1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
21 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
22 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
23 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
24 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
26 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
27 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
28 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
29 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
31 ;;; This file is part of GNU Guix.
33 ;;; GNU Guix is free software; you can redistribute it and/or modify it
34 ;;; under the terms of the GNU General Public License as published by
35 ;;; the Free Software Foundation; either version 3 of the License, or (at
36 ;;; your option) any later version.
38 ;;; GNU Guix is distributed in the hope that it will be useful, but
39 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
40 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
41 ;;; GNU General Public License for more details.
43 ;;; You should have received a copy of the GNU General Public License
44 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
46 (define-module (gnu packages cran)
47 #:use-module ((guix licenses) #:prefix license:)
48 #:use-module (guix packages)
49 #:use-module (guix download)
50 #:use-module (guix git-download)
51 #:use-module (guix utils)
52 #:use-module (guix build-system r)
53 #:use-module (gnu packages)
54 #:use-module (gnu packages algebra)
55 #:use-module (gnu packages autotools)
56 #:use-module (gnu packages base)
57 #:use-module (gnu packages bioinformatics)
58 #:use-module (gnu packages c)
59 #:use-module (gnu packages compression)
60 #:use-module (gnu packages curl)
61 #:use-module (gnu packages databases)
62 #:use-module (gnu packages fontutils)
63 #:use-module (gnu packages gcc)
64 #:use-module (gnu packages geo)
65 #:use-module (gnu packages ghostscript)
66 #:use-module (gnu packages gl)
67 #:use-module (gnu packages gnome)
68 #:use-module (gnu packages graph)
69 #:use-module (gnu packages gtk)
70 #:use-module (gnu packages haskell-xyz)
71 #:use-module (gnu packages icu4c)
72 #:use-module (gnu packages image)
73 #:use-module (gnu packages imagemagick)
74 #:use-module (gnu packages java)
75 #:use-module (gnu packages javascript)
76 #:use-module (gnu packages libevent)
77 #:use-module (gnu packages lisp-xyz)
78 #:use-module (gnu packages machine-learning)
79 #:use-module (gnu packages maths)
80 #:use-module (gnu packages mpi)
81 #:use-module (gnu packages multiprecision)
82 #:use-module (gnu packages networking)
83 #:use-module (gnu packages node)
84 #:use-module (gnu packages pcre)
85 #:use-module (gnu packages perl)
86 #:use-module (gnu packages pkg-config)
87 #:use-module (gnu packages pulseaudio) ;libsndfile
88 #:use-module (gnu packages python)
89 #:use-module (gnu packages python-xyz)
90 #:use-module (gnu packages statistics)
91 #:use-module (gnu packages tcl)
92 #:use-module (gnu packages tls)
93 #:use-module (gnu packages web)
94 #:use-module (gnu packages xorg))
96 (define-public r-rticles
103 (uri (cran-uri "rticles" version))
106 "0svh2bcqnlqdxdpw5afz1b980i2q13k8cxpq6flfqbi3dlwf3h8l"))))
107 (properties `((upstream-name . "rticles")))
108 (build-system r-build-system)
110 `(("r-knitr" ,r-knitr)
111 ("r-rmarkdown" ,r-rmarkdown)
112 ("r-tinytex" ,r-tinytex)
115 (home-page "https://github.com/rstudio/rticles")
116 (synopsis "Article formats for R Markdown")
118 "This package provides a suite of custom R Markdown formats and templates
119 for authoring journal articles and conference submissions.")
120 (license license:gpl3)))
122 (define-public r-bezier
128 (uri (cran-uri "bezier" version))
131 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
132 (build-system r-build-system)
133 (home-page "https://cran.r-project.org/web/packages/bezier/")
134 (synopsis "Bezier curve and spline toolkit")
136 "This package is a toolkit for working with Bezier curves and splines.
137 The package provides functions for point generation, arc length estimation,
138 degree elevation and curve fitting.")
139 (license license:gpl2+)))
148 (uri (cran-uri "V8" version))
151 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
152 (properties `((upstream-name . "V8")))
153 (build-system r-build-system)
156 (modify-phases %standard-phases
157 (add-after 'unpack 'find-v8
158 (lambda* (#:key inputs #:allow-other-keys)
159 (substitute* "configure"
161 (string-append "PKG_LIBS="
162 (assoc-ref inputs "node")
163 "/lib/libnode.so.64\n")))
164 (setenv "INCLUDE_DIR"
166 (assoc-ref inputs "node")
170 (assoc-ref inputs "node") "/lib"))
173 `(("node" ,libnode)))
176 ("r-jsonlite" ,r-jsonlite)
179 `(("r-knitr" ,r-knitr)))
180 (home-page "https://jeroen.cran.dev/V8")
181 (synopsis "Embedded JavaScript and WebAssembly engine for R")
183 "This package provides an R interface to V8: Google's JavaScript and
184 WebAssembly engine.")
185 (license license:expat)))
194 (uri (cran-uri "DOT" version))
197 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
198 (properties `((upstream-name . "DOT")))
199 (build-system r-build-system)
202 (home-page "http://haghish.com/dot")
203 (synopsis "Render and Export DOT Graphs in R")
205 "This package provides tools to render DOT diagram markup language in R
206 and also provides the possibility to export the graphs in PostScript and
207 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
208 programming packages such as @code{knitr} and @code{rmarkdown}.")
209 (license license:expat)))
211 (define-public r-clipr
218 (uri (cran-uri "clipr" version))
221 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
222 (build-system r-build-system)
223 (home-page "https://github.com/mdlincoln/clipr")
224 (synopsis "Read and write from the system clipboard")
226 "This package provides simple utility functions to read from and write to
227 the system clipboards.")
228 (license license:gpl3)))
236 (uri (cran-uri "zoo" version))
239 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
240 (build-system r-build-system)
242 `(("r-lattice" ,r-lattice)))
243 (home-page "http://zoo.R-Forge.R-project.org/")
244 (synopsis "S3 infrastructure for regular and irregular time series")
245 (description "This package contains an S3 class with methods for totally
246 ordered indexed observations. It is particularly aimed at irregular time
247 series of numeric vectors/matrices and factors.")
248 (license license:gpl2+)))
250 (define-public r-ggpmisc
256 (uri (cran-uri "ggpmisc" version))
259 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
260 (build-system r-build-system)
262 `(("r-broom" ,r-broom)
264 ("r-ggplot2" ,r-ggplot2)
265 ("r-gridextra" ,r-gridextra)
266 ("r-lubridate" ,r-lubridate)
267 ("r-magrittr" ,r-magrittr)
270 ("r-polynom" ,r-polynom)
272 ("r-scales" ,r-scales)
273 ("r-splus2r" ,r-splus2r)
274 ("r-stringr" ,r-stringr)
275 ("r-tibble" ,r-tibble)
279 `(("r-knitr" ,r-knitr)))
280 (home-page "https://www.r4photobiology.info/")
281 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
282 (description "This package provides extensions to @code{ggplot2},
283 respecting the grammar of its graphics paradigm.")
284 (license license:gpl2+)))
286 (define-public r-gprofiler
293 (uri (cran-uri "gProfileR" version))
296 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
297 (properties `((upstream-name . "gProfileR")))
298 (build-system r-build-system)
301 ("r-rcurl" ,r-rcurl)))
302 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
303 (synopsis "Interface to the g:Profiler toolkit")
305 "This package provides tools for functional enrichment analysis,
306 gene identifier conversion and mapping homologous genes across related
307 organisms via the @code{g:Profiler} toolkit.")
308 (license license:gpl2+)))
310 (define-public r-gprofiler2
312 (name "r-gprofiler2")
317 (uri (cran-uri "gprofiler2" version))
320 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
321 (properties `((upstream-name . "gprofiler2")))
322 (build-system r-build-system)
324 `(("r-crosstalk" ,r-crosstalk)
326 ("r-ggplot2" ,r-ggplot2)
327 ("r-gridextra" ,r-gridextra)
328 ("r-jsonlite" ,r-jsonlite)
329 ("r-plotly" ,r-plotly)
332 ("r-viridislite" ,r-viridislite)))
333 (native-inputs `(("r-knitr" ,r-knitr)))
334 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
335 (synopsis "Interface to the g:Profiler toolset")
337 "This package provides a toolset for functional enrichment analysis and
338 visualization, gene/protein/SNP identifier conversion and mapping orthologous
339 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
343 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
345 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
347 @item @code{g:Orth}, orthology search across species;
348 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
349 genes and variant effects.
352 This package is an R interface corresponding to the 2019 update of
353 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
355 (license license:gpl2+)))
357 (define-public r-oenb
364 (uri (cran-uri "oenb" version))
367 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
368 (properties `((upstream-name . "oenb")))
369 (build-system r-build-system)
371 `(("r-dplyr" ,r-dplyr)
373 (native-inputs `(("r-knitr" ,r-knitr)))
374 (home-page "https://github.com/franzmohr/oenb")
375 (synopsis "Tools for the OeNB Data Web Service")
377 "Tools to access data from the data web service of the
378 @acronym{OeNB, Oesterreichische Nationalbank},
379 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
380 (license license:gpl2+)))
382 (define-public r-scales
389 (uri (cran-uri "scales" version))
391 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
392 (build-system r-build-system)
394 `(("r-farver" ,r-farver)
395 ("r-labeling" ,r-labeling)
396 ("r-lifecycle" ,r-lifecycle)
397 ("r-munsell" ,r-munsell)
398 ("r-rcolorbrewer" ,r-rcolorbrewer)
400 ("r-viridislite" ,r-viridislite)))
401 (home-page "https://github.com/hadley/scales")
402 (synopsis "Scale functions for visualization")
404 "This package provides graphical scales that map data to aesthetics, and
405 provides methods for automatically determining breaks and labels for axes and
407 (license license:expat)))
409 (define-public r-pheatmap
416 (uri (cran-uri "pheatmap" version))
419 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
420 (build-system r-build-system)
422 `(("r-gtable" ,r-gtable)
423 ("r-rcolorbrewer" ,r-rcolorbrewer)
424 ("r-scales" ,r-scales)))
425 (home-page "https://cran.r-project.org/web/packages/pheatmap")
426 (synopsis "Pretty heatmaps")
428 "This package provides an implementation of heatmaps that offers more
429 control over dimensions and appearance.")
430 (license license:gpl2+)))
438 (uri (cran-uri "ecp" version))
441 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
442 (build-system r-build-system)
444 `(("r-rcpp" ,r-rcpp)))
445 (home-page "https://cran.r-project.org/web/packages/ecp/")
446 (synopsis "Multiple change-point analysis of multivariate data")
448 "This package implements various procedures for finding multiple
449 change-points. Two methods make use of dynamic programming and pruning, with
450 no distributional assumptions other than the existence of certain absolute
451 moments in one method. Hierarchical and exact search methods are included.
452 All methods return the set of estimated change-points as well as other summary
454 (license license:gpl2+)))
456 (define-public r-ellipsis
463 (uri (cran-uri "ellipsis" version))
466 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
467 (build-system r-build-system)
469 `(("r-rlang" ,r-rlang)))
470 (home-page "https://github.com/hadley/ellipsis")
471 (synopsis "Tools for working with additional arguments")
473 "In S3 generics, it's useful to take @code{...} so that methods can have
474 additional arguments. But this flexibility comes at a cost: misspelled
475 arguments will be silently ignored. The @code{ellipsis} package is an
476 experiment that allows a generic to warn if any arguments passed in @code{...}
478 (license license:gpl3)))
487 (uri (cran-uri "grr" version))
490 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
491 (build-system r-build-system)
492 (home-page "https://cran.r-project.org/web/packages/grr")
493 (synopsis "Alternative implementations of base R functions")
495 "This package provides alternative implementations of some base R
496 functions, including @code{sort}, @code{order}, and @code{match}. The
497 functions are simplified but can be faster or have other advantages.")
498 (license license:gpl3)))
500 (define-public r-matrix-utils
502 (name "r-matrix-utils")
507 (uri (cran-uri "Matrix.utils" version))
510 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
511 (properties `((upstream-name . "Matrix.utils")))
512 (build-system r-build-system)
515 ("r-matrix" ,r-matrix)))
516 (home-page "https://github.com/cvarrichio/Matrix.utils")
518 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
520 "This package implements data manipulation methods such as @code{cast},
521 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
523 (license license:gpl3)))
525 (define-public r-mboost
531 (uri (cran-uri "mboost" version))
534 "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf"))))
535 (build-system r-build-system)
537 `(("r-lattice" ,r-lattice)
538 ("r-matrix" ,r-matrix)
540 ("r-partykit" ,r-partykit)
541 ("r-quadprog" ,r-quadprog)
543 ("r-survival" ,r-survival)))
544 (home-page "https://github.com/boost-R/mboost")
545 (synopsis "Model-based boosting")
547 "This package provides a functional gradient descent algorithm (boosting)
548 for optimizing general risk functions utilizing component-wise (penalised)
549 least squares estimates or regression trees as base-learners for fitting
550 generalized linear, additive and interaction models to potentially
551 high-dimensional data.")
552 (license license:gpl2)))
561 (uri (cran-uri "sys" version))
564 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
565 (build-system r-build-system)
566 (home-page "https://github.com/jeroen/sys")
567 (synopsis "Powerful and reliable tools for running system commands in R")
569 "This package provides drop-in replacements for the base @code{system2()}
570 function with fine control and consistent behavior across platforms. It
571 supports clean interruption, timeout, background tasks, and streaming STDIN /
572 STDOUT / STDERR over binary or text connections. The package also provides
573 functions for evaluating expressions inside a temporary fork. Such
574 evaluations have no side effects on the main R process, and support reliable
575 interrupts and timeouts. This provides the basis for a sandboxing
577 (license license:expat)))
579 (define-public r-askpass
586 (uri (cran-uri "askpass" version))
589 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
590 (build-system r-build-system)
591 (propagated-inputs `(("r-sys" ,r-sys)))
592 (home-page "https://github.com/jeroen/askpass")
593 (synopsis "Safe password entry for R")
595 "This package provides cross-platform utilities for prompting the user
596 for credentials or a passphrase, for example to authenticate with a server or
597 read a protected key.")
598 (license license:expat)))
600 (define-public r-vegan
607 (uri (cran-uri "vegan" version))
610 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
611 (build-system r-build-system)
613 `(("gfortran" ,gfortran)))
615 `(("r-cluster" ,r-cluster)
616 ("r-knitr" ,r-knitr) ; needed for vignettes
617 ("r-lattice" ,r-lattice)
620 ("r-permute" ,r-permute)))
621 (home-page "https://cran.r-project.org/web/packages/vegan")
622 (synopsis "Functions for community ecology")
624 "The vegan package provides tools for descriptive community ecology. It
625 has most basic functions of diversity analysis, community ordination and
626 dissimilarity analysis. Most of its multivariate tools can be used for other
627 data types as well.")
628 (license license:gpl2+)))
630 (define-public r-tidyverse
637 (uri (cran-uri "tidyverse" version))
640 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
641 (build-system r-build-system)
643 `(("r-broom" ,r-broom)
645 ("r-crayon" ,r-crayon)
646 ("r-dbplyr" ,r-dbplyr)
648 ("r-forcats" ,r-forcats)
649 ("r-ggplot2" ,r-ggplot2)
653 ("r-jsonlite" ,r-jsonlite)
654 ("r-lubridate" ,r-lubridate)
655 ("r-magrittr" ,r-magrittr)
656 ("r-modelr" ,r-modelr)
657 ("r-pillar" ,r-pillar)
660 ("r-readxl" ,r-readxl)
661 ("r-reprex" ,r-reprex)
663 ("r-rstudioapi" ,r-rstudioapi)
665 ("r-stringr" ,r-stringr)
666 ("r-tibble" ,r-tibble)
669 (home-page "https://tidyverse.tidyverse.org")
670 (synopsis "Install and load packages from the \"Tidyverse\"")
672 "The @code{tidyverse} is a set of packages that work in harmony because
673 they share common data representations and API design. This package is
674 designed to make it easy to install and load multiple tidyverse packages in a
676 (license license:gpl3)))
678 (define-public r-rvest
685 (uri (cran-uri "rvest" version))
687 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
688 (build-system r-build-system)
691 ("r-magrittr" ,r-magrittr)
692 ("r-selectr" ,r-selectr)
695 `(("r-knitr" ,r-knitr)))
696 (home-page "https://github.com/hadley/rvest")
697 (synopsis "Simple web scraping for R")
699 "@code{r-rvest} helps you scrape information from web pages. It is
700 designed to work with @code{magrittr} to make it easy to express common web
701 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
702 (license license:gpl3)))
704 (define-public r-selectr
711 (uri (cran-uri "selectr" version))
713 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
714 (build-system r-build-system)
716 `(("r-stringr" ,r-stringr)
718 (home-page "https://sjp.co.nz/projects/selectr/")
719 (synopsis "Translate CSS selectors to XPath expressions")
721 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
722 expression. This allows you to use CSS selectors when working with the XML
723 package as it can only evaluate XPath expressions. Also provided are
724 convenience functions useful for using CSS selectors on XML nodes. This
725 package is a port of the Python package @code{cssselect}.")
726 (license license:bsd-3)))
728 (define-public r-reprex
735 (uri (cran-uri "reprex" version))
738 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
739 (build-system r-build-system)
741 `(("r-callr" ,r-callr)
745 ("r-rmarkdown" ,r-rmarkdown)
746 ("r-whisker" ,r-whisker)
747 ("r-withr" ,r-withr)))
748 (home-page "https://github.com/tidyverse/reprex")
749 (synopsis "Prepare reproducible R code examples for sharing")
751 "This package provides a convenience wrapper that uses the
752 @code{rmarkdown} package to render small snippets of code to target formats
753 that include both code and output. The goal is to encourage the sharing of
754 small, reproducible, and runnable examples on code-oriented websites or email.
755 @code{reprex} also extracts clean, runnable R code from various common formats,
756 such as copy/paste from an R session.")
757 (license license:expat)))
759 (define-public r-reordercluster
761 (name "r-reordercluster")
765 (uri (cran-uri "ReorderCluster" version))
768 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
769 (build-system r-build-system)
771 `(("r-gplots" ,r-gplots)
773 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
774 (synopsis "Reordering the dendrogram according to the class labels")
775 (description "This package provides tools for performing the leaf reordering
776 for the dendrogram that preserves the hierarchical clustering result and at the
777 same time tries to group instances from the same class together.")
778 (license license:gpl3+)))
780 (define-public r-callr
787 (uri (cran-uri "callr" version))
790 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
791 (build-system r-build-system)
794 ("r-processx" ,r-processx)))
795 (home-page "https://github.com/r-lib/callr#readme")
796 (synopsis "Call R from R")
798 "It is sometimes useful to perform a computation in a separate R process,
799 without affecting the current R process at all. This package does exactly
801 (license license:expat)))
803 (define-public r-readxl
810 (uri (cran-uri "readxl" version))
813 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
814 (build-system r-build-system)
816 `(("r-cellranger" ,r-cellranger)
817 ("r-progress" ,r-progress)
819 ("r-tibble" ,r-tibble)))
820 (home-page "https://readxl.tidyverse.org")
821 (synopsis "Read Excel files")
823 "This package lets you import Excel files into R. It supports
824 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
825 the embedded @code{RapidXML} C++ library.")
826 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
827 ;; 'rapidxml' which is Boost.
828 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
830 (define-public r-modelr
837 (uri (cran-uri "modelr" version))
840 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
841 (build-system r-build-system)
843 `(("r-broom" ,r-broom)
844 ("r-magrittr" ,r-magrittr)
847 ("r-tibble" ,r-tibble)
849 ("r-tidyselect" ,r-tidyselect)
850 ("r-vctrs" ,r-vctrs)))
851 (home-page "https://github.com/tidyverse/modelr")
852 (synopsis "Helper functions for modelling in pipelines")
854 "Functions for modelling that help you seamlessly integrate modelling
855 into a pipeline of data manipulation and visualisation.")
856 (license license:gpl3)))
858 (define-public r-httpuv
864 (uri (cran-uri "httpuv" version))
867 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))
868 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
869 ;; only contains fixes for building on Solaris.
870 (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch"))
871 (modules '((guix build utils)
876 (delete-file-recursively "src/libuv")
877 ;; Cannot unbundle http-parser, because it contains local
880 (build-system r-build-system)
883 (modify-phases %standard-phases
884 (add-after 'unpack 'unbundle-libuv
885 (lambda* (#:key outputs #:allow-other-keys)
886 (substitute* (find-files "src" "\\.cpp$|\\.h$")
887 (("\"libuv/include/uv\\.h\"")
889 ;; Fix https://github.com/rstudio/httpuv/issues/282
890 (substitute* "src/http.cpp"
891 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
892 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
899 ("r-promises" ,r-promises)
902 (home-page "https://github.com/rstudio/httpuv")
903 (synopsis "HTTP and WebSocket server library for R")
905 "The httpuv package provides low-level socket and protocol support for
906 handling HTTP and WebSocket requests directly from within R. It is primarily
907 intended as a building block for other packages, rather than making it
908 particularly easy to create complete web applications using httpuv alone.")
909 ;; This package includes third-party code that was originally released
910 ;; under various non-copyleft licenses. Full licensing information can be
911 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
912 (license license:gpl3+)))
914 (define-public r-jsonlite
920 (uri (cran-uri "jsonlite" version))
923 "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
924 (build-system r-build-system)
926 `(("r-knitr" ,r-knitr)))
927 (home-page "https://arxiv.org/abs/1403.2805")
928 (synopsis "Robust, high performance JSON parser and generator for R")
930 "The jsonlite package provides a fast JSON parser and generator optimized
931 for statistical data and the web. It offers flexible, robust, high
932 performance tools for working with JSON in R and is particularly powerful for
933 building pipelines and interacting with a web API. In addition to converting
934 JSON data from/to R objects, jsonlite contains functions to stream, validate,
935 and prettify JSON data. The unit tests included with the package verify that
936 all edge cases are encoded and decoded consistently for use with dynamic data
937 in systems and applications.")
938 (license license:expat)))
940 (define-public r-servr
946 (uri (cran-uri "servr" version))
949 "0xfbf1a1w34hbsx4jrdr4rqf22v7gf1p37ngknglv1dyxih7ipja"))))
950 (build-system r-build-system)
952 `(("r-httpuv" ,r-httpuv)
953 ("r-jsonlite" ,r-jsonlite)
956 (home-page "https://github.com/yihui/servr")
957 (synopsis "Simple HTTP server to serve static files or dynamic documents")
959 "Servr provides an HTTP server in R to serve static files, or dynamic
960 documents that can be converted to HTML files (e.g., R Markdown) under a given
962 (license license:expat)))
964 (define-public r-htmltools
970 (uri (cran-uri "htmltools" version))
973 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
974 (build-system r-build-system)
976 `(("r-base64enc" ,r-base64enc)
977 ("r-digest" ,r-digest)
978 ("r-rlang" ,r-rlang)))
979 (home-page "https://cran.r-project.org/web/packages/htmltools")
980 (synopsis "R tools for HTML")
982 "This package provides tools for HTML generation and output in R.")
983 (license license:expat)))
985 (define-public r-htmlwidgets
987 (name "r-htmlwidgets")
991 (uri (cran-uri "htmlwidgets" version))
994 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
995 (build-system r-build-system)
997 `(("r-htmltools" ,r-htmltools)
998 ("r-jsonlite" ,r-jsonlite)
1000 (home-page "https://github.com/ramnathv/htmlwidgets")
1001 (synopsis "HTML Widgets for R")
1003 "HTML widgets is a framework for creating HTML widgets that render in
1004 various contexts including the R console, R Markdown documents, and Shiny web
1006 (license license:expat)))
1008 (define-public r-htmltable
1010 (name "r-htmltable")
1015 (uri (cran-uri "htmlTable" version))
1017 (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
1018 (properties `((upstream-name . "htmlTable")))
1019 (build-system r-build-system)
1021 `(("r-checkmate" ,r-checkmate)
1022 ("r-htmltools" ,r-htmltools)
1023 ("r-htmlwidgets" ,r-htmlwidgets)
1024 ("r-knitr" ,r-knitr)
1025 ("r-magrittr" ,r-magrittr)
1026 ("r-rstudioapi" ,r-rstudioapi)
1027 ("r-stringr" ,r-stringr)))
1029 `(("r-knitr" ,r-knitr)))
1030 (home-page "http://gforge.se/packages/")
1031 (synopsis "Advanced tables for Markdown/HTML")
1033 "This package provides functions to build tables with advanced layout
1034 elements such as row spanners, column spanners, table spanners, zebra
1035 striping, and more. While allowing advanced layout, the underlying
1036 CSS-structure is simple in order to maximize compatibility with word
1037 processors such as LibreOffice. The package also contains a few text
1038 formatting functions that help outputting text compatible with HTML or
1040 (license license:gpl3+)))
1042 (define-public r-curl
1048 (uri (cran-uri "curl" version))
1051 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1052 (build-system r-build-system)
1055 (modify-phases %standard-phases
1056 ;; The environment variable CURL_CA_BUNDLE is only respected when
1057 ;; running Windows, so we disable the platform checks.
1058 ;; This can be removed once the libcurl has been patched.
1059 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1061 (substitute* "R/onload.R"
1062 (("if \\(!grepl\\(\"mingw\".*")
1064 (substitute* "src/handle.c"
1065 (("/\\* Only set" m)
1067 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1068 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1075 `(("pkg-config" ,pkg-config)))
1076 (home-page "https://github.com/jeroenooms/curl")
1077 (synopsis "HTTP client for R")
1079 "The @code{curl()} and @code{curl_download()} functions provide highly
1080 configurable drop-in replacements for base @code{url()} and
1081 @code{download.file()} with better performance, support for encryption, gzip
1082 compression, authentication, and other @code{libcurl} goodies. The core of
1083 the package implements a framework for performing fully customized requests
1084 where data can be processed either in memory, on disk, or streaming via the
1085 callback or connection interfaces.")
1086 (license license:expat)))
1088 (define-public r-hwriter
1095 (uri (cran-uri "hwriter" version))
1098 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1099 (build-system r-build-system)
1100 (home-page "https://cran.r-project.org/web/packages/hwriter")
1101 (synopsis "Output R objects in HTML format")
1103 "This package provides easy-to-use and versatile functions to output R
1104 objects in HTML format.")
1105 (license license:lgpl2.1+)))
1107 (define-public r-rjson
1114 (uri (cran-uri "rjson" version))
1117 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1118 (build-system r-build-system)
1119 (home-page "https://cran.r-project.org/web/packages/rjson")
1120 (synopsis "JSON library for R")
1122 "This package provides functions to convert R objects into JSON objects
1124 (license license:gpl2+)))
1126 (define-public r-fastmap
1133 (uri (cran-uri "fastmap" version))
1136 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1137 (properties `((upstream-name . "fastmap")))
1138 (build-system r-build-system)
1139 (home-page "https://r-lib.github.io/fastmap/")
1140 (synopsis "Fast implementation of a key-value store")
1142 "This package provides a fast implementation of a key-value store.
1143 Environments are commonly used as key-value stores, but every time a new key
1144 is used, it is added to R's global symbol table, causing a small amount of
1145 memory leakage. This can be problematic in cases where many different keys
1146 are used. Fastmap avoids this memory leak issue by implementing the map using
1147 data structures in C++.")
1148 (license license:expat)))
1150 (define-public r-shiny
1158 (url "https://github.com/rstudio/shiny")
1159 (commit (string-append "v" version))))
1160 (file-name (git-file-name name version))
1163 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1164 (build-system r-build-system)
1166 `(#:modules ((guix build r-build-system)
1167 (guix build minify-build-system)
1170 #:imported-modules (,@%r-build-system-modules
1171 (guix build minify-build-system))
1173 (modify-phases (@ (guix build r-build-system) %standard-phases)
1174 (add-after 'unpack 'replace-bundled-minified-JavaScript
1175 (lambda* (#:key inputs #:allow-other-keys)
1176 (let ((replace-file (lambda (old new)
1177 (format #t "replacing ~a with ~a\n" old new)
1179 (symlink new old))))
1180 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1181 ;; contain just data. They are not minified code, so we don't
1183 (with-directory-excursion "inst/www/shared"
1184 (replace-file "bootstrap/shim/respond.min.js"
1185 (string-append (assoc-ref inputs "js-respond")
1186 "/share/javascript/respond.min.js"))
1187 (replace-file "bootstrap/shim/html5shiv.min.js"
1188 (string-append (assoc-ref inputs "js-html5shiv")
1189 "/share/javascript/html5shiv.min.js"))
1190 (replace-file "json2-min.js"
1191 (string-append (assoc-ref inputs "js-json2")
1192 "/share/javascript/json2-min.js"))
1193 (replace-file "strftime/strftime-min.js"
1194 (string-append (assoc-ref inputs "js-strftime")
1195 "/share/javascript/strftime.min.js"))
1196 (replace-file "highlight/highlight.pack.js"
1197 (string-append (assoc-ref inputs "js-highlight")
1198 "/share/javascript/highlight.min.js"))
1199 (replace-file "datatables/js/jquery.dataTables.min.js"
1200 (string-append (assoc-ref inputs "js-datatables")
1201 "/share/javascript/jquery.dataTables.min.js"))
1202 (replace-file "selectize/js/selectize.min.js"
1203 (string-append (assoc-ref inputs "js-selectize")
1204 "/share/javascript/selectize.min.js"))
1205 (replace-file "selectize/js/es5-shim.min.js"
1206 (string-append (assoc-ref inputs "js-es5-shim")
1207 "/share/javascript/es5-shim.min.js"))
1208 (for-each (match-lambda
1210 (delete-file target)
1211 (minify source #:target target)))
1212 '(("jqueryui/jquery-ui.js" .
1213 "jqueryui/jquery-ui.min.js")
1214 ("datepicker/js/bootstrap-datepicker.js" .
1215 "datepicker/js/bootstrap-datepicker.min.js")
1216 ("ionrangeslider/js/ion.rangeSlider.js" .
1217 "ionrangeslider/js/ion.rangeSlider.min.js")
1218 ("bootstrap/js/bootstrap.js" .
1219 "bootstrap/js/bootstrap.min.js")
1224 ("legacy/jquery.js" .
1225 "legacy/jquery.min.js")
1226 ("showdown/src/showdown.js" .
1227 "showdown/compressed/showdown.js")))))
1230 `(("r-crayon" ,r-crayon)
1231 ("r-digest" ,r-digest)
1232 ("r-fastmap" ,r-fastmap)
1233 ("r-htmltools" ,r-htmltools)
1234 ("r-httpuv" ,r-httpuv)
1235 ("r-jsonlite" ,r-jsonlite)
1236 ("r-later" ,r-later)
1238 ("r-promises" ,r-promises)
1240 ("r-rlang" ,r-rlang)
1241 ("r-sourcetools" ,r-sourcetools)
1242 ("r-withr" ,r-withr)
1243 ("r-xtable" ,r-xtable)))
1245 `(("js-datatables" ,js-datatables)
1246 ("js-html5shiv" ,js-html5shiv)
1247 ("js-json2" ,js-json2)
1248 ("js-respond" ,js-respond)
1249 ("js-selectize" ,js-selectize)
1250 ("js-strftime" ,js-strftime)
1251 ("js-highlight" ,js-highlight)
1252 ("js-es5-shim" ,js-es5-shim)))
1254 `(("uglify-js" ,uglify-js)
1255 ("gfortran" ,gfortran)))
1256 (home-page "http://shiny.rstudio.com")
1257 (synopsis "Easy interactive web applications with R")
1259 "Makes it incredibly easy to build interactive web applications
1260 with R. Automatic \"reactive\" binding between inputs and outputs and
1261 extensive prebuilt widgets make it possible to build beautiful,
1262 responsive, and powerful applications with minimal effort.")
1263 (license license:artistic2.0)))
1265 ;; This package includes minified JavaScript files. When upgrading please
1266 ;; check that there are no new minified JavaScript files.
1267 (define-public r-shinytree
1269 (name "r-shinytree")
1274 (uri (cran-uri "shinyTree" version))
1277 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1278 (modules '((guix build utils)))
1281 ;; Delete minified JavaScript
1282 (for-each delete-file
1283 '("inst/www/jsTree-3.3.7/libs/require.js"
1284 "inst/www/jsTree-3.3.7/libs/jquery.js"
1285 "inst/www/jsTree-3.3.7/jstree.min.js"))
1287 (properties `((upstream-name . "shinyTree")))
1288 (build-system r-build-system)
1290 `(#:modules ((guix build utils)
1291 (guix build r-build-system)
1295 (modify-phases %standard-phases
1296 (add-after 'unpack 'replace-minified-javascript
1297 (lambda* (#:key inputs #:allow-other-keys)
1298 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1299 (symlink (string-append (assoc-ref inputs "js-requirejs")
1300 "/share/javascript/require.min.js")
1305 `((,(assoc-ref inputs "js-jquery")
1309 (lambda (sources targets)
1310 (for-each (lambda (source target)
1311 (format #t "Processing ~a --> ~a~%"
1313 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1314 (call-with-output-file target
1316 (dump-port minified port)))))
1320 `(("r-htmlwidgets" ,r-htmlwidgets)
1321 ("r-jsonlite" ,r-jsonlite)
1322 ("r-promises" ,r-promises)
1323 ("r-shiny" ,r-shiny)
1324 ("r-stringr" ,r-stringr)))
1326 `(("js-requirejs" ,js-requirejs)))
1328 `(("uglify-js" ,uglify-js)
1332 (uri "https://code.jquery.com/jquery-3.3.1.js")
1335 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1336 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1337 (synopsis "jsTree bindings for Shiny")
1339 "This package exposes R bindings to jsTree, a JavaScript library that
1340 supports interactive trees, to enable rich, editable trees in Shiny.")
1341 (license license:expat)))
1343 (define-public r-shinydashboard
1345 (name "r-shinydashboard")
1349 (uri (cran-uri "shinydashboard" version))
1352 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1353 (build-system r-build-system)
1354 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1355 ;; Regenerate it from the included sources.
1357 `(#:modules ((guix build utils)
1358 (guix build r-build-system)
1361 (modify-phases %standard-phases
1362 (add-after 'unpack 'generate-minified-javascript
1364 (with-directory-excursion "inst/AdminLTE"
1365 (delete-file "app.min.js")
1366 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1367 (call-with-output-file "app.min.js"
1369 (dump-port minified port))))))))))
1371 `(("r-htmltools" ,r-htmltools)
1372 ("r-promises" ,r-promises)
1373 ("r-shiny" ,r-shiny)))
1375 `(("uglify-js" ,uglify-js)))
1376 (home-page "https://rstudio.github.io/shinydashboard/")
1377 (synopsis "Create dashboards with shiny")
1378 (description "This package provides an extension to the Shiny web
1379 application framework for R, making it easy to create attractive dashboards.")
1380 ;; This package includes software that was released under the Expat
1381 ;; license, but the whole package is released under GPL version 2 or
1383 (license license:gpl2+)))
1385 (define-public r-shinyfiles
1387 (name "r-shinyfiles")
1392 (uri (cran-uri "shinyFiles" version))
1394 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1395 (properties `((upstream-name . "shinyFiles")))
1396 (build-system r-build-system)
1399 ("r-htmltools" ,r-htmltools)
1400 ("r-jsonlite" ,r-jsonlite)
1401 ("r-shiny" ,r-shiny)
1402 ("r-tibble" ,r-tibble)))
1403 (home-page "https://github.com/thomasp85/shinyFiles")
1404 (synopsis "Server-side file system viewer for Shiny")
1406 "This package provides functionality for client-side navigation of the
1407 server side file system in shiny apps. In case the app is running locally
1408 this gives the user direct access to the file system without the need to
1409 \"download\" files to a temporary location. Both file and folder selection as
1410 well as file saving is available.")
1411 (license license:gpl2+)))
1413 (define-public r-shinythemes
1415 (name "r-shinythemes")
1420 (uri (cran-uri "shinythemes" version))
1423 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1424 (properties `((upstream-name . "shinythemes")))
1425 (build-system r-build-system)
1426 (propagated-inputs `(("r-shiny" ,r-shiny)))
1427 (home-page "https://rstudio.github.io/shinythemes/")
1428 (synopsis "Themes for Shiny")
1430 "This package provides themes for use with Shiny. It includes several
1431 Bootstrap themes, which are packaged for use with Shiny applications.")
1432 ;; The package is released under version 3 of the GPL, but it includes
1433 ;; source files that are covered by the Expat license. It also includes
1434 ;; fonts under SIL or the ASL.
1435 (license (list license:gpl3 license:expat
1436 license:silofl1.1 license:asl2.0))))
1438 ;; The package sources include minified variants of d3.js and non-minified
1439 ;; source code of d3-jetpack.
1440 (define-public r-d3r
1447 (uri (cran-uri "d3r" version))
1450 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1451 (build-system r-build-system)
1453 `(#:modules ((guix build utils)
1454 (guix build r-build-system)
1458 (modify-phases %standard-phases
1459 (add-after 'unpack 'process-javascript
1460 (lambda* (#:key inputs #:allow-other-keys)
1461 (with-directory-excursion "inst/www/d3/"
1465 `((,(assoc-ref inputs "d3.v3.js")
1466 "v3/dist/d3.min.js")
1467 (,(assoc-ref inputs "d3.v4.js")
1468 "v4/dist/d3.min.js")
1469 (,(assoc-ref inputs "d3.v5.js")
1470 "v5/dist/d3.min.js"))))
1471 (lambda (sources targets)
1472 (for-each (lambda (source target)
1473 (format #t "Processing ~a --> ~a~%"
1475 (delete-file target)
1476 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1477 (call-with-output-file target
1479 (dump-port minified port)))))
1483 `(("r-dplyr" ,r-dplyr)
1484 ("r-htmltools" ,r-htmltools)
1485 ("r-rlang" ,r-rlang)
1486 ("r-tidyr" ,r-tidyr)))
1488 `(("uglify-js" ,uglify-js)
1492 (uri "https://d3js.org/d3.v3.js")
1495 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1499 (uri "https://d3js.org/d3.v4.js")
1502 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1506 (uri "https://d3js.org/d3.v5.js")
1509 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1510 (home-page "https://github.com/timelyportfolio/d3r")
1511 (synopsis "d3.js utilities for R")
1513 "This package provides a suite of functions to help ease the use of the
1514 d3.js visualization library in R. These helpers include
1515 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1516 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1517 R objects into the JSON format that the d3.js library expects.")
1518 (license license:bsd-3)))
1520 ;; We use the latest commit here because the last release was in 2016 while
1521 ;; the latest commit was in 2018.
1522 (define-public r-sankeyd3
1523 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1527 (version (git-version "0.3.2" revision commit))
1532 (url "https://github.com/fbreitwieser/sankeyD3")
1534 (file-name (git-file-name name version))
1537 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1538 (build-system r-build-system)
1541 ("r-htmlwidgets" ,r-htmlwidgets)
1542 ("r-shiny" ,r-shiny)
1543 ("r-magrittr" ,r-magrittr)))
1544 (home-page "https://github.com/fbreitwieser/sankeyD3")
1545 (synopsis "Sankey network graphs from R")
1547 "This package provides an R library to generate Sankey network graphs
1548 in R and Shiny via the D3 visualization library.")
1549 ;; The R code is licensed under GPLv3+. It includes the non-minified
1550 ;; JavaScript source code of d3-sankey, which is released under the
1551 ;; 3-clause BSD license.
1552 (license (list license:gpl3+ license:bsd-3)))))
1554 (define-public r-crosstalk
1556 (name "r-crosstalk")
1561 (uri (cran-uri "crosstalk" version))
1564 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1565 (build-system r-build-system)
1567 `(("r-htmltools" ,r-htmltools)
1568 ("r-jsonlite" ,r-jsonlite)
1569 ("r-lazyeval" ,r-lazyeval)
1571 (home-page "https://rstudio.github.io/crosstalk/")
1572 (synopsis "Inter-widget interactivity for HTML widgets")
1574 "This package provides building blocks for allowing HTML widgets to
1575 communicate with each other, with Shiny or without (i.e. static @code{.html}
1576 files). It currently supports linked brushing and filtering.")
1577 (license license:expat)))
1579 (define-public r-rook
1586 (uri (cran-uri "Rook" version))
1589 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1590 (properties `((upstream-name . "Rook")))
1591 (build-system r-build-system)
1592 (propagated-inputs `(("r-brew" ,r-brew)))
1593 (home-page "https://cran.r-project.org/web/packages/Rook")
1594 (synopsis "Web server interface for R")
1596 "This package contains the Rook specification and convenience software
1597 for building and running Rook applications. A Rook application is an R
1598 reference class object that implements a @code{call} method or an R closure
1599 that takes exactly one argument, an environment, and returns a list with three
1600 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1601 (license license:gpl2)))
1603 (define-public r-miniui
1610 (uri (cran-uri "miniUI" version))
1613 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1614 (properties `((upstream-name . "miniUI")))
1615 (build-system r-build-system)
1617 `(("r-htmltools" ,r-htmltools)
1618 ("r-shiny" ,r-shiny)))
1619 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1620 (synopsis "Shiny UI widgets for small screens")
1622 "This package provides UI widget and layout functions for writing Shiny apps that
1623 work well on small screens.")
1624 (license license:gpl3)))
1626 (define-public r-feather
1633 (uri (cran-uri "feather" version))
1636 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1637 (build-system r-build-system)
1641 ("r-tibble" ,r-tibble)))
1642 (home-page "https://github.com/wesm/feather")
1643 (synopsis "R Bindings to the Feather API")
1644 (description "Read and write feather files, a lightweight binary columnar
1645 data store designed for maximum speed.")
1646 (license license:asl2.0)))
1648 (define-public r-maps
1655 (uri (cran-uri "maps" version))
1658 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1659 (build-system r-build-system)
1660 (home-page "https://cran.r-project.org/web/packages/maps")
1661 (synopsis "Draw geographical maps")
1662 (description "This package provides an R module for display of maps.
1663 Projection code and larger maps are in separate packages (@code{mapproj} and
1665 (license license:gpl2)))
1667 (define-public r-mapproj
1674 (uri (cran-uri "mapproj" version))
1677 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1678 (build-system r-build-system)
1679 (propagated-inputs `(("r-maps" ,r-maps)))
1680 (home-page "https://cran.r-project.org/web/packages/mapproj")
1681 (synopsis "Map projection in R")
1682 (description "This package converts latitude/longitude into projected
1684 (license (list license:gpl2 ; The R interface
1685 (license:non-copyleft ; The C code
1686 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1687 "Lucent Public License Version 1.02")))))
1689 (define-public r-rgooglemaps
1691 (name "r-rgooglemaps")
1696 (uri (cran-uri "RgoogleMaps" version))
1699 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1700 (properties `((upstream-name . "RgoogleMaps")))
1701 (build-system r-build-system)
1705 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1706 (synopsis "Use Google Maps in R")
1707 (description "This package serves two purposes:
1709 @item Provide a comfortable R interface to query the Google server for static
1711 @item Use the map as a background image to overlay plots within R. This
1712 requires proper coordinate scaling.
1714 (license license:gpl2+)))
1716 (define-public r-geosphere
1718 (name "r-geosphere")
1723 (uri (cran-uri "geosphere" version))
1726 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1727 (build-system r-build-system)
1728 (propagated-inputs `(("r-sp" ,r-sp)))
1729 (home-page "https://cran.r-project.org/web/packages/geosphere")
1730 (synopsis "Spherical trigonometry")
1731 (description "This package computes spherical trigonometry for geographic
1732 applications. That is, compute distances and related measures for angular
1733 (longitude/latitude) locations.")
1734 (license license:gpl3+)))
1736 (define-public r-jpeg
1743 (uri (cran-uri "jpeg" version))
1746 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1747 (build-system r-build-system)
1748 (inputs `(("libjpeg" ,libjpeg-turbo)))
1749 (home-page "https://www.rforge.net/jpeg/")
1750 (synopsis "Read and write JPEG images with R")
1751 (description "This package provides a way to read, write and display
1752 bitmap images stored in the JPEG format with R. It can read and write both
1753 files and in-memory raw vectors.")
1754 (license license:gpl2+)))
1756 (define-public r-ggmap
1763 (uri (cran-uri "ggmap" version))
1766 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1767 (build-system r-build-system)
1769 `(("r-bitops" ,r-bitops)
1770 ("r-digest" ,r-digest)
1771 ("r-dplyr" ,r-dplyr)
1772 ("r-ggplot2" ,r-ggplot2)
1776 ("r-magrittr" ,r-magrittr)
1779 ("r-purrr" ,r-purrr)
1780 ("r-rgooglemaps" ,r-rgooglemaps)
1781 ("r-rjson" ,r-rjson)
1782 ("r-scales" ,r-scales)
1783 ("r-stringr" ,r-stringr)
1784 ("r-tibble" ,r-tibble)
1785 ("r-tidyr" ,r-tidyr)))
1786 (home-page "https://github.com/dkahle/ggmap")
1787 (synopsis "Spatial visualization with ggplot2")
1788 (description "This package provides a collection of functions to visualize
1789 spatial data and models on top of static maps from various online sources (e.g
1790 Google Maps and Stamen Maps). It includes tools common to those tasks,
1791 including functions for geolocation and routing.")
1792 (license license:gpl2)))
1794 (define-public r-haven
1801 (uri (cran-uri "haven" version))
1804 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1805 (build-system r-build-system)
1809 `(("r-knitr" ,r-knitr)))
1811 `(("r-forcats" ,r-forcats)
1814 ("r-rlang" ,r-rlang)
1815 ("r-readr" ,r-readr)
1816 ("r-tibble" ,r-tibble)
1817 ("r-tidyselect" ,r-tidyselect)
1818 ("r-vctrs" ,r-vctrs)))
1819 (home-page "https://haven.tidyverse.org")
1820 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1822 "This package lets you mport foreign statistical formats into R via the
1823 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1824 (license license:expat)))
1826 (define-public r-amap
1832 (uri (cran-uri "amap" version))
1835 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1836 (build-system r-build-system)
1838 `(("gfortran" ,gfortran)))
1839 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1840 (synopsis "Another multidimensional analysis package")
1841 (description "This package provides tools for clustering and principal
1842 component analysis (with robust methods, and parallelized functions).")
1843 (license license:gpl2+)))
1845 (define-public r-ape
1852 (uri (cran-uri "ape" version))
1855 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
1856 (build-system r-build-system)
1858 `(("r-lattice" ,r-lattice)
1860 ("r-rcpp" ,r-rcpp)))
1861 (home-page "http://ape-package.ird.fr/")
1862 (synopsis "Analyses of phylogenetics and evolution")
1864 "This package provides functions for reading, writing, plotting, and
1865 manipulating phylogenetic trees, analyses of comparative data in a
1866 phylogenetic framework, ancestral character analyses, analyses of
1867 diversification and macroevolution, computing distances from DNA sequences,
1868 and several other tools.")
1869 (license license:gpl2+)))
1871 (define-public r-abbyyr
1878 (uri (cran-uri "abbyyR" version))
1881 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1882 (properties `((upstream-name . "abbyyR")))
1883 (build-system r-build-system)
1885 `(("r-curl" ,r-curl)
1888 ("r-progress" ,r-progress)
1889 ("r-readr" ,r-readr)
1891 (home-page "https://github.com/soodoku/abbyyR")
1892 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1894 "This package provides tools to get text from images of text using Abbyy
1895 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1896 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1897 passports and get the results in a variety of formats including plain text and
1898 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1899 (license license:expat)))
1901 (define-public r-colorspace
1903 (name "r-colorspace")
1908 (uri (cran-uri "colorspace" version))
1910 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1911 (build-system r-build-system)
1912 (home-page "https://cran.r-project.org/web/packages/colorspace")
1913 (synopsis "Color space manipulation")
1915 "This package carries out a mapping between assorted color spaces
1916 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1917 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1918 colors are provided.")
1919 (license license:bsd-3)))
1921 (define-public r-glue
1928 (uri (cran-uri "glue" version))
1931 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
1932 (build-system r-build-system)
1933 ;; knitr depends on glue, so we can't add knitr here to build the
1937 `(("r-knitr" ,r-knitr)))
1938 (home-page "https://github.com/tidyverse/glue")
1939 (synopsis "Interpreted string literals")
1941 "This package provides an implementation of interpreted string literals,
1942 inspired by Python's Literal String Interpolation (PEP-0498) and
1943 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1944 (license license:expat)))
1946 (define-public r-pastecs
1952 (uri (cran-uri "pastecs" version))
1955 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1956 (build-system r-build-system)
1958 `(("r-boot" ,r-boot)))
1959 (home-page "http://www.sciviews.org/pastecs")
1960 (synopsis "Analysis of space-time ecological series")
1962 "This package provides functions for regulation, decomposition and analysis
1963 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1964 initiative to bring PASSTEC 2000 functionalities to R.")
1965 (license license:gpl2+)))
1967 (define-public r-partykit
1973 (uri (cran-uri "partykit" version))
1976 "18nc6vvj1cy8ly2hqixg544sbg8vbpzwsr1cdlzrqfykd0pzgkvf"))))
1977 (build-system r-build-system)
1979 `(("r-formula" ,r-formula)
1981 ("r-libcoin" ,r-libcoin)
1982 ("r-mvtnorm" ,r-mvtnorm)
1983 ("r-rpart" ,r-rpart)
1984 ("r-survival" ,r-survival)))
1985 (home-page "http://partykit.R-Forge.R-project.org/partykit")
1986 (synopsis "Toolkit for recursive partytioning")
1988 "This package provides a toolkit with infrastructure for representing,
1989 summarizing, and visualizing tree-structured regression and classification
1991 (license license:gpl2+)))
1993 (define-public r-plogr
2000 (uri (cran-uri "plogr" version))
2003 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2004 (build-system r-build-system)
2005 (home-page "https://github.com/krlmlr/plogr")
2006 (synopsis "R bindings for the plog C++ logging library")
2008 "This package provides the header files for a stripped-down version of
2009 the plog header-only C++ logging library, and a method to log to R's standard
2011 (license license:expat)))
2013 (define-public r-pls
2020 (uri (cran-uri "pls" version))
2022 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2023 (build-system r-build-system)
2024 (home-page "https://mevik.net/work/software/pls.html")
2025 (synopsis "Partial Least Squares and Principal Component Regression")
2027 "The pls package implements multivariate regression methods: Partial Least
2028 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2029 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2032 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2033 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2034 @item multi-response models (or @dfn{PLS2})
2035 @item flexible cross-validation
2036 @item Jackknife variance estimates of regression coefficients
2037 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2038 (R)MSEP, R², and correlation loadings
2039 @item formula interface, modelled after @code{lm()}, with methods for predict,
2040 print, summary, plot, update, etc.
2041 @item extraction functions for coefficients, scores, and loadings
2042 @item MSEP, RMSEP, and R² estimates
2043 @item multiplicative scatter correction (@dfn{MSC})
2045 (license license:gpl2)))
2054 (uri (cran-uri "ps" version))
2056 (base32 "1cxfhnff22fbsr9vynhql0rhhrqfxvkb6kv11h2m740r9scwcs44"))))
2057 (build-system r-build-system)
2058 (home-page "https://ps.r-lib.org")
2059 (synopsis "List, query, and manipulate system processes")
2061 "The ps package implements an API to list, query, and manipulate system
2062 processes. Most of its code is based on the @code{psutil} Python package.")
2063 (license license:bsd-3)))
2065 (define-public r-pkgbuild
2072 (uri (cran-uri "pkgbuild" version))
2074 (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk"))))
2075 (build-system r-build-system)
2077 `(("r-callr" ,r-callr)
2079 ("r-crayon" ,r-crayon)
2081 ("r-prettyunits" ,r-prettyunits)
2083 ("r-rprojroot" ,r-rprojroot)
2084 ("r-withr" ,r-withr)))
2085 (home-page "https://github.com/r-pkgs/pkgbuild")
2086 (synopsis "Find tools needed to build R packages")
2088 "This package provides functions used to build R packages. It locates
2089 compilers needed to build R packages on various platforms and ensures the PATH
2090 is configured appropriately so R can use them.")
2091 (license license:gpl3)))
2093 (define-public r-pkgload
2100 (uri (cran-uri "pkgload" version))
2103 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2104 (build-system r-build-system)
2107 ("r-crayon" ,r-crayon)
2109 ("r-pkgbuild" ,r-pkgbuild)
2110 ("r-rlang" ,r-rlang)
2111 ("r-rprojroot" ,r-rprojroot)
2112 ("r-rstudioapi" ,r-rstudioapi)
2113 ("r-withr" ,r-withr)))
2114 (home-page "https://github.com/r-lib/pkgload")
2115 (synopsis "Simulate package installation and attach")
2117 "This package simulates the process of installing a package and then
2118 attaching it. This is a key part of the @code{devtools} package as it allows
2119 you to rapidly iterate while developing a package.")
2120 (license license:gpl3)))
2122 (define-public r-rcpp
2129 (uri (cran-uri "Rcpp" version))
2131 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2132 (build-system r-build-system)
2133 (home-page "http://www.rcpp.org")
2134 (synopsis "Seamless R and C++ integration")
2136 "The Rcpp package provides R functions as well as C++ classes which offer
2137 a seamless integration of R and C++. Many R data types and objects can be
2138 mapped back and forth to C++ equivalents which facilitates both writing of new
2139 code as well as easier integration of third-party libraries. Documentation
2140 about Rcpp is provided by several vignettes included in this package, via the
2141 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2142 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2143 @code{citation(\"Rcpp\")} for details on these last two.")
2144 (license license:gpl2+)))
2146 (define-public r-bindr
2153 (uri (cran-uri "bindr" version))
2156 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2157 (build-system r-build-system)
2158 (home-page "https://github.com/krlmlr/bindr")
2159 (synopsis "Parametrized active bindings")
2161 "This package provides a simple interface for creating active bindings
2162 where the bound function accepts additional arguments.")
2163 (license license:expat)))
2165 (define-public r-bindrcpp
2172 (uri (cran-uri "bindrcpp" version))
2175 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2176 (build-system r-build-system)
2178 `(("r-bindr" ,r-bindr)
2179 ("r-plogr" ,r-plogr)
2180 ("r-rcpp" ,r-rcpp)))
2181 (home-page "https://github.com/krlmlr/bindrcpp")
2182 (synopsis "Rcpp interface to active bindings")
2184 "This package provides an easy way to fill an environment with active
2185 bindings that call a C++ function.")
2186 (license license:expat)))
2188 (define-public r-bisquerna
2190 (name "r-bisquerna")
2194 (uri (cran-uri "BisqueRNA" version))
2197 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2198 (properties `((upstream-name . "BisqueRNA")))
2199 (build-system r-build-system)
2201 `(("r-biobase" ,r-biobase)
2202 ("r-limsolve" ,r-limsolve)))
2203 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2204 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2205 (description "This package provides tools to accurately estimate cell type
2206 abundances from heterogeneous bulk expression. A reference-based method
2207 utilizes single-cell information to generate a signature matrix and
2208 transformation of bulk expression for accurate regression based estimates.
2209 A marker-based method utilizes known cell-specific marker genes to measure
2210 relative abundances across samples.")
2211 (license license:gpl3)))
2213 (define-public r-auc
2220 (uri (cran-uri "AUC" version))
2223 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2224 (properties `((upstream-name . "AUC")))
2225 (build-system r-build-system)
2226 (home-page "https://cran.r-project.org/web/packages/AUC")
2227 (synopsis "Compute the area under the curve of selected measures")
2229 "This package includes functions to compute the area under the curve of
2230 selected measures: the area under the sensitivity curve (AUSEC), the area
2231 under the specificity curve (AUSPC), the area under the accuracy
2232 curve (AUACC), and the area under the receiver operating characteristic
2233 curve (AUROC). The curves can also be visualized. Support for partial areas
2235 (license license:gpl2+)))
2237 (define-public r-calibrate
2239 (name "r-calibrate")
2244 (uri (cran-uri "calibrate" version))
2246 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2247 (build-system r-build-system)
2249 `(("r-mass" ,r-mass)))
2250 (home-page "https://cran.r-project.org/web/packages/calibrate")
2251 (synopsis "Calibration of scatterplot and biplot axes")
2253 "This is a package for drawing calibrated scales with tick marks
2254 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2255 (license license:gpl2)))
2257 (define-public r-shape
2264 (uri (cran-uri "shape" version))
2267 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2268 (build-system r-build-system)
2269 (home-page "https://cran.r-project.org/web/packages/shape")
2270 (synopsis "Functions for plotting graphical shapes")
2272 "This package provides functions for plotting graphical shapes such as
2273 ellipses, circles, cylinders, arrows, ...")
2274 (license license:gpl3+)))
2276 (define-public r-globaloptions
2278 (name "r-globaloptions")
2283 (uri (cran-uri "GlobalOptions" version))
2285 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2286 (properties `((upstream-name . "GlobalOptions")))
2287 (build-system r-build-system)
2289 `(("r-knitr" ,r-knitr)))
2290 (home-page "https://github.com/jokergoo/GlobalOptions")
2291 (synopsis "Generate functions to get or set global options")
2293 "This package provides more controls on the option values such as
2294 validation and filtering on the values, making options invisible or private.")
2295 (license license:gpl2+)))
2297 (define-public r-circlize
2304 (uri (cran-uri "circlize" version))
2307 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2308 (build-system r-build-system)
2310 `(("r-colorspace" ,r-colorspace)
2311 ("r-globaloptions" ,r-globaloptions)
2312 ("r-shape" ,r-shape)))
2314 `(("r-knitr" ,r-knitr)))
2315 (home-page "https://github.com/jokergoo/circlize")
2316 (synopsis "Circular visualization")
2318 "Circular layout is an efficient way to visualise huge amounts of
2319 information. This package provides an implementation of circular layout
2320 generation in R as well as an enhancement of available software. Its
2321 flexibility is based on the usage of low-level graphics functions such that
2322 self-defined high-level graphics can be easily implemented by users for
2323 specific purposes. Together with the seamless connection between the powerful
2324 computational and visual environment in R, it gives users more convenience and
2325 freedom to design figures for better understanding complex patterns behind
2326 multi-dimensional data.")
2327 (license license:gpl2+)))
2329 (define-public r-powerlaw
2336 (uri (cran-uri "poweRlaw" version))
2338 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2339 (properties `((upstream-name . "poweRlaw")))
2340 (build-system r-build-system)
2342 `(("r-pracma" ,r-pracma)))
2344 `(("r-knitr" ,r-knitr)))
2345 (home-page "https://github.com/csgillespie/poweRlaw")
2346 (synopsis "Tools for the analysis of heavy tailed distributions")
2348 "This package provides an implementation of maximum likelihood estimators
2349 for a variety of heavy tailed distributions, including both the discrete and
2350 continuous power law distributions. Additionally, a goodness-of-fit based
2351 approach is used to estimate the lower cut-off for the scaling region.")
2352 ;; Any of these GPL versions.
2353 (license (list license:gpl2 license:gpl3))))
2355 (define-public r-compare
2362 (uri (cran-uri "compare" version))
2365 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2366 (build-system r-build-system)
2367 (home-page "https://cran.r-project.org/web/packages/compare")
2368 (synopsis "Comparing objects for differences")
2370 "This package provides functions to compare a model object to a
2371 comparison object. If the objects are not identical, the functions can be
2372 instructed to explore various modifications of the objects (e.g., sorting
2373 rows, dropping names) to see if the modified versions are identical.")
2374 (license license:gpl2+)))
2376 (define-public r-dendextend
2378 (name "r-dendextend")
2383 (uri (cran-uri "dendextend" version))
2386 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2387 (build-system r-build-system)
2389 `(("r-ggplot2" ,r-ggplot2)
2390 ("r-magrittr" ,r-magrittr)
2391 ("r-viridis" ,r-viridis)))
2393 `(("r-knitr" ,r-knitr)))
2394 (home-page "https://cran.r-project.org/web/packages/dendextend")
2395 (synopsis "Extending 'dendrogram' functionality in R")
2397 "This package offers a set of functions for extending @code{dendrogram}
2398 objects in R, letting you visualize and compare trees of hierarchical
2399 clusterings. You can adjust a tree's graphical parameters (the color, size,
2400 type, etc of its branches, nodes and labels) and visually and statistically
2401 compare different dendrograms to one another.")
2402 ;; Any of these versions
2403 (license (list license:gpl2 license:gpl3))))
2405 (define-public r-getoptlong
2407 (name "r-getoptlong")
2412 (uri (cran-uri "GetoptLong" version))
2415 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2416 (properties `((upstream-name . "GetoptLong")))
2417 (build-system r-build-system)
2421 `(("r-crayon" ,r-crayon)
2422 ("r-globaloptions" ,r-globaloptions)
2423 ("r-rjson" ,r-rjson)))
2425 `(("r-knitr" ,r-knitr)))
2426 (home-page "https://github.com/jokergoo/GetoptLong")
2427 (synopsis "Parsing command-line arguments and variable interpolation")
2429 "This is yet another command-line argument parser which wraps the
2430 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2431 use in R. It also provides a simple way for variable interpolation in R.")
2432 (license license:gpl2+)))
2434 (define-public r-fastmatch
2436 (name "r-fastmatch")
2441 (uri (cran-uri "fastmatch" version))
2444 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2445 (build-system r-build-system)
2446 (home-page "https://www.rforge.net/fastmatch")
2447 (synopsis "Fast match function")
2449 "This package provides a fast @code{match} replacement for cases that
2450 require repeated look-ups. It is slightly faster that R's built-in
2451 @code{match} function on first match against a table, but extremely fast on
2452 any subsequent lookup as it keeps the hash table in memory.")
2453 (license license:gpl2)))
2462 (uri (cran-uri "ff" version))
2465 "1qbfmhk4v76q145yalqaiaffklvkfs615b5m0imxyjyjcvx1nbn0"))))
2466 (build-system r-build-system)
2467 (propagated-inputs `(("r-bit" ,r-bit)))
2468 (home-page "http://ff.r-forge.r-project.org/")
2469 (synopsis "Memory-efficient storage of large data on disk and access functions")
2471 "This package provides data structures that are stored on disk but
2472 behave (almost) as if they were in RAM by transparently mapping only a section
2474 ;; error Architecture not supported.
2475 (supported-systems (delete "aarch64-linux" %supported-systems))
2476 (license license:gpl2)))
2478 (define-public r-ffbase
2485 (uri (cran-uri "ffbase" version))
2488 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2489 (build-system r-build-system)
2492 ("r-fastmatch" ,r-fastmatch)
2494 (home-page "https://github.com/edwindj/ffbase")
2495 (synopsis "Basic statistical functions for package 'ff'")
2497 "This package extends the out of memory vectors of @code{ff} with
2498 statistical functions and other utilities to ease their usage.")
2499 (license license:gpl3)))
2501 (define-public r-prettyunits
2503 (name "r-prettyunits")
2508 (uri (cran-uri "prettyunits" version))
2511 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2512 (build-system r-build-system)
2513 (home-page "https://github.com/gaborcsardi/prettyunits")
2514 (synopsis "Pretty, human readable formatting of quantities")
2516 "This package provides tools for pretty, human readable formatting of
2518 (license license:expat)))
2520 (define-public r-reshape
2527 (uri (cran-uri "reshape" version))
2530 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2531 (build-system r-build-system)
2533 `(("r-plyr" ,r-plyr)
2534 ("r-rcpp" ,r-rcpp)))
2535 (home-page "http://had.co.nz/reshape")
2536 (synopsis "Flexibly reshape data")
2538 "Flexibly restructure and aggregate data using just two functions:
2539 @code{melt} and @code{cast}. This package provides them.")
2540 (license license:expat)))
2542 (define-public r-progress
2549 (uri (cran-uri "progress" version))
2552 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2553 (build-system r-build-system)
2555 `(("r-crayon" ,r-crayon)
2557 ("r-prettyunits" ,r-prettyunits)
2559 (home-page "https://github.com/gaborcsardi/progress")
2560 (synopsis "Terminal progress bars")
2562 "This package provides configurable progress bars. They may include
2563 percentage, elapsed time, and/or the estimated completion time. They work in
2564 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2565 package also provides a C++ API, that works with or without Rcpp.")
2566 (license license:expat)))
2568 (define-public r-ggally
2575 (uri (cran-uri "GGally" version))
2578 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2579 (properties `((upstream-name . "GGally")))
2580 (build-system r-build-system)
2582 `(("libressl" ,libressl)))
2584 `(("r-ggplot2" ,r-ggplot2)
2585 ("r-gtable" ,r-gtable)
2586 ("r-lifecycle" ,r-lifecycle)
2588 ("r-progress" ,r-progress)
2589 ("r-rcolorbrewer" ,r-rcolorbrewer)
2590 ("r-reshape" ,r-reshape)
2591 ("r-rlang" ,r-rlang)
2592 ("r-scales" ,r-scales)))
2593 (home-page "https://ggobi.github.io/ggally")
2594 (synopsis "Extension to ggplot2")
2596 "The R package ggplot2 is a plotting system based on the grammar of
2597 graphics. GGally extends ggplot2 by adding several functions to reduce the
2598 complexity of combining geometric objects with transformed data. Some of
2599 these functions include a pairwise plot matrix, a two group pairwise plot
2600 matrix, a parallel coordinates plot, a survival plot, and several functions to
2602 (license license:gpl2+)))
2604 (define-public r-proxy
2611 (uri (cran-uri "proxy" version))
2614 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2615 (build-system r-build-system)
2616 (home-page "https://cran.r-project.org/web/packages/proxy")
2617 (synopsis "Distance and similarity measures")
2619 "This package provides an extensible framework for the efficient
2620 calculation of auto- and cross-proximities, along with implementations of the
2621 most popular ones.")
2622 (license license:gpl2)))
2631 (uri (cran-uri "sp" version))
2633 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2634 (build-system r-build-system)
2636 `(("r-lattice" ,r-lattice)))
2637 (home-page "https://cran.r-project.org/web/packages/sp")
2638 (synopsis "Classes and methods for spatial data")
2640 "This package provides classes and methods for spatial data; the classes
2641 document where the spatial location information resides, for 2D or 3D data.
2642 Utility functions are provided, e.g. for plotting data as maps, spatial
2643 selection, as well as methods for retrieving coordinates, for subsetting,
2644 print, summary, etc.")
2645 (license license:gpl2+)))
2647 (define-public r-laplacesdemon
2649 (name "r-laplacesdemon")
2654 (uri (cran-uri "LaplacesDemon" version))
2656 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
2657 (properties `((upstream-name . "LaplacesDemon")))
2658 (build-system r-build-system)
2659 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
2660 (synopsis "Complete environment for Bayesian inference")
2662 "This package provides a complete environment for Bayesian inference using
2663 a variety of different samplers.")
2664 (license license:expat)))
2666 (define-public r-rmtstat
2673 (uri (cran-uri "RMTstat" version))
2676 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2677 (properties `((upstream-name . "RMTstat")))
2678 (build-system r-build-system)
2679 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2680 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2682 "This package provides functions for working with the Tracy-Widom laws
2683 and other distributions related to the eigenvalues of large Wishart
2685 (license license:bsd-3)))
2687 (define-public r-rmpi
2693 (uri (cran-uri "Rmpi" version))
2696 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2697 (properties `((upstream-name . "Rmpi")))
2698 (build-system r-build-system)
2700 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2701 #:phases (modify-phases %standard-phases
2702 (add-before 'install 'mpi-setup
2705 `(("openmpi" ,openmpi)))
2707 `(("pkg-config" ,pkg-config)))
2708 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2709 (synopsis "R interface to message-passing interface (MPI)")
2711 "This package provides an interface (wrapper) to MPI APIs. It also
2712 provides an interactive R manager and worker environment.")
2713 (license license:gpl2+)))
2715 (define-public r-lmoments
2722 (uri (cran-uri "Lmoments" version))
2725 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2726 (properties `((upstream-name . "Lmoments")))
2727 (build-system r-build-system)
2729 `(("r-rcpp" ,r-rcpp)
2730 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2731 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2732 (synopsis "L-moments and quantile mixtures")
2734 "This package contains functions to estimate L-moments and trimmed
2735 L-moments from the data. It also contains functions to estimate the
2736 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2737 quantile mixture from L-moments and trimmed L-moments.")
2738 (license license:gpl2)))
2740 (define-public r-distillery
2742 (name "r-distillery")
2747 (uri (cran-uri "distillery" version))
2750 "15qhvhg6wmvlxrvvw70sk8pv76z5pd04vyasgczvxa0599ih7bzh"))))
2751 (build-system r-build-system)
2752 (home-page "https://ral.ucar.edu/staff/ericg/")
2753 (synopsis "Functions for confidence intervals and object information")
2755 "This package provides some very simple method functions for confidence
2756 interval calculation and to distill pertinent information from a potentially
2757 complex object; primarily used in common with the packages extRemes and
2759 (license license:gpl2+)))
2761 (define-public r-extremes
2768 (uri (cran-uri "extRemes" version))
2771 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2772 (properties `((upstream-name . "extRemes")))
2773 (build-system r-build-system)
2775 `(("r-distillery" ,r-distillery)
2776 ("r-lmoments" ,r-lmoments)))
2777 (home-page "https://www.assessment.ucar.edu/toolkit/")
2778 (synopsis "Extreme value analysis")
2780 "ExtRemes is a suite of functions for carrying out analyses on the
2781 extreme values of a process of interest; be they block maxima over long blocks
2782 or excesses over a high threshold.")
2783 (license license:gpl2+)))
2785 (define-public r-lmtest
2792 (uri (cran-uri "lmtest" version))
2795 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2796 (build-system r-build-system)
2798 `(("r-zoo" ,r-zoo)))
2800 `(("gfortran" ,gfortran)))
2801 (home-page "https://cran.r-project.org/web/packages/lmtest")
2802 (synopsis "Testing linear regression models")
2804 "This package provides a collection of tests, data sets, and examples for
2805 diagnostic checking in linear regression models. Furthermore, some generic
2806 tools for inference in parametric models are provided.")
2807 ;; Either version is okay
2808 (license (list license:gpl2 license:gpl3))))
2810 (define-public r-idr
2816 (uri (cran-uri "idr" version))
2819 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2820 (build-system r-build-system)
2821 (home-page "https://cran.r-project.org/web/packages/idr/")
2822 (synopsis "Irreproducible discovery rate")
2824 "This is a package for estimating the copula mixture model and plotting
2825 correspondence curves in \"Measuring reproducibility of high-throughput
2826 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2827 by Li, Brown, Huang, and Bickel")
2828 (license license:gpl2+)))
2830 (define-public r-inline
2836 (uri (cran-uri "inline" version))
2839 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2840 (build-system r-build-system)
2841 (home-page "https://cran.r-project.org/web/packages/inline")
2842 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2844 "This package provides functionality to dynamically define R functions
2845 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2846 @code{.Call} calling conventions.")
2847 ;; Any version of the LGPL.
2848 (license license:lgpl3+)))
2850 (define-public r-inum
2856 (uri (cran-uri "inum" version))
2859 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2860 (build-system r-build-system)
2862 `(("r-libcoin" ,r-libcoin)))
2863 (home-page "https://cran.r-project.org/web/packages/inum/")
2864 (synopsis "Interval and enum-type representation of vectors")
2866 "This package provides an enum-type representation of vectors and
2867 representation of intervals, including a method of coercing variables
2869 (license license:gpl2)))
2871 (define-public r-bdsmatrix
2873 (name "r-bdsmatrix")
2878 (uri (cran-uri "bdsmatrix" version))
2881 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2882 (properties `((upstream-name . "bdsmatrix")))
2883 (build-system r-build-system)
2884 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2885 (synopsis "Routines for block diagonal symmetric matrices")
2887 "This package provides procedures to work with block diagonal symmetric
2888 matrices, a special case of sparse matrices.")
2889 (license license:lgpl2.0)))
2891 (define-public r-bbmle
2894 (version "1.0.23.1")
2898 (uri (cran-uri "bbmle" version))
2901 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2902 (build-system r-build-system)
2904 `(("r-bdsmatrix" ,r-bdsmatrix)
2905 ("r-lattice" ,r-lattice)
2907 ("r-matrix" ,r-matrix)
2908 ("r-mvtnorm" ,r-mvtnorm)
2909 ("r-numderiv" ,r-numderiv)))
2910 (home-page "https://cran.r-project.org/web/packages/bbmle")
2911 (synopsis "Tools for General Maximum Likelihood Estimation")
2913 "This package provides methods and functions for fitting maximum
2914 likelihood models in R. This package modifies and extends the @code{mle}
2915 classes in the @code{stats4} package.")
2916 ;; Any version of the GPL
2917 (license license:gpl2+)))
2919 (define-public r-emdbook
2926 (uri (cran-uri "emdbook" version))
2929 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2930 (build-system r-build-system)
2932 `(("r-bbmle" ,r-bbmle)
2934 ("r-lattice" ,r-lattice)
2936 ("r-plyr" ,r-plyr)))
2937 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2938 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2940 "This package provides auxiliary functions and data sets for \"Ecological
2941 Models and Data\", a book presenting maximum likelihood estimation and related
2942 topics for ecologists (ISBN 978-0-691-12522-0).")
2944 (license (list license:gpl2 license:gpl3))))
2946 (define-public r-lpsolve
2953 (uri (cran-uri "lpSolve" version))
2956 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2957 (properties `((upstream-name . "lpSolve")))
2958 (build-system r-build-system)
2959 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2960 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2962 "Lp_solve is software for solving linear, integer and mixed integer
2963 programs. This implementation supplies a \"wrapper\" function in C and some R
2964 functions that solve general linear/integer problems, assignment problems, and
2965 transportation problems.")
2966 (license license:lgpl2.0)))
2968 (define-public r-limsolve
2975 (uri (cran-uri "limSolve" version))
2978 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2979 (properties `((upstream-name . "limSolve")))
2980 (build-system r-build-system)
2982 `(("r-lpsolve" ,r-lpsolve)
2984 ("r-quadprog" ,r-quadprog)))
2985 (native-inputs `(("gfortran" ,gfortran)))
2986 (home-page "https://cran.r-project.org/web/packages/limSolve")
2987 (synopsis "Solving linear inverse models")
2989 "This package provides functions that:
2992 @item find the minimum/maximum of a linear or quadratic function,
2993 @item sample an underdetermined or overdetermined system,
2994 @item solve a linear system Ax=B for the unknown x.
2997 It includes banded and tridiagonal linear systems. The package calls Fortran
2998 functions from LINPACK.")
3000 (license (list license:gpl2+ license:gpl3+))))
3002 (define-public r-fitdistrplus
3004 (name "r-fitdistrplus")
3009 (uri (cran-uri "fitdistrplus" version))
3012 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
3013 (build-system r-build-system)
3015 `(("r-mass" ,r-mass)
3016 ("r-survival" ,r-survival)))
3018 `(("r-knitr" ,r-knitr)))
3019 (home-page "http://riskassessment.r-forge.r-project.org")
3020 (synopsis "Fitting a parametric distribution from data")
3022 "This package extends the @code{fitdistr} function of the MASS package
3023 with several functions to help the fit of a parametric distribution to
3024 non-censored or censored data. Censored data may contain left-censored,
3025 right-censored and interval-censored values, with several lower and upper
3026 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3027 provides moment matching (MME), quantile matching (QME) and maximum
3028 goodness-of-fit estimation (MGE) methods (available only for non-censored
3029 data). Weighted versions of MLE, MME and QME are available.")
3030 (license license:gpl2+)))
3032 (define-public r-energy
3039 (uri (cran-uri "energy" version))
3042 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3043 (build-system r-build-system)
3045 `(("r-boot" ,r-boot)
3046 ("r-rcpp" ,r-rcpp)))
3047 (home-page "https://cran.r-project.org/web/packages/energy")
3048 (synopsis "Multivariate inference via the energy of data")
3050 "This package provides e-statistics (energy) tests and statistics for
3051 multivariate and univariate inference, including distance correlation,
3052 one-sample, two-sample, and multi-sample tests for comparing multivariate
3053 distributions, are implemented. Measuring and testing multivariate
3054 independence based on distance correlation, partial distance correlation,
3055 multivariate goodness-of-fit tests, clustering based on energy distance,
3056 testing for multivariate normality, distance components (disco) for
3057 non-parametric analysis of structured data, and other energy
3058 statistics/methods are implemented.")
3059 (license license:gpl2+)))
3061 (define-public r-suppdists
3063 (name "r-suppdists")
3068 (uri (cran-uri "SuppDists" version))
3071 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3072 (properties `((upstream-name . "SuppDists")))
3073 (build-system r-build-system)
3074 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3075 (synopsis "Supplementary distributions")
3077 "This package provides ten distributions supplementing those built into
3078 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3079 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3080 coefficient, Johnson distributions, normal scores and generalized
3081 hypergeometric distributions. In addition two random number generators of
3082 George Marsaglia are included.")
3083 (license license:gpl2+)))
3085 (define-public r-ksamples
3092 (uri (cran-uri "kSamples" version))
3095 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3096 (properties `((upstream-name . "kSamples")))
3097 (build-system r-build-system)
3099 `(("r-suppdists" ,r-suppdists)))
3100 (home-page "https://cran.r-project.org/web/packages/kSamples")
3101 (synopsis "K-Sample rank tests and their combinations")
3103 "This package provides tools to compares k samples using the
3104 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3105 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3106 test. It computes asymptotic, simulated or (limited) exact P-values, all
3107 valid under randomization, with or without ties, or conditionally under random
3108 sampling from populations, given the observed tie pattern. Except for Steel's
3109 test and the JT test it also combines these tests across several blocks of
3111 (license license:gpl2+)))
3113 (define-public r-cvst
3120 (uri (cran-uri "CVST" version))
3123 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3124 (properties `((upstream-name . "CVST")))
3125 (build-system r-build-system)
3127 `(("r-kernlab" ,r-kernlab)
3128 ("r-matrix" ,r-matrix)))
3129 (home-page "https://cran.r-project.org/web/packages/CVST")
3130 (synopsis "Fast cross-validation via sequential testing")
3132 "This package implements the fast cross-validation via sequential
3133 testing (CVST) procedure. CVST is an improved cross-validation procedure
3134 which uses non-parametric testing coupled with sequential analysis to
3135 determine the best parameter set on linearly increasing subsets of the data.
