1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
33 ;;; This file is part of GNU Guix.
35 ;;; GNU Guix is free software; you can redistribute it and/or modify it
36 ;;; under the terms of the GNU General Public License as published by
37 ;;; the Free Software Foundation; either version 3 of the License, or (at
38 ;;; your option) any later version.
40 ;;; GNU Guix is distributed in the hope that it will be useful, but
41 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
42 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
43 ;;; GNU General Public License for more details.
45 ;;; You should have received a copy of the GNU General Public License
46 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
48 (define-module (gnu packages cran)
49 #:use-module ((guix licenses) #:prefix license:)
50 #:use-module (guix packages)
51 #:use-module (guix download)
52 #:use-module (guix git-download)
53 #:use-module (guix utils)
54 #:use-module (guix build-system r)
55 #:use-module (gnu packages)
56 #:use-module (gnu packages algebra)
57 #:use-module (gnu packages autotools)
58 #:use-module (gnu packages base)
59 #:use-module (gnu packages bioinformatics)
60 #:use-module (gnu packages c)
61 #:use-module (gnu packages compression)
62 #:use-module (gnu packages curl)
63 #:use-module (gnu packages databases)
64 #:use-module (gnu packages fontutils)
65 #:use-module (gnu packages gcc)
66 #:use-module (gnu packages geo)
67 #:use-module (gnu packages ghostscript)
68 #:use-module (gnu packages gl)
69 #:use-module (gnu packages gnome)
70 #:use-module (gnu packages graph)
71 #:use-module (gnu packages gtk)
72 #:use-module (gnu packages haskell-xyz)
73 #:use-module (gnu packages icu4c)
74 #:use-module (gnu packages image)
75 #:use-module (gnu packages imagemagick)
76 #:use-module (gnu packages java)
77 #:use-module (gnu packages javascript)
78 #:use-module (gnu packages libevent)
79 #:use-module (gnu packages lisp-xyz)
80 #:use-module (gnu packages machine-learning)
81 #:use-module (gnu packages maths)
82 #:use-module (gnu packages mpi)
83 #:use-module (gnu packages multiprecision)
84 #:use-module (gnu packages networking)
85 #:use-module (gnu packages node)
86 #:use-module (gnu packages pcre)
87 #:use-module (gnu packages perl)
88 #:use-module (gnu packages pkg-config)
89 #:use-module (gnu packages pulseaudio) ;libsndfile
90 #:use-module (gnu packages python)
91 #:use-module (gnu packages python-xyz)
92 #:use-module (gnu packages statistics)
93 #:use-module (gnu packages tcl)
94 #:use-module (gnu packages tls)
95 #:use-module (gnu packages web)
96 #:use-module (gnu packages xml)
97 #:use-module (gnu packages xorg))
99 (define-public r-rticles
106 (uri (cran-uri "rticles" version))
109 "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l"))))
110 (properties `((upstream-name . "rticles")))
111 (build-system r-build-system)
113 `(("r-knitr" ,r-knitr)
114 ("r-rmarkdown" ,r-rmarkdown)
115 ("r-tinytex" ,r-tinytex)
118 (home-page "https://github.com/rstudio/rticles")
119 (synopsis "Article formats for R Markdown")
121 "This package provides a suite of custom R Markdown formats and templates
122 for authoring journal articles and conference submissions.")
123 (license license:gpl3)))
125 (define-public r-bezier
131 (uri (cran-uri "bezier" version))
134 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
135 (build-system r-build-system)
136 (home-page "https://cran.r-project.org/web/packages/bezier/")
137 (synopsis "Bezier curve and spline toolkit")
139 "This package is a toolkit for working with Bezier curves and splines.
140 The package provides functions for point generation, arc length estimation,
141 degree elevation and curve fitting.")
142 (license license:gpl2+)))
151 (uri (cran-uri "V8" version))
154 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
155 (properties `((upstream-name . "V8")))
156 (build-system r-build-system)
159 (modify-phases %standard-phases
160 (add-after 'unpack 'find-v8
161 (lambda* (#:key inputs #:allow-other-keys)
162 (substitute* "configure"
164 (string-append "PKG_LIBS="
165 (assoc-ref inputs "node")
166 "/lib/libnode.so.64\n")))
167 (setenv "INCLUDE_DIR"
169 (assoc-ref inputs "node")
173 (assoc-ref inputs "node") "/lib"))
176 `(("node" ,libnode)))
179 ("r-jsonlite" ,r-jsonlite)
182 `(("r-knitr" ,r-knitr)))
183 (home-page "https://jeroen.cran.dev/V8")
184 (synopsis "Embedded JavaScript and WebAssembly engine for R")
186 "This package provides an R interface to V8: Google's JavaScript and
187 WebAssembly engine.")
188 (license license:expat)))
197 (uri (cran-uri "DOT" version))
200 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
201 (properties `((upstream-name . "DOT")))
202 (build-system r-build-system)
205 (home-page "http://haghish.com/dot")
206 (synopsis "Render and Export DOT Graphs in R")
208 "This package provides tools to render DOT diagram markup language in R
209 and also provides the possibility to export the graphs in PostScript and
210 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
211 programming packages such as @code{knitr} and @code{rmarkdown}.")
212 (license license:expat)))
214 (define-public r-clipr
221 (uri (cran-uri "clipr" version))
224 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
225 (build-system r-build-system)
226 (home-page "https://github.com/mdlincoln/clipr")
227 (synopsis "Read and write from the system clipboard")
229 "This package provides simple utility functions to read from and write to
230 the system clipboards.")
231 (license license:gpl3)))
239 (uri (cran-uri "zoo" version))
242 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
243 (build-system r-build-system)
245 `(("r-lattice" ,r-lattice)))
246 (home-page "http://zoo.R-Forge.R-project.org/")
247 (synopsis "S3 infrastructure for regular and irregular time series")
248 (description "This package contains an S3 class with methods for totally
249 ordered indexed observations. It is particularly aimed at irregular time
250 series of numeric vectors/matrices and factors.")
251 (license license:gpl2+)))
253 (define-public r-ggpmisc
259 (uri (cran-uri "ggpmisc" version))
262 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
263 (build-system r-build-system)
265 `(("r-broom" ,r-broom)
267 ("r-ggplot2" ,r-ggplot2)
268 ("r-gridextra" ,r-gridextra)
269 ("r-lubridate" ,r-lubridate)
270 ("r-magrittr" ,r-magrittr)
273 ("r-polynom" ,r-polynom)
275 ("r-scales" ,r-scales)
276 ("r-splus2r" ,r-splus2r)
277 ("r-stringr" ,r-stringr)
278 ("r-tibble" ,r-tibble)
282 `(("r-knitr" ,r-knitr)))
283 (home-page "https://www.r4photobiology.info/")
284 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
285 (description "This package provides extensions to @code{ggplot2},
286 respecting the grammar of its graphics paradigm.")
287 (license license:gpl2+)))
289 (define-public r-gprofiler
296 (uri (cran-uri "gProfileR" version))
299 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
300 (properties `((upstream-name . "gProfileR")))
301 (build-system r-build-system)
304 ("r-rcurl" ,r-rcurl)))
305 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
306 (synopsis "Interface to the g:Profiler toolkit")
308 "This package provides tools for functional enrichment analysis,
309 gene identifier conversion and mapping homologous genes across related
310 organisms via the @code{g:Profiler} toolkit.")
311 (license license:gpl2+)))
313 (define-public r-gprofiler2
315 (name "r-gprofiler2")
320 (uri (cran-uri "gprofiler2" version))
323 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
324 (properties `((upstream-name . "gprofiler2")))
325 (build-system r-build-system)
327 `(("r-crosstalk" ,r-crosstalk)
329 ("r-ggplot2" ,r-ggplot2)
330 ("r-gridextra" ,r-gridextra)
331 ("r-jsonlite" ,r-jsonlite)
332 ("r-plotly" ,r-plotly)
335 ("r-viridislite" ,r-viridislite)))
336 (native-inputs `(("r-knitr" ,r-knitr)))
337 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
338 (synopsis "Interface to the g:Profiler toolset")
340 "This package provides a toolset for functional enrichment analysis and
341 visualization, gene/protein/SNP identifier conversion and mapping orthologous
342 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
346 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
348 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
350 @item @code{g:Orth}, orthology search across species;
351 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
352 genes and variant effects.
355 This package is an R interface corresponding to the 2019 update of
356 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
358 (license license:gpl2+)))
360 (define-public r-oenb
367 (uri (cran-uri "oenb" version))
370 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
371 (properties `((upstream-name . "oenb")))
372 (build-system r-build-system)
374 `(("r-dplyr" ,r-dplyr)
376 (native-inputs `(("r-knitr" ,r-knitr)))
377 (home-page "https://github.com/franzmohr/oenb")
378 (synopsis "Tools for the OeNB Data Web Service")
380 "Tools to access data from the data web service of the
381 @acronym{OeNB, Oesterreichische Nationalbank},
382 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
383 (license license:gpl2+)))
385 (define-public r-scales
392 (uri (cran-uri "scales" version))
394 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
395 (build-system r-build-system)
397 `(("r-farver" ,r-farver)
398 ("r-labeling" ,r-labeling)
399 ("r-lifecycle" ,r-lifecycle)
400 ("r-munsell" ,r-munsell)
401 ("r-rcolorbrewer" ,r-rcolorbrewer)
403 ("r-viridislite" ,r-viridislite)))
404 (home-page "https://github.com/hadley/scales")
405 (synopsis "Scale functions for visualization")
407 "This package provides graphical scales that map data to aesthetics, and
408 provides methods for automatically determining breaks and labels for axes and
410 (license license:expat)))
412 (define-public r-pheatmap
419 (uri (cran-uri "pheatmap" version))
422 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
423 (build-system r-build-system)
425 `(("r-gtable" ,r-gtable)
426 ("r-rcolorbrewer" ,r-rcolorbrewer)
427 ("r-scales" ,r-scales)))
428 (home-page "https://cran.r-project.org/web/packages/pheatmap")
429 (synopsis "Pretty heatmaps")
431 "This package provides an implementation of heatmaps that offers more
432 control over dimensions and appearance.")
433 (license license:gpl2+)))
441 (uri (cran-uri "ecp" version))
444 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
445 (build-system r-build-system)
447 `(("r-rcpp" ,r-rcpp)))
448 (home-page "https://cran.r-project.org/web/packages/ecp/")
449 (synopsis "Multiple change-point analysis of multivariate data")
451 "This package implements various procedures for finding multiple
452 change-points. Two methods make use of dynamic programming and pruning, with
453 no distributional assumptions other than the existence of certain absolute
454 moments in one method. Hierarchical and exact search methods are included.
455 All methods return the set of estimated change-points as well as other summary
457 (license license:gpl2+)))
459 (define-public r-ellipsis
466 (uri (cran-uri "ellipsis" version))
469 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
470 (build-system r-build-system)
472 `(("r-rlang" ,r-rlang)))
473 (home-page "https://github.com/hadley/ellipsis")
474 (synopsis "Tools for working with additional arguments")
476 "In S3 generics, it's useful to take @code{...} so that methods can have
477 additional arguments. But this flexibility comes at a cost: misspelled
478 arguments will be silently ignored. The @code{ellipsis} package is an
479 experiment that allows a generic to warn if any arguments passed in @code{...}
481 (license license:gpl3)))
490 (uri (cran-uri "grr" version))
493 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
494 (build-system r-build-system)
495 (home-page "https://cran.r-project.org/web/packages/grr")
496 (synopsis "Alternative implementations of base R functions")
498 "This package provides alternative implementations of some base R
499 functions, including @code{sort}, @code{order}, and @code{match}. The
500 functions are simplified but can be faster or have other advantages.")
501 (license license:gpl3)))
503 (define-public r-matrix-utils
505 (name "r-matrix-utils")
510 (uri (cran-uri "Matrix.utils" version))
513 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
514 (properties `((upstream-name . "Matrix.utils")))
515 (build-system r-build-system)
518 ("r-matrix" ,r-matrix)))
519 (home-page "https://github.com/cvarrichio/Matrix.utils")
521 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
523 "This package implements data manipulation methods such as @code{cast},
524 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
526 (license license:gpl3)))
528 (define-public r-mboost
534 (uri (cran-uri "mboost" version))
537 "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
538 (build-system r-build-system)
540 `(("r-lattice" ,r-lattice)
541 ("r-matrix" ,r-matrix)
543 ("r-partykit" ,r-partykit)
544 ("r-quadprog" ,r-quadprog)
546 ("r-survival" ,r-survival)))
547 (home-page "https://github.com/boost-R/mboost")
548 (synopsis "Model-based boosting")
550 "This package provides a functional gradient descent algorithm (boosting)
551 for optimizing general risk functions utilizing component-wise (penalised)
552 least squares estimates or regression trees as base-learners for fitting
553 generalized linear, additive and interaction models to potentially
554 high-dimensional data.")
555 (license license:gpl2)))
564 (uri (cran-uri "sys" version))
567 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
568 (build-system r-build-system)
569 (home-page "https://github.com/jeroen/sys")
570 (synopsis "Powerful and reliable tools for running system commands in R")
572 "This package provides drop-in replacements for the base @code{system2()}
573 function with fine control and consistent behavior across platforms. It
574 supports clean interruption, timeout, background tasks, and streaming STDIN /
575 STDOUT / STDERR over binary or text connections. The package also provides
576 functions for evaluating expressions inside a temporary fork. Such
577 evaluations have no side effects on the main R process, and support reliable
578 interrupts and timeouts. This provides the basis for a sandboxing
580 (license license:expat)))
582 (define-public r-askpass
589 (uri (cran-uri "askpass" version))
592 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
593 (build-system r-build-system)
594 (propagated-inputs `(("r-sys" ,r-sys)))
595 (home-page "https://github.com/jeroen/askpass")
596 (synopsis "Safe password entry for R")
598 "This package provides cross-platform utilities for prompting the user
599 for credentials or a passphrase, for example to authenticate with a server or
600 read a protected key.")
601 (license license:expat)))
603 (define-public r-vegan
610 (uri (cran-uri "vegan" version))
613 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
614 (build-system r-build-system)
616 `(("gfortran" ,gfortran)))
618 `(("r-cluster" ,r-cluster)
619 ("r-knitr" ,r-knitr) ; needed for vignettes
620 ("r-lattice" ,r-lattice)
623 ("r-permute" ,r-permute)))
624 (home-page "https://cran.r-project.org/web/packages/vegan")
625 (synopsis "Functions for community ecology")
627 "The vegan package provides tools for descriptive community ecology. It
628 has most basic functions of diversity analysis, community ordination and
629 dissimilarity analysis. Most of its multivariate tools can be used for other
630 data types as well.")
631 (license license:gpl2+)))
633 (define-public r-tidyverse
640 (uri (cran-uri "tidyverse" version))
643 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
644 (build-system r-build-system)
646 `(("r-broom" ,r-broom)
648 ("r-crayon" ,r-crayon)
649 ("r-dbplyr" ,r-dbplyr)
651 ("r-forcats" ,r-forcats)
652 ("r-ggplot2" ,r-ggplot2)
656 ("r-jsonlite" ,r-jsonlite)
657 ("r-lubridate" ,r-lubridate)
658 ("r-magrittr" ,r-magrittr)
659 ("r-modelr" ,r-modelr)
660 ("r-pillar" ,r-pillar)
663 ("r-readxl" ,r-readxl)
664 ("r-reprex" ,r-reprex)
666 ("r-rstudioapi" ,r-rstudioapi)
668 ("r-stringr" ,r-stringr)
669 ("r-tibble" ,r-tibble)
672 (home-page "https://tidyverse.tidyverse.org")
673 (synopsis "Install and load packages from the \"Tidyverse\"")
675 "The @code{tidyverse} is a set of packages that work in harmony because
676 they share common data representations and API design. This package is
677 designed to make it easy to install and load multiple tidyverse packages in a
679 (license license:gpl3)))
681 (define-public r-rvest
688 (uri (cran-uri "rvest" version))
690 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
691 (build-system r-build-system)
694 ("r-magrittr" ,r-magrittr)
695 ("r-selectr" ,r-selectr)
698 `(("r-knitr" ,r-knitr)))
699 (home-page "https://github.com/hadley/rvest")
700 (synopsis "Simple web scraping for R")
702 "@code{r-rvest} helps you scrape information from web pages. It is
703 designed to work with @code{magrittr} to make it easy to express common web
704 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
705 (license license:gpl3)))
707 (define-public r-selectr
714 (uri (cran-uri "selectr" version))
716 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
717 (build-system r-build-system)
719 `(("r-stringr" ,r-stringr)
721 (home-page "https://sjp.co.nz/projects/selectr/")
722 (synopsis "Translate CSS selectors to XPath expressions")
724 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
725 expression. This allows you to use CSS selectors when working with the XML
726 package as it can only evaluate XPath expressions. Also provided are
727 convenience functions useful for using CSS selectors on XML nodes. This
728 package is a port of the Python package @code{cssselect}.")
729 (license license:bsd-3)))
731 (define-public r-reprex
738 (uri (cran-uri "reprex" version))
741 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
742 (build-system r-build-system)
744 `(("r-callr" ,r-callr)
748 ("r-rmarkdown" ,r-rmarkdown)
749 ("r-whisker" ,r-whisker)
750 ("r-withr" ,r-withr)))
751 (home-page "https://github.com/tidyverse/reprex")
752 (synopsis "Prepare reproducible R code examples for sharing")
754 "This package provides a convenience wrapper that uses the
755 @code{rmarkdown} package to render small snippets of code to target formats
756 that include both code and output. The goal is to encourage the sharing of
757 small, reproducible, and runnable examples on code-oriented websites or email.
758 @code{reprex} also extracts clean, runnable R code from various common formats,
759 such as copy/paste from an R session.")
760 (license license:expat)))
762 (define-public r-reordercluster
764 (name "r-reordercluster")
768 (uri (cran-uri "ReorderCluster" version))
771 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
772 (build-system r-build-system)
774 `(("r-gplots" ,r-gplots)
776 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
777 (synopsis "Reordering the dendrogram according to the class labels")
778 (description "This package provides tools for performing the leaf reordering
779 for the dendrogram that preserves the hierarchical clustering result and at the
780 same time tries to group instances from the same class together.")
781 (license license:gpl3+)))
783 (define-public r-callr
790 (uri (cran-uri "callr" version))
793 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
794 (build-system r-build-system)
797 ("r-processx" ,r-processx)))
798 (home-page "https://github.com/r-lib/callr#readme")
799 (synopsis "Call R from R")
801 "It is sometimes useful to perform a computation in a separate R process,
802 without affecting the current R process at all. This package does exactly
804 (license license:expat)))
806 (define-public r-readxl
813 (uri (cran-uri "readxl" version))
816 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
817 (build-system r-build-system)
819 `(("r-cellranger" ,r-cellranger)
820 ("r-progress" ,r-progress)
822 ("r-tibble" ,r-tibble)))
823 (home-page "https://readxl.tidyverse.org")
824 (synopsis "Read Excel files")
826 "This package lets you import Excel files into R. It supports
827 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
828 the embedded @code{RapidXML} C++ library.")
829 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
830 ;; 'rapidxml' which is Boost.
831 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
833 (define-public r-modelr
840 (uri (cran-uri "modelr" version))
843 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
844 (build-system r-build-system)
846 `(("r-broom" ,r-broom)
847 ("r-magrittr" ,r-magrittr)
850 ("r-tibble" ,r-tibble)
852 ("r-tidyselect" ,r-tidyselect)
853 ("r-vctrs" ,r-vctrs)))
854 (home-page "https://github.com/tidyverse/modelr")
855 (synopsis "Helper functions for modelling in pipelines")
857 "Functions for modelling that help you seamlessly integrate modelling
858 into a pipeline of data manipulation and visualisation.")
859 (license license:gpl3)))
861 (define-public r-httpuv
867 (uri (cran-uri "httpuv" version))
870 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
871 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
872 ;; only contains fixes for building on Solaris.
873 (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
874 (modules '((guix build utils)
879 (delete-file-recursively "src/libuv")
880 ;; Cannot unbundle http-parser, because it contains local
883 (build-system r-build-system)
886 (modify-phases %standard-phases
887 (add-after 'unpack 'unbundle-libuv
888 (lambda* (#:key outputs #:allow-other-keys)
889 (substitute* (find-files "src" "\\.cpp$|\\.h$")
890 (("\"libuv/include/uv\\.h\"")
892 ;; Fix https://github.com/rstudio/httpuv/issues/282
893 (substitute* "src/http.cpp"
894 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
895 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
902 ("r-promises" ,r-promises)
905 (home-page "https://github.com/rstudio/httpuv")
906 (synopsis "HTTP and WebSocket server library for R")
908 "The httpuv package provides low-level socket and protocol support for
909 handling HTTP and WebSocket requests directly from within R. It is primarily
910 intended as a building block for other packages, rather than making it
911 particularly easy to create complete web applications using httpuv alone.")
912 ;; This package includes third-party code that was originally released
913 ;; under various non-copyleft licenses. Full licensing information can be
914 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
915 (license license:gpl3+)))
917 (define-public r-jsonlite
923 (uri (cran-uri "jsonlite" version))
926 "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
927 (build-system r-build-system)
929 `(("r-knitr" ,r-knitr)))
930 (home-page "https://arxiv.org/abs/1403.2805")
931 (synopsis "Robust, high performance JSON parser and generator for R")
933 "The jsonlite package provides a fast JSON parser and generator optimized
934 for statistical data and the web. It offers flexible, robust, high
935 performance tools for working with JSON in R and is particularly powerful for
936 building pipelines and interacting with a web API. In addition to converting
937 JSON data from/to R objects, jsonlite contains functions to stream, validate,
938 and prettify JSON data. The unit tests included with the package verify that
939 all edge cases are encoded and decoded consistently for use with dynamic data
940 in systems and applications.")
941 (license license:expat)))
943 (define-public r-servr
949 (uri (cran-uri "servr" version))
952 "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja"))))
953 (build-system r-build-system)
955 `(("r-httpuv" ,r-httpuv)
956 ("r-jsonlite" ,r-jsonlite)
959 (home-page "https://github.com/yihui/servr")
960 (synopsis "Simple HTTP server to serve static files or dynamic documents")
962 "Servr provides an HTTP server in R to serve static files, or dynamic
963 documents that can be converted to HTML files (e.g., R Markdown) under a given
965 (license license:expat)))
967 (define-public r-htmltools
973 (uri (cran-uri "htmltools" version))
976 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
977 (build-system r-build-system)
979 `(("r-base64enc" ,r-base64enc)
980 ("r-digest" ,r-digest)
981 ("r-rlang" ,r-rlang)))
982 (home-page "https://cran.r-project.org/web/packages/htmltools")
983 (synopsis "R tools for HTML")
985 "This package provides tools for HTML generation and output in R.")
986 (license license:expat)))
988 (define-public r-htmlwidgets
990 (name "r-htmlwidgets")
994 (uri (cran-uri "htmlwidgets" version))
997 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
998 (build-system r-build-system)
1000 `(("r-htmltools" ,r-htmltools)
1001 ("r-jsonlite" ,r-jsonlite)
1002 ("r-yaml" ,r-yaml)))
1003 (home-page "https://github.com/ramnathv/htmlwidgets")
1004 (synopsis "HTML Widgets for R")
1006 "HTML widgets is a framework for creating HTML widgets that render in
1007 various contexts including the R console, R Markdown documents, and Shiny web
1009 (license license:expat)))
1011 (define-public r-htmltable
1013 (name "r-htmltable")
1018 (uri (cran-uri "htmlTable" version))
1020 (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
1021 (properties `((upstream-name . "htmlTable")))
1022 (build-system r-build-system)
1024 `(("r-checkmate" ,r-checkmate)
1025 ("r-htmltools" ,r-htmltools)
1026 ("r-htmlwidgets" ,r-htmlwidgets)
1027 ("r-knitr" ,r-knitr)
1028 ("r-magrittr" ,r-magrittr)
1029 ("r-rstudioapi" ,r-rstudioapi)
1030 ("r-stringr" ,r-stringr)))
1032 `(("r-knitr" ,r-knitr)))
1033 (home-page "http://gforge.se/packages/")
1034 (synopsis "Advanced tables for Markdown/HTML")
1036 "This package provides functions to build tables with advanced layout
1037 elements such as row spanners, column spanners, table spanners, zebra
1038 striping, and more. While allowing advanced layout, the underlying
1039 CSS-structure is simple in order to maximize compatibility with word
1040 processors such as LibreOffice. The package also contains a few text
1041 formatting functions that help outputting text compatible with HTML or
1043 (license license:gpl3+)))
1045 (define-public r-curl
1051 (uri (cran-uri "curl" version))
1054 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1055 (build-system r-build-system)
1058 (modify-phases %standard-phases
1059 ;; The environment variable CURL_CA_BUNDLE is only respected when
1060 ;; running Windows, so we disable the platform checks.
1061 ;; This can be removed once the libcurl has been patched.
1062 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1064 (substitute* "R/onload.R"
1065 (("if \\(!grepl\\(\"mingw\".*")
1067 (substitute* "src/handle.c"
1068 (("/\\* Only set" m)
1070 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1071 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1078 `(("pkg-config" ,pkg-config)))
1079 (home-page "https://github.com/jeroenooms/curl")
1080 (synopsis "HTTP client for R")
1082 "The @code{curl()} and @code{curl_download()} functions provide highly
1083 configurable drop-in replacements for base @code{url()} and
1084 @code{download.file()} with better performance, support for encryption, gzip
1085 compression, authentication, and other @code{libcurl} goodies. The core of
1086 the package implements a framework for performing fully customized requests
1087 where data can be processed either in memory, on disk, or streaming via the
1088 callback or connection interfaces.")
1089 (license license:expat)))
1091 (define-public r-hwriter
1098 (uri (cran-uri "hwriter" version))
1101 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1102 (build-system r-build-system)
1103 (home-page "https://cran.r-project.org/web/packages/hwriter")
1104 (synopsis "Output R objects in HTML format")
1106 "This package provides easy-to-use and versatile functions to output R
1107 objects in HTML format.")
1108 (license license:lgpl2.1+)))
1110 (define-public r-rjson
1117 (uri (cran-uri "rjson" version))
1120 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1121 (build-system r-build-system)
1122 (home-page "https://cran.r-project.org/web/packages/rjson")
1123 (synopsis "JSON library for R")
1125 "This package provides functions to convert R objects into JSON objects
1127 (license license:gpl2+)))
1129 (define-public r-fastmap
1136 (uri (cran-uri "fastmap" version))
1139 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1140 (properties `((upstream-name . "fastmap")))
1141 (build-system r-build-system)
1142 (home-page "https://r-lib.github.io/fastmap/")
1143 (synopsis "Fast implementation of a key-value store")
1145 "This package provides a fast implementation of a key-value store.
1146 Environments are commonly used as key-value stores, but every time a new key
1147 is used, it is added to R's global symbol table, causing a small amount of
1148 memory leakage. This can be problematic in cases where many different keys
1149 are used. Fastmap avoids this memory leak issue by implementing the map using
1150 data structures in C++.")
1151 (license license:expat)))
1153 (define-public r-shiny
1161 (url "https://github.com/rstudio/shiny")
1162 (commit (string-append "v" version))))
1163 (file-name (git-file-name name version))
1166 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1167 (build-system r-build-system)
1169 `(#:modules ((guix build r-build-system)
1170 (guix build minify-build-system)
1173 #:imported-modules (,@%r-build-system-modules
1174 (guix build minify-build-system))
1176 (modify-phases (@ (guix build r-build-system) %standard-phases)
1177 (add-after 'unpack 'replace-bundled-minified-JavaScript
1178 (lambda* (#:key inputs #:allow-other-keys)
1179 (let ((replace-file (lambda (old new)
1180 (format #t "replacing ~a with ~a\n" old new)
1182 (symlink new old))))
1183 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1184 ;; contain just data. They are not minified code, so we don't
1186 (with-directory-excursion "inst/www/shared"
1187 (replace-file "bootstrap/shim/respond.min.js"
1188 (string-append (assoc-ref inputs "js-respond")
1189 "/share/javascript/respond.min.js"))
1190 (replace-file "bootstrap/shim/html5shiv.min.js"
1191 (string-append (assoc-ref inputs "js-html5shiv")
1192 "/share/javascript/html5shiv.min.js"))
1193 (replace-file "json2-min.js"
1194 (string-append (assoc-ref inputs "js-json2")
1195 "/share/javascript/json2-min.js"))
1196 (replace-file "strftime/strftime-min.js"
1197 (string-append (assoc-ref inputs "js-strftime")
1198 "/share/javascript/strftime.min.js"))
1199 (replace-file "highlight/highlight.pack.js"
1200 (string-append (assoc-ref inputs "js-highlight")
1201 "/share/javascript/highlight.min.js"))
1202 (replace-file "datatables/js/jquery.dataTables.min.js"
1203 (string-append (assoc-ref inputs "js-datatables")
1204 "/share/javascript/jquery.dataTables.min.js"))
1205 (replace-file "selectize/js/selectize.min.js"
1206 (string-append (assoc-ref inputs "js-selectize")
1207 "/share/javascript/selectize.min.js"))
1208 (replace-file "selectize/js/es5-shim.min.js"
1209 (string-append (assoc-ref inputs "js-es5-shim")
1210 "/share/javascript/es5-shim.min.js"))
1211 (for-each (match-lambda
1213 (delete-file target)
1214 (minify source #:target target)))
1215 '(("jqueryui/jquery-ui.js" .
1216 "jqueryui/jquery-ui.min.js")
1217 ("datepicker/js/bootstrap-datepicker.js" .
1218 "datepicker/js/bootstrap-datepicker.min.js")
1219 ("ionrangeslider/js/ion.rangeSlider.js" .
1220 "ionrangeslider/js/ion.rangeSlider.min.js")
1221 ("bootstrap/js/bootstrap.js" .
1222 "bootstrap/js/bootstrap.min.js")
1227 ("legacy/jquery.js" .
1228 "legacy/jquery.min.js")
1229 ("showdown/src/showdown.js" .
1230 "showdown/compressed/showdown.js")))))
1233 `(("r-crayon" ,r-crayon)
1234 ("r-digest" ,r-digest)
1235 ("r-fastmap" ,r-fastmap)
1236 ("r-htmltools" ,r-htmltools)
1237 ("r-httpuv" ,r-httpuv)
1238 ("r-jsonlite" ,r-jsonlite)
1239 ("r-later" ,r-later)
1241 ("r-promises" ,r-promises)
1243 ("r-rlang" ,r-rlang)
1244 ("r-sourcetools" ,r-sourcetools)
1245 ("r-withr" ,r-withr)
1246 ("r-xtable" ,r-xtable)))
1248 `(("js-datatables" ,js-datatables)
1249 ("js-html5shiv" ,js-html5shiv)
1250 ("js-json2" ,js-json2)
1251 ("js-respond" ,js-respond)
1252 ("js-selectize" ,js-selectize)
1253 ("js-strftime" ,js-strftime)
1254 ("js-highlight" ,js-highlight)
1255 ("js-es5-shim" ,js-es5-shim)))
1257 `(("uglify-js" ,uglify-js)
1258 ("gfortran" ,gfortran)))
1259 (home-page "http://shiny.rstudio.com")
1260 (synopsis "Easy interactive web applications with R")
1262 "Makes it incredibly easy to build interactive web applications
1263 with R. Automatic \"reactive\" binding between inputs and outputs and
1264 extensive prebuilt widgets make it possible to build beautiful,
1265 responsive, and powerful applications with minimal effort.")
1266 (license license:artistic2.0)))
1268 ;; This package includes minified JavaScript files. When upgrading please
1269 ;; check that there are no new minified JavaScript files.
1270 (define-public r-shinytree
1272 (name "r-shinytree")
1277 (uri (cran-uri "shinyTree" version))
1280 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1281 (modules '((guix build utils)))
1284 ;; Delete minified JavaScript
1285 (for-each delete-file
1286 '("inst/www/jsTree-3.3.7/libs/require.js"
1287 "inst/www/jsTree-3.3.7/libs/jquery.js"
1288 "inst/www/jsTree-3.3.7/jstree.min.js"))
1290 (properties `((upstream-name . "shinyTree")))
1291 (build-system r-build-system)
1293 `(#:modules ((guix build utils)
1294 (guix build r-build-system)
1298 (modify-phases %standard-phases
1299 (add-after 'unpack 'replace-minified-javascript
1300 (lambda* (#:key inputs #:allow-other-keys)
1301 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1302 (symlink (string-append (assoc-ref inputs "js-requirejs")
1303 "/share/javascript/require.min.js")
1308 `((,(assoc-ref inputs "js-jquery")
1312 (lambda (sources targets)
1313 (for-each (lambda (source target)
1314 (format #t "Processing ~a --> ~a~%"
1316 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1317 (call-with-output-file target
1319 (dump-port minified port)))))
1323 `(("r-htmlwidgets" ,r-htmlwidgets)
1324 ("r-jsonlite" ,r-jsonlite)
1325 ("r-promises" ,r-promises)
1326 ("r-shiny" ,r-shiny)
1327 ("r-stringr" ,r-stringr)))
1329 `(("js-requirejs" ,js-requirejs)))
1331 `(("uglify-js" ,uglify-js)
1335 (uri "https://code.jquery.com/jquery-3.3.1.js")
1338 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1339 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1340 (synopsis "jsTree bindings for Shiny")
1342 "This package exposes R bindings to jsTree, a JavaScript library that
1343 supports interactive trees, to enable rich, editable trees in Shiny.")
1344 (license license:expat)))
1346 (define-public r-shinydashboard
1348 (name "r-shinydashboard")
1352 (uri (cran-uri "shinydashboard" version))
1355 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1356 (build-system r-build-system)
1357 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1358 ;; Regenerate it from the included sources.
1360 `(#:modules ((guix build utils)
1361 (guix build r-build-system)
1364 (modify-phases %standard-phases
1365 (add-after 'unpack 'generate-minified-javascript
1367 (with-directory-excursion "inst/AdminLTE"
1368 (delete-file "app.min.js")
1369 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1370 (call-with-output-file "app.min.js"
1372 (dump-port minified port))))))))))
1374 `(("r-htmltools" ,r-htmltools)
1375 ("r-promises" ,r-promises)
1376 ("r-shiny" ,r-shiny)))
1378 `(("uglify-js" ,uglify-js)))
1379 (home-page "https://rstudio.github.io/shinydashboard/")
1380 (synopsis "Create dashboards with shiny")
1381 (description "This package provides an extension to the Shiny web
1382 application framework for R, making it easy to create attractive dashboards.")
1383 ;; This package includes software that was released under the Expat
1384 ;; license, but the whole package is released under GPL version 2 or
1386 (license license:gpl2+)))
1388 (define-public r-shinyfiles
1390 (name "r-shinyfiles")
1395 (uri (cran-uri "shinyFiles" version))
1397 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1398 (properties `((upstream-name . "shinyFiles")))
1399 (build-system r-build-system)
1402 ("r-htmltools" ,r-htmltools)
1403 ("r-jsonlite" ,r-jsonlite)
1404 ("r-shiny" ,r-shiny)
1405 ("r-tibble" ,r-tibble)))
1406 (home-page "https://github.com/thomasp85/shinyFiles")
1407 (synopsis "Server-side file system viewer for Shiny")
1409 "This package provides functionality for client-side navigation of the
1410 server side file system in shiny apps. In case the app is running locally
1411 this gives the user direct access to the file system without the need to
1412 \"download\" files to a temporary location. Both file and folder selection as
1413 well as file saving is available.")
1414 (license license:gpl2+)))
1416 (define-public r-shinythemes
1418 (name "r-shinythemes")
1423 (uri (cran-uri "shinythemes" version))
1426 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1427 (properties `((upstream-name . "shinythemes")))
1428 (build-system r-build-system)
1429 (propagated-inputs `(("r-shiny" ,r-shiny)))
1430 (home-page "https://rstudio.github.io/shinythemes/")
1431 (synopsis "Themes for Shiny")
1433 "This package provides themes for use with Shiny. It includes several
1434 Bootstrap themes, which are packaged for use with Shiny applications.")
1435 ;; The package is released under version 3 of the GPL, but it includes
1436 ;; source files that are covered by the Expat license. It also includes
1437 ;; fonts under SIL or the ASL.
1438 (license (list license:gpl3 license:expat
1439 license:silofl1.1 license:asl2.0))))
1441 ;; The package sources include minified variants of d3.js and non-minified
1442 ;; source code of d3-jetpack.
1443 (define-public r-d3r
1450 (uri (cran-uri "d3r" version))
1453 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1454 (build-system r-build-system)
1456 `(#:modules ((guix build utils)
1457 (guix build r-build-system)
1461 (modify-phases %standard-phases
1462 (add-after 'unpack 'process-javascript
1463 (lambda* (#:key inputs #:allow-other-keys)
1464 (with-directory-excursion "inst/www/d3/"
1468 `((,(assoc-ref inputs "d3.v3.js")
1469 "v3/dist/d3.min.js")
1470 (,(assoc-ref inputs "d3.v4.js")
1471 "v4/dist/d3.min.js")
1472 (,(assoc-ref inputs "d3.v5.js")
1473 "v5/dist/d3.min.js"))))
1474 (lambda (sources targets)
1475 (for-each (lambda (source target)
1476 (format #t "Processing ~a --> ~a~%"
1478 (delete-file target)
1479 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1480 (call-with-output-file target
1482 (dump-port minified port)))))
1486 `(("r-dplyr" ,r-dplyr)
1487 ("r-htmltools" ,r-htmltools)
1488 ("r-rlang" ,r-rlang)
1489 ("r-tidyr" ,r-tidyr)))
1491 `(("uglify-js" ,uglify-js)
1495 (uri "https://d3js.org/d3.v3.js")
1498 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1502 (uri "https://d3js.org/d3.v4.js")
1505 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1509 (uri "https://d3js.org/d3.v5.js")
1512 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1513 (home-page "https://github.com/timelyportfolio/d3r")
1514 (synopsis "d3.js utilities for R")
1516 "This package provides a suite of functions to help ease the use of the
1517 d3.js visualization library in R. These helpers include
1518 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1519 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1520 R objects into the JSON format that the d3.js library expects.")
1521 (license license:bsd-3)))
1523 ;; We use the latest commit here because the last release was in 2016 while
1524 ;; the latest commit was in 2018.
1525 (define-public r-sankeyd3
1526 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1530 (version (git-version "0.3.2" revision commit))
1535 (url "https://github.com/fbreitwieser/sankeyD3")
1537 (file-name (git-file-name name version))
1540 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1541 (build-system r-build-system)
1544 ("r-htmlwidgets" ,r-htmlwidgets)
1545 ("r-shiny" ,r-shiny)
1546 ("r-magrittr" ,r-magrittr)))
1547 (home-page "https://github.com/fbreitwieser/sankeyD3")
1548 (synopsis "Sankey network graphs from R")
1550 "This package provides an R library to generate Sankey network graphs
1551 in R and Shiny via the D3 visualization library.")
1552 ;; The R code is licensed under GPLv3+. It includes the non-minified
1553 ;; JavaScript source code of d3-sankey, which is released under the
1554 ;; 3-clause BSD license.
1555 (license (list license:gpl3+ license:bsd-3)))))
1557 (define-public r-crosstalk
1559 (name "r-crosstalk")
1564 (uri (cran-uri "crosstalk" version))
1567 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1568 (build-system r-build-system)
1570 `(("r-htmltools" ,r-htmltools)
1571 ("r-jsonlite" ,r-jsonlite)
1572 ("r-lazyeval" ,r-lazyeval)
1574 (home-page "https://rstudio.github.io/crosstalk/")
1575 (synopsis "Inter-widget interactivity for HTML widgets")
1577 "This package provides building blocks for allowing HTML widgets to
1578 communicate with each other, with Shiny or without (i.e. static @code{.html}
1579 files). It currently supports linked brushing and filtering.")
1580 (license license:expat)))
1582 (define-public r-rook
1589 (uri (cran-uri "Rook" version))
1592 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1593 (properties `((upstream-name . "Rook")))
1594 (build-system r-build-system)
1595 (propagated-inputs `(("r-brew" ,r-brew)))
1596 (home-page "https://cran.r-project.org/web/packages/Rook")
1597 (synopsis "Web server interface for R")
1599 "This package contains the Rook specification and convenience software
1600 for building and running Rook applications. A Rook application is an R
1601 reference class object that implements a @code{call} method or an R closure
1602 that takes exactly one argument, an environment, and returns a list with three
1603 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1604 (license license:gpl2)))
1606 (define-public r-miniui
1613 (uri (cran-uri "miniUI" version))
1616 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1617 (properties `((upstream-name . "miniUI")))
1618 (build-system r-build-system)
1620 `(("r-htmltools" ,r-htmltools)
1621 ("r-shiny" ,r-shiny)))
1622 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1623 (synopsis "Shiny UI widgets for small screens")
1625 "This package provides UI widget and layout functions for writing Shiny apps that
1626 work well on small screens.")
1627 (license license:gpl3)))
1629 (define-public r-feather
1636 (uri (cran-uri "feather" version))
1639 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1640 (build-system r-build-system)
1644 ("r-tibble" ,r-tibble)))
1645 (home-page "https://github.com/wesm/feather")
1646 (synopsis "R Bindings to the Feather API")
1647 (description "Read and write feather files, a lightweight binary columnar
1648 data store designed for maximum speed.")
1649 (license license:asl2.0)))
1651 (define-public r-maps
1658 (uri (cran-uri "maps" version))
1661 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1662 (build-system r-build-system)
1663 (home-page "https://cran.r-project.org/web/packages/maps")
1664 (synopsis "Draw geographical maps")
1665 (description "This package provides an R module for display of maps.
1666 Projection code and larger maps are in separate packages (@code{mapproj} and
1668 (license license:gpl2)))
1670 (define-public r-mapproj
1677 (uri (cran-uri "mapproj" version))
1680 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1681 (build-system r-build-system)
1682 (propagated-inputs `(("r-maps" ,r-maps)))
1683 (home-page "https://cran.r-project.org/web/packages/mapproj")
1684 (synopsis "Map projection in R")
1685 (description "This package converts latitude/longitude into projected
1687 (license (list license:gpl2 ; The R interface
1688 (license:non-copyleft ; The C code
1689 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1690 "Lucent Public License Version 1.02")))))
1692 (define-public r-rgooglemaps
1694 (name "r-rgooglemaps")
1699 (uri (cran-uri "RgoogleMaps" version))
1702 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1703 (properties `((upstream-name . "RgoogleMaps")))
1704 (build-system r-build-system)
1708 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1709 (synopsis "Use Google Maps in R")
1710 (description "This package serves two purposes:
1712 @item Provide a comfortable R interface to query the Google server for static
1714 @item Use the map as a background image to overlay plots within R. This
1715 requires proper coordinate scaling.
1717 (license license:gpl2+)))
1719 (define-public r-geosphere
1721 (name "r-geosphere")
1726 (uri (cran-uri "geosphere" version))
1729 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1730 (build-system r-build-system)
1731 (propagated-inputs `(("r-sp" ,r-sp)))
1732 (home-page "https://cran.r-project.org/web/packages/geosphere")
1733 (synopsis "Spherical trigonometry")
1734 (description "This package computes spherical trigonometry for geographic
1735 applications. That is, compute distances and related measures for angular
1736 (longitude/latitude) locations.")
1737 (license license:gpl3+)))
1739 (define-public r-jpeg
1746 (uri (cran-uri "jpeg" version))
1749 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1750 (build-system r-build-system)
1751 (inputs `(("libjpeg" ,libjpeg-turbo)))
1752 (home-page "https://www.rforge.net/jpeg/")
1753 (synopsis "Read and write JPEG images with R")
1754 (description "This package provides a way to read, write and display
1755 bitmap images stored in the JPEG format with R. It can read and write both
1756 files and in-memory raw vectors.")
1757 (license license:gpl2+)))
1759 (define-public r-ggmap
1766 (uri (cran-uri "ggmap" version))
1769 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1770 (build-system r-build-system)
1772 `(("r-bitops" ,r-bitops)
1773 ("r-digest" ,r-digest)
1774 ("r-dplyr" ,r-dplyr)
1775 ("r-ggplot2" ,r-ggplot2)
1779 ("r-magrittr" ,r-magrittr)
1782 ("r-purrr" ,r-purrr)
1783 ("r-rgooglemaps" ,r-rgooglemaps)
1784 ("r-rjson" ,r-rjson)
1785 ("r-scales" ,r-scales)
1786 ("r-stringr" ,r-stringr)
1787 ("r-tibble" ,r-tibble)
1788 ("r-tidyr" ,r-tidyr)))
1789 (home-page "https://github.com/dkahle/ggmap")
1790 (synopsis "Spatial visualization with ggplot2")
1791 (description "This package provides a collection of functions to visualize
1792 spatial data and models on top of static maps from various online sources (e.g
1793 Google Maps and Stamen Maps). It includes tools common to those tasks,
1794 including functions for geolocation and routing.")
1795 (license license:gpl2)))
1797 (define-public r-haven
1804 (uri (cran-uri "haven" version))
1807 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1808 (build-system r-build-system)
1812 `(("r-knitr" ,r-knitr)))
1814 `(("r-forcats" ,r-forcats)
1817 ("r-rlang" ,r-rlang)
1818 ("r-readr" ,r-readr)
1819 ("r-tibble" ,r-tibble)
1820 ("r-tidyselect" ,r-tidyselect)
1821 ("r-vctrs" ,r-vctrs)))
1822 (home-page "https://haven.tidyverse.org")
1823 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1825 "This package lets you mport foreign statistical formats into R via the
1826 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1827 (license license:expat)))
1829 (define-public r-amap
1835 (uri (cran-uri "amap" version))
1838 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1839 (build-system r-build-system)
1841 `(("gfortran" ,gfortran)))
1842 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1843 (synopsis "Another multidimensional analysis package")
1844 (description "This package provides tools for clustering and principal
1845 component analysis (with robust methods, and parallelized functions).")
1846 (license license:gpl2+)))
1848 (define-public r-ape
1855 (uri (cran-uri "ape" version))
1858 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
1859 (build-system r-build-system)
1861 `(("r-lattice" ,r-lattice)
1863 ("r-rcpp" ,r-rcpp)))
1864 (home-page "http://ape-package.ird.fr/")
1865 (synopsis "Analyses of phylogenetics and evolution")
1867 "This package provides functions for reading, writing, plotting, and
1868 manipulating phylogenetic trees, analyses of comparative data in a
1869 phylogenetic framework, ancestral character analyses, analyses of
1870 diversification and macroevolution, computing distances from DNA sequences,
1871 and several other tools.")
1872 (license license:gpl2+)))
1874 (define-public r-abbyyr
1881 (uri (cran-uri "abbyyR" version))
1884 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1885 (properties `((upstream-name . "abbyyR")))
1886 (build-system r-build-system)
1888 `(("r-curl" ,r-curl)
1891 ("r-progress" ,r-progress)
1892 ("r-readr" ,r-readr)
1894 (home-page "https://github.com/soodoku/abbyyR")
1895 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1897 "This package provides tools to get text from images of text using Abbyy
1898 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1899 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1900 passports and get the results in a variety of formats including plain text and
1901 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1902 (license license:expat)))
1904 (define-public r-colorspace
1906 (name "r-colorspace")
1911 (uri (cran-uri "colorspace" version))
1913 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1914 (build-system r-build-system)
1915 (home-page "https://cran.r-project.org/web/packages/colorspace")
1916 (synopsis "Color space manipulation")
1918 "This package carries out a mapping between assorted color spaces
1919 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1920 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1921 colors are provided.")
1922 (license license:bsd-3)))
1924 (define-public r-glue
1931 (uri (cran-uri "glue" version))
1934 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
1935 (build-system r-build-system)
1936 ;; knitr depends on glue, so we can't add knitr here to build the
1940 `(("r-knitr" ,r-knitr)))
1941 (home-page "https://github.com/tidyverse/glue")
1942 (synopsis "Interpreted string literals")
1944 "This package provides an implementation of interpreted string literals,
1945 inspired by Python's Literal String Interpolation (PEP-0498) and
1946 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1947 (license license:expat)))
1949 (define-public r-pastecs
1955 (uri (cran-uri "pastecs" version))
1958 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1959 (build-system r-build-system)
1961 `(("r-boot" ,r-boot)))
1962 (home-page "http://www.sciviews.org/pastecs")
1963 (synopsis "Analysis of space-time ecological series")
1965 "This package provides functions for regulation, decomposition and analysis
1966 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1967 initiative to bring PASSTEC 2000 functionalities to R.")
1968 (license license:gpl2+)))
1970 (define-public r-partykit
1976 (uri (cran-uri "partykit" version))
1979 "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf"))))
1980 (build-system r-build-system)
1982 `(("r-formula" ,r-formula)
1984 ("r-libcoin" ,r-libcoin)
1985 ("r-mvtnorm" ,r-mvtnorm)
1986 ("r-rpart" ,r-rpart)
1987 ("r-survival" ,r-survival)))
1988 (home-page "http://partykit.R-Forge.R-project.org/partykit")
1989 (synopsis "Toolkit for recursive partytioning")
1991 "This package provides a toolkit with infrastructure for representing,
1992 summarizing, and visualizing tree-structured regression and classification
1994 (license license:gpl2+)))
1996 (define-public r-plogr
2003 (uri (cran-uri "plogr" version))
2006 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2007 (build-system r-build-system)
2008 (home-page "https://github.com/krlmlr/plogr")
2009 (synopsis "R bindings for the plog C++ logging library")
2011 "This package provides the header files for a stripped-down version of
2012 the plog header-only C++ logging library, and a method to log to R's standard
2014 (license license:expat)))
2016 (define-public r-pls
2023 (uri (cran-uri "pls" version))
2025 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2026 (build-system r-build-system)
2027 (home-page "https://mevik.net/work/software/pls.html")
2028 (synopsis "Partial Least Squares and Principal Component Regression")
2030 "The pls package implements multivariate regression methods: Partial Least
2031 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2032 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2035 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2036 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2037 @item multi-response models (or @dfn{PLS2})
2038 @item flexible cross-validation
2039 @item Jackknife variance estimates of regression coefficients
2040 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2041 (R)MSEP, R², and correlation loadings
2042 @item formula interface, modelled after @code{lm()}, with methods for predict,
2043 print, summary, plot, update, etc.
2044 @item extraction functions for coefficients, scores, and loadings
2045 @item MSEP, RMSEP, and R² estimates
2046 @item multiplicative scatter correction (@dfn{MSC})
2048 (license license:gpl2)))
2057 (uri (cran-uri "ps" version))
2059 (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44"))))
2060 (build-system r-build-system)
2061 (home-page "https://ps.r-lib.org")
2062 (synopsis "List, query, and manipulate system processes")
2064 "The ps package implements an API to list, query, and manipulate system
2065 processes. Most of its code is based on the @code{psutil} Python package.")
2066 (license license:bsd-3)))
2068 (define-public r-pkgbuild
2075 (uri (cran-uri "pkgbuild" version))
2077 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
2078 (build-system r-build-system)
2080 `(("r-callr" ,r-callr)
2082 ("r-crayon" ,r-crayon)
2084 ("r-prettyunits" ,r-prettyunits)
2086 ("r-rprojroot" ,r-rprojroot)
2087 ("r-withr" ,r-withr)))
2088 (home-page "https://github.com/r-pkgs/pkgbuild")
2089 (synopsis "Find tools needed to build R packages")
2091 "This package provides functions used to build R packages. It locates
2092 compilers needed to build R packages on various platforms and ensures the PATH
2093 is configured appropriately so R can use them.")
2094 (license license:gpl3)))
2096 (define-public r-pkgload
2103 (uri (cran-uri "pkgload" version))
2106 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2107 (build-system r-build-system)
2110 ("r-crayon" ,r-crayon)
2112 ("r-pkgbuild" ,r-pkgbuild)
2113 ("r-rlang" ,r-rlang)
2114 ("r-rprojroot" ,r-rprojroot)
2115 ("r-rstudioapi" ,r-rstudioapi)
2116 ("r-withr" ,r-withr)))
2117 (home-page "https://github.com/r-lib/pkgload")
2118 (synopsis "Simulate package installation and attach")
2120 "This package simulates the process of installing a package and then
2121 attaching it. This is a key part of the @code{devtools} package as it allows
2122 you to rapidly iterate while developing a package.")
2123 (license license:gpl3)))
2125 (define-public r-rcpp
2132 (uri (cran-uri "Rcpp" version))
2134 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2135 (build-system r-build-system)
2136 (home-page "http://www.rcpp.org")
2137 (synopsis "Seamless R and C++ integration")
2139 "The Rcpp package provides R functions as well as C++ classes which offer
2140 a seamless integration of R and C++. Many R data types and objects can be
2141 mapped back and forth to C++ equivalents which facilitates both writing of new
2142 code as well as easier integration of third-party libraries. Documentation
2143 about Rcpp is provided by several vignettes included in this package, via the
2144 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2145 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2146 @code{citation(\"Rcpp\")} for details on these last two.")
2147 (license license:gpl2+)))
2149 (define-public r-bindr
2156 (uri (cran-uri "bindr" version))
2159 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2160 (build-system r-build-system)
2161 (home-page "https://github.com/krlmlr/bindr")
2162 (synopsis "Parametrized active bindings")
2164 "This package provides a simple interface for creating active bindings
2165 where the bound function accepts additional arguments.")
2166 (license license:expat)))
2168 (define-public r-bindrcpp
2175 (uri (cran-uri "bindrcpp" version))
2178 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2179 (build-system r-build-system)
2181 `(("r-bindr" ,r-bindr)
2182 ("r-plogr" ,r-plogr)
2183 ("r-rcpp" ,r-rcpp)))
2184 (home-page "https://github.com/krlmlr/bindrcpp")
2185 (synopsis "Rcpp interface to active bindings")
2187 "This package provides an easy way to fill an environment with active
2188 bindings that call a C++ function.")
2189 (license license:expat)))
2191 (define-public r-bisquerna
2193 (name "r-bisquerna")
2197 (uri (cran-uri "BisqueRNA" version))
2200 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2201 (properties `((upstream-name . "BisqueRNA")))
2202 (build-system r-build-system)
2204 `(("r-biobase" ,r-biobase)
2205 ("r-limsolve" ,r-limsolve)))
2206 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2207 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2208 (description "This package provides tools to accurately estimate cell type
2209 abundances from heterogeneous bulk expression. A reference-based method
2210 utilizes single-cell information to generate a signature matrix and
2211 transformation of bulk expression for accurate regression based estimates.
2212 A marker-based method utilizes known cell-specific marker genes to measure
2213 relative abundances across samples.")
2214 (license license:gpl3)))
2216 (define-public r-auc
2223 (uri (cran-uri "AUC" version))
2226 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2227 (properties `((upstream-name . "AUC")))
2228 (build-system r-build-system)
2229 (home-page "https://cran.r-project.org/web/packages/AUC")
2230 (synopsis "Compute the area under the curve of selected measures")
2232 "This package includes functions to compute the area under the curve of
2233 selected measures: the area under the sensitivity curve (AUSEC), the area
2234 under the specificity curve (AUSPC), the area under the accuracy
2235 curve (AUACC), and the area under the receiver operating characteristic
2236 curve (AUROC). The curves can also be visualized. Support for partial areas
2238 (license license:gpl2+)))
2240 (define-public r-calibrate
2242 (name "r-calibrate")
2247 (uri (cran-uri "calibrate" version))
2249 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2250 (build-system r-build-system)
2252 `(("r-mass" ,r-mass)))
2253 (home-page "https://cran.r-project.org/web/packages/calibrate")
2254 (synopsis "Calibration of scatterplot and biplot axes")
2256 "This is a package for drawing calibrated scales with tick marks
2257 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2258 (license license:gpl2)))
2260 (define-public r-shape
2267 (uri (cran-uri "shape" version))
2270 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2271 (build-system r-build-system)
2272 (home-page "https://cran.r-project.org/web/packages/shape")
2273 (synopsis "Functions for plotting graphical shapes")
2275 "This package provides functions for plotting graphical shapes such as
2276 ellipses, circles, cylinders, arrows, ...")
2277 (license license:gpl3+)))
2279 (define-public r-globaloptions
2281 (name "r-globaloptions")
2286 (uri (cran-uri "GlobalOptions" version))
2288 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2289 (properties `((upstream-name . "GlobalOptions")))
2290 (build-system r-build-system)
2292 `(("r-knitr" ,r-knitr)))
2293 (home-page "https://github.com/jokergoo/GlobalOptions")
2294 (synopsis "Generate functions to get or set global options")
2296 "This package provides more controls on the option values such as
2297 validation and filtering on the values, making options invisible or private.")
2298 (license license:gpl2+)))
2300 (define-public r-circlize
2307 (uri (cran-uri "circlize" version))
2310 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2311 (build-system r-build-system)
2313 `(("r-colorspace" ,r-colorspace)
2314 ("r-globaloptions" ,r-globaloptions)
2315 ("r-shape" ,r-shape)))
2317 `(("r-knitr" ,r-knitr)))
2318 (home-page "https://github.com/jokergoo/circlize")
2319 (synopsis "Circular visualization")
2321 "Circular layout is an efficient way to visualise huge amounts of
2322 information. This package provides an implementation of circular layout
2323 generation in R as well as an enhancement of available software. Its
2324 flexibility is based on the usage of low-level graphics functions such that
2325 self-defined high-level graphics can be easily implemented by users for
2326 specific purposes. Together with the seamless connection between the powerful
2327 computational and visual environment in R, it gives users more convenience and
2328 freedom to design figures for better understanding complex patterns behind
2329 multi-dimensional data.")
2330 (license license:gpl2+)))
2332 (define-public r-powerlaw
2339 (uri (cran-uri "poweRlaw" version))
2341 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2342 (properties `((upstream-name . "poweRlaw")))
2343 (build-system r-build-system)
2345 `(("r-pracma" ,r-pracma)))
2347 `(("r-knitr" ,r-knitr)))
2348 (home-page "https://github.com/csgillespie/poweRlaw")
2349 (synopsis "Tools for the analysis of heavy tailed distributions")
2351 "This package provides an implementation of maximum likelihood estimators
2352 for a variety of heavy tailed distributions, including both the discrete and
2353 continuous power law distributions. Additionally, a goodness-of-fit based
2354 approach is used to estimate the lower cut-off for the scaling region.")
2355 ;; Any of these GPL versions.
2356 (license (list license:gpl2 license:gpl3))))
2358 (define-public r-compare
2365 (uri (cran-uri "compare" version))
2368 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2369 (build-system r-build-system)
2370 (home-page "https://cran.r-project.org/web/packages/compare")
2371 (synopsis "Comparing objects for differences")
2373 "This package provides functions to compare a model object to a
2374 comparison object. If the objects are not identical, the functions can be
2375 instructed to explore various modifications of the objects (e.g., sorting
2376 rows, dropping names) to see if the modified versions are identical.")
2377 (license license:gpl2+)))
2379 (define-public r-dendextend
2381 (name "r-dendextend")
2386 (uri (cran-uri "dendextend" version))
2389 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2390 (build-system r-build-system)
2392 `(("r-ggplot2" ,r-ggplot2)
2393 ("r-magrittr" ,r-magrittr)
2394 ("r-viridis" ,r-viridis)))
2396 `(("r-knitr" ,r-knitr)))
2397 (home-page "https://cran.r-project.org/web/packages/dendextend")
2398 (synopsis "Extending 'dendrogram' functionality in R")
2400 "This package offers a set of functions for extending @code{dendrogram}
2401 objects in R, letting you visualize and compare trees of hierarchical
2402 clusterings. You can adjust a tree's graphical parameters (the color, size,
2403 type, etc of its branches, nodes and labels) and visually and statistically
2404 compare different dendrograms to one another.")
2405 ;; Any of these versions
2406 (license (list license:gpl2 license:gpl3))))
2408 (define-public r-getoptlong
2410 (name "r-getoptlong")
2415 (uri (cran-uri "GetoptLong" version))
2418 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2419 (properties `((upstream-name . "GetoptLong")))
2420 (build-system r-build-system)
2424 `(("r-crayon" ,r-crayon)
2425 ("r-globaloptions" ,r-globaloptions)
2426 ("r-rjson" ,r-rjson)))
2428 `(("r-knitr" ,r-knitr)))
2429 (home-page "https://github.com/jokergoo/GetoptLong")
2430 (synopsis "Parsing command-line arguments and variable interpolation")
2432 "This is yet another command-line argument parser which wraps the
2433 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2434 use in R. It also provides a simple way for variable interpolation in R.")
2435 (license license:gpl2+)))
2437 (define-public r-fastmatch
2439 (name "r-fastmatch")
2444 (uri (cran-uri "fastmatch" version))
2447 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2448 (build-system r-build-system)
2449 (home-page "https://www.rforge.net/fastmatch")
2450 (synopsis "Fast match function")
2452 "This package provides a fast @code{match} replacement for cases that
2453 require repeated look-ups. It is slightly faster that R's built-in
2454 @code{match} function on first match against a table, but extremely fast on
2455 any subsequent lookup as it keeps the hash table in memory.")
2456 (license license:gpl2)))
2465 (uri (cran-uri "ff" version))
2468 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0"))))
2469 (build-system r-build-system)
2470 (propagated-inputs `(("r-bit" ,r-bit)))
2471 (home-page "http://ff.r-forge.r-project.org/")
2472 (synopsis "Memory-efficient storage of large data on disk and access functions")
2474 "This package provides data structures that are stored on disk but
2475 behave (almost) as if they were in RAM by transparently mapping only a section
2477 ;; error Architecture not supported.
2478 (supported-systems (delete "aarch64-linux" %supported-systems))
2479 (license license:gpl2)))
2481 (define-public r-ffbase
2488 (uri (cran-uri "ffbase" version))
2491 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2492 (build-system r-build-system)
2495 ("r-fastmatch" ,r-fastmatch)
2497 (home-page "https://github.com/edwindj/ffbase")
2498 (synopsis "Basic statistical functions for package 'ff'")
2500 "This package extends the out of memory vectors of @code{ff} with
2501 statistical functions and other utilities to ease their usage.")
2502 (license license:gpl3)))
2504 (define-public r-prettyunits
2506 (name "r-prettyunits")
2511 (uri (cran-uri "prettyunits" version))
2514 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2515 (build-system r-build-system)
2516 (home-page "https://github.com/gaborcsardi/prettyunits")
2517 (synopsis "Pretty, human readable formatting of quantities")
2519 "This package provides tools for pretty, human readable formatting of
2521 (license license:expat)))
2523 (define-public r-reshape
2530 (uri (cran-uri "reshape" version))
2533 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2534 (build-system r-build-system)
2536 `(("r-plyr" ,r-plyr)
2537 ("r-rcpp" ,r-rcpp)))
2538 (home-page "http://had.co.nz/reshape")
2539 (synopsis "Flexibly reshape data")
2541 "Flexibly restructure and aggregate data using just two functions:
2542 @code{melt} and @code{cast}. This package provides them.")
2543 (license license:expat)))
2545 (define-public r-progress
2552 (uri (cran-uri "progress" version))
2555 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2556 (build-system r-build-system)
2558 `(("r-crayon" ,r-crayon)
2560 ("r-prettyunits" ,r-prettyunits)
2562 (home-page "https://github.com/gaborcsardi/progress")
2563 (synopsis "Terminal progress bars")
2565 "This package provides configurable progress bars. They may include
2566 percentage, elapsed time, and/or the estimated completion time. They work in
2567 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2568 package also provides a C++ API, that works with or without Rcpp.")
2569 (license license:expat)))
2571 (define-public r-ggally
2578 (uri (cran-uri "GGally" version))
2581 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2582 (properties `((upstream-name . "GGally")))
2583 (build-system r-build-system)
2585 `(("libressl" ,libressl)))
2587 `(("r-ggplot2" ,r-ggplot2)
2588 ("r-gtable" ,r-gtable)
2589 ("r-lifecycle" ,r-lifecycle)
2591 ("r-progress" ,r-progress)
2592 ("r-rcolorbrewer" ,r-rcolorbrewer)
2593 ("r-reshape" ,r-reshape)
2594 ("r-rlang" ,r-rlang)
2595 ("r-scales" ,r-scales)))
2596 (home-page "https://ggobi.github.io/ggally")
2597 (synopsis "Extension to ggplot2")
2599 "The R package ggplot2 is a plotting system based on the grammar of
2600 graphics. GGally extends ggplot2 by adding several functions to reduce the
2601 complexity of combining geometric objects with transformed data. Some of
2602 these functions include a pairwise plot matrix, a two group pairwise plot
2603 matrix, a parallel coordinates plot, a survival plot, and several functions to
2605 (license license:gpl2+)))
2607 (define-public r-proxy
2614 (uri (cran-uri "proxy" version))
2617 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2618 (build-system r-build-system)
2619 (home-page "https://cran.r-project.org/web/packages/proxy")
2620 (synopsis "Distance and similarity measures")
2622 "This package provides an extensible framework for the efficient
2623 calculation of auto- and cross-proximities, along with implementations of the
2624 most popular ones.")
2625 (license license:gpl2)))
2634 (uri (cran-uri "sp" version))
2636 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2637 (build-system r-build-system)
2639 `(("r-lattice" ,r-lattice)))
2640 (home-page "https://cran.r-project.org/web/packages/sp")
2641 (synopsis "Classes and methods for spatial data")
2643 "This package provides classes and methods for spatial data; the classes
2644 document where the spatial location information resides, for 2D or 3D data.
2645 Utility functions are provided, e.g. for plotting data as maps, spatial
2646 selection, as well as methods for retrieving coordinates, for subsetting,
2647 print, summary, etc.")
2648 (license license:gpl2+)))
2650 (define-public r-laplacesdemon
2652 (name "r-laplacesdemon")
2657 (uri (cran-uri "LaplacesDemon" version))
2659 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
2660 (properties `((upstream-name . "LaplacesDemon")))
2661 (build-system r-build-system)
2662 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
2663 (synopsis "Complete environment for Bayesian inference")
2665 "This package provides a complete environment for Bayesian inference using
2666 a variety of different samplers.")
2667 (license license:expat)))
2669 (define-public r-rmtstat
2676 (uri (cran-uri "RMTstat" version))
2679 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2680 (properties `((upstream-name . "RMTstat")))
2681 (build-system r-build-system)
2682 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2683 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2685 "This package provides functions for working with the Tracy-Widom laws
2686 and other distributions related to the eigenvalues of large Wishart
2688 (license license:bsd-3)))
2690 (define-public r-rmpi
2696 (uri (cran-uri "Rmpi" version))
2699 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2700 (properties `((upstream-name . "Rmpi")))
2701 (build-system r-build-system)
2703 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2704 #:phases (modify-phases %standard-phases
2705 (add-before 'install 'mpi-setup
2708 `(("openmpi" ,openmpi)))
2710 `(("pkg-config" ,pkg-config)))
2711 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2712 (synopsis "R interface to message-passing interface (MPI)")
2714 "This package provides an interface (wrapper) to MPI APIs. It also
2715 provides an interactive R manager and worker environment.")
2716 (license license:gpl2+)))
2718 (define-public r-lmoments
2725 (uri (cran-uri "Lmoments" version))
2728 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2729 (properties `((upstream-name . "Lmoments")))
2730 (build-system r-build-system)
2732 `(("r-rcpp" ,r-rcpp)
2733 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2734 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2735 (synopsis "L-moments and quantile mixtures")
2737 "This package contains functions to estimate L-moments and trimmed
2738 L-moments from the data. It also contains functions to estimate the
2739 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2740 quantile mixture from L-moments and trimmed L-moments.")
2741 (license license:gpl2)))
2743 (define-public r-distillery
2745 (name "r-distillery")
2750 (uri (cran-uri "distillery" version))
2753 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2754 (build-system r-build-system)
2755 (home-page "https://ral.ucar.edu/staff/ericg/")
2756 (synopsis "Functions for confidence intervals and object information")
2758 "This package provides some very simple method functions for confidence
2759 interval calculation and to distill pertinent information from a potentially
2760 complex object; primarily used in common with the packages extRemes and
2762 (license license:gpl2+)))
2764 (define-public r-extremes
2771 (uri (cran-uri "extRemes" version))
2774 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2775 (properties `((upstream-name . "extRemes")))
2776 (build-system r-build-system)
2778 `(("r-distillery" ,r-distillery)
2779 ("r-lmoments" ,r-lmoments)))
2780 (home-page "https://www.assessment.ucar.edu/toolkit/")
2781 (synopsis "Extreme value analysis")
2783 "ExtRemes is a suite of functions for carrying out analyses on the
2784 extreme values of a process of interest; be they block maxima over long blocks
2785 or excesses over a high threshold.")
2786 (license license:gpl2+)))
2788 (define-public r-lmtest
2795 (uri (cran-uri "lmtest" version))
2798 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2799 (build-system r-build-system)
2801 `(("r-zoo" ,r-zoo)))
2803 `(("gfortran" ,gfortran)))
2804 (home-page "https://cran.r-project.org/web/packages/lmtest")
2805 (synopsis "Testing linear regression models")
2807 "This package provides a collection of tests, data sets, and examples for
2808 diagnostic checking in linear regression models. Furthermore, some generic
2809 tools for inference in parametric models are provided.")
2810 ;; Either version is okay
2811 (license (list license:gpl2 license:gpl3))))
2813 (define-public r-idr
2819 (uri (cran-uri "idr" version))
2822 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2823 (build-system r-build-system)
2824 (home-page "https://cran.r-project.org/web/packages/idr/")
2825 (synopsis "Irreproducible discovery rate")
2827 "This is a package for estimating the copula mixture model and plotting
2828 correspondence curves in \"Measuring reproducibility of high-throughput
2829 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2830 by Li, Brown, Huang, and Bickel")
2831 (license license:gpl2+)))
2833 (define-public r-inline
2839 (uri (cran-uri "inline" version))
2842 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2843 (build-system r-build-system)
2844 (home-page "https://cran.r-project.org/web/packages/inline")
2845 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2847 "This package provides functionality to dynamically define R functions
2848 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2849 @code{.Call} calling conventions.")
2850 ;; Any version of the LGPL.
2851 (license license:lgpl3+)))
2853 (define-public r-inum
2859 (uri (cran-uri "inum" version))
2862 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2863 (build-system r-build-system)
2865 `(("r-libcoin" ,r-libcoin)))
2866 (home-page "https://cran.r-project.org/web/packages/inum/")
2867 (synopsis "Interval and enum-type representation of vectors")
2869 "This package provides an enum-type representation of vectors and
2870 representation of intervals, including a method of coercing variables
2872 (license license:gpl2)))
2874 (define-public r-bdsmatrix
2876 (name "r-bdsmatrix")
2881 (uri (cran-uri "bdsmatrix" version))
2884 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2885 (properties `((upstream-name . "bdsmatrix")))
2886 (build-system r-build-system)
2887 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2888 (synopsis "Routines for block diagonal symmetric matrices")
2890 "This package provides procedures to work with block diagonal symmetric
2891 matrices, a special case of sparse matrices.")
2892 (license license:lgpl2.0)))
2894 (define-public r-bbmle
2897 (version "1.0.23.1")
2901 (uri (cran-uri "bbmle" version))
2904 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2905 (build-system r-build-system)
2907 `(("r-bdsmatrix" ,r-bdsmatrix)
2908 ("r-lattice" ,r-lattice)
2910 ("r-matrix" ,r-matrix)
2911 ("r-mvtnorm" ,r-mvtnorm)
2912 ("r-numderiv" ,r-numderiv)))
2913 (home-page "https://cran.r-project.org/web/packages/bbmle")
2914 (synopsis "Tools for General Maximum Likelihood Estimation")
2916 "This package provides methods and functions for fitting maximum
2917 likelihood models in R. This package modifies and extends the @code{mle}
2918 classes in the @code{stats4} package.")
2919 ;; Any version of the GPL
2920 (license license:gpl2+)))
2922 (define-public r-emdbook
2929 (uri (cran-uri "emdbook" version))
2932 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2933 (build-system r-build-system)
2935 `(("r-bbmle" ,r-bbmle)
2937 ("r-lattice" ,r-lattice)
2939 ("r-plyr" ,r-plyr)))
2940 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2941 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2943 "This package provides auxiliary functions and data sets for \"Ecological
2944 Models and Data\", a book presenting maximum likelihood estimation and related
2945 topics for ecologists (ISBN 978-0-691-12522-0).")
2947 (license (list license:gpl2 license:gpl3))))
2949 (define-public r-lpsolve
2956 (uri (cran-uri "lpSolve" version))
2959 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2960 (properties `((upstream-name . "lpSolve")))
2961 (build-system r-build-system)
2962 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2963 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2965 "Lp_solve is software for solving linear, integer and mixed integer
2966 programs. This implementation supplies a \"wrapper\" function in C and some R
2967 functions that solve general linear/integer problems, assignment problems, and
2968 transportation problems.")
2969 (license license:lgpl2.0)))
2971 (define-public r-limsolve
2978 (uri (cran-uri "limSolve" version))
2981 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2982 (properties `((upstream-name . "limSolve")))
2983 (build-system r-build-system)
2985 `(("r-lpsolve" ,r-lpsolve)
2987 ("r-quadprog" ,r-quadprog)))
2988 (native-inputs `(("gfortran" ,gfortran)))
2989 (home-page "https://cran.r-project.org/web/packages/limSolve")
2990 (synopsis "Solving linear inverse models")
2992 "This package provides functions that:
2995 @item find the minimum/maximum of a linear or quadratic function,
2996 @item sample an underdetermined or overdetermined system,
2997 @item solve a linear system Ax=B for the unknown x.
3000 It includes banded and tridiagonal linear systems. The package calls Fortran
3001 functions from LINPACK.")
3003 (license (list license:gpl2+ license:gpl3+))))
3005 (define-public r-fitdistrplus
3007 (name "r-fitdistrplus")
3012 (uri (cran-uri "fitdistrplus" version))
3015 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
3016 (build-system r-build-system)
3018 `(("r-mass" ,r-mass)
3019 ("r-survival" ,r-survival)))
3021 `(("r-knitr" ,r-knitr)))
3022 (home-page "http://riskassessment.r-forge.r-project.org")
3023 (synopsis "Fitting a parametric distribution from data")
3025 "This package extends the @code{fitdistr} function of the MASS package
3026 with several functions to help the fit of a parametric distribution to
3027 non-censored or censored data. Censored data may contain left-censored,
3028 right-censored and interval-censored values, with several lower and upper
3029 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3030 provides moment matching (MME), quantile matching (QME) and maximum
3031 goodness-of-fit estimation (MGE) methods (available only for non-censored
3032 data). Weighted versions of MLE, MME and QME are available.")
3033 (license license:gpl2+)))
3035 (define-public r-energy
3042 (uri (cran-uri "energy" version))
3045 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3046 (build-system r-build-system)
3048 `(("r-boot" ,r-boot)
3049 ("r-rcpp" ,r-rcpp)))
3050 (home-page "https://cran.r-project.org/web/packages/energy")
3051 (synopsis "Multivariate inference via the energy of data")
3053 "This package provides e-statistics (energy) tests and statistics for
3054 multivariate and univariate inference, including distance correlation,
3055 one-sample, two-sample, and multi-sample tests for comparing multivariate
3056 distributions, are implemented. Measuring and testing multivariate
3057 independence based on distance correlation, partial distance correlation,
3058 multivariate goodness-of-fit tests, clustering based on energy distance,
3059 testing for multivariate normality, distance components (disco) for
3060 non-parametric analysis of structured data, and other energy
3061 statistics/methods are implemented.")
3062 (license license:gpl2+)))
3064 (define-public r-suppdists
3066 (name "r-suppdists")
3071 (uri (cran-uri "SuppDists" version))
3074 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3075 (properties `((upstream-name . "SuppDists")))
3076 (build-system r-build-system)
3077 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3078 (synopsis "Supplementary distributions")
3080 "This package provides ten distributions supplementing those built into
3081 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3082 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3083 coefficient, Johnson distributions, normal scores and generalized
3084 hypergeometric distributions. In addition two random number generators of
3085 George Marsaglia are included.")
3086 (license license:gpl2+)))
3088 (define-public r-ksamples
3095 (uri (cran-uri "kSamples" version))
3098 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3099 (properties `((upstream-name . "kSamples")))
3100 (build-system r-build-system)
3102 `(("r-suppdists" ,r-suppdists)))
3103 (home-page "https://cran.r-project.org/web/packages/kSamples")
3104 (synopsis "K-Sample rank tests and their combinations")
3106 "This package provides tools to compares k samples using the
3107 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3108 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3109 test. It computes asymptotic, simulated or (limited) exact P-values, all
3110 valid under randomization, with or without ties, or conditionally under random
3111 sampling from populations, given the observed tie pattern. Except for Steel's
3112 test and the JT test it also combines these tests across several blocks of
3114 (license license:gpl2+)))
3116 (define-public r-cvst
3123 (uri (cran-uri "CVST" version))
3126 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3127 (properties `((upstream-name . "CVST")))
3128 (build-system r-build-system)
3130 `(("r-kernlab" ,r-kernlab)
3131 ("r-matrix" ,r-matrix)))
3132 (home-page "https://cran.r-project.org/web/packages/CVST")
3133 (synopsis "Fast cross-validation via sequential testing")
3135 "This package implements the fast cross-validation via sequential
3136 testing (CVST) procedure. CVST is an improved cross-validation procedure
3137 which uses non-parametric testing coupled with sequential analysis to
3138 determine the best parameter set on linearly increasing subsets of the data.
3139 Additionally to the CVST the package contains an implementation of the
3140 ordinary k-fold cross-validation with a flexible and powerful set of helper
3141 objects and methods to handle the overall model selection process. The
3142 implementations of the Cochran's Q test with permutations and the sequential
3143 testing framework of Wald are generic and can therefore also be used in other
3145 (license license:gpl2+)))
3147 (define-public r-squarem
3154 (uri (cran-uri "SQUAREM" version))
3157 "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb"))))
3158 (properties `((upstream-name . "SQUAREM")))
3159 (build-system r-build-system)
3160 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3161 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3163 "This package provides algorithms for accelerating the convergence of
3164 slow, monotone sequences from smooth, contraction mapping such as the EM
3165 algorithm. It can be used to accelerate any smooth, linearly convergent
3166 acceleration scheme. A tutorial style introduction to this package is
3167 available in a vignette.")
