1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
21 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
22 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
23 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
24 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
26 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
28 ;;; This file is part of GNU Guix.
30 ;;; GNU Guix is free software; you can redistribute it and/or modify it
31 ;;; under the terms of the GNU General Public License as published by
32 ;;; the Free Software Foundation; either version 3 of the License, or (at
33 ;;; your option) any later version.
35 ;;; GNU Guix is distributed in the hope that it will be useful, but
36 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
37 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
38 ;;; GNU General Public License for more details.
40 ;;; You should have received a copy of the GNU General Public License
41 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
43 (define-module (gnu packages cran)
44 #:use-module ((guix licenses) #:prefix license:)
45 #:use-module (guix packages)
46 #:use-module (guix download)
47 #:use-module (guix git-download)
48 #:use-module (guix utils)
49 #:use-module (guix build-system r)
50 #:use-module (gnu packages algebra)
51 #:use-module (gnu packages autotools)
52 #:use-module (gnu packages base)
53 #:use-module (gnu packages bioinformatics)
54 #:use-module (gnu packages c)
55 #:use-module (gnu packages compression)
56 #:use-module (gnu packages curl)
57 #:use-module (gnu packages databases)
58 #:use-module (gnu packages fontutils)
59 #:use-module (gnu packages gcc)
60 #:use-module (gnu packages geo)
61 #:use-module (gnu packages ghostscript)
62 #:use-module (gnu packages gl)
63 #:use-module (gnu packages gnome)
64 #:use-module (gnu packages graph)
65 #:use-module (gnu packages gtk)
66 #:use-module (gnu packages haskell-xyz)
67 #:use-module (gnu packages icu4c)
68 #:use-module (gnu packages image)
69 #:use-module (gnu packages imagemagick)
70 #:use-module (gnu packages java)
71 #:use-module (gnu packages javascript)
72 #:use-module (gnu packages lisp-xyz)
73 #:use-module (gnu packages machine-learning)
74 #:use-module (gnu packages maths)
75 #:use-module (gnu packages mpi)
76 #:use-module (gnu packages multiprecision)
77 #:use-module (gnu packages networking)
78 #:use-module (gnu packages node)
79 #:use-module (gnu packages pcre)
80 #:use-module (gnu packages perl)
81 #:use-module (gnu packages pkg-config)
82 #:use-module (gnu packages pulseaudio) ;libsndfile
83 #:use-module (gnu packages python)
84 #:use-module (gnu packages python-xyz)
85 #:use-module (gnu packages statistics)
86 #:use-module (gnu packages tcl)
87 #:use-module (gnu packages tls)
88 #:use-module (gnu packages web)
89 #:use-module (gnu packages xorg))
91 (define-public r-rticles
98 (uri (cran-uri "rticles" version))
101 "1377fib4asazhhki4aajvld0wa35vd3zjvyl3lf2hjm2qk3vyak7"))))
102 (properties `((upstream-name . "rticles")))
103 (build-system r-build-system)
105 `(("r-knitr" ,r-knitr)
106 ("r-rmarkdown" ,r-rmarkdown)
107 ("r-tinytex" ,r-tinytex)
110 (home-page "https://github.com/rstudio/rticles")
111 (synopsis "Article formats for R Markdown")
113 "This package provides a suite of custom R Markdown formats and templates
114 for authoring journal articles and conference submissions.")
115 (license license:gpl3)))
117 (define-public r-bezier
123 (uri (cran-uri "bezier" version))
126 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
127 (build-system r-build-system)
128 (home-page "https://cran.r-project.org/web/packages/bezier/")
129 (synopsis "Bezier curve and spline toolkit")
131 "This package is a toolkit for working with Bezier curves and splines.
132 The package provides functions for point generation, arc length estimation,
133 degree elevation and curve fitting.")
134 (license license:gpl2+)))
143 (uri (cran-uri "V8" version))
146 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
147 (properties `((upstream-name . "V8")))
148 (build-system r-build-system)
151 (modify-phases %standard-phases
152 (add-after 'unpack 'find-v8
153 (lambda* (#:key inputs #:allow-other-keys)
154 (substitute* "configure"
156 (string-append "PKG_LIBS="
157 (assoc-ref inputs "node")
158 "/lib/libnode.so.64\n")))
159 (setenv "INCLUDE_DIR"
161 (assoc-ref inputs "node")
165 (assoc-ref inputs "node") "/lib"))
168 `(("node" ,libnode)))
171 ("r-jsonlite" ,r-jsonlite)
174 `(("r-knitr" ,r-knitr)))
175 (home-page "https://jeroen.cran.dev/V8")
176 (synopsis "Embedded JavaScript and WebAssembly engine for R")
178 "This package provides an R interface to V8: Google's JavaScript and
179 WebAssembly engine.")
180 (license license:expat)))
189 (uri (cran-uri "DOT" version))
192 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
193 (properties `((upstream-name . "DOT")))
194 (build-system r-build-system)
197 (home-page "http://haghish.com/dot")
198 (synopsis "Render and Export DOT Graphs in R")
200 "This package provides tools to render DOT diagram markup language in R
201 and also provides the possibility to export the graphs in PostScript and
202 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
203 programming packages such as @code{knitr} and @code{rmarkdown}.")
204 (license license:expat)))
206 (define-public r-clipr
213 (uri (cran-uri "clipr" version))
216 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
217 (build-system r-build-system)
218 (home-page "https://github.com/mdlincoln/clipr")
219 (synopsis "Read and write from the system clipboard")
221 "This package provides simple utility functions to read from and write to
222 the system clipboards.")
223 (license license:gpl3)))
231 (uri (cran-uri "zoo" version))
234 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
235 (build-system r-build-system)
237 `(("r-lattice" ,r-lattice)))
238 (home-page "http://zoo.R-Forge.R-project.org/")
239 (synopsis "S3 infrastructure for regular and irregular time series")
240 (description "This package contains an S3 class with methods for totally
241 ordered indexed observations. It is particularly aimed at irregular time
242 series of numeric vectors/matrices and factors.")
243 (license license:gpl2+)))
245 (define-public r-ggpmisc
251 (uri (cran-uri "ggpmisc" version))
254 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
255 (build-system r-build-system)
257 `(("r-broom" ,r-broom)
259 ("r-ggplot2" ,r-ggplot2)
260 ("r-gridextra" ,r-gridextra)
261 ("r-lubridate" ,r-lubridate)
262 ("r-magrittr" ,r-magrittr)
265 ("r-polynom" ,r-polynom)
267 ("r-scales" ,r-scales)
268 ("r-splus2r" ,r-splus2r)
269 ("r-stringr" ,r-stringr)
270 ("r-tibble" ,r-tibble)
274 `(("r-knitr" ,r-knitr)))
275 (home-page "https://www.r4photobiology.info/")
276 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
277 (description "This package provides extensions to @code{ggplot2},
278 respecting the grammar of its graphics paradigm.")
279 (license license:gpl2+)))
281 (define-public r-gprofiler
288 (uri (cran-uri "gProfileR" version))
291 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
292 (properties `((upstream-name . "gProfileR")))
293 (build-system r-build-system)
296 ("r-rcurl" ,r-rcurl)))
297 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
298 (synopsis "Interface to the g:Profiler toolkit")
300 "This package provides tools for functional enrichment analysis,
301 gene identifier conversion and mapping homologous genes across related
302 organisms via the @code{g:Profiler} toolkit.")
303 (license license:gpl2+)))
305 (define-public r-gprofiler2
307 (name "r-gprofiler2")
312 (uri (cran-uri "gprofiler2" version))
315 "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
316 (properties `((upstream-name . "gprofiler2")))
317 (build-system r-build-system)
319 `(("r-crosstalk" ,r-crosstalk)
321 ("r-ggplot2" ,r-ggplot2)
322 ("r-gridextra" ,r-gridextra)
323 ("r-jsonlite" ,r-jsonlite)
324 ("r-plotly" ,r-plotly)
327 ("r-viridislite" ,r-viridislite)))
328 (native-inputs `(("r-knitr" ,r-knitr)))
329 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
330 (synopsis "Interface to the g:Profiler toolset")
332 "This package provides a toolset for functional enrichment analysis and
333 visualization, gene/protein/SNP identifier conversion and mapping orthologous
334 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
338 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
340 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
342 @item @code{g:Orth}, orthology search across species;
343 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
344 genes and variant effects.
347 This package is an R interface corresponding to the 2019 update of
348 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
350 (license license:gpl2+)))
352 (define-public r-oenb
359 (uri (cran-uri "oenb" version))
362 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
363 (properties `((upstream-name . "oenb")))
364 (build-system r-build-system)
366 `(("r-dplyr" ,r-dplyr)
368 (native-inputs `(("r-knitr" ,r-knitr)))
369 (home-page "https://github.com/franzmohr/oenb")
370 (synopsis "Tools for the OeNB Data Web Service")
372 "Tools to access data from the data web service of the
373 @acronym{OeNB, Oesterreichische Nationalbank},
374 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
375 (license license:gpl2+)))
377 (define-public r-scales
384 (uri (cran-uri "scales" version))
386 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
387 (build-system r-build-system)
389 `(("r-farver" ,r-farver)
390 ("r-labeling" ,r-labeling)
391 ("r-lifecycle" ,r-lifecycle)
392 ("r-munsell" ,r-munsell)
393 ("r-rcolorbrewer" ,r-rcolorbrewer)
395 ("r-viridislite" ,r-viridislite)))
396 (home-page "https://github.com/hadley/scales")
397 (synopsis "Scale functions for visualization")
399 "This package provides graphical scales that map data to aesthetics, and
400 provides methods for automatically determining breaks and labels for axes and
402 (license license:expat)))
404 (define-public r-pheatmap
411 (uri (cran-uri "pheatmap" version))
414 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
415 (build-system r-build-system)
417 `(("r-gtable" ,r-gtable)
418 ("r-rcolorbrewer" ,r-rcolorbrewer)
419 ("r-scales" ,r-scales)))
420 (home-page "https://cran.r-project.org/web/packages/pheatmap")
421 (synopsis "Pretty heatmaps")
423 "This package provides an implementation of heatmaps that offers more
424 control over dimensions and appearance.")
425 (license license:gpl2+)))
433 (uri (cran-uri "ecp" version))
436 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
437 (build-system r-build-system)
439 `(("r-rcpp" ,r-rcpp)))
440 (home-page "https://cran.r-project.org/web/packages/ecp/")
441 (synopsis "Multiple change-point analysis of multivariate data")
443 "This package implements various procedures for finding multiple
444 change-points. Two methods make use of dynamic programming and pruning, with
445 no distributional assumptions other than the existence of certain absolute
446 moments in one method. Hierarchical and exact search methods are included.
447 All methods return the set of estimated change-points as well as other summary
449 (license license:gpl2+)))
451 (define-public r-ellipsis
458 (uri (cran-uri "ellipsis" version))
461 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
462 (build-system r-build-system)
464 `(("r-rlang" ,r-rlang)))
465 (home-page "https://github.com/hadley/ellipsis")
466 (synopsis "Tools for working with additional arguments")
468 "In S3 generics, it's useful to take @code{...} so that methods can have
469 additional arguments. But this flexibility comes at a cost: misspelled
470 arguments will be silently ignored. The @code{ellipsis} package is an
471 experiment that allows a generic to warn if any arguments passed in @code{...}
473 (license license:gpl3)))
482 (uri (cran-uri "grr" version))
485 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
486 (build-system r-build-system)
487 (home-page "https://cran.r-project.org/web/packages/grr")
488 (synopsis "Alternative implementations of base R functions")
490 "This package provides alternative implementations of some base R
491 functions, including @code{sort}, @code{order}, and @code{match}. The
492 functions are simplified but can be faster or have other advantages.")
493 (license license:gpl3)))
495 (define-public r-matrix-utils
497 (name "r-matrix-utils")
502 (uri (cran-uri "Matrix.utils" version))
505 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
506 (properties `((upstream-name . "Matrix.utils")))
507 (build-system r-build-system)
510 ("r-matrix" ,r-matrix)))
511 (home-page "https://github.com/cvarrichio/Matrix.utils")
513 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
515 "This package implements data manipulation methods such as @code{cast},
516 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
518 (license license:gpl3)))
527 (uri (cran-uri "sys" version))
530 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
531 (build-system r-build-system)
532 (home-page "https://github.com/jeroen/sys")
533 (synopsis "Powerful and reliable tools for running system commands in R")
535 "This package provides drop-in replacements for the base @code{system2()}
536 function with fine control and consistent behavior across platforms. It
537 supports clean interruption, timeout, background tasks, and streaming STDIN /
538 STDOUT / STDERR over binary or text connections. The package also provides
539 functions for evaluating expressions inside a temporary fork. Such
540 evaluations have no side effects on the main R process, and support reliable
541 interrupts and timeouts. This provides the basis for a sandboxing
543 (license license:expat)))
545 (define-public r-askpass
552 (uri (cran-uri "askpass" version))
555 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
556 (build-system r-build-system)
557 (propagated-inputs `(("r-sys" ,r-sys)))
558 (home-page "https://github.com/jeroen/askpass")
559 (synopsis "Safe password entry for R")
561 "This package provides cross-platform utilities for prompting the user
562 for credentials or a passphrase, for example to authenticate with a server or
563 read a protected key.")
564 (license license:expat)))
566 (define-public r-vegan
573 (uri (cran-uri "vegan" version))
576 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
577 (build-system r-build-system)
579 `(("gfortran" ,gfortran)))
581 `(("r-cluster" ,r-cluster)
582 ("r-knitr" ,r-knitr) ; needed for vignettes
583 ("r-lattice" ,r-lattice)
586 ("r-permute" ,r-permute)))
587 (home-page "https://cran.r-project.org/web/packages/vegan")
588 (synopsis "Functions for community ecology")
590 "The vegan package provides tools for descriptive community ecology. It
591 has most basic functions of diversity analysis, community ordination and
592 dissimilarity analysis. Most of its multivariate tools can be used for other
593 data types as well.")
594 (license license:gpl2+)))
596 (define-public r-tidyverse
603 (uri (cran-uri "tidyverse" version))
606 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
607 (build-system r-build-system)
609 `(("r-broom" ,r-broom)
611 ("r-crayon" ,r-crayon)
612 ("r-dbplyr" ,r-dbplyr)
614 ("r-forcats" ,r-forcats)
615 ("r-ggplot2" ,r-ggplot2)
619 ("r-jsonlite" ,r-jsonlite)
620 ("r-lubridate" ,r-lubridate)
621 ("r-magrittr" ,r-magrittr)
622 ("r-modelr" ,r-modelr)
623 ("r-pillar" ,r-pillar)
626 ("r-readxl" ,r-readxl)
627 ("r-reprex" ,r-reprex)
629 ("r-rstudioapi" ,r-rstudioapi)
631 ("r-stringr" ,r-stringr)
632 ("r-tibble" ,r-tibble)
635 (home-page "https://tidyverse.tidyverse.org")
636 (synopsis "Install and load packages from the \"Tidyverse\"")
638 "The @code{tidyverse} is a set of packages that work in harmony because
639 they share common data representations and API design. This package is
640 designed to make it easy to install and load multiple tidyverse packages in a
642 (license license:gpl3)))
644 (define-public r-rvest
651 (uri (cran-uri "rvest" version))
653 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
654 (build-system r-build-system)
657 ("r-magrittr" ,r-magrittr)
658 ("r-selectr" ,r-selectr)
660 (home-page "https://github.com/hadley/rvest")
661 (synopsis "Simple web scraping for R")
663 "@code{r-rvest} helps you scrape information from web pages. It is
664 designed to work with @code{magrittr} to make it easy to express common web
665 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
666 (license license:gpl3)))
668 (define-public r-selectr
675 (uri (cran-uri "selectr" version))
677 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
678 (build-system r-build-system)
680 `(("r-stringr" ,r-stringr)
682 (home-page "https://sjp.co.nz/projects/selectr/")
683 (synopsis "Translate CSS selectors to XPath expressions")
685 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
686 expression. This allows you to use CSS selectors when working with the XML
687 package as it can only evaluate XPath expressions. Also provided are
688 convenience functions useful for using CSS selectors on XML nodes. This
689 package is a port of the Python package @code{cssselect}.")
690 (license license:bsd-3)))
692 (define-public r-reprex
699 (uri (cran-uri "reprex" version))
702 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
703 (build-system r-build-system)
705 `(("r-callr" ,r-callr)
709 ("r-rmarkdown" ,r-rmarkdown)
710 ("r-whisker" ,r-whisker)
711 ("r-withr" ,r-withr)))
712 (home-page "https://github.com/tidyverse/reprex")
713 (synopsis "Prepare reproducible R code examples for sharing")
715 "This package provides a convenience wrapper that uses the
716 @code{rmarkdown} package to render small snippets of code to target formats
717 that include both code and output. The goal is to encourage the sharing of
718 small, reproducible, and runnable examples on code-oriented websites or email.
719 @code{reprex} also extracts clean, runnable R code from various common formats,
720 such as copy/paste from an R session.")
721 (license license:expat)))
723 (define-public r-reordercluster
725 (name "r-reordercluster")
729 (uri (cran-uri "ReorderCluster" version))
732 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
733 (build-system r-build-system)
735 `(("r-gplots" ,r-gplots)
737 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
738 (synopsis "Reordering the dendrogram according to the class labels")
739 (description "This package provides tools for performing the leaf reordering
740 for the dendrogram that preserves the hierarchical clustering result and at the
741 same time tries to group instances from the same class together.")
742 (license license:gpl3+)))
744 (define-public r-callr
751 (uri (cran-uri "callr" version))
754 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
755 (build-system r-build-system)
758 ("r-processx" ,r-processx)))
759 (home-page "https://github.com/r-lib/callr#readme")
760 (synopsis "Call R from R")
762 "It is sometimes useful to perform a computation in a separate R process,
763 without affecting the current R process at all. This package does exactly
765 (license license:expat)))
767 (define-public r-readxl
774 (uri (cran-uri "readxl" version))
777 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
778 (build-system r-build-system)
780 `(("r-cellranger" ,r-cellranger)
781 ("r-progress" ,r-progress)
783 ("r-tibble" ,r-tibble)))
784 (home-page "https://readxl.tidyverse.org")
785 (synopsis "Read Excel files")
787 "This package lets you import Excel files into R. It supports
788 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
789 the embedded @code{RapidXML} C++ library.")
790 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
791 ;; 'rapidxml' which is Boost.
792 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
794 (define-public r-modelr
801 (uri (cran-uri "modelr" version))
804 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
805 (build-system r-build-system)
807 `(("r-broom" ,r-broom)
808 ("r-magrittr" ,r-magrittr)
811 ("r-tibble" ,r-tibble)
813 ("r-tidyselect" ,r-tidyselect)
814 ("r-vctrs" ,r-vctrs)))
815 (home-page "https://github.com/tidyverse/modelr")
816 (synopsis "Helper functions for modelling in pipelines")
818 "Functions for modelling that help you seamlessly integrate modelling
819 into a pipeline of data manipulation and visualisation.")
820 (license license:gpl3)))
822 (define-public r-httpuv
828 (uri (cran-uri "httpuv" version))
831 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
832 (build-system r-build-system)
836 ("r-promises" ,r-promises)
839 (home-page "https://github.com/rstudio/httpuv")
840 (synopsis "HTTP and WebSocket server library for R")
842 "The httpuv package provides low-level socket and protocol support for
843 handling HTTP and WebSocket requests directly from within R. It is primarily
844 intended as a building block for other packages, rather than making it
845 particularly easy to create complete web applications using httpuv alone.")
846 ;; This package includes third-party code that was originally released
847 ;; under various non-copyleft licenses. Full licensing information can be
848 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
849 (license license:gpl3+)))
851 (define-public r-jsonlite
857 (uri (cran-uri "jsonlite" version))
860 "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
861 (build-system r-build-system)
863 `(("r-knitr" ,r-knitr)))
864 (home-page "https://arxiv.org/abs/1403.2805")
865 (synopsis "Robust, high performance JSON parser and generator for R")
867 "The jsonlite package provides a fast JSON parser and generator optimized
868 for statistical data and the web. It offers flexible, robust, high
869 performance tools for working with JSON in R and is particularly powerful for
870 building pipelines and interacting with a web API. In addition to converting
871 JSON data from/to R objects, jsonlite contains functions to stream, validate,
872 and prettify JSON data. The unit tests included with the package verify that
873 all edge cases are encoded and decoded consistently for use with dynamic data
874 in systems and applications.")
875 (license license:expat)))
877 (define-public r-servr
883 (uri (cran-uri "servr" version))
886 "0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7"))))
887 (build-system r-build-system)
889 `(("r-httpuv" ,r-httpuv)
890 ("r-jsonlite" ,r-jsonlite)
893 (home-page "https://github.com/yihui/servr")
894 (synopsis "Simple HTTP server to serve static files or dynamic documents")
896 "Servr provides an HTTP server in R to serve static files, or dynamic
897 documents that can be converted to HTML files (e.g., R Markdown) under a given
899 (license license:expat)))
901 (define-public r-htmltools
907 (uri (cran-uri "htmltools" version))
910 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
911 (build-system r-build-system)
913 `(("r-base64enc" ,r-base64enc)
914 ("r-digest" ,r-digest)
915 ("r-rlang" ,r-rlang)))
916 (home-page "https://cran.r-project.org/web/packages/htmltools")
917 (synopsis "R tools for HTML")
919 "This package provides tools for HTML generation and output in R.")
920 (license license:expat)))
922 (define-public r-htmlwidgets
924 (name "r-htmlwidgets")
928 (uri (cran-uri "htmlwidgets" version))
931 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
932 (build-system r-build-system)
934 `(("r-htmltools" ,r-htmltools)
935 ("r-jsonlite" ,r-jsonlite)
937 (home-page "https://github.com/ramnathv/htmlwidgets")
938 (synopsis "HTML Widgets for R")
940 "HTML widgets is a framework for creating HTML widgets that render in
941 various contexts including the R console, R Markdown documents, and Shiny web
943 (license license:expat)))
945 (define-public r-htmltable
952 (uri (cran-uri "htmlTable" version))
954 (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6"))))
955 (properties `((upstream-name . "htmlTable")))
956 (build-system r-build-system)
958 `(("r-checkmate" ,r-checkmate)
959 ("r-htmltools" ,r-htmltools)
960 ("r-htmlwidgets" ,r-htmlwidgets)
962 ("r-magrittr" ,r-magrittr)
963 ("r-rstudioapi" ,r-rstudioapi)
964 ("r-stringr" ,r-stringr)))
966 `(("r-knitr" ,r-knitr)))
967 (home-page "http://gforge.se/packages/")
968 (synopsis "Advanced tables for Markdown/HTML")
970 "This package provides functions to build tables with advanced layout
971 elements such as row spanners, column spanners, table spanners, zebra
972 striping, and more. While allowing advanced layout, the underlying
973 CSS-structure is simple in order to maximize compatibility with word
974 processors such as LibreOffice. The package also contains a few text
975 formatting functions that help outputting text compatible with HTML or
977 (license license:gpl3+)))
979 (define-public r-curl
985 (uri (cran-uri "curl" version))
988 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
989 (build-system r-build-system)
992 (modify-phases %standard-phases
993 ;; The environment variable CURL_CA_BUNDLE is only respected when
994 ;; running Windows, so we disable the platform checks.
995 ;; This can be removed once the libcurl has been patched.
996 (add-after 'unpack 'allow-CURL_CA_BUNDLE
998 (substitute* "R/onload.R"
999 (("if \\(!grepl\\(\"mingw\".*")
1001 (substitute* "src/handle.c"
1002 (("/\\* Only set" m)
1004 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1005 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1012 `(("pkg-config" ,pkg-config)))
1013 (home-page "https://github.com/jeroenooms/curl")
1014 (synopsis "HTTP client for R")
1016 "The @code{curl()} and @code{curl_download()} functions provide highly
1017 configurable drop-in replacements for base @code{url()} and
1018 @code{download.file()} with better performance, support for encryption, gzip
1019 compression, authentication, and other @code{libcurl} goodies. The core of
1020 the package implements a framework for performing fully customized requests
1021 where data can be processed either in memory, on disk, or streaming via the
1022 callback or connection interfaces.")
1023 (license license:expat)))
1025 (define-public r-hwriter
1032 (uri (cran-uri "hwriter" version))
1035 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1036 (build-system r-build-system)
1037 (home-page "https://cran.r-project.org/web/packages/hwriter")
1038 (synopsis "Output R objects in HTML format")
1040 "This package provides easy-to-use and versatile functions to output R
1041 objects in HTML format.")
1042 (license license:lgpl2.1+)))
1044 (define-public r-rjson
1051 (uri (cran-uri "rjson" version))
1054 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1055 (build-system r-build-system)
1056 (home-page "https://cran.r-project.org/web/packages/rjson")
1057 (synopsis "JSON library for R")
1059 "This package provides functions to convert R objects into JSON objects
1061 (license license:gpl2+)))
1063 (define-public r-fastmap
1070 (uri (cran-uri "fastmap" version))
1073 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1074 (properties `((upstream-name . "fastmap")))
1075 (build-system r-build-system)
1076 (home-page "https://r-lib.github.io/fastmap/")
1077 (synopsis "Fast implementation of a key-value store")
1079 "This package provides a fast implementation of a key-value store.
1080 Environments are commonly used as key-value stores, but every time a new key
1081 is used, it is added to R's global symbol table, causing a small amount of
1082 memory leakage. This can be problematic in cases where many different keys
1083 are used. Fastmap avoids this memory leak issue by implementing the map using
1084 data structures in C++.")
1085 (license license:expat)))
1087 (define-public r-shiny
1095 (url "https://github.com/rstudio/shiny")
1096 (commit (string-append "v" version))))
1097 (file-name (git-file-name name version))
1100 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1101 (build-system r-build-system)
1103 `(#:modules ((guix build r-build-system)
1104 (guix build minify-build-system)
1107 #:imported-modules (,@%r-build-system-modules
1108 (guix build minify-build-system))
1110 (modify-phases (@ (guix build r-build-system) %standard-phases)
1111 (add-after 'unpack 'replace-bundled-minified-JavaScript
1112 (lambda* (#:key inputs #:allow-other-keys)
1113 (let ((replace-file (lambda (old new)
1114 (format #t "replacing ~a with ~a\n" old new)
1116 (symlink new old))))
1117 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1118 ;; contain just data. They are not minified code, so we don't
1120 (with-directory-excursion "inst/www/shared"
1121 (replace-file "bootstrap/shim/respond.min.js"
1122 (string-append (assoc-ref inputs "js-respond")
1123 "/share/javascript/respond.min.js"))
1124 (replace-file "bootstrap/shim/html5shiv.min.js"
1125 (string-append (assoc-ref inputs "js-html5shiv")
1126 "/share/javascript/html5shiv.min.js"))
1127 (replace-file "json2-min.js"
1128 (string-append (assoc-ref inputs "js-json2")
1129 "/share/javascript/json2-min.js"))
1130 (replace-file "strftime/strftime-min.js"
1131 (string-append (assoc-ref inputs "js-strftime")
1132 "/share/javascript/strftime.min.js"))
1133 (replace-file "highlight/highlight.pack.js"
1134 (string-append (assoc-ref inputs "js-highlight")
1135 "/share/javascript/highlight.min.js"))
1136 (replace-file "datatables/js/jquery.dataTables.min.js"
1137 (string-append (assoc-ref inputs "js-datatables")
1138 "/share/javascript/jquery.dataTables.min.js"))
1139 (replace-file "selectize/js/selectize.min.js"
1140 (string-append (assoc-ref inputs "js-selectize")
1141 "/share/javascript/selectize.min.js"))
1142 (replace-file "selectize/js/es5-shim.min.js"
1143 (string-append (assoc-ref inputs "js-es5-shim")
1144 "/share/javascript/es5-shim.min.js"))
1145 (for-each (match-lambda
1147 (delete-file target)
1148 (minify source #:target target)))
1149 '(("jqueryui/jquery-ui.js" .
1150 "jqueryui/jquery-ui.min.js")
1151 ("datepicker/js/bootstrap-datepicker.js" .
1152 "datepicker/js/bootstrap-datepicker.min.js")
1153 ("ionrangeslider/js/ion.rangeSlider.js" .
1154 "ionrangeslider/js/ion.rangeSlider.min.js")
1155 ("bootstrap/js/bootstrap.js" .
1156 "bootstrap/js/bootstrap.min.js")
1161 ("legacy/jquery.js" .
1162 "legacy/jquery.min.js")
1163 ("showdown/src/showdown.js" .
1164 "showdown/compressed/showdown.js")))))
1167 `(("r-crayon" ,r-crayon)
1168 ("r-digest" ,r-digest)
1169 ("r-fastmap" ,r-fastmap)
1170 ("r-htmltools" ,r-htmltools)
1171 ("r-httpuv" ,r-httpuv)
1172 ("r-jsonlite" ,r-jsonlite)
1173 ("r-later" ,r-later)
1175 ("r-promises" ,r-promises)
1177 ("r-rlang" ,r-rlang)
1178 ("r-sourcetools" ,r-sourcetools)
1179 ("r-withr" ,r-withr)
1180 ("r-xtable" ,r-xtable)))
1182 `(("js-datatables" ,js-datatables)
1183 ("js-html5shiv" ,js-html5shiv)
1184 ("js-json2" ,js-json2)
1185 ("js-respond" ,js-respond)
1186 ("js-selectize" ,js-selectize)
1187 ("js-strftime" ,js-strftime)
1188 ("js-highlight" ,js-highlight)
1189 ("js-es5-shim" ,js-es5-shim)))
1191 `(("uglify-js" ,uglify-js)
1192 ("gfortran" ,gfortran)))
1193 (home-page "http://shiny.rstudio.com")
1194 (synopsis "Easy interactive web applications with R")
1196 "Makes it incredibly easy to build interactive web applications
1197 with R. Automatic \"reactive\" binding between inputs and outputs and
1198 extensive prebuilt widgets make it possible to build beautiful,
1199 responsive, and powerful applications with minimal effort.")
1200 (license license:artistic2.0)))
1202 ;; This package includes minified JavaScript files. When upgrading please
1203 ;; check that there are no new minified JavaScript files.
1204 (define-public r-shinytree
1206 (name "r-shinytree")
1211 (uri (cran-uri "shinyTree" version))
1214 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1215 (modules '((guix build utils)))
1218 ;; Delete minified JavaScript
1219 (for-each delete-file
1220 '("inst/www/jsTree-3.3.7/libs/require.js"
1221 "inst/www/jsTree-3.3.7/libs/jquery.js"
1222 "inst/www/jsTree-3.3.7/jstree.min.js"))
1224 (properties `((upstream-name . "shinyTree")))
1225 (build-system r-build-system)
1227 `(#:modules ((guix build utils)
1228 (guix build r-build-system)
1232 (modify-phases %standard-phases
1233 (add-after 'unpack 'replace-minified-javascript
1234 (lambda* (#:key inputs #:allow-other-keys)
1235 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1236 (symlink (string-append (assoc-ref inputs "js-requirejs")
1237 "/share/javascript/require.min.js")
1242 `((,(assoc-ref inputs "js-jquery")
1246 (lambda (sources targets)
1247 (for-each (lambda (source target)
1248 (format #t "Processing ~a --> ~a~%"
1250 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1251 (call-with-output-file target
1253 (dump-port minified port)))))
1257 `(("r-htmlwidgets" ,r-htmlwidgets)
1258 ("r-jsonlite" ,r-jsonlite)
1259 ("r-promises" ,r-promises)
1260 ("r-shiny" ,r-shiny)
1261 ("r-stringr" ,r-stringr)))
1263 `(("js-requirejs" ,js-requirejs)))
1265 `(("uglify-js" ,uglify-js)
1269 (uri "https://code.jquery.com/jquery-3.3.1.js")
1272 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1273 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1274 (synopsis "jsTree bindings for Shiny")
1276 "This package exposes R bindings to jsTree, a JavaScript library that
1277 supports interactive trees, to enable rich, editable trees in Shiny.")
1278 (license license:expat)))
1280 (define-public r-shinydashboard
1282 (name "r-shinydashboard")
1286 (uri (cran-uri "shinydashboard" version))
1289 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1290 (build-system r-build-system)
1291 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1292 ;; Regenerate it from the included sources.
1294 `(#:modules ((guix build utils)
1295 (guix build r-build-system)
1298 (modify-phases %standard-phases
1299 (add-after 'unpack 'generate-minified-javascript
1301 (with-directory-excursion "inst/AdminLTE"
1302 (delete-file "app.min.js")
1303 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1304 (call-with-output-file "app.min.js"
1306 (dump-port minified port))))))))))
1308 `(("r-htmltools" ,r-htmltools)
1309 ("r-promises" ,r-promises)
1310 ("r-shiny" ,r-shiny)))
1312 `(("uglify-js" ,uglify-js)))
1313 (home-page "https://rstudio.github.io/shinydashboard/")
1314 (synopsis "Create dashboards with shiny")
1315 (description "This package provides an extension to the Shiny web
1316 application framework for R, making it easy to create attractive dashboards.")
1317 ;; This package includes software that was released under the Expat
1318 ;; license, but the whole package is released under GPL version 2 or
1320 (license license:gpl2+)))
1322 (define-public r-shinyfiles
1324 (name "r-shinyfiles")
1329 (uri (cran-uri "shinyFiles" version))
1331 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1332 (properties `((upstream-name . "shinyFiles")))
1333 (build-system r-build-system)
1336 ("r-htmltools" ,r-htmltools)
1337 ("r-jsonlite" ,r-jsonlite)
1338 ("r-shiny" ,r-shiny)
1339 ("r-tibble" ,r-tibble)))
1340 (home-page "https://github.com/thomasp85/shinyFiles")
1341 (synopsis "Server-side file system viewer for Shiny")
1343 "This package provides functionality for client-side navigation of the
1344 server side file system in shiny apps. In case the app is running locally
1345 this gives the user direct access to the file system without the need to
1346 \"download\" files to a temporary location. Both file and folder selection as
1347 well as file saving is available.")
1348 (license license:gpl2+)))
1350 (define-public r-shinythemes
1352 (name "r-shinythemes")
1357 (uri (cran-uri "shinythemes" version))
1360 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1361 (properties `((upstream-name . "shinythemes")))
1362 (build-system r-build-system)
1363 (propagated-inputs `(("r-shiny" ,r-shiny)))
1364 (home-page "https://rstudio.github.io/shinythemes/")
1365 (synopsis "Themes for Shiny")
1367 "This package provides themes for use with Shiny. It includes several
1368 Bootstrap themes, which are packaged for use with Shiny applications.")
1369 ;; The package is released under version 3 of the GPL, but it includes
1370 ;; source files that are covered by the Expat license. It also includes
1371 ;; fonts under SIL or the ASL.
1372 (license (list license:gpl3 license:expat
1373 license:silofl1.1 license:asl2.0))))
1375 ;; The package sources include minified variants of d3.js and non-minified
1376 ;; source code of d3-jetpack.
1377 (define-public r-d3r
1384 (uri (cran-uri "d3r" version))
1387 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1388 (build-system r-build-system)
1390 `(#:modules ((guix build utils)
1391 (guix build r-build-system)
1395 (modify-phases %standard-phases
1396 (add-after 'unpack 'process-javascript
1397 (lambda* (#:key inputs #:allow-other-keys)
1398 (with-directory-excursion "inst/www/d3/"
1402 `((,(assoc-ref inputs "d3.v3.js")
1403 "v3/dist/d3.min.js")
1404 (,(assoc-ref inputs "d3.v4.js")
1405 "v4/dist/d3.min.js")
1406 (,(assoc-ref inputs "d3.v5.js")
1407 "v5/dist/d3.min.js"))))
1408 (lambda (sources targets)
1409 (for-each (lambda (source target)
1410 (format #t "Processing ~a --> ~a~%"
1412 (delete-file target)
1413 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1414 (call-with-output-file target
1416 (dump-port minified port)))))
1420 `(("r-dplyr" ,r-dplyr)
1421 ("r-htmltools" ,r-htmltools)
1422 ("r-rlang" ,r-rlang)
1423 ("r-tidyr" ,r-tidyr)))
1425 `(("uglify-js" ,uglify-js)
1429 (uri "https://d3js.org/d3.v3.js")
1432 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1436 (uri "https://d3js.org/d3.v4.js")
1439 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1443 (uri "https://d3js.org/d3.v5.js")
1446 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1447 (home-page "https://github.com/timelyportfolio/d3r")
1448 (synopsis "d3.js utilities for R")
1450 "This package provides a suite of functions to help ease the use of the
1451 d3.js visualization library in R. These helpers include
1452 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1453 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1454 R objects into the JSON format that the d3.js library expects.")
1455 (license license:bsd-3)))
1457 ;; We use the latest commit here because the last release was in 2016 while
1458 ;; the latest commit was in 2018.
1459 (define-public r-sankeyd3
1460 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1464 (version (git-version "0.3.2" revision commit))
1469 (url "https://github.com/fbreitwieser/sankeyD3")
1471 (file-name (git-file-name name version))
1474 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1475 (build-system r-build-system)
1478 ("r-htmlwidgets" ,r-htmlwidgets)
1479 ("r-shiny" ,r-shiny)
1480 ("r-magrittr" ,r-magrittr)))
1481 (home-page "https://github.com/fbreitwieser/sankeyD3")
1482 (synopsis "Sankey network graphs from R")
1484 "This package provides an R library to generate Sankey network graphs
1485 in R and Shiny via the D3 visualization library.")
1486 ;; The R code is licensed under GPLv3+. It includes the non-minified
1487 ;; JavaScript source code of d3-sankey, which is released under the
1488 ;; 3-clause BSD license.
1489 (license (list license:gpl3+ license:bsd-3)))))
1491 (define-public r-crosstalk
1493 (name "r-crosstalk")
1498 (uri (cran-uri "crosstalk" version))
1501 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1502 (build-system r-build-system)
1504 `(("r-htmltools" ,r-htmltools)
1505 ("r-jsonlite" ,r-jsonlite)
1506 ("r-lazyeval" ,r-lazyeval)
1508 (home-page "https://rstudio.github.io/crosstalk/")
1509 (synopsis "Inter-widget interactivity for HTML widgets")
1511 "This package provides building blocks for allowing HTML widgets to
1512 communicate with each other, with Shiny or without (i.e. static @code{.html}
1513 files). It currently supports linked brushing and filtering.")
1514 (license license:expat)))
1516 (define-public r-rook
1523 (uri (cran-uri "Rook" version))
1526 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1527 (properties `((upstream-name . "Rook")))
1528 (build-system r-build-system)
1529 (propagated-inputs `(("r-brew" ,r-brew)))
1530 (home-page "https://cran.r-project.org/web/packages/Rook")
1531 (synopsis "Web server interface for R")
1533 "This package contains the Rook specification and convenience software
1534 for building and running Rook applications. A Rook application is an R
1535 reference class object that implements a @code{call} method or an R closure
1536 that takes exactly one argument, an environment, and returns a list with three
1537 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1538 (license license:gpl2)))
1540 (define-public r-miniui
1547 (uri (cran-uri "miniUI" version))
1550 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1551 (properties `((upstream-name . "miniUI")))
1552 (build-system r-build-system)
1554 `(("r-htmltools" ,r-htmltools)
1555 ("r-shiny" ,r-shiny)))
1556 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1557 (synopsis "Shiny UI widgets for small screens")
1559 "This package provides UI widget and layout functions for writing Shiny apps that
1560 work well on small screens.")
1561 (license license:gpl3)))
1563 (define-public r-feather
1570 (uri (cran-uri "feather" version))
1573 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1574 (build-system r-build-system)
1578 ("r-tibble" ,r-tibble)))
1579 (home-page "https://github.com/wesm/feather")
1580 (synopsis "R Bindings to the Feather API")
1581 (description "Read and write feather files, a lightweight binary columnar
1582 data store designed for maximum speed.")
1583 (license license:asl2.0)))
1585 (define-public r-maps
1592 (uri (cran-uri "maps" version))
1595 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1596 (build-system r-build-system)
1597 (home-page "https://cran.r-project.org/web/packages/maps")
1598 (synopsis "Draw geographical maps")
1599 (description "This package provides an R module for display of maps.
1600 Projection code and larger maps are in separate packages (@code{mapproj} and
1602 (license license:gpl2)))
1604 (define-public r-mapproj
1611 (uri (cran-uri "mapproj" version))
1614 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1615 (build-system r-build-system)
1616 (propagated-inputs `(("r-maps" ,r-maps)))
1617 (home-page "https://cran.r-project.org/web/packages/mapproj")
1618 (synopsis "Map projection in R")
1619 (description "This package converts latitude/longitude into projected
1621 (license (list license:gpl2 ; The R interface
1622 (license:non-copyleft ; The C code
1623 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1624 "Lucent Public License Version 1.02")))))
1626 (define-public r-rgooglemaps
1628 (name "r-rgooglemaps")
1633 (uri (cran-uri "RgoogleMaps" version))
1636 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1637 (properties `((upstream-name . "RgoogleMaps")))
1638 (build-system r-build-system)
1642 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1643 (synopsis "Use Google Maps in R")
1644 (description "This package serves two purposes:
1646 @item Provide a comfortable R interface to query the Google server for static
1648 @item Use the map as a background image to overlay plots within R. This
1649 requires proper coordinate scaling.
1651 (license license:gpl2+)))
1653 (define-public r-geosphere
1655 (name "r-geosphere")
1660 (uri (cran-uri "geosphere" version))
1663 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1664 (build-system r-build-system)
1665 (propagated-inputs `(("r-sp" ,r-sp)))
1666 (home-page "https://cran.r-project.org/web/packages/geosphere")
1667 (synopsis "Spherical trigonometry")
1668 (description "This package computes spherical trigonometry for geographic
1669 applications. That is, compute distances and related measures for angular
1670 (longitude/latitude) locations.")
1671 (license license:gpl3+)))
1673 (define-public r-jpeg
1680 (uri (cran-uri "jpeg" version))
1683 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1684 (build-system r-build-system)
1685 (inputs `(("libjpeg" ,libjpeg-turbo)))
1686 (home-page "https://www.rforge.net/jpeg/")
1687 (synopsis "Read and write JPEG images with R")
1688 (description "This package provides a way to read, write and display
1689 bitmap images stored in the JPEG format with R. It can read and write both
1690 files and in-memory raw vectors.")
1691 (license license:gpl2+)))
1693 (define-public r-ggmap
1700 (uri (cran-uri "ggmap" version))
1703 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1704 (build-system r-build-system)
1706 `(("r-bitops" ,r-bitops)
1707 ("r-digest" ,r-digest)
1708 ("r-dplyr" ,r-dplyr)
1709 ("r-ggplot2" ,r-ggplot2)
1713 ("r-magrittr" ,r-magrittr)
1716 ("r-purrr" ,r-purrr)
1717 ("r-rgooglemaps" ,r-rgooglemaps)
1718 ("r-rjson" ,r-rjson)
1719 ("r-scales" ,r-scales)
1720 ("r-stringr" ,r-stringr)
1721 ("r-tibble" ,r-tibble)
1722 ("r-tidyr" ,r-tidyr)))
1723 (home-page "https://github.com/dkahle/ggmap")
1724 (synopsis "Spatial visualization with ggplot2")
1725 (description "This package provides a collection of functions to visualize
1726 spatial data and models on top of static maps from various online sources (e.g
1727 Google Maps and Stamen Maps). It includes tools common to those tasks,
1728 including functions for geolocation and routing.")
1729 (license license:gpl2)))
1731 (define-public r-haven
1738 (uri (cran-uri "haven" version))
1741 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1742 (build-system r-build-system)
1746 `(("r-knitr" ,r-knitr)))
1748 `(("r-forcats" ,r-forcats)
1751 ("r-rlang" ,r-rlang)
1752 ("r-readr" ,r-readr)
1753 ("r-tibble" ,r-tibble)
1754 ("r-tidyselect" ,r-tidyselect)
1755 ("r-vctrs" ,r-vctrs)))
1756 (home-page "https://haven.tidyverse.org")
1757 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1759 "This package lets you mport foreign statistical formats into R via the
1760 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1761 (license license:expat)))
1763 (define-public r-amap
1769 (uri (cran-uri "amap" version))
1772 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1773 (build-system r-build-system)
1775 `(("gfortran" ,gfortran)))
1776 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1777 (synopsis "Another multidimensional analysis package")
1778 (description "This package provides tools for clustering and principal
1779 component analysis (with robust methods, and parallelized functions).")
1780 (license license:gpl2+)))
1782 (define-public r-ape
1789 (uri (cran-uri "ape" version))
1792 "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
1793 (build-system r-build-system)
1795 `(("r-lattice" ,r-lattice)
1797 ("r-rcpp" ,r-rcpp)))
1798 (home-page "http://ape-package.ird.fr/")
1799 (synopsis "Analyses of phylogenetics and evolution")
1801 "This package provides functions for reading, writing, plotting, and
1802 manipulating phylogenetic trees, analyses of comparative data in a
1803 phylogenetic framework, ancestral character analyses, analyses of
1804 diversification and macroevolution, computing distances from DNA sequences,
1805 and several other tools.")
1806 (license license:gpl2+)))
1808 (define-public r-abbyyr
1815 (uri (cran-uri "abbyyR" version))
1818 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1819 (properties `((upstream-name . "abbyyR")))
1820 (build-system r-build-system)
1822 `(("r-curl" ,r-curl)
1825 ("r-progress" ,r-progress)
1826 ("r-readr" ,r-readr)
1828 (home-page "https://github.com/soodoku/abbyyR")
1829 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1831 "This package provides tools to get text from images of text using Abbyy
1832 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1833 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1834 passports and get the results in a variety of formats including plain text and
1835 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1836 (license license:expat)))
1838 (define-public r-colorspace
1840 (name "r-colorspace")
1845 (uri (cran-uri "colorspace" version))
1847 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1848 (build-system r-build-system)
1849 (home-page "https://cran.r-project.org/web/packages/colorspace")
1850 (synopsis "Color space manipulation")
1852 "This package carries out a mapping between assorted color spaces
1853 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1854 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1855 colors are provided.")
1856 (license license:bsd-3)))
1858 (define-public r-glue
1865 (uri (cran-uri "glue" version))
1868 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1869 (build-system r-build-system)
1870 ;; knitr depends on glue, so we can't add knitr here to build the
1874 `(("r-knitr" ,r-knitr)))
1875 (home-page "https://github.com/tidyverse/glue")
1876 (synopsis "Interpreted string literals")
1878 "This package provides an implementation of interpreted string literals,
1879 inspired by Python's Literal String Interpolation (PEP-0498) and
1880 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1881 (license license:expat)))
1883 (define-public r-pastecs
1889 (uri (cran-uri "pastecs" version))
1892 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1893 (build-system r-build-system)
1895 `(("r-boot" ,r-boot)))
1896 (home-page "http://www.sciviews.org/pastecs")
1897 (synopsis "Analysis of space-time ecological series")
1899 "This package provides functions for regulation, decomposition and analysis
1900 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1901 initiative to bring PASSTEC 2000 functionalities to R.")
1902 (license license:gpl2+)))
1904 (define-public r-plogr
1911 (uri (cran-uri "plogr" version))
1914 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1915 (build-system r-build-system)
1916 (home-page "https://github.com/krlmlr/plogr")
1917 (synopsis "R bindings for the plog C++ logging library")
1919 "This package provides the header files for a stripped-down version of
1920 the plog header-only C++ logging library, and a method to log to R's standard
1922 (license license:expat)))
1924 (define-public r-pls
1931 (uri (cran-uri "pls" version))
1933 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1934 (build-system r-build-system)
1935 (home-page "https://mevik.net/work/software/pls.html")
1936 (synopsis "Partial Least Squares and Principal Component Regression")
1938 "The pls package implements multivariate regression methods: Partial Least
1939 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1940 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1943 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1944 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1945 @item multi-response models (or @dfn{PLS2})
1946 @item flexible cross-validation
1947 @item Jackknife variance estimates of regression coefficients
1948 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1949 (R)MSEP, R², and correlation loadings
1950 @item formula interface, modelled after @code{lm()}, with methods for predict,
1951 print, summary, plot, update, etc.
1952 @item extraction functions for coefficients, scores, and loadings
1953 @item MSEP, RMSEP, and R² estimates
1954 @item multiplicative scatter correction (@dfn{MSC})
1956 (license license:gpl2)))
1965 (uri (cran-uri "ps" version))
1967 (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
1968 (build-system r-build-system)
1969 (home-page "https://ps.r-lib.org")
1970 (synopsis "List, query, and manipulate system processes")
1972 "The ps package implements an API to list, query, and manipulate system
1973 processes. Most of its code is based on the @code{psutil} Python package.")
1974 (license license:bsd-3)))
1976 (define-public r-pkgbuild
1983 (uri (cran-uri "pkgbuild" version))
1985 (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
1986 (build-system r-build-system)
1988 `(("r-callr" ,r-callr)
1990 ("r-crayon" ,r-crayon)
1992 ("r-prettyunits" ,r-prettyunits)
1994 ("r-rprojroot" ,r-rprojroot)
1995 ("r-withr" ,r-withr)))
1996 (home-page "https://github.com/r-pkgs/pkgbuild")
1997 (synopsis "Find tools needed to build R packages")
1999 "This package provides functions used to build R packages. It locates
2000 compilers needed to build R packages on various platforms and ensures the PATH
2001 is configured appropriately so R can use them.")
2002 (license license:gpl3)))
2004 (define-public r-pkgload
2011 (uri (cran-uri "pkgload" version))
2014 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2015 (build-system r-build-system)
2018 ("r-crayon" ,r-crayon)
2020 ("r-pkgbuild" ,r-pkgbuild)
2021 ("r-rlang" ,r-rlang)
2022 ("r-rprojroot" ,r-rprojroot)
2023 ("r-rstudioapi" ,r-rstudioapi)
2024 ("r-withr" ,r-withr)))
2025 (home-page "https://github.com/r-lib/pkgload")
2026 (synopsis "Simulate package installation and attach")
2028 "This package simulates the process of installing a package and then
2029 attaching it. This is a key part of the @code{devtools} package as it allows
2030 you to rapidly iterate while developing a package.")
2031 (license license:gpl3)))
2033 (define-public r-rcpp
2040 (uri (cran-uri "Rcpp" version))
2042 (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq"))))
2043 (build-system r-build-system)
2044 (home-page "http://www.rcpp.org")
2045 (synopsis "Seamless R and C++ integration")
2047 "The Rcpp package provides R functions as well as C++ classes which offer
2048 a seamless integration of R and C++. Many R data types and objects can be
2049 mapped back and forth to C++ equivalents which facilitates both writing of new
2050 code as well as easier integration of third-party libraries. Documentation
2051 about Rcpp is provided by several vignettes included in this package, via the
2052 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2053 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2054 @code{citation(\"Rcpp\")} for details on these last two.")
2055 (license license:gpl2+)))
2057 (define-public r-bindr
2064 (uri (cran-uri "bindr" version))
2067 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2068 (build-system r-build-system)
2069 (home-page "https://github.com/krlmlr/bindr")
2070 (synopsis "Parametrized active bindings")
2072 "This package provides a simple interface for creating active bindings
2073 where the bound function accepts additional arguments.")
2074 (license license:expat)))
2076 (define-public r-bindrcpp
2083 (uri (cran-uri "bindrcpp" version))
2086 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2087 (build-system r-build-system)
2089 `(("r-bindr" ,r-bindr)
2090 ("r-plogr" ,r-plogr)
2091 ("r-rcpp" ,r-rcpp)))
2092 (home-page "https://github.com/krlmlr/bindrcpp")
2093 (synopsis "Rcpp interface to active bindings")
2095 "This package provides an easy way to fill an environment with active
2096 bindings that call a C++ function.")
2097 (license license:expat)))
2099 (define-public r-auc
2106 (uri (cran-uri "AUC" version))
2109 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2110 (properties `((upstream-name . "AUC")))
2111 (build-system r-build-system)
2112 (home-page "https://cran.r-project.org/web/packages/AUC")
2113 (synopsis "Compute the area under the curve of selected measures")
2115 "This package includes functions to compute the area under the curve of
2116 selected measures: the area under the sensitivity curve (AUSEC), the area
2117 under the specificity curve (AUSPC), the area under the accuracy
2118 curve (AUACC), and the area under the receiver operating characteristic
2119 curve (AUROC). The curves can also be visualized. Support for partial areas
2121 (license license:gpl2+)))
2123 (define-public r-calibrate
2125 (name "r-calibrate")
2130 (uri (cran-uri "calibrate" version))
2132 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2133 (build-system r-build-system)
2135 `(("r-mass" ,r-mass)))
2136 (home-page "https://cran.r-project.org/web/packages/calibrate")
2137 (synopsis "Calibration of scatterplot and biplot axes")
2139 "This is a package for drawing calibrated scales with tick marks
2140 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2141 (license license:gpl2)))
2143 (define-public r-shape
2150 (uri (cran-uri "shape" version))
2153 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2154 (build-system r-build-system)
2155 (home-page "https://cran.r-project.org/web/packages/shape")
2156 (synopsis "Functions for plotting graphical shapes")
2158 "This package provides functions for plotting graphical shapes such as
2159 ellipses, circles, cylinders, arrows, ...")
2160 (license license:gpl3+)))
2162 (define-public r-globaloptions
2164 (name "r-globaloptions")
2169 (uri (cran-uri "GlobalOptions" version))
2171 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2172 (properties `((upstream-name . "GlobalOptions")))
2173 (build-system r-build-system)
2175 `(("r-knitr" ,r-knitr)))
2176 (home-page "https://github.com/jokergoo/GlobalOptions")
2177 (synopsis "Generate functions to get or set global options")
2179 "This package provides more controls on the option values such as
2180 validation and filtering on the values, making options invisible or private.")
2181 (license license:gpl2+)))
2183 (define-public r-circlize
2190 (uri (cran-uri "circlize" version))
2193 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2194 (build-system r-build-system)
2196 `(("r-colorspace" ,r-colorspace)
2197 ("r-globaloptions" ,r-globaloptions)
2198 ("r-shape" ,r-shape)))
2200 `(("r-knitr" ,r-knitr)))
2201 (home-page "https://github.com/jokergoo/circlize")
2202 (synopsis "Circular visualization")
2204 "Circular layout is an efficient way to visualise huge amounts of
2205 information. This package provides an implementation of circular layout
2206 generation in R as well as an enhancement of available software. Its
2207 flexibility is based on the usage of low-level graphics functions such that
2208 self-defined high-level graphics can be easily implemented by users for
2209 specific purposes. Together with the seamless connection between the powerful
2210 computational and visual environment in R, it gives users more convenience and
2211 freedom to design figures for better understanding complex patterns behind
2212 multi-dimensional data.")
2213 (license license:gpl2+)))
2215 (define-public r-powerlaw
2222 (uri (cran-uri "poweRlaw" version))
2224 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2225 (properties `((upstream-name . "poweRlaw")))
2226 (build-system r-build-system)
2228 `(("r-pracma" ,r-pracma)))
2230 `(("r-knitr" ,r-knitr)))
2231 (home-page "https://github.com/csgillespie/poweRlaw")
2232 (synopsis "Tools for the analysis of heavy tailed distributions")
2234 "This package provides an implementation of maximum likelihood estimators
2235 for a variety of heavy tailed distributions, including both the discrete and
2236 continuous power law distributions. Additionally, a goodness-of-fit based
2237 approach is used to estimate the lower cut-off for the scaling region.")
2238 ;; Any of these GPL versions.
2239 (license (list license:gpl2 license:gpl3))))
2241 (define-public r-compare
2248 (uri (cran-uri "compare" version))
2251 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2252 (build-system r-build-system)
2253 (home-page "https://cran.r-project.org/web/packages/compare")
2254 (synopsis "Comparing objects for differences")
2256 "This package provides functions to compare a model object to a
2257 comparison object. If the objects are not identical, the functions can be
2258 instructed to explore various modifications of the objects (e.g., sorting
2259 rows, dropping names) to see if the modified versions are identical.")
2260 (license license:gpl2+)))
2262 (define-public r-dendextend
2264 (name "r-dendextend")
2269 (uri (cran-uri "dendextend" version))
2272 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2273 (build-system r-build-system)
2275 `(("r-ggplot2" ,r-ggplot2)
2276 ("r-magrittr" ,r-magrittr)
2277 ("r-viridis" ,r-viridis)))
2278 (home-page "https://cran.r-project.org/web/packages/dendextend")
2279 (synopsis "Extending 'dendrogram' functionality in R")
2281 "This package offers a set of functions for extending @code{dendrogram}
2282 objects in R, letting you visualize and compare trees of hierarchical
2283 clusterings. You can adjust a tree's graphical parameters (the color, size,
2284 type, etc of its branches, nodes and labels) and visually and statistically
2285 compare different dendrograms to one another.")
2286 ;; Any of these versions
2287 (license (list license:gpl2 license:gpl3))))
2289 (define-public r-getoptlong
2291 (name "r-getoptlong")
2296 (uri (cran-uri "GetoptLong" version))
2299 "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l"))))
2300 (properties `((upstream-name . "GetoptLong")))
2301 (build-system r-build-system)
2305 `(("r-crayon" ,r-crayon)
2306 ("r-globaloptions" ,r-globaloptions)
2307 ("r-rjson" ,r-rjson)))
2309 `(("r-knitr" ,r-knitr)))
2310 (home-page "https://github.com/jokergoo/GetoptLong")
2311 (synopsis "Parsing command-line arguments and variable interpolation")
2313 "This is yet another command-line argument parser which wraps the
2314 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2315 use in R. It also provides a simple way for variable interpolation in R.")
2316 (license license:gpl2+)))
2318 (define-public r-fastmatch
2320 (name "r-fastmatch")
2325 (uri (cran-uri "fastmatch" version))
2328 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2329 (build-system r-build-system)
2330 (home-page "https://www.rforge.net/fastmatch")
2331 (synopsis "Fast match function")
2333 "This package provides a fast @code{match} replacement for cases that
2334 require repeated look-ups. It is slightly faster that R's built-in
2335 @code{match} function on first match against a table, but extremely fast on
2336 any subsequent lookup as it keeps the hash table in memory.")
2337 (license license:gpl2)))
2342 (version "2.2-14.2")
2346 (uri (cran-uri "ff" version))
2349 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2350 (build-system r-build-system)
2351 (propagated-inputs `(("r-bit" ,r-bit)))
2352 (home-page "http://ff.r-forge.r-project.org/")
2353 (synopsis "Memory-efficient storage of large data on disk and access functions")
2355 "This package provides data structures that are stored on disk but
2356 behave (almost) as if they were in RAM by transparently mapping only a section
2358 ;; error Architecture not supported.
2359 (supported-systems (delete "aarch64-linux" %supported-systems))
2360 (license license:gpl2)))
2362 (define-public r-ffbase
2369 (uri (cran-uri "ffbase" version))
2372 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2373 (build-system r-build-system)
2376 ("r-fastmatch" ,r-fastmatch)
2378 (home-page "https://github.com/edwindj/ffbase")
2379 (synopsis "Basic statistical functions for package 'ff'")
2381 "This package extends the out of memory vectors of @code{ff} with
2382 statistical functions and other utilities to ease their usage.")
2383 (license license:gpl3)))
2385 (define-public r-prettyunits
2387 (name "r-prettyunits")
2392 (uri (cran-uri "prettyunits" version))
2395 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2396 (build-system r-build-system)
2397 (home-page "https://github.com/gaborcsardi/prettyunits")
2398 (synopsis "Pretty, human readable formatting of quantities")
2400 "This package provides tools for pretty, human readable formatting of
2402 (license license:expat)))
2404 (define-public r-reshape
2411 (uri (cran-uri "reshape" version))
2414 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2415 (build-system r-build-system)
2417 `(("r-plyr" ,r-plyr)
2418 ("r-rcpp" ,r-rcpp)))
2419 (home-page "http://had.co.nz/reshape")
2420 (synopsis "Flexibly reshape data")
2422 "Flexibly restructure and aggregate data using just two functions:
2423 @code{melt} and @code{cast}. This package provides them.")
2424 (license license:expat)))
2426 (define-public r-progress
2433 (uri (cran-uri "progress" version))
2436 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2437 (build-system r-build-system)
2439 `(("r-crayon" ,r-crayon)
2441 ("r-prettyunits" ,r-prettyunits)
2443 (home-page "https://github.com/gaborcsardi/progress")
2444 (synopsis "Terminal progress bars")
2446 "This package provides configurable progress bars. They may include
2447 percentage, elapsed time, and/or the estimated completion time. They work in
2448 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2449 package also provides a C++ API, that works with or without Rcpp.")
2450 (license license:expat)))
2452 (define-public r-ggally
2459 (uri (cran-uri "GGally" version))
2462 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2463 (properties `((upstream-name . "GGally")))
2464 (build-system r-build-system)
2466 `(("libressl" ,libressl)))
2468 `(("r-ggplot2" ,r-ggplot2)
2469 ("r-gtable" ,r-gtable)
2470 ("r-lifecycle" ,r-lifecycle)
2472 ("r-progress" ,r-progress)
2473 ("r-rcolorbrewer" ,r-rcolorbrewer)
2474 ("r-reshape" ,r-reshape)
2475 ("r-rlang" ,r-rlang)
2476 ("r-scales" ,r-scales)))
2477 (home-page "https://ggobi.github.io/ggally")
2478 (synopsis "Extension to ggplot2")
2480 "The R package ggplot2 is a plotting system based on the grammar of
2481 graphics. GGally extends ggplot2 by adding several functions to reduce the
2482 complexity of combining geometric objects with transformed data. Some of
2483 these functions include a pairwise plot matrix, a two group pairwise plot
2484 matrix, a parallel coordinates plot, a survival plot, and several functions to
2486 (license license:gpl2+)))
2488 (define-public r-proxy
2495 (uri (cran-uri "proxy" version))
2498 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2499 (build-system r-build-system)
2500 (home-page "https://cran.r-project.org/web/packages/proxy")
2501 (synopsis "Distance and similarity measures")
2503 "This package provides an extensible framework for the efficient
2504 calculation of auto- and cross-proximities, along with implementations of the
2505 most popular ones.")
2506 (license license:gpl2)))
2515 (uri (cran-uri "sp" version))
2517 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2518 (build-system r-build-system)
2520 `(("r-lattice" ,r-lattice)))
2521 (home-page "https://cran.r-project.org/web/packages/sp")
2522 (synopsis "Classes and methods for spatial data")
2524 "This package provides classes and methods for spatial data; the classes
2525 document where the spatial location information resides, for 2D or 3D data.
2526 Utility functions are provided, e.g. for plotting data as maps, spatial
2527 selection, as well as methods for retrieving coordinates, for subsetting,
2528 print, summary, etc.")
2529 (license license:gpl2+)))
2531 (define-public r-rmtstat
2538 (uri (cran-uri "RMTstat" version))
2541 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2542 (properties `((upstream-name . "RMTstat")))
2543 (build-system r-build-system)
2544 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2545 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2547 "This package provides functions for working with the Tracy-Widom laws
2548 and other distributions related to the eigenvalues of large Wishart
2550 (license license:bsd-3)))
2552 (define-public r-rmpi
2558 (uri (cran-uri "Rmpi" version))
2561 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2562 (properties `((upstream-name . "Rmpi")))
2563 (build-system r-build-system)
2565 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2566 #:phases (modify-phases %standard-phases
2567 (add-before 'install 'mpi-setup
2570 `(("openmpi" ,openmpi)))
2572 `(("pkg-config" ,pkg-config)))
2573 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2574 (synopsis "R interface to message-passing interface (MPI)")
2576 "This package provides an interface (wrapper) to MPI APIs. It also
2577 provides an interactive R manager and worker environment.")
2578 (license license:gpl2+)))
2580 (define-public r-lmoments
2587 (uri (cran-uri "Lmoments" version))
2590 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2591 (properties `((upstream-name . "Lmoments")))
2592 (build-system r-build-system)
2594 `(("r-rcpp" ,r-rcpp)
2595 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2596 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2597 (synopsis "L-moments and quantile mixtures")
2599 "This package contains functions to estimate L-moments and trimmed
2600 L-moments from the data. It also contains functions to estimate the
2601 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2602 quantile mixture from L-moments and trimmed L-moments.")
2603 (license license:gpl2)))
2605 (define-public r-distillery
2607 (name "r-distillery")
2612 (uri (cran-uri "distillery" version))
2615 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2616 (build-system r-build-system)
2617 (home-page "https://ral.ucar.edu/staff/ericg/")
2618 (synopsis "Functions for confidence intervals and object information")
2620 "This package provides some very simple method functions for confidence
2621 interval calculation and to distill pertinent information from a potentially
2622 complex object; primarily used in common with the packages extRemes and
2624 (license license:gpl2+)))
2626 (define-public r-extremes
2633 (uri (cran-uri "extRemes" version))
2636 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2637 (properties `((upstream-name . "extRemes")))
2638 (build-system r-build-system)
2640 `(("r-distillery" ,r-distillery)
2641 ("r-lmoments" ,r-lmoments)))
2642 (home-page "https://www.assessment.ucar.edu/toolkit/")
2643 (synopsis "Extreme value analysis")
2645 "ExtRemes is a suite of functions for carrying out analyses on the
2646 extreme values of a process of interest; be they block maxima over long blocks
2647 or excesses over a high threshold.")
2648 (license license:gpl2+)))
2650 (define-public r-lmtest
2657 (uri (cran-uri "lmtest" version))
2660 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2661 (build-system r-build-system)
2663 `(("r-zoo" ,r-zoo)))
2665 `(("gfortran" ,gfortran)))
2666 (home-page "https://cran.r-project.org/web/packages/lmtest")
2667 (synopsis "Testing linear regression models")
2669 "This package provides a collection of tests, data sets, and examples for
2670 diagnostic checking in linear regression models. Furthermore, some generic
2671 tools for inference in parametric models are provided.")
2672 ;; Either version is okay
2673 (license (list license:gpl2 license:gpl3))))
2675 (define-public r-idr
2681 (uri (cran-uri "idr" version))
2684 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2685 (build-system r-build-system)
2686 (home-page "https://cran.r-project.org/web/packages/idr/")
2687 (synopsis "Irreproducible discovery rate")
2689 "This is a package for estimating the copula mixture model and plotting
2690 correspondence curves in \"Measuring reproducibility of high-throughput
2691 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2692 by Li, Brown, Huang, and Bickel")
2693 (license license:gpl2+)))
2695 (define-public r-inline
2701 (uri (cran-uri "inline" version))
2704 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2705 (build-system r-build-system)
2706 (home-page "https://cran.r-project.org/web/packages/inline")
2707 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2709 "This package provides functionality to dynamically define R functions
2710 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2711 @code{.Call} calling conventions.")
2712 ;; Any version of the LGPL.
2713 (license license:lgpl3+)))
2715 (define-public r-inum
2721 (uri (cran-uri "inum" version))
2724 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2725 (build-system r-build-system)
2727 `(("r-libcoin" ,r-libcoin)))
2728 (home-page "https://cran.r-project.org/web/packages/inum/")
2729 (synopsis "Interval and enum-type representation of vectors")
2731 "This package provides an enum-type representation of vectors and
2732 representation of intervals, including a method of coercing variables
2734 (license license:gpl2)))
2736 (define-public r-bdsmatrix
2738 (name "r-bdsmatrix")
2743 (uri (cran-uri "bdsmatrix" version))
2746 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2747 (properties `((upstream-name . "bdsmatrix")))
2748 (build-system r-build-system)
2749 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2750 (synopsis "Routines for block diagonal symmetric matrices")
2752 "This package provides procedures to work with block diagonal symmetric
2753 matrices, a special case of sparse matrices.")
2754 (license license:lgpl2.0)))
2756 (define-public r-bbmle
2759 (version "1.0.23.1")
2763 (uri (cran-uri "bbmle" version))
2766 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2767 (build-system r-build-system)
2769 `(("r-bdsmatrix" ,r-bdsmatrix)
2770 ("r-lattice" ,r-lattice)
2772 ("r-matrix" ,r-matrix)
2773 ("r-mvtnorm" ,r-mvtnorm)
2774 ("r-numderiv" ,r-numderiv)))
2775 (home-page "https://cran.r-project.org/web/packages/bbmle")
2776 (synopsis "Tools for General Maximum Likelihood Estimation")
2778 "This package provides methods and functions for fitting maximum
2779 likelihood models in R. This package modifies and extends the @code{mle}
2780 classes in the @code{stats4} package.")
2781 ;; Any version of the GPL
2782 (license license:gpl2+)))
2784 (define-public r-emdbook
2791 (uri (cran-uri "emdbook" version))
2794 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2795 (build-system r-build-system)
2797 `(("r-bbmle" ,r-bbmle)
2799 ("r-lattice" ,r-lattice)
2801 ("r-plyr" ,r-plyr)))
2802 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2803 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2805 "This package provides auxiliary functions and data sets for \"Ecological
2806 Models and Data\", a book presenting maximum likelihood estimation and related
2807 topics for ecologists (ISBN 978-0-691-12522-0).")
2809 (license (list license:gpl2 license:gpl3))))
2811 (define-public r-lpsolve
2818 (uri (cran-uri "lpSolve" version))
2821 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2822 (properties `((upstream-name . "lpSolve")))
2823 (build-system r-build-system)
2824 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2825 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2827 "Lp_solve is software for solving linear, integer and mixed integer
2828 programs. This implementation supplies a \"wrapper\" function in C and some R
2829 functions that solve general linear/integer problems, assignment problems, and
2830 transportation problems.")
2831 (license license:lgpl2.0)))
2833 (define-public r-limsolve
2840 (uri (cran-uri "limSolve" version))
2843 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2844 (properties `((upstream-name . "limSolve")))
2845 (build-system r-build-system)
2847 `(("r-lpsolve" ,r-lpsolve)
2849 ("r-quadprog" ,r-quadprog)))
2850 (native-inputs `(("gfortran" ,gfortran)))
2851 (home-page "https://cran.r-project.org/web/packages/limSolve")
2852 (synopsis "Solving linear inverse models")
2854 "This package provides functions that:
2857 @item find the minimum/maximum of a linear or quadratic function,
2858 @item sample an underdetermined or overdetermined system,
2859 @item solve a linear system Ax=B for the unknown x.
2862 It includes banded and tridiagonal linear systems. The package calls Fortran
2863 functions from LINPACK.")
2865 (license (list license:gpl2+ license:gpl3+))))
2867 (define-public r-fitdistrplus
2869 (name "r-fitdistrplus")
2874 (uri (cran-uri "fitdistrplus" version))
2877 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2878 (build-system r-build-system)
2880 `(("r-mass" ,r-mass)
2881 ("r-survival" ,r-survival)))
2883 `(("r-knitr" ,r-knitr)))
2884 (home-page "http://riskassessment.r-forge.r-project.org")
2885 (synopsis "Fitting a parametric distribution from data")
2887 "This package extends the @code{fitdistr} function of the MASS package
2888 with several functions to help the fit of a parametric distribution to
2889 non-censored or censored data. Censored data may contain left-censored,
2890 right-censored and interval-censored values, with several lower and upper
2891 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2892 provides moment matching (MME), quantile matching (QME) and maximum
2893 goodness-of-fit estimation (MGE) methods (available only for non-censored
2894 data). Weighted versions of MLE, MME and QME are available.")
2895 (license license:gpl2+)))
2897 (define-public r-energy
2904 (uri (cran-uri "energy" version))
2907 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2908 (build-system r-build-system)
2910 `(("r-boot" ,r-boot)
2911 ("r-rcpp" ,r-rcpp)))
2912 (home-page "https://cran.r-project.org/web/packages/energy")
2913 (synopsis "Multivariate inference via the energy of data")
2915 "This package provides e-statistics (energy) tests and statistics for
2916 multivariate and univariate inference, including distance correlation,
2917 one-sample, two-sample, and multi-sample tests for comparing multivariate
2918 distributions, are implemented. Measuring and testing multivariate
2919 independence based on distance correlation, partial distance correlation,
2920 multivariate goodness-of-fit tests, clustering based on energy distance,
2921 testing for multivariate normality, distance components (disco) for
2922 non-parametric analysis of structured data, and other energy
2923 statistics/methods are implemented.")