3136 Additionally to the CVST the package contains an implementation of the
3137 ordinary k-fold cross-validation with a flexible and powerful set of helper
3138 objects and methods to handle the overall model selection process. The
3139 implementations of the Cochran's Q test with permutations and the sequential
3140 testing framework of Wald are generic and can therefore also be used in other
3142 (license license:gpl2+)))
3144 (define-public r-squarem
3151 (uri (cran-uri "SQUAREM" version))
3154 "1r2yxfiqbpwy5ccg94r7f6sz7lh5aq0xjpf632s42wgmml1dvlzb"))))
3155 (properties `((upstream-name . "SQUAREM")))
3156 (build-system r-build-system)
3157 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3158 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3160 "This package provides algorithms for accelerating the convergence of
3161 slow, monotone sequences from smooth, contraction mapping such as the EM
3162 algorithm. It can be used to accelerate any smooth, linearly convergent
3163 acceleration scheme. A tutorial style introduction to this package is
3164 available in a vignette.")
3165 (license license:gpl2+)))
3167 (define-public r-lava
3174 (uri (cran-uri "lava" version))
3177 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3178 (build-system r-build-system)
3180 `(("r-numderiv" ,r-numderiv)
3181 ("r-squarem" ,r-squarem)
3182 ("r-survival" ,r-survival)))
3183 (home-page "https://github.com/kkholst/lava")
3184 (synopsis "Latent variable models")
3186 "This package provides tools for the estimation and simulation of latent
3188 (license license:gpl3)))
3190 (define-public r-drr
3197 (uri (cran-uri "DRR" version))
3200 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3201 (properties `((upstream-name . "DRR")))
3202 (build-system r-build-system)
3204 `(("r-cvst" ,r-cvst)
3205 ("r-kernlab" ,r-kernlab)
3206 ("r-matrix" ,r-matrix)))
3207 (home-page "https://cran.r-project.org/web/packages/DRR")
3208 (synopsis "Dimensionality reduction via regression")
3210 "This package provides an implementation of dimensionality reduction via
3211 regression using Kernel Ridge Regression.")
3212 (license license:gpl3)))
3214 (define-public r-prodlim
3217 (version "2019.11.13")
3221 (uri (cran-uri "prodlim" version))
3224 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3225 (build-system r-build-system)
3227 `(("r-kernsmooth" ,r-kernsmooth)
3230 ("r-survival" ,r-survival)))
3231 (home-page "https://cran.r-project.org/web/packages/prodlim")
3232 (synopsis "Product-limit estimation for censored event history analysis")
3234 "This package provides a fast and user-friendly implementation of
3235 nonparametric estimators for censored event history (survival) analysis with
3236 the Kaplan-Meier and Aalen-Johansen methods.")
3237 (license license:gpl2+)))
3239 (define-public r-dimred
3246 (uri (cran-uri "dimRed" version))
3249 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3250 (properties `((upstream-name . "dimRed")))
3251 (build-system r-build-system)
3254 ("r-magrittr" ,r-magrittr)))
3255 (home-page "https://github.com/gdkrmr/dimRed")
3256 (synopsis "Framework for dimensionality reduction")
3258 "This package provides a collection of dimensionality reduction
3259 techniques from R packages and provides a common interface for calling the
3261 (license license:gpl3)))
3263 (define-public r-timedate
3266 (version "3043.102")
3270 (uri (cran-uri "timeDate" version))
3273 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3274 (properties `((upstream-name . "timeDate")))
3275 (build-system r-build-system)
3276 (home-page "https://www.rmetrics.org")
3277 (synopsis "Chronological and calendar objects")
3279 "This package provides an environment for teaching \"Financial
3280 Engineering and Computational Finance\" and for managing chronological and
3282 (license license:gpl2+)))
3284 (define-public r-magic
3291 (uri (cran-uri "magic" version))
3294 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3295 (build-system r-build-system)
3297 `(("r-abind" ,r-abind)))
3298 (home-page "https://github.com/RobinHankin/magic.git")
3299 (synopsis "Create and investigate magic squares")
3301 "This package provides a collection of efficient, vectorized algorithms
3302 for the creation and investigation of magic squares and hypercubes, including
3303 a variety of functions for the manipulation and analysis of arbitrarily
3304 dimensioned arrays.")
3305 (license license:gpl2)))
3307 (define-public r-rmysql
3314 (uri (cran-uri "RMySQL" version))
3317 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3318 (properties `((upstream-name . "RMySQL")))
3319 (build-system r-build-system)
3321 `(("mariadb" ,mariadb "lib")
3322 ("mariadb-dev" ,mariadb "dev")
3325 `(("r-dbi" ,r-dbi)))
3326 (home-page "https://github.com/r-dbi/RMySQL")
3327 (synopsis "Database interface and MySQL driver for R")
3329 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3330 package contains an old implementation based on legacy code from S-PLUS which
3331 is being phased out. A modern MySQL client based on Rcpp is available from
3332 the RMariaDB package.")
3333 (license license:gpl2)))
3335 (define-public r-rpostgresql
3337 (name "r-rpostgresql")
3342 (uri (cran-uri "RPostgreSQL" version))
3345 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3346 (properties `((upstream-name . "RPostgreSQL")))
3347 (build-system r-build-system)
3349 `(("postgresql" ,postgresql)))
3351 `(("r-dbi" ,r-dbi)))
3352 (home-page "https://github.com/tomoakin/RPostgreSQL")
3353 (synopsis "R interface to the PostgreSQL database system")
3355 "This package provides a Database Interface (DBI) compliant driver for R
3356 to access PostgreSQL database systems.")
3357 ;; The whole package is released under GPL version 2. It includes code
3358 ;; under the PostgreSQL license.
3359 (license license:gpl2)))
3361 (define-public r-linprog
3368 (uri (cran-uri "linprog" version))
3371 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3372 (build-system r-build-system)
3373 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3374 (home-page "http://linprog.r-forge.r-project.org/")
3375 (synopsis "Linear programming and optimization")
3377 "This package can be used to solve Linear Programming / Linear
3378 Optimization problems by using the simplex algorithm.")
3379 (license license:gpl2+)))
3381 (define-public r-geometry
3388 (uri (cran-uri "geometry" version))
3391 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3392 (build-system r-build-system)
3394 `(("r-magic" ,r-magic)
3395 ("r-linprog" ,r-linprog)
3396 ("r-lpsolve" ,r-lpsolve)
3398 ("r-rcppprogress" ,r-rcppprogress)))
3399 (home-page "http://geometry.r-forge.r-project.org/")
3400 (synopsis "Mesh generation and surface tesselation")
3402 "This package makes the qhull library available in R, in a similar manner
3403 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3404 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3405 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3406 and higher dimensions. It implements the Quickhull algorithm for computing
3407 the convex hull. Qhull does not support constrained Delaunay triangulations,
3408 or mesh generation of non-convex objects, but the package does include some R
3409 functions that allow for this. Currently the package only gives access to
3410 Delaunay triangulation and convex hull computation.")
3411 ;; The Qhull sources are included and are distributed under a custom
3412 ;; non-copyleft license. The R sources are released under GPL version 2.
3413 (license (list license:gpl2
3414 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3416 (define-public r-ddalpha
3423 (uri (cran-uri "ddalpha" version))
3426 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3427 (build-system r-build-system)
3430 ("r-class" ,r-class)
3431 ("r-geometry" ,r-geometry)
3434 ("r-robustbase" ,r-robustbase)
3435 ("r-sfsmisc" ,r-sfsmisc)))
3437 `(("gfortran" ,gfortran)))
3438 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3439 (synopsis "Depth-Based classification and calculation of data depth")
3441 "This package contains procedures for depth-based supervised learning,
3442 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3443 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3444 statistical depth function to a compact low-dimensional space, where the final
3445 classification is done. It also offers an extension to functional data and
3446 routines for calculating certain notions of statistical depth functions. 50
3447 multivariate and 5 functional classification problems are included.")
3448 (license license:gpl2)))
3450 (define-public r-gower
3457 (uri (cran-uri "gower" version))
3460 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3461 (build-system r-build-system)
3462 (home-page "https://github.com/markvanderloo/gower")
3463 (synopsis "Gower's distance")
3465 "This package provides tools to compute Gower's distance (or similarity)
3466 coefficient between records, and to compute the top-n matches between records.
3467 Core algorithms are executed in parallel on systems supporting OpenMP.")
3468 (license license:gpl3)))
3470 (define-public r-rcpproll
3477 (uri (cran-uri "RcppRoll" version))
3480 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3481 (properties `((upstream-name . "RcppRoll")))
3482 (build-system r-build-system)
3484 `(("r-rcpp" ,r-rcpp)))
3485 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3486 (synopsis "Efficient rolling and windowed operations")
3488 "This package provides fast and efficient routines for common rolling /
3489 windowed operations. Routines for the efficient computation of windowed mean,
3490 median, sum, product, minimum, maximum, standard deviation and variance are
3492 (license license:gpl2+)))
3494 (define-public r-ipred
3501 (uri (cran-uri "ipred" version))
3504 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3505 (build-system r-build-system)
3507 `(("r-class" ,r-class)
3510 ("r-prodlim" ,r-prodlim)
3511 ("r-rpart" ,r-rpart)
3512 ("r-survival" ,r-survival)))
3513 (home-page "https://cran.r-project.org/web/packages/ipred")
3514 (synopsis "Improved predictors")
3516 "This package provides improved predictive models by indirect
3517 classification and bagging for classification, regression and survival
3518 problems as well as resampling based estimators of prediction error.")
3519 (license license:gpl2+)))
3521 (define-public r-psych
3528 (uri (cran-uri "psych" version))
3531 "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
3532 (build-system r-build-system)
3534 `(("r-lattice" ,r-lattice)
3535 ("r-mnormt" ,r-mnormt)
3536 ("r-nlme" ,r-nlme)))
3537 (home-page "https://cran.r-project.org/web/packages/psych/")
3538 (synopsis "Procedures for psychological, psychometric, and personality research")
3540 "This package provides a general purpose toolbox for personality,
3541 psychometric theory and experimental psychology. Functions are primarily for
3542 multivariate analysis and scale construction using factor analysis, principal
3543 component analysis, cluster analysis and reliability analysis, although others
3544 provide basic descriptive statistics. Item Response Theory is done using
3545 factor analysis of tetrachoric and polychoric correlations. Functions for
3546 analyzing data at multiple levels include within and between group statistics,
3547 including correlations and factor analysis. Functions for simulating and
3548 testing particular item and test structures are included. Several functions
3549 serve as a useful front end for structural equation modeling. Graphical
3550 displays of path diagrams, factor analysis and structural equation models are
3551 created using basic graphics.")
3552 (license license:gpl2+)))
3554 (define-public r-generics
3561 (uri (cran-uri "generics" version))
3564 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3565 (build-system r-build-system)
3566 (home-page "https://github.com/r-lib/generics")
3567 (synopsis "Common S3 generics not provided by base R methods")
3569 "In order to reduce potential package dependencies and conflicts,
3570 generics provides a number of commonly used S3 generics that are not provided
3571 by base R methods related to model fitting.")
3572 (license license:gpl2)))
3574 (define-public r-broom
3581 (uri (cran-uri "broom" version))
3584 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3585 (build-system r-build-system)
3587 `(("r-backports" ,r-backports)
3588 ("r-dplyr" ,r-dplyr)
3589 ("r-ellipsis" ,r-ellipsis)
3590 ("r-generics" ,r-generics)
3592 ("r-purrr" ,r-purrr)
3593 ("r-rlang" ,r-rlang)
3594 ("r-stringr" ,r-stringr)
3595 ("r-tibble" ,r-tibble)
3596 ("r-tidyr" ,r-tidyr)))
3598 `(("r-knitr" ,r-knitr)))
3599 (home-page "https://github.com/tidyverse/broom")
3600 (synopsis "Convert statistical analysis objects into tidy data frames")
3602 "This package provides tools to convert statistical analysis objects from
3603 R into tidy data frames, so that they can more easily be combined, reshaped
3604 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3605 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3606 summarizes a model's statistical findings such as coefficients of a
3607 regression; @code{augment}, which adds columns to the original data such as
3608 predictions, residuals and cluster assignments; and @code{glance}, which
3609 provides a one-row summary of model-level statistics.")
3610 (license license:expat)))
3612 (define-public r-recipes
3619 (uri (cran-uri "recipes" version))
3622 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3623 (build-system r-build-system)
3625 `(("r-dplyr" ,r-dplyr)
3626 ("r-generics" ,r-generics)
3628 ("r-gower" ,r-gower)
3629 ("r-ipred" ,r-ipred)
3630 ("r-lifecycle" ,r-lifecycle)
3631 ("r-lubridate" ,r-lubridate)
3632 ("r-magrittr" ,r-magrittr)
3633 ("r-matrix" ,r-matrix)
3634 ("r-purrr" ,r-purrr)
3635 ("r-rlang" ,r-rlang)
3636 ("r-tibble" ,r-tibble)
3637 ("r-tidyr" ,r-tidyr)
3638 ("r-tidyselect" ,r-tidyselect)
3639 ("r-timedate" ,r-timedate)
3640 ("r-withr" ,r-withr)))
3642 `(("r-knitr" ,r-knitr)))
3643 (home-page "https://github.com/topepo/recipes")
3644 (synopsis "Preprocessing tools to create design matrices")
3646 "Recipes is an extensible framework to create and preprocess design
3647 matrices. Recipes consist of one or more data manipulation and analysis
3648 \"steps\". Statistical parameters for the steps can be estimated from an
3649 initial data set and then applied to other data sets. The resulting design
3650 matrices can then be used as inputs into statistical or machine learning
3652 (license license:gpl2)))
3654 (define-public r-pdist
3661 (uri (cran-uri "pdist" version))
3664 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3665 (build-system r-build-system)
3666 (home-page "https://github.com/jeffwong/pdist")
3667 (synopsis "Partitioned distance function")
3669 "Pdist computes the euclidean distance between rows of a matrix X and
3670 rows of another matrix Y. Previously, this could be done by binding the two
3671 matrices together and calling @code{dist}, but this creates unnecessary
3672 computation by computing the distances between a row of X and another row of
3673 X, and likewise for Y. Pdist strictly computes distances across the two
3674 matrices, not within the same matrix, making computations significantly faster
3675 for certain use cases.")
3676 (license license:gpl3+)))
3678 (define-public r-ggrepel
3685 (uri (cran-uri "ggrepel" version))
3688 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3689 (build-system r-build-system)
3691 `(("r-ggplot2" ,r-ggplot2)
3693 ("r-scales" ,r-scales)))
3695 `(("r-knitr" ,r-knitr))) ; for vignettes
3696 (home-page "https://github.com/slowkow/ggrepel")
3697 (synopsis "Repulsive text and label geometries for ggplot2")
3699 "This package provides text and label geometries for ggplot2 that help to
3700 avoid overlapping text labels. Labels repel away from each other and away
3701 from the data points.")
3702 (license license:gpl3)))
3704 (define-public r-corrplot
3711 (uri (cran-uri "corrplot" version))
3714 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3715 (build-system r-build-system)
3716 (home-page "https://github.com/taiyun/corrplot")
3717 (synopsis "Visualization of a correlation matrix")
3719 "This package provides a graphical display of a correlation matrix or
3720 general matrix. It also contains some algorithms to do matrix reordering. In
3721 addition, corrplot is good at details, including choosing color, text labels,
3722 color labels, layout, etc.")
3723 ;; Any version of the GPL
3724 (license license:gpl2+)))
3726 (define-public r-stringdist
3728 (name "r-stringdist")
3733 (uri (cran-uri "stringdist" version))
3735 (base32 "0nb3iwpl4f3xxirns1frwvarpyrl4i5f74h8r6h80cg0a4mpdgcb"))))
3736 (build-system r-build-system)
3737 (home-page "https://github.com/markvanderloo/stringdist")
3738 (synopsis "Approximate string matching and string distance functions")
3740 "This package implements an approximate string matching version of R's
3741 native @code{match} function. It can calculate various string distances based
3742 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3743 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3744 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3745 can be computed between character vectors while taking proper care of encoding
3746 or between integer vectors representing generic sequences.")
3747 (license license:gpl3+)))
3749 (define-public r-ucminf
3756 (uri (cran-uri "ucminf" version))
3759 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3760 (build-system r-build-system)
3761 (native-inputs `(("gfortran" ,gfortran)))
3762 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3763 (synopsis "General-purpose unconstrained non-linear optimization")
3765 "This package provides an implementation of an algorithm for
3766 general-purpose unconstrained non-linear optimization. The algorithm is of
3767 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3768 search with a trust region type monitoring of the input to the line search
3769 algorithm. The interface of @code{ucminf} is designed for easy interchange
3770 with the package @code{optim}.")
3771 (license license:gpl2+)))
3773 (define-public r-useful
3779 (uri (cran-uri "useful" version))
3782 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
3783 (properties `((upstream-name . "useful")))
3784 (build-system r-build-system)
3786 `(("r-assertthat" ,r-assertthat)
3787 ("r-dplyr" ,r-dplyr)
3788 ("r-ggplot2" ,r-ggplot2)
3789 ("r-magrittr" ,r-magrittr)
3790 ("r-matrix" ,r-matrix)
3792 ("r-purrr" ,r-purrr)
3793 ("r-scales" ,r-scales)))
3794 (home-page "https://github.com/jaredlander/useful")
3795 (synopsis "Collection of handy, useful functions")
3796 (description "This package provides a set of little functions that have been
3797 found useful to do little odds and ends such as plotting the results of K-means
3798 clustering, substituting special text characters, viewing parts of a
3799 @code{data.frame}, constructing formulas from text and building design and
3800 response matrices.")
3801 (license license:bsd-3)))
3803 (define-public r-ordinal
3806 (version "2019.12-10")
3810 (uri (cran-uri "ordinal" version))
3813 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3814 (build-system r-build-system)
3816 `(("r-mass" ,r-mass)
3817 ("r-matrix" ,r-matrix)
3818 ("r-numderiv" ,r-numderiv)
3819 ("r-ucminf" ,r-ucminf)))
3820 (home-page "https://github.com/runehaubo/ordinal")
3821 (synopsis "Regression models for ordinal data")
3823 "This package provides an implementation of cumulative link (mixed)
3824 models also known as ordered regression models, proportional odds models,
3825 proportional hazards models for grouped survival times and ordered models.
3826 Estimation is via maximum likelihood and mixed models are fitted with the
3827 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3828 (license license:gpl2+)))
3830 (define-public r-jomo
3837 (uri (cran-uri "jomo" version))
3840 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
3841 (build-system r-build-system)
3843 `(("r-lme4" ,r-lme4)
3845 ("r-ordinal" ,r-ordinal)
3846 ("r-survival" ,r-survival)))
3847 (home-page "https://cran.r-project.org/web/packages/jomo/")
3848 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3850 "Similarly to Schafer's package pan, jomo is a package for multilevel
3851 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3852 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3853 possibility of handling binary and categorical data through latent normal
3854 variables, the option to use cluster-specific covariance matrices and to
3855 impute compatibly with the substantive model.")
3856 (license license:gpl2)))
3858 (define-public r-pan
3865 (uri (cran-uri "pan" version))
3868 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3869 (build-system r-build-system)
3870 (native-inputs `(("gfortran" ,gfortran)))
3871 (home-page "https://cran.r-project.org/web/packages/pan/")
3872 (synopsis "Multiple imputation for multivariate panel or clustered data")
3874 "This package implements multiple imputation for multivariate panel or
3876 (license license:gpl3)))
3878 (define-public r-mitml
3885 (uri (cran-uri "mitml" version))
3888 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3889 (build-system r-build-system)
3891 `(("r-haven" ,r-haven)
3894 (home-page "https://cran.r-project.org/web/packages/mitml/")
3895 (synopsis "Tools for multiple imputation in multilevel modeling")
3897 "This package provides tools for multiple imputation of missing data in
3898 multilevel modeling. It includes a user-friendly interface to the packages
3899 pan and jomo, and several functions for visualization, data management and the
3900 analysis of multiply imputed data sets.")
3901 (license license:gpl2+)))
3903 (define-public r-mice
3910 (uri (cran-uri "mice" version))
3913 "1gawccw32l00rcriyxys0mzbxh44x04rziy0cbycc3i1qm39d4fq"))))
3914 (build-system r-build-system)
3916 `(("r-broom" ,r-broom)
3917 ("r-dplyr" ,r-dplyr)
3918 ("r-generics" ,r-generics)
3919 ("r-lattice" ,r-lattice)
3921 ("r-tidyr" ,r-tidyr)))
3922 (home-page "https://cran.r-project.org/web/packages/mice/")
3923 (synopsis "Multivariate imputation by chained equations")
3925 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3926 implemented by the MICE algorithm as described in @url{Van Buuren and
3927 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3928 variable has its own imputation model. Built-in imputation models are
3929 provided for continuous data (predictive mean matching, normal), binary
3930 data (logistic regression), unordered categorical data (polytomous logistic
3931 regression) and ordered categorical data (proportional odds). MICE can also
3932 impute continuous two-level data (normal model, pan, second-level variables).
3933 Passive imputation can be used to maintain consistency between variables.
3934 Various diagnostic plots are available to inspect the quality of the
3936 ;; Any of these two versions.
3937 (license (list license:gpl2 license:gpl3))))
3939 (define-public r-truncnorm
3941 (name "r-truncnorm")
3946 (uri (cran-uri "truncnorm" version))
3949 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3950 (build-system r-build-system)
3951 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3952 (synopsis "Truncated normal distribution")
3953 (description "This package provides functions for the truncated normal
3954 distribution with mean equal to @code{mean} and standard deviation equal to
3955 @code{sd}. It includes density, distribution, quantile, and expected value
3956 functions, as well as a random generation function.")
3957 (license license:gpl2)))
3959 (define-public r-rsolnp
3966 (uri (cran-uri "Rsolnp" version))
3969 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3970 (properties `((upstream-name . "Rsolnp")))
3971 (build-system r-build-system)
3973 `(("r-truncnorm" ,r-truncnorm)))
3974 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3975 (synopsis "General non-linear optimization")
3976 (description "The Rsolnp package implements a general non-linear augmented
3977 Lagrange multiplier method solver, a @dfn{sequential quadratic
3978 programming} (SQP) based solver).")
3979 ;; Any version of the GPL.
3980 (license license:gpl2+)))
3982 (define-public r-hardyweinberg
3984 (name "r-hardyweinberg")
3989 (uri (cran-uri "HardyWeinberg" version))
3992 "1qn1bbzfk4w3mqrzisshw5xx7x249sgmj6qdi39lkqb58a4mf4kh"))))
3993 (properties `((upstream-name . "HardyWeinberg")))
3994 (build-system r-build-system)
3996 `(("r-mice" ,r-mice)
3998 ("r-rsolnp" ,r-rsolnp)))
3999 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4000 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4002 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4003 diallelic genetic marker data. All classical tests (chi-square, exact,
4004 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4005 included in the package, as well as functions for power computation and for
4006 the simulation of marker data under equilibrium and disequilibrium. Routines
4007 for dealing with markers on the X-chromosome are included. Functions for
4008 testing equilibrium in the presence of missing data by using multiple
4009 imputation are also provided. Implements several graphics for exploring the
4010 equilibrium status of a large set of diallelic markers: ternary plots with
4011 acceptance regions, log-ratio plots and Q-Q plots.")
4012 (license license:gpl2+)))
4021 (uri (cran-uri "sm" version))
4024 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4025 (build-system r-build-system)
4026 (native-inputs `(("gfortran" ,gfortran)))
4027 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4028 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4030 "This is software accompanying the book 'Applied Smoothing Techniques for
4031 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4032 University Press. It provides smoothing methods for nonparametric regression
4033 and density estimation")
4034 (license license:gpl2+)))
4036 (define-public r-venndiagram
4038 (name "r-venndiagram")
4042 (uri (cran-uri "VennDiagram" version))
4045 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4046 (properties `((upstream-name . "VennDiagram")))
4047 (build-system r-build-system)
4049 `(("r-futile-logger" ,r-futile-logger)))
4050 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4051 (synopsis "Generate High-Resolution Venn and Euler Plots")
4053 "This package provides a set of functions to generate high-resolution
4054 Venn and Euler plots. It includes handling for several special cases,
4055 including two-case scaling, and extensive customization of plot shape and
4057 (license license:gpl2+)))
4059 (define-public r-vioplot
4066 (uri (cran-uri "vioplot" version))
4069 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4070 (build-system r-build-system)
4075 `(("r-knitr" ,r-knitr)))
4076 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4077 (synopsis "Violin plot")
4079 "This package provides a violin plot, which is a combination of a box
4080 plot and a kernel density plot.")
4081 (license license:bsd-3)))
4083 (define-public r-rsofia
4089 ;; This package has been removed from CRAN, so we can
4090 ;; only fetch it from the archives.
4091 (uri (string-append "https://cran.r-project.org/src/"
4092 "contrib/Archive/RSofia/RSofia_"
4096 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4097 (properties `((upstream-name . "RSofia")))
4098 (build-system r-build-system)
4100 `(("r-rcpp" ,r-rcpp)))
4101 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4102 (synopsis "Port of sofia-ml to R")
4103 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4104 suite of fast incremental algorithms for machine learning that can be used for
4105 training models for classification or ranking.")
4106 (license license:asl2.0)))
4108 (define-public r-xts
4115 (uri (cran-uri "xts" version))
4118 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
4119 (build-system r-build-system)
4120 (propagated-inputs `(("r-zoo" ,r-zoo)))
4121 (home-page "https://github.com/joshuaulrich/xts")
4122 (synopsis "Extensible time series")
4124 "This package provides for uniform handling of R's different time-based
4125 data classes by extending @code{zoo}, maximizing native format information
4126 preservation and allowing for user-level customization and extension, while
4127 simplifying cross-class interoperability.")
4128 (license license:gpl2+)))
4130 (define-public r-performanceanalytics
4132 (name "r-performanceanalytics")
4137 (uri (cran-uri "PerformanceAnalytics" version))
4140 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4142 `((upstream-name . "PerformanceAnalytics")))
4143 (build-system r-build-system)
4145 `(("r-quadprog" ,r-quadprog)
4148 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4149 (synopsis "Econometric tools for performance and risk analysis")
4150 (description "This is a collection of econometric functions for
4151 performance and risk analysis. This package aims to aid practitioners and
4152 researchers in utilizing the latest research in analysis of non-normal return
4153 streams. In general, it is most tested on return (rather than price) data on
4154 a regular scale, but most functions will work with irregular return data as
4155 well, and increasing numbers of functions will work with P&L or price data
4157 ;; Either version may be picked.
4158 (license (list license:gpl2 license:gpl3))))
4160 (define-public r-laeken
4167 (uri (cran-uri "laeken" version))
4170 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4171 (build-system r-build-system)
4173 `(("r-boot" ,r-boot)
4174 ("r-mass" ,r-mass)))
4175 (home-page "https://cran.r-project.org/web/packages/laeken/")
4176 (synopsis "Estimation of indicators on social exclusion and poverty")
4177 (description "This package provides tools for the estimation of indicators
4178 on social exclusion and poverty, as well as an implementation of Pareto tail
4179 modeling for empirical income distributions.")
4180 (license license:gpl2+)))
4182 (define-public r-vcd
4189 (uri (cran-uri "vcd" version))
4192 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4193 (build-system r-build-system)
4195 `(("r-colorspace" ,r-colorspace)
4196 ("r-lmtest" ,r-lmtest)
4197 ("r-mass" ,r-mass)))
4198 (home-page "https://cran.r-project.org/web/packages/vcd/")
4199 (synopsis "Visualizing categorical data")
4200 (description "This package provides visualization techniques, data sets,
4201 summary and inference procedures aimed particularly at categorical data.
4202 Special emphasis is given to highly extensible grid graphics. The package was
4203 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4204 Friendly and is now the main support package for a new book, \"Discrete Data
4205 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4206 (license license:gpl2)))
4208 (define-public r-ica
4215 (uri (cran-uri "ica" version))
4218 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4219 (build-system r-build-system)
4220 (home-page "https://cran.r-project.org/web/packages/ica/")
4221 (synopsis "Independent component analysis")
4222 (description "This package provides tools for @dfn{Independent Component
4223 Analysis} (ICA) using various algorithms: FastICA,
4224 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4225 of Eigenmatrices} (JADE).")
4226 (license license:gpl2+)))
4228 (define-public r-dtw
4235 (uri (cran-uri "dtw" version))
4238 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4239 (build-system r-build-system)
4240 (propagated-inputs `(("r-proxy" ,r-proxy)))
4241 (home-page "http://dtw.r-forge.r-project.org/")
4242 (synopsis "Dynamic Time Warping Algorithms")
4243 (description "This package provides a comprehensive implementation of
4244 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4245 optimal (least cumulative distance) alignment between points of two time
4246 series. Common DTW variants covered include local (slope) and global (window)
4247 constraints, subsequence matches, arbitrary distance definitions,
4248 normalizations, minimum variance matching, and so on.")
4249 (license license:gpl2+)))
4251 (define-public r-sdmtools
4254 (version "1.1-221.2")
4258 (uri (cran-uri "SDMTools" version))
4261 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4262 (properties `((upstream-name . "SDMTools")))
4263 (build-system r-build-system)
4264 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4265 (home-page "https://www.rforge.net/SDMTools/")
4266 (synopsis "Species distribution modelling tools")
4267 (description "This package provides a set of tools for post processing
4268 the outcomes of species distribution modeling exercises. It includes novel
4269 methods for comparing models and tracking changes in distributions through
4270 time. It further includes methods for visualizing outcomes, selecting
4271 thresholds, calculating measures of accuracy and landscape fragmentation
4273 (license license:gpl3+)))
4275 (define-public r-scatterplot3d
4277 (name "r-scatterplot3d")
4282 (uri (cran-uri "scatterplot3d" version))
4285 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4286 (build-system r-build-system)
4287 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4288 (synopsis "3D scatter plot")
4289 (description "This package provides an implementation of scatter plots for
4290 plotting. a three dimensional point cloud.")
4291 (license license:gpl2)))
4293 (define-public r-ggridges
4300 (uri (cran-uri "ggridges" version))
4303 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4304 (build-system r-build-system)
4306 `(("r-ggplot2" ,r-ggplot2)
4308 ("r-scales" ,r-scales)
4309 ("r-withr" ,r-withr)))
4310 (home-page "https://github.com/clauswilke/ggridges")
4311 (synopsis "Ridgeline plots in ggplot2")
4313 "Ridgeline plots provide a convenient way of visualizing changes in
4314 distributions over time or space. This package enables the creation of such
4315 plots in @code{ggplot2}.")
4316 (license license:gpl2)))
4318 (define-public r-ggjoy
4325 (uri (cran-uri "ggjoy" version))
4328 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4329 (build-system r-build-system)
4331 `(("r-ggplot2" ,r-ggplot2)
4332 ("r-ggridges" ,r-ggridges)))
4333 (home-page "https://github.com/clauswilke/ggjoy")
4334 (synopsis "Joyplots in ggplot2")
4335 (description "Joyplots provide a convenient way of visualizing changes in
4336 distributions over time or space. This package enables the creation of such
4337 plots in @code{ggplot2}.")
4338 (license license:gpl2)))
4340 (define-public r-cli
4347 (uri (cran-uri "cli" version))
4350 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4351 (build-system r-build-system)
4353 `(("r-assertthat" ,r-assertthat)
4354 ("r-crayon" ,r-crayon)
4355 ("r-fansi" ,r-fansi)
4356 ("r-glue" ,r-glue)))
4357 (home-page "https://github.com/r-lib/cli#readme")
4358 (synopsis "Helpers for developing command line interfaces")
4359 (description "This package provides a suite of tools designed to build
4360 attractive command line interfaces (CLIs). It includes tools for drawing
4361 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4362 (license license:expat)))
4364 (define-public r-argparser
4366 (name "r-argparser")
4371 (uri (cran-uri "argparser" version))
4374 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4375 (build-system r-build-system)
4376 (home-page "https://bitbucket.org/djhshih/argparser")
4377 (synopsis "Command-line argument parser")
4379 "This package provides a cross-platform command-line argument parser
4380 written purely in R with no external dependencies. It is useful with the
4381 Rscript front-end and facilitates turning an R script into an executable
4383 (license license:gpl3+)))
4385 (define-public r-debugme
4392 (uri (cran-uri "debugme" version))
4395 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4396 (build-system r-build-system)
4397 (propagated-inputs `(("r-crayon" ,r-crayon)))
4398 (home-page "https://github.com/r-lib/debugme#readme")
4399 (synopsis "Debug R packages")
4401 "This package allows the user to specify debug messages as special string
4402 constants, and control debugging of packages via environment variables.")
4403 (license license:expat)))
4405 (define-public r-processx
4412 (uri (cran-uri "processx" version))
4414 (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
4415 (build-system r-build-system)
4419 (home-page "https://github.com/r-lib/processx3")
4420 (synopsis "Execute and control system processes")
4422 "This package provides portable tools to run system processes in the
4423 background. It can check if a background process is running; wait on a
4424 background process to finish; get the exit status of finished processes; kill
4425 background processes and their children; restart processes. It can read the
4426 standard output and error of the processes, using non-blocking connections.
4427 @code{processx} can poll a process for standard output or error, with a
4428 timeout. It can also poll several processes at once.")
4429 (license license:expat)))
4431 (define-public r-tsp
4438 (uri (cran-uri "TSP" version))
4441 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4442 (properties `((upstream-name . "TSP")))
4443 (build-system r-build-system)
4444 (propagated-inputs `(("r-foreach" ,r-foreach)))
4445 (home-page "https://cran.r-project.org/web/packages/TSP/")
4446 (synopsis "Traveling salesperson problem (TSP)")
4447 (description "This package provides basic infrastructure and some
4448 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4449 traveling salesman problem).")
4450 (license license:gpl3)))
4452 (define-public r-qap
4459 (uri (cran-uri "qap" version))
4462 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4463 (build-system r-build-system)
4464 (native-inputs `(("gfortran" ,gfortran)))
4465 (home-page "https://cran.r-project.org/web/packages/qap/")
4466 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4467 (description "This package implements heuristics for the @dfn{quadratic
4468 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4470 (license license:gpl3)))
4472 (define-public r-gclus
4479 (uri (cran-uri "gclus" version))
4482 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4483 (build-system r-build-system)
4484 (propagated-inputs `(("r-cluster" ,r-cluster)))
4485 (home-page "https://cran.r-project.org/web/packages/gclus/")
4486 (synopsis "Clustering graphics")
4487 (description "This package orders panels in scatterplot matrices and
4488 parallel coordinate displays by some merit index. It contains various indices
4489 of merit, ordering functions, and enhanced versions of @code{pairs} and
4490 @code{parcoord} which color panels according to their merit level.")
4491 (license license:gpl2+)))
4493 (define-public r-webshot
4500 (uri (cran-uri "webshot" version))
4503 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4504 (build-system r-build-system)
4506 `(("r-callr" ,r-callr)
4507 ("r-jsonlite" ,r-jsonlite)
4508 ("r-magrittr" ,r-magrittr)))
4509 (home-page "https://github.com/wch/webshot/")
4510 (synopsis "Take screenshots of web pages")
4512 "Webshot makes it easy to take screenshots of web pages from within R.
4513 It can also run Shiny applications locally and take screenshots of the
4514 application; and it can render and screenshot static as well as interactive R
4515 Markdown documents.")
4516 (license license:gpl2)))
4518 (define-public r-seriation
4520 (name "r-seriation")
4525 (uri (cran-uri "seriation" version))
4528 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4529 (build-system r-build-system)
4531 `(("r-cluster" ,r-cluster)
4532 ("r-colorspace" ,r-colorspace)
4533 ("r-dendextend" ,r-dendextend)
4534 ("r-gclus" ,r-gclus)
4535 ("r-gplots" ,r-gplots)
4538 ("r-registry" ,r-registry)
4540 (native-inputs `(("gfortran" ,gfortran)))
4541 (home-page "https://s2.smu.edu/IDA/seriation/")
4542 (synopsis "Infrastructure for ordering objects using seriation")
4544 "This package provides infrastructure for seriation with an
4545 implementation of several seriation/sequencing techniques to reorder matrices,
4546 dissimilarity matrices, and dendrograms. It also provides (optimally)
4547 reordered heatmaps, color images and clustering visualizations like
4548 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4550 (license license:gpl3)))
4552 (define-public r-xfun
4559 (uri (cran-uri "xfun" version))
4561 (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
4562 (build-system r-build-system)
4563 ;; knitr itself depends on xfun
4566 `(("r-knitr" ,r-knitr)))
4567 (home-page "https://github.com/yihui/xfun")
4568 (synopsis "Miscellaneous functions")
4570 "This package provides miscellaneous functions commonly used in other
4571 packages maintained by Yihui Xie.")
4572 (license license:expat)))
4574 (define-public r-utf8
4581 (uri (cran-uri "utf8" version))
4584 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4585 (build-system r-build-system)
4586 (home-page "https://github.com/patperry/r-utf8")
4587 (synopsis "Unicode text processing")
4589 "This package provides tools to process and print UTF-8 encoded
4590 international text (Unicode). Input, validate, normalize, encode, format, and
4592 (license license:asl2.0)))
4594 (define-public r-zeallot
4601 (uri (cran-uri "zeallot" version))
4604 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4605 (build-system r-build-system)
4606 (home-page "https://github.com/nteetor/zeallot")
4607 (synopsis "Multiple, unpacking, and destructuring assignment")
4609 "This package provides a @code{%<-%} operator to perform multiple,
4610 unpacking, and destructuring assignment in R. The operator unpacks the
4611 right-hand side of an assignment into multiple values and assigns these values
4612 to variables on the left-hand side of the assignment.")
4613 (license license:expat)))
4615 (define-public r-vctrs
4622 (uri (cran-uri "vctrs" version))
4625 "0xvqgc36zhd9y1xsm7kwrbr5sxwnd3jbr9qrb1gma2lqkqf42izb"))))
4626 (build-system r-build-system)
4628 `(("r-digest" ,r-digest)
4629 ("r-ellipsis" ,r-ellipsis)
4631 ("r-rlang" ,r-rlang)))
4633 `(("r-knitr" ,r-knitr)))
4634 (home-page "https://github.com/r-lib/vctrs")
4635 (synopsis "Vector helpers")
4637 "There are three main goals to the @code{vctrs} package:
4640 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4641 @code{length()} and @code{class()}. These definitions are paired with a
4642 framework for type-coercion and size-recycling.
4643 @item To define type- and size-stability as desirable function properties, use
4644 them to analyse existing base function, and to propose better alternatives.
4645 This work has been particularly motivated by thinking about the ideal
4646 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4647 @item To provide a new @code{vctr} base class that makes it easy to create new
4648 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4649 a few new @code{vctrs} generics, making implementation considerably simpler
4652 (license license:gpl3)))
4654 (define-public r-pillar
4661 (uri (cran-uri "pillar" version))
4664 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4665 (build-system r-build-system)
4668 ("r-crayon" ,r-crayon)
4669 ("r-ellipsis" ,r-ellipsis)
4670 ("r-fansi" ,r-fansi)
4671 ("r-lifecycle" ,r-lifecycle)
4672 ("r-rlang" ,r-rlang)
4674 ("r-vctrs" ,r-vctrs)))
4675 (home-page "https://github.com/r-lib/pillar")
4676 (synopsis "Coloured formatting for columns")
4678 "This package provides a @code{pillar} generic designed for formatting
4679 columns of data using the full range of colours provided by modern
4681 (license license:gpl3)))
4683 (define-public r-uuid
4690 (uri (cran-uri "uuid" version))
4693 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4694 (build-system r-build-system)
4695 (home-page "https://www.rforge.net/uuid")
4696 (synopsis "Tools for generating and handling of UUIDs")
4698 "This package provides tools for generating and handling of
4699 @dfn{Universally Unique Identifiers} (UUIDs).")
4700 (license license:expat)))
4702 (define-public r-tinytex
4709 (uri (cran-uri "tinytex" version))
4712 "0zbhzxxjlkdj9byxyab477p7cnws5y87nyg989lkzarxdc7dglza"))))
4713 (build-system r-build-system)
4715 `(("r-xfun" ,r-xfun)))
4716 (home-page "https://github.com/yihui/tinytex")
4717 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4719 "This package provides helper functions to install and maintain the LaTeX
4720 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4721 easy-to-maintain version of TeX Live. This package also contains helper
4722 functions to compile LaTeX documents, and install missing LaTeX packages
4724 (license license:expat)))
4726 (define-public r-network
4733 (uri (cran-uri "network" version))
4736 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4737 (build-system r-build-system)
4739 `(("r-magrittr" ,r-magrittr)
4740 ("r-tibble" ,r-tibble)))
4741 (home-page "https://statnet.org/")
4742 (synopsis "Classes for relational data")
4744 "This package provides tools to create and modify network objects. The
4745 @code{network} class can represent a range of relational data types, and
4746 supports arbitrary vertex/edge/graph attributes.")
4747 (license license:gpl2+)))
4749 (define-public r-stabs
4756 (uri (cran-uri "stabs" version))
4759 "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
4760 (build-system r-build-system)
4761 (home-page "https://github.com/hofnerb/stabs")
4762 (synopsis "Stability selection with error control")
4764 "This package provides resampling procedures to assess the stability of
4765 selected variables with additional finite sample error control for
4766 high-dimensional variable selection procedures such as Lasso or boosting.
4767 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
4768 complementary pairs stability selection with improved error bounds
4769 (Shah & Samworth, 2013) are implemented. The package can be combined with
4770 arbitrary user specified variable selection approaches.")
4771 (license license:gpl2)))
4773 (define-public r-statnet-common
4775 (name "r-statnet-common")
4780 (uri (cran-uri "statnet.common" version))
4783 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4785 `((upstream-name . "statnet.common")))
4786 (build-system r-build-system)
4788 `(("r-coda" ,r-coda)))
4789 (home-page "https://statnet.org")
4790 (synopsis "R scripts and utilities used by the Statnet software")
4791 (description "This package provides non-statistical utilities used by the
4792 software developed by the Statnet Project.")
4793 (license license:gpl3)))
4795 (define-public r-statcheck
4797 (name "r-statcheck")
4802 (uri (cran-uri "statcheck" version))
4805 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4806 (build-system r-build-system)
4808 `(("r-ggplot2" ,r-ggplot2)
4810 ("r-rmarkdown" ,r-rmarkdown)))
4811 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4812 (synopsis "Extract statistics from articles and recompute p-values")
4813 (description "This package can automatically extract statistical
4814 null-hypothesis significant testing (NHST) results from articles and recompute
4815 the p-values based on the reported test statistic and degrees of freedom to
4816 detect possible inconsistencies.")
4817 (license license:gpl2)))
4819 (define-public r-sna
4826 (uri (cran-uri "sna" version))
4829 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4830 (build-system r-build-system)
4832 `(("r-network" ,r-network)
4833 ("r-statnet-common" ,r-statnet-common)))
4834 (home-page "https://statnet.org")
4835 (synopsis "Tools for social network analysis")
4837 "This package provides a range of tools for social network analysis,
4838 including node and graph-level indices, structural distance and covariance
4839 methods, structural equivalence detection, network regression, random graph
4840 generation, and 2D/3D network visualization.")
4841 (license license:gpl2+)))
4843 (define-public r-tfisher
4850 (uri (cran-uri "TFisher" version))
4853 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4854 (properties `((upstream-name . "TFisher")))
4855 (build-system r-build-system)
4857 `(("r-matrix" ,r-matrix)
4858 ("r-mvtnorm" ,r-mvtnorm)
4860 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4861 (synopsis "Optimal thresholding Fisher's p-value combination method")
4863 "This package provides the @dfn{cumulative distribution function} (CDF),
4864 quantile, and statistical power calculator for a collection of thresholding
4865 Fisher's p-value combination methods, including Fisher's p-value combination
4866 method, truncated product method and, in particular, soft-thresholding
4867 Fisher's p-value combination method which is proven to be optimal in some
4868 context of signal detection. The p-value calculator for the omnibus version
4869 of these tests are also included.")
4870 (license license:gpl2)))
4872 (define-public r-ttr
4879 (uri (cran-uri "TTR" version))
4882 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
4883 (properties `((upstream-name . "TTR")))
4884 (build-system r-build-system)
4886 `(("r-curl" ,r-curl)
4889 (home-page "https://github.com/joshuaulrich/TTR")
4890 (synopsis "Technical trading rules")
4892 "This package provides functions and data to construct technical trading
4894 (license license:gpl2)))
4896 (define-public r-leaps
4903 (uri (cran-uri "leaps" version))
4906 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4907 (build-system r-build-system)
4908 (native-inputs `(("gfortran" ,gfortran)))
4909 (home-page "https://cran.r-project.org/web/packages/leaps/")
4910 (synopsis "Regression subset selection")
4912 "This package provides tools for regression subset selection, including
4913 exhaustive search.")
4914 (license license:gpl2+)))
4916 (define-public r-splus2r
4923 (uri (cran-uri "splus2R" version))
4926 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4927 (properties `((upstream-name . "splus2R")))
4928 (build-system r-build-system)
4929 (native-inputs `(("gfortran" ,gfortran)))
4930 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4931 (synopsis "Supplemental S-PLUS functionality in R")
4933 "Currently there are many functions in S-PLUS that are missing in R. To
4934 facilitate the conversion of S-PLUS packages to R packages, this package
4935 provides some missing S-PLUS functionality in R.")
4936 (license license:gpl2)))
4938 (define-public r-ifultools
4940 (name "r-ifultools")
4945 (uri (cran-uri "ifultools" version))
4948 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4949 (build-system r-build-system)
4951 `(("r-mass" ,r-mass)
4952 ("r-splus2r" ,r-splus2r)))
4953 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4954 (synopsis "Insightful research tools")
4955 (description "This package provides C code used by the wmtsa, fractal, and
4957 (license license:gpl2)))
4959 (define-public r-sapa
4966 (uri (cran-uri "sapa" version))
4969 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4970 (build-system r-build-system)
4972 `(("r-ifultools" ,r-ifultools)
4973 ("r-splus2r" ,r-splus2r)))
4974 (home-page "https://cran.r-project.org/web/packages/sapa/")
4975 (synopsis "Spectral analysis for physical applications")
4976 (description "This package provides software for the book Spectral
4977 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4978 Cambridge University Press, 1993.")
4979 (license license:gpl2)))
4981 (define-public r-aggregation
4983 (name "r-aggregation")
4988 (uri (cran-uri "aggregation" version))
4991 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4992 (build-system r-build-system)
4993 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4994 (synopsis "Methods for p-value aggregation")
4996 "This package contains functionality for performing the following methods
4997 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4998 Fisher's method), and Sidak correction.")
4999 (license license:gpl3)))
5001 (define-public r-quantmod
5008 (uri (cran-uri "quantmod" version))
5011 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
5012 (build-system r-build-system)
5014 `(("r-curl" ,r-curl)
5018 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5019 (synopsis "Quantitative financial modelling framework")
5020 (description "This package provides a quantitative financial modelling
5021 framework to allow users to specify, build, trade, and analyse quantitative
5022 financial trading strategies.")
5023 (license license:gpl3)))
5025 (define-public r-tseries
5032 (uri (cran-uri "tseries" version))
5035 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
5036 (build-system r-build-system)
5038 `(("r-quadprog" ,r-quadprog)
5039 ("r-quantmod" ,r-quantmod)
5042 `(("gfortran" ,gfortran)))
5043 (home-page "https://cran.r-project.org/web/packages/tseries/")
5044 (synopsis "Time series analysis and computational finance")
5046 "This package provides functions relating to time series analysis and
5047 computational finance.")
5048 (license license:gpl2)))
5050 (define-public r-wmtsa
5057 (uri (cran-uri "wmtsa" version))
5060 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5061 (build-system r-build-system)
5063 `(("r-ifultools" ,r-ifultools)
5065 ("r-splus2r" ,r-splus2r)))
5066 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5067 (synopsis "Wavelet methods for time series analysis")
5069 "This package provides software to accompany the book \"Wavelet Methods
5070 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5071 University Press, 2000.")
5072 (license license:gpl2)))
5074 (define-public r-tsa
5081 (uri (cran-uri "TSA" version))
5084 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
5085 (properties `((upstream-name . "TSA")))
5086 (build-system r-build-system)
5088 `(("r-leaps" ,r-leaps)
5089 ("r-locfit" ,r-locfit)
5090 ("r-mgcv" ,r-mgcv)))
5091 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5092 (synopsis "Time series analysis")
5094 "This package contains R functions and datasets detailed in the book
5095 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5096 Cryer and Kung-Sik Chan.")
5097 (license license:gpl2+)))
5099 (define-public r-extradistr
5101 (name "r-extradistr")
5106 (uri (cran-uri "extraDistr" version))
5109 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
5110 (properties `((upstream-name . "extraDistr")))
5111 (build-system r-build-system)
5113 `(("r-rcpp" ,r-rcpp)))
5114 (home-page "https://github.com/twolodzko/extraDistr")
5115 (synopsis "Additional univariate and multivariate distributions")
5117 "This package implements density, distribution functions, quantile
5118 functions and random generation functions for a large number of univariate and
5119 multivariate distributions.")
5120 (license license:gpl2)))
5122 (define-public r-fractal
5129 (uri (cran-uri "fractal" version))
5132 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5133 (build-system r-build-system)
5135 `(("r-ifultools" ,r-ifultools)
5138 ("r-scatterplot3d" ,r-scatterplot3d)
5139 ("r-splus2r" ,r-splus2r)
5140 ("r-wmtsa" ,r-wmtsa)))
5141 (home-page "https://cran.r-project.org/web/packages/fractal/")
5142 (synopsis "Fractal time series modeling and analysis")
5144 "This package provides tools for stochastic fractal and deterministic
5145 chaotic time series analysis.")
5146 (license license:gpl2)))
5148 (define-public r-urca
5155 (uri (cran-uri "urca" version))
5158 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5159 (build-system r-build-system)
5160 (propagated-inputs `(("r-nlme" ,r-nlme)))
5161 (native-inputs `(("gfortran" ,gfortran)))
5162 (home-page "https://cran.r-project.org/web/packages/urca/")
5163 (synopsis "Unit root and cointegration tests for time series data")
5165 "This package provides unit root and cointegration tests encountered in
5166 applied econometric analysis.")
5167 (license license:gpl2+)))
5169 (define-public r-cubature
5176 (uri (cran-uri "cubature" version))
5179 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5180 (build-system r-build-system)
5182 `(("r-rcpp" ,r-rcpp)))
5184 `(("r-knitr" ,r-knitr)))
5185 (home-page "https://github.com/bnaras/cubature")
5186 (synopsis "Adaptive multivariate integration over hypercubes")
5188 "This package is an R wrapper around the cubature C library for adaptive
5189 multivariate integration over hypercubes. This version provides both
5190 @code{hcubature} and @code{pcubature} routines in addition to a vector
5192 ;; The included cubature C library is released under GPLv2+, but the
5193 ;; wrapper declares the license to be GPLv3+.
5194 (license (list license:gpl2+ license:gpl3+))))
5196 (define-public r-trend
5203 (uri (cran-uri "trend" version))
5206 "0bj40acr1sc7vfxdcsdja3g28xsmrclmgb3n94p89gfjcgp8nv1d"))))
5207 (build-system r-build-system)
5209 `(("r-extradistr" ,r-extradistr)))
5211 `(("gfortran" ,gfortran)))
5212 (home-page "https://cran.r-project.org/web/packages/trend/")
5213 (synopsis "Non-parametric trend tests and change-point detection")
5215 "The analysis of environmental data often requires the detection of
5216 trends and change-points. This package includes tests for trend
5217 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5218 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5219 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5220 correlation trend test), change-point detection (Lanzante's test procedures,
5221 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5222 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5223 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5224 sample Robust Rank-Order Distributional Test.")
5225 (license license:gpl3)))
5227 (define-public r-expm
5234 (uri (cran-uri "expm" version))
5237 "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7"))))
5238 (build-system r-build-system)
5239 (propagated-inputs `(("r-matrix" ,r-matrix)))
5240 (native-inputs `(("gfortran" ,gfortran)))
5241 (home-page "https://r-forge.r-project.org/projects/expm/")
5242 (synopsis "Tools for matrix exponentials and related quantities")
5244 "This package provides tools for the computation of the matrix
5245 exponential, logarithm, square root, and related quantities.")
5246 (license license:gpl2+)))
5248 (define-public r-complexplus
5250 (name "r-complexplus")
5255 (uri (cran-uri "complexplus" version))
5258 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5259 (build-system r-build-system)
5261 `(("r-expm" ,r-expm)
5262 ("r-matrix" ,r-matrix)))
5263 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5264 (synopsis "Functions of complex or real variables")
5266 "This package extends several functions to the complex domain, including
5267 the matrix exponential and logarithm, and the determinant.")
5268 (license license:gpl2)))
5270 (define-public r-phontools
5272 (name "r-phontools")
5277 (uri (cran-uri "phonTools" version))
5280 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5281 (properties `((upstream-name . "phonTools")))
5282 (build-system r-build-system)
5283 (home-page "http://www.santiagobarreda.com/rscripts.html")
5284 (synopsis "Tools for phonetic and acoustic analyses")
5286 "This package contains tools for the organization, display, and analysis
5287 of the sorts of data frequently encountered in phonetics research and
5288 experimentation, including the easy creation of IPA vowel plots, and the
5289 creation and manipulation of WAVE audio files.")
5290 (license license:bsd-2)))
5299 (uri (cran-uri "np" version))
5302 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5303 (build-system r-build-system)
5305 `(("r-boot" ,r-boot)
5306 ("r-cubature" ,r-cubature)
5307 ("r-quadprog" ,r-quadprog)
5308 ("r-quantreg" ,r-quantreg)))
5309 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5310 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5311 (description "This package provides non-parametric (and semi-parametric)
5312 kernel methods that seamlessly handle a mix of continuous, unordered, and
5313 ordered factor data types.")
5314 ;; Any version of the GPL.
5315 (license license:gpl3+)))
5317 (define-public r-powerplus
5319 (name "r-powerplus")
5324 (uri (cran-uri "powerplus" version))
5327 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5328 (build-system r-build-system)
5330 `(("r-complexplus" ,r-complexplus)
5333 ("r-matrix" ,r-matrix)
5334 ("r-phontools" ,r-phontools)))
5335 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5336 (synopsis "Exponentiation operations")
5338 "This package provides tools for the computation of matrix and scalar
5340 (license license:gpl2)))
5342 (define-public r-egg
5349 (uri (cran-uri "egg" version))
5352 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5353 (properties `((upstream-name . "egg")))
5354 (build-system r-build-system)
5356 `(("r-ggplot2" ,r-ggplot2)
5357 ("r-gridextra" ,r-gridextra)
5358 ("r-gtable" ,r-gtable)))
5359 (home-page "https://cran.r-project.org/web/packages/egg")
5360 (synopsis "Extensions for ggplot2")
5362 "This package provides miscellaneous functions to help customize ggplot2
5363 objects. High-level functions are provided to post-process ggplot2 layouts
5364 and allow alignment between plot panels, as well as setting panel sizes to
5365 fixed values. Other functions include a custom @code{geom}, and helper
5366 functions to enforce symmetric scales or add tags to facetted plots.")
5367 (license license:gpl3)))
5369 (define-public r-heatmaply
5371 (name "r-heatmaply")
5376 (uri (cran-uri "heatmaply" version))
5379 "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
5380 (build-system r-build-system)
5382 `(("r-assertthat" ,r-assertthat)
5383 ("r-colorspace" ,r-colorspace)
5384 ("r-dendextend" ,r-dendextend)
5386 ("r-ggplot2" ,r-ggplot2)
5387 ("r-htmlwidgets" ,r-htmlwidgets)
5388 ("r-magrittr" ,r-magrittr)
5389 ("r-plotly" ,r-plotly)
5390 ("r-rcolorbrewer" ,r-rcolorbrewer)
5391 ("r-reshape2" ,r-reshape2)
5392 ("r-scales" ,r-scales)
5393 ("r-seriation" ,r-seriation)
5394 ("r-viridis" ,r-viridis)
5395 ("r-webshot" ,r-webshot)))
5397 `(("r-knitr" ,r-knitr)))
5398 (home-page "https://cran.r-project.org/package=heatmaply")
5399 (synopsis "Interactive cluster heat maps using plotly")
5401 "This package enables you to create interactive cluster heatmaps that can
5402 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5403 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5404 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5405 a popular graphical method for visualizing high-dimensional data, in which a
5406 table of numbers is encoded as a grid of colored cells. The rows and columns
5407 of the matrix are ordered to highlight patterns and are often accompanied by
5409 ;; Either version of the license.
5410 (license (list license:gpl2 license:gpl3))))
5419 (uri (cran-uri "h5" version))
5422 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5423 (build-system r-build-system)
5428 `(("which" ,which)))
5430 `(("r-rcpp" ,r-rcpp)))
5431 (home-page "https://github.com/mannau/h5")
5432 (synopsis "Interface to the HDF5 Library")
5434 "This package provides an S4 interface to the HDF5 library supporting
5435 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5436 binary files in a language independent format. The HDF5 format can therefore
5437 be used as an alternative to R's save/load mechanism. Since h5 is able to
5438 access only subsets of stored data it can also handle data sets which do not
5440 (license license:bsd-2)))
5442 (define-public r-cgdsr
5449 (uri (cran-uri "cgdsr" version))
5452 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5453 (build-system r-build-system)
5455 `(("r-httr" ,r-httr)
5456 ("r-r-methodss3" ,r-r-methodss3)
5457 ("r-r-oo" ,r-r-oo)))
5458 (home-page "https://github.com/cBioPortal/cgdsr")
5459 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5461 "This package provides a basic set of R functions for querying the Cancer
5462 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5463 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5464 (license license:lgpl3)))
5466 (define-public r-import
5473 (uri (cran-uri "import" version))
5476 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5477 (build-system r-build-system)
5478 (home-page "https://github.com/smbache/import")
5479 (synopsis "Import mechanism for R")
5481 "This is an alternative mechanism for importing objects from packages.
5482 The syntax allows for importing multiple objects from a package with a single
5483 command in an expressive way. The import package bridges some of the gap
5484 between using @code{library} (or @code{require}) and direct (single-object)
5485 imports. Furthermore the imported objects are not placed in the current
5486 environment. It is also possible to import objects from stand-alone @code{.R}
5488 (license license:expat)))
5490 (define-public r-shinyace
5497 (uri (cran-uri "shinyAce" version))
5500 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5501 (properties `((upstream-name . "shinyAce")))
5502 (build-system r-build-system)
5504 `(("r-shiny" ,r-shiny)
5505 ("r-jsonlite" ,r-jsonlite)))
5506 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5507 (synopsis "Ace editor bindings for Shiny")
5509 "This package provides Ace editor bindings to enable a rich text editing
5510 environment within Shiny.")
5511 (license license:expat)))
5513 (define-public r-randomizr
5515 (name "r-randomizr")
5520 (uri (cran-uri "randomizr" version))
5523 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5524 (properties `((upstream-name . "randomizr")))
5525 (build-system r-build-system)
5527 `(("r-knitr" ,r-knitr)))
5528 (home-page "https://declaredesign.org/r/randomizr/")
5529 (synopsis "Tools for common forms of random assignment and sampling")
5531 "This package provides tools for generating random assignments for common
5532 experimental designs and random samples for common sampling designs.")
5533 (license license:expat)))
5535 (define-public r-base64url
5537 (name "r-base64url")
5542 (uri (cran-uri "base64url" version))
5545 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5546 (build-system r-build-system)
5548 `(("r-backports" ,r-backports)))
5549 (home-page "https://github.com/mllg/base64url")
5550 (synopsis "Fast and URL-safe base64 encoder and decoder")
5552 "This package provides a URL-safe base64 encoder and decoder. In
5553 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5554 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5555 encoder does not fill the string with trailing @code{=}. The resulting
5556 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5557 and thus are safe to use in URLs or for file names. The package also comes
5558 with a simple base32 encoder/decoder suited for case insensitive file
5560 (license license:gpl3)))
5562 (define-public r-radiant-data
5564 (name "r-radiant-data")
5569 (uri (cran-uri "radiant.data" version))
5572 "09a3wn3gl1zjq5zsc5zaxyq71dg5qnpk57bmwd6qy8w99g2clm8c"))
5573 (modules '((guix build utils)))
5576 ;; Delete files that are under CC-NC-SA.
5577 (delete-file-recursively "inst/app/tools/help")
5579 (properties `((upstream-name . "radiant.data")))
5580 (build-system r-build-system)
5582 `(("r-base64enc" ,r-base64enc)
5583 ("r-broom" ,r-broom)
5586 ("r-dplyr" ,r-dplyr)
5589 ("r-ggplot2" ,r-ggplot2)
5590 ("r-import" ,r-import)
5591 ("r-jsonlite" ,r-jsonlite)
5592 ("r-knitr" ,r-knitr)
5593 ("r-lubridate" ,r-lubridate)
5594 ("r-magrittr" ,r-magrittr)
5595 ("r-markdown" ,r-markdown)
5597 ("r-patchwork" ,r-patchwork)
5598 ("r-plotly" ,r-plotly)
5599 ("r-psych" ,r-psych)
5600 ("r-randomizr" ,r-randomizr)
5601 ("r-readr" ,r-readr)
5602 ("r-readxl" ,r-readxl)
5603 ("r-rlang" ,r-rlang)
5604 ("r-rmarkdown" ,r-rmarkdown)
5605 ("r-rstudioapi" ,r-rstudioapi)
5606 ("r-scales" ,r-scales)
5607 ("r-shiny" ,r-shiny)
5608 ("r-shinyfiles" ,r-shinyfiles)
5609 ("r-shinyace" ,r-shinyace)
5610 ("r-stringi" ,r-stringi)
5611 ("r-tibble" ,r-tibble)
5612 ("r-tidyr" ,r-tidyr)
5613 ("r-writexl" ,r-writexl)))
5614 (home-page "https://github.com/radiant-rstats/radiant.data")
5615 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5617 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5618 visualizing, summarizing, transforming, and combining data. It also contains
5619 functionality to generate reproducible reports of the analyses conducted in
5621 (license license:agpl3)))
5623 (define-public r-algdesign
5625 (name "r-algdesign")
5630 (uri (cran-uri "AlgDesign" version))
5632 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5633 (properties `((upstream-name . "AlgDesign")))
5634 (build-system r-build-system)
5635 (home-page "https://github.com/jvbraun/AlgDesign")
5636 (synopsis "Algorithmic experimental design")
5638 "This package provides tools to calculate exact and approximate theory
5639 experimental designs for D, A, and I criteria. Very large designs may be
5640 created. Experimental designs may be blocked or blocked designs created from
5641 a candidate list, using several criteria. The blocking can be done when whole
5642 and within plot factors interact.")
5643 (license license:gpl2+)))
5645 (define-public r-signal
5652 (uri (cran-uri "signal" version))
5655 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5656 (build-system r-build-system)
5657 (propagated-inputs `(("r-mass" ,r-mass)))
5658 (native-inputs `(("gfortran" ,gfortran)))
5659 (home-page "https://cran.r-project.org/web/packages/signal/")
5660 (synopsis "Signal processing")
5662 "This package provides a set of signal processing functions originally
5663 written for Matlab and GNU Octave. It includes filter generation utilities,
5664 filtering functions, resampling routines, and visualization of filter models.
5665 It also includes interpolation functions.")
5666 (license license:gpl2)))
5668 (define-public r-gsubfn
5675 (uri (cran-uri "gsubfn" version))
5678 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5679 (build-system r-build-system)
5680 (propagated-inputs `(("r-proto" ,r-proto)))
5681 (home-page "https://code.google.com/archive/p/gsubfn/")
5682 (synopsis "Utilities for strings and function arguments.")
5684 "This package provides @code{gsubfn} which is like @code{gsub} but can
5685 take a replacement function or certain other objects instead of the
5686 replacement string. Matches and back references are input to the replacement
5687 function and replaced by the function output. @code{gsubfn} can be used to
5688 split strings based on content rather than delimiters and for quasi-perl-style
5689 string interpolation. The package also has facilities for translating
5690 formulas to functions and allowing such formulas in function calls instead of
5692 (license license:gpl2+)))
5694 (define-public r-sqldf
5701 (uri (cran-uri "sqldf" version))
5704 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5705 (build-system r-build-system)
5707 `(("r-chron" ,r-chron)
5709 ("r-gsubfn" ,r-gsubfn)
5710 ("r-proto" ,r-proto)
5711 ("r-rsqlite" ,r-rsqlite)))
5712 (home-page "https://github.com/ggrothendieck/sqldf")
5713 (synopsis "Manipulate R data frames using SQL")
5715 "The @code{sqldf} function is typically passed a single argument which is
5716 an SQL select statement where the table names are ordinary R data frame names.
5717 @code{sqldf} transparently sets up a database, imports the data frames into
5718 that database, performs the SQL statement and returns the result using a
5719 heuristic to determine which class to assign to each column of the returned
5720 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5721 used to read filtered files into R even if the original files are larger than
5722 R itself can handle.")
5723 (license license:gpl2)))
5725 (define-public r-abind
5732 (uri (cran-uri "abind" version))
5735 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5736 (build-system r-build-system)
5737 (home-page "https://cran.r-project.org/web/packages/abind/")
5738 (synopsis "Combine multidimensional arrays")
5740 "This package provides tools to combine multidimensional arrays into a
5741 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5742 works with vectors, matrices, and higher-dimensional arrays. It also provides
5743 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5744 extracting and replacing data in arrays.")
5745 (license license:lgpl2.0+)))
5747 (define-public r-prroc
5754 (uri (cran-uri "PRROC" version))
5757 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5758 (properties `((upstream-name . "PRROC")))
5759 (build-system r-build-system)
5760 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5761 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5763 "This package computes the areas under the @dfn{precision-recall} (PR)
5764 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5765 contrast to other implementations, the interpolation between points of the PR
5766 curve is done by a non-linear piecewise function. In addition to the areas
5767 under the curves, the curves themselves can also be computed and plotted by a
5768 specific S3-method.")
5769 (license license:gpl3)))
5771 (define-public r-vim
5778 (uri (cran-uri "VIM" version))
5781 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5782 (properties `((upstream-name . "VIM")))
5783 (build-system r-build-system)
5786 ("r-colorspace" ,r-colorspace)
5787 ("r-data-table" ,r-data-table)
5788 ("r-e1071" ,r-e1071)
5789 ("r-laeken" ,r-laeken)
5790 ("r-magrittr" ,r-magrittr)
5793 ("r-ranger" ,r-ranger)
5795 ("r-robustbase" ,r-robustbase)
5799 `(("r-knitr" ,r-knitr)))
5800 (home-page "https://github.com/alexkowa/VIM")
5801 (synopsis "Visualization and imputation of missing values")
5803 "This package provides tools for the visualization of missing and/or
5804 imputed values are introduced, which can be used for exploring the data and
5805 the structure of the missing and/or imputed values. Depending on this
5806 structure of the missing values, the corresponding methods may help to
5807 identify the mechanism generating the missing values and allows to explore the
5808 data including missing values. In addition, the quality of imputation can be
5809 visually explored using various univariate, bivariate, multiple and
5810 multivariate plot methods.")
5811 (license license:gpl2+)))
5813 (define-public r-fnn
5820 (uri (cran-uri "FNN" version))
5823 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5824 (properties `((upstream-name . "FNN")))
5825 (build-system r-build-system)
5826 (home-page "https://cran.r-project.org/web/packages/FNN")
5827 (synopsis "Fast nearest neighbor search algorithms and applications")
5829 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5830 search algorithms. Related applications including KNN classification,
5831 regression and information measures are implemented.")
5832 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5833 ;; later can be used.
5834 (license license:gpl2+)))
5836 (define-public r-smoother
5843 (uri (cran-uri "smoother" version))
5846 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5847 (build-system r-build-system)
5849 `(("r-ttr" ,r-ttr)))
5850 (home-page "https://cran.r-project.org/web/packages/smoother")
5851 (synopsis "Functions relating to the smoothing of numerical data")
5853 "This package provides a collection of methods for smoothing numerical
5854 data, commencing with a port of the Matlab gaussian window smoothing function.
5855 In addition, several functions typically used in smoothing of financial data
5857 (license license:gpl2)))
5859 (define-public r-riverplot
5861 (name "r-riverplot")
5866 (uri (cran-uri "riverplot" version))
5869 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5870 (build-system r-build-system)
5871 (home-page "https://logfc.wordpress.com")
5872 (synopsis "Sankey or ribbon plots")
5874 "Sankey plots are a type of diagram that is convenient to illustrate how
5875 flow of information, resources etc. separates and joins, much like observing
5876 how rivers split and merge. For example, they can be used to compare
5877 different clusterings. This package provides an implementation of Sankey
5879 (license license:gpl2+)))
5881 (define-public r-dyn
5888 (uri (cran-uri "dyn" version))
5891 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5892 (build-system r-build-system)
5894 `(("r-zoo" ,r-zoo)))
5895 (home-page "https://cran.r-project.org/web/packages/dyn")
5896 (synopsis "Time series regression")
5898 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5899 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5900 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5901 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5902 @code{randomForest::randomForest()} and other regression functions, allowing
5903 those functions to be used with time series including specifications that may
5904 contain lags, diffs and missing values.")
5906 (license license:gpl2+)))
5908 (define-public r-catdap
5915 (uri (cran-uri "catdap" version))
5918 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5919 (build-system r-build-system)
5921 `(("gfortran" ,gfortran)))
5922 (home-page "https://cran.r-project.org/web/packages/catdap/")
5923 (synopsis "Tools for categorical data analysis")
5925 "This package provides functions for analyzing multivariate data.
5926 Dependencies of the distribution of the specified variable (response
5927 variable) to other variables (explanatory variables) are derived and
5928 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5929 (license license:gpl2+)))
5931 (define-public r-arules
5938 (uri (cran-uri "arules" version))
5941 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5942 (build-system r-build-system)
5944 `(("r-matrix" ,r-matrix)))
5945 (home-page "https://github.com/mhahsler/arules")
5946 (synopsis "Mining association rules and frequent itemsets")
5948 "This package provides an infrastructure for representing, manipulating
5949 and analyzing transaction data and patterns (frequent itemsets and association rules).
5950 It also provides C implementations of the association mining algorithms Apriori
5952 (license license:gpl3)))
5954 (define-public r-parsedate
5956 (name "r-parsedate")
5961 (uri (cran-uri "parsedate" version))
5964 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5965 (build-system r-build-system)
5967 `(("r-rematch2" ,r-rematch2)))
5968 (home-page "https://github.com/gaborcsardi/parsedate")
5970 "Recognize and parse dates in various formats")
5972 "This package provides three functions for dealing with dates:
5973 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5974 time formats, @code{parse_date} parses dates in unspecified formats,
5975 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5976 (license license:gpl2)))
5978 (define-public r-abc-data
5985 (uri (cran-uri "abc.data" version))
5988 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5989 (properties `((upstream-name . "abc.data")))
5990 (build-system r-build-system)
5991 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5992 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5994 "This package contains data which are used by functions of the abc
5995 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5996 algorithms for performing parameter estimation, model selection, and
5998 (license license:gpl3+)))
6000 (define-public r-abc
6007 (uri (cran-uri "abc" version))
6010 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6011 (build-system r-build-system)
6013 `(("r-abc-data" ,r-abc-data)
6014 ("r-locfit" ,r-locfit)
6017 ("r-quantreg" ,r-quantreg)))
6018 (home-page "https://cran.r-project.org/web/packages/abc/")
6019 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6021 "This package implements several @dfn{Approximate Bayesian
6022 Computation} (ABC) algorithms for performing parameter estimation, model
6023 selection, and goodness-of-fit. Cross-validation tools are also available for
6024 measuring the accuracy of ABC estimates, and to calculate the
6025 misclassification probabilities of different models.")
6026 (license license:gpl3+)))
6028 (define-public r-zip
6035 (uri (cran-uri "zip" version))
6038 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6039 (build-system r-build-system)
6040 (home-page "https://github.com/gaborcsardi/zip")
6041 (synopsis "Cross-platform Zip compression")
6043 "This package provides a cross-platform Zip compression library for R.
6044 It is a replacement for the @code{zip} function, that does not require any
6045 additional external tools on any platform.")
6046 (license license:cc0)))
6048 (define-public r-openxlsx
6055 (uri (cran-uri "openxlsx" version))
6058 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
6059 (build-system r-build-system)
6061 `(("r-rcpp" ,r-rcpp)
6062 ("r-stringi" ,r-stringi)
6065 `(("r-knitr" ,r-knitr)))
6066 (home-page "https://github.com/awalker89/openxlsx")
6067 (synopsis "Read, write and edit XLSX files")
6069 "This package simplifies the creation of Excel @code{.xlsx} files by
6070 providing a high level interface to writing, styling and editing worksheets.
6071 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6072 and @code{XLConnect} packages with the added benefit of removing the
6073 dependency on Java.")
6074 (license license:gpl3)))
6076 (define-public r-rio
6083 (uri (cran-uri "rio" version))
6086 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6087 (build-system r-build-system)
6089 `(("r-curl" ,r-curl)
6090 ("r-data-table" ,r-data-table)
6091 ("r-foreign" ,r-foreign)
6092 ("r-haven" ,r-haven)
6093 ("r-openxlsx" ,r-openxlsx)
6094 ("r-readxl" ,r-readxl)
6095 ("r-tibble" ,r-tibble)))
6096 (home-page "https://github.com/leeper/rio")
6097 (synopsis "Swiss-army knife for data I/O")
6099 "This package provides streamlined data import and export infrastructure
6100 by making assumptions that the user is probably willing to make: @code{import}
6101 and @code{export} determine the data structure from the file extension,
6102 reasonable defaults are used for data import and export (e.g.,
6103 @code{stringsAsFactors=FALSE}), web-based import is natively
6104 supported (including from SSL/HTTPS), compressed files can be read directly
6105 without explicit decompression, and fast import packages are used where
6106 appropriate. An additional convenience function, @code{convert}, provides a
6107 simple method for converting between file types.")
6108 (license license:gpl2)))
6110 (define-public r-maptools
6117 (uri (cran-uri "maptools" version))
6120 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6121 (build-system r-build-system)
6123 `(("r-foreign" ,r-foreign)
6124 ("r-lattice" ,r-lattice)
6126 (home-page "https://r-forge.r-project.org/projects/maptools/")
6127 (synopsis "Tools for reading and handling spatial objects")
6129 "This package provides a set of tools for manipulating and reading
6130 geographic data, in particular ESRI Shapefiles. It includes binary access to
6131 GSHHG shoreline files. The package also provides interface wrappers for
6132 exchanging spatial objects with other R packages.")
6133 ;; The C source files from shapelib are released under the Expat license.
6134 ;; The R code is released under GPL version 2 or later.
6135 (license (list license:gpl2+
6138 (define-public r-later
6145 (uri (cran-uri "later" version))
6148 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6149 (build-system r-build-system)
6153 ("r-rlang" ,r-rlang)))
6155 `(("r-knitr" ,r-knitr)))
6156 (home-page "https://github.com/r-lib/later")
6157 (synopsis "Utilities for delaying function execution")
6159 "This package provides tools to execute arbitrary R or C functions some
6160 time after the current time, after the R execution stack has emptied.")
6161 (license license:gpl2+)))
6163 (define-public r-promises
6170 (uri (cran-uri "promises" version))
6173 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6174 (build-system r-build-system)
6176 `(("r-later" ,r-later)
6177 ("r-magrittr" ,r-magrittr)
6180 ("r-rlang" ,r-rlang)))
6182 `(("r-knitr" ,r-knitr)))
6183 (home-page "https://rstudio.github.io/promises")
6184 (synopsis "Abstractions for promise-based asynchronous programming")
6186 "This package provides fundamental abstractions for doing asynchronous
6187 programming in R using promises. Asynchronous programming is useful for
6188 allowing a single R process to orchestrate multiple tasks in the background
6189 while also attending to something else. Semantics are similar to JavaScript
6190 promises, but with a syntax that is idiomatic R.")
6191 (license license:expat)))
6193 (define-public r-dosnow
6200 (uri (cran-uri "doSNOW" version))
6203 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6204 (properties `((upstream-name . "doSNOW")))
6205 (build-system r-build-system)
6207 `(("r-foreach" ,r-foreach)
6208 ("r-iterators" ,r-iterators)
6209 ("r-snow" ,r-snow)))
6210 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6211 (synopsis "Foreach parallel adaptor for the snow package")
6213 "This package provides a parallel backend for the @code{%dopar%} function
6214 using the @code{snow} package.")
6215 (license license:gpl2)))
6217 (define-public r-snowfall
6220 (version "1.84-6.1")
6223 (uri (cran-uri "snowfall" version))
6225 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6226 (build-system r-build-system)
6228 `(("r-snow" ,r-snow)))
6229 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6230 (synopsis "Easier cluster computing")
6231 (description "This package is a usability wrapper around snow for easier
6232 development of parallel R programs. This package offers e.g. extended error
6233 checks, and additional functions. All functions work in sequential mode, too,
6234 if no cluster is present or wished. The package is also designed as connector
6235 to the cluster management tool @code{sfCluster}, but can also used without
6237 (license license:gpl2+)))
6239 (define-public r-rappdirs
6246 (uri (cran-uri "rappdirs" version))
6249 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6250 (build-system r-build-system)
6251 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6252 (synopsis "Determine where to save data, caches, and logs")
6254 "This package provides an easy way to determine which directories on the
6255 user's computer should be used to save data, caches and logs. It is a port of
6256 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6257 (license license:expat)))
6259 (define-public r-renv
6266 (uri (cran-uri "renv" version))
6269 "1jwm1ik600xswb53i1swjsnfrjjdffmmyk5k9hjc7kc8nlfl0ay5"))))
6270 (properties `((upstream-name . "renv")))
6271 (build-system r-build-system)
6273 `(("r-knitr" ,r-knitr)))
6274 (home-page "https://rstudio.github.io/renv")
6275 (synopsis "Project environments")
6277 "This package provides a dependency management toolkit for R. Using
6278 renv, you can create and manage project-local R libraries, save the state of
6279 these libraries to a lockfile, and later restore your library as required.