3168 (license license:gpl2+)))
3170 (define-public r-lava
3177 (uri (cran-uri "lava" version))
3180 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3181 (build-system r-build-system)
3183 `(("r-numderiv" ,r-numderiv)
3184 ("r-squarem" ,r-squarem)
3185 ("r-survival" ,r-survival)))
3186 (home-page "https://github.com/kkholst/lava")
3187 (synopsis "Latent variable models")
3189 "This package provides tools for the estimation and simulation of latent
3191 (license license:gpl3)))
3193 (define-public r-drr
3200 (uri (cran-uri "DRR" version))
3203 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3204 (properties `((upstream-name . "DRR")))
3205 (build-system r-build-system)
3207 `(("r-cvst" ,r-cvst)
3208 ("r-kernlab" ,r-kernlab)
3209 ("r-matrix" ,r-matrix)))
3210 (home-page "https://cran.r-project.org/web/packages/DRR")
3211 (synopsis "Dimensionality reduction via regression")
3213 "This package provides an implementation of dimensionality reduction via
3214 regression using Kernel Ridge Regression.")
3215 (license license:gpl3)))
3217 (define-public r-prodlim
3220 (version "2019.11.13")
3224 (uri (cran-uri "prodlim" version))
3227 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3228 (build-system r-build-system)
3230 `(("r-kernsmooth" ,r-kernsmooth)
3233 ("r-survival" ,r-survival)))
3234 (home-page "https://cran.r-project.org/web/packages/prodlim")
3235 (synopsis "Product-limit estimation for censored event history analysis")
3237 "This package provides a fast and user-friendly implementation of
3238 nonparametric estimators for censored event history (survival) analysis with
3239 the Kaplan-Meier and Aalen-Johansen methods.")
3240 (license license:gpl2+)))
3242 (define-public r-dimred
3249 (uri (cran-uri "dimRed" version))
3252 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3253 (properties `((upstream-name . "dimRed")))
3254 (build-system r-build-system)
3257 ("r-magrittr" ,r-magrittr)))
3258 (home-page "https://github.com/gdkrmr/dimRed")
3259 (synopsis "Framework for dimensionality reduction")
3261 "This package provides a collection of dimensionality reduction
3262 techniques from R packages and provides a common interface for calling the
3264 (license license:gpl3)))
3266 (define-public r-timedate
3269 (version "3043.102")
3273 (uri (cran-uri "timeDate" version))
3276 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3277 (properties `((upstream-name . "timeDate")))
3278 (build-system r-build-system)
3279 (home-page "https://www.rmetrics.org")
3280 (synopsis "Chronological and calendar objects")
3282 "This package provides an environment for teaching \"Financial
3283 Engineering and Computational Finance\" and for managing chronological and
3285 (license license:gpl2+)))
3287 (define-public r-magic
3294 (uri (cran-uri "magic" version))
3297 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3298 (build-system r-build-system)
3300 `(("r-abind" ,r-abind)))
3301 (home-page "https://github.com/RobinHankin/magic.git")
3302 (synopsis "Create and investigate magic squares")
3304 "This package provides a collection of efficient, vectorized algorithms
3305 for the creation and investigation of magic squares and hypercubes, including
3306 a variety of functions for the manipulation and analysis of arbitrarily
3307 dimensioned arrays.")
3308 (license license:gpl2)))
3310 (define-public r-rmysql
3317 (uri (cran-uri "RMySQL" version))
3320 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3321 (properties `((upstream-name . "RMySQL")))
3322 (build-system r-build-system)
3324 `(("mariadb" ,mariadb "lib")
3325 ("mariadb-dev" ,mariadb "dev")
3328 `(("r-dbi" ,r-dbi)))
3329 (home-page "https://github.com/r-dbi/RMySQL")
3330 (synopsis "Database interface and MySQL driver for R")
3332 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3333 package contains an old implementation based on legacy code from S-PLUS which
3334 is being phased out. A modern MySQL client based on Rcpp is available from
3335 the RMariaDB package.")
3336 (license license:gpl2)))
3338 (define-public r-rpostgresql
3340 (name "r-rpostgresql")
3345 (uri (cran-uri "RPostgreSQL" version))
3348 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3349 (properties `((upstream-name . "RPostgreSQL")))
3350 (build-system r-build-system)
3352 `(("postgresql" ,postgresql)))
3354 `(("r-dbi" ,r-dbi)))
3355 (home-page "https://github.com/tomoakin/RPostgreSQL")
3356 (synopsis "R interface to the PostgreSQL database system")
3358 "This package provides a Database Interface (DBI) compliant driver for R
3359 to access PostgreSQL database systems.")
3360 ;; The whole package is released under GPL version 2. It includes code
3361 ;; under the PostgreSQL license.
3362 (license license:gpl2)))
3364 (define-public r-linprog
3371 (uri (cran-uri "linprog" version))
3374 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3375 (build-system r-build-system)
3376 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3377 (home-page "http://linprog.r-forge.r-project.org/")
3378 (synopsis "Linear programming and optimization")
3380 "This package can be used to solve Linear Programming / Linear
3381 Optimization problems by using the simplex algorithm.")
3382 (license license:gpl2+)))
3384 (define-public r-geometry
3391 (uri (cran-uri "geometry" version))
3394 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3395 (build-system r-build-system)
3397 `(("r-magic" ,r-magic)
3398 ("r-linprog" ,r-linprog)
3399 ("r-lpsolve" ,r-lpsolve)
3401 ("r-rcppprogress" ,r-rcppprogress)))
3402 (home-page "http://geometry.r-forge.r-project.org/")
3403 (synopsis "Mesh generation and surface tesselation")
3405 "This package makes the qhull library available in R, in a similar manner
3406 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3407 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3408 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3409 and higher dimensions. It implements the Quickhull algorithm for computing
3410 the convex hull. Qhull does not support constrained Delaunay triangulations,
3411 or mesh generation of non-convex objects, but the package does include some R
3412 functions that allow for this. Currently the package only gives access to
3413 Delaunay triangulation and convex hull computation.")
3414 ;; The Qhull sources are included and are distributed under a custom
3415 ;; non-copyleft license. The R sources are released under GPL version 2.
3416 (license (list license:gpl2
3417 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3419 (define-public r-ddalpha
3426 (uri (cran-uri "ddalpha" version))
3429 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3430 (build-system r-build-system)
3433 ("r-class" ,r-class)
3434 ("r-geometry" ,r-geometry)
3437 ("r-robustbase" ,r-robustbase)
3438 ("r-sfsmisc" ,r-sfsmisc)))
3440 `(("gfortran" ,gfortran)))
3441 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3442 (synopsis "Depth-Based classification and calculation of data depth")
3444 "This package contains procedures for depth-based supervised learning,
3445 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3446 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3447 statistical depth function to a compact low-dimensional space, where the final
3448 classification is done. It also offers an extension to functional data and
3449 routines for calculating certain notions of statistical depth functions. 50
3450 multivariate and 5 functional classification problems are included.")
3451 (license license:gpl2)))
3453 (define-public r-gower
3460 (uri (cran-uri "gower" version))
3463 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3464 (build-system r-build-system)
3465 (home-page "https://github.com/markvanderloo/gower")
3466 (synopsis "Gower's distance")
3468 "This package provides tools to compute Gower's distance (or similarity)
3469 coefficient between records, and to compute the top-n matches between records.
3470 Core algorithms are executed in parallel on systems supporting OpenMP.")
3471 (license license:gpl3)))
3473 (define-public r-rcpproll
3480 (uri (cran-uri "RcppRoll" version))
3483 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3484 (properties `((upstream-name . "RcppRoll")))
3485 (build-system r-build-system)
3487 `(("r-rcpp" ,r-rcpp)))
3488 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3489 (synopsis "Efficient rolling and windowed operations")
3491 "This package provides fast and efficient routines for common rolling /
3492 windowed operations. Routines for the efficient computation of windowed mean,
3493 median, sum, product, minimum, maximum, standard deviation and variance are
3495 (license license:gpl2+)))
3497 (define-public r-ipred
3504 (uri (cran-uri "ipred" version))
3507 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3508 (build-system r-build-system)
3510 `(("r-class" ,r-class)
3513 ("r-prodlim" ,r-prodlim)
3514 ("r-rpart" ,r-rpart)
3515 ("r-survival" ,r-survival)))
3516 (home-page "https://cran.r-project.org/web/packages/ipred")
3517 (synopsis "Improved predictors")
3519 "This package provides improved predictive models by indirect
3520 classification and bagging for classification, regression and survival
3521 problems as well as resampling based estimators of prediction error.")
3522 (license license:gpl2+)))
3524 (define-public r-psych
3531 (uri (cran-uri "psych" version))
3534 "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
3535 (build-system r-build-system)
3537 `(("r-lattice" ,r-lattice)
3538 ("r-mnormt" ,r-mnormt)
3539 ("r-nlme" ,r-nlme)))
3540 (home-page "https://cran.r-project.org/web/packages/psych/")
3541 (synopsis "Procedures for psychological, psychometric, and personality research")
3543 "This package provides a general purpose toolbox for personality,
3544 psychometric theory and experimental psychology. Functions are primarily for
3545 multivariate analysis and scale construction using factor analysis, principal
3546 component analysis, cluster analysis and reliability analysis, although others
3547 provide basic descriptive statistics. Item Response Theory is done using
3548 factor analysis of tetrachoric and polychoric correlations. Functions for
3549 analyzing data at multiple levels include within and between group statistics,
3550 including correlations and factor analysis. Functions for simulating and
3551 testing particular item and test structures are included. Several functions
3552 serve as a useful front end for structural equation modeling. Graphical
3553 displays of path diagrams, factor analysis and structural equation models are
3554 created using basic graphics.")
3555 (license license:gpl2+)))
3557 (define-public r-generics
3564 (uri (cran-uri "generics" version))
3567 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3568 (build-system r-build-system)
3569 (home-page "https://github.com/r-lib/generics")
3570 (synopsis "Common S3 generics not provided by base R methods")
3572 "In order to reduce potential package dependencies and conflicts,
3573 generics provides a number of commonly used S3 generics that are not provided
3574 by base R methods related to model fitting.")
3575 (license license:gpl2)))
3577 (define-public r-broom
3584 (uri (cran-uri "broom" version))
3587 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3588 (build-system r-build-system)
3590 `(("r-backports" ,r-backports)
3591 ("r-dplyr" ,r-dplyr)
3592 ("r-ellipsis" ,r-ellipsis)
3593 ("r-generics" ,r-generics)
3595 ("r-purrr" ,r-purrr)
3596 ("r-rlang" ,r-rlang)
3597 ("r-stringr" ,r-stringr)
3598 ("r-tibble" ,r-tibble)
3599 ("r-tidyr" ,r-tidyr)))
3601 `(("r-knitr" ,r-knitr)))
3602 (home-page "https://github.com/tidyverse/broom")
3603 (synopsis "Convert statistical analysis objects into tidy data frames")
3605 "This package provides tools to convert statistical analysis objects from
3606 R into tidy data frames, so that they can more easily be combined, reshaped
3607 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3608 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3609 summarizes a model's statistical findings such as coefficients of a
3610 regression; @code{augment}, which adds columns to the original data such as
3611 predictions, residuals and cluster assignments; and @code{glance}, which
3612 provides a one-row summary of model-level statistics.")
3613 (license license:expat)))
3615 (define-public r-recipes
3622 (uri (cran-uri "recipes" version))
3625 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3626 (build-system r-build-system)
3628 `(("r-dplyr" ,r-dplyr)
3629 ("r-generics" ,r-generics)
3631 ("r-gower" ,r-gower)
3632 ("r-ipred" ,r-ipred)
3633 ("r-lifecycle" ,r-lifecycle)
3634 ("r-lubridate" ,r-lubridate)
3635 ("r-magrittr" ,r-magrittr)
3636 ("r-matrix" ,r-matrix)
3637 ("r-purrr" ,r-purrr)
3638 ("r-rlang" ,r-rlang)
3639 ("r-tibble" ,r-tibble)
3640 ("r-tidyr" ,r-tidyr)
3641 ("r-tidyselect" ,r-tidyselect)
3642 ("r-timedate" ,r-timedate)
3643 ("r-withr" ,r-withr)))
3645 `(("r-knitr" ,r-knitr)))
3646 (home-page "https://github.com/topepo/recipes")
3647 (synopsis "Preprocessing tools to create design matrices")
3649 "Recipes is an extensible framework to create and preprocess design
3650 matrices. Recipes consist of one or more data manipulation and analysis
3651 \"steps\". Statistical parameters for the steps can be estimated from an
3652 initial data set and then applied to other data sets. The resulting design
3653 matrices can then be used as inputs into statistical or machine learning
3655 (license license:gpl2)))
3657 (define-public r-pdist
3664 (uri (cran-uri "pdist" version))
3667 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3668 (build-system r-build-system)
3669 (home-page "https://github.com/jeffwong/pdist")
3670 (synopsis "Partitioned distance function")
3672 "Pdist computes the euclidean distance between rows of a matrix X and
3673 rows of another matrix Y. Previously, this could be done by binding the two
3674 matrices together and calling @code{dist}, but this creates unnecessary
3675 computation by computing the distances between a row of X and another row of
3676 X, and likewise for Y. Pdist strictly computes distances across the two
3677 matrices, not within the same matrix, making computations significantly faster
3678 for certain use cases.")
3679 (license license:gpl3+)))
3681 (define-public r-ggrepel
3688 (uri (cran-uri "ggrepel" version))
3691 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3692 (build-system r-build-system)
3694 `(("r-ggplot2" ,r-ggplot2)
3696 ("r-scales" ,r-scales)))
3698 `(("r-knitr" ,r-knitr))) ; for vignettes
3699 (home-page "https://github.com/slowkow/ggrepel")
3700 (synopsis "Repulsive text and label geometries for ggplot2")
3702 "This package provides text and label geometries for ggplot2 that help to
3703 avoid overlapping text labels. Labels repel away from each other and away
3704 from the data points.")
3705 (license license:gpl3)))
3707 (define-public r-corrplot
3714 (uri (cran-uri "corrplot" version))
3717 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3718 (build-system r-build-system)
3719 (home-page "https://github.com/taiyun/corrplot")
3720 (synopsis "Visualization of a correlation matrix")
3722 "This package provides a graphical display of a correlation matrix or
3723 general matrix. It also contains some algorithms to do matrix reordering. In
3724 addition, corrplot is good at details, including choosing color, text labels,
3725 color labels, layout, etc.")
3726 ;; Any version of the GPL
3727 (license license:gpl2+)))
3729 (define-public r-stringdist
3731 (name "r-stringdist")
3736 (uri (cran-uri "stringdist" version))
3738 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb"))))
3739 (build-system r-build-system)
3740 (home-page "https://github.com/markvanderloo/stringdist")
3741 (synopsis "Approximate string matching and string distance functions")
3743 "This package implements an approximate string matching version of R's
3744 native @code{match} function. It can calculate various string distances based
3745 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3746 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3747 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3748 can be computed between character vectors while taking proper care of encoding
3749 or between integer vectors representing generic sequences.")
3750 (license license:gpl3+)))
3752 (define-public r-ucminf
3759 (uri (cran-uri "ucminf" version))
3762 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3763 (build-system r-build-system)
3764 (native-inputs `(("gfortran" ,gfortran)))
3765 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3766 (synopsis "General-purpose unconstrained non-linear optimization")
3768 "This package provides an implementation of an algorithm for
3769 general-purpose unconstrained non-linear optimization. The algorithm is of
3770 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3771 search with a trust region type monitoring of the input to the line search
3772 algorithm. The interface of @code{ucminf} is designed for easy interchange
3773 with the package @code{optim}.")
3774 (license license:gpl2+)))
3776 (define-public r-useful
3782 (uri (cran-uri "useful" version))
3785 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
3786 (properties `((upstream-name . "useful")))
3787 (build-system r-build-system)
3789 `(("r-assertthat" ,r-assertthat)
3790 ("r-dplyr" ,r-dplyr)
3791 ("r-ggplot2" ,r-ggplot2)
3792 ("r-magrittr" ,r-magrittr)
3793 ("r-matrix" ,r-matrix)
3795 ("r-purrr" ,r-purrr)
3796 ("r-scales" ,r-scales)))
3797 (home-page "https://github.com/jaredlander/useful")
3798 (synopsis "Collection of handy, useful functions")
3799 (description "This package provides a set of little functions that have been
3800 found useful to do little odds and ends such as plotting the results of K-means
3801 clustering, substituting special text characters, viewing parts of a
3802 @code{data.frame}, constructing formulas from text and building design and
3803 response matrices.")
3804 (license license:bsd-3)))
3806 (define-public r-ordinal
3809 (version "2019.12-10")
3813 (uri (cran-uri "ordinal" version))
3816 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3817 (build-system r-build-system)
3819 `(("r-mass" ,r-mass)
3820 ("r-matrix" ,r-matrix)
3821 ("r-numderiv" ,r-numderiv)
3822 ("r-ucminf" ,r-ucminf)))
3823 (home-page "https://github.com/runehaubo/ordinal")
3824 (synopsis "Regression models for ordinal data")
3826 "This package provides an implementation of cumulative link (mixed)
3827 models also known as ordered regression models, proportional odds models,
3828 proportional hazards models for grouped survival times and ordered models.
3829 Estimation is via maximum likelihood and mixed models are fitted with the
3830 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3831 (license license:gpl2+)))
3833 (define-public r-jomo
3840 (uri (cran-uri "jomo" version))
3843 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3844 (build-system r-build-system)
3846 `(("r-lme4" ,r-lme4)
3848 ("r-ordinal" ,r-ordinal)
3849 ("r-survival" ,r-survival)))
3850 (home-page "https://cran.r-project.org/web/packages/jomo/")
3851 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3853 "Similarly to Schafer's package pan, jomo is a package for multilevel
3854 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3855 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3856 possibility of handling binary and categorical data through latent normal
3857 variables, the option to use cluster-specific covariance matrices and to
3858 impute compatibly with the substantive model.")
3859 (license license:gpl2)))
3861 (define-public r-pan
3868 (uri (cran-uri "pan" version))
3871 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3872 (build-system r-build-system)
3873 (native-inputs `(("gfortran" ,gfortran)))
3874 (home-page "https://cran.r-project.org/web/packages/pan/")
3875 (synopsis "Multiple imputation for multivariate panel or clustered data")
3877 "This package implements multiple imputation for multivariate panel or
3879 (license license:gpl3)))
3881 (define-public r-mitml
3888 (uri (cran-uri "mitml" version))
3891 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3892 (build-system r-build-system)
3894 `(("r-haven" ,r-haven)
3897 (home-page "https://cran.r-project.org/web/packages/mitml/")
3898 (synopsis "Tools for multiple imputation in multilevel modeling")
3900 "This package provides tools for multiple imputation of missing data in
3901 multilevel modeling. It includes a user-friendly interface to the packages
3902 pan and jomo, and several functions for visualization, data management and the
3903 analysis of multiply imputed data sets.")
3904 (license license:gpl2+)))
3906 (define-public r-mice
3913 (uri (cran-uri "mice" version))
3916 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3917 (build-system r-build-system)
3919 `(("r-broom" ,r-broom)
3920 ("r-dplyr" ,r-dplyr)
3921 ("r-generics" ,r-generics)
3922 ("r-lattice" ,r-lattice)
3924 ("r-tidyr" ,r-tidyr)))
3925 (home-page "https://cran.r-project.org/web/packages/mice/")
3926 (synopsis "Multivariate imputation by chained equations")
3928 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3929 implemented by the MICE algorithm as described in @url{Van Buuren and
3930 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3931 variable has its own imputation model. Built-in imputation models are
3932 provided for continuous data (predictive mean matching, normal), binary
3933 data (logistic regression), unordered categorical data (polytomous logistic
3934 regression) and ordered categorical data (proportional odds). MICE can also
3935 impute continuous two-level data (normal model, pan, second-level variables).
3936 Passive imputation can be used to maintain consistency between variables.
3937 Various diagnostic plots are available to inspect the quality of the
3939 ;; Any of these two versions.
3940 (license (list license:gpl2 license:gpl3))))
3942 (define-public r-truncnorm
3944 (name "r-truncnorm")
3949 (uri (cran-uri "truncnorm" version))
3952 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3953 (build-system r-build-system)
3954 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3955 (synopsis "Truncated normal distribution")
3956 (description "This package provides functions for the truncated normal
3957 distribution with mean equal to @code{mean} and standard deviation equal to
3958 @code{sd}. It includes density, distribution, quantile, and expected value
3959 functions, as well as a random generation function.")
3960 (license license:gpl2)))
3962 (define-public r-rsolnp
3969 (uri (cran-uri "Rsolnp" version))
3972 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3973 (properties `((upstream-name . "Rsolnp")))
3974 (build-system r-build-system)
3976 `(("r-truncnorm" ,r-truncnorm)))
3977 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3978 (synopsis "General non-linear optimization")
3979 (description "The Rsolnp package implements a general non-linear augmented
3980 Lagrange multiplier method solver, a @dfn{sequential quadratic
3981 programming} (SQP) based solver).")
3982 ;; Any version of the GPL.
3983 (license license:gpl2+)))
3985 (define-public r-hardyweinberg
3987 (name "r-hardyweinberg")
3992 (uri (cran-uri "HardyWeinberg" version))
3995 "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh"))))
3996 (properties `((upstream-name . "HardyWeinberg")))
3997 (build-system r-build-system)
3999 `(("r-mice" ,r-mice)
4001 ("r-rsolnp" ,r-rsolnp)))
4002 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4003 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4005 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4006 diallelic genetic marker data. All classical tests (chi-square, exact,
4007 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4008 included in the package, as well as functions for power computation and for
4009 the simulation of marker data under equilibrium and disequilibrium. Routines
4010 for dealing with markers on the X-chromosome are included. Functions for
4011 testing equilibrium in the presence of missing data by using multiple
4012 imputation are also provided. Implements several graphics for exploring the
4013 equilibrium status of a large set of diallelic markers: ternary plots with
4014 acceptance regions, log-ratio plots and Q-Q plots.")
4015 (license license:gpl2+)))
4024 (uri (cran-uri "sm" version))
4027 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4028 (build-system r-build-system)
4029 (native-inputs `(("gfortran" ,gfortran)))
4030 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4031 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4033 "This is software accompanying the book 'Applied Smoothing Techniques for
4034 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4035 University Press. It provides smoothing methods for nonparametric regression
4036 and density estimation")
4037 (license license:gpl2+)))
4039 (define-public r-venndiagram
4041 (name "r-venndiagram")
4045 (uri (cran-uri "VennDiagram" version))
4048 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4049 (properties `((upstream-name . "VennDiagram")))
4050 (build-system r-build-system)
4052 `(("r-futile-logger" ,r-futile-logger)))
4053 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4054 (synopsis "Generate High-Resolution Venn and Euler Plots")
4056 "This package provides a set of functions to generate high-resolution
4057 Venn and Euler plots. It includes handling for several special cases,
4058 including two-case scaling, and extensive customization of plot shape and
4060 (license license:gpl2+)))
4062 (define-public r-vioplot
4069 (uri (cran-uri "vioplot" version))
4072 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4073 (build-system r-build-system)
4078 `(("r-knitr" ,r-knitr)))
4079 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4080 (synopsis "Violin plot")
4082 "This package provides a violin plot, which is a combination of a box
4083 plot and a kernel density plot.")
4084 (license license:bsd-3)))
4086 (define-public r-rsofia
4092 ;; This package has been removed from CRAN, so we can
4093 ;; only fetch it from the archives.
4094 (uri (string-append "https://cran.r-project.org/src/"
4095 "contrib/Archive/RSofia/RSofia_"
4099 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4100 (properties `((upstream-name . "RSofia")))
4101 (build-system r-build-system)
4103 `(("r-rcpp" ,r-rcpp)))
4104 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4105 (synopsis "Port of sofia-ml to R")
4106 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4107 suite of fast incremental algorithms for machine learning that can be used for
4108 training models for classification or ranking.")
4109 (license license:asl2.0)))
4111 (define-public r-xts
4118 (uri (cran-uri "xts" version))
4121 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
4122 (build-system r-build-system)
4123 (propagated-inputs `(("r-zoo" ,r-zoo)))
4124 (home-page "https://github.com/joshuaulrich/xts")
4125 (synopsis "Extensible time series")
4127 "This package provides for uniform handling of R's different time-based
4128 data classes by extending @code{zoo}, maximizing native format information
4129 preservation and allowing for user-level customization and extension, while
4130 simplifying cross-class interoperability.")
4131 (license license:gpl2+)))
4133 (define-public r-performanceanalytics
4135 (name "r-performanceanalytics")
4140 (uri (cran-uri "PerformanceAnalytics" version))
4143 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4145 `((upstream-name . "PerformanceAnalytics")))
4146 (build-system r-build-system)
4148 `(("r-quadprog" ,r-quadprog)
4151 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4152 (synopsis "Econometric tools for performance and risk analysis")
4153 (description "This is a collection of econometric functions for
4154 performance and risk analysis. This package aims to aid practitioners and
4155 researchers in utilizing the latest research in analysis of non-normal return
4156 streams. In general, it is most tested on return (rather than price) data on
4157 a regular scale, but most functions will work with irregular return data as
4158 well, and increasing numbers of functions will work with P&L or price data
4160 ;; Either version may be picked.
4161 (license (list license:gpl2 license:gpl3))))
4163 (define-public r-laeken
4170 (uri (cran-uri "laeken" version))
4173 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4174 (build-system r-build-system)
4176 `(("r-boot" ,r-boot)
4177 ("r-mass" ,r-mass)))
4178 (home-page "https://cran.r-project.org/web/packages/laeken/")
4179 (synopsis "Estimation of indicators on social exclusion and poverty")
4180 (description "This package provides tools for the estimation of indicators
4181 on social exclusion and poverty, as well as an implementation of Pareto tail
4182 modeling for empirical income distributions.")
4183 (license license:gpl2+)))
4185 (define-public r-vcd
4192 (uri (cran-uri "vcd" version))
4195 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4196 (build-system r-build-system)
4198 `(("r-colorspace" ,r-colorspace)
4199 ("r-lmtest" ,r-lmtest)
4200 ("r-mass" ,r-mass)))
4201 (home-page "https://cran.r-project.org/web/packages/vcd/")
4202 (synopsis "Visualizing categorical data")
4203 (description "This package provides visualization techniques, data sets,
4204 summary and inference procedures aimed particularly at categorical data.
4205 Special emphasis is given to highly extensible grid graphics. The package was
4206 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4207 Friendly and is now the main support package for a new book, \"Discrete Data
4208 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4209 (license license:gpl2)))
4211 (define-public r-ica
4218 (uri (cran-uri "ica" version))
4221 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4222 (build-system r-build-system)
4223 (home-page "https://cran.r-project.org/web/packages/ica/")
4224 (synopsis "Independent component analysis")
4225 (description "This package provides tools for @dfn{Independent Component
4226 Analysis} (ICA) using various algorithms: FastICA,
4227 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4228 of Eigenmatrices} (JADE).")
4229 (license license:gpl2+)))
4231 (define-public r-dtw
4238 (uri (cran-uri "dtw" version))
4241 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4242 (build-system r-build-system)
4243 (propagated-inputs `(("r-proxy" ,r-proxy)))
4244 (home-page "http://dtw.r-forge.r-project.org/")
4245 (synopsis "Dynamic Time Warping Algorithms")
4246 (description "This package provides a comprehensive implementation of
4247 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4248 optimal (least cumulative distance) alignment between points of two time
4249 series. Common DTW variants covered include local (slope) and global (window)
4250 constraints, subsequence matches, arbitrary distance definitions,
4251 normalizations, minimum variance matching, and so on.")
4252 (license license:gpl2+)))
4254 (define-public r-sdmtools
4257 (version "1.1-221.2")
4261 (uri (cran-uri "SDMTools" version))
4264 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4265 (properties `((upstream-name . "SDMTools")))
4266 (build-system r-build-system)
4267 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4268 (home-page "https://www.rforge.net/SDMTools/")
4269 (synopsis "Species distribution modelling tools")
4270 (description "This package provides a set of tools for post processing
4271 the outcomes of species distribution modeling exercises. It includes novel
4272 methods for comparing models and tracking changes in distributions through
4273 time. It further includes methods for visualizing outcomes, selecting
4274 thresholds, calculating measures of accuracy and landscape fragmentation
4276 (license license:gpl3+)))
4278 (define-public r-scatterplot3d
4280 (name "r-scatterplot3d")
4285 (uri (cran-uri "scatterplot3d" version))
4288 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4289 (build-system r-build-system)
4290 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4291 (synopsis "3D scatter plot")
4292 (description "This package provides an implementation of scatter plots for
4293 plotting. a three dimensional point cloud.")
4294 (license license:gpl2)))
4296 (define-public r-ggridges
4303 (uri (cran-uri "ggridges" version))
4306 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4307 (build-system r-build-system)
4309 `(("r-ggplot2" ,r-ggplot2)
4311 ("r-scales" ,r-scales)
4312 ("r-withr" ,r-withr)))
4313 (home-page "https://github.com/clauswilke/ggridges")
4314 (synopsis "Ridgeline plots in ggplot2")
4316 "Ridgeline plots provide a convenient way of visualizing changes in
4317 distributions over time or space. This package enables the creation of such
4318 plots in @code{ggplot2}.")
4319 (license license:gpl2)))
4321 (define-public r-ggjoy
4328 (uri (cran-uri "ggjoy" version))
4331 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4332 (build-system r-build-system)
4334 `(("r-ggplot2" ,r-ggplot2)
4335 ("r-ggridges" ,r-ggridges)))
4336 (home-page "https://github.com/clauswilke/ggjoy")
4337 (synopsis "Joyplots in ggplot2")
4338 (description "Joyplots provide a convenient way of visualizing changes in
4339 distributions over time or space. This package enables the creation of such
4340 plots in @code{ggplot2}.")
4341 (license license:gpl2)))
4343 (define-public r-cli
4350 (uri (cran-uri "cli" version))
4353 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4354 (build-system r-build-system)
4356 `(("r-assertthat" ,r-assertthat)
4357 ("r-crayon" ,r-crayon)
4358 ("r-fansi" ,r-fansi)
4359 ("r-glue" ,r-glue)))
4360 (home-page "https://github.com/r-lib/cli#readme")
4361 (synopsis "Helpers for developing command line interfaces")
4362 (description "This package provides a suite of tools designed to build
4363 attractive command line interfaces (CLIs). It includes tools for drawing
4364 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4365 (license license:expat)))
4367 (define-public r-argparser
4369 (name "r-argparser")
4374 (uri (cran-uri "argparser" version))
4377 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4378 (build-system r-build-system)
4379 (home-page "https://bitbucket.org/djhshih/argparser")
4380 (synopsis "Command-line argument parser")
4382 "This package provides a cross-platform command-line argument parser
4383 written purely in R with no external dependencies. It is useful with the
4384 Rscript front-end and facilitates turning an R script into an executable
4386 (license license:gpl3+)))
4388 (define-public r-debugme
4395 (uri (cran-uri "debugme" version))
4398 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4399 (build-system r-build-system)
4400 (propagated-inputs `(("r-crayon" ,r-crayon)))
4401 (home-page "https://github.com/r-lib/debugme#readme")
4402 (synopsis "Debug R packages")
4404 "This package allows the user to specify debug messages as special string
4405 constants, and control debugging of packages via environment variables.")
4406 (license license:expat)))
4408 (define-public r-processx
4415 (uri (cran-uri "processx" version))
4417 (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
4418 (build-system r-build-system)
4422 (home-page "https://github.com/r-lib/processx3")
4423 (synopsis "Execute and control system processes")
4425 "This package provides portable tools to run system processes in the
4426 background. It can check if a background process is running; wait on a
4427 background process to finish; get the exit status of finished processes; kill
4428 background processes and their children; restart processes. It can read the
4429 standard output and error of the processes, using non-blocking connections.
4430 @code{processx} can poll a process for standard output or error, with a
4431 timeout. It can also poll several processes at once.")
4432 (license license:expat)))
4434 (define-public r-tsp
4441 (uri (cran-uri "TSP" version))
4444 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4445 (properties `((upstream-name . "TSP")))
4446 (build-system r-build-system)
4447 (propagated-inputs `(("r-foreach" ,r-foreach)))
4448 (home-page "https://cran.r-project.org/web/packages/TSP/")
4449 (synopsis "Traveling salesperson problem (TSP)")
4450 (description "This package provides basic infrastructure and some
4451 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4452 traveling salesman problem).")
4453 (license license:gpl3)))
4455 (define-public r-qap
4462 (uri (cran-uri "qap" version))
4465 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4466 (build-system r-build-system)
4467 (native-inputs `(("gfortran" ,gfortran)))
4468 (home-page "https://cran.r-project.org/web/packages/qap/")
4469 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4470 (description "This package implements heuristics for the @dfn{quadratic
4471 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4473 (license license:gpl3)))
4475 (define-public r-gclus
4482 (uri (cran-uri "gclus" version))
4485 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4486 (build-system r-build-system)
4487 (propagated-inputs `(("r-cluster" ,r-cluster)))
4488 (home-page "https://cran.r-project.org/web/packages/gclus/")
4489 (synopsis "Clustering graphics")
4490 (description "This package orders panels in scatterplot matrices and
4491 parallel coordinate displays by some merit index. It contains various indices
4492 of merit, ordering functions, and enhanced versions of @code{pairs} and
4493 @code{parcoord} which color panels according to their merit level.")
4494 (license license:gpl2+)))
4496 (define-public r-webshot
4503 (uri (cran-uri "webshot" version))
4506 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4507 (build-system r-build-system)
4509 `(("r-callr" ,r-callr)
4510 ("r-jsonlite" ,r-jsonlite)
4511 ("r-magrittr" ,r-magrittr)))
4512 (home-page "https://github.com/wch/webshot/")
4513 (synopsis "Take screenshots of web pages")
4515 "Webshot makes it easy to take screenshots of web pages from within R.
4516 It can also run Shiny applications locally and take screenshots of the
4517 application; and it can render and screenshot static as well as interactive R
4518 Markdown documents.")
4519 (license license:gpl2)))
4521 (define-public r-seriation
4523 (name "r-seriation")
4528 (uri (cran-uri "seriation" version))
4531 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4532 (build-system r-build-system)
4534 `(("r-cluster" ,r-cluster)
4535 ("r-colorspace" ,r-colorspace)
4536 ("r-dendextend" ,r-dendextend)
4537 ("r-gclus" ,r-gclus)
4538 ("r-gplots" ,r-gplots)
4541 ("r-registry" ,r-registry)
4543 (native-inputs `(("gfortran" ,gfortran)))
4544 (home-page "https://s2.smu.edu/IDA/seriation/")
4545 (synopsis "Infrastructure for ordering objects using seriation")
4547 "This package provides infrastructure for seriation with an
4548 implementation of several seriation/sequencing techniques to reorder matrices,
4549 dissimilarity matrices, and dendrograms. It also provides (optimally)
4550 reordered heatmaps, color images and clustering visualizations like
4551 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4553 (license license:gpl3)))
4555 (define-public r-xfun
4562 (uri (cran-uri "xfun" version))
4564 (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
4565 (build-system r-build-system)
4566 ;; knitr itself depends on xfun
4569 `(("r-knitr" ,r-knitr)))
4570 (home-page "https://github.com/yihui/xfun")
4571 (synopsis "Miscellaneous functions")
4573 "This package provides miscellaneous functions commonly used in other
4574 packages maintained by Yihui Xie.")
4575 (license license:expat)))
4577 (define-public r-utf8
4584 (uri (cran-uri "utf8" version))
4587 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4588 (build-system r-build-system)
4589 (home-page "https://github.com/patperry/r-utf8")
4590 (synopsis "Unicode text processing")
4592 "This package provides tools to process and print UTF-8 encoded
4593 international text (Unicode). Input, validate, normalize, encode, format, and
4595 (license license:asl2.0)))
4597 (define-public r-zeallot
4604 (uri (cran-uri "zeallot" version))
4607 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4608 (build-system r-build-system)
4609 (home-page "https://github.com/nteetor/zeallot")
4610 (synopsis "Multiple, unpacking, and destructuring assignment")
4612 "This package provides a @code{%<-%} operator to perform multiple,
4613 unpacking, and destructuring assignment in R. The operator unpacks the
4614 right-hand side of an assignment into multiple values and assigns these values
4615 to variables on the left-hand side of the assignment.")
4616 (license license:expat)))
4618 (define-public r-vctrs
4625 (uri (cran-uri "vctrs" version))
4628 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
4629 (build-system r-build-system)
4631 `(("r-digest" ,r-digest)
4632 ("r-ellipsis" ,r-ellipsis)
4634 ("r-rlang" ,r-rlang)))
4636 `(("r-knitr" ,r-knitr)))
4637 (home-page "https://github.com/r-lib/vctrs")
4638 (synopsis "Vector helpers")
4640 "There are three main goals to the @code{vctrs} package:
4643 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4644 @code{length()} and @code{class()}. These definitions are paired with a
4645 framework for type-coercion and size-recycling.
4646 @item To define type- and size-stability as desirable function properties, use
4647 them to analyse existing base function, and to propose better alternatives.
4648 This work has been particularly motivated by thinking about the ideal
4649 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4650 @item To provide a new @code{vctr} base class that makes it easy to create new
4651 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4652 a few new @code{vctrs} generics, making implementation considerably simpler
4655 (license license:gpl3)))
4657 (define-public r-pillar
4664 (uri (cran-uri "pillar" version))
4667 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4668 (build-system r-build-system)
4671 ("r-crayon" ,r-crayon)
4672 ("r-ellipsis" ,r-ellipsis)
4673 ("r-fansi" ,r-fansi)
4674 ("r-lifecycle" ,r-lifecycle)
4675 ("r-rlang" ,r-rlang)
4677 ("r-vctrs" ,r-vctrs)))
4678 (home-page "https://github.com/r-lib/pillar")
4679 (synopsis "Coloured formatting for columns")
4681 "This package provides a @code{pillar} generic designed for formatting
4682 columns of data using the full range of colours provided by modern
4684 (license license:gpl3)))
4686 (define-public r-uuid
4693 (uri (cran-uri "uuid" version))
4696 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4697 (build-system r-build-system)
4698 (home-page "https://www.rforge.net/uuid")
4699 (synopsis "Tools for generating and handling of UUIDs")
4701 "This package provides tools for generating and handling of
4702 @dfn{Universally Unique Identifiers} (UUIDs).")
4703 (license license:expat)))
4705 (define-public r-tinytex
4712 (uri (cran-uri "tinytex" version))
4715 "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza"))))
4716 (build-system r-build-system)
4718 `(("r-xfun" ,r-xfun)))
4719 (home-page "https://github.com/yihui/tinytex")
4720 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4722 "This package provides helper functions to install and maintain the LaTeX
4723 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4724 easy-to-maintain version of TeX Live. This package also contains helper
4725 functions to compile LaTeX documents, and install missing LaTeX packages
4727 (license license:expat)))
4729 (define-public r-network
4736 (uri (cran-uri "network" version))
4739 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4740 (build-system r-build-system)
4742 `(("r-magrittr" ,r-magrittr)
4743 ("r-tibble" ,r-tibble)))
4744 (home-page "https://statnet.org/")
4745 (synopsis "Classes for relational data")
4747 "This package provides tools to create and modify network objects. The
4748 @code{network} class can represent a range of relational data types, and
4749 supports arbitrary vertex/edge/graph attributes.")
4750 (license license:gpl2+)))
4752 (define-public r-stabs
4759 (uri (cran-uri "stabs" version))
4762 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
4763 (build-system r-build-system)
4764 (home-page "https://github.com/hofnerb/stabs")
4765 (synopsis "Stability selection with error control")
4767 "This package provides resampling procedures to assess the stability of
4768 selected variables with additional finite sample error control for
4769 high-dimensional variable selection procedures such as Lasso or boosting.
4770 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
4771 complementary pairs stability selection with improved error bounds
4772 (Shah & Samworth, 2013) are implemented. The package can be combined with
4773 arbitrary user specified variable selection approaches.")
4774 (license license:gpl2)))
4776 (define-public r-statnet-common
4778 (name "r-statnet-common")
4783 (uri (cran-uri "statnet.common" version))
4786 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4788 `((upstream-name . "statnet.common")))
4789 (build-system r-build-system)
4791 `(("r-coda" ,r-coda)))
4792 (home-page "https://statnet.org")
4793 (synopsis "R scripts and utilities used by the Statnet software")
4794 (description "This package provides non-statistical utilities used by the
4795 software developed by the Statnet Project.")
4796 (license license:gpl3)))
4798 (define-public r-statcheck
4800 (name "r-statcheck")
4805 (uri (cran-uri "statcheck" version))
4808 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4809 (build-system r-build-system)
4811 `(("r-ggplot2" ,r-ggplot2)
4813 ("r-rmarkdown" ,r-rmarkdown)))
4814 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4815 (synopsis "Extract statistics from articles and recompute p-values")
4816 (description "This package can automatically extract statistical
4817 null-hypothesis significant testing (NHST) results from articles and recompute
4818 the p-values based on the reported test statistic and degrees of freedom to
4819 detect possible inconsistencies.")
4820 (license license:gpl2)))
4822 (define-public r-sna
4829 (uri (cran-uri "sna" version))
4832 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4833 (build-system r-build-system)
4835 `(("r-network" ,r-network)
4836 ("r-statnet-common" ,r-statnet-common)))
4837 (home-page "https://statnet.org")
4838 (synopsis "Tools for social network analysis")
4840 "This package provides a range of tools for social network analysis,
4841 including node and graph-level indices, structural distance and covariance
4842 methods, structural equivalence detection, network regression, random graph
4843 generation, and 2D/3D network visualization.")
4844 (license license:gpl2+)))
4846 (define-public r-tfisher
4853 (uri (cran-uri "TFisher" version))
4856 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4857 (properties `((upstream-name . "TFisher")))
4858 (build-system r-build-system)
4860 `(("r-matrix" ,r-matrix)
4861 ("r-mvtnorm" ,r-mvtnorm)
4863 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4864 (synopsis "Optimal thresholding Fisher's p-value combination method")
4866 "This package provides the @dfn{cumulative distribution function} (CDF),
4867 quantile, and statistical power calculator for a collection of thresholding
4868 Fisher's p-value combination methods, including Fisher's p-value combination
4869 method, truncated product method and, in particular, soft-thresholding
4870 Fisher's p-value combination method which is proven to be optimal in some
4871 context of signal detection. The p-value calculator for the omnibus version
4872 of these tests are also included.")
4873 (license license:gpl2)))
4875 (define-public r-ttr
4882 (uri (cran-uri "TTR" version))
4885 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
4886 (properties `((upstream-name . "TTR")))
4887 (build-system r-build-system)
4889 `(("r-curl" ,r-curl)
4892 (home-page "https://github.com/joshuaulrich/TTR")
4893 (synopsis "Technical trading rules")
4895 "This package provides functions and data to construct technical trading
4897 (license license:gpl2)))
4899 (define-public r-leaps
4906 (uri (cran-uri "leaps" version))
4909 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4910 (build-system r-build-system)
4911 (native-inputs `(("gfortran" ,gfortran)))
4912 (home-page "https://cran.r-project.org/web/packages/leaps/")
4913 (synopsis "Regression subset selection")
4915 "This package provides tools for regression subset selection, including
4916 exhaustive search.")
4917 (license license:gpl2+)))
4919 (define-public r-splus2r
4926 (uri (cran-uri "splus2R" version))
4929 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4930 (properties `((upstream-name . "splus2R")))
4931 (build-system r-build-system)
4932 (native-inputs `(("gfortran" ,gfortran)))
4933 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4934 (synopsis "Supplemental S-PLUS functionality in R")
4936 "Currently there are many functions in S-PLUS that are missing in R. To
4937 facilitate the conversion of S-PLUS packages to R packages, this package
4938 provides some missing S-PLUS functionality in R.")
4939 (license license:gpl2)))
4941 (define-public r-ifultools
4943 (name "r-ifultools")
4948 (uri (cran-uri "ifultools" version))
4951 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4952 (build-system r-build-system)
4954 `(("r-mass" ,r-mass)
4955 ("r-splus2r" ,r-splus2r)))
4956 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4957 (synopsis "Insightful research tools")
4958 (description "This package provides C code used by the wmtsa, fractal, and
4960 (license license:gpl2)))
4962 (define-public r-sapa
4969 (uri (cran-uri "sapa" version))
4972 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4973 (build-system r-build-system)
4975 `(("r-ifultools" ,r-ifultools)
4976 ("r-splus2r" ,r-splus2r)))
4977 (home-page "https://cran.r-project.org/web/packages/sapa/")
4978 (synopsis "Spectral analysis for physical applications")
4979 (description "This package provides software for the book Spectral
4980 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4981 Cambridge University Press, 1993.")
4982 (license license:gpl2)))
4984 (define-public r-aggregation
4986 (name "r-aggregation")
4991 (uri (cran-uri "aggregation" version))
4994 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4995 (build-system r-build-system)
4996 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4997 (synopsis "Methods for p-value aggregation")
4999 "This package contains functionality for performing the following methods
5000 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5001 Fisher's method), and Sidak correction.")
5002 (license license:gpl3)))
5004 (define-public r-quantmod
5011 (uri (cran-uri "quantmod" version))
5014 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
5015 (build-system r-build-system)
5017 `(("r-curl" ,r-curl)
5021 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5022 (synopsis "Quantitative financial modelling framework")
5023 (description "This package provides a quantitative financial modelling
5024 framework to allow users to specify, build, trade, and analyse quantitative
5025 financial trading strategies.")
5026 (license license:gpl3)))
5028 (define-public r-tseries
5035 (uri (cran-uri "tseries" version))
5038 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
5039 (build-system r-build-system)
5041 `(("r-quadprog" ,r-quadprog)
5042 ("r-quantmod" ,r-quantmod)
5045 `(("gfortran" ,gfortran)))
5046 (home-page "https://cran.r-project.org/web/packages/tseries/")
5047 (synopsis "Time series analysis and computational finance")
5049 "This package provides functions relating to time series analysis and
5050 computational finance.")
5051 (license license:gpl2)))
5053 (define-public r-wmtsa
5060 (uri (cran-uri "wmtsa" version))
5063 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5064 (build-system r-build-system)
5066 `(("r-ifultools" ,r-ifultools)
5068 ("r-splus2r" ,r-splus2r)))
5069 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5070 (synopsis "Wavelet methods for time series analysis")
5072 "This package provides software to accompany the book \"Wavelet Methods
5073 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5074 University Press, 2000.")
5075 (license license:gpl2)))
5077 (define-public r-tsa
5084 (uri (cran-uri "TSA" version))
5087 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
5088 (properties `((upstream-name . "TSA")))
5089 (build-system r-build-system)
5091 `(("r-leaps" ,r-leaps)
5092 ("r-locfit" ,r-locfit)
5093 ("r-mgcv" ,r-mgcv)))
5094 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5095 (synopsis "Time series analysis")
5097 "This package contains R functions and datasets detailed in the book
5098 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5099 Cryer and Kung-Sik Chan.")
5100 (license license:gpl2+)))
5102 (define-public r-extradistr
5104 (name "r-extradistr")
5109 (uri (cran-uri "extraDistr" version))
5112 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
5113 (properties `((upstream-name . "extraDistr")))
5114 (build-system r-build-system)
5116 `(("r-rcpp" ,r-rcpp)))
5117 (home-page "https://github.com/twolodzko/extraDistr")
5118 (synopsis "Additional univariate and multivariate distributions")
5120 "This package implements density, distribution functions, quantile
5121 functions and random generation functions for a large number of univariate and
5122 multivariate distributions.")
5123 (license license:gpl2)))
5125 (define-public r-fractal
5132 (uri (cran-uri "fractal" version))
5135 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5136 (build-system r-build-system)
5138 `(("r-ifultools" ,r-ifultools)
5141 ("r-scatterplot3d" ,r-scatterplot3d)
5142 ("r-splus2r" ,r-splus2r)
5143 ("r-wmtsa" ,r-wmtsa)))
5144 (home-page "https://cran.r-project.org/web/packages/fractal/")
5145 (synopsis "Fractal time series modeling and analysis")
5147 "This package provides tools for stochastic fractal and deterministic
5148 chaotic time series analysis.")
5149 (license license:gpl2)))
5151 (define-public r-urca
5158 (uri (cran-uri "urca" version))
5161 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5162 (build-system r-build-system)
5163 (propagated-inputs `(("r-nlme" ,r-nlme)))
5164 (native-inputs `(("gfortran" ,gfortran)))
5165 (home-page "https://cran.r-project.org/web/packages/urca/")
5166 (synopsis "Unit root and cointegration tests for time series data")
5168 "This package provides unit root and cointegration tests encountered in
5169 applied econometric analysis.")
5170 (license license:gpl2+)))
5172 (define-public r-cubature
5179 (uri (cran-uri "cubature" version))
5182 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5183 (build-system r-build-system)
5185 `(("r-rcpp" ,r-rcpp)))
5187 `(("r-knitr" ,r-knitr)))
5188 (home-page "https://github.com/bnaras/cubature")
5189 (synopsis "Adaptive multivariate integration over hypercubes")
5191 "This package is an R wrapper around the cubature C library for adaptive
5192 multivariate integration over hypercubes. This version provides both
5193 @code{hcubature} and @code{pcubature} routines in addition to a vector
5195 ;; The included cubature C library is released under GPLv2+, but the
5196 ;; wrapper declares the license to be GPLv3+.
5197 (license (list license:gpl2+ license:gpl3+))))
5199 (define-public r-trend
5206 (uri (cran-uri "trend" version))
5209 "0bj40acr1sc7vfxdcsdja3g28xsmrclmgb3n94p89gfjcgp8nv1d"))))
5210 (build-system r-build-system)
5212 `(("r-extradistr" ,r-extradistr)))
5214 `(("gfortran" ,gfortran)))
5215 (home-page "https://cran.r-project.org/web/packages/trend/")
5216 (synopsis "Non-parametric trend tests and change-point detection")
5218 "The analysis of environmental data often requires the detection of
5219 trends and change-points. This package includes tests for trend
5220 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5221 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5222 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5223 correlation trend test), change-point detection (Lanzante's test procedures,
5224 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5225 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5226 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5227 sample Robust Rank-Order Distributional Test.")
5228 (license license:gpl3)))
5230 (define-public r-expm
5237 (uri (cran-uri "expm" version))
5240 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5241 (build-system r-build-system)
5242 (propagated-inputs `(("r-matrix" ,r-matrix)))
5243 (native-inputs `(("gfortran" ,gfortran)))
5244 (home-page "https://r-forge.r-project.org/projects/expm/")
5245 (synopsis "Tools for matrix exponentials and related quantities")
5247 "This package provides tools for the computation of the matrix
5248 exponential, logarithm, square root, and related quantities.")
5249 (license license:gpl2+)))
5251 (define-public r-complexplus
5253 (name "r-complexplus")
5258 (uri (cran-uri "complexplus" version))
5261 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5262 (build-system r-build-system)
5264 `(("r-expm" ,r-expm)
5265 ("r-matrix" ,r-matrix)))
5266 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5267 (synopsis "Functions of complex or real variables")
5269 "This package extends several functions to the complex domain, including
5270 the matrix exponential and logarithm, and the determinant.")
5271 (license license:gpl2)))
5273 (define-public r-phontools
5275 (name "r-phontools")
5280 (uri (cran-uri "phonTools" version))
5283 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5284 (properties `((upstream-name . "phonTools")))
5285 (build-system r-build-system)
5286 (home-page "http://www.santiagobarreda.com/rscripts.html")
5287 (synopsis "Tools for phonetic and acoustic analyses")
5289 "This package contains tools for the organization, display, and analysis
5290 of the sorts of data frequently encountered in phonetics research and
5291 experimentation, including the easy creation of IPA vowel plots, and the
5292 creation and manipulation of WAVE audio files.")
5293 (license license:bsd-2)))
5302 (uri (cran-uri "np" version))
5305 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5306 (build-system r-build-system)
5308 `(("r-boot" ,r-boot)
5309 ("r-cubature" ,r-cubature)
5310 ("r-quadprog" ,r-quadprog)
5311 ("r-quantreg" ,r-quantreg)))
5312 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5313 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5314 (description "This package provides non-parametric (and semi-parametric)
5315 kernel methods that seamlessly handle a mix of continuous, unordered, and
5316 ordered factor data types.")
5317 ;; Any version of the GPL.
5318 (license license:gpl3+)))
5320 (define-public r-powerplus
5322 (name "r-powerplus")
5327 (uri (cran-uri "powerplus" version))
5330 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5331 (build-system r-build-system)
5333 `(("r-complexplus" ,r-complexplus)
5336 ("r-matrix" ,r-matrix)
5337 ("r-phontools" ,r-phontools)))
5338 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5339 (synopsis "Exponentiation operations")
5341 "This package provides tools for the computation of matrix and scalar
5343 (license license:gpl2)))
5345 (define-public r-egg
5352 (uri (cran-uri "egg" version))
5355 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5356 (properties `((upstream-name . "egg")))
5357 (build-system r-build-system)
5359 `(("r-ggplot2" ,r-ggplot2)
5360 ("r-gridextra" ,r-gridextra)
5361 ("r-gtable" ,r-gtable)))
5362 (home-page "https://cran.r-project.org/web/packages/egg")
5363 (synopsis "Extensions for ggplot2")
5365 "This package provides miscellaneous functions to help customize ggplot2
5366 objects. High-level functions are provided to post-process ggplot2 layouts
5367 and allow alignment between plot panels, as well as setting panel sizes to
5368 fixed values. Other functions include a custom @code{geom}, and helper
5369 functions to enforce symmetric scales or add tags to facetted plots.")
5370 (license license:gpl3)))
5372 (define-public r-heatmaply
5374 (name "r-heatmaply")
5379 (uri (cran-uri "heatmaply" version))
5382 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5383 (build-system r-build-system)
5385 `(("r-assertthat" ,r-assertthat)
5386 ("r-colorspace" ,r-colorspace)
5387 ("r-dendextend" ,r-dendextend)
5389 ("r-ggplot2" ,r-ggplot2)
5390 ("r-htmlwidgets" ,r-htmlwidgets)
5391 ("r-magrittr" ,r-magrittr)
5392 ("r-plotly" ,r-plotly)
5393 ("r-rcolorbrewer" ,r-rcolorbrewer)
5394 ("r-reshape2" ,r-reshape2)
5395 ("r-scales" ,r-scales)
5396 ("r-seriation" ,r-seriation)
5397 ("r-viridis" ,r-viridis)
5398 ("r-webshot" ,r-webshot)))
5400 `(("r-knitr" ,r-knitr)))
5401 (home-page "https://cran.r-project.org/package=heatmaply")
5402 (synopsis "Interactive cluster heat maps using plotly")
5404 "This package enables you to create interactive cluster heatmaps that can
5405 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5406 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5407 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5408 a popular graphical method for visualizing high-dimensional data, in which a
5409 table of numbers is encoded as a grid of colored cells. The rows and columns
5410 of the matrix are ordered to highlight patterns and are often accompanied by
5412 ;; Either version of the license.
5413 (license (list license:gpl2 license:gpl3))))
5422 (uri (cran-uri "h5" version))
5425 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5426 (build-system r-build-system)
5431 `(("which" ,which)))
5433 `(("r-rcpp" ,r-rcpp)))
5434 (home-page "https://github.com/mannau/h5")
5435 (synopsis "Interface to the HDF5 Library")
5437 "This package provides an S4 interface to the HDF5 library supporting
5438 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5439 binary files in a language independent format. The HDF5 format can therefore
5440 be used as an alternative to R's save/load mechanism. Since h5 is able to
5441 access only subsets of stored data it can also handle data sets which do not
5443 (license license:bsd-2)))
5445 (define-public r-cgdsr
5452 (uri (cran-uri "cgdsr" version))
5455 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5456 (build-system r-build-system)
5458 `(("r-httr" ,r-httr)
5459 ("r-r-methodss3" ,r-r-methodss3)
5460 ("r-r-oo" ,r-r-oo)))
5461 (home-page "https://github.com/cBioPortal/cgdsr")
5462 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5464 "This package provides a basic set of R functions for querying the Cancer
5465 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5466 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5467 (license license:lgpl3)))
5469 (define-public r-import
5476 (uri (cran-uri "import" version))
5479 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5480 (build-system r-build-system)
5481 (home-page "https://github.com/smbache/import")
5482 (synopsis "Import mechanism for R")
5484 "This is an alternative mechanism for importing objects from packages.
5485 The syntax allows for importing multiple objects from a package with a single
5486 command in an expressive way. The import package bridges some of the gap
5487 between using @code{library} (or @code{require}) and direct (single-object)
5488 imports. Furthermore the imported objects are not placed in the current
5489 environment. It is also possible to import objects from stand-alone @code{.R}
5491 (license license:expat)))
5493 (define-public r-shinyace
5500 (uri (cran-uri "shinyAce" version))
5503 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5504 (properties `((upstream-name . "shinyAce")))
5505 (build-system r-build-system)
5507 `(("r-shiny" ,r-shiny)
5508 ("r-jsonlite" ,r-jsonlite)))
5509 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5510 (synopsis "Ace editor bindings for Shiny")
5512 "This package provides Ace editor bindings to enable a rich text editing
5513 environment within Shiny.")
5514 (license license:expat)))
5516 (define-public r-randomizr
5518 (name "r-randomizr")
5523 (uri (cran-uri "randomizr" version))
5526 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5527 (properties `((upstream-name . "randomizr")))
5528 (build-system r-build-system)
5530 `(("r-knitr" ,r-knitr)))
5531 (home-page "https://declaredesign.org/r/randomizr/")
5532 (synopsis "Tools for common forms of random assignment and sampling")
5534 "This package provides tools for generating random assignments for common
5535 experimental designs and random samples for common sampling designs.")
5536 (license license:expat)))
5538 (define-public r-base64url
5540 (name "r-base64url")
5545 (uri (cran-uri "base64url" version))
5548 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5549 (build-system r-build-system)
5551 `(("r-backports" ,r-backports)))
5552 (home-page "https://github.com/mllg/base64url")
5553 (synopsis "Fast and URL-safe base64 encoder and decoder")
5555 "This package provides a URL-safe base64 encoder and decoder. In
5556 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5557 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5558 encoder does not fill the string with trailing @code{=}. The resulting
5559 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5560 and thus are safe to use in URLs or for file names. The package also comes
5561 with a simple base32 encoder/decoder suited for case insensitive file
5563 (license license:gpl3)))
5565 (define-public r-radiant-data
5567 (name "r-radiant-data")
5572 (uri (cran-uri "radiant.data" version))
5575 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5576 (modules '((guix build utils)))
5579 ;; Delete files that are under CC-NC-SA.
5580 (delete-file-recursively "inst/app/tools/help")
5582 (properties `((upstream-name . "radiant.data")))
5583 (build-system r-build-system)
5585 `(("r-base64enc" ,r-base64enc)
5586 ("r-broom" ,r-broom)
5589 ("r-dplyr" ,r-dplyr)
5592 ("r-ggplot2" ,r-ggplot2)
5593 ("r-import" ,r-import)
5594 ("r-jsonlite" ,r-jsonlite)
5595 ("r-knitr" ,r-knitr)
5596 ("r-lubridate" ,r-lubridate)
5597 ("r-magrittr" ,r-magrittr)
5598 ("r-markdown" ,r-markdown)
5600 ("r-patchwork" ,r-patchwork)
5601 ("r-plotly" ,r-plotly)
5602 ("r-psych" ,r-psych)
5603 ("r-randomizr" ,r-randomizr)
5604 ("r-readr" ,r-readr)
5605 ("r-readxl" ,r-readxl)
5606 ("r-rlang" ,r-rlang)
5607 ("r-rmarkdown" ,r-rmarkdown)
5608 ("r-rstudioapi" ,r-rstudioapi)
5609 ("r-scales" ,r-scales)
5610 ("r-shiny" ,r-shiny)
5611 ("r-shinyfiles" ,r-shinyfiles)
5612 ("r-shinyace" ,r-shinyace)
5613 ("r-stringi" ,r-stringi)
5614 ("r-tibble" ,r-tibble)
5615 ("r-tidyr" ,r-tidyr)
5616 ("r-writexl" ,r-writexl)))
5617 (home-page "https://github.com/radiant-rstats/radiant.data")
5618 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5620 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5621 visualizing, summarizing, transforming, and combining data. It also contains
5622 functionality to generate reproducible reports of the analyses conducted in
5624 (license license:agpl3)))
5626 (define-public r-algdesign
5628 (name "r-algdesign")
5633 (uri (cran-uri "AlgDesign" version))
5635 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5636 (properties `((upstream-name . "AlgDesign")))
5637 (build-system r-build-system)
5638 (home-page "https://github.com/jvbraun/AlgDesign")
5639 (synopsis "Algorithmic experimental design")
5641 "This package provides tools to calculate exact and approximate theory
5642 experimental designs for D, A, and I criteria. Very large designs may be
5643 created. Experimental designs may be blocked or blocked designs created from
5644 a candidate list, using several criteria. The blocking can be done when whole
5645 and within plot factors interact.")
5646 (license license:gpl2+)))
5648 (define-public r-signal
5655 (uri (cran-uri "signal" version))
5658 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5659 (build-system r-build-system)
5660 (propagated-inputs `(("r-mass" ,r-mass)))
5661 (native-inputs `(("gfortran" ,gfortran)))
5662 (home-page "https://cran.r-project.org/web/packages/signal/")
5663 (synopsis "Signal processing")
5665 "This package provides a set of signal processing functions originally
5666 written for Matlab and GNU Octave. It includes filter generation utilities,
5667 filtering functions, resampling routines, and visualization of filter models.
5668 It also includes interpolation functions.")
5669 (license license:gpl2)))
5671 (define-public r-gsubfn
5678 (uri (cran-uri "gsubfn" version))
5681 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5682 (build-system r-build-system)
5683 (propagated-inputs `(("r-proto" ,r-proto)))
5684 (home-page "https://code.google.com/archive/p/gsubfn/")
5685 (synopsis "Utilities for strings and function arguments.")
5687 "This package provides @code{gsubfn} which is like @code{gsub} but can
5688 take a replacement function or certain other objects instead of the
5689 replacement string. Matches and back references are input to the replacement
5690 function and replaced by the function output. @code{gsubfn} can be used to
5691 split strings based on content rather than delimiters and for quasi-perl-style
5692 string interpolation. The package also has facilities for translating
5693 formulas to functions and allowing such formulas in function calls instead of
5695 (license license:gpl2+)))
5697 (define-public r-sqldf
5704 (uri (cran-uri "sqldf" version))
5707 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5708 (build-system r-build-system)
5710 `(("r-chron" ,r-chron)
5712 ("r-gsubfn" ,r-gsubfn)
5713 ("r-proto" ,r-proto)
5714 ("r-rsqlite" ,r-rsqlite)))
5715 (home-page "https://github.com/ggrothendieck/sqldf")
5716 (synopsis "Manipulate R data frames using SQL")
5718 "The @code{sqldf} function is typically passed a single argument which is
5719 an SQL select statement where the table names are ordinary R data frame names.
5720 @code{sqldf} transparently sets up a database, imports the data frames into
5721 that database, performs the SQL statement and returns the result using a
5722 heuristic to determine which class to assign to each column of the returned
5723 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5724 used to read filtered files into R even if the original files are larger than
5725 R itself can handle.")
5726 (license license:gpl2)))
5728 (define-public r-abind
5735 (uri (cran-uri "abind" version))
5738 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5739 (build-system r-build-system)
5740 (home-page "https://cran.r-project.org/web/packages/abind/")
5741 (synopsis "Combine multidimensional arrays")
5743 "This package provides tools to combine multidimensional arrays into a
5744 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5745 works with vectors, matrices, and higher-dimensional arrays. It also provides
5746 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5747 extracting and replacing data in arrays.")
5748 (license license:lgpl2.0+)))
5750 (define-public r-prroc
5757 (uri (cran-uri "PRROC" version))
5760 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5761 (properties `((upstream-name . "PRROC")))
5762 (build-system r-build-system)
5763 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5764 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5766 "This package computes the areas under the @dfn{precision-recall} (PR)
5767 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5768 contrast to other implementations, the interpolation between points of the PR
5769 curve is done by a non-linear piecewise function. In addition to the areas
5770 under the curves, the curves themselves can also be computed and plotted by a
5771 specific S3-method.")
5772 (license license:gpl3)))
5774 (define-public r-vim
5781 (uri (cran-uri "VIM" version))
5784 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5785 (properties `((upstream-name . "VIM")))
5786 (build-system r-build-system)
5789 ("r-colorspace" ,r-colorspace)
5790 ("r-data-table" ,r-data-table)
5791 ("r-e1071" ,r-e1071)
5792 ("r-laeken" ,r-laeken)
5793 ("r-magrittr" ,r-magrittr)
5796 ("r-ranger" ,r-ranger)
5798 ("r-robustbase" ,r-robustbase)
5802 `(("r-knitr" ,r-knitr)))
5803 (home-page "https://github.com/alexkowa/VIM")
5804 (synopsis "Visualization and imputation of missing values")
5806 "This package provides tools for the visualization of missing and/or
5807 imputed values are introduced, which can be used for exploring the data and
5808 the structure of the missing and/or imputed values. Depending on this
5809 structure of the missing values, the corresponding methods may help to
5810 identify the mechanism generating the missing values and allows to explore the
5811 data including missing values. In addition, the quality of imputation can be
5812 visually explored using various univariate, bivariate, multiple and
5813 multivariate plot methods.")
5814 (license license:gpl2+)))
5816 (define-public r-fnn
5823 (uri (cran-uri "FNN" version))
5826 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5827 (properties `((upstream-name . "FNN")))
5828 (build-system r-build-system)
5829 (home-page "https://cran.r-project.org/web/packages/FNN")
5830 (synopsis "Fast nearest neighbor search algorithms and applications")
5832 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5833 search algorithms. Related applications including KNN classification,
5834 regression and information measures are implemented.")
5835 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5836 ;; later can be used.
5837 (license license:gpl2+)))
5839 (define-public r-smoother
5846 (uri (cran-uri "smoother" version))
5849 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5850 (build-system r-build-system)
5852 `(("r-ttr" ,r-ttr)))
5853 (home-page "https://cran.r-project.org/web/packages/smoother")
5854 (synopsis "Functions relating to the smoothing of numerical data")
5856 "This package provides a collection of methods for smoothing numerical
5857 data, commencing with a port of the Matlab gaussian window smoothing function.
5858 In addition, several functions typically used in smoothing of financial data
5860 (license license:gpl2)))
5862 (define-public r-riverplot
5864 (name "r-riverplot")
5869 (uri (cran-uri "riverplot" version))
5872 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5873 (build-system r-build-system)
5874 (home-page "https://logfc.wordpress.com")
5875 (synopsis "Sankey or ribbon plots")
5877 "Sankey plots are a type of diagram that is convenient to illustrate how
5878 flow of information, resources etc. separates and joins, much like observing
5879 how rivers split and merge. For example, they can be used to compare
5880 different clusterings. This package provides an implementation of Sankey
5882 (license license:gpl2+)))
5884 (define-public r-dyn
5891 (uri (cran-uri "dyn" version))
5894 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5895 (build-system r-build-system)
5897 `(("r-zoo" ,r-zoo)))
5898 (home-page "https://cran.r-project.org/web/packages/dyn")
5899 (synopsis "Time series regression")
5901 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5902 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5903 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5904 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5905 @code{randomForest::randomForest()} and other regression functions, allowing
5906 those functions to be used with time series including specifications that may
5907 contain lags, diffs and missing values.")
5909 (license license:gpl2+)))
5911 (define-public r-catdap
5918 (uri (cran-uri "catdap" version))
5921 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5922 (build-system r-build-system)
5924 `(("gfortran" ,gfortran)))
5925 (home-page "https://cran.r-project.org/web/packages/catdap/")
5926 (synopsis "Tools for categorical data analysis")
5928 "This package provides functions for analyzing multivariate data.
5929 Dependencies of the distribution of the specified variable (response
5930 variable) to other variables (explanatory variables) are derived and
5931 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5932 (license license:gpl2+)))
5934 (define-public r-arules
5941 (uri (cran-uri "arules" version))
5944 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5945 (build-system r-build-system)
5947 `(("r-matrix" ,r-matrix)))
5948 (home-page "https://github.com/mhahsler/arules")
5949 (synopsis "Mining association rules and frequent itemsets")
5951 "This package provides an infrastructure for representing, manipulating
5952 and analyzing transaction data and patterns (frequent itemsets and association rules).
5953 It also provides C implementations of the association mining algorithms Apriori
5955 (license license:gpl3)))
5957 (define-public r-parsedate
5959 (name "r-parsedate")
5964 (uri (cran-uri "parsedate" version))
5967 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5968 (build-system r-build-system)
5970 `(("r-rematch2" ,r-rematch2)))
5971 (home-page "https://github.com/gaborcsardi/parsedate")
5973 "Recognize and parse dates in various formats")
5975 "This package provides three functions for dealing with dates:
5976 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5977 time formats, @code{parse_date} parses dates in unspecified formats,
5978 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5979 (license license:gpl2)))
5981 (define-public r-abc-data
5988 (uri (cran-uri "abc.data" version))
5991 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5992 (properties `((upstream-name . "abc.data")))
5993 (build-system r-build-system)
5994 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5995 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5997 "This package contains data which are used by functions of the abc
5998 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5999 algorithms for performing parameter estimation, model selection, and
6001 (license license:gpl3+)))
6003 (define-public r-abc
6010 (uri (cran-uri "abc" version))
6013 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6014 (build-system r-build-system)
6016 `(("r-abc-data" ,r-abc-data)
6017 ("r-locfit" ,r-locfit)
6020 ("r-quantreg" ,r-quantreg)))
6021 (home-page "https://cran.r-project.org/web/packages/abc/")
6022 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6024 "This package implements several @dfn{Approximate Bayesian
6025 Computation} (ABC) algorithms for performing parameter estimation, model
6026 selection, and goodness-of-fit. Cross-validation tools are also available for
6027 measuring the accuracy of ABC estimates, and to calculate the
6028 misclassification probabilities of different models.")
6029 (license license:gpl3+)))
6031 (define-public r-zip
6038 (uri (cran-uri "zip" version))
6041 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6042 (build-system r-build-system)
6043 (home-page "https://github.com/gaborcsardi/zip")
6044 (synopsis "Cross-platform Zip compression")
6046 "This package provides a cross-platform Zip compression library for R.
6047 It is a replacement for the @code{zip} function, that does not require any
6048 additional external tools on any platform.")
6049 (license license:cc0)))
6051 (define-public r-openxlsx
6058 (uri (cran-uri "openxlsx" version))
6061 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
6062 (build-system r-build-system)
6064 `(("r-rcpp" ,r-rcpp)
6065 ("r-stringi" ,r-stringi)
6068 `(("r-knitr" ,r-knitr)))
6069 (home-page "https://github.com/awalker89/openxlsx")
6070 (synopsis "Read, write and edit XLSX files")
6072 "This package simplifies the creation of Excel @code{.xlsx} files by
6073 providing a high level interface to writing, styling and editing worksheets.
6074 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6075 and @code{XLConnect} packages with the added benefit of removing the
6076 dependency on Java.")
6077 (license license:gpl3)))
6079 (define-public r-rio
6086 (uri (cran-uri "rio" version))
6089 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6090 (build-system r-build-system)
6092 `(("r-curl" ,r-curl)
6093 ("r-data-table" ,r-data-table)
6094 ("r-foreign" ,r-foreign)
6095 ("r-haven" ,r-haven)
6096 ("r-openxlsx" ,r-openxlsx)
6097 ("r-readxl" ,r-readxl)
6098 ("r-tibble" ,r-tibble)))
6099 (home-page "https://github.com/leeper/rio")
6100 (synopsis "Swiss-army knife for data I/O")
6102 "This package provides streamlined data import and export infrastructure
6103 by making assumptions that the user is probably willing to make: @code{import}
6104 and @code{export} determine the data structure from the file extension,
6105 reasonable defaults are used for data import and export (e.g.,
6106 @code{stringsAsFactors=FALSE}), web-based import is natively
6107 supported (including from SSL/HTTPS), compressed files can be read directly
6108 without explicit decompression, and fast import packages are used where
6109 appropriate. An additional convenience function, @code{convert}, provides a
6110 simple method for converting between file types.")
6111 (license license:gpl2)))
6113 (define-public r-maptools
6120 (uri (cran-uri "maptools" version))
6123 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6124 (build-system r-build-system)
6126 `(("r-foreign" ,r-foreign)
6127 ("r-lattice" ,r-lattice)
6129 (home-page "https://r-forge.r-project.org/projects/maptools/")
6130 (synopsis "Tools for reading and handling spatial objects")
6132 "This package provides a set of tools for manipulating and reading
6133 geographic data, in particular ESRI Shapefiles. It includes binary access to
6134 GSHHG shoreline files. The package also provides interface wrappers for
6135 exchanging spatial objects with other R packages.")
6136 ;; The C source files from shapelib are released under the Expat license.
6137 ;; The R code is released under GPL version 2 or later.
6138 (license (list license:gpl2+
6141 (define-public r-later
6148 (uri (cran-uri "later" version))
6151 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6152 (build-system r-build-system)
6156 ("r-rlang" ,r-rlang)))
6158 `(("r-knitr" ,r-knitr)))
6159 (home-page "https://github.com/r-lib/later")
6160 (synopsis "Utilities for delaying function execution")
6162 "This package provides tools to execute arbitrary R or C functions some
6163 time after the current time, after the R execution stack has emptied.")
6164 (license license:gpl2+)))
6166 (define-public r-promises
6173 (uri (cran-uri "promises" version))
6176 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6177 (build-system r-build-system)
6179 `(("r-later" ,r-later)
6180 ("r-magrittr" ,r-magrittr)
6183 ("r-rlang" ,r-rlang)))
6185 `(("r-knitr" ,r-knitr)))
6186 (home-page "https://rstudio.github.io/promises")
6187 (synopsis "Abstractions for promise-based asynchronous programming")
6189 "This package provides fundamental abstractions for doing asynchronous
6190 programming in R using promises. Asynchronous programming is useful for
6191 allowing a single R process to orchestrate multiple tasks in the background
6192 while also attending to something else. Semantics are similar to JavaScript
6193 promises, but with a syntax that is idiomatic R.")
6194 (license license:expat)))
6196 (define-public r-dosnow
6203 (uri (cran-uri "doSNOW" version))
6206 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6207 (properties `((upstream-name . "doSNOW")))
6208 (build-system r-build-system)
6210 `(("r-foreach" ,r-foreach)
6211 ("r-iterators" ,r-iterators)
6212 ("r-snow" ,r-snow)))
6213 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6214 (synopsis "Foreach parallel adaptor for the snow package")
6216 "This package provides a parallel backend for the @code{%dopar%} function
6217 using the @code{snow} package.")
6218 (license license:gpl2)))
6220 (define-public r-snowfall
6223 (version "1.84-6.1")
6226 (uri (cran-uri "snowfall" version))
6228 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6229 (build-system r-build-system)
6231 `(("r-snow" ,r-snow)))
6232 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6233 (synopsis "Easier cluster computing")
6234 (description "This package is a usability wrapper around snow for easier
6235 development of parallel R programs. This package offers e.g. extended error
6236 checks, and additional functions. All functions work in sequential mode, too,
6237 if no cluster is present or wished. The package is also designed as connector
6238 to the cluster management tool @code{sfCluster}, but can also used without
6240 (license license:gpl2+)))
6242 (define-public r-rappdirs
6249 (uri (cran-uri "rappdirs" version))
6252 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6253 (build-system r-build-system)
6254 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6255 (synopsis "Determine where to save data, caches, and logs")
6257 "This package provides an easy way to determine which directories on the
6258 user's computer should be used to save data, caches and logs. It is a port of
6259 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6260 (license license:expat)))
6262 (define-public r-renv
6269 (uri (cran-uri "renv" version))
6272 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
6273 (properties `((upstream-name . "renv")))
6274 (build-system r-build-system)
6276 `(("r-knitr" ,r-knitr)))
6277 (home-page "https://rstudio.github.io/renv")
6278 (synopsis "Project environments")
6280 "This package provides a dependency management toolkit for R. Using
6281 renv, you can create and manage project-local R libraries, save the state of
6282 these libraries to a lockfile, and later restore your library as required.
6283 Together, these tools can help make your projects more isolated, portable, and
6285 (license license:expat)))
6287 (define-public r-learnr
6294 (uri (cran-uri "learnr" version))
6297 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6298 (build-system r-build-system)
6300 `(("r-checkmate" ,r-checkmate)
6301 ("r-ellipsis" ,r-ellipsis)
6302 ("r-evaluate" ,r-evaluate)
6303 ("r-htmltools" ,r-htmltools)
6304 ("r-htmlwidgets" ,r-htmlwidgets)
6305 ("r-jsonlite" ,r-jsonlite)
6306 ("r-knitr" ,r-knitr)
6307 ("r-markdown" ,r-markdown)
6308 ("r-rappdirs" ,r-rappdirs)
6310 ("r-rmarkdown" ,r-rmarkdown)
6311 ("r-rprojroot" ,r-rprojroot)
6312 ("r-shiny" ,r-shiny)
6313 ("r-withr" ,r-withr)))
6314 (home-page "https://rstudio.github.io/learnr/")
6315 (synopsis "Interactive tutorials for R")
6317 "This package provides tools to create interactive tutorials using R
6318 Markdown. Use a combination of narrative, figures, videos, exercises, and
6319 quizzes to create self-paced tutorials for learning about R and R packages.")