2924 (license license:gpl2+)))
2926 (define-public r-suppdists
2928 (name "r-suppdists")
2933 (uri (cran-uri "SuppDists" version))
2936 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2937 (properties `((upstream-name . "SuppDists")))
2938 (build-system r-build-system)
2939 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2940 (synopsis "Supplementary distributions")
2942 "This package provides ten distributions supplementing those built into
2943 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2944 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2945 coefficient, Johnson distributions, normal scores and generalized
2946 hypergeometric distributions. In addition two random number generators of
2947 George Marsaglia are included.")
2948 (license license:gpl2+)))
2950 (define-public r-ksamples
2957 (uri (cran-uri "kSamples" version))
2960 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2961 (properties `((upstream-name . "kSamples")))
2962 (build-system r-build-system)
2964 `(("r-suppdists" ,r-suppdists)))
2965 (home-page "https://cran.r-project.org/web/packages/kSamples")
2966 (synopsis "K-Sample rank tests and their combinations")
2968 "This package provides tools to compares k samples using the
2969 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2970 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2971 test. It computes asymptotic, simulated or (limited) exact P-values, all
2972 valid under randomization, with or without ties, or conditionally under random
2973 sampling from populations, given the observed tie pattern. Except for Steel's
2974 test and the JT test it also combines these tests across several blocks of
2976 (license license:gpl2+)))
2978 (define-public r-cvst
2985 (uri (cran-uri "CVST" version))
2988 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2989 (properties `((upstream-name . "CVST")))
2990 (build-system r-build-system)
2992 `(("r-kernlab" ,r-kernlab)
2993 ("r-matrix" ,r-matrix)))
2994 (home-page "https://cran.r-project.org/web/packages/CVST")
2995 (synopsis "Fast cross-validation via sequential testing")
2997 "This package implements the fast cross-validation via sequential
2998 testing (CVST) procedure. CVST is an improved cross-validation procedure
2999 which uses non-parametric testing coupled with sequential analysis to
3000 determine the best parameter set on linearly increasing subsets of the data.
3001 Additionally to the CVST the package contains an implementation of the
3002 ordinary k-fold cross-validation with a flexible and powerful set of helper
3003 objects and methods to handle the overall model selection process. The
3004 implementations of the Cochran's Q test with permutations and the sequential
3005 testing framework of Wald are generic and can therefore also be used in other
3007 (license license:gpl2+)))
3009 (define-public r-squarem
3016 (uri (cran-uri "SQUAREM" version))
3019 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
3020 (properties `((upstream-name . "SQUAREM")))
3021 (build-system r-build-system)
3022 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3023 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3025 "This package provides algorithms for accelerating the convergence of
3026 slow, monotone sequences from smooth, contraction mapping such as the EM
3027 algorithm. It can be used to accelerate any smooth, linearly convergent
3028 acceleration scheme. A tutorial style introduction to this package is
3029 available in a vignette.")
3030 (license license:gpl2+)))
3032 (define-public r-lava
3039 (uri (cran-uri "lava" version))
3042 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3043 (build-system r-build-system)
3045 `(("r-numderiv" ,r-numderiv)
3046 ("r-squarem" ,r-squarem)
3047 ("r-survival" ,r-survival)))
3048 (home-page "https://github.com/kkholst/lava")
3049 (synopsis "Latent variable models")
3051 "This package provides tools for the estimation and simulation of latent
3053 (license license:gpl3)))
3055 (define-public r-drr
3062 (uri (cran-uri "DRR" version))
3065 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3066 (properties `((upstream-name . "DRR")))
3067 (build-system r-build-system)
3069 `(("r-cvst" ,r-cvst)
3070 ("r-kernlab" ,r-kernlab)
3071 ("r-matrix" ,r-matrix)))
3072 (home-page "https://cran.r-project.org/web/packages/DRR")
3073 (synopsis "Dimensionality reduction via regression")
3075 "This package provides an implementation of dimensionality reduction via
3076 regression using Kernel Ridge Regression.")
3077 (license license:gpl3)))
3079 (define-public r-prodlim
3082 (version "2019.11.13")
3086 (uri (cran-uri "prodlim" version))
3089 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3090 (build-system r-build-system)
3092 `(("r-kernsmooth" ,r-kernsmooth)
3095 ("r-survival" ,r-survival)))
3096 (home-page "https://cran.r-project.org/web/packages/prodlim")
3097 (synopsis "Product-limit estimation for censored event history analysis")
3099 "This package provides a fast and user-friendly implementation of
3100 nonparametric estimators for censored event history (survival) analysis with
3101 the Kaplan-Meier and Aalen-Johansen methods.")
3102 (license license:gpl2+)))
3104 (define-public r-dimred
3111 (uri (cran-uri "dimRed" version))
3114 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3115 (properties `((upstream-name . "dimRed")))
3116 (build-system r-build-system)
3119 ("r-magrittr" ,r-magrittr)))
3120 (home-page "https://github.com/gdkrmr/dimRed")
3121 (synopsis "Framework for dimensionality reduction")
3123 "This package provides a collection of dimensionality reduction
3124 techniques from R packages and provides a common interface for calling the
3126 (license license:gpl3)))
3128 (define-public r-timedate
3131 (version "3043.102")
3135 (uri (cran-uri "timeDate" version))
3138 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3139 (properties `((upstream-name . "timeDate")))
3140 (build-system r-build-system)
3141 (home-page "https://www.rmetrics.org")
3142 (synopsis "Chronological and calendar objects")
3144 "This package provides an environment for teaching \"Financial
3145 Engineering and Computational Finance\" and for managing chronological and
3147 (license license:gpl2+)))
3149 (define-public r-magic
3156 (uri (cran-uri "magic" version))
3159 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3160 (build-system r-build-system)
3162 `(("r-abind" ,r-abind)))
3163 (home-page "https://github.com/RobinHankin/magic.git")
3164 (synopsis "Create and investigate magic squares")
3166 "This package provides a collection of efficient, vectorized algorithms
3167 for the creation and investigation of magic squares and hypercubes, including
3168 a variety of functions for the manipulation and analysis of arbitrarily
3169 dimensioned arrays.")
3170 (license license:gpl2)))
3172 (define-public r-rmysql
3179 (uri (cran-uri "RMySQL" version))
3182 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3183 (properties `((upstream-name . "RMySQL")))
3184 (build-system r-build-system)
3186 `(("mariadb" ,mariadb "lib")
3187 ("mariadb-dev" ,mariadb "dev")
3190 `(("r-dbi" ,r-dbi)))
3191 (home-page "https://github.com/r-dbi/RMySQL")
3192 (synopsis "Database interface and MySQL driver for R")
3194 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3195 package contains an old implementation based on legacy code from S-PLUS which
3196 is being phased out. A modern MySQL client based on Rcpp is available from
3197 the RMariaDB package.")
3198 (license license:gpl2)))
3200 (define-public r-rpostgresql
3202 (name "r-rpostgresql")
3207 (uri (cran-uri "RPostgreSQL" version))
3210 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3211 (properties `((upstream-name . "RPostgreSQL")))
3212 (build-system r-build-system)
3214 `(("postgresql" ,postgresql)))
3216 `(("r-dbi" ,r-dbi)))
3217 (home-page "https://github.com/tomoakin/RPostgreSQL")
3218 (synopsis "R interface to the PostgreSQL database system")
3220 "This package provides a Database Interface (DBI) compliant driver for R
3221 to access PostgreSQL database systems.")
3222 ;; The whole package is released under GPL version 2. It includes code
3223 ;; under the PostgreSQL license.
3224 (license license:gpl2)))
3226 (define-public r-linprog
3233 (uri (cran-uri "linprog" version))
3236 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3237 (build-system r-build-system)
3238 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3239 (home-page "http://linprog.r-forge.r-project.org/")
3240 (synopsis "Linear programming and optimization")
3242 "This package can be used to solve Linear Programming / Linear
3243 Optimization problems by using the simplex algorithm.")
3244 (license license:gpl2+)))
3246 (define-public r-geometry
3253 (uri (cran-uri "geometry" version))
3256 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3257 (build-system r-build-system)
3259 `(("r-magic" ,r-magic)
3260 ("r-linprog" ,r-linprog)
3261 ("r-lpsolve" ,r-lpsolve)
3263 ("r-rcppprogress" ,r-rcppprogress)))
3264 (home-page "http://geometry.r-forge.r-project.org/")
3265 (synopsis "Mesh generation and surface tesselation")
3267 "This package makes the qhull library available in R, in a similar manner
3268 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3269 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3270 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3271 and higher dimensions. It implements the Quickhull algorithm for computing
3272 the convex hull. Qhull does not support constrained Delaunay triangulations,
3273 or mesh generation of non-convex objects, but the package does include some R
3274 functions that allow for this. Currently the package only gives access to
3275 Delaunay triangulation and convex hull computation.")
3276 ;; The Qhull sources are included and are distributed under a custom
3277 ;; non-copyleft license. The R sources are released under GPL version 2.
3278 (license (list license:gpl2
3279 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3281 (define-public r-ddalpha
3288 (uri (cran-uri "ddalpha" version))
3291 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3292 (build-system r-build-system)
3295 ("r-class" ,r-class)
3296 ("r-geometry" ,r-geometry)
3299 ("r-robustbase" ,r-robustbase)
3300 ("r-sfsmisc" ,r-sfsmisc)))
3302 `(("gfortran" ,gfortran)))
3303 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3304 (synopsis "Depth-Based classification and calculation of data depth")
3306 "This package contains procedures for depth-based supervised learning,
3307 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3308 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3309 statistical depth function to a compact low-dimensional space, where the final
3310 classification is done. It also offers an extension to functional data and
3311 routines for calculating certain notions of statistical depth functions. 50
3312 multivariate and 5 functional classification problems are included.")
3313 (license license:gpl2)))
3315 (define-public r-gower
3322 (uri (cran-uri "gower" version))
3325 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3326 (build-system r-build-system)
3327 (home-page "https://github.com/markvanderloo/gower")
3328 (synopsis "Gower's distance")
3330 "This package provides tools to compute Gower's distance (or similarity)
3331 coefficient between records, and to compute the top-n matches between records.
3332 Core algorithms are executed in parallel on systems supporting OpenMP.")
3333 (license license:gpl3)))
3335 (define-public r-rcpproll
3342 (uri (cran-uri "RcppRoll" version))
3345 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3346 (properties `((upstream-name . "RcppRoll")))
3347 (build-system r-build-system)
3349 `(("r-rcpp" ,r-rcpp)))
3350 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3351 (synopsis "Efficient rolling and windowed operations")
3353 "This package provides fast and efficient routines for common rolling /
3354 windowed operations. Routines for the efficient computation of windowed mean,
3355 median, sum, product, minimum, maximum, standard deviation and variance are
3357 (license license:gpl2+)))
3359 (define-public r-ipred
3366 (uri (cran-uri "ipred" version))
3369 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3370 (build-system r-build-system)
3372 `(("r-class" ,r-class)
3375 ("r-prodlim" ,r-prodlim)
3376 ("r-rpart" ,r-rpart)
3377 ("r-survival" ,r-survival)))
3378 (home-page "https://cran.r-project.org/web/packages/ipred")
3379 (synopsis "Improved predictors")
3381 "This package provides improved predictive models by indirect
3382 classification and bagging for classification, regression and survival
3383 problems as well as resampling based estimators of prediction error.")
3384 (license license:gpl2+)))
3386 (define-public r-psych
3389 (version "1.9.12.31")
3393 (uri (cran-uri "psych" version))
3396 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3397 (build-system r-build-system)
3399 `(("r-lattice" ,r-lattice)
3400 ("r-mnormt" ,r-mnormt)
3401 ("r-nlme" ,r-nlme)))
3402 (home-page "https://cran.r-project.org/web/packages/psych/")
3403 (synopsis "Procedures for psychological, psychometric, and personality research")
3405 "This package provides a general purpose toolbox for personality,
3406 psychometric theory and experimental psychology. Functions are primarily for
3407 multivariate analysis and scale construction using factor analysis, principal
3408 component analysis, cluster analysis and reliability analysis, although others
3409 provide basic descriptive statistics. Item Response Theory is done using
3410 factor analysis of tetrachoric and polychoric correlations. Functions for
3411 analyzing data at multiple levels include within and between group statistics,
3412 including correlations and factor analysis. Functions for simulating and
3413 testing particular item and test structures are included. Several functions
3414 serve as a useful front end for structural equation modeling. Graphical
3415 displays of path diagrams, factor analysis and structural equation models are
3416 created using basic graphics.")
3417 (license license:gpl2+)))
3419 (define-public r-generics
3426 (uri (cran-uri "generics" version))
3429 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3430 (build-system r-build-system)
3431 (home-page "https://github.com/r-lib/generics")
3432 (synopsis "Common S3 generics not provided by base R methods")
3434 "In order to reduce potential package dependencies and conflicts,
3435 generics provides a number of commonly used S3 generics that are not provided
3436 by base R methods related to model fitting.")
3437 (license license:gpl2)))
3439 (define-public r-broom
3446 (uri (cran-uri "broom" version))
3449 "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5"))))
3450 (build-system r-build-system)
3452 `(("r-backports" ,r-backports)
3453 ("r-dplyr" ,r-dplyr)
3454 ("r-ellipsis" ,r-ellipsis)
3455 ("r-generics" ,r-generics)
3457 ("r-purrr" ,r-purrr)
3458 ("r-rlang" ,r-rlang)
3459 ("r-stringr" ,r-stringr)
3460 ("r-tibble" ,r-tibble)
3461 ("r-tidyr" ,r-tidyr)))
3463 `(("r-knitr" ,r-knitr)))
3464 (home-page "https://github.com/tidyverse/broom")
3465 (synopsis "Convert statistical analysis objects into tidy data frames")
3467 "This package provides tools to convert statistical analysis objects from
3468 R into tidy data frames, so that they can more easily be combined, reshaped
3469 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3470 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3471 summarizes a model's statistical findings such as coefficients of a
3472 regression; @code{augment}, which adds columns to the original data such as
3473 predictions, residuals and cluster assignments; and @code{glance}, which
3474 provides a one-row summary of model-level statistics.")
3475 (license license:expat)))
3477 (define-public r-recipes
3484 (uri (cran-uri "recipes" version))
3487 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3488 (build-system r-build-system)
3490 `(("r-dplyr" ,r-dplyr)
3491 ("r-generics" ,r-generics)
3493 ("r-gower" ,r-gower)
3494 ("r-ipred" ,r-ipred)
3495 ("r-lifecycle" ,r-lifecycle)
3496 ("r-lubridate" ,r-lubridate)
3497 ("r-magrittr" ,r-magrittr)
3498 ("r-matrix" ,r-matrix)
3499 ("r-purrr" ,r-purrr)
3500 ("r-rlang" ,r-rlang)
3501 ("r-tibble" ,r-tibble)
3502 ("r-tidyr" ,r-tidyr)
3503 ("r-tidyselect" ,r-tidyselect)
3504 ("r-timedate" ,r-timedate)
3505 ("r-withr" ,r-withr)))
3507 `(("r-knitr" ,r-knitr)))
3508 (home-page "https://github.com/topepo/recipes")
3509 (synopsis "Preprocessing tools to create design matrices")
3511 "Recipes is an extensible framework to create and preprocess design
3512 matrices. Recipes consist of one or more data manipulation and analysis
3513 \"steps\". Statistical parameters for the steps can be estimated from an
3514 initial data set and then applied to other data sets. The resulting design
3515 matrices can then be used as inputs into statistical or machine learning
3517 (license license:gpl2)))
3519 (define-public r-pdist
3526 (uri (cran-uri "pdist" version))
3529 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3530 (build-system r-build-system)
3531 (home-page "https://github.com/jeffwong/pdist")
3532 (synopsis "Partitioned distance function")
3534 "Pdist computes the euclidean distance between rows of a matrix X and
3535 rows of another matrix Y. Previously, this could be done by binding the two
3536 matrices together and calling @code{dist}, but this creates unnecessary
3537 computation by computing the distances between a row of X and another row of
3538 X, and likewise for Y. Pdist strictly computes distances across the two
3539 matrices, not within the same matrix, making computations significantly faster
3540 for certain use cases.")
3541 (license license:gpl3+)))
3543 (define-public r-ggrepel
3550 (uri (cran-uri "ggrepel" version))
3553 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3554 (build-system r-build-system)
3556 `(("r-ggplot2" ,r-ggplot2)
3558 ("r-scales" ,r-scales)))
3560 `(("r-knitr" ,r-knitr))) ; for vignettes
3561 (home-page "https://github.com/slowkow/ggrepel")
3562 (synopsis "Repulsive text and label geometries for ggplot2")
3564 "This package provides text and label geometries for ggplot2 that help to
3565 avoid overlapping text labels. Labels repel away from each other and away
3566 from the data points.")
3567 (license license:gpl3)))
3569 (define-public r-corrplot
3576 (uri (cran-uri "corrplot" version))
3579 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3580 (build-system r-build-system)
3581 (home-page "https://github.com/taiyun/corrplot")
3582 (synopsis "Visualization of a correlation matrix")
3584 "This package provides a graphical display of a correlation matrix or
3585 general matrix. It also contains some algorithms to do matrix reordering. In
3586 addition, corrplot is good at details, including choosing color, text labels,
3587 color labels, layout, etc.")
3588 ;; Any version of the GPL
3589 (license license:gpl2+)))
3591 (define-public r-stringdist
3593 (name "r-stringdist")
3598 (uri (cran-uri "stringdist" version))
3600 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3601 (build-system r-build-system)
3602 (home-page "https://github.com/markvanderloo/stringdist")
3603 (synopsis "Approximate string matching and string distance functions")
3605 "This package implements an approximate string matching version of R's
3606 native @code{match} function. It can calculate various string distances based
3607 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3608 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3609 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3610 can be computed between character vectors while taking proper care of encoding
3611 or between integer vectors representing generic sequences.")
3612 (license license:gpl3+)))
3614 (define-public r-ucminf
3621 (uri (cran-uri "ucminf" version))
3624 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3625 (build-system r-build-system)
3626 (native-inputs `(("gfortran" ,gfortran)))
3627 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3628 (synopsis "General-purpose unconstrained non-linear optimization")
3630 "This package provides an implementation of an algorithm for
3631 general-purpose unconstrained non-linear optimization. The algorithm is of
3632 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3633 search with a trust region type monitoring of the input to the line search
3634 algorithm. The interface of @code{ucminf} is designed for easy interchange
3635 with the package @code{optim}.")
3636 (license license:gpl2+)))
3638 (define-public r-ordinal
3641 (version "2019.12-10")
3645 (uri (cran-uri "ordinal" version))
3648 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3649 (build-system r-build-system)
3651 `(("r-mass" ,r-mass)
3652 ("r-matrix" ,r-matrix)
3653 ("r-numderiv" ,r-numderiv)
3654 ("r-ucminf" ,r-ucminf)))
3655 (home-page "https://github.com/runehaubo/ordinal")
3656 (synopsis "Regression models for ordinal data")
3658 "This package provides an implementation of cumulative link (mixed)
3659 models also known as ordered regression models, proportional odds models,
3660 proportional hazards models for grouped survival times and ordered models.
3661 Estimation is via maximum likelihood and mixed models are fitted with the
3662 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3663 (license license:gpl2+)))
3665 (define-public r-jomo
3672 (uri (cran-uri "jomo" version))
3675 "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w"))))
3676 (build-system r-build-system)
3678 `(("r-lme4" ,r-lme4)
3680 ("r-ordinal" ,r-ordinal)
3681 ("r-survival" ,r-survival)))
3682 (home-page "https://cran.r-project.org/web/packages/jomo/")
3683 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3685 "Similarly to Schafer's package pan, jomo is a package for multilevel
3686 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3687 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3688 possibility of handling binary and categorical data through latent normal
3689 variables, the option to use cluster-specific covariance matrices and to
3690 impute compatibly with the substantive model.")
3691 (license license:gpl2)))
3693 (define-public r-pan
3700 (uri (cran-uri "pan" version))
3703 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3704 (build-system r-build-system)
3705 (native-inputs `(("gfortran" ,gfortran)))
3706 (home-page "https://cran.r-project.org/web/packages/pan/")
3707 (synopsis "Multiple imputation for multivariate panel or clustered data")
3709 "This package implements multiple imputation for multivariate panel or
3711 (license license:gpl3)))
3713 (define-public r-mitml
3720 (uri (cran-uri "mitml" version))
3723 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3724 (build-system r-build-system)
3726 `(("r-haven" ,r-haven)
3729 (home-page "https://cran.r-project.org/web/packages/mitml/")
3730 (synopsis "Tools for multiple imputation in multilevel modeling")
3732 "This package provides tools for multiple imputation of missing data in
3733 multilevel modeling. It includes a user-friendly interface to the packages
3734 pan and jomo, and several functions for visualization, data management and the
3735 analysis of multiply imputed data sets.")
3736 (license license:gpl2+)))
3738 (define-public r-mice
3745 (uri (cran-uri "mice" version))
3748 "0w81shmd2crpdlh66pnm27v4n06aayganq6kkalirln4c0ci2nyi"))))
3749 (build-system r-build-system)
3751 `(("r-broom" ,r-broom)
3752 ("r-dplyr" ,r-dplyr)
3753 ("r-generics" ,r-generics)
3754 ("r-lattice" ,r-lattice)
3756 ("r-tidyr" ,r-tidyr)))
3757 (home-page "https://cran.r-project.org/web/packages/mice/")
3758 (synopsis "Multivariate imputation by chained equations")
3760 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3761 implemented by the MICE algorithm as described in @url{Van Buuren and
3762 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3763 variable has its own imputation model. Built-in imputation models are
3764 provided for continuous data (predictive mean matching, normal), binary
3765 data (logistic regression), unordered categorical data (polytomous logistic
3766 regression) and ordered categorical data (proportional odds). MICE can also
3767 impute continuous two-level data (normal model, pan, second-level variables).
3768 Passive imputation can be used to maintain consistency between variables.
3769 Various diagnostic plots are available to inspect the quality of the
3771 ;; Any of these two versions.
3772 (license (list license:gpl2 license:gpl3))))
3774 (define-public r-truncnorm
3776 (name "r-truncnorm")
3781 (uri (cran-uri "truncnorm" version))
3784 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3785 (build-system r-build-system)
3786 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3787 (synopsis "Truncated normal distribution")
3788 (description "This package provides functions for the truncated normal
3789 distribution with mean equal to @code{mean} and standard deviation equal to
3790 @code{sd}. It includes density, distribution, quantile, and expected value
3791 functions, as well as a random generation function.")
3792 (license license:gpl2)))
3794 (define-public r-rsolnp
3801 (uri (cran-uri "Rsolnp" version))
3804 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3805 (properties `((upstream-name . "Rsolnp")))
3806 (build-system r-build-system)
3808 `(("r-truncnorm" ,r-truncnorm)))
3809 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3810 (synopsis "General non-linear optimization")
3811 (description "The Rsolnp package implements a general non-linear augmented
3812 Lagrange multiplier method solver, a @dfn{sequential quadratic
3813 programming} (SQP) based solver).")
3814 ;; Any version of the GPL.
3815 (license license:gpl2+)))
3817 (define-public r-hardyweinberg
3819 (name "r-hardyweinberg")
3824 (uri (cran-uri "HardyWeinberg" version))
3827 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3828 (properties `((upstream-name . "HardyWeinberg")))
3829 (build-system r-build-system)
3831 `(("r-mice" ,r-mice)
3833 ("r-rsolnp" ,r-rsolnp)))
3834 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3835 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3837 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3838 diallelic genetic marker data. All classical tests (chi-square, exact,
3839 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3840 included in the package, as well as functions for power computation and for
3841 the simulation of marker data under equilibrium and disequilibrium. Routines
3842 for dealing with markers on the X-chromosome are included. Functions for
3843 testing equilibrium in the presence of missing data by using multiple
3844 imputation are also provided. Implements several graphics for exploring the
3845 equilibrium status of a large set of diallelic markers: ternary plots with
3846 acceptance regions, log-ratio plots and Q-Q plots.")
3847 (license license:gpl2+)))
3856 (uri (cran-uri "sm" version))
3859 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3860 (build-system r-build-system)
3861 (native-inputs `(("gfortran" ,gfortran)))
3862 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3863 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3865 "This is software accompanying the book 'Applied Smoothing Techniques for
3866 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3867 University Press. It provides smoothing methods for nonparametric regression
3868 and density estimation")
3869 (license license:gpl2+)))
3871 (define-public r-venndiagram
3873 (name "r-venndiagram")
3877 (uri (cran-uri "VennDiagram" version))
3880 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3881 (properties `((upstream-name . "VennDiagram")))
3882 (build-system r-build-system)
3884 `(("r-futile-logger" ,r-futile-logger)))
3885 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3886 (synopsis "Generate High-Resolution Venn and Euler Plots")
3888 "This package provides a set of functions to generate high-resolution
3889 Venn and Euler plots. It includes handling for several special cases,
3890 including two-case scaling, and extensive customization of plot shape and
3892 (license license:gpl2+)))
3894 (define-public r-vioplot
3901 (uri (cran-uri "vioplot" version))
3904 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3905 (build-system r-build-system)
3910 `(("r-knitr" ,r-knitr)))
3911 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3912 (synopsis "Violin plot")
3914 "This package provides a violin plot, which is a combination of a box
3915 plot and a kernel density plot.")
3916 (license license:bsd-3)))
3918 (define-public r-rsofia
3924 ;; This package has been removed from CRAN, so we can
3925 ;; only fetch it from the archives.
3926 (uri (string-append "https://cran.r-project.org/src/"
3927 "contrib/Archive/RSofia/RSofia_"
3931 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3932 (properties `((upstream-name . "RSofia")))
3933 (build-system r-build-system)
3935 `(("r-rcpp" ,r-rcpp)))
3936 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3937 (synopsis "Port of sofia-ml to R")
3938 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3939 suite of fast incremental algorithms for machine learning that can be used for
3940 training models for classification or ranking.")
3941 (license license:asl2.0)))
3943 (define-public r-xts
3950 (uri (cran-uri "xts" version))
3953 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3954 (build-system r-build-system)
3955 (propagated-inputs `(("r-zoo" ,r-zoo)))
3956 (home-page "https://github.com/joshuaulrich/xts")
3957 (synopsis "Extensible time series")
3959 "This package provides for uniform handling of R's different time-based
3960 data classes by extending @code{zoo}, maximizing native format information
3961 preservation and allowing for user-level customization and extension, while
3962 simplifying cross-class interoperability.")
3963 (license license:gpl2+)))
3965 (define-public r-performanceanalytics
3967 (name "r-performanceanalytics")
3972 (uri (cran-uri "PerformanceAnalytics" version))
3975 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3977 `((upstream-name . "PerformanceAnalytics")))
3978 (build-system r-build-system)
3980 `(("r-quadprog" ,r-quadprog)
3983 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3984 (synopsis "Econometric tools for performance and risk analysis")
3985 (description "This is a collection of econometric functions for
3986 performance and risk analysis. This package aims to aid practitioners and
3987 researchers in utilizing the latest research in analysis of non-normal return
3988 streams. In general, it is most tested on return (rather than price) data on
3989 a regular scale, but most functions will work with irregular return data as
3990 well, and increasing numbers of functions will work with P&L or price data
3992 ;; Either version may be picked.
3993 (license (list license:gpl2 license:gpl3))))
3995 (define-public r-laeken
4002 (uri (cran-uri "laeken" version))
4005 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4006 (build-system r-build-system)
4008 `(("r-boot" ,r-boot)
4009 ("r-mass" ,r-mass)))
4010 (home-page "https://cran.r-project.org/web/packages/laeken/")
4011 (synopsis "Estimation of indicators on social exclusion and poverty")
4012 (description "This package provides tools for the estimation of indicators
4013 on social exclusion and poverty, as well as an implementation of Pareto tail
4014 modeling for empirical income distributions.")
4015 (license license:gpl2+)))
4017 (define-public r-vcd
4024 (uri (cran-uri "vcd" version))
4027 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
4028 (build-system r-build-system)
4030 `(("r-colorspace" ,r-colorspace)
4031 ("r-lmtest" ,r-lmtest)
4032 ("r-mass" ,r-mass)))
4033 (home-page "https://cran.r-project.org/web/packages/vcd/")
4034 (synopsis "Visualizing categorical data")
4035 (description "This package provides visualization techniques, data sets,
4036 summary and inference procedures aimed particularly at categorical data.
4037 Special emphasis is given to highly extensible grid graphics. The package was
4038 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4039 Friendly and is now the main support package for a new book, \"Discrete Data
4040 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4041 (license license:gpl2)))
4043 (define-public r-ica
4050 (uri (cran-uri "ica" version))
4053 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4054 (build-system r-build-system)
4055 (home-page "https://cran.r-project.org/web/packages/ica/")
4056 (synopsis "Independent component analysis")
4057 (description "This package provides tools for @dfn{Independent Component
4058 Analysis} (ICA) using various algorithms: FastICA,
4059 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4060 of Eigenmatrices} (JADE).")
4061 (license license:gpl2+)))
4063 (define-public r-dtw
4070 (uri (cran-uri "dtw" version))
4073 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4074 (build-system r-build-system)
4075 (propagated-inputs `(("r-proxy" ,r-proxy)))
4076 (home-page "http://dtw.r-forge.r-project.org/")
4077 (synopsis "Dynamic Time Warping Algorithms")
4078 (description "This package provides a comprehensive implementation of
4079 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4080 optimal (least cumulative distance) alignment between points of two time
4081 series. Common DTW variants covered include local (slope) and global (window)
4082 constraints, subsequence matches, arbitrary distance definitions,
4083 normalizations, minimum variance matching, and so on.")
4084 (license license:gpl2+)))
4086 (define-public r-sdmtools
4089 (version "1.1-221.2")
4093 (uri (cran-uri "SDMTools" version))
4096 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4097 (properties `((upstream-name . "SDMTools")))
4098 (build-system r-build-system)
4099 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4100 (home-page "https://www.rforge.net/SDMTools/")
4101 (synopsis "Species distribution modelling tools")
4102 (description "This package provides a set of tools for post processing
4103 the outcomes of species distribution modeling exercises. It includes novel
4104 methods for comparing models and tracking changes in distributions through
4105 time. It further includes methods for visualizing outcomes, selecting
4106 thresholds, calculating measures of accuracy and landscape fragmentation
4108 (license license:gpl3+)))
4110 (define-public r-scatterplot3d
4112 (name "r-scatterplot3d")
4117 (uri (cran-uri "scatterplot3d" version))
4120 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4121 (build-system r-build-system)
4122 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4123 (synopsis "3D scatter plot")
4124 (description "This package provides an implementation of scatter plots for
4125 plotting. a three dimensional point cloud.")
4126 (license license:gpl2)))
4128 (define-public r-ggridges
4135 (uri (cran-uri "ggridges" version))
4138 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4139 (build-system r-build-system)
4141 `(("r-ggplot2" ,r-ggplot2)
4143 ("r-scales" ,r-scales)
4144 ("r-withr" ,r-withr)))
4145 (home-page "https://github.com/clauswilke/ggridges")
4146 (synopsis "Ridgeline plots in ggplot2")
4148 "Ridgeline plots provide a convenient way of visualizing changes in
4149 distributions over time or space. This package enables the creation of such
4150 plots in @code{ggplot2}.")
4151 (license license:gpl2)))
4153 (define-public r-ggjoy
4160 (uri (cran-uri "ggjoy" version))
4163 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4164 (build-system r-build-system)
4166 `(("r-ggplot2" ,r-ggplot2)
4167 ("r-ggridges" ,r-ggridges)))
4168 (home-page "https://github.com/clauswilke/ggjoy")
4169 (synopsis "Joyplots in ggplot2")
4170 (description "Joyplots provide a convenient way of visualizing changes in
4171 distributions over time or space. This package enables the creation of such
4172 plots in @code{ggplot2}.")
4173 (license license:gpl2)))
4175 (define-public r-cli
4182 (uri (cran-uri "cli" version))
4185 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4186 (build-system r-build-system)
4188 `(("r-assertthat" ,r-assertthat)
4189 ("r-crayon" ,r-crayon)
4190 ("r-fansi" ,r-fansi)
4191 ("r-glue" ,r-glue)))
4192 (home-page "https://github.com/r-lib/cli#readme")
4193 (synopsis "Helpers for developing command line interfaces")
4194 (description "This package provides a suite of tools designed to build
4195 attractive command line interfaces (CLIs). It includes tools for drawing
4196 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4197 (license license:expat)))
4199 (define-public r-argparser
4201 (name "r-argparser")
4206 (uri (cran-uri "argparser" version))
4209 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4210 (build-system r-build-system)
4211 (home-page "https://bitbucket.org/djhshih/argparser")
4212 (synopsis "Command-line argument parser")
4214 "This package provides a cross-platform command-line argument parser
4215 written purely in R with no external dependencies. It is useful with the
4216 Rscript front-end and facilitates turning an R script into an executable
4218 (license license:gpl3+)))
4220 (define-public r-debugme
4227 (uri (cran-uri "debugme" version))
4230 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4231 (build-system r-build-system)
4232 (propagated-inputs `(("r-crayon" ,r-crayon)))
4233 (home-page "https://github.com/r-lib/debugme#readme")
4234 (synopsis "Debug R packages")
4236 "This package allows the user to specify debug messages as special string
4237 constants, and control debugging of packages via environment variables.")
4238 (license license:expat)))
4240 (define-public r-processx
4247 (uri (cran-uri "processx" version))
4249 (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
4250 (build-system r-build-system)
4254 (home-page "https://github.com/r-lib/processx3")
4255 (synopsis "Execute and control system processes")
4257 "This package provides portable tools to run system processes in the
4258 background. It can check if a background process is running; wait on a
4259 background process to finish; get the exit status of finished processes; kill
4260 background processes and their children; restart processes. It can read the
4261 standard output and error of the processes, using non-blocking connections.
4262 @code{processx} can poll a process for standard output or error, with a
4263 timeout. It can also poll several processes at once.")
4264 (license license:expat)))
4266 (define-public r-tsp
4273 (uri (cran-uri "TSP" version))
4276 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4277 (properties `((upstream-name . "TSP")))
4278 (build-system r-build-system)
4279 (propagated-inputs `(("r-foreach" ,r-foreach)))
4280 (home-page "https://cran.r-project.org/web/packages/TSP/")
4281 (synopsis "Traveling salesperson problem (TSP)")
4282 (description "This package provides basic infrastructure and some
4283 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4284 traveling salesman problem).")
4285 (license license:gpl3)))
4287 (define-public r-qap
4294 (uri (cran-uri "qap" version))
4297 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4298 (build-system r-build-system)
4299 (native-inputs `(("gfortran" ,gfortran)))
4300 (home-page "https://cran.r-project.org/web/packages/qap/")
4301 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4302 (description "This package implements heuristics for the @dfn{quadratic
4303 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4305 (license license:gpl3)))
4307 (define-public r-gclus
4314 (uri (cran-uri "gclus" version))
4317 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4318 (build-system r-build-system)
4319 (propagated-inputs `(("r-cluster" ,r-cluster)))
4320 (home-page "https://cran.r-project.org/web/packages/gclus/")
4321 (synopsis "Clustering graphics")
4322 (description "This package orders panels in scatterplot matrices and
4323 parallel coordinate displays by some merit index. It contains various indices
4324 of merit, ordering functions, and enhanced versions of @code{pairs} and
4325 @code{parcoord} which color panels according to their merit level.")
4326 (license license:gpl2+)))
4328 (define-public r-webshot
4335 (uri (cran-uri "webshot" version))
4338 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4339 (build-system r-build-system)
4341 `(("r-callr" ,r-callr)
4342 ("r-jsonlite" ,r-jsonlite)
4343 ("r-magrittr" ,r-magrittr)))
4344 (home-page "https://github.com/wch/webshot/")
4345 (synopsis "Take screenshots of web pages")
4347 "Webshot makes it easy to take screenshots of web pages from within R.
4348 It can also run Shiny applications locally and take screenshots of the
4349 application; and it can render and screenshot static as well as interactive R
4350 Markdown documents.")
4351 (license license:gpl2)))
4353 (define-public r-seriation
4355 (name "r-seriation")
4360 (uri (cran-uri "seriation" version))
4363 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4364 (build-system r-build-system)
4366 `(("r-cluster" ,r-cluster)
4367 ("r-colorspace" ,r-colorspace)
4368 ("r-dendextend" ,r-dendextend)
4369 ("r-gclus" ,r-gclus)
4370 ("r-gplots" ,r-gplots)
4373 ("r-registry" ,r-registry)
4375 (native-inputs `(("gfortran" ,gfortran)))
4376 (home-page "https://s2.smu.edu/IDA/seriation/")
4377 (synopsis "Infrastructure for ordering objects using seriation")
4379 "This package provides infrastructure for seriation with an
4380 implementation of several seriation/sequencing techniques to reorder matrices,
4381 dissimilarity matrices, and dendrograms. It also provides (optimally)
4382 reordered heatmaps, color images and clustering visualizations like
4383 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4385 (license license:gpl3)))
4387 (define-public r-xfun
4394 (uri (cran-uri "xfun" version))
4396 (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj"))))
4397 (build-system r-build-system)
4398 ;; knitr itself depends on xfun
4401 `(("r-knitr" ,r-knitr)))
4402 (home-page "https://github.com/yihui/xfun")
4403 (synopsis "Miscellaneous functions")
4405 "This package provides miscellaneous functions commonly used in other
4406 packages maintained by Yihui Xie.")
4407 (license license:expat)))
4409 (define-public r-utf8
4416 (uri (cran-uri "utf8" version))
4419 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4420 (build-system r-build-system)
4421 (home-page "https://github.com/patperry/r-utf8")
4422 (synopsis "Unicode text processing")
4424 "This package provides tools to process and print UTF-8 encoded
4425 international text (Unicode). Input, validate, normalize, encode, format, and
4427 (license license:asl2.0)))
4429 (define-public r-zeallot
4436 (uri (cran-uri "zeallot" version))
4439 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4440 (build-system r-build-system)
4441 (home-page "https://github.com/nteetor/zeallot")
4442 (synopsis "Multiple, unpacking, and destructuring assignment")
4444 "This package provides a @code{%<-%} operator to perform multiple,
4445 unpacking, and destructuring assignment in R. The operator unpacks the
4446 right-hand side of an assignment into multiple values and assigns these values
4447 to variables on the left-hand side of the assignment.")
4448 (license license:expat)))
4450 (define-public r-vctrs
4457 (uri (cran-uri "vctrs" version))
4460 "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp"))))
4461 (build-system r-build-system)
4463 `(("r-digest" ,r-digest)
4464 ("r-ellipsis" ,r-ellipsis)
4466 ("r-rlang" ,r-rlang)))
4468 `(("r-knitr" ,r-knitr)))
4469 (home-page "https://github.com/r-lib/vctrs")
4470 (synopsis "Vector helpers")
4472 "There are three main goals to the @code{vctrs} package:
4475 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4476 @code{length()} and @code{class()}. These definitions are paired with a
4477 framework for type-coercion and size-recycling.
4478 @item To define type- and size-stability as desirable function properties, use
4479 them to analyse existing base function, and to propose better alternatives.
4480 This work has been particularly motivated by thinking about the ideal
4481 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4482 @item To provide a new @code{vctr} base class that makes it easy to create new
4483 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4484 a few new @code{vctrs} generics, making implementation considerably simpler
4487 (license license:gpl3)))
4489 (define-public r-pillar
4496 (uri (cran-uri "pillar" version))
4499 "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj"))))
4500 (build-system r-build-system)
4503 ("r-crayon" ,r-crayon)
4504 ("r-ellipsis" ,r-ellipsis)
4505 ("r-fansi" ,r-fansi)
4506 ("r-lifecycle" ,r-lifecycle)
4507 ("r-rlang" ,r-rlang)
4509 ("r-vctrs" ,r-vctrs)))
4510 (home-page "https://github.com/r-lib/pillar")
4511 (synopsis "Coloured formatting for columns")
4513 "This package provides a @code{pillar} generic designed for formatting
4514 columns of data using the full range of colours provided by modern
4516 (license license:gpl3)))
4518 (define-public r-uuid
4525 (uri (cran-uri "uuid" version))
4528 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4529 (build-system r-build-system)
4530 (home-page "https://www.rforge.net/uuid")
4531 (synopsis "Tools for generating and handling of UUIDs")
4533 "This package provides tools for generating and handling of
4534 @dfn{Universally Unique Identifiers} (UUIDs).")
4535 (license license:expat)))
4537 (define-public r-tinytex
4544 (uri (cran-uri "tinytex" version))
4547 "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr"))))
4548 (build-system r-build-system)
4550 `(("r-xfun" ,r-xfun)))
4551 (home-page "https://github.com/yihui/tinytex")
4552 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4554 "This package provides helper functions to install and maintain the LaTeX
4555 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4556 easy-to-maintain version of TeX Live. This package also contains helper
4557 functions to compile LaTeX documents, and install missing LaTeX packages
4559 (license license:expat)))
4561 (define-public r-network
4568 (uri (cran-uri "network" version))
4571 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4572 (build-system r-build-system)
4574 `(("r-magrittr" ,r-magrittr)
4575 ("r-tibble" ,r-tibble)))
4576 (home-page "https://statnet.org/")
4577 (synopsis "Classes for relational data")
4579 "This package provides tools to create and modify network objects. The
4580 @code{network} class can represent a range of relational data types, and
4581 supports arbitrary vertex/edge/graph attributes.")
4582 (license license:gpl2+)))
4584 (define-public r-statnet-common
4586 (name "r-statnet-common")
4591 (uri (cran-uri "statnet.common" version))
4594 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4596 `((upstream-name . "statnet.common")))
4597 (build-system r-build-system)
4599 `(("r-coda" ,r-coda)))
4600 (home-page "https://statnet.org")
4601 (synopsis "R scripts and utilities used by the Statnet software")
4602 (description "This package provides non-statistical utilities used by the
4603 software developed by the Statnet Project.")
4604 (license license:gpl3)))
4606 (define-public r-statcheck
4608 (name "r-statcheck")
4613 (uri (cran-uri "statcheck" version))
4616 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4617 (build-system r-build-system)
4619 `(("r-ggplot2" ,r-ggplot2)
4621 ("r-rmarkdown" ,r-rmarkdown)))
4622 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4623 (synopsis "Extract statistics from articles and recompute p-values")
4624 (description "This package can automatically extract statistical
4625 null-hypothesis significant testing (NHST) results from articles and recompute
4626 the p-values based on the reported test statistic and degrees of freedom to
4627 detect possible inconsistencies.")
4628 (license license:gpl2)))
4630 (define-public r-sna
4637 (uri (cran-uri "sna" version))
4640 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4641 (build-system r-build-system)
4643 `(("r-network" ,r-network)
4644 ("r-statnet-common" ,r-statnet-common)))
4645 (home-page "https://statnet.org")
4646 (synopsis "Tools for social network analysis")
4648 "This package provides a range of tools for social network analysis,
4649 including node and graph-level indices, structural distance and covariance
4650 methods, structural equivalence detection, network regression, random graph
4651 generation, and 2D/3D network visualization.")
4652 (license license:gpl2+)))
4654 (define-public r-tfisher
4661 (uri (cran-uri "TFisher" version))
4664 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4665 (properties `((upstream-name . "TFisher")))
4666 (build-system r-build-system)
4668 `(("r-matrix" ,r-matrix)
4669 ("r-mvtnorm" ,r-mvtnorm)
4671 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4672 (synopsis "Optimal thresholding Fisher's p-value combination method")
4674 "This package provides the @dfn{cumulative distribution function} (CDF),
4675 quantile, and statistical power calculator for a collection of thresholding
4676 Fisher's p-value combination methods, including Fisher's p-value combination
4677 method, truncated product method and, in particular, soft-thresholding
4678 Fisher's p-value combination method which is proven to be optimal in some
4679 context of signal detection. The p-value calculator for the omnibus version
4680 of these tests are also included.")
4681 (license license:gpl2)))
4683 (define-public r-ttr
4690 (uri (cran-uri "TTR" version))
4693 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4694 (properties `((upstream-name . "TTR")))
4695 (build-system r-build-system)
4697 `(("r-curl" ,r-curl)
4700 (home-page "https://github.com/joshuaulrich/TTR")
4701 (synopsis "Technical trading rules")
4703 "This package provides functions and data to construct technical trading
4705 (license license:gpl2)))
4707 (define-public r-leaps
4714 (uri (cran-uri "leaps" version))
4717 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4718 (build-system r-build-system)
4719 (native-inputs `(("gfortran" ,gfortran)))
4720 (home-page "https://cran.r-project.org/web/packages/leaps/")
4721 (synopsis "Regression subset selection")
4723 "This package provides tools for regression subset selection, including
4724 exhaustive search.")
4725 (license license:gpl2+)))
4727 (define-public r-splus2r
4734 (uri (cran-uri "splus2R" version))
4737 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4738 (properties `((upstream-name . "splus2R")))
4739 (build-system r-build-system)
4740 (native-inputs `(("gfortran" ,gfortran)))
4741 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4742 (synopsis "Supplemental S-PLUS functionality in R")
4744 "Currently there are many functions in S-PLUS that are missing in R. To
4745 facilitate the conversion of S-PLUS packages to R packages, this package
4746 provides some missing S-PLUS functionality in R.")
4747 (license license:gpl2)))
4749 (define-public r-ifultools
4751 (name "r-ifultools")
4756 (uri (cran-uri "ifultools" version))
4759 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4760 (build-system r-build-system)
4762 `(("r-mass" ,r-mass)
4763 ("r-splus2r" ,r-splus2r)))
4764 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4765 (synopsis "Insightful research tools")
4766 (description "This package provides C code used by the wmtsa, fractal, and
4768 (license license:gpl2)))
4770 (define-public r-sapa
4777 (uri (cran-uri "sapa" version))
4780 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4781 (build-system r-build-system)
4783 `(("r-ifultools" ,r-ifultools)
4784 ("r-splus2r" ,r-splus2r)))
4785 (home-page "https://cran.r-project.org/web/packages/sapa/")
4786 (synopsis "Spectral analysis for physical applications")
4787 (description "This package provides software for the book Spectral
4788 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4789 Cambridge University Press, 1993.")
4790 (license license:gpl2)))
4792 (define-public r-aggregation
4794 (name "r-aggregation")
4799 (uri (cran-uri "aggregation" version))
4802 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4803 (build-system r-build-system)
4804 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4805 (synopsis "Methods for p-value aggregation")
4807 "This package contains functionality for performing the following methods
4808 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4809 Fisher's method), and Sidak correction.")
4810 (license license:gpl3)))
4812 (define-public r-quantmod
4819 (uri (cran-uri "quantmod" version))
4822 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4823 (build-system r-build-system)
4825 `(("r-curl" ,r-curl)
4829 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4830 (synopsis "Quantitative financial modelling framework")
4831 (description "This package provides a quantitative financial modelling
4832 framework to allow users to specify, build, trade, and analyse quantitative
4833 financial trading strategies.")
4834 (license license:gpl3)))
4836 (define-public r-tseries
4843 (uri (cran-uri "tseries" version))
4846 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4847 (build-system r-build-system)
4849 `(("r-quadprog" ,r-quadprog)
4850 ("r-quantmod" ,r-quantmod)
4853 `(("gfortran" ,gfortran)))
4854 (home-page "https://cran.r-project.org/web/packages/tseries/")
4855 (synopsis "Time series analysis and computational finance")
4857 "This package provides functions relating to time series analysis and
4858 computational finance.")
4859 (license license:gpl2)))
4861 (define-public r-wmtsa
4868 (uri (cran-uri "wmtsa" version))
4871 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4872 (build-system r-build-system)
4874 `(("r-ifultools" ,r-ifultools)
4876 ("r-splus2r" ,r-splus2r)))
4877 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4878 (synopsis "Wavelet methods for time series analysis")
4880 "This package provides software to accompany the book \"Wavelet Methods
4881 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4882 University Press, 2000.")
4883 (license license:gpl2)))
4885 (define-public r-tsa
4892 (uri (cran-uri "TSA" version))
4895 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4896 (properties `((upstream-name . "TSA")))
4897 (build-system r-build-system)
4899 `(("r-leaps" ,r-leaps)
4900 ("r-locfit" ,r-locfit)
4901 ("r-mgcv" ,r-mgcv)))
4902 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4903 (synopsis "Time series analysis")
4905 "This package contains R functions and datasets detailed in the book
4906 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4907 Cryer and Kung-Sik Chan.")
4908 (license license:gpl2+)))
4910 (define-public r-extradistr
4912 (name "r-extradistr")
4917 (uri (cran-uri "extraDistr" version))
4920 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4921 (properties `((upstream-name . "extraDistr")))
4922 (build-system r-build-system)
4924 `(("r-rcpp" ,r-rcpp)))
4925 (home-page "https://github.com/twolodzko/extraDistr")
4926 (synopsis "Additional univariate and multivariate distributions")
4928 "This package implements density, distribution functions, quantile
4929 functions and random generation functions for a large number of univariate and
4930 multivariate distributions.")
4931 (license license:gpl2)))
4933 (define-public r-fractal
4940 (uri (cran-uri "fractal" version))
4943 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4944 (build-system r-build-system)
4946 `(("r-ifultools" ,r-ifultools)
4949 ("r-scatterplot3d" ,r-scatterplot3d)
4950 ("r-splus2r" ,r-splus2r)
4951 ("r-wmtsa" ,r-wmtsa)))
4952 (home-page "https://cran.r-project.org/web/packages/fractal/")
4953 (synopsis "Fractal time series modeling and analysis")
4955 "This package provides tools for stochastic fractal and deterministic
4956 chaotic time series analysis.")
4957 (license license:gpl2)))
4959 (define-public r-urca
4966 (uri (cran-uri "urca" version))
4969 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4970 (build-system r-build-system)
4971 (propagated-inputs `(("r-nlme" ,r-nlme)))
4972 (native-inputs `(("gfortran" ,gfortran)))
4973 (home-page "https://cran.r-project.org/web/packages/urca/")
4974 (synopsis "Unit root and cointegration tests for time series data")
4976 "This package provides unit root and cointegration tests encountered in
4977 applied econometric analysis.")
4978 (license license:gpl2+)))
4980 (define-public r-cubature
4987 (uri (cran-uri "cubature" version))
4990 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
4991 (build-system r-build-system)
4993 `(("r-rcpp" ,r-rcpp)))
4995 `(("r-knitr" ,r-knitr)))
4996 (home-page "https://github.com/bnaras/cubature")
4997 (synopsis "Adaptive multivariate integration over hypercubes")
4999 "This package is an R wrapper around the cubature C library for adaptive
5000 multivariate integration over hypercubes. This version provides both
5001 @code{hcubature} and @code{pcubature} routines in addition to a vector
5003 ;; The included cubature C library is released under GPLv2+, but the
5004 ;; wrapper declares the license to be GPLv3+.
5005 (license (list license:gpl2+ license:gpl3+))))
5007 (define-public r-trend
5014 (uri (cran-uri "trend" version))
5017 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
5018 (build-system r-build-system)
5020 `(("r-extradistr" ,r-extradistr)))
5022 `(("gfortran" ,gfortran)))
5023 (home-page "https://cran.r-project.org/web/packages/trend/")
5024 (synopsis "Non-parametric trend tests and change-point detection")
5026 "The analysis of environmental data often requires the detection of
5027 trends and change-points. This package includes tests for trend
5028 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5029 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5030 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5031 correlation trend test), change-point detection (Lanzante's test procedures,
5032 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5033 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5034 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5035 sample Robust Rank-Order Distributional Test.")
5036 (license license:gpl3)))
5038 (define-public r-expm
5045 (uri (cran-uri "expm" version))
5048 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
5049 (build-system r-build-system)
5050 (propagated-inputs `(("r-matrix" ,r-matrix)))
5051 (native-inputs `(("gfortran" ,gfortran)))
5052 (home-page "https://r-forge.r-project.org/projects/expm/")
5053 (synopsis "Tools for matrix exponentials and related quantities")
5055 "This package provides tools for the computation of the matrix
5056 exponential, logarithm, square root, and related quantities.")
5057 (license license:gpl2+)))
5059 (define-public r-complexplus
5061 (name "r-complexplus")
5066 (uri (cran-uri "complexplus" version))
5069 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5070 (build-system r-build-system)
5072 `(("r-expm" ,r-expm)
5073 ("r-matrix" ,r-matrix)))
5074 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5075 (synopsis "Functions of complex or real variables")
5077 "This package extends several functions to the complex domain, including
5078 the matrix exponential and logarithm, and the determinant.")
5079 (license license:gpl2)))
5081 (define-public r-phontools
5083 (name "r-phontools")
5088 (uri (cran-uri "phonTools" version))
5091 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5092 (properties `((upstream-name . "phonTools")))
5093 (build-system r-build-system)
5094 (home-page "http://www.santiagobarreda.com/rscripts.html")
5095 (synopsis "Tools for phonetic and acoustic analyses")
5097 "This package contains tools for the organization, display, and analysis
5098 of the sorts of data frequently encountered in phonetics research and
5099 experimentation, including the easy creation of IPA vowel plots, and the
5100 creation and manipulation of WAVE audio files.")
5101 (license license:bsd-2)))
5110 (uri (cran-uri "np" version))
5113 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5114 (build-system r-build-system)
5116 `(("r-boot" ,r-boot)
5117 ("r-cubature" ,r-cubature)
5118 ("r-quadprog" ,r-quadprog)
5119 ("r-quantreg" ,r-quantreg)))
5120 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5121 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5122 (description "This package provides non-parametric (and semi-parametric)
5123 kernel methods that seamlessly handle a mix of continuous, unordered, and
5124 ordered factor data types.")
5125 ;; Any version of the GPL.
5126 (license license:gpl3+)))
5128 (define-public r-powerplus
5130 (name "r-powerplus")
5135 (uri (cran-uri "powerplus" version))
5138 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5139 (build-system r-build-system)
5141 `(("r-complexplus" ,r-complexplus)
5144 ("r-matrix" ,r-matrix)
5145 ("r-phontools" ,r-phontools)))
5146 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5147 (synopsis "Exponentiation operations")
5149 "This package provides tools for the computation of matrix and scalar
5151 (license license:gpl2)))
5153 (define-public r-egg
5160 (uri (cran-uri "egg" version))
5163 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5164 (properties `((upstream-name . "egg")))
5165 (build-system r-build-system)
5167 `(("r-ggplot2" ,r-ggplot2)
5168 ("r-gridextra" ,r-gridextra)
5169 ("r-gtable" ,r-gtable)))
5170 (home-page "https://cran.r-project.org/web/packages/egg")
5171 (synopsis "Extensions for ggplot2")
5173 "This package provides miscellaneous functions to help customize ggplot2
5174 objects. High-level functions are provided to post-process ggplot2 layouts
5175 and allow alignment between plot panels, as well as setting panel sizes to
5176 fixed values. Other functions include a custom @code{geom}, and helper
5177 functions to enforce symmetric scales or add tags to facetted plots.")
5178 (license license:gpl3)))
5180 (define-public r-heatmaply
5182 (name "r-heatmaply")
5187 (uri (cran-uri "heatmaply" version))
5190 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5191 (build-system r-build-system)
5193 `(("r-assertthat" ,r-assertthat)
5194 ("r-colorspace" ,r-colorspace)
5195 ("r-dendextend" ,r-dendextend)
5197 ("r-ggplot2" ,r-ggplot2)
5198 ("r-htmlwidgets" ,r-htmlwidgets)
5199 ("r-magrittr" ,r-magrittr)
5200 ("r-plotly" ,r-plotly)
5201 ("r-rcolorbrewer" ,r-rcolorbrewer)
5202 ("r-reshape2" ,r-reshape2)
5203 ("r-scales" ,r-scales)
5204 ("r-seriation" ,r-seriation)
5205 ("r-viridis" ,r-viridis)
5206 ("r-webshot" ,r-webshot)))
5208 `(("r-knitr" ,r-knitr)))
5209 (home-page "https://cran.r-project.org/package=heatmaply")
5210 (synopsis "Interactive cluster heat maps using plotly")
5212 "This package enables you to create interactive cluster heatmaps that can
5213 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5214 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5215 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5216 a popular graphical method for visualizing high-dimensional data, in which a
5217 table of numbers is encoded as a grid of colored cells. The rows and columns
5218 of the matrix are ordered to highlight patterns and are often accompanied by
5220 ;; Either version of the license.
5221 (license (list license:gpl2 license:gpl3))))
5230 (uri (cran-uri "h5" version))
5233 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5234 (build-system r-build-system)
5239 `(("which" ,which)))
5241 `(("r-rcpp" ,r-rcpp)))
5242 (home-page "https://github.com/mannau/h5")
5243 (synopsis "Interface to the HDF5 Library")
5245 "This package provides an S4 interface to the HDF5 library supporting
5246 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5247 binary files in a language independent format. The HDF5 format can therefore
5248 be used as an alternative to R's save/load mechanism. Since h5 is able to
5249 access only subsets of stored data it can also handle data sets which do not
5251 (license license:bsd-2)))
5253 (define-public r-cgdsr
5260 (uri (cran-uri "cgdsr" version))
5263 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5264 (build-system r-build-system)
5266 `(("r-httr" ,r-httr)
5267 ("r-r-methodss3" ,r-r-methodss3)
5268 ("r-r-oo" ,r-r-oo)))
5269 (home-page "https://github.com/cBioPortal/cgdsr")
5270 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5272 "This package provides a basic set of R functions for querying the Cancer
5273 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5274 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5275 (license license:lgpl3)))
5277 (define-public r-import
5284 (uri (cran-uri "import" version))
5287 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5288 (build-system r-build-system)
5289 (home-page "https://github.com/smbache/import")
5290 (synopsis "Import mechanism for R")
5292 "This is an alternative mechanism for importing objects from packages.
5293 The syntax allows for importing multiple objects from a package with a single
5294 command in an expressive way. The import package bridges some of the gap
5295 between using @code{library} (or @code{require}) and direct (single-object)
5296 imports. Furthermore the imported objects are not placed in the current
5297 environment. It is also possible to import objects from stand-alone @code{.R}
5299 (license license:expat)))
5301 (define-public r-shinyace
5308 (uri (cran-uri "shinyAce" version))
5311 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5312 (properties `((upstream-name . "shinyAce")))
5313 (build-system r-build-system)
5315 `(("r-shiny" ,r-shiny)
5316 ("r-jsonlite" ,r-jsonlite)))
5317 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5318 (synopsis "Ace editor bindings for Shiny")
5320 "This package provides Ace editor bindings to enable a rich text editing
5321 environment within Shiny.")
5322 (license license:expat)))
5324 (define-public r-randomizr
5326 (name "r-randomizr")
5331 (uri (cran-uri "randomizr" version))
5334 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5335 (properties `((upstream-name . "randomizr")))
5336 (build-system r-build-system)
5338 `(("r-knitr" ,r-knitr)))
5339 (home-page "https://declaredesign.org/r/randomizr/")
5340 (synopsis "Tools for common forms of random assignment and sampling")
5342 "This package provides tools for generating random assignments for common
5343 experimental designs and random samples for common sampling designs.")
5344 (license license:expat)))
5346 (define-public r-base64url
5348 (name "r-base64url")
5353 (uri (cran-uri "base64url" version))
5356 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5357 (build-system r-build-system)
5359 `(("r-backports" ,r-backports)))
5360 (home-page "https://github.com/mllg/base64url")
5361 (synopsis "Fast and URL-safe base64 encoder and decoder")
5363 "This package provides a URL-safe base64 encoder and decoder. In
5364 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5365 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5366 encoder does not fill the string with trailing @code{=}. The resulting
5367 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5368 and thus are safe to use in URLs or for file names. The package also comes
5369 with a simple base32 encoder/decoder suited for case insensitive file
5371 (license license:gpl3)))
5373 (define-public r-radiant-data
5375 (name "r-radiant-data")
5380 (uri (cran-uri "radiant.data" version))
5383 "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0"))
5384 (modules '((guix build utils)))
5387 ;; Delete files that are under CC-NC-SA.
5388 (delete-file-recursively "inst/app/tools/help")
5390 (properties `((upstream-name . "radiant.data")))
5391 (build-system r-build-system)
5393 `(("r-base64enc" ,r-base64enc)
5394 ("r-broom" ,r-broom)
5397 ("r-dplyr" ,r-dplyr)
5400 ("r-ggplot2" ,r-ggplot2)
5401 ("r-import" ,r-import)
5402 ("r-jsonlite" ,r-jsonlite)
5403 ("r-knitr" ,r-knitr)
5404 ("r-lubridate" ,r-lubridate)
5405 ("r-magrittr" ,r-magrittr)
5406 ("r-markdown" ,r-markdown)
5408 ("r-patchwork" ,r-patchwork)
5409 ("r-plotly" ,r-plotly)
5410 ("r-psych" ,r-psych)
5411 ("r-randomizr" ,r-randomizr)
5412 ("r-readr" ,r-readr)
5413 ("r-readxl" ,r-readxl)
5414 ("r-rlang" ,r-rlang)
5415 ("r-rmarkdown" ,r-rmarkdown)
5416 ("r-rstudioapi" ,r-rstudioapi)
5417 ("r-scales" ,r-scales)
5418 ("r-shiny" ,r-shiny)
5419 ("r-shinyfiles" ,r-shinyfiles)
5420 ("r-shinyace" ,r-shinyace)
5421 ("r-stringi" ,r-stringi)
5422 ("r-tibble" ,r-tibble)
5423 ("r-tidyr" ,r-tidyr)
5424 ("r-writexl" ,r-writexl)))
5425 (home-page "https://github.com/radiant-rstats/radiant.data")
5426 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5428 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5429 visualizing, summarizing, transforming, and combining data. It also contains
5430 functionality to generate reproducible reports of the analyses conducted in
5432 (license license:agpl3)))
5434 (define-public r-algdesign
5436 (name "r-algdesign")
5441 (uri (cran-uri "AlgDesign" version))
5443 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5444 (properties `((upstream-name . "AlgDesign")))
5445 (build-system r-build-system)
5446 (home-page "https://github.com/jvbraun/AlgDesign")
5447 (synopsis "Algorithmic experimental design")
5449 "This package provides tools to calculate exact and approximate theory
5450 experimental designs for D, A, and I criteria. Very large designs may be
5451 created. Experimental designs may be blocked or blocked designs created from
5452 a candidate list, using several criteria. The blocking can be done when whole
5453 and within plot factors interact.")
5454 (license license:gpl2+)))
5456 (define-public r-signal
5463 (uri (cran-uri "signal" version))
5466 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5467 (build-system r-build-system)
5468 (propagated-inputs `(("r-mass" ,r-mass)))
5469 (native-inputs `(("gfortran" ,gfortran)))
5470 (home-page "https://cran.r-project.org/web/packages/signal/")
5471 (synopsis "Signal processing")
5473 "This package provides a set of signal processing functions originally
5474 written for Matlab and GNU Octave. It includes filter generation utilities,
5475 filtering functions, resampling routines, and visualization of filter models.
5476 It also includes interpolation functions.")
5477 (license license:gpl2)))
5479 (define-public r-gsubfn
5486 (uri (cran-uri "gsubfn" version))
5489 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5490 (build-system r-build-system)
5491 (propagated-inputs `(("r-proto" ,r-proto)))
5492 (home-page "https://code.google.com/archive/p/gsubfn/")
5493 (synopsis "Utilities for strings and function arguments.")
5495 "This package provides @code{gsubfn} which is like @code{gsub} but can
5496 take a replacement function or certain other objects instead of the
5497 replacement string. Matches and back references are input to the replacement
5498 function and replaced by the function output. @code{gsubfn} can be used to
5499 split strings based on content rather than delimiters and for quasi-perl-style
5500 string interpolation. The package also has facilities for translating
5501 formulas to functions and allowing such formulas in function calls instead of
5503 (license license:gpl2+)))
5505 (define-public r-sqldf
5512 (uri (cran-uri "sqldf" version))
5515 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5516 (build-system r-build-system)
5518 `(("r-chron" ,r-chron)
5520 ("r-gsubfn" ,r-gsubfn)
5521 ("r-proto" ,r-proto)
5522 ("r-rsqlite" ,r-rsqlite)))
5523 (home-page "https://github.com/ggrothendieck/sqldf")
5524 (synopsis "Manipulate R data frames using SQL")
5526 "The @code{sqldf} function is typically passed a single argument which is
5527 an SQL select statement where the table names are ordinary R data frame names.
5528 @code{sqldf} transparently sets up a database, imports the data frames into
5529 that database, performs the SQL statement and returns the result using a
5530 heuristic to determine which class to assign to each column of the returned
5531 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5532 used to read filtered files into R even if the original files are larger than
5533 R itself can handle.")
5534 (license license:gpl2)))
5536 (define-public r-abind
5543 (uri (cran-uri "abind" version))
5546 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5547 (build-system r-build-system)
5548 (home-page "https://cran.r-project.org/web/packages/abind/")
5549 (synopsis "Combine multidimensional arrays")
5551 "This package provides tools to combine multidimensional arrays into a
5552 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5553 works with vectors, matrices, and higher-dimensional arrays. It also provides
5554 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5555 extracting and replacing data in arrays.")
5556 (license license:lgpl2.0+)))
5558 (define-public r-prroc
5565 (uri (cran-uri "PRROC" version))
5568 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5569 (properties `((upstream-name . "PRROC")))
5570 (build-system r-build-system)
5571 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5572 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5574 "This package computes the areas under the @dfn{precision-recall} (PR)
5575 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5576 contrast to other implementations, the interpolation between points of the PR
5577 curve is done by a non-linear piecewise function. In addition to the areas
5578 under the curves, the curves themselves can also be computed and plotted by a
5579 specific S3-method.")
5580 (license license:gpl3)))
5582 (define-public r-vim
5589 (uri (cran-uri "VIM" version))
5592 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5593 (properties `((upstream-name . "VIM")))
5594 (build-system r-build-system)
5597 ("r-colorspace" ,r-colorspace)
5598 ("r-data-table" ,r-data-table)
5599 ("r-e1071" ,r-e1071)
5600 ("r-laeken" ,r-laeken)
5601 ("r-magrittr" ,r-magrittr)
5604 ("r-ranger" ,r-ranger)
5606 ("r-robustbase" ,r-robustbase)
5610 `(("r-knitr" ,r-knitr)))
5611 (home-page "https://github.com/alexkowa/VIM")
5612 (synopsis "Visualization and imputation of missing values")
5614 "This package provides tools for the visualization of missing and/or
5615 imputed values are introduced, which can be used for exploring the data and
5616 the structure of the missing and/or imputed values. Depending on this
5617 structure of the missing values, the corresponding methods may help to
5618 identify the mechanism generating the missing values and allows to explore the
5619 data including missing values. In addition, the quality of imputation can be
5620 visually explored using various univariate, bivariate, multiple and
5621 multivariate plot methods.")
5622 (license license:gpl2+)))
5624 (define-public r-fnn
5631 (uri (cran-uri "FNN" version))
5634 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5635 (properties `((upstream-name . "FNN")))
5636 (build-system r-build-system)
5637 (home-page "https://cran.r-project.org/web/packages/FNN")
5638 (synopsis "Fast nearest neighbor search algorithms and applications")
5640 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5641 search algorithms. Related applications including KNN classification,
5642 regression and information measures are implemented.")
5643 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5644 ;; later can be used.
5645 (license license:gpl2+)))
5647 (define-public r-smoother
5654 (uri (cran-uri "smoother" version))
5657 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5658 (build-system r-build-system)
5660 `(("r-ttr" ,r-ttr)))
5661 (home-page "https://cran.r-project.org/web/packages/smoother")
5662 (synopsis "Functions relating to the smoothing of numerical data")
5664 "This package provides a collection of methods for smoothing numerical
5665 data, commencing with a port of the Matlab gaussian window smoothing function.
5666 In addition, several functions typically used in smoothing of financial data
5668 (license license:gpl2)))
5670 (define-public r-riverplot
5672 (name "r-riverplot")
5677 (uri (cran-uri "riverplot" version))
5680 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5681 (build-system r-build-system)
5682 (home-page "https://logfc.wordpress.com")
5683 (synopsis "Sankey or ribbon plots")
5685 "Sankey plots are a type of diagram that is convenient to illustrate how
5686 flow of information, resources etc. separates and joins, much like observing
5687 how rivers split and merge. For example, they can be used to compare
5688 different clusterings. This package provides an implementation of Sankey
5690 (license license:gpl2+)))
5692 (define-public r-dyn
5699 (uri (cran-uri "dyn" version))
5702 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5703 (build-system r-build-system)
5705 `(("r-zoo" ,r-zoo)))
5706 (home-page "https://cran.r-project.org/web/packages/dyn")
5707 (synopsis "Time series regression")
5709 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5710 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5711 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5712 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5713 @code{randomForest::randomForest()} and other regression functions, allowing
5714 those functions to be used with time series including specifications that may
5715 contain lags, diffs and missing values.")
5717 (license license:gpl2+)))
5719 (define-public r-catdap
5726 (uri (cran-uri "catdap" version))
5729 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5730 (build-system r-build-system)
5732 `(("gfortran" ,gfortran)))
5733 (home-page "https://cran.r-project.org/web/packages/catdap/")
5734 (synopsis "Tools for categorical data analysis")
5736 "This package provides functions for analyzing multivariate data.
5737 Dependencies of the distribution of the specified variable (response
5738 variable) to other variables (explanatory variables) are derived and
5739 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5740 (license license:gpl2+)))
5742 (define-public r-arules
5749 (uri (cran-uri "arules" version))
5752 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5753 (build-system r-build-system)
5755 `(("r-matrix" ,r-matrix)))
5756 (home-page "https://github.com/mhahsler/arules")
5757 (synopsis "Mining association rules and frequent itemsets")
5759 "This package provides an infrastructure for representing, manipulating
5760 and analyzing transaction data and patterns (frequent itemsets and association rules).
5761 It also provides C implementations of the association mining algorithms Apriori
5763 (license license:gpl3)))
5765 (define-public r-parsedate
5767 (name "r-parsedate")
5772 (uri (cran-uri "parsedate" version))
5775 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5776 (build-system r-build-system)
5778 `(("r-rematch2" ,r-rematch2)))
5779 (home-page "https://github.com/gaborcsardi/parsedate")
5781 "Recognize and parse dates in various formats")
5783 "This package provides three functions for dealing with dates:
5784 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5785 time formats, @code{parse_date} parses dates in unspecified formats,
5786 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5787 (license license:gpl2)))
5789 (define-public r-abc-data
5796 (uri (cran-uri "abc.data" version))
5799 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5800 (properties `((upstream-name . "abc.data")))
5801 (build-system r-build-system)
5802 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5803 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5805 "This package contains data which are used by functions of the abc
5806 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5807 algorithms for performing parameter estimation, model selection, and
5809 (license license:gpl3+)))
5811 (define-public r-abc
5818 (uri (cran-uri "abc" version))
5821 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5822 (build-system r-build-system)
5824 `(("r-abc-data" ,r-abc-data)
5825 ("r-locfit" ,r-locfit)
5828 ("r-quantreg" ,r-quantreg)))
5829 (home-page "https://cran.r-project.org/web/packages/abc/")
5830 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5832 "This package implements several @dfn{Approximate Bayesian
5833 Computation} (ABC) algorithms for performing parameter estimation, model
5834 selection, and goodness-of-fit. Cross-validation tools are also available for
5835 measuring the accuracy of ABC estimates, and to calculate the
5836 misclassification probabilities of different models.")
5837 (license license:gpl3+)))
5839 (define-public r-zip
5846 (uri (cran-uri "zip" version))
5849 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5850 (build-system r-build-system)
5851 (home-page "https://github.com/gaborcsardi/zip")
5852 (synopsis "Cross-platform Zip compression")
5854 "This package provides a cross-platform Zip compression library for R.
5855 It is a replacement for the @code{zip} function, that does not require any
5856 additional external tools on any platform.")
