r-subplex
16863 (uri (cran-uri "subplex" version))
16866 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16867 (build-system r-build-system)
16869 `(("gfortran" ,gfortran)))
16870 (home-page "https://cran.r-project.org/web/packages/subplex")
16871 (synopsis "Unconstrained optimization using the subplex algorithm")
16873 "This package implements the Subplex optimization algorithm.
16874 It solves unconstrained optimization problems using a simplex method on
16875 subspaces. The method is well suited for optimizing objective functions that
16876 are noisy or are discontinuous at the solution.")
16877 (license license:gpl3+)))
16879 (define-public r-txtplot
16886 (uri (cran-uri "txtplot" version))
16889 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16890 (build-system r-build-system)
16891 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16892 (synopsis "Text-based plotting")
16893 (description "This package provides functions to produce rudimentary ASCII
16894 graphics directly in the terminal window. This package provides a basic
16895 plotting function (and equivalents of curve, density, acf and barplot) as well
16896 as a boxplot function.")
16897 (license license:lgpl3+)))
16899 (define-public r-bio3d
16906 (uri (cran-uri "bio3d" version))
16909 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16910 (properties `((upstream-name . "bio3d")))
16911 (build-system r-build-system)
16912 (inputs `(("zlib" ,zlib)))
16913 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16914 (home-page "http://thegrantlab.org/bio3d/")
16915 (synopsis "Biological structure analysis")
16917 "This package provides utilities to process, organize and explore protein
16918 structure, sequence and dynamics data. Features include the ability to read
16919 and write structure, sequence and dynamic trajectory data, perform sequence
16920 and structure database searches, data summaries, atom selection, alignment,
16921 superposition, rigid core identification, clustering, torsion analysis,
16922 distance matrix analysis, structure and sequence conservation analysis, normal
16923 mode analysis, principal component analysis of heterogeneous structure data,
16924 and correlation network analysis from normal mode and molecular dynamics data.
16925 In addition, various utility functions are provided to enable the statistical
16926 and graphical power of the R environment to work with biological sequence and
16928 (license license:gpl2+)))
16930 (define-public r-bios2cor
16932 (name "r-bios2cor")
16937 (uri (cran-uri "Bios2cor" version))
16940 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16941 (properties `((upstream-name . "Bios2cor")))
16942 (build-system r-build-system)
16944 `(("r-bigmemory" ,r-bigmemory)
16945 ("r-bio3d" ,r-bio3d)
16946 ("r-circular" ,r-circular)
16947 ("r-igraph" ,r-igraph)))
16948 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16949 (synopsis "From biological sequences and simulations to correlation analysis")
16951 "This package provides utilities for computation and analysis of
16952 correlation/covariation in multiple sequence alignments and in side chain
16953 motions during molecular dynamics simulations. Features include the
16954 computation of correlation/covariation scores using a variety of scoring
16955 functions between either sequence positions in alignments or side chain
16956 dihedral angles in molecular dynamics simulations and utilities to analyze the
16957 correlation/covariation matrix through a variety of tools including network
16958 representation and principal components analysis. In addition, several
16959 utility functions are based on the R graphical environment to provide friendly
16960 tools for help in data interpretation.")
16961 (license license:gpl2+)))
16963 ;; This package includes minified JavaScript files. When upgrading please
16964 ;; check that there are no new minified JavaScript files.
16965 (define-public r-networkd3
16967 (name "r-networkd3")
16972 (uri (cran-uri "networkD3" version))
16975 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16978 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16980 (properties `((upstream-name . "networkD3")))
16981 (build-system r-build-system)
16983 `(#:modules ((guix build utils)
16984 (guix build r-build-system)
16988 (modify-phases %standard-phases
16989 (add-after 'unpack 'process-javascript
16990 (lambda* (#:key inputs #:allow-other-keys)
16991 (with-directory-excursion "inst/htmlwidgets/lib/"
16995 `((,(assoc-ref inputs "d3.v4.js")
16996 "d3-4.5.0/d3.min.js"))))
16997 (lambda (sources targets)
16998 (for-each (lambda (source target)
16999 (format #t "Processing ~a --> ~a~%"
17001 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17002 (call-with-output-file target
17004 (dump-port minified port)))))
17005 sources targets))))
17008 `(("uglify-js" ,uglify-js)
17009 ;; NOTE: Make sure that this version of d3 is still valid when
17010 ;; upgrading the package.
17014 (uri "https://d3js.org/d3.v4.js")
17017 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17019 `(("r-htmlwidgets" ,r-htmlwidgets)
17020 ("r-igraph" ,r-igraph)
17021 ("r-magrittr" ,r-magrittr)))
17022 (home-page "https://cran.r-project.org/package=networkD3")
17023 (synopsis "D3 JavaScript network graphs from R")
17025 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17027 (license license:gpl3+)))
17029 (define-public r-aasea
17036 (uri (cran-uri "aaSEA" version))
17039 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17040 (properties `((upstream-name . "aaSEA")))
17041 (build-system r-build-system)
17043 `(("r-bios2cor" ,r-bios2cor)
17045 ("r-hmisc" ,r-hmisc)
17046 ("r-magrittr" ,r-magrittr)
17047 ("r-networkd3" ,r-networkd3)
17048 ("r-plotly" ,r-plotly)
17049 ("r-seqinr" ,r-seqinr)
17050 ("r-shiny" ,r-shiny)
17051 ("r-shinydashboard" ,r-shinydashboard)))
17052 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17053 (synopsis "Amino acid substitution effect analyzer")
17055 "Given a protein multiple sequence alignment, it is a daunting task to
17056 assess the effects of substitutions along sequence length. The aaSEA package
17057 is intended to help researchers to rapidly analyze property changes caused by
17058 single, multiple and correlated amino acid substitutions in proteins.")
17059 (license license:gpl3)))
17061 (define-public r-abacus
17068 (uri (cran-uri "ABACUS" version))
17071 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17072 (properties `((upstream-name . "ABACUS")))
17073 (build-system r-build-system)
17075 `(("r-ggplot2" ,r-ggplot2)
17076 ("r-shiny" ,r-shiny)))
17077 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17078 (synopsis "Apps-based activities for communicating and understanding statistics")
17080 "This package provides a set of Shiny apps for effective communication
17081 and understanding in statistics. The current version includes properties of
17082 normal distribution, properties of sampling distribution, one-sample z and t
17083 tests, two samples independent (unpaired) t test and analysis of variance.")
17084 (license license:gpl3)))
17086 (define-public r-abc-rap
17093 (uri (cran-uri "ABC.RAP" version))
17096 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17097 (properties `((upstream-name . "ABC.RAP")))
17098 (build-system r-build-system)
17099 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17100 (synopsis "Array-based CpG region analysis pipeline")
17102 "This package aims to identify candidate genes that are differentially
17103 methylated between cases and controls. It applies Student's t-test and delta
17104 beta analysis to identify candidate genes containing multiple CpG sites.")
17105 (license license:gpl3)))
17107 (define-public r-abcadm
17114 (uri (cran-uri "abcADM" version))
17117 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17118 (properties `((upstream-name . "abcADM")))
17119 (build-system r-build-system)
17122 ("r-rcpp" ,r-rcpp)))
17123 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17124 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17126 "This package provides tools to estimate parameters of accumulated
17127 damage (load duration) models based on failure time data under a Bayesian
17128 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17129 long-term reliability under stochastic load profiles.")
17130 (license license:gpl3)))
17132 (define-public r-rglpk
17139 (uri (cran-uri "Rglpk" version))
17142 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17143 (properties `((upstream-name . "Rglpk")))
17144 (build-system r-build-system)
17146 `(("r-slam" ,r-slam)))
17149 (home-page "https://r-forge.r-project.org/projects/rglp/")
17150 (synopsis "R interface to the GNU Linear Programming Kit")
17152 "This package provides an R interface to the GNU Linear Programming Kit,
17153 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17154 integer linear programming} (MILP) and other related problems.")
17156 (license (list license:gpl2 license:gpl3))))
17158 (define-public r-abcdefba
17160 (name "r-abcdefba")
17165 (uri (cran-uri "abcdeFBA" version))
17168 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17169 (properties `((upstream-name . "abcdeFBA")))
17170 (build-system r-build-system)
17172 `(("r-corrplot" ,r-corrplot)
17173 ("r-lattice" ,r-lattice)
17175 ("r-rglpk" ,r-rglpk)))
17176 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17177 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17179 "This package provides functions for Constraint Based Simulation using
17180 Flux Balance Analysis and informative analysis of the data generated during
17182 (license license:gpl2)))
17184 (define-public r-abcrlda
17191 (uri (cran-uri "abcrlda" version))
17194 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17195 (properties `((upstream-name . "abcrlda")))
17196 (build-system r-build-system)
17197 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17198 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17200 "This package offers methods to perform @dfn{asymptotically
17201 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17202 cost-sensitive binary classification. The bias-correction is an estimate of
17203 the bias term added to regularized discriminant analysis that minimizes the
17205 (license license:gpl3)))
17207 (define-public r-abemus
17214 (uri (cran-uri "abemus" version))
17217 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17218 (properties `((upstream-name . "abemus")))
17219 (build-system r-build-system)
17221 `(("r-data-table" ,r-data-table)))
17222 (home-page "https://cran.r-project.org/web/packages/abemus/")
17223 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17225 "This package provides an implementation of @dfn{Adaptive Base Error
17226 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17227 platform-specific genetic knowledge and empirical signal to readily detect and
17228 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17229 cell free DNA} (cfDNA).")
17230 (license license:gpl3)))
17232 ;; This package includes minified JavaScript files. When upgrading please
17233 ;; check that there are no new minified JavaScript files.
17234 (define-public r-rintrojs
17236 (name "r-rintrojs")
17241 (uri (cran-uri "rintrojs" version))
17244 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17245 (properties `((upstream-name . "rintrojs")))
17246 (build-system r-build-system)
17248 `(#:modules ((guix build utils)
17249 (guix build r-build-system)
17253 (modify-phases %standard-phases
17254 (add-after 'unpack 'process-javascript
17255 (lambda* (#:key inputs #:allow-other-keys)
17256 (with-directory-excursion "inst/javascript/introjs/"
17260 `((,(assoc-ref inputs "intro.js")
17262 (lambda (sources targets)
17263 (for-each (lambda (source target)
17264 (format #t "Processing ~a --> ~a~%"
17266 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17267 (call-with-output-file target
17269 (dump-port minified port)))))
17270 sources targets))))
17273 `(("uglify-js" ,uglify-js)
17277 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17280 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17282 `(("r-jsonlite" ,r-jsonlite)
17283 ("r-shiny" ,r-shiny)))
17284 (home-page "https://github.com/carlganz/rintrojs")
17285 (synopsis "Wrapper for the Intro.js library")
17287 "This package provides a wrapper for the @url{http://www.introjs.com,
17288 Intro.js} library. This package makes it easy to include step-by-step
17289 introductions, and clickable hints in a Shiny application. It supports both
17290 static introductions in the UI, and programmatic introductions from the
17292 (license license:agpl3+)))
17294 (define-public r-sysfonts
17296 (name "r-sysfonts")
17301 (uri (cran-uri "sysfonts" version))
17304 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17305 (properties `((upstream-name . "sysfonts")))
17306 (build-system r-build-system)
17308 `(("freetype" ,freetype)
17312 `(("pkg-config" ,pkg-config)))
17313 (home-page "https://github.com/yixuan/sysfonts")
17314 (synopsis "Loading fonts into R")
17316 "This is a package to simplify loading of system fonts and Google Fonts
17317 into R, in order to support other packages.")
17318 (license license:gpl2)))
17320 (define-public r-showtextdb
17322 (name "r-showtextdb")
17327 (uri (cran-uri "showtextdb" version))
17330 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17331 (properties `((upstream-name . "showtextdb")))
17332 (build-system r-build-system)
17334 `(("r-sysfonts" ,r-sysfonts)))
17335 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17336 (synopsis "Font files for the 'showtext' package")
17338 "This package provides font files that can be used by the @code{showtext}
17340 (license license:asl2.0)))
17342 (define-public r-showtext
17344 (name "r-showtext")
17349 (uri (cran-uri "showtext" version))
17352 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17353 (properties `((upstream-name . "showtext")))
17354 (build-system r-build-system)
17356 `(("freetype" ,freetype)
17360 `(("r-showtextdb" ,r-showtextdb)
17361 ("r-sysfonts" ,r-sysfonts)))
17363 `(("pkg-config" ,pkg-config)
17364 ("r-knitr" ,r-knitr)))
17365 (home-page "https://github.com/yixuan/showtext")
17366 (synopsis "Using fonts more easily in R graphs")
17368 "This package aims to make it easy to use various types of
17369 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17370 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17371 will be converted into polygons or raster images, hence after the plot has
17372 been created, it no longer relies on the font files. No external software
17373 such as Ghostscript is needed to use this package.")
17374 (license license:asl2.0)))
17376 (define-public r-emojifont
17378 (name "r-emojifont")
17383 (uri (cran-uri "emojifont" version))
17386 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17387 (properties `((upstream-name . "emojifont")))
17388 (build-system r-build-system)
17390 `(("r-ggplot2" ,r-ggplot2)
17391 ("r-proto" ,r-proto)
17392 ("r-showtext" ,r-showtext)
17393 ("r-sysfonts" ,r-sysfonts)))
17394 (home-page "https://guangchuangyu.github.io/emojifont")
17395 (synopsis "Emoji and Font Awesome in R graphics")
17397 "This package enables the use of emoji and the Font Awesome glyphs in
17398 both base and ggplot2 graphics.")
17399 (license license:artistic2.0)))
17401 (define-public r-abstractr
17403 (name "r-abstractr")
17408 (uri (cran-uri "abstractr" version))
17411 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17412 (properties `((upstream-name . "abstractr")))
17413 (build-system r-build-system)
17415 `(("r-colourpicker" ,r-colourpicker)
17416 ("r-emojifont" ,r-emojifont)
17417 ("r-ggplot2" ,r-ggplot2)
17418 ("r-gridextra" ,r-gridextra)
17419 ("r-rintrojs" ,r-rintrojs)
17420 ("r-shiny" ,r-shiny)
17421 ("r-shinythemes" ,r-shinythemes)))
17422 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17423 (synopsis "R-Shiny application for creating visual abstracts")
17425 "This package provides an R Shiny application to create visual abstracts
17426 for original research. A variety of user defined options and formatting are
17428 (license license:gpl3)))
17430 (define-public r-qgam
17437 (uri (cran-uri "qgam" version))
17440 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17441 (properties `((upstream-name . "qgam")))
17442 (build-system r-build-system)
17444 `(("r-doparallel" ,r-doparallel)
17447 ("r-shiny" ,r-shiny)))
17448 (native-inputs `(("r-knitr" ,r-knitr)))
17449 (home-page "https://cran.r-project.org/web/packages/qgam/")
17450 (synopsis "Smooth additive quantile regression models")
17452 "This package provides smooth additive quantile regression models, fitted
17453 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17454 the smoothing parameters are estimated automatically by marginal loss
17455 minimization, while the regression coefficients are estimated using either
17456 PIRLS or Newton algorithm. The learning rate is determined so that the
17457 Bayesian credible intervals of the estimated effects have approximately the
17458 correct coverage. The main function is @code{qgam()} which is similar to
17459 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17460 regression models.")
17461 (license license:gpl2+)))
17463 (define-public r-abtest
17470 (uri (cran-uri "abtest" version))
17473 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17474 (properties `((upstream-name . "abtest")))
17475 (build-system r-build-system)
17477 `(("r-matrix" ,r-matrix)
17478 ("r-mvtnorm" ,r-mvtnorm)
17479 ("r-plotrix" ,r-plotrix)
17481 ("r-rcolorbrewer" ,r-rcolorbrewer)
17484 ("r-truncnorm" ,r-truncnorm)))
17485 (home-page "https://cran.r-project.org/web/packages/abtest/")
17486 (synopsis "Bayesian A/B testing")
17488 "This package provides functions for Bayesian A/B testing including prior
17489 elicitation options based on Kass and Vaidyanathan (1992)
17490 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17491 (license license:gpl2+)))
17493 (define-public r-accept
17500 (uri (cran-uri "accept" version))
17503 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17504 (properties `((upstream-name . "accept")))
17505 (build-system r-build-system)
17507 `(("r-dplyr" ,r-dplyr)
17508 ("r-extrafont" ,r-extrafont)
17510 ("r-plotly" ,r-plotly)
17511 ("r-stringr" ,r-stringr)
17512 ("r-viridis" ,r-viridis)))
17513 (home-page "https://cran.r-project.org/web/packages/accept/")
17514 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17516 "This package allows clinicians to predict the rate and severity of
17517 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17518 Disease} (COPD) patients, based on the clinical prediction model published in
17519 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17520 (license license:gpl3)))
17522 (define-public r-smpracticals
17524 (name "r-smpracticals")
17529 (uri (cran-uri "SMPracticals" version))
17532 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17533 (properties `((upstream-name . "SMPracticals")))
17534 (build-system r-build-system)
17536 `(("r-ellipse" ,r-ellipse)
17539 ("r-survival" ,r-survival)))
17540 (home-page "http://statwww.epfl.ch/davison/SM/")
17541 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17543 "This package contains the datasets and a few functions for use with the
17544 practicals outlined in Appendix A of the book Statistical Models (Davison,
17545 2003, Cambridge University Press). The practicals themselves can be found at
17546 @url{http://statwww.epfl.ch/davison/SM/}.")
17547 (license license:gpl2+)))
17549 (define-public r-fgui
17556 (uri (cran-uri "fgui" version))
17559 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17560 (properties `((upstream-name . "fgui")))
17561 (build-system r-build-system)
17563 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17564 (synopsis "Create GUI for R functions")
17566 "Rapidly create a GUI for a function you created by automatically
17567 creating widgets for arguments of the function. This package automatically
17568 parses help routines for context-sensitive help to these arguments. The
17569 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17570 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17571 incorporated into the interface for greater customization for the more
17573 ;; Any version of the GPL.
17574 (license (list license:gpl2+ license:gpl3+))))
17576 (define-public r-tcltk2
17583 (uri (cran-uri "tcltk2" version))
17586 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17587 (properties `((upstream-name . "tcltk2")))
17588 (build-system r-build-system)
17592 (home-page "https://www.sciviews.org/SciViews-R")
17593 (synopsis "Tcl/Tk additions")
17595 "This package provides a series of additional Tcl commands and Tk widgets
17596 with style and various functions to supplement the tcltk package")
17597 (license license:lgpl3)))
17599 (define-public r-accrual
17606 (uri (cran-uri "accrual" version))
17609 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17610 (properties `((upstream-name . "accrual")))
17611 (build-system r-build-system)
17613 `(("r-fgui" ,r-fgui)
17614 ("r-smpracticals" ,r-smpracticals)
17615 ("r-tcltk2" ,r-tcltk2)))
17616 (home-page "https://cran.r-project.org/web/packages/accrual/")
17617 (synopsis "Bayesian accrual prediction")
17619 "Subject recruitment for medical research is challenging. Slow patient
17620 accrual leads to delay in research. Accrual monitoring during the process of
17621 recruitment is critical. Researchers need reliable tools to manage the
17622 accrual rate. This package provides an implementation of a Bayesian method
17623 that integrates researcher's experience on previous trials and data from the
17624 current study, providing reliable prediction on accrual rate for clinical
17625 studies. It provides functions for Bayesian accrual prediction which can be
17626 easily used by statisticians and clinical researchers.")
17627 (license license:gpl2)))
17629 (define-public r-accrued
17636 (uri (cran-uri "accrued" version))
17639 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17640 (properties `((upstream-name . "accrued")))
17641 (build-system r-build-system)
17642 (home-page "https://cran.r-project.org/web/packages/accrued/")
17643 (synopsis "Data quality visualization tools for partially accruing data")
17645 "This is a package for visualizing data quality of partially accruing
17647 (license license:gpl3)))
17649 (define-public r-mda
17656 (uri (cran-uri "mda" version))
17659 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17660 (properties `((upstream-name . "mda")))
17661 (build-system r-build-system)
17662 (propagated-inputs `(("r-class" ,r-class)))
17663 (native-inputs `(("gfortran" ,gfortran)))
17664 (home-page "https://cran.r-project.org/web/packages/mda/")
17665 (synopsis "Mixture and flexible discriminant analysis")
17667 "This is a package for mixture and flexible discriminant analysis,
17668 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17669 (license license:gpl2)))
17671 (define-public r-elasticnet
17673 (name "r-elasticnet")
17678 (uri (cran-uri "elasticnet" version))
17681 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17682 (properties `((upstream-name . "elasticnet")))
17683 (build-system r-build-system)
17685 `(("r-lars" ,r-lars)))
17686 (home-page "http://users.stat.umn.edu/~zouxx019/")
17687 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17689 "This package provides functions for fitting the entire solution path of
17690 the Elastic-Net and also provides functions for estimating sparse Principal
17691 Components. The Lasso solution paths can be computed by the same function.")
17692 (license license:gpl2+)))
17694 (define-public r-sparselda
17696 (name "r-sparselda")
17701 (uri (cran-uri "sparseLDA" version))
17704 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17705 (properties `((upstream-name . "sparseLDA")))
17706 (build-system r-build-system)
17708 `(("r-elasticnet" ,r-elasticnet)
17711 (home-page "https://www.imm.dtu.dk/~lkhc/")
17712 (synopsis "Sparse discriminant analysis")
17714 "This package performs sparse linear discriminant analysis for Gaussians
17715 and mixture of Gaussian models.")