6280 Together, these tools can help make your projects more isolated, portable, and
6282 (license license:expat)))
6284 (define-public r-learnr
6291 (uri (cran-uri "learnr" version))
6294 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6295 (build-system r-build-system)
6297 `(("r-checkmate" ,r-checkmate)
6298 ("r-ellipsis" ,r-ellipsis)
6299 ("r-evaluate" ,r-evaluate)
6300 ("r-htmltools" ,r-htmltools)
6301 ("r-htmlwidgets" ,r-htmlwidgets)
6302 ("r-jsonlite" ,r-jsonlite)
6303 ("r-knitr" ,r-knitr)
6304 ("r-markdown" ,r-markdown)
6305 ("r-rappdirs" ,r-rappdirs)
6307 ("r-rmarkdown" ,r-rmarkdown)
6308 ("r-rprojroot" ,r-rprojroot)
6309 ("r-shiny" ,r-shiny)
6310 ("r-withr" ,r-withr)))
6311 (home-page "https://rstudio.github.io/learnr/")
6312 (synopsis "Interactive tutorials for R")
6314 "This package provides tools to create interactive tutorials using R
6315 Markdown. Use a combination of narrative, figures, videos, exercises, and
6316 quizzes to create self-paced tutorials for learning about R and R packages.")
6317 (license license:asl2.0)))
6319 (define-public r-analytics
6321 (name "r-analytics")
6326 (uri (cran-uri "analytics" version))
6329 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6330 (build-system r-build-system)
6333 ("r-cluster" ,r-cluster)
6334 ("r-fractal" ,r-fractal)
6335 ("r-lmtest" ,r-lmtest)
6338 ("r-powerplus" ,r-powerplus)
6339 ("r-robust" ,r-robust)
6340 ("r-trend" ,r-trend)
6344 (home-page "https://cran.r-project.org/web/packages/analytics/")
6345 (synopsis "Collection of data analysis tools")
6347 "This package is a collection of data analysis tools. It includes tools
6348 for regression outlier detection in a fitted linear model, stationary
6349 bootstrap using a truncated geometric distribution, a comprehensive test for
6350 weak stationarity, column means by group, weighted biplots, and a heuristic to
6351 obtain a better initial configuration in non-metric MDS.")
6352 (license license:gpl2)))
6354 (define-public r-reticulate
6356 (name "r-reticulate")
6361 (uri (cran-uri "reticulate" version))
6364 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6365 (build-system r-build-system)
6366 (inputs `(("python" ,python)))
6368 `(("r-rappdirs" ,r-rappdirs)
6369 ("r-jsonlite" ,r-jsonlite)
6370 ("r-matrix" ,r-matrix)
6371 ("r-rcpp" ,r-rcpp)))
6373 `(("r-knitr" ,r-knitr)))
6374 (home-page "https://github.com/rstudio/reticulate")
6375 (synopsis "R interface to Python")
6377 "This package provides an interface from R to Python modules, classes,
6378 and functions. When calling into Python, R data types are automatically
6379 converted to their equivalent Python types. When values are returned from
6380 Python to R they are converted back to R types.")
6381 (license license:asl2.0)))
6383 (define-public r-bibtex
6390 (uri (cran-uri "bibtex" version))
6393 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6394 (build-system r-build-system)
6395 (propagated-inputs `(("r-stringr" ,r-stringr)))
6396 (home-page "https://github.com/romainfrancois/bibtex")
6397 (synopsis "Bibtex parser")
6398 (description "This package provides a utility for R to parse a bibtex
6400 (license license:gpl2+)))
6402 (define-public r-ggseqlogo
6404 (name "r-ggseqlogo")
6409 (uri (cran-uri "ggseqlogo" version))
6412 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6413 (build-system r-build-system)
6414 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6415 (home-page "https://github.com/omarwagih/ggseqlogo")
6416 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6418 "The range of functions provided by this package makes it possible to
6419 draw highly versatile genomic sequence logos. Features include, but are not
6420 limited to, modifying colour schemes and fonts used to draw the logo,
6421 generating multiple logo plots, and aiding the visualisation with annotations.
6422 Sequence logos can easily be combined with other ggplot2 plots.")
6423 ;; Unspecified version of the LGPL.
6424 (license license:lgpl3+)))
6426 (define-public r-ggsci
6433 (uri (cran-uri "ggsci" version))
6436 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6437 (build-system r-build-system)
6439 `(("r-ggplot2" ,r-ggplot2)
6440 ("r-scales" ,r-scales)))
6441 (home-page "https://nanx.me/ggsci/")
6442 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6444 "This package provides a collection of ggplot2 color palettes inspired by
6445 plots in scientific journals, data visualization libraries, science fiction
6446 movies, and TV shows.")
6447 (license license:gpl3)))
6449 (define-public r-ggsignif
6456 (uri (cran-uri "ggsignif" version))
6459 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6460 (build-system r-build-system)
6462 `(("r-knitr" ,r-knitr)))
6464 `(("r-ggplot2" ,r-ggplot2)))
6465 (home-page "https://github.com/const-ae/ggsignif")
6466 (synopsis "Significance brackets for ggplot2")
6468 "Enrich your ggplots with group-wise comparisons. This package provides
6469 an easy way to indicate if two groups are significantly different. Commonly
6470 this is shown by a bracket on top connecting the groups of interest which
6471 itself is annotated with the level of significance. The package provides a
6472 single layer that takes the groups for comparison and the test as arguments
6473 and adds the annotation to the plot.")
6474 (license license:gpl3)))
6476 (define-public r-rstatix
6483 (uri (cran-uri "rstatix" version))
6486 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6487 (properties `((upstream-name . "rstatix")))
6488 (build-system r-build-system)
6490 `(("r-broom" ,r-broom)
6492 ("r-corrplot" ,r-corrplot)
6493 ("r-dplyr" ,r-dplyr)
6494 ("r-generics" ,r-generics)
6495 ("r-magrittr" ,r-magrittr)
6496 ("r-purrr" ,r-purrr)
6497 ("r-rlang" ,r-rlang)
6498 ("r-tibble" ,r-tibble)
6499 ("r-tidyr" ,r-tidyr)
6500 ("r-tidyselect" ,r-tidyselect)))
6501 (home-page "https://rpkgs.datanovia.com/rstatix/")
6502 (synopsis "Pipe-friendly framework for basic statistical tests")
6504 "This package provides a simple and intuitive pipe-friendly framework,
6505 coherent with the @code{tidyverse} design philosophy, for performing basic
6506 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6507 correlation analyses. The output of each test is automatically transformed
6508 into a tidy data frame to facilitate visualization. Additional functions are
6509 available for reshaping, reordering, manipulating and visualizing correlation
6511 (license license:gpl2)))
6513 (define-public r-ggpubr
6520 (uri (cran-uri "ggpubr" version))
6523 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6524 (build-system r-build-system)
6526 `(("r-cowplot" ,r-cowplot)
6527 ("r-dplyr" ,r-dplyr)
6528 ("r-ggplot2" ,r-ggplot2)
6529 ("r-ggrepel" ,r-ggrepel)
6530 ("r-ggsci" ,r-ggsci)
6531 ("r-ggsignif" ,r-ggsignif)
6533 ("r-gridextra" ,r-gridextra)
6534 ("r-magrittr" ,r-magrittr)
6535 ("r-polynom" ,r-polynom)
6536 ("r-purrr" ,r-purrr)
6537 ("r-rlang" ,r-rlang)
6538 ("r-scales" ,r-scales)
6539 ("r-rstatix" ,r-rstatix)
6540 ("r-tibble" ,r-tibble)
6541 ("r-tidyr" ,r-tidyr)))
6542 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6543 (synopsis "ggplot2-based publication-ready plots")
6545 "The ggplot2 package is an excellent and flexible package for elegant
6546 data visualization in R. However the default generated plots require some
6547 formatting before we can send them for publication. The ggpubr package
6548 provides some easy-to-use functions for creating and customizing ggplot2-based
6549 publication-ready plots.")
6550 (license license:gpl2)))
6552 (define-public r-ellipse
6559 (uri (cran-uri "ellipse" version))
6562 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6563 (build-system r-build-system)
6564 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6565 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6567 "This package contains various routines for drawing ellipses and
6568 ellipse-like confidence regions, implementing the plots described in Murdoch
6569 and Chow (1996), A graphical display of large correlation matrices, The
6570 American Statistician 50, 178-180. There are also routines implementing the
6571 profile plots described in Bates and Watts (1988), Nonlinear Regression
6572 Analysis and its Applications.")
6573 (license license:gpl2+)))
6575 (define-public r-flashclust
6577 (name "r-flashclust")
6582 (uri (cran-uri "flashClust" version))
6585 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6586 (properties `((upstream-name . "flashClust")))
6587 (build-system r-build-system)
6588 (native-inputs `(("gfortran" ,gfortran)))
6589 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6590 (synopsis "Implementation of optimal hierarchical clustering")
6592 "This package provides a fast implementation of hierarchical
6594 (license license:gpl2+)))
6596 (define-public r-factominer
6598 (name "r-factominer")
6603 (uri (cran-uri "FactoMineR" version))
6606 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6607 (properties `((upstream-name . "FactoMineR")))
6608 (build-system r-build-system)
6611 ("r-cluster" ,r-cluster)
6612 ("r-ellipse" ,r-ellipse)
6613 ("r-flashclust" ,r-flashclust)
6614 ("r-ggplot2" ,r-ggplot2)
6615 ("r-ggrepel" ,r-ggrepel)
6616 ("r-lattice" ,r-lattice)
6617 ("r-leaps" ,r-leaps)
6619 ("r-scatterplot3d" ,r-scatterplot3d)))
6620 (home-page "http://factominer.free.fr")
6621 (synopsis "Multivariate exploratory data analysis and data mining")
6623 "This package provides exploratory data analysis methods to summarize,
6624 visualize and describe datasets. The main principal component methods are
6625 available, those with the largest potential in terms of applications:
6626 principal component analysis (PCA) when variables are quantitative,
6627 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6628 variables are categorical, Multiple Factor Analysis when variables are
6629 structured in groups, etc. and hierarchical cluster analysis.")
6630 (license license:gpl2+)))
6632 (define-public r-factoextra
6634 (name "r-factoextra")
6639 (uri (cran-uri "factoextra" version))
6642 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6643 (build-system r-build-system)
6645 `(("r-abind" ,r-abind)
6646 ("r-cluster" ,r-cluster)
6647 ("r-dendextend" ,r-dendextend)
6648 ("r-factominer" ,r-factominer)
6649 ("r-ggplot2" ,r-ggplot2)
6650 ("r-ggpubr" ,r-ggpubr)
6651 ("r-ggrepel" ,r-ggrepel)
6652 ("r-reshape2" ,r-reshape2)
6653 ("r-tidyr" ,r-tidyr)))
6654 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6655 (synopsis "Extract and visualize the results of multivariate data analyses")
6657 "This package provides some easy-to-use functions to extract and
6658 visualize the output of multivariate data analyses, including
6659 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6660 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6661 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6662 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6663 packages. It contains also functions for simplifying some clustering analysis
6664 steps and provides ggplot2-based elegant data visualization.")
6665 (license license:gpl2)))
6667 (define-public r-fansi
6674 (uri (cran-uri "fansi" version))
6677 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6678 (build-system r-build-system)
6680 `(("r-knitr" ,r-knitr))) ; for vignettes
6681 (home-page "https://github.com/brodieG/fansi")
6682 (synopsis "ANSI control sequence aware string functions")
6684 "This package provides counterparts to R string manipulation functions
6685 that account for the effects of ANSI text formatting control sequences.")
6686 (license license:gpl2+)))
6688 (define-public r-nbclust
6695 (uri (cran-uri "NbClust" version))
6698 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6699 (properties `((upstream-name . "NbClust")))
6700 (build-system r-build-system)
6701 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6702 (synopsis "Determine the best number of clusters in a data set")
6704 "NbClust provides 30 indexes for determining the optimal number of
6705 clusters in a data set and offers the best clustering scheme from different
6706 results to the user.")
6707 (license license:gpl2)))
6709 (define-public r-hdf5r
6716 (uri (cran-uri "hdf5r" version))
6719 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
6720 (build-system r-build-system)
6725 `(("r-bit64" ,r-bit64)
6728 `(("r-knitr" ,r-knitr)))
6729 (home-page "https://hhoeflin.github.io/hdf5r")
6730 (synopsis "Interface to the HDF5 binary data format")
6732 "HDF5 is a data model, library and file format for storing and managing
6733 large amounts of data. This package provides a nearly feature complete,
6734 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6735 functionality is added so that HDF5 objects behave very similar to their
6736 corresponding R counterparts.")
6737 (license license:asl2.0)))
6739 (define-public r-itertools
6741 (name "r-itertools")
6746 (uri (cran-uri "itertools" version))
6749 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6750 (build-system r-build-system)
6752 `(("r-iterators" ,r-iterators)))
6753 (home-page "https://cran.r-project.org/web/packages/itertools/")
6754 (synopsis "Iterator tools")
6756 "This package provides various tools for creating iterators, many
6757 patterned after functions in the Python @code{itertools} module, and others
6758 patterned after functions in the snow package.")
6759 (license license:gpl2)))
6761 (define-public r-polynom
6768 (uri (cran-uri "polynom" version))
6771 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6772 (build-system r-build-system)
6773 (home-page "https://cran.r-project.org/web/packages/polynom/")
6774 (synopsis "Functions for univariate polynomial manipulations")
6776 "This package provides a collection of functions to implement a class for
6777 univariate polynomial manipulations.")
6778 (license license:gpl2)))
6780 (define-public r-gbrd
6787 (uri (cran-uri "gbRd" version))
6790 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6791 (properties `((upstream-name . "gbRd")))
6792 (build-system r-build-system)
6793 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6794 (synopsis "Utilities for processing Rd objects and files")
6796 "This package provides utilities for processing Rd objects and files.
6797 Extract argument descriptions and other parts of the help pages of
6799 (license license:gpl2+)))
6801 (define-public r-rjags
6808 (uri (cran-uri "rjags" version))
6811 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6812 (build-system r-build-system)
6814 `(("r-coda" ,r-coda)))
6818 `(("pkg-config" ,pkg-config)))
6819 (home-page "http://mcmc-jags.sourceforge.net")
6820 (synopsis "Bayesian graphical models using MCMC")
6822 "This package provides an R interface to the JAGS MCMC library. JAGS is
6823 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6824 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6825 (license license:gpl2)))
6827 (define-public r-rdpack
6834 (uri (cran-uri "Rdpack" version))
6837 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6838 (properties `((upstream-name . "Rdpack")))
6839 (build-system r-build-system)
6841 `(("r-bibtex" ,r-bibtex)
6842 ("r-gbrd" ,r-gbrd)))
6843 (home-page "https://github.com/GeoBosh/Rdpack")
6844 (synopsis "Update and manipulate Rd documentation objects")
6846 "This package provides functions for manipulation of R documentation
6847 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6848 updating Rd documentation for functions, methods and classes; it also includes
6849 Rd macros for citations and import of references from bibtex files for use in
6850 Rd files and roxygen2 comments, as well as many functions for manipulation of
6851 references and Rd files.")
6852 (license license:gpl2+)))
6854 (define-public r-officer
6861 (uri (cran-uri "officer" version))
6864 "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
6865 (build-system r-build-system)
6867 `(("r-magrittr" ,r-magrittr)
6873 `(("r-knitr" ,r-knitr)))
6874 (home-page "https://davidgohel.github.io/officer")
6875 (synopsis "Manipulation of Word and PowerPoint documents")
6877 "This package provides tools to access and manipulate Word and PowerPoint
6878 documents from R. The package focuses on tabular and graphical reporting from
6879 R; it also provides two functions that let users get document content into
6880 data objects. A set of functions lets add and remove images, tables and
6881 paragraphs of text in new or existing documents. When working with PowerPoint
6882 presentations, slides can be added or removed; shapes inside slides can also
6883 be added or removed. When working with Word documents, a cursor can be used
6884 to help insert or delete content at a specific location in the document.")
6885 (license license:gpl3)))
6887 (define-public r-profilemodel
6889 (name "r-profilemodel")
6894 (uri (cran-uri "profileModel" version))
6897 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6898 (properties `((upstream-name . "profileModel")))
6899 (build-system r-build-system)
6900 (home-page "https://github.com/ikosmidis/profileModel")
6901 (synopsis "Profiling inference functions for various model classes")
6903 "This package provides tools that can be used to calculate, evaluate,
6904 plot and use for inference the profiles of *arbitrary* inference functions for
6905 arbitrary @code{glm}-like fitted models with linear predictors. More information
6906 on the methods that are implemented can be found in Kosmidis (2008)
6907 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6908 (license license:gpl2+)))
6910 (define-public r-brglm
6917 (uri (cran-uri "brglm" version))
6920 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6921 (properties `((upstream-name . "brglm")))
6922 (build-system r-build-system)
6924 `(("r-profilemodel" ,r-profilemodel)))
6925 (home-page "https://github.com/ikosmidis/brglm")
6926 (synopsis "Bias reduction in binomial-response generalized linear models")
6928 "Fit generalized linear models with binomial responses using either an
6929 adjusted-score approach to bias reduction or maximum penalized likelihood
6930 where penalization is by Jeffreys invariant prior. These procedures return
6931 estimates with improved frequentist properties (bias, mean squared error) that
6932 are always finite even in cases where the maximum likelihood estimates are
6933 infinite (data separation). Fitting takes place by fitting generalized linear
6934 models on iteratively updated pseudo-data. The interface is essentially the
6935 same as @code{glm}. More flexibility is provided by the fact that custom
6936 pseudo-data representations can be specified and used for model fitting.
6937 Functions are provided for the construction of confidence intervals for the
6938 reduced-bias estimates.")
6939 (license license:gpl2+)))
6941 (define-public r-entropy
6948 (uri (cran-uri "entropy" version))
6951 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6952 (properties `((upstream-name . "entropy")))
6953 (build-system r-build-system)
6954 (home-page "https://www.strimmerlab.org/software/entropy/")
6955 (synopsis "Estimation of entropy, mutual information and related quantities")
6957 "This package implements various estimators of entropy, such as the
6958 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6959 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6960 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6961 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6962 mutual information, and chi-squared statistic of independence. In addition
6963 there are functions for discretizing continuous random variables.")
6964 (license license:gpl3+)))
6966 (define-public r-abn
6973 (uri (cran-uri "abn" version))
6976 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6977 (build-system r-build-system)
6981 `(("r-boot" ,r-boot)
6982 ("r-brglm" ,r-brglm)
6983 ("r-entropy" ,r-entropy)
6986 ("r-moments" ,r-moments)
6989 ("r-rcpparmadillo" ,r-rcpparmadillo)
6990 ("r-rjags" ,r-rjags)))
6991 (home-page "https://r-bayesian-networks.org/")
6992 (synopsis "Modelling multivariate data with additive bayesian networks")
6994 "Bayesian network analysis is a form of probabilistic graphical models
6995 which derives from empirical data a directed acyclic graph, DAG, describing
6996 the dependency structure between random variables. An additive Bayesian
6997 network model consists of a form of a DAG where each node comprises a
6998 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6999 equivalent to Bayesian multivariate regression using graphical modelling, they
7000 generalises the usual multivariable regression, GLM, to multiple dependent
7001 variables. This package provides routines to help determine optimal Bayesian
7002 network models for a given data set, where these models are used to identify
7003 statistical dependencies in messy, complex data.")
7004 (license license:gpl2+)))
7006 (define-public r-acd
7013 (uri (cran-uri "ACD" version))
7016 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7017 (properties `((upstream-name . "ACD")))
7018 (build-system r-build-system)
7019 (home-page "https://cran.r-project.org/web/packages/ACD/")
7020 (synopsis "Categorical data analysis with complete or missing responses")
7022 "This package provides tools for categorical data analysis with complete
7023 or missing responses.")
7024 (license license:gpl2+)))
7026 (define-public r-acdm
7033 (uri (cran-uri "ACDm" version))
7036 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7037 (properties `((upstream-name . "ACDm")))
7038 (build-system r-build-system)
7040 `(("r-dplyr" ,r-dplyr)
7041 ("r-ggplot2" ,r-ggplot2)
7043 ("r-rsolnp" ,r-rsolnp)
7045 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7046 (synopsis "Tools for Autoregressive Conditional Duration Models")
7048 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7049 and Russell, 1998) models. It creates trade, price or volume durations from
7050 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7052 (license license:gpl2+)))
7054 (define-public r-overlap
7061 (uri (cran-uri "overlap" version))
7064 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7065 (build-system r-build-system)
7066 (home-page "https://cran.r-project.org/web/packages/overlap/")
7067 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7069 "This package provides functions to fit kernel density functions to data
7070 on temporal activity patterns of animals; estimate coefficients of overlapping
7071 of densities for two species; and calculate bootstrap estimates of confidence
7073 (license license:gpl3+)))
7075 (define-public r-snakecase
7077 (name "r-snakecase")
7082 (uri (cran-uri "snakecase" version))
7085 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7086 (build-system r-build-system)
7088 `(("r-stringi" ,r-stringi)
7089 ("r-stringr" ,r-stringr)))
7090 (home-page "https://github.com/Tazinho/snakecase")
7091 (synopsis "Convert strings into any case")
7093 "This package provides a consistent, flexible and easy to use tool to
7094 parse and convert strings into cases like snake or camel among others.")
7095 (license license:gpl3)))
7097 (define-public r-prediction
7099 (name "r-prediction")
7104 (uri (cran-uri "prediction" version))
7107 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7108 (build-system r-build-system)
7110 `(("r-data-table" ,r-data-table)))
7111 (home-page "https://github.com/leeper/prediction")
7112 (synopsis "Tidy, type-safe prediction methods")
7114 "This package provides the @code{prediction()} function, a type-safe
7115 alternative to @code{predict()} that always returns a data frame. The package
7116 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7117 from the @code{stats} package, as well as numerous other model classes from
7118 other add-on packages.")
7119 (license license:expat)))
7121 (define-public r-insight
7128 (uri (cran-uri "insight" version))
7131 "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
7132 (build-system r-build-system)
7134 `(("r-knitr" ,r-knitr)))
7135 (home-page "https://easystats.github.io/insight/")
7136 (synopsis "Easy access to model information for various model objects")
7138 "This package provides a tool to provide an easy, intuitive and
7139 consistent access to information contained in various R models, like model
7140 formulas, model terms, information about random effects, data that was used to
7141 fit the model or data from response variables. The package mainly revolves
7142 around two types of functions: Functions that find (the names of) information,
7143 starting with @code{find_}, and functions that get the underlying data,
7144 starting with @code{get_}. The package has a consistent syntax and works with
7145 many different model objects, where otherwise functions to access these
7146 information are missing.")
7147 (license license:gpl3)))
7149 (define-public r-sjlabelled
7151 (name "r-sjlabelled")
7156 (uri (cran-uri "sjlabelled" version))
7159 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
7160 (build-system r-build-system)
7162 `(("r-insight" ,r-insight)))
7164 `(("r-knitr" ,r-knitr)))
7165 (home-page "https://github.com/strengejacke/sjlabelled")
7166 (synopsis "Labelled data utility functions")
7168 "This package provides a collection of functions dealing with labelled
7169 data, like reading and writing data between R and other statistical software
7170 packages. This includes easy ways to get, set or change value and variable
7171 label attributes, to convert labelled vectors into factors or numeric (and
7172 vice versa), or to deal with multiple declared missing values.")
7173 (license license:gpl3)))
7175 (define-public r-sjmisc
7182 (uri (cran-uri "sjmisc" version))
7185 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
7186 (build-system r-build-system)
7188 `(("r-dplyr" ,r-dplyr)
7189 ("r-insight" ,r-insight)
7190 ("r-magrittr" ,r-magrittr)
7191 ("r-purrr" ,r-purrr)
7192 ("r-rlang" ,r-rlang)
7193 ("r-sjlabelled" ,r-sjlabelled)
7194 ("r-tidyselect" ,r-tidyselect)))
7196 `(("r-knitr" ,r-knitr)))
7197 (home-page "https://github.com/strengejacke/sjmisc")
7198 (synopsis "Data and variable transformation functions")
7200 "This package is a collection of miscellaneous utility functions,
7201 supporting data transformation tasks like recoding, dichotomizing or grouping
7202 variables, setting and replacing missing values. The data transformation
7203 functions also support labelled data, and all integrate seamlessly into a
7204 tidyverse workflow.")
7205 (license license:gpl3)))
7207 (define-public r-nortest
7214 (uri (cran-uri "nortest" version))
7217 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7218 (build-system r-build-system)
7219 (home-page "https://cran.r-project.org/web/packages/nortest/")
7220 (synopsis "Tests for normality")
7222 "This package provides five omnibus tests for testing the composite
7223 hypothesis of normality.")
7224 (license license:gpl2+)))
7226 (define-public r-moonbook
7233 (uri (cran-uri "moonBook" version))
7236 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7237 (properties `((upstream-name . "moonBook")))
7238 (build-system r-build-system)
7240 `(("r-magrittr" ,r-magrittr)
7241 ("r-nortest" ,r-nortest)
7242 ("r-purrr" ,r-purrr)
7243 ("r-sjmisc" ,r-sjmisc)
7244 ("r-stringr" ,r-stringr)
7245 ("r-survival" ,r-survival)))
7246 (home-page "https://github.com/cardiomoon/moonBook")
7247 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7249 "This package provides several analysis-related functions for the book
7250 entitled \"R statistics and graph for medical articles\" (written in Korean),
7251 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7253 (license license:gpl2)))
7255 (define-public r-flextable
7257 (name "r-flextable")
7262 (uri (cran-uri "flextable" version))
7265 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7266 (build-system r-build-system)
7268 `(("r-base64enc" ,r-base64enc)
7269 ("r-data-table" ,r-data-table)
7270 ("r-gdtools" ,r-gdtools)
7271 ("r-htmltools" ,r-htmltools)
7272 ("r-knitr" ,r-knitr)
7273 ("r-officer" ,r-officer)
7274 ("r-rlang" ,r-rlang)
7275 ("r-rmarkdown" ,r-rmarkdown)
7277 ("r-xml2" ,r-xml2)))
7278 (home-page "https://davidgohel.github.io/flextable")
7279 (synopsis "Functions for tabular reporting")
7281 "This package provides tools to create pretty tables for HTML documents
7282 and other formats. Functions are provided to let users create tables, modify
7283 and format their content. It extends the @code{officer} package and can be
7284 used within R markdown documents when rendering to HTML and to Word
7286 (license license:gpl3)))
7288 (define-public r-writexl
7295 (uri (cran-uri "writexl" version))
7298 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
7299 (build-system r-build-system)
7300 (inputs `(("zlib" ,zlib)))
7301 (home-page "https://github.com/ropensci/writexl")
7302 (synopsis "Export data frames to xlsx format")
7304 "This package provides a data frame to xlsx exporter based on
7306 (license license:bsd-2)))
7308 (define-public r-biasedurn
7310 (name "r-biasedurn")
7315 (uri (cran-uri "BiasedUrn" version))
7318 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7319 (properties `((upstream-name . "BiasedUrn")))
7320 (build-system r-build-system)
7321 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7322 (synopsis "Biased Urn model distributions")
7324 "This package provides statistical models of biased sampling in the form
7325 of univariate and multivariate noncentral hypergeometric distributions,
7326 including Wallenius' noncentral hypergeometric distribution and Fisher's
7327 noncentral hypergeometric distribution (also called extended hypergeometric
7329 (license license:gpl3)))
7331 (define-public r-goplot
7338 (uri (cran-uri "GOplot" version))
7341 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7342 (properties `((upstream-name . "GOplot")))
7343 (build-system r-build-system)
7345 `(("r-ggdendro" ,r-ggdendro)
7346 ("r-ggplot2" ,r-ggplot2)
7347 ("r-gridextra" ,r-gridextra)
7348 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7349 (home-page "https://github.com/wencke/wencke.github.io")
7350 (synopsis "Visualization of functional analysis data")
7352 "This package provides an implementation of multilayered visualizations
7353 for enhanced graphical representation of functional analysis data. It
7354 combines and integrates omics data derived from expression and functional
7355 annotation enrichment analyses. Its plotting functions have been developed
7356 with an hierarchical structure in mind: starting from a general overview to
7357 identify the most enriched categories (modified bar plot, bubble plot) to a
7358 more detailed one displaying different types of relevant information for the
7359 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7360 Venn diagram, heatmap).")
7361 (license license:gpl2)))
7363 (define-public r-getopt
7370 (uri (cran-uri "getopt" version))
7373 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7374 (build-system r-build-system)
7375 (home-page "https://github.com/trevorld/getopt")
7376 (synopsis "Command-line option processor for R")
7378 "This package is designed to be used with Rscript to write shebang
7379 scripts that accept short and long options. Many users will prefer to
7380 use the packages @code{optparse} or @code{argparse} which add extra
7381 features like automatically generated help options and usage texts,
7382 support for default values, positional argument support, etc.")
7383 (license license:gpl2+)))
7385 (define-public r-findpython
7387 (name "r-findpython")
7392 (uri (cran-uri "findpython" version))
7395 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7396 (build-system r-build-system)
7397 (home-page "https://github.com/trevorld/findpython")
7398 (synopsis "Functions to find an acceptable Python binary")
7400 "This package was designed to find an acceptable Python binary that
7401 matches version and feature constraints.")
7402 (license license:expat)))
7404 ;; This in not the same as "r-argparser"
7405 (define-public r-argparse
7412 (uri (cran-uri "argparse" version))
7415 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7416 (build-system r-build-system)
7417 (inputs `(("python" ,python)))
7419 `(("r-findpython" ,r-findpython)
7420 ("r-jsonlite" ,r-jsonlite)
7422 (home-page "https://github.com/trevorld/argparse")
7423 (synopsis "Command line optional and positional argument parser")
7425 "This package provides a command line parser to be used with Rscript to
7426 write shebang scripts that gracefully accept positional and optional arguments
7427 and automatically generate usage notices.")
7428 (license license:gpl2+)))
7430 (define-public r-hash
7437 (uri (cran-uri "hash" version))
7440 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7441 (build-system r-build-system)
7442 (home-page "https://cran.r-project.org/web/packages/hash/")
7443 (synopsis "Implementation of hash/associated arrays/dictionaries")
7445 "This package implements a data structure similar to hashes in Perl and
7446 dictionaries in Python but with a purposefully R flavor. For objects of
7447 appreciable size, access using hashes outperforms native named lists and
7449 (license license:gpl2+)))
7451 (define-public r-orddom
7458 (uri (cran-uri "orddom" version))
7461 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7462 (build-system r-build-system)
7463 (propagated-inputs `(("r-psych" ,r-psych)))
7464 (home-page "https://cran.r-project.org/web/packages/orddom/")
7465 (synopsis "Ordinal dominance statistics")
7467 "This package provides tools to compute ordinal, statistics and effect
7468 sizes as an alternative to mean comparison: Cliff's delta or success rate
7469 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7470 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7471 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7472 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7473 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7474 Group (Non-)Overlap considerations.")
7475 (license license:gpl2)))
7477 (define-public r-deriv
7484 (uri (cran-uri "Deriv" version))
7487 "16rq65x1xhxvqwn4p427divay3b9fgam2lxccxb8529adnrxmw6p"))))
7488 (properties `((upstream-name . "Deriv")))
7489 (build-system r-build-system)
7490 (home-page "https://cran.r-project.org/web/packages/Deriv")
7491 (synopsis "Symbolic differentiation")
7493 "This package provides an R-based solution for symbolic differentiation.
7494 It admits user-defined functions as well as function substitution in arguments
7495 of functions to be differentiated. Some symbolic simplification is part of
7497 (license license:gpl3+)))
7499 (define-public r-doby
7506 (uri (cran-uri "doBy" version))
7509 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7510 (properties `((upstream-name . "doBy")))
7511 (build-system r-build-system)
7513 `(("r-broom" ,r-broom)
7514 ("r-deriv" ,r-deriv)
7515 ("r-dplyr" ,r-dplyr)
7516 ("r-ggplot2" ,r-ggplot2)
7517 ("r-magrittr" ,r-magrittr)
7519 ("r-matrix" ,r-matrix)
7520 ("r-pbkrtest" ,r-pbkrtest)
7521 ("r-tibble" ,r-tibble)))
7523 `(("r-knitr" ,r-knitr)))
7524 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7525 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7527 "This package contains:
7530 @item facilities for working with grouped data: @code{do}
7531 something to data stratified @code{by} some variables.
7532 @item implementations of least-squares means, general linear contrasts, and
7533 @item miscellaneous other utilities.
7535 (license license:gpl2+)))
7537 (define-public r-refgenome
7539 (name "r-refgenome")
7544 (uri (cran-uri "refGenome" version))
7547 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7548 (properties `((upstream-name . "refGenome")))
7549 (build-system r-build-system)
7553 ("r-rsqlite" ,r-rsqlite)))
7554 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7556 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7558 "This package contains functionality for importing and managing of
7559 downloaded genome annotation data from the Ensembl genome browser (European
7560 Bioinformatics Institute) and from the UCSC genome browser (University of
7561 California, Santa Cruz) and annotation routines for genomic positions and
7562 splice site positions.")
7563 (license license:gpl2)))
7565 (define-public r-basix
7572 (uri (cran-uri "BASIX" version))
7575 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7576 (properties `((upstream-name . "BASIX")))
7577 (build-system r-build-system)
7578 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7579 (synopsis "Efficient C/C++ toolset for R")
7581 "BASIX provides some efficient C/C++ implementations of native R
7582 procedures to speed up calculations in R.")
7583 (license license:gpl2)))
7585 (define-public r-blockfest
7587 (name "r-blockfest")
7592 (uri (cran-uri "BlockFeST" version))
7595 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7596 (properties `((upstream-name . "BlockFeST")))
7597 (build-system r-build-system)
7598 (propagated-inputs `(("r-basix" ,r-basix)))
7599 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7600 (synopsis "Bayesian calculation of region-specific fixation index")
7602 "This package provides an R implementation of an extension of the
7603 BayeScan software for codominant markers, adding the option to group
7604 individual SNPs into pre-defined blocks. A typical application of this new
7605 approach is the identification of genomic regions, genes, or gene sets
7606 containing one or more SNPs that evolved under directional selection.")
7607 (license license:gpl2)))
7609 (define-public r-proc
7616 (uri (cran-uri "pROC" version))
7619 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7620 (properties `((upstream-name . "pROC")))
7621 (build-system r-build-system)
7623 `(("r-plyr" ,r-plyr)
7624 ("r-rcpp" ,r-rcpp)))
7625 (home-page "https://web.expasy.org/pROC/")
7626 (synopsis "Display and analyze ROC curves")
7628 "This package provides tools for visualizing, smoothing and comparing
7629 receiver operating characteristic (ROC curves). The area under the
7630 curve (AUC) can be compared with statistical tests based on U-statistics or
7631 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7632 (license license:gpl3+)))
7634 (define-public r-rootsolve
7636 (name "r-rootsolve")
7641 (uri (cran-uri "rootSolve" version))
7644 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7645 (properties `((upstream-name . "rootSolve")))
7646 (build-system r-build-system)
7647 (native-inputs `(("gfortran" ,gfortran)))
7648 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7649 (synopsis "Tools for the analysis of ordinary differential equations")
7651 "This package provides routines to find the root of nonlinear functions,
7652 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7653 differential equations} (ODE). It includes routines that:
7656 @item generate gradient and jacobian matrices (full and banded),
7657 @item find roots of non-linear equations by the Newton-Raphson method,
7658 @item estimate steady-state conditions of a system of (differential) equations
7659 in full, banded or sparse form, using the Newton-Raphson method, or by
7660 dynamically running,
7661 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7662 and 3-D partial differential equations, that have been converted to ordinary
7663 differential equations by numerical differencing (using the method-of-lines
7666 (license license:gpl2+)))
7668 (define-public r-abcanalysis
7670 (name "r-abcanalysis")
7675 (uri (cran-uri "ABCanalysis" version))
7677 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7678 (properties `((upstream-name . "ABCanalysis")))
7679 (build-system r-build-system)
7680 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7681 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7682 (synopsis "Computed ABC Analysis")
7684 "Multivariate data sets often differ in several factors or derived statistical
7685 parameters, which have to be selected for a valid interpretation. Basing this
7686 selection on traditional statistical limits leads occasionally to the perception
7687 of losing information from a data set. This package provides tools to calculate
7688 these limits on the basis of the mathematical properties of the distribution of
7689 the analyzed items.")
7690 (license license:gpl3)))
7692 (define-public r-slam
7699 (uri (cran-uri "slam" version))
7701 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7702 (build-system r-build-system)
7703 (home-page "https://cran.r-project.org/web/packages/slam/")
7704 (synopsis "Sparse lightweight arrays and matrices")
7706 "This package contains data structures and algorithms for sparse arrays and matrices,
7707 based on index arrays and simple triplet representations, respectively.")
7708 (license license:gpl2)))
7710 (define-public r-manipulatewidget
7712 (name "r-manipulatewidget")
7717 (uri (cran-uri "manipulateWidget" version))
7719 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7721 `((upstream-name . "manipulateWidget")))
7722 (build-system r-build-system)
7724 `(("r-base64enc" ,r-base64enc)
7725 ("r-codetools" ,r-codetools)
7726 ("r-htmltools" ,r-htmltools)
7727 ("r-htmlwidgets" ,r-htmlwidgets)
7728 ("r-knitr" ,r-knitr)
7729 ("r-miniui" ,r-miniui)
7730 ("r-shiny" ,r-shiny)
7731 ("r-webshot" ,r-webshot)))
7732 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7733 (synopsis "Add even more interactivity to interactive charts")
7735 "This package lets you create in just a few lines of R code a nice user interface to
7736 modify the data or the graphical parameters of one or multiple interactive
7737 charts. It is useful to quickly explore visually some data or for package
7738 developers to generate user interfaces easy to maintain.")
7739 (license license:gpl2+)))
7748 (uri (cran-uri "A3" version))
7750 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7751 (properties `((upstream-name . "A3")))
7752 (build-system r-build-system)
7754 `(("r-pbapply" ,r-pbapply)
7755 ("r-xtable" ,r-xtable)))
7756 (home-page "https://cran.r-project.org/web/packages/A3/")
7757 (synopsis "Error metrics for predictive models")
7759 "This package supplies tools for tabulating and analyzing the results of predictive
7760 models. The methods employed are applicable to virtually any predictive model
7761 and make comparisons between different methodologies straightforward.")
7762 (license license:gpl2+)))
7764 (define-public r-infotheo
7771 (uri (cran-uri "infotheo" version))
7774 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7775 (build-system r-build-system)
7776 (home-page "http://homepage.meyerp.com/software")
7777 (synopsis "Information-theoretic measures")
7779 "This package implements various measures of information theory based on
7780 several entropy estimators.")
7781 (license license:gpl3+)))
7783 (define-public r-abcoptim
7790 (uri (cran-uri "ABCoptim" version))
7792 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7793 (properties `((upstream-name . "ABCoptim")))
7794 (build-system r-build-system)
7795 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7796 (home-page "https://github.com/gvegayon/ABCoptim/")
7797 (synopsis "Optimization of Artificial Bee Colony algorithm")
7799 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7800 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7801 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7802 algorithms, and uses only common control parameters such as colony size and
7803 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7804 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7805 This version is a work-in-progress and is written in R code.")
7806 (license license:expat)))
7808 (define-public r-abcp2
7815 (uri (cran-uri "ABCp2" version))
7817 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7818 (properties `((upstream-name . "ABCp2")))
7819 (build-system r-build-system)
7820 (propagated-inputs `(("r-mass" ,r-mass)))
7821 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7822 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7824 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7825 Poisson, and Gamma distribution and estimates the proportional paternity of the
7826 second male (P2) based on the best fit distribution.")
7827 (license license:gpl2)))
7829 (define-public r-abcrf
7836 (uri (cran-uri "abcrf" version))
7838 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7839 (build-system r-build-system)
7841 `(("r-doparallel" ,r-doparallel)
7842 ("r-foreach" ,r-foreach)
7844 ("r-matrixstats" ,r-matrixstats)
7845 ("r-ranger" ,r-ranger)
7847 ("r-rcpparmadillo" ,r-rcpparmadillo)
7848 ("r-readr" ,r-readr)
7849 ("r-stringr" ,r-stringr)))
7850 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7851 (synopsis "Approximate bayesian computation via random forests")
7853 "This package performs approximate bayesian computation (ABC) model choice and
7854 parameter inference via random forests. This machine learning tool named random
7855 forests (RF) can conduct selection among the highly complex models covered by
7857 (license license:gpl2+)))
7859 (define-public r-abctools
7866 (uri (cran-uri "abctools" version))
7868 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7869 (build-system r-build-system)
7872 ("r-abind" ,r-abind)
7873 ("r-hmisc" ,r-hmisc)
7874 ("r-plyr" ,r-plyr)))
7875 (home-page "https://github.com/dennisprangle/abctools/")
7876 (synopsis "Tools for ABC analyses")
7878 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7879 including summary statistic selection and assessing coverage. This includes
7880 recent dimension reduction algorithms to tune the choice of summary statistics,
7881 and coverage methods to tune the choice of threshold.")
7882 (license license:gpl2+)))
7884 (define-public r-ggstance
7891 (uri (cran-uri "ggstance" version))
7893 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7894 (build-system r-build-system)
7896 `(("r-ggplot2" ,r-ggplot2)
7898 ("r-rlang" ,r-rlang)
7899 ("r-withr" ,r-withr)))
7900 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7901 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7903 "This package is a @code{r-ggplot2} extension that provides flipped components:
7905 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7906 @item vertical versions of @code{r-ggplot2} positions.
7908 (license license:gpl3)))
7910 (define-public r-mosaiccore
7912 (name "r-mosaiccore")
7917 (uri (cran-uri "mosaicCore" version))
7919 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7920 (properties `((upstream-name . "mosaicCore")))
7921 (build-system r-build-system)
7923 `(("r-dplyr" ,r-dplyr)
7924 ("r-lazyeval" ,r-lazyeval)
7926 ("r-rlang" ,r-rlang)
7927 ("r-tidyr" ,r-tidyr)))
7928 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7929 (synopsis "Common utilities for mosaic family packages")
7931 "Common utilities used in other Mosaic family packages are collected here.")
7932 (license license:gpl2+)))
7934 (define-public r-ggformula
7936 (name "r-ggformula")
7941 (uri (cran-uri "ggformula" version))
7943 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7944 (build-system r-build-system)
7946 `(("r-ggforce" ,r-ggforce)
7947 ("r-ggplot2" ,r-ggplot2)
7948 ("r-ggstance" ,r-ggstance)
7949 ("r-magrittr" ,r-magrittr)
7950 ("r-mosaiccore" ,r-mosaiccore)
7951 ("r-rlang" ,r-rlang)
7952 ("r-stringr" ,r-stringr)
7953 ("r-tibble" ,r-tibble)))
7954 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7955 (synopsis "Formula interface for the @code{r-ggplot2}")
7957 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7958 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7959 and extends the excellent simplicity of the lattice-graphics formula interface,
7960 while providing the intuitive capabilities of @code{r-ggplot2}.")
7961 (license license:expat)))
7963 (define-public r-mosaicdata
7965 (name "r-mosaicdata")
7970 (uri (cran-uri "mosaicData" version))
7972 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7973 (properties `((upstream-name . "mosaicData")))
7974 (build-system r-build-system)
7975 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7976 (synopsis "Data sets for project Mosaic")
7978 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7979 used to teach mathematics, statistics, computation and modeling.")
7980 (license license:gpl2+)))
7982 (define-public r-raster
7989 (uri (cran-uri "raster" version))
7992 "1s6457rq94qvm3s2lqscs2c2gn5kzcpxa13i8nhlgb1klx5kams7"))))
7993 (build-system r-build-system)
7995 `(("r-rcpp" ,r-rcpp)
7997 (home-page "https://www.rspatial.org/")
7998 (synopsis "Geographic data analysis and modeling")
8000 "The package implements basic and high-level functions for reading,
8001 writing, manipulating, analyzing and modeling of gridded spatial data.
8002 Processing of very large files is supported.")
8003 (license license:gpl3+)))
8005 (define-public r-mosaic
8012 (uri (cran-uri "mosaic" version))
8014 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8015 (build-system r-build-system)
8017 `(("r-broom" ,r-broom)
8018 ("r-dplyr" ,r-dplyr)
8019 ("r-ggdendro" ,r-ggdendro)
8020 ("r-ggformula" ,r-ggformula)
8021 ("r-ggplot2" ,r-ggplot2)
8022 ("r-ggrepel" ,r-ggrepel)
8024 ("r-gridextra" ,r-gridextra)
8025 ("r-lattice" ,r-lattice)
8026 ("r-latticeextra" ,r-latticeextra)
8027 ("r-lazyeval" ,r-lazyeval)
8029 ("r-matrix" ,r-matrix)
8030 ("r-mosaiccore" ,r-mosaiccore)
8031 ("r-mosaicdata" ,r-mosaicdata)
8032 ("r-readr" ,r-readr)
8033 ("r-tidyr" ,r-tidyr)))
8035 `(("r-knitr" ,r-knitr)))
8036 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8037 (synopsis "Mathematics, statistics, and computation teaching utilities")
8039 "This package contain data sets and utilities from
8040 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8041 statistics, computation and modeling. Project MOSAIC is a community of
8042 educators working to tie together aspects of quantitative work that students
8043 in science, technology, engineering and mathematics will need in their
8044 professional lives, but which are usually taught in isolation, if at all.")
8045 (license license:gpl2+)))
8047 (define-public r-abd
8054 (uri (cran-uri "abd" version))
8056 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8057 (build-system r-build-system)
8059 `(("r-lattice" ,r-lattice)
8060 ("r-mosaic" ,r-mosaic)
8061 ("r-nlme" ,r-nlme)))
8062 (home-page "https://cran.r-project.org/web/packages/abd/")
8063 (synopsis "Analysis of biological data")
8065 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8066 biological data by Michael Whitlock and Dolph Schluter.")
8067 (license license:gpl2)))
8069 (define-public r-svgui
8076 (uri (cran-uri "svGUI" version))
8078 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8079 (properties `((upstream-name . "svGUI")))
8080 (build-system r-build-system)
8081 (home-page "https://github.com/SciViews/svGUI/")
8082 (synopsis "Functions for managing GUI clients in R")
8084 "The SciViews @code{svGUI} package eases the management of Graphical User
8085 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8086 centralizes info about GUI elements currently used, and it dispatches GUI
8087 calls to the particular toolkits in use in function of the context.")
8088 (license license:gpl2)))
8090 (define-public r-svdialogs
8092 (name "r-svdialogs")
8097 (uri (cran-uri "svDialogs" version))
8099 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8100 (properties `((upstream-name . "svDialogs")))
8101 (build-system r-build-system)
8104 ("zenity" ,zenity)))
8106 `(("r-rstudioapi" ,r-rstudioapi)
8107 ("r-svgui" ,r-svgui)))
8108 (home-page "https://github.com/SciViews/svDialogs/")
8109 (synopsis "Portable dialog boxes")
8111 "This package helps to construct standard dialog boxes for your GUI, including
8112 message boxes, input boxes, list, file or directory selection, and others. In
8113 case R cannot display GUI dialog boxes, a simpler command line version of these
8114 interactive elements is also provided as a fallback solution.")
8115 (license license:gpl2)))
8117 (define-public r-abe
8124 (uri (cran-uri "abe" version))
8127 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8128 (build-system r-build-system)
8129 (home-page "https://cran.r-project.org/web/packages/abe/")
8130 (synopsis "Augmented backward elimination")
8132 "This package performs augmented backward elimination and checks the
8133 stability of the obtained model. Augmented backward elimination combines
8134 significance or information based criteria with the change in estimate to
8135 either select the optimal model for prediction purposes or to serve as a tool
8136 to obtain a practically sound, highly interpretable model.")
8137 (license license:gpl2+)))
8139 (define-public r-abf2
8146 (uri (cran-uri "abf2" version))
8148 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8149 (build-system r-build-system)
8150 (home-page "https://cran.r-project.org/web/packages/abf2/")
8151 (synopsis "Load gap-free axon @code{r-abf2} files")
8153 "This package loads electrophysiology data from ABF2 files, as created by
8154 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8155 mode are currently supported.")
8156 (license license:artistic2.0)))
8158 (define-public r-abhgenotyper
8160 (name "r-abhgenotyper")
8165 (uri (cran-uri "ABHgenotypeR" version))
8167 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8168 (properties `((upstream-name . "ABHgenotypeR")))
8169 (build-system r-build-system)
8171 `(("r-ggplot2" ,r-ggplot2)
8172 ("r-reshape2" ,r-reshape2)))
8173 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8174 (synopsis "Visualize and manipulate ABH genotypes")
8176 "The @code{r-abhgenotyper} package provides simple imputation,
8177 error-correction and plotting capacities for genotype data. The package is
8178 supposed to serve as an intermediate but independent analysis tool between the
8179 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8180 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8181 genotypes as \"graphical genotypes\".")
8182 (license license:gpl3)))
8184 (define-public r-furrr
8191 (uri (cran-uri "furrr" version))
8194 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8195 (build-system r-build-system)
8197 `(("r-future" ,r-future)
8198 ("r-globals" ,r-globals)
8199 ("r-purrr" ,r-purrr)
8200 ("r-rlang" ,r-rlang)))
8201 (home-page "https://github.com/DavisVaughan/furrr")
8202 (synopsis "Apply mapping functions in parallel using futures")
8204 "This package provides implementations of the family of @code{map()}
8205 functions from the @code{purrr} package that can be resolved using any
8206 @code{future}-supported backend, e.g. parallel on the local machine or
8207 distributed on a compute cluster.")
8208 (license license:lgpl2.1+)))
8210 (define-public r-abjutils
8217 (uri (cran-uri "abjutils" version))
8219 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
8220 (build-system r-build-system)
8222 `(("r-dplyr" ,r-dplyr)
8223 ("r-magrittr" ,r-magrittr)
8224 ("r-purrr" ,r-purrr)
8225 ("r-rlang" ,r-rlang)
8226 ("r-rstudioapi" ,r-rstudioapi)
8227 ("r-stringi" ,r-stringi)
8228 ("r-stringr" ,r-stringr)
8229 ("r-tidyr" ,r-tidyr)))
8230 (home-page "https://github.com/abjur/abjutils/")
8231 (synopsis "Collection of tools for jurimetrical analysis")
8233 "This package implements general purpose tools, such as functions for
8234 sampling and basic manipulation of Brazilian lawsuits identification number.
8235 It also implements functions for text cleaning, such as accentuation
8237 (license license:expat)))
8239 (define-public r-abnormality
8241 (name "r-abnormality")
8246 (uri (cran-uri "abnormality" version))
8248 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8249 (build-system r-build-system)
8251 `(("r-mass" ,r-mass)
8252 ("r-matrix" ,r-matrix)))
8253 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8254 (synopsis "Measure a subject's abnormality with respect to a reference population")
8256 "This package contains functions to implement the methodology and
8257 considerations laid out by Marks et al. in the article \"Measuring abnormality
8258 in high dimensional spaces: applications in biomechanical gait analysis\".
8259 Using high-dimensional datasets to measure a subject's overall level of
8260 abnormality as compared to a reference population is often needed in outcomes
8262 (license license:expat)))
8264 (define-public r-abodoutlier
8266 (name "r-abodoutlier")
8271 (uri (cran-uri "abodOutlier" version))
8273 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8274 (properties `((upstream-name . "abodOutlier")))
8275 (build-system r-build-system)
8277 `(("r-cluster" ,r-cluster)))
8278 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8279 (synopsis "Angle-based outlier detection")
8281 "This package performs angle-based outlier detection on a given data
8282 frame. It offers three methods to process data:
8284 @item full but slow implementation using all the data that has cubic
8286 @item a fully randomized method;
8287 @item a method using k-nearest neighbours.
8289 These algorithms are well suited for high dimensional data outlier
8291 (license license:expat)))
8293 (define-public r-abps
8300 (uri (cran-uri "ABPS" version))
8302 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8303 (properties `((upstream-name . "ABPS")))
8304 (build-system r-build-system)
8305 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8306 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8307 (synopsis "Abnormal blood profile score to detect blood doping")
8309 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8310 The ABPS is a part of the Athlete biological passport program of the World
8311 anti-doping agency, which combines several blood parameters into a single
8312 score in order to detect blood doping. The package also contains functions to
8313 calculate other scores used in anti-doping programs, such as the ratio of
8314 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8315 (license license:gpl2+)))
8317 (define-public r-parmigene
8319 (name "r-parmigene")
8324 (uri (cran-uri "parmigene" version))
8327 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
8328 (build-system r-build-system)
8329 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8330 (synopsis "Mutual information estimation for gene network reconstruction")
8332 "This package provides a parallel estimation of the mutual information
8333 based on entropy estimates from k-nearest neighbors distances and algorithms
8334 for the reconstruction of gene regulatory networks.")
8335 (license license:agpl3+)))
8337 (define-public r-pscl
8344 (uri (cran-uri "pscl" version))
8346 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8347 (build-system r-build-system)
8349 `(("r-mass" ,r-mass)))
8350 (home-page "https://github.com/atahk/pscl/")
8351 (synopsis "Political science computational laboratory")
8353 "The @code{pscl} is an R package providing classes and methods for:
8355 @item Bayesian analysis of roll call data (item-response models);
8356 @item elementary Bayesian statistics;
8357 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8359 @item utility functions.
8361 (license license:gpl2)))
8363 (define-public r-accelmissing
8365 (name "r-accelmissing")
8370 (uri (cran-uri "accelmissing" version))
8372 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8373 (build-system r-build-system)
8375 `(("r-mice" ,r-mice)
8376 ("r-pscl" ,r-pscl)))
8377 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8378 (synopsis "Missing value imputation for accelerometer data")
8380 "This package provides a statistical method to impute the missing values in
8381 accelerometer data. The methodology includes both parametric and
8382 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8383 model. It also provides multiple functions to preprocess the accelerometer data
8384 previous to the missing data imputation. These include detecting the wearing
8385 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8386 (license license:gpl2+)))
8388 (define-public r-mhsmm
8395 (uri (cran-uri "mhsmm" version))
8397 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8398 (build-system r-build-system)
8399 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8400 (home-page "https://github.com/jaredo/mhsmm/")
8401 (synopsis "Inference for hidden Markov and semi-Markov models")
8403 "The @code{r-mhsmm} package implements estimation and prediction methods for
8404 hidden Markov and semi-Markov models for multiple observation sequences. Such
8405 techniques are of interest when observed data is thought to be dependent on some
8406 unobserved (or hidden) state. Also, this package is suitable for equidistant
8407 time series data, with multivariate and/or missing data. Allows user defined
8408 emission distributions.")
8409 (license license:gpl2+)))
8411 (define-public r-nleqslv
8418 (uri (cran-uri "nleqslv" version))
8420 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8421 (build-system r-build-system)
8422 (native-inputs `(("gfortran" ,gfortran)))
8423 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8424 (synopsis "Solve systems of nonlinear equations")
8426 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8427 Broyden or a Newton method with a choice of global strategies such as line
8428 search and trust region. There are options for using a numerical or user
8429 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8430 singular or ill-conditioned Jacobian.")
8431 (license license:gpl2+)))
8433 (define-public r-physicalactivity
8435 (name "r-physicalactivity")
8440 (uri (cran-uri "PhysicalActivity" version))
8442 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8444 `((upstream-name . "PhysicalActivity")))
8445 (build-system r-build-system)
8446 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8447 (synopsis "Procesing accelerometer data for physical activity measurement")
8449 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8450 for classification of monitor wear and nonwear time intervals in accelerometer
8451 data collected to assess physical activity. The package also contains functions
8452 for making plots of accelerometer data and obtaining the summary of various
8453 information including daily monitor wear time and the mean monitor wear time
8454 during valid days. The revised package version 0.2-1 improved the functions
8455 regarding speed, robustness and add better support for time zones and daylight
8456 saving. In addition, several functions were added:
8458 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8459 @item the @code{markPAI} can categorize physical activity intensity level based
8460 on user-defined cut-points of accelerometer counts.
8462 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8463 @code{queryActigraph} functions.")
8464 (license license:gpl3+)))
8466 (define-public r-acc
8473 (uri (cran-uri "acc" version))
8475 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8476 (build-system r-build-system)
8478 `(("r-circlize" ,r-circlize)
8480 ("r-ggplot2" ,r-ggplot2)
8481 ("r-iterators" ,r-iterators)
8482 ("r-mhsmm" ,r-mhsmm)
8483 ("r-nleqslv" ,r-nleqslv)
8484 ("r-physicalactivity" ,r-physicalactivity)
8486 ("r-r-utils" ,r-r-utils)
8488 ("r-rcpparmadillo" ,r-rcpparmadillo)
8489 ("r-rsqlite" ,r-rsqlite)
8491 (home-page "https://cran.r-project.org/web/packages/acc/")
8492 (synopsis "Exploring accelerometer data")
8494 "This package processes accelerometer data from uni-axial and tri-axial devices
8495 and generates data summaries. Also, includes functions to plot, analyze, and
8496 simulate accelerometer data.")
8497 (license license:gpl2+)))
8499 (define-public r-rbenchmark
8501 (name "r-rbenchmark")
8506 (uri (cran-uri "rbenchmark" version))
8508 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8509 (build-system r-build-system)
8510 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8511 (synopsis "Benchmarking routine for R")
8513 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8514 and is intended to facilitate benchmarking of arbitrary R code. The library
8515 consists of just one function, benchmark, which is a simple wrapper around
8516 system.time. Given a specification of the benchmarking process (counts of
8517 replications, evaluation environment) and an arbitrary number of expressions,
8518 benchmark evaluates each of the expressions in the specified environment,
8519 replicating the evaluation as many times as specified, and returning the results
8520 conveniently wrapped into a data frame.")
8521 (license license:gpl2+)))
8523 (define-public r-mitools
8530 (uri (cran-uri "mitools" version))
8533 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8534 (build-system r-build-system)
8535 (propagated-inputs `(("r-dbi" ,r-dbi)))
8536 (home-page "https://cran.r-project.org/web/packages/mitools/")
8537 (synopsis "Tools for multiple imputation of missing data")
8539 "This package provides tools to perform analyses and combine results from
8540 multiple-imputation datasets.")
8541 (license license:gpl2)))
8543 (define-public r-magick
8550 (uri (cran-uri "magick" version))
8553 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8554 (build-system r-build-system)
8556 `(("imagemagick" ,imagemagick)
8559 `(("r-curl" ,r-curl)
8560 ("r-magrittr" ,r-magrittr)
8561 ("r-rcpp" ,r-rcpp)))
8563 `(("pkg-config" ,pkg-config)
8564 ("r-knitr" ,r-knitr)))
8565 (home-page "https://github.com/ropensci/magick")
8566 (synopsis "Advanced graphics and image-processing in R")
8568 "This package provides bindings to ImageMagick, a comprehensive image
8569 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8570 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8571 operations are vectorized via the Magick++ STL meaning they operate either on
8572 a single frame or a series of frames for working with layers, collages, or
8573 animation. In RStudio, images are automatically previewed when printed to the
8574 console, resulting in an interactive editing environment.")
8575 (license license:expat)))
8577 (define-public r-survey
8584 (uri (cran-uri "survey" version))
8587 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8588 (build-system r-build-system)
8590 `(("r-lattice" ,r-lattice)
8591 ("r-matrix" ,r-matrix)
8592 ("r-minqa" ,r-minqa)
8593 ("r-mitools" ,r-mitools)
8594 ("r-numderiv" ,r-numderiv)
8595 ("r-survival" ,r-survival)))
8596 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8597 (synopsis "Analysis of complex survey samples")
8599 "This package provides tools for the analysis of complex survey samples.
8600 The provided features include: summary statistics, two-sample tests, rank
8601 tests, generalised linear models, cumulative link models, Cox models,
8602 loglinear models, and general maximum pseudolikelihood estimation for
8603 multistage stratified, cluster-sampled, unequally weighted survey samples;
8604 variances by Taylor series linearisation or replicate weights;
8605 post-stratification, calibration, and raking; two-phase subsampling designs;
8606 graphics; PPS sampling without replacement; principal components, and factor
8608 ;; Either version of the GPL.
8609 (license (list license:gpl2 license:gpl3))))
8611 (define-public r-gee
8618 (uri (cran-uri "gee" version))
8621 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8622 (properties `((upstream-name . "gee")))
8623 (build-system r-build-system)
8625 `(("gfortran" ,gfortran)))
8626 (home-page "https://cran.r-project.org/web/packages/gee/")
8627 (synopsis "Generalized estimation equation solver")
8629 "This package provides a solver for generalized estimation equations.")
8630 (license license:gpl2)))
8632 (define-public r-tab
8639 (uri (cran-uri "tab" version))
8642 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8643 (properties `((upstream-name . "tab")))
8644 (build-system r-build-system)
8646 `(("r-dplyr" ,r-dplyr)
8648 ("r-knitr" ,r-knitr)
8650 ("r-survey" ,r-survey)
8651 ("r-survival" ,r-survival)
8652 ("r-xtable" ,r-xtable)))
8653 (home-page "https://cran.r-project.org/web/packages/tab/")
8654 (synopsis "Create summary tables for statistical reports")
8656 "This package contains functions for creating various types of summary
8657 tables, e.g. comparing characteristics across levels of a categorical variable
8658 and summarizing fitted generalized linear models, generalized estimating
8659 equations, and Cox proportional hazards models. Functions are available to
8660 handle data from simple random samples as well as complex surveys.")
8661 (license license:gpl3+)))
8663 (define-public r-dvmisc
8670 (uri (cran-uri "dvmisc" version))
8672 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8673 (build-system r-build-system)
8675 `(("r-cubature" ,r-cubature)
8676 ("r-data-table" ,r-data-table)
8677 ("r-dplyr" ,r-dplyr)
8678 ("r-ggplot2" ,r-ggplot2)
8680 ("r-mvtnorm" ,r-mvtnorm)
8681 ("r-pracma" ,r-pracma)
8682 ("r-rbenchmark" ,r-rbenchmark)
8684 ("r-survey" ,r-survey)
8686 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8687 (synopsis "Faster computation of common statistics and miscellaneous functions")
8689 "This package implements faster versions of base R functions (e.g. mean, standard
8690 deviation, covariance, weighted mean), mostly written in C++, along with
8691 miscellaneous functions for various purposes (e.g. create the histogram with
8692 fitted probability density function or probability mass function curve, create
8693 the body mass index groups, assess the linearity assumption in logistic
8695 (license license:gpl2)))
8697 (define-public r-accelerometry
8699 (name "r-accelerometry")
8704 (uri (cran-uri "accelerometry" version))
8706 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8707 (build-system r-build-system)
8709 `(("r-dvmisc" ,r-dvmisc)
8710 ("r-rcpp" ,r-rcpp)))
8711 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8712 (synopsis "Functions for processing accelerometer data")
8714 "This package provides a collection of functions that perform operations on
8715 time-series accelerometer data, such as identify the non-wear time, flag minutes
8716 that are part of an activity bout, and find the maximum 10-minute average count
8717 value. The functions are generally very flexible, allowing for a variety of
8718 algorithms to be implemented.")
8719 (license license:gpl3)))
8721 (define-public r-absim
8728 (uri (cran-uri "AbSim" version))
8730 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8731 (properties `((upstream-name . "AbSim")))
8732 (build-system r-build-system)
8735 ("r-powerlaw" ,r-powerlaw)))
8736 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8737 (synopsis "Time resolved simulations of antibody repertoires")
8739 "This package provides simulation methods for the evolution of antibody repertoires.
8740 The heavy and light chain variable region of both human and C57BL/6 mice can
8741 be simulated in a time-dependent fashion. Both single lineages using one set of
8742 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8743 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8744 Upon completion, the main loop of the algorithm begins, with each iteration
8745 representing one simulated time step. Various mutation events are possible at
8746 each time step, contributing to a diverse final repertoire.")
8747 (license license:gpl2)))
8749 (define-public r-quic
8756 (uri (cran-uri "QUIC" version))
8758 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8759 (properties `((upstream-name . "QUIC")))
8760 (build-system r-build-system)
8761 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8762 (synopsis "Regularized sparse inverse covariance matrix estimation")
8764 "This package implements the regularized Gaussian maximum likelihood
8765 estimation of the inverse of a covariance matrix. It uses Newton's method and
8766 coordinate descent to solve the regularized inverse covariance matrix
8767 estimation problem.")
8768 ;; The project home page states that the release is under GPLv3 or later.
8769 ;; The CRAN page only says GPL-3.
8770 (license license:gpl3+)))
8772 (define-public r-abundant
8779 (uri (cran-uri "abundant" version))
8781 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8782 (build-system r-build-system)
8784 `(("r-quic" ,r-quic)))
8785 (home-page "https://cran.r-project.org/web/packages/abundant/")
8786 (synopsis "Abundant regression and high-dimensional principal fitted components")
8788 "This package provides tools to fit and predict with the high-dimensional
8789 principal fitted components model. This model is described by Cook, Forzani,
8790 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8791 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8792 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8793 (license license:gpl2+)))
8795 (define-public r-ac3net
8802 (uri (cran-uri "Ac3net" version))
8804 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8805 (properties `((upstream-name . "Ac3net")))
8806 (build-system r-build-system)
8808 `(("r-data-table" ,r-data-table)))
8809 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8810 (synopsis "Inferring directional conservative causal core gene networks")
8811 (description "This package infers directional Conservative causal core
8812 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8813 directional network.")
8814 (license license:gpl3+)))
8816 (define-public r-aca
8823 (uri (cran-uri "ACA" version))
8825 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8826 (properties `((upstream-name . "ACA")))
8827 (build-system r-build-system)
8828 (home-page "https://cran.r-project.org/web/packages/ACA/")
8829 (synopsis "Abrupt change-point or aberration detection in point series")
8831 "This package offers an interactive function for the detection of breakpoints in
8833 ;; Any version of the GPL
8834 (license (list license:gpl2+ license:gpl3+))))
8836 (define-public r-acceptancesampling
8838 (name "r-acceptancesampling")
8843 (uri (cran-uri "AcceptanceSampling" version))
8845 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8847 `((upstream-name . "AcceptanceSampling")))
8848 (build-system r-build-system)
8849 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8850 (synopsis "Creation and evaluation of acceptance sampling plans")
8852 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8853 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8854 in quality control and improvement. International standards of acceptance
8855 sampling provide sampling plans for specific circumstances. The aim of this
8856 package is to provide an easy-to-use interface to visualize single, double or
8857 multiple sampling plans. In addition, methods have been provided to enable the
8858 user to assess sampling plans against pre-specified levels of performance, as
8859 measured by the probability of acceptance for a given level of quality in the
8861 (license license:gpl3+)))
8863 (define-public r-acclma
8870 (uri (cran-uri "ACCLMA" version))
8872 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8873 (properties `((upstream-name . "ACCLMA")))
8874 (build-system r-build-system)
8875 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8876 (synopsis "ACC & LMA graph plotting")
8878 "This package contains a function that imports data from a @acronym{CSV,
8879 Comma-Separated Values} file, or uses manually entered data from the format (x,
8880 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8881 Curve} vs @acronym{LOI, Line of Independence} graph and
8882 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8883 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8884 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8885 string) was passed, a manual data entry window is opened. The header parameter
8886 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8887 a header row or not. The dataset should contain only one independent variable
8888 (x) and one dependent variable (y) and can contain a weight for each
8890 (license license:gpl2)))
8892 (define-public r-aspi
8899 (uri (cran-uri "aspi" version))
8901 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8902 (build-system r-build-system)
8904 "https://cran.r-project.org/web/packages/aspi/")
8906 "Analysis of symmetry of parasitic infections")
8908 "This package provides tools for the analysis and visualization of bilateral
8909 asymmetry in parasitic infections.")
8910 (license license:gpl3+)))
8912 (define-public r-sandwich
8919 (uri (cran-uri "sandwich" version))
8922 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8923 (build-system r-build-system)
8925 `(("r-zoo" ,r-zoo)))
8926 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8927 (synopsis "Robust Covariance Matrix Estimators")
8929 "This package provides model-robust standard error estimators for
8930 cross-sectional, time series, clustered, panel, and longitudinal data.")
8931 ;; Either version of the license.
8932 (license (list license:gpl2 license:gpl3))))
8934 (define-public r-th-data
8941 (uri (cran-uri "TH.data" version))
8944 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8945 (properties `((upstream-name . "TH.data")))
8946 (build-system r-build-system)
8948 `(("r-mass" ,r-mass)
8949 ("r-survival" ,r-survival)))
8950 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8951 (synopsis "Shared data sets")
8953 "This package contains supporting data sets that are used in other
8954 packages maintained by Torsten Hothorn.")
8955 (license license:gpl3)))
8957 (define-public r-multcomp
8964 (uri (cran-uri "multcomp" version))
8967 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8968 (build-system r-build-system)
8970 `(("r-codetools" ,r-codetools)
8971 ("r-mvtnorm" ,r-mvtnorm)
8972 ("r-sandwich" ,r-sandwich)
8973 ("r-survival" ,r-survival)
8974 ("r-th-data" ,r-th-data)))
8975 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8976 (synopsis "Simultaneous inference in general parametric models")
8978 "Simultaneous tests and confidence intervals for general linear
8979 hypotheses in parametric models, including linear, generalized linear, linear
8980 mixed effects, and survival models. The package includes demos reproducing
8981 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8982 Hothorn, Westfall, 2010, CRC Press).")
8983 (license license:gpl2)))
8985 (define-public r-emmeans
8992 (uri (cran-uri "emmeans" version))
8995 "09nap4aazpbsswqzk0d4kjngwd8sib222s31yd08sd1sqw432c6k"))))
8996 (build-system r-build-system)
8998 `(("r-estimability" ,r-estimability)
8999 ("r-mvtnorm" ,r-mvtnorm)
9000 ("r-numderiv" ,r-numderiv)
9002 ("r-xtable" ,r-xtable)))
9004 `(("r-knitr" ,r-knitr)))
9005 (home-page "https://github.com/rvlenth/emmeans")
9006 (synopsis "Estimated marginal means, aka least-squares means")
9008 "This package provides tools to obtain @dfn{estimated marginal
9009 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9010 be used to compute contrasts or linear functions of EMMs, trends, and
9011 comparisons of slopes.")
9012 ;; Either version of the license.
9013 (license (list license:gpl2 license:gpl3))))
9015 (define-public r-pwr
9022 (uri (cran-uri "pwr" version))
9025 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9026 (build-system r-build-system)
9028 `(("r-knitr" ,r-knitr)))
9029 (home-page "https://github.com/heliosdrm/pwr")
9030 (synopsis "Basic functions for power analysis")
9032 "This package provides power analysis functions along the lines of
9034 (license license:gpl3+)))
9036 (define-public r-libcoin
9043 (uri (cran-uri "libcoin" version))
9045 (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8"))))
9046 (build-system r-build-system)
9047 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9048 (home-page "https://cran.r-project.org/web/packages/libcoin")
9049 (synopsis "Linear test statistics for permutation inference")
9051 "This package provides basic infrastructure for linear test statistics
9052 and permutation inference in the framework of Strasser and Weber (1999).")
9053 (license license:gpl2)))
9055 (define-public r-coin
9062 (uri (cran-uri "coin" version))
9065 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
9066 (build-system r-build-system)
9068 `(("r-libcoin" ,r-libcoin)
9069 ("r-matrixstats" ,r-matrixstats)
9070 ("r-modeltools" ,r-modeltools)
9071 ("r-multcomp" ,r-multcomp)
9072 ("r-mvtnorm" ,r-mvtnorm)
9073 ("r-survival" ,r-survival)))
9074 (home-page "http://coin.r-forge.r-project.org")
9075 (synopsis "Conditional inference procedures in a permutation test framework")
9077 "This package provides conditional inference procedures for the general
9078 independence problem including two-sample, K-sample (non-parametric ANOVA),
9079 correlation, censored, ordered and multivariate problems.")
9080 (license license:gpl2)))
9082 (define-public r-bayesplot
9084 (name "r-bayesplot")
9089 (uri (cran-uri "bayesplot" version))
9092 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
9093 (build-system r-build-system)
9095 `(("pandoc" ,pandoc)
9096 ("pandoc-citeproc" ,pandoc-citeproc)))
9098 `(("r-knitr" ,r-knitr)))
9100 `(("r-dplyr" ,r-dplyr)
9101 ("r-ggplot2" ,r-ggplot2)
9102 ("r-ggridges" ,r-ggridges)
9104 ("r-reshape2" ,r-reshape2)
9105 ("r-rlang" ,r-rlang)
9106 ("r-tibble" ,r-tibble)
9107 ("r-tidyselect" ,r-tidyselect)))
9108 (home-page "https://mc-stan.org/bayesplot")
9109 (synopsis "Plotting for Bayesian models")
9111 "This package provides plotting functions for posterior analysis, model
9112 checking, and MCMC diagnostics. The package is designed not only to provide
9113 convenient functionality for users, but also a common set of functions that
9114 can be easily used by developers working on a variety of R packages for
9115 Bayesian modeling.")
9116 (license license:gpl3+)))
9118 (define-public r-tmb
9125 (uri (cran-uri "TMB" version))
9128 "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
9129 (properties `((upstream-name . "TMB")))
9130 (build-system r-build-system)
9132 `(("r-matrix" ,r-matrix)
9133 ("r-rcppeigen" ,r-rcppeigen)))
9134 (home-page "http://tmb-project.org")
9135 (synopsis "Template model builder: a general random effect tool")
9137 "With this tool, a user should be able to quickly implement complex
9138 random effect models through simple C++ templates. The package combines
9139 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9140 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9141 from R) to obtain an efficient implementation of the applied Laplace
9142 approximation with exact derivatives. Key features are: Automatic sparseness
9143 detection, parallelism through BLAS and parallel user templates.")
9144 (license license:gpl2)))
9146 (define-public r-sjstats
9153 (uri (cran-uri "sjstats" version))
9155 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
9156 (build-system r-build-system)
9158 `(("r-bayestestr" ,r-bayestestr)
9159 ("r-broom" ,r-broom)
9160 ("r-dplyr" ,r-dplyr)
9161 ("r-effectsize" ,r-effectsize)
9162 ("r-emmeans" ,r-emmeans)
9163 ("r-insight" ,r-insight)
9165 ("r-magrittr" ,r-magrittr)
9167 ("r-modelr" ,r-modelr)
9168 ("r-parameters" ,r-parameters)
9169 ("r-performance" ,r-performance)
9170 ("r-purrr" ,r-purrr)
9171 ("r-rlang" ,r-rlang)
9172 ("r-sjlabelled" ,r-sjlabelled)
9173 ("r-sjmisc" ,r-sjmisc)
9174 ("r-tidyr" ,r-tidyr)))
9175 (home-page "https://github.com/strengejacke/sjstats")
9176 (synopsis "Functions for common statistical computations")
9178 "This package provides a collection of convenient functions for common
9179 statistical computations, which are not directly provided by R's @code{base}
9180 or @code{stats} packages. This package aims at providing, first, shortcuts
9181 for statistical measures, which otherwise could only be calculated with
9182 additional effort. Second, these shortcut functions are generic, and can be
9183 applied not only to vectors, but also to other objects as well. The focus of
9184 most functions lies on summary statistics or fit measures for regression
9185 models, including generalized linear models, mixed effects models and Bayesian
9187 (license license:gpl3)))
9189 (define-public r-glmmtmb
9196 (uri (cran-uri "glmmTMB" version))
9199 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9200 (properties `((upstream-name . "glmmTMB")))
9201 (build-system r-build-system)
9203 `(("r-lme4" ,r-lme4)
9204 ("r-matrix" ,r-matrix)
9206 ("r-rcppeigen" ,r-rcppeigen)
9209 `(("r-knitr" ,r-knitr))) ; for vignettes
9210 (home-page "https://github.com/glmmTMB")
9211 (synopsis "Generalized linear mixed models")
9213 "Fit linear and generalized linear mixed models with various extensions,
9214 including zero-inflation. The models are fitted using maximum likelihood
9215 estimation via the Template Model Builder. Random effects are assumed to be
9216 Gaussian on the scale of the linear predictor and are integrated out using the
9217 Laplace approximation. Gradients are calculated using automatic
9219 (license license:agpl3+)))
9221 (define-public r-bayestestr
9223 (name "r-bayestestr")
9228 (uri (cran-uri "bayestestR" version))
9231 "1c82bpxg2ha93rna4sy9pdp422dnk6b378dcg8x04clfg0y0lsi2"))))
9232 (properties `((upstream-name . "bayestestR")))
9233 (build-system r-build-system)
9235 `(("r-insight" ,r-insight)))
9237 `(("r-knitr" ,r-knitr)))
9238 (home-page "https://github.com/easystats/bayestestR")
9239 (synopsis "Describe Bayesian models and posterior distributions")
9241 "This package provides utilities to understand and describe posterior
9242 distributions and Bayesian models. It includes point-estimates such as
9243 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9244 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9245 ROPE percentage and pd).")