5857 (license license:cc0)))
5859 (define-public r-openxlsx
5866 (uri (cran-uri "openxlsx" version))
5869 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5870 (build-system r-build-system)
5872 `(("r-rcpp" ,r-rcpp)
5873 ("r-stringi" ,r-stringi)
5876 `(("r-knitr" ,r-knitr)))
5877 (home-page "https://github.com/awalker89/openxlsx")
5878 (synopsis "Read, write and edit XLSX files")
5880 "This package simplifies the creation of Excel @code{.xlsx} files by
5881 providing a high level interface to writing, styling and editing worksheets.
5882 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5883 and @code{XLConnect} packages with the added benefit of removing the
5884 dependency on Java.")
5885 (license license:gpl3)))
5887 (define-public r-rio
5894 (uri (cran-uri "rio" version))
5897 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5898 (build-system r-build-system)
5900 `(("r-curl" ,r-curl)
5901 ("r-data-table" ,r-data-table)
5902 ("r-foreign" ,r-foreign)
5903 ("r-haven" ,r-haven)
5904 ("r-openxlsx" ,r-openxlsx)
5905 ("r-readxl" ,r-readxl)
5906 ("r-tibble" ,r-tibble)))
5907 (home-page "https://github.com/leeper/rio")
5908 (synopsis "Swiss-army knife for data I/O")
5910 "This package provides streamlined data import and export infrastructure
5911 by making assumptions that the user is probably willing to make: @code{import}
5912 and @code{export} determine the data structure from the file extension,
5913 reasonable defaults are used for data import and export (e.g.,
5914 @code{stringsAsFactors=FALSE}), web-based import is natively
5915 supported (including from SSL/HTTPS), compressed files can be read directly
5916 without explicit decompression, and fast import packages are used where
5917 appropriate. An additional convenience function, @code{convert}, provides a
5918 simple method for converting between file types.")
5919 (license license:gpl2)))
5921 (define-public r-maptools
5928 (uri (cran-uri "maptools" version))
5931 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5932 (build-system r-build-system)
5934 `(("r-foreign" ,r-foreign)
5935 ("r-lattice" ,r-lattice)
5937 (home-page "https://r-forge.r-project.org/projects/maptools/")
5938 (synopsis "Tools for reading and handling spatial objects")
5940 "This package provides a set of tools for manipulating and reading
5941 geographic data, in particular ESRI Shapefiles. It includes binary access to
5942 GSHHG shoreline files. The package also provides interface wrappers for
5943 exchanging spatial objects with other R packages.")
5944 ;; The C source files from shapelib are released under the Expat license.
5945 ;; The R code is released under GPL version 2 or later.
5946 (license (list license:gpl2+
5949 (define-public r-later
5956 (uri (cran-uri "later" version))
5959 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5960 (build-system r-build-system)
5964 ("r-rlang" ,r-rlang)))
5966 `(("r-knitr" ,r-knitr)))
5967 (home-page "https://github.com/r-lib/later")
5968 (synopsis "Utilities for delaying function execution")
5970 "This package provides tools to execute arbitrary R or C functions some
5971 time after the current time, after the R execution stack has emptied.")
5972 (license license:gpl2+)))
5974 (define-public r-promises
5981 (uri (cran-uri "promises" version))
5984 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5985 (build-system r-build-system)
5987 `(("r-later" ,r-later)
5988 ("r-magrittr" ,r-magrittr)
5991 ("r-rlang" ,r-rlang)))
5993 `(("r-knitr" ,r-knitr)))
5994 (home-page "https://rstudio.github.io/promises")
5995 (synopsis "Abstractions for promise-based asynchronous programming")
5997 "This package provides fundamental abstractions for doing asynchronous
5998 programming in R using promises. Asynchronous programming is useful for
5999 allowing a single R process to orchestrate multiple tasks in the background
6000 while also attending to something else. Semantics are similar to JavaScript
6001 promises, but with a syntax that is idiomatic R.")
6002 (license license:expat)))
6004 (define-public r-dosnow
6011 (uri (cran-uri "doSNOW" version))
6014 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
6015 (properties `((upstream-name . "doSNOW")))
6016 (build-system r-build-system)
6018 `(("r-foreach" ,r-foreach)
6019 ("r-iterators" ,r-iterators)
6020 ("r-snow" ,r-snow)))
6021 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6022 (synopsis "Foreach parallel adaptor for the snow package")
6024 "This package provides a parallel backend for the @code{%dopar%} function
6025 using the @code{snow} package.")
6026 (license license:gpl2)))
6028 (define-public r-snowfall
6031 (version "1.84-6.1")
6034 (uri (cran-uri "snowfall" version))
6036 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6037 (build-system r-build-system)
6039 `(("r-snow" ,r-snow)))
6040 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6041 (synopsis "Easier cluster computing")
6042 (description "This package is a usability wrapper around snow for easier
6043 development of parallel R programs. This package offers e.g. extended error
6044 checks, and additional functions. All functions work in sequential mode, too,
6045 if no cluster is present or wished. The package is also designed as connector
6046 to the cluster management tool @code{sfCluster}, but can also used without
6048 (license license:gpl2+)))
6050 (define-public r-rappdirs
6057 (uri (cran-uri "rappdirs" version))
6060 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6061 (build-system r-build-system)
6062 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6063 (synopsis "Determine where to save data, caches, and logs")
6065 "This package provides an easy way to determine which directories on the
6066 user's computer should be used to save data, caches and logs. It is a port of
6067 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6068 (license license:expat)))
6070 (define-public r-renv
6077 (uri (cran-uri "renv" version))
6080 "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3"))))
6081 (properties `((upstream-name . "renv")))
6082 (build-system r-build-system)
6084 `(("r-knitr" ,r-knitr)))
6085 (home-page "https://rstudio.github.io/renv")
6086 (synopsis "Project environments")
6088 "This package provides a dependency management toolkit for R. Using
6089 renv, you can create and manage project-local R libraries, save the state of
6090 these libraries to a lockfile, and later restore your library as required.
6091 Together, these tools can help make your projects more isolated, portable, and
6093 (license license:expat)))
6095 (define-public r-learnr
6102 (uri (cran-uri "learnr" version))
6105 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6106 (build-system r-build-system)
6108 `(("r-checkmate" ,r-checkmate)
6109 ("r-ellipsis" ,r-ellipsis)
6110 ("r-evaluate" ,r-evaluate)
6111 ("r-htmltools" ,r-htmltools)
6112 ("r-htmlwidgets" ,r-htmlwidgets)
6113 ("r-jsonlite" ,r-jsonlite)
6114 ("r-knitr" ,r-knitr)
6115 ("r-markdown" ,r-markdown)
6116 ("r-rappdirs" ,r-rappdirs)
6118 ("r-rmarkdown" ,r-rmarkdown)
6119 ("r-rprojroot" ,r-rprojroot)
6120 ("r-shiny" ,r-shiny)
6121 ("r-withr" ,r-withr)))
6122 (home-page "https://rstudio.github.io/learnr/")
6123 (synopsis "Interactive tutorials for R")
6125 "This package provides tools to create interactive tutorials using R
6126 Markdown. Use a combination of narrative, figures, videos, exercises, and
6127 quizzes to create self-paced tutorials for learning about R and R packages.")
6128 (license license:asl2.0)))
6130 (define-public r-analytics
6132 (name "r-analytics")
6137 (uri (cran-uri "analytics" version))
6140 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6141 (build-system r-build-system)
6144 ("r-cluster" ,r-cluster)
6145 ("r-fractal" ,r-fractal)
6146 ("r-lmtest" ,r-lmtest)
6149 ("r-powerplus" ,r-powerplus)
6150 ("r-robust" ,r-robust)
6151 ("r-trend" ,r-trend)
6155 (home-page "https://cran.r-project.org/web/packages/analytics/")
6156 (synopsis "Collection of data analysis tools")
6158 "This package is a collection of data analysis tools. It includes tools
6159 for regression outlier detection in a fitted linear model, stationary
6160 bootstrap using a truncated geometric distribution, a comprehensive test for
6161 weak stationarity, column means by group, weighted biplots, and a heuristic to
6162 obtain a better initial configuration in non-metric MDS.")
6163 (license license:gpl2)))
6165 (define-public r-reticulate
6167 (name "r-reticulate")
6172 (uri (cran-uri "reticulate" version))
6175 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6176 (build-system r-build-system)
6177 (inputs `(("python" ,python)))
6179 `(("r-rappdirs" ,r-rappdirs)
6180 ("r-jsonlite" ,r-jsonlite)
6181 ("r-matrix" ,r-matrix)
6182 ("r-rcpp" ,r-rcpp)))
6184 `(("r-knitr" ,r-knitr)))
6185 (home-page "https://github.com/rstudio/reticulate")
6186 (synopsis "R interface to Python")
6188 "This package provides an interface from R to Python modules, classes,
6189 and functions. When calling into Python, R data types are automatically
6190 converted to their equivalent Python types. When values are returned from
6191 Python to R they are converted back to R types.")
6192 (license license:asl2.0)))
6194 (define-public r-bibtex
6201 (uri (cran-uri "bibtex" version))
6204 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6205 (build-system r-build-system)
6206 (propagated-inputs `(("r-stringr" ,r-stringr)))
6207 (home-page "https://github.com/romainfrancois/bibtex")
6208 (synopsis "Bibtex parser")
6209 (description "This package provides a utility for R to parse a bibtex
6211 (license license:gpl2+)))
6213 (define-public r-ggseqlogo
6215 (name "r-ggseqlogo")
6220 (uri (cran-uri "ggseqlogo" version))
6223 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6224 (build-system r-build-system)
6225 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6226 (home-page "https://github.com/omarwagih/ggseqlogo")
6227 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6229 "The range of functions provided by this package makes it possible to
6230 draw highly versatile genomic sequence logos. Features include, but are not
6231 limited to, modifying colour schemes and fonts used to draw the logo,
6232 generating multiple logo plots, and aiding the visualisation with annotations.
6233 Sequence logos can easily be combined with other ggplot2 plots.")
6234 ;; Unspecified version of the LGPL.
6235 (license license:lgpl3+)))
6237 (define-public r-ggsci
6244 (uri (cran-uri "ggsci" version))
6247 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6248 (build-system r-build-system)
6250 `(("r-ggplot2" ,r-ggplot2)
6251 ("r-scales" ,r-scales)))
6252 (home-page "https://nanx.me/ggsci/")
6253 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6255 "This package provides a collection of ggplot2 color palettes inspired by
6256 plots in scientific journals, data visualization libraries, science fiction
6257 movies, and TV shows.")
6258 (license license:gpl3)))
6260 (define-public r-ggsignif
6267 (uri (cran-uri "ggsignif" version))
6270 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6271 (build-system r-build-system)
6273 `(("r-knitr" ,r-knitr)))
6275 `(("r-ggplot2" ,r-ggplot2)))
6276 (home-page "https://github.com/const-ae/ggsignif")
6277 (synopsis "Significance brackets for ggplot2")
6279 "Enrich your ggplots with group-wise comparisons. This package provides
6280 an easy way to indicate if two groups are significantly different. Commonly
6281 this is shown by a bracket on top connecting the groups of interest which
6282 itself is annotated with the level of significance. The package provides a
6283 single layer that takes the groups for comparison and the test as arguments
6284 and adds the annotation to the plot.")
6285 (license license:gpl3)))
6287 (define-public r-rstatix
6294 (uri (cran-uri "rstatix" version))
6297 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6298 (properties `((upstream-name . "rstatix")))
6299 (build-system r-build-system)
6301 `(("r-broom" ,r-broom)
6303 ("r-corrplot" ,r-corrplot)
6304 ("r-dplyr" ,r-dplyr)
6305 ("r-generics" ,r-generics)
6306 ("r-magrittr" ,r-magrittr)
6307 ("r-purrr" ,r-purrr)
6308 ("r-rlang" ,r-rlang)
6309 ("r-tibble" ,r-tibble)
6310 ("r-tidyr" ,r-tidyr)
6311 ("r-tidyselect" ,r-tidyselect)))
6312 (home-page "https://rpkgs.datanovia.com/rstatix/")
6313 (synopsis "Pipe-friendly framework for basic statistical tests")
6315 "This package provides a simple and intuitive pipe-friendly framework,
6316 coherent with the @code{tidyverse} design philosophy, for performing basic
6317 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6318 correlation analyses. The output of each test is automatically transformed
6319 into a tidy data frame to facilitate visualization. Additional functions are
6320 available for reshaping, reordering, manipulating and visualizing correlation
6322 (license license:gpl2)))
6324 (define-public r-ggpubr
6331 (uri (cran-uri "ggpubr" version))
6334 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6335 (build-system r-build-system)
6337 `(("r-cowplot" ,r-cowplot)
6338 ("r-dplyr" ,r-dplyr)
6339 ("r-ggplot2" ,r-ggplot2)
6340 ("r-ggrepel" ,r-ggrepel)
6341 ("r-ggsci" ,r-ggsci)
6342 ("r-ggsignif" ,r-ggsignif)
6344 ("r-gridextra" ,r-gridextra)
6345 ("r-magrittr" ,r-magrittr)
6346 ("r-polynom" ,r-polynom)
6347 ("r-purrr" ,r-purrr)
6348 ("r-rlang" ,r-rlang)
6349 ("r-scales" ,r-scales)
6350 ("r-rstatix" ,r-rstatix)
6351 ("r-tibble" ,r-tibble)
6352 ("r-tidyr" ,r-tidyr)))
6353 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6354 (synopsis "ggplot2-based publication-ready plots")
6356 "The ggplot2 package is an excellent and flexible package for elegant
6357 data visualization in R. However the default generated plots require some
6358 formatting before we can send them for publication. The ggpubr package
6359 provides some easy-to-use functions for creating and customizing ggplot2-based
6360 publication-ready plots.")
6361 (license license:gpl2)))
6363 (define-public r-ellipse
6370 (uri (cran-uri "ellipse" version))
6373 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6374 (build-system r-build-system)
6375 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6376 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6378 "This package contains various routines for drawing ellipses and
6379 ellipse-like confidence regions, implementing the plots described in Murdoch
6380 and Chow (1996), A graphical display of large correlation matrices, The
6381 American Statistician 50, 178-180. There are also routines implementing the
6382 profile plots described in Bates and Watts (1988), Nonlinear Regression
6383 Analysis and its Applications.")
6384 (license license:gpl2+)))
6386 (define-public r-flashclust
6388 (name "r-flashclust")
6393 (uri (cran-uri "flashClust" version))
6396 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6397 (properties `((upstream-name . "flashClust")))
6398 (build-system r-build-system)
6399 (native-inputs `(("gfortran" ,gfortran)))
6400 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6401 (synopsis "Implementation of optimal hierarchical clustering")
6403 "This package provides a fast implementation of hierarchical
6405 (license license:gpl2+)))
6407 (define-public r-factominer
6409 (name "r-factominer")
6414 (uri (cran-uri "FactoMineR" version))
6417 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6418 (properties `((upstream-name . "FactoMineR")))
6419 (build-system r-build-system)
6422 ("r-cluster" ,r-cluster)
6423 ("r-ellipse" ,r-ellipse)
6424 ("r-flashclust" ,r-flashclust)
6425 ("r-ggplot2" ,r-ggplot2)
6426 ("r-ggrepel" ,r-ggrepel)
6427 ("r-lattice" ,r-lattice)
6428 ("r-leaps" ,r-leaps)
6430 ("r-scatterplot3d" ,r-scatterplot3d)))
6431 (home-page "http://factominer.free.fr")
6432 (synopsis "Multivariate exploratory data analysis and data mining")
6434 "This package provides exploratory data analysis methods to summarize,
6435 visualize and describe datasets. The main principal component methods are
6436 available, those with the largest potential in terms of applications:
6437 principal component analysis (PCA) when variables are quantitative,
6438 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6439 variables are categorical, Multiple Factor Analysis when variables are
6440 structured in groups, etc. and hierarchical cluster analysis.")
6441 (license license:gpl2+)))
6443 (define-public r-factoextra
6445 (name "r-factoextra")
6450 (uri (cran-uri "factoextra" version))
6453 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6454 (build-system r-build-system)
6456 `(("r-abind" ,r-abind)
6457 ("r-cluster" ,r-cluster)
6458 ("r-dendextend" ,r-dendextend)
6459 ("r-factominer" ,r-factominer)
6460 ("r-ggplot2" ,r-ggplot2)
6461 ("r-ggpubr" ,r-ggpubr)
6462 ("r-ggrepel" ,r-ggrepel)
6463 ("r-reshape2" ,r-reshape2)
6464 ("r-tidyr" ,r-tidyr)))
6465 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6466 (synopsis "Extract and visualize the results of multivariate data analyses")
6468 "This package provides some easy-to-use functions to extract and
6469 visualize the output of multivariate data analyses, including
6470 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6471 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6472 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6473 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6474 packages. It contains also functions for simplifying some clustering analysis
6475 steps and provides ggplot2-based elegant data visualization.")
6476 (license license:gpl2)))
6478 (define-public r-fansi
6485 (uri (cran-uri "fansi" version))
6488 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6489 (build-system r-build-system)
6491 `(("r-knitr" ,r-knitr))) ; for vignettes
6492 (home-page "https://github.com/brodieG/fansi")
6493 (synopsis "ANSI control sequence aware string functions")
6495 "This package provides counterparts to R string manipulation functions
6496 that account for the effects of ANSI text formatting control sequences.")
6497 (license license:gpl2+)))
6499 (define-public r-nbclust
6506 (uri (cran-uri "NbClust" version))
6509 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6510 (properties `((upstream-name . "NbClust")))
6511 (build-system r-build-system)
6512 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6513 (synopsis "Determine the best number of clusters in a data set")
6515 "NbClust provides 30 indexes for determining the optimal number of
6516 clusters in a data set and offers the best clustering scheme from different
6517 results to the user.")
6518 (license license:gpl2)))
6520 (define-public r-hdf5r
6527 (uri (cran-uri "hdf5r" version))
6530 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6531 (build-system r-build-system)
6536 `(("r-bit64" ,r-bit64)
6539 `(("r-knitr" ,r-knitr)))
6540 (home-page "https://hhoeflin.github.io/hdf5r")
6541 (synopsis "Interface to the HDF5 binary data format")
6543 "HDF5 is a data model, library and file format for storing and managing
6544 large amounts of data. This package provides a nearly feature complete,
6545 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6546 functionality is added so that HDF5 objects behave very similar to their
6547 corresponding R counterparts.")
6548 (license license:asl2.0)))
6550 (define-public r-itertools
6552 (name "r-itertools")
6557 (uri (cran-uri "itertools" version))
6560 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6561 (build-system r-build-system)
6563 `(("r-iterators" ,r-iterators)))
6564 (home-page "https://cran.r-project.org/web/packages/itertools/")
6565 (synopsis "Iterator tools")
6567 "This package provides various tools for creating iterators, many
6568 patterned after functions in the Python @code{itertools} module, and others
6569 patterned after functions in the snow package.")
6570 (license license:gpl2)))
6572 (define-public r-polynom
6579 (uri (cran-uri "polynom" version))
6582 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6583 (build-system r-build-system)
6584 (home-page "https://cran.r-project.org/web/packages/polynom/")
6585 (synopsis "Functions for univariate polynomial manipulations")
6587 "This package provides a collection of functions to implement a class for
6588 univariate polynomial manipulations.")
6589 (license license:gpl2)))
6591 (define-public r-gbrd
6598 (uri (cran-uri "gbRd" version))
6601 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6602 (properties `((upstream-name . "gbRd")))
6603 (build-system r-build-system)
6604 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6605 (synopsis "Utilities for processing Rd objects and files")
6607 "This package provides utilities for processing Rd objects and files.
6608 Extract argument descriptions and other parts of the help pages of
6610 (license license:gpl2+)))
6612 (define-public r-rjags
6619 (uri (cran-uri "rjags" version))
6622 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6623 (build-system r-build-system)
6625 `(("r-coda" ,r-coda)))
6629 `(("pkg-config" ,pkg-config)))
6630 (home-page "http://mcmc-jags.sourceforge.net")
6631 (synopsis "Bayesian graphical models using MCMC")
6633 "This package provides an R interface to the JAGS MCMC library. JAGS is
6634 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6635 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6636 (license license:gpl2)))
6638 (define-public r-rdpack
6645 (uri (cran-uri "Rdpack" version))
6648 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6649 (properties `((upstream-name . "Rdpack")))
6650 (build-system r-build-system)
6652 `(("r-bibtex" ,r-bibtex)
6653 ("r-gbrd" ,r-gbrd)))
6654 (home-page "https://github.com/GeoBosh/Rdpack")
6655 (synopsis "Update and manipulate Rd documentation objects")
6657 "This package provides functions for manipulation of R documentation
6658 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6659 updating Rd documentation for functions, methods and classes; it also includes
6660 Rd macros for citations and import of references from bibtex files for use in
6661 Rd files and roxygen2 comments, as well as many functions for manipulation of
6662 references and Rd files.")
6663 (license license:gpl2+)))
6665 (define-public r-officer
6672 (uri (cran-uri "officer" version))
6675 "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x"))))
6676 (build-system r-build-system)
6678 `(("r-magrittr" ,r-magrittr)
6684 `(("r-knitr" ,r-knitr)))
6685 (home-page "https://davidgohel.github.io/officer")
6686 (synopsis "Manipulation of Word and PowerPoint documents")
6688 "This package provides tools to access and manipulate Word and PowerPoint
6689 documents from R. The package focuses on tabular and graphical reporting from
6690 R; it also provides two functions that let users get document content into
6691 data objects. A set of functions lets add and remove images, tables and
6692 paragraphs of text in new or existing documents. When working with PowerPoint
6693 presentations, slides can be added or removed; shapes inside slides can also
6694 be added or removed. When working with Word documents, a cursor can be used
6695 to help insert or delete content at a specific location in the document.")
6696 (license license:gpl3)))
6698 (define-public r-profilemodel
6700 (name "r-profilemodel")
6705 (uri (cran-uri "profileModel" version))
6708 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6709 (properties `((upstream-name . "profileModel")))
6710 (build-system r-build-system)
6711 (home-page "https://github.com/ikosmidis/profileModel")
6712 (synopsis "Profiling inference functions for various model classes")
6714 "This package provides tools that can be used to calculate, evaluate,
6715 plot and use for inference the profiles of *arbitrary* inference functions for
6716 arbitrary @code{glm}-like fitted models with linear predictors. More information
6717 on the methods that are implemented can be found in Kosmidis (2008)
6718 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6719 (license license:gpl2+)))
6721 (define-public r-brglm
6728 (uri (cran-uri "brglm" version))
6731 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6732 (properties `((upstream-name . "brglm")))
6733 (build-system r-build-system)
6735 `(("r-profilemodel" ,r-profilemodel)))
6736 (home-page "https://github.com/ikosmidis/brglm")
6737 (synopsis "Bias reduction in binomial-response generalized linear models")
6739 "Fit generalized linear models with binomial responses using either an
6740 adjusted-score approach to bias reduction or maximum penalized likelihood
6741 where penalization is by Jeffreys invariant prior. These procedures return
6742 estimates with improved frequentist properties (bias, mean squared error) that
6743 are always finite even in cases where the maximum likelihood estimates are
6744 infinite (data separation). Fitting takes place by fitting generalized linear
6745 models on iteratively updated pseudo-data. The interface is essentially the
6746 same as @code{glm}. More flexibility is provided by the fact that custom
6747 pseudo-data representations can be specified and used for model fitting.
6748 Functions are provided for the construction of confidence intervals for the
6749 reduced-bias estimates.")
6750 (license license:gpl2+)))
6752 (define-public r-entropy
6759 (uri (cran-uri "entropy" version))
6762 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6763 (properties `((upstream-name . "entropy")))
6764 (build-system r-build-system)
6765 (home-page "https://www.strimmerlab.org/software/entropy/")
6766 (synopsis "Estimation of entropy, mutual information and related quantities")
6768 "This package implements various estimators of entropy, such as the
6769 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6770 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6771 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6772 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6773 mutual information, and chi-squared statistic of independence. In addition
6774 there are functions for discretizing continuous random variables.")
6775 (license license:gpl3+)))
6777 (define-public r-abn
6784 (uri (cran-uri "abn" version))
6787 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6788 (build-system r-build-system)
6792 `(("r-boot" ,r-boot)
6793 ("r-brglm" ,r-brglm)
6794 ("r-entropy" ,r-entropy)
6797 ("r-moments" ,r-moments)
6800 ("r-rcpparmadillo" ,r-rcpparmadillo)
6801 ("r-rjags" ,r-rjags)))
6802 (home-page "https://r-bayesian-networks.org/")
6803 (synopsis "Modelling multivariate data with additive bayesian networks")
6805 "Bayesian network analysis is a form of probabilistic graphical models
6806 which derives from empirical data a directed acyclic graph, DAG, describing
6807 the dependency structure between random variables. An additive Bayesian
6808 network model consists of a form of a DAG where each node comprises a
6809 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6810 equivalent to Bayesian multivariate regression using graphical modelling, they
6811 generalises the usual multivariable regression, GLM, to multiple dependent
6812 variables. This package provides routines to help determine optimal Bayesian
6813 network models for a given data set, where these models are used to identify
6814 statistical dependencies in messy, complex data.")
6815 (license license:gpl2+)))
6817 (define-public r-acd
6824 (uri (cran-uri "ACD" version))
6827 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6828 (properties `((upstream-name . "ACD")))
6829 (build-system r-build-system)
6830 (home-page "https://cran.r-project.org/web/packages/ACD/")
6831 (synopsis "Categorical data analysis with complete or missing responses")
6833 "This package provides tools for categorical data analysis with complete
6834 or missing responses.")
6835 (license license:gpl2+)))
6837 (define-public r-acdm
6844 (uri (cran-uri "ACDm" version))
6847 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6848 (properties `((upstream-name . "ACDm")))
6849 (build-system r-build-system)
6851 `(("r-dplyr" ,r-dplyr)
6852 ("r-ggplot2" ,r-ggplot2)
6854 ("r-rsolnp" ,r-rsolnp)
6856 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6857 (synopsis "Tools for Autoregressive Conditional Duration Models")
6859 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6860 and Russell, 1998) models. It creates trade, price or volume durations from
6861 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6863 (license license:gpl2+)))
6865 (define-public r-overlap
6872 (uri (cran-uri "overlap" version))
6875 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6876 (build-system r-build-system)
6877 (home-page "https://cran.r-project.org/web/packages/overlap/")
6878 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6880 "This package provides functions to fit kernel density functions to data
6881 on temporal activity patterns of animals; estimate coefficients of overlapping
6882 of densities for two species; and calculate bootstrap estimates of confidence
6884 (license license:gpl3+)))
6886 (define-public r-snakecase
6888 (name "r-snakecase")
6893 (uri (cran-uri "snakecase" version))
6896 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6897 (build-system r-build-system)
6899 `(("r-stringi" ,r-stringi)
6900 ("r-stringr" ,r-stringr)))
6901 (home-page "https://github.com/Tazinho/snakecase")
6902 (synopsis "Convert strings into any case")
6904 "This package provides a consistent, flexible and easy to use tool to
6905 parse and convert strings into cases like snake or camel among others.")
6906 (license license:gpl3)))
6908 (define-public r-prediction
6910 (name "r-prediction")
6915 (uri (cran-uri "prediction" version))
6918 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6919 (build-system r-build-system)
6921 `(("r-data-table" ,r-data-table)))
6922 (home-page "https://github.com/leeper/prediction")
6923 (synopsis "Tidy, type-safe prediction methods")
6925 "This package provides the @code{prediction()} function, a type-safe
6926 alternative to @code{predict()} that always returns a data frame. The package
6927 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6928 from the @code{stats} package, as well as numerous other model classes from
6929 other add-on packages.")
6930 (license license:expat)))
6932 (define-public r-insight
6939 (uri (cran-uri "insight" version))
6942 "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k"))))
6943 (build-system r-build-system)
6945 `(("r-knitr" ,r-knitr)))
6946 (home-page "https://easystats.github.io/insight/")
6947 (synopsis "Easy access to model information for various model objects")
6949 "This package provides a tool to provide an easy, intuitive and
6950 consistent access to information contained in various R models, like model
6951 formulas, model terms, information about random effects, data that was used to
6952 fit the model or data from response variables. The package mainly revolves
6953 around two types of functions: Functions that find (the names of) information,
6954 starting with @code{find_}, and functions that get the underlying data,
6955 starting with @code{get_}. The package has a consistent syntax and works with
6956 many different model objects, where otherwise functions to access these
6957 information are missing.")
6958 (license license:gpl3)))
6960 (define-public r-sjlabelled
6962 (name "r-sjlabelled")
6967 (uri (cran-uri "sjlabelled" version))
6970 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
6971 (build-system r-build-system)
6973 `(("r-insight" ,r-insight)))
6975 `(("r-knitr" ,r-knitr)))
6976 (home-page "https://github.com/strengejacke/sjlabelled")
6977 (synopsis "Labelled data utility functions")
6979 "This package provides a collection of functions dealing with labelled
6980 data, like reading and writing data between R and other statistical software
6981 packages. This includes easy ways to get, set or change value and variable
6982 label attributes, to convert labelled vectors into factors or numeric (and
6983 vice versa), or to deal with multiple declared missing values.")
6984 (license license:gpl3)))
6986 (define-public r-sjmisc
6993 (uri (cran-uri "sjmisc" version))
6996 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6997 (build-system r-build-system)
6999 `(("r-dplyr" ,r-dplyr)
7000 ("r-insight" ,r-insight)
7001 ("r-magrittr" ,r-magrittr)
7002 ("r-purrr" ,r-purrr)
7003 ("r-rlang" ,r-rlang)
7004 ("r-sjlabelled" ,r-sjlabelled)
7005 ("r-tidyselect" ,r-tidyselect)))
7007 `(("r-knitr" ,r-knitr)))
7008 (home-page "https://github.com/strengejacke/sjmisc")
7009 (synopsis "Data and variable transformation functions")
7011 "This package is a collection of miscellaneous utility functions,
7012 supporting data transformation tasks like recoding, dichotomizing or grouping
7013 variables, setting and replacing missing values. The data transformation
7014 functions also support labelled data, and all integrate seamlessly into a
7015 tidyverse workflow.")
7016 (license license:gpl3)))
7018 (define-public r-nortest
7025 (uri (cran-uri "nortest" version))
7028 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7029 (build-system r-build-system)
7030 (home-page "https://cran.r-project.org/web/packages/nortest/")
7031 (synopsis "Tests for normality")
7033 "This package provides five omnibus tests for testing the composite
7034 hypothesis of normality.")
7035 (license license:gpl2+)))
7037 (define-public r-moonbook
7044 (uri (cran-uri "moonBook" version))
7047 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7048 (properties `((upstream-name . "moonBook")))
7049 (build-system r-build-system)
7051 `(("r-magrittr" ,r-magrittr)
7052 ("r-nortest" ,r-nortest)
7053 ("r-purrr" ,r-purrr)
7054 ("r-sjmisc" ,r-sjmisc)
7055 ("r-stringr" ,r-stringr)
7056 ("r-survival" ,r-survival)))
7057 (home-page "https://github.com/cardiomoon/moonBook")
7058 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7060 "This package provides several analysis-related functions for the book
7061 entitled \"R statistics and graph for medical articles\" (written in Korean),
7062 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7064 (license license:gpl2)))
7066 (define-public r-flextable
7068 (name "r-flextable")
7073 (uri (cran-uri "flextable" version))
7076 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7077 (build-system r-build-system)
7079 `(("r-base64enc" ,r-base64enc)
7080 ("r-data-table" ,r-data-table)
7081 ("r-gdtools" ,r-gdtools)
7082 ("r-htmltools" ,r-htmltools)
7083 ("r-knitr" ,r-knitr)
7084 ("r-officer" ,r-officer)
7085 ("r-rlang" ,r-rlang)
7086 ("r-rmarkdown" ,r-rmarkdown)
7088 ("r-xml2" ,r-xml2)))
7089 (home-page "https://davidgohel.github.io/flextable")
7090 (synopsis "Functions for tabular reporting")
7092 "This package provides tools to create pretty tables for HTML documents
7093 and other formats. Functions are provided to let users create tables, modify
7094 and format their content. It extends the @code{officer} package and can be
7095 used within R markdown documents when rendering to HTML and to Word
7097 (license license:gpl3)))
7099 (define-public r-writexl
7106 (uri (cran-uri "writexl" version))
7109 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7110 (build-system r-build-system)
7111 (inputs `(("zlib" ,zlib)))
7112 (home-page "https://github.com/ropensci/writexl")
7113 (synopsis "Export data frames to xlsx format")
7115 "This package provides a data frame to xlsx exporter based on
7117 (license license:bsd-2)))
7119 (define-public r-biasedurn
7121 (name "r-biasedurn")
7126 (uri (cran-uri "BiasedUrn" version))
7129 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7130 (properties `((upstream-name . "BiasedUrn")))
7131 (build-system r-build-system)
7132 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7133 (synopsis "Biased Urn model distributions")
7135 "This package provides statistical models of biased sampling in the form
7136 of univariate and multivariate noncentral hypergeometric distributions,
7137 including Wallenius' noncentral hypergeometric distribution and Fisher's
7138 noncentral hypergeometric distribution (also called extended hypergeometric
7140 (license license:gpl3)))
7142 (define-public r-goplot
7149 (uri (cran-uri "GOplot" version))
7152 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7153 (properties `((upstream-name . "GOplot")))
7154 (build-system r-build-system)
7156 `(("r-ggdendro" ,r-ggdendro)
7157 ("r-ggplot2" ,r-ggplot2)
7158 ("r-gridextra" ,r-gridextra)
7159 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7160 (home-page "https://github.com/wencke/wencke.github.io")
7161 (synopsis "Visualization of functional analysis data")
7163 "This package provides an implementation of multilayered visualizations
7164 for enhanced graphical representation of functional analysis data. It
7165 combines and integrates omics data derived from expression and functional
7166 annotation enrichment analyses. Its plotting functions have been developed
7167 with an hierarchical structure in mind: starting from a general overview to
7168 identify the most enriched categories (modified bar plot, bubble plot) to a
7169 more detailed one displaying different types of relevant information for the
7170 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7171 Venn diagram, heatmap).")
7172 (license license:gpl2)))
7174 (define-public r-getopt
7181 (uri (cran-uri "getopt" version))
7184 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7185 (build-system r-build-system)
7186 (home-page "https://github.com/trevorld/getopt")
7187 (synopsis "Command-line option processor for R")
7189 "This package is designed to be used with Rscript to write shebang
7190 scripts that accept short and long options. Many users will prefer to
7191 use the packages @code{optparse} or @code{argparse} which add extra
7192 features like automatically generated help options and usage texts,
7193 support for default values, positional argument support, etc.")
7194 (license license:gpl2+)))
7196 (define-public r-findpython
7198 (name "r-findpython")
7203 (uri (cran-uri "findpython" version))
7206 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7207 (build-system r-build-system)
7208 (home-page "https://github.com/trevorld/findpython")
7209 (synopsis "Functions to find an acceptable Python binary")
7211 "This package was designed to find an acceptable Python binary that
7212 matches version and feature constraints.")
7213 (license license:expat)))
7215 ;; This in not the same as "r-argparser"
7216 (define-public r-argparse
7223 (uri (cran-uri "argparse" version))
7226 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7227 (build-system r-build-system)
7228 (inputs `(("python" ,python)))
7230 `(("r-findpython" ,r-findpython)
7231 ("r-jsonlite" ,r-jsonlite)
7233 (home-page "https://github.com/trevorld/argparse")
7234 (synopsis "Command line optional and positional argument parser")
7236 "This package provides a command line parser to be used with Rscript to
7237 write shebang scripts that gracefully accept positional and optional arguments
7238 and automatically generate usage notices.")
7239 (license license:gpl2+)))
7241 (define-public r-hash
7248 (uri (cran-uri "hash" version))
7251 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7252 (build-system r-build-system)
7253 (home-page "https://cran.r-project.org/web/packages/hash/")
7254 (synopsis "Implementation of hash/associated arrays/dictionaries")
7256 "This package implements a data structure similar to hashes in Perl and
7257 dictionaries in Python but with a purposefully R flavor. For objects of
7258 appreciable size, access using hashes outperforms native named lists and
7260 (license license:gpl2+)))
7262 (define-public r-orddom
7269 (uri (cran-uri "orddom" version))
7272 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7273 (build-system r-build-system)
7274 (propagated-inputs `(("r-psych" ,r-psych)))
7275 (home-page "https://cran.r-project.org/web/packages/orddom/")
7276 (synopsis "Ordinal dominance statistics")
7278 "This package provides tools to compute ordinal, statistics and effect
7279 sizes as an alternative to mean comparison: Cliff's delta or success rate
7280 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7281 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7282 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7283 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7284 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7285 Group (Non-)Overlap considerations.")
7286 (license license:gpl2)))
7288 (define-public r-deriv
7295 (uri (cran-uri "Deriv" version))
7298 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7299 (properties `((upstream-name . "Deriv")))
7300 (build-system r-build-system)
7301 (home-page "https://cran.r-project.org/web/packages/Deriv")
7302 (synopsis "Symbolic differentiation")
7304 "This package provides an R-based solution for symbolic differentiation.
7305 It admits user-defined functions as well as function substitution in arguments
7306 of functions to be differentiated. Some symbolic simplification is part of
7308 (license license:gpl3+)))
7310 (define-public r-doby
7317 (uri (cran-uri "doBy" version))
7320 "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk"))))
7321 (properties `((upstream-name . "doBy")))
7322 (build-system r-build-system)
7324 `(("r-broom" ,r-broom)
7325 ("r-deriv" ,r-deriv)
7326 ("r-dplyr" ,r-dplyr)
7327 ("r-ggplot2" ,r-ggplot2)
7328 ("r-magrittr" ,r-magrittr)
7330 ("r-matrix" ,r-matrix)
7331 ("r-pbkrtest" ,r-pbkrtest)
7332 ("r-tibble" ,r-tibble)))
7334 `(("r-knitr" ,r-knitr)))
7335 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7336 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7338 "This package contains:
7341 @item facilities for working with grouped data: @code{do}
7342 something to data stratified @code{by} some variables.
7343 @item implementations of least-squares means, general linear contrasts, and
7344 @item miscellaneous other utilities.
7346 (license license:gpl2+)))
7348 (define-public r-refgenome
7350 (name "r-refgenome")
7355 (uri (cran-uri "refGenome" version))
7358 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7359 (properties `((upstream-name . "refGenome")))
7360 (build-system r-build-system)
7364 ("r-rsqlite" ,r-rsqlite)))
7365 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7367 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7369 "This package contains functionality for importing and managing of
7370 downloaded genome annotation data from the Ensembl genome browser (European
7371 Bioinformatics Institute) and from the UCSC genome browser (University of
7372 California, Santa Cruz) and annotation routines for genomic positions and
7373 splice site positions.")
7374 (license license:gpl2)))
7376 (define-public r-basix
7383 (uri (cran-uri "BASIX" version))
7386 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7387 (properties `((upstream-name . "BASIX")))
7388 (build-system r-build-system)
7389 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7390 (synopsis "Efficient C/C++ toolset for R")
7392 "BASIX provides some efficient C/C++ implementations of native R
7393 procedures to speed up calculations in R.")
7394 (license license:gpl2)))
7396 (define-public r-blockfest
7398 (name "r-blockfest")
7403 (uri (cran-uri "BlockFeST" version))
7406 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7407 (properties `((upstream-name . "BlockFeST")))
7408 (build-system r-build-system)
7409 (propagated-inputs `(("r-basix" ,r-basix)))
7410 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7411 (synopsis "Bayesian calculation of region-specific fixation index")
7413 "This package provides an R implementation of an extension of the
7414 BayeScan software for codominant markers, adding the option to group
7415 individual SNPs into pre-defined blocks. A typical application of this new
7416 approach is the identification of genomic regions, genes, or gene sets
7417 containing one or more SNPs that evolved under directional selection.")
7418 (license license:gpl2)))
7420 (define-public r-proc
7427 (uri (cran-uri "pROC" version))
7430 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7431 (properties `((upstream-name . "pROC")))
7432 (build-system r-build-system)
7434 `(("r-plyr" ,r-plyr)
7435 ("r-rcpp" ,r-rcpp)))
7436 (home-page "https://web.expasy.org/pROC/")
7437 (synopsis "Display and analyze ROC curves")
7439 "This package provides tools for visualizing, smoothing and comparing
7440 receiver operating characteristic (ROC curves). The area under the
7441 curve (AUC) can be compared with statistical tests based on U-statistics or
7442 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7443 (license license:gpl3+)))
7445 (define-public r-rootsolve
7447 (name "r-rootsolve")
7452 (uri (cran-uri "rootSolve" version))
7455 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7456 (properties `((upstream-name . "rootSolve")))
7457 (build-system r-build-system)
7458 (native-inputs `(("gfortran" ,gfortran)))
7459 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7460 (synopsis "Tools for the analysis of ordinary differential equations")
7462 "This package provides routines to find the root of nonlinear functions,
7463 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7464 differential equations} (ODE). It includes routines that:
7467 @item generate gradient and jacobian matrices (full and banded),
7468 @item find roots of non-linear equations by the Newton-Raphson method,
7469 @item estimate steady-state conditions of a system of (differential) equations
7470 in full, banded or sparse form, using the Newton-Raphson method, or by
7471 dynamically running,
7472 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7473 and 3-D partial differential equations, that have been converted to ordinary
7474 differential equations by numerical differencing (using the method-of-lines
7477 (license license:gpl2+)))
7479 (define-public r-abcanalysis
7481 (name "r-abcanalysis")
7486 (uri (cran-uri "ABCanalysis" version))
7488 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7489 (properties `((upstream-name . "ABCanalysis")))
7490 (build-system r-build-system)
7491 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7492 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7493 (synopsis "Computed ABC Analysis")
7495 "Multivariate data sets often differ in several factors or derived statistical
7496 parameters, which have to be selected for a valid interpretation. Basing this
7497 selection on traditional statistical limits leads occasionally to the perception
7498 of losing information from a data set. This package provides tools to calculate
7499 these limits on the basis of the mathematical properties of the distribution of
7500 the analyzed items.")
7501 (license license:gpl3)))
7503 (define-public r-slam
7510 (uri (cran-uri "slam" version))
7512 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7513 (build-system r-build-system)
7514 (home-page "https://cran.r-project.org/web/packages/slam/")
7515 (synopsis "Sparse lightweight arrays and matrices")
7517 "This package contains data structures and algorithms for sparse arrays and matrices,
7518 based on index arrays and simple triplet representations, respectively.")
7519 (license license:gpl2)))
7521 (define-public r-manipulatewidget
7523 (name "r-manipulatewidget")
7528 (uri (cran-uri "manipulateWidget" version))
7530 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7532 `((upstream-name . "manipulateWidget")))
7533 (build-system r-build-system)
7535 `(("r-base64enc" ,r-base64enc)
7536 ("r-codetools" ,r-codetools)
7537 ("r-htmltools" ,r-htmltools)
7538 ("r-htmlwidgets" ,r-htmlwidgets)
7539 ("r-knitr" ,r-knitr)
7540 ("r-miniui" ,r-miniui)
7541 ("r-shiny" ,r-shiny)
7542 ("r-webshot" ,r-webshot)))
7543 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7544 (synopsis "Add even more interactivity to interactive charts")
7546 "This package lets you create in just a few lines of R code a nice user interface to
7547 modify the data or the graphical parameters of one or multiple interactive
7548 charts. It is useful to quickly explore visually some data or for package
7549 developers to generate user interfaces easy to maintain.")
7550 (license license:gpl2+)))
7559 (uri (cran-uri "A3" version))
7561 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7562 (properties `((upstream-name . "A3")))
7563 (build-system r-build-system)
7565 `(("r-pbapply" ,r-pbapply)
7566 ("r-xtable" ,r-xtable)))
7567 (home-page "https://cran.r-project.org/web/packages/A3/")
7568 (synopsis "Error metrics for predictive models")
7570 "This package supplies tools for tabulating and analyzing the results of predictive
7571 models. The methods employed are applicable to virtually any predictive model
7572 and make comparisons between different methodologies straightforward.")
7573 (license license:gpl2+)))
7575 (define-public r-infotheo
7582 (uri (cran-uri "infotheo" version))
7585 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7586 (build-system r-build-system)
7587 (home-page "http://homepage.meyerp.com/software")
7588 (synopsis "Information-theoretic measures")
7590 "This package implements various measures of information theory based on
7591 several entropy estimators.")
7592 (license license:gpl3+)))
7594 (define-public r-abcoptim
7601 (uri (cran-uri "ABCoptim" version))
7603 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7604 (properties `((upstream-name . "ABCoptim")))
7605 (build-system r-build-system)
7606 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7607 (home-page "https://github.com/gvegayon/ABCoptim/")
7608 (synopsis "Optimization of Artificial Bee Colony algorithm")
7610 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7611 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7612 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7613 algorithms, and uses only common control parameters such as colony size and
7614 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7615 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7616 This version is a work-in-progress and is written in R code.")
7617 (license license:expat)))
7619 (define-public r-abcp2
7626 (uri (cran-uri "ABCp2" version))
7628 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7629 (properties `((upstream-name . "ABCp2")))
7630 (build-system r-build-system)
7631 (propagated-inputs `(("r-mass" ,r-mass)))
7632 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7633 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7635 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7636 Poisson, and Gamma distribution and estimates the proportional paternity of the
7637 second male (P2) based on the best fit distribution.")
7638 (license license:gpl2)))
7640 (define-public r-abcrf
7647 (uri (cran-uri "abcrf" version))
7649 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7650 (build-system r-build-system)
7652 `(("r-doparallel" ,r-doparallel)
7653 ("r-foreach" ,r-foreach)
7655 ("r-matrixstats" ,r-matrixstats)
7656 ("r-ranger" ,r-ranger)
7658 ("r-rcpparmadillo" ,r-rcpparmadillo)
7659 ("r-readr" ,r-readr)
7660 ("r-stringr" ,r-stringr)))
7661 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7662 (synopsis "Approximate bayesian computation via random forests")
7664 "This package performs approximate bayesian computation (ABC) model choice and
7665 parameter inference via random forests. This machine learning tool named random
7666 forests (RF) can conduct selection among the highly complex models covered by
7668 (license license:gpl2+)))
7670 (define-public r-abctools
7677 (uri (cran-uri "abctools" version))
7679 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7680 (build-system r-build-system)
7683 ("r-abind" ,r-abind)
7684 ("r-hmisc" ,r-hmisc)
7685 ("r-plyr" ,r-plyr)))
7686 (home-page "https://github.com/dennisprangle/abctools/")
7687 (synopsis "Tools for ABC analyses")
7689 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7690 including summary statistic selection and assessing coverage. This includes
7691 recent dimension reduction algorithms to tune the choice of summary statistics,
7692 and coverage methods to tune the choice of threshold.")
7693 (license license:gpl2+)))
7695 (define-public r-ggstance
7702 (uri (cran-uri "ggstance" version))
7704 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7705 (build-system r-build-system)
7707 `(("r-ggplot2" ,r-ggplot2)
7709 ("r-rlang" ,r-rlang)
7710 ("r-withr" ,r-withr)))
7711 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7712 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7714 "This package is a @code{r-ggplot2} extension that provides flipped components:
7716 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7717 @item vertical versions of @code{r-ggplot2} positions.
7719 (license license:gpl3)))
7721 (define-public r-mosaiccore
7723 (name "r-mosaiccore")
7728 (uri (cran-uri "mosaicCore" version))
7730 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7731 (properties `((upstream-name . "mosaicCore")))
7732 (build-system r-build-system)
7734 `(("r-dplyr" ,r-dplyr)
7735 ("r-lazyeval" ,r-lazyeval)
7737 ("r-rlang" ,r-rlang)
7738 ("r-tidyr" ,r-tidyr)))
7739 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7740 (synopsis "Common utilities for mosaic family packages")
7742 "Common utilities used in other Mosaic family packages are collected here.")
7743 (license license:gpl2+)))
7745 (define-public r-ggformula
7747 (name "r-ggformula")
7752 (uri (cran-uri "ggformula" version))
7754 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7755 (build-system r-build-system)
7757 `(("r-ggforce" ,r-ggforce)
7758 ("r-ggplot2" ,r-ggplot2)
7759 ("r-ggstance" ,r-ggstance)
7760 ("r-magrittr" ,r-magrittr)
7761 ("r-mosaiccore" ,r-mosaiccore)
7762 ("r-rlang" ,r-rlang)
7763 ("r-stringr" ,r-stringr)
7764 ("r-tibble" ,r-tibble)))
7765 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7766 (synopsis "Formula interface for the @code{r-ggplot2}")
7768 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7769 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7770 and extends the excellent simplicity of the lattice-graphics formula interface,
7771 while providing the intuitive capabilities of @code{r-ggplot2}.")
7772 (license license:expat)))
7774 (define-public r-mosaicdata
7776 (name "r-mosaicdata")
7781 (uri (cran-uri "mosaicData" version))
7783 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7784 (properties `((upstream-name . "mosaicData")))
7785 (build-system r-build-system)
7786 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7787 (synopsis "Data sets for project Mosaic")
7789 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7790 used to teach mathematics, statistics, computation and modeling.")
7791 (license license:gpl2+)))
7793 (define-public r-raster
7800 (uri (cran-uri "raster" version))
7803 "144mva2dx7ffkq7z0fixr4z76ci1s4lizlyv5r7v07fd4nzg5hby"))))
7804 (build-system r-build-system)
7806 `(("r-rcpp" ,r-rcpp)
7808 (home-page "https://www.rspatial.org/")
7809 (synopsis "Geographic data analysis and modeling")
7811 "The package implements basic and high-level functions for reading,
7812 writing, manipulating, analyzing and modeling of gridded spatial data.
7813 Processing of very large files is supported.")
7814 (license license:gpl3+)))
7816 (define-public r-mosaic
7823 (uri (cran-uri "mosaic" version))
7825 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7826 (build-system r-build-system)
7828 `(("r-broom" ,r-broom)
7829 ("r-dplyr" ,r-dplyr)
7830 ("r-ggdendro" ,r-ggdendro)
7831 ("r-ggformula" ,r-ggformula)
7832 ("r-ggplot2" ,r-ggplot2)
7833 ("r-ggrepel" ,r-ggrepel)
7835 ("r-gridextra" ,r-gridextra)
7836 ("r-lattice" ,r-lattice)
7837 ("r-latticeextra" ,r-latticeextra)
7838 ("r-lazyeval" ,r-lazyeval)
7840 ("r-matrix" ,r-matrix)
7841 ("r-mosaiccore" ,r-mosaiccore)
7842 ("r-mosaicdata" ,r-mosaicdata)
7843 ("r-readr" ,r-readr)
7844 ("r-tidyr" ,r-tidyr)))
7846 `(("r-knitr" ,r-knitr)))
7847 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7848 (synopsis "Mathematics, statistics, and computation teaching utilities")
7850 "This package contain data sets and utilities from
7851 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7852 statistics, computation and modeling. Project MOSAIC is a community of
7853 educators working to tie together aspects of quantitative work that students
7854 in science, technology, engineering and mathematics will need in their
7855 professional lives, but which are usually taught in isolation, if at all.")
7856 (license license:gpl2+)))
7858 (define-public r-abd
7865 (uri (cran-uri "abd" version))
7867 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7868 (build-system r-build-system)
7870 `(("r-lattice" ,r-lattice)
7871 ("r-mosaic" ,r-mosaic)
7872 ("r-nlme" ,r-nlme)))
7873 (home-page "https://cran.r-project.org/web/packages/abd/")
7874 (synopsis "Analysis of biological data")
7876 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7877 biological data by Michael Whitlock and Dolph Schluter.")
7878 (license license:gpl2)))
7880 (define-public r-svgui
7887 (uri (cran-uri "svGUI" version))
7889 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7890 (properties `((upstream-name . "svGUI")))
7891 (build-system r-build-system)
7892 (home-page "https://github.com/SciViews/svGUI/")
7893 (synopsis "Functions for managing GUI clients in R")
7895 "The SciViews @code{svGUI} package eases the management of Graphical User
7896 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7897 centralizes info about GUI elements currently used, and it dispatches GUI
7898 calls to the particular toolkits in use in function of the context.")
7899 (license license:gpl2)))
7901 (define-public r-svdialogs
7903 (name "r-svdialogs")
7908 (uri (cran-uri "svDialogs" version))
7910 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7911 (properties `((upstream-name . "svDialogs")))
7912 (build-system r-build-system)
7915 ("zenity" ,zenity)))
7917 `(("r-rstudioapi" ,r-rstudioapi)
7918 ("r-svgui" ,r-svgui)))
7919 (home-page "https://github.com/SciViews/svDialogs/")
7920 (synopsis "Portable dialog boxes")
7922 "This package helps to construct standard dialog boxes for your GUI, including
7923 message boxes, input boxes, list, file or directory selection, and others. In
7924 case R cannot display GUI dialog boxes, a simpler command line version of these
7925 interactive elements is also provided as a fallback solution.")
7926 (license license:gpl2)))
7928 (define-public r-abe
7935 (uri (cran-uri "abe" version))
7938 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7939 (build-system r-build-system)
7940 (home-page "https://cran.r-project.org/web/packages/abe/")
7941 (synopsis "Augmented backward elimination")
7943 "This package performs augmented backward elimination and checks the
7944 stability of the obtained model. Augmented backward elimination combines
7945 significance or information based criteria with the change in estimate to
7946 either select the optimal model for prediction purposes or to serve as a tool
7947 to obtain a practically sound, highly interpretable model.")
7948 (license license:gpl2+)))
7950 (define-public r-abf2
7957 (uri (cran-uri "abf2" version))
7959 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7960 (build-system r-build-system)
7961 (home-page "https://cran.r-project.org/web/packages/abf2/")
7962 (synopsis "Load gap-free axon @code{r-abf2} files")
7964 "This package loads electrophysiology data from ABF2 files, as created by
7965 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7966 mode are currently supported.")
7967 (license license:artistic2.0)))
7969 (define-public r-abhgenotyper
7971 (name "r-abhgenotyper")
7976 (uri (cran-uri "ABHgenotypeR" version))
7978 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7979 (properties `((upstream-name . "ABHgenotypeR")))
7980 (build-system r-build-system)
7982 `(("r-ggplot2" ,r-ggplot2)
7983 ("r-reshape2" ,r-reshape2)))
7984 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7985 (synopsis "Visualize and manipulate ABH genotypes")
7987 "The @code{r-abhgenotyper} package provides simple imputation,
7988 error-correction and plotting capacities for genotype data. The package is
7989 supposed to serve as an intermediate but independent analysis tool between the
7990 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7991 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7992 genotypes as \"graphical genotypes\".")
7993 (license license:gpl3)))
7995 (define-public r-furrr
8002 (uri (cran-uri "furrr" version))
8005 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
8006 (build-system r-build-system)
8008 `(("r-future" ,r-future)
8009 ("r-globals" ,r-globals)
8010 ("r-purrr" ,r-purrr)
8011 ("r-rlang" ,r-rlang)))
8012 (home-page "https://github.com/DavisVaughan/furrr")
8013 (synopsis "Apply mapping functions in parallel using futures")
8015 "This package provides implementations of the family of @code{map()}
8016 functions from the @code{purrr} package that can be resolved using any
8017 @code{future}-supported backend, e.g. parallel on the local machine or
8018 distributed on a compute cluster.")
8019 (license license:lgpl2.1+)))
8021 (define-public r-abjutils
8028 (uri (cran-uri "abjutils" version))
8030 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
8031 (build-system r-build-system)
8033 `(("r-devtools" ,r-devtools)
8034 ("r-dplyr" ,r-dplyr)
8035 ("r-furrr" ,r-furrr)
8036 ("r-future" ,r-future)
8039 ("r-magrittr" ,r-magrittr)
8040 ("r-progress" ,r-progress)
8041 ("r-purrr" ,r-purrr)
8042 ("r-readr" ,r-readr)
8043 ("r-rlang" ,r-rlang)
8044 ("r-rstudioapi" ,r-rstudioapi)
8045 ("r-scales" ,r-scales)
8046 ("r-stringi" ,r-stringi)
8047 ("r-stringr" ,r-stringr)
8048 ("r-tibble" ,r-tibble)
8049 ("r-tidyr" ,r-tidyr)))
8050 (home-page "https://github.com/abjur/abjutils/")
8051 (synopsis "Collection of tools for jurimetrical analysis")
8053 "This package implements general purpose tools, such as functions for
8054 sampling and basic manipulation of Brazilian lawsuits identification number.
8055 It also implements functions for text cleaning, such as accentuation
8057 (license license:expat)))
8059 (define-public r-abnormality
8061 (name "r-abnormality")
8066 (uri (cran-uri "abnormality" version))
8068 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8069 (build-system r-build-system)
8071 `(("r-mass" ,r-mass)
8072 ("r-matrix" ,r-matrix)))
8073 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8074 (synopsis "Measure a subject's abnormality with respect to a reference population")
8076 "This package contains functions to implement the methodology and
8077 considerations laid out by Marks et al. in the article \"Measuring abnormality
8078 in high dimensional spaces: applications in biomechanical gait analysis\".
8079 Using high-dimensional datasets to measure a subject's overall level of
8080 abnormality as compared to a reference population is often needed in outcomes
8082 (license license:expat)))
8084 (define-public r-abodoutlier
8086 (name "r-abodoutlier")
8091 (uri (cran-uri "abodOutlier" version))
8093 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8094 (properties `((upstream-name . "abodOutlier")))
8095 (build-system r-build-system)
8097 `(("r-cluster" ,r-cluster)))
8098 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8099 (synopsis "Angle-based outlier detection")
8101 "This package performs angle-based outlier detection on a given data
8102 frame. It offers three methods to process data:
8104 @item full but slow implementation using all the data that has cubic
8106 @item a fully randomized method;
8107 @item a method using k-nearest neighbours.
8109 These algorithms are well suited for high dimensional data outlier
8111 (license license:expat)))
8113 (define-public r-abps
8120 (uri (cran-uri "ABPS" version))
8122 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8123 (properties `((upstream-name . "ABPS")))
8124 (build-system r-build-system)
8125 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8126 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8127 (synopsis "Abnormal blood profile score to detect blood doping")
8129 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8130 The ABPS is a part of the Athlete biological passport program of the World
8131 anti-doping agency, which combines several blood parameters into a single
8132 score in order to detect blood doping. The package also contains functions to
8133 calculate other scores used in anti-doping programs, such as the ratio of
8134 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8135 (license license:gpl2+)))
8137 (define-public r-parmigene
8139 (name "r-parmigene")
8144 (uri (cran-uri "parmigene" version))
8147 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
8148 (build-system r-build-system)
8149 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8150 (synopsis "Mutual information estimation for gene network reconstruction")
8152 "This package provides a parallel estimation of the mutual information
8153 based on entropy estimates from k-nearest neighbors distances and algorithms
8154 for the reconstruction of gene regulatory networks.")
8155 (license license:agpl3+)))
8157 (define-public r-pscl
8164 (uri (cran-uri "pscl" version))
8166 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8167 (build-system r-build-system)
8169 `(("r-mass" ,r-mass)))
8170 (home-page "https://github.com/atahk/pscl/")
8171 (synopsis "Political science computational laboratory")
8173 "The @code{pscl} is an R package providing classes and methods for:
8175 @item Bayesian analysis of roll call data (item-response models);
8176 @item elementary Bayesian statistics;
8177 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8179 @item utility functions.
8181 (license license:gpl2)))
8183 (define-public r-accelmissing
8185 (name "r-accelmissing")
8190 (uri (cran-uri "accelmissing" version))
8192 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8193 (build-system r-build-system)
8195 `(("r-mice" ,r-mice)
8196 ("r-pscl" ,r-pscl)))
8197 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8198 (synopsis "Missing value imputation for accelerometer data")
8200 "This package provides a statistical method to impute the missing values in
8201 accelerometer data. The methodology includes both parametric and
8202 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8203 model. It also provides multiple functions to preprocess the accelerometer data
8204 previous to the missing data imputation. These include detecting the wearing
8205 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8206 (license license:gpl2+)))
8208 (define-public r-mhsmm
8215 (uri (cran-uri "mhsmm" version))
8217 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8218 (build-system r-build-system)
8219 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8220 (home-page "https://github.com/jaredo/mhsmm/")
8221 (synopsis "Inference for hidden Markov and semi-Markov models")
8223 "The @code{r-mhsmm} package implements estimation and prediction methods for
8224 hidden Markov and semi-Markov models for multiple observation sequences. Such
8225 techniques are of interest when observed data is thought to be dependent on some
8226 unobserved (or hidden) state. Also, this package is suitable for equidistant
8227 time series data, with multivariate and/or missing data. Allows user defined
8228 emission distributions.")
8229 (license license:gpl2+)))
8231 (define-public r-nleqslv
8238 (uri (cran-uri "nleqslv" version))
8240 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8241 (build-system r-build-system)
8242 (native-inputs `(("gfortran" ,gfortran)))
8243 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8244 (synopsis "Solve systems of nonlinear equations")
8246 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8247 Broyden or a Newton method with a choice of global strategies such as line
8248 search and trust region. There are options for using a numerical or user
8249 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8250 singular or ill-conditioned Jacobian.")
8251 (license license:gpl2+)))
8253 (define-public r-physicalactivity
8255 (name "r-physicalactivity")
8260 (uri (cran-uri "PhysicalActivity" version))
8262 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8264 `((upstream-name . "PhysicalActivity")))
8265 (build-system r-build-system)
8266 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8267 (synopsis "Procesing accelerometer data for physical activity measurement")
8269 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8270 for classification of monitor wear and nonwear time intervals in accelerometer
8271 data collected to assess physical activity. The package also contains functions
8272 for making plots of accelerometer data and obtaining the summary of various
8273 information including daily monitor wear time and the mean monitor wear time
8274 during valid days. The revised package version 0.2-1 improved the functions
8275 regarding speed, robustness and add better support for time zones and daylight
8276 saving. In addition, several functions were added:
8278 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8279 @item the @code{markPAI} can categorize physical activity intensity level based
8280 on user-defined cut-points of accelerometer counts.
8282 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8283 @code{queryActigraph} functions.")
8284 (license license:gpl3+)))
8286 (define-public r-acc
8293 (uri (cran-uri "acc" version))
8295 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8296 (build-system r-build-system)
8298 `(("r-circlize" ,r-circlize)
8300 ("r-ggplot2" ,r-ggplot2)
8301 ("r-iterators" ,r-iterators)
8302 ("r-mhsmm" ,r-mhsmm)
8303 ("r-nleqslv" ,r-nleqslv)
8304 ("r-physicalactivity" ,r-physicalactivity)
8306 ("r-r-utils" ,r-r-utils)
8308 ("r-rcpparmadillo" ,r-rcpparmadillo)
8309 ("r-rsqlite" ,r-rsqlite)
8311 (home-page "https://cran.r-project.org/web/packages/acc/")
8312 (synopsis "Exploring accelerometer data")
8314 "This package processes accelerometer data from uni-axial and tri-axial devices
8315 and generates data summaries. Also, includes functions to plot, analyze, and
8316 simulate accelerometer data.")
8317 (license license:gpl2+)))
8319 (define-public r-rbenchmark
8321 (name "r-rbenchmark")
8326 (uri (cran-uri "rbenchmark" version))
8328 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8329 (build-system r-build-system)
8330 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8331 (synopsis "Benchmarking routine for R")
8333 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8334 and is intended to facilitate benchmarking of arbitrary R code. The library
8335 consists of just one function, benchmark, which is a simple wrapper around
8336 system.time. Given a specification of the benchmarking process (counts of
8337 replications, evaluation environment) and an arbitrary number of expressions,
8338 benchmark evaluates each of the expressions in the specified environment,
8339 replicating the evaluation as many times as specified, and returning the results
8340 conveniently wrapped into a data frame.")
8341 (license license:gpl2+)))
8343 (define-public r-mitools
8350 (uri (cran-uri "mitools" version))
8353 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8354 (build-system r-build-system)
8355 (propagated-inputs `(("r-dbi" ,r-dbi)))
8356 (home-page "https://cran.r-project.org/web/packages/mitools/")
8357 (synopsis "Tools for multiple imputation of missing data")
8359 "This package provides tools to perform analyses and combine results from
8360 multiple-imputation datasets.")
8361 (license license:gpl2)))
8363 (define-public r-magick
8370 (uri (cran-uri "magick" version))
8373 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8374 (build-system r-build-system)
8376 `(("imagemagick" ,imagemagick)
8379 `(("r-curl" ,r-curl)
8380 ("r-magrittr" ,r-magrittr)
8381 ("r-rcpp" ,r-rcpp)))
8383 `(("pkg-config" ,pkg-config)
8384 ("r-knitr" ,r-knitr)))
8385 (home-page "https://github.com/ropensci/magick")
8386 (synopsis "Advanced graphics and image-processing in R")
8388 "This package provides bindings to ImageMagick, a comprehensive image
8389 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8390 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8391 operations are vectorized via the Magick++ STL meaning they operate either on
8392 a single frame or a series of frames for working with layers, collages, or
8393 animation. In RStudio, images are automatically previewed when printed to the
8394 console, resulting in an interactive editing environment.")
8395 (license license:expat)))
8397 (define-public r-survey
8404 (uri (cran-uri "survey" version))
8407 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8408 (build-system r-build-system)
8410 `(("r-lattice" ,r-lattice)
8411 ("r-matrix" ,r-matrix)
8412 ("r-minqa" ,r-minqa)
8413 ("r-mitools" ,r-mitools)
8414 ("r-numderiv" ,r-numderiv)
8415 ("r-survival" ,r-survival)))
8416 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8417 (synopsis "Analysis of complex survey samples")
8419 "This package provides tools for the analysis of complex survey samples.
8420 The provided features include: summary statistics, two-sample tests, rank
8421 tests, generalised linear models, cumulative link models, Cox models,
8422 loglinear models, and general maximum pseudolikelihood estimation for
8423 multistage stratified, cluster-sampled, unequally weighted survey samples;
8424 variances by Taylor series linearisation or replicate weights;
8425 post-stratification, calibration, and raking; two-phase subsampling designs;
8426 graphics; PPS sampling without replacement; principal components, and factor
8428 ;; Either version of the GPL.
8429 (license (list license:gpl2 license:gpl3))))
8431 (define-public r-gee
8438 (uri (cran-uri "gee" version))
8441 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8442 (properties `((upstream-name . "gee")))
8443 (build-system r-build-system)
8445 `(("gfortran" ,gfortran)))
8446 (home-page "https://cran.r-project.org/web/packages/gee/")
8447 (synopsis "Generalized estimation equation solver")
8449 "This package provides a solver for generalized estimation equations.")
8450 (license license:gpl2)))
8452 (define-public r-tab
8459 (uri (cran-uri "tab" version))
8462 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8463 (properties `((upstream-name . "tab")))
8464 (build-system r-build-system)
8466 `(("r-dplyr" ,r-dplyr)
8468 ("r-knitr" ,r-knitr)
8470 ("r-survey" ,r-survey)
8471 ("r-survival" ,r-survival)
8472 ("r-xtable" ,r-xtable)))
8473 (home-page "https://cran.r-project.org/web/packages/tab/")
8474 (synopsis "Create summary tables for statistical reports")
8476 "This package contains functions for creating various types of summary
8477 tables, e.g. comparing characteristics across levels of a categorical variable
8478 and summarizing fitted generalized linear models, generalized estimating
8479 equations, and Cox proportional hazards models. Functions are available to
8480 handle data from simple random samples as well as complex surveys.")
8481 (license license:gpl3+)))
8483 (define-public r-dvmisc
8490 (uri (cran-uri "dvmisc" version))
8492 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8493 (build-system r-build-system)
8495 `(("r-cubature" ,r-cubature)
8496 ("r-data-table" ,r-data-table)
8497 ("r-dplyr" ,r-dplyr)
8498 ("r-ggplot2" ,r-ggplot2)
8500 ("r-mvtnorm" ,r-mvtnorm)
8501 ("r-pracma" ,r-pracma)
8502 ("r-rbenchmark" ,r-rbenchmark)
8504 ("r-survey" ,r-survey)
8506 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8507 (synopsis "Faster computation of common statistics and miscellaneous functions")
8509 "This package implements faster versions of base R functions (e.g. mean, standard
8510 deviation, covariance, weighted mean), mostly written in C++, along with
8511 miscellaneous functions for various purposes (e.g. create the histogram with
8512 fitted probability density function or probability mass function curve, create
8513 the body mass index groups, assess the linearity assumption in logistic
8515 (license license:gpl2)))
8517 (define-public r-accelerometry
8519 (name "r-accelerometry")
8524 (uri (cran-uri "accelerometry" version))
8526 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8527 (build-system r-build-system)
8529 `(("r-dvmisc" ,r-dvmisc)
8530 ("r-rcpp" ,r-rcpp)))
8531 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8532 (synopsis "Functions for processing accelerometer data")
8534 "This package provides a collection of functions that perform operations on
8535 time-series accelerometer data, such as identify the non-wear time, flag minutes
8536 that are part of an activity bout, and find the maximum 10-minute average count
8537 value. The functions are generally very flexible, allowing for a variety of
8538 algorithms to be implemented.")
8539 (license license:gpl3)))
8541 (define-public r-absim
8548 (uri (cran-uri "AbSim" version))
8550 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8551 (properties `((upstream-name . "AbSim")))
8552 (build-system r-build-system)
8555 ("r-powerlaw" ,r-powerlaw)))
8556 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8557 (synopsis "Time resolved simulations of antibody repertoires")
8559 "This package provides simulation methods for the evolution of antibody repertoires.
8560 The heavy and light chain variable region of both human and C57BL/6 mice can
8561 be simulated in a time-dependent fashion. Both single lineages using one set of
8562 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8563 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8564 Upon completion, the main loop of the algorithm begins, with each iteration
8565 representing one simulated time step. Various mutation events are possible at
8566 each time step, contributing to a diverse final repertoire.")
8567 (license license:gpl2)))
8569 (define-public r-quic
8576 (uri (cran-uri "QUIC" version))
8578 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8579 (properties `((upstream-name . "QUIC")))
8580 (build-system r-build-system)
8581 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8582 (synopsis "Regularized sparse inverse covariance matrix estimation")
8584 "This package implements the regularized Gaussian maximum likelihood
8585 estimation of the inverse of a covariance matrix. It uses Newton's method and
8586 coordinate descent to solve the regularized inverse covariance matrix
8587 estimation problem.")
8588 ;; The project home page states that the release is under GPLv3 or later.
8589 ;; The CRAN page only says GPL-3.
8590 (license license:gpl3+)))
8592 (define-public r-abundant
8599 (uri (cran-uri "abundant" version))
8601 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8602 (build-system r-build-system)
8604 `(("r-quic" ,r-quic)))
8605 (home-page "https://cran.r-project.org/web/packages/abundant/")
8606 (synopsis "Abundant regression and high-dimensional principal fitted components")
8608 "This package provides tools to fit and predict with the high-dimensional
8609 principal fitted components model. This model is described by Cook, Forzani,
8610 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8611 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8612 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8613 (license license:gpl2+)))
8615 (define-public r-ac3net
8622 (uri (cran-uri "Ac3net" version))
8624 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8625 (properties `((upstream-name . "Ac3net")))
8626 (build-system r-build-system)
8628 `(("r-data-table" ,r-data-table)))
8629 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8630 (synopsis "Inferring directional conservative causal core gene networks")
8631 (description "This package infers directional Conservative causal core
8632 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8633 directional network.")