17716 (license license:gpl2+)))
17718 (define-public r-accsda
17725 (uri (cran-uri "accSDA" version))
17728 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17729 (properties `((upstream-name . "accSDA")))
17730 (build-system r-build-system)
17732 `(("r-ggplot2" ,r-ggplot2)
17733 ("r-ggthemes" ,r-ggthemes)
17734 ("r-gridextra" ,r-gridextra)
17736 ("r-rarpack" ,r-rarpack)
17737 ("r-sparselda" ,r-sparselda)))
17738 (home-page "https://github.com/gumeo/accSDA/wiki")
17739 (synopsis "Accelerated sparse discriminant analysis")
17741 "This package provides an implementation of sparse linear discriminant
17742 analysis, which is a supervised classification method for multiple classes.
17743 Various novel optimization approaches to this problem are implemented
17744 including @dfn{alternating direction method of multipliers} (ADMM),
17745 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17746 Functions for performing cross validation are also supplied along with basic
17747 prediction and plotting functions. @dfn{Sparse zero variance
17748 discriminant} (SZVD) analysis is also included in the package.")
17749 (license license:gpl2+)))
17751 (define-public r-ace2fastq
17753 (name "r-ace2fastq")
17758 (uri (cran-uri "ace2fastq" version))
17761 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17762 (properties `((upstream-name . "ace2fastq")))
17763 (build-system r-build-system)
17765 `(("r-stringr" ,r-stringr)))
17766 (home-page "https://github.com/c5sire/ace2fastq")
17767 (synopsis "ACE file to FASTQ converter")
17769 "The ACE file format is used in genomics to store contigs from sequencing
17770 machines. This tools converts it into FASTQ format. Both formats contain the
17771 sequence characters and their corresponding quality information. Unlike the
17772 FASTQ file, the ACE file stores the quality values numerically. The
17773 conversion algorithm uses the standard Sanger formula. The package
17774 facilitates insertion into pipelines, and content inspection.")
17775 (license license:gpl3)))
17777 (define-public r-rngwell
17784 (uri (cran-uri "rngWELL" version))
17787 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17788 (properties `((upstream-name . "rngWELL")))
17789 (build-system r-build-system)
17790 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17791 (synopsis "Toolbox for WELL random number generators")
17793 "This is a dedicated package to WELL pseudo random generators, which were
17794 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17795 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17796 (license license:bsd-3)))
17798 (define-public r-randtoolbox
17800 (name "r-randtoolbox")
17805 (uri (cran-uri "randtoolbox" version))
17808 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17809 (properties `((upstream-name . "randtoolbox")))
17810 (build-system r-build-system)
17812 `(("r-rngwell" ,r-rngwell)))
17814 `(("gfortran" ,gfortran)))
17815 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17816 (synopsis "Toolbox for pseudo and quasi random number generation")
17818 "This package provides
17821 @item pseudo random generators, such as general linear
17822 congruential generators, multiple recursive generators and generalized
17823 feedback shift register (SF-Mersenne Twister algorithm and WELL
17826 @item quasi random generators, such as the Torus algorithm, the Sobol
17827 sequence, the Halton sequence (including the Van der Corput sequence), and
17829 @item some generator tests: the gap test, the serial test, the poker test.
17832 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17833 (license license:bsd-3)))
17835 (define-public r-lhs
17842 (uri (cran-uri "lhs" version))
17845 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17846 (properties `((upstream-name . "lhs")))
17847 (build-system r-build-system)
17848 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17850 `(("r-knitr" ,r-knitr)))
17851 (home-page "https://github.com/bertcarnell/lhs")
17852 (synopsis "Latin Hypercube Samples")
17854 "This package provides a number of methods for creating and augmenting
17855 Latin Hypercube Samples.")
17856 (license license:gpl3)))
17858 (define-public r-acebayes
17860 (name "r-acebayes")
17865 (uri (cran-uri "acebayes" version))
17868 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17869 (properties `((upstream-name . "acebayes")))
17870 (build-system r-build-system)
17872 `(("r-compare" ,r-compare)
17874 ("r-randtoolbox" ,r-randtoolbox)
17876 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17877 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17878 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17880 "Finding an optimal Bayesian experimental design involves maximizing an
17881 objective function given by the expectation of some appropriately chosen
17882 utility function with respect to the joint distribution of unknown
17883 quantities (including responses). This objective function is usually not
17884 available in closed form and the design space can be continuous and of high
17885 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17886 to maximise an approximation to the expectation of the utility function.")
17887 (license license:gpl2)))
17889 (define-public r-acet
17896 (uri (cran-uri "ACEt" version))
17899 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17900 (properties `((upstream-name . "ACEt")))
17901 (build-system r-build-system)
17906 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17907 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17908 (synopsis "Estimating dynamic heritability and twin model comparison")
17910 "This package supports twin models that are able to estimate the dynamic
17911 behaviour of the variance components in the classical twin models with respect
17912 to age using B-splines and P-splines.")
17913 (license license:gpl2+)))
17915 (define-public r-acfmperiod
17917 (name "r-acfmperiod")
17922 (uri (cran-uri "acfMPeriod" version))
17925 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17926 (properties `((upstream-name . "acfMPeriod")))
17927 (build-system r-build-system)
17929 `(("r-mass" ,r-mass)))
17930 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17931 (synopsis "Estimation of the ACF from the M-periodogram")
17933 "This package support non-robust and robust computations of the sample
17934 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17935 univariate and multivariate processes. The methodology consists in reversing
17936 the diagonalization procedure involving the periodogram or the
17937 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17938 ACOVF or the ACF as discussed in Fuller (1995)
17939 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17940 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17941 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17942 (license license:gpl2+)))
17944 (define-public r-gamlss-data
17946 (name "r-gamlss-data")
17951 (uri (cran-uri "gamlss.data" version))
17954 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17955 (properties `((upstream-name . "gamlss.data")))
17956 (build-system r-build-system)
17957 (home-page "http://www.gamlss.org/")
17958 (synopsis "GAMLSS data")
17960 "This package provides data used as examples to demonstrate GAMLSS
17962 ;; Either version of the license
17963 (license (list license:gpl2 license:gpl3))))
17965 (define-public r-gamlss
17972 (uri (cran-uri "gamlss" version))
17975 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
17976 (properties `((upstream-name . "gamlss")))
17977 (build-system r-build-system)
17979 `(("r-gamlss-data" ,r-gamlss-data)
17980 ("r-gamlss-dist" ,r-gamlss-dist)
17983 ("r-survival" ,r-survival)))
17984 (home-page "http://www.gamlss.org/")
17985 (synopsis "Generalized additive models for location scale and shape")
17987 "This package provides functions for fitting the generalized additive
17988 models for location scale and shape introduced by Rigby and
17989 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17990 use a distributional regression approach where all the parameters of the
17991 conditional distribution of the response variable are modelled using
17992 explanatory variables.")
17993 ;; Either version of the license
17994 (license (list license:gpl2 license:gpl3))))
17996 (define-public r-acid
18003 (uri (cran-uri "acid" version))
18006 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18007 (properties `((upstream-name . "acid")))
18008 (build-system r-build-system)
18010 `(("r-gamlss" ,r-gamlss)
18011 ("r-gamlss-dist" ,r-gamlss-dist)
18012 ("r-hmisc" ,r-hmisc)))
18013 (home-page "https://cran.r-project.org/web/packages/acid/")
18014 (synopsis "Analysing conditional income distributions")
18016 "This package provides functions for the analysis of income distributions
18017 for subgroups of the population as defined by a set of variables like age,
18018 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18019 distribution as well as functions for moments, inequality measures, entropy
18020 measures and polarisation measures of income distributions. This package thus
18021 aides the analysis of income inequality by offering tools for the exploratory
18022 analysis of income distributions at the disaggregated level.")
18023 (license license:gpl3)))
18025 (define-public r-acm4r
18032 (uri (cran-uri "acm4r" version))
18035 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18036 (properties `((upstream-name . "acm4r")))
18037 (build-system r-build-system)
18038 (propagated-inputs `(("r-mass" ,r-mass)))
18039 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18040 (synopsis "Align-and-count method comparisons of RFLP data")
18042 "This is a package to compare sequence fragment lengths or molecular
18043 weights from pairs of lanes. The number of matching bands in the
18044 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18045 the align-and-count method.")
18046 ;; Any version of the GPL
18047 (license (list license:gpl2+ license:gpl3+))))
18049 (define-public r-filematrix
18051 (name "r-filematrix")
18056 (uri (cran-uri "filematrix" version))
18059 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18060 (properties `((upstream-name . "filematrix")))
18061 (build-system r-build-system)
18062 ;; These inputs are needed for vignettes
18064 `(("r-knitr" ,r-knitr)
18065 ("r-rmarkdown" ,r-rmarkdown)
18066 ("pandoc-citeproc" ,pandoc-citeproc)))
18067 (home-page "https://github.com/andreyshabalin/filematrix")
18068 (synopsis "File-backed matrix class with convenient read and write access")
18070 "This package provides an interface for working with large matrices
18071 stored in files, not in computer memory. It supports multiple non-character
18072 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18073 byte real values). Access to parts of the matrix is done by indexing, exactly
18074 as with usual R matrices. It supports very large matrices; the package has
18075 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18076 columns, ad allows for quick addition of extra columns to a filematrix.")
18077 (license license:lgpl3)))
18079 (define-public r-acmeeqtl
18081 (name "r-acmeeqtl")
18086 (uri (cran-uri "ACMEeqtl" version))
18089 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18090 (properties `((upstream-name . "ACMEeqtl")))
18091 (build-system r-build-system)
18093 `(("r-filematrix" ,r-filematrix)))
18094 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18095 (synopsis "Estimation of interpretable eQTL effect sizes")
18097 "This package provides a non-linear model, termed ACME, that reflects a
18098 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18099 With non-linear least-squares algorithm the maximum likelihood parameters can
18100 be estimated. The ACME model provides interpretable effect size estimates and
18101 p-values with well controlled Type-I error.")
18102 (license license:lgpl3)))
18104 (define-public r-acmer
18111 (uri (cran-uri "acmeR" version))
18114 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18115 (properties `((upstream-name . "acmeR")))
18116 (build-system r-build-system)
18117 (propagated-inputs `(("r-foreign" ,r-foreign)))
18118 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18119 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18121 "This package provides an implementation of the ACME estimator, described
18122 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18123 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18124 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18125 as carcasses age; variable bleed-through at successive searches; and interval
18126 mortality estimates. The package provides, based on search data, functions
18127 for estimating the mortality inflation factor in Frequentist and Bayesian
18129 (license license:expat)))
18131 (define-public r-r-huge
18138 (uri (cran-uri "R.huge" version))
18141 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18142 (properties `((upstream-name . "R.huge")))
18143 (build-system r-build-system)
18145 `(("r-r-methodss3" ,r-r-methodss3)
18147 ("r-r-utils" ,r-r-utils)))
18148 (home-page "https://github.com/HenrikBengtsson/R.huge")
18149 (synopsis "Methods for accessing huge amounts of data")
18151 "This is a deprecated package for accessing huge amounts of data.
18152 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18153 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18154 the @code{aroma.affymetrix} package.")
18155 (license license:lgpl2.1+)))
18157 (define-public r-r-filesets
18159 (name "r-r-filesets")
18164 (uri (cran-uri "R.filesets" version))
18167 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18168 (properties `((upstream-name . "R.filesets")))
18169 (build-system r-build-system)
18171 `(("r-digest" ,r-digest)
18172 ("r-r-cache" ,r-r-cache)
18173 ("r-r-methodss3" ,r-r-methodss3)
18175 ("r-r-utils" ,r-r-utils)))
18176 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18177 (synopsis "Easy handling of and access to files")
18179 "This package provides classes and methods to locate, setup, subset,
18180 navigate and iterate file sets, i.e. sets of files located in one or more
18181 directories on the file system. The API is designed such that these classes
18182 can be extended via inheritance to provide a richer API for special file
18183 formats. Moreover, a specific name format is defined such that filenames and
18184 directories can be considered to have full names which consists of a name
18185 followed by comma-separated tags. This adds additional flexibility to
18186 identify file sets and individual files.")
18187 (license license:lgpl2.1+)))
18189 (define-public r-r-devices
18191 (name "r-r-devices")
18196 (uri (cran-uri "R.devices" version))
18199 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18200 (properties `((upstream-name . "R.devices")))
18201 (build-system r-build-system)
18203 `(("r-base64enc" ,r-base64enc)
18204 ("r-r-methodss3" ,r-r-methodss3)
18206 ("r-r-utils" ,r-r-utils)))
18207 (home-page "https://github.com/HenrikBengtsson/R.devices")
18208 (synopsis "Unified handling of graphics devices")
18210 "This package provides functions for creating plots and image files in a
18211 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18212 Default device options as well as scales and aspect ratios are controlled in a
18213 uniform way across all device types. Switching output format requires minimal
18214 changes in code. This package is ideal for large-scale batch processing,
18215 because it will never leave open graphics devices or incomplete image files
18216 behind, even on errors or user interrupts.")
18217 (license license:lgpl2.1+)))
18219 (define-public r-acnr
18226 (uri (cran-uri "acnr" version))
18229 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18230 (properties `((upstream-name . "acnr")))
18231 (build-system r-build-system)
18232 (home-page "https://github.com/mpierrejean/acnr")
18233 (synopsis "Annotated copy-number regions")
18235 "This package provides SNP array data from different types of copy-number
18236 regions. These regions were identified manually by the authors of the package
18237 and may be used to generate realistic data sets with known truth.")
18238 (license license:lgpl2.1+)))
18240 (define-public r-acopula
18247 (uri (cran-uri "acopula" version))
18250 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18251 (properties `((upstream-name . "acopula")))
18252 (build-system r-build-system)
18253 (home-page "https://cran.r-project.org/web/packages/acopula/")
18254 (synopsis "Modelling dependence with multivariate Archimax copulas")
18256 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18257 package provides definitions of several parametric families of generator and
18258 dependence function, computes CDF and PDF, estimates parameters, tests for
18259 goodness of fit, generates random sample and checks copula properties for
18260 custom constructs. In the 2-dimensional case explicit formulas for density
18261 are used, contrary to higher dimensions when all derivatives are linearly
18262 approximated. Several non-archimax families (normal, FGM, Plackett) are
18263 provided as well.")
18264 (license license:gpl2)))
18266 (define-public r-tuner
18273 (uri (cran-uri "tuneR" version))
18276 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18277 (properties `((upstream-name . "tuneR")))
18278 (build-system r-build-system)
18279 (propagated-inputs `(("r-signal" ,r-signal)))
18280 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18281 (synopsis "Analysis of music and speech")
18283 "This is a package for the analysis of music and speech. Analyze music
18284 and speech, extract features like MFCCs, handle wave files and their
18285 representation in various ways, read MP3, read MIDI, perform steps of a
18286 transcription, ...")
18287 ;; Either of these versions.
18288 (license (list license:gpl2 license:gpl3))))
18290 (define-public r-seewave
18297 (uri (cran-uri "seewave" version))
18300 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18301 (properties `((upstream-name . "seewave")))
18302 (build-system r-build-system)
18304 `(("libsndfile" ,libsndfile)))
18306 `(("r-tuner" ,r-tuner)))
18307 (home-page "http://rug.mnhn.fr/seewave")
18308 (synopsis "Sound analysis and synthesis")
18310 "This package provides functions for analysing, manipulating, displaying,
18311 editing and synthesizing time waves (particularly sound). This package
18312 processes time analysis (oscillograms and envelopes), spectral content,
18313 resonance quality factor, entropy, cross correlation and autocorrelation,
18314 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18315 and 3D spectrograms and many other analyses.")
18316 (license license:gpl2+)))
18318 (define-public r-acousticndlcoder
18320 (name "r-acousticndlcoder")
18325 (uri (cran-uri "AcousticNDLCodeR" version))
18328 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18330 `((upstream-name . "AcousticNDLCodeR")))
18331 (build-system r-build-system)
18333 `(("r-seewave" ,r-seewave)
18334 ("r-tuner" ,r-tuner)
18336 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18337 (synopsis "Coding sound files for use with NDL")
18339 "Make acoustic cues to use with the R package @code{ndl}.
18340 The package implements functions used in the PLoS ONE paper \"Words from
18341 spontaneous conversational speech can be recognized with human-like accuracy
18342 by an error-driven learning algorithm that discriminates between meanings
18343 straight from smart acoustic features, bypassing the phoneme as recognition
18344 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18345 (license license:gpl2+)))
18347 (define-public r-acp
18354 (uri (cran-uri "acp" version))
18357 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18358 (properties `((upstream-name . "acp")))
18359 (build-system r-build-system)
18361 `(("r-quantmod" ,r-quantmod)
18362 ("r-tseries" ,r-tseries)))
18363 (home-page "https://cran.r-project.org/web/packages/acp/")
18364 (synopsis "Autoregressive conditional Poisson")
18366 "This package supports the analysis of count data exhibiting
18367 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18368 model (ACP(p,q)) proposed by Heinen (2003).")
18369 (license license:gpl2)))
18371 (define-public r-ada
18378 (uri (cran-uri "ada" version))
18381 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18382 (properties `((upstream-name . "ada")))
18383 (build-system r-build-system)
18384 (propagated-inputs `(("r-rpart" ,r-rpart)))
18385 (home-page "https://cran.r-project.org/web/packages/ada/")
18386 (synopsis "Stochastic boosting")
18388 "This package provides a straightforward, well-documented, and broad
18389 boosting routine for classification, ideally suited for small to
18390 moderate-sized data sets. It performs discrete, real, and gentle boost under
18391 both exponential and logistic loss on a given data set.")
18392 ;; Any version of the GPL.
18393 (license (list license:gpl2+ license:gpl3+))))
18395 (define-public r-genalg
18402 (uri (cran-uri "genalg" version))
18405 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18406 (properties `((upstream-name . "genalg")))
18407 (build-system r-build-system)
18408 (home-page "https://github.com/egonw/genalg")
18409 (synopsis "R based genetic algorithm")
18411 "This package provides an R based genetic algorithm for binary and
18412 floating point chromosomes.")
18413 (license license:gpl2)))
18415 (define-public r-kernelfactory
18417 (name "r-kernelfactory")
18422 (uri (cran-uri "kernelFactory" version))
18425 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18426 (properties `((upstream-name . "kernelFactory")))
18427 (build-system r-build-system)
18430 ("r-genalg" ,r-genalg)
18431 ("r-kernlab" ,r-kernlab)
18432 ("r-randomforest" ,r-randomforest)))
18433 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18434 (synopsis "Ensemble of kernel machines")
18436 "Kernel factory is an ensemble method where each base classifier (random
18437 forest) is fit on the kernel matrix of a subset of the training data.")
18438 (license license:gpl2+)))
18440 (define-public r-dummies
18447 (uri (cran-uri "dummies" version))
18450 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18451 (properties `((upstream-name . "dummies")))
18452 (build-system r-build-system)
18453 (home-page "https://decisionpatterns.com")
18454 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18456 "This package lets you expand factors, characters and other eligible
18457 classes into dummy/indicator variables.")
18458 (license license:gpl2+)))
18460 (define-public r-acrm
18467 (uri (cran-uri "aCRM" version))
18470 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18471 (properties `((upstream-name . "aCRM")))
18472 (build-system r-build-system)
18475 ("r-dummies" ,r-dummies)
18476 ("r-kernelfactory" ,r-kernelfactory)
18477 ("r-randomforest" ,r-randomforest)))
18478 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18479 (synopsis "Convenience functions for analytical customer relationship management")
18481 "This package provides convenience functions for data preparation and
18482 modeling often used in @dfn{analytical customer relationship
18483 management} (aCRM).")