9246 (license license:gpl3)))
9248 (define-public r-performance
9250 (name "r-performance")
9255 (uri (cran-uri "performance" version))
9258 "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
9259 (build-system r-build-system)
9261 `(("r-bayestestr" ,r-bayestestr)
9262 ("r-insight" ,r-insight)))
9263 (home-page "https://easystats.github.io/performance/")
9264 (synopsis "Assessment of regression models performance")
9266 "This package provides utilities for computing measures to assess model
9267 quality, which are not directly provided by R's @code{base} or @code{stats}
9268 packages. These include e.g. measures like r-squared, intraclass correlation
9269 coefficient, root mean squared error or functions to check models for
9270 overdispersion, singularity or zero-inflation and more. Functions apply to a
9271 large variety of regression models, including generalized linear models, mixed
9272 effects models and Bayesian models.")
9273 (license license:gpl3)))
9275 (define-public r-ggeffects
9277 (name "r-ggeffects")
9282 (uri (cran-uri "ggeffects" version))
9285 "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
9286 (build-system r-build-system)
9288 `(("r-insight" ,r-insight)
9290 ("r-sjlabelled" ,r-sjlabelled)))
9292 `(("r-knitr" ,r-knitr)))
9293 (home-page "https://github.com/strengejacke/ggeffects")
9294 (synopsis "Create tidy data frames of marginal effects for ggplot")
9296 "This package provides tools to compute marginal effects from statistical
9297 models and return the result as tidy data frames. These data frames are ready
9298 to use with the @code{ggplot2} package. Marginal effects can be calculated
9299 for many different models. Interaction terms, splines and polynomial terms
9300 are also supported. The two main functions are @code{ggpredict()} and
9301 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9302 results using @code{ggplot2}.")
9303 (license license:gpl3)))
9305 (define-public r-effectsize
9307 (name "r-effectsize")
9312 (uri (cran-uri "effectsize" version))
9315 "0h9f260gb8707pcssf8dq7dakpq1ggkxr5kpbrbl8sn8h3qbvws9"))))
9316 (properties `((upstream-name . "effectsize")))
9317 (build-system r-build-system)
9319 `(("r-bayestestr" ,r-bayestestr)
9320 ("r-insight" ,r-insight)
9321 ("r-parameters" ,r-parameters)))
9323 `(("r-knitr" ,r-knitr)))
9324 (home-page "https://github.com/easystats/effectsize")
9325 (synopsis "Indices of effect size and standardized parameters")
9327 "This package provides utilities to work with indices of effect size and
9328 standardized parameters for a wide variety of models, allowing computation and
9329 conversion of indices such as Cohen's d, r, odds, etc.")
9330 (license license:gpl3)))
9332 (define-public r-sjplot
9339 (uri (cran-uri "sjPlot" version))
9341 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9342 (properties `((upstream-name . "sjPlot")))
9343 (build-system r-build-system)
9345 `(("r-bayestestr" ,r-bayestestr)
9346 ("r-dplyr" ,r-dplyr)
9347 ("r-effectsize" ,r-effectsize)
9348 ("r-ggeffects" ,r-ggeffects)
9349 ("r-ggplot2" ,r-ggplot2)
9350 ("r-insight" ,r-insight)
9351 ("r-knitr" ,r-knitr)
9353 ("r-parameters" ,r-parameters)
9354 ("r-performance" ,r-performance)
9355 ("r-purrr" ,r-purrr)
9356 ("r-rlang" ,r-rlang)
9357 ("r-scales" ,r-scales)
9358 ("r-sjlabelled" ,r-sjlabelled)
9359 ("r-sjmisc" ,r-sjmisc)
9360 ("r-sjstats" ,r-sjstats)
9361 ("r-tidyr" ,r-tidyr)))
9363 `(("r-knitr" ,r-knitr)))
9364 (home-page "https://strengejacke.github.io/sjPlot/")
9365 (synopsis "Data visualization for statistics in social science")
9367 "This package represents a collection of plotting and table output
9368 functions for data visualization. Results of various statistical
9369 analyses (that are commonly used in social sciences) can be visualized using
9370 this package, including simple and cross tabulated frequencies, histograms,
9371 box plots, (generalized) linear models, mixed effects models, principal
9372 component analysis and correlation matrices, cluster analyses, scatter plots,
9373 stacked scales, effects plots of regression models (including interaction
9374 terms) and much more. This package supports labelled data.")
9375 (license license:gpl3)))
9377 (define-public r-ini
9384 (uri (cran-uri "ini" version))
9387 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9388 (build-system r-build-system)
9389 (home-page "https://github.com/dvdscripter/ini")
9390 (synopsis "Read and write configuration files")
9392 "This package provides tools to parse simple @code{.ini} configuration
9393 files to an structured list. Users can manipulate this resulting list with
9394 @code{lapply()} functions. This same structured list can be used to write
9395 back to file after modifications.")
9396 (license license:gpl3)))
9405 (uri (cran-uri "gh" version))
9408 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9409 (build-system r-build-system)
9414 ("r-jsonlite" ,r-jsonlite)))
9415 (home-page "https://github.com/r-lib/gh#readme")
9416 (synopsis "Access the GitHub API via R")
9418 "This package provides a minimal R client to access the GitHub API.")
9419 (license license:expat)))
9428 (uri (cran-uri "fs" version))
9431 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
9432 (build-system r-build-system)
9434 `(("r-knitr" ,r-knitr)))
9435 (home-page "https://fs.r-lib.org")
9436 (synopsis "Cross-platform file system operations based on libuv")
9438 "This package provides a cross-platform interface to file system
9439 operations, built on top of the libuv C library.")
9440 (license license:gpl3)))
9442 (define-public r-clisymbols
9444 (name "r-clisymbols")
9449 (uri (cran-uri "clisymbols" version))
9452 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9453 (build-system r-build-system)
9454 (home-page "https://github.com/gaborcsardi/clisymbols")
9455 (synopsis "Unicode symbols at the R prompt")
9457 "This package provides a small subset of Unicode symbols, that are useful
9458 when building command line applications. They fall back to alternatives on
9459 terminals that do not support Unicode.")
9460 (license license:expat)))
9462 (define-public r-usethis
9469 (uri (cran-uri "usethis" version))
9472 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9473 (build-system r-build-system)
9476 ("r-clipr" ,r-clipr)
9477 ("r-crayon" ,r-crayon)
9482 ("r-git2r" ,r-git2r)
9484 ("r-purrr" ,r-purrr)
9485 ("r-rematch2" ,r-rematch2)
9486 ("r-rlang" ,r-rlang)
9487 ("r-rprojroot" ,r-rprojroot)
9488 ("r-rstudioapi" ,r-rstudioapi)
9489 ("r-whisker" ,r-whisker)
9490 ("r-withr" ,r-withr)
9491 ("r-yaml" ,r-yaml)))
9492 (home-page "https://github.com/r-lib/usethis")
9493 (synopsis "Automate R package and project setup")
9495 "This package helps you to automate R package and project setup tasks
9496 that are otherwise performed manually. This includes setting up unit testing,
9497 test coverage, continuous integration, Git, GitHub integration, licenses,
9498 Rcpp, RStudio projects, and more.")
9499 (license license:gpl3)))
9501 (define-public r-sessioninfo
9503 (name "r-sessioninfo")
9508 (uri (cran-uri "sessioninfo" version))
9511 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9512 (build-system r-build-system)
9515 ("r-withr" ,r-withr)))
9516 (home-page "https://github.com/r-lib/sessioninfo#readme")
9517 (synopsis "R session information")
9519 "This package provides tools to query and print information about the
9520 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9521 more information about packages, and where they were installed from.")
9522 (license license:gpl2)))
9524 (define-public r-remotes
9531 (uri (cran-uri "remotes" version))
9534 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
9535 (build-system r-build-system)
9537 `(("r-knitr" ,r-knitr)))
9538 (home-page "https://github.com/r-lib/remotes#readme")
9539 (synopsis "R package installation from remote repositories")
9541 "Download and install R packages stored in GitHub, BitBucket, or plain
9542 subversion or git repositories. This package is a lightweight replacement of
9543 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9544 the code was copied over from @code{devtools}.")
9545 (license license:gpl2+)))
9547 (define-public r-xopen
9554 (uri (cran-uri "xopen" version))
9557 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9558 (build-system r-build-system)
9560 `(("r-processx" ,r-processx)))
9561 (home-page "https://github.com/r-lib/xopen#readme")
9562 (synopsis "Open system files, URLs, anything")
9564 "This package provides a cross-platform solution to open files,
9565 directories or URLs with their associated programs.")
9566 (license license:expat)))
9568 (define-public r-rcmdcheck
9570 (name "r-rcmdcheck")
9575 (uri (cran-uri "rcmdcheck" version))
9578 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9579 (build-system r-build-system)
9581 `(("r-callr" ,r-callr)
9583 ("r-crayon" ,r-crayon)
9585 ("r-digest" ,r-digest)
9586 ("r-pkgbuild" ,r-pkgbuild)
9587 ("r-prettyunits" ,r-prettyunits)
9589 ("r-rprojroot" ,r-rprojroot)
9590 ("r-sessioninfo" ,r-sessioninfo)
9591 ("r-withr" ,r-withr)
9592 ("r-xopen" ,r-xopen)))
9593 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9594 (synopsis "Run R CMD check from R and capture results")
9596 "Run @code{R CMD check} from R programmatically, and capture the results
9597 of the individual checks.")
9598 (license license:expat)))
9600 (define-public r-rapportools
9602 (name "r-rapportools")
9607 (uri (cran-uri "rapportools" version))
9610 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9611 (build-system r-build-system)
9613 `(("r-pander" ,r-pander)
9615 ("r-reshape" ,r-reshape)))
9616 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9617 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9619 "This package provides helper functions that act as wrappers to more
9620 advanced statistical methods with the advantage of having sane defaults for
9622 (license license:agpl3+)))
9624 (define-public r-pander
9631 (uri (cran-uri "pander" version))
9634 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9635 (build-system r-build-system)
9637 `(("r-digest" ,r-digest)
9638 ("r-rcpp" ,r-rcpp)))
9639 (home-page "https://rapporter.github.io/pander")
9640 (synopsis "Render R objects into Pandoc's markdown")
9642 "The main aim of the pander R package is to provide a minimal and easy
9643 tool for rendering R objects into Pandoc's markdown. The package is also
9644 capable of exporting/converting complex Pandoc documents (reports) in various
9646 ;; This package is licensed under either the AGPLv3+ or the very rarely
9648 (license license:agpl3+)))
9650 (define-public r-summarytools
9652 (name "r-summarytools")
9657 (uri (cran-uri "summarytools" version))
9660 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9661 (build-system r-build-system)
9663 `(("r-base64enc" ,r-base64enc)
9664 ("r-checkmate" ,r-checkmate)
9665 ("r-dplyr" ,r-dplyr)
9666 ("r-htmltools" ,r-htmltools)
9667 ("r-lubridate" ,r-lubridate)
9668 ("r-magick" ,r-magick)
9669 ("r-matrixstats" ,r-matrixstats)
9670 ("r-pander" ,r-pander)
9672 ("r-rapportools" ,r-rapportools)
9673 ("r-tibble" ,r-tibble)
9674 ("r-tidyr" ,r-tidyr)))
9675 (home-page "https://github.com/dcomtois/summarytools")
9676 (synopsis "Tools to quickly and neatly summarize data")
9678 "This package provides tools for data frame summaries, cross-tabulations,
9679 weight-enabled frequency tables and common univariate statistics in concise
9680 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9681 good point-of-entry for exploring data, both for experienced and new R
9683 (license license:gpl2)))
9685 (define-public r-lsei
9692 (uri (cran-uri "lsei" version))
9695 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9696 (build-system r-build-system)
9698 `(("gfortran" ,gfortran)))
9699 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9700 (synopsis "Solve regression problems under equality/inequality constraints")
9702 "It contains functions that solve least squares linear regression
9703 problems under linear equality/inequality constraints. Functions for solving
9704 quadratic programming problems are also available, which transform such
9705 problems into least squares ones first.")
9706 (license license:gpl2+)))
9708 (define-public r-npsurv
9715 (uri (cran-uri "npsurv" version))
9718 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9719 (build-system r-build-system)
9721 `(("r-lsei" ,r-lsei)))
9722 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9723 (synopsis "Nonparametric survival analysis")
9725 "This package contains functions for non-parametric survival analysis of
9726 exact and interval-censored observations.")
9727 (license license:gpl2+)))
9729 (define-public r-clusteval
9731 (name "r-clusteval")
9736 (uri (cran-uri "clusteval" version))
9739 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9740 (build-system r-build-system)
9742 `(("r-mvtnorm" ,r-mvtnorm)
9743 ("r-rcpp" ,r-rcpp)))
9744 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9745 (synopsis "Evaluation of clustering algorithms")
9747 "This R package provides a suite of tools to evaluate clustering
9748 algorithms, clusterings, and individual clusters.")
9749 (license license:expat)))
9751 (define-public r-tweedie
9758 (uri (cran-uri "tweedie" version))
9761 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9762 (build-system r-build-system)
9763 (native-inputs `(("gfortran" ,gfortran)))
9764 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9765 (synopsis "Evaluation of Tweedie exponential family models")
9767 "Maximum likelihood computations for Tweedie families, including the
9768 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9769 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9770 and related methods.")
9771 (license license:gpl2+)))
9773 (define-public r-rcppgsl
9780 (uri (cran-uri "RcppGSL" version))
9782 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9783 (properties `((upstream-name . "RcppGSL")))
9784 (build-system r-build-system)
9786 `(("r-rcpp" ,r-rcpp)
9788 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9789 (synopsis "Rcpp integration for GSL vectors and matrices")
9791 "The GNU Scientific Library (or GSL) is a collection of numerical
9792 routines for scientific computing. It is particularly useful for C and C++
9793 programs as it provides a standard C interface to a wide range of mathematical
9794 routines. There are over 1000 functions in total with an extensive test
9795 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9796 structures and R using concepts from Rcpp which is itself a package that eases
9797 the interfaces between R and C++.")
9798 (license license:gpl2+)))
9800 (define-public r-mvabund
9807 (uri (cran-uri "mvabund" version))
9810 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9811 (build-system r-build-system)
9813 `(("r-mass" ,r-mass)
9815 ("r-rcppgsl" ,r-rcppgsl)
9816 ("r-statmod" ,r-statmod)
9817 ("r-tweedie" ,r-tweedie)))
9818 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9819 (synopsis "Statistical methods for analysing multivariate abundance data")
9821 "This package provides a set of tools for displaying, modeling and
9822 analysing multivariate abundance data in community ecology.")
9823 (license license:lgpl2.1+)))
9825 (define-public r-afex
9832 (uri (cran-uri "afex" version))
9835 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9836 (build-system r-build-system)
9840 ("r-lmertest" ,r-lmertest)
9841 ("r-pbkrtest" ,r-pbkrtest)
9842 ("r-reshape2" ,r-reshape2)))
9844 `(("r-knitr" ,r-knitr)))
9845 (home-page "https://afex.singmann.science/")
9846 (synopsis "Analysis of factorial experiments")
9848 "This package provides convenience functions for analyzing factorial
9849 experiments using ANOVA or mixed models.")
9850 (license license:gpl2+)))
9852 (define-public r-lmertest
9859 (uri (cran-uri "lmerTest" version))
9862 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9863 (properties `((upstream-name . "lmerTest")))
9864 (build-system r-build-system)
9866 `(("r-ggplot2" ,r-ggplot2)
9869 ("r-numderiv" ,r-numderiv)))
9870 (home-page "https://github.com/runehaubo/lmerTestR")
9871 (synopsis "Tests in linear mixed effects models")
9873 "This package provides p-values in type I, II or III anova and summary
9874 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9875 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9876 package. Model selection methods include step, drop1 and anova-like tables
9877 for random effects (ranova). Methods for Least-Square means (LS-means) and
9878 tests of linear contrasts of fixed effects are also available.")
9879 (license license:gpl2+)))
9881 (define-public r-r2glmm
9888 (uri (cran-uri "r2glmm" version))
9891 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9892 (build-system r-build-system)
9894 `(("r-afex" ,r-afex)
9895 ("r-data-table" ,r-data-table)
9896 ("r-dplyr" ,r-dplyr)
9897 ("r-ggplot2" ,r-ggplot2)
9898 ("r-gridextra" ,r-gridextra)
9899 ("r-lmertest" ,r-lmertest)
9901 ("r-matrix" ,r-matrix)
9903 ("r-pbkrtest" ,r-pbkrtest)))
9904 (home-page "https://github.com/bcjaeger/r2glmm")
9905 (synopsis "Compute R squared for mixed (multilevel) models")
9907 "This package computes model and semi partial R squared with confidence
9908 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9909 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9910 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9912 (license license:gpl2)))
9914 (define-public r-weights
9921 (uri (cran-uri "weights" version))
9924 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9925 (build-system r-build-system)
9927 `(("r-gdata" ,r-gdata)
9928 ("r-hmisc" ,r-hmisc)
9929 ("r-mice" ,r-mice)))
9931 "https://cran.r-project.org/web/packages/weights/")
9932 (synopsis "Weighting and weighted statistics")
9933 (description "This package Provides a variety of functions for producing
9934 simple weighted statistics, such as weighted Pearson's correlations, partial
9935 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9936 includes some software for quickly recoding survey data and plotting point
9937 estimates from interaction terms in regressions (and multiply imputed
9938 regressions). NOTE: Weighted partial correlation calculations pulled to
9940 (license license:gpl2+)))
9942 (define-public r-rcppannoy
9944 (name "r-rcppannoy")
9949 (uri (cran-uri "RcppAnnoy" version))
9952 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9953 (properties `((upstream-name . "RcppAnnoy")))
9954 (build-system r-build-system)
9956 `(("r-rcpp" ,r-rcpp)))
9957 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9958 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9960 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9961 for efficient memory usage as well an ability to load from and save to disk.
9962 This package provides an R interface.")
9963 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9965 (license (list license:gpl2+ license:asl2.0))))
9967 (define-public r-rcpphnsw
9974 (uri (cran-uri "RcppHNSW" version))
9977 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9978 (properties `((upstream-name . "RcppHNSW")))
9979 (build-system r-build-system)
9980 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9981 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9982 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9984 "Hnswlib is a C++ library for approximate nearest neighbors. This
9985 package provides a minimal R interface by relying on the Rcpp package.")
9986 ;; hnswlib is released under Version 2.0 of the Apache License.
9987 (license (list license:gpl3 license:asl2.0))))
9989 (define-public r-rcppparallel
9991 (name "r-rcppparallel")
9996 (uri (cran-uri "RcppParallel" version))
9999 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10000 (properties `((upstream-name . "RcppParallel")))
10001 (build-system r-build-system)
10002 (home-page "https://rcppcore.github.io/RcppParallel/")
10003 (synopsis "Parallel programming tools for Rcpp")
10005 "This package provides high level functions for parallel programming with
10006 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10007 the work of a standard serial @code{for} loop into a parallel one and the
10008 @code{parallelReduce()} function can be used for accumulating aggregates or
10010 (license license:gpl2)))
10012 (define-public r-ncdf4
10019 (uri (cran-uri "ncdf4" version))
10022 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10023 (build-system r-build-system)
10025 `(("netcdf" ,netcdf)
10027 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10028 (synopsis "R interface to Unidata netCDF format data files")
10030 "This package provides a high-level R interface to data files written
10031 using Unidata's netCDF library (version 4 or earlier), which are binary data
10032 files that are portable across platforms and include metadata information in
10033 addition to the data sets. Using this package, netCDF files can be opened and
10034 data sets read in easily. It is also easy to create new netCDF dimensions,
10035 variables, and files, in either version 3 or 4 format, and manipulate existing
10037 (license license:gpl3+)))
10039 (define-public r-biocmanager
10041 (name "r-biocmanager")
10042 (version "1.30.10")
10046 (uri (cran-uri "BiocManager" version))
10048 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10049 (properties `((upstream-name . "BiocManager")))
10050 (build-system r-build-system)
10051 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10052 (synopsis "Access the Bioconductor project package repository")
10054 "This package provides a convenient tool to install and update
10055 Bioconductor packages.")
10056 (license license:artistic2.0)))
10058 (define-public r-rgl
10061 (version "0.100.54")
10065 (uri (cran-uri "rgl" version))
10068 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
10069 (build-system r-build-system)
10071 `(("pkg-config" ,pkg-config)))
10073 `(("freetype" ,freetype)
10080 `(("r-crosstalk" ,r-crosstalk)
10081 ("r-htmltools" ,r-htmltools)
10082 ("r-htmlwidgets" ,r-htmlwidgets)
10083 ("r-jsonlite" ,r-jsonlite)
10084 ("r-knitr" ,r-knitr)
10085 ("r-magrittr" ,r-magrittr)
10086 ("r-manipulatewidget" ,r-manipulatewidget)
10087 ("r-shiny" ,r-shiny)))
10088 (home-page "https://r-forge.r-project.org/projects/rgl/")
10089 (synopsis "3D visualization using OpenGL")
10091 "This package provides medium to high level functions for 3D interactive graphics,
10092 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
10093 as functions for constructing representations of geometric
10094 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
10095 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
10096 image formats, including PNG, Postscript, SVG, PGF.")
10097 ;; Any version of the GPL.
10098 (license (list license:gpl2+ license:gpl3+))))
10100 (define-public r-multicool
10102 (name "r-multicool")
10107 (uri (cran-uri "multicool" version))
10110 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
10111 (build-system r-build-system)
10112 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10113 (home-page "https://cran.r-project.org/web/packages/multicool/")
10114 (synopsis "Permutations of multisets in cool-lex order")
10116 "This package provides a set of tools to permute multisets without loops
10117 or hash tables and to generate integer partitions. Cool-lex order is similar
10118 to colexicographical order.")
10119 (license license:gpl2)))
10121 (define-public r-misc3d
10128 (uri (cran-uri "misc3d" version))
10131 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
10132 (build-system r-build-system)
10133 (home-page "https://cran.r-project.org/web/packages/misc3d/")
10134 (synopsis "Miscellaneous 3D Plots")
10136 "This package provides a collection of miscellaneous 3d plots, including
10138 ;; Any version of the GPL.
10139 (license (list license:gpl2+ license:gpl3+))))
10141 (define-public r-ks
10148 (uri (cran-uri "ks" version))
10150 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
10151 (build-system r-build-system)
10154 ("r-kernlab" ,r-kernlab)
10155 ("r-kernsmooth" ,r-kernsmooth)
10156 ("r-matrix" ,r-matrix)
10157 ("r-mclust" ,r-mclust)
10159 ("r-multicool" ,r-multicool)
10160 ("r-mvtnorm" ,r-mvtnorm)))
10161 (home-page "http://www.mvstat.net/tduong/")
10162 (synopsis "Kernel smoothing")
10164 "This package provides kernel smoothers for univariate and multivariate
10165 data, including density functions, density derivatives, cumulative
10166 distributions, modal clustering, discriminant analysis, and two-sample
10167 hypothesis testing.")
10168 ;; Either version of the GPL.
10169 (license (list license:gpl2 license:gpl3))))
10171 (define-public r-feature
10178 (uri (cran-uri "feature" version))
10181 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
10182 (build-system r-build-system)
10185 ("r-misc3d" ,r-misc3d)
10187 (home-page "http://www.mvstat.net/tduong/")
10188 (synopsis "Inferential feature significance for kernel density estimation")
10190 "The feature package contains functions to display and compute kernel
10191 density estimates, significant gradient and significant curvature regions.
10192 Significant gradient and/or curvature regions often correspond to significant
10193 features (e.g. local modes).")
10194 ;; Either version of the GPL.
10195 (license (list license:gpl2 license:gpl3))))
10197 (define-public r-arm
10204 (uri (cran-uri "arm" version))
10207 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
10208 (build-system r-build-system)
10210 `(("r-abind" ,r-abind)
10212 ("r-hmisc" ,r-hmisc)
10215 ("r-matrix" ,r-matrix)
10216 ("r-nlme" ,r-nlme)))
10217 (home-page "https://cran.r-project.org/web/packages/arm/")
10218 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10220 "This package provides functions to accompany A. Gelman and J. Hill,
10221 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10222 University Press, 2007.")
10223 (license license:gpl3+)))
10225 (define-public r-circular
10227 (name "r-circular")
10232 (uri (cran-uri "circular" version))
10235 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10236 (build-system r-build-system)
10238 `(("r-boot" ,r-boot)
10239 ("r-mvtnorm" ,r-mvtnorm)))
10241 `(("gfortran" ,gfortran)))
10242 (home-page "https://cran.r-project.org/web/packages/circular/")
10243 (synopsis "Circular statistics")
10245 "This package provides tools for circular statistics, from \"Topics in
10246 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10248 (license license:gpl2+)))
10250 (define-public r-activity
10252 (name "r-activity")
10257 (uri (cran-uri "activity" version))
10260 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10261 (build-system r-build-system)
10263 `(("r-circular" ,r-circular)
10264 ("r-insol" ,r-insol)
10265 ("r-pbapply" ,r-pbapply)))
10266 (home-page "https://cran.r-project.org/web/packages/activity/")
10267 (synopsis "Animal activity statistics")
10269 "This package provides functions to fit kernel density functions to
10270 animal activity time data; plot activity distributions; quantify overall
10271 levels of activity; statistically compare activity metrics through
10272 bootstrapping; and evaluate variation in linear variables with time (or other
10273 circular variables).")
10274 (license license:gpl3)))
10276 (define-public r-ouch
10283 (uri (cran-uri "ouch" version))
10286 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10287 (build-system r-build-system)
10288 (propagated-inputs `(("r-subplex" ,r-subplex)))
10289 (home-page "https://kingaa.github.io/ouch/")
10290 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10292 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10293 for evolution along a phylogenetic tree.")
10294 (license license:gpl2+)))
10296 (define-public r-fmsb
10303 (uri (cran-uri "fmsb" version))
10306 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10307 (build-system r-build-system)
10308 (home-page "http://minato.sip21c.org/msb/")
10309 (synopsis "Functions for medical statistics book with demographic data")
10311 "This package provides several utility functions for the book entitled
10312 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10313 Japan, 2007) with Japanese demographic data and some demographic analysis
10314 related functions.")
10315 (license license:gpl2+)))
10317 (define-public r-stabledist
10319 (name "r-stabledist")
10324 (uri (cran-uri "stabledist" version))
10327 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10328 (build-system r-build-system)
10329 (home-page "https://www.rmetrics.org")
10330 (synopsis "Stable distribution functions")
10332 "This package provides density, probability and quantile functions, and
10333 random number generation for (skew) stable distributions, using the
10334 parametrizations of Nolan.")
10335 (license license:gpl2+)))
10337 (define-public r-gsl
10344 (uri (cran-uri "gsl" version))
10347 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10348 (build-system r-build-system)
10351 (home-page "https://cran.r-project.org/web/packages/gsl")
10352 (synopsis "Wrapper for the GNU Scientific Library")
10354 "This package provides an R wrapper for the special functions and quasi
10355 random number generators of the GNU Scientific Library.")
10356 (license license:gpl2+)))
10358 (define-public r-adgoftest
10360 (name "r-adgoftest")
10365 (uri (cran-uri "ADGofTest" version))
10368 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10369 (properties `((upstream-name . "ADGofTest")))
10370 (build-system r-build-system)
10371 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10372 (synopsis "Anderson-Darling GoF test")
10374 "This package provides an implementation of the Anderson-Darling GoF test
10375 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10376 Anderson-Darling Distribution\".")
10377 ;; Any version of the GPL.
10378 (license license:gpl3+)))
10380 (define-public r-softimpute
10382 (name "r-softimpute")
10387 (uri (cran-uri "softImpute" version))
10390 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10391 (properties `((upstream-name . "softImpute")))
10392 (build-system r-build-system)
10394 `(("r-matrix" ,r-matrix)))
10396 `(("gfortran" ,gfortran)))
10397 (home-page "https://cran.r-project.org/web/packages/softImpute")
10398 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10400 "This package provides iterative methods for matrix completion that use
10401 nuclear-norm regularization. The package includes procedures for centering
10402 and scaling rows, columns or both, and for computing low-rank @dfn{single
10403 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10405 (license license:gpl2)))
10407 (define-public r-fftwtools
10409 (name "r-fftwtools")
10414 (uri (cran-uri "fftwtools" version))
10417 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10418 (build-system r-build-system)
10419 (inputs `(("fftw" ,fftw)))
10420 (home-page "https://github.com/krahim/fftwtools")
10421 (synopsis "Wrapper for FFTW3")
10423 "This package provides a wrapper for several FFTW functions. It provides
10424 access to the two-dimensional FFT, the multivariate FFT, and the
10425 one-dimensional real to complex FFT using the FFTW3 library. The package
10426 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10427 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10428 The FFT functions have a parameter that allows them to not return the
10429 redundant complex conjugate when the input is real data.")
10430 (license license:gpl2+)))
10432 (define-public r-tiff
10439 (uri (cran-uri "tiff" version))
10442 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10443 (build-system r-build-system)
10445 `(("libtiff" ,libtiff)
10446 ("libjpeg" ,libjpeg-turbo)
10448 (home-page "https://www.rforge.net/tiff/")
10449 (synopsis "Read and write TIFF images")
10451 "This package provides an easy and simple way to read, write and display
10452 bitmap images stored in the TIFF format. It can read and write both files and
10453 in-memory raw vectors.")
10454 ;; Either of these two license versions.
10455 (license (list license:gpl2 license:gpl3))))
10457 (define-public r-nlp
10464 (uri (cran-uri "NLP" version))
10467 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10468 (properties `((upstream-name . "NLP")))
10469 (build-system r-build-system)
10470 (home-page "https://cran.r-project.org/web/packages/NLP/")
10471 (synopsis "Natural language processing infrastructure")
10473 "This package provides basic classes and methods for Natural Language
10475 (license license:gpl3)))
10477 (define-public r-tm
10484 (uri (cran-uri "tm" version))
10487 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10488 (properties `((upstream-name . "tm")))
10489 (build-system r-build-system)
10495 ("r-xml2" ,r-xml2)))
10496 (home-page "http://tm.r-forge.r-project.org/")
10497 (synopsis "Text mining package")
10499 "This package provides a framework for text mining applications within R.")
10500 (license license:gpl3)))
10502 (define-public r-waveslim
10504 (name "r-waveslim")
10509 (uri (cran-uri "waveslim" version))
10512 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10513 (build-system r-build-system)
10515 `(("gfortran" ,gfortran)))
10516 (home-page "http://waveslim.blogspot.com")
10517 (synopsis "Basic wavelet routines for signal processing")
10519 "This package provides basic wavelet routines for time series (1D),
10520 image (2D) and array (3D) analysis. The code provided here is based on
10521 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10522 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10523 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10524 pairs (Selesnick 2001, 2002).")
10525 (license license:bsd-3)))
10527 (define-public r-wordcloud
10529 (name "r-wordcloud")
10534 (uri (cran-uri "wordcloud" version))
10537 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10538 (build-system r-build-system)
10540 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10542 ;; The "tm" package is only "suggested" according to CRAN, but the
10543 ;; wordcloud package cannot be loaded without it.
10545 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10546 (synopsis "Word clouds")
10548 "This package provides functionality to create pretty word clouds,
10549 visualize differences and similarity between documents, and avoid
10550 over-plotting in scatter plots with text.")
10551 (license license:lgpl2.1)))
10553 (define-public r-colorramps
10555 (name "r-colorramps")
10560 (uri (cran-uri "colorRamps" version))
10563 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10564 (properties `((upstream-name . "colorRamps")))
10565 (build-system r-build-system)
10566 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10567 (synopsis "Build color tables")
10568 (description "This package provides features to build gradient color
10570 ;; Any version of the GPL
10571 (license license:gpl3+)))
10573 (define-public r-tidytree
10575 (name "r-tidytree")
10580 (uri (cran-uri "tidytree" version))
10582 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10583 (build-system r-build-system)
10586 ("r-dplyr" ,r-dplyr)
10587 ("r-lazyeval" ,r-lazyeval)
10588 ("r-magrittr" ,r-magrittr)
10589 ("r-rlang" ,r-rlang)
10590 ("r-tibble" ,r-tibble)))
10592 `(("r-knitr" ,r-knitr)))
10593 (home-page "https://github.com/GuangchuangYu/tidytree")
10594 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10596 "Phylogenetic trees generally contain multiple components including nodes,
10597 edges, branches and associated data. This package provides an approach to
10598 convert tree objects to tidy data frames. It also provides tidy interfaces to
10599 manipulate tree data.")
10600 (license license:artistic2.0)))
10602 (define-public r-rvcheck
10609 (uri (cran-uri "rvcheck" version))
10611 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10612 (build-system r-build-system)
10614 `(("r-biocmanager" ,r-biocmanager)
10615 ("r-rlang" ,r-rlang)))
10616 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10617 (synopsis "R package version check")
10619 "This package provides tools to check the latest release version of R and
10620 R packages (on CRAN, Bioconductor or Github).")
10621 (license license:artistic2.0)))
10623 (define-public r-docopt
10630 (uri (cran-uri "docopt" version))
10633 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10634 (build-system r-build-system)
10635 (home-page "https://github.com/docopt/docopt.R")
10636 (synopsis "Command-line interface specification language")
10638 "This package enables you to define a command-line interface by just
10639 giving it a description in the specific format.")
10640 (license license:expat)))
10642 (define-public r-sparsesvd
10644 (name "r-sparsesvd")
10649 (uri (cran-uri "sparsesvd" version))
10652 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10653 (build-system r-build-system)
10654 (propagated-inputs `(("r-matrix" ,r-matrix)))
10655 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10656 (synopsis "Sparse truncated singular value decomposition")
10658 "This package provides a Wrapper around the SVDLIBC library
10659 for (truncated) singular value decomposition of a sparse matrix. Currently,
10660 only sparse real matrices in Matrix package format are supported.")
10661 ;; SVDLIBC is released under BSD-2. The R interface is released under
10663 (license (list license:bsd-3 license:bsd-2))))
10665 (define-public r-speedglm
10667 (name "r-speedglm")
10672 (uri (cran-uri "speedglm" version))
10675 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10676 (build-system r-build-system)
10678 `(("r-mass" ,r-mass)
10679 ("r-matrix" ,r-matrix)))
10680 (home-page "https://cran.r-project.org/web/packages/speedglm")
10681 (synopsis "Fit linear and generalized linear models to large data sets")
10683 "This package provides tools for fitting linear models and generalized
10684 linear models to large data sets by updating algorithms.")
10685 ;; Any version of the GPL
10686 (license license:gpl2+)))
10688 (define-public r-densityclust
10690 (name "r-densityclust")
10695 (uri (cran-uri "densityClust" version))
10698 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10699 (properties `((upstream-name . "densityClust")))
10700 (build-system r-build-system)
10703 ("r-ggplot2" ,r-ggplot2)
10704 ("r-ggrepel" ,r-ggrepel)
10705 ("r-gridextra" ,r-gridextra)
10706 ("r-rcolorbrewer" ,r-rcolorbrewer)
10708 ("r-rtsne" ,r-rtsne)))
10709 (home-page "https://cran.r-project.org/web/packages/densityClust")
10710 (synopsis "Clustering by fast search and find of density peaks")
10712 "This package provides an improved implementation (based on k-nearest
10713 neighbors) of the density peak clustering algorithm, originally described by
10714 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10715 large datasets (> 100,000 samples) very efficiently.")
10716 (license license:gpl2+)))
10718 (define-public r-combinat
10720 (name "r-combinat")
10725 (uri (cran-uri "combinat" version))
10728 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10729 (build-system r-build-system)
10730 (home-page "https://cran.r-project.org/web/packages/combinat")
10731 (synopsis "Combinatorics utilities")
10732 (description "This package provides assorted routines for combinatorics.")
10733 (license license:gpl2)))
10735 (define-public r-qlcmatrix
10737 (name "r-qlcmatrix")
10742 (uri (cran-uri "qlcMatrix" version))
10745 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10746 (properties `((upstream-name . "qlcMatrix")))
10747 (build-system r-build-system)
10749 `(("r-docopt" ,r-docopt)
10750 ("r-matrix" ,r-matrix)
10752 ("r-sparsesvd" ,r-sparsesvd)))
10753 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10754 (synopsis "Sparse matrix functions for quantitative language comparison")
10756 "This package provides an extension of the functionality of the Matrix
10757 package for using sparse matrices. Some of the functions are very general,
10758 while other are highly specific for the special data format used for
10759 @dfn{quantitative language comparison} (QLC).")
10760 (license license:gpl3)))
10762 (define-public r-ddrtree
10769 (uri (cran-uri "DDRTree" version))
10772 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10773 (properties `((upstream-name . "DDRTree")))
10774 (build-system r-build-system)
10777 ("r-irlba" ,r-irlba)
10779 ("r-rcppeigen" ,r-rcppeigen)))
10780 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10781 (synopsis "Learning principal graphs with DDRTree")
10783 "This package provides an implementation of the framework of
10784 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10785 dimensional space while constructs a principal tree which passes through the
10786 middle of the data simultaneously. DDRTree shows superiority to
10787 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10788 intrinsic structure of single cell genomics data. In general, it could be
10789 used to reconstruct the temporal progression as well as the bifurcation
10790 structure of any data type.")
10791 (license license:asl2.0)))
10793 (define-public r-corpcor
10800 (uri (cran-uri "corpcor" version))
10803 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10804 (build-system r-build-system)
10805 (home-page "http://strimmerlab.org/software/corpcor/")
10806 (synopsis "Efficient estimation of covariance and (partial) correlation")
10808 "This package implements a James-Stein-type shrinkage estimator for the
10809 covariance matrix, with separate shrinkage for variances and correlations.
10810 Furthermore, functions are available for fast singular value decomposition,
10811 for computing the pseudoinverse, and for checking the rank and positive
10812 definiteness of a matrix.")
10813 (license license:gpl3+)))
10815 (define-public r-rspectra
10817 (name "r-rspectra")
10822 (uri (cran-uri "RSpectra" version))
10825 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10826 (properties `((upstream-name . "RSpectra")))
10827 (build-system r-build-system)
10829 `(("r-matrix" ,r-matrix)
10831 ("r-rcppeigen" ,r-rcppeigen)))
10832 (home-page "https://github.com/yixuan/RSpectra")
10833 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10835 "This package provides an R interface to the Spectra library for
10836 large-scale eigenvalue and SVD problems. It is typically used to compute a
10837 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10838 which is usually more efficient than @code{eigen()} if k << n.")
10840 (license license:mpl2.0)))
10842 (define-public r-vbsr
10849 (uri (cran-uri "vbsr" version))
10852 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10853 (build-system r-build-system)
10854 (home-page "https://cran.r-project.org/web/packages/vbsr")
10855 (synopsis "Variational Bayes spike regression regularized linear models")
10857 "This package provides an efficient algorithm for solving ultra-sparse
10858 regularized regression models using a variational Bayes algorithm with a spike
10859 prior. The algorithm is solved on a path, with coordinate updates, and is
10860 capable of generating very sparse models. Very general model
10861 diagnostics for controlling type-1 errors are also provided.")
10862 (license license:gpl2)))
10864 (define-public r-flare
10867 (version "1.6.0.2")
10871 (uri (cran-uri "flare" version))
10874 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10875 (build-system r-build-system)
10877 `(("r-igraph" ,r-igraph)
10878 ("r-lattice" ,r-lattice)
10880 ("r-matrix" ,r-matrix)))
10881 (home-page "https://cran.r-project.org/web/packages/flare")
10882 (synopsis "Family of Lasso regression implementations")
10884 "This package provides implementations of a family of Lasso variants
10885 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10886 high dimensional sparse linear models.")
10887 (license license:gpl2)))
10889 (define-public r-lassopv
10896 (uri (cran-uri "lassopv" version))
10899 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10900 (build-system r-build-system)
10901 (propagated-inputs `(("r-lars" ,r-lars)))
10902 (home-page "https://github.com/lingfeiwang/lassopv")
10903 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10905 "This package enables you to estimate the p-values for predictors x
10906 against target variable y in Lasso regression, using the regularization
10907 strength when each predictor enters the active set of regularization path for
10908 the first time as the statistic.")
10909 (license license:gpl3)))
10911 (define-public r-splitstackshape
10913 (name "r-splitstackshape")
10918 (uri (cran-uri "splitstackshape" version))
10921 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10922 (build-system r-build-system)
10924 `(("r-data-table" ,r-data-table)))
10925 (home-page "https://github.com/mrdwab/splitstackshape")
10926 (synopsis "Stack and reshape datasets after splitting concatenated values")
10928 "Online data collection tools like Google Forms often export
10929 multiple-response questions with data concatenated in cells. The
10930 @code{concat.split} (cSplit) family of functions provided by this package
10931 splits such data into separate cells. This package also includes functions to
10932 stack groups of columns and to reshape wide data, even when the data are
10933 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10934 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10936 (license license:gpl3)))
10938 (define-public r-tfmpvalue
10940 (name "r-tfmpvalue")
10945 (uri (cran-uri "TFMPvalue" version))
10948 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10949 (properties `((upstream-name . "TFMPvalue")))
10950 (build-system r-build-system)
10951 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10952 (home-page "https://github.com/ge11232002/TFMPvalue")
10953 (synopsis "P-value computation for position weight matrices")
10955 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10956 identification from sequence/alignments, we are interested in the significance
10957 of certain match scores. TFMPvalue provides the accurate calculation of a
10958 p-value with a score threshold for position weight matrices, or the score with
10959 a given p-value. It is an interface to code originally made available by
10960 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10961 Touzet and Varre (2007).")
10962 (license license:gpl2)))
10964 (define-public r-rnifti
10971 (uri (cran-uri "RNifti" version))
10974 "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
10975 (properties `((upstream-name . "RNifti")))
10976 (build-system r-build-system)
10977 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10978 (home-page "https://github.com/jonclayden/RNifti")
10979 (synopsis "Fast R and C++ access to NIfTI images")
10981 "This package provides very fast read and write access to images stored
10982 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10983 compiled C and interpreted R code. It also provides a C/C++ API that can be
10984 used by other packages.")
10985 (license license:gpl2)))
10987 (define-public r-shades
10994 (uri (cran-uri "shades" version))
10997 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10998 (build-system r-build-system)
10999 (home-page "https://github.com/jonclayden/shades")
11000 (synopsis "Simple color manipulation")
11002 "This package provides functions for easily manipulating colors,
11003 creating color scales and calculating color distances.")
11004 (license license:bsd-3)))
11006 (define-public r-ore
11013 (uri (cran-uri "ore" version))
11015 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11016 (build-system r-build-system)
11017 (home-page "https://github.com/jonclayden/ore")
11018 (synopsis "R interface to the Onigmo regular expression library")
11020 "This package provides an alternative to R's built-in functionality for
11021 handling regular expressions, based on the Onigmo library. It offers
11022 first-class compiled regex objects, partial matching and function-based
11023 substitutions, amongst other features.")
11024 (license license:bsd-3)))
11026 (define-public r-reportr
11033 (uri (cran-uri "reportr" version))
11036 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11037 (build-system r-build-system)
11038 (propagated-inputs `(("r-ore" ,r-ore)))
11039 (home-page "https://github.com/jonclayden/reportr")
11040 (synopsis "General message and error reporting system")
11042 "This package provides a system for reporting messages, which offers
11043 certain useful features over the standard R system, such as the incorporation
11044 of output consolidation, message filtering, assertions, expression
11045 substitution, automatic generation of stack traces for debugging, and
11046 conditional reporting based on the current \"output level\".")
11047 (license license:gpl2)))
11049 (define-public r-tractor-base
11051 (name "r-tractor-base")
11056 (uri (cran-uri "tractor.base" version))
11059 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
11060 (properties `((upstream-name . "tractor.base")))
11061 (build-system r-build-system)
11064 ("r-reportr" ,r-reportr)
11065 ("r-rnifti" ,r-rnifti)
11066 ("r-shades" ,r-shades)))
11067 (home-page "https://www.tractor-mri.org.uk")
11068 (synopsis "Read, manipulate and visualize magnetic resonance images")
11070 "This package provides functions for working with magnetic resonance
11071 images. It supports reading and writing of popular file formats (DICOM,
11072 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
11073 visualization; flexible image manipulation; metadata and sparse image
11075 (license license:gpl2)))
11077 (define-public r-grimport
11079 (name "r-grimport")
11084 (uri (cran-uri "grImport" version))
11087 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
11088 (properties `((upstream-name . "grImport")))
11089 (build-system r-build-system)
11091 `(("ghostscript" ,ghostscript)))
11093 `(("r-xml" ,r-xml)))
11094 (home-page "https://cran.r-project.org/web/packages/grImport")
11095 (synopsis "Convert, import, and draw PostScript pictures")
11097 "This package provides functions for converting, importing, and drawing
11098 PostScript pictures in R plots.")
11099 (license license:gpl2+)))
11101 (define-public r-grimport2
11103 (name "r-grimport2")
11108 (uri (cran-uri "grImport2" version))
11111 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
11112 (properties `((upstream-name . "grImport2")))
11113 (build-system r-build-system)
11115 `(("r-base64enc" ,r-base64enc)
11119 (home-page "https://cran.r-project.org/web/packages/grImport2/")
11120 (synopsis "Import SVG graphics")
11122 "This package provides functions for importing external vector images and
11123 drawing them as part of R plots. This package is different from the
11124 @code{grImport} package because, where that package imports PostScript format
11125 images, this package imports SVG format images. Furthermore, this package
11126 imports a specific subset of SVG, so external images must be preprocessed
11127 using a package like @code{rsvg} to produce SVG that this package can import.
11128 SVG features that are not supported by R graphics, such as gradient fills, can
11129 be imported and then exported via the @code{gridSVG} package.")
11130 (license license:gpl2+)))
11132 (define-public r-kohonen
11139 (uri (cran-uri "kohonen" version))
11142 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
11143 (build-system r-build-system)
11145 `(("r-rcpp" ,r-rcpp)))
11146 (home-page "https://cran.r-project.org/web/packages/kohonen")
11147 (synopsis "Supervised and unsupervised self-organising maps")
11149 "This package provides functions to train @dfn{self-organising
11150 maps} (SOMs). Also interrogation of the maps and prediction using trained
11151 maps are supported. The name of the package refers to Teuvo Kohonen, the
11152 inventor of the SOM.")
11153 (license license:gpl2+)))
11155 (define-public r-nnls
11162 (uri (cran-uri "nnls" version))
11165 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
11166 (build-system r-build-system)
11167 (native-inputs `(("gfortran" ,gfortran)))
11168 (home-page "https://cran.r-project.org/web/packages/nnls")
11169 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
11171 "This package provides an R interface to the Lawson-Hanson implementation
11172 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
11173 the combination of non-negative and non-positive constraints.")
11174 (license license:gpl2+)))
11176 (define-public r-iso
11179 (version "0.0-18.1")
11183 (uri (cran-uri "Iso" version))
11186 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11187 (properties `((upstream-name . "Iso")))
11188 (build-system r-build-system)
11189 (native-inputs `(("gfortran" ,gfortran)))
11190 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11191 (synopsis "Functions to perform isotonic regression")
11193 "This package provides support for linear order and unimodal
11194 order (univariate) isotonic regression and bivariate isotonic regression with
11195 linear order on both variables.")
11196 (license license:gpl2+)))
11198 (define-public r-chemometricswithr
11200 (name "r-chemometricswithr")
11205 (uri (cran-uri "ChemometricsWithR" version))
11208 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11210 `((upstream-name . "ChemometricsWithR")))
11211 (build-system r-build-system)
11213 `(("r-devtools" ,r-devtools)
11214 ("r-kohonen" ,r-kohonen)
11217 (home-page "https://github.com/rwehrens/CWR")
11218 (synopsis "Chemometrics with R")
11220 "This package provides functions and scripts used in the book
11221 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11222 Life Sciences\" by Ron Wehrens, Springer (2011).")
11223 (license license:gpl2+)))
11225 (define-public r-als
11232 (uri (cran-uri "ALS" version))
11235 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11236 (properties `((upstream-name . "ALS")))
11237 (build-system r-build-system)
11240 ("r-nnls" ,r-nnls)))
11241 (home-page "https://cran.r-project.org/web/packages/ALS")
11242 (synopsis "Multivariate curve resolution alternating least squares")
11244 "Alternating least squares is often used to resolve components
11245 contributing to data with a bilinear structure; the basic technique may be
11246 extended to alternating constrained least squares. This package provides an
11247 implementation of @dfn{multivariate curve resolution alternating least
11248 squares} (MCR-ALS).
11250 Commonly applied constraints include unimodality, non-negativity, and
11251 normalization of components. Several data matrices may be decomposed
11252 simultaneously by assuming that one of the two matrices in the bilinear
11253 decomposition is shared between datasets.")
11254 (license license:gpl2+)))
11256 (define-public r-strucchange
11258 (name "r-strucchange")
11263 (uri (cran-uri "strucchange" version))
11266 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11267 (build-system r-build-system)
11269 `(("r-sandwich" ,r-sandwich)
11271 (home-page "https://cran.r-project.org/web/packages/strucchange")
11272 (synopsis "Testing, monitoring, and dating structural changes")
11274 "This package provides tools for testing, monitoring and dating
11275 structural changes in (linear) regression models. It features tests/methods
11276 from the generalized fluctuation test framework as well as from the F
11277 test (Chow test) framework. This includes methods to fit, plot and test
11278 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11279 statistics, respectively. It is possible to monitor incoming data online
11280 using fluctuation processes. Finally, the breakpoints in regression models
11281 with structural changes can be estimated together with confidence intervals.
11282 Emphasis is always given to methods for visualizing the data.")
11283 ;; Either of these two GPL versions
11284 (license (list license:gpl2 license:gpl3))))
11286 (define-public r-pixmap
11293 (uri (cran-uri "pixmap" version))
11296 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11297 (build-system r-build-system)
11298 (home-page "https://cran.r-project.org/web/packages/pixmap")
11299 (synopsis "Tools for bitmap images")
11301 "This package provides functions for importing, exporting, plotting and
11302 other manipulations of bitmapped images.")
11303 (license license:gpl2)))
11305 (define-public r-rapidjsonr
11307 (name "r-rapidjsonr")
11312 (uri (cran-uri "rapidjsonr" version))
11315 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11316 (build-system r-build-system)
11317 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11318 (synopsis "JSON parser")
11320 "This package provides JSON parsing capability through the Rapidjson
11322 (license license:expat)))
11324 (define-public r-ontologyindex
11326 (name "r-ontologyindex")
11331 (uri (cran-uri "ontologyIndex" version))
11334 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11335 (properties `((upstream-name . "ontologyIndex")))
11336 (build-system r-build-system)
11337 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11338 (synopsis "Functions for processing ontologies in R")
11340 "This package provides functions for reading ontologies into R as lists
11341 and manipulating sets of ontological terms.")
11342 (license license:gpl2+)))
11344 (define-public r-gargle
11351 (uri (cran-uri "gargle" version))
11354 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11355 (build-system r-build-system)
11360 ("r-jsonlite" ,r-jsonlite)
11361 ("r-rlang" ,r-rlang)
11362 ("r-withr" ,r-withr)))
11364 `(("r-knitr" ,r-knitr)))
11365 (home-page "https://gargle.r-lib.org")
11366 (synopsis "Utilities for working with Google APIs")
11368 "This package provides utilities for working with Google APIs. This
11369 includes functions and classes for handling common credential types and for
11370 preparing, executing, and processing HTTP requests.")
11371 (license license:expat)))
11373 (define-public r-bigrquery
11375 (name "r-bigrquery")
11380 (uri (cran-uri "bigrquery" version))
11383 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11384 (build-system r-build-system)
11386 `(("r-assertthat" ,r-assertthat)
11387 ("r-bit64" ,r-bit64)
11390 ("r-gargle" ,r-gargle)
11393 ("r-jsonlite" ,r-jsonlite)
11394 ("r-prettyunits" ,r-prettyunits)
11395 ("r-progress" ,r-progress)
11396 ("r-rapidjsonr" ,r-rapidjsonr)
11398 ("r-rlang" ,r-rlang)
11399 ("r-tibble" ,r-tibble)))
11400 (home-page "https://github.com/rstats-db/bigrquery")
11401 (synopsis "R interface to Google's BigQuery API")
11403 "This package provides an R interface to Google's BigQuery database.")
11404 (license license:gpl3)))
11406 (define-public r-gmp
11413 (uri (cran-uri "gmp" version))
11416 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11417 (build-system r-build-system)
11420 (modify-phases %standard-phases
11421 (add-after 'unpack 'set-CC
11422 (lambda _ (setenv "CC" "gcc") #t)))))
11423 (inputs `(("gmp" ,gmp)))
11424 (home-page "https://cran.r-project.org/web/packages/gmp")
11425 (synopsis "Multiple precision arithmetic")
11427 "This package supports multiple precision arithmetic (big integers and
11428 rationals, prime number tests, matrix computation), \"arithmetic without
11429 limitations\" using the GNU Multiple Precision library.")
11430 ;; Any version of the GPL.
11431 (license license:gpl3+)))
11433 (define-public r-rmpfr
11440 (uri (cran-uri "Rmpfr" version))
11443 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11444 (properties `((upstream-name . "Rmpfr")))
11445 (build-system r-build-system)
11450 `(("r-gmp" ,r-gmp)))
11452 `(("pkg-config" ,pkg-config)))
11453 (home-page "http://rmpfr.r-forge.r-project.org/")
11454 (synopsis "R bindings to the MPFR library")
11456 "This package supports arithmetic (via S4 classes and methods) for
11457 arbitrary precision floating point numbers, including transcendental
11458 functions. To this end, the package interfaces with the @dfn{Multiple
11459 Precision Floating-Point Reliable} (MPFR) library.")
11460 (license license:gpl2+)))
11462 (define-public r-assertive-base
11464 (name "r-assertive-base")
11469 (uri (cran-uri "assertive.base" version))
11472 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11474 `((upstream-name . "assertive.base")))
11475 (build-system r-build-system)
11476 (home-page "https://bitbucket.org/richierocks/assertive.base")
11477 (synopsis "Core of the assertive package")
11479 "This package provides a minimal set of predicates and assertions used by
11480 the assertive package. This is mainly for use by other package developers who
11481 want to include run-time testing features in their own packages.")
11482 (license license:gpl3+)))
11484 (define-public r-assertive-properties
11486 (name "r-assertive-properties")
11491 (uri (cran-uri "assertive.properties" version))
11494 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11496 `((upstream-name . "assertive.properties")))
11497 (build-system r-build-system)
11499 `(("r-assertive-base" ,r-assertive-base)))
11500 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11501 (synopsis "Assertions to check properties of variables")
11503 "This package provides a set of predicates and assertions for checking
11504 the properties of variables, such as length, names and attributes. This is
11505 mainly for use by other package developers who want to include run-time
11506 testing features in their own packages.")
11507 (license license:gpl3+)))
11509 (define-public r-assertive-numbers
11511 (name "r-assertive-numbers")
11516 (uri (cran-uri "assertive.numbers" version))
11519 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11521 `((upstream-name . "assertive.numbers")))
11522 (build-system r-build-system)
11524 `(("r-assertive-base" ,r-assertive-base)))
11525 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11526 (synopsis "Assertions to check properties of numbers")
11528 "This package provides a set of predicates and assertions for checking
11529 the properties of numbers. This is mainly for use by other package developers
11530 who want to include run-time testing features in their own packages.")
11531 (license license:gpl3+)))
11533 (define-public r-assertive-sets
11535 (name "r-assertive-sets")
11540 (uri (cran-uri "assertive.sets" version))
11543 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11545 `((upstream-name . "assertive.sets")))
11546 (build-system r-build-system)
11548 `(("r-assertive-base" ,r-assertive-base)))
11549 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11550 (synopsis "Assertions to check properties of sets")
11552 "This package provides a set of predicates and assertions for checking
11553 the properties of sets. This is mainly for use by other package developers
11554 who want to include run-time testing features in their own packages.")
11555 (license license:gpl3+)))
11557 (define-public r-assertive-matrices
11559 (name "r-assertive-matrices")
11564 (uri (cran-uri "assertive.matrices" version))
11567 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11569 `((upstream-name . "assertive.matrices")))
11570 (build-system r-build-system)
11572 `(("r-assertive-base" ,r-assertive-base)))
11573 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11574 (synopsis "Assertions to check properties of matrices")
11576 "This package provides a set of predicates and assertions for checking
11577 the properties of matrices. This is mainly for use by other package
11578 developers who want to include run-time testing features in their own
11580 (license license:gpl3+)))
11582 (define-public r-assertive-models
11584 (name "r-assertive-models")
11589 (uri (cran-uri "assertive.models" version))
11592 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11594 `((upstream-name . "assertive.models")))
11595 (build-system r-build-system)
11597 `(("r-assertive-base" ,r-assertive-base)))
11598 (home-page "https://bitbucket.org/richierocks/assertive.models")
11599 (synopsis "Assertions to check properties of models")
11601 "This package provides a set of predicates and assertions for checking
11602 the properties of models. This is mainly for use by other package developers
11603 who want to include run-time testing features in their own packages.")
11604 (license license:gpl3+)))
11606 (define-public r-assertive-reflection
11608 (name "r-assertive-reflection")
11613 (uri (cran-uri "assertive.reflection" version))
11616 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
11618 `((upstream-name . "assertive.reflection")))
11619 (build-system r-build-system)
11621 `(("r-assertive-base" ,r-assertive-base)))
11622 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11623 (synopsis "Assertions for checking the state of R")
11625 "This package provides a set of predicates and assertions for checking
11626 the state and capabilities of R, the operating system it is running on, and
11627 the IDE being used. This is mainly for use by other package developers who
11628 want to include run-time testing features in their own packages.")
11629 (license license:gpl3+)))
11631 (define-public r-assertive-types
11633 (name "r-assertive-types")
11638 (uri (cran-uri "assertive.types" version))
11641 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11643 `((upstream-name . "assertive.types")))
11644 (build-system r-build-system)
11646 `(("r-assertive-base" ,r-assertive-base)
11647 ("r-assertive-properties" ,r-assertive-properties)
11648 ("r-codetools" ,r-codetools)))
11649 (home-page "https://bitbucket.org/richierocks/assertive.types")
11650 (synopsis "Assertions to check types of variables")
11652 "This package provides a set of predicates and assertions for checking
11653 the types of variables. This is mainly for use by other package developers
11654 who want to include run-time testing features in their own packages.")
11655 (license license:gpl3+)))
11657 (define-public r-assertive-files
11659 (name "r-assertive-files")
11664 (uri (cran-uri "assertive.files" version))
11667 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11669 `((upstream-name . "assertive.files")))
11670 (build-system r-build-system)
11672 `(("r-assertive-base" ,r-assertive-base)
11673 ("r-assertive-numbers" ,r-assertive-numbers)))
11674 (home-page "https://bitbucket.org/richierocks/assertive.files")
11675 (synopsis "Assertions to check properties of files")
11677 "This package provides a set of predicates and assertions for checking
11678 the properties of files and connections. This is mainly for use by other
11679 package developers who want to include run-time testing features in their own
11681 (license license:gpl3+)))
11683 (define-public r-assertive-code
11685 (name "r-assertive-code")
11690 (uri (cran-uri "assertive.code" version))
11693 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11695 `((upstream-name . "assertive.code")))
11696 (build-system r-build-system)
11698 `(("r-assertive-base" ,r-assertive-base)
11699 ("r-assertive-properties" ,r-assertive-properties)
11700 ("r-assertive-types" ,r-assertive-types)))
11701 (home-page "https://bitbucket.org/richierocks/assertive.code")
11702 (synopsis "Assertions to check properties of code")
11704 "This package provides a set of predicates and assertions for checking
11705 the properties of code. This is mainly for use by other package developers
11706 who want to include run-time testing features in their own packages.")
11707 (license license:gpl3+)))
11709 (define-public r-assertive-datetimes
11711 (name "r-assertive-datetimes")
11716 (uri (cran-uri "assertive.datetimes" version))
11719 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
11721 `((upstream-name . "assertive.datetimes")))
11722 (build-system r-build-system)
11724 `(("r-assertive-base" ,r-assertive-base)
11725 ("r-assertive-types" ,r-assertive-types)))
11726 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11727 (synopsis "Assertions to check properties of dates and times")
11729 "This package provides a set of predicates and assertions for checking
11730 the properties of dates and times. This is mainly for use by other package
11731 developers who want to include run-time testing features in their own
11733 (license license:gpl3+)))
11735 (define-public r-assertive-strings
11737 (name "r-assertive-strings")
11742 (uri (cran-uri "assertive.strings" version))
11745 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11747 `((upstream-name . "assertive.strings")))
11748 (build-system r-build-system)
11750 `(("r-assertive-base" ,r-assertive-base)
11751 ("r-assertive-types" ,r-assertive-types)
11752 ("r-stringi" ,r-stringi)))
11753 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11754 (synopsis "Assertions to check properties of strings")
11756 "This package provides a set of predicates and assertions for checking
11757 the properties of strings. This is mainly for use by other package developers
11758 who want to include run-time testing features in their own packages.")
11759 (license license:gpl3+)))
11761 (define-public r-assertive-data-us
11763 (name "r-assertive-data-us")
11768 (uri (cran-uri "assertive.data.us" version))
11771 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11773 `((upstream-name . "assertive.data.us")))
11774 (build-system r-build-system)
11776 `(("r-assertive-base" ,r-assertive-base)
11777 ("r-assertive-strings" ,r-assertive-strings)))
11778 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11779 (synopsis "Assertions to check properties of strings")
11781 "This package provides a set of predicates and assertions for checking
11782 the properties of US-specific complex data types. This is mainly for use by
11783 other package developers who want to include run-time testing features in
11784 their own packages.")
11785 (license license:gpl3+)))
11787 (define-public r-assertive-data-uk
11789 (name "r-assertive-data-uk")
11794 (uri (cran-uri "assertive.data.uk" version))
11797 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11799 `((upstream-name . "assertive.data.uk")))
11800 (build-system r-build-system)
11802 `(("r-assertive-base" ,r-assertive-base)
11803 ("r-assertive-strings" ,r-assertive-strings)))
11804 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11805 (synopsis "Assertions to check properties of strings")
11807 "This package provides a set of predicates and assertions for checking
11808 the properties of UK-specific complex data types. This is mainly for use by
11809 other package developers who want to include run-time testing features in
11810 their own packages.")
11811 (license license:gpl3+)))
11813 (define-public r-assertive-data
11815 (name "r-assertive-data")
11820 (uri (cran-uri "assertive.data" version))
11823 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11825 `((upstream-name . "assertive.data")))
11826 (build-system r-build-system)
11828 `(("r-assertive-base" ,r-assertive-base)
11829 ("r-assertive-strings" ,r-assertive-strings)))
11830 (home-page "https://bitbucket.org/richierocks/assertive.data")
11831 (synopsis "Assertions to check properties of data")
11833 "This package provides a set of predicates and assertions for checking
11834 the properties of (country independent) complex data types. This is mainly
11835 for use by other package developers who want to include run-time testing
11836 features in their own packages.")
11837 (license license:gpl3+)))
11839 (define-public r-assertive
11841 (name "r-assertive")
11846 (uri (cran-uri "assertive" version))
11849 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
11850 (build-system r-build-system)
11852 `(("r-assertive-base" ,r-assertive-base)
11853 ("r-assertive-code" ,r-assertive-code)
11854 ("r-assertive-data" ,r-assertive-data)
11855 ("r-assertive-data-uk" ,r-assertive-data-uk)
11856 ("r-assertive-data-us" ,r-assertive-data-us)
11857 ("r-assertive-datetimes" ,r-assertive-datetimes)
11858 ("r-assertive-files" ,r-assertive-files)
11859 ("r-assertive-matrices" ,r-assertive-matrices)
11860 ("r-assertive-models" ,r-assertive-models)
11861 ("r-assertive-numbers" ,r-assertive-numbers)
11862 ("r-assertive-properties" ,r-assertive-properties)
11863 ("r-assertive-reflection" ,r-assertive-reflection)
11864 ("r-assertive-sets" ,r-assertive-sets)
11865 ("r-assertive-strings" ,r-assertive-strings)
11866 ("r-assertive-types" ,r-assertive-types)
11867 ("r-knitr" ,r-knitr)))
11869 `(("r-knitr" ,r-knitr)))
11870 (home-page "https://bitbucket.org/richierocks/assertive")
11871 (synopsis "Readable check functions to ensure code integrity")
11873 "This package provides lots of predicates (@code{is_*} functions) to
11874 check the state of your variables, and assertions (@code{assert_*} functions)
11875 to throw errors if they aren't in the right form.")
11876 (license license:gpl3+)))
11878 (define-public r-dotcall64
11880 (name "r-dotcall64")
11885 (uri (cran-uri "dotCall64" version))
11888 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11889 (properties `((upstream-name . "dotCall64")))
11890 (build-system r-build-system)
11891 (native-inputs `(("gfortran" ,gfortran)))
11892 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11893 (synopsis "Enhanced foreign function interface supporting long vectors")
11895 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11896 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11897 supports long vectors, arguments of type 64-bit integer, and provides a
11898 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11899 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11900 (license license:gpl2+)))
11902 (define-public r-spam
11909 (uri (cran-uri "spam" version))
11911 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11912 (build-system r-build-system)
11914 `(("r-dotcall64" ,r-dotcall64)))
11915 (native-inputs `(("gfortran" ,gfortran)))
11916 (home-page "https://www.math.uzh.ch/pages/spam/")
11917 (synopsis "Sparse matrix algebra")
11919 "This package provides a set of functions for sparse matrix algebra.
11920 Differences with other sparse matrix packages are:
11923 @item it only supports (essentially) one sparse matrix format;
11924 @item it is based on transparent and simple structure(s);
11925 @item it is tailored for MCMC calculations within G(M)RF;
11926 @item and it is fast and scalable (with the extension package @code{spam64}).
11928 ;; Either of these licenses
11929 (license (list license:bsd-3 license:lgpl2.0))))
11931 (define-public r-fields
11938 (uri (cran-uri "fields" version))
11940 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11941 (build-system r-build-system)
11943 `(("r-maps" ,r-maps)
11944 ("r-spam" ,r-spam)))
11946 `(("gfortran" ,gfortran)))
11947 (home-page "https://www.image.ucar.edu/fields")
11948 (synopsis "Tools for spatial data")
11950 "This is a package for curve, surface and function fitting with an
11951 emphasis on splines, spatial data and spatial statistics. The major methods
11952 include cubic, and thin plate splines, Kriging, and compactly supported
11953 covariance functions for large data sets.")
11954 (license license:gpl2+)))
11956 (define-public r-spatialextremes
11958 (name "r-spatialextremes")
11963 (uri (cran-uri "SpatialExtremes" version))
11966 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11968 `((upstream-name . "SpatialExtremes")))
11969 (build-system r-build-system)
11971 `(("r-fields" ,r-fields)
11972 ("r-maps" ,r-maps)))
11973 (home-page "http://spatialextremes.r-forge.r-project.org/")
11974 (synopsis "Modelling spatial extremes")
11976 "This package provides tools for the statistical modelling of spatial
11977 extremes using max-stable processes, copula or Bayesian hierarchical models.
11978 More precisely, this package allows (conditional) simulations from various
11979 parametric max-stable models, analysis of the extremal spatial dependence, the
11980 fitting of such processes using composite likelihoods or least square (simple
11981 max-stable processes only), model checking and selection and prediction.")
11982 (license license:gpl2+)))
11984 (define-public r-drc
11991 (uri (cran-uri "drc" version))
11994 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11995 (build-system r-build-system)
11998 ("r-gtools" ,r-gtools)
12000 ("r-multcomp" ,r-multcomp)
12001 ("r-plotrix" ,r-plotrix)
12002 ("r-scales" ,r-scales)))
12003 (home-page "https://cran.r-project.org/web/packages/drc")
12004 (synopsis "Analysis of dose-response curves")
12006 "This package provides a suite of flexible and versatile model fitting
12007 and after-fitting functions for the analysis of dose-response data.")
12008 (license license:gpl2+)))
12010 (define-public r-rmeta
12017 (uri (cran-uri "rmeta" version))
12020 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12021 (build-system r-build-system)
12022 (home-page "https://cran.r-project.org/web/packages/rmeta")
12023 (synopsis "Tools for meta-analysis")
12025 "This package provides functions for simple fixed and random effects
12026 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12027 draws standard summary plots, funnel plots, and computes summaries and tests
12028 for association and heterogeneity.")
12029 (license license:gpl2)))
12031 (define-public r-bootstrap
12033 (name "r-bootstrap")
12038 (uri (cran-uri "bootstrap" version))
12041 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
12042 (build-system r-build-system)
12043 (native-inputs `(("gfortran" ,gfortran)))
12044 (home-page "https://cran.r-project.org/web/packages/bootstrap")
12045 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
12047 "This package provides software and data for the book \"An Introduction
12048 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
12049 This package is primarily provided for projects already based on it, and for
12050 support of the book. New projects should preferentially use the recommended
12051 package \"boot\".")
12052 (license license:bsd-3)))
12054 (define-public r-survivalroc
12056 (name "r-survivalroc")
12061 (uri (cran-uri "survivalROC" version))
12064 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
12065 (properties `((upstream-name . "survivalROC")))
12066 (build-system r-build-system)
12067 (home-page "https://cran.r-project.org/web/packages/survivalROC")
12068 (synopsis "Time-dependent ROC curve estimation from censored survival data")
12070 "Compute time-dependent ROC curve from censored survival data using
12071 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
12072 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
12073 (license license:gpl2+)))
12075 (define-public r-longitudinal
12077 (name "r-longitudinal")
12082 (uri (cran-uri "longitudinal" version))
12085 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
12086 (build-system r-build-system)
12087 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
12088 (home-page "http://strimmerlab.org/software/longitudinal/")
12089 (synopsis "Analysis of multiple time course data")
12091 "This package contains general data structures and functions for
12092 longitudinal data with multiple variables, repeated measurements, and
12093 irregularly spaced time points. It also implements a shrinkage estimator of
12094 dynamical correlation and dynamical covariance.")
12095 (license license:gpl3+)))
12097 (define-public r-genenet
12104 (uri (cran-uri "GeneNet" version))
12107 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
12108 (properties `((upstream-name . "GeneNet")))
12109 (build-system r-build-system)
12111 `(("r-corpcor" ,r-corpcor)
12112 ("r-fdrtool" ,r-fdrtool)
12113 ("r-longitudinal" ,r-longitudinal)))
12114 (home-page "http://strimmerlab.org/software/genenet/")
12115 (synopsis "Modeling and inferring gene networks")
12117 "This package analyzes gene expression (time series) data with focus on
12118 the inference of gene networks. In particular, GeneNet implements the methods
12119 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
12120 for learning large-scale gene association networks (including assignment of
12121 putative directions).")
12122 (license license:gpl3+)))
12124 (define-public r-rbamtools
12126 (name "r-rbamtools")
12127 (version "2.16.17")
12131 (uri (cran-uri "rbamtools" version))
12134 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
12135 (build-system r-build-system)
12136 (inputs `(("zlib" ,zlib)))
12138 `(("r-refgenome" ,r-refgenome)))
12139 (home-page "https://cran.r-project.org/web/packages/rbamtools")
12140 (synopsis "Read and write BAM (binary alignment) files")
12142 "This package provides an R interface to functions of the SAMtools
12144 (license license:artistic2.0)))
12146 (define-public r-protviz
12153 (uri (cran-uri "protViz" version))
12156 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
12157 (properties `((upstream-name . "protViz")))
12158 (build-system r-build-system)
12159 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12160 (home-page "https://github.com/protViz/protViz/")
12161 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
12163 "This package helps with quality checks, visualizations and analysis of
12164 mass spectrometry data, coming from proteomics experiments. The package is
12165 developed, tested and used at the Functional Genomics Center Zurich, where it
12166 is used mainly for prototyping, teaching, and having fun with proteomics data.
12167 But it can also be used to do data analysis for small scale data sets.")
12168 (license license:gpl3)))
12170 (define-public r-cmprsk
12177 (uri (cran-uri "cmprsk" version))
12179 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
12180 (build-system r-build-system)
12182 `(("r-survival" ,r-survival)))
12184 `(("gfortran" ,gfortran)))
12185 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12186 (synopsis "Subdistribution analysis of competing risks")
12188 "This package provides tool for estimation, testing and regression
12189 modeling of subdistribution functions in competing risks, as described in
12190 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12191 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12192 A proportional hazards model for the subdistribution of a competing risk,
12193 JASA, 94:496-509.")
12194 (license license:gpl2+)))
12196 (define-public r-etm
12203 (uri (cran-uri "etm" version))
12206 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12207 (build-system r-build-system)
12209 `(("r-data-table" ,r-data-table)
12210 ("r-lattice" ,r-lattice)
12212 ("r-rcpparmadillo" ,r-rcpparmadillo)
12213 ("r-survival" ,r-survival)))
12214 (home-page "https://cran.r-project.org/web/packages/etm")
12215 (synopsis "Empirical transition matrix")
12217 "The @dfn{empirical transition matrix} (etm) package estimates
12218 the matrix of transition probabilities for any time-inhomogeneous multistate
12219 model with finite state space using the Aalen-Johansen estimator.")
12220 (license license:expat)))
12222 (define-public r-epi
12229 (uri (cran-uri "Epi" version))
12232 "09miba6zk63bwc79n3030kgzlvy3whkq968pgqyghxnsjfh5ckp5"))))
12233 (properties `((upstream-name . "Epi")))
12234 (build-system r-build-system)
12236 `(("r-cmprsk" ,r-cmprsk)
12237 ("r-data-table" ,r-data-table)
12240 ("r-matrix" ,r-matrix)
12242 ("r-numderiv" ,r-numderiv)
12244 ("r-survival" ,r-survival)
12246 (home-page "https://BendixCarstensen.com/Epi/")
12247 (synopsis "Statistical analysis in epidemiology")
12249 "This package provides functions for demographic and epidemiological
12250 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12251 particular representation, manipulation and simulation of multistate data -
12252 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12253 @code{etm} and @code{cmprsk} packages. It also contains functions for
12254 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12255 data and some useful functions for tabulation and plotting, as well as a
12256 number of epidemiological data sets.")
12257 (license license:gpl2)))
12259 (define-public r-ppls
12262 (version "1.6-1.1")
12266 (uri (cran-uri "ppls" version))
12269 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12270 (build-system r-build-system)
12271 (propagated-inputs `(("r-mass" ,r-mass)))
12272 (home-page "https://cran.r-project.org/web/packages/ppls")
12273 (synopsis "Penalized partial least squares")
12275 "This package contains linear and nonlinear regression methods based on
12276 partial least squares and penalization techniques. Model parameters are
12277 selected via cross-validation, and confidence intervals ans tests for the
12278 regression coefficients can be conducted via jackknifing.")
12279 (license license:gpl2+)))
12281 (define-public r-huge
12284 (version "1.3.4.1")
12288 (uri (cran-uri "huge" version))
12290 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12291 (build-system r-build-system)
12293 `(("r-igraph" ,r-igraph)
12295 ("r-matrix" ,r-matrix)
12297 ("r-rcppeigen" ,r-rcppeigen)))
12298 (home-page "https://cran.r-project.org/web/packages/huge")
12299 (synopsis "High-dimensional undirected graph estimation")
12301 "This package provides a general framework for high-dimensional
12302 undirected graph estimation. It integrates data preprocessing, neighborhood
12303 screening, graph estimation, and model selection techniques into a pipeline.")
12304 (license license:gpl2)))
12306 (define-public r-parcor
12313 (uri (cran-uri "parcor" version))
12316 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12317 (build-system r-build-system)
12320 ("r-genenet" ,r-genenet)
12321 ("r-glmnet" ,r-glmnet)
12323 ("r-ppls" ,r-ppls)))
12324 (home-page "https://cran.r-project.org/web/packages/parcor")
12325 (synopsis "Regularized estimation of partial correlation matrices")
12327 "This package estimates the matrix of partial correlations based on
12328 different regularized regression methods: lasso, adaptive lasso, PLS, and
12329 Ridge Regression. In addition, the package provides model selection for
12330 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12331 (license license:gpl2+)))
12333 (define-public r-mcmc
12340 (uri (cran-uri "mcmc" version))
12343 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12344 (build-system r-build-system)
12345 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12346 (synopsis "Markov chain Monte Carlo")
12348 "This package simulates continuous distributions of random vectors using
12349 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12350 function that evaluates the log unnormalized density. Algorithms are random
12351 walk Metropolis algorithm (function @code{metrop}), simulated
12352 tempering (function @code{temper}), and morphometric random walk
12353 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12354 by change of variable.")
12355 (license license:expat)))
12357 (define-public r-listenv
12364 (uri (cran-uri "listenv" version))
12367 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12368 (build-system r-build-system)
12370 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12371 (home-page "https://github.com/HenrikBengtsson/listenv")
12372 (synopsis "Environments behaving (almost) as lists")
12374 "This package implements list environments. List environments are
12375 environments that have list-like properties. For instance, the elements of a
12376 list environment are ordered and can be accessed and iterated over using index
12378 (license license:lgpl2.1+)))
12380 (define-public r-globals
12387 (uri (cran-uri "globals" version))
12390 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12391 (build-system r-build-system)
12393 `(("r-codetools" ,r-codetools)))
12394 (home-page "https://github.com/HenrikBengtsson/globals")
12395 (synopsis "Identify global objects in R expressions")
12397 "This package provides tools to identify global (\"unknown\" or \"free\")
12398 objects in R expressions by code inspection using various strategies, e.g.
12399 conservative or liberal. The objective of this package is to make it as
12400 simple as possible to identify global objects for the purpose of exporting
12401 them in distributed compute environments.")