8634 (license license:gpl3+)))
8636 (define-public r-aca
8643 (uri (cran-uri "ACA" version))
8645 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8646 (properties `((upstream-name . "ACA")))
8647 (build-system r-build-system)
8648 (home-page "https://cran.r-project.org/web/packages/ACA/")
8649 (synopsis "Abrupt change-point or aberration detection in point series")
8651 "This package offers an interactive function for the detection of breakpoints in
8653 ;; Any version of the GPL
8654 (license (list license:gpl2+ license:gpl3+))))
8656 (define-public r-acceptancesampling
8658 (name "r-acceptancesampling")
8663 (uri (cran-uri "AcceptanceSampling" version))
8665 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8667 `((upstream-name . "AcceptanceSampling")))
8668 (build-system r-build-system)
8669 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8670 (synopsis "Creation and evaluation of acceptance sampling plans")
8672 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8673 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8674 in quality control and improvement. International standards of acceptance
8675 sampling provide sampling plans for specific circumstances. The aim of this
8676 package is to provide an easy-to-use interface to visualize single, double or
8677 multiple sampling plans. In addition, methods have been provided to enable the
8678 user to assess sampling plans against pre-specified levels of performance, as
8679 measured by the probability of acceptance for a given level of quality in the
8681 (license license:gpl3+)))
8683 (define-public r-acclma
8690 (uri (cran-uri "ACCLMA" version))
8692 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8693 (properties `((upstream-name . "ACCLMA")))
8694 (build-system r-build-system)
8695 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8696 (synopsis "ACC & LMA graph plotting")
8698 "This package contains a function that imports data from a @acronym{CSV,
8699 Comma-Separated Values} file, or uses manually entered data from the format (x,
8700 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8701 Curve} vs @acronym{LOI, Line of Independence} graph and
8702 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8703 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8704 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8705 string) was passed, a manual data entry window is opened. The header parameter
8706 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8707 a header row or not. The dataset should contain only one independent variable
8708 (x) and one dependent variable (y) and can contain a weight for each
8710 (license license:gpl2)))
8712 (define-public r-aspi
8719 (uri (cran-uri "aspi" version))
8721 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8722 (build-system r-build-system)
8724 "https://cran.r-project.org/web/packages/aspi/")
8726 "Analysis of symmetry of parasitic infections")
8728 "This package provides tools for the analysis and visualization of bilateral
8729 asymmetry in parasitic infections.")
8730 (license license:gpl3+)))
8732 (define-public r-sandwich
8739 (uri (cran-uri "sandwich" version))
8742 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8743 (build-system r-build-system)
8745 `(("r-zoo" ,r-zoo)))
8746 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8747 (synopsis "Robust Covariance Matrix Estimators")
8749 "This package provides model-robust standard error estimators for
8750 cross-sectional, time series, clustered, panel, and longitudinal data.")
8751 ;; Either version of the license.
8752 (license (list license:gpl2 license:gpl3))))
8754 (define-public r-th-data
8761 (uri (cran-uri "TH.data" version))
8764 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8765 (properties `((upstream-name . "TH.data")))
8766 (build-system r-build-system)
8768 `(("r-mass" ,r-mass)
8769 ("r-survival" ,r-survival)))
8770 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8771 (synopsis "Shared data sets")
8773 "This package contains supporting data sets that are used in other
8774 packages maintained by Torsten Hothorn.")
8775 (license license:gpl3)))
8777 (define-public r-multcomp
8784 (uri (cran-uri "multcomp" version))
8787 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8788 (build-system r-build-system)
8790 `(("r-codetools" ,r-codetools)
8791 ("r-mvtnorm" ,r-mvtnorm)
8792 ("r-sandwich" ,r-sandwich)
8793 ("r-survival" ,r-survival)
8794 ("r-th-data" ,r-th-data)))
8795 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8796 (synopsis "Simultaneous inference in general parametric models")
8798 "Simultaneous tests and confidence intervals for general linear
8799 hypotheses in parametric models, including linear, generalized linear, linear
8800 mixed effects, and survival models. The package includes demos reproducing
8801 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8802 Hothorn, Westfall, 2010, CRC Press).")
8803 (license license:gpl2)))
8805 (define-public r-emmeans
8812 (uri (cran-uri "emmeans" version))
8815 "0h884qn4cip03w0h5psrz5y9zkm2wppklrhdz2chm2xk13zqnq5k"))))
8816 (build-system r-build-system)
8818 `(("r-estimability" ,r-estimability)
8819 ("r-mvtnorm" ,r-mvtnorm)
8820 ("r-numderiv" ,r-numderiv)
8822 ("r-xtable" ,r-xtable)))
8824 `(("r-knitr" ,r-knitr)))
8825 (home-page "https://github.com/rvlenth/emmeans")
8826 (synopsis "Estimated marginal means, aka least-squares means")
8828 "This package provides tools to obtain @dfn{estimated marginal
8829 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8830 be used to compute contrasts or linear functions of EMMs, trends, and
8831 comparisons of slopes.")
8832 ;; Either version of the license.
8833 (license (list license:gpl2 license:gpl3))))
8835 (define-public r-pwr
8842 (uri (cran-uri "pwr" version))
8845 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8846 (build-system r-build-system)
8848 `(("r-knitr" ,r-knitr)))
8849 (home-page "https://github.com/heliosdrm/pwr")
8850 (synopsis "Basic functions for power analysis")
8852 "This package provides power analysis functions along the lines of
8854 (license license:gpl3+)))
8856 (define-public r-libcoin
8863 (uri (cran-uri "libcoin" version))
8866 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8867 (build-system r-build-system)
8868 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8869 (home-page "https://cran.r-project.org/web/packages/libcoin")
8870 (synopsis "Linear test statistics for permutation inference")
8872 "This package provides basic infrastructure for linear test statistics
8873 and permutation inference in the framework of Strasser and Weber (1999).")
8874 (license license:gpl2)))
8876 (define-public r-coin
8883 (uri (cran-uri "coin" version))
8886 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8887 (build-system r-build-system)
8889 `(("r-libcoin" ,r-libcoin)
8890 ("r-matrixstats" ,r-matrixstats)
8891 ("r-modeltools" ,r-modeltools)
8892 ("r-multcomp" ,r-multcomp)
8893 ("r-mvtnorm" ,r-mvtnorm)
8894 ("r-survival" ,r-survival)))
8895 (home-page "http://coin.r-forge.r-project.org")
8896 (synopsis "Conditional inference procedures in a permutation test framework")
8898 "This package provides conditional inference procedures for the general
8899 independence problem including two-sample, K-sample (non-parametric ANOVA),
8900 correlation, censored, ordered and multivariate problems.")
8901 (license license:gpl2)))
8903 (define-public r-bayesplot
8905 (name "r-bayesplot")
8910 (uri (cran-uri "bayesplot" version))
8913 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8914 (build-system r-build-system)
8916 `(("pandoc" ,ghc-pandoc)
8917 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8919 `(("r-knitr" ,r-knitr)))
8921 `(("r-dplyr" ,r-dplyr)
8922 ("r-ggplot2" ,r-ggplot2)
8923 ("r-ggridges" ,r-ggridges)
8925 ("r-reshape2" ,r-reshape2)
8926 ("r-rlang" ,r-rlang)
8927 ("r-tibble" ,r-tibble)
8928 ("r-tidyselect" ,r-tidyselect)))
8929 (home-page "https://mc-stan.org/bayesplot")
8930 (synopsis "Plotting for Bayesian models")
8932 "This package provides plotting functions for posterior analysis, model
8933 checking, and MCMC diagnostics. The package is designed not only to provide
8934 convenient functionality for users, but also a common set of functions that
8935 can be easily used by developers working on a variety of R packages for
8936 Bayesian modeling.")
8937 (license license:gpl3+)))
8939 (define-public r-tmb
8946 (uri (cran-uri "TMB" version))
8949 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8950 (properties `((upstream-name . "TMB")))
8951 (build-system r-build-system)
8953 `(("r-matrix" ,r-matrix)
8954 ("r-rcppeigen" ,r-rcppeigen)))
8955 (home-page "http://tmb-project.org")
8956 (synopsis "Template model builder: a general random effect tool")
8958 "With this tool, a user should be able to quickly implement complex
8959 random effect models through simple C++ templates. The package combines
8960 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8961 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8962 from R) to obtain an efficient implementation of the applied Laplace
8963 approximation with exact derivatives. Key features are: Automatic sparseness
8964 detection, parallelism through BLAS and parallel user templates.")
8965 (license license:gpl2)))
8967 (define-public r-sjstats
8974 (uri (cran-uri "sjstats" version))
8976 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8977 (build-system r-build-system)
8979 `(("r-bayestestr" ,r-bayestestr)
8980 ("r-broom" ,r-broom)
8981 ("r-dplyr" ,r-dplyr)
8982 ("r-effectsize" ,r-effectsize)
8983 ("r-emmeans" ,r-emmeans)
8984 ("r-insight" ,r-insight)
8986 ("r-magrittr" ,r-magrittr)
8988 ("r-modelr" ,r-modelr)
8989 ("r-parameters" ,r-parameters)
8990 ("r-performance" ,r-performance)
8991 ("r-purrr" ,r-purrr)
8992 ("r-rlang" ,r-rlang)
8993 ("r-sjlabelled" ,r-sjlabelled)
8994 ("r-sjmisc" ,r-sjmisc)
8995 ("r-tidyr" ,r-tidyr)))
8996 (home-page "https://github.com/strengejacke/sjstats")
8997 (synopsis "Functions for common statistical computations")
8999 "This package provides a collection of convenient functions for common
9000 statistical computations, which are not directly provided by R's @code{base}
9001 or @code{stats} packages. This package aims at providing, first, shortcuts
9002 for statistical measures, which otherwise could only be calculated with
9003 additional effort. Second, these shortcut functions are generic, and can be
9004 applied not only to vectors, but also to other objects as well. The focus of
9005 most functions lies on summary statistics or fit measures for regression
9006 models, including generalized linear models, mixed effects models and Bayesian
9008 (license license:gpl3)))
9010 (define-public r-glmmtmb
9017 (uri (cran-uri "glmmTMB" version))
9020 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
9021 (properties `((upstream-name . "glmmTMB")))
9022 (build-system r-build-system)
9024 `(("r-lme4" ,r-lme4)
9025 ("r-matrix" ,r-matrix)
9027 ("r-rcppeigen" ,r-rcppeigen)
9030 `(("r-knitr" ,r-knitr))) ; for vignettes
9031 (home-page "https://github.com/glmmTMB")
9032 (synopsis "Generalized linear mixed models")
9034 "Fit linear and generalized linear mixed models with various extensions,
9035 including zero-inflation. The models are fitted using maximum likelihood
9036 estimation via the Template Model Builder. Random effects are assumed to be
9037 Gaussian on the scale of the linear predictor and are integrated out using the
9038 Laplace approximation. Gradients are calculated using automatic
9040 (license license:agpl3+)))
9042 (define-public r-bayestestr
9044 (name "r-bayestestr")
9049 (uri (cran-uri "bayestestR" version))
9052 "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd"))))
9053 (properties `((upstream-name . "bayestestR")))
9054 (build-system r-build-system)
9056 `(("r-insight" ,r-insight)))
9058 `(("r-knitr" ,r-knitr)))
9059 (home-page "https://github.com/easystats/bayestestR")
9060 (synopsis "Describe Bayesian models and posterior distributions")
9062 "This package provides utilities to understand and describe posterior
9063 distributions and Bayesian models. It includes point-estimates such as
9064 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9065 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9066 ROPE percentage and pd).")
9067 (license license:gpl3)))
9069 (define-public r-performance
9071 (name "r-performance")
9076 (uri (cran-uri "performance" version))
9079 "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
9080 (build-system r-build-system)
9082 `(("r-bayestestr" ,r-bayestestr)
9083 ("r-insight" ,r-insight)))
9084 (home-page "https://easystats.github.io/performance/")
9085 (synopsis "Assessment of regression models performance")
9087 "This package provides utilities for computing measures to assess model
9088 quality, which are not directly provided by R's @code{base} or @code{stats}
9089 packages. These include e.g. measures like r-squared, intraclass correlation
9090 coefficient, root mean squared error or functions to check models for
9091 overdispersion, singularity or zero-inflation and more. Functions apply to a
9092 large variety of regression models, including generalized linear models, mixed
9093 effects models and Bayesian models.")
9094 (license license:gpl3)))
9096 (define-public r-ggeffects
9098 (name "r-ggeffects")
9103 (uri (cran-uri "ggeffects" version))
9106 "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r"))))
9107 (build-system r-build-system)
9109 `(("r-insight" ,r-insight)
9111 ("r-sjlabelled" ,r-sjlabelled)))
9113 `(("r-knitr" ,r-knitr)))
9114 (home-page "https://github.com/strengejacke/ggeffects")
9115 (synopsis "Create tidy data frames of marginal effects for ggplot")
9117 "This package provides tools to compute marginal effects from statistical
9118 models and return the result as tidy data frames. These data frames are ready
9119 to use with the @code{ggplot2} package. Marginal effects can be calculated
9120 for many different models. Interaction terms, splines and polynomial terms
9121 are also supported. The two main functions are @code{ggpredict()} and
9122 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9123 results using @code{ggplot2}.")
9124 (license license:gpl3)))
9126 (define-public r-effectsize
9128 (name "r-effectsize")
9133 (uri (cran-uri "effectsize" version))
9136 "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
9137 (properties `((upstream-name . "effectsize")))
9138 (build-system r-build-system)
9140 `(("r-bayestestr" ,r-bayestestr)
9141 ("r-insight" ,r-insight)
9142 ("r-parameters" ,r-parameters)))
9144 `(("r-knitr" ,r-knitr)))
9145 (home-page "https://github.com/easystats/effectsize")
9146 (synopsis "Indices of effect size and standardized parameters")
9148 "This package provides utilities to work with indices of effect size and
9149 standardized parameters for a wide variety of models, allowing computation and
9150 conversion of indices such as Cohen's d, r, odds, etc.")
9151 (license license:gpl3)))
9153 (define-public r-sjplot
9160 (uri (cran-uri "sjPlot" version))
9162 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9163 (properties `((upstream-name . "sjPlot")))
9164 (build-system r-build-system)
9166 `(("r-bayestestr" ,r-bayestestr)
9167 ("r-dplyr" ,r-dplyr)
9168 ("r-effectsize" ,r-effectsize)
9169 ("r-ggeffects" ,r-ggeffects)
9170 ("r-ggplot2" ,r-ggplot2)
9171 ("r-insight" ,r-insight)
9172 ("r-knitr" ,r-knitr)
9174 ("r-parameters" ,r-parameters)
9175 ("r-performance" ,r-performance)
9176 ("r-purrr" ,r-purrr)
9177 ("r-rlang" ,r-rlang)
9178 ("r-scales" ,r-scales)
9179 ("r-sjlabelled" ,r-sjlabelled)
9180 ("r-sjmisc" ,r-sjmisc)
9181 ("r-sjstats" ,r-sjstats)
9182 ("r-tidyr" ,r-tidyr)))
9184 `(("r-knitr" ,r-knitr)))
9185 (home-page "https://strengejacke.github.io/sjPlot/")
9186 (synopsis "Data visualization for statistics in social science")
9188 "This package represents a collection of plotting and table output
9189 functions for data visualization. Results of various statistical
9190 analyses (that are commonly used in social sciences) can be visualized using
9191 this package, including simple and cross tabulated frequencies, histograms,
9192 box plots, (generalized) linear models, mixed effects models, principal
9193 component analysis and correlation matrices, cluster analyses, scatter plots,
9194 stacked scales, effects plots of regression models (including interaction
9195 terms) and much more. This package supports labelled data.")
9196 (license license:gpl3)))
9198 (define-public r-ini
9205 (uri (cran-uri "ini" version))
9208 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9209 (build-system r-build-system)
9210 (home-page "https://github.com/dvdscripter/ini")
9211 (synopsis "Read and write configuration files")
9213 "This package provides tools to parse simple @code{.ini} configuration
9214 files to an structured list. Users can manipulate this resulting list with
9215 @code{lapply()} functions. This same structured list can be used to write
9216 back to file after modifications.")
9217 (license license:gpl3)))
9226 (uri (cran-uri "gh" version))
9229 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9230 (build-system r-build-system)
9235 ("r-jsonlite" ,r-jsonlite)))
9236 (home-page "https://github.com/r-lib/gh#readme")
9237 (synopsis "Access the GitHub API via R")
9239 "This package provides a minimal R client to access the GitHub API.")
9240 (license license:expat)))
9249 (uri (cran-uri "fs" version))
9252 "09rpazjba9jy448j6rq989fw3wv3xhng7fn8p8gr22gyx0n0y1zr"))))
9253 (build-system r-build-system)
9255 `(("pkg-config" ,pkg-config)
9256 ("r-knitr" ,r-knitr)))
9257 (home-page "https://fs.r-lib.org")
9258 (synopsis "Cross-platform file system operations based on libuv")
9260 "This package provides a cross-platform interface to file system
9261 operations, built on top of the libuv C library.")
9262 (license license:gpl3)))
9264 (define-public r-clisymbols
9266 (name "r-clisymbols")
9271 (uri (cran-uri "clisymbols" version))
9274 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9275 (build-system r-build-system)
9276 (home-page "https://github.com/gaborcsardi/clisymbols")
9277 (synopsis "Unicode symbols at the R prompt")
9279 "This package provides a small subset of Unicode symbols, that are useful
9280 when building command line applications. They fall back to alternatives on
9281 terminals that do not support Unicode.")
9282 (license license:expat)))
9284 (define-public r-usethis
9291 (uri (cran-uri "usethis" version))
9294 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9295 (build-system r-build-system)
9298 ("r-clipr" ,r-clipr)
9299 ("r-crayon" ,r-crayon)
9304 ("r-git2r" ,r-git2r)
9306 ("r-purrr" ,r-purrr)
9307 ("r-rematch2" ,r-rematch2)
9308 ("r-rlang" ,r-rlang)
9309 ("r-rprojroot" ,r-rprojroot)
9310 ("r-rstudioapi" ,r-rstudioapi)
9311 ("r-whisker" ,r-whisker)
9312 ("r-withr" ,r-withr)
9313 ("r-yaml" ,r-yaml)))
9314 (home-page "https://github.com/r-lib/usethis")
9315 (synopsis "Automate R package and project setup")
9317 "This package helps you to automate R package and project setup tasks
9318 that are otherwise performed manually. This includes setting up unit testing,
9319 test coverage, continuous integration, Git, GitHub integration, licenses,
9320 Rcpp, RStudio projects, and more.")
9321 (license license:gpl3)))
9323 (define-public r-sessioninfo
9325 (name "r-sessioninfo")
9330 (uri (cran-uri "sessioninfo" version))
9333 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9334 (build-system r-build-system)
9337 ("r-withr" ,r-withr)))
9338 (home-page "https://github.com/r-lib/sessioninfo#readme")
9339 (synopsis "R session information")
9341 "This package provides tools to query and print information about the
9342 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9343 more information about packages, and where they were installed from.")
9344 (license license:gpl2)))
9346 (define-public r-remotes
9353 (uri (cran-uri "remotes" version))
9356 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
9357 (build-system r-build-system)
9358 (home-page "https://github.com/r-lib/remotes#readme")
9359 (synopsis "R package installation from remote repositories")
9361 "Download and install R packages stored in GitHub, BitBucket, or plain
9362 subversion or git repositories. This package is a lightweight replacement of
9363 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9364 the code was copied over from @code{devtools}.")
9365 (license license:gpl2+)))
9367 (define-public r-xopen
9374 (uri (cran-uri "xopen" version))
9377 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9378 (build-system r-build-system)
9380 `(("r-processx" ,r-processx)))
9381 (home-page "https://github.com/r-lib/xopen#readme")
9382 (synopsis "Open system files, URLs, anything")
9384 "This package provides a cross-platform solution to open files,
9385 directories or URLs with their associated programs.")
9386 (license license:expat)))
9388 (define-public r-rcmdcheck
9390 (name "r-rcmdcheck")
9395 (uri (cran-uri "rcmdcheck" version))
9398 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9399 (build-system r-build-system)
9401 `(("r-callr" ,r-callr)
9403 ("r-crayon" ,r-crayon)
9405 ("r-digest" ,r-digest)
9406 ("r-pkgbuild" ,r-pkgbuild)
9407 ("r-prettyunits" ,r-prettyunits)
9409 ("r-rprojroot" ,r-rprojroot)
9410 ("r-sessioninfo" ,r-sessioninfo)
9411 ("r-withr" ,r-withr)
9412 ("r-xopen" ,r-xopen)))
9413 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9414 (synopsis "Run R CMD check from R and capture results")
9416 "Run @code{R CMD check} from R programmatically, and capture the results
9417 of the individual checks.")
9418 (license license:expat)))
9420 (define-public r-rapportools
9422 (name "r-rapportools")
9427 (uri (cran-uri "rapportools" version))
9430 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9431 (build-system r-build-system)
9433 `(("r-pander" ,r-pander)
9435 ("r-reshape" ,r-reshape)))
9436 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9437 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9439 "This package provides helper functions that act as wrappers to more
9440 advanced statistical methods with the advantage of having sane defaults for
9442 (license license:agpl3+)))
9444 (define-public r-pander
9451 (uri (cran-uri "pander" version))
9454 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9455 (build-system r-build-system)
9457 `(("r-digest" ,r-digest)
9458 ("r-rcpp" ,r-rcpp)))
9459 (home-page "https://rapporter.github.io/pander")
9460 (synopsis "Render R objects into Pandoc's markdown")
9462 "The main aim of the pander R package is to provide a minimal and easy
9463 tool for rendering R objects into Pandoc's markdown. The package is also
9464 capable of exporting/converting complex Pandoc documents (reports) in various
9466 ;; This package is licensed under either the AGPLv3+ or the very rarely
9468 (license license:agpl3+)))
9470 (define-public r-summarytools
9472 (name "r-summarytools")
9477 (uri (cran-uri "summarytools" version))
9480 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9481 (build-system r-build-system)
9483 `(("r-base64enc" ,r-base64enc)
9484 ("r-checkmate" ,r-checkmate)
9485 ("r-dplyr" ,r-dplyr)
9486 ("r-htmltools" ,r-htmltools)
9487 ("r-lubridate" ,r-lubridate)
9488 ("r-magick" ,r-magick)
9489 ("r-matrixstats" ,r-matrixstats)
9490 ("r-pander" ,r-pander)
9492 ("r-rapportools" ,r-rapportools)
9493 ("r-tibble" ,r-tibble)
9494 ("r-tidyr" ,r-tidyr)))
9495 (home-page "https://github.com/dcomtois/summarytools")
9496 (synopsis "Tools to quickly and neatly summarize data")
9498 "This package provides tools for data frame summaries, cross-tabulations,
9499 weight-enabled frequency tables and common univariate statistics in concise
9500 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9501 good point-of-entry for exploring data, both for experienced and new R
9503 (license license:gpl2)))
9505 (define-public r-lsei
9512 (uri (cran-uri "lsei" version))
9515 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9516 (build-system r-build-system)
9518 `(("gfortran" ,gfortran)))
9519 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9520 (synopsis "Solve regression problems under equality/inequality constraints")
9522 "It contains functions that solve least squares linear regression
9523 problems under linear equality/inequality constraints. Functions for solving
9524 quadratic programming problems are also available, which transform such
9525 problems into least squares ones first.")
9526 (license license:gpl2+)))
9528 (define-public r-npsurv
9535 (uri (cran-uri "npsurv" version))
9538 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9539 (build-system r-build-system)
9541 `(("r-lsei" ,r-lsei)))
9542 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9543 (synopsis "Nonparametric survival analysis")
9545 "This package contains functions for non-parametric survival analysis of
9546 exact and interval-censored observations.")
9547 (license license:gpl2+)))
9549 (define-public r-clusteval
9551 (name "r-clusteval")
9556 (uri (cran-uri "clusteval" version))
9559 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9560 (build-system r-build-system)
9562 `(("r-mvtnorm" ,r-mvtnorm)
9563 ("r-rcpp" ,r-rcpp)))
9564 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9565 (synopsis "Evaluation of clustering algorithms")
9567 "This R package provides a suite of tools to evaluate clustering
9568 algorithms, clusterings, and individual clusters.")
9569 (license license:expat)))
9571 (define-public r-tweedie
9578 (uri (cran-uri "tweedie" version))
9581 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9582 (build-system r-build-system)
9583 (native-inputs `(("gfortran" ,gfortran)))
9584 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9585 (synopsis "Evaluation of Tweedie exponential family models")
9587 "Maximum likelihood computations for Tweedie families, including the
9588 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9589 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9590 and related methods.")
9591 (license license:gpl2+)))
9593 (define-public r-rcppgsl
9600 (uri (cran-uri "RcppGSL" version))
9602 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9603 (properties `((upstream-name . "RcppGSL")))
9604 (build-system r-build-system)
9606 `(("r-rcpp" ,r-rcpp)
9608 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9609 (synopsis "Rcpp integration for GSL vectors and matrices")
9611 "The GNU Scientific Library (or GSL) is a collection of numerical
9612 routines for scientific computing. It is particularly useful for C and C++
9613 programs as it provides a standard C interface to a wide range of mathematical
9614 routines. There are over 1000 functions in total with an extensive test
9615 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9616 structures and R using concepts from Rcpp which is itself a package that eases
9617 the interfaces between R and C++.")
9618 (license license:gpl2+)))
9620 (define-public r-mvabund
9627 (uri (cran-uri "mvabund" version))
9630 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9631 (build-system r-build-system)
9633 `(("r-mass" ,r-mass)
9635 ("r-rcppgsl" ,r-rcppgsl)
9636 ("r-statmod" ,r-statmod)
9637 ("r-tweedie" ,r-tweedie)))
9638 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9639 (synopsis "Statistical methods for analysing multivariate abundance data")
9641 "This package provides a set of tools for displaying, modeling and
9642 analysing multivariate abundance data in community ecology.")
9643 (license license:lgpl2.1+)))
9645 (define-public r-afex
9652 (uri (cran-uri "afex" version))
9655 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9656 (build-system r-build-system)
9660 ("r-lmertest" ,r-lmertest)
9661 ("r-pbkrtest" ,r-pbkrtest)
9662 ("r-reshape2" ,r-reshape2)))
9664 `(("r-knitr" ,r-knitr)))
9665 (home-page "https://afex.singmann.science/")
9666 (synopsis "Analysis of factorial experiments")
9668 "This package provides convenience functions for analyzing factorial
9669 experiments using ANOVA or mixed models.")
9670 (license license:gpl2+)))
9672 (define-public r-lmertest
9679 (uri (cran-uri "lmerTest" version))
9682 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9683 (properties `((upstream-name . "lmerTest")))
9684 (build-system r-build-system)
9686 `(("r-ggplot2" ,r-ggplot2)
9689 ("r-numderiv" ,r-numderiv)))
9690 (home-page "https://github.com/runehaubo/lmerTestR")
9691 (synopsis "Tests in linear mixed effects models")
9693 "This package provides p-values in type I, II or III anova and summary
9694 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9695 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9696 package. Model selection methods include step, drop1 and anova-like tables
9697 for random effects (ranova). Methods for Least-Square means (LS-means) and
9698 tests of linear contrasts of fixed effects are also available.")
9699 (license license:gpl2+)))
9701 (define-public r-r2glmm
9708 (uri (cran-uri "r2glmm" version))
9711 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9712 (build-system r-build-system)
9714 `(("r-afex" ,r-afex)
9715 ("r-data-table" ,r-data-table)
9716 ("r-dplyr" ,r-dplyr)
9717 ("r-ggplot2" ,r-ggplot2)
9718 ("r-gridextra" ,r-gridextra)
9719 ("r-lmertest" ,r-lmertest)
9721 ("r-matrix" ,r-matrix)
9723 ("r-pbkrtest" ,r-pbkrtest)))
9724 (home-page "https://github.com/bcjaeger/r2glmm")
9725 (synopsis "Compute R squared for mixed (multilevel) models")
9727 "This package computes model and semi partial R squared with confidence
9728 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9729 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9730 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9732 (license license:gpl2)))
9734 (define-public r-weights
9741 (uri (cran-uri "weights" version))
9744 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9745 (build-system r-build-system)
9747 `(("r-gdata" ,r-gdata)
9748 ("r-hmisc" ,r-hmisc)
9749 ("r-mice" ,r-mice)))
9751 "https://cran.r-project.org/web/packages/weights/")
9752 (synopsis "Weighting and weighted statistics")
9753 (description "This package Provides a variety of functions for producing
9754 simple weighted statistics, such as weighted Pearson's correlations, partial
9755 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9756 includes some software for quickly recoding survey data and plotting point
9757 estimates from interaction terms in regressions (and multiply imputed
9758 regressions). NOTE: Weighted partial correlation calculations pulled to
9760 (license license:gpl2+)))
9762 (define-public r-rcppannoy
9764 (name "r-rcppannoy")
9769 (uri (cran-uri "RcppAnnoy" version))
9772 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9773 (properties `((upstream-name . "RcppAnnoy")))
9774 (build-system r-build-system)
9776 `(("r-rcpp" ,r-rcpp)))
9777 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9778 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9780 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9781 for efficient memory usage as well an ability to load from and save to disk.
9782 This package provides an R interface.")
9783 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9785 (license (list license:gpl2+ license:asl2.0))))
9787 (define-public r-rcpphnsw
9794 (uri (cran-uri "RcppHNSW" version))
9797 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9798 (properties `((upstream-name . "RcppHNSW")))
9799 (build-system r-build-system)
9800 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9801 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9802 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9804 "Hnswlib is a C++ library for approximate nearest neighbors. This
9805 package provides a minimal R interface by relying on the Rcpp package.")
9806 ;; hnswlib is released under Version 2.0 of the Apache License.
9807 (license (list license:gpl3 license:asl2.0))))
9809 (define-public r-rcppparallel
9811 (name "r-rcppparallel")
9816 (uri (cran-uri "RcppParallel" version))
9819 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
9820 (properties `((upstream-name . "RcppParallel")))
9821 (build-system r-build-system)
9822 (home-page "https://rcppcore.github.io/RcppParallel/")
9823 (synopsis "Parallel programming tools for Rcpp")
9825 "This package provides high level functions for parallel programming with
9826 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9827 the work of a standard serial @code{for} loop into a parallel one and the
9828 @code{parallelReduce()} function can be used for accumulating aggregates or
9830 (license license:gpl2)))
9832 (define-public r-ncdf4
9839 (uri (cran-uri "ncdf4" version))
9842 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9843 (build-system r-build-system)
9845 `(("netcdf" ,netcdf)
9847 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9848 (synopsis "R interface to Unidata netCDF format data files")
9850 "This package provides a high-level R interface to data files written
9851 using Unidata's netCDF library (version 4 or earlier), which are binary data
9852 files that are portable across platforms and include metadata information in
9853 addition to the data sets. Using this package, netCDF files can be opened and
9854 data sets read in easily. It is also easy to create new netCDF dimensions,
9855 variables, and files, in either version 3 or 4 format, and manipulate existing
9857 (license license:gpl3+)))
9859 (define-public r-biocmanager
9861 (name "r-biocmanager")
9866 (uri (cran-uri "BiocManager" version))
9868 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9869 (properties `((upstream-name . "BiocManager")))
9870 (build-system r-build-system)
9871 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9872 (synopsis "Access the Bioconductor project package repository")
9874 "This package provides a convenient tool to install and update
9875 Bioconductor packages.")
9876 (license license:artistic2.0)))
9878 (define-public r-rgl
9881 (version "0.100.54")
9885 (uri (cran-uri "rgl" version))
9888 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9889 (build-system r-build-system)
9891 `(("pkg-config" ,pkg-config)))
9893 `(("freetype" ,freetype)
9897 ("ghc-pandoc" ,ghc-pandoc)
9900 `(("r-crosstalk" ,r-crosstalk)
9901 ("r-htmltools" ,r-htmltools)
9902 ("r-htmlwidgets" ,r-htmlwidgets)
9903 ("r-jsonlite" ,r-jsonlite)
9904 ("r-knitr" ,r-knitr)
9905 ("r-magrittr" ,r-magrittr)
9906 ("r-manipulatewidget" ,r-manipulatewidget)
9907 ("r-shiny" ,r-shiny)))
9908 (home-page "https://r-forge.r-project.org/projects/rgl/")
9909 (synopsis "3D visualization using OpenGL")
9911 "This package provides medium to high level functions for 3D interactive graphics,
9912 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9913 as functions for constructing representations of geometric
9914 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9915 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9916 image formats, including PNG, Postscript, SVG, PGF.")
9917 ;; Any version of the GPL.
9918 (license (list license:gpl2+ license:gpl3+))))
9920 (define-public r-multicool
9922 (name "r-multicool")
9927 (uri (cran-uri "multicool" version))
9930 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9931 (build-system r-build-system)
9932 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9933 (home-page "https://cran.r-project.org/web/packages/multicool/")
9934 (synopsis "Permutations of multisets in cool-lex order")
9936 "This package provides a set of tools to permute multisets without loops
9937 or hash tables and to generate integer partitions. Cool-lex order is similar
9938 to colexicographical order.")
9939 (license license:gpl2)))
9941 (define-public r-misc3d
9948 (uri (cran-uri "misc3d" version))
9951 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9952 (build-system r-build-system)
9953 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9954 (synopsis "Miscellaneous 3D Plots")
9956 "This package provides a collection of miscellaneous 3d plots, including
9958 ;; Any version of the GPL.
9959 (license (list license:gpl2+ license:gpl3+))))
9968 (uri (cran-uri "ks" version))
9970 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9971 (build-system r-build-system)
9974 ("r-kernlab" ,r-kernlab)
9975 ("r-kernsmooth" ,r-kernsmooth)
9976 ("r-matrix" ,r-matrix)
9977 ("r-mclust" ,r-mclust)
9979 ("r-multicool" ,r-multicool)
9980 ("r-mvtnorm" ,r-mvtnorm)))
9981 (home-page "http://www.mvstat.net/tduong/")
9982 (synopsis "Kernel smoothing")
9984 "This package provides kernel smoothers for univariate and multivariate
9985 data, including density functions, density derivatives, cumulative
9986 distributions, modal clustering, discriminant analysis, and two-sample
9987 hypothesis testing.")
9988 ;; Either version of the GPL.
9989 (license (list license:gpl2 license:gpl3))))
9991 (define-public r-feature
9998 (uri (cran-uri "feature" version))
10001 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
10002 (build-system r-build-system)
10005 ("r-misc3d" ,r-misc3d)
10007 (home-page "http://www.mvstat.net/tduong/")
10008 (synopsis "Inferential feature significance for kernel density estimation")
10010 "The feature package contains functions to display and compute kernel
10011 density estimates, significant gradient and significant curvature regions.
10012 Significant gradient and/or curvature regions often correspond to significant
10013 features (e.g. local modes).")
10014 ;; Either version of the GPL.
10015 (license (list license:gpl2 license:gpl3))))
10017 (define-public r-arm
10024 (uri (cran-uri "arm" version))
10027 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
10028 (build-system r-build-system)
10030 `(("r-abind" ,r-abind)
10034 ("r-matrix" ,r-matrix)
10035 ("r-nlme" ,r-nlme)))
10036 (home-page "https://cran.r-project.org/web/packages/arm/")
10037 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10039 "This package provides functions to accompany A. Gelman and J. Hill,
10040 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10041 University Press, 2007.")
10042 (license license:gpl3+)))
10044 (define-public r-circular
10046 (name "r-circular")
10051 (uri (cran-uri "circular" version))
10054 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10055 (build-system r-build-system)
10057 `(("r-boot" ,r-boot)
10058 ("r-mvtnorm" ,r-mvtnorm)))
10060 `(("gfortran" ,gfortran)))
10061 (home-page "https://cran.r-project.org/web/packages/circular/")
10062 (synopsis "Circular statistics")
10064 "This package provides tools for circular statistics, from \"Topics in
10065 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10067 (license license:gpl2+)))
10069 (define-public r-activity
10071 (name "r-activity")
10076 (uri (cran-uri "activity" version))
10079 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10080 (build-system r-build-system)
10082 `(("r-circular" ,r-circular)
10083 ("r-insol" ,r-insol)
10084 ("r-pbapply" ,r-pbapply)))
10085 (home-page "https://cran.r-project.org/web/packages/activity/")
10086 (synopsis "Animal activity statistics")
10088 "This package provides functions to fit kernel density functions to
10089 animal activity time data; plot activity distributions; quantify overall
10090 levels of activity; statistically compare activity metrics through
10091 bootstrapping; and evaluate variation in linear variables with time (or other
10092 circular variables).")
10093 (license license:gpl3)))
10095 (define-public r-ouch
10102 (uri (cran-uri "ouch" version))
10105 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10106 (build-system r-build-system)
10107 (propagated-inputs `(("r-subplex" ,r-subplex)))
10108 (home-page "https://kingaa.github.io/ouch/")
10109 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10111 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10112 for evolution along a phylogenetic tree.")
10113 (license license:gpl2+)))
10115 (define-public r-fmsb
10122 (uri (cran-uri "fmsb" version))
10125 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10126 (build-system r-build-system)
10127 (home-page "http://minato.sip21c.org/msb/")
10128 (synopsis "Functions for medical statistics book with demographic data")
10130 "This package provides several utility functions for the book entitled
10131 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10132 Japan, 2007) with Japanese demographic data and some demographic analysis
10133 related functions.")
10134 (license license:gpl2+)))
10136 (define-public r-stabledist
10138 (name "r-stabledist")
10143 (uri (cran-uri "stabledist" version))
10146 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10147 (build-system r-build-system)
10148 (home-page "https://www.rmetrics.org")
10149 (synopsis "Stable distribution functions")
10151 "This package provides density, probability and quantile functions, and
10152 random number generation for (skew) stable distributions, using the
10153 parametrizations of Nolan.")
10154 (license license:gpl2+)))
10156 (define-public r-gsl
10163 (uri (cran-uri "gsl" version))
10166 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10167 (build-system r-build-system)
10170 (home-page "https://cran.r-project.org/web/packages/gsl")
10171 (synopsis "Wrapper for the GNU Scientific Library")
10173 "This package provides an R wrapper for the special functions and quasi
10174 random number generators of the GNU Scientific Library.")
10175 (license license:gpl2+)))
10177 (define-public r-adgoftest
10179 (name "r-adgoftest")
10184 (uri (cran-uri "ADGofTest" version))
10187 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10188 (properties `((upstream-name . "ADGofTest")))
10189 (build-system r-build-system)
10190 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10191 (synopsis "Anderson-Darling GoF test")
10193 "This package provides an implementation of the Anderson-Darling GoF test
10194 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10195 Anderson-Darling Distribution\".")
10196 ;; Any version of the GPL.
10197 (license license:gpl3+)))
10199 (define-public r-softimpute
10201 (name "r-softimpute")
10206 (uri (cran-uri "softImpute" version))
10209 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10210 (properties `((upstream-name . "softImpute")))
10211 (build-system r-build-system)
10213 `(("r-matrix" ,r-matrix)))
10215 `(("gfortran" ,gfortran)))
10216 (home-page "https://cran.r-project.org/web/packages/softImpute")
10217 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10219 "This package provides iterative methods for matrix completion that use
10220 nuclear-norm regularization. The package includes procedures for centering
10221 and scaling rows, columns or both, and for computing low-rank @dfn{single
10222 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10224 (license license:gpl2)))
10226 (define-public r-fftwtools
10228 (name "r-fftwtools")
10233 (uri (cran-uri "fftwtools" version))
10236 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10237 (build-system r-build-system)
10238 (inputs `(("fftw" ,fftw)))
10239 (home-page "https://github.com/krahim/fftwtools")
10240 (synopsis "Wrapper for FFTW3")
10242 "This package provides a wrapper for several FFTW functions. It provides
10243 access to the two-dimensional FFT, the multivariate FFT, and the
10244 one-dimensional real to complex FFT using the FFTW3 library. The package
10245 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10246 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10247 The FFT functions have a parameter that allows them to not return the
10248 redundant complex conjugate when the input is real data.")
10249 (license license:gpl2+)))
10251 (define-public r-tiff
10258 (uri (cran-uri "tiff" version))
10261 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10262 (build-system r-build-system)
10264 `(("libtiff" ,libtiff)
10265 ("libjpeg" ,libjpeg-turbo)
10267 (home-page "https://www.rforge.net/tiff/")
10268 (synopsis "Read and write TIFF images")
10270 "This package provides an easy and simple way to read, write and display
10271 bitmap images stored in the TIFF format. It can read and write both files and
10272 in-memory raw vectors.")
10273 ;; Either of these two license versions.
10274 (license (list license:gpl2 license:gpl3))))
10276 (define-public r-nlp
10283 (uri (cran-uri "NLP" version))
10286 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10287 (properties `((upstream-name . "NLP")))
10288 (build-system r-build-system)
10289 (home-page "https://cran.r-project.org/web/packages/NLP/")
10290 (synopsis "Natural language processing infrastructure")
10292 "This package provides basic classes and methods for Natural Language
10294 (license license:gpl3)))
10296 (define-public r-tm
10303 (uri (cran-uri "tm" version))
10306 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10307 (properties `((upstream-name . "tm")))
10308 (build-system r-build-system)
10314 ("r-xml2" ,r-xml2)))
10315 (home-page "http://tm.r-forge.r-project.org/")
10316 (synopsis "Text mining package")
10318 "This package provides a framework for text mining applications within R.")
10319 (license license:gpl3)))
10321 (define-public r-waveslim
10323 (name "r-waveslim")
10328 (uri (cran-uri "waveslim" version))
10331 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10332 (build-system r-build-system)
10334 `(("gfortran" ,gfortran)))
10335 (home-page "http://waveslim.blogspot.com")
10336 (synopsis "Basic wavelet routines for signal processing")
10338 "This package provides basic wavelet routines for time series (1D),
10339 image (2D) and array (3D) analysis. The code provided here is based on
10340 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10341 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10342 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10343 pairs (Selesnick 2001, 2002).")
10344 (license license:bsd-3)))
10346 (define-public r-wordcloud
10348 (name "r-wordcloud")
10353 (uri (cran-uri "wordcloud" version))
10356 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10357 (build-system r-build-system)
10359 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10361 ;; The "tm" package is only "suggested" according to CRAN, but the
10362 ;; wordcloud package cannot be loaded without it.
10364 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10365 (synopsis "Word clouds")
10367 "This package provides functionality to create pretty word clouds,
10368 visualize differences and similarity between documents, and avoid
10369 over-plotting in scatter plots with text.")
10370 (license license:lgpl2.1)))
10372 (define-public r-colorramps
10374 (name "r-colorramps")
10379 (uri (cran-uri "colorRamps" version))
10382 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10383 (properties `((upstream-name . "colorRamps")))
10384 (build-system r-build-system)
10385 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10386 (synopsis "Build color tables")
10387 (description "This package provides features to build gradient color
10389 ;; Any version of the GPL
10390 (license license:gpl3+)))
10392 (define-public r-tidytree
10394 (name "r-tidytree")
10399 (uri (cran-uri "tidytree" version))
10401 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10402 (build-system r-build-system)
10405 ("r-dplyr" ,r-dplyr)
10406 ("r-lazyeval" ,r-lazyeval)
10407 ("r-magrittr" ,r-magrittr)
10408 ("r-rlang" ,r-rlang)
10409 ("r-tibble" ,r-tibble)))
10411 `(("r-knitr" ,r-knitr)))
10412 (home-page "https://github.com/GuangchuangYu/tidytree")
10413 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10415 "Phylogenetic trees generally contain multiple components including nodes,
10416 edges, branches and associated data. This package provides an approach to
10417 convert tree objects to tidy data frames. It also provides tidy interfaces to
10418 manipulate tree data.")
10419 (license license:artistic2.0)))
10421 (define-public r-rvcheck
10428 (uri (cran-uri "rvcheck" version))
10430 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10431 (build-system r-build-system)
10433 `(("r-biocmanager" ,r-biocmanager)
10434 ("r-rlang" ,r-rlang)))
10435 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10436 (synopsis "R package version check")
10438 "This package provides tools to check the latest release version of R and
10439 R packages (on CRAN, Bioconductor or Github).")
10440 (license license:artistic2.0)))
10442 (define-public r-docopt
10449 (uri (cran-uri "docopt" version))
10452 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10453 (build-system r-build-system)
10454 (home-page "https://github.com/docopt/docopt.R")
10455 (synopsis "Command-line interface specification language")
10457 "This package enables you to define a command-line interface by just
10458 giving it a description in the specific format.")
10459 (license license:expat)))
10461 (define-public r-sparsesvd
10463 (name "r-sparsesvd")
10468 (uri (cran-uri "sparsesvd" version))
10471 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10472 (build-system r-build-system)
10473 (propagated-inputs `(("r-matrix" ,r-matrix)))
10474 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10475 (synopsis "Sparse truncated singular value decomposition")
10477 "This package provides a Wrapper around the SVDLIBC library
10478 for (truncated) singular value decomposition of a sparse matrix. Currently,
10479 only sparse real matrices in Matrix package format are supported.")
10480 ;; SVDLIBC is released under BSD-2. The R interface is released under
10482 (license (list license:bsd-3 license:bsd-2))))
10484 (define-public r-speedglm
10486 (name "r-speedglm")
10491 (uri (cran-uri "speedglm" version))
10494 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10495 (build-system r-build-system)
10497 `(("r-mass" ,r-mass)
10498 ("r-matrix" ,r-matrix)))
10499 (home-page "https://cran.r-project.org/web/packages/speedglm")
10500 (synopsis "Fit linear and generalized linear models to large data sets")
10502 "This package provides tools for fitting linear models and generalized
10503 linear models to large data sets by updating algorithms.")
10504 ;; Any version of the GPL
10505 (license license:gpl2+)))
10507 (define-public r-densityclust
10509 (name "r-densityclust")
10514 (uri (cran-uri "densityClust" version))
10517 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10518 (properties `((upstream-name . "densityClust")))
10519 (build-system r-build-system)
10522 ("r-ggplot2" ,r-ggplot2)
10523 ("r-ggrepel" ,r-ggrepel)
10524 ("r-gridextra" ,r-gridextra)
10525 ("r-rcolorbrewer" ,r-rcolorbrewer)
10527 ("r-rtsne" ,r-rtsne)))
10528 (home-page "https://cran.r-project.org/web/packages/densityClust")
10529 (synopsis "Clustering by fast search and find of density peaks")
10531 "This package provides an improved implementation (based on k-nearest
10532 neighbors) of the density peak clustering algorithm, originally described by
10533 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10534 large datasets (> 100,000 samples) very efficiently.")
10535 (license license:gpl2+)))
10537 (define-public r-combinat
10539 (name "r-combinat")
10544 (uri (cran-uri "combinat" version))
10547 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10548 (build-system r-build-system)
10549 (home-page "https://cran.r-project.org/web/packages/combinat")
10550 (synopsis "Combinatorics utilities")
10551 (description "This package provides assorted routines for combinatorics.")
10552 (license license:gpl2)))
10554 (define-public r-qlcmatrix
10556 (name "r-qlcmatrix")
10561 (uri (cran-uri "qlcMatrix" version))
10564 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10565 (properties `((upstream-name . "qlcMatrix")))
10566 (build-system r-build-system)
10568 `(("r-docopt" ,r-docopt)
10569 ("r-matrix" ,r-matrix)
10571 ("r-sparsesvd" ,r-sparsesvd)))
10572 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10573 (synopsis "Sparse matrix functions for quantitative language comparison")
10575 "This package provides an extension of the functionality of the Matrix
10576 package for using sparse matrices. Some of the functions are very general,
10577 while other are highly specific for the special data format used for
10578 @dfn{quantitative language comparison} (QLC).")
10579 (license license:gpl3)))
10581 (define-public r-ddrtree
10588 (uri (cran-uri "DDRTree" version))
10591 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10592 (properties `((upstream-name . "DDRTree")))
10593 (build-system r-build-system)
10596 ("r-irlba" ,r-irlba)
10598 ("r-rcppeigen" ,r-rcppeigen)))
10599 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10600 (synopsis "Learning principal graphs with DDRTree")
10602 "This package provides an implementation of the framework of
10603 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10604 dimensional space while constructs a principal tree which passes through the
10605 middle of the data simultaneously. DDRTree shows superiority to
10606 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10607 intrinsic structure of single cell genomics data. In general, it could be
10608 used to reconstruct the temporal progression as well as the bifurcation
10609 structure of any data type.")
10610 (license license:asl2.0)))
10612 (define-public r-corpcor
10619 (uri (cran-uri "corpcor" version))
10622 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10623 (build-system r-build-system)
10624 (home-page "http://strimmerlab.org/software/corpcor/")
10625 (synopsis "Efficient estimation of covariance and (partial) correlation")
10627 "This package implements a James-Stein-type shrinkage estimator for the
10628 covariance matrix, with separate shrinkage for variances and correlations.
10629 Furthermore, functions are available for fast singular value decomposition,
10630 for computing the pseudoinverse, and for checking the rank and positive
10631 definiteness of a matrix.")
10632 (license license:gpl3+)))
10634 (define-public r-rspectra
10636 (name "r-rspectra")
10641 (uri (cran-uri "RSpectra" version))
10644 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10645 (properties `((upstream-name . "RSpectra")))
10646 (build-system r-build-system)
10648 `(("r-matrix" ,r-matrix)
10650 ("r-rcppeigen" ,r-rcppeigen)))
10651 (home-page "https://github.com/yixuan/RSpectra")
10652 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10654 "This package provides an R interface to the Spectra library for
10655 large-scale eigenvalue and SVD problems. It is typically used to compute a
10656 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10657 which is usually more efficient than @code{eigen()} if k << n.")
10659 (license license:mpl2.0)))
10661 (define-public r-vbsr
10668 (uri (cran-uri "vbsr" version))
10671 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10672 (build-system r-build-system)
10673 (home-page "https://cran.r-project.org/web/packages/vbsr")
10674 (synopsis "Variational Bayes spike regression regularized linear models")
10676 "This package provides an efficient algorithm for solving ultra-sparse
10677 regularized regression models using a variational Bayes algorithm with a spike
10678 prior. The algorithm is solved on a path, with coordinate updates, and is
10679 capable of generating very sparse models. Very general model
10680 diagnostics for controlling type-1 errors are also provided.")
10681 (license license:gpl2)))
10683 (define-public r-flare
10686 (version "1.6.0.2")
10690 (uri (cran-uri "flare" version))
10693 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10694 (build-system r-build-system)
10696 `(("r-igraph" ,r-igraph)
10697 ("r-lattice" ,r-lattice)
10699 ("r-matrix" ,r-matrix)))
10700 (home-page "https://cran.r-project.org/web/packages/flare")
10701 (synopsis "Family of Lasso regression implementations")
10703 "This package provides implementations of a family of Lasso variants
10704 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10705 high dimensional sparse linear models.")
10706 (license license:gpl2)))
10708 (define-public r-lassopv
10715 (uri (cran-uri "lassopv" version))
10718 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10719 (build-system r-build-system)
10720 (propagated-inputs `(("r-lars" ,r-lars)))
10721 (home-page "https://github.com/lingfeiwang/lassopv")
10722 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10724 "This package enables you to estimate the p-values for predictors x
10725 against target variable y in Lasso regression, using the regularization
10726 strength when each predictor enters the active set of regularization path for
10727 the first time as the statistic.")
10728 (license license:gpl3)))
10730 (define-public r-splitstackshape
10732 (name "r-splitstackshape")
10737 (uri (cran-uri "splitstackshape" version))
10740 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10741 (build-system r-build-system)
10743 `(("r-data-table" ,r-data-table)))
10744 (home-page "https://github.com/mrdwab/splitstackshape")
10745 (synopsis "Stack and reshape datasets after splitting concatenated values")
10747 "Online data collection tools like Google Forms often export
10748 multiple-response questions with data concatenated in cells. The
10749 @code{concat.split} (cSplit) family of functions provided by this package
10750 splits such data into separate cells. This package also includes functions to
10751 stack groups of columns and to reshape wide data, even when the data are
10752 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10753 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10755 (license license:gpl3)))
10757 (define-public r-tfmpvalue
10759 (name "r-tfmpvalue")
10764 (uri (cran-uri "TFMPvalue" version))
10767 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10768 (properties `((upstream-name . "TFMPvalue")))
10769 (build-system r-build-system)
10770 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10771 (home-page "https://github.com/ge11232002/TFMPvalue")
10772 (synopsis "P-value computation for position weight matrices")
10774 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10775 identification from sequence/alignments, we are interested in the significance
10776 of certain match scores. TFMPvalue provides the accurate calculation of a
10777 p-value with a score threshold for position weight matrices, or the score with
10778 a given p-value. It is an interface to code originally made available by
10779 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10780 Touzet and Varre (2007).")
10781 (license license:gpl2)))
10783 (define-public r-rnifti
10790 (uri (cran-uri "RNifti" version))
10793 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10794 (properties `((upstream-name . "RNifti")))
10795 (build-system r-build-system)
10796 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10797 (home-page "https://github.com/jonclayden/RNifti")
10798 (synopsis "Fast R and C++ access to NIfTI images")
10800 "This package provides very fast read and write access to images stored
10801 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10802 compiled C and interpreted R code. It also provides a C/C++ API that can be
10803 used by other packages.")
10804 (license license:gpl2)))
10806 (define-public r-shades
10813 (uri (cran-uri "shades" version))
10816 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10817 (build-system r-build-system)
10818 (home-page "https://github.com/jonclayden/shades")
10819 (synopsis "Simple color manipulation")
10821 "This package provides functions for easily manipulating colors,
10822 creating color scales and calculating color distances.")
10823 (license license:bsd-3)))
10825 (define-public r-ore
10832 (uri (cran-uri "ore" version))
10834 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10835 (build-system r-build-system)
10836 (home-page "https://github.com/jonclayden/ore")
10837 (synopsis "R interface to the Onigmo regular expression library")
10839 "This package provides an alternative to R's built-in functionality for
10840 handling regular expressions, based on the Onigmo library. It offers
10841 first-class compiled regex objects, partial matching and function-based
10842 substitutions, amongst other features.")
10843 (license license:bsd-3)))
10845 (define-public r-reportr
10852 (uri (cran-uri "reportr" version))
10855 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10856 (build-system r-build-system)
10857 (propagated-inputs `(("r-ore" ,r-ore)))
10858 (home-page "https://github.com/jonclayden/reportr")
10859 (synopsis "General message and error reporting system")
10861 "This package provides a system for reporting messages, which offers
10862 certain useful features over the standard R system, such as the incorporation
10863 of output consolidation, message filtering, assertions, expression
10864 substitution, automatic generation of stack traces for debugging, and
10865 conditional reporting based on the current \"output level\".")
10866 (license license:gpl2)))
10868 (define-public r-tractor-base
10870 (name "r-tractor-base")
10875 (uri (cran-uri "tractor.base" version))
10878 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10879 (properties `((upstream-name . "tractor.base")))
10880 (build-system r-build-system)
10883 ("r-reportr" ,r-reportr)
10884 ("r-rnifti" ,r-rnifti)
10885 ("r-shades" ,r-shades)))
10886 (home-page "https://www.tractor-mri.org.uk")
10887 (synopsis "Read, manipulate and visualize magnetic resonance images")
10889 "This package provides functions for working with magnetic resonance
10890 images. It supports reading and writing of popular file formats (DICOM,
10891 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10892 visualization; flexible image manipulation; metadata and sparse image
10894 (license license:gpl2)))
10896 (define-public r-grimport
10898 (name "r-grimport")
10903 (uri (cran-uri "grImport" version))
10906 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10907 (properties `((upstream-name . "grImport")))
10908 (build-system r-build-system)
10910 `(("ghostscript" ,ghostscript)))
10912 `(("r-xml" ,r-xml)))
10913 (home-page "https://cran.r-project.org/web/packages/grImport")
10914 (synopsis "Convert, import, and draw PostScript pictures")
10916 "This package provides functions for converting, importing, and drawing
10917 PostScript pictures in R plots.")
10918 (license license:gpl2+)))
10920 (define-public r-grimport2
10922 (name "r-grimport2")
10927 (uri (cran-uri "grImport2" version))
10930 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10931 (properties `((upstream-name . "grImport2")))
10932 (build-system r-build-system)
10934 `(("r-base64enc" ,r-base64enc)
10938 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10939 (synopsis "Import SVG graphics")
10941 "This package provides functions for importing external vector images and
10942 drawing them as part of R plots. This package is different from the
10943 @code{grImport} package because, where that package imports PostScript format
10944 images, this package imports SVG format images. Furthermore, this package
10945 imports a specific subset of SVG, so external images must be preprocessed
10946 using a package like @code{rsvg} to produce SVG that this package can import.
10947 SVG features that are not supported by R graphics, such as gradient fills, can
10948 be imported and then exported via the @code{gridSVG} package.")
10949 (license license:gpl2+)))
10951 (define-public r-kohonen
10958 (uri (cran-uri "kohonen" version))
10961 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10962 (build-system r-build-system)
10964 `(("r-rcpp" ,r-rcpp)))
10965 (home-page "https://cran.r-project.org/web/packages/kohonen")
10966 (synopsis "Supervised and unsupervised self-organising maps")
10968 "This package provides functions to train @dfn{self-organising
10969 maps} (SOMs). Also interrogation of the maps and prediction using trained
10970 maps are supported. The name of the package refers to Teuvo Kohonen, the
10971 inventor of the SOM.")
10972 (license license:gpl2+)))
10974 (define-public r-nnls
10981 (uri (cran-uri "nnls" version))
10984 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10985 (build-system r-build-system)
10986 (native-inputs `(("gfortran" ,gfortran)))
10987 (home-page "https://cran.r-project.org/web/packages/nnls")
10988 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10990 "This package provides an R interface to the Lawson-Hanson implementation
10991 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10992 the combination of non-negative and non-positive constraints.")
10993 (license license:gpl2+)))
10995 (define-public r-iso
10998 (version "0.0-18.1")
11002 (uri (cran-uri "Iso" version))
11005 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
11006 (properties `((upstream-name . "Iso")))
11007 (build-system r-build-system)
11008 (native-inputs `(("gfortran" ,gfortran)))
11009 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
11010 (synopsis "Functions to perform isotonic regression")
11012 "This package provides support for linear order and unimodal
11013 order (univariate) isotonic regression and bivariate isotonic regression with
11014 linear order on both variables.")
11015 (license license:gpl2+)))
11017 (define-public r-chemometricswithr
11019 (name "r-chemometricswithr")
11024 (uri (cran-uri "ChemometricsWithR" version))
11027 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
11029 `((upstream-name . "ChemometricsWithR")))
11030 (build-system r-build-system)
11032 `(("r-devtools" ,r-devtools)
11033 ("r-kohonen" ,r-kohonen)
11036 (home-page "https://github.com/rwehrens/CWR")
11037 (synopsis "Chemometrics with R")
11039 "This package provides functions and scripts used in the book
11040 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11041 Life Sciences\" by Ron Wehrens, Springer (2011).")
11042 (license license:gpl2+)))
11044 (define-public r-als
11051 (uri (cran-uri "ALS" version))
11054 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11055 (properties `((upstream-name . "ALS")))
11056 (build-system r-build-system)
11059 ("r-nnls" ,r-nnls)))
11060 (home-page "https://cran.r-project.org/web/packages/ALS")
11061 (synopsis "Multivariate curve resolution alternating least squares")
11063 "Alternating least squares is often used to resolve components
11064 contributing to data with a bilinear structure; the basic technique may be
11065 extended to alternating constrained least squares. This package provides an
11066 implementation of @dfn{multivariate curve resolution alternating least
11067 squares} (MCR-ALS).
11069 Commonly applied constraints include unimodality, non-negativity, and
11070 normalization of components. Several data matrices may be decomposed
11071 simultaneously by assuming that one of the two matrices in the bilinear
11072 decomposition is shared between datasets.")
11073 (license license:gpl2+)))
11075 (define-public r-strucchange
11077 (name "r-strucchange")
11082 (uri (cran-uri "strucchange" version))
11085 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11086 (build-system r-build-system)
11088 `(("r-sandwich" ,r-sandwich)
11090 (home-page "https://cran.r-project.org/web/packages/strucchange")
11091 (synopsis "Testing, monitoring, and dating structural changes")
11093 "This package provides tools for testing, monitoring and dating
11094 structural changes in (linear) regression models. It features tests/methods
11095 from the generalized fluctuation test framework as well as from the F
11096 test (Chow test) framework. This includes methods to fit, plot and test
11097 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11098 statistics, respectively. It is possible to monitor incoming data online
11099 using fluctuation processes. Finally, the breakpoints in regression models
11100 with structural changes can be estimated together with confidence intervals.
11101 Emphasis is always given to methods for visualizing the data.")
11102 ;; Either of these two GPL versions
11103 (license (list license:gpl2 license:gpl3))))
11105 (define-public r-pixmap
11112 (uri (cran-uri "pixmap" version))
11115 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11116 (build-system r-build-system)
11117 (home-page "https://cran.r-project.org/web/packages/pixmap")
11118 (synopsis "Tools for bitmap images")
11120 "This package provides functions for importing, exporting, plotting and
11121 other manipulations of bitmapped images.")
11122 (license license:gpl2)))
11124 (define-public r-rapidjsonr
11126 (name "r-rapidjsonr")
11131 (uri (cran-uri "rapidjsonr" version))
11134 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11135 (build-system r-build-system)
11136 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11137 (synopsis "JSON parser")
11139 "This package provides JSON parsing capability through the Rapidjson
11141 (license license:expat)))
11143 (define-public r-ontologyindex
11145 (name "r-ontologyindex")
11150 (uri (cran-uri "ontologyIndex" version))
11153 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11154 (properties `((upstream-name . "ontologyIndex")))
11155 (build-system r-build-system)
11156 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11157 (synopsis "Functions for processing ontologies in R")
11159 "This package provides functions for reading ontologies into R as lists
11160 and manipulating sets of ontological terms.")
11161 (license license:gpl2+)))
11163 (define-public r-gargle
11170 (uri (cran-uri "gargle" version))
11173 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11174 (build-system r-build-system)
11179 ("r-jsonlite" ,r-jsonlite)
11180 ("r-rlang" ,r-rlang)
11181 ("r-withr" ,r-withr)))
11183 `(("r-knitr" ,r-knitr)))
11184 (home-page "https://gargle.r-lib.org")
11185 (synopsis "Utilities for working with Google APIs")
11187 "This package provides utilities for working with Google APIs. This
11188 includes functions and classes for handling common credential types and for
11189 preparing, executing, and processing HTTP requests.")
11190 (license license:expat)))
11192 (define-public r-bigrquery
11194 (name "r-bigrquery")
11199 (uri (cran-uri "bigrquery" version))
11202 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11203 (build-system r-build-system)
11205 `(("r-assertthat" ,r-assertthat)
11206 ("r-bit64" ,r-bit64)
11209 ("r-gargle" ,r-gargle)
11212 ("r-jsonlite" ,r-jsonlite)
11213 ("r-prettyunits" ,r-prettyunits)
11214 ("r-progress" ,r-progress)
11215 ("r-rapidjsonr" ,r-rapidjsonr)
11217 ("r-rlang" ,r-rlang)
11218 ("r-tibble" ,r-tibble)))
11219 (home-page "https://github.com/rstats-db/bigrquery")
11220 (synopsis "R interface to Google's BigQuery API")
11222 "This package provides an R interface to Google's BigQuery database.")
11223 (license license:gpl3)))
11225 (define-public r-gmp
11232 (uri (cran-uri "gmp" version))
11235 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11236 (build-system r-build-system)
11239 (modify-phases %standard-phases
11240 (add-after 'unpack 'set-CC
11241 (lambda _ (setenv "CC" "gcc") #t)))))
11242 (inputs `(("gmp" ,gmp)))
11243 (home-page "https://cran.r-project.org/web/packages/gmp")
11244 (synopsis "Multiple precision arithmetic")
11246 "This package supports multiple precision arithmetic (big integers and
11247 rationals, prime number tests, matrix computation), \"arithmetic without
11248 limitations\" using the GNU Multiple Precision library.")
11249 ;; Any version of the GPL.
11250 (license license:gpl3+)))
11252 (define-public r-rmpfr
11259 (uri (cran-uri "Rmpfr" version))
11262 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11263 (properties `((upstream-name . "Rmpfr")))
11264 (build-system r-build-system)
11269 `(("r-gmp" ,r-gmp)))
11271 `(("pkg-config" ,pkg-config)))
11272 (home-page "http://rmpfr.r-forge.r-project.org/")
11273 (synopsis "R bindings to the MPFR library")
11275 "This package supports arithmetic (via S4 classes and methods) for
11276 arbitrary precision floating point numbers, including transcendental
11277 functions. To this end, the package interfaces with the @dfn{Multiple
11278 Precision Floating-Point Reliable} (MPFR) library.")
11279 (license license:gpl2+)))
11281 (define-public r-assertive-base
11283 (name "r-assertive-base")
11288 (uri (cran-uri "assertive.base" version))
11291 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11293 `((upstream-name . "assertive.base")))
11294 (build-system r-build-system)
11295 (home-page "https://bitbucket.org/richierocks/assertive.base")
11296 (synopsis "Core of the assertive package")
11298 "This package provides a minimal set of predicates and assertions used by
11299 the assertive package. This is mainly for use by other package developers who
11300 want to include run-time testing features in their own packages.")
11301 (license license:gpl3+)))
11303 (define-public r-assertive-properties
11305 (name "r-assertive-properties")
11310 (uri (cran-uri "assertive.properties" version))
11313 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11315 `((upstream-name . "assertive.properties")))
11316 (build-system r-build-system)
11318 `(("r-assertive-base" ,r-assertive-base)))
11319 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11320 (synopsis "Assertions to check properties of variables")
11322 "This package provides a set of predicates and assertions for checking
11323 the properties of variables, such as length, names and attributes. This is
11324 mainly for use by other package developers who want to include run-time
11325 testing features in their own packages.")
11326 (license license:gpl3+)))
11328 (define-public r-assertive-numbers
11330 (name "r-assertive-numbers")
11335 (uri (cran-uri "assertive.numbers" version))
11338 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11340 `((upstream-name . "assertive.numbers")))
11341 (build-system r-build-system)
11343 `(("r-assertive-base" ,r-assertive-base)))
11344 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11345 (synopsis "Assertions to check properties of numbers")
11347 "This package provides a set of predicates and assertions for checking
11348 the properties of numbers. This is mainly for use by other package developers
11349 who want to include run-time testing features in their own packages.")
11350 (license license:gpl3+)))
11352 (define-public r-assertive-sets
11354 (name "r-assertive-sets")
11359 (uri (cran-uri "assertive.sets" version))
11362 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11364 `((upstream-name . "assertive.sets")))
11365 (build-system r-build-system)
11367 `(("r-assertive-base" ,r-assertive-base)))
11368 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11369 (synopsis "Assertions to check properties of sets")
11371 "This package provides a set of predicates and assertions for checking
11372 the properties of sets. This is mainly for use by other package developers
11373 who want to include run-time testing features in their own packages.")
11374 (license license:gpl3+)))
11376 (define-public r-assertive-matrices
11378 (name "r-assertive-matrices")
11383 (uri (cran-uri "assertive.matrices" version))
11386 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11388 `((upstream-name . "assertive.matrices")))
11389 (build-system r-build-system)
11391 `(("r-assertive-base" ,r-assertive-base)))
11392 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11393 (synopsis "Assertions to check properties of matrices")
11395 "This package provides a set of predicates and assertions for checking
11396 the properties of matrices. This is mainly for use by other package
11397 developers who want to include run-time testing features in their own
11399 (license license:gpl3+)))
11401 (define-public r-assertive-models
11403 (name "r-assertive-models")
11408 (uri (cran-uri "assertive.models" version))
11411 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11413 `((upstream-name . "assertive.models")))
11414 (build-system r-build-system)
11416 `(("r-assertive-base" ,r-assertive-base)))
11417 (home-page "https://bitbucket.org/richierocks/assertive.models")
11418 (synopsis "Assertions to check properties of models")
11420 "This package provides a set of predicates and assertions for checking
11421 the properties of models. This is mainly for use by other package developers
11422 who want to include run-time testing features in their own packages.")
11423 (license license:gpl3+)))
11425 (define-public r-assertive-reflection
11427 (name "r-assertive-reflection")
11432 (uri (cran-uri "assertive.reflection" version))
11435 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11437 `((upstream-name . "assertive.reflection")))
11438 (build-system r-build-system)
11440 `(("r-assertive-base" ,r-assertive-base)))
11441 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11442 (synopsis "Assertions for checking the state of R")
11444 "This package provides a set of predicates and assertions for checking
11445 the state and capabilities of R, the operating system it is running on, and
11446 the IDE being used. This is mainly for use by other package developers who
11447 want to include run-time testing features in their own packages.")
11448 (license license:gpl3+)))
11450 (define-public r-assertive-types
11452 (name "r-assertive-types")
11457 (uri (cran-uri "assertive.types" version))
11460 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11462 `((upstream-name . "assertive.types")))
11463 (build-system r-build-system)
11465 `(("r-assertive-base" ,r-assertive-base)
11466 ("r-assertive-properties" ,r-assertive-properties)
11467 ("r-codetools" ,r-codetools)))
11468 (home-page "https://bitbucket.org/richierocks/assertive.types")
11469 (synopsis "Assertions to check types of variables")
11471 "This package provides a set of predicates and assertions for checking
11472 the types of variables. This is mainly for use by other package developers
11473 who want to include run-time testing features in their own packages.")
11474 (license license:gpl3+)))
11476 (define-public r-assertive-files
11478 (name "r-assertive-files")
11483 (uri (cran-uri "assertive.files" version))
11486 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11488 `((upstream-name . "assertive.files")))
11489 (build-system r-build-system)
11491 `(("r-assertive-base" ,r-assertive-base)
11492 ("r-assertive-numbers" ,r-assertive-numbers)))
11493 (home-page "https://bitbucket.org/richierocks/assertive.files")
11494 (synopsis "Assertions to check properties of files")
11496 "This package provides a set of predicates and assertions for checking
11497 the properties of files and connections. This is mainly for use by other
11498 package developers who want to include run-time testing features in their own
11500 (license license:gpl3+)))
11502 (define-public r-assertive-code
11504 (name "r-assertive-code")
11509 (uri (cran-uri "assertive.code" version))
11512 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11514 `((upstream-name . "assertive.code")))
11515 (build-system r-build-system)
11517 `(("r-assertive-base" ,r-assertive-base)
11518 ("r-assertive-properties" ,r-assertive-properties)
11519 ("r-assertive-types" ,r-assertive-types)))
11520 (home-page "https://bitbucket.org/richierocks/assertive.code")
11521 (synopsis "Assertions to check properties of code")
11523 "This package provides a set of predicates and assertions for checking
11524 the properties of code. This is mainly for use by other package developers
11525 who want to include run-time testing features in their own packages.")
11526 (license license:gpl3+)))
11528 (define-public r-assertive-datetimes
11530 (name "r-assertive-datetimes")
11535 (uri (cran-uri "assertive.datetimes" version))
11538 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11540 `((upstream-name . "assertive.datetimes")))
11541 (build-system r-build-system)
11543 `(("r-assertive-base" ,r-assertive-base)
11544 ("r-assertive-types" ,r-assertive-types)))
11545 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11546 (synopsis "Assertions to check properties of dates and times")
11548 "This package provides a set of predicates and assertions for checking
11549 the properties of dates and times. This is mainly for use by other package
11550 developers who want to include run-time testing features in their own
11552 (license license:gpl3+)))
11554 (define-public r-assertive-strings
11556 (name "r-assertive-strings")
11561 (uri (cran-uri "assertive.strings" version))
11564 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11566 `((upstream-name . "assertive.strings")))
11567 (build-system r-build-system)
11569 `(("r-assertive-base" ,r-assertive-base)
11570 ("r-assertive-types" ,r-assertive-types)
11571 ("r-stringi" ,r-stringi)))
11572 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11573 (synopsis "Assertions to check properties of strings")
11575 "This package provides a set of predicates and assertions for checking
11576 the properties of strings. This is mainly for use by other package developers
11577 who want to include run-time testing features in their own packages.")