18484 (license license:gpl2+)))
18486 (define-public r-treeclust
18488 (name "r-treeclust")
18493 (uri (cran-uri "treeClust" version))
18496 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18497 (properties `((upstream-name . "treeClust")))
18498 (build-system r-build-system)
18500 `(("r-cluster" ,r-cluster)
18501 ("r-rpart" ,r-rpart)))
18502 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18503 (synopsis "Cluster distances through trees")
18505 "This package provides tools to create a measure of inter-point
18506 dissimilarity useful for clustering mixed data, and, optionally, perform the
18508 (license license:gpl2+)))
18510 (define-public r-acrosstic
18512 (name "r-acrosstic")
18517 (uri (cran-uri "AcrossTic" version))
18520 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18521 (properties `((upstream-name . "AcrossTic")))
18522 (build-system r-build-system)
18524 `(("r-lpsolve" ,r-lpsolve)
18525 ("r-treeclust" ,r-treeclust)))
18526 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18527 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18529 "This is a package for constructing minimum-cost regular spanning
18530 subgraph as part of a non-parametric two-sample test for equality of
18532 (license license:gpl2+)))
18534 (define-public r-acrt
18541 (uri (cran-uri "acrt" version))
18544 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18545 (properties `((upstream-name . "acrt")))
18546 (build-system r-build-system)
18548 `(("r-rcpp" ,r-rcpp)
18549 ("r-rcppeigen" ,r-rcppeigen)
18550 ("r-sandwich" ,r-sandwich)))
18551 (home-page "https://cran.r-project.org/web/packages/acrt/")
18552 (synopsis "Autocorrelation robust testing")
18554 "This package provides functions for testing affine hypotheses on the
18555 regression coefficient vector in regression models with autocorrelated
18557 (license license:gpl2)))
18559 (define-public r-acs
18566 (uri (cran-uri "acs" version))
18569 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18570 (properties `((upstream-name . "acs")))
18571 (build-system r-build-system)
18573 `(("r-httr" ,r-httr)
18576 ("r-stringr" ,r-stringr)
18578 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18579 (synopsis "Work with data from the US Census")
18581 "This package provides a general toolkit for downloading, managing,
18582 analyzing, and presenting data from the
18583 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18584 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18585 American Community Survey (ACS). Confidence intervals provided with ACS data
18586 are converted to standard errors to be bundled with estimates in complex
18587 @code{acs} objects. The package provides new methods to conduct standard
18588 operations on @code{acs} objects and present/plot data in statistically
18589 appropriate ways.")
18590 (license license:gpl3)))
18592 (define-public r-acss-data
18594 (name "r-acss-data")
18599 (uri (cran-uri "acss.data" version))
18602 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18603 (properties `((upstream-name . "acss.data")))
18604 (build-system r-build-system)
18605 (home-page "http://complexitycalculator.com/methodology.html")
18606 (synopsis "Data for algorithmic complexity of short strings")
18608 "This is a data only package providing the algorithmic complexity of
18609 short strings, computed using the coding theorem method. For a given set of
18610 symbols in a string, all possible or a large number of random samples of
18611 Turing machines with a given number of states (e.g., 5) and number of symbols
18612 corresponding to the number of symbols in the strings were simulated until
18613 they reached a halting state or failed to end. This package contains data on
18614 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18615 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18616 distribution of the halting states.")
18617 (license license:gpl2+)))
18619 (define-public r-acss
18626 (uri (cran-uri "acss" version))
18629 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18630 (properties `((upstream-name . "acss")))
18631 (build-system r-build-system)
18633 `(("r-acss-data" ,r-acss-data)
18635 (home-page "http://complexitycalculator.com/methodology.html")
18636 (synopsis "Algorithmic complexity for short strings")
18638 "The main purpose of this package is to provide the algorithmic
18639 complexity for short strings, an approximation of the Kolmogorov Complexity of
18640 a short string using the coding theorem method. While the database containing
18641 the complexity is provided in the data only package @code{acss.data}, this
18642 package provides functions accessing the data such as @code{prob_random}
18643 returning the posterior probability that a given string was produced by a
18644 random process. In addition, two traditional (but problematic) measures of
18645 complexity are also provided: entropy and change complexity.")
18646 (license license:gpl2+)))
18648 (define-public r-acswr
18655 (uri (cran-uri "ACSWR" version))
18658 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18659 (properties `((upstream-name . "ACSWR")))
18660 (build-system r-build-system)
18662 `(("r-mass" ,r-mass)))
18663 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18664 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18666 "This is a companion package for the book \"A Course in Statistics with
18667 R\" (ISBN 978-1-119-15272-9.)")
18668 (license license:gpl2)))
18670 (define-public r-alabama
18673 (version "2015.3-1")
18677 (uri (cran-uri "alabama" version))
18680 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18681 (properties `((upstream-name . "alabama")))
18682 (build-system r-build-system)
18683 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18684 (home-page "https://cran.r-project.org/web/packages/alabama/")
18685 (synopsis "Constrained nonlinear optimization")
18687 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18688 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18689 constraints. Linear or nonlinear equality and inequality constraints are
18691 (license license:gpl2+)))
18693 (define-public r-gdina
18700 (uri (cran-uri "GDINA" version))
18703 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18704 (properties `((upstream-name . "GDINA")))
18705 (build-system r-build-system)
18707 `(("r-alabama" ,r-alabama)
18708 ("r-ggplot2" ,r-ggplot2)
18710 ("r-nloptr" ,r-nloptr)
18711 ("r-numderiv" ,r-numderiv)
18713 ("r-rcpparmadillo" ,r-rcpparmadillo)
18714 ("r-rsolnp" ,r-rsolnp)
18715 ("r-shiny" ,r-shiny)
18716 ("r-shinydashboard" ,r-shinydashboard)))
18718 `(("r-knitr" ,r-knitr)))
18719 (home-page "https://github.com/Wenchao-Ma/GDINA")
18720 (synopsis "Generalized DINA model framework")
18722 "This package provides a set of psychometric tools for cognitive
18723 diagnosis modeling based on the generalized deterministic inputs, noisy and
18724 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18725 and its extensions, including the sequential G-DINA model by Ma and de la
18726 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18727 polytomous G-DINA model by Chen and de la Torre
18728 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18729 distribution can be independent, saturated, higher-order, loglinear smoothed
18730 or structured. Q-matrix validation, item and model fit statistics, model
18731 comparison at test and item level and differential item functioning can also
18732 be conducted. A graphical user interface is also provided.")
18733 (license license:gpl3)))
18735 (define-public r-actcd
18742 (uri (cran-uri "ACTCD" version))
18745 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18746 (properties `((upstream-name . "ACTCD")))
18747 (build-system r-build-system)
18749 `(("r-gdina" ,r-gdina)
18750 ("r-r-methodss3" ,r-r-methodss3)))
18752 `(("gfortran" ,gfortran)))
18753 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18754 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18756 "This is a package supporting cluster analysis for cognitive diagnosis
18757 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18758 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18759 sum-scores, cluster analysis techniques can be used to classify examinees into
18760 latent classes based on their attribute patterns. In addition to the
18761 algorithms used to classify data, three labeling approaches are proposed to
18762 label clusters so that examinees' attribute profiles can be obtained.")
18763 (license license:gpl2+)))
18765 (define-public r-ineq
18772 (uri (cran-uri "ineq" version))
18775 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18776 (properties `((upstream-name . "ineq")))
18777 (build-system r-build-system)
18778 (home-page "https://cran.r-project.org/web/packages/ineq/")
18779 (synopsis "Measuring inequality, concentration, and poverty")
18781 "This package provides tools for measuring inequality, concentration, and
18782 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18783 ;; Either of these two versions.
18784 (license (list license:gpl2 license:gpl3))))
18786 (define-public r-actfrag
18793 (uri (cran-uri "ActFrag" version))
18796 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18797 (properties `((upstream-name . "ActFrag")))
18798 (build-system r-build-system)
18800 `(("r-accelerometry" ,r-accelerometry)
18801 ("r-dplyr" ,r-dplyr)
18803 ("r-survival" ,r-survival)
18804 ("r-tidyr" ,r-tidyr)))
18805 (home-page "https://github.com/junruidi/ActFrag")
18806 (synopsis "Activity fragmentation metrics extraction")
18808 "This package provides functions to extract commonly used fragmentation
18809 metrics to quantify time accumulation strategies based on minute level
18810 actigraphy-measured activity counts data.")
18811 (license license:gpl3)))
18813 (define-public r-fda
18816 (version "5.1.5.1")
18820 (uri (cran-uri "fda" version))
18823 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
18824 (properties `((upstream-name . "fda")))
18825 (build-system r-build-system)
18827 `(("r-matrix" ,r-matrix)))
18828 (home-page "https://www.functionaldata.org")
18829 (synopsis "Functional data analysis")
18831 "These functions were developed to support functional data analysis as
18832 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18833 Analysis. The package includes data sets and script files working many
18835 (license license:gpl2+)))
18837 (define-public r-actigraphy
18839 (name "r-actigraphy")
18844 (uri (cran-uri "Actigraphy" version))
18847 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18848 (properties `((upstream-name . "Actigraphy")))
18849 (build-system r-build-system)
18851 `(("r-fda" ,r-fda)))
18852 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18853 (synopsis "Actigraphy data analysis")
18855 "This package provides tools for functional linear modeling and analysis
18856 of actigraphy data.")
18857 (license license:asl2.0)))
18859 (define-public r-activedriver
18861 (name "r-activedriver")
18866 (uri (cran-uri "ActiveDriver" version))
18869 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18870 (properties `((upstream-name . "ActiveDriver")))
18871 (build-system r-build-system)
18873 `(("r-mass" ,r-mass)))
18874 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18875 (synopsis "Tools for finding cancer driver proteins")
18877 "This package provides a mutation analysis tool that discovers cancer
18878 driver genes with frequent mutations in protein signalling sites such as
18879 post-translational modifications (phosphorylation, ubiquitination, etc). The
18880 Poisson generalized linear regression model identifies genes where cancer
18881 mutations in signalling sites are more frequent than expected from the
18882 sequence of the entire gene. Integration of mutations with signalling
18883 information helps find new driver genes and propose candidate mechanisms to
18885 (license license:gpl2+)))
18887 (define-public r-activitycounts
18889 (name "r-activitycounts")
18894 (uri (cran-uri "activityCounts" version))
18897 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18899 `((upstream-name . "activityCounts")))
18900 (build-system r-build-system)
18902 `(("r-lubridate" ,r-lubridate)
18903 ("r-magrittr" ,r-magrittr)
18904 ("r-seewave" ,r-seewave)
18905 ("r-signal" ,r-signal)
18906 ("r-tibble" ,r-tibble)))
18907 (home-page "https://github.com/walkabillylab/activityCounts")
18908 (synopsis "Generate ActiLife counts")
18910 "ActiLife generates activity counts from data collected by Actigraph
18911 accelerometers. Actigraph is one of the most common research-grade
18912 accelerometers. There is considerable research validating and developing
18913 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18914 counts are proprietary and difficult to implement if researchers use different
18915 accelerometer brands. The code creates ActiLife counts from raw acceleration
18916 data for different accelerometer brands.")
18917 (license license:gpl3)))
18919 (define-public r-activityindex
18921 (name "r-activityindex")
18926 (uri (cran-uri "ActivityIndex" version))
18929 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18930 (properties `((upstream-name . "ActivityIndex")))
18931 (build-system r-build-system)
18933 `(("r-data-table" ,r-data-table)
18934 ("r-matrixstats" ,r-matrixstats)
18935 ("r-r-utils" ,r-r-utils)))
18936 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18937 (synopsis "Activity Index calculation using raw accelerometry data")
18939 "This is a package to read raw accelerometry from GT3X+ accelerometry
18940 data and plain table data to calculate the Activity Index from Bai et
18941 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18942 (license license:gpl3)))
18944 (define-public r-activpal
18946 (name "r-activpal")
18951 (uri (cran-uri "activPAL" version))
18954 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18955 (properties `((upstream-name . "activPAL")))
18956 (build-system r-build-system)
18958 `(("r-devtools" ,r-devtools)
18959 ("r-dplyr" ,r-dplyr)
18960 ("r-ggplot2" ,r-ggplot2)
18961 ("r-lubridate" ,r-lubridate)
18962 ("r-magrittr" ,r-magrittr)
18963 ("r-tidyr" ,r-tidyr)))
18964 (home-page "https://cran.r-project.org/web/packages/activPAL")
18965 (synopsis "Processing and chart generation from activPAL events files")
18967 "This package contains functions to generate pre-defined summary
18968 statistics from activPAL events files. The package also contains functions to
18969 produce informative graphics that visualize physical activity behaviour and
18970 trends. This includes generating graphs that align physical activity
18971 behaviour with additional time based observations described by other data
18972 sets, such as sleep diaries and continuous glucose monitoring data.")
18973 (license license:gpl3)))
18975 (define-public r-activpalprocessing
18977 (name "r-activpalprocessing")
18982 (uri (cran-uri "activpalProcessing" version))
18985 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18987 `((upstream-name . "activpalProcessing")))
18988 (build-system r-build-system)
18990 `(("r-chron" ,r-chron)))
18991 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18992 (synopsis "Process activPAL events files")
18994 "This package performs estimation of physical activity and sedentary
18995 behavior variables from activPAL events files.")
18996 ;; Either version of the GPL.
18997 (license (list license:gpl2 license:gpl3))))
18999 (define-public r-actogrammr
19001 (name "r-actogrammr")
19006 (uri (cran-uri "actogrammr" version))
19009 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19010 (properties `((upstream-name . "actogrammr")))
19011 (build-system r-build-system)
19013 `(("r-dplyr" ,r-dplyr)
19014 ("r-ggplot2" ,r-ggplot2)
19015 ("r-lubridate" ,r-lubridate)
19016 ("r-readr" ,r-readr)
19017 ("r-tidyr" ,r-tidyr)))
19018 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19019 (synopsis "Read in activity data and plot actograms")
19021 "Read in activity measurements from standard file formats used by
19022 circadian rhythm researchers, currently only ClockLab format, and process and
19023 plot the data. The central type of plot is the actogram, as first described
19024 in \"Activity and distribution of certain wild mice in relation to biotic
19025 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19026 (license license:gpl3)))
19028 (define-public r-expint
19035 (uri (cran-uri "expint" version))
19038 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19039 (properties `((upstream-name . "expint")))
19040 (build-system r-build-system)
19041 (home-page "https://gitlab.com/vigou3/expint")
19042 (synopsis "Exponential integral and incomplete Gamma function")
19044 "This package provides the exponential integrals @code{E_1(x)},
19045 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19046 function @code{G(a, x)} defined for negative values of its first argument.
19047 The package also gives easy access to the underlying C routines through an
19048 API; see the package vignette for details.")
19049 (license license:gpl2+)))
19051 (define-public r-actuar
19058 (uri (cran-uri "actuar" version))
19061 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19062 (properties `((upstream-name . "actuar")))
19063 (build-system r-build-system)
19064 (propagated-inputs `(("r-expint" ,r-expint)))
19065 (home-page "https://gitlab.com/vigou3/actuar")
19066 (synopsis "Actuarial functions and heavy tailed distributions")
19068 "This package provides functions and data sets for actuarial science:
19069 modeling of loss distributions; risk theory and ruin theory; simulation of
19070 compound models, discrete mixtures and compound hierarchical models;
19071 credibility theory. It boasts support for many additional probability
19072 distributions to model insurance loss amounts and loss frequency: 19
19073 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19074 distribution; zero-truncated and zero-modified extensions of the standard
19075 discrete distributions. It also supports phase-type distributions commonly
19076 used to compute ruin probabilities.")
19077 (license license:gpl2+)))
19079 (define-public r-bmp
19086 (uri (cran-uri "bmp" version))
19089 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19090 (properties `((upstream-name . "bmp")))
19091 (build-system r-build-system)
19092 (home-page "https://cran.r-project.org/web/packages/bmp/")
19093 (synopsis "Read Bitmap (BMP) images")
19095 "This package provides pure R tools to read BMP format images. It is
19096 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19097 (license license:gpl2+)))
19099 (define-public r-readbitmap
19101 (name "r-readbitmap")
19106 (uri (cran-uri "readbitmap" version))
19109 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19110 (properties `((upstream-name . "readbitmap")))
19111 (build-system r-build-system)
19113 `(("libjpeg" ,libjpeg-turbo)
19114 ("libpng" ,libpng)))
19119 ("r-tiff" ,r-tiff)))
19120 (home-page "https://github.com/jefferis/readbitmap")
19121 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19123 "This package provides tools to identify and read BMP, JPEG, PNG, and
19124 TIFF format bitmap images. Identification defaults to the use of the magic
19125 number embedded in the file rather than the file extension.")
19126 (license license:gpl2+)))
19128 (define-public r-imager
19135 (uri (cran-uri "imager" version))
19138 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19139 (properties `((upstream-name . "imager")))
19140 (build-system r-build-system)
19143 ("libtiff" ,libtiff)
19147 `(("r-downloader" ,r-downloader)
19148 ("r-igraph" ,r-igraph)
19150 ("r-magrittr" ,r-magrittr)
19152 ("r-purrr" ,r-purrr)
19154 ("r-readbitmap" ,r-readbitmap)
19155 ("r-stringr" ,r-stringr)))
19157 `(("pkg-config" ,pkg-config)
19158 ("r-knitr" ,r-knitr)))
19159 (home-page "https://dahtah.github.io/imager/")
19160 (synopsis "Image processing library")
19162 "This is a package for fast image processing for images in up to 4
19163 dimensions (two spatial dimensions, one time/depth dimension, one color
19164 dimension). It provides most traditional image processing tools (filtering,
19165 morphology, transformations, etc.) as well as various functions for easily
19166 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19167 simple, modern C++ library for image processing.")
19168 (license license:lgpl3)))
19170 (define-public r-acuityview
19172 (name "r-acuityview")
19177 (uri (cran-uri "AcuityView" version))
19180 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19181 (properties `((upstream-name . "AcuityView")))
19182 (build-system r-build-system)
19184 `(("r-fftwtools" ,r-fftwtools)
19185 ("r-imager" ,r-imager)
19186 ("r-plotrix" ,r-plotrix)))
19187 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19188 (synopsis "Display scenes as seen by an animal with less acute vision")
19190 "This package provides a simple method for representing a visual scene as
19191 it may be seen by an animal with less acute vision.")
19192 (license license:gpl2+)))
19194 (define-public r-caret
19201 (uri (cran-uri "caret" version))
19204 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19205 (build-system r-build-system)
19207 `(("r-foreach" ,r-foreach)
19208 ("r-ggplot2" ,r-ggplot2)
19209 ("r-lattice" ,r-lattice)
19210 ("r-modelmetrics" ,r-modelmetrics)
19214 ("r-recipes" ,r-recipes)
19215 ("r-reshape2" ,r-reshape2)
19216 ("r-withr" ,r-withr)))
19218 `(("r-knitr" ,r-knitr)))
19219 (home-page "https://github.com/topepo/caret")
19220 (synopsis "Classification and regression training")
19222 "This package provides miscellaneous functions for training and plotting
19223 classification and regression models.")
19224 (license license:gpl2+)))
19226 (define-public r-adabag
19233 (uri (cran-uri "adabag" version))
19236 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19237 (properties `((upstream-name . "adabag")))
19238 (build-system r-build-system)
19240 `(("r-caret" ,r-caret)
19241 ("r-doparallel" ,r-doparallel)
19242 ("r-foreach" ,r-foreach)
19243 ("r-rpart" ,r-rpart)))
19244 (home-page "https://cran.r-project.org/web/packages/adabag/")
19245 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19247 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19248 Breiman's Bagging algorithm using classification trees as individual
19249 classifiers. Once these classifiers have been trained, they can be used to
19250 predict on new data. Also, cross validation estimation of the error can be
19252 (license license:gpl2+)))
19254 (define-public r-adagio
19261 (uri (cran-uri "adagio" version))
19264 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19265 (properties `((upstream-name . "adagio")))
19266 (build-system r-build-system)
19267 (native-inputs `(("gfortran" ,gfortran)))
19268 (home-page "https://cran.r-project.org/web/packages/adagio/")
19269 (synopsis "Discrete and global optimization routines")
19271 "This package provides methods and algorithms for discrete optimization,
19272 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19273 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19275 (license license:gpl3+)))
19277 (define-public r-univoutl
19279 (name "r-univoutl")
19284 (uri (cran-uri "univOutl" version))
19287 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19288 (properties `((upstream-name . "univOutl")))
19289 (build-system r-build-system)
19291 `(("r-hmisc" ,r-hmisc)
19292 ("r-robustbase" ,r-robustbase)))
19293 (home-page "https://github.com/marcellodo/univOutl")
19294 (synopsis "Detection of univariate outliers")
19296 "This package provides well-known outlier detection techniques in the
19297 univariate case. Methods to deal with skewed distribution are included too.