6320 (license license:asl2.0)))
6322 (define-public r-analytics
6324 (name "r-analytics")
6329 (uri (cran-uri "analytics" version))
6332 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6333 (build-system r-build-system)
6336 ("r-cluster" ,r-cluster)
6337 ("r-fractal" ,r-fractal)
6338 ("r-lmtest" ,r-lmtest)
6341 ("r-powerplus" ,r-powerplus)
6342 ("r-robust" ,r-robust)
6343 ("r-trend" ,r-trend)
6347 (home-page "https://cran.r-project.org/web/packages/analytics/")
6348 (synopsis "Collection of data analysis tools")
6350 "This package is a collection of data analysis tools. It includes tools
6351 for regression outlier detection in a fitted linear model, stationary
6352 bootstrap using a truncated geometric distribution, a comprehensive test for
6353 weak stationarity, column means by group, weighted biplots, and a heuristic to
6354 obtain a better initial configuration in non-metric MDS.")
6355 (license license:gpl2)))
6357 (define-public r-reticulate
6359 (name "r-reticulate")
6364 (uri (cran-uri "reticulate" version))
6367 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6368 (build-system r-build-system)
6369 (inputs `(("python" ,python)))
6371 `(("r-rappdirs" ,r-rappdirs)
6372 ("r-jsonlite" ,r-jsonlite)
6373 ("r-matrix" ,r-matrix)
6374 ("r-rcpp" ,r-rcpp)))
6376 `(("r-knitr" ,r-knitr)))
6377 (home-page "https://github.com/rstudio/reticulate")
6378 (synopsis "R interface to Python")
6380 "This package provides an interface from R to Python modules, classes,
6381 and functions. When calling into Python, R data types are automatically
6382 converted to their equivalent Python types. When values are returned from
6383 Python to R they are converted back to R types.")
6384 (license license:asl2.0)))
6386 (define-public r-bibtex
6393 (uri (cran-uri "bibtex" version))
6396 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6397 (build-system r-build-system)
6398 (propagated-inputs `(("r-stringr" ,r-stringr)))
6399 (home-page "https://github.com/romainfrancois/bibtex")
6400 (synopsis "Bibtex parser")
6401 (description "This package provides a utility for R to parse a bibtex
6403 (license license:gpl2+)))
6405 (define-public r-ggseqlogo
6407 (name "r-ggseqlogo")
6412 (uri (cran-uri "ggseqlogo" version))
6415 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6416 (build-system r-build-system)
6417 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6418 (home-page "https://github.com/omarwagih/ggseqlogo")
6419 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6421 "The range of functions provided by this package makes it possible to
6422 draw highly versatile genomic sequence logos. Features include, but are not
6423 limited to, modifying colour schemes and fonts used to draw the logo,
6424 generating multiple logo plots, and aiding the visualisation with annotations.
6425 Sequence logos can easily be combined with other ggplot2 plots.")
6426 ;; Unspecified version of the LGPL.
6427 (license license:lgpl3+)))
6429 (define-public r-ggsci
6436 (uri (cran-uri "ggsci" version))
6439 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6440 (build-system r-build-system)
6442 `(("r-ggplot2" ,r-ggplot2)
6443 ("r-scales" ,r-scales)))
6444 (home-page "https://nanx.me/ggsci/")
6445 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6447 "This package provides a collection of ggplot2 color palettes inspired by
6448 plots in scientific journals, data visualization libraries, science fiction
6449 movies, and TV shows.")
6450 (license license:gpl3)))
6452 (define-public r-ggsignif
6459 (uri (cran-uri "ggsignif" version))
6462 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6463 (build-system r-build-system)
6465 `(("r-knitr" ,r-knitr)))
6467 `(("r-ggplot2" ,r-ggplot2)))
6468 (home-page "https://github.com/const-ae/ggsignif")
6469 (synopsis "Significance brackets for ggplot2")
6471 "Enrich your ggplots with group-wise comparisons. This package provides
6472 an easy way to indicate if two groups are significantly different. Commonly
6473 this is shown by a bracket on top connecting the groups of interest which
6474 itself is annotated with the level of significance. The package provides a
6475 single layer that takes the groups for comparison and the test as arguments
6476 and adds the annotation to the plot.")
6477 (license license:gpl3)))
6479 (define-public r-rstatix
6486 (uri (cran-uri "rstatix" version))
6489 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6490 (properties `((upstream-name . "rstatix")))
6491 (build-system r-build-system)
6493 `(("r-broom" ,r-broom)
6495 ("r-corrplot" ,r-corrplot)
6496 ("r-dplyr" ,r-dplyr)
6497 ("r-generics" ,r-generics)
6498 ("r-magrittr" ,r-magrittr)
6499 ("r-purrr" ,r-purrr)
6500 ("r-rlang" ,r-rlang)
6501 ("r-tibble" ,r-tibble)
6502 ("r-tidyr" ,r-tidyr)
6503 ("r-tidyselect" ,r-tidyselect)))
6504 (home-page "https://rpkgs.datanovia.com/rstatix/")
6505 (synopsis "Pipe-friendly framework for basic statistical tests")
6507 "This package provides a simple and intuitive pipe-friendly framework,
6508 coherent with the @code{tidyverse} design philosophy, for performing basic
6509 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6510 correlation analyses. The output of each test is automatically transformed
6511 into a tidy data frame to facilitate visualization. Additional functions are
6512 available for reshaping, reordering, manipulating and visualizing correlation
6514 (license license:gpl2)))
6516 (define-public r-ggpubr
6523 (uri (cran-uri "ggpubr" version))
6526 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6527 (build-system r-build-system)
6529 `(("r-cowplot" ,r-cowplot)
6530 ("r-dplyr" ,r-dplyr)
6531 ("r-ggplot2" ,r-ggplot2)
6532 ("r-ggrepel" ,r-ggrepel)
6533 ("r-ggsci" ,r-ggsci)
6534 ("r-ggsignif" ,r-ggsignif)
6536 ("r-gridextra" ,r-gridextra)
6537 ("r-magrittr" ,r-magrittr)
6538 ("r-polynom" ,r-polynom)
6539 ("r-purrr" ,r-purrr)
6540 ("r-rlang" ,r-rlang)
6541 ("r-scales" ,r-scales)
6542 ("r-rstatix" ,r-rstatix)
6543 ("r-tibble" ,r-tibble)
6544 ("r-tidyr" ,r-tidyr)))
6545 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6546 (synopsis "ggplot2-based publication-ready plots")
6548 "The ggplot2 package is an excellent and flexible package for elegant
6549 data visualization in R. However the default generated plots require some
6550 formatting before we can send them for publication. The ggpubr package
6551 provides some easy-to-use functions for creating and customizing ggplot2-based
6552 publication-ready plots.")
6553 (license license:gpl2)))
6555 (define-public r-ellipse
6562 (uri (cran-uri "ellipse" version))
6565 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6566 (build-system r-build-system)
6567 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6568 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6570 "This package contains various routines for drawing ellipses and
6571 ellipse-like confidence regions, implementing the plots described in Murdoch
6572 and Chow (1996), A graphical display of large correlation matrices, The
6573 American Statistician 50, 178-180. There are also routines implementing the
6574 profile plots described in Bates and Watts (1988), Nonlinear Regression
6575 Analysis and its Applications.")
6576 (license license:gpl2+)))
6578 (define-public r-flashclust
6580 (name "r-flashclust")
6585 (uri (cran-uri "flashClust" version))
6588 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6589 (properties `((upstream-name . "flashClust")))
6590 (build-system r-build-system)
6591 (native-inputs `(("gfortran" ,gfortran)))
6592 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6593 (synopsis "Implementation of optimal hierarchical clustering")
6595 "This package provides a fast implementation of hierarchical
6597 (license license:gpl2+)))
6599 (define-public r-factominer
6601 (name "r-factominer")
6606 (uri (cran-uri "FactoMineR" version))
6609 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6610 (properties `((upstream-name . "FactoMineR")))
6611 (build-system r-build-system)
6614 ("r-cluster" ,r-cluster)
6615 ("r-ellipse" ,r-ellipse)
6616 ("r-flashclust" ,r-flashclust)
6617 ("r-ggplot2" ,r-ggplot2)
6618 ("r-ggrepel" ,r-ggrepel)
6619 ("r-lattice" ,r-lattice)
6620 ("r-leaps" ,r-leaps)
6622 ("r-scatterplot3d" ,r-scatterplot3d)))
6623 (home-page "http://factominer.free.fr")
6624 (synopsis "Multivariate exploratory data analysis and data mining")
6626 "This package provides exploratory data analysis methods to summarize,
6627 visualize and describe datasets. The main principal component methods are
6628 available, those with the largest potential in terms of applications:
6629 principal component analysis (PCA) when variables are quantitative,
6630 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6631 variables are categorical, Multiple Factor Analysis when variables are
6632 structured in groups, etc. and hierarchical cluster analysis.")
6633 (license license:gpl2+)))
6635 (define-public r-factoextra
6637 (name "r-factoextra")
6642 (uri (cran-uri "factoextra" version))
6645 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6646 (build-system r-build-system)
6648 `(("r-abind" ,r-abind)
6649 ("r-cluster" ,r-cluster)
6650 ("r-dendextend" ,r-dendextend)
6651 ("r-factominer" ,r-factominer)
6652 ("r-ggplot2" ,r-ggplot2)
6653 ("r-ggpubr" ,r-ggpubr)
6654 ("r-ggrepel" ,r-ggrepel)
6655 ("r-reshape2" ,r-reshape2)
6656 ("r-tidyr" ,r-tidyr)))
6657 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6658 (synopsis "Extract and visualize the results of multivariate data analyses")
6660 "This package provides some easy-to-use functions to extract and
6661 visualize the output of multivariate data analyses, including
6662 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6663 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6664 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6665 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6666 packages. It contains also functions for simplifying some clustering analysis
6667 steps and provides ggplot2-based elegant data visualization.")
6668 (license license:gpl2)))
6670 (define-public r-fansi
6677 (uri (cran-uri "fansi" version))
6680 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6681 (build-system r-build-system)
6683 `(("r-knitr" ,r-knitr))) ; for vignettes
6684 (home-page "https://github.com/brodieG/fansi")
6685 (synopsis "ANSI control sequence aware string functions")
6687 "This package provides counterparts to R string manipulation functions
6688 that account for the effects of ANSI text formatting control sequences.")
6689 (license license:gpl2+)))
6691 (define-public r-nbclust
6698 (uri (cran-uri "NbClust" version))
6701 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6702 (properties `((upstream-name . "NbClust")))
6703 (build-system r-build-system)
6704 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6705 (synopsis "Determine the best number of clusters in a data set")
6707 "NbClust provides 30 indexes for determining the optimal number of
6708 clusters in a data set and offers the best clustering scheme from different
6709 results to the user.")
6710 (license license:gpl2)))
6712 (define-public r-hdf5r
6719 (uri (cran-uri "hdf5r" version))
6722 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6723 (build-system r-build-system)
6728 `(("r-bit64" ,r-bit64)
6731 `(("r-knitr" ,r-knitr)))
6732 (home-page "https://hhoeflin.github.io/hdf5r")
6733 (synopsis "Interface to the HDF5 binary data format")
6735 "HDF5 is a data model, library and file format for storing and managing
6736 large amounts of data. This package provides a nearly feature complete,
6737 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6738 functionality is added so that HDF5 objects behave very similar to their
6739 corresponding R counterparts.")
6740 (license license:asl2.0)))
6742 (define-public r-itertools
6744 (name "r-itertools")
6749 (uri (cran-uri "itertools" version))
6752 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6753 (build-system r-build-system)
6755 `(("r-iterators" ,r-iterators)))
6756 (home-page "https://cran.r-project.org/web/packages/itertools/")
6757 (synopsis "Iterator tools")
6759 "This package provides various tools for creating iterators, many
6760 patterned after functions in the Python @code{itertools} module, and others
6761 patterned after functions in the snow package.")
6762 (license license:gpl2)))
6764 (define-public r-polynom
6771 (uri (cran-uri "polynom" version))
6774 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6775 (build-system r-build-system)
6776 (home-page "https://cran.r-project.org/web/packages/polynom/")
6777 (synopsis "Functions for univariate polynomial manipulations")
6779 "This package provides a collection of functions to implement a class for
6780 univariate polynomial manipulations.")
6781 (license license:gpl2)))
6783 (define-public r-gbrd
6790 (uri (cran-uri "gbRd" version))
6793 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6794 (properties `((upstream-name . "gbRd")))
6795 (build-system r-build-system)
6796 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6797 (synopsis "Utilities for processing Rd objects and files")
6799 "This package provides utilities for processing Rd objects and files.
6800 Extract argument descriptions and other parts of the help pages of
6802 (license license:gpl2+)))
6804 (define-public r-rjags
6811 (uri (cran-uri "rjags" version))
6814 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6815 (build-system r-build-system)
6817 `(("r-coda" ,r-coda)))
6821 `(("pkg-config" ,pkg-config)))
6822 (home-page "http://mcmc-jags.sourceforge.net")
6823 (synopsis "Bayesian graphical models using MCMC")
6825 "This package provides an R interface to the JAGS MCMC library. JAGS is
6826 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6827 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6828 (license license:gpl2)))
6830 (define-public r-rdpack
6837 (uri (cran-uri "Rdpack" version))
6840 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6841 (properties `((upstream-name . "Rdpack")))
6842 (build-system r-build-system)
6844 `(("r-bibtex" ,r-bibtex)
6845 ("r-gbrd" ,r-gbrd)))
6846 (home-page "https://github.com/GeoBosh/Rdpack")
6847 (synopsis "Update and manipulate Rd documentation objects")
6849 "This package provides functions for manipulation of R documentation
6850 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6851 updating Rd documentation for functions, methods and classes; it also includes
6852 Rd macros for citations and import of references from bibtex files for use in
6853 Rd files and roxygen2 comments, as well as many functions for manipulation of
6854 references and Rd files.")
6855 (license license:gpl2+)))
6857 (define-public r-officer
6864 (uri (cran-uri "officer" version))
6867 "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
6868 (build-system r-build-system)
6870 `(("r-magrittr" ,r-magrittr)
6876 `(("r-knitr" ,r-knitr)))
6877 (home-page "https://davidgohel.github.io/officer")
6878 (synopsis "Manipulation of Word and PowerPoint documents")
6880 "This package provides tools to access and manipulate Word and PowerPoint
6881 documents from R. The package focuses on tabular and graphical reporting from
6882 R; it also provides two functions that let users get document content into
6883 data objects. A set of functions lets add and remove images, tables and
6884 paragraphs of text in new or existing documents. When working with PowerPoint
6885 presentations, slides can be added or removed; shapes inside slides can also
6886 be added or removed. When working with Word documents, a cursor can be used
6887 to help insert or delete content at a specific location in the document.")
6888 (license license:gpl3)))
6890 (define-public r-profilemodel
6892 (name "r-profilemodel")
6897 (uri (cran-uri "profileModel" version))
6900 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6901 (properties `((upstream-name . "profileModel")))
6902 (build-system r-build-system)
6903 (home-page "https://github.com/ikosmidis/profileModel")
6904 (synopsis "Profiling inference functions for various model classes")
6906 "This package provides tools that can be used to calculate, evaluate,
6907 plot and use for inference the profiles of *arbitrary* inference functions for
6908 arbitrary @code{glm}-like fitted models with linear predictors. More information
6909 on the methods that are implemented can be found in Kosmidis (2008)
6910 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6911 (license license:gpl2+)))
6913 (define-public r-brglm
6920 (uri (cran-uri "brglm" version))
6923 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6924 (properties `((upstream-name . "brglm")))
6925 (build-system r-build-system)
6927 `(("r-profilemodel" ,r-profilemodel)))
6928 (home-page "https://github.com/ikosmidis/brglm")
6929 (synopsis "Bias reduction in binomial-response generalized linear models")
6931 "Fit generalized linear models with binomial responses using either an
6932 adjusted-score approach to bias reduction or maximum penalized likelihood
6933 where penalization is by Jeffreys invariant prior. These procedures return
6934 estimates with improved frequentist properties (bias, mean squared error) that
6935 are always finite even in cases where the maximum likelihood estimates are
6936 infinite (data separation). Fitting takes place by fitting generalized linear
6937 models on iteratively updated pseudo-data. The interface is essentially the
6938 same as @code{glm}. More flexibility is provided by the fact that custom
6939 pseudo-data representations can be specified and used for model fitting.
6940 Functions are provided for the construction of confidence intervals for the
6941 reduced-bias estimates.")
6942 (license license:gpl2+)))
6944 (define-public r-entropy
6951 (uri (cran-uri "entropy" version))
6954 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6955 (properties `((upstream-name . "entropy")))
6956 (build-system r-build-system)
6957 (home-page "https://www.strimmerlab.org/software/entropy/")
6958 (synopsis "Estimation of entropy, mutual information and related quantities")
6960 "This package implements various estimators of entropy, such as the
6961 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6962 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6963 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6964 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6965 mutual information, and chi-squared statistic of independence. In addition
6966 there are functions for discretizing continuous random variables.")
6967 (license license:gpl3+)))
6969 (define-public r-abn
6976 (uri (cran-uri "abn" version))
6979 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6980 (build-system r-build-system)
6984 `(("r-boot" ,r-boot)
6985 ("r-brglm" ,r-brglm)
6986 ("r-entropy" ,r-entropy)
6989 ("r-moments" ,r-moments)
6992 ("r-rcpparmadillo" ,r-rcpparmadillo)
6993 ("r-rjags" ,r-rjags)))
6994 (home-page "https://r-bayesian-networks.org/")
6995 (synopsis "Modelling multivariate data with additive bayesian networks")
6997 "Bayesian network analysis is a form of probabilistic graphical models
6998 which derives from empirical data a directed acyclic graph, DAG, describing
6999 the dependency structure between random variables. An additive Bayesian
7000 network model consists of a form of a DAG where each node comprises a
7001 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
7002 equivalent to Bayesian multivariate regression using graphical modelling, they
7003 generalises the usual multivariable regression, GLM, to multiple dependent
7004 variables. This package provides routines to help determine optimal Bayesian
7005 network models for a given data set, where these models are used to identify
7006 statistical dependencies in messy, complex data.")
7007 (license license:gpl2+)))
7009 (define-public r-acd
7016 (uri (cran-uri "ACD" version))
7019 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7020 (properties `((upstream-name . "ACD")))
7021 (build-system r-build-system)
7022 (home-page "https://cran.r-project.org/web/packages/ACD/")
7023 (synopsis "Categorical data analysis with complete or missing responses")
7025 "This package provides tools for categorical data analysis with complete
7026 or missing responses.")
7027 (license license:gpl2+)))
7029 (define-public r-acdm
7036 (uri (cran-uri "ACDm" version))
7039 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7040 (properties `((upstream-name . "ACDm")))
7041 (build-system r-build-system)
7043 `(("r-dplyr" ,r-dplyr)
7044 ("r-ggplot2" ,r-ggplot2)
7046 ("r-rsolnp" ,r-rsolnp)
7048 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7049 (synopsis "Tools for Autoregressive Conditional Duration Models")
7051 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7052 and Russell, 1998) models. It creates trade, price or volume durations from
7053 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7055 (license license:gpl2+)))
7057 (define-public r-overlap
7064 (uri (cran-uri "overlap" version))
7067 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7068 (build-system r-build-system)
7069 (home-page "https://cran.r-project.org/web/packages/overlap/")
7070 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7072 "This package provides functions to fit kernel density functions to data
7073 on temporal activity patterns of animals; estimate coefficients of overlapping
7074 of densities for two species; and calculate bootstrap estimates of confidence
7076 (license license:gpl3+)))
7078 (define-public r-snakecase
7080 (name "r-snakecase")
7085 (uri (cran-uri "snakecase" version))
7088 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7089 (build-system r-build-system)
7091 `(("r-stringi" ,r-stringi)
7092 ("r-stringr" ,r-stringr)))
7093 (home-page "https://github.com/Tazinho/snakecase")
7094 (synopsis "Convert strings into any case")
7096 "This package provides a consistent, flexible and easy to use tool to
7097 parse and convert strings into cases like snake or camel among others.")
7098 (license license:gpl3)))
7100 (define-public r-prediction
7102 (name "r-prediction")
7107 (uri (cran-uri "prediction" version))
7110 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7111 (build-system r-build-system)
7113 `(("r-data-table" ,r-data-table)))
7114 (home-page "https://github.com/leeper/prediction")
7115 (synopsis "Tidy, type-safe prediction methods")
7117 "This package provides the @code{prediction()} function, a type-safe
7118 alternative to @code{predict()} that always returns a data frame. The package
7119 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7120 from the @code{stats} package, as well as numerous other model classes from
7121 other add-on packages.")
7122 (license license:expat)))
7124 (define-public r-insight
7131 (uri (cran-uri "insight" version))
7134 "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
7135 (build-system r-build-system)
7137 `(("r-knitr" ,r-knitr)))
7138 (home-page "https://easystats.github.io/insight/")
7139 (synopsis "Easy access to model information for various model objects")
7141 "This package provides a tool to provide an easy, intuitive and
7142 consistent access to information contained in various R models, like model
7143 formulas, model terms, information about random effects, data that was used to
7144 fit the model or data from response variables. The package mainly revolves
7145 around two types of functions: Functions that find (the names of) information,
7146 starting with @code{find_}, and functions that get the underlying data,
7147 starting with @code{get_}. The package has a consistent syntax and works with
7148 many different model objects, where otherwise functions to access these
7149 information are missing.")
7150 (license license:gpl3)))
7152 (define-public r-sjlabelled
7154 (name "r-sjlabelled")
7159 (uri (cran-uri "sjlabelled" version))
7162 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
7163 (build-system r-build-system)
7165 `(("r-insight" ,r-insight)))
7167 `(("r-knitr" ,r-knitr)))
7168 (home-page "https://github.com/strengejacke/sjlabelled")
7169 (synopsis "Labelled data utility functions")
7171 "This package provides a collection of functions dealing with labelled
7172 data, like reading and writing data between R and other statistical software
7173 packages. This includes easy ways to get, set or change value and variable
7174 label attributes, to convert labelled vectors into factors or numeric (and
7175 vice versa), or to deal with multiple declared missing values.")
7176 (license license:gpl3)))
7178 (define-public r-sjmisc
7185 (uri (cran-uri "sjmisc" version))
7188 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7189 (build-system r-build-system)
7191 `(("r-dplyr" ,r-dplyr)
7192 ("r-insight" ,r-insight)
7193 ("r-magrittr" ,r-magrittr)
7194 ("r-purrr" ,r-purrr)
7195 ("r-rlang" ,r-rlang)
7196 ("r-sjlabelled" ,r-sjlabelled)
7197 ("r-tidyselect" ,r-tidyselect)))
7199 `(("r-knitr" ,r-knitr)))
7200 (home-page "https://github.com/strengejacke/sjmisc")
7201 (synopsis "Data and variable transformation functions")
7203 "This package is a collection of miscellaneous utility functions,
7204 supporting data transformation tasks like recoding, dichotomizing or grouping
7205 variables, setting and replacing missing values. The data transformation
7206 functions also support labelled data, and all integrate seamlessly into a
7207 tidyverse workflow.")
7208 (license license:gpl3)))
7210 (define-public r-nortest
7217 (uri (cran-uri "nortest" version))
7220 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7221 (build-system r-build-system)
7222 (home-page "https://cran.r-project.org/web/packages/nortest/")
7223 (synopsis "Tests for normality")
7225 "This package provides five omnibus tests for testing the composite
7226 hypothesis of normality.")
7227 (license license:gpl2+)))
7229 (define-public r-moonbook
7236 (uri (cran-uri "moonBook" version))
7239 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7240 (properties `((upstream-name . "moonBook")))
7241 (build-system r-build-system)
7243 `(("r-magrittr" ,r-magrittr)
7244 ("r-nortest" ,r-nortest)
7245 ("r-purrr" ,r-purrr)
7246 ("r-sjmisc" ,r-sjmisc)
7247 ("r-stringr" ,r-stringr)
7248 ("r-survival" ,r-survival)))
7249 (home-page "https://github.com/cardiomoon/moonBook")
7250 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7252 "This package provides several analysis-related functions for the book
7253 entitled \"R statistics and graph for medical articles\" (written in Korean),
7254 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7256 (license license:gpl2)))
7258 (define-public r-flextable
7260 (name "r-flextable")
7265 (uri (cran-uri "flextable" version))
7268 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7269 (build-system r-build-system)
7271 `(("r-base64enc" ,r-base64enc)
7272 ("r-data-table" ,r-data-table)
7273 ("r-gdtools" ,r-gdtools)
7274 ("r-htmltools" ,r-htmltools)
7275 ("r-knitr" ,r-knitr)
7276 ("r-officer" ,r-officer)
7277 ("r-rlang" ,r-rlang)
7278 ("r-rmarkdown" ,r-rmarkdown)
7280 ("r-xml2" ,r-xml2)))
7281 (home-page "https://davidgohel.github.io/flextable")
7282 (synopsis "Functions for tabular reporting")
7284 "This package provides tools to create pretty tables for HTML documents
7285 and other formats. Functions are provided to let users create tables, modify
7286 and format their content. It extends the @code{officer} package and can be
7287 used within R markdown documents when rendering to HTML and to Word
7289 (license license:gpl3)))
7291 (define-public r-writexl
7298 (uri (cran-uri "writexl" version))
7301 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7302 (build-system r-build-system)
7303 (inputs `(("zlib" ,zlib)))
7304 (home-page "https://github.com/ropensci/writexl")
7305 (synopsis "Export data frames to xlsx format")
7307 "This package provides a data frame to xlsx exporter based on
7309 (license license:bsd-2)))
7311 (define-public r-biasedurn
7313 (name "r-biasedurn")
7318 (uri (cran-uri "BiasedUrn" version))
7321 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7322 (properties `((upstream-name . "BiasedUrn")))
7323 (build-system r-build-system)
7324 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7325 (synopsis "Biased Urn model distributions")
7327 "This package provides statistical models of biased sampling in the form
7328 of univariate and multivariate noncentral hypergeometric distributions,
7329 including Wallenius' noncentral hypergeometric distribution and Fisher's
7330 noncentral hypergeometric distribution (also called extended hypergeometric
7332 (license license:gpl3)))
7334 (define-public r-goplot
7341 (uri (cran-uri "GOplot" version))
7344 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7345 (properties `((upstream-name . "GOplot")))
7346 (build-system r-build-system)
7348 `(("r-ggdendro" ,r-ggdendro)
7349 ("r-ggplot2" ,r-ggplot2)
7350 ("r-gridextra" ,r-gridextra)
7351 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7352 (home-page "https://github.com/wencke/wencke.github.io")
7353 (synopsis "Visualization of functional analysis data")
7355 "This package provides an implementation of multilayered visualizations
7356 for enhanced graphical representation of functional analysis data. It
7357 combines and integrates omics data derived from expression and functional
7358 annotation enrichment analyses. Its plotting functions have been developed
7359 with an hierarchical structure in mind: starting from a general overview to
7360 identify the most enriched categories (modified bar plot, bubble plot) to a
7361 more detailed one displaying different types of relevant information for the
7362 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7363 Venn diagram, heatmap).")
7364 (license license:gpl2)))
7366 (define-public r-getopt
7373 (uri (cran-uri "getopt" version))
7376 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7377 (build-system r-build-system)
7378 (home-page "https://github.com/trevorld/getopt")
7379 (synopsis "Command-line option processor for R")
7381 "This package is designed to be used with Rscript to write shebang
7382 scripts that accept short and long options. Many users will prefer to
7383 use the packages @code{optparse} or @code{argparse} which add extra
7384 features like automatically generated help options and usage texts,
7385 support for default values, positional argument support, etc.")
7386 (license license:gpl2+)))
7388 (define-public r-findpython
7390 (name "r-findpython")
7395 (uri (cran-uri "findpython" version))
7398 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7399 (build-system r-build-system)
7400 (home-page "https://github.com/trevorld/findpython")
7401 (synopsis "Functions to find an acceptable Python binary")
7403 "This package was designed to find an acceptable Python binary that
7404 matches version and feature constraints.")
7405 (license license:expat)))
7407 ;; This in not the same as "r-argparser"
7408 (define-public r-argparse
7415 (uri (cran-uri "argparse" version))
7418 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7419 (build-system r-build-system)
7420 (inputs `(("python" ,python)))
7422 `(("r-findpython" ,r-findpython)
7423 ("r-jsonlite" ,r-jsonlite)
7425 (home-page "https://github.com/trevorld/argparse")
7426 (synopsis "Command line optional and positional argument parser")
7428 "This package provides a command line parser to be used with Rscript to
7429 write shebang scripts that gracefully accept positional and optional arguments
7430 and automatically generate usage notices.")
7431 (license license:gpl2+)))
7433 (define-public r-hash
7440 (uri (cran-uri "hash" version))
7443 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7444 (build-system r-build-system)
7445 (home-page "https://cran.r-project.org/web/packages/hash/")
7446 (synopsis "Implementation of hash/associated arrays/dictionaries")
7448 "This package implements a data structure similar to hashes in Perl and
7449 dictionaries in Python but with a purposefully R flavor. For objects of
7450 appreciable size, access using hashes outperforms native named lists and
7452 (license license:gpl2+)))
7454 (define-public r-orddom
7461 (uri (cran-uri "orddom" version))
7464 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7465 (build-system r-build-system)
7466 (propagated-inputs `(("r-psych" ,r-psych)))
7467 (home-page "https://cran.r-project.org/web/packages/orddom/")
7468 (synopsis "Ordinal dominance statistics")
7470 "This package provides tools to compute ordinal, statistics and effect
7471 sizes as an alternative to mean comparison: Cliff's delta or success rate
7472 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7473 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7474 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7475 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7476 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7477 Group (Non-)Overlap considerations.")
7478 (license license:gpl2)))
7480 (define-public r-deriv
7487 (uri (cran-uri "Deriv" version))
7490 "16rq65x1xhxvqwn4p427divay3b9fgam2lxccxb8529adnrxmw6p"))))
7491 (properties `((upstream-name . "Deriv")))
7492 (build-system r-build-system)
7493 (home-page "https://cran.r-project.org/web/packages/Deriv")
7494 (synopsis "Symbolic differentiation")
7496 "This package provides an R-based solution for symbolic differentiation.
7497 It admits user-defined functions as well as function substitution in arguments
7498 of functions to be differentiated. Some symbolic simplification is part of
7500 (license license:gpl3+)))
7502 (define-public r-doby
7509 (uri (cran-uri "doBy" version))
7512 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7513 (properties `((upstream-name . "doBy")))
7514 (build-system r-build-system)
7516 `(("r-broom" ,r-broom)
7517 ("r-deriv" ,r-deriv)
7518 ("r-dplyr" ,r-dplyr)
7519 ("r-ggplot2" ,r-ggplot2)
7520 ("r-magrittr" ,r-magrittr)
7522 ("r-matrix" ,r-matrix)
7523 ("r-pbkrtest" ,r-pbkrtest)
7524 ("r-tibble" ,r-tibble)))
7526 `(("r-knitr" ,r-knitr)))
7527 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7528 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7530 "This package contains:
7533 @item facilities for working with grouped data: @code{do}
7534 something to data stratified @code{by} some variables.
7535 @item implementations of least-squares means, general linear contrasts, and
7536 @item miscellaneous other utilities.
7538 (license license:gpl2+)))
7540 (define-public r-refgenome
7542 (name "r-refgenome")
7547 (uri (cran-uri "refGenome" version))
7550 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7551 (properties `((upstream-name . "refGenome")))
7552 (build-system r-build-system)
7556 ("r-rsqlite" ,r-rsqlite)))
7557 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7559 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7561 "This package contains functionality for importing and managing of
7562 downloaded genome annotation data from the Ensembl genome browser (European
7563 Bioinformatics Institute) and from the UCSC genome browser (University of
7564 California, Santa Cruz) and annotation routines for genomic positions and
7565 splice site positions.")
7566 (license license:gpl2)))
7568 (define-public r-basix
7575 (uri (cran-uri "BASIX" version))
7578 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7579 (properties `((upstream-name . "BASIX")))
7580 (build-system r-build-system)
7581 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7582 (synopsis "Efficient C/C++ toolset for R")
7584 "BASIX provides some efficient C/C++ implementations of native R
7585 procedures to speed up calculations in R.")
7586 (license license:gpl2)))
7588 (define-public r-blockfest
7590 (name "r-blockfest")
7595 (uri (cran-uri "BlockFeST" version))
7598 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7599 (properties `((upstream-name . "BlockFeST")))
7600 (build-system r-build-system)
7601 (propagated-inputs `(("r-basix" ,r-basix)))
7602 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7603 (synopsis "Bayesian calculation of region-specific fixation index")
7605 "This package provides an R implementation of an extension of the
7606 BayeScan software for codominant markers, adding the option to group
7607 individual SNPs into pre-defined blocks. A typical application of this new
7608 approach is the identification of genomic regions, genes, or gene sets
7609 containing one or more SNPs that evolved under directional selection.")
7610 (license license:gpl2)))
7612 (define-public r-proc
7619 (uri (cran-uri "pROC" version))
7622 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7623 (properties `((upstream-name . "pROC")))
7624 (build-system r-build-system)
7626 `(("r-plyr" ,r-plyr)
7627 ("r-rcpp" ,r-rcpp)))
7628 (home-page "https://web.expasy.org/pROC/")
7629 (synopsis "Display and analyze ROC curves")
7631 "This package provides tools for visualizing, smoothing and comparing
7632 receiver operating characteristic (ROC curves). The area under the
7633 curve (AUC) can be compared with statistical tests based on U-statistics or
7634 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7635 (license license:gpl3+)))
7637 (define-public r-rootsolve
7639 (name "r-rootsolve")
7644 (uri (cran-uri "rootSolve" version))
7647 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7648 (properties `((upstream-name . "rootSolve")))
7649 (build-system r-build-system)
7650 (native-inputs `(("gfortran" ,gfortran)))
7651 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7652 (synopsis "Tools for the analysis of ordinary differential equations")
7654 "This package provides routines to find the root of nonlinear functions,
7655 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7656 differential equations} (ODE). It includes routines that:
7659 @item generate gradient and jacobian matrices (full and banded),
7660 @item find roots of non-linear equations by the Newton-Raphson method,
7661 @item estimate steady-state conditions of a system of (differential) equations
7662 in full, banded or sparse form, using the Newton-Raphson method, or by
7663 dynamically running,
7664 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7665 and 3-D partial differential equations, that have been converted to ordinary
7666 differential equations by numerical differencing (using the method-of-lines
7669 (license license:gpl2+)))
7671 (define-public r-abcanalysis
7673 (name "r-abcanalysis")
7678 (uri (cran-uri "ABCanalysis" version))
7680 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7681 (properties `((upstream-name . "ABCanalysis")))
7682 (build-system r-build-system)
7683 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7684 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7685 (synopsis "Computed ABC Analysis")
7687 "Multivariate data sets often differ in several factors or derived statistical
7688 parameters, which have to be selected for a valid interpretation. Basing this
7689 selection on traditional statistical limits leads occasionally to the perception
7690 of losing information from a data set. This package provides tools to calculate
7691 these limits on the basis of the mathematical properties of the distribution of
7692 the analyzed items.")
7693 (license license:gpl3)))
7695 (define-public r-slam
7702 (uri (cran-uri "slam" version))
7704 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7705 (build-system r-build-system)
7706 (home-page "https://cran.r-project.org/web/packages/slam/")
7707 (synopsis "Sparse lightweight arrays and matrices")
7709 "This package contains data structures and algorithms for sparse arrays and matrices,
7710 based on index arrays and simple triplet representations, respectively.")
7711 (license license:gpl2)))
7713 (define-public r-manipulatewidget
7715 (name "r-manipulatewidget")
7720 (uri (cran-uri "manipulateWidget" version))
7722 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7724 `((upstream-name . "manipulateWidget")))
7725 (build-system r-build-system)
7727 `(("r-base64enc" ,r-base64enc)
7728 ("r-codetools" ,r-codetools)
7729 ("r-htmltools" ,r-htmltools)
7730 ("r-htmlwidgets" ,r-htmlwidgets)
7731 ("r-knitr" ,r-knitr)
7732 ("r-miniui" ,r-miniui)
7733 ("r-shiny" ,r-shiny)
7734 ("r-webshot" ,r-webshot)))
7735 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7736 (synopsis "Add even more interactivity to interactive charts")
7738 "This package lets you create in just a few lines of R code a nice user interface to
7739 modify the data or the graphical parameters of one or multiple interactive
7740 charts. It is useful to quickly explore visually some data or for package
7741 developers to generate user interfaces easy to maintain.")
7742 (license license:gpl2+)))
7751 (uri (cran-uri "A3" version))
7753 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7754 (properties `((upstream-name . "A3")))
7755 (build-system r-build-system)
7757 `(("r-pbapply" ,r-pbapply)
7758 ("r-xtable" ,r-xtable)))
7759 (home-page "https://cran.r-project.org/web/packages/A3/")
7760 (synopsis "Error metrics for predictive models")
7762 "This package supplies tools for tabulating and analyzing the results of predictive
7763 models. The methods employed are applicable to virtually any predictive model
7764 and make comparisons between different methodologies straightforward.")
7765 (license license:gpl2+)))
7767 (define-public r-infotheo
7774 (uri (cran-uri "infotheo" version))
7777 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7778 (build-system r-build-system)
7779 (home-page "http://homepage.meyerp.com/software")
7780 (synopsis "Information-theoretic measures")
7782 "This package implements various measures of information theory based on
7783 several entropy estimators.")
7784 (license license:gpl3+)))
7786 (define-public r-abcoptim
7793 (uri (cran-uri "ABCoptim" version))
7795 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7796 (properties `((upstream-name . "ABCoptim")))
7797 (build-system r-build-system)
7798 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7799 (home-page "https://github.com/gvegayon/ABCoptim/")
7800 (synopsis "Optimization of Artificial Bee Colony algorithm")
7802 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7803 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7804 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7805 algorithms, and uses only common control parameters such as colony size and
7806 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7807 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7808 This version is a work-in-progress and is written in R code.")
7809 (license license:expat)))
7811 (define-public r-abcp2
7818 (uri (cran-uri "ABCp2" version))
7820 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7821 (properties `((upstream-name . "ABCp2")))
7822 (build-system r-build-system)
7823 (propagated-inputs `(("r-mass" ,r-mass)))
7824 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7825 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7827 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7828 Poisson, and Gamma distribution and estimates the proportional paternity of the
7829 second male (P2) based on the best fit distribution.")
7830 (license license:gpl2)))
7832 (define-public r-abcrf
7839 (uri (cran-uri "abcrf" version))
7841 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7842 (build-system r-build-system)
7844 `(("r-doparallel" ,r-doparallel)
7845 ("r-foreach" ,r-foreach)
7847 ("r-matrixstats" ,r-matrixstats)
7848 ("r-ranger" ,r-ranger)
7850 ("r-rcpparmadillo" ,r-rcpparmadillo)
7851 ("r-readr" ,r-readr)
7852 ("r-stringr" ,r-stringr)))
7853 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7854 (synopsis "Approximate bayesian computation via random forests")
7856 "This package performs approximate bayesian computation (ABC) model choice and
7857 parameter inference via random forests. This machine learning tool named random
7858 forests (RF) can conduct selection among the highly complex models covered by
7860 (license license:gpl2+)))
7862 (define-public r-abctools
7869 (uri (cran-uri "abctools" version))
7871 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7872 (build-system r-build-system)
7875 ("r-abind" ,r-abind)
7876 ("r-hmisc" ,r-hmisc)
7877 ("r-plyr" ,r-plyr)))
7878 (home-page "https://github.com/dennisprangle/abctools/")
7879 (synopsis "Tools for ABC analyses")
7881 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7882 including summary statistic selection and assessing coverage. This includes
7883 recent dimension reduction algorithms to tune the choice of summary statistics,
7884 and coverage methods to tune the choice of threshold.")
7885 (license license:gpl2+)))
7887 (define-public r-ggstance
7894 (uri (cran-uri "ggstance" version))
7896 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7897 (build-system r-build-system)
7899 `(("r-ggplot2" ,r-ggplot2)
7901 ("r-rlang" ,r-rlang)
7902 ("r-withr" ,r-withr)))
7903 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7904 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7906 "This package is a @code{r-ggplot2} extension that provides flipped components:
7908 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7909 @item vertical versions of @code{r-ggplot2} positions.
7911 (license license:gpl3)))
7913 (define-public r-mosaiccore
7915 (name "r-mosaiccore")
7920 (uri (cran-uri "mosaicCore" version))
7922 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7923 (properties `((upstream-name . "mosaicCore")))
7924 (build-system r-build-system)
7926 `(("r-dplyr" ,r-dplyr)
7927 ("r-lazyeval" ,r-lazyeval)
7929 ("r-rlang" ,r-rlang)
7930 ("r-tidyr" ,r-tidyr)))
7931 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7932 (synopsis "Common utilities for mosaic family packages")
7934 "Common utilities used in other Mosaic family packages are collected here.")
7935 (license license:gpl2+)))
7937 (define-public r-ggformula
7939 (name "r-ggformula")
7944 (uri (cran-uri "ggformula" version))
7946 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7947 (build-system r-build-system)
7949 `(("r-ggforce" ,r-ggforce)
7950 ("r-ggplot2" ,r-ggplot2)
7951 ("r-ggstance" ,r-ggstance)
7952 ("r-magrittr" ,r-magrittr)
7953 ("r-mosaiccore" ,r-mosaiccore)
7954 ("r-rlang" ,r-rlang)
7955 ("r-stringr" ,r-stringr)
7956 ("r-tibble" ,r-tibble)))
7957 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7958 (synopsis "Formula interface for the @code{r-ggplot2}")
7960 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7961 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7962 and extends the excellent simplicity of the lattice-graphics formula interface,
7963 while providing the intuitive capabilities of @code{r-ggplot2}.")
7964 (license license:expat)))
7966 (define-public r-mosaicdata
7968 (name "r-mosaicdata")
7973 (uri (cran-uri "mosaicData" version))
7975 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7976 (properties `((upstream-name . "mosaicData")))
7977 (build-system r-build-system)
7978 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7979 (synopsis "Data sets for project Mosaic")
7981 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7982 used to teach mathematics, statistics, computation and modeling.")
7983 (license license:gpl2+)))
7985 (define-public r-raster
7992 (uri (cran-uri "raster" version))
7995 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7996 (build-system r-build-system)
7998 `(("r-rcpp" ,r-rcpp)
8000 (home-page "https://www.rspatial.org/")
8001 (synopsis "Geographic data analysis and modeling")
8003 "The package implements basic and high-level functions for reading,
8004 writing, manipulating, analyzing and modeling of gridded spatial data.
8005 Processing of very large files is supported.")
8006 (license license:gpl3+)))
8008 (define-public r-mosaic
8015 (uri (cran-uri "mosaic" version))
8017 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8018 (build-system r-build-system)
8020 `(("r-broom" ,r-broom)
8021 ("r-dplyr" ,r-dplyr)
8022 ("r-ggdendro" ,r-ggdendro)
8023 ("r-ggformula" ,r-ggformula)
8024 ("r-ggplot2" ,r-ggplot2)
8025 ("r-ggrepel" ,r-ggrepel)
8027 ("r-gridextra" ,r-gridextra)
8028 ("r-lattice" ,r-lattice)
8029 ("r-latticeextra" ,r-latticeextra)
8030 ("r-lazyeval" ,r-lazyeval)
8032 ("r-matrix" ,r-matrix)
8033 ("r-mosaiccore" ,r-mosaiccore)
8034 ("r-mosaicdata" ,r-mosaicdata)
8035 ("r-readr" ,r-readr)
8036 ("r-tidyr" ,r-tidyr)))
8038 `(("r-knitr" ,r-knitr)))
8039 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8040 (synopsis "Mathematics, statistics, and computation teaching utilities")
8042 "This package contain data sets and utilities from
8043 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8044 statistics, computation and modeling. Project MOSAIC is a community of
8045 educators working to tie together aspects of quantitative work that students
8046 in science, technology, engineering and mathematics will need in their
8047 professional lives, but which are usually taught in isolation, if at all.")
8048 (license license:gpl2+)))
8050 (define-public r-abd
8057 (uri (cran-uri "abd" version))
8059 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8060 (build-system r-build-system)
8062 `(("r-lattice" ,r-lattice)
8063 ("r-mosaic" ,r-mosaic)
8064 ("r-nlme" ,r-nlme)))
8065 (home-page "https://cran.r-project.org/web/packages/abd/")
8066 (synopsis "Analysis of biological data")
8068 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8069 biological data by Michael Whitlock and Dolph Schluter.")
8070 (license license:gpl2)))
8072 (define-public r-svgui
8079 (uri (cran-uri "svGUI" version))
8081 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8082 (properties `((upstream-name . "svGUI")))
8083 (build-system r-build-system)
8084 (home-page "https://github.com/SciViews/svGUI/")
8085 (synopsis "Functions for managing GUI clients in R")
8087 "The SciViews @code{svGUI} package eases the management of Graphical User
8088 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8089 centralizes info about GUI elements currently used, and it dispatches GUI
8090 calls to the particular toolkits in use in function of the context.")
8091 (license license:gpl2)))
8093 (define-public r-svdialogs
8095 (name "r-svdialogs")
8100 (uri (cran-uri "svDialogs" version))
8102 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8103 (properties `((upstream-name . "svDialogs")))
8104 (build-system r-build-system)
8107 ("zenity" ,zenity)))
8109 `(("r-rstudioapi" ,r-rstudioapi)
8110 ("r-svgui" ,r-svgui)))
8111 (home-page "https://github.com/SciViews/svDialogs/")
8112 (synopsis "Portable dialog boxes")
8114 "This package helps to construct standard dialog boxes for your GUI, including
8115 message boxes, input boxes, list, file or directory selection, and others. In
8116 case R cannot display GUI dialog boxes, a simpler command line version of these
8117 interactive elements is also provided as a fallback solution.")
8118 (license license:gpl2)))
8120 (define-public r-abe
8127 (uri (cran-uri "abe" version))
8130 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8131 (build-system r-build-system)
8132 (home-page "https://cran.r-project.org/web/packages/abe/")
8133 (synopsis "Augmented backward elimination")
8135 "This package performs augmented backward elimination and checks the
8136 stability of the obtained model. Augmented backward elimination combines
8137 significance or information based criteria with the change in estimate to
8138 either select the optimal model for prediction purposes or to serve as a tool
8139 to obtain a practically sound, highly interpretable model.")
8140 (license license:gpl2+)))
8142 (define-public r-abf2
8149 (uri (cran-uri "abf2" version))
8151 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8152 (build-system r-build-system)
8153 (home-page "https://cran.r-project.org/web/packages/abf2/")
8154 (synopsis "Load gap-free axon @code{r-abf2} files")
8156 "This package loads electrophysiology data from ABF2 files, as created by
8157 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8158 mode are currently supported.")
8159 (license license:artistic2.0)))
8161 (define-public r-abhgenotyper
8163 (name "r-abhgenotyper")
8168 (uri (cran-uri "ABHgenotypeR" version))
8170 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8171 (properties `((upstream-name . "ABHgenotypeR")))
8172 (build-system r-build-system)
8174 `(("r-ggplot2" ,r-ggplot2)
8175 ("r-reshape2" ,r-reshape2)))
8176 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8177 (synopsis "Visualize and manipulate ABH genotypes")
8179 "The @code{r-abhgenotyper} package provides simple imputation,
8180 error-correction and plotting capacities for genotype data. The package is
8181 supposed to serve as an intermediate but independent analysis tool between the
8182 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8183 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8184 genotypes as \"graphical genotypes\".")
8185 (license license:gpl3)))
8187 (define-public r-furrr
8194 (uri (cran-uri "furrr" version))
8197 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8198 (build-system r-build-system)
8200 `(("r-future" ,r-future)
8201 ("r-globals" ,r-globals)
8202 ("r-purrr" ,r-purrr)
8203 ("r-rlang" ,r-rlang)))
8204 (home-page "https://github.com/DavisVaughan/furrr")
8205 (synopsis "Apply mapping functions in parallel using futures")
8207 "This package provides implementations of the family of @code{map()}
8208 functions from the @code{purrr} package that can be resolved using any
8209 @code{future}-supported backend, e.g. parallel on the local machine or
8210 distributed on a compute cluster.")
8211 (license license:lgpl2.1+)))
8213 (define-public r-abjutils
8220 (uri (cran-uri "abjutils" version))
8222 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8223 (build-system r-build-system)
8225 `(("r-dplyr" ,r-dplyr)
8226 ("r-magrittr" ,r-magrittr)
8227 ("r-purrr" ,r-purrr)
8228 ("r-rlang" ,r-rlang)
8229 ("r-rstudioapi" ,r-rstudioapi)
8230 ("r-stringi" ,r-stringi)
8231 ("r-stringr" ,r-stringr)
8232 ("r-tidyr" ,r-tidyr)))
8233 (home-page "https://github.com/abjur/abjutils/")
8234 (synopsis "Collection of tools for jurimetrical analysis")
8236 "This package implements general purpose tools, such as functions for
8237 sampling and basic manipulation of Brazilian lawsuits identification number.
8238 It also implements functions for text cleaning, such as accentuation
8240 (license license:expat)))
8242 (define-public r-abnormality
8244 (name "r-abnormality")
8249 (uri (cran-uri "abnormality" version))
8251 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8252 (build-system r-build-system)
8254 `(("r-mass" ,r-mass)
8255 ("r-matrix" ,r-matrix)))
8256 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8257 (synopsis "Measure a subject's abnormality with respect to a reference population")
8259 "This package contains functions to implement the methodology and
8260 considerations laid out by Marks et al. in the article \"Measuring abnormality
8261 in high dimensional spaces: applications in biomechanical gait analysis\".
8262 Using high-dimensional datasets to measure a subject's overall level of
8263 abnormality as compared to a reference population is often needed in outcomes
8265 (license license:expat)))
8267 (define-public r-abodoutlier
8269 (name "r-abodoutlier")
8274 (uri (cran-uri "abodOutlier" version))
8276 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8277 (properties `((upstream-name . "abodOutlier")))
8278 (build-system r-build-system)
8280 `(("r-cluster" ,r-cluster)))
8281 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8282 (synopsis "Angle-based outlier detection")
8284 "This package performs angle-based outlier detection on a given data
8285 frame. It offers three methods to process data:
8287 @item full but slow implementation using all the data that has cubic
8289 @item a fully randomized method;
8290 @item a method using k-nearest neighbours.
8292 These algorithms are well suited for high dimensional data outlier
8294 (license license:expat)))
8296 (define-public r-abps
8303 (uri (cran-uri "ABPS" version))
8305 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8306 (properties `((upstream-name . "ABPS")))
8307 (build-system r-build-system)
8308 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8309 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8310 (synopsis "Abnormal blood profile score to detect blood doping")
8312 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8313 The ABPS is a part of the Athlete biological passport program of the World
8314 anti-doping agency, which combines several blood parameters into a single
8315 score in order to detect blood doping. The package also contains functions to
8316 calculate other scores used in anti-doping programs, such as the ratio of
8317 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8318 (license license:gpl2+)))
8320 (define-public r-parmigene
8322 (name "r-parmigene")
8327 (uri (cran-uri "parmigene" version))
8330 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8331 (build-system r-build-system)
8332 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8333 (synopsis "Mutual information estimation for gene network reconstruction")
8335 "This package provides a parallel estimation of the mutual information
8336 based on entropy estimates from k-nearest neighbors distances and algorithms
8337 for the reconstruction of gene regulatory networks.")
8338 (license license:agpl3+)))
8340 (define-public r-pscl
8347 (uri (cran-uri "pscl" version))
8349 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8350 (build-system r-build-system)
8352 `(("r-mass" ,r-mass)))
8353 (home-page "https://github.com/atahk/pscl/")
8354 (synopsis "Political science computational laboratory")
8356 "The @code{pscl} is an R package providing classes and methods for:
8358 @item Bayesian analysis of roll call data (item-response models);
8359 @item elementary Bayesian statistics;
8360 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8362 @item utility functions.
8364 (license license:gpl2)))
8366 (define-public r-accelmissing
8368 (name "r-accelmissing")
8373 (uri (cran-uri "accelmissing" version))
8375 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8376 (build-system r-build-system)
8378 `(("r-mice" ,r-mice)
8379 ("r-pscl" ,r-pscl)))
8380 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8381 (synopsis "Missing value imputation for accelerometer data")
8383 "This package provides a statistical method to impute the missing values in
8384 accelerometer data. The methodology includes both parametric and
8385 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8386 model. It also provides multiple functions to preprocess the accelerometer data
8387 previous to the missing data imputation. These include detecting the wearing
8388 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8389 (license license:gpl2+)))
8391 (define-public r-mhsmm
8398 (uri (cran-uri "mhsmm" version))
8400 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8401 (build-system r-build-system)
8402 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8403 (home-page "https://github.com/jaredo/mhsmm/")
8404 (synopsis "Inference for hidden Markov and semi-Markov models")
8406 "The @code{r-mhsmm} package implements estimation and prediction methods for
8407 hidden Markov and semi-Markov models for multiple observation sequences. Such
8408 techniques are of interest when observed data is thought to be dependent on some
8409 unobserved (or hidden) state. Also, this package is suitable for equidistant
8410 time series data, with multivariate and/or missing data. Allows user defined
8411 emission distributions.")
8412 (license license:gpl2+)))
8414 (define-public r-nleqslv
8421 (uri (cran-uri "nleqslv" version))
8423 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8424 (build-system r-build-system)
8425 (native-inputs `(("gfortran" ,gfortran)))
8426 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8427 (synopsis "Solve systems of nonlinear equations")
8429 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8430 Broyden or a Newton method with a choice of global strategies such as line
8431 search and trust region. There are options for using a numerical or user
8432 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8433 singular or ill-conditioned Jacobian.")
8434 (license license:gpl2+)))
8436 (define-public r-physicalactivity
8438 (name "r-physicalactivity")
8443 (uri (cran-uri "PhysicalActivity" version))
8445 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8447 `((upstream-name . "PhysicalActivity")))
8448 (build-system r-build-system)
8449 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8450 (synopsis "Procesing accelerometer data for physical activity measurement")
8452 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8453 for classification of monitor wear and nonwear time intervals in accelerometer
8454 data collected to assess physical activity. The package also contains functions
8455 for making plots of accelerometer data and obtaining the summary of various
8456 information including daily monitor wear time and the mean monitor wear time
8457 during valid days. The revised package version 0.2-1 improved the functions
8458 regarding speed, robustness and add better support for time zones and daylight
8459 saving. In addition, several functions were added:
8461 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8462 @item the @code{markPAI} can categorize physical activity intensity level based
8463 on user-defined cut-points of accelerometer counts.
8465 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8466 @code{queryActigraph} functions.")
8467 (license license:gpl3+)))
8469 (define-public r-acc
8476 (uri (cran-uri "acc" version))
8478 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8479 (build-system r-build-system)
8481 `(("r-circlize" ,r-circlize)
8483 ("r-ggplot2" ,r-ggplot2)
8484 ("r-iterators" ,r-iterators)
8485 ("r-mhsmm" ,r-mhsmm)
8486 ("r-nleqslv" ,r-nleqslv)
8487 ("r-physicalactivity" ,r-physicalactivity)
8489 ("r-r-utils" ,r-r-utils)
8491 ("r-rcpparmadillo" ,r-rcpparmadillo)
8492 ("r-rsqlite" ,r-rsqlite)
8494 (home-page "https://cran.r-project.org/web/packages/acc/")
8495 (synopsis "Exploring accelerometer data")
8497 "This package processes accelerometer data from uni-axial and tri-axial devices
8498 and generates data summaries. Also, includes functions to plot, analyze, and
8499 simulate accelerometer data.")
8500 (license license:gpl2+)))
8502 (define-public r-rbenchmark
8504 (name "r-rbenchmark")
8509 (uri (cran-uri "rbenchmark" version))
8511 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8512 (build-system r-build-system)
8513 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8514 (synopsis "Benchmarking routine for R")
8516 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8517 and is intended to facilitate benchmarking of arbitrary R code. The library
8518 consists of just one function, benchmark, which is a simple wrapper around
8519 system.time. Given a specification of the benchmarking process (counts of
8520 replications, evaluation environment) and an arbitrary number of expressions,
8521 benchmark evaluates each of the expressions in the specified environment,
8522 replicating the evaluation as many times as specified, and returning the results
8523 conveniently wrapped into a data frame.")
8524 (license license:gpl2+)))
8526 (define-public r-mitools
8533 (uri (cran-uri "mitools" version))
8536 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8537 (build-system r-build-system)
8538 (propagated-inputs `(("r-dbi" ,r-dbi)))
8539 (home-page "https://cran.r-project.org/web/packages/mitools/")
8540 (synopsis "Tools for multiple imputation of missing data")
8542 "This package provides tools to perform analyses and combine results from
8543 multiple-imputation datasets.")
8544 (license license:gpl2)))
8546 (define-public r-magick
8553 (uri (cran-uri "magick" version))
8556 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8557 (build-system r-build-system)
8559 `(("imagemagick" ,imagemagick)
8562 `(("r-curl" ,r-curl)
8563 ("r-magrittr" ,r-magrittr)
8564 ("r-rcpp" ,r-rcpp)))
8566 `(("pkg-config" ,pkg-config)
8567 ("r-knitr" ,r-knitr)))
8568 (home-page "https://github.com/ropensci/magick")
8569 (synopsis "Advanced graphics and image-processing in R")
8571 "This package provides bindings to ImageMagick, a comprehensive image
8572 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8573 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8574 operations are vectorized via the Magick++ STL meaning they operate either on
8575 a single frame or a series of frames for working with layers, collages, or
8576 animation. In RStudio, images are automatically previewed when printed to the
8577 console, resulting in an interactive editing environment.")
8578 (license license:expat)))
8580 (define-public r-survey
8587 (uri (cran-uri "survey" version))
8590 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8591 (build-system r-build-system)
8593 `(("r-lattice" ,r-lattice)
8594 ("r-matrix" ,r-matrix)
8595 ("r-minqa" ,r-minqa)
8596 ("r-mitools" ,r-mitools)
8597 ("r-numderiv" ,r-numderiv)
8598 ("r-survival" ,r-survival)))
8599 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8600 (synopsis "Analysis of complex survey samples")
8602 "This package provides tools for the analysis of complex survey samples.
8603 The provided features include: summary statistics, two-sample tests, rank
8604 tests, generalised linear models, cumulative link models, Cox models,
8605 loglinear models, and general maximum pseudolikelihood estimation for
8606 multistage stratified, cluster-sampled, unequally weighted survey samples;
8607 variances by Taylor series linearisation or replicate weights;
8608 post-stratification, calibration, and raking; two-phase subsampling designs;
8609 graphics; PPS sampling without replacement; principal components, and factor
8611 ;; Either version of the GPL.
8612 (license (list license:gpl2 license:gpl3))))
8614 (define-public r-gee
8621 (uri (cran-uri "gee" version))
8624 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8625 (properties `((upstream-name . "gee")))
8626 (build-system r-build-system)
8628 `(("gfortran" ,gfortran)))
8629 (home-page "https://cran.r-project.org/web/packages/gee/")
8630 (synopsis "Generalized estimation equation solver")
8632 "This package provides a solver for generalized estimation equations.")
8633 (license license:gpl2)))
8635 (define-public r-tab
8642 (uri (cran-uri "tab" version))
8645 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8646 (properties `((upstream-name . "tab")))
8647 (build-system r-build-system)
8649 `(("r-dplyr" ,r-dplyr)
8651 ("r-knitr" ,r-knitr)
8653 ("r-survey" ,r-survey)
8654 ("r-survival" ,r-survival)
8655 ("r-xtable" ,r-xtable)))
8656 (home-page "https://cran.r-project.org/web/packages/tab/")
8657 (synopsis "Create summary tables for statistical reports")
8659 "This package contains functions for creating various types of summary
8660 tables, e.g. comparing characteristics across levels of a categorical variable
8661 and summarizing fitted generalized linear models, generalized estimating
8662 equations, and Cox proportional hazards models. Functions are available to
8663 handle data from simple random samples as well as complex surveys.")
8664 (license license:gpl3+)))
8666 (define-public r-dvmisc
8673 (uri (cran-uri "dvmisc" version))
8675 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8676 (build-system r-build-system)
8678 `(("r-cubature" ,r-cubature)
8679 ("r-data-table" ,r-data-table)
8680 ("r-dplyr" ,r-dplyr)
8681 ("r-ggplot2" ,r-ggplot2)
8683 ("r-mvtnorm" ,r-mvtnorm)
8684 ("r-pracma" ,r-pracma)
8685 ("r-rbenchmark" ,r-rbenchmark)
8687 ("r-survey" ,r-survey)
8689 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8690 (synopsis "Faster computation of common statistics and miscellaneous functions")
8692 "This package implements faster versions of base R functions (e.g. mean, standard
8693 deviation, covariance, weighted mean), mostly written in C++, along with
8694 miscellaneous functions for various purposes (e.g. create the histogram with
8695 fitted probability density function or probability mass function curve, create
8696 the body mass index groups, assess the linearity assumption in logistic
8698 (license license:gpl2)))
8700 (define-public r-accelerometry
8702 (name "r-accelerometry")
8707 (uri (cran-uri "accelerometry" version))
8709 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8710 (build-system r-build-system)
8712 `(("r-dvmisc" ,r-dvmisc)
8713 ("r-rcpp" ,r-rcpp)))
8714 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8715 (synopsis "Functions for processing accelerometer data")
8717 "This package provides a collection of functions that perform operations on
8718 time-series accelerometer data, such as identify the non-wear time, flag minutes
8719 that are part of an activity bout, and find the maximum 10-minute average count
8720 value. The functions are generally very flexible, allowing for a variety of
8721 algorithms to be implemented.")
8722 (license license:gpl3)))
8724 (define-public r-absim
8731 (uri (cran-uri "AbSim" version))
8733 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8734 (properties `((upstream-name . "AbSim")))
8735 (build-system r-build-system)
8738 ("r-powerlaw" ,r-powerlaw)))
8739 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8740 (synopsis "Time resolved simulations of antibody repertoires")
8742 "This package provides simulation methods for the evolution of antibody repertoires.
8743 The heavy and light chain variable region of both human and C57BL/6 mice can
8744 be simulated in a time-dependent fashion. Both single lineages using one set of
8745 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8746 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8747 Upon completion, the main loop of the algorithm begins, with each iteration
8748 representing one simulated time step. Various mutation events are possible at
8749 each time step, contributing to a diverse final repertoire.")
8750 (license license:gpl2)))
8752 (define-public r-quic
8759 (uri (cran-uri "QUIC" version))
8761 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8762 (properties `((upstream-name . "QUIC")))
8763 (build-system r-build-system)
8764 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8765 (synopsis "Regularized sparse inverse covariance matrix estimation")
8767 "This package implements the regularized Gaussian maximum likelihood
8768 estimation of the inverse of a covariance matrix. It uses Newton's method and
8769 coordinate descent to solve the regularized inverse covariance matrix
8770 estimation problem.")
8771 ;; The project home page states that the release is under GPLv3 or later.
8772 ;; The CRAN page only says GPL-3.
8773 (license license:gpl3+)))
8775 (define-public r-abundant
8782 (uri (cran-uri "abundant" version))
8784 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8785 (build-system r-build-system)
8787 `(("r-quic" ,r-quic)))
8788 (home-page "https://cran.r-project.org/web/packages/abundant/")
8789 (synopsis "Abundant regression and high-dimensional principal fitted components")
8791 "This package provides tools to fit and predict with the high-dimensional
8792 principal fitted components model. This model is described by Cook, Forzani,
8793 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8794 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8795 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8796 (license license:gpl2+)))
8798 (define-public r-ac3net
8805 (uri (cran-uri "Ac3net" version))
8807 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8808 (properties `((upstream-name . "Ac3net")))
8809 (build-system r-build-system)
8811 `(("r-data-table" ,r-data-table)))
8812 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8813 (synopsis "Inferring directional conservative causal core gene networks")
8814 (description "This package infers directional Conservative causal core
8815 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8816 directional network.")
8817 (license license:gpl3+)))
8819 (define-public r-aca
8826 (uri (cran-uri "ACA" version))
8828 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8829 (properties `((upstream-name . "ACA")))
8830 (build-system r-build-system)
8831 (home-page "https://cran.r-project.org/web/packages/ACA/")
8832 (synopsis "Abrupt change-point or aberration detection in point series")
8834 "This package offers an interactive function for the detection of breakpoints in
8836 ;; Any version of the GPL
8837 (license (list license:gpl2+ license:gpl3+))))
8839 (define-public r-acceptancesampling
8841 (name "r-acceptancesampling")
8846 (uri (cran-uri "AcceptanceSampling" version))
8848 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8850 `((upstream-name . "AcceptanceSampling")))
8851 (build-system r-build-system)
8852 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8853 (synopsis "Creation and evaluation of acceptance sampling plans")
8855 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8856 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8857 in quality control and improvement. International standards of acceptance
8858 sampling provide sampling plans for specific circumstances. The aim of this
8859 package is to provide an easy-to-use interface to visualize single, double or
8860 multiple sampling plans. In addition, methods have been provided to enable the
8861 user to assess sampling plans against pre-specified levels of performance, as
8862 measured by the probability of acceptance for a given level of quality in the
8864 (license license:gpl3+)))
8866 (define-public r-acclma
8873 (uri (cran-uri "ACCLMA" version))
8875 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8876 (properties `((upstream-name . "ACCLMA")))
8877 (build-system r-build-system)
8878 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8879 (synopsis "ACC & LMA graph plotting")
8881 "This package contains a function that imports data from a @acronym{CSV,
8882 Comma-Separated Values} file, or uses manually entered data from the format (x,
8883 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8884 Curve} vs @acronym{LOI, Line of Independence} graph and
8885 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8886 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8887 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8888 string) was passed, a manual data entry window is opened. The header parameter
8889 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8890 a header row or not. The dataset should contain only one independent variable
8891 (x) and one dependent variable (y) and can contain a weight for each
8893 (license license:gpl2)))
8895 (define-public r-aspi
8902 (uri (cran-uri "aspi" version))
8904 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8905 (build-system r-build-system)
8907 "https://cran.r-project.org/web/packages/aspi/")
8909 "Analysis of symmetry of parasitic infections")
8911 "This package provides tools for the analysis and visualization of bilateral
8912 asymmetry in parasitic infections.")
8913 (license license:gpl3+)))
8915 (define-public r-sandwich
8922 (uri (cran-uri "sandwich" version))
8925 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8926 (build-system r-build-system)
8928 `(("r-zoo" ,r-zoo)))
8929 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8930 (synopsis "Robust Covariance Matrix Estimators")
8932 "This package provides model-robust standard error estimators for
8933 cross-sectional, time series, clustered, panel, and longitudinal data.")
8934 ;; Either version of the license.
8935 (license (list license:gpl2 license:gpl3))))
8937 (define-public r-th-data
8944 (uri (cran-uri "TH.data" version))
8947 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8948 (properties `((upstream-name . "TH.data")))
8949 (build-system r-build-system)
8951 `(("r-mass" ,r-mass)
8952 ("r-survival" ,r-survival)))
8953 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8954 (synopsis "Shared data sets")
8956 "This package contains supporting data sets that are used in other
8957 packages maintained by Torsten Hothorn.")
8958 (license license:gpl3)))
8960 (define-public r-multcomp
8967 (uri (cran-uri "multcomp" version))
8970 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8971 (build-system r-build-system)
8973 `(("r-codetools" ,r-codetools)
8974 ("r-mvtnorm" ,r-mvtnorm)
8975 ("r-sandwich" ,r-sandwich)
8976 ("r-survival" ,r-survival)
8977 ("r-th-data" ,r-th-data)))
8978 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8979 (synopsis "Simultaneous inference in general parametric models")
8981 "Simultaneous tests and confidence intervals for general linear
8982 hypotheses in parametric models, including linear, generalized linear, linear
8983 mixed effects, and survival models. The package includes demos reproducing
8984 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8985 Hothorn, Westfall, 2010, CRC Press).")
8986 (license license:gpl2)))
8988 (define-public r-emmeans
8995 (uri (cran-uri "emmeans" version))
8998 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
8999 (build-system r-build-system)
9001 `(("r-estimability" ,r-estimability)
9002 ("r-mvtnorm" ,r-mvtnorm)
9003 ("r-numderiv" ,r-numderiv)
9005 ("r-xtable" ,r-xtable)))
9007 `(("r-knitr" ,r-knitr)))
9008 (home-page "https://github.com/rvlenth/emmeans")
9009 (synopsis "Estimated marginal means, aka least-squares means")
9011 "This package provides tools to obtain @dfn{estimated marginal
9012 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9013 be used to compute contrasts or linear functions of EMMs, trends, and
9014 comparisons of slopes.")
9015 ;; Either version of the license.
9016 (license (list license:gpl2 license:gpl3))))
9018 (define-public r-pwr
9025 (uri (cran-uri "pwr" version))
9028 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9029 (build-system r-build-system)
9031 `(("r-knitr" ,r-knitr)))
9032 (home-page "https://github.com/heliosdrm/pwr")
9033 (synopsis "Basic functions for power analysis")
9035 "This package provides power analysis functions along the lines of
9037 (license license:gpl3+)))
9039 (define-public r-libcoin
9046 (uri (cran-uri "libcoin" version))
9048 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9049 (build-system r-build-system)
9050 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9051 (home-page "https://cran.r-project.org/web/packages/libcoin")
9052 (synopsis "Linear test statistics for permutation inference")
9054 "This package provides basic infrastructure for linear test statistics
9055 and permutation inference in the framework of Strasser and Weber (1999).")
9056 (license license:gpl2)))
9058 (define-public r-coin
9065 (uri (cran-uri "coin" version))
9068 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9069 (build-system r-build-system)
9071 `(("r-libcoin" ,r-libcoin)
9072 ("r-matrixstats" ,r-matrixstats)
9073 ("r-modeltools" ,r-modeltools)
9074 ("r-multcomp" ,r-multcomp)
9075 ("r-mvtnorm" ,r-mvtnorm)
9076 ("r-survival" ,r-survival)))
9077 (home-page "http://coin.r-forge.r-project.org")
9078 (synopsis "Conditional inference procedures in a permutation test framework")
9080 "This package provides conditional inference procedures for the general
9081 independence problem including two-sample, K-sample (non-parametric ANOVA),
9082 correlation, censored, ordered and multivariate problems.")
9083 (license license:gpl2)))
9085 (define-public r-bayesplot
9087 (name "r-bayesplot")
9092 (uri (cran-uri "bayesplot" version))
9095 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9096 (build-system r-build-system)
9098 `(("pandoc" ,pandoc)
9099 ("pandoc-citeproc" ,pandoc-citeproc)))
9101 `(("r-knitr" ,r-knitr)))
9103 `(("r-dplyr" ,r-dplyr)
9104 ("r-ggplot2" ,r-ggplot2)
9105 ("r-ggridges" ,r-ggridges)
9107 ("r-reshape2" ,r-reshape2)
9108 ("r-rlang" ,r-rlang)
9109 ("r-tibble" ,r-tibble)
9110 ("r-tidyselect" ,r-tidyselect)))
9111 (home-page "https://mc-stan.org/bayesplot")
9112 (synopsis "Plotting for Bayesian models")
9114 "This package provides plotting functions for posterior analysis, model
9115 checking, and MCMC diagnostics. The package is designed not only to provide
9116 convenient functionality for users, but also a common set of functions that
9117 can be easily used by developers working on a variety of R packages for
9118 Bayesian modeling.")
9119 (license license:gpl3+)))
9121 (define-public r-tmb
9128 (uri (cran-uri "TMB" version))
9131 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9132 (properties `((upstream-name . "TMB")))
9133 (build-system r-build-system)
9135 `(("r-matrix" ,r-matrix)
9136 ("r-rcppeigen" ,r-rcppeigen)))
9137 (home-page "http://tmb-project.org")
9138 (synopsis "Template model builder: a general random effect tool")
9140 "With this tool, a user should be able to quickly implement complex
9141 random effect models through simple C++ templates. The package combines
9142 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9143 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9144 from R) to obtain an efficient implementation of the applied Laplace
9145 approximation with exact derivatives. Key features are: Automatic sparseness
9146 detection, parallelism through BLAS and parallel user templates.")
9147 (license license:gpl2)))
9149 (define-public r-sjstats
9156 (uri (cran-uri "sjstats" version))
9158 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9159 (build-system r-build-system)
9161 `(("r-bayestestr" ,r-bayestestr)
9162 ("r-broom" ,r-broom)
9163 ("r-dplyr" ,r-dplyr)
9164 ("r-effectsize" ,r-effectsize)
9165 ("r-emmeans" ,r-emmeans)
9166 ("r-insight" ,r-insight)
9168 ("r-magrittr" ,r-magrittr)
9170 ("r-modelr" ,r-modelr)
9171 ("r-parameters" ,r-parameters)
9172 ("r-performance" ,r-performance)
9173 ("r-purrr" ,r-purrr)
9174 ("r-rlang" ,r-rlang)
9175 ("r-sjlabelled" ,r-sjlabelled)
9176 ("r-sjmisc" ,r-sjmisc)
9177 ("r-tidyr" ,r-tidyr)))
9178 (home-page "https://github.com/strengejacke/sjstats")
9179 (synopsis "Functions for common statistical computations")
9181 "This package provides a collection of convenient functions for common
9182 statistical computations, which are not directly provided by R's @code{base}
9183 or @code{stats} packages. This package aims at providing, first, shortcuts
9184 for statistical measures, which otherwise could only be calculated with
9185 additional effort. Second, these shortcut functions are generic, and can be
9186 applied not only to vectors, but also to other objects as well. The focus of
9187 most functions lies on summary statistics or fit measures for regression
9188 models, including generalized linear models, mixed effects models and Bayesian
9190 (license license:gpl3)))
9192 (define-public r-glmmtmb
9199 (uri (cran-uri "glmmTMB" version))
9202 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9203 (properties `((upstream-name . "glmmTMB")))
9204 (build-system r-build-system)
9206 `(("r-lme4" ,r-lme4)
9207 ("r-matrix" ,r-matrix)
9209 ("r-rcppeigen" ,r-rcppeigen)
9212 `(("r-knitr" ,r-knitr))) ; for vignettes
9213 (home-page "https://github.com/glmmTMB")
9214 (synopsis "Generalized linear mixed models")
9216 "Fit linear and generalized linear mixed models with various extensions,
9217 including zero-inflation. The models are fitted using maximum likelihood
9218 estimation via the Template Model Builder. Random effects are assumed to be
9219 Gaussian on the scale of the linear predictor and are integrated out using the
9220 Laplace approximation. Gradients are calculated using automatic
9222 (license license:agpl3+)))
9224 (define-public r-bayestestr
9226 (name "r-bayestestr")
9231 (uri (cran-uri "bayestestR" version))
9234 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9235 (properties `((upstream-name . "bayestestR")))
9236 (build-system r-build-system)
9238 `(("r-insight" ,r-insight)))
9240 `(("r-knitr" ,r-knitr)))
9241 (home-page "https://github.com/easystats/bayestestR")
9242 (synopsis "Describe Bayesian models and posterior distributions")
9244 "This package provides utilities to understand and describe posterior
9245 distributions and Bayesian models. It includes point-estimates such as
9246 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9247 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9248 ROPE percentage and pd).")
9249 (license license:gpl3)))
9251 (define-public r-performance
9253 (name "r-performance")
9258 (uri (cran-uri "performance" version))
9261 "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
9262 (build-system r-build-system)
9264 `(("r-bayestestr" ,r-bayestestr)
9265 ("r-insight" ,r-insight)))
9266 (home-page "https://easystats.github.io/performance/")
9267 (synopsis "Assessment of regression models performance")
9269 "This package provides utilities for computing measures to assess model
9270 quality, which are not directly provided by R's @code{base} or @code{stats}
9271 packages. These include e.g. measures like r-squared, intraclass correlation
9272 coefficient, root mean squared error or functions to check models for
9273 overdispersion, singularity or zero-inflation and more. Functions apply to a
9274 large variety of regression models, including generalized linear models, mixed
9275 effects models and Bayesian models.")
9276 (license license:gpl3)))
9278 (define-public r-ggeffects
9280 (name "r-ggeffects")
9285 (uri (cran-uri "ggeffects" version))
9288 "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
9289 (build-system r-build-system)
9291 `(("r-insight" ,r-insight)
9293 ("r-sjlabelled" ,r-sjlabelled)))
9295 `(("r-knitr" ,r-knitr)))
9296 (home-page "https://github.com/strengejacke/ggeffects")
9297 (synopsis "Create tidy data frames of marginal effects for ggplot")
9299 "This package provides tools to compute marginal effects from statistical
9300 models and return the result as tidy data frames. These data frames are ready
9301 to use with the @code{ggplot2} package. Marginal effects can be calculated
9302 for many different models. Interaction terms, splines and polynomial terms
9303 are also supported. The two main functions are @code{ggpredict()} and
9304 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9305 results using @code{ggplot2}.")
9306 (license license:gpl3)))
9308 (define-public r-effectsize
9310 (name "r-effectsize")
9315 (uri (cran-uri "effectsize" version))
9318 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9319 (properties `((upstream-name . "effectsize")))
9320 (build-system r-build-system)
9322 `(("r-bayestestr" ,r-bayestestr)
9323 ("r-insight" ,r-insight)
9324 ("r-parameters" ,r-parameters)))
9326 `(("r-knitr" ,r-knitr)))
9327 (home-page "https://github.com/easystats/effectsize")
9328 (synopsis "Indices of effect size and standardized parameters")
9330 "This package provides utilities to work with indices of effect size and
9331 standardized parameters for a wide variety of models, allowing computation and
9332 conversion of indices such as Cohen's d, r, odds, etc.")