11578 (license license:gpl3+)))
11580 (define-public r-assertive-data-us
11582 (name "r-assertive-data-us")
11587 (uri (cran-uri "assertive.data.us" version))
11590 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11592 `((upstream-name . "assertive.data.us")))
11593 (build-system r-build-system)
11595 `(("r-assertive-base" ,r-assertive-base)
11596 ("r-assertive-strings" ,r-assertive-strings)))
11597 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11598 (synopsis "Assertions to check properties of strings")
11600 "This package provides a set of predicates and assertions for checking
11601 the properties of US-specific complex data types. This is mainly for use by
11602 other package developers who want to include run-time testing features in
11603 their own packages.")
11604 (license license:gpl3+)))
11606 (define-public r-assertive-data-uk
11608 (name "r-assertive-data-uk")
11613 (uri (cran-uri "assertive.data.uk" version))
11616 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11618 `((upstream-name . "assertive.data.uk")))
11619 (build-system r-build-system)
11621 `(("r-assertive-base" ,r-assertive-base)
11622 ("r-assertive-strings" ,r-assertive-strings)))
11623 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11624 (synopsis "Assertions to check properties of strings")
11626 "This package provides a set of predicates and assertions for checking
11627 the properties of UK-specific complex data types. This is mainly for use by
11628 other package developers who want to include run-time testing features in
11629 their own packages.")
11630 (license license:gpl3+)))
11632 (define-public r-assertive-data
11634 (name "r-assertive-data")
11639 (uri (cran-uri "assertive.data" version))
11642 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11644 `((upstream-name . "assertive.data")))
11645 (build-system r-build-system)
11647 `(("r-assertive-base" ,r-assertive-base)
11648 ("r-assertive-strings" ,r-assertive-strings)))
11649 (home-page "https://bitbucket.org/richierocks/assertive.data")
11650 (synopsis "Assertions to check properties of data")
11652 "This package provides a set of predicates and assertions for checking
11653 the properties of (country independent) complex data types. This is mainly
11654 for use by other package developers who want to include run-time testing
11655 features in their own packages.")
11656 (license license:gpl3+)))
11658 (define-public r-assertive
11660 (name "r-assertive")
11665 (uri (cran-uri "assertive" version))
11668 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11669 (build-system r-build-system)
11671 `(("r-assertive-base" ,r-assertive-base)
11672 ("r-assertive-code" ,r-assertive-code)
11673 ("r-assertive-data" ,r-assertive-data)
11674 ("r-assertive-data-uk" ,r-assertive-data-uk)
11675 ("r-assertive-data-us" ,r-assertive-data-us)
11676 ("r-assertive-datetimes" ,r-assertive-datetimes)
11677 ("r-assertive-files" ,r-assertive-files)
11678 ("r-assertive-matrices" ,r-assertive-matrices)
11679 ("r-assertive-models" ,r-assertive-models)
11680 ("r-assertive-numbers" ,r-assertive-numbers)
11681 ("r-assertive-properties" ,r-assertive-properties)
11682 ("r-assertive-reflection" ,r-assertive-reflection)
11683 ("r-assertive-sets" ,r-assertive-sets)
11684 ("r-assertive-strings" ,r-assertive-strings)
11685 ("r-assertive-types" ,r-assertive-types)
11686 ("r-knitr" ,r-knitr)))
11687 (home-page "https://bitbucket.org/richierocks/assertive")
11688 (synopsis "Readable check functions to ensure code integrity")
11690 "This package provides lots of predicates (@code{is_*} functions) to
11691 check the state of your variables, and assertions (@code{assert_*} functions)
11692 to throw errors if they aren't in the right form.")
11693 (license license:gpl3+)))
11695 (define-public r-dotcall64
11697 (name "r-dotcall64")
11702 (uri (cran-uri "dotCall64" version))
11705 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11706 (properties `((upstream-name . "dotCall64")))
11707 (build-system r-build-system)
11708 (native-inputs `(("gfortran" ,gfortran)))
11709 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11710 (synopsis "Enhanced foreign function interface supporting long vectors")
11712 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11713 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11714 supports long vectors, arguments of type 64-bit integer, and provides a
11715 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11716 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11717 (license license:gpl2+)))
11719 (define-public r-spam
11726 (uri (cran-uri "spam" version))
11728 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11729 (build-system r-build-system)
11731 `(("r-dotcall64" ,r-dotcall64)))
11732 (native-inputs `(("gfortran" ,gfortran)))
11733 (home-page "https://www.math.uzh.ch/pages/spam/")
11734 (synopsis "Sparse matrix algebra")
11736 "This package provides a set of functions for sparse matrix algebra.
11737 Differences with other sparse matrix packages are:
11740 @item it only supports (essentially) one sparse matrix format;
11741 @item it is based on transparent and simple structure(s);
11742 @item it is tailored for MCMC calculations within G(M)RF;
11743 @item and it is fast and scalable (with the extension package @code{spam64}).
11745 ;; Either of these licenses
11746 (license (list license:bsd-3 license:lgpl2.0))))
11748 (define-public r-fields
11755 (uri (cran-uri "fields" version))
11757 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11758 (build-system r-build-system)
11760 `(("r-maps" ,r-maps)
11761 ("r-spam" ,r-spam)))
11763 `(("gfortran" ,gfortran)))
11764 (home-page "https://www.image.ucar.edu/fields")
11765 (synopsis "Tools for spatial data")
11767 "This is a package for curve, surface and function fitting with an
11768 emphasis on splines, spatial data and spatial statistics. The major methods
11769 include cubic, and thin plate splines, Kriging, and compactly supported
11770 covariance functions for large data sets.")
11771 (license license:gpl2+)))
11773 (define-public r-spatialextremes
11775 (name "r-spatialextremes")
11780 (uri (cran-uri "SpatialExtremes" version))
11783 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11785 `((upstream-name . "SpatialExtremes")))
11786 (build-system r-build-system)
11788 `(("r-fields" ,r-fields)
11789 ("r-maps" ,r-maps)))
11790 (home-page "http://spatialextremes.r-forge.r-project.org/")
11791 (synopsis "Modelling spatial extremes")
11793 "This package provides tools for the statistical modelling of spatial
11794 extremes using max-stable processes, copula or Bayesian hierarchical models.
11795 More precisely, this package allows (conditional) simulations from various
11796 parametric max-stable models, analysis of the extremal spatial dependence, the
11797 fitting of such processes using composite likelihoods or least square (simple
11798 max-stable processes only), model checking and selection and prediction.")
11799 (license license:gpl2+)))
11801 (define-public r-drc
11808 (uri (cran-uri "drc" version))
11811 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11812 (build-system r-build-system)
11815 ("r-gtools" ,r-gtools)
11817 ("r-multcomp" ,r-multcomp)
11818 ("r-plotrix" ,r-plotrix)
11819 ("r-scales" ,r-scales)))
11820 (home-page "https://cran.r-project.org/web/packages/drc")
11821 (synopsis "Analysis of dose-response curves")
11823 "This package provides a suite of flexible and versatile model fitting
11824 and after-fitting functions for the analysis of dose-response data.")
11825 (license license:gpl2+)))
11827 (define-public r-rmeta
11834 (uri (cran-uri "rmeta" version))
11837 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11838 (build-system r-build-system)
11839 (home-page "https://cran.r-project.org/web/packages/rmeta")
11840 (synopsis "Tools for meta-analysis")
11842 "This package provides functions for simple fixed and random effects
11843 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11844 draws standard summary plots, funnel plots, and computes summaries and tests
11845 for association and heterogeneity.")
11846 (license license:gpl2)))
11848 (define-public r-bootstrap
11850 (name "r-bootstrap")
11855 (uri (cran-uri "bootstrap" version))
11858 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11859 (build-system r-build-system)
11860 (native-inputs `(("gfortran" ,gfortran)))
11861 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11862 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11864 "This package provides software and data for the book \"An Introduction
11865 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11866 This package is primarily provided for projects already based on it, and for
11867 support of the book. New projects should preferentially use the recommended
11868 package \"boot\".")
11869 (license license:bsd-3)))
11871 (define-public r-survivalroc
11873 (name "r-survivalroc")
11878 (uri (cran-uri "survivalROC" version))
11881 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11882 (properties `((upstream-name . "survivalROC")))
11883 (build-system r-build-system)
11884 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11885 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11887 "Compute time-dependent ROC curve from censored survival data using
11888 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11889 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11890 (license license:gpl2+)))
11892 (define-public r-longitudinal
11894 (name "r-longitudinal")
11899 (uri (cran-uri "longitudinal" version))
11902 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11903 (build-system r-build-system)
11904 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11905 (home-page "http://strimmerlab.org/software/longitudinal/")
11906 (synopsis "Analysis of multiple time course data")
11908 "This package contains general data structures and functions for
11909 longitudinal data with multiple variables, repeated measurements, and
11910 irregularly spaced time points. It also implements a shrinkage estimator of
11911 dynamical correlation and dynamical covariance.")
11912 (license license:gpl3+)))
11914 (define-public r-genenet
11921 (uri (cran-uri "GeneNet" version))
11924 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11925 (properties `((upstream-name . "GeneNet")))
11926 (build-system r-build-system)
11928 `(("r-corpcor" ,r-corpcor)
11929 ("r-fdrtool" ,r-fdrtool)
11930 ("r-longitudinal" ,r-longitudinal)))
11931 (home-page "http://strimmerlab.org/software/genenet/")
11932 (synopsis "Modeling and inferring gene networks")
11934 "This package analyzes gene expression (time series) data with focus on
11935 the inference of gene networks. In particular, GeneNet implements the methods
11936 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11937 for learning large-scale gene association networks (including assignment of
11938 putative directions).")
11939 (license license:gpl3+)))
11941 (define-public r-rbamtools
11943 (name "r-rbamtools")
11944 (version "2.16.17")
11948 (uri (cran-uri "rbamtools" version))
11951 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11952 (build-system r-build-system)
11953 (inputs `(("zlib" ,zlib)))
11955 `(("r-refgenome" ,r-refgenome)))
11956 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11957 (synopsis "Read and write BAM (binary alignment) files")
11959 "This package provides an R interface to functions of the SAMtools
11961 (license license:artistic2.0)))
11963 (define-public r-protviz
11970 (uri (cran-uri "protViz" version))
11973 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11974 (properties `((upstream-name . "protViz")))
11975 (build-system r-build-system)
11976 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11977 (home-page "https://github.com/protViz/protViz/")
11978 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11980 "This package helps with quality checks, visualizations and analysis of
11981 mass spectrometry data, coming from proteomics experiments. The package is
11982 developed, tested and used at the Functional Genomics Center Zurich, where it
11983 is used mainly for prototyping, teaching, and having fun with proteomics data.
11984 But it can also be used to do data analysis for small scale data sets.")
11985 (license license:gpl3)))
11987 (define-public r-cmprsk
11994 (uri (cran-uri "cmprsk" version))
11996 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11997 (build-system r-build-system)
11999 `(("r-survival" ,r-survival)))
12001 `(("gfortran" ,gfortran)))
12002 (home-page "https://cran.r-project.org/web/packages/cmprsk")
12003 (synopsis "Subdistribution analysis of competing risks")
12005 "This package provides tool for estimation, testing and regression
12006 modeling of subdistribution functions in competing risks, as described in
12007 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
12008 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
12009 A proportional hazards model for the subdistribution of a competing risk,
12010 JASA, 94:496-509.")
12011 (license license:gpl2+)))
12013 (define-public r-etm
12020 (uri (cran-uri "etm" version))
12023 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
12024 (build-system r-build-system)
12026 `(("r-data-table" ,r-data-table)
12027 ("r-lattice" ,r-lattice)
12029 ("r-rcpparmadillo" ,r-rcpparmadillo)
12030 ("r-survival" ,r-survival)))
12031 (home-page "https://cran.r-project.org/web/packages/etm")
12032 (synopsis "Empirical transition matrix")
12034 "The @dfn{empirical transition matrix} (etm) package estimates
12035 the matrix of transition probabilities for any time-inhomogeneous multistate
12036 model with finite state space using the Aalen-Johansen estimator.")
12037 (license license:expat)))
12039 (define-public r-epi
12046 (uri (cran-uri "Epi" version))
12049 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
12050 (properties `((upstream-name . "Epi")))
12051 (build-system r-build-system)
12053 `(("r-cmprsk" ,r-cmprsk)
12054 ("r-data-table" ,r-data-table)
12057 ("r-matrix" ,r-matrix)
12059 ("r-numderiv" ,r-numderiv)
12061 ("r-survival" ,r-survival)
12063 (home-page "https://BendixCarstensen.com/Epi/")
12064 (synopsis "Statistical analysis in epidemiology")
12066 "This package provides functions for demographic and epidemiological
12067 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12068 particular representation, manipulation and simulation of multistate data -
12069 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12070 @code{etm} and @code{cmprsk} packages. It also contains functions for
12071 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12072 data and some useful functions for tabulation and plotting, as well as a
12073 number of epidemiological data sets.")
12074 (license license:gpl2)))
12076 (define-public r-ppls
12079 (version "1.6-1.1")
12083 (uri (cran-uri "ppls" version))
12086 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12087 (build-system r-build-system)
12088 (propagated-inputs `(("r-mass" ,r-mass)))
12089 (home-page "https://cran.r-project.org/web/packages/ppls")
12090 (synopsis "Penalized partial least squares")
12092 "This package contains linear and nonlinear regression methods based on
12093 partial least squares and penalization techniques. Model parameters are
12094 selected via cross-validation, and confidence intervals ans tests for the
12095 regression coefficients can be conducted via jackknifing.")
12096 (license license:gpl2+)))
12098 (define-public r-huge
12101 (version "1.3.4.1")
12105 (uri (cran-uri "huge" version))
12107 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12108 (build-system r-build-system)
12110 `(("r-igraph" ,r-igraph)
12112 ("r-matrix" ,r-matrix)
12114 ("r-rcppeigen" ,r-rcppeigen)))
12115 (home-page "https://cran.r-project.org/web/packages/huge")
12116 (synopsis "High-dimensional undirected graph estimation")
12118 "This package provides a general framework for high-dimensional
12119 undirected graph estimation. It integrates data preprocessing, neighborhood
12120 screening, graph estimation, and model selection techniques into a pipeline.")
12121 (license license:gpl2)))
12123 (define-public r-parcor
12130 (uri (cran-uri "parcor" version))
12133 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12134 (build-system r-build-system)
12137 ("r-genenet" ,r-genenet)
12138 ("r-glmnet" ,r-glmnet)
12140 ("r-ppls" ,r-ppls)))
12141 (home-page "https://cran.r-project.org/web/packages/parcor")
12142 (synopsis "Regularized estimation of partial correlation matrices")
12144 "This package estimates the matrix of partial correlations based on
12145 different regularized regression methods: lasso, adaptive lasso, PLS, and
12146 Ridge Regression. In addition, the package provides model selection for
12147 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12148 (license license:gpl2+)))
12150 (define-public r-mcmc
12157 (uri (cran-uri "mcmc" version))
12160 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12161 (build-system r-build-system)
12162 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12163 (synopsis "Markov chain Monte Carlo")
12165 "This package simulates continuous distributions of random vectors using
12166 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12167 function that evaluates the log unnormalized density. Algorithms are random
12168 walk Metropolis algorithm (function @code{metrop}), simulated
12169 tempering (function @code{temper}), and morphometric random walk
12170 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12171 by change of variable.")
12172 (license license:expat)))
12174 (define-public r-listenv
12181 (uri (cran-uri "listenv" version))
12184 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12185 (build-system r-build-system)
12187 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12188 (home-page "https://github.com/HenrikBengtsson/listenv")
12189 (synopsis "Environments behaving (almost) as lists")
12191 "This package implements list environments. List environments are
12192 environments that have list-like properties. For instance, the elements of a
12193 list environment are ordered and can be accessed and iterated over using index
12195 (license license:lgpl2.1+)))
12197 (define-public r-globals
12204 (uri (cran-uri "globals" version))
12207 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12208 (build-system r-build-system)
12210 `(("r-codetools" ,r-codetools)))
12211 (home-page "https://github.com/HenrikBengtsson/globals")
12212 (synopsis "Identify global objects in R expressions")
12214 "This package provides tools to identify global (\"unknown\" or \"free\")
12215 objects in R expressions by code inspection using various strategies, e.g.
12216 conservative or liberal. The objective of this package is to make it as
12217 simple as possible to identify global objects for the purpose of exporting
12218 them in distributed compute environments.")
12219 (license license:lgpl2.1+)))
12221 (define-public r-future
12228 (uri (cran-uri "future" version))
12231 "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f"))))
12232 (build-system r-build-system)
12234 `(("r-digest" ,r-digest)
12235 ("r-globals" ,r-globals)
12236 ("r-listenv" ,r-listenv)))
12238 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12239 (home-page "https://github.com/HenrikBengtsson/future")
12240 (synopsis "Unified parallel and distributed processing in R")
12242 "The purpose of this package is to provide a lightweight and unified
12243 Future API for sequential and parallel processing of R expression via futures.
12244 This package implements sequential, multicore, multisession, and cluster
12245 futures. With these, R expressions can be evaluated on the local machine, in
12246 parallel a set of local machines, or distributed on a mix of local and remote
12247 machines. Extensions to this package implement additional backends for
12248 processing futures via compute cluster schedulers etc. Because of its unified
12249 API, there is no need to modify any code in order to switch from sequential on
12250 the local machine to, say, distributed processing on a remote compute cluster.")
12251 (license license:lgpl2.1+)))
12253 (define-public r-future-apply
12255 (name "r-future-apply")
12260 (uri (cran-uri "future.apply" version))
12263 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12264 (properties `((upstream-name . "future.apply")))
12265 (build-system r-build-system)
12267 `(("r-future" ,r-future)
12268 ("r-globals" ,r-globals)))
12270 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12271 (home-page "https://github.com/HenrikBengtsson/future.apply")
12272 (synopsis "Apply function to elements in parallel using futures")
12274 "This package provides implementations of @code{apply()},
12275 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12276 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12277 can be resolved using any future-supported backend, e.g. parallel on the local
12278 machine or distributed on a compute cluster.")
12279 (license license:gpl2+)))
12281 (define-public r-rsvd
12288 (uri (cran-uri "rsvd" version))
12291 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12292 (build-system r-build-system)
12294 `(("r-matrix" ,r-matrix)))
12295 (home-page "https://github.com/erichson/rSVD")
12296 (synopsis "Randomized singular value decomposition")
12298 "Low-rank matrix decompositions are fundamental tools and widely used for
12299 data analysis, dimension reduction, and data compression. Classically, highly
12300 accurate deterministic matrix algorithms are used for this task. However, the
12301 emergence of large-scale data has severely challenged our computational
12302 ability to analyze big data. The concept of randomness has been demonstrated
12303 as an effective strategy to quickly produce approximate answers to familiar
12304 problems such as the @dfn{singular value decomposition} (SVD). This package
12305 provides several randomized matrix algorithms such as the randomized singular
12306 value decomposition (@code{rsvd}), randomized principal component
12307 analysis (@code{rpca}), randomized robust principal component
12308 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12309 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12310 functions are provided.")
12311 (license license:gpl3+)))
12313 (define-public r-sloop
12320 (uri (cran-uri "sloop" version))
12323 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12324 (build-system r-build-system)
12326 `(("r-codetools" ,r-codetools)
12327 ("r-crayon" ,r-crayon)
12328 ("r-purrr" ,r-purrr)
12329 ("r-rlang" ,r-rlang)
12330 ("r-tibble" ,r-tibble)))
12331 (home-page "https://github.com/r-lib/sloop")
12332 (synopsis "Helpers for object-oriented programming in R")
12334 "This package provides a collection of helper functions designed to
12335 help you to better understand object oriented programming in R, particularly
12337 (license license:gpl3)))
12339 (define-public r-capushe
12346 (uri (cran-uri "capushe" version))
12349 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12350 (build-system r-build-system)
12351 (propagated-inputs `(("r-mass" ,r-mass)))
12352 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12353 (synopsis "Calibrating penalties using slope heuristics")
12355 "This package provides tools for the calibration of penalized criteria
12356 for model selection. The calibration methods available are based on the slope
12358 (license license:gpl2+)))
12360 (define-public r-dorng
12367 (uri (cran-uri "doRNG" version))
12370 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12371 (properties `((upstream-name . "doRNG")))
12372 (build-system r-build-system)
12374 `(("r-foreach" ,r-foreach)
12375 ("r-iterators" ,r-iterators)
12376 ("r-rngtools" ,r-rngtools)))
12377 (home-page "https://renozao.github.io/doRNG/")
12378 (synopsis "Generic reproducible parallel backend for foreach loops")
12380 "This package provides functions to perform reproducible parallel
12381 @code{foreach} loops, using independent random streams as generated by
12382 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12383 convert standard @code{%dopar%} loops into fully reproducible loops,
12384 independently of the number of workers, the task scheduling strategy, or the
12385 chosen parallel environment and associated foreach backend.")
12386 (license license:gpl2+)))
12388 (define-public r-blockmodeling
12390 (name "r-blockmodeling")
12395 (uri (cran-uri "blockmodeling" version))
12398 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12399 (build-system r-build-system)
12401 `(("r-matrix" ,r-matrix)))
12402 (native-inputs `(("gfortran" ,gfortran)))
12403 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12404 (synopsis "Generalized and classical blockmodeling of valued networks")
12406 "This package is primarily meant as an implementation of generalized
12407 blockmodeling for valued networks. In addition, measures of similarity or
12408 dissimilarity based on structural equivalence and regular equivalence (REGE
12409 algorithms) can be computed and partitioned matrices can be plotted.")
12410 (license license:gpl2+)))
12412 (define-public r-upsetr
12419 (uri (cran-uri "UpSetR" version))
12422 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12423 (properties `((upstream-name . "UpSetR")))
12424 (build-system r-build-system)
12426 `(("r-ggplot2" ,r-ggplot2)
12427 ("r-gridextra" ,r-gridextra)
12429 ("r-scales" ,r-scales)))
12430 (home-page "https://github.com/hms-dbmi/UpSetR")
12431 (synopsis "Visualize intersecting sets")
12433 "This package provides a more scalable alternative to Venn and Euler
12434 diagrams for visualizing intersecting sets. Create visualizations of
12435 intersecting sets using a novel matrix design, along with visualizations of
12436 several common set, element and attribute related tasks.")
12437 (license license:expat)))
12439 ;; This package includes a JavaScript file, which is not minified. When
12440 ;; upgrading please check that there are no new minified JavaScript files.
12441 (define-public r-shinybs
12448 (uri (cran-uri "shinyBS" version))
12451 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12452 (properties `((upstream-name . "shinyBS")))
12453 (build-system r-build-system)
12454 ;; The tests spawn Shiny browser apps. They cannot be run
12455 ;; non-interactively.
12456 (arguments '(#:tests? #f))
12458 `(("r-htmltools" ,r-htmltools)
12459 ("r-shiny" ,r-shiny)))
12460 (home-page "https://ebailey78.github.io/shinyBS/")
12461 (synopsis "Twitter Bootstrap components for Shiny")
12463 "This package adds additional Twitter Bootstrap components to Shiny.")
12464 (license license:gpl3)))
12466 (define-public r-outliers
12468 (name "r-outliers")
12473 (uri (cran-uri "outliers" version))
12476 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12477 (build-system r-build-system)
12478 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12479 (synopsis "Tests for outliers")
12481 "This package provides a collection of some tests commonly used for
12482 identifying outliers.")
12483 (license license:gpl2+)))
12485 (define-public r-bayesm
12492 (uri (cran-uri "bayesm" version))
12494 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12495 (build-system r-build-system)
12497 `(("r-rcpp" ,r-rcpp)
12498 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12499 (home-page "http://www.perossi.org/home/bsm-1")
12500 (synopsis "Bayesian inference for marketing/micro-econometrics")
12502 "This package covers many important models used in marketing and
12503 micro-econometrics applications, including Bayes Regression (univariate or
12504 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12505 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12506 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12507 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12508 Estimation with normal base, Hierarchical Linear Models with normal prior and
12509 covariates, Hierarchical Linear Models with a mixture of normals prior and
12510 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12511 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12512 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12513 analysis of choice-based conjoint data, Bayesian treatment of linear
12514 instrumental variables models, Analysis of Multivariate Ordinal survey data
12515 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12516 Coefficient Logit Models.")
12517 (license license:gpl2+)))
12519 (define-public r-tensora
12526 (uri (cran-uri "tensorA" version))
12529 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12530 (properties `((upstream-name . "tensorA")))
12531 (build-system r-build-system)
12532 (home-page "http://www.stat.boogaart.de/tensorA")
12533 (synopsis "Advanced tensor arithmetic with named indices")
12535 "This package provides convenience functions for advanced linear algebra
12536 with tensors and computation with datasets of tensors on a higher level
12537 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12538 co- and contravariate indices, and parallel computations on sequences of
12540 (license license:gpl2+)))
12542 (define-public r-rarpack
12549 (uri (cran-uri "rARPACK" version))
12552 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12553 (properties `((upstream-name . "rARPACK")))
12554 (build-system r-build-system)
12555 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12556 (home-page "https://github.com/yixuan/rARPACK")
12557 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12559 "This package was previously an R wrapper of the ARPACK library, and now
12560 a shell of the R package RSpectra, an R interface to the Spectra library for
12561 solving large scale eigenvalue/vector problems. The current version of
12562 rARPACK simply imports and exports the functions provided by RSpectra. New
12563 users of rARPACK are advised to switch to the RSpectra package.")
12564 (license license:bsd-3)))
12566 (define-public r-compositions
12568 (name "r-compositions")
12573 (uri (cran-uri "compositions" version))
12576 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12577 (build-system r-build-system)
12579 `(("r-bayesm" ,r-bayesm)
12580 ("r-robustbase" ,r-robustbase)
12581 ("r-tensora" ,r-tensora)))
12582 (home-page "http://www.stat.boogaart.de/compositions")
12583 (synopsis "Compositional data analysis")
12585 "This package provides functions for the consistent analysis of
12586 compositional data (e.g. portions of substances) and positive
12587 numbers (e.g. concentrations).")
12588 (license license:gpl2+)))
12590 (define-public r-cobs
12597 (uri (cran-uri "cobs" version))
12600 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12601 (build-system r-build-system)
12603 `(("r-quantreg" ,r-quantreg)
12604 ("r-sparsem" ,r-sparsem)))
12605 (home-page "https://cran.r-project.org/web/packages/cobs")
12606 (synopsis "Constrained B-Splines (sparse matrix based)")
12608 "This package provides qualitatively constrained (regression) smoothing
12609 splines via linear programming and sparse matrices.")
12610 (license license:gpl2+)))
12612 (define-public r-drimpute
12614 (name "r-drimpute")
12619 (uri (cran-uri "DrImpute" version))
12622 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12623 (properties `((upstream-name . "DrImpute")))
12624 (build-system r-build-system)
12626 `(("r-rcpp" ,r-rcpp)
12627 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12628 (home-page "https://github.com/ikwak2/DrImpute")
12629 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12631 "This is an R package for imputing dropout events. Many statistical
12632 methods in cell type identification, visualization and lineage reconstruction
12633 do not account for dropout events. DrImpute can improve the performance of
12634 such software by imputing dropout events.")
12635 (license license:gpl3)))
12637 (define-public r-gamlss-dist
12639 (name "r-gamlss-dist")
12644 (uri (cran-uri "gamlss.dist" version))
12646 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
12647 (properties `((upstream-name . "gamlss.dist")))
12648 (build-system r-build-system)
12649 (propagated-inputs `(("r-mass" ,r-mass)))
12650 (home-page "http://www.gamlss.org/")
12651 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12653 "This package provides a set of distributions which can be used for
12654 modelling the response variables in Generalized Additive Models for Location
12655 Scale and Shape. The distributions can be continuous, discrete or mixed
12656 distributions. Extra distributions can be created, by transforming, any
12657 continuous distribution defined on the real line, to a distribution defined on
12658 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12659 transformation, respectively.")
12660 ;; Either version of the GPL.
12661 (license (list license:gpl2 license:gpl3))))
12663 ;; This package includes JavaScript files, which are not minified. When
12664 ;; upgrading please check that there are no new minified JavaScript files.
12665 (define-public r-shinyjs
12672 (uri (cran-uri "shinyjs" version))
12675 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12676 (build-system r-build-system)
12678 `(("r-digest" ,r-digest)
12679 ("r-htmltools" ,r-htmltools)
12680 ("r-jsonlite" ,r-jsonlite)
12681 ("r-shiny" ,r-shiny)))
12682 (home-page "https://deanattali.com/shinyjs")
12683 (synopsis "Improve the user experience of your Shiny apps")
12685 "Perform common useful JavaScript operations in Shiny apps that will
12686 greatly improve your apps without having to know any JavaScript. Examples
12687 include: hiding an element, disabling an input, resetting an input back to its
12688 original value, delaying code execution by a few seconds, and many more useful
12689 functions for both the end user and the developer. Shinyjs can also be used
12690 to easily call your own custom JavaScript functions from R.")
12691 (license license:agpl3+)))
12693 ;; This package includes minified JavaScript files. When upgrading please
12694 ;; check that there are no new minified JavaScript files.
12695 (define-public r-colourpicker
12697 (name "r-colourpicker")
12702 (uri (cran-uri "colourpicker" version))
12705 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12706 (build-system r-build-system)
12708 `(#:modules ((guix build utils)
12709 (guix build r-build-system)
12713 (modify-phases %standard-phases
12714 (add-after 'unpack 'process-javascript
12715 (lambda* (#:key inputs #:allow-other-keys)
12716 (with-directory-excursion "inst"
12720 `((,(assoc-ref inputs "js-salvattore")
12721 "examples/colourInput/www/salvattore.min.js")
12722 (,(assoc-ref inputs "js-jquery")
12723 "htmlwidgets/lib/jquery/jquery.min.js")
12724 ("www/shared/colourpicker/js/colourpicker.js"
12725 "www/shared/colourpicker/js/colourpicker.min.js"))))
12726 (lambda (sources targets)
12727 (for-each (lambda (source target)
12728 (format #t "Processing ~a --> ~a~%"
12730 (delete-file target)
12731 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12732 (call-with-output-file target
12734 (dump-port minified port)))))
12735 sources targets))))
12738 `(("r-ggplot2" ,r-ggplot2)
12739 ("r-htmltools" ,r-htmltools)
12740 ("r-htmlwidgets" ,r-htmlwidgets)
12741 ("r-jsonlite" ,r-jsonlite)
12742 ("r-miniui" ,r-miniui)
12743 ("r-shiny" ,r-shiny)
12744 ("r-shinyjs" ,r-shinyjs)))
12746 `(("uglify-js" ,uglify-js)
12750 (uri "https://code.jquery.com/jquery-3.3.1.js")
12753 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12757 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12760 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12761 (home-page "https://github.com/daattali/colourpicker")
12762 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12764 "This package provides a color picker that can be used as an input in
12765 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12766 custom color palettes, and many more options. A plot color helper tool is
12767 available as an RStudio Addin, which helps you pick colors to use in your
12768 plots. A more generic color picker RStudio Addin is also provided to let you
12769 select colors to use in your R code.")
12770 (license license:expat)))
12772 (define-public r-ggextra
12779 (uri (cran-uri "ggExtra" version))
12782 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12783 (properties `((upstream-name . "ggExtra")))
12784 (build-system r-build-system)
12786 `(("r-colourpicker" ,r-colourpicker)
12787 ("r-ggplot2" ,r-ggplot2)
12788 ("r-gtable" ,r-gtable)
12789 ("r-miniui" ,r-miniui)
12791 ("r-scales" ,r-scales)
12792 ("r-shiny" ,r-shiny)
12793 ("r-shinyjs" ,r-shinyjs)))
12795 `(("r-knitr" ,r-knitr)))
12796 (home-page "https://github.com/daattali/ggExtra")
12797 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12799 "This package is a collection of functions and layers to enhance ggplot2.
12800 The flagship function is @code{ggMarginal()}, which can be used to add
12801 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12802 (license license:expat)))
12804 (define-public r-minpack-lm
12806 (name "r-minpack-lm")
12811 (uri (cran-uri "minpack.lm" version))
12814 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12815 (properties `((upstream-name . "minpack.lm")))
12816 (build-system r-build-system)
12817 (native-inputs `(("gfortran" ,gfortran)))
12818 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12819 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12821 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12822 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12823 problems by a modification of the Levenberg-Marquardt algorithm, with support
12824 for lower and upper parameter bounds. The implementation can be used via
12825 @code{nls}-like calls using the @code{nlsLM} function.")
12826 (license license:gpl3)))
12828 (define-public r-moments
12835 (uri (cran-uri "moments" version))
12838 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12839 (build-system r-build-system)
12840 (home-page "https://cran.r-project.org/web/packages/moments")
12841 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12843 "This package provides functions to calculate: moments, Pearson's
12844 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12845 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12846 (license license:gpl2+)))
12848 (define-public r-msir
12855 (uri (cran-uri "msir" version))
12858 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12859 (build-system r-build-system)
12861 `(("r-mclust" ,r-mclust)))
12862 (home-page "https://cran.r-project.org/web/packages/msir")
12863 (synopsis "Model-based sliced inverse regression")
12865 "This is an R package for dimension reduction based on finite Gaussian
12866 mixture modeling of inverse regression.")
12867 (license license:gpl2+)))
12869 (define-public r-pbivnorm
12871 (name "r-pbivnorm")
12876 (uri (cran-uri "pbivnorm" version))
12879 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12880 (build-system r-build-system)
12881 (native-inputs `(("gfortran" ,gfortran)))
12882 (home-page "https://github.com/brentonk/pbivnorm")
12883 (synopsis "Vectorized bivariate normal CDF")
12885 "This package provides a vectorized R function for calculating
12886 probabilities from a standard bivariate normal CDF.")
12887 (license license:gpl2+)))
12889 (define-public r-lavaan
12896 (uri (cran-uri "lavaan" version))
12899 "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
12900 (build-system r-build-system)
12902 `(("r-mass" ,r-mass)
12903 ("r-mnormt" ,r-mnormt)
12904 ("r-numderiv" ,r-numderiv)
12905 ("r-pbivnorm" ,r-pbivnorm)))
12906 (home-page "http://lavaan.ugent.be")
12907 (synopsis "Latent variable analysis")
12909 "This package provides tools to fit a variety of latent variable models,
12910 including confirmatory factor analysis, structural equation modeling and
12911 latent growth curve models.")
12912 (license license:gpl2+)))
12914 (define-public r-nonnest2
12916 (name "r-nonnest2")
12921 (uri (cran-uri "nonnest2" version))
12924 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
12925 (build-system r-build-system)
12927 `(("r-compquadform" ,r-compquadform)
12928 ("r-lavaan" ,r-lavaan)
12929 ("r-mvtnorm" ,r-mvtnorm)
12930 ("r-sandwich" ,r-sandwich)))
12932 `(("r-knitr" ,r-knitr)))
12933 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12934 (synopsis "Tests of non-nested models")
12936 "This package allows for testing of non-nested models. It includes tests
12937 of model distinguishability and of model fit that can be applied to both
12938 nested and non-nested models. The package also includes functionality to
12939 obtain confidence intervals associated with AIC and BIC.")
12940 ;; Either version of the GPL.
12941 (license (list license:gpl2 license:gpl3))))
12943 (define-public r-penalized
12945 (name "r-penalized")
12950 (uri (cran-uri "penalized" version))
12953 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12954 (build-system r-build-system)
12956 `(("r-rcpp" ,r-rcpp)
12957 ("r-rcpparmadillo" ,r-rcpparmadillo)
12958 ("r-survival" ,r-survival)))
12959 (home-page "https://cran.r-project.org/web/packages/penalized/")
12960 (synopsis "Penalized estimation in GLMs and in the Cox model")
12962 "This package provides tools for fitting possibly high dimensional
12963 penalized regression models. The penalty structure can be any combination of
12964 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12965 constraint on the regression coefficients. The supported regression models
12966 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12967 model. Cross-validation routines allow optimization of the tuning
12969 (license license:gpl2+)))
12971 (define-public r-zim
12978 (uri (cran-uri "ZIM" version))
12981 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12982 (properties `((upstream-name . "ZIM")))
12983 (build-system r-build-system)
12984 (propagated-inputs `(("r-mass" ,r-mass)))
12985 (home-page "https://github.com/biostatstudio/ZIM")
12986 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12988 "Analyze count time series with excess zeros. Two types of statistical
12989 models are supported: Markov regression and state-space models. They are also
12990 known as observation-driven and parameter-driven models respectively in the
12991 time series literature. The functions used for Markov regression or
12992 observation-driven models can also be used to fit ordinary regression models
12993 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12994 negative binomial (ZINB) assumption. The package also contains miscellaneous
12995 functions to compute density, distribution, quantile, and generate random
12996 numbers from ZIP and ZINB distributions.")
12997 (license license:gpl3)))
12999 (define-public r-nor1mix
13006 (uri (cran-uri "nor1mix" version))
13009 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
13010 (build-system r-build-system)
13011 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
13012 (synopsis "Normal (1-d) mixture models")
13014 "This package provides S3 classes and methods for one-dimensional normal
13015 mixture models, for, e.g., density estimation or clustering algorithms
13016 research and teaching; it provides the widely used Marron-Wand densities. It
13017 also provides tools for efficient random number generation and graphics.")
13018 (license license:gpl2+)))
13020 (define-public r-beanplot
13022 (name "r-beanplot")
13027 (uri (cran-uri "beanplot" version))
13030 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
13031 (build-system r-build-system)
13032 (home-page "https://cran.r-project.org/web/packages/beanplot/")
13033 (synopsis "Visualization via beanplots")
13035 "This package provides beanplots, an alternative to
13036 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13038 (license license:gpl2)))
13040 (define-public r-pbdzmq
13047 (uri (cran-uri "pbdZMQ" version))
13050 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13051 (properties `((upstream-name . "pbdZMQ")))
13052 (build-system r-build-system)
13054 `(("zeromq" ,zeromq)
13057 `(("pkg-config" ,pkg-config)))
13058 (home-page "https://pbdr.org/")
13059 (synopsis "R interface to ZeroMQ")
13061 "ZeroMQ is a well-known library for high-performance asynchronous
13062 messaging in scalable, distributed applications. This package provides high
13063 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13064 interactive client/server programming frameworks. A few wrapper functions
13065 compatible with @code{rzmq} are also provided.")
13066 (license license:gpl3)))
13068 (define-public r-repr
13075 (uri (cran-uri "repr" version))
13078 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13079 (build-system r-build-system)
13081 `(("r-base64enc" ,r-base64enc)
13082 ("r-htmltools" ,r-htmltools)
13083 ("r-jsonlite" ,r-jsonlite)
13084 ("r-pillar" ,r-pillar)))
13085 (home-page "https://cran.r-project.org/web/packages/repr/")
13086 (synopsis "Serializable representations")
13088 "This package provides string and binary representations of objects for
13089 several formats and MIME types.")
13090 (license license:gpl3)))
13092 (define-public r-irdisplay
13094 (name "r-irdisplay")
13099 (uri (cran-uri "IRdisplay" version))
13102 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13103 (properties `((upstream-name . "IRdisplay")))
13104 (build-system r-build-system)
13106 `(("r-repr" ,r-repr)))
13107 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13108 (synopsis "Jupyter display machinery")
13110 "This package provides an interface to the rich display capabilities of
13111 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13112 running IRkernel session.")
13113 (license license:expat)))
13115 (define-public r-irkernel
13117 (name "r-irkernel")
13122 (uri (cran-uri "IRkernel" version))
13125 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
13126 (properties `((upstream-name . "IRkernel")))
13127 (build-system r-build-system)
13130 (modify-phases %standard-phases
13131 (add-after 'install 'install-kernelspec
13132 (lambda* (#:key outputs #:allow-other-keys)
13133 (let ((out (assoc-ref outputs "out")))
13134 (setenv "HOME" "/tmp")
13135 (invoke "jupyter" "kernelspec" "install"
13138 (string-append out "/site-library/IRkernel/kernelspec"))
13139 ;; Record the absolute file name of the 'R' executable in
13141 (substitute* (string-append out "/share/jupyter"
13142 "/kernels/ir/kernel.json")
13144 (string-append "[\"" (which "R") "\",")))
13147 `(("jupyter" ,jupyter)))
13149 `(("r-crayon" ,r-crayon)
13150 ("r-digest" ,r-digest)
13151 ("r-evaluate" ,r-evaluate)
13152 ("r-irdisplay" ,r-irdisplay)
13153 ("r-jsonlite" ,r-jsonlite)
13154 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13155 ("r-minimal" ,r-minimal)
13156 ("r-pbdzmq" ,r-pbdzmq)
13158 ("r-uuid" ,r-uuid)))
13159 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13160 (synopsis "Native R kernel for Jupyter")
13162 "The R kernel for the Jupyter environment executes R code which the
13163 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13165 (license license:expat)))
13167 (define-public r-gmodels
13174 (uri (cran-uri "gmodels" version))
13177 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13178 (build-system r-build-system)
13180 `(("r-gdata" ,r-gdata)
13181 ("r-mass" ,r-mass)))
13182 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13183 (synopsis "Various R programming tools for model fitting")
13185 "This package provides various R programming tools for model fitting.")
13186 (license license:gpl2)))
13188 (define-public r-apcluster
13190 (name "r-apcluster")
13195 (uri (cran-uri "apcluster" version))
13198 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13199 (build-system r-build-system)
13201 `(("r-matrix" ,r-matrix)
13202 ("r-rcpp" ,r-rcpp)))
13203 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13204 (synopsis "Affinity propagation clustering")
13206 "This package implements affinity propagation clustering introduced by
13207 Frey and Dueck (2007). The package further provides leveraged affinity
13208 propagation and an algorithm for exemplar-based agglomerative clustering that
13209 can also be used to join clusters obtained from affinity propagation. Various
13210 plotting functions are available for analyzing clustering results.")
13211 (license license:gpl2+)))
13213 (define-public r-valr
13220 (uri (cran-uri "valr" version))
13223 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13224 (build-system r-build-system)
13226 `(("r-broom" ,r-broom)
13227 ("r-dplyr" ,r-dplyr)
13228 ("r-ggplot2" ,r-ggplot2)
13230 ("r-readr" ,r-readr)
13231 ("r-rlang" ,r-rlang)
13232 ("r-stringr" ,r-stringr)
13233 ("r-tibble" ,r-tibble)))
13235 `(("r-knitr" ,r-knitr)))
13236 (home-page "https://github.com/rnabioco/valr")
13237 (synopsis "Genome interval arithmetic in R")
13239 "This package enables you to read and manipulate genome intervals and
13240 signals. It provides functionality similar to command-line tool suites within
13241 R, enabling interactive analysis and visualization of genome-scale data.")
13242 (license license:expat)))
13244 (define-public r-rematch2
13246 (name "r-rematch2")
13251 (uri (cran-uri "rematch2" version))
13254 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13255 (build-system r-build-system)
13257 `(("r-tibble" ,r-tibble)))
13258 (home-page "https://github.com/r-lib/rematch2")
13259 (synopsis "Tidy output from regular expression matching")
13261 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13262 return the match results in tidy data frames.")
13263 (license license:expat)))
13265 (define-public r-picante
13272 (uri (cran-uri "picante" version))
13275 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13276 (build-system r-build-system)
13280 ("r-vegan" ,r-vegan)))
13281 (home-page "https://cran.r-project.org/web/packages/picante/")
13282 (synopsis "Integrating phylogenies and ecology")
13284 "This package provides functions for phylocom integration, community
13285 analyses, null-models, traits and evolution. It implements numerous
13286 ecophylogenetic approaches including measures of community phylogenetic and
13287 trait diversity, phylogenetic signal, estimation of trait values for
13288 unobserved taxa, null models for community and phylogeny randomizations, and
13289 utility functions for data input/output and phylogeny plotting. A full
13290 description of package functionality and methods are provided by Kembel et
13292 (license license:gpl2)))
13294 (define-public r-reinforcelearn
13296 (name "r-reinforcelearn")
13301 (uri (cran-uri "reinforcelearn" version))
13304 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13305 (build-system r-build-system)
13307 `(("r-checkmate" ,r-checkmate)
13309 ("r-purrr" ,r-purrr)
13311 (home-page "https://markusdumke.github.io/reinforcelearn")
13312 (synopsis "Reinforcement learning")
13314 "This package implements reinforcement learning environments and
13315 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13316 can be used with function approximation, eligibility traces (Singh & Sutton,
13317 1996) and experience replay (Mnih et al., 2013).")
13318 (license license:expat)))
13320 (define-public r-lemon
13327 (uri (cran-uri "lemon" version))
13330 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13331 (build-system r-build-system)
13333 `(("r-ggplot2" ,r-ggplot2)
13334 ("r-gridextra" ,r-gridextra)
13335 ("r-gtable" ,r-gtable)
13336 ("r-knitr" ,r-knitr)
13337 ("r-lattice" ,r-lattice)
13339 ("r-rlang" ,r-rlang)
13340 ("r-scales" ,r-scales)))
13342 `(("r-knitr" ,r-knitr)))
13343 (home-page "https://github.com/stefanedwards/lemon")
13344 (synopsis "Freshen up your ggplot2 plots")
13346 "This package provides functions for working with legends and axis lines
13347 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13349 (license license:gpl3)))
13351 (define-public r-wgaim
13358 (uri (cran-uri "wgaim" version))
13360 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13361 (build-system r-build-system)
13363 `(("r-ggplot2" ,r-ggplot2)
13365 (home-page "https://cran.r-project.org/web/packages/wgaim")
13366 (synopsis "Whole genome average interval mapping for QTL detection")
13368 "This package integrates sophisticated mixed modelling methods with a
13369 whole genome approach to detecting significant QTL in linkage maps.")
13370 (license license:gpl2+)))
13372 (define-public r-bedr
13379 (uri (cran-uri "bedr" version))
13382 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13383 (build-system r-build-system)
13385 `(("r-data-table" ,r-data-table)
13386 ("r-r-utils" ,r-r-utils)
13387 ("r-testthat" ,r-testthat)
13388 ("r-venndiagram" ,r-venndiagram)
13391 ("bedtools" ,bedtools)
13392 ("htslib" ,htslib))) ; for tabix
13394 `(("r-knitr" ,r-knitr))) ; for vignettes
13395 (home-page "https://cran.r-project.org/web/packages/bedr")
13396 (synopsis "Genomic region processing")
13398 "This package is for genomic regions processing using command line tools
13399 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13400 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13401 The bedr package's API enhances access to these tools as well as offers
13402 additional utilities for genomic regions processing.")
13403 (license license:gpl2)))
13405 (define-public r-sets
13412 (uri (cran-uri "sets" version))
13415 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13416 (properties `((upstream-name . "sets")))
13417 (build-system r-build-system)
13418 (home-page "https://cran.r-project.org/web/packages/sets")
13419 (synopsis "Sets, generalized sets, customizable sets and intervals")
13421 "This package provides data structures and basic operations for ordinary
13422 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13423 customizable sets, and intervals.")
13424 (license license:gpl2)))
13426 (define-public r-partitions
13428 (name "r-partitions")
13433 (uri (cran-uri "partitions" version))
13436 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13437 (build-system r-build-system)
13440 ("r-polynom" ,r-polynom)
13441 ("r-sets" ,r-sets)))
13442 (home-page "https://cran.r-project.org/web/packages/partitions")
13443 (synopsis "Additive partitions of integers")
13445 "This package provides tools to enumerates the partitions, unequal
13446 partitions, and restricted partitions of an integer; the three corresponding
13447 partition functions are also given.")
13448 ;; Any version of the GPL
13449 (license license:gpl2+)))
13451 (define-public r-brobdingnag
13453 (name "r-brobdingnag")
13458 (uri (cran-uri "Brobdingnag" version))
13461 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13462 (properties `((upstream-name . "Brobdingnag")))
13463 (build-system r-build-system)
13464 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13465 (synopsis "Very large numbers in R")
13467 "This package handles very large numbers in R. Real numbers are held
13468 using their natural logarithms, plus a logical flag indicating sign. The
13469 package includes a vignette that gives a step-by-step introduction to using S4
13471 ;; Any version of the GPL
13472 (license license:gpl2+)))
13474 (define-public r-untb
13481 (uri (cran-uri "untb" version))
13484 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13485 (build-system r-build-system)
13487 `(("r-brobdingnag" ,r-brobdingnag)
13488 ("r-partitions" ,r-partitions)
13489 ("r-polynom" ,r-polynom)))
13490 (home-page "https://github.com/RobinHankin/untb.git")
13491 (synopsis "Ecological drift under the UNTB")
13493 "This package provides numerical simulations, and visualizations, of
13494 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13495 (license license:gpl2+)))
13497 (define-public r-stepwise
13499 (name "r-stepwise")
13504 (uri (cran-uri "stepwise" version))
13507 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13508 (build-system r-build-system)
13509 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13510 (synopsis "Stepwise detection of recombination breakpoints")
13512 "This package provides a stepwise approach to identifying recombination
13513 breakpoints in a genomic sequence alignment.")
13514 (license license:gpl2+)))
13516 (define-public r-snpmaxsel
13518 (name "r-snpmaxsel")
13523 (uri (cran-uri "SNPmaxsel" version))
13526 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13527 (properties `((upstream-name . "SNPmaxsel")))
13528 (build-system r-build-system)
13530 `(("r-combinat" ,r-combinat)
13531 ("r-mvtnorm" ,r-mvtnorm)))
13532 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13533 (synopsis "Maximally selected statistics for SNP data")
13535 "This package implements asymptotic methods related to maximally selected
13536 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13538 (license license:gpl2+)))
13540 (define-public r-acsnminer
13542 (name "r-acsnminer")
13543 (version "0.16.8.25")
13546 (uri (cran-uri "ACSNMineR" version))
13549 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13550 (properties `((upstream-name . "ACSNMineR")))
13551 (build-system r-build-system)
13553 `(("r-ggplot2" ,r-ggplot2)
13554 ("r-gridextra" ,r-gridextra)))
13555 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13556 (synopsis "Gene enrichment analysis")
13558 "This package provides tools to compute and represent gene set enrichment
13559 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13560 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13561 enrichment can be run with hypergeometric test or Fisher exact test, and can
13562 use multiple corrections. Visualization of data can be done either by
13563 barplots or heatmaps.")
13564 (license license:gpl2+)))
13566 (define-public r-seqinr
13573 (uri (cran-uri "seqinr" version))
13576 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13577 (build-system r-build-system)
13579 `(("r-ade4" ,r-ade4)
13580 ("r-segmented" ,r-segmented)))
13583 (home-page "http://seqinr.r-forge.r-project.org/")
13584 (synopsis "Biological sequences retrieval and analysis")
13586 "This package provides tools for exploratory data analysis and data
13587 visualization of biological sequence (DNA and protein) data. It also includes
13588 utilities for sequence data management under the ACNUC system.")
13589 (license license:gpl2+)))
13591 (define-public r-units
13598 (uri (cran-uri "units" version))
13601 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13602 (build-system r-build-system)
13604 `(("udunits" ,udunits)))
13606 `(("r-rcpp" ,r-rcpp)))
13608 `(("r-knitr" ,r-knitr)))
13609 (home-page "https://github.com/r-quantities/units/")
13610 (synopsis "Measurement Units for R Vectors")
13612 "This package provides support for measurement units in R vectors,
13613 matrices and arrays: automatic propagation, conversion, derivation and
13614 simplification of units; raising errors in case of unit incompatibility. It
13615 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13617 (license license:gpl2)))
13619 (define-public r-classint
13621 (name "r-classint")
13626 (uri (cran-uri "classInt" version))
13629 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13630 (properties `((upstream-name . "classInt")))
13631 (build-system r-build-system)
13633 `(("r-class" ,r-class)
13634 ("r-e1071" ,r-e1071)
13635 ("r-kernsmooth" ,r-kernsmooth)))
13637 `(("gfortran" ,gfortran)
13638 ("r-knitr" ,r-knitr)))
13639 (home-page "https://github.com/r-spatial/classInt/")
13640 (synopsis "Choose univariate class intervals")
13642 "This package provides selected commonly used methods for choosing
13643 univariate class intervals for mapping or other graphics purposes.")
13644 (license license:gpl2+)))
13646 (define-public r-spdata
13653 (uri (cran-uri "spData" version))
13656 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
13657 (properties `((upstream-name . "spData")))
13658 (build-system r-build-system)
13660 `(("r-raster" ,r-raster)
13662 (home-page "https://github.com/Nowosad/spData")
13663 (synopsis "Datasets for spatial analysis")
13665 "This a package containing diverse spatial datasets for demonstrating,
13666 benchmarking and teaching spatial data analysis. It includes R data of class
13667 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13668 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13669 of the datasets are designed to illustrate specific analysis techniques.
13670 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13671 illustrate point pattern analysis techniques.")
13672 (license license:cc0)))
13674 (define-public r-learnbayes
13676 (name "r-learnbayes")
13681 (uri (cran-uri "LearnBayes" version))
13684 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13685 (properties `((upstream-name . "LearnBayes")))
13686 (build-system r-build-system)
13687 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13688 (synopsis "Functions for learning Bayesian inference")
13690 "This package provides a collection of functions helpful in learning the
13691 basic tenets of Bayesian statistical inference. It contains functions for
13692 summarizing basic one and two parameter posterior distributions and predictive
13693 distributions. It contains MCMC algorithms for summarizing posterior
13694 distributions defined by the user. It also contains functions for regression
13695 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13697 (license license:gpl2+)))
13699 (define-public r-deldir
13706 (uri (cran-uri "deldir" version))
13709 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13710 (build-system r-build-system)
13711 (native-inputs `(("gfortran" ,gfortran)))
13712 (home-page "https://cran.r-project.org/web/packages/deldir")
13713 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13715 "This package provides tools for calculating the Delaunay triangulation
13716 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13717 of a planar point set. It plots triangulations and tessellations in various
13718 ways, clips tessellations to sub-windows, calculates perimeters of
13719 tessellations, and summarizes information about the tiles of the
13721 (license license:gpl2+)))
13723 (define-public r-sf
13730 (uri (cran-uri "sf" version))
13733 "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
13734 (build-system r-build-system)
13741 `(("r-classint" ,r-classint)
13743 ("r-magrittr" ,r-magrittr)
13745 ("r-units" ,r-units)))
13747 `(("pkg-config" ,pkg-config)
13748 ("r-knitr" ,r-knitr)))
13749 (home-page "https://github.com/r-spatial/sf/")
13750 (synopsis "Simple features for R")
13752 "This package provides support for simple features, a standardized way to
13753 encode spatial vector data. It binds to GDAL for reading and writing data, to
13754 GEOS for geometrical operations, and to PROJ for projection conversions and
13755 datum transformations.")
13756 ;; Either of these licenses
13757 (license (list license:gpl2 license:expat))))
13759 (define-public r-spdep
13766 (uri (cran-uri "spdep" version))
13769 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13770 (build-system r-build-system)
13772 `(("r-boot" ,r-boot)
13774 ("r-deldir" ,r-deldir)
13776 ("r-gmodels" ,r-gmodels)
13777 ("r-learnbayes" ,r-learnbayes)
13779 ("r-matrix" ,r-matrix)
13783 ("r-spdata" ,r-spdata)))
13785 `(("r-knitr" ,r-knitr)))
13786 (home-page "https://github.com/r-spatial/spdep/")
13787 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13789 "This package provides a collection of functions to create spatial
13790 weights matrix objects from polygon contiguities, from point patterns by
13791 distance and tessellations, for summarizing these objects, and for permitting
13792 their use in spatial data analysis, including regional aggregation by minimum
13794 (license license:gpl2+)))
13796 (define-public r-adegenet
13798 (name "r-adegenet")
13803 (uri (cran-uri "adegenet" version))
13806 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13807 (build-system r-build-system)
13809 `(("r-ade4" ,r-ade4)
13812 ("r-dplyr" ,r-dplyr)
13813 ("r-ggplot2" ,r-ggplot2)
13814 ("r-igraph" ,r-igraph)
13816 ("r-reshape2" ,r-reshape2)
13817 ("r-seqinr" ,r-seqinr)
13818 ("r-shiny" ,r-shiny)
13819 ("r-spdep" ,r-spdep)
13820 ("r-vegan" ,r-vegan)))
13821 (home-page "https://github.com/thibautjombart/adegenet")
13822 (synopsis "Exploratory analysis of genetic and genomic data")
13824 "This package provides a toolset for the exploration of genetic and
13825 genomic data. Adegenet provides formal (S4) classes for storing and handling
13826 various genetic data, including genetic markers with varying ploidy and
13827 hierarchical population structure (@code{genind} class), alleles counts by
13828 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13829 also implements original multivariate methods (DAPC, sPCA), graphics,
13830 statistical tests, simulation tools, distance and similarity measures, and
13831 several spatial methods. A range of both empirical and simulated datasets is
13832 also provided to illustrate various methods.")
13833 (license license:gpl2+)))
13835 (define-public r-pegas
13842 (uri (cran-uri "pegas" version))
13844 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13845 (build-system r-build-system)
13847 `(("r-adegenet" ,r-adegenet)
13849 (home-page "http://ape-package.ird.fr/pegas.html")
13850 (synopsis "Population and evolutionary genetics analysis system")
13852 "This package provides functions for reading, writing, plotting,
13853 analysing, and manipulating allelic and haplotypic data, including from VCF
13854 files, and for the analysis of population nucleotide sequences and
13855 micro-satellites including coalescent analyses, linkage disequilibrium,
13856 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13857 minimum spanning tree and network, and median-joining networks.")
13858 (license license:gpl2+)))
13860 (define-public r-rmetasim
13862 (name "r-rmetasim")
13867 (uri (cran-uri "rmetasim" version))
13870 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13871 (build-system r-build-system)
13873 `(("r-ade4" ,r-ade4)
13874 ("r-adegenet" ,r-adegenet)
13875 ("r-gtools" ,r-gtools)
13876 ("r-pegas" ,r-pegas)))
13877 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13878 (synopsis "Individual-based population genetic simulation environment")
13880 "This package provides an interface between R and the metasim simulation
13881 engine. The simulation environment is documented in: Strand, A.(2002),
13882 Metasim 1.0: an individual-based environment for simulating population
13883 genetics of complex population dynamics.")
13885 (license license:gpl2+)))
13887 (define-public r-genetics
13889 (name "r-genetics")
13890 (version "1.3.8.1.2")
13894 (uri (cran-uri "genetics" version))
13897 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13898 (build-system r-build-system)
13900 `(("r-combinat" ,r-combinat)
13901 ("r-gdata" ,r-gdata)
13902 ("r-gtools" ,r-gtools)
13904 ("r-mvtnorm" ,r-mvtnorm)))
13905 (home-page "https://cran.r-project.org/web/packages/genetics/")
13906 (synopsis "Population genetics")
13908 "This package provides classes and methods for handling genetic data.
13909 It includes classes to represent genotypes and haplotypes at single markers up
13910 to multiple markers on multiple chromosomes. Function include allele
13911 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13912 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13913 and testing for linkage disequilibrium, ...")
13914 ;; Any GPL version.
13915 (license license:gpl2+)))
13917 (define-public r-snp-plotter
13919 (name "r-snp-plotter")
13924 (uri (cran-uri "snp.plotter" version))
13927 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13928 (properties `((upstream-name . "snp.plotter")))
13929 (build-system r-build-system)
13930 (propagated-inputs `(("r-genetics" ,r-genetics)))
13931 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13932 (synopsis "Plot p-values using single SNP and/or haplotype data")
13934 "This package helps you create plots of p-values using single SNP and/or
13935 haplotype data. Main features of the package include options to display a
13936 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13937 datasets simultaneously. Plots can be created using global and/or individual
13938 haplotype p-values along with single SNP p-values. Images are created as
13939 either PDF/EPS files.")
13940 (license license:gpl2+)))
13942 (define-public r-polspline
13944 (name "r-polspline")
13949 (uri (cran-uri "polspline" version))
13951 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13952 (build-system r-build-system)
13953 (native-inputs `(("gfortran" ,gfortran)))
13954 (home-page "https://cran.r-project.org/web/packages/polspline/")
13955 (synopsis "Polynomial spline routines")
13957 "This package provides routines for the polynomial spline fitting
13958 routines hazard regression, hazard estimation with flexible tails, logspline,
13959 lspec, polyclass, and polymars.")
13960 (license license:gpl2+)))
13962 (define-public r-rms
13969 (uri (cran-uri "rms" version))
13971 (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
13972 (build-system r-build-system)
13974 `(("r-cluster" ,r-cluster)
13975 ("r-digest" ,r-digest)
13976 ("r-ggplot2" ,r-ggplot2)
13977 ("r-hmisc" ,r-hmisc)
13978 ("r-htmltable" ,r-htmltable)
13979 ("r-htmltools" ,r-htmltools)
13980 ("r-lattice" ,r-lattice)
13982 ("r-multcomp" ,r-multcomp)
13984 ("r-polspline" ,r-polspline)
13985 ("r-quantreg" ,r-quantreg)
13986 ("r-rpart" ,r-rpart)
13987 ("r-sparsem" ,r-sparsem)
13988 ("r-survival" ,r-survival)))
13989 (native-inputs `(("gfortran" ,gfortran)))
13990 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13991 (synopsis "Regression modeling strategies")
13993 "This is a package for regression modeling, testing, estimation,
13994 validation, graphics, prediction, and typesetting by storing enhanced model
13995 design attributes in the fit. The rms package is a collection of functions
13996 that assist with and streamline modeling. It also contains functions for
13997 binary and ordinal logistic regression models, ordinal models for continuous Y
13998 with a variety of distribution families, and the Buckley-James multiple
13999 regression model for right-censored responses, and implements penalized
14000 maximum likelihood estimation for logistic and ordinary linear models. The
14001 package works with almost any regression model, but it was especially written
14002 to work with binary or ordinal regression models, Cox regression, accelerated
14003 failure time models, ordinary linear models, the Buckley-James model,
14004 generalized least squares for serially or spatially correlated observations,
14005 generalized linear models, and quantile regression.")
14006 (license license:gpl2+)))
14008 (define-public r-haplo-stats
14010 (name "r-haplo-stats")
14015 (uri (cran-uri "haplo.stats" version))
14018 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
14019 (properties `((upstream-name . "haplo.stats")))
14020 (build-system r-build-system)
14022 `(("r-rms" ,r-rms)))
14024 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
14025 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
14026 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
14028 "This package provides routines for the analysis of indirectly measured
14029 haplotypes. The statistical methods assume that all subjects are unrelated
14030 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
14031 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
14032 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
14033 examples in the vignette.")
14034 (license license:gpl2+)))
14036 (define-public r-bqtl
14043 (uri (cran-uri "bqtl" version))
14046 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14047 (build-system r-build-system)
14048 (native-inputs `(("gfortran" ,gfortran)))
14049 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14050 (synopsis "Bayesian QTL mapping toolkit")
14052 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14053 lines. It includes maximum likelihood and Bayesian tools.")
14054 (license license:gpl2+)))
14056 (define-public r-ibdreg
14063 (uri (cran-uri "ibdreg" version))
14066 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
14067 (build-system r-build-system)
14068 (home-page "https://www.mayo.edu/research/labs/\
14069 statistical-genetics-genetic-epidemiology/software")
14070 (synopsis "Regression methods for IBD linkage with covariates")
14072 "This package provides a method to test genetic linkage with covariates
14073 by regression methods with response IBD sharing for relative pairs. Account
14074 for correlations of IBD statistics and covariates for relative pairs within
14075 the same pedigree.")
14076 (license license:gpl2+)))
14078 (define-public r-dlmap
14085 (uri (cran-uri "dlmap" version))
14088 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14089 (build-system r-build-system)
14091 `(("r-ibdreg" ,r-ibdreg)
14095 ("r-wgaim" ,r-wgaim)))
14096 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14097 (synopsis "Detection localization mapping for QTL")
14099 "This is package for QTL mapping in a mixed model framework with separate
14100 detection and localization stages. The first stage detects the number of QTL
14101 on each chromosome based on the genetic variation due to grouped markers on
14102 the chromosome; the second stage uses this information to determine the most
14103 likely QTL positions. The mixed model can accommodate general fixed and
14104 random effects, including spatial effects in field trials and pedigree
14105 effects. It is applicable to backcrosses, doubled haploids, recombinant
14106 inbred lines, F2 intercrosses, and association mapping populations.")
14107 (license license:gpl2)))
14109 (define-public r-ldheatmap
14111 (name "r-ldheatmap")
14116 (uri (cran-uri "LDheatmap" version))
14119 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14120 (properties `((upstream-name . "LDheatmap")))
14121 (build-system r-build-system)
14123 `(("r-genetics" ,r-genetics)
14125 ("r-snpstats" ,r-snpstats)))
14126 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14127 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14129 "This package provides tools to produce a graphical display, as a heat
14130 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14131 optionally include the physical locations or genetic map distances of each SNP
14133 (license license:gpl3)))
14135 (define-public r-hwde
14142 (uri (cran-uri "hwde" version))
14145 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14146 (build-system r-build-system)
14147 (home-page "https://cran.r-project.org/web/packages/hwde/")
14148 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14150 "This package fits models for genotypic disequilibria, as described in
14151 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14152 terms are available that account for first order interactions between loci.
14153 It also implements, for a single locus in a single population, a conditional
14154 exact test for Hardy-Weinberg equilibrium.")
14155 (license license:gpl2+)))
14157 (define-public r-tdthap
14164 (uri (cran-uri "tdthap" version))
14167 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14168 (build-system r-build-system)
14169 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14170 (synopsis "TDT tests for extended haplotypes")
14172 "Functions and examples are provided for transmission/disequilibrium
14173 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14174 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14175 (license license:artistic2.0)))
14177 (define-public r-sparql
14183 (uri (cran-uri "SPARQL" version))
14186 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14187 (properties `((upstream-name . "SPARQL")))
14188 (build-system r-build-system)
14190 `(("r-rcurl" ,r-rcurl)
14192 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14193 (synopsis "SPARQL client for R")
14194 (description "This package provides an interface to use SPARQL to pose
14195 SELECT or UPDATE queries to an end-point.")
14196 ;; The only license indication is found in the DESCRIPTION file,
14197 ;; which states GPL-3. So we cannot assume GPLv3+.
14198 (license license:gpl3)))
14200 (define-public r-bookdown
14202 (name "r-bookdown")
14206 (uri (cran-uri "bookdown" version))
14209 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14210 (build-system r-build-system)
14212 `(("r-htmltools" ,r-htmltools)
14213 ("r-knitr" ,r-knitr)
14214 ("r-rmarkdown" ,r-rmarkdown)
14215 ("r-tinytex" ,r-tinytex)
14217 ("pandoc" ,ghc-pandoc)))
14218 (home-page "https://github.com/rstudio/bookdown")
14219 (synopsis "Authoring books and technical documents with R markdown")
14220 (description "This package provides output formats and utilities for
14221 authoring books and technical documents with R Markdown.")
14222 (license license:gpl3)))
14224 (define-public r-optparse
14226 (name "r-optparse")
14231 (uri (cran-uri "optparse" version))
14234 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14235 (build-system r-build-system)
14237 `(("r-getopt" ,r-getopt)))
14239 `(("r-knitr" ,r-knitr)))
14240 (home-page "https://github.com/trevorld/optparse")
14241 (synopsis "Command line option parser")
14243 "This package provides a command line parser inspired by Python's
14244 @code{optparse} library to be used with Rscript to write shebang scripts
14245 that accept short and long options.")
14246 (license license:gpl2+)))
14248 (define-public r-wgcna
14255 (uri (cran-uri "WGCNA" version))
14258 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14259 (properties `((upstream-name . "WGCNA")))
14260 (build-system r-build-system)
14262 `(("r-annotationdbi" ,r-annotationdbi)
14263 ("r-doparallel" ,r-doparallel)
14264 ("r-dynamictreecut" ,r-dynamictreecut)
14265 ("r-fastcluster" ,r-fastcluster)
14266 ("r-foreach" ,r-foreach)
14267 ("r-go-db" ,r-go-db)
14268 ("r-hmisc" ,r-hmisc)
14269 ("r-impute" ,r-impute)
14271 ("r-survival" ,r-survival)
14272 ("r-matrixstats" ,r-matrixstats)
14273 ("r-preprocesscore" ,r-preprocesscore)))
14275 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14276 (synopsis "Weighted correlation network analysis")
14278 "This package provides functions necessary to perform Weighted
14279 Correlation Network Analysis on high-dimensional data. It includes functions
14280 for rudimentary data cleaning, construction and summarization of correlation
14281 networks, module identification and functions for relating both variables and
14282 modules to sample traits. It also includes a number of utility functions for
14283 data manipulation and visualization.")
14284 (license license:gpl2+)))
14286 (define-public r-kernlab
14293 (uri (cran-uri "kernlab" version))
14295 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14296 (build-system r-build-system)
14297 (home-page "https://cran.r-project.org/web/packages/kernlab")
14298 (synopsis "Kernel-based machine learning tools")
14300 "This package provides kernel-based machine learning methods for
14301 classification, regression, clustering, novelty detection, quantile regression
14302 and dimensionality reduction. Among other methods @code{kernlab} includes
14303 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14305 (license license:gpl2)))
14307 (define-public r-hierfstat
14309 (name "r-hierfstat")
14310 (version "0.04-22")
14314 (uri (cran-uri "hierfstat" version))
14317 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
14318 (build-system r-build-system)
14320 `(("r-ade4" ,r-ade4)
14321 ("r-adegenet" ,r-adegenet)
14322 ("r-gtools" ,r-gtools)))
14323 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14324 (synopsis "Estimation and tests of hierarchical F-statistics")
14326 "This package allows the estimation of hierarchical F-statistics from
14327 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14328 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14329 are also given to test via randomisations the significance of each F and
14330 variance components, using the likelihood-ratio statistics G.")
14331 (license license:gpl2+)))
14333 (define-public r-hapassoc
14335 (name "r-hapassoc")
14340 (uri (cran-uri "hapassoc" version))
14343 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14344 (build-system r-build-system)
14345 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14346 (synopsis "Inference of trait associations with SNP haplotypes")
14348 "Hapassoc performs likelihood inference of trait associations with
14349 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14350 functions are developed primarily for data collected in cohort or
14351 cross-sectional studies. They can accommodate uncertain haplotype phase and
14352 handle missing genotypes at some SNPs.")
14353 (license license:gpl2)))
14355 (define-public r-sampling
14357 (name "r-sampling")
14362 (uri (cran-uri "sampling" version))
14365 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14366 (build-system r-build-system)
14368 `(("r-lpsolve" ,r-lpsolve)
14369 ("r-mass" ,r-mass)))
14370 (home-page "https://cran.r-project.org/web/packages/sampling/")
14371 (synopsis "Survey sampling")
14373 "This package provides functions for drawing and calibrating samples.")
14374 (license license:gpl2+)))
14376 (define-public r-r2html
14383 (uri (cran-uri "R2HTML" version))
14386 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14387 (properties `((upstream-name . "R2HTML")))
14388 (build-system r-build-system)
14389 (home-page "https://github.com/nalimilan/R2HTML")
14390 (synopsis "HTML export for R objects")
14392 "This package includes HTML functions and methods to write in an HTML
14393 file. Thus, making HTML reports is easy. It includes a function that allows
14394 redirection on the fly, which appears to be very useful for teaching purposes,
14395 as the student can keep a copy of the produced output to keep all that they
14396 did during the course. The package comes with a vignette describing how to
14397 write HTML reports for statistical analysis. Finally, a driver for Sweave
14398 parses HTML flat files containing R code and to automatically write
14399 the corresponding outputs (tables and graphs).")
14400 (license license:gpl2+)))
14402 (define-public r-rjava
14409 (uri (cran-uri "rJava" version))
14412 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
14413 (properties `((upstream-name . "rJava")))
14414 (build-system r-build-system)
14416 `(#:modules ((guix build utils)
14417 (guix build r-build-system)
14420 (modify-phases %standard-phases
14421 (add-after 'unpack 'set-JAVA_HOME
14422 (lambda* (#:key inputs #:allow-other-keys)
14423 (let ((jdk (assoc-ref inputs "jdk")))
14424 (setenv "JAVA_HOME" jdk)
14425 (setenv "JAVA" (which "java"))
14426 (setenv "JAR" (which "jar"))
14427 (setenv "JAVAC" (which "javac"))
14428 (setenv "JAVAH" (which "javah"))
14429 (setenv "JAVA_CPPFLAGS"
14430 (string-append "-I" jdk "/include "
14431 "-I" jdk "/include/linux"))
14432 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14433 ((lib) (setenv "JAVA_LIBS" lib))
14434 (_ (error "Could not find libjvm.so"))))
14438 ("jdk" ,icedtea-8 "jdk")
14441 (home-page "https://www.rforge.net/rJava/")
14442 (synopsis "Low-Level R to Java interface")
14444 "This package provides a low-level interface to the Java VM very much
14445 like .C/.Call and friends. It allows the creation of objects, calling methods
14446 and accessing fields.")