19298 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19299 historical data is implemented as well. When available, survey weights can be
19300 used in outliers detection.")
19301 (license license:gpl2+)))
19303 (define-public r-tolerance
19305 (name "r-tolerance")
19310 (uri (cran-uri "tolerance" version))
19313 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19314 (properties `((upstream-name . "tolerance")))
19315 (build-system r-build-system)
19317 `(("r-mass" ,r-mass)
19319 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19320 (synopsis "Statistical tolerance intervals and regions")
19322 "This package provides functions for estimating tolerance
19323 limits (intervals) for various univariate distributions (binomial, Cauchy,
19324 discrete Pareto, exponential, two-parameter exponential, extreme value,
19325 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19326 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19327 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19328 nonparametric tolerance intervals, tolerance bands for regression
19329 settings (linear regression, nonlinear regression, nonparametric regression,
19330 and multivariate regression), and analysis of variance tolerance intervals.
19331 Visualizations are also available for most of these settings.")
19332 (license license:gpl2+)))
19334 (define-public r-additivitytests
19336 (name "r-additivitytests")
19341 (uri (cran-uri "additivityTests" version))
19344 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19346 `((upstream-name . "additivityTests")))
19347 (build-system r-build-system)
19348 (home-page "https://github.com/simecek/additivityTests")
19349 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19351 "This package provides an implementation of the Tukey, Mandel,
19352 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19353 (license license:gpl3)))
19355 (define-public r-flexclust
19357 (name "r-flexclust")
19362 (uri (cran-uri "flexclust" version))
19365 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19366 (properties `((upstream-name . "flexclust")))
19367 (build-system r-build-system)
19369 `(("r-class" ,r-class)
19370 ("r-lattice" ,r-lattice)
19371 ("r-modeltools" ,r-modeltools)))
19372 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19373 (synopsis "Flexible cluster algorithms")
19375 "The main function @code{kcca} implements a general framework for
19376 k-centroids cluster analysis supporting arbitrary distance measures and
19377 centroid computation. Further cluster methods include hard competitive
19378 learning, neural gas, and QT clustering. There are numerous visualization
19379 methods for cluster results (neighborhood graphs, convex cluster hulls,
19380 barcharts of centroids, ...), and bootstrap methods for the analysis of
19381 cluster stability.")
19382 (license license:gpl2)))
19384 (define-public r-biclust
19391 (uri (cran-uri "biclust" version))
19394 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19395 (properties `((upstream-name . "biclust")))
19396 (build-system r-build-system)
19398 `(("r-additivitytests" ,r-additivitytests)
19399 ("r-colorspace" ,r-colorspace)
19400 ("r-flexclust" ,r-flexclust)
19401 ("r-ggplot2" ,r-ggplot2)
19402 ("r-lattice" ,r-lattice)
19404 ("r-tidyr" ,r-tidyr)))
19405 (home-page "https://cran.r-project.org/web/packages/biclust/")
19406 (synopsis "BiCluster algorithms")
19408 "The main function @code{biclust()} provides several algorithms to find
19409 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19410 In addition, the package provides methods for data
19411 preprocessing (normalization and discretization), visualization, and
19412 validation of bicluster solutions.")
19413 (license license:gpl3)))
19415 (define-public r-icge
19422 (uri (cran-uri "ICGE" version))
19425 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19426 (properties `((upstream-name . "ICGE")))
19427 (build-system r-build-system)
19429 `(("r-cluster" ,r-cluster)
19430 ("r-mass" ,r-mass)))
19431 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19432 (synopsis "Cluster estimation and identification of atypical units")
19434 "ICGE is a package that helps to estimate the number of real clusters in
19435 data as well as to identify atypical units. The underlying methods are based
19436 on distances rather than on unit x variables.")
19437 (license license:gpl2+)))
19439 (define-public r-depth
19442 (version "2.1-1.1")
19446 (uri (cran-uri "depth" version))
19449 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19450 (properties `((upstream-name . "depth")))
19451 (build-system r-build-system)
19453 `(("r-abind" ,r-abind)
19454 ("r-circular" ,r-circular)
19457 `(("gfortran" ,gfortran)))
19458 (home-page "https://cran.r-project.org/web/packages/depth/")
19459 (synopsis "Nonparametric depth functions for multivariate analysis")
19461 "This package provides tools for depth functions methodology applied to
19462 multivariate analysis. Besides allowing calculation of depth values and
19463 depth-based location estimators, the package includes functions or drawing
19464 contour plots and perspective plots of depth functions. Euclidian and
19465 spherical depths are supported.")
19466 (license license:gpl2)))
19468 (define-public r-archetypes
19470 (name "r-archetypes")
19471 (version "2.2-0.1")
19475 (uri (cran-uri "archetypes" version))
19478 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19479 (properties `((upstream-name . "archetypes")))
19480 (build-system r-build-system)
19482 `(("r-modeltools" ,r-modeltools)
19483 ("r-nnls" ,r-nnls)))
19484 (home-page "https://cran.r-project.org/web/packages/archetypes")
19485 (synopsis "Archetypal analysis")
19487 "The main function @code{archetypes} implements a framework for
19488 archetypal analysis supporting arbitrary problem solving mechanisms for the
19489 different conceptual parts of the algorithm.")
19490 (license license:gpl2+)))
19492 (define-public r-shapes
19499 (uri (cran-uri "shapes" version))
19502 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19503 (properties `((upstream-name . "shapes")))
19504 (build-system r-build-system)
19506 `(("r-mass" ,r-mass)
19507 ("r-minpack-lm" ,r-minpack-lm)
19509 ("r-scatterplot3d" ,r-scatterplot3d)))
19510 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19511 (synopsis "Statistical shape analysis")
19513 "This package provides routines for the statistical analysis of landmark
19514 shapes, including Procrustes analysis, graphical displays, principal
19515 components analysis, permutation and bootstrap tests, thin-plate spline
19516 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19517 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19518 Edition), John Wiley and Sons.")
19519 (license license:gpl2)))
19521 (define-public r-anthropometry
19523 (name "r-anthropometry")
19528 (uri (cran-uri "Anthropometry" version))
19531 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19532 (properties `((upstream-name . "Anthropometry")))
19533 (build-system r-build-system)
19535 `(("r-archetypes" ,r-archetypes)
19536 ("r-biclust" ,r-biclust)
19537 ("r-cluster" ,r-cluster)
19538 ("r-depth" ,r-depth)
19543 ("r-shapes" ,r-shapes)))
19545 `(("r-knitr" ,r-knitr)))
19546 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19547 (synopsis "Statistical methods for anthropometric data")
19549 "This package provides statistical methods especially developed to
19550 analyze anthropometric data. These methods are aimed at providing effective
19551 solutions to some commons problems related to Ergonomics and Anthropometry.
19552 They are based on clustering, the statistical concept of data depth,
19553 statistical shape analysis and archetypal analysis.")
19554 (license license:gpl2+)))
19556 (define-public r-adamethods
19558 (name "r-adamethods")
19563 (uri (cran-uri "adamethods" version))
19566 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19567 (properties `((upstream-name . "adamethods")))
19568 (build-system r-build-system)
19570 `(("r-anthropometry" ,r-anthropometry)
19571 ("r-archetypes" ,r-archetypes)
19573 ("r-foreach" ,r-foreach)
19575 ("r-tolerance" ,r-tolerance)
19576 ("r-univoutl" ,r-univoutl)))
19577 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19578 (synopsis "Archetypoid algorithms and anomaly detection")
19580 "This package is a collection of several algorithms to obtain
19581 archetypoids with small and large databases and with both classical
19582 multivariate data and functional data (univariate and multivariate). Some of
19583 these algorithms also allow to detect anomalies (outliers).")
19584 (license license:gpl2+)))
19586 (define-public r-idpmisc
19593 (uri (cran-uri "IDPmisc" version))
19596 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19597 (properties `((upstream-name . "IDPmisc")))
19598 (build-system r-build-system)
19600 `(("r-lattice" ,r-lattice)))
19601 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19602 (synopsis "Functions for data analyses and visualization")
19604 "This package provides different high-level graphics functions for
19605 displaying large datasets, displaying circular data in a very flexible way,
19606 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19607 2D-plots, creating figures with differently colored margin and plot region.
19608 In addition, the package contains auxiliary functions for data manipulation
19609 like omitting observations with irregular values or selecting data by logical
19610 vectors, which include NAs. Other functions are especially useful in
19611 spectroscopy and analyses of environmental data: robust baseline fitting,
19612 finding peaks in spectra, converting humidity measures.")
19613 (license license:gpl3+)))
19615 (define-public r-qqman
19622 (uri (cran-uri "qqman" version))
19625 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19626 (properties `((upstream-name . "qqman")))
19627 (build-system r-build-system)
19629 `(("r-calibrate" ,r-calibrate)))
19630 (home-page "https://cran.r-project.org/web/packages/qqman/")
19631 (synopsis "Q-Q and Manhattan plots for GWAS data")
19633 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19634 from PLINK results.")
19635 (license license:gpl3)))
19637 (define-public r-ggplot-multistats
19639 (name "r-ggplot-multistats")
19644 (uri (cran-uri "ggplot.multistats" version))
19647 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19649 `((upstream-name . "ggplot.multistats")))
19650 (build-system r-build-system)
19652 `(("r-ggplot2" ,r-ggplot2)
19653 ("r-hexbin" ,r-hexbin)
19654 ("r-rlang" ,r-rlang)
19655 ("r-scales" ,r-scales)))
19656 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19657 (synopsis "Multiple summary statistics for binned stats/geometries")
19659 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19660 which functions similar to its singular form, but allows the use of multiple
19661 statistics per bin. Those statistics can be mapped to multiple bin
19663 (license license:gpl3)))
19665 (define-public r-knn-covertree
19667 (name "r-knn-covertree")
19672 (uri (cran-uri "knn.covertree" version))
19675 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19676 (properties `((upstream-name . "knn.covertree")))
19677 (build-system r-build-system)
19679 `(("r-matrix" ,r-matrix)
19681 ("r-rcppeigen" ,r-rcppeigen)))
19682 (home-page "https://github.com/flying-sheep/knn.covertree")
19683 (synopsis "Accurate kNN Implementation with multiple distance measures")
19685 "Similarly to the FNN package, this package allows calculation of the k
19686 nearest neighbors (kNN) of a data matrix. The implementation is based on
19687 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19688 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19689 (license license:agpl3+)))
19691 (define-public r-poibin
19698 (uri (cran-uri "poibin" version))
19701 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19702 (properties `((upstream-name . "poibin")))
19703 (build-system r-build-system)
19704 (home-page "https://cran.r-project.org/web/packages/poibin/")
19705 (synopsis "Poisson binomial distribution")
19707 "This package provides an implementation of both the exact and
19708 approximation methods for computing the @dfn{cumulative distribution
19709 function} (CDF) of the Poisson binomial distribution. It also provides the
19710 @dfn{probability mass function} (PMF), quantile function, and random number
19711 generation for the Poisson binomial distribution.")
19712 (license license:gpl2)))
19714 (define-public r-diagram
19721 (uri (cran-uri "diagram" version))
19724 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19725 (properties `((upstream-name . "diagram")))
19726 (build-system r-build-system)
19728 `(("r-shape" ,r-shape)))
19729 (home-page "https://cran.r-project.org/web/packages/diagram/")
19730 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19732 "This package provides tools to visualize simple graphs (networks) based
19733 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19734 electrical networks, etc. It also includes supporting material for the book
19735 \"A practical guide to ecological modelling - using R as a simulation
19736 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19737 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19738 Francesca Mazzia (2012).")
19739 (license license:gpl2+)))
19741 (define-public r-lim
19748 (uri (cran-uri "LIM" version))
19751 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19752 (properties `((upstream-name . "LIM")))
19753 (build-system r-build-system)
19755 `(("r-diagram" ,r-diagram)
19756 ("r-limsolve" ,r-limsolve)))
19757 (home-page "https://cran.r-project.org/web/packages/LIM/")
19758 (synopsis "Linear inverse model examples and solution methods")
19760 "This package provides functions that read and solve linear inverse
19761 problems (food web problems, linear programming problems).")
19762 (license license:gpl2+)))
19764 (define-public r-shinycssloaders
19766 (name "r-shinycssloaders")
19771 (uri (cran-uri "shinycssloaders" version))
19774 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19776 `((upstream-name . "shinycssloaders")))
19777 (build-system r-build-system)
19779 `(("r-digest" ,r-digest)
19781 ("r-shiny" ,r-shiny)))
19782 (home-page "https://github.com/andrewsali/shinycssloaders")
19783 (synopsis "Add CSS loading animations to Shiny outputs")
19785 "This package provides tools to create a lightweight Shiny wrapper for
19786 the css-loaders created by Luke Hass
19787 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19788 automatically show a loader when the output is (re)calculating.")
19789 (license license:gpl3)))
19791 (define-public r-rsvg
19798 (uri (cran-uri "rsvg" version))
19801 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19802 (properties `((upstream-name . "rsvg")))
19803 (build-system r-build-system)
19805 `(("librsvg" ,librsvg)
19808 `(("pkg-config" ,pkg-config)
19809 ("r-knitr" ,r-knitr)))
19810 (home-page "https://github.com/jeroen/rsvg#readme")
19811 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19813 "This package allows you to render vector-based SVG images into
19814 high-quality custom-size bitmap arrays using the librsvg2 library. The
19815 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19816 addition, the package can convert images directly to various formats such as
19817 PDF or PostScript.")
19818 (license license:expat)))
19820 (define-public r-influencer
19822 (name "r-influencer")
19827 (uri (cran-uri "influenceR" version))
19830 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19831 (properties `((upstream-name . "influenceR")))
19832 (build-system r-build-system)
19834 `(("r-igraph" ,r-igraph)
19835 ("r-matrix" ,r-matrix)))
19836 (home-page "https://github.com/rcc-uchicago/influenceR")
19837 (synopsis "Tools to quantify structural importance of nodes in a network")
19839 "This package provides functionality to compute various node centrality
19840 measures on networks. Included are functions to compute betweenness
19841 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19842 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19843 algorithm to identify key players, and Valente's bridging metric. The
19844 betweenness, Key Players, and bridging implementations are parallelized with
19846 (license license:gpl2)))
19848 (define-public r-emplik
19855 (uri (cran-uri "emplik" version))
19858 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19859 (properties `((upstream-name . "emplik")))
19860 (build-system r-build-system)
19862 `(("r-quantreg" ,r-quantreg)))
19863 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19864 (synopsis "Empirical likelihood ratio for censored/truncated data")
19866 "This package provides empirical likelihood ratio tests for
19867 means/quantiles/hazards from possibly censored and/or truncated data. It also
19869 (license license:gpl2+)))
19871 (define-public r-imputeyn
19873 (name "r-imputeyn")
19878 (uri (cran-uri "imputeYn" version))
19881 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19882 (properties `((upstream-name . "imputeYn")))
19883 (build-system r-build-system)
19885 `(("r-boot" ,r-boot)
19886 ("r-emplik" ,r-emplik)
19887 ("r-mvtnorm" ,r-mvtnorm)
19888 ("r-quadprog" ,r-quadprog)
19889 ("r-survival" ,r-survival)))
19890 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19891 (synopsis "Impute last largest censored observation under weighted least squares")
19893 "This package allows for the imputation of the last largest censored
19894 observantions. This method brings less bias and more efficient estimates for
19896 (license license:gpl2)))
19898 (define-public r-adapenetclass
19900 (name "r-adapenetclass")
19905 (uri (cran-uri "AdapEnetClass" version))
19908 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19909 (properties `((upstream-name . "AdapEnetClass")))
19910 (build-system r-build-system)
19912 `(("r-glmnet" ,r-glmnet)
19913 ("r-imputeyn" ,r-imputeyn)
19915 ("r-quadprog" ,r-quadprog)))
19916 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19917 (synopsis "Class of adaptive elastic net methods for censored data")
19919 "This package provides methods for variable selection for AFT models.")
19920 (license license:gpl2)))
19922 (define-public r-flock
19929 (uri (cran-uri "flock" version))
19932 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19933 (properties `((upstream-name . "flock")))
19934 (build-system r-build-system)
19935 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19936 (home-page "https://cran.r-project.org/web/packages/flock/")
19937 (synopsis "Process synchronization using file locks")
19939 "This package implements synchronization between R processes (spawned by
19940 using the @code{parallel} package for instance) using file locks. It supports
19941 both exclusive and shared locking.")
19942 (license license:asl2.0)))
19944 (define-public r-archivist
19946 (name "r-archivist")
19951 (uri (cran-uri "archivist" version))
19954 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19955 (properties `((upstream-name . "archivist")))
19956 (build-system r-build-system)
19959 ("r-digest" ,r-digest)
19960 ("r-flock" ,r-flock)
19962 ("r-lubridate" ,r-lubridate)
19963 ("r-magrittr" ,r-magrittr)
19964 ("r-rcurl" ,r-rcurl)
19965 ("r-rsqlite" ,r-rsqlite)))
19966 (home-page "https://pbiecek.github.io/archivist/")
19967 (synopsis "Tools for storing, restoring and searching for R objects")
19969 "Data exploration and modelling is a process in which a lot of data
19970 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19971 statistical models, different versions of data sets and different versions of
19972 results. Archivist helps to store and manage artifacts created in R. It
19973 allows you to store selected artifacts as binary files together with their
19974 metadata and relations. Archivist allows sharing artifacts with others. It
19975 can look for already created artifacts by using its class, name, date of the
19976 creation or other properties. It also makes it easy to restore such
19978 (license license:gpl2)))
19980 (define-public r-versions
19982 (name "r-versions")
19987 (uri (cran-uri "versions" version))
19990 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19991 (properties `((upstream-name . "versions")))
19992 (build-system r-build-system)
19993 (home-page "https://cran.r-project.org/web/packages/versions/")
19994 (synopsis "Query and install specific versions of CRAN packages")
19996 "This package allows you to install specified versions of R packages
19997 hosted on CRAN and provides functions to list available versions and the
19998 versions of currently installed packages.")
19999 (license license:bsd-3)))
20001 (define-public r-adapr
20008 (uri (cran-uri "adapr" version))
20011 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20012 (properties `((upstream-name . "adapr")))
20013 (build-system r-build-system)
20015 `(("r-archivist" ,r-archivist)
20016 ("r-devtools" ,r-devtools)
20017 ("r-digest" ,r-digest)
20018 ("r-doparallel" ,r-doparallel)
20019 ("r-gdata" ,r-gdata)
20020 ("r-ggplot2" ,r-ggplot2)
20021 ("r-git2r" ,r-git2r)
20022 ("r-igraph" ,r-igraph)
20023 ("r-knitr" ,r-knitr)
20024 ("r-plotly" ,r-plotly)
20026 ("r-rmarkdown" ,r-rmarkdown)
20027 ("r-shiny" ,r-shiny)
20028 ("r-shinydashboard" ,r-shinydashboard)
20029 ("r-versions" ,r-versions)))
20030 (home-page "https://cran.r-project.org/web/packages/adapr/")
20031 (synopsis "Implementation of an accountable data analysis process")
20033 "This package tracks reading and writing within R scripts that are
20034 organized into a directed acyclic graph. It contains an interactive Shiny
20035 application @code{adaprApp()}. It uses Git and file hashes to track version
20036 histories of inputs and outputs.")