12402 (license license:lgpl2.1+)))
12404 (define-public r-future
12411 (uri (cran-uri "future" version))
12414 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12415 (build-system r-build-system)
12417 `(("r-digest" ,r-digest)
12418 ("r-globals" ,r-globals)
12419 ("r-listenv" ,r-listenv)))
12421 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12422 (home-page "https://github.com/HenrikBengtsson/future")
12423 (synopsis "Unified parallel and distributed processing in R")
12425 "The purpose of this package is to provide a lightweight and unified
12426 Future API for sequential and parallel processing of R expression via futures.
12427 This package implements sequential, multicore, multisession, and cluster
12428 futures. With these, R expressions can be evaluated on the local machine, in
12429 parallel a set of local machines, or distributed on a mix of local and remote
12430 machines. Extensions to this package implement additional backends for
12431 processing futures via compute cluster schedulers etc. Because of its unified
12432 API, there is no need to modify any code in order to switch from sequential on
12433 the local machine to, say, distributed processing on a remote compute cluster.")
12434 (license license:lgpl2.1+)))
12436 (define-public r-future-apply
12438 (name "r-future-apply")
12443 (uri (cran-uri "future.apply" version))
12446 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12447 (properties `((upstream-name . "future.apply")))
12448 (build-system r-build-system)
12450 `(("r-future" ,r-future)
12451 ("r-globals" ,r-globals)))
12453 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12454 (home-page "https://github.com/HenrikBengtsson/future.apply")
12455 (synopsis "Apply function to elements in parallel using futures")
12457 "This package provides implementations of @code{apply()},
12458 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12459 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12460 can be resolved using any future-supported backend, e.g. parallel on the local
12461 machine or distributed on a compute cluster.")
12462 (license license:gpl2+)))
12464 (define-public r-rsvd
12471 (uri (cran-uri "rsvd" version))
12474 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12475 (build-system r-build-system)
12477 `(("r-matrix" ,r-matrix)))
12478 (home-page "https://github.com/erichson/rSVD")
12479 (synopsis "Randomized singular value decomposition")
12481 "Low-rank matrix decompositions are fundamental tools and widely used for
12482 data analysis, dimension reduction, and data compression. Classically, highly
12483 accurate deterministic matrix algorithms are used for this task. However, the
12484 emergence of large-scale data has severely challenged our computational
12485 ability to analyze big data. The concept of randomness has been demonstrated
12486 as an effective strategy to quickly produce approximate answers to familiar
12487 problems such as the @dfn{singular value decomposition} (SVD). This package
12488 provides several randomized matrix algorithms such as the randomized singular
12489 value decomposition (@code{rsvd}), randomized principal component
12490 analysis (@code{rpca}), randomized robust principal component
12491 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12492 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12493 functions are provided.")
12494 (license license:gpl3+)))
12496 (define-public r-sloop
12503 (uri (cran-uri "sloop" version))
12506 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12507 (build-system r-build-system)
12509 `(("r-codetools" ,r-codetools)
12510 ("r-crayon" ,r-crayon)
12511 ("r-purrr" ,r-purrr)
12512 ("r-rlang" ,r-rlang)
12513 ("r-tibble" ,r-tibble)))
12514 (home-page "https://github.com/r-lib/sloop")
12515 (synopsis "Helpers for object-oriented programming in R")
12517 "This package provides a collection of helper functions designed to
12518 help you to better understand object oriented programming in R, particularly
12520 (license license:gpl3)))
12522 (define-public r-capushe
12529 (uri (cran-uri "capushe" version))
12532 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12533 (build-system r-build-system)
12534 (propagated-inputs `(("r-mass" ,r-mass)))
12535 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12536 (synopsis "Calibrating penalties using slope heuristics")
12538 "This package provides tools for the calibration of penalized criteria
12539 for model selection. The calibration methods available are based on the slope
12541 (license license:gpl2+)))
12543 (define-public r-dorng
12550 (uri (cran-uri "doRNG" version))
12553 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12554 (properties `((upstream-name . "doRNG")))
12555 (build-system r-build-system)
12557 `(("r-foreach" ,r-foreach)
12558 ("r-iterators" ,r-iterators)
12559 ("r-rngtools" ,r-rngtools)))
12560 (home-page "https://renozao.github.io/doRNG/")
12561 (synopsis "Generic reproducible parallel backend for foreach loops")
12563 "This package provides functions to perform reproducible parallel
12564 @code{foreach} loops, using independent random streams as generated by
12565 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12566 convert standard @code{%dopar%} loops into fully reproducible loops,
12567 independently of the number of workers, the task scheduling strategy, or the
12568 chosen parallel environment and associated foreach backend.")
12569 (license license:gpl2+)))
12571 (define-public r-blockmodeling
12573 (name "r-blockmodeling")
12578 (uri (cran-uri "blockmodeling" version))
12581 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12582 (build-system r-build-system)
12584 `(("r-matrix" ,r-matrix)))
12585 (native-inputs `(("gfortran" ,gfortran)))
12586 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12587 (synopsis "Generalized and classical blockmodeling of valued networks")
12589 "This package is primarily meant as an implementation of generalized
12590 blockmodeling for valued networks. In addition, measures of similarity or
12591 dissimilarity based on structural equivalence and regular equivalence (REGE
12592 algorithms) can be computed and partitioned matrices can be plotted.")
12593 (license license:gpl2+)))
12595 (define-public r-upsetr
12602 (uri (cran-uri "UpSetR" version))
12605 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12606 (properties `((upstream-name . "UpSetR")))
12607 (build-system r-build-system)
12609 `(("r-ggplot2" ,r-ggplot2)
12610 ("r-gridextra" ,r-gridextra)
12612 ("r-scales" ,r-scales)))
12613 (home-page "https://github.com/hms-dbmi/UpSetR")
12614 (synopsis "Visualize intersecting sets")
12616 "This package provides a more scalable alternative to Venn and Euler
12617 diagrams for visualizing intersecting sets. Create visualizations of
12618 intersecting sets using a novel matrix design, along with visualizations of
12619 several common set, element and attribute related tasks.")
12620 (license license:expat)))
12622 ;; This package includes a JavaScript file, which is not minified. When
12623 ;; upgrading please check that there are no new minified JavaScript files.
12624 (define-public r-shinybs
12631 (uri (cran-uri "shinyBS" version))
12634 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12635 (properties `((upstream-name . "shinyBS")))
12636 (build-system r-build-system)
12637 ;; The tests spawn Shiny browser apps. They cannot be run
12638 ;; non-interactively.
12639 (arguments '(#:tests? #f))
12641 `(("r-htmltools" ,r-htmltools)
12642 ("r-shiny" ,r-shiny)))
12643 (home-page "https://ebailey78.github.io/shinyBS/")
12644 (synopsis "Twitter Bootstrap components for Shiny")
12646 "This package adds additional Twitter Bootstrap components to Shiny.")
12647 (license license:gpl3)))
12649 (define-public r-outliers
12651 (name "r-outliers")
12656 (uri (cran-uri "outliers" version))
12659 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12660 (build-system r-build-system)
12661 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12662 (synopsis "Tests for outliers")
12664 "This package provides a collection of some tests commonly used for
12665 identifying outliers.")
12666 (license license:gpl2+)))
12668 (define-public r-bayesm
12675 (uri (cran-uri "bayesm" version))
12677 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12678 (build-system r-build-system)
12680 `(("r-rcpp" ,r-rcpp)
12681 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12682 (home-page "http://www.perossi.org/home/bsm-1")
12683 (synopsis "Bayesian inference for marketing/micro-econometrics")
12685 "This package covers many important models used in marketing and
12686 micro-econometrics applications, including Bayes Regression (univariate or
12687 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12688 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12689 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12690 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12691 Estimation with normal base, Hierarchical Linear Models with normal prior and
12692 covariates, Hierarchical Linear Models with a mixture of normals prior and
12693 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12694 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12695 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12696 analysis of choice-based conjoint data, Bayesian treatment of linear
12697 instrumental variables models, Analysis of Multivariate Ordinal survey data
12698 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12699 Coefficient Logit Models.")
12700 (license license:gpl2+)))
12702 (define-public r-tensora
12709 (uri (cran-uri "tensorA" version))
12712 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12713 (properties `((upstream-name . "tensorA")))
12714 (build-system r-build-system)
12715 (home-page "http://www.stat.boogaart.de/tensorA")
12716 (synopsis "Advanced tensor arithmetic with named indices")
12718 "This package provides convenience functions for advanced linear algebra
12719 with tensors and computation with datasets of tensors on a higher level
12720 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12721 co- and contravariate indices, and parallel computations on sequences of
12723 (license license:gpl2+)))
12725 (define-public r-rarpack
12732 (uri (cran-uri "rARPACK" version))
12735 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12736 (properties `((upstream-name . "rARPACK")))
12737 (build-system r-build-system)
12738 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12739 (home-page "https://github.com/yixuan/rARPACK")
12740 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12742 "This package was previously an R wrapper of the ARPACK library, and now
12743 a shell of the R package RSpectra, an R interface to the Spectra library for
12744 solving large scale eigenvalue/vector problems. The current version of
12745 rARPACK simply imports and exports the functions provided by RSpectra. New
12746 users of rARPACK are advised to switch to the RSpectra package.")
12747 (license license:bsd-3)))
12749 (define-public r-compositions
12751 (name "r-compositions")
12756 (uri (cran-uri "compositions" version))
12759 "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr"))))
12760 (build-system r-build-system)
12762 `(("r-bayesm" ,r-bayesm)
12764 ("r-robustbase" ,r-robustbase)
12765 ("r-tensora" ,r-tensora)))
12767 `(("r-knitr" ,r-knitr)))
12768 (home-page "http://www.stat.boogaart.de/compositions")
12769 (synopsis "Compositional data analysis")
12771 "This package provides functions for the consistent analysis of
12772 compositional data (e.g. portions of substances) and positive
12773 numbers (e.g. concentrations).")
12774 (license license:gpl2+)))
12776 (define-public r-cobs
12783 (uri (cran-uri "cobs" version))
12786 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12787 (build-system r-build-system)
12789 `(("r-quantreg" ,r-quantreg)
12790 ("r-sparsem" ,r-sparsem)))
12791 (home-page "https://cran.r-project.org/web/packages/cobs")
12792 (synopsis "Constrained B-Splines (sparse matrix based)")
12794 "This package provides qualitatively constrained (regression) smoothing
12795 splines via linear programming and sparse matrices.")
12796 (license license:gpl2+)))
12798 (define-public r-drimpute
12800 (name "r-drimpute")
12805 (uri (cran-uri "DrImpute" version))
12808 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12809 (properties `((upstream-name . "DrImpute")))
12810 (build-system r-build-system)
12812 `(("r-rcpp" ,r-rcpp)
12813 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12814 (home-page "https://github.com/ikwak2/DrImpute")
12815 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12817 "This is an R package for imputing dropout events. Many statistical
12818 methods in cell type identification, visualization and lineage reconstruction
12819 do not account for dropout events. DrImpute can improve the performance of
12820 such software by imputing dropout events.")
12821 (license license:gpl3)))
12823 (define-public r-gamlss-dist
12825 (name "r-gamlss-dist")
12830 (uri (cran-uri "gamlss.dist" version))
12832 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12833 (properties `((upstream-name . "gamlss.dist")))
12834 (build-system r-build-system)
12835 (propagated-inputs `(("r-mass" ,r-mass)))
12836 (home-page "http://www.gamlss.org/")
12837 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12839 "This package provides a set of distributions which can be used for
12840 modelling the response variables in Generalized Additive Models for Location
12841 Scale and Shape. The distributions can be continuous, discrete or mixed
12842 distributions. Extra distributions can be created, by transforming, any
12843 continuous distribution defined on the real line, to a distribution defined on
12844 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12845 transformation, respectively.")
12846 ;; Either version of the GPL.
12847 (license (list license:gpl2 license:gpl3))))
12849 ;; This package includes JavaScript files, which are not minified. When
12850 ;; upgrading please check that there are no new minified JavaScript files.
12851 (define-public r-shinyjs
12858 (uri (cran-uri "shinyjs" version))
12861 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12862 (build-system r-build-system)
12864 `(("r-digest" ,r-digest)
12865 ("r-htmltools" ,r-htmltools)
12866 ("r-jsonlite" ,r-jsonlite)
12867 ("r-shiny" ,r-shiny)))
12868 (home-page "https://deanattali.com/shinyjs")
12869 (synopsis "Improve the user experience of your Shiny apps")
12871 "Perform common useful JavaScript operations in Shiny apps that will
12872 greatly improve your apps without having to know any JavaScript. Examples
12873 include: hiding an element, disabling an input, resetting an input back to its
12874 original value, delaying code execution by a few seconds, and many more useful
12875 functions for both the end user and the developer. Shinyjs can also be used
12876 to easily call your own custom JavaScript functions from R.")
12877 (license license:agpl3+)))
12879 ;; This package includes minified JavaScript files. When upgrading please
12880 ;; check that there are no new minified JavaScript files.
12881 (define-public r-colourpicker
12883 (name "r-colourpicker")
12888 (uri (cran-uri "colourpicker" version))
12891 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12892 (build-system r-build-system)
12894 `(#:modules ((guix build utils)
12895 (guix build r-build-system)
12899 (modify-phases %standard-phases
12900 (add-after 'unpack 'process-javascript
12901 (lambda* (#:key inputs #:allow-other-keys)
12902 (with-directory-excursion "inst"
12906 `((,(assoc-ref inputs "js-salvattore")
12907 "examples/colourInput/www/salvattore.min.js")
12908 (,(assoc-ref inputs "js-jquery")
12909 "htmlwidgets/lib/jquery/jquery.min.js")
12910 ("www/shared/colourpicker/js/colourpicker.js"
12911 "www/shared/colourpicker/js/colourpicker.min.js"))))
12912 (lambda (sources targets)
12913 (for-each (lambda (source target)
12914 (format #t "Processing ~a --> ~a~%"
12916 (delete-file target)
12917 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12918 (call-with-output-file target
12920 (dump-port minified port)))))
12921 sources targets))))
12924 `(("r-ggplot2" ,r-ggplot2)
12925 ("r-htmltools" ,r-htmltools)
12926 ("r-htmlwidgets" ,r-htmlwidgets)
12927 ("r-jsonlite" ,r-jsonlite)
12928 ("r-miniui" ,r-miniui)
12929 ("r-shiny" ,r-shiny)
12930 ("r-shinyjs" ,r-shinyjs)))
12932 `(("uglify-js" ,uglify-js)
12936 (uri "https://code.jquery.com/jquery-3.3.1.js")
12939 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12943 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12946 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12947 (home-page "https://github.com/daattali/colourpicker")
12948 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12950 "This package provides a color picker that can be used as an input in
12951 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12952 custom color palettes, and many more options. A plot color helper tool is
12953 available as an RStudio Addin, which helps you pick colors to use in your
12954 plots. A more generic color picker RStudio Addin is also provided to let you
12955 select colors to use in your R code.")
12956 (license license:expat)))
12958 (define-public r-ggextra
12965 (uri (cran-uri "ggExtra" version))
12968 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12969 (properties `((upstream-name . "ggExtra")))
12970 (build-system r-build-system)
12972 `(("r-colourpicker" ,r-colourpicker)
12973 ("r-ggplot2" ,r-ggplot2)
12974 ("r-gtable" ,r-gtable)
12975 ("r-miniui" ,r-miniui)
12977 ("r-scales" ,r-scales)
12978 ("r-shiny" ,r-shiny)
12979 ("r-shinyjs" ,r-shinyjs)))
12981 `(("r-knitr" ,r-knitr)))
12982 (home-page "https://github.com/daattali/ggExtra")
12983 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12985 "This package is a collection of functions and layers to enhance ggplot2.
12986 The flagship function is @code{ggMarginal()}, which can be used to add
12987 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12988 (license license:expat)))
12990 (define-public r-minpack-lm
12992 (name "r-minpack-lm")
12997 (uri (cran-uri "minpack.lm" version))
13000 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
13001 (properties `((upstream-name . "minpack.lm")))
13002 (build-system r-build-system)
13003 (native-inputs `(("gfortran" ,gfortran)))
13004 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
13005 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
13007 "The @code{nls.lm} function provides an R interface to @code{lmder} and
13008 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
13009 problems by a modification of the Levenberg-Marquardt algorithm, with support
13010 for lower and upper parameter bounds. The implementation can be used via
13011 @code{nls}-like calls using the @code{nlsLM} function.")
13012 (license license:gpl3)))
13014 (define-public r-moments
13021 (uri (cran-uri "moments" version))
13024 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
13025 (build-system r-build-system)
13026 (home-page "https://cran.r-project.org/web/packages/moments")
13027 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
13029 "This package provides functions to calculate: moments, Pearson's
13030 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
13031 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
13032 (license license:gpl2+)))
13034 (define-public r-msir
13041 (uri (cran-uri "msir" version))
13044 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
13045 (build-system r-build-system)
13047 `(("r-mclust" ,r-mclust)))
13048 (home-page "https://cran.r-project.org/web/packages/msir")
13049 (synopsis "Model-based sliced inverse regression")
13051 "This is an R package for dimension reduction based on finite Gaussian
13052 mixture modeling of inverse regression.")
13053 (license license:gpl2+)))
13055 (define-public r-pbivnorm
13057 (name "r-pbivnorm")
13062 (uri (cran-uri "pbivnorm" version))
13065 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
13066 (build-system r-build-system)
13067 (native-inputs `(("gfortran" ,gfortran)))
13068 (home-page "https://github.com/brentonk/pbivnorm")
13069 (synopsis "Vectorized bivariate normal CDF")
13071 "This package provides a vectorized R function for calculating
13072 probabilities from a standard bivariate normal CDF.")
13073 (license license:gpl2+)))
13075 (define-public r-lavaan
13082 (uri (cran-uri "lavaan" version))
13085 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
13086 (build-system r-build-system)
13088 `(("r-mass" ,r-mass)
13089 ("r-mnormt" ,r-mnormt)
13090 ("r-numderiv" ,r-numderiv)
13091 ("r-pbivnorm" ,r-pbivnorm)))
13092 (home-page "http://lavaan.ugent.be")
13093 (synopsis "Latent variable analysis")
13095 "This package provides tools to fit a variety of latent variable models,
13096 including confirmatory factor analysis, structural equation modeling and
13097 latent growth curve models.")
13098 (license license:gpl2+)))
13100 (define-public r-nonnest2
13102 (name "r-nonnest2")
13107 (uri (cran-uri "nonnest2" version))
13110 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
13111 (build-system r-build-system)
13113 `(("r-compquadform" ,r-compquadform)
13114 ("r-lavaan" ,r-lavaan)
13115 ("r-mvtnorm" ,r-mvtnorm)
13116 ("r-sandwich" ,r-sandwich)))
13118 `(("r-knitr" ,r-knitr)))
13119 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
13120 (synopsis "Tests of non-nested models")
13122 "This package allows for testing of non-nested models. It includes tests
13123 of model distinguishability and of model fit that can be applied to both
13124 nested and non-nested models. The package also includes functionality to
13125 obtain confidence intervals associated with AIC and BIC.")
13126 ;; Either version of the GPL.
13127 (license (list license:gpl2 license:gpl3))))
13129 (define-public r-penalized
13131 (name "r-penalized")
13136 (uri (cran-uri "penalized" version))
13139 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
13140 (build-system r-build-system)
13142 `(("r-rcpp" ,r-rcpp)
13143 ("r-rcpparmadillo" ,r-rcpparmadillo)
13144 ("r-survival" ,r-survival)))
13145 (home-page "https://cran.r-project.org/web/packages/penalized/")
13146 (synopsis "Penalized estimation in GLMs and in the Cox model")
13148 "This package provides tools for fitting possibly high dimensional
13149 penalized regression models. The penalty structure can be any combination of
13150 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
13151 constraint on the regression coefficients. The supported regression models
13152 are linear, logistic and Poisson regression and the Cox Proportional Hazards
13153 model. Cross-validation routines allow optimization of the tuning
13155 (license license:gpl2+)))
13157 (define-public r-zim
13164 (uri (cran-uri "ZIM" version))
13167 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
13168 (properties `((upstream-name . "ZIM")))
13169 (build-system r-build-system)
13170 (propagated-inputs `(("r-mass" ,r-mass)))
13171 (home-page "https://github.com/biostatstudio/ZIM")
13172 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
13174 "Analyze count time series with excess zeros. Two types of statistical
13175 models are supported: Markov regression and state-space models. They are also
13176 known as observation-driven and parameter-driven models respectively in the
13177 time series literature. The functions used for Markov regression or
13178 observation-driven models can also be used to fit ordinary regression models
13179 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
13180 negative binomial (ZINB) assumption. The package also contains miscellaneous
13181 functions to compute density, distribution, quantile, and generate random
13182 numbers from ZIP and ZINB distributions.")
13183 (license license:gpl3)))
13185 (define-public r-nor1mix
13192 (uri (cran-uri "nor1mix" version))
13195 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13196 (build-system r-build-system)
13197 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13198 (synopsis "Normal (1-d) mixture models")
13200 "This package provides S3 classes and methods for one-dimensional normal
13201 mixture models, for, e.g., density estimation or clustering algorithms
13202 research and teaching; it provides the widely used Marron-Wand densities. It
13203 also provides tools for efficient random number generation and graphics.")
13204 (license license:gpl2+)))
13206 (define-public r-beanplot
13208 (name "r-beanplot")
13213 (uri (cran-uri "beanplot" version))
13216 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13217 (build-system r-build-system)
13218 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13219 (synopsis "Visualization via beanplots")
13221 "This package provides beanplots, an alternative to
13222 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13224 (license license:gpl2)))
13226 (define-public r-pbdzmq
13233 (uri (cran-uri "pbdZMQ" version))
13236 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13237 (properties `((upstream-name . "pbdZMQ")))
13238 (build-system r-build-system)
13240 `(("zeromq" ,zeromq)
13243 `(("pkg-config" ,pkg-config)))
13244 (home-page "https://pbdr.org/")
13245 (synopsis "R interface to ZeroMQ")
13247 "ZeroMQ is a well-known library for high-performance asynchronous
13248 messaging in scalable, distributed applications. This package provides high
13249 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13250 interactive client/server programming frameworks. A few wrapper functions
13251 compatible with @code{rzmq} are also provided.")
13252 (license license:gpl3)))
13254 (define-public r-repr
13261 (uri (cran-uri "repr" version))
13264 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13265 (build-system r-build-system)
13267 `(("r-base64enc" ,r-base64enc)
13268 ("r-htmltools" ,r-htmltools)
13269 ("r-jsonlite" ,r-jsonlite)
13270 ("r-pillar" ,r-pillar)))
13271 (home-page "https://cran.r-project.org/web/packages/repr/")
13272 (synopsis "Serializable representations")
13274 "This package provides string and binary representations of objects for
13275 several formats and MIME types.")
13276 (license license:gpl3)))
13278 (define-public r-irdisplay
13280 (name "r-irdisplay")
13285 (uri (cran-uri "IRdisplay" version))
13288 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13289 (properties `((upstream-name . "IRdisplay")))
13290 (build-system r-build-system)
13292 `(("r-repr" ,r-repr)))
13293 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13294 (synopsis "Jupyter display machinery")
13296 "This package provides an interface to the rich display capabilities of
13297 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13298 running IRkernel session.")
13299 (license license:expat)))
13301 (define-public r-irkernel
13303 (name "r-irkernel")
13308 (uri (cran-uri "IRkernel" version))
13311 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
13312 (properties `((upstream-name . "IRkernel")))
13313 (build-system r-build-system)
13316 (modify-phases %standard-phases
13317 (add-after 'install 'install-kernelspec
13318 (lambda* (#:key outputs #:allow-other-keys)
13319 (let ((out (assoc-ref outputs "out")))
13320 (setenv "HOME" "/tmp")
13321 (invoke "jupyter" "kernelspec" "install"
13324 (string-append out "/site-library/IRkernel/kernelspec"))
13325 ;; Record the absolute file name of the 'R' executable in
13327 (substitute* (string-append out "/share/jupyter"
13328 "/kernels/ir/kernel.json")
13330 (string-append "[\"" (which "R") "\",")))
13333 `(("jupyter" ,jupyter)))
13335 `(("r-crayon" ,r-crayon)
13336 ("r-digest" ,r-digest)
13337 ("r-evaluate" ,r-evaluate)
13338 ("r-irdisplay" ,r-irdisplay)
13339 ("r-jsonlite" ,r-jsonlite)
13340 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13341 ("r-minimal" ,r-minimal)
13342 ("r-pbdzmq" ,r-pbdzmq)
13344 ("r-uuid" ,r-uuid)))
13345 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13346 (synopsis "Native R kernel for Jupyter")
13348 "The R kernel for the Jupyter environment executes R code which the
13349 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13351 (license license:expat)))
13353 (define-public r-gmodels
13360 (uri (cran-uri "gmodels" version))
13363 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13364 (build-system r-build-system)
13366 `(("r-gdata" ,r-gdata)
13367 ("r-mass" ,r-mass)))
13368 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13369 (synopsis "Various R programming tools for model fitting")
13371 "This package provides various R programming tools for model fitting.")
13372 (license license:gpl2)))
13374 (define-public r-apcluster
13376 (name "r-apcluster")
13381 (uri (cran-uri "apcluster" version))
13384 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13385 (build-system r-build-system)
13387 `(("r-matrix" ,r-matrix)
13388 ("r-rcpp" ,r-rcpp)))
13389 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13390 (synopsis "Affinity propagation clustering")
13392 "This package implements affinity propagation clustering introduced by
13393 Frey and Dueck (2007). The package further provides leveraged affinity
13394 propagation and an algorithm for exemplar-based agglomerative clustering that
13395 can also be used to join clusters obtained from affinity propagation. Various
13396 plotting functions are available for analyzing clustering results.")
13397 (license license:gpl2+)))
13399 (define-public r-valr
13406 (uri (cran-uri "valr" version))
13409 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13410 (build-system r-build-system)
13412 `(("r-broom" ,r-broom)
13413 ("r-dplyr" ,r-dplyr)
13414 ("r-ggplot2" ,r-ggplot2)
13416 ("r-readr" ,r-readr)
13417 ("r-rlang" ,r-rlang)
13418 ("r-stringr" ,r-stringr)
13419 ("r-tibble" ,r-tibble)))
13421 `(("r-knitr" ,r-knitr)))
13422 (home-page "https://github.com/rnabioco/valr")
13423 (synopsis "Genome interval arithmetic in R")
13425 "This package enables you to read and manipulate genome intervals and
13426 signals. It provides functionality similar to command-line tool suites within
13427 R, enabling interactive analysis and visualization of genome-scale data.")
13428 (license license:expat)))
13430 (define-public r-rematch2
13432 (name "r-rematch2")
13437 (uri (cran-uri "rematch2" version))
13440 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13441 (build-system r-build-system)
13443 `(("r-tibble" ,r-tibble)))
13444 (home-page "https://github.com/r-lib/rematch2")
13445 (synopsis "Tidy output from regular expression matching")
13447 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13448 return the match results in tidy data frames.")
13449 (license license:expat)))
13451 (define-public r-picante
13458 (uri (cran-uri "picante" version))
13461 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13462 (build-system r-build-system)
13466 ("r-vegan" ,r-vegan)))
13467 (home-page "https://cran.r-project.org/web/packages/picante/")
13468 (synopsis "Integrating phylogenies and ecology")
13470 "This package provides functions for phylocom integration, community
13471 analyses, null-models, traits and evolution. It implements numerous
13472 ecophylogenetic approaches including measures of community phylogenetic and
13473 trait diversity, phylogenetic signal, estimation of trait values for
13474 unobserved taxa, null models for community and phylogeny randomizations, and
13475 utility functions for data input/output and phylogeny plotting. A full
13476 description of package functionality and methods are provided by Kembel et
13478 (license license:gpl2)))
13480 (define-public r-reinforcelearn
13482 (name "r-reinforcelearn")
13487 (uri (cran-uri "reinforcelearn" version))
13490 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13491 (build-system r-build-system)
13493 `(("r-checkmate" ,r-checkmate)
13495 ("r-purrr" ,r-purrr)
13497 (home-page "https://markusdumke.github.io/reinforcelearn")
13498 (synopsis "Reinforcement learning")
13500 "This package implements reinforcement learning environments and
13501 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13502 can be used with function approximation, eligibility traces (Singh & Sutton,
13503 1996) and experience replay (Mnih et al., 2013).")
13504 (license license:expat)))
13506 (define-public r-lemon
13513 (uri (cran-uri "lemon" version))
13516 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13517 (build-system r-build-system)
13519 `(("r-ggplot2" ,r-ggplot2)
13520 ("r-gridextra" ,r-gridextra)
13521 ("r-gtable" ,r-gtable)
13522 ("r-knitr" ,r-knitr)
13523 ("r-lattice" ,r-lattice)
13525 ("r-rlang" ,r-rlang)
13526 ("r-scales" ,r-scales)))
13528 `(("r-knitr" ,r-knitr)))
13529 (home-page "https://github.com/stefanedwards/lemon")
13530 (synopsis "Freshen up your ggplot2 plots")
13532 "This package provides functions for working with legends and axis lines
13533 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13535 (license license:gpl3)))
13537 (define-public r-wgaim
13544 (uri (cran-uri "wgaim" version))
13546 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13547 (build-system r-build-system)
13549 `(("r-ggplot2" ,r-ggplot2)
13551 (home-page "https://cran.r-project.org/web/packages/wgaim")
13552 (synopsis "Whole genome average interval mapping for QTL detection")
13554 "This package integrates sophisticated mixed modelling methods with a
13555 whole genome approach to detecting significant QTL in linkage maps.")
13556 (license license:gpl2+)))
13558 (define-public r-bedr
13565 (uri (cran-uri "bedr" version))
13568 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13569 (build-system r-build-system)
13571 `(("r-data-table" ,r-data-table)
13572 ("r-r-utils" ,r-r-utils)
13573 ("r-testthat" ,r-testthat)
13574 ("r-venndiagram" ,r-venndiagram)
13577 ("bedtools" ,bedtools)
13578 ("htslib" ,htslib))) ; for tabix
13580 `(("r-knitr" ,r-knitr))) ; for vignettes
13581 (home-page "https://cran.r-project.org/web/packages/bedr")
13582 (synopsis "Genomic region processing")
13584 "This package is for genomic regions processing using command line tools
13585 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13586 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13587 The bedr package's API enhances access to these tools as well as offers
13588 additional utilities for genomic regions processing.")
13589 (license license:gpl2)))
13591 (define-public r-sets
13598 (uri (cran-uri "sets" version))
13601 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13602 (properties `((upstream-name . "sets")))
13603 (build-system r-build-system)
13604 (home-page "https://cran.r-project.org/web/packages/sets")
13605 (synopsis "Sets, generalized sets, customizable sets and intervals")
13607 "This package provides data structures and basic operations for ordinary
13608 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13609 customizable sets, and intervals.")
13610 (license license:gpl2)))
13612 (define-public r-partitions
13614 (name "r-partitions")
13619 (uri (cran-uri "partitions" version))
13622 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13623 (build-system r-build-system)
13626 ("r-polynom" ,r-polynom)
13627 ("r-sets" ,r-sets)))
13628 (home-page "https://cran.r-project.org/web/packages/partitions")
13629 (synopsis "Additive partitions of integers")
13631 "This package provides tools to enumerates the partitions, unequal
13632 partitions, and restricted partitions of an integer; the three corresponding
13633 partition functions are also given.")
13634 ;; Any version of the GPL
13635 (license license:gpl2+)))
13637 (define-public r-brobdingnag
13639 (name "r-brobdingnag")
13644 (uri (cran-uri "Brobdingnag" version))
13647 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13648 (properties `((upstream-name . "Brobdingnag")))
13649 (build-system r-build-system)
13650 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13651 (synopsis "Very large numbers in R")
13653 "This package handles very large numbers in R. Real numbers are held
13654 using their natural logarithms, plus a logical flag indicating sign. The
13655 package includes a vignette that gives a step-by-step introduction to using S4
13657 ;; Any version of the GPL
13658 (license license:gpl2+)))
13660 (define-public r-untb
13667 (uri (cran-uri "untb" version))
13670 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13671 (build-system r-build-system)
13673 `(("r-brobdingnag" ,r-brobdingnag)
13674 ("r-partitions" ,r-partitions)
13675 ("r-polynom" ,r-polynom)))
13676 (home-page "https://github.com/RobinHankin/untb.git")
13677 (synopsis "Ecological drift under the UNTB")
13679 "This package provides numerical simulations, and visualizations, of
13680 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13681 (license license:gpl2+)))
13683 (define-public r-stepwise
13685 (name "r-stepwise")
13690 (uri (cran-uri "stepwise" version))
13693 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13694 (build-system r-build-system)
13695 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13696 (synopsis "Stepwise detection of recombination breakpoints")
13698 "This package provides a stepwise approach to identifying recombination
13699 breakpoints in a genomic sequence alignment.")
13700 (license license:gpl2+)))
13702 (define-public r-snpmaxsel
13704 (name "r-snpmaxsel")
13709 (uri (cran-uri "SNPmaxsel" version))
13712 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13713 (properties `((upstream-name . "SNPmaxsel")))
13714 (build-system r-build-system)
13716 `(("r-combinat" ,r-combinat)
13717 ("r-mvtnorm" ,r-mvtnorm)))
13718 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13719 (synopsis "Maximally selected statistics for SNP data")
13721 "This package implements asymptotic methods related to maximally selected
13722 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13724 (license license:gpl2+)))
13726 (define-public r-acsnminer
13728 (name "r-acsnminer")
13729 (version "0.16.8.25")
13732 (uri (cran-uri "ACSNMineR" version))
13735 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13736 (properties `((upstream-name . "ACSNMineR")))
13737 (build-system r-build-system)
13739 `(("r-ggplot2" ,r-ggplot2)
13740 ("r-gridextra" ,r-gridextra)))
13741 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13742 (synopsis "Gene enrichment analysis")
13744 "This package provides tools to compute and represent gene set enrichment
13745 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13746 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13747 enrichment can be run with hypergeometric test or Fisher exact test, and can
13748 use multiple corrections. Visualization of data can be done either by
13749 barplots or heatmaps.")
13750 (license license:gpl2+)))
13752 (define-public r-seqinr
13759 (uri (cran-uri "seqinr" version))
13762 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13763 (build-system r-build-system)
13765 `(("r-ade4" ,r-ade4)
13766 ("r-segmented" ,r-segmented)))
13769 (home-page "http://seqinr.r-forge.r-project.org/")
13770 (synopsis "Biological sequences retrieval and analysis")
13772 "This package provides tools for exploratory data analysis and data
13773 visualization of biological sequence (DNA and protein) data. It also includes
13774 utilities for sequence data management under the ACNUC system.")
13775 (license license:gpl2+)))
13777 (define-public r-units
13784 (uri (cran-uri "units" version))
13787 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13788 (build-system r-build-system)
13790 `(("udunits" ,udunits)))
13792 `(("r-rcpp" ,r-rcpp)))
13794 `(("r-knitr" ,r-knitr)))
13795 (home-page "https://github.com/r-quantities/units/")
13796 (synopsis "Measurement Units for R Vectors")
13798 "This package provides support for measurement units in R vectors,
13799 matrices and arrays: automatic propagation, conversion, derivation and
13800 simplification of units; raising errors in case of unit incompatibility. It
13801 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13803 (license license:gpl2)))
13805 (define-public r-classint
13807 (name "r-classint")
13812 (uri (cran-uri "classInt" version))
13815 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13816 (properties `((upstream-name . "classInt")))
13817 (build-system r-build-system)
13819 `(("r-class" ,r-class)
13820 ("r-e1071" ,r-e1071)
13821 ("r-kernsmooth" ,r-kernsmooth)))
13823 `(("gfortran" ,gfortran)
13824 ("r-knitr" ,r-knitr)))
13825 (home-page "https://github.com/r-spatial/classInt/")
13826 (synopsis "Choose univariate class intervals")
13828 "This package provides selected commonly used methods for choosing
13829 univariate class intervals for mapping or other graphics purposes.")
13830 (license license:gpl2+)))
13832 (define-public r-spdata
13839 (uri (cran-uri "spData" version))
13842 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13843 (properties `((upstream-name . "spData")))
13844 (build-system r-build-system)
13846 `(("r-raster" ,r-raster)
13848 (home-page "https://github.com/Nowosad/spData")
13849 (synopsis "Datasets for spatial analysis")
13851 "This a package containing diverse spatial datasets for demonstrating,
13852 benchmarking and teaching spatial data analysis. It includes R data of class
13853 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13854 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13855 of the datasets are designed to illustrate specific analysis techniques.
13856 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13857 illustrate point pattern analysis techniques.")
13858 (license license:cc0)))
13860 (define-public r-learnbayes
13862 (name "r-learnbayes")
13867 (uri (cran-uri "LearnBayes" version))
13870 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13871 (properties `((upstream-name . "LearnBayes")))
13872 (build-system r-build-system)
13873 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13874 (synopsis "Functions for learning Bayesian inference")
13876 "This package provides a collection of functions helpful in learning the
13877 basic tenets of Bayesian statistical inference. It contains functions for
13878 summarizing basic one and two parameter posterior distributions and predictive
13879 distributions. It contains MCMC algorithms for summarizing posterior
13880 distributions defined by the user. It also contains functions for regression
13881 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13883 (license license:gpl2+)))
13885 (define-public r-deldir
13892 (uri (cran-uri "deldir" version))
13895 "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
13896 (build-system r-build-system)
13897 (native-inputs `(("gfortran" ,gfortran)))
13898 (home-page "https://cran.r-project.org/web/packages/deldir")
13899 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13901 "This package provides tools for calculating the Delaunay triangulation
13902 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13903 of a planar point set. It plots triangulations and tessellations in various
13904 ways, clips tessellations to sub-windows, calculates perimeters of
13905 tessellations, and summarizes information about the tiles of the
13907 (license license:gpl2+)))
13909 (define-public r-sf
13916 (uri (cran-uri "sf" version))
13919 "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
13920 (build-system r-build-system)
13927 `(("r-classint" ,r-classint)
13929 ("r-magrittr" ,r-magrittr)
13931 ("r-units" ,r-units)))
13933 `(("pkg-config" ,pkg-config)
13934 ("r-knitr" ,r-knitr)))
13935 (home-page "https://github.com/r-spatial/sf/")
13936 (synopsis "Simple features for R")
13938 "This package provides support for simple features, a standardized way to
13939 encode spatial vector data. It binds to GDAL for reading and writing data, to
13940 GEOS for geometrical operations, and to PROJ for projection conversions and
13941 datum transformations.")
13942 ;; Either of these licenses
13943 (license (list license:gpl2 license:expat))))
13945 (define-public r-spdep
13952 (uri (cran-uri "spdep" version))
13955 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13956 (build-system r-build-system)
13958 `(("r-boot" ,r-boot)
13960 ("r-deldir" ,r-deldir)
13962 ("r-gmodels" ,r-gmodels)
13963 ("r-learnbayes" ,r-learnbayes)
13965 ("r-matrix" ,r-matrix)
13969 ("r-spdata" ,r-spdata)))
13971 `(("r-knitr" ,r-knitr)))
13972 (home-page "https://github.com/r-spatial/spdep/")
13973 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13975 "This package provides a collection of functions to create spatial
13976 weights matrix objects from polygon contiguities, from point patterns by
13977 distance and tessellations, for summarizing these objects, and for permitting
13978 their use in spatial data analysis, including regional aggregation by minimum
13980 (license license:gpl2+)))
13982 (define-public r-adegenet
13984 (name "r-adegenet")
13989 (uri (cran-uri "adegenet" version))
13992 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13993 (build-system r-build-system)
13995 `(("r-ade4" ,r-ade4)
13998 ("r-dplyr" ,r-dplyr)
13999 ("r-ggplot2" ,r-ggplot2)
14000 ("r-igraph" ,r-igraph)
14002 ("r-reshape2" ,r-reshape2)
14003 ("r-seqinr" ,r-seqinr)
14004 ("r-shiny" ,r-shiny)
14005 ("r-spdep" ,r-spdep)
14006 ("r-vegan" ,r-vegan)))
14007 (home-page "https://github.com/thibautjombart/adegenet")
14008 (synopsis "Exploratory analysis of genetic and genomic data")
14010 "This package provides a toolset for the exploration of genetic and
14011 genomic data. Adegenet provides formal (S4) classes for storing and handling
14012 various genetic data, including genetic markers with varying ploidy and
14013 hierarchical population structure (@code{genind} class), alleles counts by
14014 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
14015 also implements original multivariate methods (DAPC, sPCA), graphics,
14016 statistical tests, simulation tools, distance and similarity measures, and
14017 several spatial methods. A range of both empirical and simulated datasets is
14018 also provided to illustrate various methods.")
14019 (license license:gpl2+)))
14021 (define-public r-pegas
14028 (uri (cran-uri "pegas" version))
14030 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
14031 (build-system r-build-system)
14033 `(("r-adegenet" ,r-adegenet)
14035 (home-page "http://ape-package.ird.fr/pegas.html")
14036 (synopsis "Population and evolutionary genetics analysis system")
14038 "This package provides functions for reading, writing, plotting,
14039 analysing, and manipulating allelic and haplotypic data, including from VCF
14040 files, and for the analysis of population nucleotide sequences and
14041 micro-satellites including coalescent analyses, linkage disequilibrium,
14042 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
14043 minimum spanning tree and network, and median-joining networks.")
14044 (license license:gpl2+)))
14046 (define-public r-rmetasim
14048 (name "r-rmetasim")
14053 (uri (cran-uri "rmetasim" version))
14056 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
14057 (build-system r-build-system)
14059 `(("r-ade4" ,r-ade4)
14060 ("r-adegenet" ,r-adegenet)
14061 ("r-gtools" ,r-gtools)
14062 ("r-pegas" ,r-pegas)))
14063 (home-page "https://cran.r-project.org/web/packages/rmetasim")
14064 (synopsis "Individual-based population genetic simulation environment")
14066 "This package provides an interface between R and the metasim simulation
14067 engine. The simulation environment is documented in: Strand, A.(2002),
14068 Metasim 1.0: an individual-based environment for simulating population
14069 genetics of complex population dynamics.")
14071 (license license:gpl2+)))
14073 (define-public r-genetics
14075 (name "r-genetics")
14076 (version "1.3.8.1.2")
14080 (uri (cran-uri "genetics" version))
14083 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
14084 (build-system r-build-system)
14086 `(("r-combinat" ,r-combinat)
14087 ("r-gdata" ,r-gdata)
14088 ("r-gtools" ,r-gtools)
14090 ("r-mvtnorm" ,r-mvtnorm)))
14091 (home-page "https://cran.r-project.org/web/packages/genetics/")
14092 (synopsis "Population genetics")
14094 "This package provides classes and methods for handling genetic data.
14095 It includes classes to represent genotypes and haplotypes at single markers up
14096 to multiple markers on multiple chromosomes. Function include allele
14097 frequencies, flagging homo/heterozygotes, flagging carriers of certain
14098 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
14099 and testing for linkage disequilibrium, ...")
14100 ;; Any GPL version.
14101 (license license:gpl2+)))
14103 (define-public r-snp-plotter
14105 (name "r-snp-plotter")
14110 (uri (cran-uri "snp.plotter" version))
14113 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
14114 (properties `((upstream-name . "snp.plotter")))
14115 (build-system r-build-system)
14116 (propagated-inputs `(("r-genetics" ,r-genetics)))
14117 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
14118 (synopsis "Plot p-values using single SNP and/or haplotype data")
14120 "This package helps you create plots of p-values using single SNP and/or
14121 haplotype data. Main features of the package include options to display a
14122 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
14123 datasets simultaneously. Plots can be created using global and/or individual
14124 haplotype p-values along with single SNP p-values. Images are created as
14125 either PDF/EPS files.")
14126 (license license:gpl2+)))
14128 (define-public r-polspline
14130 (name "r-polspline")
14135 (uri (cran-uri "polspline" version))
14137 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
14138 (build-system r-build-system)
14139 (native-inputs `(("gfortran" ,gfortran)))
14140 (home-page "https://cran.r-project.org/web/packages/polspline/")
14141 (synopsis "Polynomial spline routines")
14143 "This package provides routines for the polynomial spline fitting
14144 routines hazard regression, hazard estimation with flexible tails, logspline,
14145 lspec, polyclass, and polymars.")
14146 (license license:gpl2+)))
14148 (define-public r-rms
14155 (uri (cran-uri "rms" version))
14157 (base32 "1zkcsqcvldfj4kyn0346vi51igq951qrnpxlv2pfvap6n2v5wbxq"))))
14158 (build-system r-build-system)
14160 `(("r-cluster" ,r-cluster)
14161 ("r-digest" ,r-digest)
14162 ("r-ggplot2" ,r-ggplot2)
14163 ("r-hmisc" ,r-hmisc)
14164 ("r-htmltable" ,r-htmltable)
14165 ("r-htmltools" ,r-htmltools)
14166 ("r-lattice" ,r-lattice)
14168 ("r-multcomp" ,r-multcomp)
14170 ("r-polspline" ,r-polspline)
14171 ("r-quantreg" ,r-quantreg)
14172 ("r-rpart" ,r-rpart)
14173 ("r-sparsem" ,r-sparsem)
14174 ("r-survival" ,r-survival)))
14175 (native-inputs `(("gfortran" ,gfortran)))
14176 (home-page "http://biostat.mc.vanderbilt.edu/rms")
14177 (synopsis "Regression modeling strategies")
14179 "This is a package for regression modeling, testing, estimation,
14180 validation, graphics, prediction, and typesetting by storing enhanced model
14181 design attributes in the fit. The rms package is a collection of functions
14182 that assist with and streamline modeling. It also contains functions for
14183 binary and ordinal logistic regression models, ordinal models for continuous Y
14184 with a variety of distribution families, and the Buckley-James multiple
14185 regression model for right-censored responses, and implements penalized
14186 maximum likelihood estimation for logistic and ordinary linear models. The
14187 package works with almost any regression model, but it was especially written
14188 to work with binary or ordinal regression models, Cox regression, accelerated
14189 failure time models, ordinary linear models, the Buckley-James model,
14190 generalized least squares for serially or spatially correlated observations,
14191 generalized linear models, and quantile regression.")
14192 (license license:gpl2+)))
14194 (define-public r-arsenal
14201 (uri (cran-uri "arsenal" version))
14204 "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
14205 (properties `((upstream-name . "arsenal")))
14206 (build-system r-build-system)
14207 (propagated-inputs `(("r-knitr" ,r-knitr)))
14208 (native-inputs `(("r-knitr" ,r-knitr)))
14209 (home-page "https://github.com/mayoverse/arsenal")
14210 (synopsis "Functions for large-scale statistical summaries")
14212 "This package provides an arsenal of R functions for large-scale
14213 statistical summaries, which are streamlined to work within the latest
14214 reporting tools in R and RStudio and which use formulas and versatile
14215 summary statistics for summary tables and models. The primary functions
14219 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
14220 levels of one or more categorical variables;
14221 @item @code{paired}, a Table-1-like summary of multiple variable types paired
14222 across two time points;
14223 @item @code{modelsum}, which performs simple model fits on one or more
14224 endpoints for many variables (univariate or adjusted for covariates);
14225 @item @code{freqlist}, a powerful frequency table across many categorical
14227 @item @code{comparedf}, a function for comparing @code{data.frames}; and
14228 @item @code{write2}, a function to output tables to a document.
14231 (license license:gpl2+)))
14233 (define-public r-haplo-stats
14235 (name "r-haplo-stats")
14240 (uri (cran-uri "haplo.stats" version))
14243 "1f5cyyyavkf4l6kksp87s8d92vjrnhxmpz6j737pa527pn3gghf9"))))
14244 (properties `((upstream-name . "haplo.stats")))
14245 (build-system r-build-system)
14247 `(("r-arsenal" ,r-arsenal)
14250 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14251 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14252 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14254 "This package provides routines for the analysis of indirectly measured
14255 haplotypes. The statistical methods assume that all subjects are unrelated
14256 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14257 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14258 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14259 examples in the vignette.")
14260 (license license:gpl2+)))
14262 (define-public r-bqtl
14269 (uri (cran-uri "bqtl" version))
14272 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14273 (build-system r-build-system)
14274 (native-inputs `(("gfortran" ,gfortran)))
14275 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14276 (synopsis "Bayesian QTL mapping toolkit")
14278 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14279 lines. It includes maximum likelihood and Bayesian tools.")
14280 (license license:gpl2+)))
14282 (define-public r-ibdreg
14289 (uri (cran-uri "ibdreg" version))
14292 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
14293 (build-system r-build-system)
14294 (home-page "https://www.mayo.edu/research/labs/\
14295 statistical-genetics-genetic-epidemiology/software")
14296 (synopsis "Regression methods for IBD linkage with covariates")
14298 "This package provides a method to test genetic linkage with covariates
14299 by regression methods with response IBD sharing for relative pairs. Account
14300 for correlations of IBD statistics and covariates for relative pairs within
14301 the same pedigree.")
14302 (license license:gpl2+)))
14304 (define-public r-dlmap
14311 (uri (cran-uri "dlmap" version))
14314 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14315 (build-system r-build-system)
14317 `(("r-ibdreg" ,r-ibdreg)
14321 ("r-wgaim" ,r-wgaim)))
14322 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14323 (synopsis "Detection localization mapping for QTL")
14325 "This is package for QTL mapping in a mixed model framework with separate
14326 detection and localization stages. The first stage detects the number of QTL
14327 on each chromosome based on the genetic variation due to grouped markers on
14328 the chromosome; the second stage uses this information to determine the most
14329 likely QTL positions. The mixed model can accommodate general fixed and
14330 random effects, including spatial effects in field trials and pedigree
14331 effects. It is applicable to backcrosses, doubled haploids, recombinant
14332 inbred lines, F2 intercrosses, and association mapping populations.")
14333 (license license:gpl2)))
14335 (define-public r-ldheatmap
14337 (name "r-ldheatmap")
14342 (uri (cran-uri "LDheatmap" version))
14345 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14346 (properties `((upstream-name . "LDheatmap")))
14347 (build-system r-build-system)
14349 `(("r-genetics" ,r-genetics)
14351 ("r-snpstats" ,r-snpstats)))
14352 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14353 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14355 "This package provides tools to produce a graphical display, as a heat
14356 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14357 optionally include the physical locations or genetic map distances of each SNP
14359 (license license:gpl3)))
14361 (define-public r-hwde
14368 (uri (cran-uri "hwde" version))
14371 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14372 (build-system r-build-system)
14373 (home-page "https://cran.r-project.org/web/packages/hwde/")
14374 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14376 "This package fits models for genotypic disequilibria, as described in
14377 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14378 terms are available that account for first order interactions between loci.
14379 It also implements, for a single locus in a single population, a conditional
14380 exact test for Hardy-Weinberg equilibrium.")
14381 (license license:gpl2+)))
14383 (define-public r-tdthap
14390 (uri (cran-uri "tdthap" version))
14393 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14394 (build-system r-build-system)
14395 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14396 (synopsis "TDT tests for extended haplotypes")
14398 "Functions and examples are provided for transmission/disequilibrium
14399 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14400 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14401 (license license:artistic2.0)))
14403 (define-public r-sparql
14409 (uri (cran-uri "SPARQL" version))
14412 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14413 (properties `((upstream-name . "SPARQL")))
14414 (build-system r-build-system)
14416 `(("r-rcurl" ,r-rcurl)
14418 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14419 (synopsis "SPARQL client for R")
14420 (description "This package provides an interface to use SPARQL to pose
14421 SELECT or UPDATE queries to an end-point.")
14422 ;; The only license indication is found in the DESCRIPTION file,
14423 ;; which states GPL-3. So we cannot assume GPLv3+.
14424 (license license:gpl3)))
14426 (define-public r-bookdown
14428 (name "r-bookdown")
14432 (uri (cran-uri "bookdown" version))
14435 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14436 (build-system r-build-system)
14438 `(("r-htmltools" ,r-htmltools)
14439 ("r-knitr" ,r-knitr)
14440 ("r-rmarkdown" ,r-rmarkdown)
14441 ("r-tinytex" ,r-tinytex)
14443 ("pandoc" ,pandoc)))
14444 (home-page "https://github.com/rstudio/bookdown")
14445 (synopsis "Authoring books and technical documents with R markdown")
14446 (description "This package provides output formats and utilities for
14447 authoring books and technical documents with R Markdown.")
14448 (license license:gpl3)))
14450 (define-public r-optparse
14452 (name "r-optparse")
14457 (uri (cran-uri "optparse" version))
14460 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14461 (build-system r-build-system)
14463 `(("r-getopt" ,r-getopt)))
14465 `(("r-knitr" ,r-knitr)))
14466 (home-page "https://github.com/trevorld/optparse")
14467 (synopsis "Command line option parser")
14469 "This package provides a command line parser inspired by Python's
14470 @code{optparse} library to be used with Rscript to write shebang scripts
14471 that accept short and long options.")
14472 (license license:gpl2+)))
14474 (define-public r-wgcna
14481 (uri (cran-uri "WGCNA" version))
14484 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14485 (properties `((upstream-name . "WGCNA")))
14486 (build-system r-build-system)
14488 `(("r-annotationdbi" ,r-annotationdbi)
14489 ("r-doparallel" ,r-doparallel)
14490 ("r-dynamictreecut" ,r-dynamictreecut)
14491 ("r-fastcluster" ,r-fastcluster)
14492 ("r-foreach" ,r-foreach)
14493 ("r-go-db" ,r-go-db)
14494 ("r-hmisc" ,r-hmisc)
14495 ("r-impute" ,r-impute)
14497 ("r-survival" ,r-survival)
14498 ("r-matrixstats" ,r-matrixstats)
14499 ("r-preprocesscore" ,r-preprocesscore)))
14501 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14502 (synopsis "Weighted correlation network analysis")
14504 "This package provides functions necessary to perform Weighted
14505 Correlation Network Analysis on high-dimensional data. It includes functions
14506 for rudimentary data cleaning, construction and summarization of correlation
14507 networks, module identification and functions for relating both variables and
14508 modules to sample traits. It also includes a number of utility functions for
14509 data manipulation and visualization.")
14510 (license license:gpl2+)))
14512 (define-public r-kernlab
14519 (uri (cran-uri "kernlab" version))
14521 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14522 (build-system r-build-system)
14523 (home-page "https://cran.r-project.org/web/packages/kernlab")
14524 (synopsis "Kernel-based machine learning tools")
14526 "This package provides kernel-based machine learning methods for
14527 classification, regression, clustering, novelty detection, quantile regression
14528 and dimensionality reduction. Among other methods @code{kernlab} includes
14529 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14531 (license license:gpl2)))
14533 (define-public r-hierfstat
14535 (name "r-hierfstat")
14540 (uri (cran-uri "hierfstat" version))
14543 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
14544 (build-system r-build-system)
14546 `(("r-ade4" ,r-ade4)
14547 ("r-adegenet" ,r-adegenet)
14548 ("r-gaston" ,r-gaston)
14549 ("r-gtools" ,r-gtools)))
14551 `(("r-knitr" ,r-knitr)))
14552 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14553 (synopsis "Estimation and tests of hierarchical F-statistics")
14555 "This package allows the estimation of hierarchical F-statistics from
14556 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14557 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14558 are also given to test via randomisations the significance of each F and
14559 variance components, using the likelihood-ratio statistics G.")
14560 (license license:gpl2+)))
14562 (define-public r-hapassoc
14564 (name "r-hapassoc")
14569 (uri (cran-uri "hapassoc" version))
14572 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14573 (build-system r-build-system)
14574 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14575 (synopsis "Inference of trait associations with SNP haplotypes")
14577 "Hapassoc performs likelihood inference of trait associations with
14578 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14579 functions are developed primarily for data collected in cohort or
14580 cross-sectional studies. They can accommodate uncertain haplotype phase and
14581 handle missing genotypes at some SNPs.")
14582 (license license:gpl2)))
14584 (define-public r-sampling
14586 (name "r-sampling")
14591 (uri (cran-uri "sampling" version))
14594 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14595 (build-system r-build-system)
14597 `(("r-lpsolve" ,r-lpsolve)
14598 ("r-mass" ,r-mass)))
14599 (home-page "https://cran.r-project.org/web/packages/sampling/")
14600 (synopsis "Survey sampling")
14602 "This package provides functions for drawing and calibrating samples.")
14603 (license license:gpl2+)))
14605 (define-public r-r2html
14612 (uri (cran-uri "R2HTML" version))
14615 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14616 (properties `((upstream-name . "R2HTML")))
14617 (build-system r-build-system)
14618 (home-page "https://github.com/nalimilan/R2HTML")
14619 (synopsis "HTML export for R objects")
14621 "This package includes HTML functions and methods to write in an HTML
14622 file. Thus, making HTML reports is easy. It includes a function that allows
14623 redirection on the fly, which appears to be very useful for teaching purposes,
14624 as the student can keep a copy of the produced output to keep all that they
14625 did during the course. The package comes with a vignette describing how to
14626 write HTML reports for statistical analysis. Finally, a driver for Sweave
14627 parses HTML flat files containing R code and to automatically write
14628 the corresponding outputs (tables and graphs).")
14629 (license license:gpl2+)))
14631 (define-public r-rjava
14638 (uri (cran-uri "rJava" version))
14641 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14642 (properties `((upstream-name . "rJava")))
14643 (build-system r-build-system)
14645 `(#:modules ((guix build utils)
14646 (guix build r-build-system)
14649 (modify-phases %standard-phases
14650 (add-after 'unpack 'set-JAVA_HOME
14651 (lambda* (#:key inputs #:allow-other-keys)
14652 (let ((jdk (assoc-ref inputs "jdk")))
14653 (setenv "JAVA_HOME" jdk)
14654 (setenv "JAVA" (which "java"))
14655 (setenv "JAR" (which "jar"))
14656 (setenv "JAVAC" (which "javac"))
14657 (setenv "JAVAH" (which "javah"))
14658 (setenv "JAVA_CPPFLAGS"
14659 (string-append "-I" jdk "/include "
14660 "-I" jdk "/include/linux"))
14661 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14662 ((lib) (setenv "JAVA_LIBS" lib))
14663 (_ (error "Could not find libjvm.so"))))
14667 ("jdk" ,icedtea-8 "jdk")
14670 (home-page "https://www.rforge.net/rJava/")
14671 (synopsis "Low-Level R to Java interface")
14673 "This package provides a low-level interface to the Java VM very much
14674 like .C/.Call and friends. It allows the creation of objects, calling methods
14675 and accessing fields.")
14676 (license license:gpl2)))
14678 (define-public r-svmisc
14685 (uri (cran-uri "svMisc" version))
14688 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14689 (properties `((upstream-name . "svMisc")))
14690 (build-system r-build-system)
14691 (home-page "https://github.com/SciViews/svMisc")
14692 (synopsis "Miscellaneous functions for SciViews")
14694 "This package provides miscellaneous functions for SciViews or general
14695 use, including tools to manage a temporary environment attached to the search
14696 path for temporary variables you do not want to @code{save()} or
14697 @code{load()}; test the current platform; showing progress bars, etc.")
14698 (license license:gpl2)))
14700 (define-public r-xyz
14707 (uri (cran-uri "xyz" version))
14710 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14711 (build-system r-build-system)
14713 `(("r-rcpp" ,r-rcpp)))
14714 (home-page "https://cran.r-project.org/web/packages/xyz/")
14715 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14717 "High dimensional interaction search by brute force requires a quadratic
14718 computational cost in the number of variables. The xyz algorithm provably
14719 finds strong interactions in almost linear time. For details of the algorithm
14720 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14721 interaction search in high-dimensional data.")
14722 ;; Any version of the GPL.
14723 (license license:gpl2+)))
14725 (define-public r-rttf2pt1
14727 (name "r-rttf2pt1")
14732 (uri (cran-uri "Rttf2pt1" version))
14735 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14736 (properties `((upstream-name . "Rttf2pt1")))
14737 (build-system r-build-system)
14738 (home-page "https://github.com/wch/Rttf2pt1")
14739 (synopsis "Font conversion utility")
14741 "This package contains the program @code{ttf2pt1}, for use with the
14742 @code{extrafont} package.")
14743 ;; Most of the files are covered under the Expat license. Some files are
14744 ;; covered under BSD-3. Deviations for individual files are recorded in
14745 ;; the LICENSE file.
14746 (license (list license:bsd-3 license:expat
14747 (license:non-copyleft "file://LICENSE")))))
14749 (define-public r-extrafontdb
14751 (name "r-extrafontdb")
14756 (uri (cran-uri "extrafontdb" version))
14759 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14760 (build-system r-build-system)
14761 (home-page "https://github.com/wch/extrafontdb")
14762 (synopsis "Database for the extrafont package")
14764 "This package holds the database for the @code{extrafont} package.")
14765 (license license:gpl2)))
14767 (define-public r-extrafont
14769 (name "r-extrafont")
14774 (uri (cran-uri "extrafont" version))
14777 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14778 (build-system r-build-system)
14780 `(("r-extrafontdb" ,r-extrafontdb)
14781 ("r-rttf2pt1" ,r-rttf2pt1)))
14782 (home-page "https://github.com/wch/extrafont")
14783 (synopsis "Tools for using fonts in R")
14785 "The extrafont package makes it easier to use fonts other than the basic
14786 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14787 used with PDF or PostScript output files. There are two hurdles for using
14788 fonts in PDF (or Postscript) output files:
14791 @item Making R aware of the font and the dimensions of the characters.
14792 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14793 properly on a device that doesn't have the font. This is usually needed if
14794 you want to print the PDF file or share it with others.
14797 The extrafont package makes both of these things easier.")
14798 (license license:gpl2)))
14800 (define-public r-xkcd
14807 (uri (cran-uri "xkcd" version))
14810 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14811 (build-system r-build-system)
14813 `(("r-extrafont" ,r-extrafont)
14814 ("r-ggplot2" ,r-ggplot2)
14815 ("r-hmisc" ,r-hmisc)))
14816 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14817 (synopsis "Plot ggplot2 graphics in the XKCD style")
14819 "This package provides the means to plot ggplot2 graphs in the style of
14820 the XKCD web comic.")
14821 (license license:gpl3)))
14823 (define-public r-msigdbr
14830 (uri (cran-uri "msigdbr" version))
14833 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14834 (build-system r-build-system)
14836 `(("r-dplyr" ,r-dplyr)
14837 ("r-magrittr" ,r-magrittr)
14838 ("r-rlang" ,r-rlang)
14839 ("r-tibble" ,r-tibble)))
14841 `(("r-knitr" ,r-knitr)))
14842 (home-page "https://github.com/igordot/msigdbr")
14843 (synopsis "MSigDB gene sets for multiple organisms")
14845 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14846 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14847 software in a standard R data frame with key-value pairs. Included are the
14848 original human gene symbols and Entrez IDs as well as the equivalents for
14849 various frequently studied model organisms such as mouse, rat, pig, fly, and
14851 ;; The package is covered under the Expat license, but the upstream MSigDB
14852 ;; files are made available under the Creative Commons Attribution 4.0
14853 ;; International license.
14854 (license (list license:expat license:cc-by4.0))))
14856 (define-public r-gridgraphics
14858 (name "r-gridgraphics")
14863 (uri (cran-uri "gridGraphics" version))
14866 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14867 (properties `((upstream-name . "gridGraphics")))
14868 (build-system r-build-system)
14869 (home-page "https://github.com/pmur002/gridgraphics")
14870 (synopsis "Redraw base graphics using @code{grid} graphics")
14872 "This package provides functions to convert a page of plots drawn with
14873 the @code{graphics} package into identical output drawn with the @code{grid}
14874 package. The result looks like the original @code{graphics}-based plot, but
14875 consists of @code{grid} grobs and viewports that can then be manipulated with
14876 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14877 (license license:gpl2+)))
14879 (define-public r-farver
14886 (uri (cran-uri "farver" version))
14889 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14890 (build-system r-build-system)
14891 (home-page "https://github.com/thomasp85/farver")
14892 (synopsis "Vectorized color conversion and comparison")
14894 "The encoding of color can be handled in many different ways, using
14895 different color spaces. As different color spaces have different uses,
14896 efficient conversion between these representations are important. This
14897 package provides a set of functions that gives access to very fast color space
14898 conversion and comparisons implemented in C++, and offers 100-fold speed
14899 improvements over the @code{convertColor} function in the @code{grDevices}
14901 (license license:expat)))
14903 (define-public r-ggplotify
14905 (name "r-ggplotify")
14910 (uri (cran-uri "ggplotify" version))
14913 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14914 (build-system r-build-system)
14916 `(("r-ggplot2" ,r-ggplot2)
14917 ("r-gridgraphics" ,r-gridgraphics)
14918 ("r-rvcheck" ,r-rvcheck)))
14920 `(("r-knitr" ,r-knitr)))
14921 (home-page "https://github.com/GuangchuangYu/ggplotify")
14922 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14924 "This package provides tools to convert plot function calls (using
14925 expression or formula) to @code{grob} or @code{ggplot} objects that are
14926 compatible with the @code{grid} and @code{ggplot2} environment. With this
14927 package, we are able to e.g. use @code{cowplot} to align plots produced by
14928 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14929 converting them to @code{ggplot} objects.")
14930 (license license:artistic2.0)))
14932 (define-public r-triebeard
14934 (name "r-triebeard")
14939 (uri (cran-uri "triebeard" version))
14942 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14943 (build-system r-build-system)
14944 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14945 (home-page "https://github.com/Ironholds/triebeard/")
14946 (synopsis "Radix trees in Rcpp")
14948 "Radix trees, or tries, are key-value data structures optimized for
14949 efficient lookups, similar in purpose to hash tables. This package provides
14950 an implementation of radix trees for use in R programming and in developing
14951 packages with Rcpp.")
14952 (license license:expat)))
14954 (define-public r-tweenr
14961 (uri (cran-uri "tweenr" version))
14964 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14965 (build-system r-build-system)
14967 `(("r-farver" ,r-farver)
14968 ("r-magrittr" ,r-magrittr)
14970 ("r-rlang" ,r-rlang)))
14971 (home-page "https://github.com/thomasp85/tweenr")
14972 (synopsis "Interpolate data for smooth animations")
14974 "In order to create smooth animation between states of data, tweening is
14975 necessary. This package provides a range of functions for creating tweened
14976 data that can be used as basis for animation. Furthermore it adds a number of
14977 vectorized interpolaters for common R data types such as numeric, date and
14979 (license license:expat)))
14981 (define-public r-polyclip
14983 (name "r-polyclip")
14988 (uri (cran-uri "polyclip" version))
14991 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14992 (build-system r-build-system)
14993 (native-inputs `(("pkg-config" ,pkg-config)))
14994 (home-page "http://www.angusj.com/delphi/clipper.php")
14995 (synopsis "Polygon clipping")
14997 "This package provides an R port of the library Clipper. It performs
14998 polygon clipping operations (intersection, union, set minus, set difference)
14999 for polygonal regions of arbitrary complexity, including holes. It computes
15000 offset polygons (spatial buffer zones, morphological dilations, Minkowski
15001 dilations) for polygonal regions and polygonal lines. It computes the
15002 Minkowski Sum of general polygons. There is a function for removing
15003 self-intersections from polygon data.")
15004 (license license:boost1.0)))
15006 (define-public r-urltools
15008 (name "r-urltools")
15013 (uri (cran-uri "urltools" version))
15016 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
15017 (build-system r-build-system)
15019 `(("r-rcpp" ,r-rcpp)
15020 ("r-triebeard" ,r-triebeard)))
15021 (home-page "https://github.com/Ironholds/urltools/")
15022 (synopsis "Vectorized tools for URL handling and parsing")
15024 "This package provides a toolkit for all URL-handling needs, including
15025 encoding and decoding, parsing, parameter extraction and modification. All
15026 functions are designed to be both fast and entirely vectorized. It is
15027 intended to be useful for people dealing with web-related datasets, such as
15028 server-side logs, although may be useful for other situations involving large
15030 (license license:expat)))
15032 (define-public r-ggforce
15039 (uri (cran-uri "ggforce" version))
15042 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
15043 (build-system r-build-system)
15045 `(("r-ggplot2" ,r-ggplot2)
15046 ("r-gtable" ,r-gtable)
15048 ("r-polyclip" ,r-polyclip)
15050 ("r-rcppeigen" ,r-rcppeigen)
15051 ("r-rlang" ,r-rlang)
15052 ("r-scales" ,r-scales)
15053 ("r-tidyselect" ,r-tidyselect)
15054 ("r-tweenr" ,r-tweenr)
15055 ("r-withr" ,r-withr)))
15056 (home-page "https://ggforce.data-imaginist.com")
15057 (synopsis "Accelerating ggplot2")
15059 "The aim of the ggplot2 package is to aid in visual data investigations.
15060 This focus has led to a lack of facilities for composing specialized plots.
15061 Thi package aims to be a collection of mainly new statistics and geometries
15062 that fills this gap.")
15063 (license license:expat)))
15065 (define-public r-europepmc
15067 (name "r-europepmc")
15072 (uri (cran-uri "europepmc" version))
15075 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
15076 (build-system r-build-system)
15078 `(("r-dplyr" ,r-dplyr)
15080 ("r-jsonlite" ,r-jsonlite)
15082 ("r-progress" ,r-progress)
15083 ("r-purrr" ,r-purrr)
15084 ("r-rlang" ,r-rlang)
15085 ("r-tibble" ,r-tibble)
15086 ("r-tidyr" ,r-tidyr)
15087 ("r-urltools" ,r-urltools)
15088 ("r-xml2" ,r-xml2)))
15090 `(("r-knitr" ,r-knitr)))
15091 (home-page "https://github.com/ropensci/europepmc/")
15092 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
15094 "This package provides an R Client for the
15095 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
15096 Service}. It gives access to both metadata on life science literature and
15097 open access full texts. Europe PMC indexes all PubMed content and other
15098 literature sources including Agricola, a bibliographic database of citations
15099 to the agricultural literature, or Biological Patents. In addition to
15100 bibliographic metadata, the client allows users to fetch citations and
15101 reference lists. Links between life-science literature and other EBI
15102 databases, including ENA, PDB or ChEMBL are also accessible.")
15103 (license license:gpl3)))
15105 (define-public r-ggraph
15112 (uri (cran-uri "ggraph" version))
15115 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
15116 (build-system r-build-system)
15118 `(("r-digest" ,r-digest)
15119 ("r-dplyr" ,r-dplyr)
15120 ("r-ggforce" ,r-ggforce)
15121 ("r-ggplot2" ,r-ggplot2)
15122 ("r-ggrepel" ,r-ggrepel)
15123 ("r-graphlayouts" ,r-graphlayouts)
15124 ("r-gtable" ,r-gtable)
15125 ("r-igraph" ,r-igraph)
15128 ("r-rlang" ,r-rlang)
15129 ("r-scales" ,r-scales)
15130 ("r-tidygraph" ,r-tidygraph)
15131 ("r-viridis" ,r-viridis)))
15133 `(("r-knitr" ,r-knitr)))
15134 (home-page "https://cran.r-project.org/web/packages/ggraph/")
15135 (synopsis "Implementation of grammar of graphics for graphs and networks")
15137 "The grammar of graphics as implemented in ggplot2 is a poor fit for
15138 graph and network visualizations due to its reliance on tabular data input.
15139 The ggraph package is an extension of the ggplot2 API tailored to graph
15140 visualizations and provides the same flexible approach to building up plots
15142 (license license:gpl3)))
15144 (define-public r-varselrf
15146 (name "r-varselrf")
15151 (uri (cran-uri "varSelRF" version))
15154 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
15155 (properties `((upstream-name . "varSelRF")))
15156 (build-system r-build-system)
15158 `(("r-randomforest" ,r-randomforest)))
15159 (home-page "https://www.ligarto.org/rdiaz/software/software")
15160 (synopsis "Variable selection using random forests")
15162 "This package provides tools for the variable selection from random
15163 forests using both backwards variable elimination (for the selection of small
15164 sets of non-redundant variables) and selection based on the importance
15165 spectrum (somewhat similar to scree plots; for the selection of large,
15166 potentially highly-correlated variables). The main applications are in
15167 high-dimensional data (e.g., microarray data, and other genomics and
15168 proteomics applications).")
15169 (license license:gpl2+)))
15171 (define-public r-pamr
15178 (uri (cran-uri "pamr" version))
15181 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
15182 (build-system r-build-system)
15184 `(("r-cluster" ,r-cluster)
15185 ("r-survival" ,r-survival)))
15186 (native-inputs `(("gfortran" ,gfortran)))
15187 (home-page "https://cran.r-project.org/web/packages/pamr/")
15188 (synopsis "Prediction Analysis for Microarrays")
15190 "This package provides some functions for sample classification in
15192 (license license:gpl2)))
15194 (define-public r-rda
15197 (version "1.0.2-2.1")
15201 (uri (cran-uri "rda" version))
15204 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
15205 (build-system r-build-system)
15206 (home-page "https://cran.r-project.org/web/packages/rda/")
15207 (synopsis "Shrunken centroids regularized discriminant analysis")
15209 "This package provides tools for shrunken centroids regularized
15210 discriminant analysis for the purpose of classifying high dimensional data.")
15211 (license license:gpl2+)))
15213 (define-public r-ggvis
15220 (uri (cran-uri "ggvis" version))
15223 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
15224 (build-system r-build-system)
15226 `(("r-assertthat" ,r-assertthat)
15227 ("r-dplyr" ,r-dplyr)
15228 ("r-htmltools" ,r-htmltools)
15229 ("r-jsonlite" ,r-jsonlite)
15230 ("r-lazyeval" ,r-lazyeval)
15231 ("r-magrittr" ,r-magrittr)
15232 ("r-shiny" ,r-shiny)))
15233 (home-page "https://ggvis.rstudio.com/")
15234 (synopsis "Interactive grammar of graphics")
15236 "This package is a data visualization package for R providing an
15237 implementation of an interactive grammar of graphics, taking the best parts of
15238 ggplot2, combining them with the reactive framework of Shiny and drawing web
15239 graphics using Vega.")
15240 (license license:gpl2)))
15242 (define-public r-gbm
15249 (uri (cran-uri "gbm" version))
15252 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
15253 (build-system r-build-system)
15255 `(("r-lattice" ,r-lattice)
15256 ("r-survival" ,r-survival)))
15258 `(("r-knitr" ,r-knitr)))
15259 (home-page "https://github.com/gbm-developers/gbm")
15260 (synopsis "Generalized boosted regression models")
15262 "This package is an implementation of extensions to Freund and Schapire's
15263 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15264 regression methods for least squares, absolute loss, t-distribution loss,
15265 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15266 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15267 and Learning to Rank measures (LambdaMart).")
15268 (license license:gpl2+)))
15270 (define-public r-threejs
15277 (uri (cran-uri "threejs" version))
15280 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15281 (build-system r-build-system)
15283 `(#:modules ((guix build utils)
15284 (guix build r-build-system)
15288 (modify-phases %standard-phases
15289 (add-after 'unpack 'process-javascript
15290 (lambda* (#:key inputs #:allow-other-keys)
15291 (with-directory-excursion "inst"
15295 `((,(assoc-ref inputs "js-jquery")
15296 "htmlwidgets/lib/jquery/jquery.min.js")
15297 (,(assoc-ref inputs "js-threejs-111")
15298 "htmlwidgets/lib/threejs-111/three.min.js"))))
15299 (lambda (sources targets)
15300 (for-each (lambda (source target)
15301 (format #t "Processing ~a --> ~a~%"
15303 (delete-file target)
15304 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15305 (call-with-output-file target
15307 (dump-port minified port)))))
15308 sources targets))))
15311 `(("r-base64enc" ,r-base64enc)
15312 ("r-crosstalk" ,r-crosstalk)
15313 ("r-htmlwidgets" ,r-htmlwidgets)
15314 ("r-igraph" ,r-igraph)))
15316 `(("uglify-js" ,uglify-js)
15320 (uri "https://code.jquery.com/jquery-1.12.4.js")
15323 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15327 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15330 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15331 (home-page "https://bwlewis.github.io/rthreejs")
15332 (synopsis "Interactive 3D scatter plots, networks and globes")
15334 "Create interactive 3D scatter plots, network plots, and globes in R
15335 using the three.js visualization library.")
15336 (license license:expat)))
15338 (define-public r-mlbench
15345 (uri (cran-uri "mlbench" version))
15348 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15349 (build-system r-build-system)
15350 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15351 (synopsis "Machine learning benchmark problems")
15353 "This package provides a collection of artificial and real-world machine
15354 learning benchmark problems, including, e.g., several data sets from the UCI
15356 (license license:gpl2)))
15358 (define-public r-mpm
15365 (uri (cran-uri "mpm" version))
15368 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15369 (build-system r-build-system)
15371 `(("r-kernsmooth" ,r-kernsmooth)
15372 ("r-mass" ,r-mass)))
15373 (home-page "http://mpm.r-forge.r-project.org")
15374 (synopsis "Multivariate projection methods")
15376 "This is a package for exploratory graphical analysis of multivariate
15377 data, specifically gene expression data with different projection methods:
15378 principal component analysis, correspondence analysis, spectral map
15380 (license license:gpl2+)))
15382 (define-public r-png
15388 (uri (cran-uri "png" version))
15391 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15392 (build-system r-build-system)
15394 `(("libpng" ,libpng)
15396 (home-page "https://www.rforge.net/png/")
15397 (synopsis "Read and write PNG images")
15399 "This package provides an easy and simple way to read, write and display
15400 bitmap images stored in the PNG format. It can read and write both files and
15401 in-memory raw vectors.")
15402 ;; Any of these GPL versions.
15403 (license (list license:gpl2 license:gpl3))))
15405 (define-public r-ggcorrplot
15407 (name "r-ggcorrplot")
15412 (uri (cran-uri "ggcorrplot" version))
15415 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15416 (build-system r-build-system)
15418 `(("r-ggplot2" ,r-ggplot2)
15419 ("r-reshape2" ,r-reshape2)))
15420 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15421 (synopsis "Visualization of a correlation matrix using ggplot2")
15423 "The ggcorrplot package can be used to visualize easily a correlation
15424 matrix using ggplot2. It provides a solution for reordering the correlation
15425 matrix and displays the significance level on the plot. It also includes a
15426 function for computing a matrix of correlation p-values.")