14447 (license license:gpl2)))
14449 (define-public r-svmisc
14456 (uri (cran-uri "svMisc" version))
14459 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14460 (properties `((upstream-name . "svMisc")))
14461 (build-system r-build-system)
14462 (home-page "https://github.com/SciViews/svMisc")
14463 (synopsis "Miscellaneous functions for SciViews")
14465 "This package provides miscellaneous functions for SciViews or general
14466 use, including tools to manage a temporary environment attached to the search
14467 path for temporary variables you do not want to @code{save()} or
14468 @code{load()}; test the current platform; showing progress bars, etc.")
14469 (license license:gpl2)))
14471 (define-public r-xyz
14478 (uri (cran-uri "xyz" version))
14481 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14482 (build-system r-build-system)
14484 `(("r-rcpp" ,r-rcpp)))
14485 (home-page "https://cran.r-project.org/web/packages/xyz/")
14486 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14488 "High dimensional interaction search by brute force requires a quadratic
14489 computational cost in the number of variables. The xyz algorithm provably
14490 finds strong interactions in almost linear time. For details of the algorithm
14491 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14492 interaction search in high-dimensional data.")
14493 ;; Any version of the GPL.
14494 (license license:gpl2+)))
14496 (define-public r-rttf2pt1
14498 (name "r-rttf2pt1")
14503 (uri (cran-uri "Rttf2pt1" version))
14506 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14507 (properties `((upstream-name . "Rttf2pt1")))
14508 (build-system r-build-system)
14509 (home-page "https://github.com/wch/Rttf2pt1")
14510 (synopsis "Font conversion utility")
14512 "This package contains the program @code{ttf2pt1}, for use with the
14513 @code{extrafont} package.")
14514 ;; Most of the files are covered under the Expat license. Some files are
14515 ;; covered under BSD-3. Deviations for individual files are recorded in
14516 ;; the LICENSE file.
14517 (license (list license:bsd-3 license:expat
14518 (license:non-copyleft "file://LICENSE")))))
14520 (define-public r-extrafontdb
14522 (name "r-extrafontdb")
14527 (uri (cran-uri "extrafontdb" version))
14530 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14531 (build-system r-build-system)
14532 (home-page "https://github.com/wch/extrafontdb")
14533 (synopsis "Database for the extrafont package")
14535 "This package holds the database for the @code{extrafont} package.")
14536 (license license:gpl2)))
14538 (define-public r-extrafont
14540 (name "r-extrafont")
14545 (uri (cran-uri "extrafont" version))
14548 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14549 (build-system r-build-system)
14551 `(("r-extrafontdb" ,r-extrafontdb)
14552 ("r-rttf2pt1" ,r-rttf2pt1)))
14553 (home-page "https://github.com/wch/extrafont")
14554 (synopsis "Tools for using fonts in R")
14556 "The extrafont package makes it easier to use fonts other than the basic
14557 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14558 used with PDF or PostScript output files. There are two hurdles for using
14559 fonts in PDF (or Postscript) output files:
14562 @item Making R aware of the font and the dimensions of the characters.
14563 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14564 properly on a device that doesn't have the font. This is usually needed if
14565 you want to print the PDF file or share it with others.
14568 The extrafont package makes both of these things easier.")
14569 (license license:gpl2)))
14571 (define-public r-xkcd
14578 (uri (cran-uri "xkcd" version))
14581 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14582 (build-system r-build-system)
14584 `(("r-extrafont" ,r-extrafont)
14585 ("r-ggplot2" ,r-ggplot2)
14586 ("r-hmisc" ,r-hmisc)))
14587 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14588 (synopsis "Plot ggplot2 graphics in the XKCD style")
14590 "This package provides the means to plot ggplot2 graphs in the style of
14591 the XKCD web comic.")
14592 (license license:gpl3)))
14594 (define-public r-msigdbr
14601 (uri (cran-uri "msigdbr" version))
14604 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14605 (build-system r-build-system)
14607 `(("r-dplyr" ,r-dplyr)
14608 ("r-magrittr" ,r-magrittr)
14609 ("r-rlang" ,r-rlang)
14610 ("r-tibble" ,r-tibble)))
14612 `(("r-knitr" ,r-knitr)))
14613 (home-page "https://github.com/igordot/msigdbr")
14614 (synopsis "MSigDB gene sets for multiple organisms")
14616 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14617 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14618 software in a standard R data frame with key-value pairs. Included are the
14619 original human gene symbols and Entrez IDs as well as the equivalents for
14620 various frequently studied model organisms such as mouse, rat, pig, fly, and
14622 ;; The package is covered under the Expat license, but the upstream MSigDB
14623 ;; files are made available under the Creative Commons Attribution 4.0
14624 ;; International license.
14625 (license (list license:expat license:cc-by4.0))))
14627 (define-public r-gridgraphics
14629 (name "r-gridgraphics")
14634 (uri (cran-uri "gridGraphics" version))
14637 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14638 (properties `((upstream-name . "gridGraphics")))
14639 (build-system r-build-system)
14640 (home-page "https://github.com/pmur002/gridgraphics")
14641 (synopsis "Redraw base graphics using @code{grid} graphics")
14643 "This package provides functions to convert a page of plots drawn with
14644 the @code{graphics} package into identical output drawn with the @code{grid}
14645 package. The result looks like the original @code{graphics}-based plot, but
14646 consists of @code{grid} grobs and viewports that can then be manipulated with
14647 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14648 (license license:gpl2+)))
14650 (define-public r-farver
14657 (uri (cran-uri "farver" version))
14660 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14661 (build-system r-build-system)
14662 (home-page "https://github.com/thomasp85/farver")
14663 (synopsis "Vectorized color conversion and comparison")
14665 "The encoding of color can be handled in many different ways, using
14666 different color spaces. As different color spaces have different uses,
14667 efficient conversion between these representations are important. This
14668 package provides a set of functions that gives access to very fast color space
14669 conversion and comparisons implemented in C++, and offers 100-fold speed
14670 improvements over the @code{convertColor} function in the @code{grDevices}
14672 (license license:expat)))
14674 (define-public r-ggplotify
14676 (name "r-ggplotify")
14681 (uri (cran-uri "ggplotify" version))
14684 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14685 (build-system r-build-system)
14687 `(("r-ggplot2" ,r-ggplot2)
14688 ("r-gridgraphics" ,r-gridgraphics)
14689 ("r-rvcheck" ,r-rvcheck)))
14691 `(("r-knitr" ,r-knitr)))
14692 (home-page "https://github.com/GuangchuangYu/ggplotify")
14693 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14695 "This package provides tools to convert plot function calls (using
14696 expression or formula) to @code{grob} or @code{ggplot} objects that are
14697 compatible with the @code{grid} and @code{ggplot2} environment. With this
14698 package, we are able to e.g. use @code{cowplot} to align plots produced by
14699 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14700 converting them to @code{ggplot} objects.")
14701 (license license:artistic2.0)))
14703 (define-public r-triebeard
14705 (name "r-triebeard")
14710 (uri (cran-uri "triebeard" version))
14713 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14714 (build-system r-build-system)
14715 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14716 (home-page "https://github.com/Ironholds/triebeard/")
14717 (synopsis "Radix trees in Rcpp")
14719 "Radix trees, or tries, are key-value data structures optimized for
14720 efficient lookups, similar in purpose to hash tables. This package provides
14721 an implementation of radix trees for use in R programming and in developing
14722 packages with Rcpp.")
14723 (license license:expat)))
14725 (define-public r-tweenr
14732 (uri (cran-uri "tweenr" version))
14735 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14736 (build-system r-build-system)
14738 `(("r-farver" ,r-farver)
14739 ("r-magrittr" ,r-magrittr)
14741 ("r-rlang" ,r-rlang)))
14742 (home-page "https://github.com/thomasp85/tweenr")
14743 (synopsis "Interpolate data for smooth animations")
14745 "In order to create smooth animation between states of data, tweening is
14746 necessary. This package provides a range of functions for creating tweened
14747 data that can be used as basis for animation. Furthermore it adds a number of
14748 vectorized interpolaters for common R data types such as numeric, date and
14750 (license license:expat)))
14752 (define-public r-polyclip
14754 (name "r-polyclip")
14759 (uri (cran-uri "polyclip" version))
14762 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14763 (build-system r-build-system)
14764 (native-inputs `(("pkg-config" ,pkg-config)))
14765 (home-page "http://www.angusj.com/delphi/clipper.php")
14766 (synopsis "Polygon clipping")
14768 "This package provides an R port of the library Clipper. It performs
14769 polygon clipping operations (intersection, union, set minus, set difference)
14770 for polygonal regions of arbitrary complexity, including holes. It computes
14771 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14772 dilations) for polygonal regions and polygonal lines. It computes the
14773 Minkowski Sum of general polygons. There is a function for removing
14774 self-intersections from polygon data.")
14775 (license license:boost1.0)))
14777 (define-public r-urltools
14779 (name "r-urltools")
14784 (uri (cran-uri "urltools" version))
14787 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14788 (build-system r-build-system)
14790 `(("r-rcpp" ,r-rcpp)
14791 ("r-triebeard" ,r-triebeard)))
14792 (home-page "https://github.com/Ironholds/urltools/")
14793 (synopsis "Vectorized tools for URL handling and parsing")
14795 "This package provides a toolkit for all URL-handling needs, including
14796 encoding and decoding, parsing, parameter extraction and modification. All
14797 functions are designed to be both fast and entirely vectorized. It is
14798 intended to be useful for people dealing with web-related datasets, such as
14799 server-side logs, although may be useful for other situations involving large
14801 (license license:expat)))
14803 (define-public r-ggforce
14810 (uri (cran-uri "ggforce" version))
14813 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
14814 (build-system r-build-system)
14816 `(("r-ggplot2" ,r-ggplot2)
14817 ("r-gtable" ,r-gtable)
14819 ("r-polyclip" ,r-polyclip)
14821 ("r-rcppeigen" ,r-rcppeigen)
14822 ("r-rlang" ,r-rlang)
14823 ("r-scales" ,r-scales)
14824 ("r-tidyselect" ,r-tidyselect)
14825 ("r-tweenr" ,r-tweenr)
14826 ("r-withr" ,r-withr)))
14827 (home-page "https://ggforce.data-imaginist.com")
14828 (synopsis "Accelerating ggplot2")
14830 "The aim of the ggplot2 package is to aid in visual data investigations.
14831 This focus has led to a lack of facilities for composing specialized plots.
14832 Thi package aims to be a collection of mainly new statistics and geometries
14833 that fills this gap.")
14834 (license license:expat)))
14836 (define-public r-europepmc
14838 (name "r-europepmc")
14843 (uri (cran-uri "europepmc" version))
14846 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14847 (build-system r-build-system)
14849 `(("r-dplyr" ,r-dplyr)
14851 ("r-jsonlite" ,r-jsonlite)
14853 ("r-progress" ,r-progress)
14854 ("r-purrr" ,r-purrr)
14855 ("r-rlang" ,r-rlang)
14856 ("r-tibble" ,r-tibble)
14857 ("r-tidyr" ,r-tidyr)
14858 ("r-urltools" ,r-urltools)
14859 ("r-xml2" ,r-xml2)))
14861 `(("r-knitr" ,r-knitr)))
14862 (home-page "https://github.com/ropensci/europepmc/")
14863 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14865 "This package provides an R Client for the
14866 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14867 Service}. It gives access to both metadata on life science literature and
14868 open access full texts. Europe PMC indexes all PubMed content and other
14869 literature sources including Agricola, a bibliographic database of citations
14870 to the agricultural literature, or Biological Patents. In addition to
14871 bibliographic metadata, the client allows users to fetch citations and
14872 reference lists. Links between life-science literature and other EBI
14873 databases, including ENA, PDB or ChEMBL are also accessible.")
14874 (license license:gpl3)))
14876 (define-public r-ggraph
14883 (uri (cran-uri "ggraph" version))
14886 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14887 (build-system r-build-system)
14889 `(("r-digest" ,r-digest)
14890 ("r-dplyr" ,r-dplyr)
14891 ("r-ggforce" ,r-ggforce)
14892 ("r-ggplot2" ,r-ggplot2)
14893 ("r-ggrepel" ,r-ggrepel)
14894 ("r-graphlayouts" ,r-graphlayouts)
14895 ("r-gtable" ,r-gtable)
14896 ("r-igraph" ,r-igraph)
14899 ("r-rlang" ,r-rlang)
14900 ("r-scales" ,r-scales)
14901 ("r-tidygraph" ,r-tidygraph)
14902 ("r-viridis" ,r-viridis)))
14904 `(("r-knitr" ,r-knitr)))
14905 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14906 (synopsis "Implementation of grammar of graphics for graphs and networks")
14908 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14909 graph and network visualizations due to its reliance on tabular data input.
14910 The ggraph package is an extension of the ggplot2 API tailored to graph
14911 visualizations and provides the same flexible approach to building up plots
14913 (license license:gpl3)))
14915 (define-public r-varselrf
14917 (name "r-varselrf")
14922 (uri (cran-uri "varSelRF" version))
14925 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14926 (properties `((upstream-name . "varSelRF")))
14927 (build-system r-build-system)
14929 `(("r-randomforest" ,r-randomforest)))
14930 (home-page "https://www.ligarto.org/rdiaz/software/software")
14931 (synopsis "Variable selection using random forests")
14933 "This package provides tools for the variable selection from random
14934 forests using both backwards variable elimination (for the selection of small
14935 sets of non-redundant variables) and selection based on the importance
14936 spectrum (somewhat similar to scree plots; for the selection of large,
14937 potentially highly-correlated variables). The main applications are in
14938 high-dimensional data (e.g., microarray data, and other genomics and
14939 proteomics applications).")
14940 (license license:gpl2+)))
14942 (define-public r-pamr
14949 (uri (cran-uri "pamr" version))
14952 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14953 (build-system r-build-system)
14955 `(("r-cluster" ,r-cluster)
14956 ("r-survival" ,r-survival)))
14957 (native-inputs `(("gfortran" ,gfortran)))
14958 (home-page "https://cran.r-project.org/web/packages/pamr/")
14959 (synopsis "Prediction Analysis for Microarrays")
14961 "This package provides some functions for sample classification in
14963 (license license:gpl2)))
14965 (define-public r-rda
14968 (version "1.0.2-2.1")
14972 (uri (cran-uri "rda" version))
14975 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14976 (build-system r-build-system)
14977 (home-page "https://cran.r-project.org/web/packages/rda/")
14978 (synopsis "Shrunken centroids regularized discriminant analysis")
14980 "This package provides tools for shrunken centroids regularized
14981 discriminant analysis for the purpose of classifying high dimensional data.")
14982 (license license:gpl2+)))
14984 (define-public r-ggvis
14991 (uri (cran-uri "ggvis" version))
14994 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14995 (build-system r-build-system)
14997 `(("r-assertthat" ,r-assertthat)
14998 ("r-dplyr" ,r-dplyr)
14999 ("r-htmltools" ,r-htmltools)
15000 ("r-jsonlite" ,r-jsonlite)
15001 ("r-lazyeval" ,r-lazyeval)
15002 ("r-magrittr" ,r-magrittr)
15003 ("r-shiny" ,r-shiny)))
15004 (home-page "https://ggvis.rstudio.com/")
15005 (synopsis "Interactive grammar of graphics")
15007 "This package is a data visualization package for R providing an
15008 implementation of an interactive grammar of graphics, taking the best parts of
15009 ggplot2, combining them with the reactive framework of Shiny and drawing web
15010 graphics using Vega.")
15011 (license license:gpl2)))
15013 (define-public r-gbm
15020 (uri (cran-uri "gbm" version))
15023 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
15024 (build-system r-build-system)
15026 `(("r-gridextra" ,r-gridextra)
15027 ("r-lattice" ,r-lattice)
15028 ("r-survival" ,r-survival)))
15029 (home-page "https://github.com/gbm-developers/gbm")
15030 (synopsis "Generalized boosted regression models")
15032 "This package is an implementation of extensions to Freund and Schapire's
15033 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
15034 regression methods for least squares, absolute loss, t-distribution loss,
15035 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15036 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15037 and Learning to Rank measures (LambdaMart).")
15038 (license license:gpl2+)))
15040 (define-public r-threejs
15047 (uri (cran-uri "threejs" version))
15050 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15051 (build-system r-build-system)
15053 `(#:modules ((guix build utils)
15054 (guix build r-build-system)
15058 (modify-phases %standard-phases
15059 (add-after 'unpack 'process-javascript
15060 (lambda* (#:key inputs #:allow-other-keys)
15061 (with-directory-excursion "inst"
15065 `((,(assoc-ref inputs "js-jquery")
15066 "htmlwidgets/lib/jquery/jquery.min.js")
15067 (,(assoc-ref inputs "js-threejs-111")
15068 "htmlwidgets/lib/threejs-111/three.min.js"))))
15069 (lambda (sources targets)
15070 (for-each (lambda (source target)
15071 (format #t "Processing ~a --> ~a~%"
15073 (delete-file target)
15074 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15075 (call-with-output-file target
15077 (dump-port minified port)))))
15078 sources targets))))
15081 `(("r-base64enc" ,r-base64enc)
15082 ("r-crosstalk" ,r-crosstalk)
15083 ("r-htmlwidgets" ,r-htmlwidgets)
15084 ("r-igraph" ,r-igraph)))
15086 `(("uglify-js" ,uglify-js)
15090 (uri "https://code.jquery.com/jquery-1.12.4.js")
15093 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15097 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15100 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15101 (home-page "https://bwlewis.github.io/rthreejs")
15102 (synopsis "Interactive 3D scatter plots, networks and globes")
15104 "Create interactive 3D scatter plots, network plots, and globes in R
15105 using the three.js visualization library.")
15106 (license license:expat)))
15108 (define-public r-mlbench
15115 (uri (cran-uri "mlbench" version))
15118 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15119 (build-system r-build-system)
15120 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15121 (synopsis "Machine learning benchmark problems")
15123 "This package provides a collection of artificial and real-world machine
15124 learning benchmark problems, including, e.g., several data sets from the UCI
15126 (license license:gpl2)))
15128 (define-public r-mpm
15135 (uri (cran-uri "mpm" version))
15138 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15139 (build-system r-build-system)
15141 `(("r-kernsmooth" ,r-kernsmooth)
15142 ("r-mass" ,r-mass)))
15143 (home-page "http://mpm.r-forge.r-project.org")
15144 (synopsis "Multivariate projection methods")
15146 "This is a package for exploratory graphical analysis of multivariate
15147 data, specifically gene expression data with different projection methods:
15148 principal component analysis, correspondence analysis, spectral map
15150 (license license:gpl2+)))
15152 (define-public r-png
15158 (uri (cran-uri "png" version))
15161 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15162 (build-system r-build-system)
15164 `(("libpng" ,libpng)
15166 (home-page "https://www.rforge.net/png/")
15167 (synopsis "Read and write PNG images")
15169 "This package provides an easy and simple way to read, write and display
15170 bitmap images stored in the PNG format. It can read and write both files and
15171 in-memory raw vectors.")
15172 ;; Any of these GPL versions.
15173 (license (list license:gpl2 license:gpl3))))
15175 (define-public r-ggcorrplot
15177 (name "r-ggcorrplot")
15182 (uri (cran-uri "ggcorrplot" version))
15185 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15186 (build-system r-build-system)
15188 `(("r-ggplot2" ,r-ggplot2)
15189 ("r-reshape2" ,r-reshape2)))
15190 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15191 (synopsis "Visualization of a correlation matrix using ggplot2")
15193 "The ggcorrplot package can be used to visualize easily a correlation
15194 matrix using ggplot2. It provides a solution for reordering the correlation
15195 matrix and displays the significance level on the plot. It also includes a
15196 function for computing a matrix of correlation p-values.")
15197 (license license:gpl2)))
15199 ;; This package includes minified JavaScript files. When upgrading please
15200 ;; check that there are no new minified JavaScript files.
15201 (define-public r-flexdashboard
15203 (name "r-flexdashboard")
15208 (uri (cran-uri "flexdashboard" version))
15211 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15212 (modules '((guix build utils)))
15215 ;; Delete bundled minified JavaScript files
15216 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15217 (delete-file "inst/www/sly/sly.min.js")
15218 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15219 (delete-file "inst/www/prism/prism.js")
15221 (build-system r-build-system)
15223 `(#:modules ((guix build utils)
15224 (guix build r-build-system)
15228 (ice-9 textual-ports))
15230 (modify-phases %standard-phases
15231 (add-after 'unpack 'process-javascript
15232 (lambda* (#:key inputs #:allow-other-keys)
15233 (with-directory-excursion "inst"
15234 ;; Concatenate all components of prism.js
15235 (let ((contents (string-join
15236 (map (lambda (name)
15237 (call-with-input-file
15238 (assoc-ref inputs name)
15242 "js-prism-line-numbers"))
15244 (call-with-output-file "prism-src.js"
15245 (cut display contents <>)))
15249 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15250 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15252 "www/sly/sly.min.js")
15254 "www/prism/prism.js")
15255 (,(assoc-ref inputs "js-raphael")
15256 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15257 (,(assoc-ref inputs "js-featherlight")
15258 "www/featherlight/featherlight.min.js"))))
15259 (lambda (sources targets)
15260 (for-each (lambda (source target)
15261 (format #t "Processing ~a --> ~a~%"
15263 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15264 (call-with-output-file target
15266 (dump-port minified port)))))
15267 sources targets))))
15270 `(("r-htmltools" ,r-htmltools)
15271 ("r-htmlwidgets" ,r-htmlwidgets)
15272 ("r-jsonlite" ,r-jsonlite)
15273 ("r-knitr" ,r-knitr)
15274 ("r-rmarkdown" ,r-rmarkdown)
15275 ("r-shiny" ,r-shiny)))
15277 `(("uglify-js" ,uglify-js)
15281 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15284 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15288 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15291 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15295 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15298 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15299 ("js-prism-line-numbers"
15302 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15305 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15309 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15312 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15313 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15314 (synopsis "R Markdown format for flexible dashboards")
15316 "This package provides an R Markdown format for converting an R Markdown
15317 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15318 of its components to the containing web page.")
15319 (license license:expat)))
15321 (define-public r-preseqr
15328 (uri (cran-uri "preseqR" version))
15331 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15332 (properties `((upstream-name . "preseqR")))
15333 (build-system r-build-system)
15335 `(("r-polynom" ,r-polynom)))
15336 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15337 (synopsis "Predicting species accumulation curves")
15339 "This package can be used to predict the r-species accumulation
15340 curve (r-SAC), which is the number of species represented at least r times as
15341 a function of the sampling effort. When r = 1, the curve is known as the
15342 species accumulation curve, or the library complexity curve in high-throughput
15343 genomic sequencing. The package includes both parametric and nonparametric
15344 methods, as described by Deng C, et al. (2018).")
15345 (license license:gpl3)))
15347 (define-public r-mapplots
15349 (name "r-mapplots")
15354 (uri (cran-uri "mapplots" version))
15357 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15358 (build-system r-build-system)
15359 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15360 (synopsis "Data visualization on maps")
15362 "This package helps you create simple maps; add sub-plots like pie plots
15363 to a map or any other plot; format, plot and export gridded data. The package
15364 was developed for displaying fisheries data but most functions can be used for
15365 more generic data visualisation.")
15366 (license license:gpl2+)))
15368 (define-public r-pmcmr
15375 (uri (cran-uri "PMCMR" version))
15378 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15379 (properties `((upstream-name . "PMCMR")))
15380 (build-system r-build-system)
15381 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15382 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15384 "This is a deprecated package for calculating pairwise multiple
15385 comparisons of mean rank sums. This package is superseded by the novel
15386 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15387 compatibility of dependent packages for some time.")
15388 (license license:gpl3+)))
15390 (define-public r-downloader
15392 (name "r-downloader")
15397 (uri (cran-uri "downloader" version))
15400 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15401 (build-system r-build-system)
15403 `(("r-digest" ,r-digest)))
15404 (home-page "https://github.com/wch/downloader")
15405 (synopsis "Download files over HTTP and HTTPS")
15407 "This package provides a wrapper for the @code{download.file} function,
15408 making it possible to download files over HTTPS across platforms. The
15409 @code{RCurl} package provides this functionality (and much more) but has
15410 external dependencies. This package has is implemented purely in R.")
15411 (license license:gpl2)))
15413 (define-public r-rex
15420 (uri (cran-uri "rex" version))
15423 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15424 (build-system r-build-system)
15426 `(("r-lazyeval" ,r-lazyeval)))
15428 `(("r-knitr" ,r-knitr)))
15429 (home-page "https://github.com/kevinushey/rex")
15430 (synopsis "Friendly regular expressions")
15432 "This package provides a friendly interface for the construction of
15433 regular expressions. Regular expressions are a very powerful feature, however
15434 they are often difficult to interpret. Rex allows you to build complex
15435 regular expressions from human readable expressions")
15436 (license license:expat)))
15438 (define-public r-xmlparsedata
15440 (name "r-xmlparsedata")
15445 (uri (cran-uri "xmlparsedata" version))
15448 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15449 (properties `((upstream-name . "xmlparsedata")))
15450 (build-system r-build-system)
15451 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15452 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15454 "This package provides tools to convert the output of
15455 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15456 @code{XPath}, and is easier to manipulate in general.")
15457 (license license:expat)))
15459 (define-public r-cyclocomp
15461 (name "r-cyclocomp")
15466 (uri (cran-uri "cyclocomp" version))
15469 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15470 (properties `((upstream-name . "cyclocomp")))
15471 (build-system r-build-system)
15473 `(("r-callr" ,r-callr)
15474 ("r-crayon" ,r-crayon)
15476 ("r-remotes" ,r-remotes)
15477 ("r-withr" ,r-withr)))
15478 (home-page "https://github.com/MangoTheCat/cyclocomp")
15479 (synopsis "Cyclomatic complexity of R code")
15481 "Cyclomatic complexity is a software metric, used to indicate the
15482 complexity of a program. It is a quantitative measure of the number of
15483 linearly independent paths through a program's source code. This package
15484 provides tools to compute this metric.")
15485 (license license:expat)))
15487 (define-public r-lintr
15494 (uri (cran-uri "lintr" version))
15497 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15498 (properties `((upstream-name . "lintr")))
15499 (build-system r-build-system)
15501 `(("r-codetools" ,r-codetools)
15502 ("r-crayon" ,r-crayon)
15503 ("r-cyclocomp" ,r-cyclocomp)
15504 ("r-digest" ,r-digest)
15506 ("r-jsonlite" ,r-jsonlite)
15507 ("r-knitr" ,r-knitr)
15509 ("r-rstudioapi" ,r-rstudioapi)
15510 ("r-testthat" ,r-testthat)
15512 ("r-xmlparsedata" ,r-xmlparsedata)))
15513 (home-page "https://github.com/jimhester/lintr")
15514 (synopsis "Linter for R code")
15515 (description "This package checks adherence to a given style, syntax
15516 errors and possible semantic issues. It supports on the fly checking of R
15517 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15518 (license license:expat)))
15520 (define-public r-sctransform
15522 (name "r-sctransform")
15527 (uri (cran-uri "sctransform" version))
15530 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15531 (build-system r-build-system)
15533 `(("r-future-apply" ,r-future-apply)
15534 ("r-ggplot2" ,r-ggplot2)
15535 ("r-gridextra" ,r-gridextra)
15537 ("r-matrix" ,r-matrix)
15539 ("r-rcppeigen" ,r-rcppeigen)
15540 ("r-reshape2" ,r-reshape2)))
15541 (home-page "https://github.com/ChristophH/sctransform")
15542 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15544 "This package provides a normalization method for single-cell UMI count
15545 data using a variance stabilizing transformation. The transformation is based
15546 on a negative binomial regression model with regularized parameters. As part
15547 of the same regression framework, this package also provides functions for
15548 batch correction, and data correction.")
15549 (license license:gpl3)))
15551 (define-public r-styler
15558 (uri (cran-uri "styler" version))
15561 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15562 (build-system r-build-system)
15564 `(("r-backports" ,r-backports)
15566 ("r-magrittr" ,r-magrittr)
15567 ("r-purrr" ,r-purrr)
15568 ("r-r-cache" ,r-r-cache)
15569 ("r-rematch2" ,r-rematch2)
15570 ("r-rlang" ,r-rlang)
15571 ("r-rprojroot" ,r-rprojroot)
15572 ("r-tibble" ,r-tibble)
15573 ("r-withr" ,r-withr)
15574 ("r-xfun" ,r-xfun)))
15575 (home-page "https://github.com/r-lib/styler")
15576 (synopsis "Non-invasive pretty printing of R code")
15578 "This is a package for pretty-printing R code without changing the user's
15579 formatting intent.")
15580 (license license:gpl3)))
15582 (define-public r-scrime
15589 (uri (cran-uri "scrime" version))
15592 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15593 (build-system r-build-system)
15594 (home-page "https://cran.r-project.org/web/packages/scrime/")
15595 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15597 "This package provides tools for the analysis of high-dimensional data
15598 developed/implemented at the group \"Statistical Complexity Reduction In
15599 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15600 the functions can also be applied to other types of categorical data.")
15601 (license license:gpl2)))
15603 (define-public r-pbmcapply
15605 (name "r-pbmcapply")
15610 (uri (cran-uri "pbmcapply" version))
15613 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15614 (build-system r-build-system)
15615 (home-page "https://github.com/kvnkuang/pbmcapply")
15616 (synopsis "Track the progress of apply procedures with a progress bar")
15618 "This light-weight package helps you track and visualize the progress of
15619 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15620 (license license:expat)))
15622 (define-public r-blme
15629 (uri (cran-uri "blme" version))
15632 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15633 (build-system r-build-system)
15634 (propagated-inputs `(("r-lme4" ,r-lme4)))
15635 (home-page "https://github.com/vdorie/blme")
15636 (synopsis "Bayesian linear mixed-effects models")
15638 "This package provides tools for maximum a posteriori estimation for
15639 linear and generalized linear mixed-effects models in a Bayesian setting. It
15640 extends the lme4 package.")
15641 (license license:gpl2+)))
15643 (define-public r-batchtools
15645 (name "r-batchtools")
15650 (uri (cran-uri "batchtools" version))
15653 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15654 (build-system r-build-system)
15656 `(("r-backports" ,r-backports)
15657 ("r-base64url" ,r-base64url)
15659 ("r-checkmate" ,r-checkmate)
15660 ("r-data-table" ,r-data-table)
15661 ("r-digest" ,r-digest)
15663 ("r-progress" ,r-progress)
15665 ("r-rappdirs" ,r-rappdirs)
15666 ("r-stringi" ,r-stringi)
15667 ("r-withr" ,r-withr)))
15669 `(("r-knitr" ,r-knitr)))
15670 (home-page "https://github.com/mllg/batchtools")
15671 (synopsis "Tools for computation on batch systems")
15673 "As a successor of the packages BatchJobs and BatchExperiments, this
15674 package provides a parallel implementation of the Map function for high
15675 performance computing systems managed by various schedulers. A multicore and
15676 socket mode allow the parallelization on a local machines, and multiple
15677 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15678 the package provides an abstraction mechanism to define large-scale computer
15679 experiments in a well-organized and reproducible way.")
15680 (license license:lgpl3)))
15682 (define-public r-clue
15689 (uri (cran-uri "clue" version))
15692 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15693 (build-system r-build-system)
15694 (propagated-inputs `(("r-cluster" ,r-cluster)))
15695 (home-page "https://cran.r-project.org/web/packages/clue/")
15696 (synopsis "Tools for analyzing cluster ensembles")
15697 (description "Cluster ensembles are collections of individual solutions to
15698 a given clustering problem which are useful or necessary to consider in a wide
15699 range of applications. This R package provides an extensible computational
15700 environment for creating and analyzing cluster ensembles, with basic data
15701 structures for representing partitions and hierarchies, and facilities for
15702 computing on them, including methods for measuring proximity and obtaining
15703 consensus and secondary clusterings.")
15704 (license license:gpl2)))
15706 (define-public r-sitmo
15713 (uri (cran-uri "sitmo" version))
15716 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15717 (build-system r-build-system)
15718 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15719 (home-page "https://github.com/coatless/sitmo/")
15720 (synopsis "Parallel pseudo random number generator header files")
15722 "This package provides two high quality and fast PPRNGs that may be used
15723 in an OpenMP parallel environment. In addition, there is a generator for one
15724 dimensional low-discrepancy sequence.")
15725 (license license:expat)))
15727 (define-public r-dqrng
15734 (uri (cran-uri "dqrng" version))
15737 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15738 (build-system r-build-system)
15742 ("r-sitmo" ,r-sitmo)))
15743 (home-page "https://www.daqana.org/dqrng")
15744 (synopsis "Fast pseudo random number generators")
15746 "Several fast random number generators are provided as C++ header-only
15747 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15748 Additionally, fast functions for generating random numbers according to a
15749 uniform, normal and exponential distribution are included. The latter two use
15750 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15751 functions are exported to R and as a C++ interface and are enabled for use
15752 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15753 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15754 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15755 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15756 ;; whole is distributed under the terms of the AGPL 3.
15757 (license license:agpl3)))
15759 (define-public r-ingredients
15761 (name "r-ingredients")
15766 (uri (cran-uri "ingredients" version))
15769 "1mp1rgi3nnr8mjddpbyi24zvqcbihz0d8np2j13cbjc089n6jci8"))))
15770 (properties `((upstream-name . "ingredients")))
15771 (build-system r-build-system)
15773 `(("r-ggplot2" ,r-ggplot2)
15774 ("r-gridextra" ,r-gridextra)
15775 ("r-scales" ,r-scales)))
15776 (native-inputs `(("r-knitr" ,r-knitr)))
15777 (home-page "https://ModelOriented.github.io/ingredients/")
15778 (synopsis "Effects and importances of model ingredients")
15780 "This is a collection of tools for assessment of feature importance and
15781 feature effects. Key functions are:
15784 @item @code{feature_importance()} for assessment of global level feature
15786 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15787 @item @code{partial_dependence()} for partial dependence plots,
15788 @item @code{conditional_dependence()} for conditional dependence plots,
15789 @item @code{accumulated_dependence()} for accumulated local effects plots,
15790 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15791 aggregation of ceteris paribus profiles,
15792 @item generic @code{print()} and @code{plot()} for better usability of
15793 selected explainers,
15794 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15795 @item generic @code{describe()} for explanations in natural language.
15797 (license license:gpl3)))
15799 (define-public r-ibreakdown
15801 (name "r-ibreakdown")
15806 (uri (cran-uri "iBreakDown" version))
15809 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15810 (properties `((upstream-name . "iBreakDown")))
15811 (build-system r-build-system)
15812 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15813 (native-inputs `(("r-knitr" ,r-knitr)))
15814 (home-page "https://ModelOriented.github.io/iBreakDown/")
15815 (synopsis "Model agnostic instance level variable attributions")
15817 "This package provides a model agnostic tool for decomposition of
15818 predictions from black boxes. It supports additive attributions and
15819 attributions with interactions. The Break Down Table shows contributions of
15820 every variable to a final prediction. The Break Down Plot presents variable
15821 contributions in a concise graphical way. This package works for
15822 classification and regression models.")
15823 (license license:gpl3)))
15825 (define-public r-dae
15832 (uri (cran-uri "dae" version))
15835 "14q3cxhcz0zqjdkas0dl71k2bp5qwvb60gha47s78hdr38r46kml"))))
15836 (build-system r-build-system)
15838 `(("r-ggplot2" ,r-ggplot2)
15839 ("r-plyr" ,r-plyr)))
15841 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
15842 (home-page "http://chris.brien.name")
15843 (synopsis "Functions useful in the design and ANOVA of experiments")
15845 "This package provides functions useful in the design and ANOVA of
15846 experiments. The content falls into the following groupings:
15850 @item factor manipulation functions,
15851 @item design functions,
15852 @item ANOVA functions,
15853 @item matrix functions,
15854 @item projector and canonical efficiency functions, and
15855 @item miscellaneous functions.
15858 There is a vignette called @code{DesignNotes} describing how to use the design
15859 functions for randomizing and assessing designs. The ANOVA functions
15860 facilitate the extraction of information when the @code{Error} function has
15861 been used in the call to @code{aov}.")
15862 (license license:gpl2)))
15864 (define-public r-dalex
15871 (uri (cran-uri "DALEX" version))
15874 "1azbnykaddsfp2qmxmhpjz76zg78msxv6n2jqkq4gwbgqa5vdfd2"))))
15875 (properties `((upstream-name . "DALEX")))
15876 (build-system r-build-system)
15878 `(("r-ggplot2" ,r-ggplot2)
15879 ("r-ibreakdown" ,r-ibreakdown)
15880 ("r-ingredients" ,r-ingredients)))
15881 (home-page "https://pbiecek.github.io/DALEX/")
15882 (synopsis "Descriptive machine learning explanations")
15884 "Machine Learning models are widely used and have various applications in
15885 classification or regression. Models created with boosting, bagging, stacking
15886 or similar techniques are often used due to their high performance, but such
15887 black-box models usually lack interpretability. The DALEX package contains
15888 various explainers that help to understand the link between input variables
15889 and model output.")
15890 ;; Any version of the GPL
15891 (license license:gpl3+)))
15893 (define-public r-enrichr
15900 (uri (cran-uri "enrichR" version))
15903 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15904 (properties `((upstream-name . "enrichR")))
15905 (build-system r-build-system)
15907 `(("r-httr" ,r-httr)
15908 ("r-rjson" ,r-rjson)))
15909 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15910 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15912 "This package provides an R interface to all Enrichr databases, a
15913 web-based tool for analyzing gene sets and returns any enrichment of common
15914 annotated biological functions.")
15915 (license license:gpl2+)))
15917 (define-public r-plot3d
15924 (uri (cran-uri "plot3D" version))
15927 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15928 (properties `((upstream-name . "plot3D")))
15929 (build-system r-build-system)
15930 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15931 (home-page "https://cran.r-project.org/web/packages/plot3D")
15932 (synopsis "Plot multi-dimensional data")
15934 "This package provides functions for viewing 2D and 3D data, including
15935 perspective plots, slice plots, surface plots, scatter plots, etc. It
15936 includes data sets from oceanography.")
15937 (license license:gpl3+)))
15939 (define-public r-ggfortify
15941 (name "r-ggfortify")
15946 (uri (cran-uri "ggfortify" version))
15949 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15950 (build-system r-build-system)
15952 `(("r-dplyr" ,r-dplyr)
15953 ("r-ggplot2" ,r-ggplot2)
15954 ("r-gridextra" ,r-gridextra)
15955 ("r-scales" ,r-scales)
15956 ("r-stringr" ,r-stringr)
15957 ("r-tibble" ,r-tibble)
15958 ("r-tidyr" ,r-tidyr)))
15960 `(("r-knitr" ,r-knitr)))
15961 (home-page "https://github.com/sinhrks/ggfortify")
15962 (synopsis "Data visualization tools for statistical analysis results")
15964 "This package provides unified plotting tools for statistics commonly
15965 used, such as GLM, time series, PCA families, clustering and survival
15966 analysis. The package offers a single plotting interface for these analysis
15967 results and plots in a unified style using the @code{ggplot2} package.")
15968 (license license:gpl2)))
15970 (define-public r-refmanager
15972 (name "r-refmanager")
15977 (uri (cran-uri "RefManageR" version))
15980 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15981 (properties `((upstream-name . "RefManageR")))
15982 (build-system r-build-system)
15984 `(("r-bibtex" ,r-bibtex)
15986 ("r-jsonlite" ,r-jsonlite)
15987 ("r-lubridate" ,r-lubridate)
15989 ("r-stringr" ,r-stringr)
15990 ("r-xml2" ,r-xml2)))
15991 (home-page "https://github.com/ropensci/RefManageR/")
15992 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15994 "This package provides tools for importing and working with bibliographic
15995 references. It greatly enhances the @code{bibentry} class by providing a
15996 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15997 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15998 by various formats for name lists (author by last names, translator by full
15999 names, etc.). Entries can be updated, combined, sorted, printed in a number
16000 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
16001 into R and converted to @code{BibEntry} objects.")
16002 ;; Any of these licenses may be picked.
16003 (license (list license:gpl2 license:gpl3 license:bsd-3))))
16005 (define-public r-citr
16012 (uri (cran-uri "citr" version))
16015 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
16016 (build-system r-build-system)
16018 `(("r-assertthat" ,r-assertthat)
16021 ("r-miniui" ,r-miniui)
16022 ("r-refmanager" ,r-refmanager)
16023 ("r-rstudioapi" ,r-rstudioapi)
16024 ("r-shiny" ,r-shiny)
16025 ("r-shinyjs" ,r-shinyjs)
16026 ("r-yaml" ,r-yaml)))
16027 (home-page "https://github.com/crsh/citr")
16028 (synopsis "RStudio add-in to insert Markdown citations")
16030 "This package provides functions and an RStudio add-in that search a
16031 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
16032 the current document.")
16033 (license license:expat)))
16035 (define-public r-xgboost
16038 (version "1.1.1.1")
16042 (uri (cran-uri "xgboost" version))
16045 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
16046 (build-system r-build-system)
16048 `(("r-data-table" ,r-data-table)
16049 ("r-magrittr" ,r-magrittr)
16050 ("r-matrix" ,r-matrix)
16051 ("r-stringi" ,r-stringi)))
16053 `(("r-knitr" ,r-knitr)))
16054 (home-page "https://github.com/dmlc/xgboost")
16055 (synopsis "Extreme gradient boosting")
16057 "This package provides an R interface to Extreme Gradient Boosting, which
16058 is an efficient implementation of the gradient boosting framework from Chen
16059 and Guestrin (2016). The package includes efficient linear model solver and
16060 tree learning algorithms. The package can automatically do parallel
16061 computation on a single machine. It supports various objective functions,
16062 including regression, classification and ranking. The package is made to be
16063 extensible, so that users are also allowed to define their own objectives
16065 (license license:asl2.0)))
16067 (define-public r-umap
16070 (version "0.2.6.0")
16074 (uri (cran-uri "umap" version))
16077 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16078 (build-system r-build-system)
16080 `(("r-openssl" ,r-openssl)
16082 ("r-reticulate" ,r-reticulate)
16083 ("r-rspectra" ,r-rspectra)))
16085 `(("r-knitr" ,r-knitr)))
16086 (home-page "https://github.com/tkonopka/umap")
16087 (synopsis "Uniform manifold approximation and projection")
16089 "Uniform manifold approximation and projection is a technique for
16090 dimension reduction. This package provides an interface to the UMAP algorithm
16091 in R, including a translation of the original algorithm into R.")
16092 (license license:expat)))
16094 (define-public r-uwot
16101 (uri (cran-uri "uwot" version))
16104 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16105 (build-system r-build-system)
16107 `(("r-dqrng" ,r-dqrng)
16109 ("r-irlba" ,r-irlba)
16110 ("r-matrix" ,r-matrix)
16112 ("r-rcppannoy" ,r-rcppannoy)
16113 ("r-rcppprogress" ,r-rcppprogress)
16114 ("r-rspectra" ,r-rspectra)))
16115 (home-page "https://github.com/jlmelville/uwot")
16116 (synopsis "Uniform manifold approximation and projection")
16118 "This package provides an implementation of the Uniform Manifold
16119 Approximation and Projection dimensionality reduction by McInnes et
16120 al. (2018). It also provides means to transform new data and to carry out
16121 supervised dimensionality reduction. An implementation of the related
16122 LargeVis method of Tang et al. (2016) is also provided.")
16123 (license license:gpl3)))
16125 (define-public r-kableextra
16127 (name "r-kableextra")
16132 (uri (cran-uri "kableExtra" version))
16135 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16136 (properties `((upstream-name . "kableExtra")))
16137 (build-system r-build-system)
16139 `(("r-digest" ,r-digest)
16141 ("r-htmltools" ,r-htmltools)
16142 ("r-knitr" ,r-knitr)
16143 ("r-magrittr" ,r-magrittr)
16144 ("r-readr" ,r-readr)
16145 ("r-rmarkdown" ,r-rmarkdown)
16146 ("r-rstudioapi" ,r-rstudioapi)
16147 ("r-rvest" ,r-rvest)
16148 ("r-scales" ,r-scales)
16149 ("r-stringr" ,r-stringr)
16150 ("r-viridislite" ,r-viridislite)
16151 ("r-webshot" ,r-webshot)
16152 ("r-xml2" ,r-xml2)))
16153 (home-page "https://haozhu233.github.io/kableExtra/")
16154 (synopsis "Construct complex tables with pipe syntax")
16156 "Build complex HTML or LaTeX tables using @code{kable()} from
16157 @code{knitr} and the piping syntax from @code{magrittr}. The function
16158 @code{kable()} is a light weight table generator coming from @code{knitr}.
16159 This package simplifies the way to manipulate the HTML or LaTeX codes
16160 generated by @code{kable()} and allows users to construct complex tables and
16161 customize styles using a readable syntax.")
16162 (license license:expat)))
16164 (define-public r-glasso
16171 (uri (cran-uri "glasso" version))
16173 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16174 (build-system r-build-system)
16175 (native-inputs `(("gfortran" ,gfortran)))
16176 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16177 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16179 "This is a package for estimation of a sparse inverse covariance matrix
16180 using a lasso (L1) penalty. Facilities are provided for estimates along a
16181 path of values for the regularization parameter.")
16182 (license license:gpl2)))
16184 (define-public r-rhpcblasctl
16186 (name "r-rhpcblasctl")
16187 (version "0.20-137")
16191 (uri (cran-uri "RhpcBLASctl" version))
16194 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16195 (properties `((upstream-name . "RhpcBLASctl")))
16196 (build-system r-build-system)
16197 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16198 (synopsis "Control the number of threads on BLAS")
16200 "This package allows you to control the number of threads the BLAS
16201 library uses. It is also possible to control the number of threads in
16203 (license license:agpl3+)))
16205 (define-public r-lda
16212 (uri (cran-uri "lda" version))
16215 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16216 (build-system r-build-system)
16217 (home-page "https://cran.r-project.org/web/packages/lda/")
16218 (synopsis "Collapsed Gibbs sampling methods for topic models")
16220 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16221 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16222 mixed-membership stochastic blockmodel. Inference for all of these models is
16223 implemented via a fast collapsed Gibbs sampler written in C. Utility
16224 functions for reading/writing data typically used in topic models, as well as
16225 tools for examining posterior distributions are also included.")
16226 ;; Any version of the LGPL
16227 (license license:lgpl3+)))
16229 (define-public r-rann-l1
16236 (uri (cran-uri "RANN.L1" version))
16239 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16240 (properties `((upstream-name . "RANN.L1")))
16241 (build-system r-build-system)
16242 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16243 (synopsis "Fast nearest neighbour search using L1 metric")
16245 "This package provides tools to find the k nearest neighbours for every
16246 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16247 library. There is support for approximate as well as exact searches, fixed
16248 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16249 computed using the L1 (Manhattan, taxicab) metric.")
16250 (license license:gpl3+)))
16252 (define-public r-leiden
16259 (uri (cran-uri "leiden" version))
16262 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16263 (properties `((upstream-name . "leiden")))
16264 (build-system r-build-system)
16266 `(("r-igraph" ,r-igraph)
16267 ("r-matrix" ,r-matrix)
16268 ("r-reticulate" ,r-reticulate)))
16269 (home-page "https://github.com/TomKellyGenetics/leiden")
16270 (synopsis "R implementation of Leiden clustering algorithm")
16272 "This package implements the Python @code{leidenalg} module to be called
16273 in R. It enables clustering using the Leiden algorithm for partitioning a
16274 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16275 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16276 (license license:gpl3)))
16278 (define-public r-patchwork
16280 (name "r-patchwork")
16285 (uri (cran-uri "patchwork" version))
16288 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16289 (build-system r-build-system)
16291 `(("r-ggplot2" ,r-ggplot2)
16292 ("r-gtable" ,r-gtable)))
16294 `(("r-knitr" ,r-knitr)))
16295 (home-page "https://github.com/thomasp85/patchwork")
16296 (synopsis "Compose ggplot2 plots")
16298 "The @code{ggplot2} package provides a strong API for sequentially
16299 building up a plot, but does not concern itself with composition of multiple
16300 plots. Patchwork is a package that expands the API to allow for arbitrarily
16301 complex composition of plots by providing mathmatical operators for combining
16303 (license license:expat)))
16305 (define-public r-liger
16312 (uri (git-reference
16313 (url "https://github.com/MacoskoLab/liger")
16314 (commit (string-append "v" version))))
16315 (file-name (git-file-name name version))
16318 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16319 (modules '((guix build utils)))
16322 (delete-file "inst/java/ModularityOptimizer.jar")
16324 (build-system r-build-system)
16327 (modify-phases %standard-phases
16328 (add-after 'unpack 'build-java-part
16329 (lambda* (#:key inputs #:allow-other-keys)
16330 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16331 (for-each (lambda (file) (invoke "javac" file))
16332 (find-files "." "\\.java$"))
16333 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16334 (find-files "." "\\.class$"))
16337 `(("r-cowplot" ,r-cowplot)
16338 ("r-dosnow" ,r-dosnow)
16339 ("r-dplyr" ,r-dplyr)
16341 ("r-foreach" ,r-foreach)
16342 ("r-ggplot2" ,r-ggplot2)
16343 ("r-ggrepel" ,r-ggrepel)
16344 ("r-hmisc" ,r-hmisc)
16346 ("r-irlba" ,r-irlba)
16347 ("r-matrix" ,r-matrix)
16348 ("r-mclust" ,r-mclust)
16349 ("r-patchwork" ,r-patchwork)
16351 ("r-rann-l1" ,r-rann-l1)
16353 ("r-rcpparmadillo" ,r-rcpparmadillo)
16354 ("r-riverplot" ,r-riverplot)
16355 ("r-rtsne" ,r-rtsne)
16356 ("r-snow" ,r-snow)))
16358 `(("jdk" ,icedtea "jdk")
16359 ;; See https://github.com/MacoskoLab/liger/issues/96
16360 ;; The optimizer is released under the Expat license.
16364 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16367 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16369 ("r-knitr" ,r-knitr))) ; for vignettes
16370 (home-page "https://github.com/MacoskoLab/liger")
16371 (synopsis "Integrate and analyze multiple single-cell datasets")
16373 "LIGER is a package for integrating and analyzing multiple single-cell
16374 datasets, developed and maintained by the Macosko lab. It relies on
16375 integrative non-negative matrix factorization to identify shared and
16376 dataset-specific factors.")
16377 (license license:gpl3)))
16379 (define-public r-harmony
16386 (uri (git-reference
16387 (url "https://github.com/immunogenomics/harmony")
16389 (file-name (git-file-name name version))
16392 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16393 (modules '((guix build utils)))
16396 (for-each delete-file '("config.status" "configure"))
16398 (build-system r-build-system)
16400 `(("r-cowplot" ,r-cowplot)
16401 ("r-dplyr" ,r-dplyr)
16402 ("r-ggplot2" ,r-ggplot2)
16403 ("r-irlba" ,r-irlba)
16404 ("r-matrix" ,r-matrix)
16406 ("r-rcpparmadillo" ,r-rcpparmadillo)
16407 ("r-rcppprogress" ,r-rcppprogress)
16408 ("r-rlang" ,r-rlang)
16409 ("r-tibble" ,r-tibble)
16410 ("r-tidyr" ,r-tidyr)))
16412 `(("autoconf" ,autoconf)))
16413 (home-page "https://github.com/immunogenomics/harmony")
16414 (synopsis "Integration of single cell sequencing data")
16416 "This package provides an implementation of the Harmony algorithm for
16417 single cell integration, described in Korsunsky et al
16418 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16419 function and interfaces to external frameworks.")
16420 (license license:gpl3)))
16422 (define-public r-covr
16429 (uri (cran-uri "covr" version))
16431 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16432 (properties `((upstream-name . "covr")))
16433 (build-system r-build-system)
16435 `(("r-crayon" ,r-crayon)
16436 ("r-digest" ,r-digest)
16438 ("r-jsonlite" ,r-jsonlite)
16440 ("r-withr" ,r-withr)
16441 ("r-yaml" ,r-yaml)))
16443 `(("r-knitr" ,r-knitr))) ; for vignettes
16444 (home-page "https://github.com/r-lib/covr")
16445 (synopsis "Test coverage for R packages")
16447 "Thisp package enables you to track and report code coverage for your
16448 package and (optionally) upload the results to a coverage service. Code
16449 coverage is a measure of the amount of code being exercised by a set of tests.
16450 It is an indirect measure of test quality and completeness. This package is
16451 compatible with any testing methodology or framework and tracks coverage of
16452 both R code and compiled C/C++/FORTRAN code.")
16453 (license license:gpl3)))
16455 (define-public r-systemfonts
16457 (name "r-systemfonts")
16462 (uri (cran-uri "systemfonts" version))
16465 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16466 (properties `((upstream-name . "systemfonts")))
16467 (build-system r-build-system)
16469 `(("fontconfig" ,fontconfig)
16472 `(("pkg-config" ,pkg-config)
16473 ("r-knitr" ,r-knitr)))
16474 (home-page "https://github.com/r-lib/systemfonts")
16475 (synopsis "System native font finding")
16477 "This package provides system native access to the font catalogue. As
16478 font handling varies between systems it is difficult to correctly locate
16479 installed fonts across different operating systems. The 'systemfonts' package
16480 provides bindings to the native libraries for finding font files that can then
16481 be used further by e.g. graphic devices.")
16482 (license license:expat)))
16484 (define-public r-graphlayouts
16486 (name "r-graphlayouts")
16491 (uri (cran-uri "graphlayouts" version))
16494 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16495 (properties `((upstream-name . "graphlayouts")))
16496 (build-system r-build-system)
16498 `(("r-igraph" ,r-igraph)
16500 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16501 (home-page "https://github.com/schochastics/graphlayouts")
16502 (synopsis "Additional layout algorithms for network visualizations")
16504 "This package provides several layout algorithms to visualize networks
16505 which are not part of the igraph library. Most are based on the concept of
16506 stress majorization by Gansner et al. (2004)
16507 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16508 emphasize hidden group structures in networks or focus on specific nodes.")
16509 (license license:expat)))
16511 (define-public r-tidygraph
16513 (name "r-tidygraph")
16518 (uri (cran-uri "tidygraph" version))
16521 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16522 (properties `((upstream-name . "tidygraph")))
16523 (build-system r-build-system)
16525 `(("r-dplyr" ,r-dplyr)
16526 ("r-igraph" ,r-igraph)
16527 ("r-magrittr" ,r-magrittr)
16528 ("r-pillar" ,r-pillar)
16531 ("r-rlang" ,r-rlang)
16532 ("r-tibble" ,r-tibble)
16533 ("r-tidyr" ,r-tidyr)))
16534 (home-page "https://github.com/thomasp85/tidygraph")
16535 (synopsis "Tidy API for graph manipulation")
16537 "This package provides a graph implementation that can be thought of as
16538 two tidy data frames describing node and edge data respectively. It provides
16539 an approach to manipulate these two virtual data frames using the API defined
16540 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16541 common graph algorithms.")
16542 (license license:expat)))
16544 (define-public r-soupx
16545 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16549 (version (git-version "0.3.1" revision commit))
16553 (uri (git-reference
16554 (url "https://github.com/constantAmateur/SoupX")
16556 (file-name (git-file-name name version))
16559 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16560 (properties `((upstream-name . "SoupX")))
16561 (build-system r-build-system)
16563 `(("r-ggplot2" ,r-ggplot2)
16564 ("r-matrix" ,r-matrix)
16565 ("r-seurat" ,r-seurat)))
16566 (home-page "https://github.com/constantAmateur/SoupX")
16567 (synopsis "Single cell mRNA Soup eXterminator")
16569 "This package provides a package for quantifying, profiling and
16570 removing cell free mRNA contamination (the \"soup\") from droplet based single
16571 cell RNA-seq experiments.")
16572 (license license:gpl2))))
16574 (define-public r-assertr
16581 (uri (cran-uri "assertr" version))
16584 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16585 (build-system r-build-system)
16587 `(("r-dplyr" ,r-dplyr)
16589 ("r-rlang" ,r-rlang)))
16591 `(("r-knitr" ,r-knitr))) ; needed for vignette
16592 (home-page "https://github.com/ropensci/assertr")
16593 (synopsis "Assertive programming for R analysis pipelines")
16595 "This package provides functionality to assert conditions that have to be
16596 met so that errors in data used in analysis pipelines can fail quickly. It is
16597 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16599 (license license:expat)))
16601 (define-public r-parameters
16603 (name "r-parameters")
16608 (uri (cran-uri "parameters" version))
16611 "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
16612 (properties `((upstream-name . "parameters")))
16613 (build-system r-build-system)
16615 `(("r-bayestestr" ,r-bayestestr)
16616 ("r-insight" ,r-insight)))
16618 `(("r-knitr" ,r-knitr)))
16619 (home-page "https://cran.r-project.org/web/packages/parameters")
16620 (synopsis "Processing of model parameters")
16622 "This package provides utilities for processing the parameters of various
16623 statistical models. Beyond computing p values, CIs, and other indices for a
16624 wide variety of models, this package implements features like standardization
16625 or bootstrapping of parameters and models, feature reduction (feature
16626 extraction and variable selection) as well as conversion between indices of
16628 (license license:gpl3)))
16630 (define-public r-rgdal
16637 (uri (cran-uri "rgdal" version))
16639 (base32 "0jvb5ykp539mi0hqs05w4w8wz45blc4nvkhs70aqmzyx27hadfiq"))))
16640 (properties `((upstream-name . "rgdal")))
16641 (build-system r-build-system)
16649 `(("pkg-config" ,pkg-config)
16650 ("r-knitr" ,r-knitr)))
16651 (home-page "http://rgdal.r-forge.r-project.org")
16652 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16654 "This package provides bindings to the Geospatial Data Abstraction
16655 Library (GDAL) and access to projection/transformation operations from the
16657 (license license:gpl2+)))
16659 (define-public r-insol
16666 (uri (cran-uri "insol" version))
16669 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16670 (properties `((upstream-name . "insol")))
16671 (build-system r-build-system)
16673 `(("r-raster" ,r-raster)))
16675 `(("gfortran" ,gfortran)))
16676 (home-page "https://meteoexploration.com/R/insol/index.html")
16677 (synopsis "Tools for calculating solar radiation")
16679 "This package provides functions to compute insolation on tilted
16680 surfaces, computes atmospheric transmittance and related parameters such as:
16681 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16682 time, vector in the direction of the sun, vector normal to surface, and some
16683 atmospheric physics.")
16684 (license license:gpl2+)))
16686 (define-public r-lifecycle
16688 (name "r-lifecycle")
16693 (uri (cran-uri "lifecycle" version))
16696 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16697 (properties `((upstream-name . "lifecycle")))
16698 (build-system r-build-system)
16700 `(("r-glue" ,r-glue)
16701 ("r-rlang" ,r-rlang)))
16703 `(("r-knitr" ,r-knitr))) ; for vignettes
16704 (home-page "https://github.com/r-lib/lifecycle")
16705 (synopsis "Manage the life cycle of your package functions")
16707 "Manage the life cycle of your exported functions with shared
16708 conventions, documentation badges, and non-invasive deprecation warnings. The
16709 lifecycle package defines four development stages (experimental, maturing,
16710 stable, and questioning) and three deprecation stages (soft-deprecated,
16711 deprecated, and defunct). It makes it easy to insert badges corresponding to
16712 these stages in your documentation. Usage of deprecated functions are
16713 signalled with increasing levels of non-invasive verbosity.")
16714 (license license:gpl3)))
16716 (define-public r-assertable
16718 (name "r-assertable")
16723 (uri (cran-uri "assertable" version))
16726 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16727 (build-system r-build-system)
16729 `(("r-data-table" ,r-data-table)))
16730 (home-page "https://cran.r-project.org/web/packages/assertable/")
16731 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16732 (description "This package provides simple, flexible assertions on
16733 data.frame or data.table objects with verbose output for vetting. While other
16734 assertion packages apply towards more general use-cases, @code{assertable} is
16735 tailored towards tabular data. It includes functions to check variable names
16736 and values, whether the dataset contains all combinations of a given set of
16737 unique identifiers, and whether it is a certain length. In addition,
16738 @code{assertable} includes utility functions to check the existence of target
16739 files and to efficiently import multiple tabular data files into one
16741 (license license:gpl3)))
16743 (define-public r-quadprog
16745 (name "r-quadprog")
16750 (uri (cran-uri "quadprog" version))
16752 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16753 (build-system r-build-system)
16755 `(("gfortran" ,gfortran)))
16756 (home-page "https://cran.r-project.org/web/packages/quadprog")
16757 (synopsis "Functions to solve quadratic programming problems")
16759 "This package contains routines and documentation for solving quadratic
16760 programming problems.")
16761 (license license:gpl3+)))
16763 (define-public r-desolve
16770 (uri (cran-uri "deSolve" version))
16772 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16773 (properties `((upstream-name . "deSolve")))
16774 (build-system r-build-system)
16776 `(("gfortran" ,gfortran)))
16777 (home-page "https://desolve.r-forge.r-project.org/")
16778 (synopsis "Solvers for initial value problems of differential equations")
16779 (description "This package provides functions that solve initial value
16780 problems of a system of first-order @dfn{ordinary differential
16781 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16782 @dfn{differential algebraic equations} (DAE), and of delay differential
16783 equations. The functions provide an interface to the FORTRAN functions
16784 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16785 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16786 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16787 time steps. The package contains routines designed for solving ODEs resulting
16788 from 1-D, 2-D and 3-D partial differential equations that have been converted
16789 to ODEs by numerical differencing.")
16790 (license license:gpl2+)))
16792 (define-public r-pracma
16798 (uri (cran-uri "pracma" version))
16800 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16801 (build-system r-build-system)
16802 (home-page "https://cran.r-project.org/web/packages/pracma/")
16803 (synopsis "Practical numerical math functions")
16804 (description "This package provides functions for numerical analysis and
16805 linear algebra, numerical optimization, differential equations, plus some
16806 special functions. It uses Matlab function names where appropriate to simplify
16808 (license license:gpl3+)))
16810 (define-public r-subplex
16817 (uri (cran-uri "subplex" version))
16820 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16821 (build-system r-build-system)
16823 `(("gfortran" ,gfortran)))
16824 (home-page "https://cran.r-project.org/web/packages/subplex")
16825 (synopsis "Unconstrained optimization using the subplex algorithm")
16827 "This package implements the Subplex optimization algorithm.
16828 It solves unconstrained optimization problems using a simplex method on
16829 subspaces. The method is well suited for optimizing objective functions that
16830 are noisy or are discontinuous at the solution.")
16831 (license license:gpl3+)))
16833 (define-public r-txtplot
16840 (uri (cran-uri "txtplot" version))
16843 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16844 (build-system r-build-system)
16845 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16846 (synopsis "Text-based plotting")
16847 (description "This package provides functions to produce rudimentary ASCII
16848 graphics directly in the terminal window. This package provides a basic
16849 plotting function (and equivalents of curve, density, acf and barplot) as well
16850 as a boxplot function.")
16851 (license license:lgpl3+)))
16853 (define-public r-bio3d
16860 (uri (cran-uri "bio3d" version))
16863 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16864 (properties `((upstream-name . "bio3d")))
16865 (build-system r-build-system)
16866 (inputs `(("zlib" ,zlib)))
16867 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16868 (home-page "http://thegrantlab.org/bio3d/")
16869 (synopsis "Biological structure analysis")
16871 "This package provides utilities to process, organize and explore protein
16872 structure, sequence and dynamics data. Features include the ability to read
16873 and write structure, sequence and dynamic trajectory data, perform sequence
16874 and structure database searches, data summaries, atom selection, alignment,
16875 superposition, rigid core identification, clustering, torsion analysis,
16876 distance matrix analysis, structure and sequence conservation analysis, normal
16877 mode analysis, principal component analysis of heterogeneous structure data,
16878 and correlation network analysis from normal mode and molecular dynamics data.
16879 In addition, various utility functions are provided to enable the statistical
16880 and graphical power of the R environment to work with biological sequence and
16882 (license license:gpl2+)))
16884 (define-public r-bios2cor
16886 (name "r-bios2cor")
16891 (uri (cran-uri "Bios2cor" version))
16894 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16895 (properties `((upstream-name . "Bios2cor")))
16896 (build-system r-build-system)
16898 `(("r-bigmemory" ,r-bigmemory)
16899 ("r-bio3d" ,r-bio3d)
16900 ("r-circular" ,r-circular)
16901 ("r-igraph" ,r-igraph)))
16902 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16903 (synopsis "From biological sequences and simulations to correlation analysis")
16905 "This package provides utilities for computation and analysis of
16906 correlation/covariation in multiple sequence alignments and in side chain
16907 motions during molecular dynamics simulations. Features include the
16908 computation of correlation/covariation scores using a variety of scoring
16909 functions between either sequence positions in alignments or side chain
16910 dihedral angles in molecular dynamics simulations and utilities to analyze the
16911 correlation/covariation matrix through a variety of tools including network
16912 representation and principal components analysis. In addition, several
16913 utility functions are based on the R graphical environment to provide friendly
16914 tools for help in data interpretation.")
16915 (license license:gpl2+)))
16917 ;; This package includes minified JavaScript files. When upgrading please
16918 ;; check that there are no new minified JavaScript files.
16919 (define-public r-networkd3
16921 (name "r-networkd3")
16926 (uri (cran-uri "networkD3" version))
16929 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16932 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16934 (properties `((upstream-name . "networkD3")))
16935 (build-system r-build-system)
16937 `(#:modules ((guix build utils)
16938 (guix build r-build-system)
16942 (modify-phases %standard-phases
16943 (add-after 'unpack 'process-javascript
16944 (lambda* (#:key inputs #:allow-other-keys)
16945 (with-directory-excursion "inst/htmlwidgets/lib/"
16949 `((,(assoc-ref inputs "d3.v4.js")
16950 "d3-4.5.0/d3.min.js"))))
16951 (lambda (sources targets)
16952 (for-each (lambda (source target)
16953 (format #t "Processing ~a --> ~a~%"
16955 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16956 (call-with-output-file target
16958 (dump-port minified port)))))
16959 sources targets))))
16962 `(("uglify-js" ,uglify-js)
16963 ;; NOTE: Make sure that this version of d3 is still valid when
16964 ;; upgrading the package.
16968 (uri "https://d3js.org/d3.v4.js")
16971 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16973 `(("r-htmlwidgets" ,r-htmlwidgets)
16974 ("r-igraph" ,r-igraph)
16975 ("r-magrittr" ,r-magrittr)))
16976 (home-page "https://cran.r-project.org/package=networkD3")
16977 (synopsis "D3 JavaScript network graphs from R")
16979 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16981 (license license:gpl3+)))
16983 (define-public r-aasea
16990 (uri (cran-uri "aaSEA" version))
16993 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16994 (properties `((upstream-name . "aaSEA")))
16995 (build-system r-build-system)
16997 `(("r-bios2cor" ,r-bios2cor)
16999 ("r-hmisc" ,r-hmisc)
17000 ("r-magrittr" ,r-magrittr)
17001 ("r-networkd3" ,r-networkd3)
17002 ("r-plotly" ,r-plotly)
17003 ("r-seqinr" ,r-seqinr)
17004 ("r-shiny" ,r-shiny)
17005 ("r-shinydashboard" ,r-shinydashboard)))
17006 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
17007 (synopsis "Amino acid substitution effect analyzer")
17009 "Given a protein multiple sequence alignment, it is a daunting task to
17010 assess the effects of substitutions along sequence length. The aaSEA package
17011 is intended to help researchers to rapidly analyze property changes caused by
17012 single, multiple and correlated amino acid substitutions in proteins.")
17013 (license license:gpl3)))
17015 (define-public r-abacus
17022 (uri (cran-uri "ABACUS" version))
17025 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
17026 (properties `((upstream-name . "ABACUS")))
17027 (build-system r-build-system)
17029 `(("r-ggplot2" ,r-ggplot2)
17030 ("r-shiny" ,r-shiny)))
17031 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
17032 (synopsis "Apps-based activities for communicating and understanding statistics")
17034 "This package provides a set of Shiny apps for effective communication
17035 and understanding in statistics. The current version includes properties of
17036 normal distribution, properties of sampling distribution, one-sample z and t
17037 tests, two samples independent (unpaired) t test and analysis of variance.")
17038 (license license:gpl3)))
17040 (define-public r-abc-rap
17047 (uri (cran-uri "ABC.RAP" version))
17050 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
17051 (properties `((upstream-name . "ABC.RAP")))
17052 (build-system r-build-system)
17053 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
17054 (synopsis "Array-based CpG region analysis pipeline")
17056 "This package aims to identify candidate genes that are differentially
17057 methylated between cases and controls. It applies Student's t-test and delta
17058 beta analysis to identify candidate genes containing multiple CpG sites.")
17059 (license license:gpl3)))
17061 (define-public r-abcadm
17068 (uri (cran-uri "abcADM" version))
17071 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
17072 (properties `((upstream-name . "abcADM")))
17073 (build-system r-build-system)
17076 ("r-rcpp" ,r-rcpp)))
17077 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17078 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17080 "This package provides tools to estimate parameters of accumulated
17081 damage (load duration) models based on failure time data under a Bayesian
17082 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17083 long-term reliability under stochastic load profiles.")
17084 (license license:gpl3)))
17086 (define-public r-rglpk
17093 (uri (cran-uri "Rglpk" version))
17096 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17097 (properties `((upstream-name . "Rglpk")))
17098 (build-system r-build-system)
17100 `(("r-slam" ,r-slam)))
17103 (home-page "https://r-forge.r-project.org/projects/rglp/")
17104 (synopsis "R interface to the GNU Linear Programming Kit")
17106 "This package provides an R interface to the GNU Linear Programming Kit,
17107 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17108 integer linear programming} (MILP) and other related problems.")
17110 (license (list license:gpl2 license:gpl3))))
17112 (define-public r-abcdefba
17114 (name "r-abcdefba")
17119 (uri (cran-uri "abcdeFBA" version))
17122 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17123 (properties `((upstream-name . "abcdeFBA")))
17124 (build-system r-build-system)
17126 `(("r-corrplot" ,r-corrplot)
17127 ("r-lattice" ,r-lattice)
17129 ("r-rglpk" ,r-rglpk)))
17130 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17131 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17133 "This package provides functions for Constraint Based Simulation using
17134 Flux Balance Analysis and informative analysis of the data generated during
17136 (license license:gpl2)))
17138 (define-public r-abcrlda
17145 (uri (cran-uri "abcrlda" version))
17148 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17149 (properties `((upstream-name . "abcrlda")))
17150 (build-system r-build-system)
17151 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17152 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17154 "This package offers methods to perform @dfn{asymptotically
17155 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17156 cost-sensitive binary classification. The bias-correction is an estimate of
17157 the bias term added to regularized discriminant analysis that minimizes the
17159 (license license:gpl3)))
17161 (define-public r-abemus
17168 (uri (cran-uri "abemus" version))
17171 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17172 (properties `((upstream-name . "abemus")))
17173 (build-system r-build-system)
17175 `(("r-data-table" ,r-data-table)))
17176 (home-page "https://cran.r-project.org/web/packages/abemus/")
17177 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17179 "This package provides an implementation of @dfn{Adaptive Base Error
17180 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17181 platform-specific genetic knowledge and empirical signal to readily detect and
17182 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17183 cell free DNA} (cfDNA).")