20037 (license license:lgpl2.0)))
20039 (define-public r-adapsamp
20041 (name "r-adapsamp")
20046 (uri (cran-uri "AdapSamp" version))
20049 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20050 (properties `((upstream-name . "AdapSamp")))
20051 (build-system r-build-system)
20052 (propagated-inputs `(("r-pracma" ,r-pracma)))
20053 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20054 (synopsis "Adaptive sampling algorithms")
20056 "For distributions whose probability density functions are log-concave,
20057 the adaptive rejection sampling algorithm can be used to build envelope
20058 functions for sampling. For others, the modified adaptive rejection sampling
20059 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20060 adaptive slice sampling algorithm can be used. This R package mainly includes
20061 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20062 @code{rASS()}. These functions can realize sampling based on the algorithms
20064 (license license:gpl2)))
20066 (define-public r-adaptalint
20068 (name "r-adaptalint")
20073 (uri (cran-uri "adaptalint" version))
20076 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20077 (properties `((upstream-name . "adaptalint")))
20078 (build-system r-build-system)
20080 `(("r-dplyr" ,r-dplyr)
20081 ("r-lintr" ,r-lintr)
20082 ("r-purrr" ,r-purrr)))
20083 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20084 (synopsis "Check R code style")
20086 "This package provides tools to infer the code style (which style rules
20087 are followed and which ones are not) from one package and use it to check
20088 another. This makes it easier to find and correct the most important problems
20090 (license license:gpl3)))
20092 (define-public r-fracdiff
20094 (name "r-fracdiff")
20099 (uri (cran-uri "fracdiff" version))
20102 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20103 (properties `((upstream-name . "fracdiff")))
20104 (build-system r-build-system)
20105 (home-page "https://github.com/mmaechler/fracdiff")
20107 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20109 "This package provides tools for the maximum likelihood estimation of the
20110 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20111 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20112 (license license:gpl2+)))
20114 (define-public r-forecast
20116 (name "r-forecast")
20121 (uri (cran-uri "forecast" version))
20124 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20125 (properties `((upstream-name . "forecast")))
20126 (build-system r-build-system)
20128 `(("r-colorspace" ,r-colorspace)
20129 ("r-fracdiff" ,r-fracdiff)
20130 ("r-ggplot2" ,r-ggplot2)
20131 ("r-lmtest" ,r-lmtest)
20132 ("r-magrittr" ,r-magrittr)
20135 ("r-rcpparmadillo" ,r-rcpparmadillo)
20136 ("r-timedate" ,r-timedate)
20137 ("r-tseries" ,r-tseries)
20141 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20142 (home-page "https://pkg.robjhyndman.com/forecast/")
20143 (synopsis "Forecasting functions for time series and linear models")
20145 "This package provides methods and tools for displaying and analysing
20146 univariate time series forecasts including exponential smoothing via state
20147 space models and automatic ARIMA modelling.")
20148 (license license:gpl3)))
20150 (define-public r-xmisc
20157 (uri (cran-uri "Xmisc" version))
20160 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20161 (properties `((upstream-name . "Xmisc")))
20162 (build-system r-build-system)
20163 (home-page "https://cran.r-project.org/package=Xmisc")
20165 "Xiaobei's miscellaneous classes and functions")
20167 "This package provides Xiaobei's miscellaneous classes and functions,
20168 which are useful when developing R packages for @dfn{object oriented
20169 programming} (OOP) using R Reference Class.")
20170 (license license:gpl2+)))
20172 (define-public r-proxyc
20179 (uri (cran-uri "proxyC" version))
20182 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20183 (properties `((upstream-name . "proxyC")))
20184 (build-system r-build-system)
20186 `(("r-matrix" ,r-matrix)
20188 ("r-rcpparmadillo" ,r-rcpparmadillo)
20189 ("r-rcppparallel" ,r-rcppparallel)))
20190 (home-page "https://cran.r-project.org/package=proxyC")
20191 (synopsis "Compute proximity in large sparse matrices")
20193 "This package provides efficient tools to compute the proximity between
20194 rows or columns of large matrices. Functions are optimised for large sparse
20195 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20196 similarity/distance measures, computation of correlation, cosine similarity
20197 and Euclidean distance is particularly fast.")
20198 (license license:gpl3)))
20200 (define-public r-isocodes
20202 (name "r-isocodes")
20203 (version "2020.03.16")
20207 (uri (cran-uri "ISOcodes" version))
20210 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20211 (properties `((upstream-name . "ISOcodes")))
20212 (build-system r-build-system)
20213 (home-page "https://cran.r-project.org/package=ISOcodes")
20214 (synopsis "Selected ISO codes")
20216 "This package provides ISO language, territory, currency, script and
20217 character codes. It provides ISO 639 language codes, ISO 3166 territory
20218 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20219 character codes as well as the UN M.49 area codes.")
20220 (license license:gpl2)))
20222 (define-public r-stopwords
20224 (name "r-stopwords")
20229 (uri (cran-uri "stopwords" version))
20232 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20233 (properties `((upstream-name . "stopwords")))
20234 (build-system r-build-system)
20236 `(("r-desc" ,r-desc)
20237 ("r-isocodes" ,r-isocodes)
20238 ("r-usethis" ,r-usethis)))
20239 (home-page "https://github.com/quanteda/stopwords")
20240 (synopsis "Multilingual stopword lists")
20242 "This package provides multiple sources of stopwords, for use in text
20243 analysis and natural language processing.")
20244 (license license:expat)))
20246 (define-public r-spacyr
20253 (uri (cran-uri "spacyr" version))
20256 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20257 (properties `((upstream-name . "spacyr")))
20258 (build-system r-build-system)
20260 `(("r-data-table" ,r-data-table)
20261 ("r-reticulate" ,r-reticulate)))
20262 (home-page "https://spacyr.quanteda.io")
20263 (synopsis "R wrapper for the spaCy NLP library")
20265 "This package provides an R wrapper to the Python @dfn{natural language
20266 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20267 (license license:gpl3)))
20269 (define-public r-snowballc
20271 (name "r-snowballc")
20276 (uri (cran-uri "SnowballC" version))
20279 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20280 (properties `((upstream-name . "SnowballC")))
20281 (build-system r-build-system)
20282 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20283 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20285 "This package provides an R interface to the C @code{libstemmer} library
20286 that implements Porter's word stemming algorithm for collapsing words to a
20287 common root to aid comparison of vocabulary. Currently supported languages
20288 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20289 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20290 (license license:bsd-3)))
20292 (define-public r-quanteda
20294 (name "r-quanteda")
20299 (uri (cran-uri "quanteda" version))
20302 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20303 (properties `((upstream-name . "quanteda")))
20304 (build-system r-build-system)
20306 `(("r-data-table" ,r-data-table)
20307 ("r-digest" ,r-digest)
20308 ("r-extrafont" ,r-extrafont)
20309 ("r-fastmatch" ,r-fastmatch)
20310 ("r-ggplot2" ,r-ggplot2)
20311 ("r-ggrepel" ,r-ggrepel)
20312 ("r-jsonlite" ,r-jsonlite)
20313 ("r-magrittr" ,r-magrittr)
20314 ("r-matrix" ,r-matrix)
20315 ("r-network" ,r-network)
20316 ("r-proxyc" ,r-proxyc)
20318 ("r-rcpparmadillo" ,r-rcpparmadillo)
20319 ("r-rcppparallel" ,r-rcppparallel)
20321 ("r-snowballc" ,r-snowballc)
20322 ("r-stopwords" ,r-stopwords)
20323 ("r-stringi" ,r-stringi)
20325 ("r-yaml" ,r-yaml)))
20327 `(("r-knitr" ,r-knitr)))
20328 (home-page "https://quanteda.io")
20329 (synopsis "Quantitative analysis of textual data")
20331 "This package provides a fast, flexible, and comprehensive framework for
20332 quantitative text analysis in R. It provides functionality for corpus
20333 management, creating and manipulating tokens and ngrams, exploring keywords in
20334 context, forming and manipulating sparse matrices of documents by features and
20335 feature co-occurrences, analyzing keywords, computing feature similarities and
20336 distances, applying content dictionaries, applying supervised and unsupervised
20337 machine learning, visually representing text and text analyses, and more.")
20338 (license license:gpl3)))
20340 (define-public r-topicmodels
20342 (name "r-topicmodels")
20347 (uri (cran-uri "topicmodels" version))
20350 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20351 (properties `((upstream-name . "topicmodels")))
20352 (build-system r-build-system)
20356 `(("r-modeltools" ,r-modeltools)
20359 (home-page "https://cran.r-project.org/package=topicmodels")
20360 (synopsis "Topic models")
20362 "This package provides an interface to the C code for @dfn{Latent
20363 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20364 David M. Blei and co-authors and the C++ code for fitting LDA models using
20365 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20366 (license license:gpl2)))
20368 (define-public r-stm
20375 (uri (cran-uri "stm" version))
20378 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20379 (properties `((upstream-name . "stm")))
20380 (build-system r-build-system)
20382 `(("r-data-table" ,r-data-table)
20383 ("r-glmnet" ,r-glmnet)
20385 ("r-matrix" ,r-matrix)
20386 ("r-matrixstats" ,r-matrixstats)
20387 ("r-quadprog" ,r-quadprog)
20388 ("r-quanteda" ,r-quanteda)
20390 ("r-rcpparmadillo" ,r-rcpparmadillo)
20392 ("r-stringr" ,r-stringr)))
20393 (home-page "http://www.structuraltopicmodel.com/")
20394 (synopsis "Estimation of the Structural Topic Model")
20396 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20397 topic models with document-level covariates. The package also includes tools
20398 for model selection, visualization, and estimation of topic-covariate
20400 (license license:expat)))
20402 (define-public r-polycor
20409 (uri (cran-uri "polycor" version))
20412 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20413 (properties `((upstream-name . "polycor")))
20414 (build-system r-build-system)
20416 `(("r-matrix" ,r-matrix)
20417 ("r-mvtnorm" ,r-mvtnorm)))
20418 (home-page "https://r-forge.r-project.org/projects/polycor/")
20419 (synopsis "Polychoric and polyserial correlations")
20421 "This package provides tools to compute polychoric and polyserial
20422 correlations by quick \"two-step\" methods or ML, optionally with standard
20423 errors; tetrachoric and biserial correlations are special cases.")
20424 (license license:gpl2+)))
20426 (define-public r-msm
20433 (uri (cran-uri "msm" version))
20436 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20437 (properties `((upstream-name . "msm")))
20438 (build-system r-build-system)
20440 `(("r-expm" ,r-expm)
20441 ("r-mvtnorm" ,r-mvtnorm)
20442 ("r-survival" ,r-survival)))
20443 (home-page "https://github.com/chjackson/msm")
20444 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20446 "This package provides functions for fitting continuous-time Markov and
20447 hidden Markov multi-state models to longitudinal data. It was designed for
20448 processes observed at arbitrary times in continuous time (panel data) but some
20449 other observation schemes are supported. Both Markov transition rates and the
20450 hidden Markov output process can be modelled in terms of covariates, which may
20451 be constant or piecewise-constant in time.")
20452 (license license:gpl2+)))
20454 (define-public r-ltm
20461 (uri (cran-uri "ltm" version))
20464 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20465 (properties `((upstream-name . "ltm")))
20466 (build-system r-build-system)
20468 `(("r-mass" ,r-mass)
20470 ("r-polycor" ,r-polycor)))
20471 (home-page "https://github.com/drizopoulos/ltm")
20472 (synopsis "Latent trait models under IRT")
20474 "This is a package supporting the analysis of multivariate dichotomous
20475 and polytomous data using latent trait models under the Item Response Theory
20476 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20477 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20479 (license license:gpl2+)))
20481 (define-public r-mi
20488 (uri (cran-uri "mi" version))
20491 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20492 (properties `((upstream-name . "mi")))
20493 (build-system r-build-system)
20496 ("r-matrix" ,r-matrix)))
20497 (home-page "http://www.stat.columbia.edu/~gelman/")
20498 (synopsis "Missing data imputation and model checking")
20500 "This package provides functions for data manipulation, imputing missing
20501 values in an approximate Bayesian framework, diagnostics of the models used to
20502 generate the imputations, confidence-building mechanisms to validate some of
20503 the assumptions of the imputation algorithm, and functions to analyze multiply
20504 imputed data sets with the appropriate degree of sampling uncertainty.")
20505 (license license:gpl2+)))
20507 (define-public r-matrixcalc
20509 (name "r-matrixcalc")
20514 (uri (cran-uri "matrixcalc" version))
20517 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20518 (properties `((upstream-name . "matrixcalc")))
20519 (build-system r-build-system)
20520 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20521 (synopsis "Collection of functions for matrix calculations")
20523 "This package provides a collection of functions to support matrix
20524 calculations for probability, econometric and numerical analysis. There are
20525 additional functions that are comparable to APL functions which are useful for
20526 actuarial models such as pension mathematics.")
20527 (license license:gpl2+)))
20529 (define-public r-sem
20536 (uri (cran-uri "sem" version))
20539 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20540 (properties `((upstream-name . "sem")))
20541 (build-system r-build-system)
20543 `(("r-boot" ,r-boot)
20545 ("r-matrixcalc" ,r-matrixcalc)
20547 (home-page "https://cran.r-project.org/package=sem")
20548 (synopsis "Structural equation models")
20550 "This package provides functions for fitting general linear structural
20551 equation models (with observed and latent variables) using the RAM approach,
20552 and for fitting structural equations in observed-variable models by two-stage
20554 (license license:gpl2+)))
20556 (define-public r-semtools
20558 (name "r-semtools")
20563 (uri (cran-uri "semTools" version))
20566 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20567 (properties `((upstream-name . "semTools")))
20568 (build-system r-build-system)
20570 `(("r-lavaan" ,r-lavaan)))
20571 (home-page "https://github.com/simsem/semTools/wiki")
20572 (synopsis "Useful tools for structural equation modeling")
20574 "This package provides useful tools for structural equation modeling.")
20575 (license license:gpl2+)))
20577 (define-public r-regsem
20584 (uri (cran-uri "regsem" version))
20587 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20588 (properties `((upstream-name . "regsem")))
20589 (build-system r-build-system)
20591 `(("r-lavaan" ,r-lavaan)
20593 ("r-rcpparmadillo" ,r-rcpparmadillo)
20594 ("r-rsolnp" ,r-rsolnp)))
20595 (home-page "https://cran.r-project.org/package=regsem")
20596 (synopsis "Regularized structural equation modeling")
20598 "This package uses both ridge and lasso penalties (and extensions) to
20599 penalize specific parameters in structural equation models. The package
20600 offers additional cost functions, cross validation, and other extensions
20601 beyond traditional structural equation models. It also contains a function to
20602 perform @dfn{exploratory mediation} (XMed).")
20603 (license license:gpl2+)))
20605 (define-public r-stanheaders
20607 (name "r-stanheaders")
20608 (version "2.21.0-6")
20612 (uri (cran-uri "StanHeaders" version))
20615 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20616 (properties `((upstream-name . "StanHeaders")))
20617 (build-system r-build-system)
20618 (inputs `(("pandoc" ,pandoc)))
20620 `(("r-rcppeigen" ,r-rcppeigen)
20621 ("r-rcppparallel" ,r-rcppparallel)))
20623 `(("gfortran" ,gfortran)
20624 ("r-knitr" ,r-knitr))) ; for vignettes
20625 (home-page "https://mc-stan.org/")
20626 (synopsis "C++ header files for Stan")
20628 "The C++ header files of the Stan project are provided by this package.
20629 There is a shared object containing part of the @code{CVODES} library, but it
20630 is not accessible from R. @code{r-stanheaders} is only useful for developers
20631 who want to utilize the @code{LinkingTo} directive of their package's
20632 DESCRIPTION file to build on the Stan library without incurring unnecessary
20635 The Stan project develops a probabilistic programming language that implements
20636 full or approximate Bayesian statistical inference via Markov Chain Monte
20637 Carlo or variational methods and implements (optionally penalized) maximum
20638 likelihood estimation via optimization. The Stan library includes an advanced
20639 automatic differentiation scheme, templated statistical and linear algebra
20640 functions that can handle the automatically differentiable scalar types (and
20641 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20642 package provides user-facing R functions to parse, compile, test, estimate,
20643 and analyze Stan models.")
20644 (license license:bsd-3)))
20646 (define-public r-rpf
20653 (uri (cran-uri "rpf" version))
20656 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20657 (properties `((upstream-name . "rpf")))
20658 (build-system r-build-system)
20660 `(("r-lifecycle" ,r-lifecycle)
20661 ("r-mvtnorm" ,r-mvtnorm)
20663 ("r-rcppeigen" ,r-rcppeigen)))
20665 `(("r-knitr" ,r-knitr)))
20666 (home-page "https://github.com/jpritikin/rpf")
20667 (synopsis "Response probability functions")
20669 "The purpose of this package is to factor out logic and math common to
20670 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20671 core support code suitable for more specialized IRT packages to build upon.
20672 Complete access to optimized C functions is made available with
20673 @code{R_RegisterCCallable()}.")
20674 (license license:gpl3+)))
20676 (define-public r-openmx
20683 (uri (cran-uri "OpenMx" version))
20686 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20687 (properties `((upstream-name . "OpenMx")))
20688 (build-system r-build-system)
20691 ("r-digest" ,r-digest)
20692 ("r-lifecycle" ,r-lifecycle)
20694 ("r-matrix" ,r-matrix)
20696 ("r-rcppeigen" ,r-rcppeigen)
20698 ("r-stanheaders" ,r-stanheaders)))
20699 (native-inputs `(("gfortran" ,gfortran)))
20700 (home-page "http://openmx.ssri.psu.edu")
20701 (synopsis "Extended structural equation modelling")
20703 "This package allows for the estimation of a wide variety of advanced
20704 multivariate statistical models. It consists of a library of functions and
20705 optimizers that allow you to quickly and flexibly define an SEM model and
20706 estimate parameters given observed data.")
20707 (license license:asl2.0)))
20709 (define-public r-kutils
20716 (uri (cran-uri "kutils" version))
20719 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20720 (properties `((upstream-name . "kutils")))
20721 (build-system r-build-system)
20723 `(("r-foreign" ,r-foreign)
20724 ("r-openxlsx" ,r-openxlsx)
20726 ("r-runit" ,r-runit)
20727 ("r-xtable" ,r-xtable)))
20728 (home-page "https://cran.r-project.org/package=kutils")
20729 (synopsis "Project management tools")
20731 "This package provides tools for data importation, recoding, and
20732 inspection. There are functions to create new project folders, R code
20733 templates, create uniquely named output directories, and to quickly obtain a
20734 visual summary for each variable in a data frame. The main feature here is
20735 the systematic implementation of the \"variable key\" framework for data
20736 importation and recoding.")
20737 (license license:gpl2)))
20739 (define-public r-rockchalk
20741 (name "r-rockchalk")
20742 (version "1.8.144")
20746 (uri (cran-uri "rockchalk" version))
20749 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20750 (properties `((upstream-name . "rockchalk")))
20751 (build-system r-build-system)
20753 `(("r-cardata" ,r-cardata)
20754 ("r-kutils" ,r-kutils)
20756 ("r-mass" ,r-mass)))
20757 (home-page "https://cran.r-project.org/package=rockchalk")
20758 (synopsis "Regression estimation and presentation")
20760 "This package provides a collection of functions for interpretation and
20761 presentation of regression analysis. These functions are used to produce the
20762 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20763 includes regression diagnostics, regression tables, and plots of interactions
20764 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20765 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20766 fairly comprehensive overview.")
20767 (license license:gpl3+)))
20769 (define-public r-lisreltor
20771 (name "r-lisreltor")
20776 (uri (cran-uri "lisrelToR" version))
20779 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20780 (properties `((upstream-name . "lisrelToR")))
20781 (build-system r-build-system)
20782 (home-page "https://cran.r-project.org/package=lisrelToR")
20783 (synopsis "Import output from LISREL into R")
20785 "This is an unofficial package aimed at automating the import of LISREL
20787 (license license:gpl2)))
20789 (define-public r-bdgraph
20796 (uri (cran-uri "BDgraph" version))
20799 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
20800 (properties `((upstream-name . "BDgraph")))
20801 (build-system r-build-system)
20803 `(("r-igraph" ,r-igraph)))
20804 (home-page "https://www.uva.nl/profile/a.mohammadi")
20805 (synopsis "Bayesian structure learning in graphical models")
20807 "This package provides statistical tools for Bayesian structure learning
20808 in undirected graphical models for continuous, discrete, and mixed data. It
20809 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20810 on a continuous-time birth-death process.")