15427 (license license:gpl2)))
15429 ;; This package includes minified JavaScript files. When upgrading please
15430 ;; check that there are no new minified JavaScript files.
15431 (define-public r-flexdashboard
15433 (name "r-flexdashboard")
15438 (uri (cran-uri "flexdashboard" version))
15441 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15442 (modules '((guix build utils)))
15445 ;; Delete bundled minified JavaScript files
15446 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15447 (delete-file "inst/www/sly/sly.min.js")
15448 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15449 (delete-file "inst/www/prism/prism.js")
15451 (build-system r-build-system)
15453 `(#:modules ((guix build utils)
15454 (guix build r-build-system)
15458 (ice-9 textual-ports))
15460 (modify-phases %standard-phases
15461 (add-after 'unpack 'process-javascript
15462 (lambda* (#:key inputs #:allow-other-keys)
15463 (with-directory-excursion "inst"
15464 ;; Concatenate all components of prism.js
15465 (let ((contents (string-join
15466 (map (lambda (name)
15467 (call-with-input-file
15468 (assoc-ref inputs name)
15472 "js-prism-line-numbers"))
15474 (call-with-output-file "prism-src.js"
15475 (cut display contents <>)))
15479 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15480 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15482 "www/sly/sly.min.js")
15484 "www/prism/prism.js")
15485 (,(assoc-ref inputs "js-raphael")
15486 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15487 (,(assoc-ref inputs "js-featherlight")
15488 "www/featherlight/featherlight.min.js"))))
15489 (lambda (sources targets)
15490 (for-each (lambda (source target)
15491 (format #t "Processing ~a --> ~a~%"
15493 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15494 (call-with-output-file target
15496 (dump-port minified port)))))
15497 sources targets))))
15500 `(("r-htmltools" ,r-htmltools)
15501 ("r-htmlwidgets" ,r-htmlwidgets)
15502 ("r-jsonlite" ,r-jsonlite)
15503 ("r-knitr" ,r-knitr)
15504 ("r-rmarkdown" ,r-rmarkdown)
15505 ("r-shiny" ,r-shiny)))
15507 `(("uglify-js" ,uglify-js)
15511 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15514 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15518 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15521 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15525 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15528 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15529 ("js-prism-line-numbers"
15532 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15535 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15539 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15542 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15543 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15544 (synopsis "R Markdown format for flexible dashboards")
15546 "This package provides an R Markdown format for converting an R Markdown
15547 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15548 of its components to the containing web page.")
15549 (license license:expat)))
15551 (define-public r-preseqr
15558 (uri (cran-uri "preseqR" version))
15561 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15562 (properties `((upstream-name . "preseqR")))
15563 (build-system r-build-system)
15565 `(("r-polynom" ,r-polynom)))
15566 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15567 (synopsis "Predicting species accumulation curves")
15569 "This package can be used to predict the r-species accumulation
15570 curve (r-SAC), which is the number of species represented at least r times as
15571 a function of the sampling effort. When r = 1, the curve is known as the
15572 species accumulation curve, or the library complexity curve in high-throughput
15573 genomic sequencing. The package includes both parametric and nonparametric
15574 methods, as described by Deng C, et al. (2018).")
15575 (license license:gpl3)))
15577 (define-public r-mapplots
15579 (name "r-mapplots")
15584 (uri (cran-uri "mapplots" version))
15587 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15588 (build-system r-build-system)
15589 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15590 (synopsis "Data visualization on maps")
15592 "This package helps you create simple maps; add sub-plots like pie plots
15593 to a map or any other plot; format, plot and export gridded data. The package
15594 was developed for displaying fisheries data but most functions can be used for
15595 more generic data visualisation.")
15596 (license license:gpl2+)))
15598 (define-public r-pmcmr
15605 (uri (cran-uri "PMCMR" version))
15608 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15609 (properties `((upstream-name . "PMCMR")))
15610 (build-system r-build-system)
15611 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15612 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15614 "This is a deprecated package for calculating pairwise multiple
15615 comparisons of mean rank sums. This package is superseded by the novel
15616 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15617 compatibility of dependent packages for some time.")
15618 (license license:gpl3+)))
15620 (define-public r-downloader
15622 (name "r-downloader")
15627 (uri (cran-uri "downloader" version))
15630 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15631 (build-system r-build-system)
15633 `(("r-digest" ,r-digest)))
15634 (home-page "https://github.com/wch/downloader")
15635 (synopsis "Download files over HTTP and HTTPS")
15637 "This package provides a wrapper for the @code{download.file} function,
15638 making it possible to download files over HTTPS across platforms. The
15639 @code{RCurl} package provides this functionality (and much more) but has
15640 external dependencies. This package has is implemented purely in R.")
15641 (license license:gpl2)))
15643 (define-public r-rex
15650 (uri (cran-uri "rex" version))
15653 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15654 (build-system r-build-system)
15656 `(("r-lazyeval" ,r-lazyeval)))
15658 `(("r-knitr" ,r-knitr)))
15659 (home-page "https://github.com/kevinushey/rex")
15660 (synopsis "Friendly regular expressions")
15662 "This package provides a friendly interface for the construction of
15663 regular expressions. Regular expressions are a very powerful feature, however
15664 they are often difficult to interpret. Rex allows you to build complex
15665 regular expressions from human readable expressions")
15666 (license license:expat)))
15668 (define-public r-xmlparsedata
15670 (name "r-xmlparsedata")
15675 (uri (cran-uri "xmlparsedata" version))
15678 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
15679 (properties `((upstream-name . "xmlparsedata")))
15680 (build-system r-build-system)
15681 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15682 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15684 "This package provides tools to convert the output of
15685 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15686 @code{XPath}, and is easier to manipulate in general.")
15687 (license license:expat)))
15689 (define-public r-cyclocomp
15691 (name "r-cyclocomp")
15696 (uri (cran-uri "cyclocomp" version))
15699 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15700 (properties `((upstream-name . "cyclocomp")))
15701 (build-system r-build-system)
15703 `(("r-callr" ,r-callr)
15704 ("r-crayon" ,r-crayon)
15706 ("r-remotes" ,r-remotes)
15707 ("r-withr" ,r-withr)))
15708 (home-page "https://github.com/MangoTheCat/cyclocomp")
15709 (synopsis "Cyclomatic complexity of R code")
15711 "Cyclomatic complexity is a software metric, used to indicate the
15712 complexity of a program. It is a quantitative measure of the number of
15713 linearly independent paths through a program's source code. This package
15714 provides tools to compute this metric.")
15715 (license license:expat)))
15717 (define-public r-lintr
15724 (uri (cran-uri "lintr" version))
15727 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15728 (properties `((upstream-name . "lintr")))
15729 (build-system r-build-system)
15731 `(("r-codetools" ,r-codetools)
15732 ("r-crayon" ,r-crayon)
15733 ("r-cyclocomp" ,r-cyclocomp)
15734 ("r-digest" ,r-digest)
15736 ("r-jsonlite" ,r-jsonlite)
15737 ("r-knitr" ,r-knitr)
15739 ("r-rstudioapi" ,r-rstudioapi)
15740 ("r-testthat" ,r-testthat)
15742 ("r-xmlparsedata" ,r-xmlparsedata)))
15743 (home-page "https://github.com/jimhester/lintr")
15744 (synopsis "Linter for R code")
15745 (description "This package checks adherence to a given style, syntax
15746 errors and possible semantic issues. It supports on the fly checking of R
15747 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15748 (license license:expat)))
15750 (define-public r-sctransform
15752 (name "r-sctransform")
15757 (uri (cran-uri "sctransform" version))
15760 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15761 (build-system r-build-system)
15763 `(("r-future-apply" ,r-future-apply)
15764 ("r-ggplot2" ,r-ggplot2)
15765 ("r-gridextra" ,r-gridextra)
15767 ("r-matrix" ,r-matrix)
15769 ("r-rcppeigen" ,r-rcppeigen)
15770 ("r-reshape2" ,r-reshape2)))
15771 (home-page "https://github.com/ChristophH/sctransform")
15772 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15774 "This package provides a normalization method for single-cell UMI count
15775 data using a variance stabilizing transformation. The transformation is based
15776 on a negative binomial regression model with regularized parameters. As part
15777 of the same regression framework, this package also provides functions for
15778 batch correction, and data correction.")
15779 (license license:gpl3)))
15781 (define-public r-styler
15788 (uri (cran-uri "styler" version))
15791 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15792 (build-system r-build-system)
15794 `(("r-backports" ,r-backports)
15796 ("r-magrittr" ,r-magrittr)
15797 ("r-purrr" ,r-purrr)
15798 ("r-r-cache" ,r-r-cache)
15799 ("r-rematch2" ,r-rematch2)
15800 ("r-rlang" ,r-rlang)
15801 ("r-rprojroot" ,r-rprojroot)
15802 ("r-tibble" ,r-tibble)
15803 ("r-withr" ,r-withr)
15804 ("r-xfun" ,r-xfun)))
15805 (home-page "https://github.com/r-lib/styler")
15806 (synopsis "Non-invasive pretty printing of R code")
15808 "This is a package for pretty-printing R code without changing the user's
15809 formatting intent.")
15810 (license license:gpl3)))
15812 (define-public r-scrime
15819 (uri (cran-uri "scrime" version))
15822 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15823 (build-system r-build-system)
15824 (home-page "https://cran.r-project.org/web/packages/scrime/")
15825 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15827 "This package provides tools for the analysis of high-dimensional data
15828 developed/implemented at the group \"Statistical Complexity Reduction In
15829 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15830 the functions can also be applied to other types of categorical data.")
15831 (license license:gpl2)))
15833 (define-public r-pbmcapply
15835 (name "r-pbmcapply")
15840 (uri (cran-uri "pbmcapply" version))
15843 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15844 (build-system r-build-system)
15845 (home-page "https://github.com/kvnkuang/pbmcapply")
15846 (synopsis "Track the progress of apply procedures with a progress bar")
15848 "This light-weight package helps you track and visualize the progress of
15849 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15850 (license license:expat)))
15852 (define-public r-blme
15859 (uri (cran-uri "blme" version))
15862 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15863 (build-system r-build-system)
15864 (propagated-inputs `(("r-lme4" ,r-lme4)))
15865 (home-page "https://github.com/vdorie/blme")
15866 (synopsis "Bayesian linear mixed-effects models")
15868 "This package provides tools for maximum a posteriori estimation for
15869 linear and generalized linear mixed-effects models in a Bayesian setting. It
15870 extends the lme4 package.")
15871 (license license:gpl2+)))
15873 (define-public r-batchtools
15875 (name "r-batchtools")
15880 (uri (cran-uri "batchtools" version))
15883 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15884 (build-system r-build-system)
15886 `(("r-backports" ,r-backports)
15887 ("r-base64url" ,r-base64url)
15889 ("r-checkmate" ,r-checkmate)
15890 ("r-data-table" ,r-data-table)
15891 ("r-digest" ,r-digest)
15893 ("r-progress" ,r-progress)
15895 ("r-rappdirs" ,r-rappdirs)
15896 ("r-stringi" ,r-stringi)
15897 ("r-withr" ,r-withr)))
15899 `(("r-knitr" ,r-knitr)))
15900 (home-page "https://github.com/mllg/batchtools")
15901 (synopsis "Tools for computation on batch systems")
15903 "As a successor of the packages BatchJobs and BatchExperiments, this
15904 package provides a parallel implementation of the Map function for high
15905 performance computing systems managed by various schedulers. A multicore and
15906 socket mode allow the parallelization on a local machines, and multiple
15907 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15908 the package provides an abstraction mechanism to define large-scale computer
15909 experiments in a well-organized and reproducible way.")
15910 (license license:lgpl3)))
15912 (define-public r-clue
15919 (uri (cran-uri "clue" version))
15922 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15923 (build-system r-build-system)
15924 (propagated-inputs `(("r-cluster" ,r-cluster)))
15925 (home-page "https://cran.r-project.org/web/packages/clue/")
15926 (synopsis "Tools for analyzing cluster ensembles")
15927 (description "Cluster ensembles are collections of individual solutions to
15928 a given clustering problem which are useful or necessary to consider in a wide
15929 range of applications. This R package provides an extensible computational
15930 environment for creating and analyzing cluster ensembles, with basic data
15931 structures for representing partitions and hierarchies, and facilities for
15932 computing on them, including methods for measuring proximity and obtaining
15933 consensus and secondary clusterings.")
15934 (license license:gpl2)))
15936 (define-public r-sitmo
15943 (uri (cran-uri "sitmo" version))
15946 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15947 (build-system r-build-system)
15948 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15949 (home-page "https://github.com/coatless/sitmo/")
15950 (synopsis "Parallel pseudo random number generator header files")
15952 "This package provides two high quality and fast PPRNGs that may be used
15953 in an OpenMP parallel environment. In addition, there is a generator for one
15954 dimensional low-discrepancy sequence.")
15955 (license license:expat)))
15957 (define-public r-dqrng
15964 (uri (cran-uri "dqrng" version))
15967 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15968 (build-system r-build-system)
15972 ("r-sitmo" ,r-sitmo)))
15973 (home-page "https://www.daqana.org/dqrng")
15974 (synopsis "Fast pseudo random number generators")
15976 "Several fast random number generators are provided as C++ header-only
15977 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15978 Additionally, fast functions for generating random numbers according to a
15979 uniform, normal and exponential distribution are included. The latter two use
15980 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15981 functions are exported to R and as a C++ interface and are enabled for use
15982 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15983 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15984 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15985 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15986 ;; whole is distributed under the terms of the AGPL 3.
15987 (license license:agpl3)))
15989 (define-public r-ingredients
15991 (name "r-ingredients")
15996 (uri (cran-uri "ingredients" version))
15999 "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
16000 (properties `((upstream-name . "ingredients")))
16001 (build-system r-build-system)
16003 `(("r-ggplot2" ,r-ggplot2)
16004 ("r-gridextra" ,r-gridextra)
16005 ("r-scales" ,r-scales)))
16006 (native-inputs `(("r-knitr" ,r-knitr)))
16007 (home-page "https://ModelOriented.github.io/ingredients/")
16008 (synopsis "Effects and importances of model ingredients")
16010 "This is a collection of tools for assessment of feature importance and
16011 feature effects. Key functions are:
16014 @item @code{feature_importance()} for assessment of global level feature
16016 @item @code{ceteris_paribus()} for calculation of the what-if plots,
16017 @item @code{partial_dependence()} for partial dependence plots,
16018 @item @code{conditional_dependence()} for conditional dependence plots,
16019 @item @code{accumulated_dependence()} for accumulated local effects plots,
16020 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
16021 aggregation of ceteris paribus profiles,
16022 @item generic @code{print()} and @code{plot()} for better usability of
16023 selected explainers,
16024 @item generic @code{plotD3()} for interactive, D3 based explanations, and
16025 @item generic @code{describe()} for explanations in natural language.
16027 (license license:gpl3)))
16029 (define-public r-ibreakdown
16031 (name "r-ibreakdown")
16036 (uri (cran-uri "iBreakDown" version))
16039 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
16040 (properties `((upstream-name . "iBreakDown")))
16041 (build-system r-build-system)
16042 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
16043 (native-inputs `(("r-knitr" ,r-knitr)))
16044 (home-page "https://ModelOriented.github.io/iBreakDown/")
16045 (synopsis "Model agnostic instance level variable attributions")
16047 "This package provides a model agnostic tool for decomposition of
16048 predictions from black boxes. It supports additive attributions and
16049 attributions with interactions. The Break Down Table shows contributions of
16050 every variable to a final prediction. The Break Down Plot presents variable
16051 contributions in a concise graphical way. This package works for
16052 classification and regression models.")
16053 (license license:gpl3)))
16055 (define-public r-dae
16062 (uri (cran-uri "dae" version))
16065 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
16066 (build-system r-build-system)
16068 `(("r-ggplot2" ,r-ggplot2)
16069 ("r-plyr" ,r-plyr)))
16071 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
16072 (home-page "http://chris.brien.name")
16073 (synopsis "Functions useful in the design and ANOVA of experiments")
16075 "This package provides functions useful in the design and ANOVA of
16076 experiments. The content falls into the following groupings:
16080 @item factor manipulation functions,
16081 @item design functions,
16082 @item ANOVA functions,
16083 @item matrix functions,
16084 @item projector and canonical efficiency functions, and
16085 @item miscellaneous functions.
16088 There is a vignette called @code{DesignNotes} describing how to use the design
16089 functions for randomizing and assessing designs. The ANOVA functions
16090 facilitate the extraction of information when the @code{Error} function has
16091 been used in the call to @code{aov}.")
16092 (license license:gpl2)))
16094 (define-public r-dalex
16097 (version "1.3.1.1")
16101 (uri (cran-uri "DALEX" version))
16104 "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
16105 (properties `((upstream-name . "DALEX")))
16106 (build-system r-build-system)
16108 `(("r-ggplot2" ,r-ggplot2)
16109 ("r-ibreakdown" ,r-ibreakdown)
16110 ("r-ingredients" ,r-ingredients)))
16111 (home-page "https://pbiecek.github.io/DALEX/")
16112 (synopsis "Descriptive machine learning explanations")
16114 "Machine Learning models are widely used and have various applications in
16115 classification or regression. Models created with boosting, bagging, stacking
16116 or similar techniques are often used due to their high performance, but such
16117 black-box models usually lack interpretability. The DALEX package contains
16118 various explainers that help to understand the link between input variables
16119 and model output.")
16120 ;; Any version of the GPL
16121 (license license:gpl3+)))
16123 (define-public r-enrichr
16130 (uri (cran-uri "enrichR" version))
16133 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
16134 (properties `((upstream-name . "enrichR")))
16135 (build-system r-build-system)
16137 `(("r-httr" ,r-httr)
16138 ("r-rjson" ,r-rjson)))
16139 (home-page "https://cran.r-project.org/web/packages/enrichR/")
16140 (synopsis "R Interface to Enrichr database for analyzing gene sets")
16142 "This package provides an R interface to all Enrichr databases, a
16143 web-based tool for analyzing gene sets and returns any enrichment of common
16144 annotated biological functions.")
16145 (license license:gpl2+)))
16147 (define-public r-plot3d
16154 (uri (cran-uri "plot3D" version))
16157 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
16158 (properties `((upstream-name . "plot3D")))
16159 (build-system r-build-system)
16160 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
16161 (home-page "https://cran.r-project.org/web/packages/plot3D")
16162 (synopsis "Plot multi-dimensional data")
16164 "This package provides functions for viewing 2D and 3D data, including
16165 perspective plots, slice plots, surface plots, scatter plots, etc. It
16166 includes data sets from oceanography.")
16167 (license license:gpl3+)))
16169 (define-public r-ggfortify
16171 (name "r-ggfortify")
16176 (uri (cran-uri "ggfortify" version))
16179 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
16180 (build-system r-build-system)
16182 `(("r-dplyr" ,r-dplyr)
16183 ("r-ggplot2" ,r-ggplot2)
16184 ("r-gridextra" ,r-gridextra)
16185 ("r-scales" ,r-scales)
16186 ("r-stringr" ,r-stringr)
16187 ("r-tibble" ,r-tibble)
16188 ("r-tidyr" ,r-tidyr)))
16190 `(("r-knitr" ,r-knitr)))
16191 (home-page "https://github.com/sinhrks/ggfortify")
16192 (synopsis "Data visualization tools for statistical analysis results")
16194 "This package provides unified plotting tools for statistics commonly
16195 used, such as GLM, time series, PCA families, clustering and survival
16196 analysis. The package offers a single plotting interface for these analysis
16197 results and plots in a unified style using the @code{ggplot2} package.")
16198 (license license:gpl2)))
16200 (define-public r-refmanager
16202 (name "r-refmanager")
16207 (uri (cran-uri "RefManageR" version))
16210 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
16211 (properties `((upstream-name . "RefManageR")))
16212 (build-system r-build-system)
16214 `(("r-bibtex" ,r-bibtex)
16216 ("r-jsonlite" ,r-jsonlite)
16217 ("r-lubridate" ,r-lubridate)
16219 ("r-stringr" ,r-stringr)
16220 ("r-xml2" ,r-xml2)))
16221 (home-page "https://github.com/ropensci/RefManageR/")
16222 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
16224 "This package provides tools for importing and working with bibliographic
16225 references. It greatly enhances the @code{bibentry} class by providing a
16226 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
16227 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
16228 by various formats for name lists (author by last names, translator by full
16229 names, etc.). Entries can be updated, combined, sorted, printed in a number
16230 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16231 into R and converted to @code{BibEntry} objects.")
16232 ;; Any of these licenses may be picked.
16233 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16235 (define-public r-citr
16242 (uri (cran-uri "citr" version))
16245 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16246 (build-system r-build-system)
16248 `(("r-assertthat" ,r-assertthat)
16251 ("r-miniui" ,r-miniui)
16252 ("r-refmanager" ,r-refmanager)
16253 ("r-rstudioapi" ,r-rstudioapi)
16254 ("r-shiny" ,r-shiny)
16255 ("r-shinyjs" ,r-shinyjs)
16256 ("r-yaml" ,r-yaml)))
16257 (home-page "https://github.com/crsh/citr")
16258 (synopsis "RStudio add-in to insert Markdown citations")
16260 "This package provides functions and an RStudio add-in that search a
16261 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16262 the current document.")
16263 (license license:expat)))
16265 (define-public r-xgboost
16268 (version "1.2.0.1")
16272 (uri (cran-uri "xgboost" version))
16275 "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4"))))
16276 (build-system r-build-system)
16278 `(("r-data-table" ,r-data-table)
16279 ("r-magrittr" ,r-magrittr)
16280 ("r-matrix" ,r-matrix)
16281 ("r-stringi" ,r-stringi)))
16283 `(("r-knitr" ,r-knitr)))
16284 (home-page "https://github.com/dmlc/xgboost")
16285 (synopsis "Extreme gradient boosting")
16287 "This package provides an R interface to Extreme Gradient Boosting, which
16288 is an efficient implementation of the gradient boosting framework from Chen
16289 and Guestrin (2016). The package includes efficient linear model solver and
16290 tree learning algorithms. The package can automatically do parallel
16291 computation on a single machine. It supports various objective functions,
16292 including regression, classification and ranking. The package is made to be
16293 extensible, so that users are also allowed to define their own objectives
16295 (license license:asl2.0)))
16297 (define-public r-umap
16300 (version "0.2.6.0")
16304 (uri (cran-uri "umap" version))
16307 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16308 (build-system r-build-system)
16310 `(("r-openssl" ,r-openssl)
16312 ("r-reticulate" ,r-reticulate)
16313 ("r-rspectra" ,r-rspectra)))
16315 `(("r-knitr" ,r-knitr)))
16316 (home-page "https://github.com/tkonopka/umap")
16317 (synopsis "Uniform manifold approximation and projection")
16319 "Uniform manifold approximation and projection is a technique for
16320 dimension reduction. This package provides an interface to the UMAP algorithm
16321 in R, including a translation of the original algorithm into R.")
16322 (license license:expat)))
16324 (define-public r-uwot
16331 (uri (cran-uri "uwot" version))
16334 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16335 (build-system r-build-system)
16337 `(("r-dqrng" ,r-dqrng)
16339 ("r-irlba" ,r-irlba)
16340 ("r-matrix" ,r-matrix)
16342 ("r-rcppannoy" ,r-rcppannoy)
16343 ("r-rcppprogress" ,r-rcppprogress)
16344 ("r-rspectra" ,r-rspectra)))
16345 (home-page "https://github.com/jlmelville/uwot")
16346 (synopsis "Uniform manifold approximation and projection")
16348 "This package provides an implementation of the Uniform Manifold
16349 Approximation and Projection dimensionality reduction by McInnes et
16350 al. (2018). It also provides means to transform new data and to carry out
16351 supervised dimensionality reduction. An implementation of the related
16352 LargeVis method of Tang et al. (2016) is also provided.")
16353 (license license:gpl3)))
16355 (define-public r-kableextra
16357 (name "r-kableextra")
16362 (uri (cran-uri "kableExtra" version))
16365 "0n25y7zwpspvkd62rd6x8c22dg2ys27smlpdz5brqs5ddv7x9dis"))))
16366 (properties `((upstream-name . "kableExtra")))
16367 (build-system r-build-system)
16369 `(("r-digest" ,r-digest)
16371 ("r-htmltools" ,r-htmltools)
16372 ("r-knitr" ,r-knitr)
16373 ("r-magrittr" ,r-magrittr)
16374 ("r-rmarkdown" ,r-rmarkdown)
16375 ("r-rstudioapi" ,r-rstudioapi)
16376 ("r-rvest" ,r-rvest)
16377 ("r-scales" ,r-scales)
16378 ("r-stringr" ,r-stringr)
16379 ("r-viridislite" ,r-viridislite)
16380 ("r-webshot" ,r-webshot)
16381 ("r-xml2" ,r-xml2)))
16383 `(("r-knitr" ,r-knitr)))
16384 (home-page "https://haozhu233.github.io/kableExtra/")
16385 (synopsis "Construct complex tables with pipe syntax")
16387 "Build complex HTML or LaTeX tables using @code{kable()} from
16388 @code{knitr} and the piping syntax from @code{magrittr}. The function
16389 @code{kable()} is a light weight table generator coming from @code{knitr}.
16390 This package simplifies the way to manipulate the HTML or LaTeX codes
16391 generated by @code{kable()} and allows users to construct complex tables and
16392 customize styles using a readable syntax.")
16393 (license license:expat)))
16395 (define-public r-glasso
16402 (uri (cran-uri "glasso" version))
16404 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16405 (build-system r-build-system)
16406 (native-inputs `(("gfortran" ,gfortran)))
16407 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16408 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16410 "This is a package for estimation of a sparse inverse covariance matrix
16411 using a lasso (L1) penalty. Facilities are provided for estimates along a
16412 path of values for the regularization parameter.")
16413 (license license:gpl2)))
16415 (define-public r-rhpcblasctl
16417 (name "r-rhpcblasctl")
16418 (version "0.20-137")
16422 (uri (cran-uri "RhpcBLASctl" version))
16425 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16426 (properties `((upstream-name . "RhpcBLASctl")))
16427 (build-system r-build-system)
16428 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16429 (synopsis "Control the number of threads on BLAS")
16431 "This package allows you to control the number of threads the BLAS
16432 library uses. It is also possible to control the number of threads in
16434 (license license:agpl3+)))
16436 (define-public r-lda
16443 (uri (cran-uri "lda" version))
16446 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16447 (build-system r-build-system)
16448 (home-page "https://cran.r-project.org/web/packages/lda/")
16449 (synopsis "Collapsed Gibbs sampling methods for topic models")
16451 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16452 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16453 mixed-membership stochastic blockmodel. Inference for all of these models is
16454 implemented via a fast collapsed Gibbs sampler written in C. Utility
16455 functions for reading/writing data typically used in topic models, as well as
16456 tools for examining posterior distributions are also included.")
16457 ;; Any version of the LGPL
16458 (license license:lgpl3+)))
16460 (define-public r-rann-l1
16467 (uri (cran-uri "RANN.L1" version))
16470 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16471 (properties `((upstream-name . "RANN.L1")))
16472 (build-system r-build-system)
16473 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16474 (synopsis "Fast nearest neighbour search using L1 metric")
16476 "This package provides tools to find the k nearest neighbours for every
16477 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16478 library. There is support for approximate as well as exact searches, fixed
16479 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16480 computed using the L1 (Manhattan, taxicab) metric.")
16481 (license license:gpl3+)))
16483 (define-public r-leiden
16490 (uri (cran-uri "leiden" version))
16493 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16494 (properties `((upstream-name . "leiden")))
16495 (build-system r-build-system)
16497 `(("r-igraph" ,r-igraph)
16498 ("r-matrix" ,r-matrix)
16499 ("r-reticulate" ,r-reticulate)))
16500 (home-page "https://github.com/TomKellyGenetics/leiden")
16501 (synopsis "R implementation of Leiden clustering algorithm")
16503 "This package implements the Python @code{leidenalg} module to be called
16504 in R. It enables clustering using the Leiden algorithm for partitioning a
16505 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16506 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16507 (license license:gpl3)))
16509 (define-public r-patchwork
16511 (name "r-patchwork")
16516 (uri (cran-uri "patchwork" version))
16519 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16520 (build-system r-build-system)
16522 `(("r-ggplot2" ,r-ggplot2)
16523 ("r-gtable" ,r-gtable)))
16525 `(("r-knitr" ,r-knitr)))
16526 (home-page "https://github.com/thomasp85/patchwork")
16527 (synopsis "Compose ggplot2 plots")
16529 "The @code{ggplot2} package provides a strong API for sequentially
16530 building up a plot, but does not concern itself with composition of multiple
16531 plots. Patchwork is a package that expands the API to allow for arbitrarily
16532 complex composition of plots by providing mathmatical operators for combining
16534 (license license:expat)))
16536 (define-public r-liger
16543 (uri (git-reference
16544 (url "https://github.com/MacoskoLab/liger")
16545 (commit (string-append "v" version))))
16546 (file-name (git-file-name name version))
16549 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16550 (modules '((guix build utils)))
16553 (delete-file "inst/java/ModularityOptimizer.jar")
16555 (build-system r-build-system)
16558 (modify-phases %standard-phases
16559 (add-after 'unpack 'build-java-part
16560 (lambda* (#:key inputs #:allow-other-keys)
16561 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16562 (for-each (lambda (file) (invoke "javac" file))
16563 (find-files "." "\\.java$"))
16564 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16565 (find-files "." "\\.class$"))
16568 `(("r-cowplot" ,r-cowplot)
16569 ("r-dosnow" ,r-dosnow)
16570 ("r-dplyr" ,r-dplyr)
16572 ("r-foreach" ,r-foreach)
16573 ("r-ggplot2" ,r-ggplot2)
16574 ("r-ggrepel" ,r-ggrepel)
16575 ("r-hmisc" ,r-hmisc)
16577 ("r-irlba" ,r-irlba)
16578 ("r-matrix" ,r-matrix)
16579 ("r-mclust" ,r-mclust)
16580 ("r-patchwork" ,r-patchwork)
16582 ("r-rann-l1" ,r-rann-l1)
16584 ("r-rcpparmadillo" ,r-rcpparmadillo)
16585 ("r-riverplot" ,r-riverplot)
16586 ("r-rtsne" ,r-rtsne)
16587 ("r-snow" ,r-snow)))
16589 `(("jdk" ,icedtea "jdk")
16590 ;; See https://github.com/MacoskoLab/liger/issues/96
16591 ;; The optimizer is released under the Expat license.
16595 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16598 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16600 ("r-knitr" ,r-knitr))) ; for vignettes
16601 (home-page "https://github.com/MacoskoLab/liger")
16602 (synopsis "Integrate and analyze multiple single-cell datasets")
16604 "LIGER is a package for integrating and analyzing multiple single-cell
16605 datasets, developed and maintained by the Macosko lab. It relies on
16606 integrative non-negative matrix factorization to identify shared and
16607 dataset-specific factors.")
16608 (license license:gpl3)))
16610 (define-public r-harmony
16617 (uri (git-reference
16618 (url "https://github.com/immunogenomics/harmony")
16620 (file-name (git-file-name name version))
16623 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16624 (modules '((guix build utils)))
16627 (for-each delete-file '("config.status" "configure"))
16629 (build-system r-build-system)
16631 `(("r-cowplot" ,r-cowplot)
16632 ("r-dplyr" ,r-dplyr)
16633 ("r-ggplot2" ,r-ggplot2)
16634 ("r-irlba" ,r-irlba)
16635 ("r-matrix" ,r-matrix)
16637 ("r-rcpparmadillo" ,r-rcpparmadillo)
16638 ("r-rcppprogress" ,r-rcppprogress)
16639 ("r-rlang" ,r-rlang)
16640 ("r-tibble" ,r-tibble)
16641 ("r-tidyr" ,r-tidyr)))
16643 `(("autoconf" ,autoconf)))
16644 (home-page "https://github.com/immunogenomics/harmony")
16645 (synopsis "Integration of single cell sequencing data")
16647 "This package provides an implementation of the Harmony algorithm for
16648 single cell integration, described in Korsunsky et al
16649 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16650 function and interfaces to external frameworks.")
16651 (license license:gpl3)))
16653 (define-public r-covr
16660 (uri (cran-uri "covr" version))
16662 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16663 (properties `((upstream-name . "covr")))
16664 (build-system r-build-system)
16666 `(("r-crayon" ,r-crayon)
16667 ("r-digest" ,r-digest)
16669 ("r-jsonlite" ,r-jsonlite)
16671 ("r-withr" ,r-withr)
16672 ("r-yaml" ,r-yaml)))
16674 `(("r-knitr" ,r-knitr))) ; for vignettes
16675 (home-page "https://github.com/r-lib/covr")
16676 (synopsis "Test coverage for R packages")
16678 "Thisp package enables you to track and report code coverage for your
16679 package and (optionally) upload the results to a coverage service. Code
16680 coverage is a measure of the amount of code being exercised by a set of tests.
16681 It is an indirect measure of test quality and completeness. This package is
16682 compatible with any testing methodology or framework and tracks coverage of
16683 both R code and compiled C/C++/FORTRAN code.")
16684 (license license:gpl3)))
16686 (define-public r-systemfonts
16688 (name "r-systemfonts")
16693 (uri (cran-uri "systemfonts" version))
16696 "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
16697 (properties `((upstream-name . "systemfonts")))
16698 (build-system r-build-system)
16700 `(("r-cpp11" ,r-cpp11)))
16702 `(("fontconfig" ,fontconfig)
16705 `(("pkg-config" ,pkg-config)
16706 ("r-knitr" ,r-knitr)))
16707 (home-page "https://github.com/r-lib/systemfonts")
16708 (synopsis "System native font finding")
16710 "This package provides system native access to the font catalogue. As
16711 font handling varies between systems it is difficult to correctly locate
16712 installed fonts across different operating systems. The 'systemfonts' package
16713 provides bindings to the native libraries for finding font files that can then
16714 be used further by e.g. graphic devices.")
16715 (license license:expat)))
16717 (define-public r-graphlayouts
16719 (name "r-graphlayouts")
16724 (uri (cran-uri "graphlayouts" version))
16727 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16728 (properties `((upstream-name . "graphlayouts")))
16729 (build-system r-build-system)
16731 `(("r-igraph" ,r-igraph)
16733 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16734 (home-page "https://github.com/schochastics/graphlayouts")
16735 (synopsis "Additional layout algorithms for network visualizations")
16737 "This package provides several layout algorithms to visualize networks
16738 which are not part of the igraph library. Most are based on the concept of
16739 stress majorization by Gansner et al. (2004)
16740 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16741 emphasize hidden group structures in networks or focus on specific nodes.")
16742 (license license:expat)))
16744 (define-public r-tidygraph
16746 (name "r-tidygraph")
16751 (uri (cran-uri "tidygraph" version))
16754 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16755 (properties `((upstream-name . "tidygraph")))
16756 (build-system r-build-system)
16758 `(("r-dplyr" ,r-dplyr)
16759 ("r-igraph" ,r-igraph)
16760 ("r-magrittr" ,r-magrittr)
16761 ("r-pillar" ,r-pillar)
16764 ("r-rlang" ,r-rlang)
16765 ("r-tibble" ,r-tibble)
16766 ("r-tidyr" ,r-tidyr)))
16767 (home-page "https://github.com/thomasp85/tidygraph")
16768 (synopsis "Tidy API for graph manipulation")
16770 "This package provides a graph implementation that can be thought of as
16771 two tidy data frames describing node and edge data respectively. It provides
16772 an approach to manipulate these two virtual data frames using the API defined
16773 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16774 common graph algorithms.")
16775 (license license:expat)))
16777 (define-public r-soupx
16778 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16782 (version (git-version "0.3.1" revision commit))
16786 (uri (git-reference
16787 (url "https://github.com/constantAmateur/SoupX")
16789 (file-name (git-file-name name version))
16792 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16793 (properties `((upstream-name . "SoupX")))
16794 (build-system r-build-system)
16796 `(("r-ggplot2" ,r-ggplot2)
16797 ("r-matrix" ,r-matrix)
16798 ("r-seurat" ,r-seurat)))
16799 (home-page "https://github.com/constantAmateur/SoupX")
16800 (synopsis "Single cell mRNA Soup eXterminator")
16802 "This package provides a package for quantifying, profiling and
16803 removing cell free mRNA contamination (the \"soup\") from droplet based single
16804 cell RNA-seq experiments.")
16805 (license license:gpl2))))
16807 (define-public r-assertr
16814 (uri (cran-uri "assertr" version))
16817 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16818 (build-system r-build-system)
16820 `(("r-dplyr" ,r-dplyr)
16822 ("r-rlang" ,r-rlang)))
16824 `(("r-knitr" ,r-knitr))) ; needed for vignette
16825 (home-page "https://github.com/ropensci/assertr")
16826 (synopsis "Assertive programming for R analysis pipelines")
16828 "This package provides functionality to assert conditions that have to be
16829 met so that errors in data used in analysis pipelines can fail quickly. It is
16830 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16832 (license license:expat)))
16834 (define-public r-parameters
16836 (name "r-parameters")
16841 (uri (cran-uri "parameters" version))
16844 "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
16845 (properties `((upstream-name . "parameters")))
16846 (build-system r-build-system)
16848 `(("r-bayestestr" ,r-bayestestr)
16849 ("r-insight" ,r-insight)))
16851 `(("r-knitr" ,r-knitr)))
16852 (home-page "https://cran.r-project.org/web/packages/parameters")
16853 (synopsis "Processing of model parameters")
16855 "This package provides utilities for processing the parameters of various
16856 statistical models. Beyond computing p values, CIs, and other indices for a
16857 wide variety of models, this package implements features like standardization
16858 or bootstrapping of parameters and models, feature reduction (feature
16859 extraction and variable selection) as well as conversion between indices of
16861 (license license:gpl3)))
16863 (define-public r-rgdal
16870 (uri (cran-uri "rgdal" version))
16872 (base32 "0rwlsafqxgqflfid4ciaa9qz3f75fgw8hilhaqj558gdxg8bzigp"))))
16873 (properties `((upstream-name . "rgdal")))
16874 (build-system r-build-system)
16882 `(("pkg-config" ,pkg-config)
16883 ("r-knitr" ,r-knitr)))
16884 (home-page "http://rgdal.r-forge.r-project.org")
16885 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16887 "This package provides bindings to the Geospatial Data Abstraction
16888 Library (GDAL) and access to projection/transformation operations from the
16890 (license license:gpl2+)))
16892 (define-public r-insol
16899 (uri (cran-uri "insol" version))
16902 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16903 (properties `((upstream-name . "insol")))
16904 (build-system r-build-system)
16906 `(("r-raster" ,r-raster)))
16908 `(("gfortran" ,gfortran)))
16909 (home-page "https://meteoexploration.com/R/insol/index.html")
16910 (synopsis "Tools for calculating solar radiation")
16912 "This package provides functions to compute insolation on tilted
16913 surfaces, computes atmospheric transmittance and related parameters such as:
16914 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16915 time, vector in the direction of the sun, vector normal to surface, and some
16916 atmospheric physics.")
16917 (license license:gpl2+)))
16919 (define-public r-lifecycle
16921 (name "r-lifecycle")
16926 (uri (cran-uri "lifecycle" version))
16929 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16930 (properties `((upstream-name . "lifecycle")))
16931 (build-system r-build-system)
16933 `(("r-glue" ,r-glue)
16934 ("r-rlang" ,r-rlang)))
16936 `(("r-knitr" ,r-knitr))) ; for vignettes
16937 (home-page "https://github.com/r-lib/lifecycle")
16938 (synopsis "Manage the life cycle of your package functions")
16940 "Manage the life cycle of your exported functions with shared
16941 conventions, documentation badges, and non-invasive deprecation warnings. The
16942 lifecycle package defines four development stages (experimental, maturing,
16943 stable, and questioning) and three deprecation stages (soft-deprecated,
16944 deprecated, and defunct). It makes it easy to insert badges corresponding to
16945 these stages in your documentation. Usage of deprecated functions are
16946 signalled with increasing levels of non-invasive verbosity.")
16947 (license license:gpl3)))
16949 (define-public r-assertable
16951 (name "r-assertable")
16956 (uri (cran-uri "assertable" version))
16959 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16960 (build-system r-build-system)
16962 `(("r-data-table" ,r-data-table)))
16963 (home-page "https://cran.r-project.org/web/packages/assertable/")
16964 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16965 (description "This package provides simple, flexible assertions on
16966 data.frame or data.table objects with verbose output for vetting. While other
16967 assertion packages apply towards more general use-cases, @code{assertable} is
16968 tailored towards tabular data. It includes functions to check variable names
16969 and values, whether the dataset contains all combinations of a given set of
16970 unique identifiers, and whether it is a certain length. In addition,
16971 @code{assertable} includes utility functions to check the existence of target
16972 files and to efficiently import multiple tabular data files into one
16974 (license license:gpl3)))
16976 (define-public r-quadprog
16978 (name "r-quadprog")
16983 (uri (cran-uri "quadprog" version))
16985 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16986 (build-system r-build-system)
16988 `(("gfortran" ,gfortran)))
16989 (home-page "https://cran.r-project.org/web/packages/quadprog")
16990 (synopsis "Functions to solve quadratic programming problems")
16992 "This package contains routines and documentation for solving quadratic
16993 programming problems.")
16994 (license license:gpl3+)))
16996 (define-public r-desolve
17003 (uri (cran-uri "deSolve" version))
17005 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
17006 (properties `((upstream-name . "deSolve")))
17007 (build-system r-build-system)
17009 `(("gfortran" ,gfortran)))
17010 (home-page "https://desolve.r-forge.r-project.org/")
17011 (synopsis "Solvers for initial value problems of differential equations")
17012 (description "This package provides functions that solve initial value
17013 problems of a system of first-order @dfn{ordinary differential
17014 equations} (ODE), of @dfn{partial differential equations} (PDE), of
17015 @dfn{differential algebraic equations} (DAE), and of delay differential
17016 equations. The functions provide an interface to the FORTRAN functions
17017 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
17018 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
17019 C-implementation of solvers of the Runge-Kutta family with fixed or variable
17020 time steps. The package contains routines designed for solving ODEs resulting
17021 from 1-D, 2-D and 3-D partial differential equations that have been converted
17022 to ODEs by numerical differencing.")
17023 (license license:gpl2+)))
17025 (define-public r-pracma
17031 (uri (cran-uri "pracma" version))
17033 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
17034 (build-system r-build-system)
17035 (home-page "https://cran.r-project.org/web/packages/pracma/")
17036 (synopsis "Practical numerical math functions")
17037 (description "This package provides functions for numerical analysis and
17038 linear algebra, numerical optimization, differential equations, plus some
17039 special functions. It uses Matlab function names where appropriate to simplify
17041 (license license:gpl3+)))
17043 (define-public r-subplex
17050 (uri (cran-uri "subplex" version))
17053 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
17054 (build-system r-build-system)
17056 `(("gfortran" ,gfortran)))
17057 (home-page "https://cran.r-project.org/web/packages/subplex")
17058 (synopsis "Unconstrained optimization using the subplex algorithm")
17060 "This package implements the Subplex optimization algorithm.
17061 It solves unconstrained optimization problems using a simplex method on
17062 subspaces. The method is well suited for optimizing objective functions that
17063 are noisy or are discontinuous at the solution.")
17064 (license license:gpl3+)))
17066 (define-public r-txtplot
17073 (uri (cran-uri "txtplot" version))
17076 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
17077 (build-system r-build-system)
17078 (home-page "https://cran.r-project.org/web/packages/txtplot/")
17079 (synopsis "Text-based plotting")
17080 (description "This package provides functions to produce rudimentary ASCII
17081 graphics directly in the terminal window. This package provides a basic
17082 plotting function (and equivalents of curve, density, acf and barplot) as well
17083 as a boxplot function.")
17084 (license license:lgpl3+)))
17086 (define-public r-bio3d
17093 (uri (cran-uri "bio3d" version))
17096 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
17097 (properties `((upstream-name . "bio3d")))
17098 (build-system r-build-system)
17099 (inputs `(("zlib" ,zlib)))
17100 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17101 (home-page "http://thegrantlab.org/bio3d/")
17102 (synopsis "Biological structure analysis")
17104 "This package provides utilities to process, organize and explore protein
17105 structure, sequence and dynamics data. Features include the ability to read
17106 and write structure, sequence and dynamic trajectory data, perform sequence
17107 and structure database searches, data summaries, atom selection, alignment,
17108 superposition, rigid core identification, clustering, torsion analysis,
17109 distance matrix analysis, structure and sequence conservation analysis, normal
17110 mode analysis, principal component analysis of heterogeneous structure data,
17111 and correlation network analysis from normal mode and molecular dynamics data.
17112 In addition, various utility functions are provided to enable the statistical
17113 and graphical power of the R environment to work with biological sequence and
17115 (license license:gpl2+)))
17117 (define-public r-bios2cor
17119 (name "r-bios2cor")
17124 (uri (cran-uri "Bios2cor" version))
17127 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
17128 (properties `((upstream-name . "Bios2cor")))
17129 (build-system r-build-system)
17131 `(("r-bigmemory" ,r-bigmemory)
17132 ("r-bio3d" ,r-bio3d)
17133 ("r-circular" ,r-circular)
17134 ("r-igraph" ,r-igraph)))
17135 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
17136 (synopsis "From biological sequences and simulations to correlation analysis")
17138 "This package provides utilities for computation and analysis of
17139 correlation/covariation in multiple sequence alignments and in side chain
17140 motions during molecular dynamics simulations. Features include the
17141 computation of correlation/covariation scores using a variety of scoring
17142 functions between either sequence positions in alignments or side chain
17143 dihedral angles in molecular dynamics simulations and utilities to analyze the
17144 correlation/covariation matrix through a variety of tools including network
17145 representation and principal components analysis. In addition, several
17146 utility functions are based on the R graphical environment to provide friendly
17147 tools for help in data interpretation.")
17148 (license license:gpl2+)))
17150 ;; This package includes minified JavaScript files. When upgrading please
17151 ;; check that there are no new minified JavaScript files.
17152 (define-public r-networkd3
17154 (name "r-networkd3")
17159 (uri (cran-uri "networkD3" version))
17162 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
17165 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
17167 (properties `((upstream-name . "networkD3")))
17168 (build-system r-build-system)
17170 `(#:modules ((guix build utils)
17171 (guix build r-build-system)
17175 (modify-phases %standard-phases
17176 (add-after 'unpack 'process-javascript
17177 (lambda* (#:key inputs #:allow-other-keys)
17178 (with-directory-excursion "inst/htmlwidgets/lib/"
17182 `((,(assoc-ref inputs "d3.v4.js")
17183 "d3-4.5.0/d3.min.js"))))
17184 (lambda (sources targets)
17185 (for-each (lambda (source target)
17186 (format #t "Processing ~a --> ~a~%"
17188 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17189 (call-with-output-file target
17191 (dump-port minified port)))))
17192 sources targets))))
17195 `(("uglify-js" ,uglify-js)
17196 ;; NOTE: Make sure that this version of d3 is still valid when
17197 ;; upgrading the package.
17201 (uri "https://d3js.org/d3.v4.js")
17204 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
17206 `(("r-htmlwidgets" ,r-htmlwidgets)
17207 ("r-igraph" ,r-igraph)
17208 ("r-magrittr" ,r-magrittr)))
17209 (home-page "https://cran.r-project.org/package=networkD3")
17210 (synopsis "D3 JavaScript network graphs from R")
17212 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
17214 (license license:gpl3+)))
17216 (define-public r-aasea
17223 (uri (cran-uri "aaSEA" version))
17226 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
17227 (properties `((upstream-name . "aaSEA")))
17228 (build-system r-build-system)
17230 `(("r-bios2cor" ,r-bios2cor)
17232 ("r-hmisc" ,r-hmisc)
17233 ("r-magrittr" ,r-magrittr)
17234 ("r-networkd3" ,r-networkd3)
17235 ("r-plotly" ,r-plotly)
17236 ("r-seqinr" ,r-seqinr)
17237 ("r-shiny" ,r-shiny)
17238 ("r-shinydashboard" ,r-shinydashboard)))
17239 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17240 (synopsis "Amino acid substitution effect analyzer")
17242 "Given a protein multiple sequence alignment, it is a daunting task to
17243 assess the effects of substitutions along sequence length. The aaSEA package
17244 is intended to help researchers to rapidly analyze property changes caused by
17245 single, multiple and correlated amino acid substitutions in proteins.")
17246 (license license:gpl3)))
17248 (define-public r-abacus
17255 (uri (cran-uri "ABACUS" version))
17258 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17259 (properties `((upstream-name . "ABACUS")))
17260 (build-system r-build-system)
17262 `(("r-ggplot2" ,r-ggplot2)
17263 ("r-shiny" ,r-shiny)))
17264 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17265 (synopsis "Apps-based activities for communicating and understanding statistics")
17267 "This package provides a set of Shiny apps for effective communication
17268 and understanding in statistics. The current version includes properties of
17269 normal distribution, properties of sampling distribution, one-sample z and t
17270 tests, two samples independent (unpaired) t test and analysis of variance.")
17271 (license license:gpl3)))
17273 (define-public r-abc-rap
17280 (uri (cran-uri "ABC.RAP" version))
17283 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17284 (properties `((upstream-name . "ABC.RAP")))
17285 (build-system r-build-system)
17286 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17287 (synopsis "Array-based CpG region analysis pipeline")
17289 "This package aims to identify candidate genes that are differentially
17290 methylated between cases and controls. It applies Student's t-test and delta
17291 beta analysis to identify candidate genes containing multiple CpG sites.")
17292 (license license:gpl3)))
17294 (define-public r-abcadm
17301 (uri (cran-uri "abcADM" version))
17304 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17305 (properties `((upstream-name . "abcADM")))
17306 (build-system r-build-system)
17309 ("r-rcpp" ,r-rcpp)))
17310 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17311 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17313 "This package provides tools to estimate parameters of accumulated
17314 damage (load duration) models based on failure time data under a Bayesian
17315 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17316 long-term reliability under stochastic load profiles.")
17317 (license license:gpl3)))
17319 (define-public r-rglpk
17326 (uri (cran-uri "Rglpk" version))
17329 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17330 (properties `((upstream-name . "Rglpk")))
17331 (build-system r-build-system)
17333 `(("r-slam" ,r-slam)))
17336 (home-page "https://r-forge.r-project.org/projects/rglp/")
17337 (synopsis "R interface to the GNU Linear Programming Kit")
17339 "This package provides an R interface to the GNU Linear Programming Kit,
17340 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17341 integer linear programming} (MILP) and other related problems.")
17343 (license (list license:gpl2 license:gpl3))))
17345 (define-public r-abcdefba
17347 (name "r-abcdefba")
17352 (uri (cran-uri "abcdeFBA" version))
17355 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17356 (properties `((upstream-name . "abcdeFBA")))
17357 (build-system r-build-system)
17359 `(("r-corrplot" ,r-corrplot)
17360 ("r-lattice" ,r-lattice)
17362 ("r-rglpk" ,r-rglpk)))
17363 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17364 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17366 "This package provides functions for Constraint Based Simulation using
17367 Flux Balance Analysis and informative analysis of the data generated during
17369 (license license:gpl2)))
17371 (define-public r-abcrlda
17378 (uri (cran-uri "abcrlda" version))
17381 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17382 (properties `((upstream-name . "abcrlda")))
17383 (build-system r-build-system)
17384 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17385 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17387 "This package offers methods to perform @dfn{asymptotically
17388 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17389 cost-sensitive binary classification. The bias-correction is an estimate of
17390 the bias term added to regularized discriminant analysis that minimizes the
17392 (license license:gpl3)))
17394 (define-public r-abemus
17401 (uri (cran-uri "abemus" version))
17404 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17405 (properties `((upstream-name . "abemus")))
17406 (build-system r-build-system)
17408 `(("r-data-table" ,r-data-table)))
17409 (home-page "https://cran.r-project.org/web/packages/abemus/")
17410 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17412 "This package provides an implementation of @dfn{Adaptive Base Error
17413 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17414 platform-specific genetic knowledge and empirical signal to readily detect and
17415 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17416 cell free DNA} (cfDNA).")
17417 (license license:gpl3)))
17419 ;; This package includes minified JavaScript files. When upgrading please
17420 ;; check that there are no new minified JavaScript files.
17421 (define-public r-rintrojs
17423 (name "r-rintrojs")
17428 (uri (cran-uri "rintrojs" version))
17431 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17432 (properties `((upstream-name . "rintrojs")))
17433 (build-system r-build-system)
17435 `(#:modules ((guix build utils)
17436 (guix build r-build-system)
17440 (modify-phases %standard-phases
17441 (add-after 'unpack 'process-javascript
17442 (lambda* (#:key inputs #:allow-other-keys)
17443 (with-directory-excursion "inst/javascript/introjs/"
17447 `((,(assoc-ref inputs "intro.js")
17449 (lambda (sources targets)
17450 (for-each (lambda (source target)
17451 (format #t "Processing ~a --> ~a~%"
17453 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17454 (call-with-output-file target
17456 (dump-port minified port)))))
17457 sources targets))))
17460 `(("uglify-js" ,uglify-js)
17464 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17467 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17469 `(("r-jsonlite" ,r-jsonlite)
17470 ("r-shiny" ,r-shiny)))
17471 (home-page "https://github.com/carlganz/rintrojs")
17472 (synopsis "Wrapper for the Intro.js library")
17474 "This package provides a wrapper for the @url{http://www.introjs.com,
17475 Intro.js} library. This package makes it easy to include step-by-step
17476 introductions, and clickable hints in a Shiny application. It supports both
17477 static introductions in the UI, and programmatic introductions from the
17479 (license license:agpl3+)))
17481 (define-public r-sysfonts
17483 (name "r-sysfonts")
17488 (uri (cran-uri "sysfonts" version))
17491 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17492 (properties `((upstream-name . "sysfonts")))
17493 (build-system r-build-system)
17495 `(("freetype" ,freetype)
17499 `(("pkg-config" ,pkg-config)))
17500 (home-page "https://github.com/yixuan/sysfonts")
17501 (synopsis "Loading fonts into R")
17503 "This is a package to simplify loading of system fonts and Google Fonts
17504 into R, in order to support other packages.")
17505 (license license:gpl2)))
17507 (define-public r-showtextdb
17509 (name "r-showtextdb")
17514 (uri (cran-uri "showtextdb" version))
17517 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17518 (properties `((upstream-name . "showtextdb")))
17519 (build-system r-build-system)
17521 `(("r-sysfonts" ,r-sysfonts)))
17522 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17523 (synopsis "Font files for the 'showtext' package")
17525 "This package provides font files that can be used by the @code{showtext}
17527 (license license:asl2.0)))
17529 (define-public r-showtext
17531 (name "r-showtext")
17536 (uri (cran-uri "showtext" version))
17539 "11fx2vv8jlvcnybh18y7v4bn2c67aqsqwfq7y8dpywbwr4zg8jid"))))
17540 (properties `((upstream-name . "showtext")))
17541 (build-system r-build-system)
17543 `(("freetype" ,freetype)
17547 `(("r-showtextdb" ,r-showtextdb)
17548 ("r-sysfonts" ,r-sysfonts)))
17550 `(("pkg-config" ,pkg-config)
17551 ("r-knitr" ,r-knitr)))
17552 (home-page "https://github.com/yixuan/showtext")
17553 (synopsis "Using fonts more easily in R graphs")
17555 "This package aims to make it easy to use various types of
17556 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17557 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17558 will be converted into polygons or raster images, hence after the plot has
17559 been created, it no longer relies on the font files. No external software
17560 such as Ghostscript is needed to use this package.")
17561 (license license:asl2.0)))
17563 (define-public r-emojifont
17565 (name "r-emojifont")
17570 (uri (cran-uri "emojifont" version))
17573 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17574 (properties `((upstream-name . "emojifont")))
17575 (build-system r-build-system)
17577 `(("r-ggplot2" ,r-ggplot2)
17578 ("r-proto" ,r-proto)
17579 ("r-showtext" ,r-showtext)
17580 ("r-sysfonts" ,r-sysfonts)))
17581 (home-page "https://guangchuangyu.github.io/emojifont")
17582 (synopsis "Emoji and Font Awesome in R graphics")
17584 "This package enables the use of emoji and the Font Awesome glyphs in
17585 both base and ggplot2 graphics.")
17586 (license license:artistic2.0)))
17588 (define-public r-abstractr
17590 (name "r-abstractr")
17595 (uri (cran-uri "abstractr" version))
17598 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17599 (properties `((upstream-name . "abstractr")))
17600 (build-system r-build-system)
17602 `(("r-colourpicker" ,r-colourpicker)
17603 ("r-emojifont" ,r-emojifont)
17604 ("r-ggplot2" ,r-ggplot2)
17605 ("r-gridextra" ,r-gridextra)
17606 ("r-rintrojs" ,r-rintrojs)
17607 ("r-shiny" ,r-shiny)
17608 ("r-shinythemes" ,r-shinythemes)))
17609 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17610 (synopsis "R-Shiny application for creating visual abstracts")
17612 "This package provides an R Shiny application to create visual abstracts
17613 for original research. A variety of user defined options and formatting are
17615 (license license:gpl3)))
17617 (define-public r-qgam
17624 (uri (cran-uri "qgam" version))
17627 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17628 (properties `((upstream-name . "qgam")))
17629 (build-system r-build-system)
17631 `(("r-doparallel" ,r-doparallel)
17634 ("r-shiny" ,r-shiny)))
17635 (native-inputs `(("r-knitr" ,r-knitr)))
17636 (home-page "https://cran.r-project.org/web/packages/qgam/")
17637 (synopsis "Smooth additive quantile regression models")
17639 "This package provides smooth additive quantile regression models, fitted
17640 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17641 the smoothing parameters are estimated automatically by marginal loss
17642 minimization, while the regression coefficients are estimated using either
17643 PIRLS or Newton algorithm. The learning rate is determined so that the
17644 Bayesian credible intervals of the estimated effects have approximately the
17645 correct coverage. The main function is @code{qgam()} which is similar to
17646 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17647 regression models.")
17648 (license license:gpl2+)))
17650 (define-public r-abtest
17657 (uri (cran-uri "abtest" version))
17660 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17661 (properties `((upstream-name . "abtest")))
17662 (build-system r-build-system)
17664 `(("r-matrix" ,r-matrix)
17665 ("r-mvtnorm" ,r-mvtnorm)
17666 ("r-plotrix" ,r-plotrix)
17668 ("r-rcolorbrewer" ,r-rcolorbrewer)
17671 ("r-truncnorm" ,r-truncnorm)))
17672 (home-page "https://cran.r-project.org/web/packages/abtest/")
17673 (synopsis "Bayesian A/B testing")
17675 "This package provides functions for Bayesian A/B testing including prior
17676 elicitation options based on Kass and Vaidyanathan (1992)
17677 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17678 (license license:gpl2+)))
17680 (define-public r-accept
17687 (uri (cran-uri "accept" version))
17690 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17691 (properties `((upstream-name . "accept")))
17692 (build-system r-build-system)
17694 `(("r-dplyr" ,r-dplyr)
17695 ("r-extrafont" ,r-extrafont)
17697 ("r-plotly" ,r-plotly)
17698 ("r-stringr" ,r-stringr)
17699 ("r-viridis" ,r-viridis)))
17700 (home-page "https://cran.r-project.org/web/packages/accept/")
17701 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17703 "This package allows clinicians to predict the rate and severity of
17704 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17705 Disease} (COPD) patients, based on the clinical prediction model published in
17706 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17707 (license license:gpl3)))
17709 (define-public r-smpracticals
17711 (name "r-smpracticals")
17716 (uri (cran-uri "SMPracticals" version))
17719 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17720 (properties `((upstream-name . "SMPracticals")))
17721 (build-system r-build-system)
17723 `(("r-ellipse" ,r-ellipse)
17726 ("r-survival" ,r-survival)))
17727 (home-page "http://statwww.epfl.ch/davison/SM/")
17728 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17730 "This package contains the datasets and a few functions for use with the
17731 practicals outlined in Appendix A of the book Statistical Models (Davison,
17732 2003, Cambridge University Press). The practicals themselves can be found at
17733 @url{http://statwww.epfl.ch/davison/SM/}.")
17734 (license license:gpl2+)))
17736 (define-public r-fgui
17743 (uri (cran-uri "fgui" version))
17746 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17747 (properties `((upstream-name . "fgui")))
17748 (build-system r-build-system)
17750 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17751 (synopsis "Create GUI for R functions")
17753 "Rapidly create a GUI for a function you created by automatically
17754 creating widgets for arguments of the function. This package automatically
17755 parses help routines for context-sensitive help to these arguments. The
17756 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17757 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17758 incorporated into the interface for greater customization for the more
17760 ;; Any version of the GPL.
17761 (license (list license:gpl2+ license:gpl3+))))
17763 (define-public r-tcltk2
17770 (uri (cran-uri "tcltk2" version))
17773 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17774 (properties `((upstream-name . "tcltk2")))
17775 (build-system r-build-system)
17779 (home-page "https://www.sciviews.org/SciViews-R")
17780 (synopsis "Tcl/Tk additions")
17782 "This package provides a series of additional Tcl commands and Tk widgets
17783 with style and various functions to supplement the tcltk package")
17784 (license license:lgpl3)))
17786 (define-public r-accrual
17793 (uri (cran-uri "accrual" version))
17796 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17797 (properties `((upstream-name . "accrual")))
17798 (build-system r-build-system)
17800 `(("r-fgui" ,r-fgui)
17801 ("r-smpracticals" ,r-smpracticals)
17802 ("r-tcltk2" ,r-tcltk2)))
17803 (home-page "https://cran.r-project.org/web/packages/accrual/")
17804 (synopsis "Bayesian accrual prediction")
17806 "Subject recruitment for medical research is challenging. Slow patient
17807 accrual leads to delay in research. Accrual monitoring during the process of
17808 recruitment is critical. Researchers need reliable tools to manage the
17809 accrual rate. This package provides an implementation of a Bayesian method
17810 that integrates researcher's experience on previous trials and data from the
17811 current study, providing reliable prediction on accrual rate for clinical
17812 studies. It provides functions for Bayesian accrual prediction which can be
17813 easily used by statisticians and clinical researchers.")
17814 (license license:gpl2)))
17816 (define-public r-accrued
17823 (uri (cran-uri "accrued" version))
17826 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17827 (properties `((upstream-name . "accrued")))
17828 (build-system r-build-system)
17829 (home-page "https://cran.r-project.org/web/packages/accrued/")
17830 (synopsis "Data quality visualization tools for partially accruing data")
17832 "This is a package for visualizing data quality of partially accruing
17834 (license license:gpl3)))
17836 (define-public r-mda
17843 (uri (cran-uri "mda" version))
17846 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17847 (properties `((upstream-name . "mda")))
17848 (build-system r-build-system)
17849 (propagated-inputs `(("r-class" ,r-class)))
17850 (native-inputs `(("gfortran" ,gfortran)))
17851 (home-page "https://cran.r-project.org/web/packages/mda/")
17852 (synopsis "Mixture and flexible discriminant analysis")
17854 "This is a package for mixture and flexible discriminant analysis,
17855 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17856 (license license:gpl2)))
17858 (define-public r-elasticnet
17860 (name "r-elasticnet")
17865 (uri (cran-uri "elasticnet" version))
17868 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17869 (properties `((upstream-name . "elasticnet")))
17870 (build-system r-build-system)
17872 `(("r-lars" ,r-lars)))
17873 (home-page "http://users.stat.umn.edu/~zouxx019/")
17874 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17876 "This package provides functions for fitting the entire solution path of
17877 the Elastic-Net and also provides functions for estimating sparse Principal
17878 Components. The Lasso solution paths can be computed by the same function.")
17879 (license license:gpl2+)))
17881 (define-public r-sparselda
17883 (name "r-sparselda")
17888 (uri (cran-uri "sparseLDA" version))
17891 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17892 (properties `((upstream-name . "sparseLDA")))
17893 (build-system r-build-system)
17895 `(("r-elasticnet" ,r-elasticnet)
17898 (home-page "https://www.imm.dtu.dk/~lkhc/")
17899 (synopsis "Sparse discriminant analysis")
17901 "This package performs sparse linear discriminant analysis for Gaussians
17902 and mixture of Gaussian models.")
17903 (license license:gpl2+)))
17905 (define-public r-accsda
17912 (uri (cran-uri "accSDA" version))
17915 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17916 (properties `((upstream-name . "accSDA")))
17917 (build-system r-build-system)
17919 `(("r-ggplot2" ,r-ggplot2)
17920 ("r-ggthemes" ,r-ggthemes)
17921 ("r-gridextra" ,r-gridextra)
17923 ("r-rarpack" ,r-rarpack)
17924 ("r-sparselda" ,r-sparselda)))
17925 (home-page "https://github.com/gumeo/accSDA/wiki")
17926 (synopsis "Accelerated sparse discriminant analysis")
17928 "This package provides an implementation of sparse linear discriminant
17929 analysis, which is a supervised classification method for multiple classes.
17930 Various novel optimization approaches to this problem are implemented
17931 including @dfn{alternating direction method of multipliers} (ADMM),
17932 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17933 Functions for performing cross validation are also supplied along with basic
17934 prediction and plotting functions. @dfn{Sparse zero variance
17935 discriminant} (SZVD) analysis is also included in the package.")
17936 (license license:gpl2+)))
17938 (define-public r-ace2fastq
17940 (name "r-ace2fastq")
17945 (uri (cran-uri "ace2fastq" version))
17948 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17949 (properties `((upstream-name . "ace2fastq")))
17950 (build-system r-build-system)
17952 `(("r-stringr" ,r-stringr)))
17953 (home-page "https://github.com/c5sire/ace2fastq")
17954 (synopsis "ACE file to FASTQ converter")
17956 "The ACE file format is used in genomics to store contigs from sequencing
17957 machines. This tools converts it into FASTQ format. Both formats contain the
17958 sequence characters and their corresponding quality information. Unlike the
17959 FASTQ file, the ACE file stores the quality values numerically. The
17960 conversion algorithm uses the standard Sanger formula. The package
17961 facilitates insertion into pipelines, and content inspection.")
17962 (license license:gpl3)))
17964 (define-public r-rngwell
17971 (uri (cran-uri "rngWELL" version))
17974 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17975 (properties `((upstream-name . "rngWELL")))
17976 (build-system r-build-system)
17977 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17978 (synopsis "Toolbox for WELL random number generators")
17980 "This is a dedicated package to WELL pseudo random generators, which were
17981 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17982 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17983 (license license:bsd-3)))
17985 (define-public r-randtoolbox
17987 (name "r-randtoolbox")
17992 (uri (cran-uri "randtoolbox" version))
17995 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17996 (properties `((upstream-name . "randtoolbox")))
17997 (build-system r-build-system)
17999 `(("r-rngwell" ,r-rngwell)))
18001 `(("gfortran" ,gfortran)))
18002 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
18003 (synopsis "Toolbox for pseudo and quasi random number generation")
18005 "This package provides
18008 @item pseudo random generators, such as general linear
18009 congruential generators, multiple recursive generators and generalized
18010 feedback shift register (SF-Mersenne Twister algorithm and WELL
18013 @item quasi random generators, such as the Torus algorithm, the Sobol
18014 sequence, the Halton sequence (including the Van der Corput sequence), and
18016 @item some generator tests: the gap test, the serial test, the poker test.
18019 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
18020 (license license:bsd-3)))
18022 (define-public r-lhs
18029 (uri (cran-uri "lhs" version))
18032 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
18033 (properties `((upstream-name . "lhs")))
18034 (build-system r-build-system)
18035 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18037 `(("r-knitr" ,r-knitr)))
18038 (home-page "https://github.com/bertcarnell/lhs")
18039 (synopsis "Latin Hypercube Samples")
18041 "This package provides a number of methods for creating and augmenting
18042 Latin Hypercube Samples.")
18043 (license license:gpl3)))
18045 (define-public r-acebayes
18047 (name "r-acebayes")
18052 (uri (cran-uri "acebayes" version))
18055 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
18056 (properties `((upstream-name . "acebayes")))
18057 (build-system r-build-system)
18059 `(("r-compare" ,r-compare)
18061 ("r-randtoolbox" ,r-randtoolbox)
18063 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18064 (home-page "https://cran.r-project.org/web/packages/acebayes/")
18065 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
18067 "Finding an optimal Bayesian experimental design involves maximizing an
18068 objective function given by the expectation of some appropriately chosen
18069 utility function with respect to the joint distribution of unknown
18070 quantities (including responses). This objective function is usually not
18071 available in closed form and the design space can be continuous and of high
18072 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
18073 to maximise an approximation to the expectation of the utility function.")
18074 (license license:gpl2)))
18076 (define-public r-acet
18083 (uri (cran-uri "ACEt" version))
18086 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
18087 (properties `((upstream-name . "ACEt")))
18088 (build-system r-build-system)
18093 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18094 (home-page "https://cran.r-project.org/web/packages/ACEt/")
18095 (synopsis "Estimating dynamic heritability and twin model comparison")
18097 "This package supports twin models that are able to estimate the dynamic
18098 behaviour of the variance components in the classical twin models with respect
18099 to age using B-splines and P-splines.")
18100 (license license:gpl2+)))
18102 (define-public r-acfmperiod
18104 (name "r-acfmperiod")
18109 (uri (cran-uri "acfMPeriod" version))
18112 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
18113 (properties `((upstream-name . "acfMPeriod")))
18114 (build-system r-build-system)
18116 `(("r-mass" ,r-mass)))
18117 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
18118 (synopsis "Estimation of the ACF from the M-periodogram")
18120 "This package support non-robust and robust computations of the sample
18121 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
18122 univariate and multivariate processes. The methodology consists in reversing
18123 the diagonalization procedure involving the periodogram or the
18124 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
18125 ACOVF or the ACF as discussed in Fuller (1995)
18126 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
18127 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
18128 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
18129 (license license:gpl2+)))
18131 (define-public r-gamlss-data
18133 (name "r-gamlss-data")
18138 (uri (cran-uri "gamlss.data" version))
18141 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
18142 (properties `((upstream-name . "gamlss.data")))
18143 (build-system r-build-system)
18144 (home-page "http://www.gamlss.org/")
18145 (synopsis "GAMLSS data")
18147 "This package provides data used as examples to demonstrate GAMLSS
18149 ;; Either version of the license
18150 (license (list license:gpl2 license:gpl3))))
18152 (define-public r-gamlss
18159 (uri (cran-uri "gamlss" version))
18162 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
18163 (properties `((upstream-name . "gamlss")))
18164 (build-system r-build-system)
18166 `(("r-gamlss-data" ,r-gamlss-data)
18167 ("r-gamlss-dist" ,r-gamlss-dist)
18170 ("r-survival" ,r-survival)))
18171 (home-page "http://www.gamlss.org/")
18172 (synopsis "Generalized additive models for location scale and shape")
18174 "This package provides functions for fitting the generalized additive
18175 models for location scale and shape introduced by Rigby and
18176 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
18177 use a distributional regression approach where all the parameters of the
18178 conditional distribution of the response variable are modelled using
18179 explanatory variables.")
18180 ;; Either version of the license
18181 (license (list license:gpl2 license:gpl3))))
18183 (define-public r-acid
18190 (uri (cran-uri "acid" version))
18193 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
18194 (properties `((upstream-name . "acid")))
18195 (build-system r-build-system)
18197 `(("r-gamlss" ,r-gamlss)
18198 ("r-gamlss-dist" ,r-gamlss-dist)
18199 ("r-hmisc" ,r-hmisc)))
18200 (home-page "https://cran.r-project.org/web/packages/acid/")
18201 (synopsis "Analysing conditional income distributions")
18203 "This package provides functions for the analysis of income distributions
18204 for subgroups of the population as defined by a set of variables like age,
18205 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
18206 distribution as well as functions for moments, inequality measures, entropy
18207 measures and polarisation measures of income distributions. This package thus
18208 aides the analysis of income inequality by offering tools for the exploratory
18209 analysis of income distributions at the disaggregated level.")
18210 (license license:gpl3)))
18212 (define-public r-acm4r
18219 (uri (cran-uri "acm4r" version))
18222 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
18223 (properties `((upstream-name . "acm4r")))
18224 (build-system r-build-system)
18225 (propagated-inputs `(("r-mass" ,r-mass)))
18226 (home-page "https://cran.r-project.org/web/packages/acm4r/")
18227 (synopsis "Align-and-count method comparisons of RFLP data")
18229 "This is a package to compare sequence fragment lengths or molecular
18230 weights from pairs of lanes. The number of matching bands in the
18231 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
18232 the align-and-count method.")
18233 ;; Any version of the GPL
18234 (license (list license:gpl2+ license:gpl3+))))
18236 (define-public r-filematrix
18238 (name "r-filematrix")
18243 (uri (cran-uri "filematrix" version))
18246 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18247 (properties `((upstream-name . "filematrix")))
18248 (build-system r-build-system)
18249 ;; These inputs are needed for vignettes
18251 `(("r-knitr" ,r-knitr)
18252 ("r-rmarkdown" ,r-rmarkdown)
18253 ("pandoc-citeproc" ,pandoc-citeproc)))
18254 (home-page "https://github.com/andreyshabalin/filematrix")
18255 (synopsis "File-backed matrix class with convenient read and write access")
18257 "This package provides an interface for working with large matrices
18258 stored in files, not in computer memory. It supports multiple non-character
18259 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18260 byte real values). Access to parts of the matrix is done by indexing, exactly
18261 as with usual R matrices. It supports very large matrices; the package has
18262 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18263 columns, ad allows for quick addition of extra columns to a filematrix.")
18264 (license license:lgpl3)))
18266 (define-public r-acmeeqtl
18268 (name "r-acmeeqtl")
18273 (uri (cran-uri "ACMEeqtl" version))
18276 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18277 (properties `((upstream-name . "ACMEeqtl")))
18278 (build-system r-build-system)
18280 `(("r-filematrix" ,r-filematrix)))
18281 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18282 (synopsis "Estimation of interpretable eQTL effect sizes")
18284 "This package provides a non-linear model, termed ACME, that reflects a
18285 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18286 With non-linear least-squares algorithm the maximum likelihood parameters can
18287 be estimated. The ACME model provides interpretable effect size estimates and
18288 p-values with well controlled Type-I error.")
18289 (license license:lgpl3)))
18291 (define-public r-acmer
18298 (uri (cran-uri "acmeR" version))
18301 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18302 (properties `((upstream-name . "acmeR")))
18303 (build-system r-build-system)
18304 (propagated-inputs `(("r-foreign" ,r-foreign)))
18305 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18306 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18308 "This package provides an implementation of the ACME estimator, described
18309 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18310 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18311 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18312 as carcasses age; variable bleed-through at successive searches; and interval
18313 mortality estimates. The package provides, based on search data, functions
18314 for estimating the mortality inflation factor in Frequentist and Bayesian
18316 (license license:expat)))
18318 (define-public r-r-huge
18325 (uri (cran-uri "R.huge" version))
18328 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18329 (properties `((upstream-name . "R.huge")))
18330 (build-system r-build-system)
18332 `(("r-r-methodss3" ,r-r-methodss3)
18334 ("r-r-utils" ,r-r-utils)))
18335 (home-page "https://github.com/HenrikBengtsson/R.huge")
18336 (synopsis "Methods for accessing huge amounts of data")
18338 "This is a deprecated package for accessing huge amounts of data.
18339 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18340 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18341 the @code{aroma.affymetrix} package.")
18342 (license license:lgpl2.1+)))
18344 (define-public r-r-filesets
18346 (name "r-r-filesets")
18351 (uri (cran-uri "R.filesets" version))
18354 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18355 (properties `((upstream-name . "R.filesets")))
18356 (build-system r-build-system)
18358 `(("r-digest" ,r-digest)
18359 ("r-r-cache" ,r-r-cache)
18360 ("r-r-methodss3" ,r-r-methodss3)
18362 ("r-r-utils" ,r-r-utils)))
18363 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18364 (synopsis "Easy handling of and access to files")
18366 "This package provides classes and methods to locate, setup, subset,
18367 navigate and iterate file sets, i.e. sets of files located in one or more
18368 directories on the file system. The API is designed such that these classes
18369 can be extended via inheritance to provide a richer API for special file
18370 formats. Moreover, a specific name format is defined such that filenames and
18371 directories can be considered to have full names which consists of a name
18372 followed by comma-separated tags. This adds additional flexibility to
18373 identify file sets and individual files.")
18374 (license license:lgpl2.1+)))
18376 (define-public r-r-devices
18378 (name "r-r-devices")
18383 (uri (cran-uri "R.devices" version))
18386 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18387 (properties `((upstream-name . "R.devices")))
18388 (build-system r-build-system)
18390 `(("r-base64enc" ,r-base64enc)
18391 ("r-r-methodss3" ,r-r-methodss3)
18393 ("r-r-utils" ,r-r-utils)))
18394 (home-page "https://github.com/HenrikBengtsson/R.devices")
18395 (synopsis "Unified handling of graphics devices")
18397 "This package provides functions for creating plots and image files in a
18398 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18399 Default device options as well as scales and aspect ratios are controlled in a
18400 uniform way across all device types. Switching output format requires minimal
18401 changes in code. This package is ideal for large-scale batch processing,
18402 because it will never leave open graphics devices or incomplete image files
18403 behind, even on errors or user interrupts.")
18404 (license license:lgpl2.1+)))
18406 (define-public r-acnr
18413 (uri (cran-uri "acnr" version))
18416 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18417 (properties `((upstream-name . "acnr")))
18418 (build-system r-build-system)
18419 (home-page "https://github.com/mpierrejean/acnr")
18420 (synopsis "Annotated copy-number regions")
18422 "This package provides SNP array data from different types of copy-number
18423 regions. These regions were identified manually by the authors of the package
18424 and may be used to generate realistic data sets with known truth.")