9333 (license license:gpl3)))
9335 (define-public r-sjplot
9342 (uri (cran-uri "sjPlot" version))
9344 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9345 (properties `((upstream-name . "sjPlot")))
9346 (build-system r-build-system)
9348 `(("r-bayestestr" ,r-bayestestr)
9349 ("r-dplyr" ,r-dplyr)
9350 ("r-effectsize" ,r-effectsize)
9351 ("r-ggeffects" ,r-ggeffects)
9352 ("r-ggplot2" ,r-ggplot2)
9353 ("r-insight" ,r-insight)
9354 ("r-knitr" ,r-knitr)
9356 ("r-parameters" ,r-parameters)
9357 ("r-performance" ,r-performance)
9358 ("r-purrr" ,r-purrr)
9359 ("r-rlang" ,r-rlang)
9360 ("r-scales" ,r-scales)
9361 ("r-sjlabelled" ,r-sjlabelled)
9362 ("r-sjmisc" ,r-sjmisc)
9363 ("r-sjstats" ,r-sjstats)
9364 ("r-tidyr" ,r-tidyr)))
9366 `(("r-knitr" ,r-knitr)))
9367 (home-page "https://strengejacke.github.io/sjPlot/")
9368 (synopsis "Data visualization for statistics in social science")
9370 "This package represents a collection of plotting and table output
9371 functions for data visualization. Results of various statistical
9372 analyses (that are commonly used in social sciences) can be visualized using
9373 this package, including simple and cross tabulated frequencies, histograms,
9374 box plots, (generalized) linear models, mixed effects models, principal
9375 component analysis and correlation matrices, cluster analyses, scatter plots,
9376 stacked scales, effects plots of regression models (including interaction
9377 terms) and much more. This package supports labelled data.")
9378 (license license:gpl3)))
9380 (define-public r-ini
9387 (uri (cran-uri "ini" version))
9390 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9391 (build-system r-build-system)
9392 (home-page "https://github.com/dvdscripter/ini")
9393 (synopsis "Read and write configuration files")
9395 "This package provides tools to parse simple @code{.ini} configuration
9396 files to an structured list. Users can manipulate this resulting list with
9397 @code{lapply()} functions. This same structured list can be used to write
9398 back to file after modifications.")
9399 (license license:gpl3)))
9408 (uri (cran-uri "gh" version))
9411 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9412 (build-system r-build-system)
9417 ("r-jsonlite" ,r-jsonlite)))
9418 (home-page "https://github.com/r-lib/gh#readme")
9419 (synopsis "Access the GitHub API via R")
9421 "This package provides a minimal R client to access the GitHub API.")
9422 (license license:expat)))
9431 (uri (cran-uri "fs" version))
9434 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9435 (build-system r-build-system)
9437 `(("r-knitr" ,r-knitr)))
9438 (home-page "https://fs.r-lib.org")
9439 (synopsis "Cross-platform file system operations based on libuv")
9441 "This package provides a cross-platform interface to file system
9442 operations, built on top of the libuv C library.")
9443 (license license:gpl3)))
9445 (define-public r-clisymbols
9447 (name "r-clisymbols")
9452 (uri (cran-uri "clisymbols" version))
9455 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9456 (build-system r-build-system)
9457 (home-page "https://github.com/gaborcsardi/clisymbols")
9458 (synopsis "Unicode symbols at the R prompt")
9460 "This package provides a small subset of Unicode symbols, that are useful
9461 when building command line applications. They fall back to alternatives on
9462 terminals that do not support Unicode.")
9463 (license license:expat)))
9465 (define-public r-usethis
9472 (uri (cran-uri "usethis" version))
9475 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9476 (build-system r-build-system)
9479 ("r-clipr" ,r-clipr)
9480 ("r-crayon" ,r-crayon)
9485 ("r-git2r" ,r-git2r)
9487 ("r-purrr" ,r-purrr)
9488 ("r-rematch2" ,r-rematch2)
9489 ("r-rlang" ,r-rlang)
9490 ("r-rprojroot" ,r-rprojroot)
9491 ("r-rstudioapi" ,r-rstudioapi)
9492 ("r-whisker" ,r-whisker)
9493 ("r-withr" ,r-withr)
9494 ("r-yaml" ,r-yaml)))
9495 (home-page "https://github.com/r-lib/usethis")
9496 (synopsis "Automate R package and project setup")
9498 "This package helps you to automate R package and project setup tasks
9499 that are otherwise performed manually. This includes setting up unit testing,
9500 test coverage, continuous integration, Git, GitHub integration, licenses,
9501 Rcpp, RStudio projects, and more.")
9502 (license license:gpl3)))
9504 (define-public r-sessioninfo
9506 (name "r-sessioninfo")
9511 (uri (cran-uri "sessioninfo" version))
9514 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9515 (build-system r-build-system)
9518 ("r-withr" ,r-withr)))
9519 (home-page "https://github.com/r-lib/sessioninfo#readme")
9520 (synopsis "R session information")
9522 "This package provides tools to query and print information about the
9523 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9524 more information about packages, and where they were installed from.")
9525 (license license:gpl2)))
9527 (define-public r-remotes
9534 (uri (cran-uri "remotes" version))
9537 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9538 (build-system r-build-system)
9540 `(("r-knitr" ,r-knitr)))
9541 (home-page "https://github.com/r-lib/remotes#readme")
9542 (synopsis "R package installation from remote repositories")
9544 "Download and install R packages stored in GitHub, BitBucket, or plain
9545 subversion or git repositories. This package is a lightweight replacement of
9546 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9547 the code was copied over from @code{devtools}.")
9548 (license license:gpl2+)))
9550 (define-public r-xopen
9557 (uri (cran-uri "xopen" version))
9560 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9561 (build-system r-build-system)
9563 `(("r-processx" ,r-processx)))
9564 (home-page "https://github.com/r-lib/xopen#readme")
9565 (synopsis "Open system files, URLs, anything")
9567 "This package provides a cross-platform solution to open files,
9568 directories or URLs with their associated programs.")
9569 (license license:expat)))
9571 (define-public r-rcmdcheck
9573 (name "r-rcmdcheck")
9578 (uri (cran-uri "rcmdcheck" version))
9581 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9582 (build-system r-build-system)
9584 `(("r-callr" ,r-callr)
9586 ("r-crayon" ,r-crayon)
9588 ("r-digest" ,r-digest)
9589 ("r-pkgbuild" ,r-pkgbuild)
9590 ("r-prettyunits" ,r-prettyunits)
9592 ("r-rprojroot" ,r-rprojroot)
9593 ("r-sessioninfo" ,r-sessioninfo)
9594 ("r-withr" ,r-withr)
9595 ("r-xopen" ,r-xopen)))
9596 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9597 (synopsis "Run R CMD check from R and capture results")
9599 "Run @code{R CMD check} from R programmatically, and capture the results
9600 of the individual checks.")
9601 (license license:expat)))
9603 (define-public r-rapportools
9605 (name "r-rapportools")
9610 (uri (cran-uri "rapportools" version))
9613 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9614 (build-system r-build-system)
9616 `(("r-pander" ,r-pander)
9618 ("r-reshape" ,r-reshape)))
9619 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9620 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9622 "This package provides helper functions that act as wrappers to more
9623 advanced statistical methods with the advantage of having sane defaults for
9625 (license license:agpl3+)))
9627 (define-public r-pander
9634 (uri (cran-uri "pander" version))
9637 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9638 (build-system r-build-system)
9640 `(("r-digest" ,r-digest)
9641 ("r-rcpp" ,r-rcpp)))
9642 (home-page "https://rapporter.github.io/pander")
9643 (synopsis "Render R objects into Pandoc's markdown")
9645 "The main aim of the pander R package is to provide a minimal and easy
9646 tool for rendering R objects into Pandoc's markdown. The package is also
9647 capable of exporting/converting complex Pandoc documents (reports) in various
9649 ;; This package is licensed under either the AGPLv3+ or the very rarely
9651 (license license:agpl3+)))
9653 (define-public r-summarytools
9655 (name "r-summarytools")
9660 (uri (cran-uri "summarytools" version))
9663 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9664 (build-system r-build-system)
9666 `(("r-base64enc" ,r-base64enc)
9667 ("r-checkmate" ,r-checkmate)
9668 ("r-dplyr" ,r-dplyr)
9669 ("r-htmltools" ,r-htmltools)
9670 ("r-lubridate" ,r-lubridate)
9671 ("r-magick" ,r-magick)
9672 ("r-matrixstats" ,r-matrixstats)
9673 ("r-pander" ,r-pander)
9675 ("r-rapportools" ,r-rapportools)
9676 ("r-tibble" ,r-tibble)
9677 ("r-tidyr" ,r-tidyr)))
9678 (home-page "https://github.com/dcomtois/summarytools")
9679 (synopsis "Tools to quickly and neatly summarize data")
9681 "This package provides tools for data frame summaries, cross-tabulations,
9682 weight-enabled frequency tables and common univariate statistics in concise
9683 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9684 good point-of-entry for exploring data, both for experienced and new R
9686 (license license:gpl2)))
9688 (define-public r-lsei
9695 (uri (cran-uri "lsei" version))
9698 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9699 (build-system r-build-system)
9701 `(("gfortran" ,gfortran)))
9702 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9703 (synopsis "Solve regression problems under equality/inequality constraints")
9705 "It contains functions that solve least squares linear regression
9706 problems under linear equality/inequality constraints. Functions for solving
9707 quadratic programming problems are also available, which transform such
9708 problems into least squares ones first.")
9709 (license license:gpl2+)))
9711 (define-public r-npsurv
9718 (uri (cran-uri "npsurv" version))
9721 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9722 (build-system r-build-system)
9724 `(("r-lsei" ,r-lsei)))
9725 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9726 (synopsis "Nonparametric survival analysis")
9728 "This package contains functions for non-parametric survival analysis of
9729 exact and interval-censored observations.")
9730 (license license:gpl2+)))
9732 (define-public r-clusteval
9734 (name "r-clusteval")
9739 (uri (cran-uri "clusteval" version))
9742 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9743 (build-system r-build-system)
9745 `(("r-mvtnorm" ,r-mvtnorm)
9746 ("r-rcpp" ,r-rcpp)))
9747 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9748 (synopsis "Evaluation of clustering algorithms")
9750 "This R package provides a suite of tools to evaluate clustering
9751 algorithms, clusterings, and individual clusters.")
9752 (license license:expat)))
9754 (define-public r-tweedie
9761 (uri (cran-uri "tweedie" version))
9764 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9765 (build-system r-build-system)
9766 (native-inputs `(("gfortran" ,gfortran)))
9767 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9768 (synopsis "Evaluation of Tweedie exponential family models")
9770 "Maximum likelihood computations for Tweedie families, including the
9771 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9772 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9773 and related methods.")
9774 (license license:gpl2+)))
9776 (define-public r-rcppgsl
9783 (uri (cran-uri "RcppGSL" version))
9785 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9786 (properties `((upstream-name . "RcppGSL")))
9787 (build-system r-build-system)
9789 `(("r-rcpp" ,r-rcpp)
9791 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9792 (synopsis "Rcpp integration for GSL vectors and matrices")
9794 "The GNU Scientific Library (or GSL) is a collection of numerical
9795 routines for scientific computing. It is particularly useful for C and C++
9796 programs as it provides a standard C interface to a wide range of mathematical
9797 routines. There are over 1000 functions in total with an extensive test
9798 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9799 structures and R using concepts from Rcpp which is itself a package that eases
9800 the interfaces between R and C++.")
9801 (license license:gpl2+)))
9803 (define-public r-mvabund
9810 (uri (cran-uri "mvabund" version))
9813 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9814 (build-system r-build-system)
9816 `(("r-mass" ,r-mass)
9818 ("r-rcppgsl" ,r-rcppgsl)
9819 ("r-statmod" ,r-statmod)
9820 ("r-tweedie" ,r-tweedie)))
9821 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9822 (synopsis "Statistical methods for analysing multivariate abundance data")
9824 "This package provides a set of tools for displaying, modeling and
9825 analysing multivariate abundance data in community ecology.")
9826 (license license:lgpl2.1+)))
9828 (define-public r-afex
9835 (uri (cran-uri "afex" version))
9838 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9839 (build-system r-build-system)
9843 ("r-lmertest" ,r-lmertest)
9844 ("r-pbkrtest" ,r-pbkrtest)
9845 ("r-reshape2" ,r-reshape2)))
9847 `(("r-knitr" ,r-knitr)))
9848 (home-page "https://afex.singmann.science/")
9849 (synopsis "Analysis of factorial experiments")
9851 "This package provides convenience functions for analyzing factorial
9852 experiments using ANOVA or mixed models.")
9853 (license license:gpl2+)))
9855 (define-public r-lmertest
9862 (uri (cran-uri "lmerTest" version))
9865 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9866 (properties `((upstream-name . "lmerTest")))
9867 (build-system r-build-system)
9869 `(("r-ggplot2" ,r-ggplot2)
9872 ("r-numderiv" ,r-numderiv)))
9873 (home-page "https://github.com/runehaubo/lmerTestR")
9874 (synopsis "Tests in linear mixed effects models")
9876 "This package provides p-values in type I, II or III anova and summary
9877 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9878 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9879 package. Model selection methods include step, drop1 and anova-like tables
9880 for random effects (ranova). Methods for Least-Square means (LS-means) and
9881 tests of linear contrasts of fixed effects are also available.")
9882 (license license:gpl2+)))
9884 (define-public r-r2glmm
9891 (uri (cran-uri "r2glmm" version))
9894 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9895 (build-system r-build-system)
9897 `(("r-afex" ,r-afex)
9898 ("r-data-table" ,r-data-table)
9899 ("r-dplyr" ,r-dplyr)
9900 ("r-ggplot2" ,r-ggplot2)
9901 ("r-gridextra" ,r-gridextra)
9902 ("r-lmertest" ,r-lmertest)
9904 ("r-matrix" ,r-matrix)
9906 ("r-pbkrtest" ,r-pbkrtest)))
9907 (home-page "https://github.com/bcjaeger/r2glmm")
9908 (synopsis "Compute R squared for mixed (multilevel) models")
9910 "This package computes model and semi partial R squared with confidence
9911 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9912 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9913 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9915 (license license:gpl2)))
9917 (define-public r-weights
9924 (uri (cran-uri "weights" version))
9927 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9928 (build-system r-build-system)
9930 `(("r-gdata" ,r-gdata)
9931 ("r-hmisc" ,r-hmisc)
9932 ("r-mice" ,r-mice)))
9934 "https://cran.r-project.org/web/packages/weights/")
9935 (synopsis "Weighting and weighted statistics")
9936 (description "This package Provides a variety of functions for producing
9937 simple weighted statistics, such as weighted Pearson's correlations, partial
9938 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9939 includes some software for quickly recoding survey data and plotting point
9940 estimates from interaction terms in regressions (and multiply imputed
9941 regressions). NOTE: Weighted partial correlation calculations pulled to
9943 (license license:gpl2+)))
9945 (define-public r-rcppannoy
9947 (name "r-rcppannoy")
9952 (uri (cran-uri "RcppAnnoy" version))
9955 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9956 (properties `((upstream-name . "RcppAnnoy")))
9957 (build-system r-build-system)
9959 `(("r-rcpp" ,r-rcpp)))
9960 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9961 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9963 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9964 for efficient memory usage as well an ability to load from and save to disk.
9965 This package provides an R interface.")
9966 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9968 (license (list license:gpl2+ license:asl2.0))))
9970 (define-public r-rcpphnsw
9977 (uri (cran-uri "RcppHNSW" version))
9980 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9981 (properties `((upstream-name . "RcppHNSW")))
9982 (build-system r-build-system)
9983 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9984 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9985 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9987 "Hnswlib is a C++ library for approximate nearest neighbors. This
9988 package provides a minimal R interface by relying on the Rcpp package.")
9989 ;; hnswlib is released under Version 2.0 of the Apache License.
9990 (license (list license:gpl3 license:asl2.0))))
9992 (define-public r-rcppparallel
9994 (name "r-rcppparallel")
9999 (uri (cran-uri "RcppParallel" version))
10002 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10003 (properties `((upstream-name . "RcppParallel")))
10004 (build-system r-build-system)
10005 (home-page "https://rcppcore.github.io/RcppParallel/")
10006 (synopsis "Parallel programming tools for Rcpp")
10008 "This package provides high level functions for parallel programming with
10009 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10010 the work of a standard serial @code{for} loop into a parallel one and the
10011 @code{parallelReduce()} function can be used for accumulating aggregates or
10013 (license license:gpl2)))
10015 (define-public r-ncdf4
10022 (uri (cran-uri "ncdf4" version))
10025 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10026 (build-system r-build-system)
10028 `(("netcdf" ,netcdf)
10030 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10031 (synopsis "R interface to Unidata netCDF format data files")
10033 "This package provides a high-level R interface to data files written
10034 using Unidata's netCDF library (version 4 or earlier), which are binary data
10035 files that are portable across platforms and include metadata information in
10036 addition to the data sets. Using this package, netCDF files can be opened and
10037 data sets read in easily. It is also easy to create new netCDF dimensions,
10038 variables, and files, in either version 3 or 4 format, and manipulate existing
10040 (license license:gpl3+)))
10042 (define-public r-biocmanager
10044 (name "r-biocmanager")
10045 (version "1.30.10")
10049 (uri (cran-uri "BiocManager" version))
10051 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10052 (properties `((upstream-name . "BiocManager")))
10053 (build-system r-build-system)
10054 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10055 (synopsis "Access the Bioconductor project package repository")
10057 "This package provides a convenient tool to install and update
10058 Bioconductor packages.")
10059 (license license:artistic2.0)))
10061 (define-public r-rgl
10064 (version "0.100.54")
10068 (uri (cran-uri "rgl" version))
10071 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10072 (build-system r-build-system)
10074 `(("pkg-config" ,pkg-config)))
10076 `(("freetype" ,freetype)
10083 `(("r-crosstalk" ,r-crosstalk)
10084 ("r-htmltools" ,r-htmltools)
10085 ("r-htmlwidgets" ,r-htmlwidgets)
10086 ("r-jsonlite" ,r-jsonlite)
10087 ("r-knitr" ,r-knitr)
10088 ("r-magrittr" ,r-magrittr)
10089 ("r-manipulatewidget" ,r-manipulatewidget)
10090 ("r-shiny" ,r-shiny)))
10091 (home-page "https://r-forge.r-project.org/projects/rgl/")
10092 (synopsis "3D visualization using OpenGL")
10094 "This package provides medium to high level functions for 3D interactive graphics,
10095 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10096 as functions for constructing representations of geometric
10097 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10098 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10099 image formats, including PNG, Postscript, SVG, PGF.")
10100 ;; Any version of the GPL.
10101 (license (list license:gpl2+ license:gpl3+))))
10103 (define-public r-multicool
10105 (name "r-multicool")
10110 (uri (cran-uri "multicool" version))
10113 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10114 (build-system r-build-system)
10115 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10116 (home-page "https://cran.r-project.org/web/packages/multicool/")
10117 (synopsis "Permutations of multisets in cool-lex order")
10119 "This package provides a set of tools to permute multisets without loops
10120 or hash tables and to generate integer partitions. Cool-lex order is similar
10121 to colexicographical order.")
10122 (license license:gpl2)))
10124 (define-public r-misc3d
10131 (uri (cran-uri "misc3d" version))
10134 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
10135 (build-system r-build-system)
10136 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10137 (synopsis "Miscellaneous 3D Plots")
10139 "This package provides a collection of miscellaneous 3d plots, including
10141 ;; Any version of the GPL.
10142 (license (list license:gpl2+ license:gpl3+))))
10144 (define-public r-ks
10151 (uri (cran-uri "ks" version))
10153 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10154 (build-system r-build-system)
10157 ("r-kernlab" ,r-kernlab)
10158 ("r-kernsmooth" ,r-kernsmooth)
10159 ("r-matrix" ,r-matrix)
10160 ("r-mclust" ,r-mclust)
10162 ("r-multicool" ,r-multicool)
10163 ("r-mvtnorm" ,r-mvtnorm)))
10164 (home-page "http://www.mvstat.net/tduong/")
10165 (synopsis "Kernel smoothing")
10167 "This package provides kernel smoothers for univariate and multivariate
10168 data, including density functions, density derivatives, cumulative
10169 distributions, modal clustering, discriminant analysis, and two-sample
10170 hypothesis testing.")
10171 ;; Either version of the GPL.
10172 (license (list license:gpl2 license:gpl3))))
10174 (define-public r-feature
10181 (uri (cran-uri "feature" version))
10184 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
10185 (build-system r-build-system)
10188 ("r-misc3d" ,r-misc3d)
10190 (home-page "http://www.mvstat.net/tduong/")
10191 (synopsis "Inferential feature significance for kernel density estimation")
10193 "The feature package contains functions to display and compute kernel
10194 density estimates, significant gradient and significant curvature regions.
10195 Significant gradient and/or curvature regions often correspond to significant
10196 features (e.g. local modes).")
10197 ;; Either version of the GPL.
10198 (license (list license:gpl2 license:gpl3))))
10200 (define-public r-arm
10207 (uri (cran-uri "arm" version))
10210 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10211 (build-system r-build-system)
10213 `(("r-abind" ,r-abind)
10215 ("r-hmisc" ,r-hmisc)
10218 ("r-matrix" ,r-matrix)
10219 ("r-nlme" ,r-nlme)))
10220 (home-page "https://cran.r-project.org/web/packages/arm/")
10221 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10223 "This package provides functions to accompany A. Gelman and J. Hill,
10224 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10225 University Press, 2007.")
10226 (license license:gpl3+)))
10228 (define-public r-circular
10230 (name "r-circular")
10235 (uri (cran-uri "circular" version))
10238 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10239 (build-system r-build-system)
10241 `(("r-boot" ,r-boot)
10242 ("r-mvtnorm" ,r-mvtnorm)))
10244 `(("gfortran" ,gfortran)))
10245 (home-page "https://cran.r-project.org/web/packages/circular/")
10246 (synopsis "Circular statistics")
10248 "This package provides tools for circular statistics, from \"Topics in
10249 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10251 (license license:gpl2+)))
10253 (define-public r-activity
10255 (name "r-activity")
10260 (uri (cran-uri "activity" version))
10263 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10264 (build-system r-build-system)
10266 `(("r-circular" ,r-circular)
10267 ("r-insol" ,r-insol)
10268 ("r-pbapply" ,r-pbapply)))
10269 (home-page "https://cran.r-project.org/web/packages/activity/")
10270 (synopsis "Animal activity statistics")
10272 "This package provides functions to fit kernel density functions to
10273 animal activity time data; plot activity distributions; quantify overall
10274 levels of activity; statistically compare activity metrics through
10275 bootstrapping; and evaluate variation in linear variables with time (or other
10276 circular variables).")
10277 (license license:gpl3)))
10279 (define-public r-ouch
10286 (uri (cran-uri "ouch" version))
10289 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10290 (build-system r-build-system)
10291 (propagated-inputs `(("r-subplex" ,r-subplex)))
10292 (home-page "https://kingaa.github.io/ouch/")
10293 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10295 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10296 for evolution along a phylogenetic tree.")
10297 (license license:gpl2+)))
10299 (define-public r-fmsb
10306 (uri (cran-uri "fmsb" version))
10309 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10310 (build-system r-build-system)
10311 (home-page "http://minato.sip21c.org/msb/")
10312 (synopsis "Functions for medical statistics book with demographic data")
10314 "This package provides several utility functions for the book entitled
10315 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10316 Japan, 2007) with Japanese demographic data and some demographic analysis
10317 related functions.")
10318 (license license:gpl2+)))
10320 (define-public r-stabledist
10322 (name "r-stabledist")
10327 (uri (cran-uri "stabledist" version))
10330 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10331 (build-system r-build-system)
10332 (home-page "https://www.rmetrics.org")
10333 (synopsis "Stable distribution functions")
10335 "This package provides density, probability and quantile functions, and
10336 random number generation for (skew) stable distributions, using the
10337 parametrizations of Nolan.")
10338 (license license:gpl2+)))
10340 (define-public r-gsl
10347 (uri (cran-uri "gsl" version))
10350 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10351 (build-system r-build-system)
10354 (home-page "https://cran.r-project.org/web/packages/gsl")
10355 (synopsis "Wrapper for the GNU Scientific Library")
10357 "This package provides an R wrapper for the special functions and quasi
10358 random number generators of the GNU Scientific Library.")
10359 (license license:gpl2+)))
10361 (define-public r-adgoftest
10363 (name "r-adgoftest")
10368 (uri (cran-uri "ADGofTest" version))
10371 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10372 (properties `((upstream-name . "ADGofTest")))
10373 (build-system r-build-system)
10374 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10375 (synopsis "Anderson-Darling GoF test")
10377 "This package provides an implementation of the Anderson-Darling GoF test
10378 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10379 Anderson-Darling Distribution\".")
10380 ;; Any version of the GPL.
10381 (license license:gpl3+)))
10383 (define-public r-softimpute
10385 (name "r-softimpute")
10390 (uri (cran-uri "softImpute" version))
10393 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10394 (properties `((upstream-name . "softImpute")))
10395 (build-system r-build-system)
10397 `(("r-matrix" ,r-matrix)))
10399 `(("gfortran" ,gfortran)))
10400 (home-page "https://cran.r-project.org/web/packages/softImpute")
10401 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10403 "This package provides iterative methods for matrix completion that use
10404 nuclear-norm regularization. The package includes procedures for centering
10405 and scaling rows, columns or both, and for computing low-rank @dfn{single
10406 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10408 (license license:gpl2)))
10410 (define-public r-fftwtools
10412 (name "r-fftwtools")
10417 (uri (cran-uri "fftwtools" version))
10420 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10421 (build-system r-build-system)
10422 (inputs `(("fftw" ,fftw)))
10423 (home-page "https://github.com/krahim/fftwtools")
10424 (synopsis "Wrapper for FFTW3")
10426 "This package provides a wrapper for several FFTW functions. It provides
10427 access to the two-dimensional FFT, the multivariate FFT, and the
10428 one-dimensional real to complex FFT using the FFTW3 library. The package
10429 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10430 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10431 The FFT functions have a parameter that allows them to not return the
10432 redundant complex conjugate when the input is real data.")
10433 (license license:gpl2+)))
10435 (define-public r-tiff
10442 (uri (cran-uri "tiff" version))
10445 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10446 (build-system r-build-system)
10448 `(("libtiff" ,libtiff)
10449 ("libjpeg" ,libjpeg-turbo)
10451 (home-page "https://www.rforge.net/tiff/")
10452 (synopsis "Read and write TIFF images")
10454 "This package provides an easy and simple way to read, write and display
10455 bitmap images stored in the TIFF format. It can read and write both files and
10456 in-memory raw vectors.")
10457 ;; Either of these two license versions.
10458 (license (list license:gpl2 license:gpl3))))
10460 (define-public r-nlp
10467 (uri (cran-uri "NLP" version))
10470 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10471 (properties `((upstream-name . "NLP")))
10472 (build-system r-build-system)
10473 (home-page "https://cran.r-project.org/web/packages/NLP/")
10474 (synopsis "Natural language processing infrastructure")
10476 "This package provides basic classes and methods for Natural Language
10478 (license license:gpl3)))
10480 (define-public r-tm
10487 (uri (cran-uri "tm" version))
10490 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10491 (properties `((upstream-name . "tm")))
10492 (build-system r-build-system)
10498 ("r-xml2" ,r-xml2)))
10499 (home-page "http://tm.r-forge.r-project.org/")
10500 (synopsis "Text mining package")
10502 "This package provides a framework for text mining applications within R.")
10503 (license license:gpl3)))
10505 (define-public r-waveslim
10507 (name "r-waveslim")
10512 (uri (cran-uri "waveslim" version))
10515 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10516 (build-system r-build-system)
10518 `(("gfortran" ,gfortran)))
10519 (home-page "http://waveslim.blogspot.com")
10520 (synopsis "Basic wavelet routines for signal processing")
10522 "This package provides basic wavelet routines for time series (1D),
10523 image (2D) and array (3D) analysis. The code provided here is based on
10524 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10525 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10526 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10527 pairs (Selesnick 2001, 2002).")
10528 (license license:bsd-3)))
10530 (define-public r-wordcloud
10532 (name "r-wordcloud")
10537 (uri (cran-uri "wordcloud" version))
10540 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10541 (build-system r-build-system)
10543 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10545 ;; The "tm" package is only "suggested" according to CRAN, but the
10546 ;; wordcloud package cannot be loaded without it.
10548 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10549 (synopsis "Word clouds")
10551 "This package provides functionality to create pretty word clouds,
10552 visualize differences and similarity between documents, and avoid
10553 over-plotting in scatter plots with text.")
10554 (license license:lgpl2.1)))
10556 (define-public r-colorramps
10558 (name "r-colorramps")
10563 (uri (cran-uri "colorRamps" version))
10566 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10567 (properties `((upstream-name . "colorRamps")))
10568 (build-system r-build-system)
10569 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10570 (synopsis "Build color tables")
10571 (description "This package provides features to build gradient color
10573 ;; Any version of the GPL
10574 (license license:gpl3+)))
10576 (define-public r-tidytree
10578 (name "r-tidytree")
10583 (uri (cran-uri "tidytree" version))
10585 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10586 (build-system r-build-system)
10589 ("r-dplyr" ,r-dplyr)
10590 ("r-lazyeval" ,r-lazyeval)
10591 ("r-magrittr" ,r-magrittr)
10592 ("r-rlang" ,r-rlang)
10593 ("r-tibble" ,r-tibble)))
10595 `(("r-knitr" ,r-knitr)))
10596 (home-page "https://github.com/GuangchuangYu/tidytree")
10597 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10599 "Phylogenetic trees generally contain multiple components including nodes,
10600 edges, branches and associated data. This package provides an approach to
10601 convert tree objects to tidy data frames. It also provides tidy interfaces to
10602 manipulate tree data.")
10603 (license license:artistic2.0)))
10605 (define-public r-rvcheck
10612 (uri (cran-uri "rvcheck" version))
10614 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10615 (build-system r-build-system)
10617 `(("r-biocmanager" ,r-biocmanager)
10618 ("r-rlang" ,r-rlang)))
10619 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10620 (synopsis "R package version check")
10622 "This package provides tools to check the latest release version of R and
10623 R packages (on CRAN, Bioconductor or Github).")
10624 (license license:artistic2.0)))
10626 (define-public r-docopt
10633 (uri (cran-uri "docopt" version))
10636 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10637 (build-system r-build-system)
10638 (home-page "https://github.com/docopt/docopt.R")
10639 (synopsis "Command-line interface specification language")
10641 "This package enables you to define a command-line interface by just
10642 giving it a description in the specific format.")
10643 (license license:expat)))
10645 (define-public r-sparsesvd
10647 (name "r-sparsesvd")
10652 (uri (cran-uri "sparsesvd" version))
10655 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10656 (build-system r-build-system)
10657 (propagated-inputs `(("r-matrix" ,r-matrix)))
10658 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10659 (synopsis "Sparse truncated singular value decomposition")
10661 "This package provides a Wrapper around the SVDLIBC library
10662 for (truncated) singular value decomposition of a sparse matrix. Currently,
10663 only sparse real matrices in Matrix package format are supported.")
10664 ;; SVDLIBC is released under BSD-2. The R interface is released under
10666 (license (list license:bsd-3 license:bsd-2))))
10668 (define-public r-speedglm
10670 (name "r-speedglm")
10675 (uri (cran-uri "speedglm" version))
10678 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10679 (build-system r-build-system)
10681 `(("r-mass" ,r-mass)
10682 ("r-matrix" ,r-matrix)))
10683 (home-page "https://cran.r-project.org/web/packages/speedglm")
10684 (synopsis "Fit linear and generalized linear models to large data sets")
10686 "This package provides tools for fitting linear models and generalized
10687 linear models to large data sets by updating algorithms.")
10688 ;; Any version of the GPL
10689 (license license:gpl2+)))
10691 (define-public r-densityclust
10693 (name "r-densityclust")
10698 (uri (cran-uri "densityClust" version))
10701 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10702 (properties `((upstream-name . "densityClust")))
10703 (build-system r-build-system)
10706 ("r-ggplot2" ,r-ggplot2)
10707 ("r-ggrepel" ,r-ggrepel)
10708 ("r-gridextra" ,r-gridextra)
10709 ("r-rcolorbrewer" ,r-rcolorbrewer)
10711 ("r-rtsne" ,r-rtsne)))
10712 (home-page "https://cran.r-project.org/web/packages/densityClust")
10713 (synopsis "Clustering by fast search and find of density peaks")
10715 "This package provides an improved implementation (based on k-nearest
10716 neighbors) of the density peak clustering algorithm, originally described by
10717 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10718 large datasets (> 100,000 samples) very efficiently.")
10719 (license license:gpl2+)))
10721 (define-public r-combinat
10723 (name "r-combinat")
10728 (uri (cran-uri "combinat" version))
10731 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10732 (build-system r-build-system)
10733 (home-page "https://cran.r-project.org/web/packages/combinat")
10734 (synopsis "Combinatorics utilities")
10735 (description "This package provides assorted routines for combinatorics.")
10736 (license license:gpl2)))
10738 (define-public r-qlcmatrix
10740 (name "r-qlcmatrix")
10745 (uri (cran-uri "qlcMatrix" version))
10748 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10749 (properties `((upstream-name . "qlcMatrix")))
10750 (build-system r-build-system)
10752 `(("r-docopt" ,r-docopt)
10753 ("r-matrix" ,r-matrix)
10755 ("r-sparsesvd" ,r-sparsesvd)))
10756 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10757 (synopsis "Sparse matrix functions for quantitative language comparison")
10759 "This package provides an extension of the functionality of the Matrix
10760 package for using sparse matrices. Some of the functions are very general,
10761 while other are highly specific for the special data format used for
10762 @dfn{quantitative language comparison} (QLC).")
10763 (license license:gpl3)))
10765 (define-public r-ddrtree
10772 (uri (cran-uri "DDRTree" version))
10775 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10776 (properties `((upstream-name . "DDRTree")))
10777 (build-system r-build-system)
10780 ("r-irlba" ,r-irlba)
10782 ("r-rcppeigen" ,r-rcppeigen)))
10783 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10784 (synopsis "Learning principal graphs with DDRTree")
10786 "This package provides an implementation of the framework of
10787 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10788 dimensional space while constructs a principal tree which passes through the
10789 middle of the data simultaneously. DDRTree shows superiority to
10790 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10791 intrinsic structure of single cell genomics data. In general, it could be
10792 used to reconstruct the temporal progression as well as the bifurcation
10793 structure of any data type.")
10794 (license license:asl2.0)))
10796 (define-public r-corpcor
10803 (uri (cran-uri "corpcor" version))
10806 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10807 (build-system r-build-system)
10808 (home-page "http://strimmerlab.org/software/corpcor/")
10809 (synopsis "Efficient estimation of covariance and (partial) correlation")
10811 "This package implements a James-Stein-type shrinkage estimator for the
10812 covariance matrix, with separate shrinkage for variances and correlations.
10813 Furthermore, functions are available for fast singular value decomposition,
10814 for computing the pseudoinverse, and for checking the rank and positive
10815 definiteness of a matrix.")
10816 (license license:gpl3+)))
10818 (define-public r-rspectra
10820 (name "r-rspectra")
10825 (uri (cran-uri "RSpectra" version))
10828 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10829 (properties `((upstream-name . "RSpectra")))
10830 (build-system r-build-system)
10832 `(("r-matrix" ,r-matrix)
10834 ("r-rcppeigen" ,r-rcppeigen)))
10835 (home-page "https://github.com/yixuan/RSpectra")
10836 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10838 "This package provides an R interface to the Spectra library for
10839 large-scale eigenvalue and SVD problems. It is typically used to compute a
10840 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10841 which is usually more efficient than @code{eigen()} if k << n.")
10843 (license license:mpl2.0)))
10845 (define-public r-vbsr
10852 (uri (cran-uri "vbsr" version))
10855 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10856 (build-system r-build-system)
10857 (home-page "https://cran.r-project.org/web/packages/vbsr")
10858 (synopsis "Variational Bayes spike regression regularized linear models")
10860 "This package provides an efficient algorithm for solving ultra-sparse
10861 regularized regression models using a variational Bayes algorithm with a spike
10862 prior. The algorithm is solved on a path, with coordinate updates, and is
10863 capable of generating very sparse models. Very general model
10864 diagnostics for controlling type-1 errors are also provided.")
10865 (license license:gpl2)))
10867 (define-public r-flare
10870 (version "1.6.0.2")
10874 (uri (cran-uri "flare" version))
10877 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10878 (build-system r-build-system)
10880 `(("r-igraph" ,r-igraph)
10881 ("r-lattice" ,r-lattice)
10883 ("r-matrix" ,r-matrix)))
10884 (home-page "https://cran.r-project.org/web/packages/flare")
10885 (synopsis "Family of Lasso regression implementations")
10887 "This package provides implementations of a family of Lasso variants
10888 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10889 high dimensional sparse linear models.")
10890 (license license:gpl2)))
10892 (define-public r-lassopv
10899 (uri (cran-uri "lassopv" version))
10902 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10903 (build-system r-build-system)
10904 (propagated-inputs `(("r-lars" ,r-lars)))
10905 (home-page "https://github.com/lingfeiwang/lassopv")
10906 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10908 "This package enables you to estimate the p-values for predictors x
10909 against target variable y in Lasso regression, using the regularization
10910 strength when each predictor enters the active set of regularization path for
10911 the first time as the statistic.")
10912 (license license:gpl3)))
10914 (define-public r-splitstackshape
10916 (name "r-splitstackshape")
10921 (uri (cran-uri "splitstackshape" version))
10924 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10925 (build-system r-build-system)
10927 `(("r-data-table" ,r-data-table)))
10928 (home-page "https://github.com/mrdwab/splitstackshape")
10929 (synopsis "Stack and reshape datasets after splitting concatenated values")
10931 "Online data collection tools like Google Forms often export
10932 multiple-response questions with data concatenated in cells. The
10933 @code{concat.split} (cSplit) family of functions provided by this package
10934 splits such data into separate cells. This package also includes functions to
10935 stack groups of columns and to reshape wide data, even when the data are
10936 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10937 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10939 (license license:gpl3)))
10941 (define-public r-tfmpvalue
10943 (name "r-tfmpvalue")
10948 (uri (cran-uri "TFMPvalue" version))
10951 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10952 (properties `((upstream-name . "TFMPvalue")))
10953 (build-system r-build-system)
10954 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10955 (home-page "https://github.com/ge11232002/TFMPvalue")
10956 (synopsis "P-value computation for position weight matrices")
10958 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10959 identification from sequence/alignments, we are interested in the significance
10960 of certain match scores. TFMPvalue provides the accurate calculation of a
10961 p-value with a score threshold for position weight matrices, or the score with
10962 a given p-value. It is an interface to code originally made available by
10963 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10964 Touzet and Varre (2007).")
10965 (license license:gpl2)))
10967 (define-public r-rnifti
10974 (uri (cran-uri "RNifti" version))
10977 "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
10978 (properties `((upstream-name . "RNifti")))
10979 (build-system r-build-system)
10980 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10981 (home-page "https://github.com/jonclayden/RNifti")
10982 (synopsis "Fast R and C++ access to NIfTI images")
10984 "This package provides very fast read and write access to images stored
10985 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10986 compiled C and interpreted R code. It also provides a C/C++ API that can be
10987 used by other packages.")
10988 (license license:gpl2)))
10990 (define-public r-shades
10997 (uri (cran-uri "shades" version))
11000 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11001 (build-system r-build-system)
11002 (home-page "https://github.com/jonclayden/shades")
11003 (synopsis "Simple color manipulation")
11005 "This package provides functions for easily manipulating colors,
11006 creating color scales and calculating color distances.")
11007 (license license:bsd-3)))
11009 (define-public r-ore
11016 (uri (cran-uri "ore" version))
11018 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11019 (build-system r-build-system)
11020 (home-page "https://github.com/jonclayden/ore")
11021 (synopsis "R interface to the Onigmo regular expression library")
11023 "This package provides an alternative to R's built-in functionality for
11024 handling regular expressions, based on the Onigmo library. It offers
11025 first-class compiled regex objects, partial matching and function-based
11026 substitutions, amongst other features.")
11027 (license license:bsd-3)))
11029 (define-public r-reportr
11036 (uri (cran-uri "reportr" version))
11039 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11040 (build-system r-build-system)
11041 (propagated-inputs `(("r-ore" ,r-ore)))
11042 (home-page "https://github.com/jonclayden/reportr")
11043 (synopsis "General message and error reporting system")
11045 "This package provides a system for reporting messages, which offers
11046 certain useful features over the standard R system, such as the incorporation
11047 of output consolidation, message filtering, assertions, expression
11048 substitution, automatic generation of stack traces for debugging, and
11049 conditional reporting based on the current \"output level\".")
11050 (license license:gpl2)))
11052 (define-public r-tractor-base
11054 (name "r-tractor-base")
11059 (uri (cran-uri "tractor.base" version))
11062 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11063 (properties `((upstream-name . "tractor.base")))
11064 (build-system r-build-system)
11067 ("r-reportr" ,r-reportr)
11068 ("r-rnifti" ,r-rnifti)
11069 ("r-shades" ,r-shades)))
11070 (home-page "https://www.tractor-mri.org.uk")
11071 (synopsis "Read, manipulate and visualize magnetic resonance images")
11073 "This package provides functions for working with magnetic resonance
11074 images. It supports reading and writing of popular file formats (DICOM,
11075 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11076 visualization; flexible image manipulation; metadata and sparse image
11078 (license license:gpl2)))
11080 (define-public r-grimport
11082 (name "r-grimport")
11087 (uri (cran-uri "grImport" version))
11090 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11091 (properties `((upstream-name . "grImport")))
11092 (build-system r-build-system)
11094 `(("ghostscript" ,ghostscript)))
11096 `(("r-xml" ,r-xml)))
11097 (home-page "https://cran.r-project.org/web/packages/grImport")
11098 (synopsis "Convert, import, and draw PostScript pictures")
11100 "This package provides functions for converting, importing, and drawing
11101 PostScript pictures in R plots.")
11102 (license license:gpl2+)))
11104 (define-public r-grimport2
11106 (name "r-grimport2")
11111 (uri (cran-uri "grImport2" version))
11114 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11115 (properties `((upstream-name . "grImport2")))
11116 (build-system r-build-system)
11118 `(("r-base64enc" ,r-base64enc)
11122 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11123 (synopsis "Import SVG graphics")
11125 "This package provides functions for importing external vector images and
11126 drawing them as part of R plots. This package is different from the
11127 @code{grImport} package because, where that package imports PostScript format
11128 images, this package imports SVG format images. Furthermore, this package
11129 imports a specific subset of SVG, so external images must be preprocessed
11130 using a package like @code{rsvg} to produce SVG that this package can import.
11131 SVG features that are not supported by R graphics, such as gradient fills, can
11132 be imported and then exported via the @code{gridSVG} package.")
11133 (license license:gpl2+)))
11135 (define-public r-kohonen
11142 (uri (cran-uri "kohonen" version))
11145 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11146 (build-system r-build-system)
11148 `(("r-rcpp" ,r-rcpp)))
11149 (home-page "https://cran.r-project.org/web/packages/kohonen")
11150 (synopsis "Supervised and unsupervised self-organising maps")
11152 "This package provides functions to train @dfn{self-organising
11153 maps} (SOMs). Also interrogation of the maps and prediction using trained
11154 maps are supported. The name of the package refers to Teuvo Kohonen, the
11155 inventor of the SOM.")
11156 (license license:gpl2+)))
11158 (define-public r-nnls
11165 (uri (cran-uri "nnls" version))
11168 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11169 (build-system r-build-system)
11170 (native-inputs `(("gfortran" ,gfortran)))
11171 (home-page "https://cran.r-project.org/web/packages/nnls")
11172 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11174 "This package provides an R interface to the Lawson-Hanson implementation
11175 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11176 the combination of non-negative and non-positive constraints.")
11177 (license license:gpl2+)))
11179 (define-public r-iso
11182 (version "0.0-18.1")
11186 (uri (cran-uri "Iso" version))
11189 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11190 (properties `((upstream-name . "Iso")))
11191 (build-system r-build-system)
11192 (native-inputs `(("gfortran" ,gfortran)))
11193 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11194 (synopsis "Functions to perform isotonic regression")
11196 "This package provides support for linear order and unimodal
11197 order (univariate) isotonic regression and bivariate isotonic regression with
11198 linear order on both variables.")
11199 (license license:gpl2+)))
11201 (define-public r-chemometricswithr
11203 (name "r-chemometricswithr")
11208 (uri (cran-uri "ChemometricsWithR" version))
11211 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11213 `((upstream-name . "ChemometricsWithR")))
11214 (build-system r-build-system)
11216 `(("r-devtools" ,r-devtools)
11217 ("r-kohonen" ,r-kohonen)
11220 (home-page "https://github.com/rwehrens/CWR")
11221 (synopsis "Chemometrics with R")
11223 "This package provides functions and scripts used in the book
11224 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11225 Life Sciences\" by Ron Wehrens, Springer (2011).")
11226 (license license:gpl2+)))
11228 (define-public r-als
11235 (uri (cran-uri "ALS" version))
11238 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11239 (properties `((upstream-name . "ALS")))
11240 (build-system r-build-system)
11243 ("r-nnls" ,r-nnls)))
11244 (home-page "https://cran.r-project.org/web/packages/ALS")
11245 (synopsis "Multivariate curve resolution alternating least squares")
11247 "Alternating least squares is often used to resolve components
11248 contributing to data with a bilinear structure; the basic technique may be
11249 extended to alternating constrained least squares. This package provides an
11250 implementation of @dfn{multivariate curve resolution alternating least
11251 squares} (MCR-ALS).
11253 Commonly applied constraints include unimodality, non-negativity, and
11254 normalization of components. Several data matrices may be decomposed
11255 simultaneously by assuming that one of the two matrices in the bilinear
11256 decomposition is shared between datasets.")
11257 (license license:gpl2+)))
11259 (define-public r-strucchange
11261 (name "r-strucchange")
11266 (uri (cran-uri "strucchange" version))
11269 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11270 (build-system r-build-system)
11272 `(("r-sandwich" ,r-sandwich)
11274 (home-page "https://cran.r-project.org/web/packages/strucchange")
11275 (synopsis "Testing, monitoring, and dating structural changes")
11277 "This package provides tools for testing, monitoring and dating
11278 structural changes in (linear) regression models. It features tests/methods
11279 from the generalized fluctuation test framework as well as from the F
11280 test (Chow test) framework. This includes methods to fit, plot and test
11281 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11282 statistics, respectively. It is possible to monitor incoming data online
11283 using fluctuation processes. Finally, the breakpoints in regression models
11284 with structural changes can be estimated together with confidence intervals.
11285 Emphasis is always given to methods for visualizing the data.")
11286 ;; Either of these two GPL versions
11287 (license (list license:gpl2 license:gpl3))))
11289 (define-public r-pixmap
11296 (uri (cran-uri "pixmap" version))
11299 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11300 (build-system r-build-system)
11301 (home-page "https://cran.r-project.org/web/packages/pixmap")
11302 (synopsis "Tools for bitmap images")
11304 "This package provides functions for importing, exporting, plotting and
11305 other manipulations of bitmapped images.")
11306 (license license:gpl2)))
11308 (define-public r-rapidjsonr
11310 (name "r-rapidjsonr")
11315 (uri (cran-uri "rapidjsonr" version))
11318 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11319 (build-system r-build-system)
11320 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11321 (synopsis "JSON parser")
11323 "This package provides JSON parsing capability through the Rapidjson
11325 (license license:expat)))
11327 (define-public r-ontologyindex
11329 (name "r-ontologyindex")
11334 (uri (cran-uri "ontologyIndex" version))
11337 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11338 (properties `((upstream-name . "ontologyIndex")))
11339 (build-system r-build-system)
11340 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11341 (synopsis "Functions for processing ontologies in R")
11343 "This package provides functions for reading ontologies into R as lists
11344 and manipulating sets of ontological terms.")
11345 (license license:gpl2+)))
11347 (define-public r-gargle
11354 (uri (cran-uri "gargle" version))
11357 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11358 (build-system r-build-system)
11363 ("r-jsonlite" ,r-jsonlite)
11364 ("r-rlang" ,r-rlang)
11365 ("r-withr" ,r-withr)))
11367 `(("r-knitr" ,r-knitr)))
11368 (home-page "https://gargle.r-lib.org")
11369 (synopsis "Utilities for working with Google APIs")
11371 "This package provides utilities for working with Google APIs. This
11372 includes functions and classes for handling common credential types and for
11373 preparing, executing, and processing HTTP requests.")
11374 (license license:expat)))
11376 (define-public r-bigrquery
11378 (name "r-bigrquery")
11383 (uri (cran-uri "bigrquery" version))
11386 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11387 (build-system r-build-system)
11389 `(("r-assertthat" ,r-assertthat)
11390 ("r-bit64" ,r-bit64)
11393 ("r-gargle" ,r-gargle)
11396 ("r-jsonlite" ,r-jsonlite)
11397 ("r-prettyunits" ,r-prettyunits)
11398 ("r-progress" ,r-progress)
11399 ("r-rapidjsonr" ,r-rapidjsonr)
11401 ("r-rlang" ,r-rlang)
11402 ("r-tibble" ,r-tibble)))
11403 (home-page "https://github.com/rstats-db/bigrquery")
11404 (synopsis "R interface to Google's BigQuery API")
11406 "This package provides an R interface to Google's BigQuery database.")
11407 (license license:gpl3)))
11409 (define-public r-gmp
11416 (uri (cran-uri "gmp" version))
11419 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11420 (build-system r-build-system)
11423 (modify-phases %standard-phases
11424 (add-after 'unpack 'set-CC
11425 (lambda _ (setenv "CC" "gcc") #t)))))
11426 (inputs `(("gmp" ,gmp)))
11427 (home-page "https://cran.r-project.org/web/packages/gmp")
11428 (synopsis "Multiple precision arithmetic")
11430 "This package supports multiple precision arithmetic (big integers and
11431 rationals, prime number tests, matrix computation), \"arithmetic without
11432 limitations\" using the GNU Multiple Precision library.")
11433 ;; Any version of the GPL.
11434 (license license:gpl3+)))
11436 (define-public r-rmpfr
11443 (uri (cran-uri "Rmpfr" version))
11446 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11447 (properties `((upstream-name . "Rmpfr")))
11448 (build-system r-build-system)
11453 `(("r-gmp" ,r-gmp)))
11455 `(("pkg-config" ,pkg-config)))
11456 (home-page "http://rmpfr.r-forge.r-project.org/")
11457 (synopsis "R bindings to the MPFR library")
11459 "This package supports arithmetic (via S4 classes and methods) for
11460 arbitrary precision floating point numbers, including transcendental
11461 functions. To this end, the package interfaces with the @dfn{Multiple
11462 Precision Floating-Point Reliable} (MPFR) library.")
11463 (license license:gpl2+)))
11465 (define-public r-assertive-base
11467 (name "r-assertive-base")
11472 (uri (cran-uri "assertive.base" version))
11475 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11477 `((upstream-name . "assertive.base")))
11478 (build-system r-build-system)
11479 (home-page "https://bitbucket.org/richierocks/assertive.base")
11480 (synopsis "Core of the assertive package")
11482 "This package provides a minimal set of predicates and assertions used by
11483 the assertive package. This is mainly for use by other package developers who
11484 want to include run-time testing features in their own packages.")
11485 (license license:gpl3+)))
11487 (define-public r-assertive-properties
11489 (name "r-assertive-properties")
11494 (uri (cran-uri "assertive.properties" version))
11497 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11499 `((upstream-name . "assertive.properties")))
11500 (build-system r-build-system)
11502 `(("r-assertive-base" ,r-assertive-base)))
11503 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11504 (synopsis "Assertions to check properties of variables")
11506 "This package provides a set of predicates and assertions for checking
11507 the properties of variables, such as length, names and attributes. This is
11508 mainly for use by other package developers who want to include run-time
11509 testing features in their own packages.")
11510 (license license:gpl3+)))
11512 (define-public r-assertive-numbers
11514 (name "r-assertive-numbers")
11519 (uri (cran-uri "assertive.numbers" version))
11522 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11524 `((upstream-name . "assertive.numbers")))
11525 (build-system r-build-system)
11527 `(("r-assertive-base" ,r-assertive-base)))
11528 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11529 (synopsis "Assertions to check properties of numbers")
11531 "This package provides a set of predicates and assertions for checking
11532 the properties of numbers. This is mainly for use by other package developers
11533 who want to include run-time testing features in their own packages.")
11534 (license license:gpl3+)))
11536 (define-public r-assertive-sets
11538 (name "r-assertive-sets")
11543 (uri (cran-uri "assertive.sets" version))
11546 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11548 `((upstream-name . "assertive.sets")))
11549 (build-system r-build-system)
11551 `(("r-assertive-base" ,r-assertive-base)))
11552 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11553 (synopsis "Assertions to check properties of sets")
11555 "This package provides a set of predicates and assertions for checking
11556 the properties of sets. This is mainly for use by other package developers
11557 who want to include run-time testing features in their own packages.")
11558 (license license:gpl3+)))
11560 (define-public r-assertive-matrices
11562 (name "r-assertive-matrices")
11567 (uri (cran-uri "assertive.matrices" version))
11570 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11572 `((upstream-name . "assertive.matrices")))
11573 (build-system r-build-system)
11575 `(("r-assertive-base" ,r-assertive-base)))
11576 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11577 (synopsis "Assertions to check properties of matrices")
11579 "This package provides a set of predicates and assertions for checking
11580 the properties of matrices. This is mainly for use by other package
11581 developers who want to include run-time testing features in their own
11583 (license license:gpl3+)))
11585 (define-public r-assertive-models
11587 (name "r-assertive-models")
11592 (uri (cran-uri "assertive.models" version))
11595 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11597 `((upstream-name . "assertive.models")))
11598 (build-system r-build-system)
11600 `(("r-assertive-base" ,r-assertive-base)))
11601 (home-page "https://bitbucket.org/richierocks/assertive.models")
11602 (synopsis "Assertions to check properties of models")
11604 "This package provides a set of predicates and assertions for checking
11605 the properties of models. This is mainly for use by other package developers
11606 who want to include run-time testing features in their own packages.")
11607 (license license:gpl3+)))
11609 (define-public r-assertive-reflection
11611 (name "r-assertive-reflection")
11616 (uri (cran-uri "assertive.reflection" version))
11619 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11621 `((upstream-name . "assertive.reflection")))
11622 (build-system r-build-system)
11624 `(("r-assertive-base" ,r-assertive-base)))
11625 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11626 (synopsis "Assertions for checking the state of R")
11628 "This package provides a set of predicates and assertions for checking
11629 the state and capabilities of R, the operating system it is running on, and
11630 the IDE being used. This is mainly for use by other package developers who
11631 want to include run-time testing features in their own packages.")
11632 (license license:gpl3+)))
11634 (define-public r-assertive-types
11636 (name "r-assertive-types")
11641 (uri (cran-uri "assertive.types" version))
11644 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11646 `((upstream-name . "assertive.types")))
11647 (build-system r-build-system)
11649 `(("r-assertive-base" ,r-assertive-base)
11650 ("r-assertive-properties" ,r-assertive-properties)
11651 ("r-codetools" ,r-codetools)))
11652 (home-page "https://bitbucket.org/richierocks/assertive.types")
11653 (synopsis "Assertions to check types of variables")
11655 "This package provides a set of predicates and assertions for checking
11656 the types of variables. This is mainly for use by other package developers
11657 who want to include run-time testing features in their own packages.")
11658 (license license:gpl3+)))
11660 (define-public r-assertive-files
11662 (name "r-assertive-files")
11667 (uri (cran-uri "assertive.files" version))
11670 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11672 `((upstream-name . "assertive.files")))
11673 (build-system r-build-system)
11675 `(("r-assertive-base" ,r-assertive-base)
11676 ("r-assertive-numbers" ,r-assertive-numbers)))
11677 (home-page "https://bitbucket.org/richierocks/assertive.files")
11678 (synopsis "Assertions to check properties of files")
11680 "This package provides a set of predicates and assertions for checking
11681 the properties of files and connections. This is mainly for use by other
11682 package developers who want to include run-time testing features in their own
11684 (license license:gpl3+)))
11686 (define-public r-assertive-code
11688 (name "r-assertive-code")
11693 (uri (cran-uri "assertive.code" version))
11696 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11698 `((upstream-name . "assertive.code")))
11699 (build-system r-build-system)
11701 `(("r-assertive-base" ,r-assertive-base)
11702 ("r-assertive-properties" ,r-assertive-properties)
11703 ("r-assertive-types" ,r-assertive-types)))
11704 (home-page "https://bitbucket.org/richierocks/assertive.code")
11705 (synopsis "Assertions to check properties of code")
11707 "This package provides a set of predicates and assertions for checking
11708 the properties of code. This is mainly for use by other package developers
11709 who want to include run-time testing features in their own packages.")
11710 (license license:gpl3+)))
11712 (define-public r-assertive-datetimes
11714 (name "r-assertive-datetimes")
11719 (uri (cran-uri "assertive.datetimes" version))
11722 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11724 `((upstream-name . "assertive.datetimes")))
11725 (build-system r-build-system)
11727 `(("r-assertive-base" ,r-assertive-base)
11728 ("r-assertive-types" ,r-assertive-types)))
11729 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11730 (synopsis "Assertions to check properties of dates and times")
11732 "This package provides a set of predicates and assertions for checking
11733 the properties of dates and times. This is mainly for use by other package
11734 developers who want to include run-time testing features in their own
11736 (license license:gpl3+)))
11738 (define-public r-assertive-strings
11740 (name "r-assertive-strings")
11745 (uri (cran-uri "assertive.strings" version))
11748 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11750 `((upstream-name . "assertive.strings")))
11751 (build-system r-build-system)
11753 `(("r-assertive-base" ,r-assertive-base)
11754 ("r-assertive-types" ,r-assertive-types)
11755 ("r-stringi" ,r-stringi)))
11756 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11757 (synopsis "Assertions to check properties of strings")
11759 "This package provides a set of predicates and assertions for checking
11760 the properties of strings. This is mainly for use by other package developers
11761 who want to include run-time testing features in their own packages.")
11762 (license license:gpl3+)))
11764 (define-public r-assertive-data-us
11766 (name "r-assertive-data-us")
11771 (uri (cran-uri "assertive.data.us" version))
11774 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11776 `((upstream-name . "assertive.data.us")))
11777 (build-system r-build-system)
11779 `(("r-assertive-base" ,r-assertive-base)
11780 ("r-assertive-strings" ,r-assertive-strings)))
11781 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11782 (synopsis "Assertions to check properties of strings")
11784 "This package provides a set of predicates and assertions for checking
11785 the properties of US-specific complex data types. This is mainly for use by
11786 other package developers who want to include run-time testing features in
11787 their own packages.")
11788 (license license:gpl3+)))
11790 (define-public r-assertive-data-uk
11792 (name "r-assertive-data-uk")
11797 (uri (cran-uri "assertive.data.uk" version))
11800 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11802 `((upstream-name . "assertive.data.uk")))
11803 (build-system r-build-system)
11805 `(("r-assertive-base" ,r-assertive-base)
11806 ("r-assertive-strings" ,r-assertive-strings)))
11807 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11808 (synopsis "Assertions to check properties of strings")
11810 "This package provides a set of predicates and assertions for checking
11811 the properties of UK-specific complex data types. This is mainly for use by
11812 other package developers who want to include run-time testing features in
11813 their own packages.")
11814 (license license:gpl3+)))
11816 (define-public r-assertive-data
11818 (name "r-assertive-data")
11823 (uri (cran-uri "assertive.data" version))
11826 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11828 `((upstream-name . "assertive.data")))
11829 (build-system r-build-system)
11831 `(("r-assertive-base" ,r-assertive-base)
11832 ("r-assertive-strings" ,r-assertive-strings)))
11833 (home-page "https://bitbucket.org/richierocks/assertive.data")
11834 (synopsis "Assertions to check properties of data")
11836 "This package provides a set of predicates and assertions for checking
11837 the properties of (country independent) complex data types. This is mainly
11838 for use by other package developers who want to include run-time testing
11839 features in their own packages.")
11840 (license license:gpl3+)))
11842 (define-public r-assertive
11844 (name "r-assertive")
11849 (uri (cran-uri "assertive" version))
11852 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11853 (build-system r-build-system)
11855 `(("r-assertive-base" ,r-assertive-base)
11856 ("r-assertive-code" ,r-assertive-code)
11857 ("r-assertive-data" ,r-assertive-data)
11858 ("r-assertive-data-uk" ,r-assertive-data-uk)
11859 ("r-assertive-data-us" ,r-assertive-data-us)
11860 ("r-assertive-datetimes" ,r-assertive-datetimes)
11861 ("r-assertive-files" ,r-assertive-files)
11862 ("r-assertive-matrices" ,r-assertive-matrices)
11863 ("r-assertive-models" ,r-assertive-models)
11864 ("r-assertive-numbers" ,r-assertive-numbers)
11865 ("r-assertive-properties" ,r-assertive-properties)
11866 ("r-assertive-reflection" ,r-assertive-reflection)
11867 ("r-assertive-sets" ,r-assertive-sets)
11868 ("r-assertive-strings" ,r-assertive-strings)
11869 ("r-assertive-types" ,r-assertive-types)
11870 ("r-knitr" ,r-knitr)))
11872 `(("r-knitr" ,r-knitr)))
11873 (home-page "https://bitbucket.org/richierocks/assertive")
11874 (synopsis "Readable check functions to ensure code integrity")
11876 "This package provides lots of predicates (@code{is_*} functions) to
11877 check the state of your variables, and assertions (@code{assert_*} functions)
11878 to throw errors if they aren't in the right form.")
11879 (license license:gpl3+)))
11881 (define-public r-dotcall64
11883 (name "r-dotcall64")
11888 (uri (cran-uri "dotCall64" version))
11891 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11892 (properties `((upstream-name . "dotCall64")))
11893 (build-system r-build-system)
11894 (native-inputs `(("gfortran" ,gfortran)))
11895 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11896 (synopsis "Enhanced foreign function interface supporting long vectors")
11898 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11899 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11900 supports long vectors, arguments of type 64-bit integer, and provides a
11901 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11902 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11903 (license license:gpl2+)))
11905 (define-public r-spam
11912 (uri (cran-uri "spam" version))
11914 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11915 (build-system r-build-system)
11917 `(("r-dotcall64" ,r-dotcall64)))
11918 (native-inputs `(("gfortran" ,gfortran)))
11919 (home-page "https://www.math.uzh.ch/pages/spam/")
11920 (synopsis "Sparse matrix algebra")
11922 "This package provides a set of functions for sparse matrix algebra.
11923 Differences with other sparse matrix packages are:
11926 @item it only supports (essentially) one sparse matrix format;
11927 @item it is based on transparent and simple structure(s);
11928 @item it is tailored for MCMC calculations within G(M)RF;
11929 @item and it is fast and scalable (with the extension package @code{spam64}).
11931 ;; Either of these licenses
11932 (license (list license:bsd-3 license:lgpl2.0))))
11934 (define-public r-fields
11941 (uri (cran-uri "fields" version))
11943 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11944 (build-system r-build-system)
11946 `(("r-maps" ,r-maps)
11947 ("r-spam" ,r-spam)))
11949 `(("gfortran" ,gfortran)))
11950 (home-page "https://www.image.ucar.edu/fields")
11951 (synopsis "Tools for spatial data")
11953 "This is a package for curve, surface and function fitting with an
11954 emphasis on splines, spatial data and spatial statistics. The major methods
11955 include cubic, and thin plate splines, Kriging, and compactly supported
11956 covariance functions for large data sets.")
11957 (license license:gpl2+)))
11959 (define-public r-spatialextremes
11961 (name "r-spatialextremes")
11966 (uri (cran-uri "SpatialExtremes" version))
11969 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11971 `((upstream-name . "SpatialExtremes")))
11972 (build-system r-build-system)
11974 `(("r-fields" ,r-fields)
11975 ("r-maps" ,r-maps)))
11976 (home-page "http://spatialextremes.r-forge.r-project.org/")
11977 (synopsis "Modelling spatial extremes")
11979 "This package provides tools for the statistical modelling of spatial
11980 extremes using max-stable processes, copula or Bayesian hierarchical models.
11981 More precisely, this package allows (conditional) simulations from various
11982 parametric max-stable models, analysis of the extremal spatial dependence, the
11983 fitting of such processes using composite likelihoods or least square (simple
11984 max-stable processes only), model checking and selection and prediction.")
11985 (license license:gpl2+)))
11987 (define-public r-drc
11994 (uri (cran-uri "drc" version))
11997 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11998 (build-system r-build-system)
12001 ("r-gtools" ,r-gtools)
12003 ("r-multcomp" ,r-multcomp)
12004 ("r-plotrix" ,r-plotrix)
12005 ("r-scales" ,r-scales)))
12006 (home-page "https://cran.r-project.org/web/packages/drc")
12007 (synopsis "Analysis of dose-response curves")
12009 "This package provides a suite of flexible and versatile model fitting
12010 and after-fitting functions for the analysis of dose-response data.")
12011 (license license:gpl2+)))
12013 (define-public r-rmeta
12020 (uri (cran-uri "rmeta" version))
12023 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12024 (build-system r-build-system)
12025 (home-page "https://cran.r-project.org/web/packages/rmeta")
12026 (synopsis "Tools for meta-analysis")
12028 "This package provides functions for simple fixed and random effects
12029 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12030 draws standard summary plots, funnel plots, and computes summaries and tests
12031 for association and heterogeneity.")
12032 (license license:gpl2)))
12034 (define-public r-bootstrap
12036 (name "r-bootstrap")
12041 (uri (cran-uri "bootstrap" version))
12044 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12045 (build-system r-build-system)
12046 (native-inputs `(("gfortran" ,gfortran)))
12047 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12048 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12050 "This package provides software and data for the book \"An Introduction
12051 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12052 This package is primarily provided for projects already based on it, and for
12053 support of the book. New projects should preferentially use the recommended
12054 package \"boot\".")
12055 (license license:bsd-3)))
12057 (define-public r-survivalroc
12059 (name "r-survivalroc")
12064 (uri (cran-uri "survivalROC" version))
12067 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12068 (properties `((upstream-name . "survivalROC")))
12069 (build-system r-build-system)
12070 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12071 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12073 "Compute time-dependent ROC curve from censored survival data using
12074 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12075 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12076 (license license:gpl2+)))
12078 (define-public r-longitudinal
12080 (name "r-longitudinal")
12085 (uri (cran-uri "longitudinal" version))
12088 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12089 (build-system r-build-system)
12090 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12091 (home-page "http://strimmerlab.org/software/longitudinal/")
12092 (synopsis "Analysis of multiple time course data")
12094 "This package contains general data structures and functions for
12095 longitudinal data with multiple variables, repeated measurements, and
12096 irregularly spaced time points. It also implements a shrinkage estimator of
12097 dynamical correlation and dynamical covariance.")
12098 (license license:gpl3+)))
12100 (define-public r-genenet
12107 (uri (cran-uri "GeneNet" version))
12110 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12111 (properties `((upstream-name . "GeneNet")))
12112 (build-system r-build-system)
12114 `(("r-corpcor" ,r-corpcor)
12115 ("r-fdrtool" ,r-fdrtool)
12116 ("r-longitudinal" ,r-longitudinal)))
12117 (home-page "http://strimmerlab.org/software/genenet/")
12118 (synopsis "Modeling and inferring gene networks")
12120 "This package analyzes gene expression (time series) data with focus on
12121 the inference of gene networks. In particular, GeneNet implements the methods
12122 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12123 for learning large-scale gene association networks (including assignment of
12124 putative directions).")
12125 (license license:gpl3+)))
12127 (define-public r-rbamtools
12129 (name "r-rbamtools")
12130 (version "2.16.17")
12134 (uri (cran-uri "rbamtools" version))
12137 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12138 (build-system r-build-system)
12139 (inputs `(("zlib" ,zlib)))
12141 `(("r-refgenome" ,r-refgenome)))
12142 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12143 (synopsis "Read and write BAM (binary alignment) files")
12145 "This package provides an R interface to functions of the SAMtools
12147 (license license:artistic2.0)))
12149 (define-public r-protviz
12156 (uri (cran-uri "protViz" version))
12159 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12160 (properties `((upstream-name . "protViz")))
12161 (build-system r-build-system)
12162 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12163 (home-page "https://github.com/protViz/protViz/")
12164 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12166 "This package helps with quality checks, visualizations and analysis of
12167 mass spectrometry data, coming from proteomics experiments. The package is
12168 developed, tested and used at the Functional Genomics Center Zurich, where it
12169 is used mainly for prototyping, teaching, and having fun with proteomics data.
12170 But it can also be used to do data analysis for small scale data sets.")
12171 (license license:gpl3)))
12173 (define-public r-cmprsk
12180 (uri (cran-uri "cmprsk" version))
12182 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12183 (build-system r-build-system)
12185 `(("r-survival" ,r-survival)))
12187 `(("gfortran" ,gfortran)))
12188 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12189 (synopsis "Subdistribution analysis of competing risks")
12191 "This package provides tool for estimation, testing and regression
12192 modeling of subdistribution functions in competing risks, as described in
12193 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12194 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12195 A proportional hazards model for the subdistribution of a competing risk,
12196 JASA, 94:496-509.")
12197 (license license:gpl2+)))
12199 (define-public r-etm
12206 (uri (cran-uri "etm" version))
12209 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12210 (build-system r-build-system)
12212 `(("r-data-table" ,r-data-table)
12213 ("r-lattice" ,r-lattice)
12215 ("r-rcpparmadillo" ,r-rcpparmadillo)
12216 ("r-survival" ,r-survival)))
12217 (home-page "https://cran.r-project.org/web/packages/etm")
12218 (synopsis "Empirical transition matrix")
12220 "The @dfn{empirical transition matrix} (etm) package estimates
12221 the matrix of transition probabilities for any time-inhomogeneous multistate
12222 model with finite state space using the Aalen-Johansen estimator.")
12223 (license license:expat)))
12225 (define-public r-epi
12232 (uri (cran-uri "Epi" version))
12235 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12236 (properties `((upstream-name . "Epi")))
12237 (build-system r-build-system)
12239 `(("r-cmprsk" ,r-cmprsk)
12240 ("r-data-table" ,r-data-table)
12243 ("r-matrix" ,r-matrix)
12245 ("r-numderiv" ,r-numderiv)
12247 ("r-survival" ,r-survival)
12249 (home-page "https://BendixCarstensen.com/Epi/")
12250 (synopsis "Statistical analysis in epidemiology")
12252 "This package provides functions for demographic and epidemiological
12253 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12254 particular representation, manipulation and simulation of multistate data -
12255 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12256 @code{etm} and @code{cmprsk} packages. It also contains functions for
12257 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12258 data and some useful functions for tabulation and plotting, as well as a
12259 number of epidemiological data sets.")
12260 (license license:gpl2)))
12262 (define-public r-ppls
12265 (version "1.6-1.1")
12269 (uri (cran-uri "ppls" version))
12272 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12273 (build-system r-build-system)
12274 (propagated-inputs `(("r-mass" ,r-mass)))
12275 (home-page "https://cran.r-project.org/web/packages/ppls")
12276 (synopsis "Penalized partial least squares")
12278 "This package contains linear and nonlinear regression methods based on
12279 partial least squares and penalization techniques. Model parameters are
12280 selected via cross-validation, and confidence intervals ans tests for the
12281 regression coefficients can be conducted via jackknifing.")
12282 (license license:gpl2+)))
12284 (define-public r-huge
12287 (version "1.3.4.1")
12291 (uri (cran-uri "huge" version))
12293 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12294 (build-system r-build-system)
12296 `(("r-igraph" ,r-igraph)
12298 ("r-matrix" ,r-matrix)
12300 ("r-rcppeigen" ,r-rcppeigen)))
12301 (home-page "https://cran.r-project.org/web/packages/huge")
12302 (synopsis "High-dimensional undirected graph estimation")
12304 "This package provides a general framework for high-dimensional
12305 undirected graph estimation. It integrates data preprocessing, neighborhood
12306 screening, graph estimation, and model selection techniques into a pipeline.")
12307 (license license:gpl2)))
12309 (define-public r-parcor
12316 (uri (cran-uri "parcor" version))
12319 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12320 (build-system r-build-system)
12323 ("r-genenet" ,r-genenet)
12324 ("r-glmnet" ,r-glmnet)
12326 ("r-ppls" ,r-ppls)))
12327 (home-page "https://cran.r-project.org/web/packages/parcor")
12328 (synopsis "Regularized estimation of partial correlation matrices")
12330 "This package estimates the matrix of partial correlations based on
12331 different regularized regression methods: lasso, adaptive lasso, PLS, and
12332 Ridge Regression. In addition, the package provides model selection for
12333 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12334 (license license:gpl2+)))
12336 (define-public r-mcmc
12343 (uri (cran-uri "mcmc" version))
12346 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12347 (build-system r-build-system)
12348 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12349 (synopsis "Markov chain Monte Carlo")
12351 "This package simulates continuous distributions of random vectors using
12352 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12353 function that evaluates the log unnormalized density. Algorithms are random
12354 walk Metropolis algorithm (function @code{metrop}), simulated
12355 tempering (function @code{temper}), and morphometric random walk
12356 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12357 by change of variable.")
12358 (license license:expat)))
12360 (define-public r-listenv
12367 (uri (cran-uri "listenv" version))
12370 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12371 (build-system r-build-system)
12373 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12374 (home-page "https://github.com/HenrikBengtsson/listenv")
12375 (synopsis "Environments behaving (almost) as lists")
12377 "This package implements list environments. List environments are
12378 environments that have list-like properties. For instance, the elements of a
12379 list environment are ordered and can be accessed and iterated over using index
12381 (license license:lgpl2.1+)))
12383 (define-public r-globals
12390 (uri (cran-uri "globals" version))
12393 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12394 (build-system r-build-system)
12396 `(("r-codetools" ,r-codetools)))
12397 (home-page "https://github.com/HenrikBengtsson/globals")
12398 (synopsis "Identify global objects in R expressions")
12400 "This package provides tools to identify global (\"unknown\" or \"free\")
12401 objects in R expressions by code inspection using various strategies, e.g.
12402 conservative or liberal. The objective of this package is to make it as
12403 simple as possible to identify global objects for the purpose of exporting
12404 them in distributed compute environments.")
12405 (license license:lgpl2.1+)))
12407 (define-public r-future
12414 (uri (cran-uri "future" version))
12417 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12418 (build-system r-build-system)
12420 `(("r-digest" ,r-digest)
12421 ("r-globals" ,r-globals)
12422 ("r-listenv" ,r-listenv)))
12424 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12425 (home-page "https://github.com/HenrikBengtsson/future")
12426 (synopsis "Unified parallel and distributed processing in R")
12428 "The purpose of this package is to provide a lightweight and unified
12429 Future API for sequential and parallel processing of R expression via futures.
12430 This package implements sequential, multicore, multisession, and cluster
12431 futures. With these, R expressions can be evaluated on the local machine, in
12432 parallel a set of local machines, or distributed on a mix of local and remote
12433 machines. Extensions to this package implement additional backends for
12434 processing futures via compute cluster schedulers etc. Because of its unified
12435 API, there is no need to modify any code in order to switch from sequential on
12436 the local machine to, say, distributed processing on a remote compute cluster.")
12437 (license license:lgpl2.1+)))
12439 (define-public r-future-apply
12441 (name "r-future-apply")
12446 (uri (cran-uri "future.apply" version))
12449 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12450 (properties `((upstream-name . "future.apply")))
12451 (build-system r-build-system)
12453 `(("r-future" ,r-future)
12454 ("r-globals" ,r-globals)))
12456 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12457 (home-page "https://github.com/HenrikBengtsson/future.apply")
12458 (synopsis "Apply function to elements in parallel using futures")
12460 "This package provides implementations of @code{apply()},
12461 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12462 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12463 can be resolved using any future-supported backend, e.g. parallel on the local
12464 machine or distributed on a compute cluster.")
12465 (license license:gpl2+)))
12467 (define-public r-rsvd
12474 (uri (cran-uri "rsvd" version))
12477 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12478 (build-system r-build-system)
12480 `(("r-matrix" ,r-matrix)))
12481 (home-page "https://github.com/erichson/rSVD")
12482 (synopsis "Randomized singular value decomposition")
12484 "Low-rank matrix decompositions are fundamental tools and widely used for
12485 data analysis, dimension reduction, and data compression. Classically, highly
12486 accurate deterministic matrix algorithms are used for this task. However, the
12487 emergence of large-scale data has severely challenged our computational
12488 ability to analyze big data. The concept of randomness has been demonstrated
12489 as an effective strategy to quickly produce approximate answers to familiar
12490 problems such as the @dfn{singular value decomposition} (SVD). This package
12491 provides several randomized matrix algorithms such as the randomized singular
12492 value decomposition (@code{rsvd}), randomized principal component
12493 analysis (@code{rpca}), randomized robust principal component
12494 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12495 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12496 functions are provided.")