20811 (license license:gpl2+)))
20813 (define-public r-d3network
20815 (name "r-d3network")
20816 (version "0.5.2.1")
20820 (uri (cran-uri "d3Network" version))
20823 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20824 (properties `((upstream-name . "d3Network")))
20825 (build-system r-build-system)
20827 `(("r-plyr" ,r-plyr)
20828 ("r-rjson" ,r-rjson)
20829 ("r-whisker" ,r-whisker)))
20830 (home-page "http://christophergandrud.github.io/d3Network/")
20831 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20833 "This package is intended to make it easy to create D3 JavaScript
20834 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20835 (license license:gpl3+)))
20837 (define-public r-qgraph
20844 (uri (cran-uri "qgraph" version))
20847 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20848 (properties `((upstream-name . "qgraph")))
20849 (build-system r-build-system)
20851 `(("r-abind" ,r-abind)
20852 ("r-bdgraph" ,r-bdgraph)
20853 ("r-colorspace" ,r-colorspace)
20854 ("r-corpcor" ,r-corpcor)
20855 ("r-d3network" ,r-d3network)
20856 ("r-dplyr" ,r-dplyr)
20857 ("r-fdrtool" ,r-fdrtool)
20858 ("r-ggplot2" ,r-ggplot2)
20859 ("r-ggraph" ,r-ggraph)
20860 ("r-glasso" ,r-glasso)
20861 ("r-gtools" ,r-gtools)
20862 ("r-hmisc" ,r-hmisc)
20864 ("r-igraph" ,r-igraph)
20866 ("r-lavaan" ,r-lavaan)
20867 ("r-matrix" ,r-matrix)
20868 ("r-pbapply" ,r-pbapply)
20871 ("r-psych" ,r-psych)
20873 ("r-reshape2" ,r-reshape2)
20874 ("r-tidygraph" ,r-tidygraph)))
20875 (home-page "http://sachaepskamp.com/qgraph/")
20876 (synopsis "Weighted network visualization and analysis")
20878 "This package implements tools for weighted network visualization and
20879 analysis, as well as Gaussian graphical model computation. It contains graph
20880 plotting methods, and tools for psychometric data visualization and graphical
20881 model estimation. See Epskamp et al. (2012)
20882 @url{doi:10.18637/jss.v048.i04}.")
20883 (license license:gpl2)))
20885 (define-public r-semplot
20892 (uri (cran-uri "semPlot" version))
20895 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20896 (properties `((upstream-name . "semPlot")))
20897 (build-system r-build-system)
20899 `(("r-colorspace" ,r-colorspace)
20900 ("r-corpcor" ,r-corpcor)
20901 ("r-igraph" ,r-igraph)
20902 ("r-lavaan" ,r-lavaan)
20903 ("r-lisreltor" ,r-lisreltor)
20904 ("r-openmx" ,r-openmx)
20906 ("r-qgraph" ,r-qgraph)
20907 ("r-regsem" ,r-regsem)
20908 ("r-rockchalk" ,r-rockchalk)
20911 (home-page "https://github.com/SachaEpskamp/semPlot")
20912 (synopsis "Unified visualizations of structural equation models")
20914 "Structural equation modeling (SEM) has a long history of representing
20915 models graphically as path diagrams. The semPlot package for R fills the gap
20916 between advanced, but time-consuming, graphical software and the limited
20917 graphics produced automatically by SEM software. In addition, semPlot offers
20918 more functionality than drawing path diagrams: it can act as a common ground
20919 for importing SEM results into R. Any result usable as input to semPlot can
20920 also be represented in any of the three popular SEM frame-works, as well as
20921 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20922 (license license:gpl2)))
20924 (define-public r-cdm
20931 (uri (cran-uri "CDM" version))
20934 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20935 (properties `((upstream-name . "CDM")))
20936 (build-system r-build-system)
20938 `(("r-mvtnorm" ,r-mvtnorm)
20939 ("r-polycor" ,r-polycor)
20941 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20943 "https://github.com/alexanderrobitzsch/CDM")
20944 (synopsis "Cognitive diagnosis modeling")
20946 "This package provides functions for cognitive diagnosis modeling and
20947 multidimensional item response modeling for dichotomous and polytomous item
20948 responses. It enables the estimation of the DINA and DINO model, the multiple
20949 group (polytomous) GDINA model, the multiple choice DINA model, the general
20950 diagnostic model (GDM), the structured latent class model (SLCA), and
20951 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20952 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20953 estimation and the package structure. For tutorials on how to use the CDM
20954 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20955 well as Ravand and Robitzsch (2015).")
20956 (license license:gpl2+)))
20958 (define-public r-tam
20965 (uri (cran-uri "TAM" version))
20968 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20969 (properties `((upstream-name . "TAM")))
20970 (build-system r-build-system)
20974 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20975 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20976 (synopsis "Test analysis modules")
20978 "This package includes tools for marginal maximum likelihood estimation
20979 and joint maximum likelihood estimation for unidimensional and
20980 multidimensional item response models. The package functionality covers the
20981 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20982 multi-faceted Rasch model, nominal item response model, structured latent
20983 class model, mixture distribution IRT models, and located latent class models.
20984 Latent regression models and plausible value imputation are also supported.")
20985 (license license:gpl2+)))
20987 (define-public r-erm
20994 (uri (cran-uri "eRm" version))
20997 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20998 (properties `((upstream-name . "eRm")))
20999 (build-system r-build-system)
21001 `(("r-colorspace" ,r-colorspace)
21002 ("r-lattice" ,r-lattice)
21004 ("r-matrix" ,r-matrix)
21005 ("r-psych" ,r-psych)))
21006 (native-inputs `(("gfortran" ,gfortran)))
21007 (home-page "https://cran.r-project.org/package=eRm")
21008 (synopsis "Extended Rasch modeling")
21010 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21011 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21012 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21013 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21014 data matrix. Additional features are the ML estimation of the person
21015 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21016 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21017 infit and outfit measures, ICC and other plots, automated stepwise item
21018 elimination, and a simulation module for various binary data matrices.")
21019 (license license:gpl3)))
21021 (define-public r-irtoys
21028 (uri (cran-uri "irtoys" version))
21031 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21032 (properties `((upstream-name . "irtoys")))
21033 (build-system r-build-system)
21037 (home-page "https://cran.r-project.org/package=irtoys")
21038 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21040 "This package provides a collection of functions useful in learning and
21041 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21042 programs. It provides basic CTT analysis, a simple common interface to the
21043 estimation of item parameters in IRT models for binary responses with three
21044 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21045 EAP, WLE, plausible values), item and person fit statistics, scaling
21046 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21047 array of parametric and non-parametric (kernel) plots. It estimates and plots
21048 Haberman's interaction model when all items are dichotomously scored.")
21049 (license license:gpl2+)))
21051 (define-public r-iheatmapr
21053 (name "r-iheatmapr")
21058 (uri (cran-uri "iheatmapr" version))
21061 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21062 (properties `((upstream-name . "iheatmapr")))
21063 (build-system r-build-system)
21065 `(("r-fastcluster" ,r-fastcluster)
21066 ("r-ggdendro" ,r-ggdendro)
21067 ("r-htmlwidgets" ,r-htmlwidgets)
21068 ("r-jsonlite" ,r-jsonlite)
21069 ("r-knitr" ,r-knitr)
21070 ("r-magrittr" ,r-magrittr)
21071 ("r-rcolorbrewer" ,r-rcolorbrewer)
21072 ("r-scales" ,r-scales)))
21074 `(("r-knitr" ,r-knitr)))
21075 (home-page "https://docs.ropensci.org/iheatmapr")
21076 (synopsis "Interactive, Complex Heatmaps")
21078 "iheatmapr is an R package for building complex, interactive heatmaps
21079 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21080 subplots along the rows or columns of the main heatmap add more information
21081 about each row or column. For example, a one column additional heatmap may
21082 indicate what group a particular row or column belongs to. Complex heatmaps
21083 may also include multiple side by side heatmaps which show different types of
21084 data for the same conditions. Interactivity can improve complex heatmaps by
21085 providing tooltips with information about each cell and enabling zooming into
21086 interesting features. iheatmapr uses the plotly library for interactivity.")
21087 (license license:expat)))
21089 (define-public r-packrat
21096 (uri (cran-uri "packrat" version))
21099 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21100 (properties `((upstream-name . "packrat")))
21101 (build-system r-build-system)
21102 (home-page "https://github.com/rstudio/packrat/")
21103 (synopsis "Dependency management R projects")
21105 "This package provides a dependency manager for R projects that allows
21106 you to manage the R packages your project depends on in an isolated, portable,
21107 and reproducible way.")
21108 (license license:gpl2)))
21110 (define-public r-rsconnect
21112 (name "r-rsconnect")
21117 (uri (cran-uri "rsconnect" version))
21120 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21121 (properties `((upstream-name . "rsconnect")))
21122 (build-system r-build-system)
21124 `(("r-curl" ,r-curl)
21125 ("r-digest" ,r-digest)
21126 ("r-jsonlite" ,r-jsonlite)
21127 ("r-openssl" ,r-openssl)
21128 ("r-packrat" ,r-packrat)
21129 ("r-rstudioapi" ,r-rstudioapi)
21130 ("r-yaml" ,r-yaml)))
21131 (home-page "https://github.com/rstudio/rsconnect")
21132 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21134 "This package provides a programmatic deployment interface for RPubs,
21135 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21136 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21137 (license license:gpl2)))
21139 ;; This package includes minified JavaScript files. When upgrading please
21140 ;; check that there are no new minified JavaScript files.
21141 (define-public r-dygraphs
21143 (name "r-dygraphs")
21144 (version "1.1.1.6")
21148 (uri (cran-uri "dygraphs" version))
21151 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21152 (properties `((upstream-name . "dygraphs")))
21153 (build-system r-build-system)
21155 `(#:modules ((guix build utils)
21156 (guix build r-build-system)
21160 (modify-phases %standard-phases
21161 (add-after 'unpack 'process-javascript
21162 (lambda* (#:key inputs #:allow-other-keys)
21163 (with-directory-excursion "inst/htmlwidgets/lib/"
21167 `(("dygraphs/dygraph-combined-dev.js"
21168 "dygraph-combined.js")
21169 (,(assoc-ref inputs "js-jquery")
21170 "jquery/jquery.min.js")
21171 (,(assoc-ref inputs "js-fquarter")
21172 "fquarter/moment-fquarter.min.js"))))
21173 (lambda (sources targets)
21174 (for-each (lambda (source target)
21175 (format #t "Processing ~a --> ~a~%"
21177 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21178 (call-with-output-file target
21180 (dump-port minified port)))))
21181 sources targets))))
21184 `(("uglify-js" ,uglify-js)
21185 ;; They actually use version 1.11.1, but this more recent version
21186 ;; should be just fine.
21190 (uri "https://code.jquery.com/jquery-1.12.4.js")
21193 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21197 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21198 "moment-fquarter/1.0.1/moment-fquarter.js"))
21201 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21203 `(("r-htmltools" ,r-htmltools)
21204 ("r-htmlwidgets" ,r-htmlwidgets)
21205 ("r-magrittr" ,r-magrittr)
21208 (home-page "https://github.com/rstudio/dygraphs")
21209 (synopsis "Interface to Dygraphs interactive time series charting library")
21211 "This package provides an R interface to the dygraphs JavaScript charting
21212 library (a copy of which is included in the package). It provides rich
21213 facilities for charting time-series data in R, including highly configurable
21214 series- and axis-display and interactive features like zoom/pan and
21215 series/point highlighting.")
21216 (license license:expat)))
21218 (define-public r-shinystan
21220 (name "r-shinystan")
21225 (uri (cran-uri "shinystan" version))
21228 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21229 (properties `((upstream-name . "shinystan")))
21230 (build-system r-build-system)
21232 `(("r-bayesplot" ,r-bayesplot)
21233 ("r-colourpicker" ,r-colourpicker)
21235 ("r-dygraphs" ,r-dygraphs)
21236 ("r-ggplot2" ,r-ggplot2)
21237 ("r-gridextra" ,r-gridextra)
21238 ("r-gtools" ,r-gtools)
21239 ("r-markdown" ,r-markdown)
21240 ("r-reshape2" ,r-reshape2)
21241 ("r-rsconnect" ,r-rsconnect)
21242 ("r-rstan" ,r-rstan)
21243 ("r-shiny" ,r-shiny)
21244 ("r-shinyjs" ,r-shinyjs)
21245 ("r-shinythemes" ,r-shinythemes)
21246 ("r-threejs" ,r-threejs)
21247 ("r-xtable" ,r-xtable)
21249 (home-page "https://mc-stan.org/")
21250 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21252 "This package provides a graphical user interface for interactive
21253 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21254 for analyzing a posterior sample. The interface is powered by the Shiny web
21255 application framework and works with the output of MCMC programs written in
21256 any programming language (and has extended functionality for Stan models fit
21257 using the @code{rstan} and @code{rstanarm} packages).")
21258 (license license:gpl3+)))
21260 (define-public r-rstantools
21262 (name "r-rstantools")
21267 (uri (cran-uri "rstantools" version))
21270 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21271 (properties `((upstream-name . "rstantools")))
21272 (build-system r-build-system)
21273 (inputs `(("pandoc" ,pandoc)))
21275 `(("r-desc" ,r-desc)
21277 ("r-rcppparallel" ,r-rcppparallel)))
21279 `(("r-knitr" ,r-knitr)))
21280 (home-page "https://mc-stan.org/rstantools/")
21281 (synopsis "Tools for developing R packages interfacing with Stan")
21283 "This package provides various tools for developers of R packages
21284 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21285 up the required package structure, S3 generics and default methods to unify
21286 function naming across Stan-based R packages, and vignettes with
21287 recommendations for developers.")
21288 (license license:gpl3+)))
21290 (define-public r-loo
21297 (uri (cran-uri "loo" version))
21299 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21300 (properties `((upstream-name . "loo")))
21301 (build-system r-build-system)
21303 `(("pandoc" ,pandoc)
21304 ("pandoc-citeproc" ,pandoc-citeproc)))
21306 `(("r-checkmate" ,r-checkmate)
21307 ("r-matrixstats" ,r-matrixstats)))
21309 `(("r-knitr" ,r-knitr)))
21310 (home-page "https://mc-stan.org/loo/")
21311 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21313 "This package provides an implementation of efficient approximate
21314 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21315 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21316 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21317 procedure for regularizing importance weights. As a byproduct of the
21318 calculations, we also obtain approximate standard errors for estimated
21319 predictive errors and for the comparison of predictive errors between models.
21320 The package also provides methods for using stacking and other model weighting
21321 techniques to average Bayesian predictive distributions.")
21322 (license license:gpl3+)))
21324 (define-public r-rstan
21331 (uri (cran-uri "rstan" version))
21334 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21335 (properties `((upstream-name . "rstan")))
21336 (build-system r-build-system)
21339 (modify-phases %standard-phases
21340 (add-before 'install 'set-timezone
21341 ;; This package is picky about timezones.
21342 (lambda* (#:key inputs #:allow-other-keys)
21343 (setenv "TZ" "UTC+1")
21345 (string-append (assoc-ref inputs "tzdata")
21346 "/share/zoneinfo"))
21349 `(("tzdata" ,tzdata-for-tests)
21351 ("r-knitr" ,r-knitr)))
21354 ("r-ggplot2" ,r-ggplot2)
21355 ("r-gridextra" ,r-gridextra)
21356 ("r-inline" ,r-inline)
21358 ("r-pkgbuild" ,r-pkgbuild)
21360 ("r-rcppeigen" ,r-rcppeigen)
21361 ("r-rcppparallel" ,r-rcppparallel)
21362 ("r-stanheaders" ,r-stanheaders)
21364 ("r-withr" ,r-withr)))
21365 (home-page "https://discourse.mc-stan.org/")
21366 (synopsis "R interface to Stan")
21368 "User-facing R functions are provided to parse, compile, test, estimate,
21369 and analyze Stan models by accessing the header-only Stan library provided by
21370 the StanHeaders package. The Stan project develops a probabilistic
21371 programming language that implements full Bayesian statistical inference via
21372 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21373 approximation, and (optionally penalized) maximum likelihood estimation via
21374 optimization. In all three cases, automatic differentiation is used to
21375 quickly and accurately evaluate gradients without burdening the user with the
21376 need to derive the partial derivatives.")
21377 (license license:gpl3+)))
21379 (define-public r-rstanarm
21381 (name "r-rstanarm")
21386 (uri (cran-uri "rstanarm" version))
21389 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21390 (properties `((upstream-name . "rstanarm")))
21391 (build-system r-build-system)
21393 `(("pandoc" ,pandoc)
21394 ("pandoc-citeproc" ,pandoc-citeproc)))
21396 `(("r-bayesplot" ,r-bayesplot)
21398 ("r-ggplot2" ,r-ggplot2)
21401 ("r-matrix" ,r-matrix)
21404 ("r-rcppeigen" ,r-rcppeigen)
21405 ("r-rcppparallel" ,r-rcppparallel)
21406 ("r-rstan" ,r-rstan)
21407 ("r-rstantools" ,r-rstantools)
21408 ("r-shinystan" ,r-shinystan)
21409 ("r-stanheaders" ,r-stanheaders)
21410 ("r-survival" ,r-survival)))
21412 `(("r-knitr" ,r-knitr)))
21413 (home-page "https://mc-stan.org/rstanarm/")
21414 (synopsis "Bayesian applied regression modeling via Stan")
21416 "This package estimates previously compiled regression models using the
21417 @code{rstan} package, which provides the R interface to the Stan C++ library
21418 for Bayesian estimation. Users specify models via the customary R syntax with
21419 a formula and @code{data.frame} plus some additional arguments for priors.")
21420 (license license:gpl3+)))
21422 (define-public r-kendall
21429 (uri (cran-uri "Kendall" version))
21432 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21433 (properties `((upstream-name . "Kendall")))
21434 (build-system r-build-system)
21436 `(("r-boot" ,r-boot)))
21438 `(("gfortran" ,gfortran)))
21439 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21440 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21442 "This package computes the Kendall rank correlation and Mann-Kendall
21444 (license license:gpl2+)))
21446 (define-public r-zyp
21449 (version "0.10-1.1")
21453 (uri (cran-uri "zyp" version))
21456 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21457 (properties `((upstream-name . "zyp")))
21458 (build-system r-build-system)
21460 `(("r-kendall" ,r-kendall)))
21461 (home-page "https://cran.r-project.org/web/packages/zyp/")
21462 (synopsis "Zhang + Yue-Pilon Trends Package")
21464 "This package contains an efficient implementation of Sen's slope
21465 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21466 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21468 (license license:lgpl2.1)))
21470 (define-public r-rlinsolve
21472 (name "r-rlinsolve")
21477 (uri (cran-uri "Rlinsolve" version))
21480 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21481 (properties `((upstream-name . "Rlinsolve")))
21482 (build-system r-build-system)
21484 `(("r-matrix" ,r-matrix)
21486 ("r-rcpparmadillo" ,r-rcpparmadillo)
21487 ("r-rdpack" ,r-rdpack)))
21488 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21489 (synopsis "Iterative solvers for (sparse) linear system of equations")
21491 "Solving a system of linear equations is one of the most fundamental
21492 computational problems for many fields of mathematical studies, such as
21493 regression problems from statistics or numerical partial differential
21494 equations. This package provides basic stationary iterative solvers such as
21495 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21496 Nonstationary, also known as Krylov subspace methods are also provided.
21497 Sparse matrix computation is also supported in that solving large and sparse
21498 linear systems can be manageable using the @code{Matrix} package along with
21499 @code{RcppArmadillo}.")
21500 (license license:gpl3+)))
21502 (define-public r-zvcv
21509 (uri (cran-uri "ZVCV" version))
21512 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21513 (properties `((upstream-name . "ZVCV")))
21514 (build-system r-build-system)
21516 `(("r-abind" ,r-abind)
21518 ("r-dplyr" ,r-dplyr)
21519 ("r-glmnet" ,r-glmnet)
21520 ("r-magrittr" ,r-magrittr)
21521 ("r-mvtnorm" ,r-mvtnorm)
21523 ("r-rcpparmadillo" ,r-rcpparmadillo)
21524 ("r-rlinsolve" ,r-rlinsolve)))
21525 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21526 (synopsis "Zero-Variance Control Variates")
21528 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21529 to reduce the variance of Monte Carlo estimators of expectations using the
21530 derivatives of the log target. Once the derivatives are available, the only
21531 additional computational effort is in solving a linear regression problem.
21532 This method has been extended to higher dimensions using regularisation. This
21533 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21534 samples, derivatives and function evaluations are available. Additional
21535 functions for applying ZV-CV to two estimators for the normalising constant of
21536 the posterior distribution in Bayesian statistics are also supplied.")
21537 (license license:gpl2+)))
21539 (define-public r-ztype
21546 (uri (cran-uri "ztype" version))
21549 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21550 (properties `((upstream-name . "ztype")))
21551 (build-system r-build-system)
21553 `(("r-assertthat" ,r-assertthat)
21554 ("r-dplyr" ,r-dplyr)
21555 ("r-ggplot2" ,r-ggplot2)
21556 ("r-lubridate" ,r-lubridate)
21557 ("r-magrittr" ,r-magrittr)
21558 ("r-rvest" ,r-rvest)
21559 ("r-stringr" ,r-stringr)))
21560 (home-page "https://cran.r-project.org/web/packages/ztype/")
21561 (synopsis "Run a Ztype game loaded with R functions")
21563 "How fast can you type R functions on your keyboard? Find out by running
21564 a @code{zty.pe} game: export R functions as instructions to type to destroy
21565 opponents' vessels.")