18425 (license license:lgpl2.1+)))
18427 (define-public r-acopula
18434 (uri (cran-uri "acopula" version))
18437 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18438 (properties `((upstream-name . "acopula")))
18439 (build-system r-build-system)
18440 (home-page "https://cran.r-project.org/web/packages/acopula/")
18441 (synopsis "Modelling dependence with multivariate Archimax copulas")
18443 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18444 package provides definitions of several parametric families of generator and
18445 dependence function, computes CDF and PDF, estimates parameters, tests for
18446 goodness of fit, generates random sample and checks copula properties for
18447 custom constructs. In the 2-dimensional case explicit formulas for density
18448 are used, contrary to higher dimensions when all derivatives are linearly
18449 approximated. Several non-archimax families (normal, FGM, Plackett) are
18450 provided as well.")
18451 (license license:gpl2)))
18453 (define-public r-tuner
18460 (uri (cran-uri "tuneR" version))
18463 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18464 (properties `((upstream-name . "tuneR")))
18465 (build-system r-build-system)
18466 (propagated-inputs `(("r-signal" ,r-signal)))
18467 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18468 (synopsis "Analysis of music and speech")
18470 "This is a package for the analysis of music and speech. Analyze music
18471 and speech, extract features like MFCCs, handle wave files and their
18472 representation in various ways, read MP3, read MIDI, perform steps of a
18473 transcription, ...")
18474 ;; Either of these versions.
18475 (license (list license:gpl2 license:gpl3))))
18477 (define-public r-seewave
18484 (uri (cran-uri "seewave" version))
18487 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18488 (properties `((upstream-name . "seewave")))
18489 (build-system r-build-system)
18491 `(("libsndfile" ,libsndfile)))
18493 `(("r-tuner" ,r-tuner)))
18494 (home-page "http://rug.mnhn.fr/seewave")
18495 (synopsis "Sound analysis and synthesis")
18497 "This package provides functions for analysing, manipulating, displaying,
18498 editing and synthesizing time waves (particularly sound). This package
18499 processes time analysis (oscillograms and envelopes), spectral content,
18500 resonance quality factor, entropy, cross correlation and autocorrelation,
18501 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18502 and 3D spectrograms and many other analyses.")
18503 (license license:gpl2+)))
18505 (define-public r-acousticndlcoder
18507 (name "r-acousticndlcoder")
18512 (uri (cran-uri "AcousticNDLCodeR" version))
18515 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18517 `((upstream-name . "AcousticNDLCodeR")))
18518 (build-system r-build-system)
18520 `(("r-seewave" ,r-seewave)
18521 ("r-tuner" ,r-tuner)
18523 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18524 (synopsis "Coding sound files for use with NDL")
18526 "Make acoustic cues to use with the R package @code{ndl}.
18527 The package implements functions used in the PLoS ONE paper \"Words from
18528 spontaneous conversational speech can be recognized with human-like accuracy
18529 by an error-driven learning algorithm that discriminates between meanings
18530 straight from smart acoustic features, bypassing the phoneme as recognition
18531 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18532 (license license:gpl2+)))
18534 (define-public r-acp
18541 (uri (cran-uri "acp" version))
18544 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18545 (properties `((upstream-name . "acp")))
18546 (build-system r-build-system)
18548 `(("r-quantmod" ,r-quantmod)
18549 ("r-tseries" ,r-tseries)))
18550 (home-page "https://cran.r-project.org/web/packages/acp/")
18551 (synopsis "Autoregressive conditional Poisson")
18553 "This package supports the analysis of count data exhibiting
18554 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18555 model (ACP(p,q)) proposed by Heinen (2003).")
18556 (license license:gpl2)))
18558 (define-public r-ada
18565 (uri (cran-uri "ada" version))
18568 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18569 (properties `((upstream-name . "ada")))
18570 (build-system r-build-system)
18571 (propagated-inputs `(("r-rpart" ,r-rpart)))
18572 (home-page "https://cran.r-project.org/web/packages/ada/")
18573 (synopsis "Stochastic boosting")
18575 "This package provides a straightforward, well-documented, and broad
18576 boosting routine for classification, ideally suited for small to
18577 moderate-sized data sets. It performs discrete, real, and gentle boost under
18578 both exponential and logistic loss on a given data set.")
18579 ;; Any version of the GPL.
18580 (license (list license:gpl2+ license:gpl3+))))
18582 (define-public r-genalg
18589 (uri (cran-uri "genalg" version))
18592 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18593 (properties `((upstream-name . "genalg")))
18594 (build-system r-build-system)
18595 (home-page "https://github.com/egonw/genalg")
18596 (synopsis "R based genetic algorithm")
18598 "This package provides an R based genetic algorithm for binary and
18599 floating point chromosomes.")
18600 (license license:gpl2)))
18602 (define-public r-kernelfactory
18604 (name "r-kernelfactory")
18609 (uri (cran-uri "kernelFactory" version))
18612 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18613 (properties `((upstream-name . "kernelFactory")))
18614 (build-system r-build-system)
18617 ("r-genalg" ,r-genalg)
18618 ("r-kernlab" ,r-kernlab)
18619 ("r-randomforest" ,r-randomforest)))
18620 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18621 (synopsis "Ensemble of kernel machines")
18623 "Kernel factory is an ensemble method where each base classifier (random
18624 forest) is fit on the kernel matrix of a subset of the training data.")
18625 (license license:gpl2+)))
18627 (define-public r-dummies
18634 (uri (cran-uri "dummies" version))
18637 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18638 (properties `((upstream-name . "dummies")))
18639 (build-system r-build-system)
18640 (home-page "https://decisionpatterns.com")
18641 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18643 "This package lets you expand factors, characters and other eligible
18644 classes into dummy/indicator variables.")
18645 (license license:gpl2+)))
18647 (define-public r-acrm
18654 (uri (cran-uri "aCRM" version))
18657 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18658 (properties `((upstream-name . "aCRM")))
18659 (build-system r-build-system)
18662 ("r-dummies" ,r-dummies)
18663 ("r-kernelfactory" ,r-kernelfactory)
18664 ("r-randomforest" ,r-randomforest)))
18665 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18666 (synopsis "Convenience functions for analytical customer relationship management")
18668 "This package provides convenience functions for data preparation and
18669 modeling often used in @dfn{analytical customer relationship
18670 management} (aCRM).")
18671 (license license:gpl2+)))
18673 (define-public r-treeclust
18675 (name "r-treeclust")
18680 (uri (cran-uri "treeClust" version))
18683 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18684 (properties `((upstream-name . "treeClust")))
18685 (build-system r-build-system)
18687 `(("r-cluster" ,r-cluster)
18688 ("r-rpart" ,r-rpart)))
18689 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18690 (synopsis "Cluster distances through trees")
18692 "This package provides tools to create a measure of inter-point
18693 dissimilarity useful for clustering mixed data, and, optionally, perform the
18695 (license license:gpl2+)))
18697 (define-public r-acrosstic
18699 (name "r-acrosstic")
18704 (uri (cran-uri "AcrossTic" version))
18707 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18708 (properties `((upstream-name . "AcrossTic")))
18709 (build-system r-build-system)
18711 `(("r-lpsolve" ,r-lpsolve)
18712 ("r-treeclust" ,r-treeclust)))
18713 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18714 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18716 "This is a package for constructing minimum-cost regular spanning
18717 subgraph as part of a non-parametric two-sample test for equality of
18719 (license license:gpl2+)))
18721 (define-public r-acrt
18728 (uri (cran-uri "acrt" version))
18731 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18732 (properties `((upstream-name . "acrt")))
18733 (build-system r-build-system)
18735 `(("r-rcpp" ,r-rcpp)
18736 ("r-rcppeigen" ,r-rcppeigen)
18737 ("r-sandwich" ,r-sandwich)))
18738 (home-page "https://cran.r-project.org/web/packages/acrt/")
18739 (synopsis "Autocorrelation robust testing")
18741 "This package provides functions for testing affine hypotheses on the
18742 regression coefficient vector in regression models with autocorrelated
18744 (license license:gpl2)))
18746 (define-public r-acs
18753 (uri (cran-uri "acs" version))
18756 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18757 (properties `((upstream-name . "acs")))
18758 (build-system r-build-system)
18760 `(("r-httr" ,r-httr)
18763 ("r-stringr" ,r-stringr)
18765 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18766 (synopsis "Work with data from the US Census")
18768 "This package provides a general toolkit for downloading, managing,
18769 analyzing, and presenting data from the
18770 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18771 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18772 American Community Survey (ACS). Confidence intervals provided with ACS data
18773 are converted to standard errors to be bundled with estimates in complex
18774 @code{acs} objects. The package provides new methods to conduct standard
18775 operations on @code{acs} objects and present/plot data in statistically
18776 appropriate ways.")
18777 (license license:gpl3)))
18779 (define-public r-acss-data
18781 (name "r-acss-data")
18786 (uri (cran-uri "acss.data" version))
18789 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18790 (properties `((upstream-name . "acss.data")))
18791 (build-system r-build-system)
18792 (home-page "http://complexitycalculator.com/methodology.html")
18793 (synopsis "Data for algorithmic complexity of short strings")
18795 "This is a data only package providing the algorithmic complexity of
18796 short strings, computed using the coding theorem method. For a given set of
18797 symbols in a string, all possible or a large number of random samples of
18798 Turing machines with a given number of states (e.g., 5) and number of symbols
18799 corresponding to the number of symbols in the strings were simulated until
18800 they reached a halting state or failed to end. This package contains data on
18801 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18802 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18803 distribution of the halting states.")
18804 (license license:gpl2+)))
18806 (define-public r-acss
18813 (uri (cran-uri "acss" version))
18816 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18817 (properties `((upstream-name . "acss")))
18818 (build-system r-build-system)
18820 `(("r-acss-data" ,r-acss-data)
18822 (home-page "http://complexitycalculator.com/methodology.html")
18823 (synopsis "Algorithmic complexity for short strings")
18825 "The main purpose of this package is to provide the algorithmic
18826 complexity for short strings, an approximation of the Kolmogorov Complexity of
18827 a short string using the coding theorem method. While the database containing
18828 the complexity is provided in the data only package @code{acss.data}, this
18829 package provides functions accessing the data such as @code{prob_random}
18830 returning the posterior probability that a given string was produced by a
18831 random process. In addition, two traditional (but problematic) measures of
18832 complexity are also provided: entropy and change complexity.")
18833 (license license:gpl2+)))
18835 (define-public r-acswr
18842 (uri (cran-uri "ACSWR" version))
18845 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18846 (properties `((upstream-name . "ACSWR")))
18847 (build-system r-build-system)
18849 `(("r-mass" ,r-mass)))
18850 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18851 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18853 "This is a companion package for the book \"A Course in Statistics with
18854 R\" (ISBN 978-1-119-15272-9.)")
18855 (license license:gpl2)))
18857 (define-public r-alabama
18860 (version "2015.3-1")
18864 (uri (cran-uri "alabama" version))
18867 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18868 (properties `((upstream-name . "alabama")))
18869 (build-system r-build-system)
18870 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18871 (home-page "https://cran.r-project.org/web/packages/alabama/")
18872 (synopsis "Constrained nonlinear optimization")
18874 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18875 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18876 constraints. Linear or nonlinear equality and inequality constraints are
18878 (license license:gpl2+)))
18880 (define-public r-gdina
18887 (uri (cran-uri "GDINA" version))
18890 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18891 (properties `((upstream-name . "GDINA")))
18892 (build-system r-build-system)
18894 `(("r-alabama" ,r-alabama)
18895 ("r-ggplot2" ,r-ggplot2)
18897 ("r-nloptr" ,r-nloptr)
18898 ("r-numderiv" ,r-numderiv)
18900 ("r-rcpparmadillo" ,r-rcpparmadillo)
18901 ("r-rsolnp" ,r-rsolnp)
18902 ("r-shiny" ,r-shiny)
18903 ("r-shinydashboard" ,r-shinydashboard)))
18905 `(("r-knitr" ,r-knitr)))
18906 (home-page "https://github.com/Wenchao-Ma/GDINA")
18907 (synopsis "Generalized DINA model framework")
18909 "This package provides a set of psychometric tools for cognitive
18910 diagnosis modeling based on the generalized deterministic inputs, noisy and
18911 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18912 and its extensions, including the sequential G-DINA model by Ma and de la
18913 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18914 polytomous G-DINA model by Chen and de la Torre
18915 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18916 distribution can be independent, saturated, higher-order, loglinear smoothed
18917 or structured. Q-matrix validation, item and model fit statistics, model
18918 comparison at test and item level and differential item functioning can also
18919 be conducted. A graphical user interface is also provided.")
18920 (license license:gpl3)))
18922 (define-public r-actcd
18929 (uri (cran-uri "ACTCD" version))
18932 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18933 (properties `((upstream-name . "ACTCD")))
18934 (build-system r-build-system)
18936 `(("r-gdina" ,r-gdina)
18937 ("r-r-methodss3" ,r-r-methodss3)))
18939 `(("gfortran" ,gfortran)))
18940 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18941 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18943 "This is a package supporting cluster analysis for cognitive diagnosis
18944 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18945 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18946 sum-scores, cluster analysis techniques can be used to classify examinees into
18947 latent classes based on their attribute patterns. In addition to the
18948 algorithms used to classify data, three labeling approaches are proposed to
18949 label clusters so that examinees' attribute profiles can be obtained.")
18950 (license license:gpl2+)))
18952 (define-public r-ineq
18959 (uri (cran-uri "ineq" version))
18962 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18963 (properties `((upstream-name . "ineq")))
18964 (build-system r-build-system)
18965 (home-page "https://cran.r-project.org/web/packages/ineq/")
18966 (synopsis "Measuring inequality, concentration, and poverty")
18968 "This package provides tools for measuring inequality, concentration, and
18969 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18970 ;; Either of these two versions.
18971 (license (list license:gpl2 license:gpl3))))
18973 (define-public r-actfrag
18980 (uri (cran-uri "ActFrag" version))
18983 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18984 (properties `((upstream-name . "ActFrag")))
18985 (build-system r-build-system)
18987 `(("r-accelerometry" ,r-accelerometry)
18988 ("r-dplyr" ,r-dplyr)
18990 ("r-survival" ,r-survival)
18991 ("r-tidyr" ,r-tidyr)))
18992 (home-page "https://github.com/junruidi/ActFrag")
18993 (synopsis "Activity fragmentation metrics extraction")
18995 "This package provides functions to extract commonly used fragmentation
18996 metrics to quantify time accumulation strategies based on minute level
18997 actigraphy-measured activity counts data.")
18998 (license license:gpl3)))
19000 (define-public r-fda
19003 (version "5.1.5.1")
19007 (uri (cran-uri "fda" version))
19010 "0zi001cw5536x6rgr4l0skva7fk53663zf6ggnsa8znml090sihm"))))
19011 (properties `((upstream-name . "fda")))
19012 (build-system r-build-system)
19014 `(("r-matrix" ,r-matrix)))
19015 (home-page "https://www.functionaldata.org")
19016 (synopsis "Functional data analysis")
19018 "These functions were developed to support functional data analysis as
19019 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
19020 Analysis. The package includes data sets and script files working many
19022 (license license:gpl2+)))
19024 (define-public r-actigraphy
19026 (name "r-actigraphy")
19031 (uri (cran-uri "Actigraphy" version))
19034 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
19035 (properties `((upstream-name . "Actigraphy")))
19036 (build-system r-build-system)
19038 `(("r-fda" ,r-fda)))
19039 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
19040 (synopsis "Actigraphy data analysis")
19042 "This package provides tools for functional linear modeling and analysis
19043 of actigraphy data.")
19044 (license license:asl2.0)))
19046 (define-public r-activedriver
19048 (name "r-activedriver")
19053 (uri (cran-uri "ActiveDriver" version))
19056 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
19057 (properties `((upstream-name . "ActiveDriver")))
19058 (build-system r-build-system)
19060 `(("r-mass" ,r-mass)))
19061 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
19062 (synopsis "Tools for finding cancer driver proteins")
19064 "This package provides a mutation analysis tool that discovers cancer
19065 driver genes with frequent mutations in protein signalling sites such as
19066 post-translational modifications (phosphorylation, ubiquitination, etc). The
19067 Poisson generalized linear regression model identifies genes where cancer
19068 mutations in signalling sites are more frequent than expected from the
19069 sequence of the entire gene. Integration of mutations with signalling
19070 information helps find new driver genes and propose candidate mechanisms to
19072 (license license:gpl2+)))
19074 (define-public r-activitycounts
19076 (name "r-activitycounts")
19081 (uri (cran-uri "activityCounts" version))
19084 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
19086 `((upstream-name . "activityCounts")))
19087 (build-system r-build-system)
19089 `(("r-lubridate" ,r-lubridate)
19090 ("r-magrittr" ,r-magrittr)
19091 ("r-seewave" ,r-seewave)
19092 ("r-signal" ,r-signal)
19093 ("r-tibble" ,r-tibble)))
19094 (home-page "https://github.com/walkabillylab/activityCounts")
19095 (synopsis "Generate ActiLife counts")
19097 "ActiLife generates activity counts from data collected by Actigraph
19098 accelerometers. Actigraph is one of the most common research-grade
19099 accelerometers. There is considerable research validating and developing
19100 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
19101 counts are proprietary and difficult to implement if researchers use different
19102 accelerometer brands. The code creates ActiLife counts from raw acceleration
19103 data for different accelerometer brands.")
19104 (license license:gpl3)))
19106 (define-public r-activityindex
19108 (name "r-activityindex")
19113 (uri (cran-uri "ActivityIndex" version))
19116 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
19117 (properties `((upstream-name . "ActivityIndex")))
19118 (build-system r-build-system)
19120 `(("r-data-table" ,r-data-table)
19121 ("r-matrixstats" ,r-matrixstats)
19122 ("r-r-utils" ,r-r-utils)))
19123 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
19124 (synopsis "Activity Index calculation using raw accelerometry data")
19126 "This is a package to read raw accelerometry from GT3X+ accelerometry
19127 data and plain table data to calculate the Activity Index from Bai et
19128 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
19129 (license license:gpl3)))
19131 (define-public r-activpal
19133 (name "r-activpal")
19138 (uri (cran-uri "activPAL" version))
19141 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
19142 (properties `((upstream-name . "activPAL")))
19143 (build-system r-build-system)
19145 `(("r-devtools" ,r-devtools)
19146 ("r-dplyr" ,r-dplyr)
19147 ("r-ggplot2" ,r-ggplot2)
19148 ("r-lubridate" ,r-lubridate)
19149 ("r-magrittr" ,r-magrittr)
19150 ("r-tidyr" ,r-tidyr)))
19151 (home-page "https://cran.r-project.org/web/packages/activPAL")
19152 (synopsis "Processing and chart generation from activPAL events files")
19154 "This package contains functions to generate pre-defined summary
19155 statistics from activPAL events files. The package also contains functions to
19156 produce informative graphics that visualize physical activity behaviour and
19157 trends. This includes generating graphs that align physical activity
19158 behaviour with additional time based observations described by other data
19159 sets, such as sleep diaries and continuous glucose monitoring data.")
19160 (license license:gpl3)))
19162 (define-public r-activpalprocessing
19164 (name "r-activpalprocessing")
19169 (uri (cran-uri "activpalProcessing" version))
19172 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
19174 `((upstream-name . "activpalProcessing")))
19175 (build-system r-build-system)
19177 `(("r-chron" ,r-chron)))
19178 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
19179 (synopsis "Process activPAL events files")
19181 "This package performs estimation of physical activity and sedentary
19182 behavior variables from activPAL events files.")
19183 ;; Either version of the GPL.
19184 (license (list license:gpl2 license:gpl3))))
19186 (define-public r-actogrammr
19188 (name "r-actogrammr")
19193 (uri (cran-uri "actogrammr" version))
19196 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
19197 (properties `((upstream-name . "actogrammr")))
19198 (build-system r-build-system)
19200 `(("r-dplyr" ,r-dplyr)
19201 ("r-ggplot2" ,r-ggplot2)
19202 ("r-lubridate" ,r-lubridate)
19203 ("r-readr" ,r-readr)
19204 ("r-tidyr" ,r-tidyr)))
19205 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
19206 (synopsis "Read in activity data and plot actograms")
19208 "Read in activity measurements from standard file formats used by
19209 circadian rhythm researchers, currently only ClockLab format, and process and
19210 plot the data. The central type of plot is the actogram, as first described
19211 in \"Activity and distribution of certain wild mice in relation to biotic
19212 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
19213 (license license:gpl3)))
19215 (define-public r-expint
19222 (uri (cran-uri "expint" version))
19225 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
19226 (properties `((upstream-name . "expint")))
19227 (build-system r-build-system)
19228 (home-page "https://gitlab.com/vigou3/expint")
19229 (synopsis "Exponential integral and incomplete Gamma function")
19231 "This package provides the exponential integrals @code{E_1(x)},
19232 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19233 function @code{G(a, x)} defined for negative values of its first argument.
19234 The package also gives easy access to the underlying C routines through an
19235 API; see the package vignette for details.")
19236 (license license:gpl2+)))
19238 (define-public r-actuar
19245 (uri (cran-uri "actuar" version))
19248 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19249 (properties `((upstream-name . "actuar")))
19250 (build-system r-build-system)
19251 (propagated-inputs `(("r-expint" ,r-expint)))
19252 (home-page "https://gitlab.com/vigou3/actuar")
19253 (synopsis "Actuarial functions and heavy tailed distributions")
19255 "This package provides functions and data sets for actuarial science:
19256 modeling of loss distributions; risk theory and ruin theory; simulation of
19257 compound models, discrete mixtures and compound hierarchical models;
19258 credibility theory. It boasts support for many additional probability
19259 distributions to model insurance loss amounts and loss frequency: 19
19260 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19261 distribution; zero-truncated and zero-modified extensions of the standard
19262 discrete distributions. It also supports phase-type distributions commonly
19263 used to compute ruin probabilities.")
19264 (license license:gpl2+)))
19266 (define-public r-bmp
19273 (uri (cran-uri "bmp" version))
19276 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19277 (properties `((upstream-name . "bmp")))
19278 (build-system r-build-system)
19279 (home-page "https://cran.r-project.org/web/packages/bmp/")
19280 (synopsis "Read Bitmap (BMP) images")
19282 "This package provides pure R tools to read BMP format images. It is
19283 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19284 (license license:gpl2+)))
19286 (define-public r-readbitmap
19288 (name "r-readbitmap")
19293 (uri (cran-uri "readbitmap" version))
19296 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19297 (properties `((upstream-name . "readbitmap")))
19298 (build-system r-build-system)
19300 `(("libjpeg" ,libjpeg-turbo)
19301 ("libpng" ,libpng)))
19306 ("r-tiff" ,r-tiff)))
19307 (home-page "https://github.com/jefferis/readbitmap")
19308 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19310 "This package provides tools to identify and read BMP, JPEG, PNG, and
19311 TIFF format bitmap images. Identification defaults to the use of the magic
19312 number embedded in the file rather than the file extension.")
19313 (license license:gpl2+)))
19315 (define-public r-imager
19322 (uri (cran-uri "imager" version))
19325 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19326 (properties `((upstream-name . "imager")))
19327 (build-system r-build-system)
19330 ("libtiff" ,libtiff)
19334 `(("r-downloader" ,r-downloader)
19335 ("r-igraph" ,r-igraph)
19337 ("r-magrittr" ,r-magrittr)
19339 ("r-purrr" ,r-purrr)
19341 ("r-readbitmap" ,r-readbitmap)
19342 ("r-stringr" ,r-stringr)))
19344 `(("pkg-config" ,pkg-config)
19345 ("r-knitr" ,r-knitr)))
19346 (home-page "https://dahtah.github.io/imager/")
19347 (synopsis "Image processing library")
19349 "This is a package for fast image processing for images in up to 4
19350 dimensions (two spatial dimensions, one time/depth dimension, one color
19351 dimension). It provides most traditional image processing tools (filtering,
19352 morphology, transformations, etc.) as well as various functions for easily
19353 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19354 simple, modern C++ library for image processing.")
19355 (license license:lgpl3)))
19357 (define-public r-acuityview
19359 (name "r-acuityview")
19364 (uri (cran-uri "AcuityView" version))
19367 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19368 (properties `((upstream-name . "AcuityView")))
19369 (build-system r-build-system)
19371 `(("r-fftwtools" ,r-fftwtools)
19372 ("r-imager" ,r-imager)
19373 ("r-plotrix" ,r-plotrix)))
19374 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19375 (synopsis "Display scenes as seen by an animal with less acute vision")
19377 "This package provides a simple method for representing a visual scene as
19378 it may be seen by an animal with less acute vision.")
19379 (license license:gpl2+)))
19381 (define-public r-caret
19388 (uri (cran-uri "caret" version))
19391 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19392 (build-system r-build-system)
19394 `(("r-foreach" ,r-foreach)
19395 ("r-ggplot2" ,r-ggplot2)
19396 ("r-lattice" ,r-lattice)
19397 ("r-modelmetrics" ,r-modelmetrics)
19401 ("r-recipes" ,r-recipes)
19402 ("r-reshape2" ,r-reshape2)
19403 ("r-withr" ,r-withr)))
19405 `(("r-knitr" ,r-knitr)))
19406 (home-page "https://github.com/topepo/caret")
19407 (synopsis "Classification and regression training")
19409 "This package provides miscellaneous functions for training and plotting
19410 classification and regression models.")
19411 (license license:gpl2+)))
19413 (define-public r-adabag
19420 (uri (cran-uri "adabag" version))
19423 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19424 (properties `((upstream-name . "adabag")))
19425 (build-system r-build-system)
19427 `(("r-caret" ,r-caret)
19428 ("r-doparallel" ,r-doparallel)
19429 ("r-foreach" ,r-foreach)
19430 ("r-rpart" ,r-rpart)))
19431 (home-page "https://cran.r-project.org/web/packages/adabag/")
19432 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19434 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19435 Breiman's Bagging algorithm using classification trees as individual
19436 classifiers. Once these classifiers have been trained, they can be used to
19437 predict on new data. Also, cross validation estimation of the error can be
19439 (license license:gpl2+)))
19441 (define-public r-adagio
19448 (uri (cran-uri "adagio" version))
19451 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19452 (properties `((upstream-name . "adagio")))
19453 (build-system r-build-system)
19454 (native-inputs `(("gfortran" ,gfortran)))
19455 (home-page "https://cran.r-project.org/web/packages/adagio/")
19456 (synopsis "Discrete and global optimization routines")
19458 "This package provides methods and algorithms for discrete optimization,
19459 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19460 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19462 (license license:gpl3+)))
19464 (define-public r-univoutl
19466 (name "r-univoutl")
19471 (uri (cran-uri "univOutl" version))
19474 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19475 (properties `((upstream-name . "univOutl")))
19476 (build-system r-build-system)
19478 `(("r-hmisc" ,r-hmisc)
19479 ("r-robustbase" ,r-robustbase)))
19480 (home-page "https://github.com/marcellodo/univOutl")
19481 (synopsis "Detection of univariate outliers")
19483 "This package provides well-known outlier detection techniques in the
19484 univariate case. Methods to deal with skewed distribution are included too.
19485 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19486 historical data is implemented as well. When available, survey weights can be
19487 used in outliers detection.")
19488 (license license:gpl2+)))
19490 (define-public r-tolerance
19492 (name "r-tolerance")
19497 (uri (cran-uri "tolerance" version))
19500 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19501 (properties `((upstream-name . "tolerance")))
19502 (build-system r-build-system)
19504 `(("r-mass" ,r-mass)
19506 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19507 (synopsis "Statistical tolerance intervals and regions")
19509 "This package provides functions for estimating tolerance
19510 limits (intervals) for various univariate distributions (binomial, Cauchy,
19511 discrete Pareto, exponential, two-parameter exponential, extreme value,
19512 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19513 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19514 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19515 nonparametric tolerance intervals, tolerance bands for regression
19516 settings (linear regression, nonlinear regression, nonparametric regression,
19517 and multivariate regression), and analysis of variance tolerance intervals.
19518 Visualizations are also available for most of these settings.")
19519 (license license:gpl2+)))
19521 (define-public r-additivitytests
19523 (name "r-additivitytests")
19528 (uri (cran-uri "additivityTests" version))
19531 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19533 `((upstream-name . "additivityTests")))
19534 (build-system r-build-system)
19535 (home-page "https://github.com/simecek/additivityTests")
19536 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19538 "This package provides an implementation of the Tukey, Mandel,
19539 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19540 (license license:gpl3)))
19542 (define-public r-flexclust
19544 (name "r-flexclust")
19549 (uri (cran-uri "flexclust" version))
19552 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19553 (properties `((upstream-name . "flexclust")))
19554 (build-system r-build-system)
19556 `(("r-class" ,r-class)
19557 ("r-lattice" ,r-lattice)
19558 ("r-modeltools" ,r-modeltools)))
19559 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19560 (synopsis "Flexible cluster algorithms")
19562 "The main function @code{kcca} implements a general framework for
19563 k-centroids cluster analysis supporting arbitrary distance measures and
19564 centroid computation. Further cluster methods include hard competitive
19565 learning, neural gas, and QT clustering. There are numerous visualization
19566 methods for cluster results (neighborhood graphs, convex cluster hulls,
19567 barcharts of centroids, ...), and bootstrap methods for the analysis of
19568 cluster stability.")
19569 (license license:gpl2)))
19571 (define-public r-biclust
19578 (uri (cran-uri "biclust" version))
19581 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19582 (properties `((upstream-name . "biclust")))
19583 (build-system r-build-system)
19585 `(("r-additivitytests" ,r-additivitytests)
19586 ("r-colorspace" ,r-colorspace)
19587 ("r-flexclust" ,r-flexclust)
19588 ("r-ggplot2" ,r-ggplot2)
19589 ("r-lattice" ,r-lattice)
19591 ("r-tidyr" ,r-tidyr)))
19592 (home-page "https://cran.r-project.org/web/packages/biclust/")
19593 (synopsis "BiCluster algorithms")
19595 "The main function @code{biclust()} provides several algorithms to find
19596 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19597 In addition, the package provides methods for data
19598 preprocessing (normalization and discretization), visualization, and
19599 validation of bicluster solutions.")
19600 (license license:gpl3)))
19602 (define-public r-icge
19609 (uri (cran-uri "ICGE" version))
19612 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19613 (properties `((upstream-name . "ICGE")))
19614 (build-system r-build-system)
19616 `(("r-cluster" ,r-cluster)
19617 ("r-mass" ,r-mass)))
19618 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19619 (synopsis "Cluster estimation and identification of atypical units")
19621 "ICGE is a package that helps to estimate the number of real clusters in
19622 data as well as to identify atypical units. The underlying methods are based
19623 on distances rather than on unit x variables.")
19624 (license license:gpl2+)))
19626 (define-public r-depth
19629 (version "2.1-1.1")
19633 (uri (cran-uri "depth" version))
19636 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19637 (properties `((upstream-name . "depth")))
19638 (build-system r-build-system)
19640 `(("r-abind" ,r-abind)
19641 ("r-circular" ,r-circular)
19644 `(("gfortran" ,gfortran)))
19645 (home-page "https://cran.r-project.org/web/packages/depth/")
19646 (synopsis "Nonparametric depth functions for multivariate analysis")
19648 "This package provides tools for depth functions methodology applied to
19649 multivariate analysis. Besides allowing calculation of depth values and
19650 depth-based location estimators, the package includes functions or drawing
19651 contour plots and perspective plots of depth functions. Euclidian and
19652 spherical depths are supported.")
19653 (license license:gpl2)))
19655 (define-public r-archetypes
19657 (name "r-archetypes")
19658 (version "2.2-0.1")
19662 (uri (cran-uri "archetypes" version))
19665 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19666 (properties `((upstream-name . "archetypes")))
19667 (build-system r-build-system)
19669 `(("r-modeltools" ,r-modeltools)
19670 ("r-nnls" ,r-nnls)))
19671 (home-page "https://cran.r-project.org/web/packages/archetypes")
19672 (synopsis "Archetypal analysis")
19674 "The main function @code{archetypes} implements a framework for
19675 archetypal analysis supporting arbitrary problem solving mechanisms for the
19676 different conceptual parts of the algorithm.")
19677 (license license:gpl2+)))
19679 (define-public r-shapes
19686 (uri (cran-uri "shapes" version))
19689 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19690 (properties `((upstream-name . "shapes")))
19691 (build-system r-build-system)
19693 `(("r-mass" ,r-mass)
19694 ("r-minpack-lm" ,r-minpack-lm)
19696 ("r-scatterplot3d" ,r-scatterplot3d)))
19697 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19698 (synopsis "Statistical shape analysis")
19700 "This package provides routines for the statistical analysis of landmark
19701 shapes, including Procrustes analysis, graphical displays, principal
19702 components analysis, permutation and bootstrap tests, thin-plate spline
19703 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19704 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19705 Edition), John Wiley and Sons.")
19706 (license license:gpl2)))
19708 (define-public r-anthropometry
19710 (name "r-anthropometry")
19715 (uri (cran-uri "Anthropometry" version))
19718 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19719 (properties `((upstream-name . "Anthropometry")))
19720 (build-system r-build-system)
19722 `(("r-archetypes" ,r-archetypes)
19723 ("r-biclust" ,r-biclust)
19724 ("r-cluster" ,r-cluster)
19725 ("r-depth" ,r-depth)
19730 ("r-shapes" ,r-shapes)))
19732 `(("r-knitr" ,r-knitr)))
19733 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19734 (synopsis "Statistical methods for anthropometric data")
19736 "This package provides statistical methods especially developed to
19737 analyze anthropometric data. These methods are aimed at providing effective
19738 solutions to some commons problems related to Ergonomics and Anthropometry.
19739 They are based on clustering, the statistical concept of data depth,
19740 statistical shape analysis and archetypal analysis.")
19741 (license license:gpl2+)))
19743 (define-public r-adamethods
19745 (name "r-adamethods")
19750 (uri (cran-uri "adamethods" version))
19753 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
19754 (properties `((upstream-name . "adamethods")))
19755 (build-system r-build-system)
19757 `(("r-anthropometry" ,r-anthropometry)
19758 ("r-archetypes" ,r-archetypes)
19760 ("r-foreach" ,r-foreach)
19762 ("r-tolerance" ,r-tolerance)
19763 ("r-univoutl" ,r-univoutl)))
19764 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19765 (synopsis "Archetypoid algorithms and anomaly detection")
19767 "This package is a collection of several algorithms to obtain
19768 archetypoids with small and large databases and with both classical
19769 multivariate data and functional data (univariate and multivariate). Some of
19770 these algorithms also allow to detect anomalies (outliers).")
19771 (license license:gpl2+)))
19773 (define-public r-idpmisc
19780 (uri (cran-uri "IDPmisc" version))
19783 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19784 (properties `((upstream-name . "IDPmisc")))
19785 (build-system r-build-system)
19787 `(("r-lattice" ,r-lattice)))
19788 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19789 (synopsis "Functions for data analyses and visualization")
19791 "This package provides different high-level graphics functions for
19792 displaying large datasets, displaying circular data in a very flexible way,
19793 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19794 2D-plots, creating figures with differently colored margin and plot region.
19795 In addition, the package contains auxiliary functions for data manipulation
19796 like omitting observations with irregular values or selecting data by logical
19797 vectors, which include NAs. Other functions are especially useful in
19798 spectroscopy and analyses of environmental data: robust baseline fitting,
19799 finding peaks in spectra, converting humidity measures.")
19800 (license license:gpl3+)))
19802 (define-public r-qqman
19809 (uri (cran-uri "qqman" version))
19812 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19813 (properties `((upstream-name . "qqman")))
19814 (build-system r-build-system)
19816 `(("r-calibrate" ,r-calibrate)))
19817 (home-page "https://cran.r-project.org/web/packages/qqman/")
19818 (synopsis "Q-Q and Manhattan plots for GWAS data")
19820 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19821 from PLINK results.")
19822 (license license:gpl3)))
19824 (define-public r-ggplot-multistats
19826 (name "r-ggplot-multistats")
19831 (uri (cran-uri "ggplot.multistats" version))
19834 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19836 `((upstream-name . "ggplot.multistats")))
19837 (build-system r-build-system)
19839 `(("r-ggplot2" ,r-ggplot2)
19840 ("r-hexbin" ,r-hexbin)
19841 ("r-rlang" ,r-rlang)
19842 ("r-scales" ,r-scales)))
19843 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19844 (synopsis "Multiple summary statistics for binned stats/geometries")
19846 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19847 which functions similar to its singular form, but allows the use of multiple
19848 statistics per bin. Those statistics can be mapped to multiple bin
19850 (license license:gpl3)))
19852 (define-public r-knn-covertree
19854 (name "r-knn-covertree")
19859 (uri (cran-uri "knn.covertree" version))
19862 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19863 (properties `((upstream-name . "knn.covertree")))
19864 (build-system r-build-system)
19866 `(("r-matrix" ,r-matrix)
19868 ("r-rcppeigen" ,r-rcppeigen)))
19869 (home-page "https://github.com/flying-sheep/knn.covertree")
19870 (synopsis "Accurate kNN Implementation with multiple distance measures")
19872 "Similarly to the FNN package, this package allows calculation of the k
19873 nearest neighbors (kNN) of a data matrix. The implementation is based on
19874 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19875 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19876 (license license:agpl3+)))
19878 (define-public r-poibin
19885 (uri (cran-uri "poibin" version))
19888 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19889 (properties `((upstream-name . "poibin")))
19890 (build-system r-build-system)
19891 (home-page "https://cran.r-project.org/web/packages/poibin/")
19892 (synopsis "Poisson binomial distribution")
19894 "This package provides an implementation of both the exact and
19895 approximation methods for computing the @dfn{cumulative distribution
19896 function} (CDF) of the Poisson binomial distribution. It also provides the
19897 @dfn{probability mass function} (PMF), quantile function, and random number
19898 generation for the Poisson binomial distribution.")
19899 (license license:gpl2)))
19901 (define-public r-diagram
19908 (uri (cran-uri "diagram" version))
19911 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19912 (properties `((upstream-name . "diagram")))
19913 (build-system r-build-system)
19915 `(("r-shape" ,r-shape)))
19916 (home-page "https://cran.r-project.org/web/packages/diagram/")
19917 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19919 "This package provides tools to visualize simple graphs (networks) based
19920 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19921 electrical networks, etc. It also includes supporting material for the book
19922 \"A practical guide to ecological modelling - using R as a simulation
19923 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19924 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19925 Francesca Mazzia (2012).")
19926 (license license:gpl2+)))
19928 (define-public r-lim
19935 (uri (cran-uri "LIM" version))
19938 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19939 (properties `((upstream-name . "LIM")))
19940 (build-system r-build-system)
19942 `(("r-diagram" ,r-diagram)
19943 ("r-limsolve" ,r-limsolve)))
19944 (home-page "https://cran.r-project.org/web/packages/LIM/")
19945 (synopsis "Linear inverse model examples and solution methods")
19947 "This package provides functions that read and solve linear inverse
19948 problems (food web problems, linear programming problems).")
19949 (license license:gpl2+)))
19951 (define-public r-shinycssloaders
19953 (name "r-shinycssloaders")
19958 (uri (cran-uri "shinycssloaders" version))
19961 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
19963 `((upstream-name . "shinycssloaders")))
19964 (build-system r-build-system)
19966 `(("r-digest" ,r-digest)
19968 ("r-shiny" ,r-shiny)))
19969 (home-page "https://github.com/andrewsali/shinycssloaders")
19970 (synopsis "Add CSS loading animations to Shiny outputs")
19972 "This package provides tools to create a lightweight Shiny wrapper for
19973 the css-loaders created by Luke Hass
19974 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19975 automatically show a loader when the output is (re)calculating.")
19976 (license license:gpl3)))
19978 (define-public r-rsvg
19985 (uri (cran-uri "rsvg" version))
19988 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19989 (properties `((upstream-name . "rsvg")))
19990 (build-system r-build-system)
19992 `(("librsvg" ,librsvg)
19995 `(("pkg-config" ,pkg-config)
19996 ("r-knitr" ,r-knitr)))
19997 (home-page "https://github.com/jeroen/rsvg#readme")
19998 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
20000 "This package allows you to render vector-based SVG images into
20001 high-quality custom-size bitmap arrays using the librsvg2 library. The
20002 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
20003 addition, the package can convert images directly to various formats such as
20004 PDF or PostScript.")
20005 (license license:expat)))
20007 (define-public r-influencer
20009 (name "r-influencer")
20014 (uri (cran-uri "influenceR" version))
20017 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
20018 (properties `((upstream-name . "influenceR")))
20019 (build-system r-build-system)
20021 `(("r-igraph" ,r-igraph)
20022 ("r-matrix" ,r-matrix)))
20023 (home-page "https://github.com/rcc-uchicago/influenceR")
20024 (synopsis "Tools to quantify structural importance of nodes in a network")
20026 "This package provides functionality to compute various node centrality
20027 measures on networks. Included are functions to compute betweenness
20028 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
20029 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
20030 algorithm to identify key players, and Valente's bridging metric. The
20031 betweenness, Key Players, and bridging implementations are parallelized with
20033 (license license:gpl2)))
20035 (define-public r-emplik
20042 (uri (cran-uri "emplik" version))
20045 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
20046 (properties `((upstream-name . "emplik")))
20047 (build-system r-build-system)
20049 `(("r-quantreg" ,r-quantreg)))
20050 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
20051 (synopsis "Empirical likelihood ratio for censored/truncated data")
20053 "This package provides empirical likelihood ratio tests for
20054 means/quantiles/hazards from possibly censored and/or truncated data. It also
20056 (license license:gpl2+)))
20058 (define-public r-imputeyn
20060 (name "r-imputeyn")
20065 (uri (cran-uri "imputeYn" version))
20068 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
20069 (properties `((upstream-name . "imputeYn")))
20070 (build-system r-build-system)
20072 `(("r-boot" ,r-boot)
20073 ("r-emplik" ,r-emplik)
20074 ("r-mvtnorm" ,r-mvtnorm)
20075 ("r-quadprog" ,r-quadprog)
20076 ("r-survival" ,r-survival)))
20077 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
20078 (synopsis "Impute last largest censored observation under weighted least squares")
20080 "This package allows for the imputation of the last largest censored
20081 observantions. This method brings less bias and more efficient estimates for
20083 (license license:gpl2)))
20085 (define-public r-adapenetclass
20087 (name "r-adapenetclass")
20092 (uri (cran-uri "AdapEnetClass" version))
20095 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
20096 (properties `((upstream-name . "AdapEnetClass")))
20097 (build-system r-build-system)
20099 `(("r-glmnet" ,r-glmnet)
20100 ("r-imputeyn" ,r-imputeyn)
20102 ("r-quadprog" ,r-quadprog)))
20103 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
20104 (synopsis "Class of adaptive elastic net methods for censored data")
20106 "This package provides methods for variable selection for AFT models.")
20107 (license license:gpl2)))
20109 (define-public r-flock
20116 (uri (cran-uri "flock" version))
20119 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
20120 (properties `((upstream-name . "flock")))
20121 (build-system r-build-system)
20122 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
20123 (home-page "https://cran.r-project.org/web/packages/flock/")
20124 (synopsis "Process synchronization using file locks")
20126 "This package implements synchronization between R processes (spawned by
20127 using the @code{parallel} package for instance) using file locks. It supports
20128 both exclusive and shared locking.")
20129 (license license:asl2.0)))
20131 (define-public r-archivist
20133 (name "r-archivist")
20138 (uri (cran-uri "archivist" version))
20141 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
20142 (properties `((upstream-name . "archivist")))
20143 (build-system r-build-system)
20146 ("r-digest" ,r-digest)
20147 ("r-flock" ,r-flock)
20149 ("r-lubridate" ,r-lubridate)
20150 ("r-magrittr" ,r-magrittr)
20151 ("r-rcurl" ,r-rcurl)
20152 ("r-rsqlite" ,r-rsqlite)))
20153 (home-page "https://pbiecek.github.io/archivist/")
20154 (synopsis "Tools for storing, restoring and searching for R objects")
20156 "Data exploration and modelling is a process in which a lot of data
20157 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
20158 statistical models, different versions of data sets and different versions of
20159 results. Archivist helps to store and manage artifacts created in R. It
20160 allows you to store selected artifacts as binary files together with their
20161 metadata and relations. Archivist allows sharing artifacts with others. It
20162 can look for already created artifacts by using its class, name, date of the
20163 creation or other properties. It also makes it easy to restore such
20165 (license license:gpl2)))
20167 (define-public r-versions
20169 (name "r-versions")
20174 (uri (cran-uri "versions" version))
20177 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
20178 (properties `((upstream-name . "versions")))
20179 (build-system r-build-system)
20180 (home-page "https://cran.r-project.org/web/packages/versions/")
20181 (synopsis "Query and install specific versions of CRAN packages")
20183 "This package allows you to install specified versions of R packages
20184 hosted on CRAN and provides functions to list available versions and the
20185 versions of currently installed packages.")
20186 (license license:bsd-3)))
20188 (define-public r-adapr
20195 (uri (cran-uri "adapr" version))
20198 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
20199 (properties `((upstream-name . "adapr")))
20200 (build-system r-build-system)
20202 `(("r-archivist" ,r-archivist)
20203 ("r-devtools" ,r-devtools)
20204 ("r-digest" ,r-digest)
20205 ("r-doparallel" ,r-doparallel)
20206 ("r-gdata" ,r-gdata)
20207 ("r-ggplot2" ,r-ggplot2)
20208 ("r-git2r" ,r-git2r)
20209 ("r-igraph" ,r-igraph)
20210 ("r-knitr" ,r-knitr)
20211 ("r-plotly" ,r-plotly)
20213 ("r-rmarkdown" ,r-rmarkdown)
20214 ("r-shiny" ,r-shiny)
20215 ("r-shinydashboard" ,r-shinydashboard)
20216 ("r-versions" ,r-versions)))
20217 (home-page "https://cran.r-project.org/web/packages/adapr/")
20218 (synopsis "Implementation of an accountable data analysis process")
20220 "This package tracks reading and writing within R scripts that are
20221 organized into a directed acyclic graph. It contains an interactive Shiny
20222 application @code{adaprApp()}. It uses Git and file hashes to track version
20223 histories of inputs and outputs.")
20224 (license license:lgpl2.0)))
20226 (define-public r-adapsamp
20228 (name "r-adapsamp")
20233 (uri (cran-uri "AdapSamp" version))
20236 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20237 (properties `((upstream-name . "AdapSamp")))
20238 (build-system r-build-system)
20239 (propagated-inputs `(("r-pracma" ,r-pracma)))
20240 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20241 (synopsis "Adaptive sampling algorithms")
20243 "For distributions whose probability density functions are log-concave,
20244 the adaptive rejection sampling algorithm can be used to build envelope
20245 functions for sampling. For others, the modified adaptive rejection sampling
20246 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20247 adaptive slice sampling algorithm can be used. This R package mainly includes
20248 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20249 @code{rASS()}. These functions can realize sampling based on the algorithms
20251 (license license:gpl2)))
20253 (define-public r-adaptalint
20255 (name "r-adaptalint")
20260 (uri (cran-uri "adaptalint" version))
20263 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20264 (properties `((upstream-name . "adaptalint")))
20265 (build-system r-build-system)
20267 `(("r-dplyr" ,r-dplyr)
20268 ("r-lintr" ,r-lintr)
20269 ("r-purrr" ,r-purrr)))
20270 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20271 (synopsis "Check R code style")
20273 "This package provides tools to infer the code style (which style rules
20274 are followed and which ones are not) from one package and use it to check
20275 another. This makes it easier to find and correct the most important problems
20277 (license license:gpl3)))
20279 (define-public r-fracdiff
20281 (name "r-fracdiff")
20286 (uri (cran-uri "fracdiff" version))
20289 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20290 (properties `((upstream-name . "fracdiff")))
20291 (build-system r-build-system)
20292 (home-page "https://github.com/mmaechler/fracdiff")
20294 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20296 "This package provides tools for the maximum likelihood estimation of the
20297 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20298 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20299 (license license:gpl2+)))
20301 (define-public r-forecast
20303 (name "r-forecast")
20308 (uri (cran-uri "forecast" version))
20311 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20312 (properties `((upstream-name . "forecast")))
20313 (build-system r-build-system)
20315 `(("r-colorspace" ,r-colorspace)
20316 ("r-fracdiff" ,r-fracdiff)
20317 ("r-ggplot2" ,r-ggplot2)
20318 ("r-lmtest" ,r-lmtest)
20319 ("r-magrittr" ,r-magrittr)
20322 ("r-rcpparmadillo" ,r-rcpparmadillo)
20323 ("r-timedate" ,r-timedate)
20324 ("r-tseries" ,r-tseries)
20328 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20329 (home-page "https://pkg.robjhyndman.com/forecast/")
20330 (synopsis "Forecasting functions for time series and linear models")
20332 "This package provides methods and tools for displaying and analysing
20333 univariate time series forecasts including exponential smoothing via state
20334 space models and automatic ARIMA modelling.")
20335 (license license:gpl3)))
20337 (define-public r-xmisc
20344 (uri (cran-uri "Xmisc" version))
20347 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20348 (properties `((upstream-name . "Xmisc")))
20349 (build-system r-build-system)
20350 (home-page "https://cran.r-project.org/package=Xmisc")
20352 "Xiaobei's miscellaneous classes and functions")
20354 "This package provides Xiaobei's miscellaneous classes and functions,
20355 which are useful when developing R packages for @dfn{object oriented
20356 programming} (OOP) using R Reference Class.")
20357 (license license:gpl2+)))
20359 (define-public r-proxyc
20366 (uri (cran-uri "proxyC" version))
20369 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20370 (properties `((upstream-name . "proxyC")))
20371 (build-system r-build-system)
20373 `(("r-matrix" ,r-matrix)
20375 ("r-rcpparmadillo" ,r-rcpparmadillo)
20376 ("r-rcppparallel" ,r-rcppparallel)))
20377 (home-page "https://cran.r-project.org/package=proxyC")
20378 (synopsis "Compute proximity in large sparse matrices")
20380 "This package provides efficient tools to compute the proximity between
20381 rows or columns of large matrices. Functions are optimised for large sparse
20382 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20383 similarity/distance measures, computation of correlation, cosine similarity
20384 and Euclidean distance is particularly fast.")
20385 (license license:gpl3)))
20387 (define-public r-isocodes
20389 (name "r-isocodes")
20390 (version "2020.03.16")
20394 (uri (cran-uri "ISOcodes" version))
20397 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20398 (properties `((upstream-name . "ISOcodes")))
20399 (build-system r-build-system)
20400 (home-page "https://cran.r-project.org/package=ISOcodes")
20401 (synopsis "Selected ISO codes")
20403 "This package provides ISO language, territory, currency, script and
20404 character codes. It provides ISO 639 language codes, ISO 3166 territory
20405 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20406 character codes as well as the UN M.49 area codes.")
20407 (license license:gpl2)))
20409 (define-public r-stopwords
20411 (name "r-stopwords")
20416 (uri (cran-uri "stopwords" version))
20419 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20420 (properties `((upstream-name . "stopwords")))
20421 (build-system r-build-system)
20423 `(("r-desc" ,r-desc)
20424 ("r-isocodes" ,r-isocodes)
20425 ("r-usethis" ,r-usethis)))
20426 (home-page "https://github.com/quanteda/stopwords")
20427 (synopsis "Multilingual stopword lists")
20429 "This package provides multiple sources of stopwords, for use in text
20430 analysis and natural language processing.")
20431 (license license:expat)))
20433 (define-public r-spacyr
20440 (uri (cran-uri "spacyr" version))
20443 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20444 (properties `((upstream-name . "spacyr")))
20445 (build-system r-build-system)
20447 `(("r-data-table" ,r-data-table)
20448 ("r-reticulate" ,r-reticulate)))
20449 (home-page "https://spacyr.quanteda.io")
20450 (synopsis "R wrapper for the spaCy NLP library")
20452 "This package provides an R wrapper to the Python @dfn{natural language
20453 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20454 (license license:gpl3)))
20456 (define-public r-snowballc
20458 (name "r-snowballc")
20463 (uri (cran-uri "SnowballC" version))
20466 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20467 (properties `((upstream-name . "SnowballC")))
20468 (build-system r-build-system)
20469 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20470 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20472 "This package provides an R interface to the C @code{libstemmer} library
20473 that implements Porter's word stemming algorithm for collapsing words to a
20474 common root to aid comparison of vocabulary. Currently supported languages
20475 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20476 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20477 (license license:bsd-3)))
20479 (define-public r-quanteda
20481 (name "r-quanteda")
20486 (uri (cran-uri "quanteda" version))
20489 "1wlrd7g2b459pnkqhihxhn74f37py1c9pxrdzp5xzp4mnbdxcsj8"))))
20490 (properties `((upstream-name . "quanteda")))
20491 (build-system r-build-system)
20493 `(("r-data-table" ,r-data-table)
20494 ("r-digest" ,r-digest)
20495 ("r-extrafont" ,r-extrafont)
20496 ("r-fastmatch" ,r-fastmatch)
20497 ("r-ggplot2" ,r-ggplot2)
20498 ("r-ggrepel" ,r-ggrepel)
20499 ("r-jsonlite" ,r-jsonlite)
20500 ("r-magrittr" ,r-magrittr)
20501 ("r-matrix" ,r-matrix)
20502 ("r-network" ,r-network)
20503 ("r-proxyc" ,r-proxyc)
20505 ("r-rcpparmadillo" ,r-rcpparmadillo)
20506 ("r-rcppparallel" ,r-rcppparallel)
20508 ("r-snowballc" ,r-snowballc)
20509 ("r-stopwords" ,r-stopwords)
20510 ("r-stringi" ,r-stringi)
20512 ("r-yaml" ,r-yaml)))
20514 `(("r-knitr" ,r-knitr)))
20515 (home-page "https://quanteda.io")
20516 (synopsis "Quantitative analysis of textual data")
20518 "This package provides a fast, flexible, and comprehensive framework for
20519 quantitative text analysis in R. It provides functionality for corpus
20520 management, creating and manipulating tokens and ngrams, exploring keywords in
20521 context, forming and manipulating sparse matrices of documents by features and
20522 feature co-occurrences, analyzing keywords, computing feature similarities and
20523 distances, applying content dictionaries, applying supervised and unsupervised
20524 machine learning, visually representing text and text analyses, and more.")
20525 (license license:gpl3)))
20527 (define-public r-topicmodels
20529 (name "r-topicmodels")
20534 (uri (cran-uri "topicmodels" version))
20537 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20538 (properties `((upstream-name . "topicmodels")))
20539 (build-system r-build-system)
20543 `(("r-modeltools" ,r-modeltools)
20546 (home-page "https://cran.r-project.org/package=topicmodels")
20547 (synopsis "Topic models")
20549 "This package provides an interface to the C code for @dfn{Latent
20550 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20551 David M. Blei and co-authors and the C++ code for fitting LDA models using
20552 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20553 (license license:gpl2)))
20555 (define-public r-stm
20562 (uri (cran-uri "stm" version))
20565 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20566 (properties `((upstream-name . "stm")))
20567 (build-system r-build-system)
20569 `(("r-data-table" ,r-data-table)
20570 ("r-glmnet" ,r-glmnet)
20572 ("r-matrix" ,r-matrix)
20573 ("r-matrixstats" ,r-matrixstats)
20574 ("r-quadprog" ,r-quadprog)
20575 ("r-quanteda" ,r-quanteda)
20577 ("r-rcpparmadillo" ,r-rcpparmadillo)
20579 ("r-stringr" ,r-stringr)))
20580 (home-page "http://www.structuraltopicmodel.com/")
20581 (synopsis "Estimation of the Structural Topic Model")
20583 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20584 topic models with document-level covariates. The package also includes tools
20585 for model selection, visualization, and estimation of topic-covariate
20587 (license license:expat)))
20589 (define-public r-polycor
20596 (uri (cran-uri "polycor" version))
20599 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20600 (properties `((upstream-name . "polycor")))
20601 (build-system r-build-system)
20603 `(("r-matrix" ,r-matrix)
20604 ("r-mvtnorm" ,r-mvtnorm)))
20605 (home-page "https://r-forge.r-project.org/projects/polycor/")
20606 (synopsis "Polychoric and polyserial correlations")
20608 "This package provides tools to compute polychoric and polyserial
20609 correlations by quick \"two-step\" methods or ML, optionally with standard
20610 errors; tetrachoric and biserial correlations are special cases.")
20611 (license license:gpl2+)))
20613 (define-public r-msm
20620 (uri (cran-uri "msm" version))
20623 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20624 (properties `((upstream-name . "msm")))
20625 (build-system r-build-system)
20627 `(("r-expm" ,r-expm)
20628 ("r-mvtnorm" ,r-mvtnorm)
20629 ("r-survival" ,r-survival)))
20630 (home-page "https://github.com/chjackson/msm")
20631 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20633 "This package provides functions for fitting continuous-time Markov and
20634 hidden Markov multi-state models to longitudinal data. It was designed for
20635 processes observed at arbitrary times in continuous time (panel data) but some
20636 other observation schemes are supported. Both Markov transition rates and the
20637 hidden Markov output process can be modelled in terms of covariates, which may
20638 be constant or piecewise-constant in time.")
20639 (license license:gpl2+)))
20641 (define-public r-ltm
20648 (uri (cran-uri "ltm" version))
20651 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20652 (properties `((upstream-name . "ltm")))
20653 (build-system r-build-system)
20655 `(("r-mass" ,r-mass)
20657 ("r-polycor" ,r-polycor)))
20658 (home-page "https://github.com/drizopoulos/ltm")
20659 (synopsis "Latent trait models under IRT")
20661 "This is a package supporting the analysis of multivariate dichotomous
20662 and polytomous data using latent trait models under the Item Response Theory
20663 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20664 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20666 (license license:gpl2+)))
20668 (define-public r-mi
20675 (uri (cran-uri "mi" version))
20678 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20679 (properties `((upstream-name . "mi")))
20680 (build-system r-build-system)
20683 ("r-matrix" ,r-matrix)))
20684 (home-page "http://www.stat.columbia.edu/~gelman/")
20685 (synopsis "Missing data imputation and model checking")
20687 "This package provides functions for data manipulation, imputing missing
20688 values in an approximate Bayesian framework, diagnostics of the models used to
20689 generate the imputations, confidence-building mechanisms to validate some of
20690 the assumptions of the imputation algorithm, and functions to analyze multiply
20691 imputed data sets with the appropriate degree of sampling uncertainty.")
20692 (license license:gpl2+)))
20694 (define-public r-matrixcalc
20696 (name "r-matrixcalc")
20701 (uri (cran-uri "matrixcalc" version))
20704 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20705 (properties `((upstream-name . "matrixcalc")))
20706 (build-system r-build-system)
20707 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20708 (synopsis "Collection of functions for matrix calculations")
20710 "This package provides a collection of functions to support matrix
20711 calculations for probability, econometric and numerical analysis. There are
20712 additional functions that are comparable to APL functions which are useful for
20713 actuarial models such as pension mathematics.")
20714 (license license:gpl2+)))
20716 (define-public r-sem
20723 (uri (cran-uri "sem" version))
20726 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20727 (properties `((upstream-name . "sem")))
20728 (build-system r-build-system)
20730 `(("r-boot" ,r-boot)
20732 ("r-matrixcalc" ,r-matrixcalc)
20734 (home-page "https://cran.r-project.org/package=sem")
20735 (synopsis "Structural equation models")
20737 "This package provides functions for fitting general linear structural
20738 equation models (with observed and latent variables) using the RAM approach,
20739 and for fitting structural equations in observed-variable models by two-stage
20741 (license license:gpl2+)))
20743 (define-public r-semtools
20745 (name "r-semtools")
20750 (uri (cran-uri "semTools" version))
20753 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20754 (properties `((upstream-name . "semTools")))
20755 (build-system r-build-system)
20757 `(("r-lavaan" ,r-lavaan)))
20758 (home-page "https://github.com/simsem/semTools/wiki")
20759 (synopsis "Useful tools for structural equation modeling")
20761 "This package provides useful tools for structural equation modeling.")
20762 (license license:gpl2+)))
20764 (define-public r-regsem
20771 (uri (cran-uri "regsem" version))
20774 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20775 (properties `((upstream-name . "regsem")))
20776 (build-system r-build-system)
20778 `(("r-lavaan" ,r-lavaan)
20780 ("r-rcpparmadillo" ,r-rcpparmadillo)
20781 ("r-rsolnp" ,r-rsolnp)))
20782 (home-page "https://cran.r-project.org/package=regsem")
20783 (synopsis "Regularized structural equation modeling")
20785 "This package uses both ridge and lasso penalties (and extensions) to
20786 penalize specific parameters in structural equation models. The package
20787 offers additional cost functions, cross validation, and other extensions
20788 beyond traditional structural equation models. It also contains a function to
20789 perform @dfn{exploratory mediation} (XMed).")
20790 (license license:gpl2+)))
20792 (define-public r-stanheaders
20794 (name "r-stanheaders")
20795 (version "2.21.0-6")
20799 (uri (cran-uri "StanHeaders" version))
20802 "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50"))))
20803 (properties `((upstream-name . "StanHeaders")))
20804 (build-system r-build-system)
20805 (inputs `(("pandoc" ,pandoc)))
20807 `(("r-rcppeigen" ,r-rcppeigen)
20808 ("r-rcppparallel" ,r-rcppparallel)))
20810 `(("gfortran" ,gfortran)
20811 ("r-knitr" ,r-knitr))) ; for vignettes
20812 (home-page "https://mc-stan.org/")
20813 (synopsis "C++ header files for Stan")
20815 "The C++ header files of the Stan project are provided by this package.
20816 There is a shared object containing part of the @code{CVODES} library, but it
20817 is not accessible from R. @code{r-stanheaders} is only useful for developers
20818 who want to utilize the @code{LinkingTo} directive of their package's
20819 DESCRIPTION file to build on the Stan library without incurring unnecessary
20822 The Stan project develops a probabilistic programming language that implements
20823 full or approximate Bayesian statistical inference via Markov Chain Monte
20824 Carlo or variational methods and implements (optionally penalized) maximum
20825 likelihood estimation via optimization. The Stan library includes an advanced
20826 automatic differentiation scheme, templated statistical and linear algebra
20827 functions that can handle the automatically differentiable scalar types (and
20828 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20829 package provides user-facing R functions to parse, compile, test, estimate,
20830 and analyze Stan models.")
20831 (license license:bsd-3)))
20833 (define-public r-rpf
20840 (uri (cran-uri "rpf" version))
20843 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20844 (properties `((upstream-name . "rpf")))
20845 (build-system r-build-system)
20847 `(("r-lifecycle" ,r-lifecycle)
20848 ("r-mvtnorm" ,r-mvtnorm)
20850 ("r-rcppeigen" ,r-rcppeigen)))
20852 `(("r-knitr" ,r-knitr)))
20853 (home-page "https://github.com/jpritikin/rpf")
20854 (synopsis "Response probability functions")
20856 "The purpose of this package is to factor out logic and math common to
20857 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20858 core support code suitable for more specialized IRT packages to build upon.
20859 Complete access to optimized C functions is made available with
20860 @code{R_RegisterCCallable()}.")
20861 (license license:gpl3+)))
20863 (define-public r-openmx
20870 (uri (cran-uri "OpenMx" version))
20873 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
20874 (properties `((upstream-name . "OpenMx")))
20875 (build-system r-build-system)
20878 ("r-digest" ,r-digest)
20879 ("r-lifecycle" ,r-lifecycle)
20881 ("r-matrix" ,r-matrix)
20883 ("r-rcppeigen" ,r-rcppeigen)
20885 ("r-stanheaders" ,r-stanheaders)))
20886 (native-inputs `(("gfortran" ,gfortran)))
20887 (home-page "http://openmx.ssri.psu.edu")
20888 (synopsis "Extended structural equation modelling")
20890 "This package allows for the estimation of a wide variety of advanced
20891 multivariate statistical models. It consists of a library of functions and
20892 optimizers that allow you to quickly and flexibly define an SEM model and
20893 estimate parameters given observed data.")
20894 (license license:asl2.0)))
20896 (define-public r-kutils
20903 (uri (cran-uri "kutils" version))
20906 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20907 (properties `((upstream-name . "kutils")))
20908 (build-system r-build-system)
20910 `(("r-foreign" ,r-foreign)
20911 ("r-openxlsx" ,r-openxlsx)
20913 ("r-runit" ,r-runit)
20914 ("r-xtable" ,r-xtable)))
20915 (home-page "https://cran.r-project.org/package=kutils")
20916 (synopsis "Project management tools")
20918 "This package provides tools for data importation, recoding, and
20919 inspection. There are functions to create new project folders, R code
20920 templates, create uniquely named output directories, and to quickly obtain a
20921 visual summary for each variable in a data frame. The main feature here is
20922 the systematic implementation of the \"variable key\" framework for data
20923 importation and recoding.")
20924 (license license:gpl2)))
20926 (define-public r-rockchalk
20928 (name "r-rockchalk")
20929 (version "1.8.144")
20933 (uri (cran-uri "rockchalk" version))
20936 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20937 (properties `((upstream-name . "rockchalk")))
20938 (build-system r-build-system)
20940 `(("r-cardata" ,r-cardata)
20941 ("r-kutils" ,r-kutils)
20943 ("r-mass" ,r-mass)))
20944 (home-page "https://cran.r-project.org/package=rockchalk")
20945 (synopsis "Regression estimation and presentation")
20947 "This package provides a collection of functions for interpretation and
20948 presentation of regression analysis. These functions are used to produce the
20949 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20950 includes regression diagnostics, regression tables, and plots of interactions
20951 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20952 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20953 fairly comprehensive overview.")
20954 (license license:gpl3+)))
20956 (define-public r-lisreltor
20958 (name "r-lisreltor")
20963 (uri (cran-uri "lisrelToR" version))
20966 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20967 (properties `((upstream-name . "lisrelToR")))
20968 (build-system r-build-system)
20969 (home-page "https://cran.r-project.org/package=lisrelToR")
20970 (synopsis "Import output from LISREL into R")
20972 "This is an unofficial package aimed at automating the import of LISREL
20974 (license license:gpl2)))
20976 (define-public r-bdgraph
20983 (uri (cran-uri "BDgraph" version))
20986 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
20987 (properties `((upstream-name . "BDgraph")))
20988 (build-system r-build-system)
20990 `(("r-igraph" ,r-igraph)))
20991 (home-page "https://www.uva.nl/profile/a.mohammadi")
20992 (synopsis "Bayesian structure learning in graphical models")
20994 "This package provides statistical tools for Bayesian structure learning
20995 in undirected graphical models for continuous, discrete, and mixed data. It
20996 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20997 on a continuous-time birth-death process.")
20998 (license license:gpl2+)))
21000 (define-public r-d3network
21002 (name "r-d3network")
21003 (version "0.5.2.1")
21007 (uri (cran-uri "d3Network" version))
21010 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
21011 (properties `((upstream-name . "d3Network")))
21012 (build-system r-build-system)
21014 `(("r-plyr" ,r-plyr)
21015 ("r-rjson" ,r-rjson)
21016 ("r-whisker" ,r-whisker)))
21017 (home-page "http://christophergandrud.github.io/d3Network/")
21018 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
21020 "This package is intended to make it easy to create D3 JavaScript
21021 network, tree, dendrogram, and Sankey graphs from R using data frames.")
21022 (license license:gpl3+)))
21024 (define-public r-qgraph
21031 (uri (cran-uri "qgraph" version))
21034 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
21035 (properties `((upstream-name . "qgraph")))
21036 (build-system r-build-system)
21038 `(("r-abind" ,r-abind)
21039 ("r-bdgraph" ,r-bdgraph)
21040 ("r-colorspace" ,r-colorspace)
21041 ("r-corpcor" ,r-corpcor)
21042 ("r-d3network" ,r-d3network)
21043 ("r-dplyr" ,r-dplyr)
21044 ("r-fdrtool" ,r-fdrtool)
21045 ("r-ggplot2" ,r-ggplot2)
21046 ("r-ggraph" ,r-ggraph)
21047 ("r-glasso" ,r-glasso)
21048 ("r-gtools" ,r-gtools)
21049 ("r-hmisc" ,r-hmisc)
21051 ("r-igraph" ,r-igraph)
21053 ("r-lavaan" ,r-lavaan)
21054 ("r-matrix" ,r-matrix)
21055 ("r-pbapply" ,r-pbapply)
21058 ("r-psych" ,r-psych)
21060 ("r-reshape2" ,r-reshape2)
21061 ("r-tidygraph" ,r-tidygraph)))
21062 (home-page "http://sachaepskamp.com/qgraph/")
21063 (synopsis "Weighted network visualization and analysis")
21065 "This package implements tools for weighted network visualization and
21066 analysis, as well as Gaussian graphical model computation. It contains graph
21067 plotting methods, and tools for psychometric data visualization and graphical
21068 model estimation. See Epskamp et al. (2012)
21069 @url{doi:10.18637/jss.v048.i04}.")
21070 (license license:gpl2)))
21072 (define-public r-semplot
21079 (uri (cran-uri "semPlot" version))
21082 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
21083 (properties `((upstream-name . "semPlot")))
21084 (build-system r-build-system)
21086 `(("r-colorspace" ,r-colorspace)
21087 ("r-corpcor" ,r-corpcor)
21088 ("r-igraph" ,r-igraph)
21089 ("r-lavaan" ,r-lavaan)
21090 ("r-lisreltor" ,r-lisreltor)
21091 ("r-openmx" ,r-openmx)
21093 ("r-qgraph" ,r-qgraph)
21094 ("r-regsem" ,r-regsem)
21095 ("r-rockchalk" ,r-rockchalk)
21098 (home-page "https://github.com/SachaEpskamp/semPlot")
21099 (synopsis "Unified visualizations of structural equation models")
21101 "Structural equation modeling (SEM) has a long history of representing
21102 models graphically as path diagrams. The semPlot package for R fills the gap
21103 between advanced, but time-consuming, graphical software and the limited
21104 graphics produced automatically by SEM software. In addition, semPlot offers
21105 more functionality than drawing path diagrams: it can act as a common ground
21106 for importing SEM results into R. Any result usable as input to semPlot can
21107 also be represented in any of the three popular SEM frame-works, as well as
21108 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
21109 (license license:gpl2)))
21111 (define-public r-cdm
21118 (uri (cran-uri "CDM" version))
21121 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
21122 (properties `((upstream-name . "CDM")))
21123 (build-system r-build-system)
21125 `(("r-mvtnorm" ,r-mvtnorm)
21126 ("r-polycor" ,r-polycor)
21128 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21130 "https://github.com/alexanderrobitzsch/CDM")
21131 (synopsis "Cognitive diagnosis modeling")
21133 "This package provides functions for cognitive diagnosis modeling and
21134 multidimensional item response modeling for dichotomous and polytomous item
21135 responses. It enables the estimation of the DINA and DINO model, the multiple
21136 group (polytomous) GDINA model, the multiple choice DINA model, the general
21137 diagnostic model (GDM), the structured latent class model (SLCA), and
21138 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
21139 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
21140 estimation and the package structure. For tutorials on how to use the CDM
21141 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
21142 well as Ravand and Robitzsch (2015).")
21143 (license license:gpl2+)))
21145 (define-public r-tam
21152 (uri (cran-uri "TAM" version))
21155 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
21156 (properties `((upstream-name . "TAM")))
21157 (build-system r-build-system)
21161 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21162 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
21163 (synopsis "Test analysis modules")
21165 "This package includes tools for marginal maximum likelihood estimation
21166 and joint maximum likelihood estimation for unidimensional and
21167 multidimensional item response models. The package functionality covers the
21168 Rasch model, 2PL model, 3PL model, generalized partial credit model,
21169 multi-faceted Rasch model, nominal item response model, structured latent
21170 class model, mixture distribution IRT models, and located latent class models.
21171 Latent regression models and plausible value imputation are also supported.")
21172 (license license:gpl2+)))
21174 (define-public r-erm
21181 (uri (cran-uri "eRm" version))
21184 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
21185 (properties `((upstream-name . "eRm")))
21186 (build-system r-build-system)
21188 `(("r-colorspace" ,r-colorspace)
21189 ("r-lattice" ,r-lattice)
21191 ("r-matrix" ,r-matrix)
21192 ("r-psych" ,r-psych)))
21193 (native-inputs `(("gfortran" ,gfortran)))
21194 (home-page "https://cran.r-project.org/package=eRm")
21195 (synopsis "Extended Rasch modeling")
21197 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
21198 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
21199 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
21200 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
21201 data matrix. Additional features are the ML estimation of the person
21202 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
21203 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
21204 infit and outfit measures, ICC and other plots, automated stepwise item
21205 elimination, and a simulation module for various binary data matrices.")
21206 (license license:gpl3)))
21208 (define-public r-irtoys
21215 (uri (cran-uri "irtoys" version))
21218 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
21219 (properties `((upstream-name . "irtoys")))
21220 (build-system r-build-system)
21224 (home-page "https://cran.r-project.org/package=irtoys")
21225 (synopsis "Collection of functions related to Item Response Theory (IRT)")
21227 "This package provides a collection of functions useful in learning and
21228 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
21229 programs. It provides basic CTT analysis, a simple common interface to the
21230 estimation of item parameters in IRT models for binary responses with three
21231 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
21232 EAP, WLE, plausible values), item and person fit statistics, scaling
21233 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21234 array of parametric and non-parametric (kernel) plots. It estimates and plots
21235 Haberman's interaction model when all items are dichotomously scored.")
21236 (license license:gpl2+)))
21238 (define-public r-iheatmapr
21240 (name "r-iheatmapr")
21245 (uri (cran-uri "iheatmapr" version))
21248 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21249 (properties `((upstream-name . "iheatmapr")))
21250 (build-system r-build-system)
21252 `(("r-fastcluster" ,r-fastcluster)
21253 ("r-ggdendro" ,r-ggdendro)
21254 ("r-htmlwidgets" ,r-htmlwidgets)
21255 ("r-jsonlite" ,r-jsonlite)
21256 ("r-knitr" ,r-knitr)
21257 ("r-magrittr" ,r-magrittr)
21258 ("r-rcolorbrewer" ,r-rcolorbrewer)
21259 ("r-scales" ,r-scales)))
21261 `(("r-knitr" ,r-knitr)))
21262 (home-page "https://docs.ropensci.org/iheatmapr")
21263 (synopsis "Interactive, Complex Heatmaps")
21265 "iheatmapr is an R package for building complex, interactive heatmaps
21266 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21267 subplots along the rows or columns of the main heatmap add more information
21268 about each row or column. For example, a one column additional heatmap may
21269 indicate what group a particular row or column belongs to. Complex heatmaps
21270 may also include multiple side by side heatmaps which show different types of
21271 data for the same conditions. Interactivity can improve complex heatmaps by
21272 providing tooltips with information about each cell and enabling zooming into
21273 interesting features. iheatmapr uses the plotly library for interactivity.")
21274 (license license:expat)))
21276 (define-public r-packrat
21283 (uri (cran-uri "packrat" version))
21286 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21287 (properties `((upstream-name . "packrat")))
21288 (build-system r-build-system)
21289 (home-page "https://github.com/rstudio/packrat/")
21290 (synopsis "Dependency management R projects")
21292 "This package provides a dependency manager for R projects that allows
21293 you to manage the R packages your project depends on in an isolated, portable,
21294 and reproducible way.")
21295 (license license:gpl2)))
21297 (define-public r-rsconnect
21299 (name "r-rsconnect")
21304 (uri (cran-uri "rsconnect" version))
21307 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21308 (properties `((upstream-name . "rsconnect")))
21309 (build-system r-build-system)
21311 `(("r-curl" ,r-curl)
21312 ("r-digest" ,r-digest)
21313 ("r-jsonlite" ,r-jsonlite)
21314 ("r-openssl" ,r-openssl)
21315 ("r-packrat" ,r-packrat)
21316 ("r-rstudioapi" ,r-rstudioapi)
21317 ("r-yaml" ,r-yaml)))
21318 (home-page "https://github.com/rstudio/rsconnect")
21319 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21321 "This package provides a programmatic deployment interface for RPubs,
21322 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21323 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21324 (license license:gpl2)))
21326 ;; This package includes minified JavaScript files. When upgrading please
21327 ;; check that there are no new minified JavaScript files.
21328 (define-public r-dygraphs
21330 (name "r-dygraphs")
21331 (version "1.1.1.6")
21335 (uri (cran-uri "dygraphs" version))
21338 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21339 (properties `((upstream-name . "dygraphs")))
21340 (build-system r-build-system)
21342 `(#:modules ((guix build utils)
21343 (guix build r-build-system)
21347 (modify-phases %standard-phases
21348 (add-after 'unpack 'process-javascript
21349 (lambda* (#:key inputs #:allow-other-keys)
21350 (with-directory-excursion "inst/htmlwidgets/lib/"
21354 `(("dygraphs/dygraph-combined-dev.js"
21355 "dygraph-combined.js")
21356 (,(assoc-ref inputs "js-jquery")
21357 "jquery/jquery.min.js")
21358 (,(assoc-ref inputs "js-fquarter")
21359 "fquarter/moment-fquarter.min.js"))))
21360 (lambda (sources targets)
21361 (for-each (lambda (source target)
21362 (format #t "Processing ~a --> ~a~%"
21364 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21365 (call-with-output-file target
21367 (dump-port minified port)))))
21368 sources targets))))
21371 `(("uglify-js" ,uglify-js)
21372 ;; They actually use version 1.11.1, but this more recent version
21373 ;; should be just fine.