12497 (license license:gpl3+)))
12499 (define-public r-sloop
12506 (uri (cran-uri "sloop" version))
12509 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12510 (build-system r-build-system)
12512 `(("r-codetools" ,r-codetools)
12513 ("r-crayon" ,r-crayon)
12514 ("r-purrr" ,r-purrr)
12515 ("r-rlang" ,r-rlang)
12516 ("r-tibble" ,r-tibble)))
12517 (home-page "https://github.com/r-lib/sloop")
12518 (synopsis "Helpers for object-oriented programming in R")
12520 "This package provides a collection of helper functions designed to
12521 help you to better understand object oriented programming in R, particularly
12523 (license license:gpl3)))
12525 (define-public r-capushe
12532 (uri (cran-uri "capushe" version))
12535 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12536 (build-system r-build-system)
12537 (propagated-inputs `(("r-mass" ,r-mass)))
12538 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12539 (synopsis "Calibrating penalties using slope heuristics")
12541 "This package provides tools for the calibration of penalized criteria
12542 for model selection. The calibration methods available are based on the slope
12544 (license license:gpl2+)))
12546 (define-public r-dorng
12553 (uri (cran-uri "doRNG" version))
12556 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12557 (properties `((upstream-name . "doRNG")))
12558 (build-system r-build-system)
12560 `(("r-foreach" ,r-foreach)
12561 ("r-iterators" ,r-iterators)
12562 ("r-rngtools" ,r-rngtools)))
12563 (home-page "https://renozao.github.io/doRNG/")
12564 (synopsis "Generic reproducible parallel backend for foreach loops")
12566 "This package provides functions to perform reproducible parallel
12567 @code{foreach} loops, using independent random streams as generated by
12568 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12569 convert standard @code{%dopar%} loops into fully reproducible loops,
12570 independently of the number of workers, the task scheduling strategy, or the
12571 chosen parallel environment and associated foreach backend.")
12572 (license license:gpl2+)))
12574 (define-public r-blockmodeling
12576 (name "r-blockmodeling")
12581 (uri (cran-uri "blockmodeling" version))
12584 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12585 (build-system r-build-system)
12587 `(("r-matrix" ,r-matrix)))
12588 (native-inputs `(("gfortran" ,gfortran)))
12589 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12590 (synopsis "Generalized and classical blockmodeling of valued networks")
12592 "This package is primarily meant as an implementation of generalized
12593 blockmodeling for valued networks. In addition, measures of similarity or
12594 dissimilarity based on structural equivalence and regular equivalence (REGE
12595 algorithms) can be computed and partitioned matrices can be plotted.")
12596 (license license:gpl2+)))
12598 (define-public r-upsetr
12605 (uri (cran-uri "UpSetR" version))
12608 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12609 (properties `((upstream-name . "UpSetR")))
12610 (build-system r-build-system)
12612 `(("r-ggplot2" ,r-ggplot2)
12613 ("r-gridextra" ,r-gridextra)
12615 ("r-scales" ,r-scales)))
12616 (home-page "https://github.com/hms-dbmi/UpSetR")
12617 (synopsis "Visualize intersecting sets")
12619 "This package provides a more scalable alternative to Venn and Euler
12620 diagrams for visualizing intersecting sets. Create visualizations of
12621 intersecting sets using a novel matrix design, along with visualizations of
12622 several common set, element and attribute related tasks.")
12623 (license license:expat)))
12625 ;; This package includes a JavaScript file, which is not minified. When
12626 ;; upgrading please check that there are no new minified JavaScript files.
12627 (define-public r-shinybs
12634 (uri (cran-uri "shinyBS" version))
12637 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12638 (properties `((upstream-name . "shinyBS")))
12639 (build-system r-build-system)
12640 ;; The tests spawn Shiny browser apps. They cannot be run
12641 ;; non-interactively.
12642 (arguments '(#:tests? #f))
12644 `(("r-htmltools" ,r-htmltools)
12645 ("r-shiny" ,r-shiny)))
12646 (home-page "https://ebailey78.github.io/shinyBS/")
12647 (synopsis "Twitter Bootstrap components for Shiny")
12649 "This package adds additional Twitter Bootstrap components to Shiny.")
12650 (license license:gpl3)))
12652 (define-public r-outliers
12654 (name "r-outliers")
12659 (uri (cran-uri "outliers" version))
12662 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12663 (build-system r-build-system)
12664 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12665 (synopsis "Tests for outliers")
12667 "This package provides a collection of some tests commonly used for
12668 identifying outliers.")
12669 (license license:gpl2+)))
12671 (define-public r-bayesm
12678 (uri (cran-uri "bayesm" version))
12680 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12681 (build-system r-build-system)
12683 `(("r-rcpp" ,r-rcpp)
12684 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12685 (home-page "http://www.perossi.org/home/bsm-1")
12686 (synopsis "Bayesian inference for marketing/micro-econometrics")
12688 "This package covers many important models used in marketing and
12689 micro-econometrics applications, including Bayes Regression (univariate or
12690 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12691 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12692 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12693 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12694 Estimation with normal base, Hierarchical Linear Models with normal prior and
12695 covariates, Hierarchical Linear Models with a mixture of normals prior and
12696 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12697 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12698 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12699 analysis of choice-based conjoint data, Bayesian treatment of linear
12700 instrumental variables models, Analysis of Multivariate Ordinal survey data
12701 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12702 Coefficient Logit Models.")
12703 (license license:gpl2+)))
12705 (define-public r-tensora
12712 (uri (cran-uri "tensorA" version))
12715 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12716 (properties `((upstream-name . "tensorA")))
12717 (build-system r-build-system)
12718 (home-page "http://www.stat.boogaart.de/tensorA")
12719 (synopsis "Advanced tensor arithmetic with named indices")
12721 "This package provides convenience functions for advanced linear algebra
12722 with tensors and computation with datasets of tensors on a higher level
12723 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12724 co- and contravariate indices, and parallel computations on sequences of
12726 (license license:gpl2+)))
12728 (define-public r-rarpack
12735 (uri (cran-uri "rARPACK" version))
12738 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12739 (properties `((upstream-name . "rARPACK")))
12740 (build-system r-build-system)
12741 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12742 (home-page "https://github.com/yixuan/rARPACK")
12743 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12745 "This package was previously an R wrapper of the ARPACK library, and now
12746 a shell of the R package RSpectra, an R interface to the Spectra library for
12747 solving large scale eigenvalue/vector problems. The current version of
12748 rARPACK simply imports and exports the functions provided by RSpectra. New
12749 users of rARPACK are advised to switch to the RSpectra package.")
12750 (license license:bsd-3)))
12752 (define-public r-compositions
12754 (name "r-compositions")
12759 (uri (cran-uri "compositions" version))
12762 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12763 (build-system r-build-system)
12765 `(("r-bayesm" ,r-bayesm)
12767 ("r-robustbase" ,r-robustbase)
12768 ("r-tensora" ,r-tensora)))
12770 `(("r-knitr" ,r-knitr)))
12771 (home-page "http://www.stat.boogaart.de/compositions")
12772 (synopsis "Compositional data analysis")
12774 "This package provides functions for the consistent analysis of
12775 compositional data (e.g. portions of substances) and positive
12776 numbers (e.g. concentrations).")
12777 (license license:gpl2+)))
12779 (define-public r-cobs
12786 (uri (cran-uri "cobs" version))
12789 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12790 (build-system r-build-system)
12792 `(("r-quantreg" ,r-quantreg)
12793 ("r-sparsem" ,r-sparsem)))
12794 (home-page "https://cran.r-project.org/web/packages/cobs")
12795 (synopsis "Constrained B-Splines (sparse matrix based)")
12797 "This package provides qualitatively constrained (regression) smoothing
12798 splines via linear programming and sparse matrices.")
12799 (license license:gpl2+)))
12801 (define-public r-drimpute
12803 (name "r-drimpute")
12808 (uri (cran-uri "DrImpute" version))
12811 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12812 (properties `((upstream-name . "DrImpute")))
12813 (build-system r-build-system)
12815 `(("r-rcpp" ,r-rcpp)
12816 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12817 (home-page "https://github.com/ikwak2/DrImpute")
12818 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12820 "This is an R package for imputing dropout events. Many statistical
12821 methods in cell type identification, visualization and lineage reconstruction
12822 do not account for dropout events. DrImpute can improve the performance of
12823 such software by imputing dropout events.")
12824 (license license:gpl3)))
12826 (define-public r-gamlss-dist
12828 (name "r-gamlss-dist")
12833 (uri (cran-uri "gamlss.dist" version))
12835 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12836 (properties `((upstream-name . "gamlss.dist")))
12837 (build-system r-build-system)
12838 (propagated-inputs `(("r-mass" ,r-mass)))
12839 (home-page "http://www.gamlss.org/")
12840 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12842 "This package provides a set of distributions which can be used for
12843 modelling the response variables in Generalized Additive Models for Location
12844 Scale and Shape. The distributions can be continuous, discrete or mixed
12845 distributions. Extra distributions can be created, by transforming, any
12846 continuous distribution defined on the real line, to a distribution defined on
12847 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12848 transformation, respectively.")
12849 ;; Either version of the GPL.
12850 (license (list license:gpl2 license:gpl3))))
12852 ;; This package includes JavaScript files, which are not minified. When
12853 ;; upgrading please check that there are no new minified JavaScript files.
12854 (define-public r-shinyjs
12861 (uri (cran-uri "shinyjs" version))
12864 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12865 (build-system r-build-system)
12867 `(("r-digest" ,r-digest)
12868 ("r-htmltools" ,r-htmltools)
12869 ("r-jsonlite" ,r-jsonlite)
12870 ("r-shiny" ,r-shiny)))
12871 (home-page "https://deanattali.com/shinyjs")
12872 (synopsis "Improve the user experience of your Shiny apps")
12874 "Perform common useful JavaScript operations in Shiny apps that will
12875 greatly improve your apps without having to know any JavaScript. Examples
12876 include: hiding an element, disabling an input, resetting an input back to its
12877 original value, delaying code execution by a few seconds, and many more useful
12878 functions for both the end user and the developer. Shinyjs can also be used
12879 to easily call your own custom JavaScript functions from R.")
12880 (license license:agpl3+)))
12882 ;; This package includes minified JavaScript files. When upgrading please
12883 ;; check that there are no new minified JavaScript files.
12884 (define-public r-colourpicker
12886 (name "r-colourpicker")
12891 (uri (cran-uri "colourpicker" version))
12894 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12895 (build-system r-build-system)
12897 `(#:modules ((guix build utils)
12898 (guix build r-build-system)
12902 (modify-phases %standard-phases
12903 (add-after 'unpack 'process-javascript
12904 (lambda* (#:key inputs #:allow-other-keys)
12905 (with-directory-excursion "inst"
12909 `((,(assoc-ref inputs "js-salvattore")
12910 "examples/colourInput/www/salvattore.min.js")
12911 (,(assoc-ref inputs "js-jquery")
12912 "htmlwidgets/lib/jquery/jquery.min.js")
12913 ("www/shared/colourpicker/js/colourpicker.js"
12914 "www/shared/colourpicker/js/colourpicker.min.js"))))
12915 (lambda (sources targets)
12916 (for-each (lambda (source target)
12917 (format #t "Processing ~a --> ~a~%"
12919 (delete-file target)
12920 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12921 (call-with-output-file target
12923 (dump-port minified port)))))
12924 sources targets))))
12927 `(("r-ggplot2" ,r-ggplot2)
12928 ("r-htmltools" ,r-htmltools)
12929 ("r-htmlwidgets" ,r-htmlwidgets)
12930 ("r-jsonlite" ,r-jsonlite)
12931 ("r-miniui" ,r-miniui)
12932 ("r-shiny" ,r-shiny)
12933 ("r-shinyjs" ,r-shinyjs)))
12935 `(("uglify-js" ,uglify-js)
12939 (uri "https://code.jquery.com/jquery-3.3.1.js")
12942 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12946 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12949 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12950 (home-page "https://github.com/daattali/colourpicker")
12951 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12953 "This package provides a color picker that can be used as an input in
12954 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12955 custom color palettes, and many more options. A plot color helper tool is
12956 available as an RStudio Addin, which helps you pick colors to use in your
12957 plots. A more generic color picker RStudio Addin is also provided to let you
12958 select colors to use in your R code.")
12959 (license license:expat)))
12961 (define-public r-ggextra
12968 (uri (cran-uri "ggExtra" version))
12971 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12972 (properties `((upstream-name . "ggExtra")))
12973 (build-system r-build-system)
12975 `(("r-colourpicker" ,r-colourpicker)
12976 ("r-ggplot2" ,r-ggplot2)
12977 ("r-gtable" ,r-gtable)
12978 ("r-miniui" ,r-miniui)
12980 ("r-scales" ,r-scales)
12981 ("r-shiny" ,r-shiny)
12982 ("r-shinyjs" ,r-shinyjs)))
12984 `(("r-knitr" ,r-knitr)))
12985 (home-page "https://github.com/daattali/ggExtra")
12986 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12988 "This package is a collection of functions and layers to enhance ggplot2.
12989 The flagship function is @code{ggMarginal()}, which can be used to add
12990 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12991 (license license:expat)))
12993 (define-public r-minpack-lm
12995 (name "r-minpack-lm")
13000 (uri (cran-uri "minpack.lm" version))
13003 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13004 (properties `((upstream-name . "minpack.lm")))
13005 (build-system r-build-system)
13006 (native-inputs `(("gfortran" ,gfortran)))
13007 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13008 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13010 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13011 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13012 problems by a modification of the Levenberg-Marquardt algorithm, with support
13013 for lower and upper parameter bounds. The implementation can be used via
13014 @code{nls}-like calls using the @code{nlsLM} function.")
13015 (license license:gpl3)))
13017 (define-public r-moments
13024 (uri (cran-uri "moments" version))
13027 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13028 (build-system r-build-system)
13029 (home-page "https://cran.r-project.org/web/packages/moments")
13030 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13032 "This package provides functions to calculate: moments, Pearson's
13033 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13034 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13035 (license license:gpl2+)))
13037 (define-public r-msir
13044 (uri (cran-uri "msir" version))
13047 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13048 (build-system r-build-system)
13050 `(("r-mclust" ,r-mclust)))
13051 (home-page "https://cran.r-project.org/web/packages/msir")
13052 (synopsis "Model-based sliced inverse regression")
13054 "This is an R package for dimension reduction based on finite Gaussian
13055 mixture modeling of inverse regression.")
13056 (license license:gpl2+)))
13058 (define-public r-pbivnorm
13060 (name "r-pbivnorm")
13065 (uri (cran-uri "pbivnorm" version))
13068 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13069 (build-system r-build-system)
13070 (native-inputs `(("gfortran" ,gfortran)))
13071 (home-page "https://github.com/brentonk/pbivnorm")
13072 (synopsis "Vectorized bivariate normal CDF")
13074 "This package provides a vectorized R function for calculating
13075 probabilities from a standard bivariate normal CDF.")
13076 (license license:gpl2+)))
13078 (define-public r-lavaan
13085 (uri (cran-uri "lavaan" version))
13088 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13089 (build-system r-build-system)
13091 `(("r-mass" ,r-mass)
13092 ("r-mnormt" ,r-mnormt)
13093 ("r-numderiv" ,r-numderiv)
13094 ("r-pbivnorm" ,r-pbivnorm)))
13095 (home-page "http://lavaan.ugent.be")
13096 (synopsis "Latent variable analysis")
13098 "This package provides tools to fit a variety of latent variable models,
13099 including confirmatory factor analysis, structural equation modeling and
13100 latent growth curve models.")
13101 (license license:gpl2+)))
13103 (define-public r-nonnest2
13105 (name "r-nonnest2")
13110 (uri (cran-uri "nonnest2" version))
13113 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13114 (build-system r-build-system)
13116 `(("r-compquadform" ,r-compquadform)
13117 ("r-lavaan" ,r-lavaan)
13118 ("r-mvtnorm" ,r-mvtnorm)
13119 ("r-sandwich" ,r-sandwich)))
13121 `(("r-knitr" ,r-knitr)))
13122 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13123 (synopsis "Tests of non-nested models")
13125 "This package allows for testing of non-nested models. It includes tests
13126 of model distinguishability and of model fit that can be applied to both
13127 nested and non-nested models. The package also includes functionality to
13128 obtain confidence intervals associated with AIC and BIC.")
13129 ;; Either version of the GPL.
13130 (license (list license:gpl2 license:gpl3))))
13132 (define-public r-penalized
13134 (name "r-penalized")
13139 (uri (cran-uri "penalized" version))
13142 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13143 (build-system r-build-system)
13145 `(("r-rcpp" ,r-rcpp)
13146 ("r-rcpparmadillo" ,r-rcpparmadillo)
13147 ("r-survival" ,r-survival)))
13148 (home-page "https://cran.r-project.org/web/packages/penalized/")
13149 (synopsis "Penalized estimation in GLMs and in the Cox model")
13151 "This package provides tools for fitting possibly high dimensional
13152 penalized regression models. The penalty structure can be any combination of
13153 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13154 constraint on the regression coefficients. The supported regression models
13155 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13156 model. Cross-validation routines allow optimization of the tuning
13158 (license license:gpl2+)))
13160 (define-public r-zim
13167 (uri (cran-uri "ZIM" version))
13170 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13171 (properties `((upstream-name . "ZIM")))
13172 (build-system r-build-system)
13173 (propagated-inputs `(("r-mass" ,r-mass)))
13174 (home-page "https://github.com/biostatstudio/ZIM")
13175 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13177 "Analyze count time series with excess zeros. Two types of statistical
13178 models are supported: Markov regression and state-space models. They are also
13179 known as observation-driven and parameter-driven models respectively in the
13180 time series literature. The functions used for Markov regression or
13181 observation-driven models can also be used to fit ordinary regression models
13182 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13183 negative binomial (ZINB) assumption. The package also contains miscellaneous
13184 functions to compute density, distribution, quantile, and generate random
13185 numbers from ZIP and ZINB distributions.")
13186 (license license:gpl3)))
13188 (define-public r-nor1mix
13195 (uri (cran-uri "nor1mix" version))
13198 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13199 (build-system r-build-system)
13200 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13201 (synopsis "Normal (1-d) mixture models")
13203 "This package provides S3 classes and methods for one-dimensional normal
13204 mixture models, for, e.g., density estimation or clustering algorithms
13205 research and teaching; it provides the widely used Marron-Wand densities. It
13206 also provides tools for efficient random number generation and graphics.")
13207 (license license:gpl2+)))
13209 (define-public r-beanplot
13211 (name "r-beanplot")
13216 (uri (cran-uri "beanplot" version))
13219 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13220 (build-system r-build-system)
13221 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13222 (synopsis "Visualization via beanplots")
13224 "This package provides beanplots, an alternative to
13225 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13227 (license license:gpl2)))
13229 (define-public r-pbdzmq
13236 (uri (cran-uri "pbdZMQ" version))
13239 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13240 (properties `((upstream-name . "pbdZMQ")))
13241 (build-system r-build-system)
13243 `(("zeromq" ,zeromq)
13246 `(("pkg-config" ,pkg-config)))
13247 (home-page "https://pbdr.org/")
13248 (synopsis "R interface to ZeroMQ")
13250 "ZeroMQ is a well-known library for high-performance asynchronous
13251 messaging in scalable, distributed applications. This package provides high
13252 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13253 interactive client/server programming frameworks. A few wrapper functions
13254 compatible with @code{rzmq} are also provided.")
13255 (license license:gpl3)))
13257 (define-public r-repr
13264 (uri (cran-uri "repr" version))
13267 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13268 (build-system r-build-system)
13270 `(("r-base64enc" ,r-base64enc)
13271 ("r-htmltools" ,r-htmltools)
13272 ("r-jsonlite" ,r-jsonlite)
13273 ("r-pillar" ,r-pillar)))
13274 (home-page "https://cran.r-project.org/web/packages/repr/")
13275 (synopsis "Serializable representations")
13277 "This package provides string and binary representations of objects for
13278 several formats and MIME types.")
13279 (license license:gpl3)))
13281 (define-public r-irdisplay
13283 (name "r-irdisplay")
13288 (uri (cran-uri "IRdisplay" version))
13291 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13292 (properties `((upstream-name . "IRdisplay")))
13293 (build-system r-build-system)
13295 `(("r-repr" ,r-repr)))
13296 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13297 (synopsis "Jupyter display machinery")
13299 "This package provides an interface to the rich display capabilities of
13300 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13301 running IRkernel session.")
13302 (license license:expat)))
13304 (define-public r-irkernel
13306 (name "r-irkernel")
13311 (uri (cran-uri "IRkernel" version))
13314 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13315 (properties `((upstream-name . "IRkernel")))
13316 (build-system r-build-system)
13319 (modify-phases %standard-phases
13320 (add-after 'install 'install-kernelspec
13321 (lambda* (#:key outputs #:allow-other-keys)
13322 (let ((out (assoc-ref outputs "out")))
13323 (setenv "HOME" "/tmp")
13324 (invoke "jupyter" "kernelspec" "install"
13327 (string-append out "/site-library/IRkernel/kernelspec"))
13328 ;; Record the absolute file name of the 'R' executable in
13330 (substitute* (string-append out "/share/jupyter"
13331 "/kernels/ir/kernel.json")
13333 (string-append "[\"" (which "R") "\",")))
13336 `(("jupyter" ,jupyter)))
13338 `(("r-crayon" ,r-crayon)
13339 ("r-digest" ,r-digest)
13340 ("r-evaluate" ,r-evaluate)
13341 ("r-irdisplay" ,r-irdisplay)
13342 ("r-jsonlite" ,r-jsonlite)
13343 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13344 ("r-minimal" ,r-minimal)
13345 ("r-pbdzmq" ,r-pbdzmq)
13347 ("r-uuid" ,r-uuid)))
13348 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13349 (synopsis "Native R kernel for Jupyter")
13351 "The R kernel for the Jupyter environment executes R code which the
13352 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13354 (license license:expat)))
13356 (define-public r-gmodels
13363 (uri (cran-uri "gmodels" version))
13366 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13367 (build-system r-build-system)
13369 `(("r-gdata" ,r-gdata)
13370 ("r-mass" ,r-mass)))
13371 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13372 (synopsis "Various R programming tools for model fitting")
13374 "This package provides various R programming tools for model fitting.")
13375 (license license:gpl2)))
13377 (define-public r-apcluster
13379 (name "r-apcluster")
13384 (uri (cran-uri "apcluster" version))
13387 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13388 (build-system r-build-system)
13390 `(("r-matrix" ,r-matrix)
13391 ("r-rcpp" ,r-rcpp)))
13392 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13393 (synopsis "Affinity propagation clustering")
13395 "This package implements affinity propagation clustering introduced by
13396 Frey and Dueck (2007). The package further provides leveraged affinity
13397 propagation and an algorithm for exemplar-based agglomerative clustering that
13398 can also be used to join clusters obtained from affinity propagation. Various
13399 plotting functions are available for analyzing clustering results.")
13400 (license license:gpl2+)))
13402 (define-public r-valr
13409 (uri (cran-uri "valr" version))
13412 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13413 (build-system r-build-system)
13415 `(("r-broom" ,r-broom)
13416 ("r-dplyr" ,r-dplyr)
13417 ("r-ggplot2" ,r-ggplot2)
13419 ("r-readr" ,r-readr)
13420 ("r-rlang" ,r-rlang)
13421 ("r-stringr" ,r-stringr)
13422 ("r-tibble" ,r-tibble)))
13424 `(("r-knitr" ,r-knitr)))
13425 (home-page "https://github.com/rnabioco/valr")
13426 (synopsis "Genome interval arithmetic in R")
13428 "This package enables you to read and manipulate genome intervals and
13429 signals. It provides functionality similar to command-line tool suites within
13430 R, enabling interactive analysis and visualization of genome-scale data.")
13431 (license license:expat)))
13433 (define-public r-rematch2
13435 (name "r-rematch2")
13440 (uri (cran-uri "rematch2" version))
13443 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13444 (build-system r-build-system)
13446 `(("r-tibble" ,r-tibble)))
13447 (home-page "https://github.com/r-lib/rematch2")
13448 (synopsis "Tidy output from regular expression matching")
13450 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13451 return the match results in tidy data frames.")
13452 (license license:expat)))
13454 (define-public r-picante
13461 (uri (cran-uri "picante" version))
13464 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13465 (build-system r-build-system)
13469 ("r-vegan" ,r-vegan)))
13470 (home-page "https://cran.r-project.org/web/packages/picante/")
13471 (synopsis "Integrating phylogenies and ecology")
13473 "This package provides functions for phylocom integration, community
13474 analyses, null-models, traits and evolution. It implements numerous
13475 ecophylogenetic approaches including measures of community phylogenetic and
13476 trait diversity, phylogenetic signal, estimation of trait values for
13477 unobserved taxa, null models for community and phylogeny randomizations, and
13478 utility functions for data input/output and phylogeny plotting. A full
13479 description of package functionality and methods are provided by Kembel et
13481 (license license:gpl2)))
13483 (define-public r-reinforcelearn
13485 (name "r-reinforcelearn")
13490 (uri (cran-uri "reinforcelearn" version))
13493 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13494 (build-system r-build-system)
13496 `(("r-checkmate" ,r-checkmate)
13498 ("r-purrr" ,r-purrr)
13500 (home-page "https://markusdumke.github.io/reinforcelearn")
13501 (synopsis "Reinforcement learning")
13503 "This package implements reinforcement learning environments and
13504 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13505 can be used with function approximation, eligibility traces (Singh & Sutton,
13506 1996) and experience replay (Mnih et al., 2013).")
13507 (license license:expat)))
13509 (define-public r-lemon
13516 (uri (cran-uri "lemon" version))
13519 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13520 (build-system r-build-system)
13522 `(("r-ggplot2" ,r-ggplot2)
13523 ("r-gridextra" ,r-gridextra)
13524 ("r-gtable" ,r-gtable)
13525 ("r-knitr" ,r-knitr)
13526 ("r-lattice" ,r-lattice)
13528 ("r-rlang" ,r-rlang)
13529 ("r-scales" ,r-scales)))
13531 `(("r-knitr" ,r-knitr)))
13532 (home-page "https://github.com/stefanedwards/lemon")
13533 (synopsis "Freshen up your ggplot2 plots")
13535 "This package provides functions for working with legends and axis lines
13536 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13538 (license license:gpl3)))
13540 (define-public r-wgaim
13547 (uri (cran-uri "wgaim" version))
13549 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13550 (build-system r-build-system)
13552 `(("r-ggplot2" ,r-ggplot2)
13554 (home-page "https://cran.r-project.org/web/packages/wgaim")
13555 (synopsis "Whole genome average interval mapping for QTL detection")
13557 "This package integrates sophisticated mixed modelling methods with a
13558 whole genome approach to detecting significant QTL in linkage maps.")
13559 (license license:gpl2+)))
13561 (define-public r-bedr
13568 (uri (cran-uri "bedr" version))
13571 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13572 (build-system r-build-system)
13574 `(("r-data-table" ,r-data-table)
13575 ("r-r-utils" ,r-r-utils)
13576 ("r-testthat" ,r-testthat)
13577 ("r-venndiagram" ,r-venndiagram)
13580 ("bedtools" ,bedtools)
13581 ("htslib" ,htslib))) ; for tabix
13583 `(("r-knitr" ,r-knitr))) ; for vignettes
13584 (home-page "https://cran.r-project.org/web/packages/bedr")
13585 (synopsis "Genomic region processing")
13587 "This package is for genomic regions processing using command line tools
13588 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13589 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13590 The bedr package's API enhances access to these tools as well as offers
13591 additional utilities for genomic regions processing.")
13592 (license license:gpl2)))
13594 (define-public r-sets
13601 (uri (cran-uri "sets" version))
13604 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13605 (properties `((upstream-name . "sets")))
13606 (build-system r-build-system)
13607 (home-page "https://cran.r-project.org/web/packages/sets")
13608 (synopsis "Sets, generalized sets, customizable sets and intervals")
13610 "This package provides data structures and basic operations for ordinary
13611 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13612 customizable sets, and intervals.")
13613 (license license:gpl2)))
13615 (define-public r-partitions
13617 (name "r-partitions")
13622 (uri (cran-uri "partitions" version))
13625 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13626 (build-system r-build-system)
13629 ("r-polynom" ,r-polynom)
13630 ("r-sets" ,r-sets)))
13631 (home-page "https://cran.r-project.org/web/packages/partitions")
13632 (synopsis "Additive partitions of integers")
13634 "This package provides tools to enumerates the partitions, unequal
13635 partitions, and restricted partitions of an integer; the three corresponding
13636 partition functions are also given.")
13637 ;; Any version of the GPL
13638 (license license:gpl2+)))
13640 (define-public r-brobdingnag
13642 (name "r-brobdingnag")
13647 (uri (cran-uri "Brobdingnag" version))
13650 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13651 (properties `((upstream-name . "Brobdingnag")))
13652 (build-system r-build-system)
13653 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13654 (synopsis "Very large numbers in R")
13656 "This package handles very large numbers in R. Real numbers are held
13657 using their natural logarithms, plus a logical flag indicating sign. The
13658 package includes a vignette that gives a step-by-step introduction to using S4
13660 ;; Any version of the GPL
13661 (license license:gpl2+)))
13663 (define-public r-untb
13670 (uri (cran-uri "untb" version))
13673 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13674 (build-system r-build-system)
13676 `(("r-brobdingnag" ,r-brobdingnag)
13677 ("r-partitions" ,r-partitions)
13678 ("r-polynom" ,r-polynom)))
13679 (home-page "https://github.com/RobinHankin/untb.git")
13680 (synopsis "Ecological drift under the UNTB")
13682 "This package provides numerical simulations, and visualizations, of
13683 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13684 (license license:gpl2+)))
13686 (define-public r-stepwise
13688 (name "r-stepwise")
13693 (uri (cran-uri "stepwise" version))
13696 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13697 (build-system r-build-system)
13698 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13699 (synopsis "Stepwise detection of recombination breakpoints")
13701 "This package provides a stepwise approach to identifying recombination
13702 breakpoints in a genomic sequence alignment.")
13703 (license license:gpl2+)))
13705 (define-public r-snpmaxsel
13707 (name "r-snpmaxsel")
13712 (uri (cran-uri "SNPmaxsel" version))
13715 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13716 (properties `((upstream-name . "SNPmaxsel")))
13717 (build-system r-build-system)
13719 `(("r-combinat" ,r-combinat)
13720 ("r-mvtnorm" ,r-mvtnorm)))
13721 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13722 (synopsis "Maximally selected statistics for SNP data")
13724 "This package implements asymptotic methods related to maximally selected
13725 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13727 (license license:gpl2+)))
13729 (define-public r-acsnminer
13731 (name "r-acsnminer")
13732 (version "0.16.8.25")
13735 (uri (cran-uri "ACSNMineR" version))
13738 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13739 (properties `((upstream-name . "ACSNMineR")))
13740 (build-system r-build-system)
13742 `(("r-ggplot2" ,r-ggplot2)
13743 ("r-gridextra" ,r-gridextra)))
13744 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13745 (synopsis "Gene enrichment analysis")
13747 "This package provides tools to compute and represent gene set enrichment
13748 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13749 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13750 enrichment can be run with hypergeometric test or Fisher exact test, and can
13751 use multiple corrections. Visualization of data can be done either by
13752 barplots or heatmaps.")
13753 (license license:gpl2+)))
13755 (define-public r-seqinr
13762 (uri (cran-uri "seqinr" version))
13765 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13766 (build-system r-build-system)
13768 `(("r-ade4" ,r-ade4)
13769 ("r-segmented" ,r-segmented)))
13772 (home-page "http://seqinr.r-forge.r-project.org/")
13773 (synopsis "Biological sequences retrieval and analysis")
13775 "This package provides tools for exploratory data analysis and data
13776 visualization of biological sequence (DNA and protein) data. It also includes
13777 utilities for sequence data management under the ACNUC system.")
13778 (license license:gpl2+)))
13780 (define-public r-units
13787 (uri (cran-uri "units" version))
13790 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13791 (build-system r-build-system)
13793 `(("udunits" ,udunits)))
13795 `(("r-rcpp" ,r-rcpp)))
13797 `(("r-knitr" ,r-knitr)))
13798 (home-page "https://github.com/r-quantities/units/")
13799 (synopsis "Measurement Units for R Vectors")
13801 "This package provides support for measurement units in R vectors,
13802 matrices and arrays: automatic propagation, conversion, derivation and
13803 simplification of units; raising errors in case of unit incompatibility. It
13804 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13806 (license license:gpl2)))
13808 (define-public r-classint
13810 (name "r-classint")
13815 (uri (cran-uri "classInt" version))
13818 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13819 (properties `((upstream-name . "classInt")))
13820 (build-system r-build-system)
13822 `(("r-class" ,r-class)
13823 ("r-e1071" ,r-e1071)
13824 ("r-kernsmooth" ,r-kernsmooth)))
13826 `(("gfortran" ,gfortran)
13827 ("r-knitr" ,r-knitr)))
13828 (home-page "https://github.com/r-spatial/classInt/")
13829 (synopsis "Choose univariate class intervals")
13831 "This package provides selected commonly used methods for choosing
13832 univariate class intervals for mapping or other graphics purposes.")
13833 (license license:gpl2+)))
13835 (define-public r-spdata
13842 (uri (cran-uri "spData" version))
13845 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13846 (properties `((upstream-name . "spData")))
13847 (build-system r-build-system)
13849 `(("r-raster" ,r-raster)
13851 (home-page "https://github.com/Nowosad/spData")
13852 (synopsis "Datasets for spatial analysis")
13854 "This a package containing diverse spatial datasets for demonstrating,
13855 benchmarking and teaching spatial data analysis. It includes R data of class
13856 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13857 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13858 of the datasets are designed to illustrate specific analysis techniques.
13859 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13860 illustrate point pattern analysis techniques.")
13861 (license license:cc0)))
13863 (define-public r-learnbayes
13865 (name "r-learnbayes")
13870 (uri (cran-uri "LearnBayes" version))
13873 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13874 (properties `((upstream-name . "LearnBayes")))
13875 (build-system r-build-system)
13876 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13877 (synopsis "Functions for learning Bayesian inference")
13879 "This package provides a collection of functions helpful in learning the
13880 basic tenets of Bayesian statistical inference. It contains functions for
13881 summarizing basic one and two parameter posterior distributions and predictive
13882 distributions. It contains MCMC algorithms for summarizing posterior
13883 distributions defined by the user. It also contains functions for regression
13884 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13886 (license license:gpl2+)))
13888 (define-public r-deldir
13895 (uri (cran-uri "deldir" version))
13898 "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
13899 (build-system r-build-system)
13900 (native-inputs `(("gfortran" ,gfortran)))
13901 (home-page "https://cran.r-project.org/web/packages/deldir")
13902 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13904 "This package provides tools for calculating the Delaunay triangulation
13905 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13906 of a planar point set. It plots triangulations and tessellations in various
13907 ways, clips tessellations to sub-windows, calculates perimeters of
13908 tessellations, and summarizes information about the tiles of the
13910 (license license:gpl2+)))
13912 (define-public r-sf
13919 (uri (cran-uri "sf" version))
13922 "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
13923 (build-system r-build-system)
13930 `(("r-classint" ,r-classint)
13932 ("r-magrittr" ,r-magrittr)
13934 ("r-units" ,r-units)))
13936 `(("pkg-config" ,pkg-config)
13937 ("r-knitr" ,r-knitr)))
13938 (home-page "https://github.com/r-spatial/sf/")
13939 (synopsis "Simple features for R")
13941 "This package provides support for simple features, a standardized way to
13942 encode spatial vector data. It binds to GDAL for reading and writing data, to
13943 GEOS for geometrical operations, and to PROJ for projection conversions and
13944 datum transformations.")
13945 ;; Either of these licenses
13946 (license (list license:gpl2 license:expat))))
13948 (define-public r-spdep
13955 (uri (cran-uri "spdep" version))
13958 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13959 (build-system r-build-system)
13961 `(("r-boot" ,r-boot)
13963 ("r-deldir" ,r-deldir)
13965 ("r-gmodels" ,r-gmodels)
13966 ("r-learnbayes" ,r-learnbayes)
13968 ("r-matrix" ,r-matrix)
13972 ("r-spdata" ,r-spdata)))
13974 `(("r-knitr" ,r-knitr)))
13975 (home-page "https://github.com/r-spatial/spdep/")
13976 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13978 "This package provides a collection of functions to create spatial
13979 weights matrix objects from polygon contiguities, from point patterns by
13980 distance and tessellations, for summarizing these objects, and for permitting
13981 their use in spatial data analysis, including regional aggregation by minimum
13983 (license license:gpl2+)))
13985 (define-public r-adegenet
13987 (name "r-adegenet")
13992 (uri (cran-uri "adegenet" version))
13995 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13996 (build-system r-build-system)
13998 `(("r-ade4" ,r-ade4)
14001 ("r-dplyr" ,r-dplyr)
14002 ("r-ggplot2" ,r-ggplot2)
14003 ("r-igraph" ,r-igraph)
14005 ("r-reshape2" ,r-reshape2)
14006 ("r-seqinr" ,r-seqinr)
14007 ("r-shiny" ,r-shiny)
14008 ("r-spdep" ,r-spdep)
14009 ("r-vegan" ,r-vegan)))
14010 (home-page "https://github.com/thibautjombart/adegenet")
14011 (synopsis "Exploratory analysis of genetic and genomic data")
14013 "This package provides a toolset for the exploration of genetic and
14014 genomic data. Adegenet provides formal (S4) classes for storing and handling
14015 various genetic data, including genetic markers with varying ploidy and
14016 hierarchical population structure (@code{genind} class), alleles counts by
14017 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14018 also implements original multivariate methods (DAPC, sPCA), graphics,
14019 statistical tests, simulation tools, distance and similarity measures, and
14020 several spatial methods. A range of both empirical and simulated datasets is
14021 also provided to illustrate various methods.")
14022 (license license:gpl2+)))
14024 (define-public r-pegas
14031 (uri (cran-uri "pegas" version))
14033 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
14034 (build-system r-build-system)
14036 `(("r-adegenet" ,r-adegenet)
14038 (home-page "http://ape-package.ird.fr/pegas.html")
14039 (synopsis "Population and evolutionary genetics analysis system")
14041 "This package provides functions for reading, writing, plotting,
14042 analysing, and manipulating allelic and haplotypic data, including from VCF
14043 files, and for the analysis of population nucleotide sequences and
14044 micro-satellites including coalescent analyses, linkage disequilibrium,
14045 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14046 minimum spanning tree and network, and median-joining networks.")
14047 (license license:gpl2+)))
14049 (define-public r-rmetasim
14051 (name "r-rmetasim")
14056 (uri (cran-uri "rmetasim" version))
14059 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14060 (build-system r-build-system)
14062 `(("r-ade4" ,r-ade4)
14063 ("r-adegenet" ,r-adegenet)
14064 ("r-gtools" ,r-gtools)
14065 ("r-pegas" ,r-pegas)))
14066 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14067 (synopsis "Individual-based population genetic simulation environment")
14069 "This package provides an interface between R and the metasim simulation
14070 engine. The simulation environment is documented in: Strand, A.(2002),
14071 Metasim 1.0: an individual-based environment for simulating population
14072 genetics of complex population dynamics.")
14074 (license license:gpl2+)))
14076 (define-public r-genetics
14078 (name "r-genetics")
14079 (version "1.3.8.1.2")
14083 (uri (cran-uri "genetics" version))
14086 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14087 (build-system r-build-system)
14089 `(("r-combinat" ,r-combinat)
14090 ("r-gdata" ,r-gdata)
14091 ("r-gtools" ,r-gtools)
14093 ("r-mvtnorm" ,r-mvtnorm)))
14094 (home-page "https://cran.r-project.org/web/packages/genetics/")
14095 (synopsis "Population genetics")
14097 "This package provides classes and methods for handling genetic data.
14098 It includes classes to represent genotypes and haplotypes at single markers up
14099 to multiple markers on multiple chromosomes. Function include allele
14100 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14101 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14102 and testing for linkage disequilibrium, ...")
14103 ;; Any GPL version.
14104 (license license:gpl2+)))
14106 (define-public r-snp-plotter
14108 (name "r-snp-plotter")
14113 (uri (cran-uri "snp.plotter" version))
14116 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14117 (properties `((upstream-name . "snp.plotter")))
14118 (build-system r-build-system)
14119 (propagated-inputs `(("r-genetics" ,r-genetics)))
14120 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14121 (synopsis "Plot p-values using single SNP and/or haplotype data")
14123 "This package helps you create plots of p-values using single SNP and/or
14124 haplotype data. Main features of the package include options to display a
14125 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14126 datasets simultaneously. Plots can be created using global and/or individual
14127 haplotype p-values along with single SNP p-values. Images are created as
14128 either PDF/EPS files.")
14129 (license license:gpl2+)))
14131 (define-public r-polspline
14133 (name "r-polspline")
14138 (uri (cran-uri "polspline" version))
14140 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14141 (build-system r-build-system)
14142 (native-inputs `(("gfortran" ,gfortran)))
14143 (home-page "https://cran.r-project.org/web/packages/polspline/")
14144 (synopsis "Polynomial spline routines")
14146 "This package provides routines for the polynomial spline fitting
14147 routines hazard regression, hazard estimation with flexible tails, logspline,
14148 lspec, polyclass, and polymars.")
14149 (license license:gpl2+)))
14151 (define-public r-rms
14158 (uri (cran-uri "rms" version))
14160 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14161 (build-system r-build-system)
14163 `(("r-cluster" ,r-cluster)
14164 ("r-digest" ,r-digest)
14165 ("r-ggplot2" ,r-ggplot2)
14166 ("r-hmisc" ,r-hmisc)
14167 ("r-htmltable" ,r-htmltable)
14168 ("r-htmltools" ,r-htmltools)
14169 ("r-lattice" ,r-lattice)
14171 ("r-multcomp" ,r-multcomp)
14173 ("r-polspline" ,r-polspline)
14174 ("r-quantreg" ,r-quantreg)
14175 ("r-rpart" ,r-rpart)
14176 ("r-sparsem" ,r-sparsem)
14177 ("r-survival" ,r-survival)))
14178 (native-inputs `(("gfortran" ,gfortran)))
14179 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14180 (synopsis "Regression modeling strategies")
14182 "This is a package for regression modeling, testing, estimation,
14183 validation, graphics, prediction, and typesetting by storing enhanced model
14184 design attributes in the fit. The rms package is a collection of functions
14185 that assist with and streamline modeling. It also contains functions for
14186 binary and ordinal logistic regression models, ordinal models for continuous Y
14187 with a variety of distribution families, and the Buckley-James multiple
14188 regression model for right-censored responses, and implements penalized
14189 maximum likelihood estimation for logistic and ordinary linear models. The
14190 package works with almost any regression model, but it was especially written
14191 to work with binary or ordinal regression models, Cox regression, accelerated
14192 failure time models, ordinary linear models, the Buckley-James model,
14193 generalized least squares for serially or spatially correlated observations,
14194 generalized linear models, and quantile regression.")
14195 (license license:gpl2+)))
14197 (define-public r-arsenal
14204 (uri (cran-uri "arsenal" version))
14207 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14208 (properties `((upstream-name . "arsenal")))
14209 (build-system r-build-system)
14210 (propagated-inputs `(("r-knitr" ,r-knitr)))
14211 (native-inputs `(("r-knitr" ,r-knitr)))
14212 (home-page "https://github.com/mayoverse/arsenal")
14213 (synopsis "Functions for large-scale statistical summaries")
14215 "This package provides an arsenal of R functions for large-scale
14216 statistical summaries, which are streamlined to work within the latest
14217 reporting tools in R and RStudio and which use formulas and versatile
14218 summary statistics for summary tables and models. The primary functions
14222 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14223 levels of one or more categorical variables;
14224 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14225 across two time points;
14226 @item @code{modelsum}, which performs simple model fits on one or more
14227 endpoints for many variables (univariate or adjusted for covariates);
14228 @item @code{freqlist}, a powerful frequency table across many categorical
14230 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14231 @item @code{write2}, a function to output tables to a document.
14234 (license license:gpl2+)))
14236 (define-public r-haplo-stats
14238 (name "r-haplo-stats")
14243 (uri (cran-uri "haplo.stats" version))
14246 "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
14247 (properties `((upstream-name . "haplo.stats")))
14248 (build-system r-build-system)
14250 `(("r-arsenal" ,r-arsenal)
14253 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14254 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14255 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14257 "This package provides routines for the analysis of indirectly measured
14258 haplotypes. The statistical methods assume that all subjects are unrelated
14259 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14260 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14261 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14262 examples in the vignette.")
14263 (license license:gpl2+)))
14265 (define-public r-bqtl
14272 (uri (cran-uri "bqtl" version))
14275 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14276 (build-system r-build-system)
14277 (native-inputs `(("gfortran" ,gfortran)))
14278 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14279 (synopsis "Bayesian QTL mapping toolkit")
14281 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14282 lines. It includes maximum likelihood and Bayesian tools.")
14283 (license license:gpl2+)))
14285 (define-public r-ibdreg
14292 (uri (cran-uri "ibdreg" version))
14295 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14296 (build-system r-build-system)
14297 (home-page "https://www.mayo.edu/research/labs/\
14298 statistical-genetics-genetic-epidemiology/software")
14299 (synopsis "Regression methods for IBD linkage with covariates")
14301 "This package provides a method to test genetic linkage with covariates
14302 by regression methods with response IBD sharing for relative pairs. Account
14303 for correlations of IBD statistics and covariates for relative pairs within
14304 the same pedigree.")
14305 (license license:gpl2+)))
14307 (define-public r-dlmap
14314 (uri (cran-uri "dlmap" version))
14317 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14318 (build-system r-build-system)
14320 `(("r-ibdreg" ,r-ibdreg)
14324 ("r-wgaim" ,r-wgaim)))
14325 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14326 (synopsis "Detection localization mapping for QTL")
14328 "This is package for QTL mapping in a mixed model framework with separate
14329 detection and localization stages. The first stage detects the number of QTL
14330 on each chromosome based on the genetic variation due to grouped markers on
14331 the chromosome; the second stage uses this information to determine the most
14332 likely QTL positions. The mixed model can accommodate general fixed and
14333 random effects, including spatial effects in field trials and pedigree
14334 effects. It is applicable to backcrosses, doubled haploids, recombinant
14335 inbred lines, F2 intercrosses, and association mapping populations.")
14336 (license license:gpl2)))
14338 (define-public r-ldheatmap
14340 (name "r-ldheatmap")
14345 (uri (cran-uri "LDheatmap" version))
14348 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14349 (properties `((upstream-name . "LDheatmap")))
14350 (build-system r-build-system)
14352 `(("r-genetics" ,r-genetics)
14354 ("r-snpstats" ,r-snpstats)))
14355 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14356 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14358 "This package provides tools to produce a graphical display, as a heat
14359 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14360 optionally include the physical locations or genetic map distances of each SNP
14362 (license license:gpl3)))
14364 (define-public r-hwde
14371 (uri (cran-uri "hwde" version))
14374 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14375 (build-system r-build-system)
14376 (home-page "https://cran.r-project.org/web/packages/hwde/")
14377 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14379 "This package fits models for genotypic disequilibria, as described in
14380 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14381 terms are available that account for first order interactions between loci.
14382 It also implements, for a single locus in a single population, a conditional
14383 exact test for Hardy-Weinberg equilibrium.")
14384 (license license:gpl2+)))
14386 (define-public r-tdthap
14393 (uri (cran-uri "tdthap" version))
14396 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14397 (build-system r-build-system)
14398 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14399 (synopsis "TDT tests for extended haplotypes")
14401 "Functions and examples are provided for transmission/disequilibrium
14402 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14403 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14404 (license license:artistic2.0)))
14406 (define-public r-sparql
14412 (uri (cran-uri "SPARQL" version))
14415 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14416 (properties `((upstream-name . "SPARQL")))
14417 (build-system r-build-system)
14419 `(("r-rcurl" ,r-rcurl)
14421 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14422 (synopsis "SPARQL client for R")
14423 (description "This package provides an interface to use SPARQL to pose
14424 SELECT or UPDATE queries to an end-point.")
14425 ;; The only license indication is found in the DESCRIPTION file,
14426 ;; which states GPL-3. So we cannot assume GPLv3+.
14427 (license license:gpl3)))
14429 (define-public r-bookdown
14431 (name "r-bookdown")
14435 (uri (cran-uri "bookdown" version))
14438 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14439 (build-system r-build-system)
14441 `(("r-htmltools" ,r-htmltools)
14442 ("r-knitr" ,r-knitr)
14443 ("r-rmarkdown" ,r-rmarkdown)
14444 ("r-tinytex" ,r-tinytex)
14446 ("pandoc" ,pandoc)))
14447 (home-page "https://github.com/rstudio/bookdown")
14448 (synopsis "Authoring books and technical documents with R markdown")
14449 (description "This package provides output formats and utilities for
14450 authoring books and technical documents with R Markdown.")
14451 (license license:gpl3)))
14453 (define-public r-optparse
14455 (name "r-optparse")
14460 (uri (cran-uri "optparse" version))
14463 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14464 (build-system r-build-system)
14466 `(("r-getopt" ,r-getopt)))
14468 `(("r-knitr" ,r-knitr)))
14469 (home-page "https://github.com/trevorld/optparse")
14470 (synopsis "Command line option parser")
14472 "This package provides a command line parser inspired by Python's
14473 @code{optparse} library to be used with Rscript to write shebang scripts
14474 that accept short and long options.")
14475 (license license:gpl2+)))
14477 (define-public r-wgcna
14484 (uri (cran-uri "WGCNA" version))
14487 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14488 (properties `((upstream-name . "WGCNA")))
14489 (build-system r-build-system)
14491 `(("r-annotationdbi" ,r-annotationdbi)
14492 ("r-doparallel" ,r-doparallel)
14493 ("r-dynamictreecut" ,r-dynamictreecut)
14494 ("r-fastcluster" ,r-fastcluster)
14495 ("r-foreach" ,r-foreach)
14496 ("r-go-db" ,r-go-db)
14497 ("r-hmisc" ,r-hmisc)
14498 ("r-impute" ,r-impute)
14500 ("r-survival" ,r-survival)
14501 ("r-matrixstats" ,r-matrixstats)
14502 ("r-preprocesscore" ,r-preprocesscore)))
14504 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14505 (synopsis "Weighted correlation network analysis")
14507 "This package provides functions necessary to perform Weighted
14508 Correlation Network Analysis on high-dimensional data. It includes functions
14509 for rudimentary data cleaning, construction and summarization of correlation
14510 networks, module identification and functions for relating both variables and
14511 modules to sample traits. It also includes a number of utility functions for
14512 data manipulation and visualization.")
14513 (license license:gpl2+)))
14515 (define-public r-kernlab
14522 (uri (cran-uri "kernlab" version))
14524 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14525 (build-system r-build-system)
14526 (home-page "https://cran.r-project.org/web/packages/kernlab")
14527 (synopsis "Kernel-based machine learning tools")
14529 "This package provides kernel-based machine learning methods for
14530 classification, regression, clustering, novelty detection, quantile regression
14531 and dimensionality reduction. Among other methods @code{kernlab} includes
14532 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14534 (license license:gpl2)))
14536 (define-public r-hierfstat
14538 (name "r-hierfstat")
14543 (uri (cran-uri "hierfstat" version))
14546 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14547 (build-system r-build-system)
14549 `(("r-ade4" ,r-ade4)
14550 ("r-adegenet" ,r-adegenet)
14551 ("r-gaston" ,r-gaston)
14552 ("r-gtools" ,r-gtools)))
14554 `(("r-knitr" ,r-knitr)))
14555 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14556 (synopsis "Estimation and tests of hierarchical F-statistics")
14558 "This package allows the estimation of hierarchical F-statistics from
14559 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14560 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14561 are also given to test via randomisations the significance of each F and
14562 variance components, using the likelihood-ratio statistics G.")
14563 (license license:gpl2+)))
14565 (define-public r-hapassoc
14567 (name "r-hapassoc")
14572 (uri (cran-uri "hapassoc" version))
14575 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14576 (build-system r-build-system)
14577 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14578 (synopsis "Inference of trait associations with SNP haplotypes")
14580 "Hapassoc performs likelihood inference of trait associations with
14581 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14582 functions are developed primarily for data collected in cohort or
14583 cross-sectional studies. They can accommodate uncertain haplotype phase and
14584 handle missing genotypes at some SNPs.")
14585 (license license:gpl2)))
14587 (define-public r-sampling
14589 (name "r-sampling")
14594 (uri (cran-uri "sampling" version))
14597 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14598 (build-system r-build-system)
14600 `(("r-lpsolve" ,r-lpsolve)
14601 ("r-mass" ,r-mass)))
14602 (home-page "https://cran.r-project.org/web/packages/sampling/")
14603 (synopsis "Survey sampling")
14605 "This package provides functions for drawing and calibrating samples.")
14606 (license license:gpl2+)))
14608 (define-public r-r2html
14615 (uri (cran-uri "R2HTML" version))
14618 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14619 (properties `((upstream-name . "R2HTML")))
14620 (build-system r-build-system)
14621 (home-page "https://github.com/nalimilan/R2HTML")
14622 (synopsis "HTML export for R objects")
14624 "This package includes HTML functions and methods to write in an HTML
14625 file. Thus, making HTML reports is easy. It includes a function that allows
14626 redirection on the fly, which appears to be very useful for teaching purposes,
14627 as the student can keep a copy of the produced output to keep all that they
14628 did during the course. The package comes with a vignette describing how to
14629 write HTML reports for statistical analysis. Finally, a driver for Sweave
14630 parses HTML flat files containing R code and to automatically write
14631 the corresponding outputs (tables and graphs).")
14632 (license license:gpl2+)))
14634 (define-public r-rjava
14641 (uri (cran-uri "rJava" version))
14644 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14645 (properties `((upstream-name . "rJava")))
14646 (build-system r-build-system)
14648 `(#:modules ((guix build utils)
14649 (guix build r-build-system)
14652 (modify-phases %standard-phases
14653 (add-after 'unpack 'set-JAVA_HOME
14654 (lambda* (#:key inputs #:allow-other-keys)
14655 (let ((jdk (assoc-ref inputs "jdk")))
14656 (setenv "JAVA_HOME" jdk)
14657 (setenv "JAVA" (which "java"))
14658 (setenv "JAR" (which "jar"))
14659 (setenv "JAVAC" (which "javac"))
14660 (setenv "JAVAH" (which "javah"))
14661 (setenv "JAVA_CPPFLAGS"
14662 (string-append "-I" jdk "/include "
14663 "-I" jdk "/include/linux"))
14664 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14665 ((lib) (setenv "JAVA_LIBS" lib))
14666 (_ (error "Could not find libjvm.so"))))
14670 ("jdk" ,icedtea-8 "jdk")
14673 (home-page "https://www.rforge.net/rJava/")
14674 (synopsis "Low-Level R to Java interface")
14676 "This package provides a low-level interface to the Java VM very much
14677 like .C/.Call and friends. It allows the creation of objects, calling methods
14678 and accessing fields.")
14679 (license license:gpl2)))
14681 (define-public r-svmisc
14688 (uri (cran-uri "svMisc" version))
14691 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14692 (properties `((upstream-name . "svMisc")))
14693 (build-system r-build-system)
14694 (home-page "https://github.com/SciViews/svMisc")
14695 (synopsis "Miscellaneous functions for SciViews")
14697 "This package provides miscellaneous functions for SciViews or general
14698 use, including tools to manage a temporary environment attached to the search
14699 path for temporary variables you do not want to @code{save()} or
14700 @code{load()}; test the current platform; showing progress bars, etc.")
14701 (license license:gpl2)))
14703 (define-public r-xyz
14710 (uri (cran-uri "xyz" version))
14713 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14714 (build-system r-build-system)
14716 `(("r-rcpp" ,r-rcpp)))
14717 (home-page "https://cran.r-project.org/web/packages/xyz/")
14718 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14720 "High dimensional interaction search by brute force requires a quadratic
14721 computational cost in the number of variables. The xyz algorithm provably
14722 finds strong interactions in almost linear time. For details of the algorithm
14723 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14724 interaction search in high-dimensional data.")
14725 ;; Any version of the GPL.
14726 (license license:gpl2+)))
14728 (define-public r-rttf2pt1
14730 (name "r-rttf2pt1")
14735 (uri (cran-uri "Rttf2pt1" version))
14738 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14739 (properties `((upstream-name . "Rttf2pt1")))
14740 (build-system r-build-system)
14741 (home-page "https://github.com/wch/Rttf2pt1")
14742 (synopsis "Font conversion utility")
14744 "This package contains the program @code{ttf2pt1}, for use with the
14745 @code{extrafont} package.")
14746 ;; Most of the files are covered under the Expat license. Some files are
14747 ;; covered under BSD-3. Deviations for individual files are recorded in
14748 ;; the LICENSE file.
14749 (license (list license:bsd-3 license:expat
14750 (license:non-copyleft "file://LICENSE")))))
14752 (define-public r-extrafontdb
14754 (name "r-extrafontdb")
14759 (uri (cran-uri "extrafontdb" version))
14762 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14763 (build-system r-build-system)
14764 (home-page "https://github.com/wch/extrafontdb")
14765 (synopsis "Database for the extrafont package")
14767 "This package holds the database for the @code{extrafont} package.")
14768 (license license:gpl2)))
14770 (define-public r-extrafont
14772 (name "r-extrafont")
14777 (uri (cran-uri "extrafont" version))
14780 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14781 (build-system r-build-system)
14783 `(("r-extrafontdb" ,r-extrafontdb)
14784 ("r-rttf2pt1" ,r-rttf2pt1)))
14785 (home-page "https://github.com/wch/extrafont")
14786 (synopsis "Tools for using fonts in R")
14788 "The extrafont package makes it easier to use fonts other than the basic
14789 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14790 used with PDF or PostScript output files. There are two hurdles for using
14791 fonts in PDF (or Postscript) output files:
14794 @item Making R aware of the font and the dimensions of the characters.
14795 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14796 properly on a device that doesn't have the font. This is usually needed if
14797 you want to print the PDF file or share it with others.
14800 The extrafont package makes both of these things easier.")
14801 (license license:gpl2)))
14803 (define-public r-xkcd
14810 (uri (cran-uri "xkcd" version))
14813 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14814 (build-system r-build-system)
14816 `(("r-extrafont" ,r-extrafont)
14817 ("r-ggplot2" ,r-ggplot2)
14818 ("r-hmisc" ,r-hmisc)))
14819 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14820 (synopsis "Plot ggplot2 graphics in the XKCD style")
14822 "This package provides the means to plot ggplot2 graphs in the style of
14823 the XKCD web comic.")
14824 (license license:gpl3)))
14826 (define-public r-msigdbr
14833 (uri (cran-uri "msigdbr" version))
14836 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14837 (build-system r-build-system)
14839 `(("r-dplyr" ,r-dplyr)
14840 ("r-magrittr" ,r-magrittr)
14841 ("r-rlang" ,r-rlang)
14842 ("r-tibble" ,r-tibble)))
14844 `(("r-knitr" ,r-knitr)))
14845 (home-page "https://github.com/igordot/msigdbr")
14846 (synopsis "MSigDB gene sets for multiple organisms")
14848 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14849 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14850 software in a standard R data frame with key-value pairs. Included are the
14851 original human gene symbols and Entrez IDs as well as the equivalents for
14852 various frequently studied model organisms such as mouse, rat, pig, fly, and
14854 ;; The package is covered under the Expat license, but the upstream MSigDB
14855 ;; files are made available under the Creative Commons Attribution 4.0
14856 ;; International license.
14857 (license (list license:expat license:cc-by4.0))))
14859 (define-public r-gridgraphics
14861 (name "r-gridgraphics")
14866 (uri (cran-uri "gridGraphics" version))
14869 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14870 (properties `((upstream-name . "gridGraphics")))
14871 (build-system r-build-system)
14872 (home-page "https://github.com/pmur002/gridgraphics")
14873 (synopsis "Redraw base graphics using @code{grid} graphics")
14875 "This package provides functions to convert a page of plots drawn with
14876 the @code{graphics} package into identical output drawn with the @code{grid}
14877 package. The result looks like the original @code{graphics}-based plot, but
14878 consists of @code{grid} grobs and viewports that can then be manipulated with
14879 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14880 (license license:gpl2+)))
14882 (define-public r-farver
14889 (uri (cran-uri "farver" version))
14892 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14893 (build-system r-build-system)
14894 (home-page "https://github.com/thomasp85/farver")
14895 (synopsis "Vectorized color conversion and comparison")
14897 "The encoding of color can be handled in many different ways, using
14898 different color spaces. As different color spaces have different uses,
14899 efficient conversion between these representations are important. This
14900 package provides a set of functions that gives access to very fast color space
14901 conversion and comparisons implemented in C++, and offers 100-fold speed
14902 improvements over the @code{convertColor} function in the @code{grDevices}
14904 (license license:expat)))
14906 (define-public r-ggplotify
14908 (name "r-ggplotify")
14913 (uri (cran-uri "ggplotify" version))
14916 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14917 (build-system r-build-system)
14919 `(("r-ggplot2" ,r-ggplot2)
14920 ("r-gridgraphics" ,r-gridgraphics)
14921 ("r-rvcheck" ,r-rvcheck)))
14923 `(("r-knitr" ,r-knitr)))
14924 (home-page "https://github.com/GuangchuangYu/ggplotify")
14925 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14927 "This package provides tools to convert plot function calls (using
14928 expression or formula) to @code{grob} or @code{ggplot} objects that are
14929 compatible with the @code{grid} and @code{ggplot2} environment. With this
14930 package, we are able to e.g. use @code{cowplot} to align plots produced by
14931 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14932 converting them to @code{ggplot} objects.")
14933 (license license:artistic2.0)))
14935 (define-public r-triebeard
14937 (name "r-triebeard")
14942 (uri (cran-uri "triebeard" version))
14945 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14946 (build-system r-build-system)
14947 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14948 (home-page "https://github.com/Ironholds/triebeard/")
14949 (synopsis "Radix trees in Rcpp")
14951 "Radix trees, or tries, are key-value data structures optimized for
14952 efficient lookups, similar in purpose to hash tables. This package provides
14953 an implementation of radix trees for use in R programming and in developing
14954 packages with Rcpp.")
14955 (license license:expat)))
14957 (define-public r-tweenr
14964 (uri (cran-uri "tweenr" version))
14967 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14968 (build-system r-build-system)
14970 `(("r-farver" ,r-farver)
14971 ("r-magrittr" ,r-magrittr)
14973 ("r-rlang" ,r-rlang)))
14974 (home-page "https://github.com/thomasp85/tweenr")
14975 (synopsis "Interpolate data for smooth animations")
14977 "In order to create smooth animation between states of data, tweening is
14978 necessary. This package provides a range of functions for creating tweened
14979 data that can be used as basis for animation. Furthermore it adds a number of
14980 vectorized interpolaters for common R data types such as numeric, date and
14982 (license license:expat)))
14984 (define-public r-polyclip
14986 (name "r-polyclip")
14991 (uri (cran-uri "polyclip" version))
14994 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14995 (build-system r-build-system)
14996 (native-inputs `(("pkg-config" ,pkg-config)))
14997 (home-page "http://www.angusj.com/delphi/clipper.php")
14998 (synopsis "Polygon clipping")
15000 "This package provides an R port of the library Clipper. It performs
15001 polygon clipping operations (intersection, union, set minus, set difference)
15002 for polygonal regions of arbitrary complexity, including holes. It computes
15003 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15004 dilations) for polygonal regions and polygonal lines. It computes the
15005 Minkowski Sum of general polygons. There is a function for removing
15006 self-intersections from polygon data.")
15007 (license license:boost1.0)))
15009 (define-public r-urltools
15011 (name "r-urltools")
15016 (uri (cran-uri "urltools" version))
15019 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15020 (build-system r-build-system)
15022 `(("r-rcpp" ,r-rcpp)
15023 ("r-triebeard" ,r-triebeard)))
15024 (home-page "https://github.com/Ironholds/urltools/")
15025 (synopsis "Vectorized tools for URL handling and parsing")
15027 "This package provides a toolkit for all URL-handling needs, including
15028 encoding and decoding, parsing, parameter extraction and modification. All
15029 functions are designed to be both fast and entirely vectorized. It is
15030 intended to be useful for people dealing with web-related datasets, such as
15031 server-side logs, although may be useful for other situations involving large
15033 (license license:expat)))
15035 (define-public r-ggforce
15042 (uri (cran-uri "ggforce" version))
15045 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15046 (build-system r-build-system)
15048 `(("r-ggplot2" ,r-ggplot2)
15049 ("r-gtable" ,r-gtable)
15051 ("r-polyclip" ,r-polyclip)
15053 ("r-rcppeigen" ,r-rcppeigen)
15054 ("r-rlang" ,r-rlang)
15055 ("r-scales" ,r-scales)
15056 ("r-tidyselect" ,r-tidyselect)
15057 ("r-tweenr" ,r-tweenr)
15058 ("r-withr" ,r-withr)))
15059 (home-page "https://ggforce.data-imaginist.com")
15060 (synopsis "Accelerating ggplot2")
15062 "The aim of the ggplot2 package is to aid in visual data investigations.
15063 This focus has led to a lack of facilities for composing specialized plots.
15064 Thi package aims to be a collection of mainly new statistics and geometries
15065 that fills this gap.")
15066 (license license:expat)))
15068 (define-public r-europepmc
15070 (name "r-europepmc")
15075 (uri (cran-uri "europepmc" version))
15078 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15079 (build-system r-build-system)
15081 `(("r-dplyr" ,r-dplyr)
15083 ("r-jsonlite" ,r-jsonlite)
15085 ("r-progress" ,r-progress)
15086 ("r-purrr" ,r-purrr)
15087 ("r-rlang" ,r-rlang)
15088 ("r-tibble" ,r-tibble)
15089 ("r-tidyr" ,r-tidyr)
15090 ("r-urltools" ,r-urltools)
15091 ("r-xml2" ,r-xml2)))
15093 `(("r-knitr" ,r-knitr)))
15094 (home-page "https://github.com/ropensci/europepmc/")
15095 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15097 "This package provides an R Client for the
15098 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15099 Service}. It gives access to both metadata on life science literature and
15100 open access full texts. Europe PMC indexes all PubMed content and other
15101 literature sources including Agricola, a bibliographic database of citations
15102 to the agricultural literature, or Biological Patents. In addition to
15103 bibliographic metadata, the client allows users to fetch citations and
15104 reference lists. Links between life-science literature and other EBI
15105 databases, including ENA, PDB or ChEMBL are also accessible.")
15106 (license license:gpl3)))
15108 (define-public r-ggraph
15115 (uri (cran-uri "ggraph" version))
15118 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15119 (build-system r-build-system)
15121 `(("r-digest" ,r-digest)
15122 ("r-dplyr" ,r-dplyr)
15123 ("r-ggforce" ,r-ggforce)
15124 ("r-ggplot2" ,r-ggplot2)
15125 ("r-ggrepel" ,r-ggrepel)
15126 ("r-graphlayouts" ,r-graphlayouts)
15127 ("r-gtable" ,r-gtable)
15128 ("r-igraph" ,r-igraph)
15131 ("r-rlang" ,r-rlang)
15132 ("r-scales" ,r-scales)
15133 ("r-tidygraph" ,r-tidygraph)
15134 ("r-viridis" ,r-viridis)))
15136 `(("r-knitr" ,r-knitr)))
15137 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15138 (synopsis "Implementation of grammar of graphics for graphs and networks")
15140 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15141 graph and network visualizations due to its reliance on tabular data input.
15142 The ggraph package is an extension of the ggplot2 API tailored to graph
15143 visualizations and provides the same flexible approach to building up plots
15145 (license license:gpl3)))
15147 (define-public r-varselrf
15149 (name "r-varselrf")
15154 (uri (cran-uri "varSelRF" version))
15157 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15158 (properties `((upstream-name . "varSelRF")))
15159 (build-system r-build-system)
15161 `(("r-randomforest" ,r-randomforest)))
15162 (home-page "https://www.ligarto.org/rdiaz/software/software")
15163 (synopsis "Variable selection using random forests")
15165 "This package provides tools for the variable selection from random
15166 forests using both backwards variable elimination (for the selection of small
15167 sets of non-redundant variables) and selection based on the importance
15168 spectrum (somewhat similar to scree plots; for the selection of large,
15169 potentially highly-correlated variables). The main applications are in
15170 high-dimensional data (e.g., microarray data, and other genomics and
15171 proteomics applications).")
15172 (license license:gpl2+)))
15174 (define-public r-pamr
15181 (uri (cran-uri "pamr" version))
15184 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15185 (build-system r-build-system)
15187 `(("r-cluster" ,r-cluster)
15188 ("r-survival" ,r-survival)))
15189 (native-inputs `(("gfortran" ,gfortran)))
15190 (home-page "https://cran.r-project.org/web/packages/pamr/")
15191 (synopsis "Prediction Analysis for Microarrays")
15193 "This package provides some functions for sample classification in
15195 (license license:gpl2)))
15197 (define-public r-rda
15200 (version "1.0.2-2.1")
15204 (uri (cran-uri "rda" version))
15207 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15208 (build-system r-build-system)
15209 (home-page "https://cran.r-project.org/web/packages/rda/")
15210 (synopsis "Shrunken centroids regularized discriminant analysis")
15212 "This package provides tools for shrunken centroids regularized
15213 discriminant analysis for the purpose of classifying high dimensional data.")
15214 (license license:gpl2+)))
15216 (define-public r-ggvis
15223 (uri (cran-uri "ggvis" version))
15226 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15227 (build-system r-build-system)
15229 `(("r-assertthat" ,r-assertthat)
15230 ("r-dplyr" ,r-dplyr)
15231 ("r-htmltools" ,r-htmltools)
15232 ("r-jsonlite" ,r-jsonlite)
15233 ("r-lazyeval" ,r-lazyeval)
15234 ("r-magrittr" ,r-magrittr)
15235 ("r-shiny" ,r-shiny)))
15236 (home-page "https://ggvis.rstudio.com/")
15237 (synopsis "Interactive grammar of graphics")
15239 "This package is a data visualization package for R providing an
15240 implementation of an interactive grammar of graphics, taking the best parts of
15241 ggplot2, combining them with the reactive framework of Shiny and drawing web
15242 graphics using Vega.")
15243 (license license:gpl2)))
15245 (define-public r-gbm
15252 (uri (cran-uri "gbm" version))
15255 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15256 (build-system r-build-system)
15258 `(("r-lattice" ,r-lattice)
15259 ("r-survival" ,r-survival)))
15261 `(("r-knitr" ,r-knitr)))
15262 (home-page "https://github.com/gbm-developers/gbm")
15263 (synopsis "Generalized boosted regression models")
15265 "This package is an implementation of extensions to Freund and Schapire's
15266 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15267 regression methods for least squares, absolute loss, t-distribution loss,
15268 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15269 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15270 and Learning to Rank measures (LambdaMart).")
15271 (license license:gpl2+)))
15273 (define-public r-threejs
15280 (uri (cran-uri "threejs" version))
15283 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15284 (build-system r-build-system)
15286 `(#:modules ((guix build utils)
15287 (guix build r-build-system)
15291 (modify-phases %standard-phases
15292 (add-after 'unpack 'process-javascript
15293 (lambda* (#:key inputs #:allow-other-keys)
15294 (with-directory-excursion "inst"
15298 `((,(assoc-ref inputs "js-jquery")
15299 "htmlwidgets/lib/jquery/jquery.min.js")
15300 (,(assoc-ref inputs "js-threejs-111")
15301 "htmlwidgets/lib/threejs-111/three.min.js"))))
15302 (lambda (sources targets)
15303 (for-each (lambda (source target)
15304 (format #t "Processing ~a --> ~a~%"
15306 (delete-file target)
15307 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15308 (call-with-output-file target
15310 (dump-port minified port)))))
15311 sources targets))))
15314 `(("r-base64enc" ,r-base64enc)
15315 ("r-crosstalk" ,r-crosstalk)
15316 ("r-htmlwidgets" ,r-htmlwidgets)
15317 ("r-igraph" ,r-igraph)))
15319 `(("uglify-js" ,uglify-js)
15323 (uri "https://code.jquery.com/jquery-1.12.4.js")
15326 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15330 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15333 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15334 (home-page "https://bwlewis.github.io/rthreejs")
15335 (synopsis "Interactive 3D scatter plots, networks and globes")
15337 "Create interactive 3D scatter plots, network plots, and globes in R
15338 using the three.js visualization library.")
15339 (license license:expat)))
15341 (define-public r-mlbench
15348 (uri (cran-uri "mlbench" version))
15351 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15352 (build-system r-build-system)
15353 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15354 (synopsis "Machine learning benchmark problems")
15356 "This package provides a collection of artificial and real-world machine
15357 learning benchmark problems, including, e.g., several data sets from the UCI
15359 (license license:gpl2)))
15361 (define-public r-mpm
15368 (uri (cran-uri "mpm" version))
15371 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15372 (build-system r-build-system)
15374 `(("r-kernsmooth" ,r-kernsmooth)
15375 ("r-mass" ,r-mass)))
15376 (home-page "http://mpm.r-forge.r-project.org")
15377 (synopsis "Multivariate projection methods")
15379 "This is a package for exploratory graphical analysis of multivariate
15380 data, specifically gene expression data with different projection methods:
15381 principal component analysis, correspondence analysis, spectral map
15383 (license license:gpl2+)))
15385 (define-public r-png
15391 (uri (cran-uri "png" version))
15394 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15395 (build-system r-build-system)
15397 `(("libpng" ,libpng)
15399 (home-page "https://www.rforge.net/png/")
15400 (synopsis "Read and write PNG images")
15402 "This package provides an easy and simple way to read, write and display
15403 bitmap images stored in the PNG format. It can read and write both files and
15404 in-memory raw vectors.")
15405 ;; Any of these GPL versions.
15406 (license (list license:gpl2 license:gpl3))))
15408 (define-public r-ggcorrplot
15410 (name "r-ggcorrplot")
15415 (uri (cran-uri "ggcorrplot" version))
15418 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15419 (build-system r-build-system)
15421 `(("r-ggplot2" ,r-ggplot2)
15422 ("r-reshape2" ,r-reshape2)))
15423 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15424 (synopsis "Visualization of a correlation matrix using ggplot2")
15426 "The ggcorrplot package can be used to visualize easily a correlation
15427 matrix using ggplot2. It provides a solution for reordering the correlation
15428 matrix and displays the significance level on the plot. It also includes a
15429 function for computing a matrix of correlation p-values.")
15430 (license license:gpl2)))
15432 ;; This package includes minified JavaScript files. When upgrading please
15433 ;; check that there are no new minified JavaScript files.
15434 (define-public r-flexdashboard
15436 (name "r-flexdashboard")
15441 (uri (cran-uri "flexdashboard" version))
15444 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15445 (modules '((guix build utils)))
15448 ;; Delete bundled minified JavaScript files
15449 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15450 (delete-file "inst/www/sly/sly.min.js")
15451 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15452 (delete-file "inst/www/prism/prism.js")
15454 (build-system r-build-system)
15456 `(#:modules ((guix build utils)
15457 (guix build r-build-system)
15461 (ice-9 textual-ports))
15463 (modify-phases %standard-phases
15464 (add-after 'unpack 'process-javascript
15465 (lambda* (#:key inputs #:allow-other-keys)
15466 (with-directory-excursion "inst"
15467 ;; Concatenate all components of prism.js
15468 (let ((contents (string-join
15469 (map (lambda (name)
15470 (call-with-input-file
15471 (assoc-ref inputs name)
15475 "js-prism-line-numbers"))
15477 (call-with-output-file "prism-src.js"
15478 (cut display contents <>)))
15482 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15483 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15485 "www/sly/sly.min.js")
15487 "www/prism/prism.js")
15488 (,(assoc-ref inputs "js-raphael")
15489 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15490 (,(assoc-ref inputs "js-featherlight")
15491 "www/featherlight/featherlight.min.js"))))
15492 (lambda (sources targets)
15493 (for-each (lambda (source target)
15494 (format #t "Processing ~a --> ~a~%"
15496 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15497 (call-with-output-file target
15499 (dump-port minified port)))))
15500 sources targets))))
15503 `(("r-htmltools" ,r-htmltools)
15504 ("r-htmlwidgets" ,r-htmlwidgets)
15505 ("r-jsonlite" ,r-jsonlite)
15506 ("r-knitr" ,r-knitr)
15507 ("r-rmarkdown" ,r-rmarkdown)
15508 ("r-shiny" ,r-shiny)))
15510 `(("uglify-js" ,uglify-js)
15514 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15517 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15521 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15524 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15528 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15531 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15532 ("js-prism-line-numbers"
15535 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15538 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15542 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15545 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15546 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15547 (synopsis "R Markdown format for flexible dashboards")
15549 "This package provides an R Markdown format for converting an R Markdown
15550 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15551 of its components to the containing web page.")
15552 (license license:expat)))
15554 (define-public r-preseqr
15561 (uri (cran-uri "preseqR" version))
15564 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15565 (properties `((upstream-name . "preseqR")))
15566 (build-system r-build-system)
15568 `(("r-polynom" ,r-polynom)))
15569 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15570 (synopsis "Predicting species accumulation curves")
15572 "This package can be used to predict the r-species accumulation
15573 curve (r-SAC), which is the number of species represented at least r times as
15574 a function of the sampling effort. When r = 1, the curve is known as the
15575 species accumulation curve, or the library complexity curve in high-throughput
15576 genomic sequencing. The package includes both parametric and nonparametric
15577 methods, as described by Deng C, et al. (2018).")
15578 (license license:gpl3)))
15580 (define-public r-mapplots
15582 (name "r-mapplots")
15587 (uri (cran-uri "mapplots" version))
15590 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15591 (build-system r-build-system)
15592 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15593 (synopsis "Data visualization on maps")
15595 "This package helps you create simple maps; add sub-plots like pie plots
15596 to a map or any other plot; format, plot and export gridded data. The package
15597 was developed for displaying fisheries data but most functions can be used for
15598 more generic data visualisation.")
15599 (license license:gpl2+)))
15601 (define-public r-pmcmr
15608 (uri (cran-uri "PMCMR" version))
15611 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15612 (properties `((upstream-name . "PMCMR")))
15613 (build-system r-build-system)
15614 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15615 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15617 "This is a deprecated package for calculating pairwise multiple
15618 comparisons of mean rank sums. This package is superseded by the novel
15619 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15620 compatibility of dependent packages for some time.")