21566 (license license:gpl3)))
21568 (define-public r-zseq
21575 (uri (cran-uri "Zseq" version))
21578 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21579 (properties `((upstream-name . "Zseq")))
21580 (build-system r-build-system)
21582 `(("r-gmp" ,r-gmp)))
21583 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21584 (synopsis "Integer sequence generator")
21586 "This package generates well-known integer sequences. The @code{gmp}
21587 package is adopted for computing with arbitrarily large numbers. Every
21588 function has a hyperlink to its corresponding item in the @dfn{On-Line
21589 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21590 (license license:gpl3+)))
21592 (define-public r-isoband
21599 (uri (cran-uri "isoband" version))
21602 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21603 (properties `((upstream-name . "isoband")))
21604 (build-system r-build-system)
21606 `(("r-testthat" ,r-testthat)))
21608 `(("r-knitr" ,r-knitr)))
21609 (home-page "https://github.com/wilkelab/isoband")
21610 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21612 "This package provides a fast C++ implementation to generate contour
21613 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21614 containing elevation data.")
21615 (license license:expat)))
21617 (define-public r-ppcor
21624 (uri (cran-uri "ppcor" version))
21627 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21628 (properties `((upstream-name . "ppcor")))
21629 (build-system r-build-system)
21631 `(("r-mass" ,r-mass)))
21632 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21633 (synopsis "Partial and semi-partial correlation")
21635 "This package provides users not only with a function to readily
21636 calculate the higher-order partial and semi-partial correlations but also with
21637 statistics and p-values of the correlation coefficients.")
21638 (license license:gpl2)))
21640 (define-public r-hrbrthemes
21642 (name "r-hrbrthemes")
21647 (uri (cran-uri "hrbrthemes" version))
21649 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21650 (properties `((upstream-name . "hrbrthemes")))
21651 (build-system r-build-system)
21653 `(("r-extrafont" ,r-extrafont)
21654 ("r-gdtools" ,r-gdtools)
21655 ("r-ggplot2" ,r-ggplot2)
21656 ("r-htmltools" ,r-htmltools)
21657 ("r-knitr" ,r-knitr)
21658 ("r-magrittr" ,r-magrittr)
21659 ("r-rmarkdown" ,r-rmarkdown)
21660 ("r-scales" ,r-scales)))
21662 `(("r-knitr" ,r-knitr)))
21663 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21664 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21666 "This package provides a compilation of extra @code{ggplot2} themes,
21667 scales and utilities, including a spell check function for plot label fields
21668 and an overall emphasis on typography.")
21669 (license license:expat)))
21671 (define-public r-crochet
21678 (uri (cran-uri "crochet" version))
21681 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21682 (build-system r-build-system)
21684 `(("r-knitr" ,r-knitr)))
21685 (home-page "https://github.com/agrueneberg/crochet")
21686 (synopsis "Implementation Helper for Matrix-Like Types")
21688 "Functions to help implement the extraction / subsetting / indexing
21689 function @code{[} and replacement function @code{[<-} of custom matrix-like
21690 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21691 as possible (with tests to prove it).")
21692 (license license:expat)))
21694 (define-public r-boa
21697 (version "1.1.8-2")
21701 (uri (cran-uri "boa" version))
21704 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21705 (properties `((upstream-name . "boa")))
21706 (build-system r-build-system)
21707 (home-page "http://www.jstatsoft.org/v21/i11")
21708 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21710 "This package provides a menu-driven program and library of functions for
21711 carrying out convergence diagnostics and statistical and graphical analysis of
21712 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21713 (license license:gpl2+)))
21715 (define-public r-httpcode
21717 (name "r-httpcode")
21721 (uri (cran-uri "httpcode" version))
21724 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21725 (build-system r-build-system)
21726 (home-page "https://github.com/sckott/httpcode")
21727 (synopsis "HTTP status code helper")
21728 (description "@code{httpcode} provides functionality for finding and
21729 explaining the meaning of @code{HTTP} status codes. Functions are included for
21730 searching for codes by full or partial number, by message, and to get
21731 appropriate dog and cat images for many status codes.")
21732 (license license:expat)))
21734 (define-public r-latex2exp
21736 (name "r-latex2exp")
21740 (uri (cran-uri "latex2exp" version))
21743 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21744 (build-system r-build-system)
21746 `(("r-stringr" ,r-stringr)
21747 ("r-magrittr", r-magrittr)))
21748 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21749 (synopsis "Use LaTeX expressions in plots")
21750 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21751 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21752 rendered as text, axis labels, etc. throughout R's plotting system.")
21753 (license license:expat)))
21755 (define-public r-oai
21761 (uri (cran-uri "oai" version))
21764 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21765 (build-system r-build-system)
21767 `(("r-xml2" ,r-xml2)
21770 ("r-stringr" ,r-stringr)
21771 ("r-tibble" ,r-tibble)))
21772 (home-page "https://github.com/ropensci/oai/")
21773 (synopsis "General purpose OAI-PMH services client")
21774 (description "@code{oai} provides a general purpose client to work with
21775 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21776 service. Functions are provided to work with the OAI-PMH verbs:
21777 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21778 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21779 (license license:expat)))
21781 (define-public r-argon2
21788 (uri (cran-uri "argon2" version))
21791 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21792 (properties `((upstream-name . "argon2")))
21793 (build-system r-build-system)
21794 (home-page "https://github.com/wrathematics/argon2")
21795 (synopsis "Secure password hashing based on the argon2 algorithm")
21797 "This package provides utilities for secure password hashing via the
21798 argon2 algorithm.")
21799 (license license:bsd-2)))
21801 (define-public r-getpass
21808 (uri (cran-uri "getPass" version))
21811 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21812 (properties `((upstream-name . "getPass")))
21813 (build-system r-build-system)
21815 `(("r-rstudioapi" ,r-rstudioapi)))
21816 (home-page "https://github.com/wrathematics/getPass")
21817 (synopsis "Masked user input")
21819 "This package provides a micro-package for reading \"passwords\", i.e.
21820 reading user input with masking, so that the input is not displayed as it is
21821 typed. Currently, RStudio, the command line (every OS), and any platform
21822 where tcltk is present are supported.")
21823 (license license:bsd-2)))
21825 (define-public r-remoter
21832 (uri (cran-uri "remoter" version))
21835 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21836 (properties `((upstream-name . "remoter")))
21837 (build-system r-build-system)
21839 `(("r-argon2" ,r-argon2)
21840 ("r-getpass" ,r-getpass)
21841 ("r-pbdzmq" ,r-pbdzmq)
21843 (home-page "https://github.com/RBigData/remoter")
21844 (synopsis "Control a remote R session from a local one")
21846 "This package provides a set of utilities for client/server computing
21847 with R, controlling a remote R session (the server) from a local one (the
21849 (license license:bsd-2)))
21851 (define-public r-asd
21858 (uri (cran-uri "asd" version))
21861 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21862 (properties `((upstream-name . "asd")))
21863 (build-system r-build-system)
21865 `(("r-mvtnorm" ,r-mvtnorm)))
21866 (home-page "https://cran.r-project.org/web/packages/asd")
21867 (synopsis "Simulations for Adaptive Seamless Designs")
21869 "This package provdes means to run simulations for adaptive seamless
21870 designs with and without early outcomes for treatment selection and
21871 subpopulation type designs.")
21872 (license license:gpl3)))
21874 (define-public r-nbconvertr
21876 (name "r-nbconvertr")
21881 (uri (cran-uri "nbconvertR" version))
21884 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21885 (properties `((upstream-name . "nbconvertR")))
21886 (build-system r-build-system)
21888 `(("jupyter" ,python-nbconvert)
21889 ("pandoc" ,pandoc)))
21890 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21891 (synopsis "Vignette engine wrapping Jupyter notebooks")
21893 "This package calls the Jupyter script @code{nbconvert} to create
21894 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21895 containing rich text, code, and its output. Code cells can be edited and
21896 evaluated interactively.")
21897 (license license:gpl3)))
21899 (define-public r-bridgesampling
21901 (name "r-bridgesampling")
21906 (uri (cran-uri "bridgesampling" version))
21909 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21911 `((upstream-name . "bridgesampling")))
21912 (build-system r-build-system)
21914 `(("r-brobdingnag" ,r-brobdingnag)
21916 ("r-matrix" ,r-matrix)
21917 ("r-mvtnorm" ,r-mvtnorm)
21918 ("r-scales" ,r-scales)
21919 ("r-stringr" ,r-stringr)))
21921 `(("r-knitr" ,r-knitr)))
21922 (home-page "https://github.com/quentingronau/bridgesampling")
21923 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21925 "This package provides functions for estimating marginal likelihoods,
21926 Bayes factors, posterior model probabilities, and normalizing constants in
21927 general, via different versions of bridge sampling.")
21928 (license license:gpl2+)))
21930 (define-public r-tea
21937 (uri (cran-uri "tea" version))
21940 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21942 `((upstream-name . "tea")))
21943 (build-system r-build-system)
21945 `(("r-matrix" ,r-matrix)))
21946 (home-page "https://cran.r-project.org/web/packages/tea/")
21947 (synopsis "Threshold estimation approaches")
21949 "This package provides different approaches for selecting the threshold
21950 in generalized Pareto distributions. Most of them are based on minimizing the
21951 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21952 Others are heuristically motivated by searching for stable sample paths, i.e.
21953 a nearly constant region of the tail index estimator with respect to k, which
21954 is the number of data in the tail. The third class is motivated by graphical
21955 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21956 is also implemented here.")
21957 (license license:gpl3)))
21959 (define-public r-awsmethods
21961 (name "r-awsmethods")
21966 (uri (cran-uri "awsMethods" version))
21969 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21971 `((upstream-name . "awsMethods")))
21972 (build-system r-build-system)
21973 (home-page "http://www.wias-berlin.de/software/imaging/")
21974 (synopsis "Class and methods definitions")
21976 "This package defines the generic method @code{extract} and provides
21977 @code{openMP} support as needed in several packages like
21978 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21979 (license license:gpl2+)))
21981 (define-public r-aws
21988 (uri (cran-uri "aws" version))
21991 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
21993 `((upstream-name . "aws")))
21994 (build-system r-build-system)
21996 `(("r-awsmethods" ,r-awsmethods)
21999 `(("gfortran" ,gfortran)))
22000 (home-page "https://cran.r-project.org/web/packages/aws/")
22001 (synopsis "Adaptive weights smoothing")
22003 "This package provides a collection of R-functions implementing adaptive
22004 smoothing procedures in 1D, 2D and 3D. This includes the
22005 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22006 Confidence Intervals} (ICI), variational approaches, and a non-local means
22008 (license license:gpl2+)))
22010 (define-public r-sgloptim
22012 (name "r-sgloptim")
22017 (uri (cran-uri "sglOptim" version))
22020 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22022 `((upstream-name . "sglOptim")))
22023 (build-system r-build-system)
22026 ("r-doparallel" ,r-doparallel)
22027 ("r-foreach" ,r-foreach)
22028 ("r-matrix" ,r-matrix)
22030 ("r-rcpparmadillo" ,r-rcpparmadillo)
22031 ("r-rcppprogress" ,r-rcppprogress)))
22033 `(("r-knitr" ,r-knitr)))
22034 (home-page "https://github.com/nielsrhansen/sglOptim")
22035 (synopsis "Generic sparse group Lasso solver")
22037 "This package provides a fast generic solver for sparse group lasso
22038 optimization problems. The loss (objective) function must be defined in a C++
22039 module. The optimization problem is solved using a coordinate gradient
22040 descent algorithm. Convergence of the algorithm is established and the
22041 algorithm is applicable to a broad class of loss functions. Use of parallel
22042 computing for cross validation and subsampling is supported through the
22043 @code{foreach} and @code{doParallel} packages.")
22044 (license license:gpl2+)))
22046 (define-public r-grouped
22053 (uri (cran-uri "grouped" version))
22056 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22058 `((upstream-name . "grouped")))
22059 (build-system r-build-system)
22061 `(("r-mass" ,r-mass)))
22062 (home-page "https://cran.r-project.org/web/packages/grouped/")
22063 (synopsis "Regression analysis of grouped and coarse data")
22065 "This package provides regression models for grouped and coarse data,
22066 under the coarsened at random assumption.")
22067 (license license:gpl2+)))
22069 (define-public r-stam
22076 (uri (cran-uri "stam" version))
22079 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22081 `((upstream-name . "stam")))
22082 (build-system r-build-system)
22086 (home-page "https://cran.r-project.org/web/packages/stam")
22087 (synopsis "Spatio-temporal analysis and modelling")
22089 "This package provides various methods to conduct Spatio-Temporal
22090 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22091 Inferred Spatio-Temporal Modelling.")
22092 (license license:gpl2+)))
22094 (define-public r-dcv
22101 (uri (cran-uri "dcv" version))
22104 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22106 `((upstream-name . "dcv")))
22107 (build-system r-build-system)
22109 `(("r-lmtest" ,r-lmtest)))
22110 (home-page "https://cran.r-project.org/web/packages/dcv/")
22111 (synopsis "Conventional cross-validation statistics for climate-growth model")
22113 "This package performs several conventional cross-validation statistical
22114 methods for climate-growth model in the climate reconstruction from tree
22115 rings, including Sign Test statistic, Reduction of Error statistic, Product
22116 Mean Test, Durbin-Watson statistic etc.")
22117 (license license:gpl2)))
22119 (define-public r-rcdd
22126 (uri (cran-uri "rcdd" version))
22129 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22131 `((upstream-name . "rcdd")))
22132 (build-system r-build-system)
22135 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22136 (synopsis "Computational geometry")
22138 "This package converts back and forth between two representations of a
22139 convex polytope: as solution of a set of linear equalities and inequalities
22140 and as convex hull of set of points and rays. Also does linear programming
22141 and redundant generator elimination. All functions can use exact
22142 infinite-precision rational arithmetic.")
22143 (license license:gpl2)))
22145 (define-public r-rxnat
22152 (uri (cran-uri "Rxnat" version))
22155 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22157 `((upstream-name . "Rxnat")))
22158 (build-system r-build-system)
22160 `(("r-dplyr" ,r-dplyr)
22162 ("r-rcurl" ,r-rcurl)))
22164 `(("r-knitr" ,r-knitr)))
22165 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22166 (synopsis "Queries and extracts images from neuroimaging datasets")
22168 "This package allows communication with the Extensible Neuroimaging
22169 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22171 (license license:gpl2)))
22173 (define-public r-rserve
22180 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22181 version ".tar.gz"))
22184 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22185 (build-system r-build-system)
22187 `(("r-checkmate" ,r-checkmate)
22189 ("r-jsonlite" ,r-jsonlite)
22190 ("r-knitr" ,r-knitr)
22193 ("r-uuid" ,r-uuid)))
22195 `(("openssl" ,openssl)
22197 (home-page "https://github.com/s-u/Rserve")
22199 "Server providing access to R from many languages and systems")
22201 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22202 binary requests to be sent to R. Every connection has a separate workspace
22203 and working directory. Client-side implementations are available for popular
22204 languages such as C/C++ and Java, allowing any application to use facilities
22205 of R without the need of linking to R code. Rserve supports remote
22206 connection, user authentication and file transfer. A simple R client is
22207 included in this package as well.")
22208 (license license:gpl2)))
22210 (define-public r-brms
22217 (uri (cran-uri "brms" version))
22220 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22221 (properties `((upstream-name . "brms")))
22222 (build-system r-build-system)
22224 `(("r-abind" ,r-abind)
22225 ("r-backports" ,r-backports)
22226 ("r-bayesplot" ,r-bayesplot)
22227 ("r-bridgesampling" ,r-bridgesampling)
22229 ("r-future" ,r-future)
22230 ("r-ggplot2" ,r-ggplot2)
22233 ("r-matrix" ,r-matrix)
22234 ("r-matrixstats" ,r-matrixstats)
22236 ("r-nleqslv" ,r-nleqslv)
22239 ("r-rstan" ,r-rstan)
22240 ("r-rstantools" ,r-rstantools)
22241 ("r-shinystan" ,r-shinystan)))
22242 (native-inputs `(("r-knitr" ,r-knitr)))
22244 "https://github.com/paul-buerkner/brms")
22246 "Bayesian Regression Models using 'Stan'")
22248 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22249 using 'Stan' for full Bayesian inference. A wide range of distributions and
22250 link functions are supported, allowing users to fit -- among others -- linear,
22251 robust linear, count data, survival, response times, ordinal, zero-inflated,
22252 hurdle, and even self-defined mixture models all in a multilevel context.
22253 Further modeling options include non-linear and smooth terms, auto-correlation
22254 structures, censored data, meta-analytic standard errors, and quite a few
22255 more. In addition, all parameters of the response distribution can be
22256 predicted in order to perform distributional regression. Prior specifications
22257 are flexible and explicitly encourage users to apply prior distributions that
22258 actually reflect their beliefs. Model fit can easily be assessed and compared
22259 with posterior predictive checks and leave-one-out cross-validation.")
22260 (license license:gpl2)))
22262 (define-public r-mstate
22269 (uri (cran-uri "mstate" version))
22272 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22273 (properties `((upstream-name . "mstate")))
22274 (build-system r-build-system)
22276 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22277 ("r-survival" ,r-survival)))
22279 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22281 "Data Preparation, Estimation and Prediction in Multi-State Models")
22283 "Contains functions for data preparation, descriptives, hazard estimation
22284 and prediction with Aalen-Johansen or simulation in competing risks and
22285 multi-state models.")
22286 (license license:gpl2+)))
22288 (define-public r-scatterpie
22290 (name "r-scatterpie")
22295 (uri (cran-uri "scatterpie" version))
22298 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22299 (properties `((upstream-name . "scatterpie")))
22300 (build-system r-build-system)
22302 `(("r-ggforce" ,r-ggforce)
22303 ("r-ggplot2" ,r-ggplot2)
22304 ("r-rlang" ,r-rlang)
22305 ("r-rvcheck" ,r-rvcheck)
22306 ("r-tidyr" ,r-tidyr)))
22308 `(("r-knitr" ,r-knitr)))
22309 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22310 (synopsis "Scatter pie plot")
22312 "This package creates scatterpie plots, especially useful for plotting
22314 (license license:artistic2.0)))
22316 (define-public r-boruta
22323 (uri (cran-uri "Boruta" version))
22326 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22327 (properties `((upstream-name . "Boruta")))
22328 (build-system r-build-system)
22329 (propagated-inputs `(("r-ranger" ,r-ranger)))
22330 (home-page "https://gitlab.com/mbq/Boruta/")
22331 (synopsis "Wrapper algorithm for all relevant feature selection")
22333 "This package provides an all relevant feature selection wrapper
22334 algorithm. It finds relevant features by comparing original attributes'
22335 importance with importance achievable at random, estimated using their
22336 permuted copies (shadows).")
22337 (license license:gpl2+)))
22339 (define-public r-directlabels
22341 (name "r-directlabels")
22342 (version "2020.6.17")
22346 (uri (cran-uri "directlabels" version))
22349 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22350 (build-system r-build-system)
22352 `(("r-quadprog" ,r-quadprog)))
22354 `(("r-knitr" ,r-knitr)))
22355 (home-page "http://directlabels.r-forge.r-project.org/")
22356 (synopsis "Direct labels for multicolor plots")
22358 "This package provides an extensible framework for automatically placing
22359 direct labels onto multicolor plots. Label positions are described using
22360 positioning methods that can be re-used across several different plots. There
22361 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22362 inferring an appropriate positioning method.")
22363 (license license:gpl3)))
22365 (define-public r-lsd
22372 (uri (cran-uri "LSD" version))
22374 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22375 (properties `((upstream-name . "LSD")))
22376 (build-system r-build-system)
22377 (home-page "https://cran.r-project.org/web/packages/LSD/")
22378 (synopsis "Lots of superior depictions tool creates colorful plots")
22380 "This package creates lots of colorful plots in a multitude of variations.