21377 (uri "https://code.jquery.com/jquery-1.12.4.js")
21380 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21384 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21385 "moment-fquarter/1.0.1/moment-fquarter.js"))
21388 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21390 `(("r-htmltools" ,r-htmltools)
21391 ("r-htmlwidgets" ,r-htmlwidgets)
21392 ("r-magrittr" ,r-magrittr)
21395 (home-page "https://github.com/rstudio/dygraphs")
21396 (synopsis "Interface to Dygraphs interactive time series charting library")
21398 "This package provides an R interface to the dygraphs JavaScript charting
21399 library (a copy of which is included in the package). It provides rich
21400 facilities for charting time-series data in R, including highly configurable
21401 series- and axis-display and interactive features like zoom/pan and
21402 series/point highlighting.")
21403 (license license:expat)))
21405 (define-public r-shinystan
21407 (name "r-shinystan")
21412 (uri (cran-uri "shinystan" version))
21415 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21416 (properties `((upstream-name . "shinystan")))
21417 (build-system r-build-system)
21419 `(("r-bayesplot" ,r-bayesplot)
21420 ("r-colourpicker" ,r-colourpicker)
21422 ("r-dygraphs" ,r-dygraphs)
21423 ("r-ggplot2" ,r-ggplot2)
21424 ("r-gridextra" ,r-gridextra)
21425 ("r-gtools" ,r-gtools)
21426 ("r-markdown" ,r-markdown)
21427 ("r-reshape2" ,r-reshape2)
21428 ("r-rsconnect" ,r-rsconnect)
21429 ("r-rstan" ,r-rstan)
21430 ("r-shiny" ,r-shiny)
21431 ("r-shinyjs" ,r-shinyjs)
21432 ("r-shinythemes" ,r-shinythemes)
21433 ("r-threejs" ,r-threejs)
21434 ("r-xtable" ,r-xtable)
21436 (home-page "https://mc-stan.org/")
21437 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21439 "This package provides a graphical user interface for interactive
21440 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21441 for analyzing a posterior sample. The interface is powered by the Shiny web
21442 application framework and works with the output of MCMC programs written in
21443 any programming language (and has extended functionality for Stan models fit
21444 using the @code{rstan} and @code{rstanarm} packages).")
21445 (license license:gpl3+)))
21447 (define-public r-rstantools
21449 (name "r-rstantools")
21454 (uri (cran-uri "rstantools" version))
21457 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21458 (properties `((upstream-name . "rstantools")))
21459 (build-system r-build-system)
21460 (inputs `(("pandoc" ,pandoc)))
21462 `(("r-desc" ,r-desc)
21464 ("r-rcppparallel" ,r-rcppparallel)))
21466 `(("r-knitr" ,r-knitr)))
21467 (home-page "https://mc-stan.org/rstantools/")
21468 (synopsis "Tools for developing R packages interfacing with Stan")
21470 "This package provides various tools for developers of R packages
21471 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21472 up the required package structure, S3 generics and default methods to unify
21473 function naming across Stan-based R packages, and vignettes with
21474 recommendations for developers.")
21475 (license license:gpl3+)))
21477 (define-public r-loo
21484 (uri (cran-uri "loo" version))
21486 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21487 (properties `((upstream-name . "loo")))
21488 (build-system r-build-system)
21490 `(("pandoc" ,pandoc)
21491 ("pandoc-citeproc" ,pandoc-citeproc)))
21493 `(("r-checkmate" ,r-checkmate)
21494 ("r-matrixstats" ,r-matrixstats)))
21496 `(("r-knitr" ,r-knitr)))
21497 (home-page "https://mc-stan.org/loo/")
21498 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21500 "This package provides an implementation of efficient approximate
21501 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21502 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21503 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21504 procedure for regularizing importance weights. As a byproduct of the
21505 calculations, we also obtain approximate standard errors for estimated
21506 predictive errors and for the comparison of predictive errors between models.
21507 The package also provides methods for using stacking and other model weighting
21508 techniques to average Bayesian predictive distributions.")
21509 (license license:gpl3+)))
21511 (define-public r-rstan
21518 (uri (cran-uri "rstan" version))
21521 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
21522 (properties `((upstream-name . "rstan")))
21523 (build-system r-build-system)
21526 (modify-phases %standard-phases
21527 (add-before 'install 'set-timezone
21528 ;; This package is picky about timezones.
21529 (lambda* (#:key inputs #:allow-other-keys)
21530 (setenv "TZ" "UTC+1")
21532 (string-append (assoc-ref inputs "tzdata")
21533 "/share/zoneinfo"))
21536 `(("tzdata" ,tzdata-for-tests)
21538 ("r-knitr" ,r-knitr)))
21541 ("r-ggplot2" ,r-ggplot2)
21542 ("r-gridextra" ,r-gridextra)
21543 ("r-inline" ,r-inline)
21545 ("r-pkgbuild" ,r-pkgbuild)
21547 ("r-rcppeigen" ,r-rcppeigen)
21548 ("r-rcppparallel" ,r-rcppparallel)
21549 ("r-stanheaders" ,r-stanheaders)
21551 ("r-withr" ,r-withr)))
21552 (home-page "https://discourse.mc-stan.org/")
21553 (synopsis "R interface to Stan")
21555 "User-facing R functions are provided to parse, compile, test, estimate,
21556 and analyze Stan models by accessing the header-only Stan library provided by
21557 the StanHeaders package. The Stan project develops a probabilistic
21558 programming language that implements full Bayesian statistical inference via
21559 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21560 approximation, and (optionally penalized) maximum likelihood estimation via
21561 optimization. In all three cases, automatic differentiation is used to
21562 quickly and accurately evaluate gradients without burdening the user with the
21563 need to derive the partial derivatives.")
21564 (license license:gpl3+)))
21566 (define-public r-rstanarm
21568 (name "r-rstanarm")
21573 (uri (cran-uri "rstanarm" version))
21576 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
21577 (properties `((upstream-name . "rstanarm")))
21578 (build-system r-build-system)
21580 `(("pandoc" ,pandoc)
21581 ("pandoc-citeproc" ,pandoc-citeproc)))
21583 `(("r-bayesplot" ,r-bayesplot)
21585 ("r-ggplot2" ,r-ggplot2)
21588 ("r-matrix" ,r-matrix)
21591 ("r-rcppeigen" ,r-rcppeigen)
21592 ("r-rcppparallel" ,r-rcppparallel)
21593 ("r-rstan" ,r-rstan)
21594 ("r-rstantools" ,r-rstantools)
21595 ("r-shinystan" ,r-shinystan)
21596 ("r-stanheaders" ,r-stanheaders)
21597 ("r-survival" ,r-survival)))
21599 `(("r-knitr" ,r-knitr)))
21600 (home-page "https://mc-stan.org/rstanarm/")
21601 (synopsis "Bayesian applied regression modeling via Stan")
21603 "This package estimates previously compiled regression models using the
21604 @code{rstan} package, which provides the R interface to the Stan C++ library
21605 for Bayesian estimation. Users specify models via the customary R syntax with
21606 a formula and @code{data.frame} plus some additional arguments for priors.")
21607 (license license:gpl3+)))
21609 (define-public r-kendall
21616 (uri (cran-uri "Kendall" version))
21619 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21620 (properties `((upstream-name . "Kendall")))
21621 (build-system r-build-system)
21623 `(("r-boot" ,r-boot)))
21625 `(("gfortran" ,gfortran)))
21626 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21627 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21629 "This package computes the Kendall rank correlation and Mann-Kendall
21631 (license license:gpl2+)))
21633 (define-public r-zyp
21636 (version "0.10-1.1")
21640 (uri (cran-uri "zyp" version))
21643 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21644 (properties `((upstream-name . "zyp")))
21645 (build-system r-build-system)
21647 `(("r-kendall" ,r-kendall)))
21648 (home-page "https://cran.r-project.org/web/packages/zyp/")
21649 (synopsis "Zhang + Yue-Pilon Trends Package")
21651 "This package contains an efficient implementation of Sen's slope
21652 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21653 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21655 (license license:lgpl2.1)))
21657 (define-public r-rlinsolve
21659 (name "r-rlinsolve")
21664 (uri (cran-uri "Rlinsolve" version))
21667 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21668 (properties `((upstream-name . "Rlinsolve")))
21669 (build-system r-build-system)
21671 `(("r-matrix" ,r-matrix)
21673 ("r-rcpparmadillo" ,r-rcpparmadillo)
21674 ("r-rdpack" ,r-rdpack)))
21675 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21676 (synopsis "Iterative solvers for (sparse) linear system of equations")
21678 "Solving a system of linear equations is one of the most fundamental
21679 computational problems for many fields of mathematical studies, such as
21680 regression problems from statistics or numerical partial differential
21681 equations. This package provides basic stationary iterative solvers such as
21682 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21683 Nonstationary, also known as Krylov subspace methods are also provided.
21684 Sparse matrix computation is also supported in that solving large and sparse
21685 linear systems can be manageable using the @code{Matrix} package along with
21686 @code{RcppArmadillo}.")
21687 (license license:gpl3+)))
21689 (define-public r-zvcv
21696 (uri (cran-uri "ZVCV" version))
21699 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21700 (properties `((upstream-name . "ZVCV")))
21701 (build-system r-build-system)
21703 `(("r-abind" ,r-abind)
21705 ("r-dplyr" ,r-dplyr)
21706 ("r-glmnet" ,r-glmnet)
21707 ("r-magrittr" ,r-magrittr)
21708 ("r-mvtnorm" ,r-mvtnorm)
21710 ("r-rcpparmadillo" ,r-rcpparmadillo)
21711 ("r-rlinsolve" ,r-rlinsolve)))
21712 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21713 (synopsis "Zero-Variance Control Variates")
21715 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21716 to reduce the variance of Monte Carlo estimators of expectations using the
21717 derivatives of the log target. Once the derivatives are available, the only
21718 additional computational effort is in solving a linear regression problem.
21719 This method has been extended to higher dimensions using regularisation. This
21720 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21721 samples, derivatives and function evaluations are available. Additional
21722 functions for applying ZV-CV to two estimators for the normalising constant of
21723 the posterior distribution in Bayesian statistics are also supplied.")
21724 (license license:gpl2+)))
21726 (define-public r-ztype
21733 (uri (cran-uri "ztype" version))
21736 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21737 (properties `((upstream-name . "ztype")))
21738 (build-system r-build-system)
21740 `(("r-assertthat" ,r-assertthat)
21741 ("r-dplyr" ,r-dplyr)
21742 ("r-ggplot2" ,r-ggplot2)
21743 ("r-lubridate" ,r-lubridate)
21744 ("r-magrittr" ,r-magrittr)
21745 ("r-rvest" ,r-rvest)
21746 ("r-stringr" ,r-stringr)))
21747 (home-page "https://cran.r-project.org/web/packages/ztype/")
21748 (synopsis "Run a Ztype game loaded with R functions")
21750 "How fast can you type R functions on your keyboard? Find out by running
21751 a @code{zty.pe} game: export R functions as instructions to type to destroy
21752 opponents' vessels.")
21753 (license license:gpl3)))
21755 (define-public r-zseq
21762 (uri (cran-uri "Zseq" version))
21765 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21766 (properties `((upstream-name . "Zseq")))
21767 (build-system r-build-system)
21769 `(("r-gmp" ,r-gmp)))
21770 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21771 (synopsis "Integer sequence generator")
21773 "This package generates well-known integer sequences. The @code{gmp}
21774 package is adopted for computing with arbitrarily large numbers. Every
21775 function has a hyperlink to its corresponding item in the @dfn{On-Line
21776 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21777 (license license:gpl3+)))
21779 (define-public r-isoband
21786 (uri (cran-uri "isoband" version))
21789 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21790 (properties `((upstream-name . "isoband")))
21791 (build-system r-build-system)
21793 `(("r-testthat" ,r-testthat)))
21795 `(("r-knitr" ,r-knitr)))
21796 (home-page "https://github.com/wilkelab/isoband")
21797 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21799 "This package provides a fast C++ implementation to generate contour
21800 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21801 containing elevation data.")
21802 (license license:expat)))
21804 (define-public r-ppcor
21811 (uri (cran-uri "ppcor" version))
21814 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21815 (properties `((upstream-name . "ppcor")))
21816 (build-system r-build-system)
21818 `(("r-mass" ,r-mass)))
21819 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21820 (synopsis "Partial and semi-partial correlation")
21822 "This package provides users not only with a function to readily
21823 calculate the higher-order partial and semi-partial correlations but also with
21824 statistics and p-values of the correlation coefficients.")
21825 (license license:gpl2)))
21827 (define-public r-hrbrthemes
21829 (name "r-hrbrthemes")
21834 (uri (cran-uri "hrbrthemes" version))
21836 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21837 (properties `((upstream-name . "hrbrthemes")))
21838 (build-system r-build-system)
21840 `(("r-extrafont" ,r-extrafont)
21841 ("r-gdtools" ,r-gdtools)
21842 ("r-ggplot2" ,r-ggplot2)
21843 ("r-htmltools" ,r-htmltools)
21844 ("r-knitr" ,r-knitr)
21845 ("r-magrittr" ,r-magrittr)
21846 ("r-rmarkdown" ,r-rmarkdown)
21847 ("r-scales" ,r-scales)))
21849 `(("r-knitr" ,r-knitr)))
21850 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21851 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21853 "This package provides a compilation of extra @code{ggplot2} themes,
21854 scales and utilities, including a spell check function for plot label fields
21855 and an overall emphasis on typography.")
21856 (license license:expat)))
21858 (define-public r-crochet
21865 (uri (cran-uri "crochet" version))
21868 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21869 (build-system r-build-system)
21871 `(("r-knitr" ,r-knitr)))
21872 (home-page "https://github.com/agrueneberg/crochet")
21873 (synopsis "Implementation Helper for Matrix-Like Types")
21875 "Functions to help implement the extraction / subsetting / indexing
21876 function @code{[} and replacement function @code{[<-} of custom matrix-like
21877 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21878 as possible (with tests to prove it).")
21879 (license license:expat)))
21881 (define-public r-boa
21884 (version "1.1.8-2")
21888 (uri (cran-uri "boa" version))
21891 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21892 (properties `((upstream-name . "boa")))
21893 (build-system r-build-system)
21894 (home-page "http://www.jstatsoft.org/v21/i11")
21895 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21897 "This package provides a menu-driven program and library of functions for
21898 carrying out convergence diagnostics and statistical and graphical analysis of
21899 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21900 (license license:gpl2+)))
21902 (define-public r-httpcode
21904 (name "r-httpcode")
21908 (uri (cran-uri "httpcode" version))
21911 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21912 (build-system r-build-system)
21913 (home-page "https://github.com/sckott/httpcode")
21914 (synopsis "HTTP status code helper")
21915 (description "@code{httpcode} provides functionality for finding and
21916 explaining the meaning of @code{HTTP} status codes. Functions are included for
21917 searching for codes by full or partial number, by message, and to get
21918 appropriate dog and cat images for many status codes.")
21919 (license license:expat)))
21921 (define-public r-latex2exp
21923 (name "r-latex2exp")
21927 (uri (cran-uri "latex2exp" version))
21930 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21931 (build-system r-build-system)
21933 `(("r-stringr" ,r-stringr)
21934 ("r-magrittr", r-magrittr)))
21935 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21936 (synopsis "Use LaTeX expressions in plots")
21937 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21938 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21939 rendered as text, axis labels, etc. throughout R's plotting system.")
21940 (license license:expat)))
21942 (define-public r-oai
21948 (uri (cran-uri "oai" version))
21951 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21952 (build-system r-build-system)
21954 `(("r-xml2" ,r-xml2)
21957 ("r-stringr" ,r-stringr)
21958 ("r-tibble" ,r-tibble)))
21959 (home-page "https://github.com/ropensci/oai/")
21960 (synopsis "General purpose OAI-PMH services client")
21961 (description "@code{oai} provides a general purpose client to work with
21962 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21963 service. Functions are provided to work with the OAI-PMH verbs:
21964 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21965 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21966 (license license:expat)))
21968 (define-public r-argon2
21975 (uri (cran-uri "argon2" version))
21978 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21979 (properties `((upstream-name . "argon2")))
21980 (build-system r-build-system)
21981 (home-page "https://github.com/wrathematics/argon2")
21982 (synopsis "Secure password hashing based on the argon2 algorithm")
21984 "This package provides utilities for secure password hashing via the
21985 argon2 algorithm.")
21986 (license license:bsd-2)))
21988 (define-public r-getpass
21995 (uri (cran-uri "getPass" version))
21998 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21999 (properties `((upstream-name . "getPass")))
22000 (build-system r-build-system)
22002 `(("r-rstudioapi" ,r-rstudioapi)))
22003 (home-page "https://github.com/wrathematics/getPass")
22004 (synopsis "Masked user input")
22006 "This package provides a micro-package for reading \"passwords\", i.e.
22007 reading user input with masking, so that the input is not displayed as it is
22008 typed. Currently, RStudio, the command line (every OS), and any platform
22009 where tcltk is present are supported.")
22010 (license license:bsd-2)))
22012 (define-public r-remoter
22019 (uri (cran-uri "remoter" version))
22022 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
22023 (properties `((upstream-name . "remoter")))
22024 (build-system r-build-system)
22026 `(("r-argon2" ,r-argon2)
22027 ("r-getpass" ,r-getpass)
22028 ("r-pbdzmq" ,r-pbdzmq)
22030 (home-page "https://github.com/RBigData/remoter")
22031 (synopsis "Control a remote R session from a local one")
22033 "This package provides a set of utilities for client/server computing
22034 with R, controlling a remote R session (the server) from a local one (the
22036 (license license:bsd-2)))
22038 (define-public r-asd
22045 (uri (cran-uri "asd" version))
22048 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
22049 (properties `((upstream-name . "asd")))
22050 (build-system r-build-system)
22052 `(("r-mvtnorm" ,r-mvtnorm)))
22053 (home-page "https://cran.r-project.org/web/packages/asd")
22054 (synopsis "Simulations for Adaptive Seamless Designs")
22056 "This package provdes means to run simulations for adaptive seamless
22057 designs with and without early outcomes for treatment selection and
22058 subpopulation type designs.")
22059 (license license:gpl3)))
22061 (define-public r-nbconvertr
22063 (name "r-nbconvertr")
22068 (uri (cran-uri "nbconvertR" version))
22071 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
22072 (properties `((upstream-name . "nbconvertR")))
22073 (build-system r-build-system)
22075 `(("jupyter" ,python-nbconvert)
22076 ("pandoc" ,pandoc)))
22077 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
22078 (synopsis "Vignette engine wrapping Jupyter notebooks")
22080 "This package calls the Jupyter script @code{nbconvert} to create
22081 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
22082 containing rich text, code, and its output. Code cells can be edited and
22083 evaluated interactively.")
22084 (license license:gpl3)))
22086 (define-public r-bridgesampling
22088 (name "r-bridgesampling")
22093 (uri (cran-uri "bridgesampling" version))
22096 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
22098 `((upstream-name . "bridgesampling")))
22099 (build-system r-build-system)
22101 `(("r-brobdingnag" ,r-brobdingnag)
22103 ("r-matrix" ,r-matrix)
22104 ("r-mvtnorm" ,r-mvtnorm)
22105 ("r-scales" ,r-scales)
22106 ("r-stringr" ,r-stringr)))
22108 `(("r-knitr" ,r-knitr)))
22109 (home-page "https://github.com/quentingronau/bridgesampling")
22110 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
22112 "This package provides functions for estimating marginal likelihoods,
22113 Bayes factors, posterior model probabilities, and normalizing constants in
22114 general, via different versions of bridge sampling.")
22115 (license license:gpl2+)))
22117 (define-public r-tea
22124 (uri (cran-uri "tea" version))
22127 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
22129 `((upstream-name . "tea")))
22130 (build-system r-build-system)
22132 `(("r-matrix" ,r-matrix)))
22133 (home-page "https://cran.r-project.org/web/packages/tea/")
22134 (synopsis "Threshold estimation approaches")
22136 "This package provides different approaches for selecting the threshold
22137 in generalized Pareto distributions. Most of them are based on minimizing the
22138 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
22139 Others are heuristically motivated by searching for stable sample paths, i.e.
22140 a nearly constant region of the tail index estimator with respect to k, which
22141 is the number of data in the tail. The third class is motivated by graphical
22142 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
22143 is also implemented here.")
22144 (license license:gpl3)))
22146 (define-public r-awsmethods
22148 (name "r-awsmethods")
22153 (uri (cran-uri "awsMethods" version))
22156 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
22158 `((upstream-name . "awsMethods")))
22159 (build-system r-build-system)
22160 (home-page "http://www.wias-berlin.de/software/imaging/")
22161 (synopsis "Class and methods definitions")
22163 "This package defines the generic method @code{extract} and provides
22164 @code{openMP} support as needed in several packages like
22165 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
22166 (license license:gpl2+)))
22168 (define-public r-aws
22175 (uri (cran-uri "aws" version))
22178 "0ccm8ffjf8bylhfr64j9wzi49hzigz4bs172pvkb0bi4d5vdr0l5"))))
22180 `((upstream-name . "aws")))
22181 (build-system r-build-system)
22183 `(("r-awsmethods" ,r-awsmethods)
22186 `(("gfortran" ,gfortran)))
22187 (home-page "https://cran.r-project.org/web/packages/aws/")
22188 (synopsis "Adaptive weights smoothing")
22190 "This package provides a collection of R-functions implementing adaptive
22191 smoothing procedures in 1D, 2D and 3D. This includes the
22192 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
22193 Confidence Intervals} (ICI), variational approaches, and a non-local means
22195 (license license:gpl2+)))
22197 (define-public r-sgloptim
22199 (name "r-sgloptim")
22204 (uri (cran-uri "sglOptim" version))
22207 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
22209 `((upstream-name . "sglOptim")))
22210 (build-system r-build-system)
22213 ("r-doparallel" ,r-doparallel)
22214 ("r-foreach" ,r-foreach)
22215 ("r-matrix" ,r-matrix)
22217 ("r-rcpparmadillo" ,r-rcpparmadillo)
22218 ("r-rcppprogress" ,r-rcppprogress)))
22220 `(("r-knitr" ,r-knitr)))
22221 (home-page "https://github.com/nielsrhansen/sglOptim")
22222 (synopsis "Generic sparse group Lasso solver")
22224 "This package provides a fast generic solver for sparse group lasso
22225 optimization problems. The loss (objective) function must be defined in a C++
22226 module. The optimization problem is solved using a coordinate gradient
22227 descent algorithm. Convergence of the algorithm is established and the
22228 algorithm is applicable to a broad class of loss functions. Use of parallel
22229 computing for cross validation and subsampling is supported through the
22230 @code{foreach} and @code{doParallel} packages.")
22231 (license license:gpl2+)))
22233 (define-public r-grouped
22240 (uri (cran-uri "grouped" version))
22243 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22245 `((upstream-name . "grouped")))
22246 (build-system r-build-system)
22248 `(("r-mass" ,r-mass)))
22249 (home-page "https://cran.r-project.org/web/packages/grouped/")
22250 (synopsis "Regression analysis of grouped and coarse data")
22252 "This package provides regression models for grouped and coarse data,
22253 under the coarsened at random assumption.")
22254 (license license:gpl2+)))
22256 (define-public r-stam
22263 (uri (cran-uri "stam" version))
22266 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22268 `((upstream-name . "stam")))
22269 (build-system r-build-system)
22273 (home-page "https://cran.r-project.org/web/packages/stam")
22274 (synopsis "Spatio-temporal analysis and modelling")
22276 "This package provides various methods to conduct Spatio-Temporal
22277 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22278 Inferred Spatio-Temporal Modelling.")
22279 (license license:gpl2+)))
22281 (define-public r-dcv
22288 (uri (cran-uri "dcv" version))
22291 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22293 `((upstream-name . "dcv")))
22294 (build-system r-build-system)
22296 `(("r-lmtest" ,r-lmtest)))
22297 (home-page "https://cran.r-project.org/web/packages/dcv/")
22298 (synopsis "Conventional cross-validation statistics for climate-growth model")
22300 "This package performs several conventional cross-validation statistical
22301 methods for climate-growth model in the climate reconstruction from tree
22302 rings, including Sign Test statistic, Reduction of Error statistic, Product
22303 Mean Test, Durbin-Watson statistic etc.")
22304 (license license:gpl2)))
22306 (define-public r-rcdd
22313 (uri (cran-uri "rcdd" version))
22316 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22318 `((upstream-name . "rcdd")))
22319 (build-system r-build-system)
22322 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22323 (synopsis "Computational geometry")
22325 "This package converts back and forth between two representations of a
22326 convex polytope: as solution of a set of linear equalities and inequalities
22327 and as convex hull of set of points and rays. Also does linear programming
22328 and redundant generator elimination. All functions can use exact
22329 infinite-precision rational arithmetic.")
22330 (license license:gpl2)))
22332 (define-public r-rxnat
22339 (uri (cran-uri "Rxnat" version))
22342 "06w99b5lvpycykzlga6grw33zkajwbb04s89s37wy9zxy42vc4cb"))))
22344 `((upstream-name . "Rxnat")))
22345 (build-system r-build-system)
22347 `(("r-dplyr" ,r-dplyr)
22349 ("r-rcurl" ,r-rcurl)))
22351 `(("r-knitr" ,r-knitr)))
22352 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22353 (synopsis "Queries and extracts images from neuroimaging datasets")
22355 "This package allows communication with the Extensible Neuroimaging
22356 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22358 (license license:gpl2)))
22360 (define-public r-rserve
22367 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22368 version ".tar.gz"))
22371 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22372 (build-system r-build-system)
22374 `(("r-checkmate" ,r-checkmate)
22376 ("r-jsonlite" ,r-jsonlite)
22377 ("r-knitr" ,r-knitr)
22380 ("r-uuid" ,r-uuid)))
22382 `(("openssl" ,openssl)
22384 (home-page "https://github.com/s-u/Rserve")
22386 "Server providing access to R from many languages and systems")
22388 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22389 binary requests to be sent to R. Every connection has a separate workspace
22390 and working directory. Client-side implementations are available for popular
22391 languages such as C/C++ and Java, allowing any application to use facilities
22392 of R without the need of linking to R code. Rserve supports remote
22393 connection, user authentication and file transfer. A simple R client is
22394 included in this package as well.")
22395 (license license:gpl2)))
22397 (define-public r-brms
22404 (uri (cran-uri "brms" version))
22407 "0a2m5wr134sxflmiq5jzvanzn81fv7xndy9gyvrq3bay9vakic69"))))
22408 (properties `((upstream-name . "brms")))
22409 (build-system r-build-system)
22411 `(("r-abind" ,r-abind)
22412 ("r-backports" ,r-backports)
22413 ("r-bayesplot" ,r-bayesplot)
22414 ("r-bridgesampling" ,r-bridgesampling)
22416 ("r-future" ,r-future)
22417 ("r-ggplot2" ,r-ggplot2)
22420 ("r-matrix" ,r-matrix)
22421 ("r-matrixstats" ,r-matrixstats)
22423 ("r-nleqslv" ,r-nleqslv)
22426 ("r-rstan" ,r-rstan)
22427 ("r-rstantools" ,r-rstantools)
22428 ("r-shinystan" ,r-shinystan)))
22429 (native-inputs `(("r-knitr" ,r-knitr)))
22431 "https://github.com/paul-buerkner/brms")
22433 "Bayesian Regression Models using 'Stan'")
22435 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22436 using 'Stan' for full Bayesian inference. A wide range of distributions and
22437 link functions are supported, allowing users to fit -- among others -- linear,
22438 robust linear, count data, survival, response times, ordinal, zero-inflated,
22439 hurdle, and even self-defined mixture models all in a multilevel context.
22440 Further modeling options include non-linear and smooth terms, auto-correlation
22441 structures, censored data, meta-analytic standard errors, and quite a few
22442 more. In addition, all parameters of the response distribution can be
22443 predicted in order to perform distributional regression. Prior specifications
22444 are flexible and explicitly encourage users to apply prior distributions that
22445 actually reflect their beliefs. Model fit can easily be assessed and compared
22446 with posterior predictive checks and leave-one-out cross-validation.")
22447 (license license:gpl2)))
22449 (define-public r-mstate
22456 (uri (cran-uri "mstate" version))
22459 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22460 (properties `((upstream-name . "mstate")))
22461 (build-system r-build-system)
22463 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22464 ("r-survival" ,r-survival)))
22466 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22468 "Data Preparation, Estimation and Prediction in Multi-State Models")
22470 "Contains functions for data preparation, descriptives, hazard estimation
22471 and prediction with Aalen-Johansen or simulation in competing risks and
22472 multi-state models.")
22473 (license license:gpl2+)))
22475 (define-public r-scatterpie
22477 (name "r-scatterpie")
22482 (uri (cran-uri "scatterpie" version))
22485 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22486 (properties `((upstream-name . "scatterpie")))
22487 (build-system r-build-system)
22489 `(("r-ggforce" ,r-ggforce)
22490 ("r-ggplot2" ,r-ggplot2)
22491 ("r-rlang" ,r-rlang)
22492 ("r-rvcheck" ,r-rvcheck)
22493 ("r-tidyr" ,r-tidyr)))
22495 `(("r-knitr" ,r-knitr)))
22496 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22497 (synopsis "Scatter pie plot")
22499 "This package creates scatterpie plots, especially useful for plotting
22501 (license license:artistic2.0)))
22503 (define-public r-boruta
22510 (uri (cran-uri "Boruta" version))
22513 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22514 (properties `((upstream-name . "Boruta")))
22515 (build-system r-build-system)
22516 (propagated-inputs `(("r-ranger" ,r-ranger)))
22517 (home-page "https://gitlab.com/mbq/Boruta/")
22518 (synopsis "Wrapper algorithm for all relevant feature selection")
22520 "This package provides an all relevant feature selection wrapper
22521 algorithm. It finds relevant features by comparing original attributes'
22522 importance with importance achievable at random, estimated using their
22523 permuted copies (shadows).")
22524 (license license:gpl2+)))
22526 (define-public r-directlabels
22528 (name "r-directlabels")
22529 (version "2020.6.17")
22533 (uri (cran-uri "directlabels" version))
22536 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22537 (build-system r-build-system)
22539 `(("r-quadprog" ,r-quadprog)))
22541 `(("r-knitr" ,r-knitr)))
22542 (home-page "http://directlabels.r-forge.r-project.org/")
22543 (synopsis "Direct labels for multicolor plots")
22545 "This package provides an extensible framework for automatically placing
22546 direct labels onto multicolor plots. Label positions are described using
22547 positioning methods that can be re-used across several different plots. There
22548 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22549 inferring an appropriate positioning method.")
22550 (license license:gpl3)))
22552 (define-public r-lsd
22559 (uri (cran-uri "LSD" version))
22561 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22562 (properties `((upstream-name . "LSD")))
22563 (build-system r-build-system)
22564 (home-page "https://cran.r-project.org/web/packages/LSD/")
22565 (synopsis "Lots of superior depictions tool creates colorful plots")
22567 "This package creates lots of colorful plots in a multitude of variations.
22568 Try a demo of the LSD by running @code{demotour()}.")
22570 (license (list license:gpl2 license:gpl3))))
22572 (define-public r-fourcseq
22574 (name "r-fourcseq")
22579 (uri (bioconductor-uri "FourCSeq" version))
22581 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
22582 (properties `((upstream-name . "FourCSeq")))
22583 (build-system r-build-system)
22585 `(("r-biobase" ,r-biobase)
22586 ("r-biostrings" ,r-biostrings)
22587 ("r-deseq2" ,r-deseq2)
22589 ("r-genomicalignments" ,r-genomicalignments)
22590 ("r-genomicranges" ,r-genomicranges)
22591 ("r-ggbio" ,r-ggbio)
22592 ("r-ggplot2" ,r-ggplot2)
22593 ("r-gtools" ,r-gtools)
22595 ("r-matrix" ,r-matrix)
22596 ("r-reshape2" ,r-reshape2)
22597 ("r-rsamtools" ,r-rsamtools)
22598 ("r-rtracklayer" ,r-rtracklayer)
22599 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22601 `(("r-knitr" ,r-knitr)))
22603 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22604 (synopsis "Analysis of multiplexed 4C sequencing data")
22606 "This package is an R package dedicated to the analysis of (multiplexed)
22607 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22608 interactions between DNA elements and identify differential interactions
22609 between conditions. The statistical analysis in R starts with individual bam
22610 files for each sample as inputs. To obtain these files, the package contains
22611 a Python script to demultiplex libraries and trim off primer sequences. With
22612 a standard alignment software the required bam files can be then be
22614 (license license:gpl3+)))
22616 (define-public r-phylogram
22618 (name "r-phylogram")
22623 (uri (cran-uri "phylogram" version))
22625 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22626 (properties `((upstream-name . "phylogram")))
22627 (build-system r-build-system)
22628 (propagated-inputs `(("r-ape" ,r-ape)))
22629 (home-page "https://github.com/ropensci/phylogram/")
22630 (synopsis "Dendrograms for evolutionary analysis")
22632 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22633 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22634 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22635 as well as several tools for command-line tree manipulation and import/export
22636 via Newick parenthetic text. This improves accessibility to the comprehensive
22637 range of object-specific analytical and tree-visualization functions found
22638 across a wide array of bioinformatic R packages.")
22639 (license license:gpl3)))
22641 (define-public r-kmer
22648 (uri (cran-uri "kmer" version))
22650 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22651 (properties `((upstream-name . "kmer")))
22652 (build-system r-build-system)
22654 `(("r-openssl" ,r-openssl)
22655 ("r-phylogram" ,r-phylogram)
22656 ("r-rcpp" ,r-rcpp)))
22657 (home-page "https://github.com/shaunpwilkinson/kmer/")
22658 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22660 "@code{r-kmer} is an R package for rapidly computing distance matrices
22661 and clustering large sequence datasets using fast alignment-free k-mer
22662 counting and recursive k-means partitioning.")
22663 (license license:gpl3)))
22665 (define-public r-hardhat
22672 (uri (cran-uri "hardhat" version))
22675 "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
22676 (properties `((upstream-name . "hardhat")))
22677 (build-system r-build-system)
22679 `(("r-glue" ,r-glue)
22680 ("r-rlang" ,r-rlang)
22681 ("r-tibble" ,r-tibble)
22682 ("r-vctrs" ,r-vctrs)))
22684 `(("r-knitr" ,r-knitr)))
22685 (home-page "https://github.com/tidymodels/hardhat")
22686 (synopsis "Construct modeling packages")
22688 "Building modeling packages is hard. A large amount of effort generally
22689 goes into providing an implementation for a new method that is efficient,
22690 fast, and correct, but often less emphasis is put on the user interface. A
22691 good interface requires specialized knowledge about S3 methods and formulas,
22692 which the average package developer might not have. The goal of
22693 @code{hardhat} is to reduce the burden around building new modeling packages
22694 by providing functionality for preprocessing, predicting, and validating
22696 (license license:expat)))
22698 (define-public r-shapforxgboost
22700 (name "r-shapforxgboost")
22705 (uri (cran-uri "SHAPforxgboost" version))
22708 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22710 `((upstream-name . "SHAPforxgboost")))
22711 (build-system r-build-system)
22713 `(("r-bbmisc" ,r-bbmisc)
22714 ("r-data-table" ,r-data-table)
22715 ("r-ggextra" ,r-ggextra)
22716 ("r-ggforce" ,r-ggforce)
22717 ("r-ggplot2" ,r-ggplot2)
22718 ("r-ggpubr" ,r-ggpubr)
22719 ("r-rcolorbrewer" ,r-rcolorbrewer)
22720 ("r-xgboost" ,r-xgboost)))
22721 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22722 (synopsis "SHAP Plots for XGBoost")
22724 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22725 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22726 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22727 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22729 (license license:expat)))
22731 (define-public r-rismed
22738 (uri (cran-uri "RISmed" version))
22741 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22742 (properties `((upstream-name . "RISmed")))
22743 (build-system r-build-system)
22744 (home-page "https://cran.r-project.org/web/packages/RISmed")
22745 (synopsis "Download content from NCBI databases")
22747 "This package provides a set of tools to extract bibliographic
22748 content from the National Center for Biotechnology Information (NCBI)
22749 databases, including PubMed. The name RISmed is a portmanteau of
22750 RIS (for Research Information Systems, a common tag format for
22751 bibliographic data) and PubMed.")
22752 (license license:gpl2+)))
22754 (define-public r-semver
22761 (uri (cran-uri "semver" version))
22764 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22765 (properties `((upstream-name . "semver")))
22766 (build-system r-build-system)
22768 `(("r-assertthat" ,r-assertthat)
22769 ("r-rcpp" ,r-rcpp)))
22770 (native-inputs `(("r-knitr" ,r-knitr)))
22771 (home-page "https://github.com/johndharrison/semver")
22772 (synopsis "Parser for Semantic Versioning 2.0.0")
22774 "This package provides tools and functions for parsing, rendering and
22775 operating on semantic version strings. Semantic versioning is a simple set of
22776 rules and requirements that dictate how version numbers are assigned and
22777 incremented as outlined at @url{http://semver.org}.")
22778 (license license:expat)))
22780 (define-public r-binman
22787 (uri (cran-uri "binman" version))
22790 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22791 (properties `((upstream-name . "binman")))
22792 (build-system r-build-system)
22794 `(("r-assertthat" ,r-assertthat)
22796 ("r-jsonlite" ,r-jsonlite)
22797 ("r-rappdirs" ,r-rappdirs)
22798 ("r-semver" ,r-semver)
22800 ("r-yaml" ,r-yaml)))
22801 (native-inputs `(("r-knitr" ,r-knitr)))
22802 (home-page "https://github.com/ropensci/binman")
22803 (synopsis "Binary download manager")
22805 "This package provides tools and functions for managing the download of
22806 binary files. Binary repositories are defined in the YAML format. Defining
22807 new pre-download, download and post-download templates allow additional
22808 repositories to be added.")
22809 (license license:expat)))
22811 (define-public r-wdman
22818 (uri (cran-uri "wdman" version))
22821 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22822 (properties `((upstream-name . "wdman")))
22823 (build-system r-build-system)
22825 `(("r-assertthat" ,r-assertthat)
22826 ("r-binman" ,r-binman)
22827 ("r-processx" ,r-processx)
22828 ("r-semver" ,r-semver)
22829 ("r-yaml" ,r-yaml)))
22830 (native-inputs `(("r-knitr" ,r-knitr)))
22831 (home-page "https://docs.ropensci.org/wdman/")
22832 (synopsis "Webdriver/Selenium binary manager")
22834 "There are a number of binary files associated with the
22835 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22836 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22837 @url{https://github.com/mozilla/geckodriver},
22838 @url{http://phantomjs.org/download.html}, and
22839 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22840 more information). This package provides functions to download these binaries
22841 and to manage processes involving them.")
22842 (license license:expat)))
22844 (define-public r-rselenium
22846 (name "r-rselenium")
22851 (uri (cran-uri "RSelenium" version))
22854 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22855 (properties `((upstream-name . "RSelenium")))
22856 (build-system r-build-system)
22858 `(("r-binman" ,r-binman)
22859 ("r-catools" ,r-catools)
22861 ("r-openssl" ,r-openssl)
22862 ("r-wdman" ,r-wdman)
22864 (native-inputs `(("r-knitr" ,r-knitr)))
22865 (home-page "https://docs.ropensci.org/RSelenium/")
22866 (synopsis "R bindings for Selenium WebDriver")
22868 "This package provides a set of R bindings for the Selenium 2.0
22869 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22870 information) using the @code{JsonWireProtocol} (see
22871 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22872 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22873 a user would either locally or on a remote machine using the Selenium server
22874 it marks a leap forward in terms of web browser automation. Selenium
22875 automates web browsers (commonly referred to as browsers). Using RSelenium
22876 you can automate browsers locally or remotely.")
22877 (license license:agpl3+)))
22879 (define-public r-conquer
22886 (uri (cran-uri "conquer" version))
22889 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
22890 (properties `((upstream-name . "conquer")))
22891 (build-system r-build-system)
22893 `(("r-matrix" ,r-matrix)
22894 ("r-matrixstats" ,r-matrixstats)
22896 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22897 (home-page "https://github.com/XiaoouPan/conquer")
22898 (synopsis "Convolution-type smoothed quantile regression")
22900 "This package provides fast and accurate convolution-type smoothed
22901 quantile regression, implemented using Barzilai-Borwein gradient descent with
22902 a Huber regression warm start. Confidence intervals for regression
22903 coefficients are constructed using multiplier bootstrap.")
22904 (license license:gpl3)))
22906 (define-public r-fastshap
22908 (name "r-fastshap")
22913 (uri (cran-uri "fastshap" version))
22916 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22917 (properties `((upstream-name . "fastshap")))
22918 (build-system r-build-system)
22920 `(("r-abind" ,r-abind)
22921 ("r-ggplot2" ,r-ggplot2)
22922 ("r-gridextra" ,r-gridextra)
22923 ("r-matrixstats" ,r-matrixstats)
22926 ("r-rcpparmadillo" ,r-rcpparmadillo)
22927 ("r-tibble" ,r-tibble)))
22928 (home-page "https://github.com/bgreenwell/fastshap")
22929 (synopsis "Fast approximate Shapley values")
22931 "This package computes fast (relative to other implementations)
22932 approximate Shapley values for any supervised learning model. Shapley values
22933 help to explain the predictions from any black box model using ideas from game
22934 theory; see @url{Strumbel and Kononenko (2014),
22935 doi.org/10.1007/s10115-013-0679-x} for details.")
22936 (license license:gpl2+)))
22938 (define-public r-metrics
22945 (uri (cran-uri "Metrics" version))
22948 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22949 (properties `((upstream-name . "Metrics")))
22950 (build-system r-build-system)
22951 (home-page "https://github.com/mfrasco/Metrics")
22952 (synopsis "Evaluation metrics for machine learning")
22954 "This package provides an implementation of evaluation metrics in R that
22955 are commonly used in supervised machine learning. It implements metrics for
22956 regression, time series, binary classification, classification, and
22957 information retrieval problems. It has zero dependencies and a consistent,
22958 simple interface for all functions.")
22959 (license license:bsd-3)))
22961 (define-public r-iml
22968 (uri (cran-uri "iml" version))
22971 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22972 (properties `((upstream-name . "iml")))
22973 (build-system r-build-system)
22975 `(("r-checkmate" ,r-checkmate)
22976 ("r-data-table" ,r-data-table)
22977 ("r-formula" ,r-formula)
22978 ("r-future" ,r-future)
22979 ("r-future-apply" ,r-future-apply)
22980 ("r-ggplot2" ,r-ggplot2)
22981 ("r-gridextra" ,r-gridextra)
22982 ("r-metrics" ,r-metrics)
22983 ("r-prediction" ,r-prediction)
22985 (native-inputs `(("r-knitr" ,r-knitr)))
22986 (home-page "https://github.com/christophM/iml")
22987 (synopsis "Interpretable machine learning")
22989 "This package provides interpretability methods to analyze the behavior
22990 and predictions of any machine learning model. Implemented methods are:
22993 @item Feature importance described by Fisher et al. (2018),
22994 @item accumulated local effects plots described by Apley (2018),
22995 @item partial dependence plots described by Friedman (2001),
22996 @item individual conditional expectation ('ice') plots described by Goldstein
22997 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
22998 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
22999 @item the Shapley Value described by Strumbelj et. al (2014)
23000 @url{https://doi.org/10.1007/s10115-013-0679-x},
23001 @item feature interactions described by Friedman et. al
23002 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
23005 (license license:expat)))
23007 (define-public r-goftest
23014 (uri (cran-uri "goftest" version))
23017 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
23018 (properties `((upstream-name . "goftest")))
23019 (build-system r-build-system)
23020 (home-page "https://github.com/baddstats/goftest")
23021 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
23023 "This package provides Cramer-Von Mises and Anderson-Darling tests of
23024 goodness-of-fit for continuous univariate distributions, using efficient
23026 (license license:gpl2+)))
23028 (define-public r-tensor
23035 (uri (cran-uri "tensor" version))
23038 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
23039 (properties `((upstream-name . "tensor")))
23040 (build-system r-build-system)
23041 (home-page "https://cran.r-project.org/web/packages/tensor/")
23042 (synopsis "Tensor product of arrays")
23044 "The tensor product of two arrays is notionally an outer product of the
23045 arrays collapsed in specific extents by summing along the appropriate
23046 diagonals. This package allows you to compute the tensor product of arrays.")
23047 (license license:gpl2+)))
23049 (define-public r-spatstat-utils
23051 (name "r-spatstat-utils")
23056 (uri (cran-uri "spatstat.utils" version))
23059 "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r"))))
23061 `((upstream-name . "spatstat.utils")))
23062 (build-system r-build-system)
23063 (home-page "http://www.spatstat.org")
23064 (synopsis "Utility functions for spatstat")
23066 "This package contains utility functions for the @code{spatstat} package
23067 which may also be useful for other purposes.")
23068 (license license:gpl2+)))
23070 (define-public r-spatstat-data
23072 (name "r-spatstat-data")
23077 (uri (cran-uri "spatstat.data" version))
23080 "18lfj5vkwxgf5w9qz0g5al3zy8y2yi3bnd13w24hszfc82nbcmc9"))))
23081 (properties `((upstream-name . "spatstat.data")))
23082 (build-system r-build-system)
23084 `(("r-matrix" ,r-matrix)
23085 ("r-spatstat-utils" ,r-spatstat-utils)))
23086 (home-page "http://www.spatstat.org")
23087 (synopsis "Datasets for spatstat")
23089 "This package contains all the datasets for the @code{spatstat}
23091 (license license:gpl2+)))
23093 (define-public r-spatstat
23095 (name "r-spatstat")
23100 (uri (cran-uri "spatstat" version))
23103 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
23104 (properties `((upstream-name . "spatstat")))
23105 (build-system r-build-system)
23107 `(("r-abind" ,r-abind)
23108 ("r-deldir" ,r-deldir)
23109 ("r-goftest" ,r-goftest)
23110 ("r-matrix" ,r-matrix)
23113 ("r-polyclip" ,r-polyclip)
23114 ("r-rpart" ,r-rpart)
23115 ("r-spatstat-data" ,r-spatstat-data)
23116 ("r-spatstat-utils" ,r-spatstat-utils)
23117 ("r-tensor" ,r-tensor)))
23118 (home-page "http://www.spatstat.org")
23119 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
23121 "This package provides a comprehensive toolbox for analysing Spatial
23122 Point Patterns. It is focused mainly on two-dimensional point patterns,
23123 including multitype/marked points, in any spatial region. It also supports
23124 three-dimensional point patterns, space-time point patterns in any number of
23125 dimensions, point patterns on a linear network, and patterns of other
23126 geometrical objects. It supports spatial covariate data such as pixel images
23127 and contains over 2000 functions for plotting spatial data, exploratory data
23128 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
23129 formal inference.")
23130 (license license:gpl2+)))
23132 (define-public r-gaston
23139 (uri (cran-uri "gaston" version))
23142 "1bx6iqfjb9lf3vn0z7v8wjv9m7issvqsnymm4qsgl3622s6qz6rg"))))
23143 (properties `((upstream-name . "gaston")))
23144 (build-system r-build-system)
23145 (inputs `(("zlib" ,zlib)))
23147 `(("r-rcpp" ,r-rcpp)
23148 ("r-rcppeigen" ,r-rcppeigen)
23149 ("r-rcppparallel" ,r-rcppparallel)))
23150 (native-inputs `(("r-knitr" ,r-knitr)))
23151 (home-page "https://cran.r-project.org/web/packages/gaston/")
23152 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
23154 "This is a package for the manipulation of genetic data (SNPs).
23155 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
23156 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
23157 for linear mixed models (AIREML).")
23158 (license license:gpl3)))
23160 (define-public r-cpp11
23167 (uri (cran-uri "cpp11" version))
23170 "1113y61lj4cg1d2yjavdx9zih5rzb4pnxmj5v3sr4bhzlxz2scda"))))
23171 (properties `((upstream-name . "cpp11")))
23172 (build-system r-build-system)
23173 (native-inputs `(("r-knitr" ,r-knitr)))
23174 (home-page "https://github.com/r-lib/cpp11")
23175 (synopsis "C++11 Interface for R's C Interface")
23177 "This package provides a header only, C++11 interface to R's C interface.
23178 Compared to other approaches @code{cpp11} strives to be safe against long
23179 jumps from the C API as well as C++ exceptions, conform to normal R function
23180 semantics and supports interaction with @code{ALTREP} vectors.")
23181 (license license:expat)))
23183 (define-public r-rcppziggurat
23185 (name "r-rcppziggurat")
23190 (uri (cran-uri "RcppZiggurat" version))
23193 "0zmr3nvm5j0fpwxk3x9kxpwqbr66ldfvd10zy8xlgjbslz9myvfv"))))
23194 (properties `((upstream-name . "RcppZiggurat")))
23195 (build-system r-build-system)
23197 `(("r-rcpp" ,r-rcpp)
23198 ("r-rcppgsl" ,r-rcppgsl)))
23199 (native-inputs `(("r-knitr" ,r-knitr)))
23200 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
23201 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
23203 "The Ziggurat generator for normally distributed random numbers,
23204 originally proposed by Marsaglia and Tsang (2000,
23205 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
23206 times starting with Leong et al (2005,
23207 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
23208 aggregation for comparing different implementations in order to provide a
23209 'faster but good enough' alternative for use with R and C++ code.")
23210 (license license:gpl2+)))
23212 (define-public r-rfast
23219 (uri (cran-uri "Rfast" version))
23222 "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
23223 (properties `((upstream-name . "Rfast")))
23224 (build-system r-build-system)
23226 `(("r-rcpp" ,r-rcpp)
23227 ("r-rcpparmadillo" ,r-rcpparmadillo)
23228 ("r-rcppziggurat" ,r-rcppziggurat)))
23229 (home-page "https://github.com/RfastOfficial/Rfast")
23230 (synopsis "Collection of efficient and fast R functions")
23232 "This package provides a collection of fast (utility) functions for data
23233 analysis. Column- and row- wise means, medians, variances, minimums,
23234 maximums, many t, F and G-square tests, many regressions (normal, logistic,
23235 Poisson), are some of the many fast functions.")
23236 (license license:gpl2+)))
23238 (define-public r-clusterr
23240 (name "r-clusterr")
23245 (uri (cran-uri "ClusterR" version))
23248 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
23249 (properties `((upstream-name . "ClusterR")))
23250 (build-system r-build-system)
23252 `(("r-ggplot2" ,r-ggplot2)
23254 ("r-gtools" ,r-gtools)
23256 ("r-rcpparmadillo" ,r-rcpparmadillo)))
23257 (native-inputs `(("r-knitr" ,r-knitr)))
23258 (home-page "https://github.com/mlampros/ClusterR")
23259 (synopsis "Clustering")
23261 "This package provides Gaussian mixture models, k-means,
23262 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
23263 option to plot, validate, predict (new data) and estimate the optimal number
23264 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
23265 the computationally intensive parts of the functions. For more information,
23269 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
23270 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
23271 @url{https://doi.org/10.18637/jss.v001.i04};
23272 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
23273 Library, @url{https://doi.org/10.1145/1772690.1772862};
23274 @item \"Armadillo: a template-based C++ library
23275 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
23276 Software, @url{https://doi.org/10.21105/joss.00026};
23277 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
23278 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
23279 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
23282 (license license:gpl3)))
23284 (define-public r-spectrum
23286 (name "r-spectrum")
23291 (uri (cran-uri "Spectrum" version))
23294 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
23295 (properties `((upstream-name . "Spectrum")))
23296 (build-system r-build-system)
23298 `(("r-clusterr" ,r-clusterr)
23299 ("r-diptest" ,r-diptest)
23300 ("r-ggplot2" ,r-ggplot2)
23301 ("r-rfast" ,r-rfast)))
23302 (native-inputs `(("r-knitr" ,r-knitr)))
23303 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
23304 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
23306 "This package provides a self-tuning spectral clustering method for
23307 single or multi-view data. Spectrum uses a new type of adaptive density aware
23308 kernel that strengthens connections in the graph based on common nearest
23309 neighbours. It uses a tensor product graph data integration and diffusion
23310 procedure to integrate different data sources and reduce noise. Spectrum uses
23311 either the eigengap or multimodality gap heuristics to determine the number of
23312 clusters. The method is sufficiently flexible so that a wide range of
23313 Gaussian and non-Gaussian structures can be clustered with automatic selection
23315 (license license:agpl3+)))
23317 (define-public r-nabor
23324 (uri (cran-uri "nabor" version))
23327 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
23328 (properties `((upstream-name . "nabor")))
23329 (build-system r-build-system)
23333 ("r-rcppeigen" ,r-rcppeigen)))
23334 (home-page "https://cran.r-project.org/web/packages/nabor/")
23335 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
23337 "This package provides an R wrapper for libnabo, an exact or approximate
23338 k nearest neighbour library which is optimised for low dimensional
23339 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
23340 designed as a drop-in replacement for the RANN function @code{nn2}. In
23341 addition, objects which include the k-d tree search structure can be returned
23342 to speed up repeated queries of the same set of target points.")
23343 (license license:bsd-3)))
23345 (define-public r-muhaz
23348 (version "1.2.6.1")
23352 (uri (cran-uri "muhaz" version))
23355 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
23356 (properties `((upstream-name . "muhaz")))
23357 (build-system r-build-system)
23359 `(("r-survival" ,r-survival)))
23361 `(("gfortran" ,gfortran)))
23362 (home-page "https://cran.r-project.org/web/packages/muhaz/")
23363 (synopsis "Hazard function estimation in survival analysis")
23365 "This package produces a smooth estimate of the hazard function for
23367 ;; Any version of the GPL.
23368 (license license:gpl3+)))
23370 (define-public r-flexsurv
23372 (name "r-flexsurv")
23377 (uri (cran-uri "flexsurv" version))
23380 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
23381 (properties `((upstream-name . "flexsurv")))
23382 (build-system r-build-system)
23384 `(("r-desolve" ,r-desolve)
23385 ("r-mstate" ,r-mstate)
23386 ("r-muhaz" ,r-muhaz)
23387 ("r-mvtnorm" ,r-mvtnorm)
23388 ("r-quadprog" ,r-quadprog)
23390 ("r-survival" ,r-survival)
23391 ("r-tibble" ,r-tibble)
23392 ("r-tidyr" ,r-tidyr)))
23394 `(("r-knitr" ,r-knitr)))
23395 (home-page "https://github.com/chjackson/flexsurv-dev")
23396 (synopsis "Flexible parametric survival and multi-state models")
23398 "This package provides flexible parametric models for time-to-event data,
23399 including the Royston-Parmar spline model, generalized gamma and generalized F
23400 distributions. Any user-defined parametric distribution can be fitted, given
23401 at least an R function defining the probability density or hazard. There are
23402 also tools for fitting and predicting from fully parametric multi-state
23404 (license license:gpl2+)))
23406 (define-public r-transphylo
23408 (name "r-transphylo")
23413 (uri (cran-uri "TransPhylo" version))
23416 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
23417 (properties `((upstream-name . "TransPhylo")))
23418 (build-system r-build-system)
23421 ("r-rcpp" ,r-rcpp)))
23423 `(("r-knitr" ,r-knitr)))
23424 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
23425 (synopsis "Inference of transmission tree from a dated phylogeny")
23427 "This is a package to infer transmission trees from a dated phylogeny.
23428 It includes methods to simulate and analyze outbreaks. The methodology is
23429 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
23430 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
23431 (license license:gpl2+)))
23433 (define-public r-km-ci
23440 (uri (cran-uri "km.ci" version))
23443 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
23444 (properties `((upstream-name . "km.ci")))
23445 (build-system r-build-system)
23447 `(("r-survival" ,r-survival)))
23448 (home-page "https://cran.r-project.org/web/packages/km.ci/")
23449 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
23451 "This package computes various @dfn{confidence intervals} (CI) for the
23452 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
23453 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
23454 Nair and Hall and Wellner.")
23455 (license license:gpl2+)))
23457 (define-public r-kmsurv
23464 (uri (cran-uri "KMsurv" version))
23467 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
23468 (properties `((upstream-name . "KMsurv")))
23469 (build-system r-build-system)
23470 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
23471 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
23473 "This package provides data sets and functions for Klein and Moeschberger
23474 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
23476 (license license:gpl3+)))
23478 (define-public r-survmisc
23480 (name "r-survmisc")
23485 (uri (cran-uri "survMisc" version))
23488 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
23489 (properties `((upstream-name . "survMisc")))
23490 (build-system r-build-system)
23492 `(("r-data-table" ,r-data-table)
23493 ("r-ggplot2" ,r-ggplot2)
23494 ("r-gridextra" ,r-gridextra)
23495 ("r-km-ci" ,r-km-ci)
23496 ("r-kmsurv" ,r-kmsurv)
23497 ("r-knitr" ,r-knitr)
23498 ("r-survival" ,r-survival)
23499 ("r-xtable" ,r-xtable)
23502 `(("r-knitr" ,r-knitr)))
23503 (home-page "https://cran.r-project.org/web/packages/survMisc/")
23504 (synopsis "Miscellaneous functions for survival data")
23506 "This package provides a collection of functions to help in the analysis
23507 of right-censored survival data. These extend the methods available in
23508 the @code{survival} package.")
23509 (license license:gpl2)))
23511 (define-public r-exactranktests
23513 (name "r-exactranktests")
23518 (uri (cran-uri "exactRankTests" version))
23521 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
23523 `((upstream-name . "exactRankTests")))
23524 (build-system r-build-system)
23525 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
23526 (synopsis "Exact distributions for rank and permutation tests")
23528 "This package computes exact conditional p-values and quantiles using an
23529 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
23530 (license license:gpl2+)))
23532 (define-public r-maxstat
23539 (uri (cran-uri "maxstat" version))
23542 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
23543 (properties `((upstream-name . "maxstat")))
23544 (build-system r-build-system)
23546 `(("r-exactranktests" ,r-exactranktests)
23547 ("r-mvtnorm" ,r-mvtnorm)))
23548 (home-page "https://cran.r-project.org/web/packages/maxstat/")
23549 (synopsis "Maximally selected rank statistics")
23551 "This package provides maximally selected rank statistics with several
23552 p-value approximations.")
23553 (license license:gpl2+)))
23555 (define-public r-survminer
23557 (name "r-survminer")
23562 (uri (cran-uri "survminer" version))
23565 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
23566 (properties `((upstream-name . "survminer")))
23567 (build-system r-build-system)
23569 `(("r-broom" ,r-broom)
23570 ("r-dplyr" ,r-dplyr)
23571 ("r-ggplot2" ,r-ggplot2)
23572 ("r-ggpubr" ,r-ggpubr)
23573 ("r-gridextra" ,r-gridextra)
23574 ("r-magrittr" ,r-magrittr)
23575 ("r-maxstat" ,r-maxstat)
23576 ("r-purrr" ,r-purrr)
23577 ("r-rlang" ,r-rlang)
23578 ("r-scales" ,r-scales)
23579 ("r-survival" ,r-survival)
23580 ("r-survmisc" ,r-survmisc)
23581 ("r-tibble" ,r-tibble)
23582 ("r-tidyr" ,r-tidyr)))
23584 `(("r-knitr" ,r-knitr)))
23585 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
23586 (synopsis "Drawing survival curves using ggplot2")
23588 "This package contains the function @code{ggsurvplot()} for easily
23589 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
23590 risk' table and 'censoring count plot'. Other functions are also available to
23591 plot adjusted curves for Cox model and to visually examine Cox model
23593 (license license:gpl2)))
23595 (define-public r-forge
23602 (uri (cran-uri "forge" version))
23605 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
23606 (properties `((upstream-name . "forge")))
23607 (build-system r-build-system)
23609 `(("r-magrittr" ,r-magrittr)
23610 ("r-rlang" ,r-rlang)))
23611 (home-page "https://cran.r-project.org/web/packages/forge/")
23612 (synopsis "Cast values into shape")
23614 "This package provides helper functions with a consistent interface to
23615 coerce and verify the types and shapes of values for input checking.")
23616 (license license:asl2.0)))
23618 (define-public r-config
23625 (uri (cran-uri "config" version))
23628 "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs"))))
23629 (properties `((upstream-name . "config")))
23630 (build-system r-build-system)
23632 `(("r-yaml" ,r-yaml)))
23634 `(("r-knitr" ,r-knitr)))
23635 (home-page "https://github.com/rstudio/config")
23636 (synopsis "Manage environment specific configuration values")
23638 "This package lets you manage configuration values across multiple
23639 environments (e.g. development, test, production). It reads values using a
23640 function that determines the current environment and returns the appropriate
23642 (license license:gpl3)))
23644 (define-public r-workflows
23646 (name "r-workflows")
23651 (uri (cran-uri "workflows" version))
23654 "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
23655 (properties `((upstream-name . "workflows")))
23656 (build-system r-build-system)
23659 ("r-ellipsis" ,r-ellipsis)
23660 ("r-generics" ,r-generics)
23662 ("r-hardhat" ,r-hardhat)
23663 ("r-parsnip" ,r-parsnip)
23664 ("r-rlang" ,r-rlang)))
23666 `(("r-knitr" ,r-knitr)))
23667 (home-page "https://github.com/tidymodels/workflows")
23668 (synopsis "Modeling workflows")
23670 "A workflow is an object that can bundle together your pre-processing,
23671 modeling, and post-processing requests. For example, if you have a
23672 @code{recipe} and @code{parsnip} model, these can be combined into a
23673 workflow. The advantages are:
23676 @item You don’t have to keep track of separate objects in your workspace.
23677 @item The recipe prepping and model fitting can be executed using a single
23678 call to @code{fit()}.
23679 @item If you have custom tuning parameter settings, these can be defined using
23680 a simpler interface when combined with @code{tune}.
23681 @item In the future, workflows will be able to add post-processing operations,
23682 such as modifying the probability cutoff for two-class models.
23685 (license license:expat)))
23687 (define-public r-gpfit
23694 (uri (cran-uri "GPfit" version))
23697 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
23698 (properties `((upstream-name . "GPfit")))
23699 (build-system r-build-system)
23701 `(("r-lattice" ,r-lattice)
23703 (home-page "https://cran.r-project.org/web/packages/GPfit/")
23704 (synopsis "Gaussian Processes modeling")
23706 "This package provides a computationally stable approach of fitting a
23707 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
23708 (license license:gpl2)))
23710 (define-public r-yardstick
23712 (name "r-yardstick")
23717 (uri (cran-uri "yardstick" version))
23720 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
23721 (properties `((upstream-name . "yardstick")))
23722 (build-system r-build-system)
23724 `(("r-dplyr" ,r-dplyr)
23725 ("r-generics" ,r-generics)
23727 ("r-rlang" ,r-rlang)
23728 ("r-tidyselect" ,r-tidyselect)))
23730 `(("r-knitr" ,r-knitr)))
23731 (home-page "https://github.com/tidymodels/yardstick")
23732 (synopsis "Tidy characterizations of model performance")
23734 "This package provides tidy tools for quantifying how well a model fits
23735 to a data set such as confusion matrices, class probability curve summaries,
23736 and regression metrics (e.g., RMSE).")
23737 (license license:gpl2)))
23739 (define-public r-rsample
23746 (uri (cran-uri "rsample" version))
23749 "0s6hgq0rcv3ianyidq3n9z34y5ww51gaggqkwmwns9yyxmwfjcm8"))))
23750 (properties `((upstream-name . "rsample")))
23751 (build-system r-build-system)
23753 `(("r-dplyr" ,r-dplyr)
23754 ("r-furrr" ,r-furrr)
23755 ("r-generics" ,r-generics)
23756 ("r-purrr" ,r-purrr)
23757 ("r-rlang" ,r-rlang)
23758 ("r-tibble" ,r-tibble)
23759 ("r-tidyr" ,r-tidyr)
23760 ("r-tidyselect" ,r-tidyselect)
23761 ("r-vctrs" ,r-vctrs)))
23763 `(("r-knitr" ,r-knitr)))
23764 (home-page "https://rsample.tidymodels.org")
23765 (synopsis "General resampling infrastructure")
23767 "This package provides classes and functions to create and summarize
23768 different types of resampling objects (e.g. bootstrap, cross-validation).")
23769 (license license:gpl2)))
23771 (define-public r-dicedesign
23773 (name "r-dicedesign")
23778 (uri (cran-uri "DiceDesign" version))
23781 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
23782 (properties `((upstream-name . "DiceDesign")))
23783 (build-system r-build-system)
23784 (home-page "http://dice.emse.fr/")
23785 (synopsis "Designs of computer experiments")
23787 "This package provides tools to create some specific @code{Space-Filling
23788 Design} (SFD) and to test their quality.")
23789 (license license:gpl3)))
23791 (define-public r-dials
23798 (uri (cran-uri "dials" version))
23801 "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
23802 (properties `((upstream-name . "dials")))
23803 (build-system r-build-system)
23805 `(("r-dicedesign" ,r-dicedesign)
23806 ("r-dplyr" ,r-dplyr)
23808 ("r-purrr" ,r-purrr)
23809 ("r-rlang" ,r-rlang)
23810 ("r-scales" ,r-scales)
23811 ("r-tibble" ,r-tibble)
23812 ("r-vctrs" ,r-vctrs)
23813 ("r-withr" ,r-withr)))
23814 (native-inputs `(("r-knitr" ,r-knitr)))
23815 (home-page "https://dials.tidymodels.org/")
23816 (synopsis "Tools for creating tuning parameter values")
23818 "Many models contain tuning parameters (i.e. parameters that cannot be
23819 directly estimated from the data). These tools can be used to define objects
23820 for creating, simulating, or validating values for such parameters.")
23821 (license license:gpl2)))
23823 (define-public r-tune
23830 (uri (cran-uri "tune" version))
23833 "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
23834 (properties `((upstream-name . "tune")))
23835 (build-system r-build-system)
23838 ("r-crayon" ,r-crayon)
23839 ("r-dials" ,r-dials)
23840 ("r-dplyr" ,r-dplyr)
23841 ("r-foreach" ,r-foreach)
23842 ("r-ggplot2" ,r-ggplot2)
23844 ("r-gpfit" ,r-gpfit)
23845 ("r-hardhat" ,r-hardhat)
23846 ("r-lifecycle" ,r-lifecycle)
23847 ("r-parsnip" ,r-parsnip)
23848 ("r-purrr" ,r-purrr)
23849 ("r-recipes" ,r-recipes)
23850 ("r-rlang" ,r-rlang)
23851 ("r-rsample" ,r-rsample)
23852 ("r-tibble" ,r-tibble)
23853 ("r-tidyr" ,r-tidyr)
23854 ("r-vctrs" ,r-vctrs)
23855 ("r-workflows" ,r-workflows)
23856 ("r-yardstick" ,r-yardstick)))
23857 (home-page "https://github.com/tidymodels/tune")
23858 (synopsis "Tidy tuning tools")
23860 "The ability to tune models is important. @code{tune} contains functions
23861 and classes to be used in conjunction with other @code{tidymodels} packages
23862 for finding reasonable values of hyper-parameters in models, pre-processing
23863 methods, and post-processing steps.")
23864 (license license:expat)))
23866 (define-public r-tidyposterior
23868 (name "r-tidyposterior")
23873 (uri (cran-uri "tidyposterior" version))
23876 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
23877 (properties `((upstream-name . "tidyposterior")))
23878 (build-system r-build-system)
23880 `(("r-dplyr" ,r-dplyr)
23881 ("r-generics" ,r-generics)
23882 ("r-ggplot2" ,r-ggplot2)
23883 ("r-lifecycle" ,r-lifecycle)
23884 ("r-purrr" ,r-purrr)
23885 ("r-rlang" ,r-rlang)
23886 ("r-rsample" ,r-rsample)
23887 ("r-rstanarm" ,r-rstanarm)
23888 ("r-tibble" ,r-tibble)
23889 ("r-tidyr" ,r-tidyr)
23890 ("r-vctrs" ,r-vctrs)))
23892 `(("r-knitr" ,r-knitr)))
23893 (home-page "https://tidyposterior.tidymodels.org")
23894 (synopsis "Bayesian analysis to compare models using resampling statistics")
23896 "This package can be used to conduct post hoc analyses of resampling
23897 results generated by models. For example, if two models are evaluated with
23898 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
23899 are 10 paired statistics. These can be used to make comparisons between
23900 models without involving a test set.")
23901 (license license:gpl2)))
23903 (define-public r-tidypredict
23905 (name "r-tidypredict")
23910 (uri (cran-uri "tidypredict" version))
23913 "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
23914 (properties `((upstream-name . "tidypredict")))
23915 (build-system r-build-system)
23917 `(("r-dplyr" ,r-dplyr)
23918 ("r-generics" ,r-generics)
23919 ("r-knitr" ,r-knitr)
23920 ("r-purrr" ,r-purrr)
23921 ("r-rlang" ,r-rlang)
23922 ("r-tibble" ,r-tibble)))
23924 `(("r-knitr" ,r-knitr)))
23925 (home-page "https://tidypredict.tidymodels.org")
23926 (synopsis "Run predictions inside the database")
23928 "This package parses a fitted R model object, and returns a formula in
23929 Tidy Eval code that calculates the predictions. It works with several
23930 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
23931 final SQL translation of the algorithm. It currently supports @code{lm()},
23932 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
23933 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
23934 (license license:gpl3)))
23936 (define-public r-janeaustenr
23938 (name "r-janeaustenr")
23943 (uri (cran-uri "janeaustenr" version))
23946 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
23947 (properties `((upstream-name . "janeaustenr")))
23948 (build-system r-build-system)
23949 (home-page "https://github.com/juliasilge/janeaustenr")
23950 (synopsis "Jane Austen's complete novels")
23952 "This package provides the full texts for Jane Austen's six completed
23953 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
23954 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
23955 and \"Persuasion\".")
23956 (license license:expat)))
23958 (define-public r-tokenizers
23960 (name "r-tokenizers")
23965 (uri (cran-uri "tokenizers" version))
23968 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
23969 (properties `((upstream-name . "tokenizers")))
23970 (build-system r-build-system)
23972 `(("r-rcpp" ,r-rcpp)
23973 ("r-snowballc" ,r-snowballc)
23974 ("r-stringi" ,r-stringi)))
23976 `(("r-knitr" ,r-knitr)))
23977 (home-page "https://lincolnmullen.com/software/tokenizers/")
23978 (synopsis "Fast, consistent tokenization of natural language text")
23980 "This is a package for converting natural language text into tokens.
23981 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
23982 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
23983 Treebank, regular expressions, as well as functions for counting characters,
23984 words, and sentences, and a function for splitting longer texts into separate
23985 documents, each with the same number of words. The tokenizers have a
23986 consistent interface, and the package is built on the @code{stringi} and
23987 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
23988 (license license:expat)))
23990 (define-public r-hunspell
23992 (name "r-hunspell")
23997 (uri (cran-uri "hunspell" version))
24000 "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"))))
24001 (properties `((upstream-name . "hunspell")))
24002 (build-system r-build-system)
24004 `(("r-digest" ,r-digest)
24005 ("r-rcpp" ,r-rcpp)))
24007 `(("r-knitr" ,r-knitr)))
24008 (home-page "https://github.com/ropensci/hunspell#readme")
24009 (synopsis "High-performance stemmer, tokenizer, and spell checker")
24011 "This package provides a low-level spell checker and morphological
24012 analyzer based on the famous @code{hunspell} library. The package can analyze
24013 or check individual words as well as parse text, LaTeX, HTML or XML documents.
24014 For a more user-friendly interface use the @code{spelling} package which
24015 builds on this package to automate checking of files, documentation and
24016 vignettes in all common formats.")
24017 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
24018 ;; MPL; in addition to these licenses the rest of the R wrapper is also
24019 ;; available under the Expat license.
24020 (license (list license:gpl2
24025 (define-public r-tidytext
24027 (name "r-tidytext")
24032 (uri (cran-uri "tidytext" version))
24035 "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
24036 (properties `((upstream-name . "tidytext")))
24037 (build-system r-build-system)
24039 `(("r-dplyr" ,r-dplyr)
24040 ("r-generics" ,r-generics)
24041 ("r-hunspell" ,r-hunspell)
24042 ("r-janeaustenr" ,r-janeaustenr)
24043 ("r-matrix" ,r-matrix)
24044 ("r-purrr" ,r-purrr)
24045 ("r-rlang" ,r-rlang)
24046 ("r-stringr" ,r-stringr)
24047 ("r-tibble" ,r-tibble)
24048 ("r-tokenizers" ,r-tokenizers)))
24050 `(("r-knitr" ,r-knitr)))
24051 (home-page "https://github.com/juliasilge/tidytext")
24052 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
24054 "This is a package for text mining for word processing and sentiment
24055 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
24056 (license license:expat)))
24058 (define-public r-parsnip
24065 (uri (cran-uri "parsnip" version))
24068 "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
24069 (properties `((upstream-name . "parsnip")))
24070 (build-system r-build-system)
24072 `(("r-dplyr" ,r-dplyr)
24073 ("r-generics" ,r-generics)
24074 ("r-globals" ,r-globals)
24076 ("r-magrittr" ,r-magrittr)
24077 ("r-prettyunits" ,r-prettyunits)
24078 ("r-purrr" ,r-purrr)
24079 ("r-rlang" ,r-rlang)
24080 ("r-tibble" ,r-tibble)
24081 ("r-tidyr" ,r-tidyr)
24082 ("r-vctrs" ,r-vctrs)))
24084 `(("r-knitr" ,r-knitr)))
24085 (home-page "https://parsnip.tidymodels.org")
24086 (synopsis "Common API to modeling and analysis functions")
24088 "This package provides a common interface to allow users to specify a
24089 model without having to remember the different argument names across different
24090 functions or computational engines (e.g. R, Spark, Stan, etc).")
24091 (license license:gpl2)))
24093 (define-public r-infer
24100 (uri (cran-uri "infer" version))
24103 "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
24104 (properties `((upstream-name . "infer")))
24105 (build-system r-build-system)
24107 `(("r-dplyr" ,r-dplyr)
24108 ("r-ggplot2" ,r-ggplot2)
24110 ("r-magrittr" ,r-magrittr)
24111 ("r-purrr" ,r-purrr)
24112 ("r-rlang" ,r-rlang)
24113 ("r-tibble" ,r-tibble)))
24115 `(("r-knitr" ,r-knitr)))
24116 (home-page "https://github.com/tidymodels/infer")
24117 (synopsis "Tidy statistical inference")
24119 "The objective of this package is to perform inference using an
24120 expressive statistical grammar that coheres with the Tidy design framework.")
24121 (license license:cc0)))
24123 (define-public r-modeldata
24125 (name "r-modeldata")
24130 (uri (cran-uri "modeldata" version))
24133 "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
24134 (properties `((upstream-name . "modeldata")))
24135 (build-system r-build-system)
24136 (home-page "https://modeldata.tidymodels.org")
24137 (synopsis "Data sets useful for modeling packages")
24139 "This package provides data sets used for demonstrating or testing
24140 model-related packages.")
24141 (license license:expat)))
24143 (define-public r-tidymodels
24145 (name "r-tidymodels")
24150 (uri (cran-uri "tidymodels" version))
24153 "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
24154 (properties `((upstream-name . "tidymodels")))
24155 (build-system r-build-system)
24157 `(("r-broom" ,r-broom)
24159 ("r-crayon" ,r-crayon)
24160 ("r-dials" ,r-dials)
24161 ("r-dplyr" ,r-dplyr)
24162 ("r-ggplot2" ,r-ggplot2)
24163 ("r-infer" ,r-infer)
24164 ("r-magrittr" ,r-magrittr)
24165 ("r-modeldata" ,r-modeldata)
24166 ("r-parsnip" ,r-parsnip)
24167 ("r-purrr" ,r-purrr)
24168 ("r-recipes" ,r-recipes)
24169 ("r-rlang" ,r-rlang)
24170 ("r-rsample" ,r-rsample)
24171 ("r-rstudioapi" ,r-rstudioapi)
24172 ("r-tibble" ,r-tibble)
24173 ("r-tidyr" ,r-tidyr)
24175 ("r-workflows" ,r-workflows)
24176 ("r-yardstick" ,r-yardstick)))
24178 `(("r-knitr" ,r-knitr)
24179 ("r-rmarkdown" ,r-rmarkdown)
24181 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
24182 (home-page "https://github.com/tidymodels/tidymodels")
24183 (synopsis "Tidy collection for modeling and statistical analysis")
24185 "The tidy modeling \"verse\" is a collection of packages for modeling and
24186 statistical analysis that share the underlying design philosophy, grammar, and
24187 data structures of the tidyverse.")
24188 (license license:gpl3)))
24190 (define-public r-mlecens
24197 (uri (cran-uri "MLEcens" version))
24200 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
24201 (properties `((upstream-name . "MLEcens")))
24202 (build-system r-build-system)
24203 (home-page "http://stat.ethz.ch/~maathuis/")
24204 (synopsis "Computation of the MLE for bivariate (interval) censored data")
24206 "This package contains functions to compute the nonparametric
24207 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
24208 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
24209 To be more precise, we consider the situation where we observe a set of
24210 rectangles that are known to contain the unobservable realizations of (X,Y).
24211 We compute the MLE based on such a set of rectangles. The methods can also be
24212 used for univariate censored data (see data set @code{cosmesis}), and for
24213 censored data with competing risks (see data set @code{menopause}). The
24214 package also provides functions to visualize the observed data and the MLE.")
24215 (license license:gpl2+)))
24217 (define-public r-perm
24220 (version "1.0-0.0")
24224 (uri (cran-uri "perm" version))
24227 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
24228 (properties `((upstream-name . "perm")))
24229 (build-system r-build-system)
24230 (home-page "https://cran.r-project.org/web/packages/perm/")
24231 (synopsis "Exact or asymptotic permutation tests")
24233 "This package provides several methods for performing permutation tests.
24234 It has three main functions, to perform linear permutation tests. These tests
24235 are tests where the test statistic is the sum of the product of a
24236 covariate (usually group indicator) and the scores.")
24237 ;; Any version of the GPL
24238 (license license:gpl2+)))