17184 (license license:gpl3)))
17186 ;; This package includes minified JavaScript files. When upgrading please
17187 ;; check that there are no new minified JavaScript files.
17188 (define-public r-rintrojs
17190 (name "r-rintrojs")
17195 (uri (cran-uri "rintrojs" version))
17198 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17199 (properties `((upstream-name . "rintrojs")))
17200 (build-system r-build-system)
17202 `(#:modules ((guix build utils)
17203 (guix build r-build-system)
17207 (modify-phases %standard-phases
17208 (add-after 'unpack 'process-javascript
17209 (lambda* (#:key inputs #:allow-other-keys)
17210 (with-directory-excursion "inst/javascript/introjs/"
17214 `((,(assoc-ref inputs "intro.js")
17216 (lambda (sources targets)
17217 (for-each (lambda (source target)
17218 (format #t "Processing ~a --> ~a~%"
17220 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17221 (call-with-output-file target
17223 (dump-port minified port)))))
17224 sources targets))))
17227 `(("uglify-js" ,uglify-js)
17231 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17234 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17236 `(("r-jsonlite" ,r-jsonlite)
17237 ("r-shiny" ,r-shiny)))
17238 (home-page "https://github.com/carlganz/rintrojs")
17239 (synopsis "Wrapper for the Intro.js library")
17241 "This package provides a wrapper for the @url{http://www.introjs.com,
17242 Intro.js} library. This package makes it easy to include step-by-step
17243 introductions, and clickable hints in a Shiny application. It supports both
17244 static introductions in the UI, and programmatic introductions from the
17246 (license license:agpl3+)))
17248 (define-public r-sysfonts
17250 (name "r-sysfonts")
17255 (uri (cran-uri "sysfonts" version))
17258 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17259 (properties `((upstream-name . "sysfonts")))
17260 (build-system r-build-system)
17262 `(("freetype" ,freetype)
17266 `(("pkg-config" ,pkg-config)))
17267 (home-page "https://github.com/yixuan/sysfonts")
17268 (synopsis "Loading fonts into R")
17270 "This is a package to simplify loading of system fonts and Google Fonts
17271 into R, in order to support other packages.")
17272 (license license:gpl2)))
17274 (define-public r-showtextdb
17276 (name "r-showtextdb")
17281 (uri (cran-uri "showtextdb" version))
17284 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17285 (properties `((upstream-name . "showtextdb")))
17286 (build-system r-build-system)
17288 `(("r-sysfonts" ,r-sysfonts)))
17289 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17290 (synopsis "Font files for the 'showtext' package")
17292 "This package provides font files that can be used by the @code{showtext}
17294 (license license:asl2.0)))
17296 (define-public r-showtext
17298 (name "r-showtext")
17303 (uri (cran-uri "showtext" version))
17306 "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
17307 (properties `((upstream-name . "showtext")))
17308 (build-system r-build-system)
17310 `(("freetype" ,freetype)
17314 `(("r-showtextdb" ,r-showtextdb)
17315 ("r-sysfonts" ,r-sysfonts)))
17317 `(("pkg-config" ,pkg-config)
17318 ("r-knitr" ,r-knitr)))
17319 (home-page "https://github.com/yixuan/showtext")
17320 (synopsis "Using fonts more easily in R graphs")
17322 "This package aims to make it easy to use various types of
17323 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17324 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17325 will be converted into polygons or raster images, hence after the plot has
17326 been created, it no longer relies on the font files. No external software
17327 such as Ghostscript is needed to use this package.")
17328 (license license:asl2.0)))
17330 (define-public r-emojifont
17332 (name "r-emojifont")
17337 (uri (cran-uri "emojifont" version))
17340 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17341 (properties `((upstream-name . "emojifont")))
17342 (build-system r-build-system)
17344 `(("r-ggplot2" ,r-ggplot2)
17345 ("r-proto" ,r-proto)
17346 ("r-showtext" ,r-showtext)
17347 ("r-sysfonts" ,r-sysfonts)))
17348 (home-page "https://guangchuangyu.github.io/emojifont")
17349 (synopsis "Emoji and Font Awesome in R graphics")
17351 "This package enables the use of emoji and the Font Awesome glyphs in
17352 both base and ggplot2 graphics.")
17353 (license license:artistic2.0)))
17355 (define-public r-abstractr
17357 (name "r-abstractr")
17362 (uri (cran-uri "abstractr" version))
17365 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17366 (properties `((upstream-name . "abstractr")))
17367 (build-system r-build-system)
17369 `(("r-colourpicker" ,r-colourpicker)
17370 ("r-emojifont" ,r-emojifont)
17371 ("r-ggplot2" ,r-ggplot2)
17372 ("r-gridextra" ,r-gridextra)
17373 ("r-rintrojs" ,r-rintrojs)
17374 ("r-shiny" ,r-shiny)
17375 ("r-shinythemes" ,r-shinythemes)))
17376 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17377 (synopsis "R-Shiny application for creating visual abstracts")
17379 "This package provides an R Shiny application to create visual abstracts
17380 for original research. A variety of user defined options and formatting are
17382 (license license:gpl3)))
17384 (define-public r-qgam
17391 (uri (cran-uri "qgam" version))
17394 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17395 (properties `((upstream-name . "qgam")))
17396 (build-system r-build-system)
17398 `(("r-doparallel" ,r-doparallel)
17401 ("r-shiny" ,r-shiny)))
17402 (native-inputs `(("r-knitr" ,r-knitr)))
17403 (home-page "https://cran.r-project.org/web/packages/qgam/")
17404 (synopsis "Smooth additive quantile regression models")
17406 "This package provides smooth additive quantile regression models, fitted
17407 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17408 the smoothing parameters are estimated automatically by marginal loss
17409 minimization, while the regression coefficients are estimated using either
17410 PIRLS or Newton algorithm. The learning rate is determined so that the
17411 Bayesian credible intervals of the estimated effects have approximately the
17412 correct coverage. The main function is @code{qgam()} which is similar to
17413 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17414 regression models.")
17415 (license license:gpl2+)))
17417 (define-public r-abtest
17424 (uri (cran-uri "abtest" version))
17427 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17428 (properties `((upstream-name . "abtest")))
17429 (build-system r-build-system)
17431 `(("r-matrix" ,r-matrix)
17432 ("r-mvtnorm" ,r-mvtnorm)
17433 ("r-plotrix" ,r-plotrix)
17435 ("r-rcolorbrewer" ,r-rcolorbrewer)
17438 ("r-truncnorm" ,r-truncnorm)))
17439 (home-page "https://cran.r-project.org/web/packages/abtest/")
17440 (synopsis "Bayesian A/B testing")
17442 "This package provides functions for Bayesian A/B testing including prior
17443 elicitation options based on Kass and Vaidyanathan (1992)
17444 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17445 (license license:gpl2+)))
17447 (define-public r-accept
17454 (uri (cran-uri "accept" version))
17457 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17458 (properties `((upstream-name . "accept")))
17459 (build-system r-build-system)
17461 `(("r-dplyr" ,r-dplyr)
17462 ("r-extrafont" ,r-extrafont)
17464 ("r-plotly" ,r-plotly)
17465 ("r-stringr" ,r-stringr)
17466 ("r-viridis" ,r-viridis)))
17467 (home-page "https://cran.r-project.org/web/packages/accept/")
17468 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17470 "This package allows clinicians to predict the rate and severity of
17471 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17472 Disease} (COPD) patients, based on the clinical prediction model published in
17473 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17474 (license license:gpl3)))
17476 (define-public r-smpracticals
17478 (name "r-smpracticals")
17483 (uri (cran-uri "SMPracticals" version))
17486 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17487 (properties `((upstream-name . "SMPracticals")))
17488 (build-system r-build-system)
17490 `(("r-ellipse" ,r-ellipse)
17493 ("r-survival" ,r-survival)))
17494 (home-page "http://statwww.epfl.ch/davison/SM/")
17495 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17497 "This package contains the datasets and a few functions for use with the
17498 practicals outlined in Appendix A of the book Statistical Models (Davison,
17499 2003, Cambridge University Press). The practicals themselves can be found at
17500 @url{http://statwww.epfl.ch/davison/SM/}.")
17501 (license license:gpl2+)))
17503 (define-public r-fgui
17510 (uri (cran-uri "fgui" version))
17513 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17514 (properties `((upstream-name . "fgui")))
17515 (build-system r-build-system)
17517 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17518 (synopsis "Create GUI for R functions")
17520 "Rapidly create a GUI for a function you created by automatically
17521 creating widgets for arguments of the function. This package automatically
17522 parses help routines for context-sensitive help to these arguments. The
17523 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17524 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17525 incorporated into the interface for greater customization for the more
17527 ;; Any version of the GPL.
17528 (license (list license:gpl2+ license:gpl3+))))
17530 (define-public r-tcltk2
17537 (uri (cran-uri "tcltk2" version))
17540 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17541 (properties `((upstream-name . "tcltk2")))
17542 (build-system r-build-system)
17546 (home-page "https://www.sciviews.org/SciViews-R")
17547 (synopsis "Tcl/Tk additions")
17549 "This package provides a series of additional Tcl commands and Tk widgets
17550 with style and various functions to supplement the tcltk package")
17551 (license license:lgpl3)))
17553 (define-public r-accrual
17560 (uri (cran-uri "accrual" version))
17563 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17564 (properties `((upstream-name . "accrual")))
17565 (build-system r-build-system)
17567 `(("r-fgui" ,r-fgui)
17568 ("r-smpracticals" ,r-smpracticals)
17569 ("r-tcltk2" ,r-tcltk2)))
17570 (home-page "https://cran.r-project.org/web/packages/accrual/")
17571 (synopsis "Bayesian accrual prediction")
17573 "Subject recruitment for medical research is challenging. Slow patient
17574 accrual leads to delay in research. Accrual monitoring during the process of
17575 recruitment is critical. Researchers need reliable tools to manage the
17576 accrual rate. This package provides an implementation of a Bayesian method
17577 that integrates researcher's experience on previous trials and data from the
17578 current study, providing reliable prediction on accrual rate for clinical
17579 studies. It provides functions for Bayesian accrual prediction which can be
17580 easily used by statisticians and clinical researchers.")
17581 (license license:gpl2)))
17583 (define-public r-accrued
17590 (uri (cran-uri "accrued" version))
17593 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17594 (properties `((upstream-name . "accrued")))
17595 (build-system r-build-system)
17596 (home-page "https://cran.r-project.org/web/packages/accrued/")
17597 (synopsis "Data quality visualization tools for partially accruing data")
17599 "This is a package for visualizing data quality of partially accruing
17601 (license license:gpl3)))
17603 (define-public r-mda
17610 (uri (cran-uri "mda" version))
17613 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17614 (properties `((upstream-name . "mda")))
17615 (build-system r-build-system)
17616 (propagated-inputs `(("r-class" ,r-class)))
17617 (native-inputs `(("gfortran" ,gfortran)))
17618 (home-page "https://cran.r-project.org/web/packages/mda/")
17619 (synopsis "Mixture and flexible discriminant analysis")
17621 "This is a package for mixture and flexible discriminant analysis,
17622 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17623 (license license:gpl2)))
17625 (define-public r-elasticnet
17627 (name "r-elasticnet")
17632 (uri (cran-uri "elasticnet" version))
17635 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17636 (properties `((upstream-name . "elasticnet")))
17637 (build-system r-build-system)
17639 `(("r-lars" ,r-lars)))
17640 (home-page "http://users.stat.umn.edu/~zouxx019/")
17641 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17643 "This package provides functions for fitting the entire solution path of
17644 the Elastic-Net and also provides functions for estimating sparse Principal
17645 Components. The Lasso solution paths can be computed by the same function.")
17646 (license license:gpl2+)))
17648 (define-public r-sparselda
17650 (name "r-sparselda")
17655 (uri (cran-uri "sparseLDA" version))
17658 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17659 (properties `((upstream-name . "sparseLDA")))
17660 (build-system r-build-system)
17662 `(("r-elasticnet" ,r-elasticnet)
17665 (home-page "https://www.imm.dtu.dk/~lkhc/")
17666 (synopsis "Sparse discriminant analysis")
17668 "This package performs sparse linear discriminant analysis for Gaussians
17669 and mixture of Gaussian models.")
17670 (license license:gpl2+)))
17672 (define-public r-accsda
17679 (uri (cran-uri "accSDA" version))
17682 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17683 (properties `((upstream-name . "accSDA")))
17684 (build-system r-build-system)
17686 `(("r-ggplot2" ,r-ggplot2)
17687 ("r-ggthemes" ,r-ggthemes)
17688 ("r-gridextra" ,r-gridextra)
17690 ("r-rarpack" ,r-rarpack)
17691 ("r-sparselda" ,r-sparselda)))
17692 (home-page "https://github.com/gumeo/accSDA/wiki")
17693 (synopsis "Accelerated sparse discriminant analysis")
17695 "This package provides an implementation of sparse linear discriminant
17696 analysis, which is a supervised classification method for multiple classes.
17697 Various novel optimization approaches to this problem are implemented
17698 including @dfn{alternating direction method of multipliers} (ADMM),
17699 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17700 Functions for performing cross validation are also supplied along with basic
17701 prediction and plotting functions. @dfn{Sparse zero variance
17702 discriminant} (SZVD) analysis is also included in the package.")
17703 (license license:gpl2+)))
17705 (define-public r-ace2fastq
17707 (name "r-ace2fastq")
17712 (uri (cran-uri "ace2fastq" version))
17715 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17716 (properties `((upstream-name . "ace2fastq")))
17717 (build-system r-build-system)
17719 `(("r-stringr" ,r-stringr)))
17720 (home-page "https://github.com/c5sire/ace2fastq")
17721 (synopsis "ACE file to FASTQ converter")
17723 "The ACE file format is used in genomics to store contigs from sequencing
17724 machines. This tools converts it into FASTQ format. Both formats contain the
17725 sequence characters and their corresponding quality information. Unlike the
17726 FASTQ file, the ACE file stores the quality values numerically. The
17727 conversion algorithm uses the standard Sanger formula. The package
17728 facilitates insertion into pipelines, and content inspection.")
17729 (license license:gpl3)))
17731 (define-public r-rngwell
17738 (uri (cran-uri "rngWELL" version))
17741 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17742 (properties `((upstream-name . "rngWELL")))
17743 (build-system r-build-system)
17744 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17745 (synopsis "Toolbox for WELL random number generators")
17747 "This is a dedicated package to WELL pseudo random generators, which were
17748 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17749 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17750 (license license:bsd-3)))
17752 (define-public r-randtoolbox
17754 (name "r-randtoolbox")
17759 (uri (cran-uri "randtoolbox" version))
17762 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17763 (properties `((upstream-name . "randtoolbox")))
17764 (build-system r-build-system)
17766 `(("r-rngwell" ,r-rngwell)))
17768 `(("gfortran" ,gfortran)))
17769 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17770 (synopsis "Toolbox for pseudo and quasi random number generation")
17772 "This package provides
17775 @item pseudo random generators, such as general linear
17776 congruential generators, multiple recursive generators and generalized
17777 feedback shift register (SF-Mersenne Twister algorithm and WELL
17780 @item quasi random generators, such as the Torus algorithm, the Sobol
17781 sequence, the Halton sequence (including the Van der Corput sequence), and
17783 @item some generator tests: the gap test, the serial test, the poker test.
17786 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17787 (license license:bsd-3)))
17789 (define-public r-lhs
17796 (uri (cran-uri "lhs" version))
17799 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17800 (properties `((upstream-name . "lhs")))
17801 (build-system r-build-system)
17802 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17804 `(("r-knitr" ,r-knitr)))
17805 (home-page "https://github.com/bertcarnell/lhs")
17806 (synopsis "Latin Hypercube Samples")
17808 "This package provides a number of methods for creating and augmenting
17809 Latin Hypercube Samples.")
17810 (license license:gpl3)))
17812 (define-public r-acebayes
17814 (name "r-acebayes")
17819 (uri (cran-uri "acebayes" version))
17822 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17823 (properties `((upstream-name . "acebayes")))
17824 (build-system r-build-system)
17826 `(("r-compare" ,r-compare)
17828 ("r-randtoolbox" ,r-randtoolbox)
17830 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17831 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17832 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17834 "Finding an optimal Bayesian experimental design involves maximizing an
17835 objective function given by the expectation of some appropriately chosen
17836 utility function with respect to the joint distribution of unknown
17837 quantities (including responses). This objective function is usually not
17838 available in closed form and the design space can be continuous and of high
17839 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17840 to maximise an approximation to the expectation of the utility function.")
17841 (license license:gpl2)))
17843 (define-public r-acet
17850 (uri (cran-uri "ACEt" version))
17853 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17854 (properties `((upstream-name . "ACEt")))
17855 (build-system r-build-system)
17860 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17861 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17862 (synopsis "Estimating dynamic heritability and twin model comparison")
17864 "This package supports twin models that are able to estimate the dynamic
17865 behaviour of the variance components in the classical twin models with respect
17866 to age using B-splines and P-splines.")
17867 (license license:gpl2+)))
17869 (define-public r-acfmperiod
17871 (name "r-acfmperiod")
17876 (uri (cran-uri "acfMPeriod" version))
17879 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17880 (properties `((upstream-name . "acfMPeriod")))
17881 (build-system r-build-system)
17883 `(("r-mass" ,r-mass)))
17884 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17885 (synopsis "Estimation of the ACF from the M-periodogram")
17887 "This package support non-robust and robust computations of the sample
17888 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17889 univariate and multivariate processes. The methodology consists in reversing
17890 the diagonalization procedure involving the periodogram or the
17891 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17892 ACOVF or the ACF as discussed in Fuller (1995)
17893 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17894 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17895 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17896 (license license:gpl2+)))
17898 (define-public r-gamlss-data
17900 (name "r-gamlss-data")
17905 (uri (cran-uri "gamlss.data" version))
17908 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17909 (properties `((upstream-name . "gamlss.data")))
17910 (build-system r-build-system)
17911 (home-page "http://www.gamlss.org/")
17912 (synopsis "GAMLSS data")
17914 "This package provides data used as examples to demonstrate GAMLSS
17916 ;; Either version of the license
17917 (license (list license:gpl2 license:gpl3))))
17919 (define-public r-gamlss
17926 (uri (cran-uri "gamlss" version))
17929 "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
17930 (properties `((upstream-name . "gamlss")))
17931 (build-system r-build-system)
17933 `(("r-gamlss-data" ,r-gamlss-data)
17934 ("r-gamlss-dist" ,r-gamlss-dist)
17937 ("r-survival" ,r-survival)))
17938 (home-page "http://www.gamlss.org/")
17939 (synopsis "Generalized additive models for location scale and shape")
17941 "This package provides functions for fitting the generalized additive
17942 models for location scale and shape introduced by Rigby and
17943 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17944 use a distributional regression approach where all the parameters of the
17945 conditional distribution of the response variable are modelled using
17946 explanatory variables.")
17947 ;; Either version of the license
17948 (license (list license:gpl2 license:gpl3))))
17950 (define-public r-acid
17957 (uri (cran-uri "acid" version))
17960 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17961 (properties `((upstream-name . "acid")))
17962 (build-system r-build-system)
17964 `(("r-gamlss" ,r-gamlss)
17965 ("r-gamlss-dist" ,r-gamlss-dist)
17966 ("r-hmisc" ,r-hmisc)))
17967 (home-page "https://cran.r-project.org/web/packages/acid/")
17968 (synopsis "Analysing conditional income distributions")
17970 "This package provides functions for the analysis of income distributions
17971 for subgroups of the population as defined by a set of variables like age,
17972 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17973 distribution as well as functions for moments, inequality measures, entropy
17974 measures and polarisation measures of income distributions. This package thus
17975 aides the analysis of income inequality by offering tools for the exploratory
17976 analysis of income distributions at the disaggregated level.")
17977 (license license:gpl3)))
17979 (define-public r-acm4r
17986 (uri (cran-uri "acm4r" version))
17989 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17990 (properties `((upstream-name . "acm4r")))
17991 (build-system r-build-system)
17992 (propagated-inputs `(("r-mass" ,r-mass)))
17993 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17994 (synopsis "Align-and-count method comparisons of RFLP data")
17996 "This is a package to compare sequence fragment lengths or molecular
17997 weights from pairs of lanes. The number of matching bands in the
17998 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17999 the align-and-count method.")
18000 ;; Any version of the GPL
18001 (license (list license:gpl2+ license:gpl3+))))
18003 (define-public r-filematrix
18005 (name "r-filematrix")
18010 (uri (cran-uri "filematrix" version))
18013 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
18014 (properties `((upstream-name . "filematrix")))
18015 (build-system r-build-system)
18016 ;; These inputs are needed for vignettes
18018 `(("r-knitr" ,r-knitr)
18019 ("r-rmarkdown" ,r-rmarkdown)
18020 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
18021 (home-page "https://github.com/andreyshabalin/filematrix")
18022 (synopsis "File-backed matrix class with convenient read and write access")
18024 "This package provides an interface for working with large matrices
18025 stored in files, not in computer memory. It supports multiple non-character
18026 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
18027 byte real values). Access to parts of the matrix is done by indexing, exactly
18028 as with usual R matrices. It supports very large matrices; the package has
18029 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
18030 columns, ad allows for quick addition of extra columns to a filematrix.")
18031 (license license:lgpl3)))
18033 (define-public r-acmeeqtl
18035 (name "r-acmeeqtl")
18040 (uri (cran-uri "ACMEeqtl" version))
18043 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
18044 (properties `((upstream-name . "ACMEeqtl")))
18045 (build-system r-build-system)
18047 `(("r-filematrix" ,r-filematrix)))
18048 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
18049 (synopsis "Estimation of interpretable eQTL effect sizes")
18051 "This package provides a non-linear model, termed ACME, that reflects a
18052 parsimonious biological model for allelic contributions of cis-acting eQTLs.
18053 With non-linear least-squares algorithm the maximum likelihood parameters can
18054 be estimated. The ACME model provides interpretable effect size estimates and
18055 p-values with well controlled Type-I error.")
18056 (license license:lgpl3)))
18058 (define-public r-acmer
18065 (uri (cran-uri "acmeR" version))
18068 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
18069 (properties `((upstream-name . "acmeR")))
18070 (build-system r-build-system)
18071 (propagated-inputs `(("r-foreign" ,r-foreign)))
18072 (home-page "https://cran.r-project.org/web/packages/acmeR/")
18073 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18075 "This package provides an implementation of the ACME estimator, described
18076 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18077 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18078 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18079 as carcasses age; variable bleed-through at successive searches; and interval
18080 mortality estimates. The package provides, based on search data, functions
18081 for estimating the mortality inflation factor in Frequentist and Bayesian
18083 (license license:expat)))
18085 (define-public r-r-huge
18092 (uri (cran-uri "R.huge" version))
18095 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18096 (properties `((upstream-name . "R.huge")))
18097 (build-system r-build-system)
18099 `(("r-r-methodss3" ,r-r-methodss3)
18101 ("r-r-utils" ,r-r-utils)))
18102 (home-page "https://github.com/HenrikBengtsson/R.huge")
18103 (synopsis "Methods for accessing huge amounts of data")
18105 "This is a deprecated package for accessing huge amounts of data.
18106 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18107 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18108 the @code{aroma.affymetrix} package.")
18109 (license license:lgpl2.1+)))
18111 (define-public r-r-filesets
18113 (name "r-r-filesets")
18118 (uri (cran-uri "R.filesets" version))
18121 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18122 (properties `((upstream-name . "R.filesets")))
18123 (build-system r-build-system)
18125 `(("r-digest" ,r-digest)
18126 ("r-r-cache" ,r-r-cache)
18127 ("r-r-methodss3" ,r-r-methodss3)
18129 ("r-r-utils" ,r-r-utils)))
18130 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18131 (synopsis "Easy handling of and access to files")
18133 "This package provides classes and methods to locate, setup, subset,
18134 navigate and iterate file sets, i.e. sets of files located in one or more
18135 directories on the file system. The API is designed such that these classes
18136 can be extended via inheritance to provide a richer API for special file
18137 formats. Moreover, a specific name format is defined such that filenames and
18138 directories can be considered to have full names which consists of a name
18139 followed by comma-separated tags. This adds additional flexibility to
18140 identify file sets and individual files.")
18141 (license license:lgpl2.1+)))
18143 (define-public r-r-devices
18145 (name "r-r-devices")
18150 (uri (cran-uri "R.devices" version))
18153 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18154 (properties `((upstream-name . "R.devices")))
18155 (build-system r-build-system)
18157 `(("r-base64enc" ,r-base64enc)
18158 ("r-r-methodss3" ,r-r-methodss3)
18160 ("r-r-utils" ,r-r-utils)))
18161 (home-page "https://github.com/HenrikBengtsson/R.devices")
18162 (synopsis "Unified handling of graphics devices")
18164 "This package provides functions for creating plots and image files in a
18165 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18166 Default device options as well as scales and aspect ratios are controlled in a
18167 uniform way across all device types. Switching output format requires minimal
18168 changes in code. This package is ideal for large-scale batch processing,
18169 because it will never leave open graphics devices or incomplete image files
18170 behind, even on errors or user interrupts.")
18171 (license license:lgpl2.1+)))
18173 (define-public r-acnr
18180 (uri (cran-uri "acnr" version))
18183 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18184 (properties `((upstream-name . "acnr")))
18185 (build-system r-build-system)
18186 (home-page "https://github.com/mpierrejean/acnr")
18187 (synopsis "Annotated copy-number regions")
18189 "This package provides SNP array data from different types of copy-number
18190 regions. These regions were identified manually by the authors of the package
18191 and may be used to generate realistic data sets with known truth.")
18192 (license license:lgpl2.1+)))
18194 (define-public r-acopula
18201 (uri (cran-uri "acopula" version))
18204 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18205 (properties `((upstream-name . "acopula")))
18206 (build-system r-build-system)
18207 (home-page "https://cran.r-project.org/web/packages/acopula/")
18208 (synopsis "Modelling dependence with multivariate Archimax copulas")
18210 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18211 package provides definitions of several parametric families of generator and
18212 dependence function, computes CDF and PDF, estimates parameters, tests for
18213 goodness of fit, generates random sample and checks copula properties for
18214 custom constructs. In the 2-dimensional case explicit formulas for density
18215 are used, contrary to higher dimensions when all derivatives are linearly
18216 approximated. Several non-archimax families (normal, FGM, Plackett) are
18217 provided as well.")
18218 (license license:gpl2)))
18220 (define-public r-tuner
18227 (uri (cran-uri "tuneR" version))
18230 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18231 (properties `((upstream-name . "tuneR")))
18232 (build-system r-build-system)
18233 (propagated-inputs `(("r-signal" ,r-signal)))
18234 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18235 (synopsis "Analysis of music and speech")
18237 "This is a package for the analysis of music and speech. Analyze music
18238 and speech, extract features like MFCCs, handle wave files and their
18239 representation in various ways, read MP3, read MIDI, perform steps of a
18240 transcription, ...")
18241 ;; Either of these versions.
18242 (license (list license:gpl2 license:gpl3))))
18244 (define-public r-seewave
18251 (uri (cran-uri "seewave" version))
18254 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18255 (properties `((upstream-name . "seewave")))
18256 (build-system r-build-system)
18258 `(("libsndfile" ,libsndfile)))
18260 `(("r-tuner" ,r-tuner)))
18261 (home-page "http://rug.mnhn.fr/seewave")
18262 (synopsis "Sound analysis and synthesis")
18264 "This package provides functions for analysing, manipulating, displaying,
18265 editing and synthesizing time waves (particularly sound). This package
18266 processes time analysis (oscillograms and envelopes), spectral content,
18267 resonance quality factor, entropy, cross correlation and autocorrelation,
18268 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18269 and 3D spectrograms and many other analyses.")
18270 (license license:gpl2+)))
18272 (define-public r-acousticndlcoder
18274 (name "r-acousticndlcoder")
18279 (uri (cran-uri "AcousticNDLCodeR" version))
18282 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18284 `((upstream-name . "AcousticNDLCodeR")))
18285 (build-system r-build-system)
18287 `(("r-seewave" ,r-seewave)
18288 ("r-tuner" ,r-tuner)
18290 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18291 (synopsis "Coding sound files for use with NDL")
18293 "Make acoustic cues to use with the R package @code{ndl}.
18294 The package implements functions used in the PLoS ONE paper \"Words from
18295 spontaneous conversational speech can be recognized with human-like accuracy
18296 by an error-driven learning algorithm that discriminates between meanings
18297 straight from smart acoustic features, bypassing the phoneme as recognition
18298 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18299 (license license:gpl2+)))
18301 (define-public r-acp
18308 (uri (cran-uri "acp" version))
18311 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18312 (properties `((upstream-name . "acp")))
18313 (build-system r-build-system)
18315 `(("r-quantmod" ,r-quantmod)
18316 ("r-tseries" ,r-tseries)))
18317 (home-page "https://cran.r-project.org/web/packages/acp/")
18318 (synopsis "Autoregressive conditional Poisson")
18320 "This package supports the analysis of count data exhibiting
18321 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18322 model (ACP(p,q)) proposed by Heinen (2003).")
18323 (license license:gpl2)))
18325 (define-public r-ada
18332 (uri (cran-uri "ada" version))
18335 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18336 (properties `((upstream-name . "ada")))
18337 (build-system r-build-system)
18338 (propagated-inputs `(("r-rpart" ,r-rpart)))
18339 (home-page "https://cran.r-project.org/web/packages/ada/")
18340 (synopsis "Stochastic boosting")
18342 "This package provides a straightforward, well-documented, and broad
18343 boosting routine for classification, ideally suited for small to
18344 moderate-sized data sets. It performs discrete, real, and gentle boost under
18345 both exponential and logistic loss on a given data set.")
18346 ;; Any version of the GPL.
18347 (license (list license:gpl2+ license:gpl3+))))
18349 (define-public r-genalg
18356 (uri (cran-uri "genalg" version))
18359 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18360 (properties `((upstream-name . "genalg")))
18361 (build-system r-build-system)
18362 (home-page "https://github.com/egonw/genalg")
18363 (synopsis "R based genetic algorithm")
18365 "This package provides an R based genetic algorithm for binary and
18366 floating point chromosomes.")
18367 (license license:gpl2)))
18369 (define-public r-kernelfactory
18371 (name "r-kernelfactory")
18376 (uri (cran-uri "kernelFactory" version))
18379 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18380 (properties `((upstream-name . "kernelFactory")))
18381 (build-system r-build-system)
18384 ("r-genalg" ,r-genalg)
18385 ("r-kernlab" ,r-kernlab)
18386 ("r-randomforest" ,r-randomforest)))
18387 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18388 (synopsis "Ensemble of kernel machines")
18390 "Kernel factory is an ensemble method where each base classifier (random
18391 forest) is fit on the kernel matrix of a subset of the training data.")
18392 (license license:gpl2+)))
18394 (define-public r-dummies
18401 (uri (cran-uri "dummies" version))
18404 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18405 (properties `((upstream-name . "dummies")))
18406 (build-system r-build-system)
18407 (home-page "https://decisionpatterns.com")
18408 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18410 "This package lets you expand factors, characters and other eligible
18411 classes into dummy/indicator variables.")
18412 (license license:gpl2+)))
18414 (define-public r-acrm
18421 (uri (cran-uri "aCRM" version))
18424 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18425 (properties `((upstream-name . "aCRM")))
18426 (build-system r-build-system)
18429 ("r-dummies" ,r-dummies)
18430 ("r-kernelfactory" ,r-kernelfactory)
18431 ("r-randomforest" ,r-randomforest)))
18432 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18433 (synopsis "Convenience functions for analytical customer relationship management")
18435 "This package provides convenience functions for data preparation and
18436 modeling often used in @dfn{analytical customer relationship
18437 management} (aCRM).")
18438 (license license:gpl2+)))
18440 (define-public r-treeclust
18442 (name "r-treeclust")
18447 (uri (cran-uri "treeClust" version))
18450 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18451 (properties `((upstream-name . "treeClust")))
18452 (build-system r-build-system)
18454 `(("r-cluster" ,r-cluster)
18455 ("r-rpart" ,r-rpart)))
18456 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18457 (synopsis "Cluster distances through trees")
18459 "This package provides tools to create a measure of inter-point
18460 dissimilarity useful for clustering mixed data, and, optionally, perform the
18462 (license license:gpl2+)))
18464 (define-public r-acrosstic
18466 (name "r-acrosstic")
18471 (uri (cran-uri "AcrossTic" version))
18474 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18475 (properties `((upstream-name . "AcrossTic")))
18476 (build-system r-build-system)
18478 `(("r-lpsolve" ,r-lpsolve)
18479 ("r-treeclust" ,r-treeclust)))
18480 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18481 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18483 "This is a package for constructing minimum-cost regular spanning
18484 subgraph as part of a non-parametric two-sample test for equality of
18486 (license license:gpl2+)))
18488 (define-public r-acrt
18495 (uri (cran-uri "acrt" version))
18498 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18499 (properties `((upstream-name . "acrt")))
18500 (build-system r-build-system)
18502 `(("r-rcpp" ,r-rcpp)
18503 ("r-rcppeigen" ,r-rcppeigen)
18504 ("r-sandwich" ,r-sandwich)))
18505 (home-page "https://cran.r-project.org/web/packages/acrt/")
18506 (synopsis "Autocorrelation robust testing")
18508 "This package provides functions for testing affine hypotheses on the
18509 regression coefficient vector in regression models with autocorrelated
18511 (license license:gpl2)))
18513 (define-public r-acs
18520 (uri (cran-uri "acs" version))
18523 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18524 (properties `((upstream-name . "acs")))
18525 (build-system r-build-system)
18527 `(("r-httr" ,r-httr)
18530 ("r-stringr" ,r-stringr)
18532 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18533 (synopsis "Work with data from the US Census")
18535 "This package provides a general toolkit for downloading, managing,
18536 analyzing, and presenting data from the
18537 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18538 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18539 American Community Survey (ACS). Confidence intervals provided with ACS data
18540 are converted to standard errors to be bundled with estimates in complex
18541 @code{acs} objects. The package provides new methods to conduct standard
18542 operations on @code{acs} objects and present/plot data in statistically
18543 appropriate ways.")
18544 (license license:gpl3)))
18546 (define-public r-acss-data
18548 (name "r-acss-data")
18553 (uri (cran-uri "acss.data" version))
18556 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18557 (properties `((upstream-name . "acss.data")))
18558 (build-system r-build-system)
18559 (home-page "http://complexitycalculator.com/methodology.html")
18560 (synopsis "Data for algorithmic complexity of short strings")
18562 "This is a data only package providing the algorithmic complexity of
18563 short strings, computed using the coding theorem method. For a given set of
18564 symbols in a string, all possible or a large number of random samples of
18565 Turing machines with a given number of states (e.g., 5) and number of symbols
18566 corresponding to the number of symbols in the strings were simulated until
18567 they reached a halting state or failed to end. This package contains data on
18568 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18569 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18570 distribution of the halting states.")
18571 (license license:gpl2+)))
18573 (define-public r-acss
18580 (uri (cran-uri "acss" version))
18583 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18584 (properties `((upstream-name . "acss")))
18585 (build-system r-build-system)
18587 `(("r-acss-data" ,r-acss-data)
18589 (home-page "http://complexitycalculator.com/methodology.html")
18590 (synopsis "Algorithmic complexity for short strings")
18592 "The main purpose of this package is to provide the algorithmic
18593 complexity for short strings, an approximation of the Kolmogorov Complexity of
18594 a short string using the coding theorem method. While the database containing
18595 the complexity is provided in the data only package @code{acss.data}, this
18596 package provides functions accessing the data such as @code{prob_random}
18597 returning the posterior probability that a given string was produced by a
18598 random process. In addition, two traditional (but problematic) measures of
18599 complexity are also provided: entropy and change complexity.")
18600 (license license:gpl2+)))
18602 (define-public r-acswr
18609 (uri (cran-uri "ACSWR" version))
18612 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18613 (properties `((upstream-name . "ACSWR")))
18614 (build-system r-build-system)
18616 `(("r-mass" ,r-mass)))
18617 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18618 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18620 "This is a companion package for the book \"A Course in Statistics with
18621 R\" (ISBN 978-1-119-15272-9.)")
18622 (license license:gpl2)))
18624 (define-public r-alabama
18627 (version "2015.3-1")
18631 (uri (cran-uri "alabama" version))
18634 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18635 (properties `((upstream-name . "alabama")))
18636 (build-system r-build-system)
18637 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18638 (home-page "https://cran.r-project.org/web/packages/alabama/")
18639 (synopsis "Constrained nonlinear optimization")
18641 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18642 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18643 constraints. Linear or nonlinear equality and inequality constraints are
18645 (license license:gpl2+)))
18647 (define-public r-gdina
18654 (uri (cran-uri "GDINA" version))
18657 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18658 (properties `((upstream-name . "GDINA")))
18659 (build-system r-build-system)
18661 `(("r-alabama" ,r-alabama)
18662 ("r-ggplot2" ,r-ggplot2)
18664 ("r-nloptr" ,r-nloptr)
18665 ("r-numderiv" ,r-numderiv)
18667 ("r-rcpparmadillo" ,r-rcpparmadillo)
18668 ("r-rsolnp" ,r-rsolnp)
18669 ("r-shiny" ,r-shiny)
18670 ("r-shinydashboard" ,r-shinydashboard)))
18672 `(("r-knitr" ,r-knitr)))
18673 (home-page "https://github.com/Wenchao-Ma/GDINA")
18674 (synopsis "Generalized DINA model framework")
18676 "This package provides a set of psychometric tools for cognitive
18677 diagnosis modeling based on the generalized deterministic inputs, noisy and
18678 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18679 and its extensions, including the sequential G-DINA model by Ma and de la
18680 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18681 polytomous G-DINA model by Chen and de la Torre
18682 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18683 distribution can be independent, saturated, higher-order, loglinear smoothed
18684 or structured. Q-matrix validation, item and model fit statistics, model
18685 comparison at test and item level and differential item functioning can also
18686 be conducted. A graphical user interface is also provided.")
18687 (license license:gpl3)))
18689 (define-public r-actcd
18696 (uri (cran-uri "ACTCD" version))
18699 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18700 (properties `((upstream-name . "ACTCD")))
18701 (build-system r-build-system)
18703 `(("r-gdina" ,r-gdina)
18704 ("r-r-methodss3" ,r-r-methodss3)))
18706 `(("gfortran" ,gfortran)))
18707 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18708 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18710 "This is a package supporting cluster analysis for cognitive diagnosis
18711 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18712 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18713 sum-scores, cluster analysis techniques can be used to classify examinees into
18714 latent classes based on their attribute patterns. In addition to the
18715 algorithms used to classify data, three labeling approaches are proposed to
18716 label clusters so that examinees' attribute profiles can be obtained.")
18717 (license license:gpl2+)))
18719 (define-public r-ineq
18726 (uri (cran-uri "ineq" version))
18729 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18730 (properties `((upstream-name . "ineq")))
18731 (build-system r-build-system)
18732 (home-page "https://cran.r-project.org/web/packages/ineq/")
18733 (synopsis "Measuring inequality, concentration, and poverty")
18735 "This package provides tools for measuring inequality, concentration, and
18736 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18737 ;; Either of these two versions.
18738 (license (list license:gpl2 license:gpl3))))
18740 (define-public r-actfrag
18747 (uri (cran-uri "ActFrag" version))
18750 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18751 (properties `((upstream-name . "ActFrag")))
18752 (build-system r-build-system)
18754 `(("r-accelerometry" ,r-accelerometry)
18755 ("r-dplyr" ,r-dplyr)
18757 ("r-survival" ,r-survival)
18758 ("r-tidyr" ,r-tidyr)))
18759 (home-page "https://github.com/junruidi/ActFrag")
18760 (synopsis "Activity fragmentation metrics extraction")
18762 "This package provides functions to extract commonly used fragmentation
18763 metrics to quantify time accumulation strategies based on minute level
18764 actigraphy-measured activity counts data.")
18765 (license license:gpl3)))
18767 (define-public r-fda
18774 (uri (cran-uri "fda" version))
18777 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18778 (properties `((upstream-name . "fda")))
18779 (build-system r-build-system)
18781 `(("r-matrix" ,r-matrix)))
18782 (home-page "https://www.functionaldata.org")
18783 (synopsis "Functional data analysis")
18785 "These functions were developed to support functional data analysis as
18786 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18787 Analysis. The package includes data sets and script files working many
18789 (license license:gpl2+)))
18791 (define-public r-actigraphy
18793 (name "r-actigraphy")
18798 (uri (cran-uri "Actigraphy" version))
18801 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18802 (properties `((upstream-name . "Actigraphy")))
18803 (build-system r-build-system)
18805 `(("r-fda" ,r-fda)))
18806 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18807 (synopsis "Actigraphy data analysis")
18809 "This package provides tools for functional linear modeling and analysis
18810 of actigraphy data.")
18811 (license license:asl2.0)))
18813 (define-public r-activedriver
18815 (name "r-activedriver")
18820 (uri (cran-uri "ActiveDriver" version))
18823 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18824 (properties `((upstream-name . "ActiveDriver")))
18825 (build-system r-build-system)
18827 `(("r-mass" ,r-mass)))
18828 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18829 (synopsis "Tools for finding cancer driver proteins")
18831 "This package provides a mutation analysis tool that discovers cancer
18832 driver genes with frequent mutations in protein signalling sites such as
18833 post-translational modifications (phosphorylation, ubiquitination, etc). The
18834 Poisson generalized linear regression model identifies genes where cancer
18835 mutations in signalling sites are more frequent than expected from the
18836 sequence of the entire gene. Integration of mutations with signalling
18837 information helps find new driver genes and propose candidate mechanisms to
18839 (license license:gpl2+)))
18841 (define-public r-activitycounts
18843 (name "r-activitycounts")
18848 (uri (cran-uri "activityCounts" version))
18851 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18853 `((upstream-name . "activityCounts")))
18854 (build-system r-build-system)
18856 `(("r-lubridate" ,r-lubridate)
18857 ("r-magrittr" ,r-magrittr)
18858 ("r-seewave" ,r-seewave)
18859 ("r-signal" ,r-signal)
18860 ("r-tibble" ,r-tibble)))
18861 (home-page "https://github.com/walkabillylab/activityCounts")
18862 (synopsis "Generate ActiLife counts")
18864 "ActiLife generates activity counts from data collected by Actigraph
18865 accelerometers. Actigraph is one of the most common research-grade
18866 accelerometers. There is considerable research validating and developing
18867 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18868 counts are proprietary and difficult to implement if researchers use different
18869 accelerometer brands. The code creates ActiLife counts from raw acceleration
18870 data for different accelerometer brands.")
18871 (license license:gpl3)))
18873 (define-public r-activityindex
18875 (name "r-activityindex")
18880 (uri (cran-uri "ActivityIndex" version))
18883 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18884 (properties `((upstream-name . "ActivityIndex")))
18885 (build-system r-build-system)
18887 `(("r-data-table" ,r-data-table)
18888 ("r-matrixstats" ,r-matrixstats)
18889 ("r-r-utils" ,r-r-utils)))
18890 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18891 (synopsis "Activity Index calculation using raw accelerometry data")
18893 "This is a package to read raw accelerometry from GT3X+ accelerometry
18894 data and plain table data to calculate the Activity Index from Bai et
18895 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18896 (license license:gpl3)))
18898 (define-public r-activpal
18900 (name "r-activpal")
18905 (uri (cran-uri "activPAL" version))
18908 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18909 (properties `((upstream-name . "activPAL")))
18910 (build-system r-build-system)
18912 `(("r-devtools" ,r-devtools)
18913 ("r-dplyr" ,r-dplyr)
18914 ("r-ggplot2" ,r-ggplot2)
18915 ("r-lubridate" ,r-lubridate)
18916 ("r-magrittr" ,r-magrittr)
18917 ("r-tidyr" ,r-tidyr)))
18918 (home-page "https://cran.r-project.org/web/packages/activPAL")
18919 (synopsis "Processing and chart generation from activPAL events files")
18921 "This package contains functions to generate pre-defined summary
18922 statistics from activPAL events files. The package also contains functions to
18923 produce informative graphics that visualize physical activity behaviour and
18924 trends. This includes generating graphs that align physical activity
18925 behaviour with additional time based observations described by other data
18926 sets, such as sleep diaries and continuous glucose monitoring data.")
18927 (license license:gpl3)))
18929 (define-public r-activpalprocessing
18931 (name "r-activpalprocessing")
18936 (uri (cran-uri "activpalProcessing" version))
18939 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18941 `((upstream-name . "activpalProcessing")))
18942 (build-system r-build-system)
18944 `(("r-chron" ,r-chron)))
18945 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18946 (synopsis "Process activPAL events files")
18948 "This package performs estimation of physical activity and sedentary
18949 behavior variables from activPAL events files.")
18950 ;; Either version of the GPL.
18951 (license (list license:gpl2 license:gpl3))))
18953 (define-public r-actogrammr
18955 (name "r-actogrammr")
18960 (uri (cran-uri "actogrammr" version))
18963 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18964 (properties `((upstream-name . "actogrammr")))
18965 (build-system r-build-system)
18967 `(("r-dplyr" ,r-dplyr)
18968 ("r-ggplot2" ,r-ggplot2)
18969 ("r-lubridate" ,r-lubridate)
18970 ("r-readr" ,r-readr)
18971 ("r-tidyr" ,r-tidyr)))
18972 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18973 (synopsis "Read in activity data and plot actograms")
18975 "Read in activity measurements from standard file formats used by
18976 circadian rhythm researchers, currently only ClockLab format, and process and
18977 plot the data. The central type of plot is the actogram, as first described
18978 in \"Activity and distribution of certain wild mice in relation to biotic
18979 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18980 (license license:gpl3)))
18982 (define-public r-expint
18989 (uri (cran-uri "expint" version))
18992 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18993 (properties `((upstream-name . "expint")))
18994 (build-system r-build-system)
18995 (home-page "https://gitlab.com/vigou3/expint")
18996 (synopsis "Exponential integral and incomplete Gamma function")
18998 "This package provides the exponential integrals @code{E_1(x)},
18999 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
19000 function @code{G(a, x)} defined for negative values of its first argument.
19001 The package also gives easy access to the underlying C routines through an
19002 API; see the package vignette for details.")
19003 (license license:gpl2+)))
19005 (define-public r-actuar
19012 (uri (cran-uri "actuar" version))
19015 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
19016 (properties `((upstream-name . "actuar")))
19017 (build-system r-build-system)
19018 (propagated-inputs `(("r-expint" ,r-expint)))
19019 (home-page "https://gitlab.com/vigou3/actuar")
19020 (synopsis "Actuarial functions and heavy tailed distributions")
19022 "This package provides functions and data sets for actuarial science:
19023 modeling of loss distributions; risk theory and ruin theory; simulation of
19024 compound models, discrete mixtures and compound hierarchical models;
19025 credibility theory. It boasts support for many additional probability
19026 distributions to model insurance loss amounts and loss frequency: 19
19027 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
19028 distribution; zero-truncated and zero-modified extensions of the standard
19029 discrete distributions. It also supports phase-type distributions commonly
19030 used to compute ruin probabilities.")
19031 (license license:gpl2+)))
19033 (define-public r-bmp
19040 (uri (cran-uri "bmp" version))
19043 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
19044 (properties `((upstream-name . "bmp")))
19045 (build-system r-build-system)
19046 (home-page "https://cran.r-project.org/web/packages/bmp/")
19047 (synopsis "Read Bitmap (BMP) images")
19049 "This package provides pure R tools to read BMP format images. It is
19050 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
19051 (license license:gpl2+)))
19053 (define-public r-readbitmap
19055 (name "r-readbitmap")
19060 (uri (cran-uri "readbitmap" version))
19063 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
19064 (properties `((upstream-name . "readbitmap")))
19065 (build-system r-build-system)
19067 `(("libjpeg" ,libjpeg-turbo)
19068 ("libpng" ,libpng)))
19073 ("r-tiff" ,r-tiff)))
19074 (home-page "https://github.com/jefferis/readbitmap")
19075 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19077 "This package provides tools to identify and read BMP, JPEG, PNG, and
19078 TIFF format bitmap images. Identification defaults to the use of the magic
19079 number embedded in the file rather than the file extension.")
19080 (license license:gpl2+)))
19082 (define-public r-imager
19089 (uri (cran-uri "imager" version))
19092 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19093 (properties `((upstream-name . "imager")))
19094 (build-system r-build-system)
19097 ("libtiff" ,libtiff)
19101 `(("r-downloader" ,r-downloader)
19102 ("r-igraph" ,r-igraph)
19104 ("r-magrittr" ,r-magrittr)
19106 ("r-purrr" ,r-purrr)
19108 ("r-readbitmap" ,r-readbitmap)
19109 ("r-stringr" ,r-stringr)))
19111 `(("pkg-config" ,pkg-config)
19112 ("r-knitr" ,r-knitr)))
19113 (home-page "https://dahtah.github.io/imager/")
19114 (synopsis "Image processing library")
19116 "This is a package for fast image processing for images in up to 4
19117 dimensions (two spatial dimensions, one time/depth dimension, one color
19118 dimension). It provides most traditional image processing tools (filtering,
19119 morphology, transformations, etc.) as well as various functions for easily
19120 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19121 simple, modern C++ library for image processing.")
19122 (license license:lgpl3)))
19124 (define-public r-acuityview
19126 (name "r-acuityview")
19131 (uri (cran-uri "AcuityView" version))
19134 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19135 (properties `((upstream-name . "AcuityView")))
19136 (build-system r-build-system)
19138 `(("r-fftwtools" ,r-fftwtools)
19139 ("r-imager" ,r-imager)
19140 ("r-plotrix" ,r-plotrix)))
19141 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19142 (synopsis "Display scenes as seen by an animal with less acute vision")
19144 "This package provides a simple method for representing a visual scene as
19145 it may be seen by an animal with less acute vision.")
19146 (license license:gpl2+)))
19148 (define-public r-caret
19155 (uri (cran-uri "caret" version))
19158 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19159 (build-system r-build-system)
19161 `(("r-foreach" ,r-foreach)
19162 ("r-ggplot2" ,r-ggplot2)
19163 ("r-lattice" ,r-lattice)
19164 ("r-modelmetrics" ,r-modelmetrics)
19168 ("r-recipes" ,r-recipes)
19169 ("r-reshape2" ,r-reshape2)
19170 ("r-withr" ,r-withr)))
19172 `(("r-knitr" ,r-knitr)))
19173 (home-page "https://github.com/topepo/caret")
19174 (synopsis "Classification and regression training")
19176 "This package provides miscellaneous functions for training and plotting
19177 classification and regression models.")
19178 (license license:gpl2+)))
19180 (define-public r-adabag
19187 (uri (cran-uri "adabag" version))
19190 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19191 (properties `((upstream-name . "adabag")))
19192 (build-system r-build-system)
19194 `(("r-caret" ,r-caret)
19195 ("r-doparallel" ,r-doparallel)
19196 ("r-foreach" ,r-foreach)
19197 ("r-rpart" ,r-rpart)))
19198 (home-page "https://cran.r-project.org/web/packages/adabag/")
19199 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19201 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19202 Breiman's Bagging algorithm using classification trees as individual
19203 classifiers. Once these classifiers have been trained, they can be used to
19204 predict on new data. Also, cross validation estimation of the error can be
19206 (license license:gpl2+)))
19208 (define-public r-adagio
19215 (uri (cran-uri "adagio" version))
19218 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19219 (properties `((upstream-name . "adagio")))
19220 (build-system r-build-system)
19221 (native-inputs `(("gfortran" ,gfortran)))
19222 (home-page "https://cran.r-project.org/web/packages/adagio/")
19223 (synopsis "Discrete and global optimization routines")
19225 "This package provides methods and algorithms for discrete optimization,
19226 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19227 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19229 (license license:gpl3+)))
19231 (define-public r-univoutl
19233 (name "r-univoutl")
19238 (uri (cran-uri "univOutl" version))
19241 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19242 (properties `((upstream-name . "univOutl")))
19243 (build-system r-build-system)
19245 `(("r-hmisc" ,r-hmisc)
19246 ("r-robustbase" ,r-robustbase)))
19247 (home-page "https://github.com/marcellodo/univOutl")
19248 (synopsis "Detection of univariate outliers")
19250 "This package provides well-known outlier detection techniques in the
19251 univariate case. Methods to deal with skewed distribution are included too.
19252 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19253 historical data is implemented as well. When available, survey weights can be
19254 used in outliers detection.")
19255 (license license:gpl2+)))
19257 (define-public r-tolerance
19259 (name "r-tolerance")
19264 (uri (cran-uri "tolerance" version))
19267 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19268 (properties `((upstream-name . "tolerance")))
19269 (build-system r-build-system)
19271 `(("r-mass" ,r-mass)
19273 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19274 (synopsis "Statistical tolerance intervals and regions")
19276 "This package provides functions for estimating tolerance
19277 limits (intervals) for various univariate distributions (binomial, Cauchy,
19278 discrete Pareto, exponential, two-parameter exponential, extreme value,
19279 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19280 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19281 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19282 nonparametric tolerance intervals, tolerance bands for regression
19283 settings (linear regression, nonlinear regression, nonparametric regression,
19284 and multivariate regression), and analysis of variance tolerance intervals.
19285 Visualizations are also available for most of these settings.")
19286 (license license:gpl2+)))
19288 (define-public r-additivitytests
19290 (name "r-additivitytests")
19295 (uri (cran-uri "additivityTests" version))
19298 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19300 `((upstream-name . "additivityTests")))
19301 (build-system r-build-system)
19302 (home-page "https://github.com/simecek/additivityTests")
19303 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19305 "This package provides an implementation of the Tukey, Mandel,
19306 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19307 (license license:gpl3)))
19309 (define-public r-flexclust
19311 (name "r-flexclust")
19316 (uri (cran-uri "flexclust" version))
19319 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19320 (properties `((upstream-name . "flexclust")))
19321 (build-system r-build-system)
19323 `(("r-class" ,r-class)
19324 ("r-lattice" ,r-lattice)
19325 ("r-modeltools" ,r-modeltools)))
19326 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19327 (synopsis "Flexible cluster algorithms")
19329 "The main function @code{kcca} implements a general framework for
19330 k-centroids cluster analysis supporting arbitrary distance measures and
19331 centroid computation. Further cluster methods include hard competitive
19332 learning, neural gas, and QT clustering. There are numerous visualization
19333 methods for cluster results (neighborhood graphs, convex cluster hulls,
19334 barcharts of centroids, ...), and bootstrap methods for the analysis of
19335 cluster stability.")
19336 (license license:gpl2)))
19338 (define-public r-biclust
19345 (uri (cran-uri "biclust" version))
19348 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19349 (properties `((upstream-name . "biclust")))
19350 (build-system r-build-system)
19352 `(("r-additivitytests" ,r-additivitytests)
19353 ("r-colorspace" ,r-colorspace)
19354 ("r-flexclust" ,r-flexclust)
19355 ("r-ggplot2" ,r-ggplot2)
19356 ("r-lattice" ,r-lattice)
19358 ("r-tidyr" ,r-tidyr)))
19359 (home-page "https://cran.r-project.org/web/packages/biclust/")
19360 (synopsis "BiCluster algorithms")
19362 "The main function @code{biclust()} provides several algorithms to find
19363 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19364 In addition, the package provides methods for data
19365 preprocessing (normalization and discretization), visualization, and
19366 validation of bicluster solutions.")
19367 (license license:gpl3)))
19369 (define-public r-icge
19376 (uri (cran-uri "ICGE" version))
19379 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19380 (properties `((upstream-name . "ICGE")))
19381 (build-system r-build-system)
19383 `(("r-cluster" ,r-cluster)
19384 ("r-mass" ,r-mass)))
19385 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19386 (synopsis "Cluster estimation and identification of atypical units")
19388 "ICGE is a package that helps to estimate the number of real clusters in
19389 data as well as to identify atypical units. The underlying methods are based
19390 on distances rather than on unit x variables.")
19391 (license license:gpl2+)))
19393 (define-public r-depth
19396 (version "2.1-1.1")
19400 (uri (cran-uri "depth" version))
19403 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19404 (properties `((upstream-name . "depth")))
19405 (build-system r-build-system)
19407 `(("r-abind" ,r-abind)
19408 ("r-circular" ,r-circular)
19411 `(("gfortran" ,gfortran)))
19412 (home-page "https://cran.r-project.org/web/packages/depth/")
19413 (synopsis "Nonparametric depth functions for multivariate analysis")
19415 "This package provides tools for depth functions methodology applied to
19416 multivariate analysis. Besides allowing calculation of depth values and
19417 depth-based location estimators, the package includes functions or drawing
19418 contour plots and perspective plots of depth functions. Euclidian and
19419 spherical depths are supported.")
19420 (license license:gpl2)))
19422 (define-public r-archetypes
19424 (name "r-archetypes")
19425 (version "2.2-0.1")
19429 (uri (cran-uri "archetypes" version))
19432 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19433 (properties `((upstream-name . "archetypes")))
19434 (build-system r-build-system)
19436 `(("r-modeltools" ,r-modeltools)
19437 ("r-nnls" ,r-nnls)))
19438 (home-page "https://cran.r-project.org/web/packages/archetypes")
19439 (synopsis "Archetypal analysis")
19441 "The main function @code{archetypes} implements a framework for
19442 archetypal analysis supporting arbitrary problem solving mechanisms for the
19443 different conceptual parts of the algorithm.")
19444 (license license:gpl2+)))
19446 (define-public r-shapes
19453 (uri (cran-uri "shapes" version))
19456 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19457 (properties `((upstream-name . "shapes")))
19458 (build-system r-build-system)
19460 `(("r-mass" ,r-mass)
19461 ("r-minpack-lm" ,r-minpack-lm)
19463 ("r-scatterplot3d" ,r-scatterplot3d)))
19464 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19465 (synopsis "Statistical shape analysis")
19467 "This package provides routines for the statistical analysis of landmark
19468 shapes, including Procrustes analysis, graphical displays, principal
19469 components analysis, permutation and bootstrap tests, thin-plate spline
19470 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19471 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19472 Edition), John Wiley and Sons.")
19473 (license license:gpl2)))
19475 (define-public r-anthropometry
19477 (name "r-anthropometry")
19482 (uri (cran-uri "Anthropometry" version))
19485 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19486 (properties `((upstream-name . "Anthropometry")))
19487 (build-system r-build-system)
19489 `(("r-archetypes" ,r-archetypes)
19490 ("r-biclust" ,r-biclust)
19491 ("r-cluster" ,r-cluster)
19492 ("r-depth" ,r-depth)
19497 ("r-shapes" ,r-shapes)))
19499 `(("r-knitr" ,r-knitr)))
19500 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19501 (synopsis "Statistical methods for anthropometric data")
19503 "This package provides statistical methods especially developed to
19504 analyze anthropometric data. These methods are aimed at providing effective
19505 solutions to some commons problems related to Ergonomics and Anthropometry.
19506 They are based on clustering, the statistical concept of data depth,
19507 statistical shape analysis and archetypal analysis.")
19508 (license license:gpl2+)))
19510 (define-public r-adamethods
19512 (name "r-adamethods")
19517 (uri (cran-uri "adamethods" version))
19520 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19521 (properties `((upstream-name . "adamethods")))
19522 (build-system r-build-system)
19524 `(("r-anthropometry" ,r-anthropometry)
19525 ("r-archetypes" ,r-archetypes)
19527 ("r-foreach" ,r-foreach)
19529 ("r-tolerance" ,r-tolerance)
19530 ("r-univoutl" ,r-univoutl)))
19531 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19532 (synopsis "Archetypoid algorithms and anomaly detection")
19534 "This package is a collection of several algorithms to obtain
19535 archetypoids with small and large databases and with both classical
19536 multivariate data and functional data (univariate and multivariate). Some of
19537 these algorithms also allow to detect anomalies (outliers).")
19538 (license license:gpl2+)))
19540 (define-public r-idpmisc
19547 (uri (cran-uri "IDPmisc" version))
19550 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19551 (properties `((upstream-name . "IDPmisc")))
19552 (build-system r-build-system)
19554 `(("r-lattice" ,r-lattice)))
19555 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19556 (synopsis "Functions for data analyses and visualization")
19558 "This package provides different high-level graphics functions for
19559 displaying large datasets, displaying circular data in a very flexible way,
19560 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19561 2D-plots, creating figures with differently colored margin and plot region.
19562 In addition, the package contains auxiliary functions for data manipulation
19563 like omitting observations with irregular values or selecting data by logical
19564 vectors, which include NAs. Other functions are especially useful in
19565 spectroscopy and analyses of environmental data: robust baseline fitting,
19566 finding peaks in spectra, converting humidity measures.")
19567 (license license:gpl3+)))
19569 (define-public r-qqman
19576 (uri (cran-uri "qqman" version))
19579 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19580 (properties `((upstream-name . "qqman")))
19581 (build-system r-build-system)
19583 `(("r-calibrate" ,r-calibrate)))
19584 (home-page "https://cran.r-project.org/web/packages/qqman/")
19585 (synopsis "Q-Q and Manhattan plots for GWAS data")
19587 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19588 from PLINK results.")
19589 (license license:gpl3)))
19591 (define-public r-ggplot-multistats
19593 (name "r-ggplot-multistats")
19598 (uri (cran-uri "ggplot.multistats" version))
19601 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19603 `((upstream-name . "ggplot.multistats")))
19604 (build-system r-build-system)
19606 `(("r-ggplot2" ,r-ggplot2)
19607 ("r-hexbin" ,r-hexbin)
19608 ("r-rlang" ,r-rlang)
19609 ("r-scales" ,r-scales)))
19610 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19611 (synopsis "Multiple summary statistics for binned stats/geometries")
19613 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19614 which functions similar to its singular form, but allows the use of multiple
19615 statistics per bin. Those statistics can be mapped to multiple bin
19617 (license license:gpl3)))
19619 (define-public r-knn-covertree
19621 (name "r-knn-covertree")
19626 (uri (cran-uri "knn.covertree" version))
19629 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19630 (properties `((upstream-name . "knn.covertree")))
19631 (build-system r-build-system)
19633 `(("r-matrix" ,r-matrix)
19635 ("r-rcppeigen" ,r-rcppeigen)))
19636 (home-page "https://github.com/flying-sheep/knn.covertree")
19637 (synopsis "Accurate kNN Implementation with multiple distance measures")
19639 "Similarly to the FNN package, this package allows calculation of the k
19640 nearest neighbors (kNN) of a data matrix. The implementation is based on
19641 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19642 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19643 (license license:agpl3+)))
19645 (define-public r-poibin
19652 (uri (cran-uri "poibin" version))
19655 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19656 (properties `((upstream-name . "poibin")))
19657 (build-system r-build-system)
19658 (home-page "https://cran.r-project.org/web/packages/poibin/")
19659 (synopsis "Poisson binomial distribution")
19661 "This package provides an implementation of both the exact and
19662 approximation methods for computing the @dfn{cumulative distribution
19663 function} (CDF) of the Poisson binomial distribution. It also provides the
19664 @dfn{probability mass function} (PMF), quantile function, and random number
19665 generation for the Poisson binomial distribution.")
19666 (license license:gpl2)))
19668 (define-public r-diagram
19675 (uri (cran-uri "diagram" version))
19678 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19679 (properties `((upstream-name . "diagram")))
19680 (build-system r-build-system)
19682 `(("r-shape" ,r-shape)))
19683 (home-page "https://cran.r-project.org/web/packages/diagram/")
19684 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19686 "This package provides tools to visualize simple graphs (networks) based
19687 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19688 electrical networks, etc. It also includes supporting material for the book
19689 \"A practical guide to ecological modelling - using R as a simulation
19690 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19691 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19692 Francesca Mazzia (2012).")
19693 (license license:gpl2+)))
19695 (define-public r-lim
19702 (uri (cran-uri "LIM" version))
19705 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19706 (properties `((upstream-name . "LIM")))
19707 (build-system r-build-system)
19709 `(("r-diagram" ,r-diagram)
19710 ("r-limsolve" ,r-limsolve)))
19711 (home-page "https://cran.r-project.org/web/packages/LIM/")
19712 (synopsis "Linear inverse model examples and solution methods")
19714 "This package provides functions that read and solve linear inverse
19715 problems (food web problems, linear programming problems).")
19716 (license license:gpl2+)))
19718 (define-public r-shinycssloaders
19720 (name "r-shinycssloaders")
19725 (uri (cran-uri "shinycssloaders" version))
19728 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19730 `((upstream-name . "shinycssloaders")))
19731 (build-system r-build-system)
19733 `(("r-digest" ,r-digest)
19735 ("r-shiny" ,r-shiny)))
19736 (home-page "https://github.com/andrewsali/shinycssloaders")
19737 (synopsis "Add CSS loading animations to Shiny outputs")
19739 "This package provides tools to create a lightweight Shiny wrapper for
19740 the css-loaders created by Luke Hass
19741 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19742 automatically show a loader when the output is (re)calculating.")
19743 (license license:gpl3)))
19745 (define-public r-rsvg
19752 (uri (cran-uri "rsvg" version))
19755 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19756 (properties `((upstream-name . "rsvg")))
19757 (build-system r-build-system)
19759 `(("librsvg" ,librsvg)
19762 `(("pkg-config" ,pkg-config)
19763 ("r-knitr" ,r-knitr)))
19764 (home-page "https://github.com/jeroen/rsvg#readme")
19765 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19767 "This package allows you to render vector-based SVG images into
19768 high-quality custom-size bitmap arrays using the librsvg2 library. The
19769 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19770 addition, the package can convert images directly to various formats such as
19771 PDF or PostScript.")
19772 (license license:expat)))
19774 (define-public r-influencer
19776 (name "r-influencer")
19781 (uri (cran-uri "influenceR" version))
19784 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19785 (properties `((upstream-name . "influenceR")))
19786 (build-system r-build-system)
19788 `(("r-igraph" ,r-igraph)
19789 ("r-matrix" ,r-matrix)))
19790 (home-page "https://github.com/rcc-uchicago/influenceR")
19791 (synopsis "Tools to quantify structural importance of nodes in a network")
19793 "This package provides functionality to compute various node centrality
19794 measures on networks. Included are functions to compute betweenness
19795 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19796 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19797 algorithm to identify key players, and Valente's bridging metric. The
19798 betweenness, Key Players, and bridging implementations are parallelized with
19800 (license license:gpl2)))
19802 (define-public r-emplik
19809 (uri (cran-uri "emplik" version))
19812 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19813 (properties `((upstream-name . "emplik")))
19814 (build-system r-build-system)
19816 `(("r-quantreg" ,r-quantreg)))
19817 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19818 (synopsis "Empirical likelihood ratio for censored/truncated data")
19820 "This package provides empirical likelihood ratio tests for
19821 means/quantiles/hazards from possibly censored and/or truncated data. It also
19823 (license license:gpl2+)))
19825 (define-public r-imputeyn
19827 (name "r-imputeyn")
19832 (uri (cran-uri "imputeYn" version))
19835 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19836 (properties `((upstream-name . "imputeYn")))
19837 (build-system r-build-system)
19839 `(("r-boot" ,r-boot)
19840 ("r-emplik" ,r-emplik)
19841 ("r-mvtnorm" ,r-mvtnorm)
19842 ("r-quadprog" ,r-quadprog)
19843 ("r-survival" ,r-survival)))
19844 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19845 (synopsis "Impute last largest censored observation under weighted least squares")
19847 "This package allows for the imputation of the last largest censored
19848 observantions. This method brings less bias and more efficient estimates for
19850 (license license:gpl2)))
19852 (define-public r-adapenetclass
19854 (name "r-adapenetclass")
19859 (uri (cran-uri "AdapEnetClass" version))
19862 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19863 (properties `((upstream-name . "AdapEnetClass")))
19864 (build-system r-build-system)
19866 `(("r-glmnet" ,r-glmnet)
19867 ("r-imputeyn" ,r-imputeyn)
19869 ("r-quadprog" ,r-quadprog)))
19870 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19871 (synopsis "Class of adaptive elastic net methods for censored data")
19873 "This package provides methods for variable selection for AFT models.")
19874 (license license:gpl2)))
19876 (define-public r-flock
19883 (uri (cran-uri "flock" version))
19886 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19887 (properties `((upstream-name . "flock")))
19888 (build-system r-build-system)
19889 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19890 (home-page "https://cran.r-project.org/web/packages/flock/")
19891 (synopsis "Process synchronization using file locks")
19893 "This package implements synchronization between R processes (spawned by
19894 using the @code{parallel} package for instance) using file locks. It supports
19895 both exclusive and shared locking.")
19896 (license license:asl2.0)))
19898 (define-public r-archivist
19900 (name "r-archivist")
19905 (uri (cran-uri "archivist" version))
19908 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19909 (properties `((upstream-name . "archivist")))
19910 (build-system r-build-system)
19913 ("r-digest" ,r-digest)
19914 ("r-flock" ,r-flock)
19916 ("r-lubridate" ,r-lubridate)
19917 ("r-magrittr" ,r-magrittr)
19918 ("r-rcurl" ,r-rcurl)
19919 ("r-rsqlite" ,r-rsqlite)))
19920 (home-page "https://pbiecek.github.io/archivist/")
19921 (synopsis "Tools for storing, restoring and searching for R objects")
19923 "Data exploration and modelling is a process in which a lot of data
19924 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19925 statistical models, different versions of data sets and different versions of
19926 results. Archivist helps to store and manage artifacts created in R. It
19927 allows you to store selected artifacts as binary files together with their
19928 metadata and relations. Archivist allows sharing artifacts with others. It
19929 can look for already created artifacts by using its class, name, date of the
19930 creation or other properties. It also makes it easy to restore such
19932 (license license:gpl2)))
19934 (define-public r-versions
19936 (name "r-versions")
19941 (uri (cran-uri "versions" version))
19944 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19945 (properties `((upstream-name . "versions")))
19946 (build-system r-build-system)
19947 (home-page "https://cran.r-project.org/web/packages/versions/")
19948 (synopsis "Query and install specific versions of CRAN packages")
19950 "This package allows you to install specified versions of R packages
19951 hosted on CRAN and provides functions to list available versions and the
19952 versions of currently installed packages.")
19953 (license license:bsd-3)))
19955 (define-public r-adapr
19962 (uri (cran-uri "adapr" version))
19965 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19966 (properties `((upstream-name . "adapr")))
19967 (build-system r-build-system)
19969 `(("r-archivist" ,r-archivist)
19970 ("r-devtools" ,r-devtools)
19971 ("r-digest" ,r-digest)
19972 ("r-doparallel" ,r-doparallel)
19973 ("r-gdata" ,r-gdata)
19974 ("r-ggplot2" ,r-ggplot2)
19975 ("r-git2r" ,r-git2r)
19976 ("r-igraph" ,r-igraph)
19977 ("r-knitr" ,r-knitr)
19978 ("r-plotly" ,r-plotly)
19980 ("r-rmarkdown" ,r-rmarkdown)
19981 ("r-shiny" ,r-shiny)
19982 ("r-shinydashboard" ,r-shinydashboard)
19983 ("r-versions" ,r-versions)))
19984 (home-page "https://cran.r-project.org/web/packages/adapr/")
19985 (synopsis "Implementation of an accountable data analysis process")
19987 "This package tracks reading and writing within R scripts that are
19988 organized into a directed acyclic graph. It contains an interactive Shiny
19989 application @code{adaprApp()}. It uses Git and file hashes to track version
19990 histories of inputs and outputs.")