15621 (license license:gpl3+)))
15623 (define-public r-downloader
15625 (name "r-downloader")
15630 (uri (cran-uri "downloader" version))
15633 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15634 (build-system r-build-system)
15636 `(("r-digest" ,r-digest)))
15637 (home-page "https://github.com/wch/downloader")
15638 (synopsis "Download files over HTTP and HTTPS")
15640 "This package provides a wrapper for the @code{download.file} function,
15641 making it possible to download files over HTTPS across platforms. The
15642 @code{RCurl} package provides this functionality (and much more) but has
15643 external dependencies. This package has is implemented purely in R.")
15644 (license license:gpl2)))
15646 (define-public r-rex
15653 (uri (cran-uri "rex" version))
15656 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15657 (build-system r-build-system)
15659 `(("r-lazyeval" ,r-lazyeval)))
15661 `(("r-knitr" ,r-knitr)))
15662 (home-page "https://github.com/kevinushey/rex")
15663 (synopsis "Friendly regular expressions")
15665 "This package provides a friendly interface for the construction of
15666 regular expressions. Regular expressions are a very powerful feature, however
15667 they are often difficult to interpret. Rex allows you to build complex
15668 regular expressions from human readable expressions")
15669 (license license:expat)))
15671 (define-public r-xmlparsedata
15673 (name "r-xmlparsedata")
15678 (uri (cran-uri "xmlparsedata" version))
15681 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
15682 (properties `((upstream-name . "xmlparsedata")))
15683 (build-system r-build-system)
15684 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15685 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15687 "This package provides tools to convert the output of
15688 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15689 @code{XPath}, and is easier to manipulate in general.")
15690 (license license:expat)))
15692 (define-public r-cyclocomp
15694 (name "r-cyclocomp")
15699 (uri (cran-uri "cyclocomp" version))
15702 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15703 (properties `((upstream-name . "cyclocomp")))
15704 (build-system r-build-system)
15706 `(("r-callr" ,r-callr)
15707 ("r-crayon" ,r-crayon)
15709 ("r-remotes" ,r-remotes)
15710 ("r-withr" ,r-withr)))
15711 (home-page "https://github.com/MangoTheCat/cyclocomp")
15712 (synopsis "Cyclomatic complexity of R code")
15714 "Cyclomatic complexity is a software metric, used to indicate the
15715 complexity of a program. It is a quantitative measure of the number of
15716 linearly independent paths through a program's source code. This package
15717 provides tools to compute this metric.")
15718 (license license:expat)))
15720 (define-public r-lintr
15727 (uri (cran-uri "lintr" version))
15730 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15731 (properties `((upstream-name . "lintr")))
15732 (build-system r-build-system)
15734 `(("r-codetools" ,r-codetools)
15735 ("r-crayon" ,r-crayon)
15736 ("r-cyclocomp" ,r-cyclocomp)
15737 ("r-digest" ,r-digest)
15739 ("r-jsonlite" ,r-jsonlite)
15740 ("r-knitr" ,r-knitr)
15742 ("r-rstudioapi" ,r-rstudioapi)
15743 ("r-testthat" ,r-testthat)
15745 ("r-xmlparsedata" ,r-xmlparsedata)))
15746 (home-page "https://github.com/jimhester/lintr")
15747 (synopsis "Linter for R code")
15748 (description "This package checks adherence to a given style, syntax
15749 errors and possible semantic issues. It supports on the fly checking of R
15750 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15751 (license license:expat)))
15753 (define-public r-sctransform
15755 (name "r-sctransform")
15760 (uri (cran-uri "sctransform" version))
15763 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15764 (build-system r-build-system)
15766 `(("r-future-apply" ,r-future-apply)
15767 ("r-ggplot2" ,r-ggplot2)
15768 ("r-gridextra" ,r-gridextra)
15770 ("r-matrix" ,r-matrix)
15772 ("r-rcppeigen" ,r-rcppeigen)
15773 ("r-reshape2" ,r-reshape2)))
15774 (home-page "https://github.com/ChristophH/sctransform")
15775 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15777 "This package provides a normalization method for single-cell UMI count
15778 data using a variance stabilizing transformation. The transformation is based
15779 on a negative binomial regression model with regularized parameters. As part
15780 of the same regression framework, this package also provides functions for
15781 batch correction, and data correction.")
15782 (license license:gpl3)))
15784 (define-public r-styler
15791 (uri (cran-uri "styler" version))
15794 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15795 (build-system r-build-system)
15797 `(("r-backports" ,r-backports)
15799 ("r-magrittr" ,r-magrittr)
15800 ("r-purrr" ,r-purrr)
15801 ("r-r-cache" ,r-r-cache)
15802 ("r-rematch2" ,r-rematch2)
15803 ("r-rlang" ,r-rlang)
15804 ("r-rprojroot" ,r-rprojroot)
15805 ("r-tibble" ,r-tibble)
15806 ("r-withr" ,r-withr)
15807 ("r-xfun" ,r-xfun)))
15808 (home-page "https://github.com/r-lib/styler")
15809 (synopsis "Non-invasive pretty printing of R code")
15811 "This is a package for pretty-printing R code without changing the user's
15812 formatting intent.")
15813 (license license:gpl3)))
15815 (define-public r-scrime
15822 (uri (cran-uri "scrime" version))
15825 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15826 (build-system r-build-system)
15827 (home-page "https://cran.r-project.org/web/packages/scrime/")
15828 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15830 "This package provides tools for the analysis of high-dimensional data
15831 developed/implemented at the group \"Statistical Complexity Reduction In
15832 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15833 the functions can also be applied to other types of categorical data.")
15834 (license license:gpl2)))
15836 (define-public r-pbmcapply
15838 (name "r-pbmcapply")
15843 (uri (cran-uri "pbmcapply" version))
15846 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15847 (build-system r-build-system)
15848 (home-page "https://github.com/kvnkuang/pbmcapply")
15849 (synopsis "Track the progress of apply procedures with a progress bar")
15851 "This light-weight package helps you track and visualize the progress of
15852 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15853 (license license:expat)))
15855 (define-public r-blme
15862 (uri (cran-uri "blme" version))
15865 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15866 (build-system r-build-system)
15867 (propagated-inputs `(("r-lme4" ,r-lme4)))
15868 (home-page "https://github.com/vdorie/blme")
15869 (synopsis "Bayesian linear mixed-effects models")
15871 "This package provides tools for maximum a posteriori estimation for
15872 linear and generalized linear mixed-effects models in a Bayesian setting. It
15873 extends the lme4 package.")
15874 (license license:gpl2+)))
15876 (define-public r-batchtools
15878 (name "r-batchtools")
15883 (uri (cran-uri "batchtools" version))
15886 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15887 (build-system r-build-system)
15889 `(("r-backports" ,r-backports)
15890 ("r-base64url" ,r-base64url)
15892 ("r-checkmate" ,r-checkmate)
15893 ("r-data-table" ,r-data-table)
15894 ("r-digest" ,r-digest)
15896 ("r-progress" ,r-progress)
15898 ("r-rappdirs" ,r-rappdirs)
15899 ("r-stringi" ,r-stringi)
15900 ("r-withr" ,r-withr)))
15902 `(("r-knitr" ,r-knitr)))
15903 (home-page "https://github.com/mllg/batchtools")
15904 (synopsis "Tools for computation on batch systems")
15906 "As a successor of the packages BatchJobs and BatchExperiments, this
15907 package provides a parallel implementation of the Map function for high
15908 performance computing systems managed by various schedulers. A multicore and
15909 socket mode allow the parallelization on a local machines, and multiple
15910 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15911 the package provides an abstraction mechanism to define large-scale computer
15912 experiments in a well-organized and reproducible way.")
15913 (license license:lgpl3)))
15915 (define-public r-clue
15922 (uri (cran-uri "clue" version))
15925 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15926 (build-system r-build-system)
15927 (propagated-inputs `(("r-cluster" ,r-cluster)))
15928 (home-page "https://cran.r-project.org/web/packages/clue/")
15929 (synopsis "Tools for analyzing cluster ensembles")
15930 (description "Cluster ensembles are collections of individual solutions to
15931 a given clustering problem which are useful or necessary to consider in a wide
15932 range of applications. This R package provides an extensible computational
15933 environment for creating and analyzing cluster ensembles, with basic data
15934 structures for representing partitions and hierarchies, and facilities for
15935 computing on them, including methods for measuring proximity and obtaining
15936 consensus and secondary clusterings.")
15937 (license license:gpl2)))
15939 (define-public r-sitmo
15946 (uri (cran-uri "sitmo" version))
15949 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15950 (build-system r-build-system)
15951 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15952 (home-page "https://github.com/coatless/sitmo/")
15953 (synopsis "Parallel pseudo random number generator header files")
15955 "This package provides two high quality and fast PPRNGs that may be used
15956 in an OpenMP parallel environment. In addition, there is a generator for one
15957 dimensional low-discrepancy sequence.")
15958 (license license:expat)))
15960 (define-public r-dqrng
15967 (uri (cran-uri "dqrng" version))
15970 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15971 (build-system r-build-system)
15975 ("r-sitmo" ,r-sitmo)))
15976 (home-page "https://www.daqana.org/dqrng")
15977 (synopsis "Fast pseudo random number generators")
15979 "Several fast random number generators are provided as C++ header-only
15980 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15981 Additionally, fast functions for generating random numbers according to a
15982 uniform, normal and exponential distribution are included. The latter two use
15983 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15984 functions are exported to R and as a C++ interface and are enabled for use
15985 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15986 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15987 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15988 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15989 ;; whole is distributed under the terms of the AGPL 3.
15990 (license license:agpl3)))
15992 (define-public r-ingredients
15994 (name "r-ingredients")
15999 (uri (cran-uri "ingredients" version))
16002 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16003 (properties `((upstream-name . "ingredients")))
16004 (build-system r-build-system)
16006 `(("r-ggplot2" ,r-ggplot2)
16007 ("r-gridextra" ,r-gridextra)
16008 ("r-scales" ,r-scales)))
16009 (native-inputs `(("r-knitr" ,r-knitr)))
16010 (home-page "https://ModelOriented.github.io/ingredients/")
16011 (synopsis "Effects and importances of model ingredients")
16013 "This is a collection of tools for assessment of feature importance and
16014 feature effects. Key functions are:
16017 @item @code{feature_importance()} for assessment of global level feature
16019 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16020 @item @code{partial_dependence()} for partial dependence plots,
16021 @item @code{conditional_dependence()} for conditional dependence plots,
16022 @item @code{accumulated_dependence()} for accumulated local effects plots,
16023 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16024 aggregation of ceteris paribus profiles,
16025 @item generic @code{print()} and @code{plot()} for better usability of
16026 selected explainers,
16027 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16028 @item generic @code{describe()} for explanations in natural language.
16030 (license license:gpl3)))
16032 (define-public r-ibreakdown
16034 (name "r-ibreakdown")
16039 (uri (cran-uri "iBreakDown" version))
16042 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16043 (properties `((upstream-name . "iBreakDown")))
16044 (build-system r-build-system)
16045 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16046 (native-inputs `(("r-knitr" ,r-knitr)))
16047 (home-page "https://ModelOriented.github.io/iBreakDown/")
16048 (synopsis "Model agnostic instance level variable attributions")
16050 "This package provides a model agnostic tool for decomposition of
16051 predictions from black boxes. It supports additive attributions and
16052 attributions with interactions. The Break Down Table shows contributions of
16053 every variable to a final prediction. The Break Down Plot presents variable
16054 contributions in a concise graphical way. This package works for
16055 classification and regression models.")
16056 (license license:gpl3)))
16058 (define-public r-dae
16065 (uri (cran-uri "dae" version))
16068 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16069 (build-system r-build-system)
16071 `(("r-ggplot2" ,r-ggplot2)
16072 ("r-plyr" ,r-plyr)))
16074 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16075 (home-page "http://chris.brien.name")
16076 (synopsis "Functions useful in the design and ANOVA of experiments")
16078 "This package provides functions useful in the design and ANOVA of
16079 experiments. The content falls into the following groupings:
16083 @item factor manipulation functions,
16084 @item design functions,
16085 @item ANOVA functions,
16086 @item matrix functions,
16087 @item projector and canonical efficiency functions, and
16088 @item miscellaneous functions.
16091 There is a vignette called @code{DesignNotes} describing how to use the design
16092 functions for randomizing and assessing designs. The ANOVA functions
16093 facilitate the extraction of information when the @code{Error} function has
16094 been used in the call to @code{aov}.")
16095 (license license:gpl2)))
16097 (define-public r-dalex
16100 (version "1.3.1.1")
16104 (uri (cran-uri "DALEX" version))
16107 "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
16108 (properties `((upstream-name . "DALEX")))
16109 (build-system r-build-system)
16111 `(("r-ggplot2" ,r-ggplot2)
16112 ("r-ibreakdown" ,r-ibreakdown)
16113 ("r-ingredients" ,r-ingredients)))
16114 (home-page "https://pbiecek.github.io/DALEX/")
16115 (synopsis "Descriptive machine learning explanations")
16117 "Machine Learning models are widely used and have various applications in
16118 classification or regression. Models created with boosting, bagging, stacking
16119 or similar techniques are often used due to their high performance, but such
16120 black-box models usually lack interpretability. The DALEX package contains
16121 various explainers that help to understand the link between input variables
16122 and model output.")
16123 ;; Any version of the GPL
16124 (license license:gpl3+)))
16126 (define-public r-enrichr
16133 (uri (cran-uri "enrichR" version))
16136 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16137 (properties `((upstream-name . "enrichR")))
16138 (build-system r-build-system)
16140 `(("r-httr" ,r-httr)
16141 ("r-rjson" ,r-rjson)))
16142 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16143 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16145 "This package provides an R interface to all Enrichr databases, a
16146 web-based tool for analyzing gene sets and returns any enrichment of common
16147 annotated biological functions.")
16148 (license license:gpl2+)))
16150 (define-public r-plot3d
16157 (uri (cran-uri "plot3D" version))
16160 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16161 (properties `((upstream-name . "plot3D")))
16162 (build-system r-build-system)
16163 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16164 (home-page "https://cran.r-project.org/web/packages/plot3D")
16165 (synopsis "Plot multi-dimensional data")
16167 "This package provides functions for viewing 2D and 3D data, including
16168 perspective plots, slice plots, surface plots, scatter plots, etc. It
16169 includes data sets from oceanography.")
16170 (license license:gpl3+)))
16172 (define-public r-ggfortify
16174 (name "r-ggfortify")
16179 (uri (cran-uri "ggfortify" version))
16182 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
16183 (build-system r-build-system)
16185 `(("r-dplyr" ,r-dplyr)
16186 ("r-ggplot2" ,r-ggplot2)
16187 ("r-gridextra" ,r-gridextra)
16188 ("r-scales" ,r-scales)
16189 ("r-stringr" ,r-stringr)
16190 ("r-tibble" ,r-tibble)
16191 ("r-tidyr" ,r-tidyr)))
16193 `(("r-knitr" ,r-knitr)))
16194 (home-page "https://github.com/sinhrks/ggfortify")
16195 (synopsis "Data visualization tools for statistical analysis results")
16197 "This package provides unified plotting tools for statistics commonly
16198 used, such as GLM, time series, PCA families, clustering and survival
16199 analysis. The package offers a single plotting interface for these analysis
16200 results and plots in a unified style using the @code{ggplot2} package.")
16201 (license license:gpl2)))
16203 (define-public r-refmanager
16205 (name "r-refmanager")
16210 (uri (cran-uri "RefManageR" version))
16213 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16214 (properties `((upstream-name . "RefManageR")))
16215 (build-system r-build-system)
16217 `(("r-bibtex" ,r-bibtex)
16219 ("r-jsonlite" ,r-jsonlite)
16220 ("r-lubridate" ,r-lubridate)
16222 ("r-stringr" ,r-stringr)
16223 ("r-xml2" ,r-xml2)))
16224 (home-page "https://github.com/ropensci/RefManageR/")
16225 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16227 "This package provides tools for importing and working with bibliographic
16228 references. It greatly enhances the @code{bibentry} class by providing a
16229 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16230 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16231 by various formats for name lists (author by last names, translator by full
16232 names, etc.). Entries can be updated, combined, sorted, printed in a number
16233 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16234 into R and converted to @code{BibEntry} objects.")
16235 ;; Any of these licenses may be picked.
16236 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16238 (define-public r-citr
16245 (uri (cran-uri "citr" version))
16248 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16249 (build-system r-build-system)
16251 `(("r-assertthat" ,r-assertthat)
16254 ("r-miniui" ,r-miniui)
16255 ("r-refmanager" ,r-refmanager)
16256 ("r-rstudioapi" ,r-rstudioapi)
16257 ("r-shiny" ,r-shiny)
16258 ("r-shinyjs" ,r-shinyjs)
16259 ("r-yaml" ,r-yaml)))
16260 (home-page "https://github.com/crsh/citr")
16261 (synopsis "RStudio add-in to insert Markdown citations")
16263 "This package provides functions and an RStudio add-in that search a
16264 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16265 the current document.")
16266 (license license:expat)))
16268 (define-public r-xgboost
16271 (version "1.2.0.1")
16275 (uri (cran-uri "xgboost" version))
16278 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16279 (build-system r-build-system)
16281 `(("r-data-table" ,r-data-table)
16282 ("r-magrittr" ,r-magrittr)
16283 ("r-matrix" ,r-matrix)
16284 ("r-stringi" ,r-stringi)))
16286 `(("r-knitr" ,r-knitr)))
16287 (home-page "https://github.com/dmlc/xgboost")
16288 (synopsis "Extreme gradient boosting")
16290 "This package provides an R interface to Extreme Gradient Boosting, which
16291 is an efficient implementation of the gradient boosting framework from Chen
16292 and Guestrin (2016). The package includes efficient linear model solver and
16293 tree learning algorithms. The package can automatically do parallel
16294 computation on a single machine. It supports various objective functions,
16295 including regression, classification and ranking. The package is made to be
16296 extensible, so that users are also allowed to define their own objectives
16298 (license license:asl2.0)))
16300 (define-public r-umap
16303 (version "0.2.6.0")
16307 (uri (cran-uri "umap" version))
16310 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16311 (build-system r-build-system)
16313 `(("r-openssl" ,r-openssl)
16315 ("r-reticulate" ,r-reticulate)
16316 ("r-rspectra" ,r-rspectra)))
16318 `(("r-knitr" ,r-knitr)))
16319 (home-page "https://github.com/tkonopka/umap")
16320 (synopsis "Uniform manifold approximation and projection")
16322 "Uniform manifold approximation and projection is a technique for
16323 dimension reduction. This package provides an interface to the UMAP algorithm
16324 in R, including a translation of the original algorithm into R.")
16325 (license license:expat)))
16327 (define-public r-uwot
16334 (uri (cran-uri "uwot" version))
16337 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16338 (build-system r-build-system)
16340 `(("r-dqrng" ,r-dqrng)
16342 ("r-irlba" ,r-irlba)
16343 ("r-matrix" ,r-matrix)
16345 ("r-rcppannoy" ,r-rcppannoy)
16346 ("r-rcppprogress" ,r-rcppprogress)
16347 ("r-rspectra" ,r-rspectra)))
16348 (home-page "https://github.com/jlmelville/uwot")
16349 (synopsis "Uniform manifold approximation and projection")
16351 "This package provides an implementation of the Uniform Manifold
16352 Approximation and Projection dimensionality reduction by McInnes et
16353 al. (2018). It also provides means to transform new data and to carry out
16354 supervised dimensionality reduction. An implementation of the related
16355 LargeVis method of Tang et al. (2016) is also provided.")
16356 (license license:gpl3)))
16358 (define-public r-kableextra
16360 (name "r-kableextra")
16365 (uri (cran-uri "kableExtra" version))
16368 "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
16369 (properties `((upstream-name . "kableExtra")))
16370 (build-system r-build-system)
16372 `(("r-digest" ,r-digest)
16374 ("r-htmltools" ,r-htmltools)
16375 ("r-knitr" ,r-knitr)
16376 ("r-magrittr" ,r-magrittr)
16377 ("r-rmarkdown" ,r-rmarkdown)
16378 ("r-rstudioapi" ,r-rstudioapi)
16379 ("r-rvest" ,r-rvest)
16380 ("r-scales" ,r-scales)
16381 ("r-stringr" ,r-stringr)
16382 ("r-viridislite" ,r-viridislite)
16383 ("r-webshot" ,r-webshot)
16384 ("r-xml2" ,r-xml2)))
16386 `(("r-knitr" ,r-knitr)))
16387 (home-page "https://haozhu233.github.io/kableExtra/")
16388 (synopsis "Construct complex tables with pipe syntax")
16390 "Build complex HTML or LaTeX tables using @code{kable()} from
16391 @code{knitr} and the piping syntax from @code{magrittr}. The function
16392 @code{kable()} is a light weight table generator coming from @code{knitr}.
16393 This package simplifies the way to manipulate the HTML or LaTeX codes
16394 generated by @code{kable()} and allows users to construct complex tables and
16395 customize styles using a readable syntax.")
16396 (license license:expat)))
16398 (define-public r-glasso
16405 (uri (cran-uri "glasso" version))
16407 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16408 (build-system r-build-system)
16409 (native-inputs `(("gfortran" ,gfortran)))
16410 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16411 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16413 "This is a package for estimation of a sparse inverse covariance matrix
16414 using a lasso (L1) penalty. Facilities are provided for estimates along a
16415 path of values for the regularization parameter.")
16416 (license license:gpl2)))
16418 (define-public r-rhpcblasctl
16420 (name "r-rhpcblasctl")
16421 (version "0.20-137")
16425 (uri (cran-uri "RhpcBLASctl" version))
16428 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16429 (properties `((upstream-name . "RhpcBLASctl")))
16430 (build-system r-build-system)
16431 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16432 (synopsis "Control the number of threads on BLAS")
16434 "This package allows you to control the number of threads the BLAS
16435 library uses. It is also possible to control the number of threads in
16437 (license license:agpl3+)))
16439 (define-public r-lda
16446 (uri (cran-uri "lda" version))
16449 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16450 (build-system r-build-system)
16451 (home-page "https://cran.r-project.org/web/packages/lda/")
16452 (synopsis "Collapsed Gibbs sampling methods for topic models")
16454 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16455 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16456 mixed-membership stochastic blockmodel. Inference for all of these models is
16457 implemented via a fast collapsed Gibbs sampler written in C. Utility
16458 functions for reading/writing data typically used in topic models, as well as
16459 tools for examining posterior distributions are also included.")
16460 ;; Any version of the LGPL
16461 (license license:lgpl3+)))
16463 (define-public r-rann-l1
16470 (uri (cran-uri "RANN.L1" version))
16473 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16474 (properties `((upstream-name . "RANN.L1")))
16475 (build-system r-build-system)
16476 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16477 (synopsis "Fast nearest neighbour search using L1 metric")
16479 "This package provides tools to find the k nearest neighbours for every
16480 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16481 library. There is support for approximate as well as exact searches, fixed
16482 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16483 computed using the L1 (Manhattan, taxicab) metric.")
16484 (license license:gpl3+)))
16486 (define-public r-leiden
16493 (uri (cran-uri "leiden" version))
16496 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16497 (properties `((upstream-name . "leiden")))
16498 (build-system r-build-system)
16500 `(("r-igraph" ,r-igraph)
16501 ("r-matrix" ,r-matrix)
16502 ("r-reticulate" ,r-reticulate)))
16503 (home-page "https://github.com/TomKellyGenetics/leiden")
16504 (synopsis "R implementation of Leiden clustering algorithm")
16506 "This package implements the Python @code{leidenalg} module to be called
16507 in R. It enables clustering using the Leiden algorithm for partitioning a
16508 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16509 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16510 (license license:gpl3)))
16512 (define-public r-patchwork
16514 (name "r-patchwork")
16519 (uri (cran-uri "patchwork" version))
16522 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16523 (build-system r-build-system)
16525 `(("r-ggplot2" ,r-ggplot2)
16526 ("r-gtable" ,r-gtable)))
16528 `(("r-knitr" ,r-knitr)))
16529 (home-page "https://github.com/thomasp85/patchwork")
16530 (synopsis "Compose ggplot2 plots")
16532 "The @code{ggplot2} package provides a strong API for sequentially
16533 building up a plot, but does not concern itself with composition of multiple
16534 plots. Patchwork is a package that expands the API to allow for arbitrarily
16535 complex composition of plots by providing mathmatical operators for combining
16537 (license license:expat)))
16539 (define-public r-liger
16546 (uri (git-reference
16547 (url "https://github.com/MacoskoLab/liger")
16548 (commit (string-append "v" version))))
16549 (file-name (git-file-name name version))
16552 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16553 (modules '((guix build utils)))
16556 (delete-file "inst/java/ModularityOptimizer.jar")
16558 (build-system r-build-system)
16561 (modify-phases %standard-phases
16562 (add-after 'unpack 'build-java-part
16563 (lambda* (#:key inputs #:allow-other-keys)
16564 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16565 (for-each (lambda (file) (invoke "javac" file))
16566 (find-files "." "\\.java$"))
16567 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16568 (find-files "." "\\.class$"))
16571 `(("r-cowplot" ,r-cowplot)
16572 ("r-dosnow" ,r-dosnow)
16573 ("r-dplyr" ,r-dplyr)
16575 ("r-foreach" ,r-foreach)
16576 ("r-ggplot2" ,r-ggplot2)
16577 ("r-ggrepel" ,r-ggrepel)
16578 ("r-hmisc" ,r-hmisc)
16580 ("r-irlba" ,r-irlba)
16581 ("r-matrix" ,r-matrix)
16582 ("r-mclust" ,r-mclust)
16583 ("r-patchwork" ,r-patchwork)
16585 ("r-rann-l1" ,r-rann-l1)
16587 ("r-rcpparmadillo" ,r-rcpparmadillo)
16588 ("r-riverplot" ,r-riverplot)
16589 ("r-rtsne" ,r-rtsne)
16590 ("r-snow" ,r-snow)))
16592 `(("jdk" ,icedtea "jdk")
16593 ;; See https://github.com/MacoskoLab/liger/issues/96
16594 ;; The optimizer is released under the Expat license.
16598 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16601 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16603 ("r-knitr" ,r-knitr))) ; for vignettes
16604 (home-page "https://github.com/MacoskoLab/liger")
16605 (synopsis "Integrate and analyze multiple single-cell datasets")
16607 "LIGER is a package for integrating and analyzing multiple single-cell
16608 datasets, developed and maintained by the Macosko lab. It relies on
16609 integrative non-negative matrix factorization to identify shared and
16610 dataset-specific factors.")
16611 (license license:gpl3)))
16613 (define-public r-harmony
16620 (uri (git-reference
16621 (url "https://github.com/immunogenomics/harmony")
16623 (file-name (git-file-name name version))
16626 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16627 (modules '((guix build utils)))
16630 (for-each delete-file '("config.status" "configure"))
16632 (build-system r-build-system)
16634 `(("r-cowplot" ,r-cowplot)
16635 ("r-dplyr" ,r-dplyr)
16636 ("r-ggplot2" ,r-ggplot2)
16637 ("r-irlba" ,r-irlba)
16638 ("r-matrix" ,r-matrix)
16640 ("r-rcpparmadillo" ,r-rcpparmadillo)
16641 ("r-rcppprogress" ,r-rcppprogress)
16642 ("r-rlang" ,r-rlang)
16643 ("r-tibble" ,r-tibble)
16644 ("r-tidyr" ,r-tidyr)))
16646 `(("autoconf" ,autoconf)))
16647 (home-page "https://github.com/immunogenomics/harmony")
16648 (synopsis "Integration of single cell sequencing data")
16650 "This package provides an implementation of the Harmony algorithm for
16651 single cell integration, described in Korsunsky et al
16652 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16653 function and interfaces to external frameworks.")
16654 (license license:gpl3)))
16656 (define-public r-covr
16663 (uri (cran-uri "covr" version))
16665 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16666 (properties `((upstream-name . "covr")))
16667 (build-system r-build-system)
16669 `(("r-crayon" ,r-crayon)
16670 ("r-digest" ,r-digest)
16672 ("r-jsonlite" ,r-jsonlite)
16674 ("r-withr" ,r-withr)
16675 ("r-yaml" ,r-yaml)))
16677 `(("r-knitr" ,r-knitr))) ; for vignettes
16678 (home-page "https://github.com/r-lib/covr")
16679 (synopsis "Test coverage for R packages")
16681 "Thisp package enables you to track and report code coverage for your
16682 package and (optionally) upload the results to a coverage service. Code
16683 coverage is a measure of the amount of code being exercised by a set of tests.
16684 It is an indirect measure of test quality and completeness. This package is
16685 compatible with any testing methodology or framework and tracks coverage of
16686 both R code and compiled C/C++/FORTRAN code.")
16687 (license license:gpl3)))
16689 (define-public r-systemfonts
16691 (name "r-systemfonts")
16696 (uri (cran-uri "systemfonts" version))
16699 "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
16700 (properties `((upstream-name . "systemfonts")))
16701 (build-system r-build-system)
16703 `(("r-cpp11" ,r-cpp11)))
16705 `(("fontconfig" ,fontconfig)
16708 `(("pkg-config" ,pkg-config)
16709 ("r-knitr" ,r-knitr)))
16710 (home-page "https://github.com/r-lib/systemfonts")
16711 (synopsis "System native font finding")
16713 "This package provides system native access to the font catalogue. As
16714 font handling varies between systems it is difficult to correctly locate
16715 installed fonts across different operating systems. The 'systemfonts' package
16716 provides bindings to the native libraries for finding font files that can then
16717 be used further by e.g. graphic devices.")
16718 (license license:expat)))
16720 (define-public r-graphlayouts
16722 (name "r-graphlayouts")
16727 (uri (cran-uri "graphlayouts" version))
16730 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16731 (properties `((upstream-name . "graphlayouts")))
16732 (build-system r-build-system)
16734 `(("r-igraph" ,r-igraph)
16736 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16737 (home-page "https://github.com/schochastics/graphlayouts")
16738 (synopsis "Additional layout algorithms for network visualizations")
16740 "This package provides several layout algorithms to visualize networks
16741 which are not part of the igraph library. Most are based on the concept of
16742 stress majorization by Gansner et al. (2004)
16743 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16744 emphasize hidden group structures in networks or focus on specific nodes.")
16745 (license license:expat)))
16747 (define-public r-tidygraph
16749 (name "r-tidygraph")
16754 (uri (cran-uri "tidygraph" version))
16757 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16758 (properties `((upstream-name . "tidygraph")))
16759 (build-system r-build-system)
16761 `(("r-dplyr" ,r-dplyr)
16762 ("r-igraph" ,r-igraph)
16763 ("r-magrittr" ,r-magrittr)
16764 ("r-pillar" ,r-pillar)
16767 ("r-rlang" ,r-rlang)
16768 ("r-tibble" ,r-tibble)
16769 ("r-tidyr" ,r-tidyr)))
16770 (home-page "https://github.com/thomasp85/tidygraph")
16771 (synopsis "Tidy API for graph manipulation")
16773 "This package provides a graph implementation that can be thought of as
16774 two tidy data frames describing node and edge data respectively. It provides
16775 an approach to manipulate these two virtual data frames using the API defined
16776 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16777 common graph algorithms.")
16778 (license license:expat)))
16780 (define-public r-soupx
16781 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16785 (version (git-version "0.3.1" revision commit))
16789 (uri (git-reference
16790 (url "https://github.com/constantAmateur/SoupX")
16792 (file-name (git-file-name name version))
16795 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16796 (properties `((upstream-name . "SoupX")))
16797 (build-system r-build-system)
16799 `(("r-ggplot2" ,r-ggplot2)
16800 ("r-matrix" ,r-matrix)
16801 ("r-seurat" ,r-seurat)))
16802 (home-page "https://github.com/constantAmateur/SoupX")
16803 (synopsis "Single cell mRNA Soup eXterminator")
16805 "This package provides a package for quantifying, profiling and
16806 removing cell free mRNA contamination (the \"soup\") from droplet based single
16807 cell RNA-seq experiments.")
16808 (license license:gpl2))))
16810 (define-public r-assertr
16817 (uri (cran-uri "assertr" version))
16820 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16821 (build-system r-build-system)
16823 `(("r-dplyr" ,r-dplyr)
16825 ("r-rlang" ,r-rlang)))
16827 `(("r-knitr" ,r-knitr))) ; needed for vignette
16828 (home-page "https://github.com/ropensci/assertr")
16829 (synopsis "Assertive programming for R analysis pipelines")
16831 "This package provides functionality to assert conditions that have to be
16832 met so that errors in data used in analysis pipelines can fail quickly. It is
16833 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16835 (license license:expat)))
16837 (define-public r-parameters
16839 (name "r-parameters")
16844 (uri (cran-uri "parameters" version))
16847 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16848 (properties `((upstream-name . "parameters")))
16849 (build-system r-build-system)
16851 `(("r-bayestestr" ,r-bayestestr)
16852 ("r-insight" ,r-insight)))
16854 `(("r-knitr" ,r-knitr)))
16855 (home-page "https://cran.r-project.org/web/packages/parameters")
16856 (synopsis "Processing of model parameters")
16858 "This package provides utilities for processing the parameters of various
16859 statistical models. Beyond computing p values, CIs, and other indices for a
16860 wide variety of models, this package implements features like standardization
16861 or bootstrapping of parameters and models, feature reduction (feature
16862 extraction and variable selection) as well as conversion between indices of
16864 (license license:gpl3)))
16866 (define-public r-rgdal
16873 (uri (cran-uri "rgdal" version))
16875 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16876 (properties `((upstream-name . "rgdal")))
16877 (build-system r-build-system)
16885 `(("pkg-config" ,pkg-config)
16886 ("r-knitr" ,r-knitr)))
16887 (home-page "http://rgdal.r-forge.r-project.org")
16888 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16890 "This package provides bindings to the Geospatial Data Abstraction
16891 Library (GDAL) and access to projection/transformation operations from the
16893 (license license:gpl2+)))
16895 (define-public r-insol
16902 (uri (cran-uri "insol" version))
16905 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16906 (properties `((upstream-name . "insol")))
16907 (build-system r-build-system)
16909 `(("r-raster" ,r-raster)))
16911 `(("gfortran" ,gfortran)))
16912 (home-page "https://meteoexploration.com/R/insol/index.html")
16913 (synopsis "Tools for calculating solar radiation")
16915 "This package provides functions to compute insolation on tilted
16916 surfaces, computes atmospheric transmittance and related parameters such as:
16917 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16918 time, vector in the direction of the sun, vector normal to surface, and some
16919 atmospheric physics.")
16920 (license license:gpl2+)))
16922 (define-public r-lifecycle
16924 (name "r-lifecycle")
16929 (uri (cran-uri "lifecycle" version))
16932 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16933 (properties `((upstream-name . "lifecycle")))
16934 (build-system r-build-system)
16936 `(("r-glue" ,r-glue)
16937 ("r-rlang" ,r-rlang)))
16939 `(("r-knitr" ,r-knitr))) ; for vignettes
16940 (home-page "https://github.com/r-lib/lifecycle")
16941 (synopsis "Manage the life cycle of your package functions")
16943 "Manage the life cycle of your exported functions with shared
16944 conventions, documentation badges, and non-invasive deprecation warnings. The
16945 lifecycle package defines four development stages (experimental, maturing,
16946 stable, and questioning) and three deprecation stages (soft-deprecated,
16947 deprecated, and defunct). It makes it easy to insert badges corresponding to
16948 these stages in your documentation. Usage of deprecated functions are
16949 signalled with increasing levels of non-invasive verbosity.")
16950 (license license:gpl3)))
16952 (define-public r-assertable
16954 (name "r-assertable")
16959 (uri (cran-uri "assertable" version))
16962 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16963 (build-system r-build-system)
16965 `(("r-data-table" ,r-data-table)))
16966 (home-page "https://cran.r-project.org/web/packages/assertable/")
16967 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16968 (description "This package provides simple, flexible assertions on
16969 data.frame or data.table objects with verbose output for vetting. While other
16970 assertion packages apply towards more general use-cases, @code{assertable} is
16971 tailored towards tabular data. It includes functions to check variable names
16972 and values, whether the dataset contains all combinations of a given set of
16973 unique identifiers, and whether it is a certain length. In addition,
16974 @code{assertable} includes utility functions to check the existence of target
16975 files and to efficiently import multiple tabular data files into one
16977 (license license:gpl3)))
16979 (define-public r-quadprog
16981 (name "r-quadprog")
16986 (uri (cran-uri "quadprog" version))
16988 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16989 (build-system r-build-system)
16991 `(("gfortran" ,gfortran)))
16992 (home-page "https://cran.r-project.org/web/packages/quadprog")
16993 (synopsis "Functions to solve quadratic programming problems")
16995 "This package contains routines and documentation for solving quadratic
16996 programming problems.")
16997 (license license:gpl3+)))
16999 (define-public r-desolve
17006 (uri (cran-uri "deSolve" version))
17008 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17009 (properties `((upstream-name . "deSolve")))
17010 (build-system r-build-system)
17012 `(("gfortran" ,gfortran)))
17013 (home-page "https://desolve.r-forge.r-project.org/")
17014 (synopsis "Solvers for initial value problems of differential equations")
17015 (description "This package provides functions that solve initial value
17016 problems of a system of first-order @dfn{ordinary differential
17017 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17018 @dfn{differential algebraic equations} (DAE), and of delay differential
17019 equations. The functions provide an interface to the FORTRAN functions
17020 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17021 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17022 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17023 time steps. The package contains routines designed for solving ODEs resulting
17024 from 1-D, 2-D and 3-D partial differential equations that have been converted
17025 to ODEs by numerical differencing.")
17026 (license license:gpl2+)))
17028 (define-public r-pracma
17034 (uri (cran-uri "pracma" version))
17036 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17037 (build-system r-build-system)
17038 (home-page "https://cran.r-project.org/web/packages/pracma/")
17039 (synopsis "Practical numerical math functions")
17040 (description "This package provides functions for numerical analysis and
17041 linear algebra, numerical optimization, differential equations, plus some
17042 special functions. It uses Matlab function names where appropriate to simplify
17044 (license license:gpl3+)))
17046 (define-public r-subplex
17053 (uri (cran-uri "subplex" version))
17056 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17057 (build-system r-build-system)
17059 `(("gfortran" ,gfortran)))
17060 (home-page "https://cran.r-project.org/web/packages/subplex")
17061 (synopsis "Unconstrained optimization using the subplex algorithm")
17063 "This package implements the Subplex optimization algorithm.
17064 It solves unconstrained optimization problems using a simplex method on
17065 subspaces. The method is well suited for optimizing objective functions that
17066 are noisy or are discontinuous at the solution.")
17067 (license license:gpl3+)))
17069 (define-public r-txtplot
17076 (uri (cran-uri "txtplot" version))
17079 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17080 (build-system r-build-system)
17081 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17082 (synopsis "Text-based plotting")
17083 (description "This package provides functions to produce rudimentary ASCII
17084 graphics directly in the terminal window. This package provides a basic
17085 plotting function (and equivalents of curve, density, acf and barplot) as well
17086 as a boxplot function.")
17087 (license license:lgpl3+)))
17089 (define-public r-bio3d
17096 (uri (cran-uri "bio3d" version))
17099 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17100 (properties `((upstream-name . "bio3d")))
17101 (build-system r-build-system)
17102 (inputs `(("zlib" ,zlib)))
17103 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17104 (home-page "http://thegrantlab.org/bio3d/")
17105 (synopsis "Biological structure analysis")
17107 "This package provides utilities to process, organize and explore protein
17108 structure, sequence and dynamics data. Features include the ability to read
17109 and write structure, sequence and dynamic trajectory data, perform sequence
17110 and structure database searches, data summaries, atom selection, alignment,
17111 superposition, rigid core identification, clustering, torsion analysis,
17112 distance matrix analysis, structure and sequence conservation analysis, normal
17113 mode analysis, principal component analysis of heterogeneous structure data,
17114 and correlation network analysis from normal mode and molecular dynamics data.
17115 In addition, various utility functions are provided to enable the statistical
17116 and graphical power of the R environment to work with biological sequence and
17118 (license license:gpl2+)))
17120 (define-public r-bios2cor
17122 (name "r-bios2cor")
17127 (uri (cran-uri "Bios2cor" version))
17130 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
17131 (properties `((upstream-name . "Bios2cor")))
17132 (build-system r-build-system)
17134 `(("r-bigmemory" ,r-bigmemory)
17135 ("r-bio3d" ,r-bio3d)
17136 ("r-circular" ,r-circular)
17137 ("r-igraph" ,r-igraph)))
17138 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17139 (synopsis "From biological sequences and simulations to correlation analysis")
17141 "This package provides utilities for computation and analysis of
17142 correlation/covariation in multiple sequence alignments and in side chain
17143 motions during molecular dynamics simulations. Features include the
17144 computation of correlation/covariation scores using a variety of scoring
17145 functions between either sequence positions in alignments or side chain
17146 dihedral angles in molecular dynamics simulations and utilities to analyze the
17147 correlation/covariation matrix through a variety of tools including network
17148 representation and principal components analysis. In addition, several
17149 utility functions are based on the R graphical environment to provide friendly
17150 tools for help in data interpretation.")
17151 (license license:gpl2+)))
17153 ;; This package includes minified JavaScript files. When upgrading please
17154 ;; check that there are no new minified JavaScript files.
17155 (define-public r-networkd3
17157 (name "r-networkd3")
17162 (uri (cran-uri "networkD3" version))
17165 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17168 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17170 (properties `((upstream-name . "networkD3")))
17171 (build-system r-build-system)
17173 `(#:modules ((guix build utils)
17174 (guix build r-build-system)
17178 (modify-phases %standard-phases
17179 (add-after 'unpack 'process-javascript
17180 (lambda* (#:key inputs #:allow-other-keys)
17181 (with-directory-excursion "inst/htmlwidgets/lib/"
17185 `((,(assoc-ref inputs "d3.v4.js")
17186 "d3-4.5.0/d3.min.js"))))
17187 (lambda (sources targets)
17188 (for-each (lambda (source target)
17189 (format #t "Processing ~a --> ~a~%"
17191 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17192 (call-with-output-file target
17194 (dump-port minified port)))))
17195 sources targets))))
17198 `(("uglify-js" ,uglify-js)
17199 ;; NOTE: Make sure that this version of d3 is still valid when
17200 ;; upgrading the package.
17204 (uri "https://d3js.org/d3.v4.js")
17207 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17209 `(("r-htmlwidgets" ,r-htmlwidgets)
17210 ("r-igraph" ,r-igraph)
17211 ("r-magrittr" ,r-magrittr)))
17212 (home-page "https://cran.r-project.org/package=networkD3")
17213 (synopsis "D3 JavaScript network graphs from R")
17215 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17217 (license license:gpl3+)))
17219 (define-public r-aasea
17226 (uri (cran-uri "aaSEA" version))
17229 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17230 (properties `((upstream-name . "aaSEA")))
17231 (build-system r-build-system)
17233 `(("r-bios2cor" ,r-bios2cor)
17235 ("r-hmisc" ,r-hmisc)
17236 ("r-magrittr" ,r-magrittr)
17237 ("r-networkd3" ,r-networkd3)
17238 ("r-plotly" ,r-plotly)
17239 ("r-seqinr" ,r-seqinr)
17240 ("r-shiny" ,r-shiny)
17241 ("r-shinydashboard" ,r-shinydashboard)))
17242 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17243 (synopsis "Amino acid substitution effect analyzer")
17245 "Given a protein multiple sequence alignment, it is a daunting task to
17246 assess the effects of substitutions along sequence length. The aaSEA package
17247 is intended to help researchers to rapidly analyze property changes caused by
17248 single, multiple and correlated amino acid substitutions in proteins.")
17249 (license license:gpl3)))
17251 (define-public r-abacus
17258 (uri (cran-uri "ABACUS" version))
17261 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17262 (properties `((upstream-name . "ABACUS")))
17263 (build-system r-build-system)
17265 `(("r-ggplot2" ,r-ggplot2)
17266 ("r-shiny" ,r-shiny)))
17267 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17268 (synopsis "Apps-based activities for communicating and understanding statistics")
17270 "This package provides a set of Shiny apps for effective communication
17271 and understanding in statistics. The current version includes properties of
17272 normal distribution, properties of sampling distribution, one-sample z and t
17273 tests, two samples independent (unpaired) t test and analysis of variance.")
17274 (license license:gpl3)))
17276 (define-public r-abc-rap
17283 (uri (cran-uri "ABC.RAP" version))
17286 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17287 (properties `((upstream-name . "ABC.RAP")))
17288 (build-system r-build-system)
17289 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17290 (synopsis "Array-based CpG region analysis pipeline")
17292 "This package aims to identify candidate genes that are differentially
17293 methylated between cases and controls. It applies Student's t-test and delta
17294 beta analysis to identify candidate genes containing multiple CpG sites.")
17295 (license license:gpl3)))
17297 (define-public r-abcadm
17304 (uri (cran-uri "abcADM" version))
17307 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17308 (properties `((upstream-name . "abcADM")))
17309 (build-system r-build-system)
17312 ("r-rcpp" ,r-rcpp)))
17313 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17314 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17316 "This package provides tools to estimate parameters of accumulated
17317 damage (load duration) models based on failure time data under a Bayesian
17318 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17319 long-term reliability under stochastic load profiles.")
17320 (license license:gpl3)))
17322 (define-public r-rglpk
17329 (uri (cran-uri "Rglpk" version))
17332 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17333 (properties `((upstream-name . "Rglpk")))
17334 (build-system r-build-system)
17336 `(("r-slam" ,r-slam)))
17339 (home-page "https://r-forge.r-project.org/projects/rglp/")
17340 (synopsis "R interface to the GNU Linear Programming Kit")
17342 "This package provides an R interface to the GNU Linear Programming Kit,
17343 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17344 integer linear programming} (MILP) and other related problems.")
17346 (license (list license:gpl2 license:gpl3))))
17348 (define-public r-abcdefba
17350 (name "r-abcdefba")
17355 (uri (cran-uri "abcdeFBA" version))
17358 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17359 (properties `((upstream-name . "abcdeFBA")))
17360 (build-system r-build-system)
17362 `(("r-corrplot" ,r-corrplot)
17363 ("r-lattice" ,r-lattice)
17365 ("r-rglpk" ,r-rglpk)))
17366 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17367 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17369 "This package provides functions for Constraint Based Simulation using
17370 Flux Balance Analysis and informative analysis of the data generated during
17372 (license license:gpl2)))
17374 (define-public r-abcrlda
17381 (uri (cran-uri "abcrlda" version))
17384 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17385 (properties `((upstream-name . "abcrlda")))
17386 (build-system r-build-system)
17387 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17388 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17390 "This package offers methods to perform @dfn{asymptotically
17391 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17392 cost-sensitive binary classification. The bias-correction is an estimate of
17393 the bias term added to regularized discriminant analysis that minimizes the
17395 (license license:gpl3)))
17397 (define-public r-abemus
17404 (uri (cran-uri "abemus" version))
17407 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17408 (properties `((upstream-name . "abemus")))
17409 (build-system r-build-system)
17411 `(("r-data-table" ,r-data-table)))
17412 (home-page "https://cran.r-project.org/web/packages/abemus/")
17413 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17415 "This package provides an implementation of @dfn{Adaptive Base Error
17416 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17417 platform-specific genetic knowledge and empirical signal to readily detect and
17418 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17419 cell free DNA} (cfDNA).")
17420 (license license:gpl3)))
17422 ;; This package includes minified JavaScript files. When upgrading please
17423 ;; check that there are no new minified JavaScript files.
17424 (define-public r-rintrojs
17426 (name "r-rintrojs")
17431 (uri (cran-uri "rintrojs" version))
17434 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17435 (properties `((upstream-name . "rintrojs")))
17436 (build-system r-build-system)
17438 `(#:modules ((guix build utils)
17439 (guix build r-build-system)
17443 (modify-phases %standard-phases
17444 (add-after 'unpack 'process-javascript
17445 (lambda* (#:key inputs #:allow-other-keys)
17446 (with-directory-excursion "inst/javascript/introjs/"
17450 `((,(assoc-ref inputs "intro.js")
17452 (lambda (sources targets)
17453 (for-each (lambda (source target)
17454 (format #t "Processing ~a --> ~a~%"
17456 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17457 (call-with-output-file target
17459 (dump-port minified port)))))
17460 sources targets))))
17463 `(("uglify-js" ,uglify-js)
17467 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17470 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17472 `(("r-jsonlite" ,r-jsonlite)
17473 ("r-shiny" ,r-shiny)))
17474 (home-page "https://github.com/carlganz/rintrojs")
17475 (synopsis "Wrapper for the Intro.js library")
17477 "This package provides a wrapper for the @url{http://www.introjs.com,
17478 Intro.js} library. This package makes it easy to include step-by-step
17479 introductions, and clickable hints in a Shiny application. It supports both
17480 static introductions in the UI, and programmatic introductions from the
17482 (license license:agpl3+)))
17484 (define-public r-sysfonts
17486 (name "r-sysfonts")
17491 (uri (cran-uri "sysfonts" version))
17494 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17495 (properties `((upstream-name . "sysfonts")))
17496 (build-system r-build-system)
17498 `(("freetype" ,freetype)
17502 `(("pkg-config" ,pkg-config)))
17503 (home-page "https://github.com/yixuan/sysfonts")
17504 (synopsis "Loading fonts into R")
17506 "This is a package to simplify loading of system fonts and Google Fonts
17507 into R, in order to support other packages.")
17508 (license license:gpl2)))
17510 (define-public r-showtextdb
17512 (name "r-showtextdb")
17517 (uri (cran-uri "showtextdb" version))
17520 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17521 (properties `((upstream-name . "showtextdb")))
17522 (build-system r-build-system)
17524 `(("r-sysfonts" ,r-sysfonts)))
17525 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17526 (synopsis "Font files for the 'showtext' package")
17528 "This package provides font files that can be used by the @code{showtext}
17530 (license license:asl2.0)))
17532 (define-public r-showtext
17534 (name "r-showtext")
17539 (uri (cran-uri "showtext" version))
17542 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17543 (properties `((upstream-name . "showtext")))
17544 (build-system r-build-system)
17546 `(("freetype" ,freetype)
17550 `(("r-showtextdb" ,r-showtextdb)
17551 ("r-sysfonts" ,r-sysfonts)))
17553 `(("pkg-config" ,pkg-config)
17554 ("r-knitr" ,r-knitr)))
17555 (home-page "https://github.com/yixuan/showtext")
17556 (synopsis "Using fonts more easily in R graphs")
17558 "This package aims to make it easy to use various types of
17559 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17560 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17561 will be converted into polygons or raster images, hence after the plot has
17562 been created, it no longer relies on the font files. No external software
17563 such as Ghostscript is needed to use this package.")
17564 (license license:asl2.0)))
17566 (define-public r-emojifont
17568 (name "r-emojifont")
17573 (uri (cran-uri "emojifont" version))
17576 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17577 (properties `((upstream-name . "emojifont")))
17578 (build-system r-build-system)
17580 `(("r-ggplot2" ,r-ggplot2)
17581 ("r-proto" ,r-proto)
17582 ("r-showtext" ,r-showtext)
17583 ("r-sysfonts" ,r-sysfonts)))
17584 (home-page "https://guangchuangyu.github.io/emojifont")
17585 (synopsis "Emoji and Font Awesome in R graphics")
17587 "This package enables the use of emoji and the Font Awesome glyphs in
17588 both base and ggplot2 graphics.")
17589 (license license:artistic2.0)))
17591 (define-public r-abstractr
17593 (name "r-abstractr")
17598 (uri (cran-uri "abstractr" version))
17601 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17602 (properties `((upstream-name . "abstractr")))
17603 (build-system r-build-system)
17605 `(("r-colourpicker" ,r-colourpicker)
17606 ("r-emojifont" ,r-emojifont)
17607 ("r-ggplot2" ,r-ggplot2)
17608 ("r-gridextra" ,r-gridextra)
17609 ("r-rintrojs" ,r-rintrojs)
17610 ("r-shiny" ,r-shiny)
17611 ("r-shinythemes" ,r-shinythemes)))
17612 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17613 (synopsis "R-Shiny application for creating visual abstracts")
17615 "This package provides an R Shiny application to create visual abstracts
17616 for original research. A variety of user defined options and formatting are
17618 (license license:gpl3)))
17620 (define-public r-qgam
17627 (uri (cran-uri "qgam" version))
17630 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17631 (properties `((upstream-name . "qgam")))
17632 (build-system r-build-system)
17634 `(("r-doparallel" ,r-doparallel)
17637 ("r-shiny" ,r-shiny)))
17638 (native-inputs `(("r-knitr" ,r-knitr)))
17639 (home-page "https://cran.r-project.org/web/packages/qgam/")
17640 (synopsis "Smooth additive quantile regression models")
17642 "This package provides smooth additive quantile regression models, fitted
17643 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17644 the smoothing parameters are estimated automatically by marginal loss
17645 minimization, while the regression coefficients are estimated using either
17646 PIRLS or Newton algorithm. The learning rate is determined so that the
17647 Bayesian credible intervals of the estimated effects have approximately the
17648 correct coverage. The main function is @code{qgam()} which is similar to
17649 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17650 regression models.")
17651 (license license:gpl2+)))
17653 (define-public r-abtest
17660 (uri (cran-uri "abtest" version))
17663 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17664 (properties `((upstream-name . "abtest")))
17665 (build-system r-build-system)
17667 `(("r-matrix" ,r-matrix)
17668 ("r-mvtnorm" ,r-mvtnorm)
17669 ("r-plotrix" ,r-plotrix)
17671 ("r-rcolorbrewer" ,r-rcolorbrewer)
17674 ("r-truncnorm" ,r-truncnorm)))
17675 (home-page "https://cran.r-project.org/web/packages/abtest/")
17676 (synopsis "Bayesian A/B testing")
17678 "This package provides functions for Bayesian A/B testing including prior
17679 elicitation options based on Kass and Vaidyanathan (1992)
17680 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17681 (license license:gpl2+)))
17683 (define-public r-accept
17690 (uri (cran-uri "accept" version))
17693 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17694 (properties `((upstream-name . "accept")))
17695 (build-system r-build-system)
17697 `(("r-dplyr" ,r-dplyr)
17698 ("r-extrafont" ,r-extrafont)
17700 ("r-plotly" ,r-plotly)
17701 ("r-stringr" ,r-stringr)
17702 ("r-viridis" ,r-viridis)))
17703 (home-page "https://cran.r-project.org/web/packages/accept/")
17704 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17706 "This package allows clinicians to predict the rate and severity of
17707 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17708 Disease} (COPD) patients, based on the clinical prediction model published in
17709 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17710 (license license:gpl3)))
17712 (define-public r-smpracticals
17714 (name "r-smpracticals")
17719 (uri (cran-uri "SMPracticals" version))
17722 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17723 (properties `((upstream-name . "SMPracticals")))
17724 (build-system r-build-system)
17726 `(("r-ellipse" ,r-ellipse)
17729 ("r-survival" ,r-survival)))
17730 (home-page "http://statwww.epfl.ch/davison/SM/")
17731 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17733 "This package contains the datasets and a few functions for use with the
17734 practicals outlined in Appendix A of the book Statistical Models (Davison,
17735 2003, Cambridge University Press). The practicals themselves can be found at
17736 @url{http://statwww.epfl.ch/davison/SM/}.")
17737 (license license:gpl2+)))
17739 (define-public r-fgui
17746 (uri (cran-uri "fgui" version))
17749 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17750 (properties `((upstream-name . "fgui")))
17751 (build-system r-build-system)
17753 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17754 (synopsis "Create GUI for R functions")
17756 "Rapidly create a GUI for a function you created by automatically
17757 creating widgets for arguments of the function. This package automatically
17758 parses help routines for context-sensitive help to these arguments. The
17759 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17760 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17761 incorporated into the interface for greater customization for the more
17763 ;; Any version of the GPL.
17764 (license (list license:gpl2+ license:gpl3+))))
17766 (define-public r-tcltk2
17773 (uri (cran-uri "tcltk2" version))
17776 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17777 (properties `((upstream-name . "tcltk2")))
17778 (build-system r-build-system)
17782 (home-page "https://www.sciviews.org/SciViews-R")
17783 (synopsis "Tcl/Tk additions")
17785 "This package provides a series of additional Tcl commands and Tk widgets
17786 with style and various functions to supplement the tcltk package")
17787 (license license:lgpl3)))
17789 (define-public r-accrual
17796 (uri (cran-uri "accrual" version))
17799 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17800 (properties `((upstream-name . "accrual")))
17801 (build-system r-build-system)
17803 `(("r-fgui" ,r-fgui)
17804 ("r-smpracticals" ,r-smpracticals)
17805 ("r-tcltk2" ,r-tcltk2)))
17806 (home-page "https://cran.r-project.org/web/packages/accrual/")
17807 (synopsis "Bayesian accrual prediction")
17809 "Subject recruitment for medical research is challenging. Slow patient
17810 accrual leads to delay in research. Accrual monitoring during the process of
17811 recruitment is critical. Researchers need reliable tools to manage the
17812 accrual rate. This package provides an implementation of a Bayesian method
17813 that integrates researcher's experience on previous trials and data from the
17814 current study, providing reliable prediction on accrual rate for clinical
17815 studies. It provides functions for Bayesian accrual prediction which can be
17816 easily used by statisticians and clinical researchers.")
17817 (license license:gpl2)))
17819 (define-public r-accrued
17826 (uri (cran-uri "accrued" version))
17829 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17830 (properties `((upstream-name . "accrued")))
17831 (build-system r-build-system)
17832 (home-page "https://cran.r-project.org/web/packages/accrued/")
17833 (synopsis "Data quality visualization tools for partially accruing data")
17835 "This is a package for visualizing data quality of partially accruing
17837 (license license:gpl3)))
17839 (define-public r-mda
17846 (uri (cran-uri "mda" version))
17849 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17850 (properties `((upstream-name . "mda")))
17851 (build-system r-build-system)
17852 (propagated-inputs `(("r-class" ,r-class)))
17853 (native-inputs `(("gfortran" ,gfortran)))
17854 (home-page "https://cran.r-project.org/web/packages/mda/")
17855 (synopsis "Mixture and flexible discriminant analysis")
17857 "This is a package for mixture and flexible discriminant analysis,
17858 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17859 (license license:gpl2)))
17861 (define-public r-elasticnet
17863 (name "r-elasticnet")
17868 (uri (cran-uri "elasticnet" version))
17871 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17872 (properties `((upstream-name . "elasticnet")))
17873 (build-system r-build-system)
17875 `(("r-lars" ,r-lars)))
17876 (home-page "http://users.stat.umn.edu/~zouxx019/")
17877 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17879 "This package provides functions for fitting the entire solution path of
17880 the Elastic-Net and also provides functions for estimating sparse Principal
17881 Components. The Lasso solution paths can be computed by the same function.")
17882 (license license:gpl2+)))
17884 (define-public r-sparselda
17886 (name "r-sparselda")
17891 (uri (cran-uri "sparseLDA" version))
17894 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17895 (properties `((upstream-name . "sparseLDA")))
17896 (build-system r-build-system)
17898 `(("r-elasticnet" ,r-elasticnet)
17901 (home-page "https://www.imm.dtu.dk/~lkhc/")
17902 (synopsis "Sparse discriminant analysis")
17904 "This package performs sparse linear discriminant analysis for Gaussians
17905 and mixture of Gaussian models.")
17906 (license license:gpl2+)))
17908 (define-public r-accsda
17915 (uri (cran-uri "accSDA" version))
17918 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17919 (properties `((upstream-name . "accSDA")))
17920 (build-system r-build-system)
17922 `(("r-ggplot2" ,r-ggplot2)
17923 ("r-ggthemes" ,r-ggthemes)
17924 ("r-gridextra" ,r-gridextra)
17926 ("r-rarpack" ,r-rarpack)
17927 ("r-sparselda" ,r-sparselda)))
17928 (home-page "https://github.com/gumeo/accSDA/wiki")
17929 (synopsis "Accelerated sparse discriminant analysis")
17931 "This package provides an implementation of sparse linear discriminant
17932 analysis, which is a supervised classification method for multiple classes.
17933 Various novel optimization approaches to this problem are implemented
17934 including @dfn{alternating direction method of multipliers} (ADMM),
17935 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17936 Functions for performing cross validation are also supplied along with basic
17937 prediction and plotting functions. @dfn{Sparse zero variance
17938 discriminant} (SZVD) analysis is also included in the package.")
17939 (license license:gpl2+)))
17941 (define-public r-ace2fastq
17943 (name "r-ace2fastq")
17948 (uri (cran-uri "ace2fastq" version))
17951 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17952 (properties `((upstream-name . "ace2fastq")))
17953 (build-system r-build-system)
17955 `(("r-stringr" ,r-stringr)))
17956 (home-page "https://github.com/c5sire/ace2fastq")
17957 (synopsis "ACE file to FASTQ converter")
17959 "The ACE file format is used in genomics to store contigs from sequencing
17960 machines. This tools converts it into FASTQ format. Both formats contain the
17961 sequence characters and their corresponding quality information. Unlike the
17962 FASTQ file, the ACE file stores the quality values numerically. The
17963 conversion algorithm uses the standard Sanger formula. The package
17964 facilitates insertion into pipelines, and content inspection.")
17965 (license license:gpl3)))
17967 (define-public r-rngwell
17974 (uri (cran-uri "rngWELL" version))
17977 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17978 (properties `((upstream-name . "rngWELL")))
17979 (build-system r-build-system)
17980 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17981 (synopsis "Toolbox for WELL random number generators")
17983 "This is a dedicated package to WELL pseudo random generators, which were
17984 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17985 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17986 (license license:bsd-3)))
17988 (define-public r-randtoolbox
17990 (name "r-randtoolbox")
17995 (uri (cran-uri "randtoolbox" version))
17998 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17999 (properties `((upstream-name . "randtoolbox")))
18000 (build-system r-build-system)
18002 `(("r-rngwell" ,r-rngwell)))
18004 `(("gfortran" ,gfortran)))
18005 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18006 (synopsis "Toolbox for pseudo and quasi random number generation")
18008 "This package provides
18011 @item pseudo random generators, such as general linear
18012 congruential generators, multiple recursive generators and generalized
18013 feedback shift register (SF-Mersenne Twister algorithm and WELL
18016 @item quasi random generators, such as the Torus algorithm, the Sobol
18017 sequence, the Halton sequence (including the Van der Corput sequence), and
18019 @item some generator tests: the gap test, the serial test, the poker test.
18022 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18023 (license license:bsd-3)))
18025 (define-public r-lhs
18032 (uri (cran-uri "lhs" version))
18035 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
18036 (properties `((upstream-name . "lhs")))
18037 (build-system r-build-system)
18038 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18040 `(("r-knitr" ,r-knitr)))
18041 (home-page "https://github.com/bertcarnell/lhs")
18042 (synopsis "Latin Hypercube Samples")
18044 "This package provides a number of methods for creating and augmenting
18045 Latin Hypercube Samples.")
18046 (license license:gpl3)))
18048 (define-public r-acebayes
18050 (name "r-acebayes")
18055 (uri (cran-uri "acebayes" version))
18058 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
18059 (properties `((upstream-name . "acebayes")))
18060 (build-system r-build-system)
18062 `(("r-compare" ,r-compare)
18064 ("r-randtoolbox" ,r-randtoolbox)
18066 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18067 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18068 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18070 "Finding an optimal Bayesian experimental design involves maximizing an
18071 objective function given by the expectation of some appropriately chosen
18072 utility function with respect to the joint distribution of unknown
18073 quantities (including responses). This objective function is usually not
18074 available in closed form and the design space can be continuous and of high
18075 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18076 to maximise an approximation to the expectation of the utility function.")
18077 (license license:gpl2)))
18079 (define-public r-acet
18086 (uri (cran-uri "ACEt" version))
18089 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
18090 (properties `((upstream-name . "ACEt")))
18091 (build-system r-build-system)
18096 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18097 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18098 (synopsis "Estimating dynamic heritability and twin model comparison")
18100 "This package supports twin models that are able to estimate the dynamic
18101 behaviour of the variance components in the classical twin models with respect
18102 to age using B-splines and P-splines.")
18103 (license license:gpl2+)))
18105 (define-public r-acfmperiod
18107 (name "r-acfmperiod")
18112 (uri (cran-uri "acfMPeriod" version))
18115 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18116 (properties `((upstream-name . "acfMPeriod")))
18117 (build-system r-build-system)
18119 `(("r-mass" ,r-mass)))
18120 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18121 (synopsis "Estimation of the ACF from the M-periodogram")
18123 "This package support non-robust and robust computations of the sample
18124 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18125 univariate and multivariate processes. The methodology consists in reversing
18126 the diagonalization procedure involving the periodogram or the
18127 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18128 ACOVF or the ACF as discussed in Fuller (1995)
18129 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18130 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18131 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18132 (license license:gpl2+)))
18134 (define-public r-gamlss-data
18136 (name "r-gamlss-data")
18141 (uri (cran-uri "gamlss.data" version))
18144 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18145 (properties `((upstream-name . "gamlss.data")))
18146 (build-system r-build-system)
18147 (home-page "http://www.gamlss.org/")
18148 (synopsis "GAMLSS data")
18150 "This package provides data used as examples to demonstrate GAMLSS
18152 ;; Either version of the license
18153 (license (list license:gpl2 license:gpl3))))
18155 (define-public r-gamlss
18162 (uri (cran-uri "gamlss" version))
18165 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
18166 (properties `((upstream-name . "gamlss")))
18167 (build-system r-build-system)
18169 `(("r-gamlss-data" ,r-gamlss-data)
18170 ("r-gamlss-dist" ,r-gamlss-dist)
18173 ("r-survival" ,r-survival)))
18174 (home-page "http://www.gamlss.org/")
18175 (synopsis "Generalized additive models for location scale and shape")
18177 "This package provides functions for fitting the generalized additive
18178 models for location scale and shape introduced by Rigby and
18179 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18180 use a distributional regression approach where all the parameters of the
18181 conditional distribution of the response variable are modelled using
18182 explanatory variables.")
18183 ;; Either version of the license
18184 (license (list license:gpl2 license:gpl3))))
18186 (define-public r-acid
18193 (uri (cran-uri "acid" version))
18196 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18197 (properties `((upstream-name . "acid")))
18198 (build-system r-build-system)
18200 `(("r-gamlss" ,r-gamlss)
18201 ("r-gamlss-dist" ,r-gamlss-dist)
18202 ("r-hmisc" ,r-hmisc)))
18203 (home-page "https://cran.r-project.org/web/packages/acid/")
18204 (synopsis "Analysing conditional income distributions")
18206 "This package provides functions for the analysis of income distributions
18207 for subgroups of the population as defined by a set of variables like age,
18208 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18209 distribution as well as functions for moments, inequality measures, entropy
18210 measures and polarisation measures of income distributions. This package thus
18211 aides the analysis of income inequality by offering tools for the exploratory
18212 analysis of income distributions at the disaggregated level.")
18213 (license license:gpl3)))
18215 (define-public r-acm4r
18222 (uri (cran-uri "acm4r" version))
18225 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18226 (properties `((upstream-name . "acm4r")))
18227 (build-system r-build-system)
18228 (propagated-inputs `(("r-mass" ,r-mass)))
18229 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18230 (synopsis "Align-and-count method comparisons of RFLP data")
18232 "This is a package to compare sequence fragment lengths or molecular
18233 weights from pairs of lanes. The number of matching bands in the
18234 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18235 the align-and-count method.")
18236 ;; Any version of the GPL
18237 (license (list license:gpl2+ license:gpl3+))))
18239 (define-public r-filematrix
18241 (name "r-filematrix")
18246 (uri (cran-uri "filematrix" version))
18249 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18250 (properties `((upstream-name . "filematrix")))
18251 (build-system r-build-system)
18252 ;; These inputs are needed for vignettes
18254 `(("r-knitr" ,r-knitr)
18255 ("r-rmarkdown" ,r-rmarkdown)
18256 ("pandoc-citeproc" ,pandoc-citeproc)))
18257 (home-page "https://github.com/andreyshabalin/filematrix")
18258 (synopsis "File-backed matrix class with convenient read and write access")
18260 "This package provides an interface for working with large matrices
18261 stored in files, not in computer memory. It supports multiple non-character
18262 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18263 byte real values). Access to parts of the matrix is done by indexing, exactly
18264 as with usual R matrices. It supports very large matrices; the package has
18265 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18266 columns, ad allows for quick addition of extra columns to a filematrix.")
18267 (license license:lgpl3)))
18269 (define-public r-acmeeqtl
18271 (name "r-acmeeqtl")
18276 (uri (cran-uri "ACMEeqtl" version))
18279 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18280 (properties `((upstream-name . "ACMEeqtl")))
18281 (build-system r-build-system)
18283 `(("r-filematrix" ,r-filematrix)))
18284 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18285 (synopsis "Estimation of interpretable eQTL effect sizes")
18287 "This package provides a non-linear model, termed ACME, that reflects a
18288 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18289 With non-linear least-squares algorithm the maximum likelihood parameters can
18290 be estimated. The ACME model provides interpretable effect size estimates and
18291 p-values with well controlled Type-I error.")
18292 (license license:lgpl3)))
18294 (define-public r-acmer
18301 (uri (cran-uri "acmeR" version))
18304 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18305 (properties `((upstream-name . "acmeR")))
18306 (build-system r-build-system)
18307 (propagated-inputs `(("r-foreign" ,r-foreign)))
18308 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18309 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18311 "This package provides an implementation of the ACME estimator, described
18312 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18313 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18314 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18315 as carcasses age; variable bleed-through at successive searches; and interval
18316 mortality estimates. The package provides, based on search data, functions
18317 for estimating the mortality inflation factor in Frequentist and Bayesian
18319 (license license:expat)))
18321 (define-public r-r-huge
18328 (uri (cran-uri "R.huge" version))
18331 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18332 (properties `((upstream-name . "R.huge")))
18333 (build-system r-build-system)
18335 `(("r-r-methodss3" ,r-r-methodss3)
18337 ("r-r-utils" ,r-r-utils)))
18338 (home-page "https://github.com/HenrikBengtsson/R.huge")
18339 (synopsis "Methods for accessing huge amounts of data")
18341 "This is a deprecated package for accessing huge amounts of data.
18342 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18343 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18344 the @code{aroma.affymetrix} package.")
18345 (license license:lgpl2.1+)))
18347 (define-public r-r-filesets
18349 (name "r-r-filesets")
18354 (uri (cran-uri "R.filesets" version))
18357 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18358 (properties `((upstream-name . "R.filesets")))
18359 (build-system r-build-system)
18361 `(("r-digest" ,r-digest)
18362 ("r-r-cache" ,r-r-cache)
18363 ("r-r-methodss3" ,r-r-methodss3)
18365 ("r-r-utils" ,r-r-utils)))
18366 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18367 (synopsis "Easy handling of and access to files")
18369 "This package provides classes and methods to locate, setup, subset,
18370 navigate and iterate file sets, i.e. sets of files located in one or more
18371 directories on the file system. The API is designed such that these classes
18372 can be extended via inheritance to provide a richer API for special file
18373 formats. Moreover, a specific name format is defined such that filenames and
18374 directories can be considered to have full names which consists of a name
18375 followed by comma-separated tags. This adds additional flexibility to
18376 identify file sets and individual files.")
18377 (license license:lgpl2.1+)))
18379 (define-public r-r-devices
18381 (name "r-r-devices")
18386 (uri (cran-uri "R.devices" version))
18389 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18390 (properties `((upstream-name . "R.devices")))
18391 (build-system r-build-system)
18393 `(("r-base64enc" ,r-base64enc)
18394 ("r-r-methodss3" ,r-r-methodss3)
18396 ("r-r-utils" ,r-r-utils)))
18397 (home-page "https://github.com/HenrikBengtsson/R.devices")
18398 (synopsis "Unified handling of graphics devices")
18400 "This package provides functions for creating plots and image files in a
18401 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18402 Default device options as well as scales and aspect ratios are controlled in a
18403 uniform way across all device types. Switching output format requires minimal
18404 changes in code. This package is ideal for large-scale batch processing,
18405 because it will never leave open graphics devices or incomplete image files
18406 behind, even on errors or user interrupts.")
18407 (license license:lgpl2.1+)))
18409 (define-public r-acnr
18416 (uri (cran-uri "acnr" version))
18419 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18420 (properties `((upstream-name . "acnr")))
18421 (build-system r-build-system)
18422 (home-page "https://github.com/mpierrejean/acnr")
18423 (synopsis "Annotated copy-number regions")
18425 "This package provides SNP array data from different types of copy-number
18426 regions. These regions were identified manually by the authors of the package
18427 and may be used to generate realistic data sets with known truth.")
18428 (license license:lgpl2.1+)))
18430 (define-public r-acopula
18437 (uri (cran-uri "acopula" version))
18440 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18441 (properties `((upstream-name . "acopula")))
18442 (build-system r-build-system)
18443 (home-page "https://cran.r-project.org/web/packages/acopula/")
18444 (synopsis "Modelling dependence with multivariate Archimax copulas")
18446 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18447 package provides definitions of several parametric families of generator and
18448 dependence function, computes CDF and PDF, estimates parameters, tests for
18449 goodness of fit, generates random sample and checks copula properties for
18450 custom constructs. In the 2-dimensional case explicit formulas for density
18451 are used, contrary to higher dimensions when all derivatives are linearly
18452 approximated. Several non-archimax families (normal, FGM, Plackett) are
18453 provided as well.")
18454 (license license:gpl2)))
18456 (define-public r-tuner
18463 (uri (cran-uri "tuneR" version))
18466 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18467 (properties `((upstream-name . "tuneR")))
18468 (build-system r-build-system)
18469 (propagated-inputs `(("r-signal" ,r-signal)))
18470 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18471 (synopsis "Analysis of music and speech")
18473 "This is a package for the analysis of music and speech. Analyze music
18474 and speech, extract features like MFCCs, handle wave files and their
18475 representation in various ways, read MP3, read MIDI, perform steps of a
18476 transcription, ...")
18477 ;; Either of these versions.
18478 (license (list license:gpl2 license:gpl3))))
18480 (define-public r-seewave
18487 (uri (cran-uri "seewave" version))
18490 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18491 (properties `((upstream-name . "seewave")))
18492 (build-system r-build-system)
18494 `(("libsndfile" ,libsndfile)))
18496 `(("r-tuner" ,r-tuner)))
18497 (home-page "http://rug.mnhn.fr/seewave")
18498 (synopsis "Sound analysis and synthesis")
18500 "This package provides functions for analysing, manipulating, displaying,
18501 editing and synthesizing time waves (particularly sound). This package
18502 processes time analysis (oscillograms and envelopes), spectral content,
18503 resonance quality factor, entropy, cross correlation and autocorrelation,
18504 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18505 and 3D spectrograms and many other analyses.")
18506 (license license:gpl2+)))
18508 (define-public r-acousticndlcoder
18510 (name "r-acousticndlcoder")
18515 (uri (cran-uri "AcousticNDLCodeR" version))
18518 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18520 `((upstream-name . "AcousticNDLCodeR")))
18521 (build-system r-build-system)
18523 `(("r-seewave" ,r-seewave)
18524 ("r-tuner" ,r-tuner)
18526 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18527 (synopsis "Coding sound files for use with NDL")
18529 "Make acoustic cues to use with the R package @code{ndl}.
18530 The package implements functions used in the PLoS ONE paper \"Words from
18531 spontaneous conversational speech can be recognized with human-like accuracy
18532 by an error-driven learning algorithm that discriminates between meanings
18533 straight from smart acoustic features, bypassing the phoneme as recognition
18534 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18535 (license license:gpl2+)))
18537 (define-public r-acp
18544 (uri (cran-uri "acp" version))
18547 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18548 (properties `((upstream-name . "acp")))
18549 (build-system r-build-system)
18551 `(("r-quantmod" ,r-quantmod)
18552 ("r-tseries" ,r-tseries)))
18553 (home-page "https://cran.r-project.org/web/packages/acp/")
18554 (synopsis "Autoregressive conditional Poisson")
18556 "This package supports the analysis of count data exhibiting
18557 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18558 model (ACP(p,q)) proposed by Heinen (2003).")
18559 (license license:gpl2)))
18561 (define-public r-ada
18568 (uri (cran-uri "ada" version))
18571 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18572 (properties `((upstream-name . "ada")))
18573 (build-system r-build-system)
18574 (propagated-inputs `(("r-rpart" ,r-rpart)))
18575 (home-page "https://cran.r-project.org/web/packages/ada/")
18576 (synopsis "Stochastic boosting")
18578 "This package provides a straightforward, well-documented, and broad
18579 boosting routine for classification, ideally suited for small to
18580 moderate-sized data sets. It performs discrete, real, and gentle boost under
18581 both exponential and logistic loss on a given data set.")
18582 ;; Any version of the GPL.
18583 (license (list license:gpl2+ license:gpl3+))))
18585 (define-public r-genalg
18592 (uri (cran-uri "genalg" version))
18595 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18596 (properties `((upstream-name . "genalg")))
18597 (build-system r-build-system)
18598 (home-page "https://github.com/egonw/genalg")
18599 (synopsis "R based genetic algorithm")
18601 "This package provides an R based genetic algorithm for binary and
18602 floating point chromosomes.")
18603 (license license:gpl2)))
18605 (define-public r-kernelfactory
18607 (name "r-kernelfactory")
18612 (uri (cran-uri "kernelFactory" version))
18615 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18616 (properties `((upstream-name . "kernelFactory")))
18617 (build-system r-build-system)
18620 ("r-genalg" ,r-genalg)
18621 ("r-kernlab" ,r-kernlab)
18622 ("r-randomforest" ,r-randomforest)))
18623 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18624 (synopsis "Ensemble of kernel machines")
18626 "Kernel factory is an ensemble method where each base classifier (random
18627 forest) is fit on the kernel matrix of a subset of the training data.")
18628 (license license:gpl2+)))
18630 (define-public r-dummies
18637 (uri (cran-uri "dummies" version))
18640 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18641 (properties `((upstream-name . "dummies")))
18642 (build-system r-build-system)
18643 (home-page "https://decisionpatterns.com")
18644 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18646 "This package lets you expand factors, characters and other eligible
18647 classes into dummy/indicator variables.")