22381 Try a demo of the LSD by running @code{demotour()}.")
22383 (license (list license:gpl2 license:gpl3))))
22385 (define-public r-fourcseq
22387 (name "r-fourcseq")
22392 (uri (bioconductor-uri "FourCSeq" version))
22394 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22395 (properties `((upstream-name . "FourCSeq")))
22396 (build-system r-build-system)
22398 `(("r-biobase" ,r-biobase)
22399 ("r-biostrings" ,r-biostrings)
22400 ("r-deseq2" ,r-deseq2)
22402 ("r-genomicalignments" ,r-genomicalignments)
22403 ("r-genomicranges" ,r-genomicranges)
22404 ("r-ggbio" ,r-ggbio)
22405 ("r-ggplot2" ,r-ggplot2)
22406 ("r-gtools" ,r-gtools)
22408 ("r-matrix" ,r-matrix)
22409 ("r-reshape2" ,r-reshape2)
22410 ("r-rsamtools" ,r-rsamtools)
22411 ("r-rtracklayer" ,r-rtracklayer)
22412 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22414 `(("r-knitr" ,r-knitr)))
22416 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22417 (synopsis "Analysis of multiplexed 4C sequencing data")
22419 "This package is an R package dedicated to the analysis of (multiplexed)
22420 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22421 interactions between DNA elements and identify differential interactions
22422 between conditions. The statistical analysis in R starts with individual bam
22423 files for each sample as inputs. To obtain these files, the package contains
22424 a Python script to demultiplex libraries and trim off primer sequences. With
22425 a standard alignment software the required bam files can be then be
22427 (license license:gpl3+)))
22429 (define-public r-phylogram
22431 (name "r-phylogram")
22436 (uri (cran-uri "phylogram" version))
22438 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22439 (properties `((upstream-name . "phylogram")))
22440 (build-system r-build-system)
22441 (propagated-inputs `(("r-ape" ,r-ape)))
22442 (home-page "https://github.com/ropensci/phylogram/")
22443 (synopsis "Dendrograms for evolutionary analysis")
22445 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22446 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22447 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22448 as well as several tools for command-line tree manipulation and import/export
22449 via Newick parenthetic text. This improves accessibility to the comprehensive
22450 range of object-specific analytical and tree-visualization functions found
22451 across a wide array of bioinformatic R packages.")
22452 (license license:gpl3)))
22454 (define-public r-kmer
22461 (uri (cran-uri "kmer" version))
22463 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22464 (properties `((upstream-name . "kmer")))
22465 (build-system r-build-system)
22467 `(("r-openssl" ,r-openssl)
22468 ("r-phylogram" ,r-phylogram)
22469 ("r-rcpp" ,r-rcpp)))
22470 (home-page "https://github.com/shaunpwilkinson/kmer/")
22471 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22473 "@code{r-kmer} is an R package for rapidly computing distance matrices
22474 and clustering large sequence datasets using fast alignment-free k-mer
22475 counting and recursive k-means partitioning.")
22476 (license license:gpl3)))
22478 (define-public r-shapforxgboost
22480 (name "r-shapforxgboost")
22485 (uri (cran-uri "SHAPforxgboost" version))
22488 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22490 `((upstream-name . "SHAPforxgboost")))
22491 (build-system r-build-system)
22493 `(("r-bbmisc" ,r-bbmisc)
22494 ("r-data-table" ,r-data-table)
22495 ("r-ggextra" ,r-ggextra)
22496 ("r-ggforce" ,r-ggforce)
22497 ("r-ggplot2" ,r-ggplot2)
22498 ("r-ggpubr" ,r-ggpubr)
22499 ("r-rcolorbrewer" ,r-rcolorbrewer)
22500 ("r-xgboost" ,r-xgboost)))
22501 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22502 (synopsis "SHAP Plots for XGBoost")
22504 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22505 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22506 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22507 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22509 (license license:expat)))
22511 (define-public r-rismed
22518 (uri (cran-uri "RISmed" version))
22521 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22522 (properties `((upstream-name . "RISmed")))
22523 (build-system r-build-system)
22524 (home-page "https://cran.r-project.org/web/packages/RISmed")
22525 (synopsis "Download content from NCBI databases")
22527 "This package provides a set of tools to extract bibliographic
22528 content from the National Center for Biotechnology Information (NCBI)
22529 databases, including PubMed. The name RISmed is a portmanteau of
22530 RIS (for Research Information Systems, a common tag format for
22531 bibliographic data) and PubMed.")
22532 (license license:gpl2+)))
22534 (define-public r-semver
22541 (uri (cran-uri "semver" version))
22544 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22545 (properties `((upstream-name . "semver")))
22546 (build-system r-build-system)
22548 `(("r-assertthat" ,r-assertthat)
22549 ("r-rcpp" ,r-rcpp)))
22550 (native-inputs `(("r-knitr" ,r-knitr)))
22551 (home-page "https://github.com/johndharrison/semver")
22552 (synopsis "Parser for Semantic Versioning 2.0.0")
22554 "This package provides tools and functions for parsing, rendering and
22555 operating on semantic version strings. Semantic versioning is a simple set of
22556 rules and requirements that dictate how version numbers are assigned and
22557 incremented as outlined at @url{http://semver.org}.")
22558 (license license:expat)))
22560 (define-public r-binman
22567 (uri (cran-uri "binman" version))
22570 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22571 (properties `((upstream-name . "binman")))
22572 (build-system r-build-system)
22574 `(("r-assertthat" ,r-assertthat)
22576 ("r-jsonlite" ,r-jsonlite)
22577 ("r-rappdirs" ,r-rappdirs)
22578 ("r-semver" ,r-semver)
22580 ("r-yaml" ,r-yaml)))
22581 (native-inputs `(("r-knitr" ,r-knitr)))
22582 (home-page "https://github.com/ropensci/binman")
22583 (synopsis "Binary download manager")
22585 "This package provides tools and functions for managing the download of
22586 binary files. Binary repositories are defined in the YAML format. Defining
22587 new pre-download, download and post-download templates allow additional
22588 repositories to be added.")
22589 (license license:expat)))
22591 (define-public r-wdman
22598 (uri (cran-uri "wdman" version))
22601 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22602 (properties `((upstream-name . "wdman")))
22603 (build-system r-build-system)
22605 `(("r-assertthat" ,r-assertthat)
22606 ("r-binman" ,r-binman)
22607 ("r-processx" ,r-processx)
22608 ("r-semver" ,r-semver)
22609 ("r-yaml" ,r-yaml)))
22610 (native-inputs `(("r-knitr" ,r-knitr)))
22611 (home-page "https://docs.ropensci.org/wdman/")
22612 (synopsis "Webdriver/Selenium binary manager")
22614 "There are a number of binary files associated with the
22615 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22616 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22617 @url{https://github.com/mozilla/geckodriver},
22618 @url{http://phantomjs.org/download.html}, and
22619 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22620 more information). This package provides functions to download these binaries
22621 and to manage processes involving them.")
22622 (license license:expat)))
22624 (define-public r-rselenium
22626 (name "r-rselenium")
22631 (uri (cran-uri "RSelenium" version))
22634 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22635 (properties `((upstream-name . "RSelenium")))
22636 (build-system r-build-system)
22638 `(("r-binman" ,r-binman)
22639 ("r-catools" ,r-catools)
22641 ("r-openssl" ,r-openssl)
22642 ("r-wdman" ,r-wdman)
22644 (native-inputs `(("r-knitr" ,r-knitr)))
22645 (home-page "https://docs.ropensci.org/RSelenium/")
22646 (synopsis "R bindings for Selenium WebDriver")
22648 "This package provides a set of R bindings for the Selenium 2.0
22649 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22650 information) using the @code{JsonWireProtocol} (see
22651 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22652 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22653 a user would either locally or on a remote machine using the Selenium server
22654 it marks a leap forward in terms of web browser automation. Selenium
22655 automates web browsers (commonly referred to as browsers). Using RSelenium
22656 you can automate browsers locally or remotely.")
22657 (license license:agpl3+)))
22659 (define-public r-conquer
22666 (uri (cran-uri "conquer" version))
22669 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22670 (properties `((upstream-name . "conquer")))
22671 (build-system r-build-system)
22673 `(("r-matrix" ,r-matrix)
22674 ("r-matrixstats" ,r-matrixstats)
22676 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22677 (home-page "https://github.com/XiaoouPan/conquer")
22678 (synopsis "Convolution-type smoothed quantile regression")
22680 "This package provides fast and accurate convolution-type smoothed
22681 quantile regression, implemented using Barzilai-Borwein gradient descent with
22682 a Huber regression warm start. Confidence intervals for regression
22683 coefficients are constructed using multiplier bootstrap.")
22684 (license license:gpl3)))
22686 (define-public r-fastshap
22688 (name "r-fastshap")
22693 (uri (cran-uri "fastshap" version))
22696 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22697 (properties `((upstream-name . "fastshap")))
22698 (build-system r-build-system)
22700 `(("r-abind" ,r-abind)
22701 ("r-ggplot2" ,r-ggplot2)
22702 ("r-gridextra" ,r-gridextra)
22703 ("r-matrixstats" ,r-matrixstats)
22706 ("r-rcpparmadillo" ,r-rcpparmadillo)
22707 ("r-tibble" ,r-tibble)))
22708 (home-page "https://github.com/bgreenwell/fastshap")
22709 (synopsis "Fast approximate Shapley values")
22711 "This package computes fast (relative to other implementations)
22712 approximate Shapley values for any supervised learning model. Shapley values
22713 help to explain the predictions from any black box model using ideas from game
22714 theory; see @url{Strumbel and Kononenko (2014),
22715 doi.org/10.1007/s10115-013-0679-x} for details.")
22716 (license license:gpl2+)))
22718 (define-public r-metrics
22725 (uri (cran-uri "Metrics" version))
22728 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22729 (properties `((upstream-name . "Metrics")))
22730 (build-system r-build-system)
22731 (home-page "https://github.com/mfrasco/Metrics")
22732 (synopsis "Evaluation metrics for machine learning")
22734 "This package provides an implementation of evaluation metrics in R that
22735 are commonly used in supervised machine learning. It implements metrics for
22736 regression, time series, binary classification, classification, and
22737 information retrieval problems. It has zero dependencies and a consistent,
22738 simple interface for all functions.")
22739 (license license:bsd-3)))
22741 (define-public r-iml
22748 (uri (cran-uri "iml" version))
22751 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22752 (properties `((upstream-name . "iml")))
22753 (build-system r-build-system)
22755 `(("r-checkmate" ,r-checkmate)
22756 ("r-data-table" ,r-data-table)
22757 ("r-formula" ,r-formula)
22758 ("r-future" ,r-future)
22759 ("r-future-apply" ,r-future-apply)
22760 ("r-ggplot2" ,r-ggplot2)
22761 ("r-gridextra" ,r-gridextra)
22762 ("r-metrics" ,r-metrics)
22763 ("r-prediction" ,r-prediction)
22765 (native-inputs `(("r-knitr" ,r-knitr)))
22766 (home-page "https://github.com/christophM/iml")
22767 (synopsis "Interpretable machine learning")
22769 "This package provides interpretability methods to analyze the behavior
22770 and predictions of any machine learning model. Implemented methods are:
22773 @item Feature importance described by Fisher et al. (2018),
22774 @item accumulated local effects plots described by Apley (2018),
22775 @item partial dependence plots described by Friedman (2001),
22776 @item individual conditional expectation ('ice') plots described by Goldstein
22777 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
22778 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
22779 @item the Shapley Value described by Strumbelj et. al (2014)
22780 @url{https://doi.org/10.1007/s10115-013-0679-x},
22781 @item feature interactions described by Friedman et. al
22782 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
22785 (license license:expat)))
22787 (define-public r-goftest
22794 (uri (cran-uri "goftest" version))
22797 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
22798 (properties `((upstream-name . "goftest")))
22799 (build-system r-build-system)
22800 (home-page "https://github.com/baddstats/goftest")
22801 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
22803 "This package provides Cramer-Von Mises and Anderson-Darling tests of
22804 goodness-of-fit for continuous univariate distributions, using efficient
22806 (license license:gpl2+)))
22808 (define-public r-tensor
22815 (uri (cran-uri "tensor" version))
22818 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
22819 (properties `((upstream-name . "tensor")))
22820 (build-system r-build-system)
22821 (home-page "https://cran.r-project.org/web/packages/tensor/")
22822 (synopsis "Tensor product of arrays")
22824 "The tensor product of two arrays is notionally an outer product of the
22825 arrays collapsed in specific extents by summing along the appropriate
22826 diagonals. This package allows you to compute the tensor product of arrays.")
22827 (license license:gpl2+)))
22829 (define-public r-spatstat-utils
22831 (name "r-spatstat-utils")
22836 (uri (cran-uri "spatstat.utils" version))
22839 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
22841 `((upstream-name . "spatstat.utils")))
22842 (build-system r-build-system)
22843 (home-page "http://www.spatstat.org")
22844 (synopsis "Utility functions for spatstat")
22846 "This package contains utility functions for the @code{spatstat} package
22847 which may also be useful for other purposes.")
22848 (license license:gpl2+)))
22850 (define-public r-spatstat-data
22852 (name "r-spatstat-data")
22857 (uri (cran-uri "spatstat.data" version))
22860 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
22861 (properties `((upstream-name . "spatstat.data")))
22862 (build-system r-build-system)
22864 `(("r-matrix" ,r-matrix)
22865 ("r-spatstat-utils" ,r-spatstat-utils)))
22866 (home-page "http://www.spatstat.org")
22867 (synopsis "Datasets for spatstat")
22869 "This package contains all the datasets for the @code{spatstat}
22871 (license license:gpl2+)))
22873 (define-public r-spatstat
22875 (name "r-spatstat")
22880 (uri (cran-uri "spatstat" version))
22883 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
22884 (properties `((upstream-name . "spatstat")))
22885 (build-system r-build-system)
22887 `(("r-abind" ,r-abind)
22888 ("r-deldir" ,r-deldir)
22889 ("r-goftest" ,r-goftest)
22890 ("r-matrix" ,r-matrix)
22893 ("r-polyclip" ,r-polyclip)
22894 ("r-rpart" ,r-rpart)
22895 ("r-spatstat-data" ,r-spatstat-data)
22896 ("r-spatstat-utils" ,r-spatstat-utils)
22897 ("r-tensor" ,r-tensor)))
22898 (home-page "http://www.spatstat.org")
22899 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
22901 "This package provides a comprehensive toolbox for analysing Spatial
22902 Point Patterns. It is focused mainly on two-dimensional point patterns,
22903 including multitype/marked points, in any spatial region. It also supports
22904 three-dimensional point patterns, space-time point patterns in any number of
22905 dimensions, point patterns on a linear network, and patterns of other
22906 geometrical objects. It supports spatial covariate data such as pixel images
22907 and contains over 2000 functions for plotting spatial data, exploratory data
22908 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
22909 formal inference.")
22910 (license license:gpl2+)))
22912 (define-public r-gaston
22919 (uri (cran-uri "gaston" version))
22922 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
22923 (properties `((upstream-name . "gaston")))
22924 (build-system r-build-system)
22925 (inputs `(("zlib" ,zlib)))
22927 `(("r-rcpp" ,r-rcpp)
22928 ("r-rcppeigen" ,r-rcppeigen)
22929 ("r-rcppparallel" ,r-rcppparallel)))
22930 (native-inputs `(("r-knitr" ,r-knitr)))
22931 (home-page "https://cran.r-project.org/web/packages/gaston/")
22932 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
22934 "This is a package for the manipulation of genetic data (SNPs).
22935 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
22936 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
22937 for linear mixed models (AIREML).")
22938 (license license:gpl3)))
22940 (define-public r-cpp11
22947 (uri (cran-uri "cpp11" version))
22950 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
22951 (properties `((upstream-name . "cpp11")))
22952 (build-system r-build-system)
22953 (native-inputs `(("r-knitr" ,r-knitr)))
22954 (home-page "https://github.com/r-lib/cpp11")
22955 (synopsis "C++11 Interface for R's C Interface")
22957 "This package provides a header only, C++11 interface to R's C interface.
22958 Compared to other approaches @code{cpp11} strives to be safe against long
22959 jumps from the C API as well as C++ exceptions, conform to normal R function
22960 semantics and supports interaction with @code{ALTREP} vectors.")
22961 (license license:expat)))
22963 (define-public r-rcppziggurat
22965 (name "r-rcppziggurat")
22970 (uri (cran-uri "RcppZiggurat" version))
22973 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
22974 (properties `((upstream-name . "RcppZiggurat")))
22975 (build-system r-build-system)
22977 `(("r-rcpp" ,r-rcpp)
22978 ("r-rcppgsl" ,r-rcppgsl)))
22979 (native-inputs `(("r-knitr" ,r-knitr)))
22980 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
22981 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
22983 "The Ziggurat generator for normally distributed random numbers,
22984 originally proposed by Marsaglia and Tsang (2000,
22985 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
22986 times starting with Leong et al (2005,
22987 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
22988 aggregation for comparing different implementations in order to provide a
22989 'faster but good enough' alternative for use with R and C++ code.")
22990 (license license:gpl2+)))
22992 (define-public r-rfast
22999 (uri (cran-uri "Rfast" version))
23002 "18m8xhg24kygwhq7avdp1hibilicb5wppi2wdmc36fkqljc274y0"))))
23003 (properties `((upstream-name . "Rfast")))
23004 (build-system r-build-system)
23006 `(("r-rcpp" ,r-rcpp)
23007 ("r-rcpparmadillo" ,r-rcpparmadillo)
23008 ("r-rcppziggurat" ,r-rcppziggurat)))
23009 (home-page "https://github.com/RfastOfficial/Rfast")
23010 (synopsis "Collection of efficient and fast R functions")
23012 "This package provides a collection of fast (utility) functions for data
23013 analysis. Column- and row- wise means, medians, variances, minimums,
23014 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23015 Poisson), are some of the many fast functions.")
23016 (license license:gpl2+)))
23018 (define-public r-clusterr
23020 (name "r-clusterr")
23025 (uri (cran-uri "ClusterR" version))
23028 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23029 (properties `((upstream-name . "ClusterR")))
23030 (build-system r-build-system)
23032 `(("r-ggplot2" ,r-ggplot2)
23034 ("r-gtools" ,r-gtools)
23036 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23037 (native-inputs `(("r-knitr" ,r-knitr)))
23038 (home-page "https://github.com/mlampros/ClusterR")
23039 (synopsis "Clustering")
23041 "This package provides Gaussian mixture models, k-means,
23042 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23043 option to plot, validate, predict (new data) and estimate the optimal number
23044 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23045 the computationally intensive parts of the functions. For more information,
23049 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23050 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23051 @url{https://doi.org/10.18637/jss.v001.i04};
23052 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23053 Library, @url{https://doi.org/10.1145/1772690.1772862};
23054 @item \"Armadillo: a template-based C++ library
23055 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23056 Software, @url{https://doi.org/10.21105/joss.00026};
23057 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23058 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23059 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23062 (license license:gpl3)))
23064 (define-public r-spectrum
23066 (name "r-spectrum")
23071 (uri (cran-uri "Spectrum" version))
23074 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23075 (properties `((upstream-name . "Spectrum")))
23076 (build-system r-build-system)
23078 `(("r-clusterr" ,r-clusterr)
23079 ("r-diptest" ,r-diptest)
23080 ("r-ggplot2" ,r-ggplot2)
23081 ("r-rfast" ,r-rfast)))
23082 (native-inputs `(("r-knitr" ,r-knitr)))
23083 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23084 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23086 "This package provides a self-tuning spectral clustering method for
23087 single or multi-view data. Spectrum uses a new type of adaptive density aware
23088 kernel that strengthens connections in the graph based on common nearest
23089 neighbours. It uses a tensor product graph data integration and diffusion
23090 procedure to integrate different data sources and reduce noise. Spectrum uses
23091 either the eigengap or multimodality gap heuristics to determine the number of
23092 clusters. The method is sufficiently flexible so that a wide range of
23093 Gaussian and non-Gaussian structures can be clustered with automatic selection
23095 (license license:agpl3+)))
23097 (define-public r-nabor
23104 (uri (cran-uri "nabor" version))
23107 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23108 (properties `((upstream-name . "nabor")))
23109 (build-system r-build-system)
23113 ("r-rcppeigen" ,r-rcppeigen)))
23114 (home-page "https://cran.r-project.org/web/packages/nabor/")
23115 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23117 "This package provides an R wrapper for libnabo, an exact or approximate
23118 k nearest neighbour library which is optimised for low dimensional
23119 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23120 designed as a drop-in replacement for the RANN function @code{nn2}. In
23121 addition, objects which include the k-d tree search structure can be returned
23122 to speed up repeated queries of the same set of target points.")
23123 (license license:bsd-3)))