18648 (license license:gpl2+)))
18650 (define-public r-acrm
18657 (uri (cran-uri "aCRM" version))
18660 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18661 (properties `((upstream-name . "aCRM")))
18662 (build-system r-build-system)
18665 ("r-dummies" ,r-dummies)
18666 ("r-kernelfactory" ,r-kernelfactory)
18667 ("r-randomforest" ,r-randomforest)))
18668 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18669 (synopsis "Convenience functions for analytical customer relationship management")
18671 "This package provides convenience functions for data preparation and
18672 modeling often used in @dfn{analytical customer relationship
18673 management} (aCRM).")
18674 (license license:gpl2+)))
18676 (define-public r-treeclust
18678 (name "r-treeclust")
18683 (uri (cran-uri "treeClust" version))
18686 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18687 (properties `((upstream-name . "treeClust")))
18688 (build-system r-build-system)
18690 `(("r-cluster" ,r-cluster)
18691 ("r-rpart" ,r-rpart)))
18692 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18693 (synopsis "Cluster distances through trees")
18695 "This package provides tools to create a measure of inter-point
18696 dissimilarity useful for clustering mixed data, and, optionally, perform the
18698 (license license:gpl2+)))
18700 (define-public r-acrosstic
18702 (name "r-acrosstic")
18707 (uri (cran-uri "AcrossTic" version))
18710 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18711 (properties `((upstream-name . "AcrossTic")))
18712 (build-system r-build-system)
18714 `(("r-lpsolve" ,r-lpsolve)
18715 ("r-treeclust" ,r-treeclust)))
18716 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18717 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18719 "This is a package for constructing minimum-cost regular spanning
18720 subgraph as part of a non-parametric two-sample test for equality of
18722 (license license:gpl2+)))
18724 (define-public r-acrt
18731 (uri (cran-uri "acrt" version))
18734 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18735 (properties `((upstream-name . "acrt")))
18736 (build-system r-build-system)
18738 `(("r-rcpp" ,r-rcpp)
18739 ("r-rcppeigen" ,r-rcppeigen)
18740 ("r-sandwich" ,r-sandwich)))
18741 (home-page "https://cran.r-project.org/web/packages/acrt/")
18742 (synopsis "Autocorrelation robust testing")
18744 "This package provides functions for testing affine hypotheses on the
18745 regression coefficient vector in regression models with autocorrelated
18747 (license license:gpl2)))
18749 (define-public r-acs
18756 (uri (cran-uri "acs" version))
18759 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18760 (properties `((upstream-name . "acs")))
18761 (build-system r-build-system)
18763 `(("r-httr" ,r-httr)
18766 ("r-stringr" ,r-stringr)
18768 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18769 (synopsis "Work with data from the US Census")
18771 "This package provides a general toolkit for downloading, managing,
18772 analyzing, and presenting data from the
18773 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18774 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18775 American Community Survey (ACS). Confidence intervals provided with ACS data
18776 are converted to standard errors to be bundled with estimates in complex
18777 @code{acs} objects. The package provides new methods to conduct standard
18778 operations on @code{acs} objects and present/plot data in statistically
18779 appropriate ways.")
18780 (license license:gpl3)))
18782 (define-public r-acss-data
18784 (name "r-acss-data")
18789 (uri (cran-uri "acss.data" version))
18792 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18793 (properties `((upstream-name . "acss.data")))
18794 (build-system r-build-system)
18795 (home-page "http://complexitycalculator.com/methodology.html")
18796 (synopsis "Data for algorithmic complexity of short strings")
18798 "This is a data only package providing the algorithmic complexity of
18799 short strings, computed using the coding theorem method. For a given set of
18800 symbols in a string, all possible or a large number of random samples of
18801 Turing machines with a given number of states (e.g., 5) and number of symbols
18802 corresponding to the number of symbols in the strings were simulated until
18803 they reached a halting state or failed to end. This package contains data on
18804 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18805 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18806 distribution of the halting states.")
18807 (license license:gpl2+)))
18809 (define-public r-acss
18816 (uri (cran-uri "acss" version))
18819 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18820 (properties `((upstream-name . "acss")))
18821 (build-system r-build-system)
18823 `(("r-acss-data" ,r-acss-data)
18825 (home-page "http://complexitycalculator.com/methodology.html")
18826 (synopsis "Algorithmic complexity for short strings")
18828 "The main purpose of this package is to provide the algorithmic
18829 complexity for short strings, an approximation of the Kolmogorov Complexity of
18830 a short string using the coding theorem method. While the database containing
18831 the complexity is provided in the data only package @code{acss.data}, this
18832 package provides functions accessing the data such as @code{prob_random}
18833 returning the posterior probability that a given string was produced by a
18834 random process. In addition, two traditional (but problematic) measures of
18835 complexity are also provided: entropy and change complexity.")
18836 (license license:gpl2+)))
18838 (define-public r-acswr
18845 (uri (cran-uri "ACSWR" version))
18848 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18849 (properties `((upstream-name . "ACSWR")))
18850 (build-system r-build-system)
18852 `(("r-mass" ,r-mass)))
18853 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18854 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18856 "This is a companion package for the book \"A Course in Statistics with
18857 R\" (ISBN 978-1-119-15272-9.)")
18858 (license license:gpl2)))
18860 (define-public r-alabama
18863 (version "2015.3-1")
18867 (uri (cran-uri "alabama" version))
18870 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18871 (properties `((upstream-name . "alabama")))
18872 (build-system r-build-system)
18873 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18874 (home-page "https://cran.r-project.org/web/packages/alabama/")
18875 (synopsis "Constrained nonlinear optimization")
18877 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18878 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18879 constraints. Linear or nonlinear equality and inequality constraints are
18881 (license license:gpl2+)))
18883 (define-public r-gdina
18890 (uri (cran-uri "GDINA" version))
18893 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18894 (properties `((upstream-name . "GDINA")))
18895 (build-system r-build-system)
18897 `(("r-alabama" ,r-alabama)
18898 ("r-ggplot2" ,r-ggplot2)
18900 ("r-nloptr" ,r-nloptr)
18901 ("r-numderiv" ,r-numderiv)
18903 ("r-rcpparmadillo" ,r-rcpparmadillo)
18904 ("r-rsolnp" ,r-rsolnp)
18905 ("r-shiny" ,r-shiny)
18906 ("r-shinydashboard" ,r-shinydashboard)))
18908 `(("r-knitr" ,r-knitr)))
18909 (home-page "https://github.com/Wenchao-Ma/GDINA")
18910 (synopsis "Generalized DINA model framework")
18912 "This package provides a set of psychometric tools for cognitive
18913 diagnosis modeling based on the generalized deterministic inputs, noisy and
18914 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18915 and its extensions, including the sequential G-DINA model by Ma and de la
18916 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18917 polytomous G-DINA model by Chen and de la Torre
18918 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18919 distribution can be independent, saturated, higher-order, loglinear smoothed
18920 or structured. Q-matrix validation, item and model fit statistics, model
18921 comparison at test and item level and differential item functioning can also
18922 be conducted. A graphical user interface is also provided.")
18923 (license license:gpl3)))
18925 (define-public r-actcd
18932 (uri (cran-uri "ACTCD" version))
18935 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18936 (properties `((upstream-name . "ACTCD")))
18937 (build-system r-build-system)
18939 `(("r-gdina" ,r-gdina)
18940 ("r-r-methodss3" ,r-r-methodss3)))
18942 `(("gfortran" ,gfortran)))
18943 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18944 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18946 "This is a package supporting cluster analysis for cognitive diagnosis
18947 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18948 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18949 sum-scores, cluster analysis techniques can be used to classify examinees into
18950 latent classes based on their attribute patterns. In addition to the
18951 algorithms used to classify data, three labeling approaches are proposed to
18952 label clusters so that examinees' attribute profiles can be obtained.")
18953 (license license:gpl2+)))
18955 (define-public r-ineq
18962 (uri (cran-uri "ineq" version))
18965 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18966 (properties `((upstream-name . "ineq")))
18967 (build-system r-build-system)
18968 (home-page "https://cran.r-project.org/web/packages/ineq/")
18969 (synopsis "Measuring inequality, concentration, and poverty")
18971 "This package provides tools for measuring inequality, concentration, and
18972 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18973 ;; Either of these two versions.
18974 (license (list license:gpl2 license:gpl3))))
18976 (define-public r-actfrag
18983 (uri (cran-uri "ActFrag" version))
18986 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18987 (properties `((upstream-name . "ActFrag")))
18988 (build-system r-build-system)
18990 `(("r-accelerometry" ,r-accelerometry)
18991 ("r-dplyr" ,r-dplyr)
18993 ("r-survival" ,r-survival)
18994 ("r-tidyr" ,r-tidyr)))
18995 (home-page "https://github.com/junruidi/ActFrag")
18996 (synopsis "Activity fragmentation metrics extraction")
18998 "This package provides functions to extract commonly used fragmentation
18999 metrics to quantify time accumulation strategies based on minute level
19000 actigraphy-measured activity counts data.")
19001 (license license:gpl3)))
19003 (define-public r-fda
19006 (version "5.1.5.1")
19010 (uri (cran-uri "fda" version))
19013 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19014 (properties `((upstream-name . "fda")))
19015 (build-system r-build-system)
19017 `(("r-matrix" ,r-matrix)))
19018 (home-page "https://www.functionaldata.org")
19019 (synopsis "Functional data analysis")
19021 "These functions were developed to support functional data analysis as
19022 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19023 Analysis. The package includes data sets and script files working many
19025 (license license:gpl2+)))
19027 (define-public r-actigraphy
19029 (name "r-actigraphy")
19034 (uri (cran-uri "Actigraphy" version))
19037 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19038 (properties `((upstream-name . "Actigraphy")))
19039 (build-system r-build-system)
19041 `(("r-fda" ,r-fda)))
19042 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19043 (synopsis "Actigraphy data analysis")
19045 "This package provides tools for functional linear modeling and analysis
19046 of actigraphy data.")
19047 (license license:asl2.0)))
19049 (define-public r-activedriver
19051 (name "r-activedriver")
19056 (uri (cran-uri "ActiveDriver" version))
19059 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19060 (properties `((upstream-name . "ActiveDriver")))
19061 (build-system r-build-system)
19063 `(("r-mass" ,r-mass)))
19064 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19065 (synopsis "Tools for finding cancer driver proteins")
19067 "This package provides a mutation analysis tool that discovers cancer
19068 driver genes with frequent mutations in protein signalling sites such as
19069 post-translational modifications (phosphorylation, ubiquitination, etc). The
19070 Poisson generalized linear regression model identifies genes where cancer
19071 mutations in signalling sites are more frequent than expected from the
19072 sequence of the entire gene. Integration of mutations with signalling
19073 information helps find new driver genes and propose candidate mechanisms to
19075 (license license:gpl2+)))
19077 (define-public r-activitycounts
19079 (name "r-activitycounts")
19084 (uri (cran-uri "activityCounts" version))
19087 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19089 `((upstream-name . "activityCounts")))
19090 (build-system r-build-system)
19092 `(("r-lubridate" ,r-lubridate)
19093 ("r-magrittr" ,r-magrittr)
19094 ("r-seewave" ,r-seewave)
19095 ("r-signal" ,r-signal)
19096 ("r-tibble" ,r-tibble)))
19097 (home-page "https://github.com/walkabillylab/activityCounts")
19098 (synopsis "Generate ActiLife counts")
19100 "ActiLife generates activity counts from data collected by Actigraph
19101 accelerometers. Actigraph is one of the most common research-grade
19102 accelerometers. There is considerable research validating and developing
19103 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19104 counts are proprietary and difficult to implement if researchers use different
19105 accelerometer brands. The code creates ActiLife counts from raw acceleration
19106 data for different accelerometer brands.")
19107 (license license:gpl3)))
19109 (define-public r-activityindex
19111 (name "r-activityindex")
19116 (uri (cran-uri "ActivityIndex" version))
19119 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19120 (properties `((upstream-name . "ActivityIndex")))
19121 (build-system r-build-system)
19123 `(("r-data-table" ,r-data-table)
19124 ("r-matrixstats" ,r-matrixstats)
19125 ("r-r-utils" ,r-r-utils)))
19126 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19127 (synopsis "Activity Index calculation using raw accelerometry data")
19129 "This is a package to read raw accelerometry from GT3X+ accelerometry
19130 data and plain table data to calculate the Activity Index from Bai et
19131 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19132 (license license:gpl3)))
19134 (define-public r-activpal
19136 (name "r-activpal")
19141 (uri (cran-uri "activPAL" version))
19144 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19145 (properties `((upstream-name . "activPAL")))
19146 (build-system r-build-system)
19148 `(("r-devtools" ,r-devtools)
19149 ("r-dplyr" ,r-dplyr)
19150 ("r-ggplot2" ,r-ggplot2)
19151 ("r-lubridate" ,r-lubridate)
19152 ("r-magrittr" ,r-magrittr)
19153 ("r-tidyr" ,r-tidyr)))
19154 (home-page "https://cran.r-project.org/web/packages/activPAL")
19155 (synopsis "Processing and chart generation from activPAL events files")
19157 "This package contains functions to generate pre-defined summary
19158 statistics from activPAL events files. The package also contains functions to
19159 produce informative graphics that visualize physical activity behaviour and
19160 trends. This includes generating graphs that align physical activity
19161 behaviour with additional time based observations described by other data
19162 sets, such as sleep diaries and continuous glucose monitoring data.")
19163 (license license:gpl3)))
19165 (define-public r-activpalprocessing
19167 (name "r-activpalprocessing")
19172 (uri (cran-uri "activpalProcessing" version))
19175 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19177 `((upstream-name . "activpalProcessing")))
19178 (build-system r-build-system)
19180 `(("r-chron" ,r-chron)))
19181 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19182 (synopsis "Process activPAL events files")
19184 "This package performs estimation of physical activity and sedentary
19185 behavior variables from activPAL events files.")
19186 ;; Either version of the GPL.
19187 (license (list license:gpl2 license:gpl3))))
19189 (define-public r-actogrammr
19191 (name "r-actogrammr")
19196 (uri (cran-uri "actogrammr" version))
19199 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19200 (properties `((upstream-name . "actogrammr")))
19201 (build-system r-build-system)
19203 `(("r-dplyr" ,r-dplyr)
19204 ("r-ggplot2" ,r-ggplot2)
19205 ("r-lubridate" ,r-lubridate)
19206 ("r-readr" ,r-readr)
19207 ("r-tidyr" ,r-tidyr)))
19208 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19209 (synopsis "Read in activity data and plot actograms")
19211 "Read in activity measurements from standard file formats used by
19212 circadian rhythm researchers, currently only ClockLab format, and process and
19213 plot the data. The central type of plot is the actogram, as first described
19214 in \"Activity and distribution of certain wild mice in relation to biotic
19215 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19216 (license license:gpl3)))
19218 (define-public r-expint
19225 (uri (cran-uri "expint" version))
19228 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19229 (properties `((upstream-name . "expint")))
19230 (build-system r-build-system)
19231 (home-page "https://gitlab.com/vigou3/expint")
19232 (synopsis "Exponential integral and incomplete Gamma function")
19234 "This package provides the exponential integrals @code{E_1(x)},
19235 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19236 function @code{G(a, x)} defined for negative values of its first argument.
19237 The package also gives easy access to the underlying C routines through an
19238 API; see the package vignette for details.")
19239 (license license:gpl2+)))
19241 (define-public r-actuar
19248 (uri (cran-uri "actuar" version))
19251 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19252 (properties `((upstream-name . "actuar")))
19253 (build-system r-build-system)
19254 (propagated-inputs `(("r-expint" ,r-expint)))
19255 (home-page "https://gitlab.com/vigou3/actuar")
19256 (synopsis "Actuarial functions and heavy tailed distributions")
19258 "This package provides functions and data sets for actuarial science:
19259 modeling of loss distributions; risk theory and ruin theory; simulation of
19260 compound models, discrete mixtures and compound hierarchical models;
19261 credibility theory. It boasts support for many additional probability
19262 distributions to model insurance loss amounts and loss frequency: 19
19263 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19264 distribution; zero-truncated and zero-modified extensions of the standard
19265 discrete distributions. It also supports phase-type distributions commonly
19266 used to compute ruin probabilities.")
19267 (license license:gpl2+)))
19269 (define-public r-bmp
19276 (uri (cran-uri "bmp" version))
19279 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19280 (properties `((upstream-name . "bmp")))
19281 (build-system r-build-system)
19282 (home-page "https://cran.r-project.org/web/packages/bmp/")
19283 (synopsis "Read Bitmap (BMP) images")
19285 "This package provides pure R tools to read BMP format images. It is
19286 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19287 (license license:gpl2+)))
19289 (define-public r-readbitmap
19291 (name "r-readbitmap")
19296 (uri (cran-uri "readbitmap" version))
19299 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19300 (properties `((upstream-name . "readbitmap")))
19301 (build-system r-build-system)
19303 `(("libjpeg" ,libjpeg-turbo)
19304 ("libpng" ,libpng)))
19309 ("r-tiff" ,r-tiff)))
19310 (home-page "https://github.com/jefferis/readbitmap")
19311 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19313 "This package provides tools to identify and read BMP, JPEG, PNG, and
19314 TIFF format bitmap images. Identification defaults to the use of the magic
19315 number embedded in the file rather than the file extension.")
19316 (license license:gpl2+)))
19318 (define-public r-imager
19325 (uri (cran-uri "imager" version))
19328 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19329 (properties `((upstream-name . "imager")))
19330 (build-system r-build-system)
19333 ("libtiff" ,libtiff)
19337 `(("r-downloader" ,r-downloader)
19338 ("r-igraph" ,r-igraph)
19340 ("r-magrittr" ,r-magrittr)
19342 ("r-purrr" ,r-purrr)
19344 ("r-readbitmap" ,r-readbitmap)
19345 ("r-stringr" ,r-stringr)))
19347 `(("pkg-config" ,pkg-config)
19348 ("r-knitr" ,r-knitr)))
19349 (home-page "https://dahtah.github.io/imager/")
19350 (synopsis "Image processing library")
19352 "This is a package for fast image processing for images in up to 4
19353 dimensions (two spatial dimensions, one time/depth dimension, one color
19354 dimension). It provides most traditional image processing tools (filtering,
19355 morphology, transformations, etc.) as well as various functions for easily
19356 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19357 simple, modern C++ library for image processing.")
19358 (license license:lgpl3)))
19360 (define-public r-acuityview
19362 (name "r-acuityview")
19367 (uri (cran-uri "AcuityView" version))
19370 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19371 (properties `((upstream-name . "AcuityView")))
19372 (build-system r-build-system)
19374 `(("r-fftwtools" ,r-fftwtools)
19375 ("r-imager" ,r-imager)
19376 ("r-plotrix" ,r-plotrix)))
19377 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19378 (synopsis "Display scenes as seen by an animal with less acute vision")
19380 "This package provides a simple method for representing a visual scene as
19381 it may be seen by an animal with less acute vision.")
19382 (license license:gpl2+)))
19384 (define-public r-caret
19391 (uri (cran-uri "caret" version))
19394 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19395 (build-system r-build-system)
19397 `(("r-foreach" ,r-foreach)
19398 ("r-ggplot2" ,r-ggplot2)
19399 ("r-lattice" ,r-lattice)
19400 ("r-modelmetrics" ,r-modelmetrics)
19404 ("r-recipes" ,r-recipes)
19405 ("r-reshape2" ,r-reshape2)
19406 ("r-withr" ,r-withr)))
19408 `(("r-knitr" ,r-knitr)))
19409 (home-page "https://github.com/topepo/caret")
19410 (synopsis "Classification and regression training")
19412 "This package provides miscellaneous functions for training and plotting
19413 classification and regression models.")
19414 (license license:gpl2+)))
19416 (define-public r-adabag
19423 (uri (cran-uri "adabag" version))
19426 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19427 (properties `((upstream-name . "adabag")))
19428 (build-system r-build-system)
19430 `(("r-caret" ,r-caret)
19431 ("r-doparallel" ,r-doparallel)
19432 ("r-foreach" ,r-foreach)
19433 ("r-rpart" ,r-rpart)))
19434 (home-page "https://cran.r-project.org/web/packages/adabag/")
19435 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19437 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19438 Breiman's Bagging algorithm using classification trees as individual
19439 classifiers. Once these classifiers have been trained, they can be used to
19440 predict on new data. Also, cross validation estimation of the error can be
19442 (license license:gpl2+)))
19444 (define-public r-adagio
19451 (uri (cran-uri "adagio" version))
19454 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19455 (properties `((upstream-name . "adagio")))
19456 (build-system r-build-system)
19457 (native-inputs `(("gfortran" ,gfortran)))
19458 (home-page "https://cran.r-project.org/web/packages/adagio/")
19459 (synopsis "Discrete and global optimization routines")
19461 "This package provides methods and algorithms for discrete optimization,
19462 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19463 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19465 (license license:gpl3+)))
19467 (define-public r-univoutl
19469 (name "r-univoutl")
19474 (uri (cran-uri "univOutl" version))
19477 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19478 (properties `((upstream-name . "univOutl")))
19479 (build-system r-build-system)
19481 `(("r-hmisc" ,r-hmisc)
19482 ("r-robustbase" ,r-robustbase)))
19483 (home-page "https://github.com/marcellodo/univOutl")
19484 (synopsis "Detection of univariate outliers")
19486 "This package provides well-known outlier detection techniques in the
19487 univariate case. Methods to deal with skewed distribution are included too.
19488 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19489 historical data is implemented as well. When available, survey weights can be
19490 used in outliers detection.")
19491 (license license:gpl2+)))
19493 (define-public r-tolerance
19495 (name "r-tolerance")
19500 (uri (cran-uri "tolerance" version))
19503 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19504 (properties `((upstream-name . "tolerance")))
19505 (build-system r-build-system)
19507 `(("r-mass" ,r-mass)
19509 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19510 (synopsis "Statistical tolerance intervals and regions")
19512 "This package provides functions for estimating tolerance
19513 limits (intervals) for various univariate distributions (binomial, Cauchy,
19514 discrete Pareto, exponential, two-parameter exponential, extreme value,
19515 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19516 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19517 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19518 nonparametric tolerance intervals, tolerance bands for regression
19519 settings (linear regression, nonlinear regression, nonparametric regression,
19520 and multivariate regression), and analysis of variance tolerance intervals.
19521 Visualizations are also available for most of these settings.")
19522 (license license:gpl2+)))
19524 (define-public r-additivitytests
19526 (name "r-additivitytests")
19531 (uri (cran-uri "additivityTests" version))
19534 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19536 `((upstream-name . "additivityTests")))
19537 (build-system r-build-system)
19538 (home-page "https://github.com/simecek/additivityTests")
19539 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19541 "This package provides an implementation of the Tukey, Mandel,
19542 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19543 (license license:gpl3)))
19545 (define-public r-flexclust
19547 (name "r-flexclust")
19552 (uri (cran-uri "flexclust" version))
19555 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19556 (properties `((upstream-name . "flexclust")))
19557 (build-system r-build-system)
19559 `(("r-class" ,r-class)
19560 ("r-lattice" ,r-lattice)
19561 ("r-modeltools" ,r-modeltools)))
19562 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19563 (synopsis "Flexible cluster algorithms")
19565 "The main function @code{kcca} implements a general framework for
19566 k-centroids cluster analysis supporting arbitrary distance measures and
19567 centroid computation. Further cluster methods include hard competitive
19568 learning, neural gas, and QT clustering. There are numerous visualization
19569 methods for cluster results (neighborhood graphs, convex cluster hulls,
19570 barcharts of centroids, ...), and bootstrap methods for the analysis of
19571 cluster stability.")
19572 (license license:gpl2)))
19574 (define-public r-biclust
19581 (uri (cran-uri "biclust" version))
19584 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19585 (properties `((upstream-name . "biclust")))
19586 (build-system r-build-system)
19588 `(("r-additivitytests" ,r-additivitytests)
19589 ("r-colorspace" ,r-colorspace)
19590 ("r-flexclust" ,r-flexclust)
19591 ("r-ggplot2" ,r-ggplot2)
19592 ("r-lattice" ,r-lattice)
19594 ("r-tidyr" ,r-tidyr)))
19595 (home-page "https://cran.r-project.org/web/packages/biclust/")
19596 (synopsis "BiCluster algorithms")
19598 "The main function @code{biclust()} provides several algorithms to find
19599 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19600 In addition, the package provides methods for data
19601 preprocessing (normalization and discretization), visualization, and
19602 validation of bicluster solutions.")
19603 (license license:gpl3)))
19605 (define-public r-icge
19612 (uri (cran-uri "ICGE" version))
19615 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19616 (properties `((upstream-name . "ICGE")))
19617 (build-system r-build-system)
19619 `(("r-cluster" ,r-cluster)
19620 ("r-mass" ,r-mass)))
19621 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19622 (synopsis "Cluster estimation and identification of atypical units")
19624 "ICGE is a package that helps to estimate the number of real clusters in
19625 data as well as to identify atypical units. The underlying methods are based
19626 on distances rather than on unit x variables.")
19627 (license license:gpl2+)))
19629 (define-public r-depth
19632 (version "2.1-1.1")
19636 (uri (cran-uri "depth" version))
19639 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19640 (properties `((upstream-name . "depth")))
19641 (build-system r-build-system)
19643 `(("r-abind" ,r-abind)
19644 ("r-circular" ,r-circular)
19647 `(("gfortran" ,gfortran)))
19648 (home-page "https://cran.r-project.org/web/packages/depth/")
19649 (synopsis "Nonparametric depth functions for multivariate analysis")
19651 "This package provides tools for depth functions methodology applied to
19652 multivariate analysis. Besides allowing calculation of depth values and
19653 depth-based location estimators, the package includes functions or drawing
19654 contour plots and perspective plots of depth functions. Euclidian and
19655 spherical depths are supported.")
19656 (license license:gpl2)))
19658 (define-public r-archetypes
19660 (name "r-archetypes")
19661 (version "2.2-0.1")
19665 (uri (cran-uri "archetypes" version))
19668 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19669 (properties `((upstream-name . "archetypes")))
19670 (build-system r-build-system)
19672 `(("r-modeltools" ,r-modeltools)
19673 ("r-nnls" ,r-nnls)))
19674 (home-page "https://cran.r-project.org/web/packages/archetypes")
19675 (synopsis "Archetypal analysis")
19677 "The main function @code{archetypes} implements a framework for
19678 archetypal analysis supporting arbitrary problem solving mechanisms for the
19679 different conceptual parts of the algorithm.")
19680 (license license:gpl2+)))
19682 (define-public r-shapes
19689 (uri (cran-uri "shapes" version))
19692 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19693 (properties `((upstream-name . "shapes")))
19694 (build-system r-build-system)
19696 `(("r-mass" ,r-mass)
19697 ("r-minpack-lm" ,r-minpack-lm)
19699 ("r-scatterplot3d" ,r-scatterplot3d)))
19700 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19701 (synopsis "Statistical shape analysis")
19703 "This package provides routines for the statistical analysis of landmark
19704 shapes, including Procrustes analysis, graphical displays, principal
19705 components analysis, permutation and bootstrap tests, thin-plate spline
19706 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19707 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19708 Edition), John Wiley and Sons.")
19709 (license license:gpl2)))
19711 (define-public r-anthropometry
19713 (name "r-anthropometry")
19718 (uri (cran-uri "Anthropometry" version))
19721 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19722 (properties `((upstream-name . "Anthropometry")))
19723 (build-system r-build-system)
19725 `(("r-archetypes" ,r-archetypes)
19726 ("r-biclust" ,r-biclust)
19727 ("r-cluster" ,r-cluster)
19728 ("r-depth" ,r-depth)
19733 ("r-shapes" ,r-shapes)))
19735 `(("r-knitr" ,r-knitr)))
19736 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19737 (synopsis "Statistical methods for anthropometric data")
19739 "This package provides statistical methods especially developed to
19740 analyze anthropometric data. These methods are aimed at providing effective
19741 solutions to some commons problems related to Ergonomics and Anthropometry.
19742 They are based on clustering, the statistical concept of data depth,
19743 statistical shape analysis and archetypal analysis.")
19744 (license license:gpl2+)))
19746 (define-public r-adamethods
19748 (name "r-adamethods")
19753 (uri (cran-uri "adamethods" version))
19756 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19757 (properties `((upstream-name . "adamethods")))
19758 (build-system r-build-system)
19760 `(("r-anthropometry" ,r-anthropometry)
19761 ("r-archetypes" ,r-archetypes)
19763 ("r-foreach" ,r-foreach)
19765 ("r-tolerance" ,r-tolerance)
19766 ("r-univoutl" ,r-univoutl)))
19767 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19768 (synopsis "Archetypoid algorithms and anomaly detection")
19770 "This package is a collection of several algorithms to obtain
19771 archetypoids with small and large databases and with both classical
19772 multivariate data and functional data (univariate and multivariate). Some of
19773 these algorithms also allow to detect anomalies (outliers).")
19774 (license license:gpl2+)))
19776 (define-public r-idpmisc
19783 (uri (cran-uri "IDPmisc" version))
19786 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19787 (properties `((upstream-name . "IDPmisc")))
19788 (build-system r-build-system)
19790 `(("r-lattice" ,r-lattice)))
19791 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19792 (synopsis "Functions for data analyses and visualization")
19794 "This package provides different high-level graphics functions for
19795 displaying large datasets, displaying circular data in a very flexible way,
19796 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19797 2D-plots, creating figures with differently colored margin and plot region.
19798 In addition, the package contains auxiliary functions for data manipulation
19799 like omitting observations with irregular values or selecting data by logical
19800 vectors, which include NAs. Other functions are especially useful in
19801 spectroscopy and analyses of environmental data: robust baseline fitting,
19802 finding peaks in spectra, converting humidity measures.")
19803 (license license:gpl3+)))
19805 (define-public r-qqman
19812 (uri (cran-uri "qqman" version))
19815 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19816 (properties `((upstream-name . "qqman")))
19817 (build-system r-build-system)
19819 `(("r-calibrate" ,r-calibrate)))
19820 (home-page "https://cran.r-project.org/web/packages/qqman/")
19821 (synopsis "Q-Q and Manhattan plots for GWAS data")
19823 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19824 from PLINK results.")
19825 (license license:gpl3)))
19827 (define-public r-ggplot-multistats
19829 (name "r-ggplot-multistats")
19834 (uri (cran-uri "ggplot.multistats" version))
19837 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19839 `((upstream-name . "ggplot.multistats")))
19840 (build-system r-build-system)
19842 `(("r-ggplot2" ,r-ggplot2)
19843 ("r-hexbin" ,r-hexbin)
19844 ("r-rlang" ,r-rlang)
19845 ("r-scales" ,r-scales)))
19846 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19847 (synopsis "Multiple summary statistics for binned stats/geometries")
19849 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19850 which functions similar to its singular form, but allows the use of multiple
19851 statistics per bin. Those statistics can be mapped to multiple bin
19853 (license license:gpl3)))
19855 (define-public r-knn-covertree
19857 (name "r-knn-covertree")
19862 (uri (cran-uri "knn.covertree" version))
19865 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19866 (properties `((upstream-name . "knn.covertree")))
19867 (build-system r-build-system)
19869 `(("r-matrix" ,r-matrix)
19871 ("r-rcppeigen" ,r-rcppeigen)))
19872 (home-page "https://github.com/flying-sheep/knn.covertree")
19873 (synopsis "Accurate kNN Implementation with multiple distance measures")
19875 "Similarly to the FNN package, this package allows calculation of the k
19876 nearest neighbors (kNN) of a data matrix. The implementation is based on
19877 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19878 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19879 (license license:agpl3+)))
19881 (define-public r-poibin
19888 (uri (cran-uri "poibin" version))
19891 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19892 (properties `((upstream-name . "poibin")))
19893 (build-system r-build-system)
19894 (home-page "https://cran.r-project.org/web/packages/poibin/")
19895 (synopsis "Poisson binomial distribution")
19897 "This package provides an implementation of both the exact and
19898 approximation methods for computing the @dfn{cumulative distribution
19899 function} (CDF) of the Poisson binomial distribution. It also provides the
19900 @dfn{probability mass function} (PMF), quantile function, and random number
19901 generation for the Poisson binomial distribution.")
19902 (license license:gpl2)))
19904 (define-public r-diagram
19911 (uri (cran-uri "diagram" version))
19914 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19915 (properties `((upstream-name . "diagram")))
19916 (build-system r-build-system)
19918 `(("r-shape" ,r-shape)))
19919 (home-page "https://cran.r-project.org/web/packages/diagram/")
19920 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19922 "This package provides tools to visualize simple graphs (networks) based
19923 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19924 electrical networks, etc. It also includes supporting material for the book
19925 \"A practical guide to ecological modelling - using R as a simulation
19926 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19927 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19928 Francesca Mazzia (2012).")
19929 (license license:gpl2+)))
19931 (define-public r-lim
19938 (uri (cran-uri "LIM" version))
19941 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19942 (properties `((upstream-name . "LIM")))
19943 (build-system r-build-system)
19945 `(("r-diagram" ,r-diagram)
19946 ("r-limsolve" ,r-limsolve)))
19947 (home-page "https://cran.r-project.org/web/packages/LIM/")
19948 (synopsis "Linear inverse model examples and solution methods")
19950 "This package provides functions that read and solve linear inverse
19951 problems (food web problems, linear programming problems).")
19952 (license license:gpl2+)))
19954 (define-public r-shinycssloaders
19956 (name "r-shinycssloaders")
19961 (uri (cran-uri "shinycssloaders" version))
19964 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19966 `((upstream-name . "shinycssloaders")))
19967 (build-system r-build-system)
19969 `(("r-digest" ,r-digest)
19971 ("r-shiny" ,r-shiny)))
19972 (home-page "https://github.com/andrewsali/shinycssloaders")
19973 (synopsis "Add CSS loading animations to Shiny outputs")
19975 "This package provides tools to create a lightweight Shiny wrapper for
19976 the css-loaders created by Luke Hass
19977 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19978 automatically show a loader when the output is (re)calculating.")
19979 (license license:gpl3)))
19981 (define-public r-rsvg
19988 (uri (cran-uri "rsvg" version))
19991 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19992 (properties `((upstream-name . "rsvg")))
19993 (build-system r-build-system)
19995 `(("librsvg" ,librsvg)
19998 `(("pkg-config" ,pkg-config)
19999 ("r-knitr" ,r-knitr)))
20000 (home-page "https://github.com/jeroen/rsvg#readme")
20001 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20003 "This package allows you to render vector-based SVG images into
20004 high-quality custom-size bitmap arrays using the librsvg2 library. The
20005 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20006 addition, the package can convert images directly to various formats such as
20007 PDF or PostScript.")
20008 (license license:expat)))
20010 (define-public r-influencer
20012 (name "r-influencer")
20017 (uri (cran-uri "influenceR" version))
20020 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20021 (properties `((upstream-name . "influenceR")))
20022 (build-system r-build-system)
20024 `(("r-igraph" ,r-igraph)
20025 ("r-matrix" ,r-matrix)))
20026 (home-page "https://github.com/rcc-uchicago/influenceR")
20027 (synopsis "Tools to quantify structural importance of nodes in a network")
20029 "This package provides functionality to compute various node centrality
20030 measures on networks. Included are functions to compute betweenness
20031 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20032 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20033 algorithm to identify key players, and Valente's bridging metric. The
20034 betweenness, Key Players, and bridging implementations are parallelized with
20036 (license license:gpl2)))
20038 (define-public r-emplik
20045 (uri (cran-uri "emplik" version))
20048 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20049 (properties `((upstream-name . "emplik")))
20050 (build-system r-build-system)
20052 `(("r-quantreg" ,r-quantreg)))
20053 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20054 (synopsis "Empirical likelihood ratio for censored/truncated data")
20056 "This package provides empirical likelihood ratio tests for
20057 means/quantiles/hazards from possibly censored and/or truncated data. It also
20059 (license license:gpl2+)))
20061 (define-public r-imputeyn
20063 (name "r-imputeyn")
20068 (uri (cran-uri "imputeYn" version))
20071 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20072 (properties `((upstream-name . "imputeYn")))
20073 (build-system r-build-system)
20075 `(("r-boot" ,r-boot)
20076 ("r-emplik" ,r-emplik)
20077 ("r-mvtnorm" ,r-mvtnorm)
20078 ("r-quadprog" ,r-quadprog)
20079 ("r-survival" ,r-survival)))
20080 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20081 (synopsis "Impute last largest censored observation under weighted least squares")
20083 "This package allows for the imputation of the last largest censored
20084 observantions. This method brings less bias and more efficient estimates for
20086 (license license:gpl2)))
20088 (define-public r-adapenetclass
20090 (name "r-adapenetclass")
20095 (uri (cran-uri "AdapEnetClass" version))
20098 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20099 (properties `((upstream-name . "AdapEnetClass")))
20100 (build-system r-build-system)
20102 `(("r-glmnet" ,r-glmnet)
20103 ("r-imputeyn" ,r-imputeyn)
20105 ("r-quadprog" ,r-quadprog)))
20106 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20107 (synopsis "Class of adaptive elastic net methods for censored data")
20109 "This package provides methods for variable selection for AFT models.")
20110 (license license:gpl2)))
20112 (define-public r-flock
20119 (uri (cran-uri "flock" version))
20122 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20123 (properties `((upstream-name . "flock")))
20124 (build-system r-build-system)
20125 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20126 (home-page "https://cran.r-project.org/web/packages/flock/")
20127 (synopsis "Process synchronization using file locks")
20129 "This package implements synchronization between R processes (spawned by
20130 using the @code{parallel} package for instance) using file locks. It supports
20131 both exclusive and shared locking.")
20132 (license license:asl2.0)))
20134 (define-public r-archivist
20136 (name "r-archivist")
20141 (uri (cran-uri "archivist" version))
20144 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20145 (properties `((upstream-name . "archivist")))
20146 (build-system r-build-system)
20149 ("r-digest" ,r-digest)
20150 ("r-flock" ,r-flock)
20152 ("r-lubridate" ,r-lubridate)
20153 ("r-magrittr" ,r-magrittr)
20154 ("r-rcurl" ,r-rcurl)
20155 ("r-rsqlite" ,r-rsqlite)))
20156 (home-page "https://pbiecek.github.io/archivist/")
20157 (synopsis "Tools for storing, restoring and searching for R objects")
20159 "Data exploration and modelling is a process in which a lot of data
20160 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20161 statistical models, different versions of data sets and different versions of
20162 results. Archivist helps to store and manage artifacts created in R. It
20163 allows you to store selected artifacts as binary files together with their
20164 metadata and relations. Archivist allows sharing artifacts with others. It
20165 can look for already created artifacts by using its class, name, date of the
20166 creation or other properties. It also makes it easy to restore such
20168 (license license:gpl2)))
20170 (define-public r-versions
20172 (name "r-versions")
20177 (uri (cran-uri "versions" version))
20180 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20181 (properties `((upstream-name . "versions")))
20182 (build-system r-build-system)
20183 (home-page "https://cran.r-project.org/web/packages/versions/")
20184 (synopsis "Query and install specific versions of CRAN packages")
20186 "This package allows you to install specified versions of R packages
20187 hosted on CRAN and provides functions to list available versions and the
20188 versions of currently installed packages.")
20189 (license license:bsd-3)))
20191 (define-public r-adapr
20198 (uri (cran-uri "adapr" version))
20201 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20202 (properties `((upstream-name . "adapr")))
20203 (build-system r-build-system)
20205 `(("r-archivist" ,r-archivist)
20206 ("r-devtools" ,r-devtools)
20207 ("r-digest" ,r-digest)
20208 ("r-doparallel" ,r-doparallel)
20209 ("r-gdata" ,r-gdata)
20210 ("r-ggplot2" ,r-ggplot2)
20211 ("r-git2r" ,r-git2r)
20212 ("r-igraph" ,r-igraph)
20213 ("r-knitr" ,r-knitr)
20214 ("r-plotly" ,r-plotly)
20216 ("r-rmarkdown" ,r-rmarkdown)
20217 ("r-shiny" ,r-shiny)
20218 ("r-shinydashboard" ,r-shinydashboard)
20219 ("r-versions" ,r-versions)))
20220 (home-page "https://cran.r-project.org/web/packages/adapr/")
20221 (synopsis "Implementation of an accountable data analysis process")
20223 "This package tracks reading and writing within R scripts that are
20224 organized into a directed acyclic graph. It contains an interactive Shiny
20225 application @code{adaprApp()}. It uses Git and file hashes to track version
20226 histories of inputs and outputs.")
20227 (license license:lgpl2.0)))
20229 (define-public r-adapsamp
20231 (name "r-adapsamp")
20236 (uri (cran-uri "AdapSamp" version))
20239 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20240 (properties `((upstream-name . "AdapSamp")))
20241 (build-system r-build-system)
20242 (propagated-inputs `(("r-pracma" ,r-pracma)))
20243 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20244 (synopsis "Adaptive sampling algorithms")
20246 "For distributions whose probability density functions are log-concave,
20247 the adaptive rejection sampling algorithm can be used to build envelope
20248 functions for sampling. For others, the modified adaptive rejection sampling
20249 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20250 adaptive slice sampling algorithm can be used. This R package mainly includes
20251 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20252 @code{rASS()}. These functions can realize sampling based on the algorithms
20254 (license license:gpl2)))
20256 (define-public r-adaptalint
20258 (name "r-adaptalint")
20263 (uri (cran-uri "adaptalint" version))
20266 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20267 (properties `((upstream-name . "adaptalint")))
20268 (build-system r-build-system)
20270 `(("r-dplyr" ,r-dplyr)
20271 ("r-lintr" ,r-lintr)
20272 ("r-purrr" ,r-purrr)))
20273 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20274 (synopsis "Check R code style")
20276 "This package provides tools to infer the code style (which style rules
20277 are followed and which ones are not) from one package and use it to check
20278 another. This makes it easier to find and correct the most important problems
20280 (license license:gpl3)))
20282 (define-public r-fracdiff
20284 (name "r-fracdiff")
20289 (uri (cran-uri "fracdiff" version))
20292 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20293 (properties `((upstream-name . "fracdiff")))
20294 (build-system r-build-system)
20295 (home-page "https://github.com/mmaechler/fracdiff")
20297 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20299 "This package provides tools for the maximum likelihood estimation of the
20300 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20301 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20302 (license license:gpl2+)))
20304 (define-public r-forecast
20306 (name "r-forecast")
20311 (uri (cran-uri "forecast" version))
20314 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20315 (properties `((upstream-name . "forecast")))
20316 (build-system r-build-system)
20318 `(("r-colorspace" ,r-colorspace)
20319 ("r-fracdiff" ,r-fracdiff)
20320 ("r-ggplot2" ,r-ggplot2)
20321 ("r-lmtest" ,r-lmtest)
20322 ("r-magrittr" ,r-magrittr)
20325 ("r-rcpparmadillo" ,r-rcpparmadillo)
20326 ("r-timedate" ,r-timedate)
20327 ("r-tseries" ,r-tseries)
20331 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20332 (home-page "https://pkg.robjhyndman.com/forecast/")
20333 (synopsis "Forecasting functions for time series and linear models")
20335 "This package provides methods and tools for displaying and analysing
20336 univariate time series forecasts including exponential smoothing via state
20337 space models and automatic ARIMA modelling.")
20338 (license license:gpl3)))
20340 (define-public r-xmisc
20347 (uri (cran-uri "Xmisc" version))
20350 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20351 (properties `((upstream-name . "Xmisc")))
20352 (build-system r-build-system)
20353 (home-page "https://cran.r-project.org/package=Xmisc")
20355 "Xiaobei's miscellaneous classes and functions")
20357 "This package provides Xiaobei's miscellaneous classes and functions,
20358 which are useful when developing R packages for @dfn{object oriented
20359 programming} (OOP) using R Reference Class.")
20360 (license license:gpl2+)))
20362 (define-public r-proxyc
20369 (uri (cran-uri "proxyC" version))
20372 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20373 (properties `((upstream-name . "proxyC")))
20374 (build-system r-build-system)
20376 `(("r-matrix" ,r-matrix)
20378 ("r-rcpparmadillo" ,r-rcpparmadillo)
20379 ("r-rcppparallel" ,r-rcppparallel)))
20380 (home-page "https://cran.r-project.org/package=proxyC")
20381 (synopsis "Compute proximity in large sparse matrices")
20383 "This package provides efficient tools to compute the proximity between
20384 rows or columns of large matrices. Functions are optimised for large sparse
20385 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20386 similarity/distance measures, computation of correlation, cosine similarity
20387 and Euclidean distance is particularly fast.")
20388 (license license:gpl3)))
20390 (define-public r-isocodes
20392 (name "r-isocodes")
20393 (version "2020.03.16")
20397 (uri (cran-uri "ISOcodes" version))
20400 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20401 (properties `((upstream-name . "ISOcodes")))
20402 (build-system r-build-system)
20403 (home-page "https://cran.r-project.org/package=ISOcodes")
20404 (synopsis "Selected ISO codes")
20406 "This package provides ISO language, territory, currency, script and
20407 character codes. It provides ISO 639 language codes, ISO 3166 territory
20408 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20409 character codes as well as the UN M.49 area codes.")
20410 (license license:gpl2)))
20412 (define-public r-stopwords
20414 (name "r-stopwords")
20419 (uri (cran-uri "stopwords" version))
20422 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20423 (properties `((upstream-name . "stopwords")))
20424 (build-system r-build-system)
20426 `(("r-desc" ,r-desc)
20427 ("r-isocodes" ,r-isocodes)
20428 ("r-usethis" ,r-usethis)))
20429 (home-page "https://github.com/quanteda/stopwords")
20430 (synopsis "Multilingual stopword lists")
20432 "This package provides multiple sources of stopwords, for use in text
20433 analysis and natural language processing.")
20434 (license license:expat)))
20436 (define-public r-spacyr
20443 (uri (cran-uri "spacyr" version))
20446 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20447 (properties `((upstream-name . "spacyr")))
20448 (build-system r-build-system)
20450 `(("r-data-table" ,r-data-table)
20451 ("r-reticulate" ,r-reticulate)))
20452 (home-page "https://spacyr.quanteda.io")
20453 (synopsis "R wrapper for the spaCy NLP library")
20455 "This package provides an R wrapper to the Python @dfn{natural language
20456 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20457 (license license:gpl3)))
20459 (define-public r-snowballc
20461 (name "r-snowballc")
20466 (uri (cran-uri "SnowballC" version))
20469 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20470 (properties `((upstream-name . "SnowballC")))
20471 (build-system r-build-system)
20472 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20473 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20475 "This package provides an R interface to the C @code{libstemmer} library
20476 that implements Porter's word stemming algorithm for collapsing words to a
20477 common root to aid comparison of vocabulary. Currently supported languages
20478 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20479 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20480 (license license:bsd-3)))
20482 (define-public r-quanteda
20484 (name "r-quanteda")
20489 (uri (cran-uri "quanteda" version))
20492 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20493 (properties `((upstream-name . "quanteda")))
20494 (build-system r-build-system)
20496 `(("r-data-table" ,r-data-table)
20497 ("r-digest" ,r-digest)
20498 ("r-extrafont" ,r-extrafont)
20499 ("r-fastmatch" ,r-fastmatch)
20500 ("r-ggplot2" ,r-ggplot2)
20501 ("r-ggrepel" ,r-ggrepel)
20502 ("r-jsonlite" ,r-jsonlite)
20503 ("r-magrittr" ,r-magrittr)
20504 ("r-matrix" ,r-matrix)
20505 ("r-network" ,r-network)
20506 ("r-proxyc" ,r-proxyc)
20508 ("r-rcpparmadillo" ,r-rcpparmadillo)
20509 ("r-rcppparallel" ,r-rcppparallel)
20511 ("r-snowballc" ,r-snowballc)
20512 ("r-stopwords" ,r-stopwords)
20513 ("r-stringi" ,r-stringi)
20515 ("r-yaml" ,r-yaml)))
20517 `(("r-knitr" ,r-knitr)))
20518 (home-page "https://quanteda.io")
20519 (synopsis "Quantitative analysis of textual data")
20521 "This package provides a fast, flexible, and comprehensive framework for
20522 quantitative text analysis in R. It provides functionality for corpus
20523 management, creating and manipulating tokens and ngrams, exploring keywords in
20524 context, forming and manipulating sparse matrices of documents by features and
20525 feature co-occurrences, analyzing keywords, computing feature similarities and
20526 distances, applying content dictionaries, applying supervised and unsupervised
20527 machine learning, visually representing text and text analyses, and more.")
20528 (license license:gpl3)))
20530 (define-public r-topicmodels
20532 (name "r-topicmodels")
20537 (uri (cran-uri "topicmodels" version))
20540 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20541 (properties `((upstream-name . "topicmodels")))
20542 (build-system r-build-system)
20546 `(("r-modeltools" ,r-modeltools)
20549 (home-page "https://cran.r-project.org/package=topicmodels")
20550 (synopsis "Topic models")
20552 "This package provides an interface to the C code for @dfn{Latent
20553 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20554 David M. Blei and co-authors and the C++ code for fitting LDA models using
20555 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20556 (license license:gpl2)))
20558 (define-public r-stm
20565 (uri (cran-uri "stm" version))
20568 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20569 (properties `((upstream-name . "stm")))
20570 (build-system r-build-system)
20572 `(("r-data-table" ,r-data-table)
20573 ("r-glmnet" ,r-glmnet)
20575 ("r-matrix" ,r-matrix)
20576 ("r-matrixstats" ,r-matrixstats)
20577 ("r-quadprog" ,r-quadprog)
20578 ("r-quanteda" ,r-quanteda)
20580 ("r-rcpparmadillo" ,r-rcpparmadillo)
20582 ("r-stringr" ,r-stringr)))
20583 (home-page "http://www.structuraltopicmodel.com/")
20584 (synopsis "Estimation of the Structural Topic Model")
20586 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20587 topic models with document-level covariates. The package also includes tools
20588 for model selection, visualization, and estimation of topic-covariate
20590 (license license:expat)))
20592 (define-public r-polycor
20599 (uri (cran-uri "polycor" version))
20602 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20603 (properties `((upstream-name . "polycor")))
20604 (build-system r-build-system)
20606 `(("r-matrix" ,r-matrix)
20607 ("r-mvtnorm" ,r-mvtnorm)))
20608 (home-page "https://r-forge.r-project.org/projects/polycor/")
20609 (synopsis "Polychoric and polyserial correlations")
20611 "This package provides tools to compute polychoric and polyserial
20612 correlations by quick \"two-step\" methods or ML, optionally with standard
20613 errors; tetrachoric and biserial correlations are special cases.")
20614 (license license:gpl2+)))
20616 (define-public r-msm
20623 (uri (cran-uri "msm" version))
20626 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20627 (properties `((upstream-name . "msm")))
20628 (build-system r-build-system)
20630 `(("r-expm" ,r-expm)
20631 ("r-mvtnorm" ,r-mvtnorm)
20632 ("r-survival" ,r-survival)))
20633 (home-page "https://github.com/chjackson/msm")
20634 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20636 "This package provides functions for fitting continuous-time Markov and
20637 hidden Markov multi-state models to longitudinal data. It was designed for
20638 processes observed at arbitrary times in continuous time (panel data) but some
20639 other observation schemes are supported. Both Markov transition rates and the
20640 hidden Markov output process can be modelled in terms of covariates, which may
20641 be constant or piecewise-constant in time.")
20642 (license license:gpl2+)))
20644 (define-public r-ltm
20651 (uri (cran-uri "ltm" version))
20654 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20655 (properties `((upstream-name . "ltm")))
20656 (build-system r-build-system)
20658 `(("r-mass" ,r-mass)
20660 ("r-polycor" ,r-polycor)))
20661 (home-page "https://github.com/drizopoulos/ltm")
20662 (synopsis "Latent trait models under IRT")
20664 "This is a package supporting the analysis of multivariate dichotomous
20665 and polytomous data using latent trait models under the Item Response Theory
20666 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20667 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20669 (license license:gpl2+)))
20671 (define-public r-mi
20678 (uri (cran-uri "mi" version))
20681 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20682 (properties `((upstream-name . "mi")))
20683 (build-system r-build-system)
20686 ("r-matrix" ,r-matrix)))
20687 (home-page "http://www.stat.columbia.edu/~gelman/")
20688 (synopsis "Missing data imputation and model checking")
20690 "This package provides functions for data manipulation, imputing missing
20691 values in an approximate Bayesian framework, diagnostics of the models used to
20692 generate the imputations, confidence-building mechanisms to validate some of
20693 the assumptions of the imputation algorithm, and functions to analyze multiply
20694 imputed data sets with the appropriate degree of sampling uncertainty.")
20695 (license license:gpl2+)))
20697 (define-public r-matrixcalc
20699 (name "r-matrixcalc")
20704 (uri (cran-uri "matrixcalc" version))
20707 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20708 (properties `((upstream-name . "matrixcalc")))
20709 (build-system r-build-system)
20710 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20711 (synopsis "Collection of functions for matrix calculations")
20713 "This package provides a collection of functions to support matrix
20714 calculations for probability, econometric and numerical analysis. There are
20715 additional functions that are comparable to APL functions which are useful for
20716 actuarial models such as pension mathematics.")
20717 (license license:gpl2+)))
20719 (define-public r-sem
20726 (uri (cran-uri "sem" version))
20729 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20730 (properties `((upstream-name . "sem")))
20731 (build-system r-build-system)
20733 `(("r-boot" ,r-boot)
20735 ("r-matrixcalc" ,r-matrixcalc)
20737 (home-page "https://cran.r-project.org/package=sem")
20738 (synopsis "Structural equation models")
20740 "This package provides functions for fitting general linear structural
20741 equation models (with observed and latent variables) using the RAM approach,
20742 and for fitting structural equations in observed-variable models by two-stage
20744 (license license:gpl2+)))
20746 (define-public r-semtools
20748 (name "r-semtools")
20753 (uri (cran-uri "semTools" version))
20756 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20757 (properties `((upstream-name . "semTools")))
20758 (build-system r-build-system)
20760 `(("r-lavaan" ,r-lavaan)))
20761 (home-page "https://github.com/simsem/semTools/wiki")
20762 (synopsis "Useful tools for structural equation modeling")
20764 "This package provides useful tools for structural equation modeling.")
20765 (license license:gpl2+)))
20767 (define-public r-regsem
20774 (uri (cran-uri "regsem" version))
20777 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20778 (properties `((upstream-name . "regsem")))
20779 (build-system r-build-system)
20781 `(("r-lavaan" ,r-lavaan)
20783 ("r-rcpparmadillo" ,r-rcpparmadillo)
20784 ("r-rsolnp" ,r-rsolnp)))
20785 (home-page "https://cran.r-project.org/package=regsem")
20786 (synopsis "Regularized structural equation modeling")
20788 "This package uses both ridge and lasso penalties (and extensions) to
20789 penalize specific parameters in structural equation models. The package
20790 offers additional cost functions, cross validation, and other extensions
20791 beyond traditional structural equation models. It also contains a function to
20792 perform @dfn{exploratory mediation} (XMed).")
20793 (license license:gpl2+)))
20795 (define-public r-stanheaders
20797 (name "r-stanheaders")
20798 (version "2.21.0-6")
20802 (uri (cran-uri "StanHeaders" version))
20805 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20806 (properties `((upstream-name . "StanHeaders")))
20807 (build-system r-build-system)
20808 (inputs `(("pandoc" ,pandoc)))
20810 `(("r-rcppeigen" ,r-rcppeigen)
20811 ("r-rcppparallel" ,r-rcppparallel)))
20813 `(("gfortran" ,gfortran)
20814 ("r-knitr" ,r-knitr))) ; for vignettes
20815 (home-page "https://mc-stan.org/")
20816 (synopsis "C++ header files for Stan")
20818 "The C++ header files of the Stan project are provided by this package.
20819 There is a shared object containing part of the @code{CVODES} library, but it
20820 is not accessible from R. @code{r-stanheaders} is only useful for developers
20821 who want to utilize the @code{LinkingTo} directive of their package's
20822 DESCRIPTION file to build on the Stan library without incurring unnecessary
20825 The Stan project develops a probabilistic programming language that implements
20826 full or approximate Bayesian statistical inference via Markov Chain Monte
20827 Carlo or variational methods and implements (optionally penalized) maximum
20828 likelihood estimation via optimization. The Stan library includes an advanced
20829 automatic differentiation scheme, templated statistical and linear algebra
20830 functions that can handle the automatically differentiable scalar types (and
20831 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20832 package provides user-facing R functions to parse, compile, test, estimate,
20833 and analyze Stan models.")
20834 (license license:bsd-3)))
20836 (define-public r-rpf
20843 (uri (cran-uri "rpf" version))
20846 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20847 (properties `((upstream-name . "rpf")))
20848 (build-system r-build-system)
20850 `(("r-lifecycle" ,r-lifecycle)
20851 ("r-mvtnorm" ,r-mvtnorm)
20853 ("r-rcppeigen" ,r-rcppeigen)))
20855 `(("r-knitr" ,r-knitr)))
20856 (home-page "https://github.com/jpritikin/rpf")
20857 (synopsis "Response probability functions")
20859 "The purpose of this package is to factor out logic and math common to
20860 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20861 core support code suitable for more specialized IRT packages to build upon.
20862 Complete access to optimized C functions is made available with
20863 @code{R_RegisterCCallable()}.")
20864 (license license:gpl3+)))
20866 (define-public r-openmx
20873 (uri (cran-uri "OpenMx" version))
20876 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20877 (properties `((upstream-name . "OpenMx")))
20878 (build-system r-build-system)
20881 ("r-digest" ,r-digest)
20882 ("r-lifecycle" ,r-lifecycle)
20884 ("r-matrix" ,r-matrix)
20886 ("r-rcppeigen" ,r-rcppeigen)
20888 ("r-stanheaders" ,r-stanheaders)))
20889 (native-inputs `(("gfortran" ,gfortran)))
20890 (home-page "http://openmx.ssri.psu.edu")
20891 (synopsis "Extended structural equation modelling")
20893 "This package allows for the estimation of a wide variety of advanced
20894 multivariate statistical models. It consists of a library of functions and
20895 optimizers that allow you to quickly and flexibly define an SEM model and
20896 estimate parameters given observed data.")
20897 (license license:asl2.0)))
20899 (define-public r-kutils
20906 (uri (cran-uri "kutils" version))
20909 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20910 (properties `((upstream-name . "kutils")))
20911 (build-system r-build-system)
20913 `(("r-foreign" ,r-foreign)
20914 ("r-openxlsx" ,r-openxlsx)
20916 ("r-runit" ,r-runit)
20917 ("r-xtable" ,r-xtable)))
20918 (home-page "https://cran.r-project.org/package=kutils")
20919 (synopsis "Project management tools")
20921 "This package provides tools for data importation, recoding, and
20922 inspection. There are functions to create new project folders, R code
20923 templates, create uniquely named output directories, and to quickly obtain a
20924 visual summary for each variable in a data frame. The main feature here is
20925 the systematic implementation of the \"variable key\" framework for data
20926 importation and recoding.")
20927 (license license:gpl2)))
20929 (define-public r-rockchalk
20931 (name "r-rockchalk")
20932 (version "1.8.144")
20936 (uri (cran-uri "rockchalk" version))
20939 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20940 (properties `((upstream-name . "rockchalk")))
20941 (build-system r-build-system)
20943 `(("r-cardata" ,r-cardata)
20944 ("r-kutils" ,r-kutils)
20946 ("r-mass" ,r-mass)))
20947 (home-page "https://cran.r-project.org/package=rockchalk")
20948 (synopsis "Regression estimation and presentation")
20950 "This package provides a collection of functions for interpretation and
20951 presentation of regression analysis. These functions are used to produce the
20952 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20953 includes regression diagnostics, regression tables, and plots of interactions
20954 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20955 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20956 fairly comprehensive overview.")
20957 (license license:gpl3+)))
20959 (define-public r-lisreltor
20961 (name "r-lisreltor")
20966 (uri (cran-uri "lisrelToR" version))
20969 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20970 (properties `((upstream-name . "lisrelToR")))
20971 (build-system r-build-system)
20972 (home-page "https://cran.r-project.org/package=lisrelToR")
20973 (synopsis "Import output from LISREL into R")
20975 "This is an unofficial package aimed at automating the import of LISREL
20977 (license license:gpl2)))
20979 (define-public r-bdgraph
20986 (uri (cran-uri "BDgraph" version))
20989 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
20990 (properties `((upstream-name . "BDgraph")))
20991 (build-system r-build-system)
20993 `(("r-igraph" ,r-igraph)))
20994 (home-page "https://www.uva.nl/profile/a.mohammadi")
20995 (synopsis "Bayesian structure learning in graphical models")
20997 "This package provides statistical tools for Bayesian structure learning
20998 in undirected graphical models for continuous, discrete, and mixed data. It
20999 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
21000 on a continuous-time birth-death process.")
21001 (license license:gpl2+)))
21003 (define-public r-d3network
21005 (name "r-d3network")
21006 (version "0.5.2.1")
21010 (uri (cran-uri "d3Network" version))
21013 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21014 (properties `((upstream-name . "d3Network")))
21015 (build-system r-build-system)
21017 `(("r-plyr" ,r-plyr)
21018 ("r-rjson" ,r-rjson)
21019 ("r-whisker" ,r-whisker)))
21020 (home-page "http://christophergandrud.github.io/d3Network/")
21021 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21023 "This package is intended to make it easy to create D3 JavaScript
21024 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21025 (license license:gpl3+)))
21027 (define-public r-qgraph
21034 (uri (cran-uri "qgraph" version))
21037 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21038 (properties `((upstream-name . "qgraph")))
21039 (build-system r-build-system)
21041 `(("r-abind" ,r-abind)
21042 ("r-bdgraph" ,r-bdgraph)
21043 ("r-colorspace" ,r-colorspace)
21044 ("r-corpcor" ,r-corpcor)
21045 ("r-d3network" ,r-d3network)
21046 ("r-dplyr" ,r-dplyr)
21047 ("r-fdrtool" ,r-fdrtool)
21048 ("r-ggplot2" ,r-ggplot2)
21049 ("r-ggraph" ,r-ggraph)
21050 ("r-glasso" ,r-glasso)
21051 ("r-gtools" ,r-gtools)
21052 ("r-hmisc" ,r-hmisc)
21054 ("r-igraph" ,r-igraph)
21056 ("r-lavaan" ,r-lavaan)
21057 ("r-matrix" ,r-matrix)
21058 ("r-pbapply" ,r-pbapply)
21061 ("r-psych" ,r-psych)
21063 ("r-reshape2" ,r-reshape2)
21064 ("r-tidygraph" ,r-tidygraph)))
21065 (home-page "http://sachaepskamp.com/qgraph/")
21066 (synopsis "Weighted network visualization and analysis")
21068 "This package implements tools for weighted network visualization and
21069 analysis, as well as Gaussian graphical model computation. It contains graph
21070 plotting methods, and tools for psychometric data visualization and graphical
21071 model estimation. See Epskamp et al. (2012)
21072 @url{doi:10.18637/jss.v048.i04}.")
21073 (license license:gpl2)))
21075 (define-public r-semplot
21082 (uri (cran-uri "semPlot" version))
21085 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21086 (properties `((upstream-name . "semPlot")))
21087 (build-system r-build-system)
21089 `(("r-colorspace" ,r-colorspace)
21090 ("r-corpcor" ,r-corpcor)
21091 ("r-igraph" ,r-igraph)
21092 ("r-lavaan" ,r-lavaan)
21093 ("r-lisreltor" ,r-lisreltor)
21094 ("r-openmx" ,r-openmx)
21096 ("r-qgraph" ,r-qgraph)
21097 ("r-regsem" ,r-regsem)
21098 ("r-rockchalk" ,r-rockchalk)
21101 (home-page "https://github.com/SachaEpskamp/semPlot")
21102 (synopsis "Unified visualizations of structural equation models")
21104 "Structural equation modeling (SEM) has a long history of representing
21105 models graphically as path diagrams. The semPlot package for R fills the gap
21106 between advanced, but time-consuming, graphical software and the limited
21107 graphics produced automatically by SEM software. In addition, semPlot offers
21108 more functionality than drawing path diagrams: it can act as a common ground
21109 for importing SEM results into R. Any result usable as input to semPlot can
21110 also be represented in any of the three popular SEM frame-works, as well as
21111 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21112 (license license:gpl2)))
21114 (define-public r-cdm
21121 (uri (cran-uri "CDM" version))
21124 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21125 (properties `((upstream-name . "CDM")))
21126 (build-system r-build-system)
21128 `(("r-mvtnorm" ,r-mvtnorm)
21129 ("r-polycor" ,r-polycor)
21131 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21133 "https://github.com/alexanderrobitzsch/CDM")
21134 (synopsis "Cognitive diagnosis modeling")
21136 "This package provides functions for cognitive diagnosis modeling and
21137 multidimensional item response modeling for dichotomous and polytomous item
21138 responses. It enables the estimation of the DINA and DINO model, the multiple
21139 group (polytomous) GDINA model, the multiple choice DINA model, the general
21140 diagnostic model (GDM), the structured latent class model (SLCA), and
21141 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21142 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21143 estimation and the package structure. For tutorials on how to use the CDM
21144 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21145 well as Ravand and Robitzsch (2015).")
21146 (license license:gpl2+)))
21148 (define-public r-tam
21155 (uri (cran-uri "TAM" version))
21158 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21159 (properties `((upstream-name . "TAM")))
21160 (build-system r-build-system)
21164 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21165 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21166 (synopsis "Test analysis modules")
21168 "This package includes tools for marginal maximum likelihood estimation
21169 and joint maximum likelihood estimation for unidimensional and
21170 multidimensional item response models. The package functionality covers the
21171 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21172 multi-faceted Rasch model, nominal item response model, structured latent
21173 class model, mixture distribution IRT models, and located latent class models.
21174 Latent regression models and plausible value imputation are also supported.")
21175 (license license:gpl2+)))
21177 (define-public r-erm
21184 (uri (cran-uri "eRm" version))
21187 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21188 (properties `((upstream-name . "eRm")))
21189 (build-system r-build-system)
21191 `(("r-colorspace" ,r-colorspace)
21192 ("r-lattice" ,r-lattice)
21194 ("r-matrix" ,r-matrix)
21195 ("r-psych" ,r-psych)))
21196 (native-inputs `(("gfortran" ,gfortran)))
21197 (home-page "https://cran.r-project.org/package=eRm")
21198 (synopsis "Extended Rasch modeling")
21200 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21201 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21202 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21203 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21204 data matrix. Additional features are the ML estimation of the person
21205 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21206 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21207 infit and outfit measures, ICC and other plots, automated stepwise item
21208 elimination, and a simulation module for various binary data matrices.")
21209 (license license:gpl3)))
21211 (define-public r-irtoys
21218 (uri (cran-uri "irtoys" version))
21221 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21222 (properties `((upstream-name . "irtoys")))
21223 (build-system r-build-system)
21227 (home-page "https://cran.r-project.org/package=irtoys")
21228 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21230 "This package provides a collection of functions useful in learning and
21231 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21232 programs. It provides basic CTT analysis, a simple common interface to the
21233 estimation of item parameters in IRT models for binary responses with three
21234 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21235 EAP, WLE, plausible values), item and person fit statistics, scaling
21236 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21237 array of parametric and non-parametric (kernel) plots. It estimates and plots
21238 Haberman's interaction model when all items are dichotomously scored.")
21239 (license license:gpl2+)))
21241 (define-public r-iheatmapr
21243 (name "r-iheatmapr")
21248 (uri (cran-uri "iheatmapr" version))
21251 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21252 (properties `((upstream-name . "iheatmapr")))
21253 (build-system r-build-system)
21255 `(("r-fastcluster" ,r-fastcluster)
21256 ("r-ggdendro" ,r-ggdendro)
21257 ("r-htmlwidgets" ,r-htmlwidgets)
21258 ("r-jsonlite" ,r-jsonlite)
21259 ("r-knitr" ,r-knitr)
21260 ("r-magrittr" ,r-magrittr)
21261 ("r-rcolorbrewer" ,r-rcolorbrewer)
21262 ("r-scales" ,r-scales)))
21264 `(("r-knitr" ,r-knitr)))
21265 (home-page "https://docs.ropensci.org/iheatmapr")
21266 (synopsis "Interactive, Complex Heatmaps")
21268 "iheatmapr is an R package for building complex, interactive heatmaps
21269 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21270 subplots along the rows or columns of the main heatmap add more information
21271 about each row or column. For example, a one column additional heatmap may
21272 indicate what group a particular row or column belongs to. Complex heatmaps
21273 may also include multiple side by side heatmaps which show different types of
21274 data for the same conditions. Interactivity can improve complex heatmaps by
21275 providing tooltips with information about each cell and enabling zooming into
21276 interesting features. iheatmapr uses the plotly library for interactivity.")
21277 (license license:expat)))
21279 (define-public r-packrat
21286 (uri (cran-uri "packrat" version))
21289 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21290 (properties `((upstream-name . "packrat")))
21291 (build-system r-build-system)
21292 (home-page "https://github.com/rstudio/packrat/")
21293 (synopsis "Dependency management R projects")
21295 "This package provides a dependency manager for R projects that allows
21296 you to manage the R packages your project depends on in an isolated, portable,
21297 and reproducible way.")
21298 (license license:gpl2)))
21300 (define-public r-rsconnect
21302 (name "r-rsconnect")
21307 (uri (cran-uri "rsconnect" version))
21310 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21311 (properties `((upstream-name . "rsconnect")))
21312 (build-system r-build-system)
21314 `(("r-curl" ,r-curl)
21315 ("r-digest" ,r-digest)
21316 ("r-jsonlite" ,r-jsonlite)
21317 ("r-openssl" ,r-openssl)
21318 ("r-packrat" ,r-packrat)
21319 ("r-rstudioapi" ,r-rstudioapi)
21320 ("r-yaml" ,r-yaml)))
21321 (home-page "https://github.com/rstudio/rsconnect")
21322 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21324 "This package provides a programmatic deployment interface for RPubs,
21325 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21326 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21327 (license license:gpl2)))
21329 ;; This package includes minified JavaScript files. When upgrading please
21330 ;; check that there are no new minified JavaScript files.
21331 (define-public r-dygraphs
21333 (name "r-dygraphs")
21334 (version "1.1.1.6")
21338 (uri (cran-uri "dygraphs" version))
21341 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21342 (properties `((upstream-name . "dygraphs")))
21343 (build-system r-build-system)
21345 `(#:modules ((guix build utils)
21346 (guix build r-build-system)
21350 (modify-phases %standard-phases
21351 (add-after 'unpack 'process-javascript
21352 (lambda* (#:key inputs #:allow-other-keys)
21353 (with-directory-excursion "inst/htmlwidgets/lib/"
21357 `(("dygraphs/dygraph-combined-dev.js"
21358 "dygraph-combined.js")
21359 (,(assoc-ref inputs "js-jquery")
21360 "jquery/jquery.min.js")
21361 (,(assoc-ref inputs "js-fquarter")
21362 "fquarter/moment-fquarter.min.js"))))
21363 (lambda (sources targets)
21364 (for-each (lambda (source target)
21365 (format #t "Processing ~a --> ~a~%"
21367 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21368 (call-with-output-file target
21370 (dump-port minified port)))))
21371 sources targets))))
21374 `(("uglify-js" ,uglify-js)
21375 ;; They actually use version 1.11.1, but this more recent version
21376 ;; should be just fine.
21380 (uri "https://code.jquery.com/jquery-1.12.4.js")
21383 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21387 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21388 "moment-fquarter/1.0.1/moment-fquarter.js"))
21391 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21393 `(("r-htmltools" ,r-htmltools)
21394 ("r-htmlwidgets" ,r-htmlwidgets)
21395 ("r-magrittr" ,r-magrittr)
21398 (home-page "https://github.com/rstudio/dygraphs")
21399 (synopsis "Interface to Dygraphs interactive time series charting library")
21401 "This package provides an R interface to the dygraphs JavaScript charting
21402 library (a copy of which is included in the package). It provides rich
21403 facilities for charting time-series data in R, including highly configurable
21404 series- and axis-display and interactive features like zoom/pan and
21405 series/point highlighting.")
21406 (license license:expat)))
21408 (define-public r-shinystan
21410 (name "r-shinystan")
21415 (uri (cran-uri "shinystan" version))
21418 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21419 (properties `((upstream-name . "shinystan")))
21420 (build-system r-build-system)
21422 `(("r-bayesplot" ,r-bayesplot)
21423 ("r-colourpicker" ,r-colourpicker)
21425 ("r-dygraphs" ,r-dygraphs)
21426 ("r-ggplot2" ,r-ggplot2)
21427 ("r-gridextra" ,r-gridextra)
21428 ("r-gtools" ,r-gtools)
21429 ("r-markdown" ,r-markdown)
21430 ("r-reshape2" ,r-reshape2)
21431 ("r-rsconnect" ,r-rsconnect)
21432 ("r-rstan" ,r-rstan)
21433 ("r-shiny" ,r-shiny)
21434 ("r-shinyjs" ,r-shinyjs)
21435 ("r-shinythemes" ,r-shinythemes)
21436 ("r-threejs" ,r-threejs)
21437 ("r-xtable" ,r-xtable)
21439 (home-page "https://mc-stan.org/")
21440 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21442 "This package provides a graphical user interface for interactive
21443 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21444 for analyzing a posterior sample. The interface is powered by the Shiny web
21445 application framework and works with the output of MCMC programs written in
21446 any programming language (and has extended functionality for Stan models fit
21447 using the @code{rstan} and @code{rstanarm} packages).")
21448 (license license:gpl3+)))
21450 (define-public r-rstantools
21452 (name "r-rstantools")
21457 (uri (cran-uri "rstantools" version))
21460 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21461 (properties `((upstream-name . "rstantools")))
21462 (build-system r-build-system)
21463 (inputs `(("pandoc" ,pandoc)))
21465 `(("r-desc" ,r-desc)
21467 ("r-rcppparallel" ,r-rcppparallel)))
21469 `(("r-knitr" ,r-knitr)))
21470 (home-page "https://mc-stan.org/rstantools/")
21471 (synopsis "Tools for developing R packages interfacing with Stan")
21473 "This package provides various tools for developers of R packages
21474 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21475 up the required package structure, S3 generics and default methods to unify
21476 function naming across Stan-based R packages, and vignettes with
21477 recommendations for developers.")
21478 (license license:gpl3+)))
21480 (define-public r-loo
21487 (uri (cran-uri "loo" version))
21489 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21490 (properties `((upstream-name . "loo")))
21491 (build-system r-build-system)
21493 `(("pandoc" ,pandoc)
21494 ("pandoc-citeproc" ,pandoc-citeproc)))
21496 `(("r-checkmate" ,r-checkmate)
21497 ("r-matrixstats" ,r-matrixstats)))
21499 `(("r-knitr" ,r-knitr)))
21500 (home-page "https://mc-stan.org/loo/")
21501 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21503 "This package provides an implementation of efficient approximate
21504 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21505 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21506 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21507 procedure for regularizing importance weights. As a byproduct of the
21508 calculations, we also obtain approximate standard errors for estimated
21509 predictive errors and for the comparison of predictive errors between models.
21510 The package also provides methods for using stacking and other model weighting
21511 techniques to average Bayesian predictive distributions.")
21512 (license license:gpl3+)))
21514 (define-public r-rstan
21521 (uri (cran-uri "rstan" version))
21524 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21525 (properties `((upstream-name . "rstan")))
21526 (build-system r-build-system)
21529 (modify-phases %standard-phases
21530 (add-before 'install 'set-timezone
21531 ;; This package is picky about timezones.
21532 (lambda* (#:key inputs #:allow-other-keys)
21533 (setenv "TZ" "UTC+1")
21535 (string-append (assoc-ref inputs "tzdata")
21536 "/share/zoneinfo"))
21539 `(("tzdata" ,tzdata-for-tests)
21541 ("r-knitr" ,r-knitr)))
21544 ("r-ggplot2" ,r-ggplot2)
21545 ("r-gridextra" ,r-gridextra)
21546 ("r-inline" ,r-inline)
21548 ("r-pkgbuild" ,r-pkgbuild)
21550 ("r-rcppeigen" ,r-rcppeigen)
21551 ("r-rcppparallel" ,r-rcppparallel)
21552 ("r-stanheaders" ,r-stanheaders)
21554 ("r-withr" ,r-withr)))
21555 (home-page "https://discourse.mc-stan.org/")
21556 (synopsis "R interface to Stan")
21558 "User-facing R functions are provided to parse, compile, test, estimate,
21559 and analyze Stan models by accessing the header-only Stan library provided by
21560 the StanHeaders package. The Stan project develops a probabilistic
21561 programming language that implements full Bayesian statistical inference via
21562 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21563 approximation, and (optionally penalized) maximum likelihood estimation via
21564 optimization. In all three cases, automatic differentiation is used to
21565 quickly and accurately evaluate gradients without burdening the user with the
21566 need to derive the partial derivatives.")
21567 (license license:gpl3+)))
21569 (define-public r-rstanarm
21571 (name "r-rstanarm")
21576 (uri (cran-uri "rstanarm" version))
21579 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21580 (properties `((upstream-name . "rstanarm")))
21581 (build-system r-build-system)
21583 `(("pandoc" ,pandoc)
21584 ("pandoc-citeproc" ,pandoc-citeproc)))
21586 `(("r-bayesplot" ,r-bayesplot)
21588 ("r-ggplot2" ,r-ggplot2)
21591 ("r-matrix" ,r-matrix)
21594 ("r-rcppeigen" ,r-rcppeigen)
21595 ("r-rcppparallel" ,r-rcppparallel)
21596 ("r-rstan" ,r-rstan)
21597 ("r-rstantools" ,r-rstantools)
21598 ("r-shinystan" ,r-shinystan)
21599 ("r-stanheaders" ,r-stanheaders)
21600 ("r-survival" ,r-survival)))
21602 `(("r-knitr" ,r-knitr)))
21603 (home-page "https://mc-stan.org/rstanarm/")
21604 (synopsis "Bayesian applied regression modeling via Stan")
21606 "This package estimates previously compiled regression models using the
21607 @code{rstan} package, which provides the R interface to the Stan C++ library
21608 for Bayesian estimation. Users specify models via the customary R syntax with
21609 a formula and @code{data.frame} plus some additional arguments for priors.")
21610 (license license:gpl3+)))
21612 (define-public r-kendall
21619 (uri (cran-uri "Kendall" version))
21622 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21623 (properties `((upstream-name . "Kendall")))
21624 (build-system r-build-system)
21626 `(("r-boot" ,r-boot)))
21628 `(("gfortran" ,gfortran)))
21629 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21630 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21632 "This package computes the Kendall rank correlation and Mann-Kendall
21634 (license license:gpl2+)))
21636 (define-public r-zyp
21639 (version "0.10-1.1")
21643 (uri (cran-uri "zyp" version))
21646 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21647 (properties `((upstream-name . "zyp")))
21648 (build-system r-build-system)
21650 `(("r-kendall" ,r-kendall)))
21651 (home-page "https://cran.r-project.org/web/packages/zyp/")
21652 (synopsis "Zhang + Yue-Pilon Trends Package")
21654 "This package contains an efficient implementation of Sen's slope
21655 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21656 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21658 (license license:lgpl2.1)))
21660 (define-public r-rlinsolve
21662 (name "r-rlinsolve")
21667 (uri (cran-uri "Rlinsolve" version))
21670 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21671 (properties `((upstream-name . "Rlinsolve")))
21672 (build-system r-build-system)
21674 `(("r-matrix" ,r-matrix)
21676 ("r-rcpparmadillo" ,r-rcpparmadillo)
21677 ("r-rdpack" ,r-rdpack)))
21678 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21679 (synopsis "Iterative solvers for (sparse) linear system of equations")
21681 "Solving a system of linear equations is one of the most fundamental
21682 computational problems for many fields of mathematical studies, such as
21683 regression problems from statistics or numerical partial differential
21684 equations. This package provides basic stationary iterative solvers such as
21685 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21686 Nonstationary, also known as Krylov subspace methods are also provided.
21687 Sparse matrix computation is also supported in that solving large and sparse
21688 linear systems can be manageable using the @code{Matrix} package along with
21689 @code{RcppArmadillo}.")
21690 (license license:gpl3+)))
21692 (define-public r-zvcv
21699 (uri (cran-uri "ZVCV" version))
21702 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21703 (properties `((upstream-name . "ZVCV")))
21704 (build-system r-build-system)
21706 `(("r-abind" ,r-abind)
21708 ("r-dplyr" ,r-dplyr)
21709 ("r-glmnet" ,r-glmnet)
21710 ("r-magrittr" ,r-magrittr)
21711 ("r-mvtnorm" ,r-mvtnorm)
21713 ("r-rcpparmadillo" ,r-rcpparmadillo)
21714 ("r-rlinsolve" ,r-rlinsolve)))
21715 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21716 (synopsis "Zero-Variance Control Variates")
21718 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21719 to reduce the variance of Monte Carlo estimators of expectations using the
21720 derivatives of the log target. Once the derivatives are available, the only
21721 additional computational effort is in solving a linear regression problem.
21722 This method has been extended to higher dimensions using regularisation. This
21723 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21724 samples, derivatives and function evaluations are available. Additional
21725 functions for applying ZV-CV to two estimators for the normalising constant of
21726 the posterior distribution in Bayesian statistics are also supplied.")
21727 (license license:gpl2+)))
21729 (define-public r-ztype
21736 (uri (cran-uri "ztype" version))
21739 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21740 (properties `((upstream-name . "ztype")))
21741 (build-system r-build-system)
21743 `(("r-assertthat" ,r-assertthat)
21744 ("r-dplyr" ,r-dplyr)
21745 ("r-ggplot2" ,r-ggplot2)
21746 ("r-lubridate" ,r-lubridate)
21747 ("r-magrittr" ,r-magrittr)
21748 ("r-rvest" ,r-rvest)
21749 ("r-stringr" ,r-stringr)))
21750 (home-page "https://cran.r-project.org/web/packages/ztype/")
21751 (synopsis "Run a Ztype game loaded with R functions")
21753 "How fast can you type R functions on your keyboard? Find out by running
21754 a @code{zty.pe} game: export R functions as instructions to type to destroy
21755 opponents' vessels.")
21756 (license license:gpl3)))
21758 (define-public r-zseq
21765 (uri (cran-uri "Zseq" version))
21768 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21769 (properties `((upstream-name . "Zseq")))
21770 (build-system r-build-system)
21772 `(("r-gmp" ,r-gmp)))
21773 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21774 (synopsis "Integer sequence generator")
21776 "This package generates well-known integer sequences. The @code{gmp}
21777 package is adopted for computing with arbitrarily large numbers. Every
21778 function has a hyperlink to its corresponding item in the @dfn{On-Line
21779 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21780 (license license:gpl3+)))
21782 (define-public r-isoband
21789 (uri (cran-uri "isoband" version))
21792 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21793 (properties `((upstream-name . "isoband")))
21794 (build-system r-build-system)
21796 `(("r-testthat" ,r-testthat)))
21798 `(("r-knitr" ,r-knitr)))
21799 (home-page "https://github.com/wilkelab/isoband")
21800 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21802 "This package provides a fast C++ implementation to generate contour
21803 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21804 containing elevation data.")
21805 (license license:expat)))
21807 (define-public r-ppcor
21814 (uri (cran-uri "ppcor" version))
21817 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21818 (properties `((upstream-name . "ppcor")))
21819 (build-system r-build-system)
21821 `(("r-mass" ,r-mass)))
21822 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21823 (synopsis "Partial and semi-partial correlation")
21825 "This package provides users not only with a function to readily
21826 calculate the higher-order partial and semi-partial correlations but also with
21827 statistics and p-values of the correlation coefficients.")
21828 (license license:gpl2)))
21830 (define-public r-hrbrthemes
21832 (name "r-hrbrthemes")
21837 (uri (cran-uri "hrbrthemes" version))
21839 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21840 (properties `((upstream-name . "hrbrthemes")))
21841 (build-system r-build-system)
21843 `(("r-extrafont" ,r-extrafont)
21844 ("r-gdtools" ,r-gdtools)
21845 ("r-ggplot2" ,r-ggplot2)
21846 ("r-htmltools" ,r-htmltools)
21847 ("r-knitr" ,r-knitr)
21848 ("r-magrittr" ,r-magrittr)
21849 ("r-rmarkdown" ,r-rmarkdown)
21850 ("r-scales" ,r-scales)))
21852 `(("r-knitr" ,r-knitr)))
21853 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21854 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21856 "This package provides a compilation of extra @code{ggplot2} themes,
21857 scales and utilities, including a spell check function for plot label fields
21858 and an overall emphasis on typography.")
21859 (license license:expat)))
21861 (define-public r-crochet
21868 (uri (cran-uri "crochet" version))
21871 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21872 (build-system r-build-system)
21874 `(("r-knitr" ,r-knitr)))
21875 (home-page "https://github.com/agrueneberg/crochet")
21876 (synopsis "Implementation Helper for Matrix-Like Types")
21878 "Functions to help implement the extraction / subsetting / indexing
21879 function @code{[} and replacement function @code{[<-} of custom matrix-like
21880 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21881 as possible (with tests to prove it).")
21882 (license license:expat)))
21884 (define-public r-boa
21887 (version "1.1.8-2")
21891 (uri (cran-uri "boa" version))
21894 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21895 (properties `((upstream-name . "boa")))
21896 (build-system r-build-system)
21897 (home-page "http://www.jstatsoft.org/v21/i11")
21898 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21900 "This package provides a menu-driven program and library of functions for
21901 carrying out convergence diagnostics and statistical and graphical analysis of
21902 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21903 (license license:gpl2+)))
21905 (define-public r-httpcode
21907 (name "r-httpcode")
21911 (uri (cran-uri "httpcode" version))
21914 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21915 (build-system r-build-system)
21916 (home-page "https://github.com/sckott/httpcode")
21917 (synopsis "HTTP status code helper")
21918 (description "@code{httpcode} provides functionality for finding and
21919 explaining the meaning of @code{HTTP} status codes. Functions are included for
21920 searching for codes by full or partial number, by message, and to get
21921 appropriate dog and cat images for many status codes.")
21922 (license license:expat)))
21924 (define-public r-latex2exp
21926 (name "r-latex2exp")
21930 (uri (cran-uri "latex2exp" version))
21933 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21934 (build-system r-build-system)
21936 `(("r-stringr" ,r-stringr)
21937 ("r-magrittr", r-magrittr)))
21938 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21939 (synopsis "Use LaTeX expressions in plots")
21940 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21941 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21942 rendered as text, axis labels, etc. throughout R's plotting system.")
21943 (license license:expat)))
21945 (define-public r-oai
21951 (uri (cran-uri "oai" version))
21954 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21955 (build-system r-build-system)
21957 `(("r-xml2" ,r-xml2)
21960 ("r-stringr" ,r-stringr)
21961 ("r-tibble" ,r-tibble)))
21962 (home-page "https://github.com/ropensci/oai/")
21963 (synopsis "General purpose OAI-PMH services client")
21964 (description "@code{oai} provides a general purpose client to work with
21965 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21966 service. Functions are provided to work with the OAI-PMH verbs:
21967 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21968 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21969 (license license:expat)))
21971 (define-public r-argon2
21978 (uri (cran-uri "argon2" version))
21981 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21982 (properties `((upstream-name . "argon2")))
21983 (build-system r-build-system)
21984 (home-page "https://github.com/wrathematics/argon2")
21985 (synopsis "Secure password hashing based on the argon2 algorithm")
21987 "This package provides utilities for secure password hashing via the
21988 argon2 algorithm.")
21989 (license license:bsd-2)))
21991 (define-public r-getpass
21998 (uri (cran-uri "getPass" version))
22001 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
22002 (properties `((upstream-name . "getPass")))
22003 (build-system r-build-system)
22005 `(("r-rstudioapi" ,r-rstudioapi)))
22006 (home-page "https://github.com/wrathematics/getPass")
22007 (synopsis "Masked user input")
22009 "This package provides a micro-package for reading \"passwords\", i.e.
22010 reading user input with masking, so that the input is not displayed as it is
22011 typed. Currently, RStudio, the command line (every OS), and any platform
22012 where tcltk is present are supported.")
22013 (license license:bsd-2)))
22015 (define-public r-remoter
22022 (uri (cran-uri "remoter" version))
22025 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22026 (properties `((upstream-name . "remoter")))
22027 (build-system r-build-system)
22029 `(("r-argon2" ,r-argon2)
22030 ("r-getpass" ,r-getpass)
22031 ("r-pbdzmq" ,r-pbdzmq)
22033 (home-page "https://github.com/RBigData/remoter")
22034 (synopsis "Control a remote R session from a local one")
22036 "This package provides a set of utilities for client/server computing
22037 with R, controlling a remote R session (the server) from a local one (the
22039 (license license:bsd-2)))
22041 (define-public r-asd
22048 (uri (cran-uri "asd" version))
22051 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22052 (properties `((upstream-name . "asd")))
22053 (build-system r-build-system)
22055 `(("r-mvtnorm" ,r-mvtnorm)))
22056 (home-page "https://cran.r-project.org/web/packages/asd")
22057 (synopsis "Simulations for Adaptive Seamless Designs")
22059 "This package provdes means to run simulations for adaptive seamless
22060 designs with and without early outcomes for treatment selection and
22061 subpopulation type designs.")
22062 (license license:gpl3)))
22064 (define-public r-nbconvertr
22066 (name "r-nbconvertr")
22071 (uri (cran-uri "nbconvertR" version))
22074 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22075 (properties `((upstream-name . "nbconvertR")))
22076 (build-system r-build-system)
22078 `(("jupyter" ,python-nbconvert)
22079 ("pandoc" ,pandoc)))
22080 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22081 (synopsis "Vignette engine wrapping Jupyter notebooks")
22083 "This package calls the Jupyter script @code{nbconvert} to create
22084 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22085 containing rich text, code, and its output. Code cells can be edited and
22086 evaluated interactively.")
22087 (license license:gpl3)))
22089 (define-public r-bridgesampling
22091 (name "r-bridgesampling")
22096 (uri (cran-uri "bridgesampling" version))
22099 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22101 `((upstream-name . "bridgesampling")))
22102 (build-system r-build-system)
22104 `(("r-brobdingnag" ,r-brobdingnag)
22106 ("r-matrix" ,r-matrix)
22107 ("r-mvtnorm" ,r-mvtnorm)
22108 ("r-scales" ,r-scales)
22109 ("r-stringr" ,r-stringr)))
22111 `(("r-knitr" ,r-knitr)))
22112 (home-page "https://github.com/quentingronau/bridgesampling")
22113 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22115 "This package provides functions for estimating marginal likelihoods,
22116 Bayes factors, posterior model probabilities, and normalizing constants in
22117 general, via different versions of bridge sampling.")
22118 (license license:gpl2+)))
22120 (define-public r-tea
22127 (uri (cran-uri "tea" version))
22130 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22132 `((upstream-name . "tea")))
22133 (build-system r-build-system)
22135 `(("r-matrix" ,r-matrix)))
22136 (home-page "https://cran.r-project.org/web/packages/tea/")
22137 (synopsis "Threshold estimation approaches")
22139 "This package provides different approaches for selecting the threshold
22140 in generalized Pareto distributions. Most of them are based on minimizing the
22141 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
22142 Others are heuristically motivated by searching for stable sample paths, i.e.
22143 a nearly constant region of the tail index estimator with respect to k, which
22144 is the number of data in the tail. The third class is motivated by graphical
22145 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22146 is also implemented here.")
22147 (license license:gpl3)))
22149 (define-public r-awsmethods
22151 (name "r-awsmethods")
22156 (uri (cran-uri "awsMethods" version))
22159 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22161 `((upstream-name . "awsMethods")))
22162 (build-system r-build-system)
22163 (home-page "http://www.wias-berlin.de/software/imaging/")
22164 (synopsis "Class and methods definitions")
22166 "This package defines the generic method @code{extract} and provides
22167 @code{openMP} support as needed in several packages like
22168 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22169 (license license:gpl2+)))
22171 (define-public r-aws
22178 (uri (cran-uri "aws" version))
22181 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
22183 `((upstream-name . "aws")))
22184 (build-system r-build-system)
22186 `(("r-awsmethods" ,r-awsmethods)
22189 `(("gfortran" ,gfortran)))
22190 (home-page "https://cran.r-project.org/web/packages/aws/")
22191 (synopsis "Adaptive weights smoothing")
22193 "This package provides a collection of R-functions implementing adaptive
22194 smoothing procedures in 1D, 2D and 3D. This includes the
22195 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22196 Confidence Intervals} (ICI), variational approaches, and a non-local means
22198 (license license:gpl2+)))
22200 (define-public r-sgloptim
22202 (name "r-sgloptim")
22207 (uri (cran-uri "sglOptim" version))
22210 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22212 `((upstream-name . "sglOptim")))
22213 (build-system r-build-system)
22216 ("r-doparallel" ,r-doparallel)
22217 ("r-foreach" ,r-foreach)
22218 ("r-matrix" ,r-matrix)
22220 ("r-rcpparmadillo" ,r-rcpparmadillo)
22221 ("r-rcppprogress" ,r-rcppprogress)))
22223 `(("r-knitr" ,r-knitr)))
22224 (home-page "https://github.com/nielsrhansen/sglOptim")
22225 (synopsis "Generic sparse group Lasso solver")
22227 "This package provides a fast generic solver for sparse group lasso
22228 optimization problems. The loss (objective) function must be defined in a C++
22229 module. The optimization problem is solved using a coordinate gradient
22230 descent algorithm. Convergence of the algorithm is established and the
22231 algorithm is applicable to a broad class of loss functions. Use of parallel
22232 computing for cross validation and subsampling is supported through the
22233 @code{foreach} and @code{doParallel} packages.")
22234 (license license:gpl2+)))
22236 (define-public r-grouped
22243 (uri (cran-uri "grouped" version))
22246 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22248 `((upstream-name . "grouped")))
22249 (build-system r-build-system)
22251 `(("r-mass" ,r-mass)))
22252 (home-page "https://cran.r-project.org/web/packages/grouped/")
22253 (synopsis "Regression analysis of grouped and coarse data")
22255 "This package provides regression models for grouped and coarse data,
22256 under the coarsened at random assumption.")
22257 (license license:gpl2+)))
22259 (define-public r-stam
22266 (uri (cran-uri "stam" version))
22269 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22271 `((upstream-name . "stam")))
22272 (build-system r-build-system)
22276 (home-page "https://cran.r-project.org/web/packages/stam")
22277 (synopsis "Spatio-temporal analysis and modelling")
22279 "This package provides various methods to conduct Spatio-Temporal
22280 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22281 Inferred Spatio-Temporal Modelling.")
22282 (license license:gpl2+)))
22284 (define-public r-dcv
22291 (uri (cran-uri "dcv" version))
22294 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22296 `((upstream-name . "dcv")))
22297 (build-system r-build-system)
22299 `(("r-lmtest" ,r-lmtest)))
22300 (home-page "https://cran.r-project.org/web/packages/dcv/")
22301 (synopsis "Conventional cross-validation statistics for climate-growth model")
22303 "This package performs several conventional cross-validation statistical
22304 methods for climate-growth model in the climate reconstruction from tree
22305 rings, including Sign Test statistic, Reduction of Error statistic, Product
22306 Mean Test, Durbin-Watson statistic etc.")
22307 (license license:gpl2)))
22309 (define-public r-rcdd
22316 (uri (cran-uri "rcdd" version))
22319 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22321 `((upstream-name . "rcdd")))
22322 (build-system r-build-system)
22325 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22326 (synopsis "Computational geometry")
22328 "This package converts back and forth between two representations of a
22329 convex polytope: as solution of a set of linear equalities and inequalities
22330 and as convex hull of set of points and rays. Also does linear programming
22331 and redundant generator elimination. All functions can use exact
22332 infinite-precision rational arithmetic.")
22333 (license license:gpl2)))
22335 (define-public r-rxnat
22342 (uri (cran-uri "Rxnat" version))
22345 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22347 `((upstream-name . "Rxnat")))
22348 (build-system r-build-system)
22350 `(("r-dplyr" ,r-dplyr)
22352 ("r-rcurl" ,r-rcurl)))
22354 `(("r-knitr" ,r-knitr)))
22355 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22356 (synopsis "Queries and extracts images from neuroimaging datasets")
22358 "This package allows communication with the Extensible Neuroimaging
22359 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22361 (license license:gpl2)))
22363 (define-public r-rserve
22370 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22371 version ".tar.gz"))
22374 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22375 (build-system r-build-system)
22377 `(("r-checkmate" ,r-checkmate)
22379 ("r-jsonlite" ,r-jsonlite)
22380 ("r-knitr" ,r-knitr)
22383 ("r-uuid" ,r-uuid)))
22385 `(("openssl" ,openssl)
22387 (home-page "https://github.com/s-u/Rserve")
22389 "Server providing access to R from many languages and systems")
22391 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22392 binary requests to be sent to R. Every connection has a separate workspace
22393 and working directory. Client-side implementations are available for popular
22394 languages such as C/C++ and Java, allowing any application to use facilities
22395 of R without the need of linking to R code. Rserve supports remote
22396 connection, user authentication and file transfer. A simple R client is
22397 included in this package as well.")
22398 (license license:gpl2)))
22400 (define-public r-brms
22407 (uri (cran-uri "brms" version))
22410 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22411 (properties `((upstream-name . "brms")))
22412 (build-system r-build-system)
22414 `(("r-abind" ,r-abind)
22415 ("r-backports" ,r-backports)
22416 ("r-bayesplot" ,r-bayesplot)
22417 ("r-bridgesampling" ,r-bridgesampling)
22419 ("r-future" ,r-future)
22420 ("r-ggplot2" ,r-ggplot2)
22423 ("r-matrix" ,r-matrix)
22424 ("r-matrixstats" ,r-matrixstats)
22426 ("r-nleqslv" ,r-nleqslv)
22429 ("r-rstan" ,r-rstan)
22430 ("r-rstantools" ,r-rstantools)
22431 ("r-shinystan" ,r-shinystan)))
22432 (native-inputs `(("r-knitr" ,r-knitr)))
22434 "https://github.com/paul-buerkner/brms")
22436 "Bayesian Regression Models using 'Stan'")
22438 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22439 using 'Stan' for full Bayesian inference. A wide range of distributions and
22440 link functions are supported, allowing users to fit -- among others -- linear,
22441 robust linear, count data, survival, response times, ordinal, zero-inflated,
22442 hurdle, and even self-defined mixture models all in a multilevel context.
22443 Further modeling options include non-linear and smooth terms, auto-correlation
22444 structures, censored data, meta-analytic standard errors, and quite a few
22445 more. In addition, all parameters of the response distribution can be
22446 predicted in order to perform distributional regression. Prior specifications
22447 are flexible and explicitly encourage users to apply prior distributions that
22448 actually reflect their beliefs. Model fit can easily be assessed and compared
22449 with posterior predictive checks and leave-one-out cross-validation.")
22450 (license license:gpl2)))
22452 (define-public r-mstate
22459 (uri (cran-uri "mstate" version))
22462 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22463 (properties `((upstream-name . "mstate")))
22464 (build-system r-build-system)
22466 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22467 ("r-survival" ,r-survival)))
22469 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22471 "Data Preparation, Estimation and Prediction in Multi-State Models")
22473 "Contains functions for data preparation, descriptives, hazard estimation
22474 and prediction with Aalen-Johansen or simulation in competing risks and
22475 multi-state models.")
22476 (license license:gpl2+)))
22478 (define-public r-scatterpie
22480 (name "r-scatterpie")
22485 (uri (cran-uri "scatterpie" version))
22488 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22489 (properties `((upstream-name . "scatterpie")))
22490 (build-system r-build-system)
22492 `(("r-ggforce" ,r-ggforce)
22493 ("r-ggplot2" ,r-ggplot2)
22494 ("r-rlang" ,r-rlang)
22495 ("r-rvcheck" ,r-rvcheck)
22496 ("r-tidyr" ,r-tidyr)))
22498 `(("r-knitr" ,r-knitr)))
22499 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22500 (synopsis "Scatter pie plot")
22502 "This package creates scatterpie plots, especially useful for plotting
22504 (license license:artistic2.0)))
22506 (define-public r-boruta
22513 (uri (cran-uri "Boruta" version))
22516 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22517 (properties `((upstream-name . "Boruta")))
22518 (build-system r-build-system)
22519 (propagated-inputs `(("r-ranger" ,r-ranger)))
22520 (home-page "https://gitlab.com/mbq/Boruta/")
22521 (synopsis "Wrapper algorithm for all relevant feature selection")
22523 "This package provides an all relevant feature selection wrapper
22524 algorithm. It finds relevant features by comparing original attributes'
22525 importance with importance achievable at random, estimated using their
22526 permuted copies (shadows).")
22527 (license license:gpl2+)))
22529 (define-public r-directlabels
22531 (name "r-directlabels")
22532 (version "2020.6.17")
22536 (uri (cran-uri "directlabels" version))
22539 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22540 (build-system r-build-system)
22542 `(("r-quadprog" ,r-quadprog)))
22544 `(("r-knitr" ,r-knitr)))
22545 (home-page "http://directlabels.r-forge.r-project.org/")
22546 (synopsis "Direct labels for multicolor plots")
22548 "This package provides an extensible framework for automatically placing
22549 direct labels onto multicolor plots. Label positions are described using
22550 positioning methods that can be re-used across several different plots. There
22551 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22552 inferring an appropriate positioning method.")
22553 (license license:gpl3)))
22555 (define-public r-lsd
22562 (uri (cran-uri "LSD" version))
22564 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22565 (properties `((upstream-name . "LSD")))
22566 (build-system r-build-system)
22567 (home-page "https://cran.r-project.org/web/packages/LSD/")
22568 (synopsis "Lots of superior depictions tool creates colorful plots")
22570 "This package creates lots of colorful plots in a multitude of variations.
22571 Try a demo of the LSD by running @code{demotour()}.")
22573 (license (list license:gpl2 license:gpl3))))
22575 (define-public r-fourcseq
22577 (name "r-fourcseq")
22582 (uri (bioconductor-uri "FourCSeq" version))
22584 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22585 (properties `((upstream-name . "FourCSeq")))
22586 (build-system r-build-system)
22588 `(("r-biobase" ,r-biobase)
22589 ("r-biostrings" ,r-biostrings)
22590 ("r-deseq2" ,r-deseq2)
22592 ("r-genomicalignments" ,r-genomicalignments)
22593 ("r-genomicranges" ,r-genomicranges)
22594 ("r-ggbio" ,r-ggbio)
22595 ("r-ggplot2" ,r-ggplot2)
22596 ("r-gtools" ,r-gtools)
22598 ("r-matrix" ,r-matrix)
22599 ("r-reshape2" ,r-reshape2)
22600 ("r-rsamtools" ,r-rsamtools)
22601 ("r-rtracklayer" ,r-rtracklayer)
22602 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22604 `(("r-knitr" ,r-knitr)))
22606 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22607 (synopsis "Analysis of multiplexed 4C sequencing data")
22609 "This package is an R package dedicated to the analysis of (multiplexed)
22610 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22611 interactions between DNA elements and identify differential interactions
22612 between conditions. The statistical analysis in R starts with individual bam
22613 files for each sample as inputs. To obtain these files, the package contains
22614 a Python script to demultiplex libraries and trim off primer sequences. With
22615 a standard alignment software the required bam files can be then be
22617 (license license:gpl3+)))
22619 (define-public r-phylogram
22621 (name "r-phylogram")
22626 (uri (cran-uri "phylogram" version))
22628 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22629 (properties `((upstream-name . "phylogram")))
22630 (build-system r-build-system)
22631 (propagated-inputs `(("r-ape" ,r-ape)))
22632 (home-page "https://github.com/ropensci/phylogram/")
22633 (synopsis "Dendrograms for evolutionary analysis")
22635 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22636 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22637 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22638 as well as several tools for command-line tree manipulation and import/export
22639 via Newick parenthetic text. This improves accessibility to the comprehensive
22640 range of object-specific analytical and tree-visualization functions found
22641 across a wide array of bioinformatic R packages.")
22642 (license license:gpl3)))
22644 (define-public r-kmer
22651 (uri (cran-uri "kmer" version))
22653 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22654 (properties `((upstream-name . "kmer")))
22655 (build-system r-build-system)
22657 `(("r-openssl" ,r-openssl)
22658 ("r-phylogram" ,r-phylogram)
22659 ("r-rcpp" ,r-rcpp)))
22660 (home-page "https://github.com/shaunpwilkinson/kmer/")
22661 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22663 "@code{r-kmer} is an R package for rapidly computing distance matrices
22664 and clustering large sequence datasets using fast alignment-free k-mer
22665 counting and recursive k-means partitioning.")
22666 (license license:gpl3)))
22668 (define-public r-hardhat
22675 (uri (cran-uri "hardhat" version))
22678 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
22679 (properties `((upstream-name . "hardhat")))
22680 (build-system r-build-system)
22682 `(("r-glue" ,r-glue)
22683 ("r-rlang" ,r-rlang)
22684 ("r-tibble" ,r-tibble)
22685 ("r-vctrs" ,r-vctrs)))
22687 `(("r-knitr" ,r-knitr)))
22688 (home-page "https://github.com/tidymodels/hardhat")
22689 (synopsis "Construct modeling packages")
22691 "Building modeling packages is hard. A large amount of effort generally
22692 goes into providing an implementation for a new method that is efficient,
22693 fast, and correct, but often less emphasis is put on the user interface. A
22694 good interface requires specialized knowledge about S3 methods and formulas,
22695 which the average package developer might not have. The goal of
22696 @code{hardhat} is to reduce the burden around building new modeling packages
22697 by providing functionality for preprocessing, predicting, and validating
22699 (license license:expat)))
22701 (define-public r-shapforxgboost
22703 (name "r-shapforxgboost")
22708 (uri (cran-uri "SHAPforxgboost" version))
22711 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22713 `((upstream-name . "SHAPforxgboost")))
22714 (build-system r-build-system)
22716 `(("r-bbmisc" ,r-bbmisc)
22717 ("r-data-table" ,r-data-table)
22718 ("r-ggextra" ,r-ggextra)
22719 ("r-ggforce" ,r-ggforce)
22720 ("r-ggplot2" ,r-ggplot2)
22721 ("r-ggpubr" ,r-ggpubr)
22722 ("r-rcolorbrewer" ,r-rcolorbrewer)
22723 ("r-xgboost" ,r-xgboost)))
22724 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22725 (synopsis "SHAP Plots for XGBoost")
22727 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22728 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22729 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22730 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22732 (license license:expat)))
22734 (define-public r-rismed
22741 (uri (cran-uri "RISmed" version))
22744 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22745 (properties `((upstream-name . "RISmed")))
22746 (build-system r-build-system)
22747 (home-page "https://cran.r-project.org/web/packages/RISmed")
22748 (synopsis "Download content from NCBI databases")
22750 "This package provides a set of tools to extract bibliographic
22751 content from the National Center for Biotechnology Information (NCBI)
22752 databases, including PubMed. The name RISmed is a portmanteau of
22753 RIS (for Research Information Systems, a common tag format for
22754 bibliographic data) and PubMed.")
22755 (license license:gpl2+)))
22757 (define-public r-semver
22764 (uri (cran-uri "semver" version))
22767 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22768 (properties `((upstream-name . "semver")))
22769 (build-system r-build-system)
22771 `(("r-assertthat" ,r-assertthat)
22772 ("r-rcpp" ,r-rcpp)))
22773 (native-inputs `(("r-knitr" ,r-knitr)))
22774 (home-page "https://github.com/johndharrison/semver")
22775 (synopsis "Parser for Semantic Versioning 2.0.0")
22777 "This package provides tools and functions for parsing, rendering and
22778 operating on semantic version strings. Semantic versioning is a simple set of
22779 rules and requirements that dictate how version numbers are assigned and
22780 incremented as outlined at @url{http://semver.org}.")
22781 (license license:expat)))
22783 (define-public r-binman
22790 (uri (cran-uri "binman" version))
22793 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22794 (properties `((upstream-name . "binman")))
22795 (build-system r-build-system)
22797 `(("r-assertthat" ,r-assertthat)
22799 ("r-jsonlite" ,r-jsonlite)
22800 ("r-rappdirs" ,r-rappdirs)
22801 ("r-semver" ,r-semver)
22803 ("r-yaml" ,r-yaml)))
22804 (native-inputs `(("r-knitr" ,r-knitr)))
22805 (home-page "https://github.com/ropensci/binman")
22806 (synopsis "Binary download manager")
22808 "This package provides tools and functions for managing the download of
22809 binary files. Binary repositories are defined in the YAML format. Defining
22810 new pre-download, download and post-download templates allow additional
22811 repositories to be added.")
22812 (license license:expat)))
22814 (define-public r-wdman
22821 (uri (cran-uri "wdman" version))
22824 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22825 (properties `((upstream-name . "wdman")))
22826 (build-system r-build-system)
22828 `(("r-assertthat" ,r-assertthat)
22829 ("r-binman" ,r-binman)
22830 ("r-processx" ,r-processx)
22831 ("r-semver" ,r-semver)
22832 ("r-yaml" ,r-yaml)))
22833 (native-inputs `(("r-knitr" ,r-knitr)))
22834 (home-page "https://docs.ropensci.org/wdman/")
22835 (synopsis "Webdriver/Selenium binary manager")
22837 "There are a number of binary files associated with the
22838 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22839 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22840 @url{https://github.com/mozilla/geckodriver},
22841 @url{http://phantomjs.org/download.html}, and
22842 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22843 more information). This package provides functions to download these binaries
22844 and to manage processes involving them.")
22845 (license license:expat)))
22847 (define-public r-rselenium
22849 (name "r-rselenium")
22854 (uri (cran-uri "RSelenium" version))
22857 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22858 (properties `((upstream-name . "RSelenium")))
22859 (build-system r-build-system)
22861 `(("r-binman" ,r-binman)
22862 ("r-catools" ,r-catools)
22864 ("r-openssl" ,r-openssl)
22865 ("r-wdman" ,r-wdman)
22867 (native-inputs `(("r-knitr" ,r-knitr)))
22868 (home-page "https://docs.ropensci.org/RSelenium/")
22869 (synopsis "R bindings for Selenium WebDriver")
22871 "This package provides a set of R bindings for the Selenium 2.0
22872 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22873 information) using the @code{JsonWireProtocol} (see
22874 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22875 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22876 a user would either locally or on a remote machine using the Selenium server
22877 it marks a leap forward in terms of web browser automation. Selenium
22878 automates web browsers (commonly referred to as browsers). Using RSelenium
22879 you can automate browsers locally or remotely.")
22880 (license license:agpl3+)))
22882 (define-public r-conquer
22889 (uri (cran-uri "conquer" version))
22892 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22893 (properties `((upstream-name . "conquer")))
22894 (build-system r-build-system)
22896 `(("r-matrix" ,r-matrix)
22897 ("r-matrixstats" ,r-matrixstats)
22899 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22900 (home-page "https://github.com/XiaoouPan/conquer")
22901 (synopsis "Convolution-type smoothed quantile regression")
22903 "This package provides fast and accurate convolution-type smoothed
22904 quantile regression, implemented using Barzilai-Borwein gradient descent with
22905 a Huber regression warm start. Confidence intervals for regression
22906 coefficients are constructed using multiplier bootstrap.")
22907 (license license:gpl3)))
22909 (define-public r-fastshap
22911 (name "r-fastshap")
22916 (uri (cran-uri "fastshap" version))
22919 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22920 (properties `((upstream-name . "fastshap")))
22921 (build-system r-build-system)
22923 `(("r-abind" ,r-abind)
22924 ("r-ggplot2" ,r-ggplot2)
22925 ("r-gridextra" ,r-gridextra)
22926 ("r-matrixstats" ,r-matrixstats)
22929 ("r-rcpparmadillo" ,r-rcpparmadillo)
22930 ("r-tibble" ,r-tibble)))
22931 (home-page "https://github.com/bgreenwell/fastshap")
22932 (synopsis "Fast approximate Shapley values")
22934 "This package computes fast (relative to other implementations)
22935 approximate Shapley values for any supervised learning model. Shapley values
22936 help to explain the predictions from any black box model using ideas from game
22937 theory; see @url{Strumbel and Kononenko (2014),
22938 doi.org/10.1007/s10115-013-0679-x} for details.")
22939 (license license:gpl2+)))
22941 (define-public r-metrics
22948 (uri (cran-uri "Metrics" version))
22951 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22952 (properties `((upstream-name . "Metrics")))
22953 (build-system r-build-system)
22954 (home-page "https://github.com/mfrasco/Metrics")
22955 (synopsis "Evaluation metrics for machine learning")
22957 "This package provides an implementation of evaluation metrics in R that
22958 are commonly used in supervised machine learning. It implements metrics for
22959 regression, time series, binary classification, classification, and
22960 information retrieval problems. It has zero dependencies and a consistent,
22961 simple interface for all functions.")
22962 (license license:bsd-3)))
22964 (define-public r-iml
22971 (uri (cran-uri "iml" version))
22974 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22975 (properties `((upstream-name . "iml")))
22976 (build-system r-build-system)
22978 `(("r-checkmate" ,r-checkmate)
22979 ("r-data-table" ,r-data-table)
22980 ("r-formula" ,r-formula)
22981 ("r-future" ,r-future)
22982 ("r-future-apply" ,r-future-apply)
22983 ("r-ggplot2" ,r-ggplot2)
22984 ("r-gridextra" ,r-gridextra)
22985 ("r-metrics" ,r-metrics)
22986 ("r-prediction" ,r-prediction)
22988 (native-inputs `(("r-knitr" ,r-knitr)))
22989 (home-page "https://github.com/christophM/iml")
22990 (synopsis "Interpretable machine learning")
22992 "This package provides interpretability methods to analyze the behavior
22993 and predictions of any machine learning model. Implemented methods are:
22996 @item Feature importance described by Fisher et al. (2018),
22997 @item accumulated local effects plots described by Apley (2018),
22998 @item partial dependence plots described by Friedman (2001),
22999 @item individual conditional expectation ('ice') plots described by Goldstein
23000 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
23001 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
23002 @item the Shapley Value described by Strumbelj et. al (2014)
23003 @url{https://doi.org/10.1007/s10115-013-0679-x},
23004 @item feature interactions described by Friedman et. al
23005 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
23008 (license license:expat)))
23010 (define-public r-goftest
23017 (uri (cran-uri "goftest" version))
23020 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23021 (properties `((upstream-name . "goftest")))
23022 (build-system r-build-system)
23023 (home-page "https://github.com/baddstats/goftest")
23024 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23026 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23027 goodness-of-fit for continuous univariate distributions, using efficient
23029 (license license:gpl2+)))
23031 (define-public r-tensor
23038 (uri (cran-uri "tensor" version))
23041 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23042 (properties `((upstream-name . "tensor")))
23043 (build-system r-build-system)
23044 (home-page "https://cran.r-project.org/web/packages/tensor/")
23045 (synopsis "Tensor product of arrays")
23047 "The tensor product of two arrays is notionally an outer product of the
23048 arrays collapsed in specific extents by summing along the appropriate
23049 diagonals. This package allows you to compute the tensor product of arrays.")
23050 (license license:gpl2+)))
23052 (define-public r-spatstat-utils
23054 (name "r-spatstat-utils")
23059 (uri (cran-uri "spatstat.utils" version))
23062 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23064 `((upstream-name . "spatstat.utils")))
23065 (build-system r-build-system)
23066 (home-page "http://www.spatstat.org")
23067 (synopsis "Utility functions for spatstat")
23069 "This package contains utility functions for the @code{spatstat} package
23070 which may also be useful for other purposes.")
23071 (license license:gpl2+)))
23073 (define-public r-spatstat-data
23075 (name "r-spatstat-data")
23080 (uri (cran-uri "spatstat.data" version))
23083 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23084 (properties `((upstream-name . "spatstat.data")))
23085 (build-system r-build-system)
23087 `(("r-matrix" ,r-matrix)
23088 ("r-spatstat-utils" ,r-spatstat-utils)))
23089 (home-page "http://www.spatstat.org")
23090 (synopsis "Datasets for spatstat")
23092 "This package contains all the datasets for the @code{spatstat}
23094 (license license:gpl2+)))
23096 (define-public r-spatstat
23098 (name "r-spatstat")
23103 (uri (cran-uri "spatstat" version))
23106 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23107 (properties `((upstream-name . "spatstat")))
23108 (build-system r-build-system)
23110 `(("r-abind" ,r-abind)
23111 ("r-deldir" ,r-deldir)
23112 ("r-goftest" ,r-goftest)
23113 ("r-matrix" ,r-matrix)
23116 ("r-polyclip" ,r-polyclip)
23117 ("r-rpart" ,r-rpart)
23118 ("r-spatstat-data" ,r-spatstat-data)
23119 ("r-spatstat-utils" ,r-spatstat-utils)
23120 ("r-tensor" ,r-tensor)))
23121 (home-page "http://www.spatstat.org")
23122 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23124 "This package provides a comprehensive toolbox for analysing Spatial
23125 Point Patterns. It is focused mainly on two-dimensional point patterns,
23126 including multitype/marked points, in any spatial region. It also supports
23127 three-dimensional point patterns, space-time point patterns in any number of
23128 dimensions, point patterns on a linear network, and patterns of other
23129 geometrical objects. It supports spatial covariate data such as pixel images
23130 and contains over 2000 functions for plotting spatial data, exploratory data
23131 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23132 formal inference.")
23133 (license license:gpl2+)))
23135 (define-public r-gaston
23142 (uri (cran-uri "gaston" version))
23145 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
23146 (properties `((upstream-name . "gaston")))
23147 (build-system r-build-system)
23148 (inputs `(("zlib" ,zlib)))
23150 `(("r-rcpp" ,r-rcpp)
23151 ("r-rcppeigen" ,r-rcppeigen)
23152 ("r-rcppparallel" ,r-rcppparallel)))
23153 (native-inputs `(("r-knitr" ,r-knitr)))
23154 (home-page "https://cran.r-project.org/web/packages/gaston/")
23155 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23157 "This is a package for the manipulation of genetic data (SNPs).
23158 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23159 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23160 for linear mixed models (AIREML).")
23161 (license license:gpl3)))
23163 (define-public r-cpp11
23170 (uri (cran-uri "cpp11" version))
23173 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
23174 (properties `((upstream-name . "cpp11")))
23175 (build-system r-build-system)
23176 (native-inputs `(("r-knitr" ,r-knitr)))
23177 (home-page "https://github.com/r-lib/cpp11")
23178 (synopsis "C++11 Interface for R's C Interface")
23180 "This package provides a header only, C++11 interface to R's C interface.
23181 Compared to other approaches @code{cpp11} strives to be safe against long
23182 jumps from the C API as well as C++ exceptions, conform to normal R function
23183 semantics and supports interaction with @code{ALTREP} vectors.")
23184 (license license:expat)))
23186 (define-public r-rcppziggurat
23188 (name "r-rcppziggurat")
23193 (uri (cran-uri "RcppZiggurat" version))
23196 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
23197 (properties `((upstream-name . "RcppZiggurat")))
23198 (build-system r-build-system)
23200 `(("r-rcpp" ,r-rcpp)
23201 ("r-rcppgsl" ,r-rcppgsl)))
23202 (native-inputs `(("r-knitr" ,r-knitr)))
23203 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23204 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23206 "The Ziggurat generator for normally distributed random numbers,
23207 originally proposed by Marsaglia and Tsang (2000,
23208 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23209 times starting with Leong et al (2005,
23210 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23211 aggregation for comparing different implementations in order to provide a
23212 'faster but good enough' alternative for use with R and C++ code.")
23213 (license license:gpl2+)))
23215 (define-public r-rfast
23222 (uri (cran-uri "Rfast" version))
23225 "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
23226 (properties `((upstream-name . "Rfast")))
23227 (build-system r-build-system)
23229 `(("r-rcpp" ,r-rcpp)
23230 ("r-rcpparmadillo" ,r-rcpparmadillo)
23231 ("r-rcppziggurat" ,r-rcppziggurat)))
23232 (home-page "https://github.com/RfastOfficial/Rfast")
23233 (synopsis "Collection of efficient and fast R functions")
23235 "This package provides a collection of fast (utility) functions for data
23236 analysis. Column- and row- wise means, medians, variances, minimums,
23237 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23238 Poisson), are some of the many fast functions.")
23239 (license license:gpl2+)))
23241 (define-public r-clusterr
23243 (name "r-clusterr")
23248 (uri (cran-uri "ClusterR" version))
23251 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23252 (properties `((upstream-name . "ClusterR")))
23253 (build-system r-build-system)
23255 `(("r-ggplot2" ,r-ggplot2)
23257 ("r-gtools" ,r-gtools)
23259 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23260 (native-inputs `(("r-knitr" ,r-knitr)))
23261 (home-page "https://github.com/mlampros/ClusterR")
23262 (synopsis "Clustering")
23264 "This package provides Gaussian mixture models, k-means,
23265 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23266 option to plot, validate, predict (new data) and estimate the optimal number
23267 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23268 the computationally intensive parts of the functions. For more information,
23272 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23273 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23274 @url{https://doi.org/10.18637/jss.v001.i04};
23275 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23276 Library, @url{https://doi.org/10.1145/1772690.1772862};
23277 @item \"Armadillo: a template-based C++ library
23278 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23279 Software, @url{https://doi.org/10.21105/joss.00026};
23280 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23281 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23282 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23285 (license license:gpl3)))
23287 (define-public r-spectrum
23289 (name "r-spectrum")
23294 (uri (cran-uri "Spectrum" version))
23297 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23298 (properties `((upstream-name . "Spectrum")))
23299 (build-system r-build-system)
23301 `(("r-clusterr" ,r-clusterr)
23302 ("r-diptest" ,r-diptest)
23303 ("r-ggplot2" ,r-ggplot2)
23304 ("r-rfast" ,r-rfast)))
23305 (native-inputs `(("r-knitr" ,r-knitr)))
23306 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23307 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23309 "This package provides a self-tuning spectral clustering method for
23310 single or multi-view data. Spectrum uses a new type of adaptive density aware
23311 kernel that strengthens connections in the graph based on common nearest
23312 neighbours. It uses a tensor product graph data integration and diffusion
23313 procedure to integrate different data sources and reduce noise. Spectrum uses
23314 either the eigengap or multimodality gap heuristics to determine the number of
23315 clusters. The method is sufficiently flexible so that a wide range of
23316 Gaussian and non-Gaussian structures can be clustered with automatic selection
23318 (license license:agpl3+)))
23320 (define-public r-nabor
23327 (uri (cran-uri "nabor" version))
23330 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23331 (properties `((upstream-name . "nabor")))
23332 (build-system r-build-system)
23336 ("r-rcppeigen" ,r-rcppeigen)))
23337 (home-page "https://cran.r-project.org/web/packages/nabor/")
23338 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23340 "This package provides an R wrapper for libnabo, an exact or approximate
23341 k nearest neighbour library which is optimised for low dimensional
23342 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23343 designed as a drop-in replacement for the RANN function @code{nn2}. In
23344 addition, objects which include the k-d tree search structure can be returned
23345 to speed up repeated queries of the same set of target points.")
23346 (license license:bsd-3)))
23348 (define-public r-muhaz
23351 (version "1.2.6.1")
23355 (uri (cran-uri "muhaz" version))
23358 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23359 (properties `((upstream-name . "muhaz")))
23360 (build-system r-build-system)
23362 `(("r-survival" ,r-survival)))
23364 `(("gfortran" ,gfortran)))
23365 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23366 (synopsis "Hazard function estimation in survival analysis")
23368 "This package produces a smooth estimate of the hazard function for
23370 ;; Any version of the GPL.
23371 (license license:gpl3+)))
23373 (define-public r-flexsurv
23375 (name "r-flexsurv")
23380 (uri (cran-uri "flexsurv" version))
23383 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23384 (properties `((upstream-name . "flexsurv")))
23385 (build-system r-build-system)
23387 `(("r-desolve" ,r-desolve)
23388 ("r-mstate" ,r-mstate)
23389 ("r-muhaz" ,r-muhaz)
23390 ("r-mvtnorm" ,r-mvtnorm)
23391 ("r-quadprog" ,r-quadprog)
23393 ("r-survival" ,r-survival)
23394 ("r-tibble" ,r-tibble)
23395 ("r-tidyr" ,r-tidyr)))
23397 `(("r-knitr" ,r-knitr)))
23398 (home-page "https://github.com/chjackson/flexsurv-dev")
23399 (synopsis "Flexible parametric survival and multi-state models")
23401 "This package provides flexible parametric models for time-to-event data,
23402 including the Royston-Parmar spline model, generalized gamma and generalized F
23403 distributions. Any user-defined parametric distribution can be fitted, given
23404 at least an R function defining the probability density or hazard. There are
23405 also tools for fitting and predicting from fully parametric multi-state
23407 (license license:gpl2+)))
23409 (define-public r-transphylo
23411 (name "r-transphylo")
23416 (uri (cran-uri "TransPhylo" version))
23419 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23420 (properties `((upstream-name . "TransPhylo")))
23421 (build-system r-build-system)
23424 ("r-rcpp" ,r-rcpp)))
23426 `(("r-knitr" ,r-knitr)))
23427 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23428 (synopsis "Inference of transmission tree from a dated phylogeny")
23430 "This is a package to infer transmission trees from a dated phylogeny.
23431 It includes methods to simulate and analyze outbreaks. The methodology is
23432 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23433 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23434 (license license:gpl2+)))
23436 (define-public r-km-ci
23443 (uri (cran-uri "km.ci" version))
23446 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23447 (properties `((upstream-name . "km.ci")))
23448 (build-system r-build-system)
23450 `(("r-survival" ,r-survival)))
23451 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23452 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23454 "This package computes various @dfn{confidence intervals} (CI) for the
23455 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23456 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23457 Nair and Hall and Wellner.")
23458 (license license:gpl2+)))
23460 (define-public r-kmsurv
23467 (uri (cran-uri "KMsurv" version))
23470 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23471 (properties `((upstream-name . "KMsurv")))
23472 (build-system r-build-system)
23473 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23474 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23476 "This package provides data sets and functions for Klein and Moeschberger
23477 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23479 (license license:gpl3+)))
23481 (define-public r-survmisc
23483 (name "r-survmisc")
23488 (uri (cran-uri "survMisc" version))
23491 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23492 (properties `((upstream-name . "survMisc")))
23493 (build-system r-build-system)
23495 `(("r-data-table" ,r-data-table)
23496 ("r-ggplot2" ,r-ggplot2)
23497 ("r-gridextra" ,r-gridextra)
23498 ("r-km-ci" ,r-km-ci)
23499 ("r-kmsurv" ,r-kmsurv)
23500 ("r-knitr" ,r-knitr)
23501 ("r-survival" ,r-survival)
23502 ("r-xtable" ,r-xtable)
23505 `(("r-knitr" ,r-knitr)))
23506 (home-page "https://cran.r-project.org/web/packages/survMisc/")
23507 (synopsis "Miscellaneous functions for survival data")
23509 "This package provides a collection of functions to help in the analysis
23510 of right-censored survival data. These extend the methods available in
23511 the @code{survival} package.")
23512 (license license:gpl2)))
23514 (define-public r-exactranktests
23516 (name "r-exactranktests")
23521 (uri (cran-uri "exactRankTests" version))
23524 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
23526 `((upstream-name . "exactRankTests")))
23527 (build-system r-build-system)
23528 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
23529 (synopsis "Exact distributions for rank and permutation tests")
23531 "This package computes exact conditional p-values and quantiles using an
23532 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
23533 (license license:gpl2+)))
23535 (define-public r-maxstat
23542 (uri (cran-uri "maxstat" version))
23545 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
23546 (properties `((upstream-name . "maxstat")))
23547 (build-system r-build-system)
23549 `(("r-exactranktests" ,r-exactranktests)
23550 ("r-mvtnorm" ,r-mvtnorm)))
23551 (home-page "https://cran.r-project.org/web/packages/maxstat/")
23552 (synopsis "Maximally selected rank statistics")
23554 "This package provides maximally selected rank statistics with several
23555 p-value approximations.")
23556 (license license:gpl2+)))
23558 (define-public r-survminer
23560 (name "r-survminer")
23565 (uri (cran-uri "survminer" version))
23568 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
23569 (properties `((upstream-name . "survminer")))
23570 (build-system r-build-system)
23572 `(("r-broom" ,r-broom)
23573 ("r-dplyr" ,r-dplyr)
23574 ("r-ggplot2" ,r-ggplot2)
23575 ("r-ggpubr" ,r-ggpubr)
23576 ("r-gridextra" ,r-gridextra)
23577 ("r-magrittr" ,r-magrittr)
23578 ("r-maxstat" ,r-maxstat)
23579 ("r-purrr" ,r-purrr)
23580 ("r-rlang" ,r-rlang)
23581 ("r-scales" ,r-scales)
23582 ("r-survival" ,r-survival)
23583 ("r-survmisc" ,r-survmisc)
23584 ("r-tibble" ,r-tibble)
23585 ("r-tidyr" ,r-tidyr)))
23587 `(("r-knitr" ,r-knitr)))
23588 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
23589 (synopsis "Drawing survival curves using ggplot2")
23591 "This package contains the function @code{ggsurvplot()} for easily
23592 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
23593 risk' table and 'censoring count plot'. Other functions are also available to
23594 plot adjusted curves for Cox model and to visually examine Cox model
23596 (license license:gpl2)))
23598 (define-public r-forge
23605 (uri (cran-uri "forge" version))
23608 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
23609 (properties `((upstream-name . "forge")))
23610 (build-system r-build-system)
23612 `(("r-magrittr" ,r-magrittr)
23613 ("r-rlang" ,r-rlang)))
23614 (home-page "https://cran.r-project.org/web/packages/forge/")
23615 (synopsis "Cast values into shape")
23617 "This package provides helper functions with a consistent interface to
23618 coerce and verify the types and shapes of values for input checking.")
23619 (license license:asl2.0)))
23621 (define-public r-config
23628 (uri (cran-uri "config" version))
23631 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
23632 (properties `((upstream-name . "config")))
23633 (build-system r-build-system)
23635 `(("r-yaml" ,r-yaml)))
23637 `(("r-knitr" ,r-knitr)))
23638 (home-page "https://github.com/rstudio/config")
23639 (synopsis "Manage environment specific configuration values")
23641 "This package lets you manage configuration values across multiple
23642 environments (e.g. development, test, production). It reads values using a
23643 function that determines the current environment and returns the appropriate
23645 (license license:gpl3)))
23647 (define-public r-adaptivesparsity
23649 (name "r-adaptivesparsity")
23653 (uri (cran-uri "AdaptiveSparsity" version))
23656 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
23658 `((upstream-name . "AdaptiveSparsity")))
23659 (build-system r-build-system)
23662 (modify-phases %standard-phases
23663 (add-after 'unpack 'link-against-armadillo
23665 (substitute* "src/Makevars"
23666 (("PKG_LIBS=" prefix)
23667 (string-append prefix "-larmadillo"))))))))
23669 `(("r-mass" ,r-mass)
23670 ("r-matrix" ,r-matrix)
23672 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23674 `(("armadillo" ,armadillo)))
23675 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
23676 (synopsis "Adaptive sparsity models")
23678 "This package implements the Figueiredo machine learning algorithm for
23679 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
23680 geometric models.")
23681 (license license:lgpl3+)))
23683 (define-public r-diffusionmap
23685 (name "r-diffusionmap")
23690 (uri (cran-uri "diffusionMap" version))
23693 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
23694 (properties `((upstream-name . "diffusionMap")))
23695 (build-system r-build-system)
23697 `(("r-igraph" ,r-igraph)
23698 ("r-matrix" ,r-matrix)
23699 ("r-scatterplot3d" ,r-scatterplot3d)))
23700 (home-page "https://www.r-project.org")
23701 (synopsis "Diffusion map")
23702 (description "This package implements the diffusion map method of data
23703 parametrization, including creation and visualization of diffusion maps,
23704 clustering with diffusion K-means and regression using the adaptive regression
23706 (license license:gpl2)))
23708 (define-public r-igraph
23715 (uri (cran-uri "igraph" version))
23718 "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
23719 (build-system r-build-system)
23721 `(("gfortran" ,gfortran)))
23725 ("libxml2" ,libxml2)
23728 `(("r-magrittr" ,r-magrittr)
23729 ("r-matrix" ,r-matrix)
23730 ("r-pkgconfig" ,r-pkgconfig)))
23731 (home-page "https://igraph.org")
23732 (synopsis "Network analysis and visualization")
23734 "This package provides routines for simple graphs and network analysis.
23735 It can handle large graphs very well and provides functions for generating
23736 random and regular graphs, graph visualization, centrality methods and much
23738 (license license:gpl2+)))
23740 (define-public r-workflows
23742 (name "r-workflows")
23747 (uri (cran-uri "workflows" version))
23750 "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
23751 (properties `((upstream-name . "workflows")))
23752 (build-system r-build-system)
23755 ("r-ellipsis" ,r-ellipsis)
23756 ("r-generics" ,r-generics)
23758 ("r-hardhat" ,r-hardhat)
23759 ("r-parsnip" ,r-parsnip)
23760 ("r-rlang" ,r-rlang)))
23762 `(("r-knitr" ,r-knitr)))
23763 (home-page "https://github.com/tidymodels/workflows")
23764 (synopsis "Modeling workflows")
23766 "A workflow is an object that can bundle together your pre-processing,
23767 modeling, and post-processing requests. For example, if you have a
23768 @code{recipe} and @code{parsnip} model, these can be combined into a
23769 workflow. The advantages are:
23772 @item You don’t have to keep track of separate objects in your workspace.
23773 @item The recipe prepping and model fitting can be executed using a single
23774 call to @code{fit()}.
23775 @item If you have custom tuning parameter settings, these can be defined using
23776 a simpler interface when combined with @code{tune}.
23777 @item In the future, workflows will be able to add post-processing operations,
23778 such as modifying the probability cutoff for two-class models.
23781 (license license:expat)))
23783 (define-public r-gpfit
23790 (uri (cran-uri "GPfit" version))
23793 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
23794 (properties `((upstream-name . "GPfit")))
23795 (build-system r-build-system)
23797 `(("r-lattice" ,r-lattice)
23799 (home-page "https://cran.r-project.org/web/packages/GPfit/")
23800 (synopsis "Gaussian Processes modeling")
23802 "This package provides a computationally stable approach of fitting a
23803 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
23804 (license license:gpl2)))
23806 (define-public r-yardstick
23808 (name "r-yardstick")
23813 (uri (cran-uri "yardstick" version))
23816 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
23817 (properties `((upstream-name . "yardstick")))
23818 (build-system r-build-system)
23820 `(("r-dplyr" ,r-dplyr)
23821 ("r-generics" ,r-generics)
23823 ("r-rlang" ,r-rlang)
23824 ("r-tidyselect" ,r-tidyselect)))
23826 `(("r-knitr" ,r-knitr)))
23827 (home-page "https://github.com/tidymodels/yardstick")
23828 (synopsis "Tidy characterizations of model performance")
23830 "This package provides tidy tools for quantifying how well a model fits
23831 to a data set such as confusion matrices, class probability curve summaries,
23832 and regression metrics (e.g., RMSE).")
23833 (license license:gpl2)))
23835 (define-public r-rsample
23842 (uri (cran-uri "rsample" version))
23845 "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8"))))
23846 (properties `((upstream-name . "rsample")))
23847 (build-system r-build-system)
23849 `(("r-dplyr" ,r-dplyr)
23850 ("r-furrr" ,r-furrr)
23851 ("r-generics" ,r-generics)
23852 ("r-purrr" ,r-purrr)
23853 ("r-rlang" ,r-rlang)
23854 ("r-tibble" ,r-tibble)
23855 ("r-tidyr" ,r-tidyr)
23856 ("r-tidyselect" ,r-tidyselect)
23857 ("r-vctrs" ,r-vctrs)))
23859 `(("r-knitr" ,r-knitr)))
23860 (home-page "https://rsample.tidymodels.org")
23861 (synopsis "General resampling infrastructure")
23863 "This package provides classes and functions to create and summarize
23864 different types of resampling objects (e.g. bootstrap, cross-validation).")
23865 (license license:gpl2)))
23867 (define-public r-dicedesign
23869 (name "r-dicedesign")
23874 (uri (cran-uri "DiceDesign" version))
23877 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
23878 (properties `((upstream-name . "DiceDesign")))
23879 (build-system r-build-system)
23880 (home-page "http://dice.emse.fr/")
23881 (synopsis "Designs of computer experiments")
23883 "This package provides tools to create some specific @code{Space-Filling
23884 Design} (SFD) and to test their quality.")
23885 (license license:gpl3)))
23887 (define-public r-dials
23894 (uri (cran-uri "dials" version))
23897 "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
23898 (properties `((upstream-name . "dials")))
23899 (build-system r-build-system)
23901 `(("r-dicedesign" ,r-dicedesign)
23902 ("r-dplyr" ,r-dplyr)
23904 ("r-purrr" ,r-purrr)
23905 ("r-rlang" ,r-rlang)
23906 ("r-scales" ,r-scales)
23907 ("r-tibble" ,r-tibble)
23908 ("r-vctrs" ,r-vctrs)
23909 ("r-withr" ,r-withr)))
23910 (native-inputs `(("r-knitr" ,r-knitr)))
23911 (home-page "https://dials.tidymodels.org/")
23912 (synopsis "Tools for creating tuning parameter values")
23914 "Many models contain tuning parameters (i.e. parameters that cannot be
23915 directly estimated from the data). These tools can be used to define objects
23916 for creating, simulating, or validating values for such parameters.")
23917 (license license:gpl2)))
23919 (define-public r-tune
23926 (uri (cran-uri "tune" version))
23929 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
23930 (properties `((upstream-name . "tune")))
23931 (build-system r-build-system)
23934 ("r-crayon" ,r-crayon)
23935 ("r-dials" ,r-dials)
23936 ("r-dplyr" ,r-dplyr)
23937 ("r-foreach" ,r-foreach)
23938 ("r-ggplot2" ,r-ggplot2)
23940 ("r-gpfit" ,r-gpfit)
23941 ("r-hardhat" ,r-hardhat)
23942 ("r-lifecycle" ,r-lifecycle)
23943 ("r-parsnip" ,r-parsnip)
23944 ("r-purrr" ,r-purrr)
23945 ("r-recipes" ,r-recipes)
23946 ("r-rlang" ,r-rlang)
23947 ("r-rsample" ,r-rsample)
23948 ("r-tibble" ,r-tibble)
23949 ("r-tidyr" ,r-tidyr)
23950 ("r-vctrs" ,r-vctrs)
23951 ("r-workflows" ,r-workflows)
23952 ("r-yardstick" ,r-yardstick)))
23953 (home-page "https://github.com/tidymodels/tune")
23954 (synopsis "Tidy tuning tools")
23956 "The ability to tune models is important. @code{tune} contains functions
23957 and classes to be used in conjunction with other @code{tidymodels} packages
23958 for finding reasonable values of hyper-parameters in models, pre-processing
23959 methods, and post-processing steps.")
23960 (license license:expat)))
23962 (define-public r-tidyposterior
23964 (name "r-tidyposterior")
23969 (uri (cran-uri "tidyposterior" version))
23972 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
23973 (properties `((upstream-name . "tidyposterior")))
23974 (build-system r-build-system)
23976 `(("r-dplyr" ,r-dplyr)
23977 ("r-generics" ,r-generics)
23978 ("r-ggplot2" ,r-ggplot2)
23979 ("r-lifecycle" ,r-lifecycle)
23980 ("r-purrr" ,r-purrr)
23981 ("r-rlang" ,r-rlang)
23982 ("r-rsample" ,r-rsample)
23983 ("r-rstanarm" ,r-rstanarm)
23984 ("r-tibble" ,r-tibble)
23985 ("r-tidyr" ,r-tidyr)
23986 ("r-vctrs" ,r-vctrs)))
23988 `(("r-knitr" ,r-knitr)))
23989 (home-page "https://tidyposterior.tidymodels.org")
23990 (synopsis "Bayesian analysis to compare models using resampling statistics")
23992 "This package can be used to conduct post hoc analyses of resampling
23993 results generated by models. For example, if two models are evaluated with
23994 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
23995 are 10 paired statistics. These can be used to make comparisons between
23996 models without involving a test set.")
23997 (license license:gpl2)))
23999 (define-public r-tidypredict
24001 (name "r-tidypredict")
24006 (uri (cran-uri "tidypredict" version))
24009 "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
24010 (properties `((upstream-name . "tidypredict")))
24011 (build-system r-build-system)
24013 `(("r-dplyr" ,r-dplyr)
24014 ("r-generics" ,r-generics)
24015 ("r-knitr" ,r-knitr)
24016 ("r-purrr" ,r-purrr)
24017 ("r-rlang" ,r-rlang)
24018 ("r-tibble" ,r-tibble)))
24020 `(("r-knitr" ,r-knitr)))
24021 (home-page "https://tidypredict.tidymodels.org")
24022 (synopsis "Run predictions inside the database")
24024 "This package parses a fitted R model object, and returns a formula in
24025 Tidy Eval code that calculates the predictions. It works with several
24026 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
24027 final SQL translation of the algorithm. It currently supports @code{lm()},
24028 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
24029 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
24030 (license license:gpl3)))
24032 (define-public r-janeaustenr
24034 (name "r-janeaustenr")
24039 (uri (cran-uri "janeaustenr" version))
24042 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
24043 (properties `((upstream-name . "janeaustenr")))
24044 (build-system r-build-system)
24045 (home-page "https://github.com/juliasilge/janeaustenr")
24046 (synopsis "Jane Austen's complete novels")
24048 "This package provides the full texts for Jane Austen's six completed
24049 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
24050 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
24051 and \"Persuasion\".")
24052 (license license:expat)))
24054 (define-public r-tokenizers
24056 (name "r-tokenizers")
24061 (uri (cran-uri "tokenizers" version))
24064 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
24065 (properties `((upstream-name . "tokenizers")))
24066 (build-system r-build-system)
24068 `(("r-rcpp" ,r-rcpp)
24069 ("r-snowballc" ,r-snowballc)
24070 ("r-stringi" ,r-stringi)))
24072 `(("r-knitr" ,r-knitr)))
24073 (home-page "https://lincolnmullen.com/software/tokenizers/")
24074 (synopsis "Fast, consistent tokenization of natural language text")
24076 "This is a package for converting natural language text into tokens.
24077 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
24078 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
24079 Treebank, regular expressions, as well as functions for counting characters,
24080 words, and sentences, and a function for splitting longer texts into separate
24081 documents, each with the same number of words. The tokenizers have a
24082 consistent interface, and the package is built on the @code{stringi} and
24083 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
24084 (license license:expat)))
24086 (define-public r-hunspell
24088 (name "r-hunspell")
24093 (uri (cran-uri "hunspell" version))
24096 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24097 (properties `((upstream-name . "hunspell")))
24098 (build-system r-build-system)
24100 `(("r-digest" ,r-digest)
24101 ("r-rcpp" ,r-rcpp)))
24103 `(("r-knitr" ,r-knitr)))
24104 (home-page "https://github.com/ropensci/hunspell#readme")
24105 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24107 "This package provides a low-level spell checker and morphological
24108 analyzer based on the famous @code{hunspell} library. The package can analyze
24109 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24110 For a more user-friendly interface use the @code{spelling} package which
24111 builds on this package to automate checking of files, documentation and
24112 vignettes in all common formats.")
24113 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24114 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24115 ;; available under the Expat license.
24116 (license (list license:gpl2
24121 (define-public r-tidytext
24123 (name "r-tidytext")
24128 (uri (cran-uri "tidytext" version))
24131 "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
24132 (properties `((upstream-name . "tidytext")))
24133 (build-system r-build-system)
24135 `(("r-dplyr" ,r-dplyr)
24136 ("r-generics" ,r-generics)
24137 ("r-hunspell" ,r-hunspell)
24138 ("r-janeaustenr" ,r-janeaustenr)
24139 ("r-matrix" ,r-matrix)
24140 ("r-purrr" ,r-purrr)
24141 ("r-rlang" ,r-rlang)
24142 ("r-stringr" ,r-stringr)
24143 ("r-tibble" ,r-tibble)
24144 ("r-tokenizers" ,r-tokenizers)))
24146 `(("r-knitr" ,r-knitr)))
24147 (home-page "https://github.com/juliasilge/tidytext")
24148 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24150 "This is a package for text mining for word processing and sentiment
24151 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24152 (license license:expat)))
24154 (define-public r-parsnip
24161 (uri (cran-uri "parsnip" version))
24164 "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
24165 (properties `((upstream-name . "parsnip")))
24166 (build-system r-build-system)
24168 `(("r-dplyr" ,r-dplyr)
24169 ("r-generics" ,r-generics)
24170 ("r-globals" ,r-globals)
24172 ("r-magrittr" ,r-magrittr)
24173 ("r-prettyunits" ,r-prettyunits)
24174 ("r-purrr" ,r-purrr)
24175 ("r-rlang" ,r-rlang)
24176 ("r-tibble" ,r-tibble)
24177 ("r-tidyr" ,r-tidyr)
24178 ("r-vctrs" ,r-vctrs)))
24180 `(("r-knitr" ,r-knitr)))
24181 (home-page "https://parsnip.tidymodels.org")
24182 (synopsis "Common API to modeling and analysis functions")
24184 "This package provides a common interface to allow users to specify a
24185 model without having to remember the different argument names across different
24186 functions or computational engines (e.g. R, Spark, Stan, etc).")
24187 (license license:gpl2)))
24189 (define-public r-infer
24196 (uri (cran-uri "infer" version))
24199 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24200 (properties `((upstream-name . "infer")))
24201 (build-system r-build-system)
24203 `(("r-dplyr" ,r-dplyr)
24204 ("r-ggplot2" ,r-ggplot2)
24206 ("r-magrittr" ,r-magrittr)
24207 ("r-purrr" ,r-purrr)
24208 ("r-rlang" ,r-rlang)
24209 ("r-tibble" ,r-tibble)))
24211 `(("r-knitr" ,r-knitr)))
24212 (home-page "https://github.com/tidymodels/infer")
24213 (synopsis "Tidy statistical inference")
24215 "The objective of this package is to perform inference using an
24216 expressive statistical grammar that coheres with the Tidy design framework.")
24217 (license license:cc0)))
24219 (define-public r-modeldata
24221 (name "r-modeldata")
24226 (uri (cran-uri "modeldata" version))
24229 "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
24230 (properties `((upstream-name . "modeldata")))
24231 (build-system r-build-system)
24232 (home-page "https://modeldata.tidymodels.org")
24233 (synopsis "Data sets useful for modeling packages")
24235 "This package provides data sets used for demonstrating or testing
24236 model-related packages.")
24237 (license license:expat)))
24239 (define-public r-tidymodels
24241 (name "r-tidymodels")
24246 (uri (cran-uri "tidymodels" version))
24249 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24250 (properties `((upstream-name . "tidymodels")))
24251 (build-system r-build-system)
24253 `(("r-broom" ,r-broom)
24255 ("r-crayon" ,r-crayon)
24256 ("r-dials" ,r-dials)
24257 ("r-dplyr" ,r-dplyr)
24258 ("r-ggplot2" ,r-ggplot2)
24259 ("r-infer" ,r-infer)
24260 ("r-magrittr" ,r-magrittr)
24261 ("r-modeldata" ,r-modeldata)
24262 ("r-parsnip" ,r-parsnip)
24263 ("r-purrr" ,r-purrr)
24264 ("r-recipes" ,r-recipes)
24265 ("r-rlang" ,r-rlang)
24266 ("r-rsample" ,r-rsample)
24267 ("r-rstudioapi" ,r-rstudioapi)
24268 ("r-tibble" ,r-tibble)
24269 ("r-tidyr" ,r-tidyr)
24271 ("r-workflows" ,r-workflows)
24272 ("r-yardstick" ,r-yardstick)))
24274 `(("r-knitr" ,r-knitr)
24275 ("r-rmarkdown" ,r-rmarkdown)
24277 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24278 (home-page "https://github.com/tidymodels/tidymodels")
24279 (synopsis "Tidy collection for modeling and statistical analysis")
24281 "The tidy modeling \"verse\" is a collection of packages for modeling and
24282 statistical analysis that share the underlying design philosophy, grammar, and
24283 data structures of the tidyverse.")
24284 (license license:gpl3)))
24286 (define-public r-mlecens
24293 (uri (cran-uri "MLEcens" version))
24296 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24297 (properties `((upstream-name . "MLEcens")))
24298 (build-system r-build-system)
24299 (home-page "http://stat.ethz.ch/~maathuis/")
24300 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24302 "This package contains functions to compute the nonparametric
24303 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24304 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24305 To be more precise, we consider the situation where we observe a set of
24306 rectangles that are known to contain the unobservable realizations of (X,Y).
24307 We compute the MLE based on such a set of rectangles. The methods can also be
24308 used for univariate censored data (see data set @code{cosmesis}), and for
24309 censored data with competing risks (see data set @code{menopause}). The
24310 package also provides functions to visualize the observed data and the MLE.")
24311 (license license:gpl2+)))
24313 (define-public r-perm
24316 (version "1.0-0.0")
24320 (uri (cran-uri "perm" version))
24323 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24324 (properties `((upstream-name . "perm")))
24325 (build-system r-build-system)
24326 (home-page "https://cran.r-project.org/web/packages/perm/")
24327 (synopsis "Exact or asymptotic permutation tests")
24329 "This package provides several methods for performing permutation tests.
24330 It has three main functions, to perform linear permutation tests. These tests
24331 are tests where the test statistic is the sum of the product of a
24332 covariate (usually group indicator) and the scores.")
24333 ;; Any version of the GPL
24334 (license license:gpl2+)))
24336 (define-public r-qtl
24343 (uri (string-append "mirror://cran/src/contrib/qtl_"
24344 version ".tar.gz"))
24347 "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
24348 (build-system r-build-system)
24349 (home-page "https://rqtl.org/")
24350 (synopsis "R package for analyzing QTL experiments in genetics")
24351 (description "R/qtl is an extension library for the R statistics
24352 system. It is used to analyze experimental crosses for identifying
24353 genes contributing to variation in quantitative traits (so-called
24354 quantitative trait loci, QTLs).
24356 Using a hidden Markov model, R/qtl estimates genetic maps, to
24357 identify genotyping errors, and to perform single-QTL and two-QTL,
24358 two-dimensional genome scans.")
24359 (license license:gpl3)))
24361 (define-public r-qtl2
24364 (version "0.22-11")
24367 (uri (cran-uri "qtl2" version))
24369 (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
24370 (build-system r-build-system)
24372 `(("r-data-table" ,r-data-table)
24373 ("r-jsonlite" ,r-jsonlite)
24375 ("r-rcppeigen" ,r-rcppeigen)
24376 ("r-rsqlite" ,r-rsqlite)
24377 ("r-yaml" ,r-yaml)))
24378 (home-page "https://kbroman.org/qtl2/")
24379 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
24381 "This package provides a set of tools to perform @dfn{Quantitative Trait
24382 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
24383 @code{R/qtl} package to better handle high-dimensional data and complex cross
24384 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
24385 (license license:gpl3)))
24387 (define-public r-seqminer
24389 (name "r-seqminer")
24394 (uri (cran-uri "seqminer" version))
24397 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
24398 (build-system r-build-system)
24401 (home-page "http://seqminer.genomic.codes")
24402 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
24404 "This package provides tools to integrate nucleotide sequencing
24405 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
24406 ;; Any version of the GPL is acceptable
24407 (license (list license:gpl2+ license:gpl3+))))
24409 (define-public r-maldiquant
24411 (name "r-maldiquant")
24416 (uri (cran-uri "MALDIquant" version))
24419 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
24420 (properties `((upstream-name . "MALDIquant")))
24421 (build-system r-build-system)
24422 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
24423 (synopsis "Quantitative analysis of mass spectrometry data")
24425 "This package provides a complete analysis pipeline for matrix-assisted
24426 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
24427 two-dimensional mass spectrometry data. In addition to commonly used plotting
24428 and processing methods it includes distinctive features, namely baseline
24429 subtraction methods such as morphological filters (TopHat) or the
24430 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
24431 alignment using warping functions, handling of replicated measurements as well
24432 as allowing spectra with different resolutions.")
24433 (license license:gpl3+)))
24435 (define-public r-seurat
24441 (uri (cran-uri "Seurat" version))
24444 "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
24445 (properties `((upstream-name . "Seurat")))
24446 (build-system r-build-system)
24449 ("r-cluster" ,r-cluster)
24450 ("r-cowplot" ,r-cowplot)
24451 ("r-fitdistrplus" ,r-fitdistrplus)
24452 ("r-future" ,r-future)
24453 ("r-future-apply" ,r-future-apply)
24454 ("r-ggplot2" ,r-ggplot2)
24455 ("r-ggrepel" ,r-ggrepel)
24456 ("r-ggridges" ,r-ggridges)
24459 ("r-igraph" ,r-igraph)
24460 ("r-irlba" ,r-irlba)
24461 ("r-jsonlite" ,r-jsonlite)
24462 ("r-kernsmooth" ,r-kernsmooth)
24463 ("r-leiden" ,r-leiden)
24464 ("r-lmtest" ,r-lmtest)
24466 ("r-matrix" ,r-matrix)
24467 ("r-miniui" ,r-miniui)
24468 ("r-patchwork" ,r-patchwork)
24469 ("r-pbapply" ,r-pbapply)
24470 ("r-plotly" ,r-plotly)
24473 ("r-rcolorbrewer" ,r-rcolorbrewer)
24475 ("r-rcppannoy" ,r-rcppannoy)
24476 ("r-rcppeigen" ,r-rcppeigen)
24477 ("r-rcppprogress" ,r-rcppprogress)
24478 ("r-reticulate" ,r-reticulate)
24479 ("r-rlang" ,r-rlang)
24482 ("r-rtsne" ,r-rtsne)
24483 ("r-scales" ,r-scales)
24484 ("r-sctransform" ,r-sctransform)
24485 ("r-shiny" ,r-shiny)
24486 ("r-spatstat" ,r-spatstat)
24487 ("r-tibble" ,r-tibble)
24488 ("r-uwot" ,r-uwot)))
24489 (home-page "http://www.satijalab.org/seurat")
24490 (synopsis "Seurat is an R toolkit for single cell genomics")
24492 "This package is an R package designed for QC, analysis, and
24493 exploration of single cell RNA-seq data. It easily enables widely-used
24494 analytical techniques, including the identification of highly variable genes,
24495 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
24496 algorithms; density clustering, hierarchical clustering, k-means, and the
24497 discovery of differentially expressed genes and markers.")
24498 (license license:gpl3)))
24500 (define-public r-phangorn
24502 (name "r-phangorn")
24507 (uri (cran-uri "phangorn" version))
24510 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
24511 (build-system r-build-system)
24514 ("r-fastmatch" ,r-fastmatch)
24515 ("r-igraph" ,r-igraph)
24516 ("r-magrittr" ,r-magrittr)
24517 ("r-matrix" ,r-matrix)
24518 ("r-quadprog" ,r-quadprog)
24519 ("r-rcpp" ,r-rcpp)))
24520 (home-page "https://github.com/KlausVigo/phangorn")
24521 (synopsis "Phylogenetic analysis in R")
24523 "Phangorn is a package for phylogenetic analysis in R. It supports
24524 estimation of phylogenetic trees and networks using Maximum Likelihood,
24525 Maximum Parsimony, distance methods and Hadamard conjugation.")
24526 (license license:gpl2+)))