19991 (license license:lgpl2.0)))
19993 (define-public r-adapsamp
19995 (name "r-adapsamp")
20000 (uri (cran-uri "AdapSamp" version))
20003 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
20004 (properties `((upstream-name . "AdapSamp")))
20005 (build-system r-build-system)
20006 (propagated-inputs `(("r-pracma" ,r-pracma)))
20007 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
20008 (synopsis "Adaptive sampling algorithms")
20010 "For distributions whose probability density functions are log-concave,
20011 the adaptive rejection sampling algorithm can be used to build envelope
20012 functions for sampling. For others, the modified adaptive rejection sampling
20013 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
20014 adaptive slice sampling algorithm can be used. This R package mainly includes
20015 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
20016 @code{rASS()}. These functions can realize sampling based on the algorithms
20018 (license license:gpl2)))
20020 (define-public r-adaptalint
20022 (name "r-adaptalint")
20027 (uri (cran-uri "adaptalint" version))
20030 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
20031 (properties `((upstream-name . "adaptalint")))
20032 (build-system r-build-system)
20034 `(("r-dplyr" ,r-dplyr)
20035 ("r-lintr" ,r-lintr)
20036 ("r-purrr" ,r-purrr)))
20037 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
20038 (synopsis "Check R code style")
20040 "This package provides tools to infer the code style (which style rules
20041 are followed and which ones are not) from one package and use it to check
20042 another. This makes it easier to find and correct the most important problems
20044 (license license:gpl3)))
20046 (define-public r-fracdiff
20048 (name "r-fracdiff")
20053 (uri (cran-uri "fracdiff" version))
20056 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
20057 (properties `((upstream-name . "fracdiff")))
20058 (build-system r-build-system)
20059 (home-page "https://github.com/mmaechler/fracdiff")
20061 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
20063 "This package provides tools for the maximum likelihood estimation of the
20064 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
20065 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
20066 (license license:gpl2+)))
20068 (define-public r-forecast
20070 (name "r-forecast")
20075 (uri (cran-uri "forecast" version))
20078 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20079 (properties `((upstream-name . "forecast")))
20080 (build-system r-build-system)
20082 `(("r-colorspace" ,r-colorspace)
20083 ("r-fracdiff" ,r-fracdiff)
20084 ("r-ggplot2" ,r-ggplot2)
20085 ("r-lmtest" ,r-lmtest)
20086 ("r-magrittr" ,r-magrittr)
20089 ("r-rcpparmadillo" ,r-rcpparmadillo)
20090 ("r-timedate" ,r-timedate)
20091 ("r-tseries" ,r-tseries)
20095 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20096 (home-page "https://pkg.robjhyndman.com/forecast/")
20097 (synopsis "Forecasting functions for time series and linear models")
20099 "This package provides methods and tools for displaying and analysing
20100 univariate time series forecasts including exponential smoothing via state
20101 space models and automatic ARIMA modelling.")
20102 (license license:gpl3)))
20104 (define-public r-xmisc
20111 (uri (cran-uri "Xmisc" version))
20114 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20115 (properties `((upstream-name . "Xmisc")))
20116 (build-system r-build-system)
20117 (home-page "https://cran.r-project.org/package=Xmisc")
20119 "Xiaobei's miscellaneous classes and functions")
20121 "This package provides Xiaobei's miscellaneous classes and functions,
20122 which are useful when developing R packages for @dfn{object oriented
20123 programming} (OOP) using R Reference Class.")
20124 (license license:gpl2+)))
20126 (define-public r-proxyc
20133 (uri (cran-uri "proxyC" version))
20136 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20137 (properties `((upstream-name . "proxyC")))
20138 (build-system r-build-system)
20140 `(("r-matrix" ,r-matrix)
20142 ("r-rcpparmadillo" ,r-rcpparmadillo)
20143 ("r-rcppparallel" ,r-rcppparallel)))
20144 (home-page "https://cran.r-project.org/package=proxyC")
20145 (synopsis "Compute proximity in large sparse matrices")
20147 "This package provides efficient tools to compute the proximity between
20148 rows or columns of large matrices. Functions are optimised for large sparse
20149 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20150 similarity/distance measures, computation of correlation, cosine similarity
20151 and Euclidean distance is particularly fast.")
20152 (license license:gpl3)))
20154 (define-public r-isocodes
20156 (name "r-isocodes")
20157 (version "2020.03.16")
20161 (uri (cran-uri "ISOcodes" version))
20164 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20165 (properties `((upstream-name . "ISOcodes")))
20166 (build-system r-build-system)
20167 (home-page "https://cran.r-project.org/package=ISOcodes")
20168 (synopsis "Selected ISO codes")
20170 "This package provides ISO language, territory, currency, script and
20171 character codes. It provides ISO 639 language codes, ISO 3166 territory
20172 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20173 character codes as well as the UN M.49 area codes.")
20174 (license license:gpl2)))
20176 (define-public r-stopwords
20178 (name "r-stopwords")
20183 (uri (cran-uri "stopwords" version))
20186 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20187 (properties `((upstream-name . "stopwords")))
20188 (build-system r-build-system)
20190 `(("r-desc" ,r-desc)
20191 ("r-isocodes" ,r-isocodes)
20192 ("r-usethis" ,r-usethis)))
20193 (home-page "https://github.com/quanteda/stopwords")
20194 (synopsis "Multilingual stopword lists")
20196 "This package provides multiple sources of stopwords, for use in text
20197 analysis and natural language processing.")
20198 (license license:expat)))
20200 (define-public r-spacyr
20207 (uri (cran-uri "spacyr" version))
20210 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20211 (properties `((upstream-name . "spacyr")))
20212 (build-system r-build-system)
20214 `(("r-data-table" ,r-data-table)
20215 ("r-reticulate" ,r-reticulate)))
20216 (home-page "https://spacyr.quanteda.io")
20217 (synopsis "R wrapper for the spaCy NLP library")
20219 "This package provides an R wrapper to the Python @dfn{natural language
20220 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20221 (license license:gpl3)))
20223 (define-public r-snowballc
20225 (name "r-snowballc")
20230 (uri (cran-uri "SnowballC" version))
20233 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20234 (properties `((upstream-name . "SnowballC")))
20235 (build-system r-build-system)
20236 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20237 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20239 "This package provides an R interface to the C @code{libstemmer} library
20240 that implements Porter's word stemming algorithm for collapsing words to a
20241 common root to aid comparison of vocabulary. Currently supported languages
20242 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20243 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20244 (license license:bsd-3)))
20246 (define-public r-quanteda
20248 (name "r-quanteda")
20253 (uri (cran-uri "quanteda" version))
20256 "0qxvm75g6r0d1clj8b19gjqwkfrqypapf4zysb8nyfbmn33h8xc7"))))
20257 (properties `((upstream-name . "quanteda")))
20258 (build-system r-build-system)
20260 `(("r-data-table" ,r-data-table)
20261 ("r-digest" ,r-digest)
20262 ("r-extrafont" ,r-extrafont)
20263 ("r-fastmatch" ,r-fastmatch)
20264 ("r-ggplot2" ,r-ggplot2)
20265 ("r-ggrepel" ,r-ggrepel)
20266 ("r-jsonlite" ,r-jsonlite)
20267 ("r-magrittr" ,r-magrittr)
20268 ("r-matrix" ,r-matrix)
20269 ("r-network" ,r-network)
20270 ("r-proxyc" ,r-proxyc)
20272 ("r-rcpparmadillo" ,r-rcpparmadillo)
20273 ("r-rcppparallel" ,r-rcppparallel)
20275 ("r-snowballc" ,r-snowballc)
20276 ("r-stopwords" ,r-stopwords)
20277 ("r-stringi" ,r-stringi)
20279 ("r-yaml" ,r-yaml)))
20281 `(("r-knitr" ,r-knitr)))
20282 (home-page "https://quanteda.io")
20283 (synopsis "Quantitative analysis of textual data")
20285 "This package provides a fast, flexible, and comprehensive framework for
20286 quantitative text analysis in R. It provides functionality for corpus
20287 management, creating and manipulating tokens and ngrams, exploring keywords in
20288 context, forming and manipulating sparse matrices of documents by features and
20289 feature co-occurrences, analyzing keywords, computing feature similarities and
20290 distances, applying content dictionaries, applying supervised and unsupervised
20291 machine learning, visually representing text and text analyses, and more.")
20292 (license license:gpl3)))
20294 (define-public r-topicmodels
20296 (name "r-topicmodels")
20301 (uri (cran-uri "topicmodels" version))
20304 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20305 (properties `((upstream-name . "topicmodels")))
20306 (build-system r-build-system)
20310 `(("r-modeltools" ,r-modeltools)
20313 (home-page "https://cran.r-project.org/package=topicmodels")
20314 (synopsis "Topic models")
20316 "This package provides an interface to the C code for @dfn{Latent
20317 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20318 David M. Blei and co-authors and the C++ code for fitting LDA models using
20319 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20320 (license license:gpl2)))
20322 (define-public r-stm
20329 (uri (cran-uri "stm" version))
20332 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20333 (properties `((upstream-name . "stm")))
20334 (build-system r-build-system)
20336 `(("r-data-table" ,r-data-table)
20337 ("r-glmnet" ,r-glmnet)
20339 ("r-matrix" ,r-matrix)
20340 ("r-matrixstats" ,r-matrixstats)
20341 ("r-quadprog" ,r-quadprog)
20342 ("r-quanteda" ,r-quanteda)
20344 ("r-rcpparmadillo" ,r-rcpparmadillo)
20346 ("r-stringr" ,r-stringr)))
20347 (home-page "http://www.structuraltopicmodel.com/")
20348 (synopsis "Estimation of the Structural Topic Model")
20350 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20351 topic models with document-level covariates. The package also includes tools
20352 for model selection, visualization, and estimation of topic-covariate
20354 (license license:expat)))
20356 (define-public r-polycor
20363 (uri (cran-uri "polycor" version))
20366 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20367 (properties `((upstream-name . "polycor")))
20368 (build-system r-build-system)
20370 `(("r-matrix" ,r-matrix)
20371 ("r-mvtnorm" ,r-mvtnorm)))
20372 (home-page "https://r-forge.r-project.org/projects/polycor/")
20373 (synopsis "Polychoric and polyserial correlations")
20375 "This package provides tools to compute polychoric and polyserial
20376 correlations by quick \"two-step\" methods or ML, optionally with standard
20377 errors; tetrachoric and biserial correlations are special cases.")
20378 (license license:gpl2+)))
20380 (define-public r-msm
20387 (uri (cran-uri "msm" version))
20390 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20391 (properties `((upstream-name . "msm")))
20392 (build-system r-build-system)
20394 `(("r-expm" ,r-expm)
20395 ("r-mvtnorm" ,r-mvtnorm)
20396 ("r-survival" ,r-survival)))
20397 (home-page "https://github.com/chjackson/msm")
20398 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20400 "This package provides functions for fitting continuous-time Markov and
20401 hidden Markov multi-state models to longitudinal data. It was designed for
20402 processes observed at arbitrary times in continuous time (panel data) but some
20403 other observation schemes are supported. Both Markov transition rates and the
20404 hidden Markov output process can be modelled in terms of covariates, which may
20405 be constant or piecewise-constant in time.")
20406 (license license:gpl2+)))
20408 (define-public r-ltm
20415 (uri (cran-uri "ltm" version))
20418 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20419 (properties `((upstream-name . "ltm")))
20420 (build-system r-build-system)
20422 `(("r-mass" ,r-mass)
20424 ("r-polycor" ,r-polycor)))
20425 (home-page "https://github.com/drizopoulos/ltm")
20426 (synopsis "Latent trait models under IRT")
20428 "This is a package supporting the analysis of multivariate dichotomous
20429 and polytomous data using latent trait models under the Item Response Theory
20430 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20431 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20433 (license license:gpl2+)))
20435 (define-public r-mi
20442 (uri (cran-uri "mi" version))
20445 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20446 (properties `((upstream-name . "mi")))
20447 (build-system r-build-system)
20450 ("r-matrix" ,r-matrix)))
20451 (home-page "http://www.stat.columbia.edu/~gelman/")
20452 (synopsis "Missing data imputation and model checking")
20454 "This package provides functions for data manipulation, imputing missing
20455 values in an approximate Bayesian framework, diagnostics of the models used to
20456 generate the imputations, confidence-building mechanisms to validate some of
20457 the assumptions of the imputation algorithm, and functions to analyze multiply
20458 imputed data sets with the appropriate degree of sampling uncertainty.")
20459 (license license:gpl2+)))
20461 (define-public r-matrixcalc
20463 (name "r-matrixcalc")
20468 (uri (cran-uri "matrixcalc" version))
20471 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20472 (properties `((upstream-name . "matrixcalc")))
20473 (build-system r-build-system)
20474 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20475 (synopsis "Collection of functions for matrix calculations")
20477 "This package provides a collection of functions to support matrix
20478 calculations for probability, econometric and numerical analysis. There are
20479 additional functions that are comparable to APL functions which are useful for
20480 actuarial models such as pension mathematics.")
20481 (license license:gpl2+)))
20483 (define-public r-sem
20490 (uri (cran-uri "sem" version))
20493 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20494 (properties `((upstream-name . "sem")))
20495 (build-system r-build-system)
20497 `(("r-boot" ,r-boot)
20499 ("r-matrixcalc" ,r-matrixcalc)
20501 (home-page "https://cran.r-project.org/package=sem")
20502 (synopsis "Structural equation models")
20504 "This package provides functions for fitting general linear structural
20505 equation models (with observed and latent variables) using the RAM approach,
20506 and for fitting structural equations in observed-variable models by two-stage
20508 (license license:gpl2+)))
20510 (define-public r-semtools
20512 (name "r-semtools")
20517 (uri (cran-uri "semTools" version))
20520 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20521 (properties `((upstream-name . "semTools")))
20522 (build-system r-build-system)
20524 `(("r-lavaan" ,r-lavaan)))
20525 (home-page "https://github.com/simsem/semTools/wiki")
20526 (synopsis "Useful tools for structural equation modeling")
20528 "This package provides useful tools for structural equation modeling.")
20529 (license license:gpl2+)))
20531 (define-public r-regsem
20538 (uri (cran-uri "regsem" version))
20541 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20542 (properties `((upstream-name . "regsem")))
20543 (build-system r-build-system)
20545 `(("r-lavaan" ,r-lavaan)
20547 ("r-rcpparmadillo" ,r-rcpparmadillo)
20548 ("r-rsolnp" ,r-rsolnp)))
20549 (home-page "https://cran.r-project.org/package=regsem")
20550 (synopsis "Regularized structural equation modeling")
20552 "This package uses both ridge and lasso penalties (and extensions) to
20553 penalize specific parameters in structural equation models. The package
20554 offers additional cost functions, cross validation, and other extensions
20555 beyond traditional structural equation models. It also contains a function to
20556 perform @dfn{exploratory mediation} (XMed).")
20557 (license license:gpl2+)))
20559 (define-public r-stanheaders
20561 (name "r-stanheaders")
20562 (version "2.21.0-5")
20566 (uri (cran-uri "StanHeaders" version))
20569 "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
20570 (properties `((upstream-name . "StanHeaders")))
20571 (build-system r-build-system)
20572 (inputs `(("pandoc" ,ghc-pandoc)))
20574 `(("r-rcppeigen" ,r-rcppeigen)
20575 ("r-rcppparallel" ,r-rcppparallel)))
20577 `(("gfortran" ,gfortran)
20578 ("r-knitr" ,r-knitr))) ; for vignettes
20579 (home-page "https://mc-stan.org/")
20580 (synopsis "C++ header files for Stan")
20582 "The C++ header files of the Stan project are provided by this package.
20583 There is a shared object containing part of the @code{CVODES} library, but it
20584 is not accessible from R. @code{r-stanheaders} is only useful for developers
20585 who want to utilize the @code{LinkingTo} directive of their package's
20586 DESCRIPTION file to build on the Stan library without incurring unnecessary
20589 The Stan project develops a probabilistic programming language that implements
20590 full or approximate Bayesian statistical inference via Markov Chain Monte
20591 Carlo or variational methods and implements (optionally penalized) maximum
20592 likelihood estimation via optimization. The Stan library includes an advanced
20593 automatic differentiation scheme, templated statistical and linear algebra
20594 functions that can handle the automatically differentiable scalar types (and
20595 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20596 package provides user-facing R functions to parse, compile, test, estimate,
20597 and analyze Stan models.")
20598 (license license:bsd-3)))
20600 (define-public r-rpf
20607 (uri (cran-uri "rpf" version))
20610 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20611 (properties `((upstream-name . "rpf")))
20612 (build-system r-build-system)
20614 `(("r-lifecycle" ,r-lifecycle)
20615 ("r-mvtnorm" ,r-mvtnorm)
20617 ("r-rcppeigen" ,r-rcppeigen)))
20619 `(("r-knitr" ,r-knitr)))
20620 (home-page "https://github.com/jpritikin/rpf")
20621 (synopsis "Response probability functions")
20623 "The purpose of this package is to factor out logic and math common to
20624 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20625 core support code suitable for more specialized IRT packages to build upon.
20626 Complete access to optimized C functions is made available with
20627 @code{R_RegisterCCallable()}.")
20628 (license license:gpl3+)))
20630 (define-public r-openmx
20637 (uri (cran-uri "OpenMx" version))
20640 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20641 (properties `((upstream-name . "OpenMx")))
20642 (build-system r-build-system)
20645 ("r-digest" ,r-digest)
20647 ("r-matrix" ,r-matrix)
20649 ("r-rcppeigen" ,r-rcppeigen)
20651 ("r-stanheaders" ,r-stanheaders)))
20652 (native-inputs `(("gfortran" ,gfortran)))
20653 (home-page "http://openmx.ssri.psu.edu")
20654 (synopsis "Extended structural equation modelling")
20656 "This package allows for the estimation of a wide variety of advanced
20657 multivariate statistical models. It consists of a library of functions and
20658 optimizers that allow you to quickly and flexibly define an SEM model and
20659 estimate parameters given observed data.")
20660 (license license:asl2.0)))
20662 (define-public r-kutils
20669 (uri (cran-uri "kutils" version))
20672 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20673 (properties `((upstream-name . "kutils")))
20674 (build-system r-build-system)
20676 `(("r-foreign" ,r-foreign)
20677 ("r-openxlsx" ,r-openxlsx)
20679 ("r-runit" ,r-runit)
20680 ("r-xtable" ,r-xtable)))
20681 (home-page "https://cran.r-project.org/package=kutils")
20682 (synopsis "Project management tools")
20684 "This package provides tools for data importation, recoding, and
20685 inspection. There are functions to create new project folders, R code
20686 templates, create uniquely named output directories, and to quickly obtain a
20687 visual summary for each variable in a data frame. The main feature here is
20688 the systematic implementation of the \"variable key\" framework for data
20689 importation and recoding.")
20690 (license license:gpl2)))
20692 (define-public r-rockchalk
20694 (name "r-rockchalk")
20695 (version "1.8.144")
20699 (uri (cran-uri "rockchalk" version))
20702 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20703 (properties `((upstream-name . "rockchalk")))
20704 (build-system r-build-system)
20706 `(("r-cardata" ,r-cardata)
20707 ("r-kutils" ,r-kutils)
20709 ("r-mass" ,r-mass)))
20710 (home-page "https://cran.r-project.org/package=rockchalk")
20711 (synopsis "Regression estimation and presentation")
20713 "This package provides a collection of functions for interpretation and
20714 presentation of regression analysis. These functions are used to produce the
20715 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20716 includes regression diagnostics, regression tables, and plots of interactions
20717 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20718 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20719 fairly comprehensive overview.")
20720 (license license:gpl3+)))
20722 (define-public r-lisreltor
20724 (name "r-lisreltor")
20729 (uri (cran-uri "lisrelToR" version))
20732 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20733 (properties `((upstream-name . "lisrelToR")))
20734 (build-system r-build-system)
20735 (home-page "https://cran.r-project.org/package=lisrelToR")
20736 (synopsis "Import output from LISREL into R")
20738 "This is an unofficial package aimed at automating the import of LISREL
20740 (license license:gpl2)))
20742 (define-public r-bdgraph
20749 (uri (cran-uri "BDgraph" version))
20752 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20753 (properties `((upstream-name . "BDgraph")))
20754 (build-system r-build-system)
20756 `(("r-igraph" ,r-igraph)))
20757 (home-page "https://www.uva.nl/profile/a.mohammadi")
20758 (synopsis "Bayesian structure learning in graphical models")
20760 "This package provides statistical tools for Bayesian structure learning
20761 in undirected graphical models for continuous, discrete, and mixed data. It
20762 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20763 on a continuous-time birth-death process.")
20764 (license license:gpl2+)))
20766 (define-public r-d3network
20768 (name "r-d3network")
20769 (version "0.5.2.1")
20773 (uri (cran-uri "d3Network" version))
20776 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20777 (properties `((upstream-name . "d3Network")))
20778 (build-system r-build-system)
20780 `(("r-plyr" ,r-plyr)
20781 ("r-rjson" ,r-rjson)
20782 ("r-whisker" ,r-whisker)))
20783 (home-page "http://christophergandrud.github.io/d3Network/")
20784 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20786 "This package is intended to make it easy to create D3 JavaScript
20787 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20788 (license license:gpl3+)))
20790 (define-public r-qgraph
20797 (uri (cran-uri "qgraph" version))
20800 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20801 (properties `((upstream-name . "qgraph")))
20802 (build-system r-build-system)
20804 `(("r-abind" ,r-abind)
20805 ("r-bdgraph" ,r-bdgraph)
20806 ("r-colorspace" ,r-colorspace)
20807 ("r-corpcor" ,r-corpcor)
20808 ("r-d3network" ,r-d3network)
20809 ("r-dplyr" ,r-dplyr)
20810 ("r-fdrtool" ,r-fdrtool)
20811 ("r-ggplot2" ,r-ggplot2)
20812 ("r-ggraph" ,r-ggraph)
20813 ("r-glasso" ,r-glasso)
20814 ("r-gtools" ,r-gtools)
20815 ("r-hmisc" ,r-hmisc)
20817 ("r-igraph" ,r-igraph)
20819 ("r-lavaan" ,r-lavaan)
20820 ("r-matrix" ,r-matrix)
20821 ("r-pbapply" ,r-pbapply)
20824 ("r-psych" ,r-psych)
20826 ("r-reshape2" ,r-reshape2)
20827 ("r-tidygraph" ,r-tidygraph)))
20828 (home-page "http://sachaepskamp.com/qgraph/")
20829 (synopsis "Weighted network visualization and analysis")
20831 "This package implements tools for weighted network visualization and
20832 analysis, as well as Gaussian graphical model computation. It contains graph
20833 plotting methods, and tools for psychometric data visualization and graphical
20834 model estimation. See Epskamp et al. (2012)
20835 @url{doi:10.18637/jss.v048.i04}.")
20836 (license license:gpl2)))
20838 (define-public r-semplot
20845 (uri (cran-uri "semPlot" version))
20848 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20849 (properties `((upstream-name . "semPlot")))
20850 (build-system r-build-system)
20852 `(("r-colorspace" ,r-colorspace)
20853 ("r-corpcor" ,r-corpcor)
20854 ("r-igraph" ,r-igraph)
20855 ("r-lavaan" ,r-lavaan)
20856 ("r-lisreltor" ,r-lisreltor)
20857 ("r-openmx" ,r-openmx)
20859 ("r-qgraph" ,r-qgraph)
20860 ("r-regsem" ,r-regsem)
20861 ("r-rockchalk" ,r-rockchalk)
20864 (home-page "https://github.com/SachaEpskamp/semPlot")
20865 (synopsis "Unified visualizations of structural equation models")
20867 "Structural equation modeling (SEM) has a long history of representing
20868 models graphically as path diagrams. The semPlot package for R fills the gap
20869 between advanced, but time-consuming, graphical software and the limited
20870 graphics produced automatically by SEM software. In addition, semPlot offers
20871 more functionality than drawing path diagrams: it can act as a common ground
20872 for importing SEM results into R. Any result usable as input to semPlot can
20873 also be represented in any of the three popular SEM frame-works, as well as
20874 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20875 (license license:gpl2)))
20877 (define-public r-cdm
20884 (uri (cran-uri "CDM" version))
20887 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20888 (properties `((upstream-name . "CDM")))
20889 (build-system r-build-system)
20891 `(("r-mvtnorm" ,r-mvtnorm)
20892 ("r-polycor" ,r-polycor)
20894 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20896 "https://github.com/alexanderrobitzsch/CDM")
20897 (synopsis "Cognitive diagnosis modeling")
20899 "This package provides functions for cognitive diagnosis modeling and
20900 multidimensional item response modeling for dichotomous and polytomous item
20901 responses. It enables the estimation of the DINA and DINO model, the multiple
20902 group (polytomous) GDINA model, the multiple choice DINA model, the general
20903 diagnostic model (GDM), the structured latent class model (SLCA), and
20904 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20905 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20906 estimation and the package structure. For tutorials on how to use the CDM
20907 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20908 well as Ravand and Robitzsch (2015).")
20909 (license license:gpl2+)))
20911 (define-public r-tam
20918 (uri (cran-uri "TAM" version))
20921 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20922 (properties `((upstream-name . "TAM")))
20923 (build-system r-build-system)
20927 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20928 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20929 (synopsis "Test analysis modules")
20931 "This package includes tools for marginal maximum likelihood estimation
20932 and joint maximum likelihood estimation for unidimensional and
20933 multidimensional item response models. The package functionality covers the
20934 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20935 multi-faceted Rasch model, nominal item response model, structured latent
20936 class model, mixture distribution IRT models, and located latent class models.
20937 Latent regression models and plausible value imputation are also supported.")
20938 (license license:gpl2+)))
20940 (define-public r-erm
20947 (uri (cran-uri "eRm" version))
20950 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20951 (properties `((upstream-name . "eRm")))
20952 (build-system r-build-system)
20954 `(("r-colorspace" ,r-colorspace)
20955 ("r-lattice" ,r-lattice)
20957 ("r-matrix" ,r-matrix)
20958 ("r-psych" ,r-psych)))
20959 (native-inputs `(("gfortran" ,gfortran)))
20960 (home-page "https://cran.r-project.org/package=eRm")
20961 (synopsis "Extended Rasch modeling")
20963 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20964 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20965 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20966 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20967 data matrix. Additional features are the ML estimation of the person
20968 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20969 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20970 infit and outfit measures, ICC and other plots, automated stepwise item
20971 elimination, and a simulation module for various binary data matrices.")
20972 (license license:gpl3)))
20974 (define-public r-irtoys
20981 (uri (cran-uri "irtoys" version))
20984 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20985 (properties `((upstream-name . "irtoys")))
20986 (build-system r-build-system)
20990 (home-page "https://cran.r-project.org/package=irtoys")
20991 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20993 "This package provides a collection of functions useful in learning and
20994 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20995 programs. It provides basic CTT analysis, a simple common interface to the
20996 estimation of item parameters in IRT models for binary responses with three
20997 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20998 EAP, WLE, plausible values), item and person fit statistics, scaling
20999 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
21000 array of parametric and non-parametric (kernel) plots. It estimates and plots
21001 Haberman's interaction model when all items are dichotomously scored.")
21002 (license license:gpl2+)))
21004 (define-public r-iheatmapr
21006 (name "r-iheatmapr")
21011 (uri (cran-uri "iheatmapr" version))
21014 "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h"))))
21015 (properties `((upstream-name . "iheatmapr")))
21016 (build-system r-build-system)
21018 `(("r-fastcluster" ,r-fastcluster)
21019 ("r-ggdendro" ,r-ggdendro)
21020 ("r-htmlwidgets" ,r-htmlwidgets)
21021 ("r-jsonlite" ,r-jsonlite)
21022 ("r-knitr" ,r-knitr)
21023 ("r-magrittr" ,r-magrittr)
21024 ("r-rcolorbrewer" ,r-rcolorbrewer)
21025 ("r-scales" ,r-scales)))
21027 `(("r-knitr" ,r-knitr)))
21028 (home-page "https://docs.ropensci.org/iheatmapr")
21029 (synopsis "Interactive, Complex Heatmaps")
21031 "iheatmapr is an R package for building complex, interactive heatmaps
21032 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
21033 subplots along the rows or columns of the main heatmap add more information
21034 about each row or column. For example, a one column additional heatmap may
21035 indicate what group a particular row or column belongs to. Complex heatmaps
21036 may also include multiple side by side heatmaps which show different types of
21037 data for the same conditions. Interactivity can improve complex heatmaps by
21038 providing tooltips with information about each cell and enabling zooming into
21039 interesting features. iheatmapr uses the plotly library for interactivity.")
21040 (license license:expat)))
21042 (define-public r-packrat
21049 (uri (cran-uri "packrat" version))
21052 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
21053 (properties `((upstream-name . "packrat")))
21054 (build-system r-build-system)
21055 (home-page "https://github.com/rstudio/packrat/")
21056 (synopsis "Dependency management R projects")
21058 "This package provides a dependency manager for R projects that allows
21059 you to manage the R packages your project depends on in an isolated, portable,
21060 and reproducible way.")
21061 (license license:gpl2)))
21063 (define-public r-rsconnect
21065 (name "r-rsconnect")
21070 (uri (cran-uri "rsconnect" version))
21073 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
21074 (properties `((upstream-name . "rsconnect")))
21075 (build-system r-build-system)
21077 `(("r-curl" ,r-curl)
21078 ("r-digest" ,r-digest)
21079 ("r-jsonlite" ,r-jsonlite)
21080 ("r-openssl" ,r-openssl)
21081 ("r-packrat" ,r-packrat)
21082 ("r-rstudioapi" ,r-rstudioapi)
21083 ("r-yaml" ,r-yaml)))
21084 (home-page "https://github.com/rstudio/rsconnect")
21085 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21087 "This package provides a programmatic deployment interface for RPubs,
21088 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21089 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21090 (license license:gpl2)))
21092 ;; This package includes minified JavaScript files. When upgrading please
21093 ;; check that there are no new minified JavaScript files.
21094 (define-public r-dygraphs
21096 (name "r-dygraphs")
21097 (version "1.1.1.6")
21101 (uri (cran-uri "dygraphs" version))
21104 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21105 (properties `((upstream-name . "dygraphs")))
21106 (build-system r-build-system)
21108 `(#:modules ((guix build utils)
21109 (guix build r-build-system)
21113 (modify-phases %standard-phases
21114 (add-after 'unpack 'process-javascript
21115 (lambda* (#:key inputs #:allow-other-keys)
21116 (with-directory-excursion "inst/htmlwidgets/lib/"
21120 `(("dygraphs/dygraph-combined-dev.js"
21121 "dygraph-combined.js")
21122 (,(assoc-ref inputs "js-jquery")
21123 "jquery/jquery.min.js")
21124 (,(assoc-ref inputs "js-fquarter")
21125 "fquarter/moment-fquarter.min.js"))))
21126 (lambda (sources targets)
21127 (for-each (lambda (source target)
21128 (format #t "Processing ~a --> ~a~%"
21130 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21131 (call-with-output-file target
21133 (dump-port minified port)))))
21134 sources targets))))
21137 `(("uglify-js" ,uglify-js)
21138 ;; They actually use version 1.11.1, but this more recent version
21139 ;; should be just fine.
21143 (uri "https://code.jquery.com/jquery-1.12.4.js")
21146 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21150 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21151 "moment-fquarter/1.0.1/moment-fquarter.js"))
21154 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21156 `(("r-htmltools" ,r-htmltools)
21157 ("r-htmlwidgets" ,r-htmlwidgets)
21158 ("r-magrittr" ,r-magrittr)
21161 (home-page "https://github.com/rstudio/dygraphs")
21162 (synopsis "Interface to Dygraphs interactive time series charting library")
21164 "This package provides an R interface to the dygraphs JavaScript charting
21165 library (a copy of which is included in the package). It provides rich
21166 facilities for charting time-series data in R, including highly configurable
21167 series- and axis-display and interactive features like zoom/pan and
21168 series/point highlighting.")
21169 (license license:expat)))
21171 (define-public r-shinystan
21173 (name "r-shinystan")
21178 (uri (cran-uri "shinystan" version))
21181 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21182 (properties `((upstream-name . "shinystan")))
21183 (build-system r-build-system)
21185 `(("r-bayesplot" ,r-bayesplot)
21186 ("r-colourpicker" ,r-colourpicker)
21188 ("r-dygraphs" ,r-dygraphs)
21189 ("r-ggplot2" ,r-ggplot2)
21190 ("r-gridextra" ,r-gridextra)
21191 ("r-gtools" ,r-gtools)
21192 ("r-markdown" ,r-markdown)
21193 ("r-reshape2" ,r-reshape2)
21194 ("r-rsconnect" ,r-rsconnect)
21195 ("r-rstan" ,r-rstan)
21196 ("r-shiny" ,r-shiny)
21197 ("r-shinyjs" ,r-shinyjs)
21198 ("r-shinythemes" ,r-shinythemes)
21199 ("r-threejs" ,r-threejs)
21200 ("r-xtable" ,r-xtable)
21202 (home-page "https://mc-stan.org/")
21203 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21205 "This package provides a graphical user interface for interactive
21206 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21207 for analyzing a posterior sample. The interface is powered by the Shiny web
21208 application framework and works with the output of MCMC programs written in
21209 any programming language (and has extended functionality for Stan models fit
21210 using the @code{rstan} and @code{rstanarm} packages).")
21211 (license license:gpl3+)))
21213 (define-public r-rstantools
21215 (name "r-rstantools")
21220 (uri (cran-uri "rstantools" version))
21223 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
21224 (properties `((upstream-name . "rstantools")))
21225 (build-system r-build-system)
21226 (inputs `(("pandoc" ,ghc-pandoc)))
21228 `(("r-desc" ,r-desc)
21230 ("r-rcppparallel" ,r-rcppparallel)))
21232 `(("r-knitr" ,r-knitr)))
21233 (home-page "https://mc-stan.org/rstantools/")
21234 (synopsis "Tools for developing R packages interfacing with Stan")
21236 "This package provides various tools for developers of R packages
21237 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21238 up the required package structure, S3 generics and default methods to unify
21239 function naming across Stan-based R packages, and vignettes with
21240 recommendations for developers.")
21241 (license license:gpl3+)))
21243 (define-public r-loo
21250 (uri (cran-uri "loo" version))
21252 (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr"))))
21253 (properties `((upstream-name . "loo")))
21254 (build-system r-build-system)
21256 `(("pandoc" ,ghc-pandoc)
21257 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21259 `(("r-checkmate" ,r-checkmate)
21260 ("r-matrixstats" ,r-matrixstats)))
21262 `(("r-knitr" ,r-knitr)))
21263 (home-page "https://mc-stan.org/loo/")
21264 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21266 "This package provides an implementation of efficient approximate
21267 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21268 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21269 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21270 procedure for regularizing importance weights. As a byproduct of the
21271 calculations, we also obtain approximate standard errors for estimated
21272 predictive errors and for the comparison of predictive errors between models.
21273 The package also provides methods for using stacking and other model weighting
21274 techniques to average Bayesian predictive distributions.")
21275 (license license:gpl3+)))
21277 (define-public r-rstan
21284 (uri (cran-uri "rstan" version))
21287 "0fxxh2jmrgfp98195qkqli1r9ni457vnjdvqm5l91j6aagkbk8zz"))))
21288 (properties `((upstream-name . "rstan")))
21289 (build-system r-build-system)
21292 (modify-phases %standard-phases
21293 (add-before 'install 'set-timezone
21294 ;; This package is picky about timezones.
21295 (lambda* (#:key inputs #:allow-other-keys)
21296 (setenv "TZ" "UTC+1")
21298 (string-append (assoc-ref inputs "tzdata")
21299 "/share/zoneinfo"))
21302 `(("tzdata" ,tzdata-for-tests)
21303 ("pandoc" ,ghc-pandoc)
21304 ("r-knitr" ,r-knitr)))
21307 ("r-ggplot2" ,r-ggplot2)
21308 ("r-gridextra" ,r-gridextra)
21309 ("r-inline" ,r-inline)
21311 ("r-pkgbuild" ,r-pkgbuild)
21313 ("r-rcppeigen" ,r-rcppeigen)
21314 ("r-rcppparallel" ,r-rcppparallel)
21315 ("r-stanheaders" ,r-stanheaders)
21317 (home-page "https://discourse.mc-stan.org/")
21318 (synopsis "R interface to Stan")
21320 "User-facing R functions are provided to parse, compile, test, estimate,
21321 and analyze Stan models by accessing the header-only Stan library provided by
21322 the StanHeaders package. The Stan project develops a probabilistic
21323 programming language that implements full Bayesian statistical inference via
21324 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21325 approximation, and (optionally penalized) maximum likelihood estimation via
21326 optimization. In all three cases, automatic differentiation is used to
21327 quickly and accurately evaluate gradients without burdening the user with the
21328 need to derive the partial derivatives.")
21329 (license license:gpl3+)))
21331 (define-public r-rstanarm
21333 (name "r-rstanarm")
21338 (uri (cran-uri "rstanarm" version))
21341 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
21342 (properties `((upstream-name . "rstanarm")))
21343 (build-system r-build-system)
21345 `(("pandoc" ,ghc-pandoc)
21346 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21348 `(("r-bayesplot" ,r-bayesplot)
21350 ("r-ggplot2" ,r-ggplot2)
21353 ("r-matrix" ,r-matrix)
21356 ("r-rcppeigen" ,r-rcppeigen)
21357 ("r-rcppparallel" ,r-rcppparallel)
21358 ("r-rstan" ,r-rstan)
21359 ("r-rstantools" ,r-rstantools)
21360 ("r-shinystan" ,r-shinystan)
21361 ("r-stanheaders" ,r-stanheaders)
21362 ("r-survival" ,r-survival)))
21363 (home-page "https://mc-stan.org/rstanarm/")
21364 (synopsis "Bayesian applied regression modeling via Stan")
21366 "This package estimates previously compiled regression models using the
21367 @code{rstan} package, which provides the R interface to the Stan C++ library
21368 for Bayesian estimation. Users specify models via the customary R syntax with
21369 a formula and @code{data.frame} plus some additional arguments for priors.")
21370 (license license:gpl3+)))
21372 (define-public r-kendall
21379 (uri (cran-uri "Kendall" version))
21382 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21383 (properties `((upstream-name . "Kendall")))
21384 (build-system r-build-system)
21386 `(("r-boot" ,r-boot)))
21388 `(("gfortran" ,gfortran)))
21389 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21390 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21392 "This package computes the Kendall rank correlation and Mann-Kendall
21394 (license license:gpl2+)))
21396 (define-public r-zyp
21399 (version "0.10-1.1")
21403 (uri (cran-uri "zyp" version))
21406 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21407 (properties `((upstream-name . "zyp")))
21408 (build-system r-build-system)
21410 `(("r-kendall" ,r-kendall)))
21411 (home-page "https://cran.r-project.org/web/packages/zyp/")
21412 (synopsis "Zhang + Yue-Pilon Trends Package")
21414 "This package contains an efficient implementation of Sen's slope
21415 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21416 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21418 (license license:lgpl2.1)))
21420 (define-public r-rlinsolve
21422 (name "r-rlinsolve")
21427 (uri (cran-uri "Rlinsolve" version))
21430 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21431 (properties `((upstream-name . "Rlinsolve")))
21432 (build-system r-build-system)
21434 `(("r-matrix" ,r-matrix)
21436 ("r-rcpparmadillo" ,r-rcpparmadillo)
21437 ("r-rdpack" ,r-rdpack)))
21438 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21439 (synopsis "Iterative solvers for (sparse) linear system of equations")
21441 "Solving a system of linear equations is one of the most fundamental
21442 computational problems for many fields of mathematical studies, such as
21443 regression problems from statistics or numerical partial differential
21444 equations. This package provides basic stationary iterative solvers such as
21445 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21446 Nonstationary, also known as Krylov subspace methods are also provided.
21447 Sparse matrix computation is also supported in that solving large and sparse
21448 linear systems can be manageable using the @code{Matrix} package along with
21449 @code{RcppArmadillo}.")
21450 (license license:gpl3+)))
21452 (define-public r-zvcv
21459 (uri (cran-uri "ZVCV" version))
21462 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21463 (properties `((upstream-name . "ZVCV")))
21464 (build-system r-build-system)
21466 `(("r-abind" ,r-abind)
21468 ("r-dplyr" ,r-dplyr)
21469 ("r-glmnet" ,r-glmnet)
21470 ("r-magrittr" ,r-magrittr)
21471 ("r-mvtnorm" ,r-mvtnorm)
21473 ("r-rcpparmadillo" ,r-rcpparmadillo)
21474 ("r-rlinsolve" ,r-rlinsolve)))
21475 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21476 (synopsis "Zero-Variance Control Variates")
21478 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21479 to reduce the variance of Monte Carlo estimators of expectations using the
21480 derivatives of the log target. Once the derivatives are available, the only
21481 additional computational effort is in solving a linear regression problem.
21482 This method has been extended to higher dimensions using regularisation. This
21483 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21484 samples, derivatives and function evaluations are available. Additional
21485 functions for applying ZV-CV to two estimators for the normalising constant of
21486 the posterior distribution in Bayesian statistics are also supplied.")
21487 (license license:gpl2+)))
21489 (define-public r-ztype
21496 (uri (cran-uri "ztype" version))
21499 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21500 (properties `((upstream-name . "ztype")))
21501 (build-system r-build-system)
21503 `(("r-assertthat" ,r-assertthat)
21504 ("r-dplyr" ,r-dplyr)
21505 ("r-ggplot2" ,r-ggplot2)
21506 ("r-lubridate" ,r-lubridate)
21507 ("r-magrittr" ,r-magrittr)
21508 ("r-rvest" ,r-rvest)
21509 ("r-stringr" ,r-stringr)))
21510 (home-page "https://cran.r-project.org/web/packages/ztype/")
21511 (synopsis "Run a Ztype game loaded with R functions")
21513 "How fast can you type R functions on your keyboard? Find out by running
21514 a @code{zty.pe} game: export R functions as instructions to type to destroy
21515 opponents' vessels.")
21516 (license license:gpl3)))
21518 (define-public r-zseq
21525 (uri (cran-uri "Zseq" version))
21528 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21529 (properties `((upstream-name . "Zseq")))
21530 (build-system r-build-system)
21532 `(("r-gmp" ,r-gmp)))
21533 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21534 (synopsis "Integer sequence generator")
21536 "This package generates well-known integer sequences. The @code{gmp}
21537 package is adopted for computing with arbitrarily large numbers. Every
21538 function has a hyperlink to its corresponding item in the @dfn{On-Line
21539 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21540 (license license:gpl3+)))
21542 (define-public r-isoband
21549 (uri (cran-uri "isoband" version))
21552 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21553 (properties `((upstream-name . "isoband")))
21554 (build-system r-build-system)
21556 `(("r-testthat" ,r-testthat)))
21558 `(("r-knitr" ,r-knitr)))
21559 (home-page "https://github.com/wilkelab/isoband")
21560 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21562 "This package provides a fast C++ implementation to generate contour
21563 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21564 containing elevation data.")
21565 (license license:expat)))
21567 (define-public r-ppcor
21574 (uri (cran-uri "ppcor" version))
21577 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21578 (properties `((upstream-name . "ppcor")))
21579 (build-system r-build-system)
21581 `(("r-mass" ,r-mass)))
21582 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21583 (synopsis "Partial and semi-partial correlation")
21585 "This package provides users not only with a function to readily
21586 calculate the higher-order partial and semi-partial correlations but also with
21587 statistics and p-values of the correlation coefficients.")
21588 (license license:gpl2)))
21590 (define-public r-hrbrthemes
21592 (name "r-hrbrthemes")
21597 (uri (cran-uri "hrbrthemes" version))
21599 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21600 (properties `((upstream-name . "hrbrthemes")))
21601 (build-system r-build-system)
21603 `(("r-extrafont" ,r-extrafont)
21604 ("r-gdtools" ,r-gdtools)
21605 ("r-ggplot2" ,r-ggplot2)
21606 ("r-htmltools" ,r-htmltools)
21607 ("r-knitr" ,r-knitr)
21608 ("r-magrittr" ,r-magrittr)
21609 ("r-rmarkdown" ,r-rmarkdown)
21610 ("r-scales" ,r-scales)))
21612 `(("r-knitr" ,r-knitr)))
21613 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21614 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21616 "This package provides a compilation of extra @code{ggplot2} themes,
21617 scales and utilities, including a spell check function for plot label fields
21618 and an overall emphasis on typography.")
21619 (license license:expat)))
21621 (define-public r-crochet
21628 (uri (cran-uri "crochet" version))
21631 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21632 (build-system r-build-system)
21634 `(("r-knitr" ,r-knitr)))
21635 (home-page "https://github.com/agrueneberg/crochet")
21636 (synopsis "Implementation Helper for Matrix-Like Types")
21638 "Functions to help implement the extraction / subsetting / indexing
21639 function @code{[} and replacement function @code{[<-} of custom matrix-like
21640 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21641 as possible (with tests to prove it).")
21642 (license license:expat)))
21644 (define-public r-boa
21647 (version "1.1.8-2")
21651 (uri (cran-uri "boa" version))
21654 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21655 (properties `((upstream-name . "boa")))
21656 (build-system r-build-system)
21657 (home-page "http://www.jstatsoft.org/v21/i11")
21658 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21660 "This package provides a menu-driven program and library of functions for
21661 carrying out convergence diagnostics and statistical and graphical analysis of
21662 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21663 (license license:gpl2+)))
21665 (define-public r-httpcode
21667 (name "r-httpcode")
21671 (uri (cran-uri "httpcode" version))
21674 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21675 (build-system r-build-system)
21676 (home-page "https://github.com/sckott/httpcode")
21677 (synopsis "HTTP status code helper")
21678 (description "@code{httpcode} provides functionality for finding and
21679 explaining the meaning of @code{HTTP} status codes. Functions are included for
21680 searching for codes by full or partial number, by message, and to get
21681 appropriate dog and cat images for many status codes.")
21682 (license license:expat)))
21684 (define-public r-latex2exp
21686 (name "r-latex2exp")
21690 (uri (cran-uri "latex2exp" version))
21693 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21694 (build-system r-build-system)
21696 `(("r-stringr" ,r-stringr)
21697 ("r-magrittr", r-magrittr)))
21698 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21699 (synopsis "Use LaTeX expressions in plots")
21700 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21701 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21702 rendered as text, axis labels, etc. throughout R's plotting system.")
21703 (license license:expat)))
21705 (define-public r-oai
21711 (uri (cran-uri "oai" version))
21714 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21715 (build-system r-build-system)
21717 `(("r-xml2" ,r-xml2)
21720 ("r-stringr" ,r-stringr)
21721 ("r-tibble" ,r-tibble)))
21722 (home-page "https://github.com/ropensci/oai/")
21723 (synopsis "General purpose OAI-PMH services client")
21724 (description "@code{oai} provides a general purpose client to work with
21725 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21726 service. Functions are provided to work with the OAI-PMH verbs:
21727 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21728 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21729 (license license:expat)))
21731 (define-public r-argon2
21738 (uri (cran-uri "argon2" version))
21741 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21742 (properties `((upstream-name . "argon2")))
21743 (build-system r-build-system)
21744 (home-page "https://github.com/wrathematics/argon2")
21745 (synopsis "Secure password hashing based on the argon2 algorithm")
21747 "This package provides utilities for secure password hashing via the
21748 argon2 algorithm.")
21749 (license license:bsd-2)))
21751 (define-public r-getpass
21758 (uri (cran-uri "getPass" version))
21761 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21762 (properties `((upstream-name . "getPass")))
21763 (build-system r-build-system)
21765 `(("r-rstudioapi" ,r-rstudioapi)))
21766 (home-page "https://github.com/wrathematics/getPass")
21767 (synopsis "Masked user input")
21769 "This package provides a micro-package for reading \"passwords\", i.e.
21770 reading user input with masking, so that the input is not displayed as it is
21771 typed. Currently, RStudio, the command line (every OS), and any platform
21772 where tcltk is present are supported.")
21773 (license license:bsd-2)))
21775 (define-public r-remoter
21782 (uri (cran-uri "remoter" version))
21785 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21786 (properties `((upstream-name . "remoter")))
21787 (build-system r-build-system)
21789 `(("r-argon2" ,r-argon2)
21790 ("r-getpass" ,r-getpass)
21791 ("r-pbdzmq" ,r-pbdzmq)
21793 (home-page "https://github.com/RBigData/remoter")
21794 (synopsis "Control a remote R session from a local one")
21796 "This package provides a set of utilities for client/server computing
21797 with R, controlling a remote R session (the server) from a local one (the
21799 (license license:bsd-2)))
21801 (define-public r-asd
21808 (uri (cran-uri "asd" version))
21811 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21812 (properties `((upstream-name . "asd")))
21813 (build-system r-build-system)
21815 `(("r-mvtnorm" ,r-mvtnorm)))
21816 (home-page "https://cran.r-project.org/web/packages/asd")
21817 (synopsis "Simulations for Adaptive Seamless Designs")
21819 "This package provdes means to run simulations for adaptive seamless
21820 designs with and without early outcomes for treatment selection and
21821 subpopulation type designs.")
21822 (license license:gpl3)))
21824 (define-public r-nbconvertr
21826 (name "r-nbconvertr")
21831 (uri (cran-uri "nbconvertR" version))
21834 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21835 (properties `((upstream-name . "nbconvertR")))
21836 (build-system r-build-system)
21838 `(("jupyter" ,python-nbconvert)
21839 ("pandoc" ,ghc-pandoc)))
21840 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21841 (synopsis "Vignette engine wrapping Jupyter notebooks")
21843 "This package calls the Jupyter script @code{nbconvert} to create
21844 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21845 containing rich text, code, and its output. Code cells can be edited and
21846 evaluated interactively.")
21847 (license license:gpl3)))
21849 (define-public r-bridgesampling
21851 (name "r-bridgesampling")
21856 (uri (cran-uri "bridgesampling" version))
21859 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21861 `((upstream-name . "bridgesampling")))
21862 (build-system r-build-system)
21864 `(("r-brobdingnag" ,r-brobdingnag)
21866 ("r-matrix" ,r-matrix)
21867 ("r-mvtnorm" ,r-mvtnorm)
21868 ("r-scales" ,r-scales)
21869 ("r-stringr" ,r-stringr)))
21871 `(("r-knitr" ,r-knitr)))
21872 (home-page "https://github.com/quentingronau/bridgesampling")
21873 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21875 "This package provides functions for estimating marginal likelihoods,
21876 Bayes factors, posterior model probabilities, and normalizing constants in
21877 general, via different versions of bridge sampling.")
21878 (license license:gpl2+)))
21880 (define-public r-tea
21887 (uri (cran-uri "tea" version))
21890 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21892 `((upstream-name . "tea")))
21893 (build-system r-build-system)
21895 `(("r-matrix" ,r-matrix)))
21896 (home-page "https://cran.r-project.org/web/packages/tea/")
21897 (synopsis "Threshold estimation approaches")
21899 "This package provides different approaches for selecting the threshold
21900 in generalized Pareto distributions. Most of them are based on minimizing the
21901 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21902 Others are heuristically motivated by searching for stable sample paths, i.e.
21903 a nearly constant region of the tail index estimator with respect to k, which
21904 is the number of data in the tail. The third class is motivated by graphical
21905 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21906 is also implemented here.")
21907 (license license:gpl3)))
21909 (define-public r-awsmethods
21911 (name "r-awsmethods")
21916 (uri (cran-uri "awsMethods" version))
21919 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21921 `((upstream-name . "awsMethods")))
21922 (build-system r-build-system)
21923 (home-page "http://www.wias-berlin.de/software/imaging/")
21924 (synopsis "Class and methods definitions")
21926 "This package defines the generic method @code{extract} and provides
21927 @code{openMP} support as needed in several packages like
21928 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21929 (license license:gpl2+)))
21931 (define-public r-aws
21938 (uri (cran-uri "aws" version))
21941 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21943 `((upstream-name . "aws")))
21944 (build-system r-build-system)
21946 `(("r-awsmethods" ,r-awsmethods)
21949 `(("gfortran" ,gfortran)))
21950 (home-page "https://cran.r-project.org/web/packages/aws/")
21951 (synopsis "Adaptive weights smoothing")
21953 "This package provides a collection of R-functions implementing adaptive
21954 smoothing procedures in 1D, 2D and 3D. This includes the
21955 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21956 Confidence Intervals} (ICI), variational approaches, and a non-local means
21958 (license license:gpl2+)))
21960 (define-public r-sgloptim
21962 (name "r-sgloptim")
21967 (uri (cran-uri "sglOptim" version))
21970 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21972 `((upstream-name . "sglOptim")))
21973 (build-system r-build-system)
21976 ("r-doparallel" ,r-doparallel)
21977 ("r-foreach" ,r-foreach)
21978 ("r-matrix" ,r-matrix)
21980 ("r-rcpparmadillo" ,r-rcpparmadillo)
21981 ("r-rcppprogress" ,r-rcppprogress)))
21983 `(("r-knitr" ,r-knitr)))
21984 (home-page "https://github.com/nielsrhansen/sglOptim")
21985 (synopsis "Generic sparse group Lasso solver")
21987 "This package provides a fast generic solver for sparse group lasso
21988 optimization problems. The loss (objective) function must be defined in a C++
21989 module. The optimization problem is solved using a coordinate gradient
21990 descent algorithm. Convergence of the algorithm is established and the
21991 algorithm is applicable to a broad class of loss functions. Use of parallel
21992 computing for cross validation and subsampling is supported through the
21993 @code{foreach} and @code{doParallel} packages.")
21994 (license license:gpl2+)))
21996 (define-public r-grouped
22003 (uri (cran-uri "grouped" version))
22006 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
22008 `((upstream-name . "grouped")))
22009 (build-system r-build-system)
22011 `(("r-mass" ,r-mass)))
22012 (home-page "https://cran.r-project.org/web/packages/grouped/")
22013 (synopsis "Regression analysis of grouped and coarse data")
22015 "This package provides regression models for grouped and coarse data,
22016 under the coarsened at random assumption.")
22017 (license license:gpl2+)))
22019 (define-public r-stam
22026 (uri (cran-uri "stam" version))
22029 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
22031 `((upstream-name . "stam")))
22032 (build-system r-build-system)
22036 (home-page "https://cran.r-project.org/web/packages/stam")
22037 (synopsis "Spatio-temporal analysis and modelling")
22039 "This package provides various methods to conduct Spatio-Temporal
22040 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
22041 Inferred Spatio-Temporal Modelling.")
22042 (license license:gpl2+)))
22044 (define-public r-dcv
22051 (uri (cran-uri "dcv" version))
22054 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
22056 `((upstream-name . "dcv")))
22057 (build-system r-build-system)
22059 `(("r-lmtest" ,r-lmtest)))
22060 (home-page "https://cran.r-project.org/web/packages/dcv/")
22061 (synopsis "Conventional cross-validation statistics for climate-growth model")
22063 "This package performs several conventional cross-validation statistical
22064 methods for climate-growth model in the climate reconstruction from tree
22065 rings, including Sign Test statistic, Reduction of Error statistic, Product
22066 Mean Test, Durbin-Watson statistic etc.")
22067 (license license:gpl2)))
22069 (define-public r-rcdd
22076 (uri (cran-uri "rcdd" version))
22079 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
22081 `((upstream-name . "rcdd")))
22082 (build-system r-build-system)
22085 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22086 (synopsis "Computational geometry")
22088 "This package converts back and forth between two representations of a
22089 convex polytope: as solution of a set of linear equalities and inequalities
22090 and as convex hull of set of points and rays. Also does linear programming
22091 and redundant generator elimination. All functions can use exact
22092 infinite-precision rational arithmetic.")
22093 (license license:gpl2)))
22095 (define-public r-rxnat
22102 (uri (cran-uri "Rxnat" version))
22105 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
22107 `((upstream-name . "Rxnat")))
22108 (build-system r-build-system)
22110 `(("r-httr" ,r-httr)
22111 ("r-rcurl" ,r-rcurl)))
22113 `(("r-knitr" ,r-knitr)))
22114 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22115 (synopsis "Queries and extracts images from neuroimaging datasets")
22117 "This package allows communication with the Extensible Neuroimaging
22118 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22120 (license license:gpl2)))
22122 (define-public r-rserve
22129 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22130 version ".tar.gz"))
22133 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22134 (build-system r-build-system)
22136 `(("r-checkmate" ,r-checkmate)
22138 ("r-jsonlite" ,r-jsonlite)
22139 ("r-knitr" ,r-knitr)
22142 ("r-uuid" ,r-uuid)))
22144 `(("openssl" ,openssl)
22146 (home-page "https://github.com/s-u/Rserve")
22148 "Server providing access to R from many languages and systems")
22150 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22151 binary requests to be sent to R. Every connection has a separate workspace
22152 and working directory. Client-side implementations are available for popular
22153 languages such as C/C++ and Java, allowing any application to use facilities
22154 of R without the need of linking to R code. Rserve supports remote
22155 connection, user authentication and file transfer. A simple R client is
22156 included in this package as well.")
22157 (license license:gpl2)))
22159 (define-public r-brms
22166 (uri (cran-uri "brms" version))
22169 "13gnc517yssvi2mnih5bln06hcbn4y80gd9h3szacs6n3mwpig5f"))))
22170 (properties `((upstream-name . "brms")))
22171 (build-system r-build-system)
22173 `(("r-abind" ,r-abind)
22174 ("r-backports" ,r-backports)
22175 ("r-bayesplot" ,r-bayesplot)
22176 ("r-bridgesampling" ,r-bridgesampling)
22178 ("r-future" ,r-future)
22179 ("r-ggplot2" ,r-ggplot2)
22182 ("r-matrix" ,r-matrix)
22183 ("r-matrixstats" ,r-matrixstats)
22185 ("r-nleqslv" ,r-nleqslv)
22188 ("r-rstan" ,r-rstan)
22189 ("r-rstantools" ,r-rstantools)
22190 ("r-shinystan" ,r-shinystan)))
22191 (native-inputs `(("r-knitr" ,r-knitr)))
22193 "https://github.com/paul-buerkner/brms")
22195 "Bayesian Regression Models using 'Stan'")
22197 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22198 using 'Stan' for full Bayesian inference. A wide range of distributions and
22199 link functions are supported, allowing users to fit -- among others -- linear,
22200 robust linear, count data, survival, response times, ordinal, zero-inflated,
22201 hurdle, and even self-defined mixture models all in a multilevel context.
22202 Further modeling options include non-linear and smooth terms, auto-correlation
22203 structures, censored data, meta-analytic standard errors, and quite a few
22204 more. In addition, all parameters of the response distribution can be
22205 predicted in order to perform distributional regression. Prior specifications
22206 are flexible and explicitly encourage users to apply prior distributions that
22207 actually reflect their beliefs. Model fit can easily be assessed and compared
22208 with posterior predictive checks and leave-one-out cross-validation.")
22209 (license license:gpl2)))
22211 (define-public r-mstate
22218 (uri (cran-uri "mstate" version))
22221 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22222 (properties `((upstream-name . "mstate")))
22223 (build-system r-build-system)
22225 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22226 ("r-survival" ,r-survival)))
22228 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22230 "Data Preparation, Estimation and Prediction in Multi-State Models")
22232 "Contains functions for data preparation, descriptives, hazard estimation
22233 and prediction with Aalen-Johansen or simulation in competing risks and
22234 multi-state models.")
22235 (license license:gpl2+)))
22237 (define-public r-scatterpie
22239 (name "r-scatterpie")
22244 (uri (cran-uri "scatterpie" version))
22247 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22248 (properties `((upstream-name . "scatterpie")))
22249 (build-system r-build-system)
22251 `(("r-ggforce" ,r-ggforce)
22252 ("r-ggplot2" ,r-ggplot2)
22253 ("r-rlang" ,r-rlang)
22254 ("r-rvcheck" ,r-rvcheck)
22255 ("r-tidyr" ,r-tidyr)))
22257 `(("r-knitr" ,r-knitr)))
22258 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22259 (synopsis "Scatter pie plot")
22261 "This package creates scatterpie plots, especially useful for plotting
22263 (license license:artistic2.0)))
22265 (define-public r-boruta
22272 (uri (cran-uri "Boruta" version))
22275 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22276 (properties `((upstream-name . "Boruta")))
22277 (build-system r-build-system)
22278 (propagated-inputs `(("r-ranger" ,r-ranger)))
22279 (home-page "https://gitlab.com/mbq/Boruta/")
22280 (synopsis "Wrapper algorithm for all relevant feature selection")
22282 "This package provides an all relevant feature selection wrapper
22283 algorithm. It finds relevant features by comparing original attributes'
22284 importance with importance achievable at random, estimated using their
22285 permuted copies (shadows).")
22286 (license license:gpl2+)))
22288 (define-public r-directlabels
22290 (name "r-directlabels")
22291 (version "2020.6.17")
22295 (uri (cran-uri "directlabels" version))
22298 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22299 (build-system r-build-system)
22301 `(("r-quadprog" ,r-quadprog)))
22303 `(("r-knitr" ,r-knitr)))
22304 (home-page "http://directlabels.r-forge.r-project.org/")
22305 (synopsis "Direct labels for multicolor plots")
22307 "This package provides an extensible framework for automatically placing
22308 direct labels onto multicolor plots. Label positions are described using
22309 positioning methods that can be re-used across several different plots. There
22310 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22311 inferring an appropriate positioning method.")
22312 (license license:gpl3)))
22314 (define-public r-lsd
22321 (uri (cran-uri "LSD" version))
22323 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22324 (properties `((upstream-name . "LSD")))
22325 (build-system r-build-system)
22326 (home-page "https://cran.r-project.org/web/packages/LSD/")
22327 (synopsis "Lots of superior depictions tool creates colorful plots")
22329 "This package creates lots of colorful plots in a multitude of variations.
22330 Try a demo of the LSD by running @code{demotour()}.")
22332 (license (list license:gpl2 license:gpl3))))
22334 (define-public r-fourcseq
22336 (name "r-fourcseq")
22341 (uri (bioconductor-uri "FourCSeq" version))
22343 (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x"))))
22344 (properties `((upstream-name . "FourCSeq")))
22345 (build-system r-build-system)
22347 `(("r-biobase" ,r-biobase)
22348 ("r-biostrings" ,r-biostrings)
22349 ("r-deseq2" ,r-deseq2)
22351 ("r-genomicalignments" ,r-genomicalignments)
22352 ("r-genomicranges" ,r-genomicranges)
22353 ("r-ggbio" ,r-ggbio)
22354 ("r-ggplot2" ,r-ggplot2)
22355 ("r-gtools" ,r-gtools)
22357 ("r-matrix" ,r-matrix)
22358 ("r-reshape2" ,r-reshape2)
22359 ("r-rsamtools" ,r-rsamtools)
22360 ("r-rtracklayer" ,r-rtracklayer)
22361 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22363 `(("r-knitr" ,r-knitr)))
22365 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22366 (synopsis "Analysis of multiplexed 4C sequencing data")
22368 "This package is an R package dedicated to the analysis of (multiplexed)
22369 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22370 interactions between DNA elements and identify differential interactions
22371 between conditions. The statistical analysis in R starts with individual bam
22372 files for each sample as inputs. To obtain these files, the package contains
22373 a Python script to demultiplex libraries and trim off primer sequences. With
22374 a standard alignment software the required bam files can be then be
22376 (license license:gpl3+)))
22378 (define-public r-phylogram
22380 (name "r-phylogram")
22385 (uri (cran-uri "phylogram" version))
22387 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22388 (properties `((upstream-name . "phylogram")))
22389 (build-system r-build-system)
22390 (propagated-inputs `(("r-ape" ,r-ape)))
22391 (home-page "https://github.com/ropensci/phylogram/")
22392 (synopsis "Dendrograms for evolutionary analysis")
22394 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22395 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22396 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22397 as well as several tools for command-line tree manipulation and import/export
22398 via Newick parenthetic text. This improves accessibility to the comprehensive
22399 range of object-specific analytical and tree-visualization functions found
22400 across a wide array of bioinformatic R packages.")
22401 (license license:gpl3)))
22403 (define-public r-kmer
22410 (uri (cran-uri "kmer" version))
22412 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22413 (properties `((upstream-name . "kmer")))
22414 (build-system r-build-system)
22416 `(("r-openssl" ,r-openssl)
22417 ("r-phylogram" ,r-phylogram)
22418 ("r-rcpp" ,r-rcpp)))
22419 (home-page "https://github.com/shaunpwilkinson/kmer/")
22420 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22422 "@code{r-kmer} is an R package for rapidly computing distance matrices
22423 and clustering large sequence datasets using fast alignment-free k-mer
22424 counting and recursive k-means partitioning.")
22425 (license license:gpl3)))
22427 (define-public r-shapforxgboost
22429 (name "r-shapforxgboost")
22434 (uri (cran-uri "SHAPforxgboost" version))
22437 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22439 `((upstream-name . "SHAPforxgboost")))
22440 (build-system r-build-system)
22442 `(("r-bbmisc" ,r-bbmisc)
22443 ("r-data-table" ,r-data-table)
22444 ("r-ggextra" ,r-ggextra)
22445 ("r-ggforce" ,r-ggforce)
22446 ("r-ggplot2" ,r-ggplot2)
22447 ("r-ggpubr" ,r-ggpubr)
22448 ("r-rcolorbrewer" ,r-rcolorbrewer)
22449 ("r-xgboost" ,r-xgboost)))
22450 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22451 (synopsis "SHAP Plots for XGBoost")
22453 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22454 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22455 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22456 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22458 (license license:expat)))
22460 (define-public r-rismed
22467 (uri (cran-uri "RISmed" version))
22470 "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l"))))
22471 (properties `((upstream-name . "RISmed")))
22472 (build-system r-build-system)
22473 (home-page "https://cran.r-project.org/web/packages/RISmed")
22474 (synopsis "Download content from NCBI databases")
22476 "This package provides a set of tools to extract bibliographic
22477 content from the National Center for Biotechnology Information (NCBI)
22478 databases, including PubMed. The name RISmed is a portmanteau of
22479 RIS (for Research Information Systems, a common tag format for
22480 bibliographic data) and PubMed.")
22481 (license license:gpl2+)))
22483 (define-public r-semver
22490 (uri (cran-uri "semver" version))
22493 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
22494 (properties `((upstream-name . "semver")))
22495 (build-system r-build-system)
22497 `(("r-assertthat" ,r-assertthat)
22498 ("r-rcpp" ,r-rcpp)))
22499 (native-inputs `(("r-knitr" ,r-knitr)))
22500 (home-page "https://github.com/johndharrison/semver")
22501 (synopsis "Parser for Semantic Versioning 2.0.0")
22503 "This package provides tools and functions for parsing, rendering and
22504 operating on semantic version strings. Semantic versioning is a simple set of
22505 rules and requirements that dictate how version numbers are assigned and
22506 incremented as outlined at @url{http://semver.org}.")
22507 (license license:expat)))
22509 (define-public r-binman
22516 (uri (cran-uri "binman" version))
22519 "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"))))
22520 (properties `((upstream-name . "binman")))
22521 (build-system r-build-system)
22523 `(("r-assertthat" ,r-assertthat)
22525 ("r-jsonlite" ,r-jsonlite)
22526 ("r-rappdirs" ,r-rappdirs)
22527 ("r-semver" ,r-semver)
22529 ("r-yaml" ,r-yaml)))
22530 (native-inputs `(("r-knitr" ,r-knitr)))
22531 (home-page "https://github.com/ropensci/binman")
22532 (synopsis "Binary download manager")
22534 "This package provides tools and functions for managing the download of
22535 binary files. Binary repositories are defined in the YAML format. Defining
22536 new pre-download, download and post-download templates allow additional
22537 repositories to be added.")
22538 (license license:expat)))
22540 (define-public r-wdman
22547 (uri (cran-uri "wdman" version))
22550 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
22551 (properties `((upstream-name . "wdman")))
22552 (build-system r-build-system)
22554 `(("r-assertthat" ,r-assertthat)
22555 ("r-binman" ,r-binman)
22556 ("r-processx" ,r-processx)
22557 ("r-semver" ,r-semver)
22558 ("r-yaml" ,r-yaml)))
22559 (native-inputs `(("r-knitr" ,r-knitr)))
22560 (home-page "https://docs.ropensci.org/wdman/")
22561 (synopsis "Webdriver/Selenium binary manager")
22563 "There are a number of binary files associated with the
22564 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
22565 @url{https://sites.google.com/a/chromium.org/chromedriver/},
22566 @url{https://github.com/mozilla/geckodriver},
22567 @url{http://phantomjs.org/download.html}, and
22568 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
22569 more information). This package provides functions to download these binaries
22570 and to manage processes involving them.")
22571 (license license:expat)))
22573 (define-public r-rselenium
22575 (name "r-rselenium")
22580 (uri (cran-uri "RSelenium" version))
22583 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
22584 (properties `((upstream-name . "RSelenium")))
22585 (build-system r-build-system)
22587 `(("r-binman" ,r-binman)
22588 ("r-catools" ,r-catools)
22590 ("r-openssl" ,r-openssl)
22591 ("r-wdman" ,r-wdman)
22593 (native-inputs `(("r-knitr" ,r-knitr)))
22594 (home-page "https://docs.ropensci.org/RSelenium/")
22595 (synopsis "R bindings for Selenium WebDriver")
22597 "This package provides a set of R bindings for the Selenium 2.0
22598 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
22599 information) using the @code{JsonWireProtocol} (see
22600 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
22601 information). Selenium 2.0 WebDriver allows driving a web browser natively as
22602 a user would either locally or on a remote machine using the Selenium server
22603 it marks a leap forward in terms of web browser automation. Selenium
22604 automates web browsers (commonly referred to as browsers). Using RSelenium
22605 you can automate browsers locally or remotely.")
22606 (license license:agpl3+)))
22608 (define-public r-conquer
22615 (uri (cran-uri "conquer" version))
22618 "1c7id7wgspma5bdcirrhw7f9fp709zxpj31klivasdbvd4jgi4vb"))))
22619 (properties `((upstream-name . "conquer")))
22620 (build-system r-build-system)
22622 `(("r-matrix" ,r-matrix)
22623 ("r-matrixstats" ,r-matrixstats)
22625 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22626 (home-page "https://github.com/XiaoouPan/conquer")
22627 (synopsis "Convolution-type smoothed quantile regression")
22629 "This package provides fast and accurate convolution-type smoothed
22630 quantile regression, implemented using Barzilai-Borwein gradient descent with
22631 a Huber regression warm start. Confidence intervals for regression
22632 coefficients are constructed using multiplier bootstrap.")
22633 (license license:gpl3)))
22635 (define-public r-fastshap
22637 (name "r-fastshap")
22642 (uri (cran-uri "fastshap" version))
22645 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
22646 (properties `((upstream-name . "fastshap")))
22647 (build-system r-build-system)
22649 `(("r-abind" ,r-abind)
22650 ("r-ggplot2" ,r-ggplot2)
22651 ("r-gridextra" ,r-gridextra)
22652 ("r-matrixstats" ,r-matrixstats)
22655 ("r-rcpparmadillo" ,r-rcpparmadillo)
22656 ("r-tibble" ,r-tibble)))
22657 (home-page "https://github.com/bgreenwell/fastshap")
22658 (synopsis "Fast approximate Shapley values")
22660 "This package computes fast (relative to other implementations)
22661 approximate Shapley values for any supervised learning model. Shapley values
22662 help to explain the predictions from any black box model using ideas from game
22663 theory; see @url{Strumbel and Kononenko (2014),
22664 doi.org/10.1007/s10115-013-0679-x} for details.")
22665 (license license:gpl2+)))
22667 (define-public r-metrics
22674 (uri (cran-uri "Metrics" version))
22677 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
22678 (properties `((upstream-name . "Metrics")))
22679 (build-system r-build-system)
22680 (home-page "https://github.com/mfrasco/Metrics")
22681 (synopsis "Evaluation metrics for machine learning")
22683 "This package provides an implementation of evaluation metrics in R that
22684 are commonly used in supervised machine learning. It implements metrics for
22685 regression, time series, binary classification, classification, and
22686 information retrieval problems. It has zero dependencies and a consistent,
22687 simple interface for all functions.")
22688 (license license:bsd-3)))
22690 (define-public r-iml
22697 (uri (cran-uri "iml" version))
22700 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
22701 (properties `((upstream-name . "iml")))
22702 (build-system r-build-system)
22704 `(("r-checkmate" ,r-checkmate)
22705 ("r-data-table" ,r-data-table)
22706 ("r-formula" ,r-formula)
22707 ("r-future" ,r-future)
22708 ("r-future-apply" ,r-future-apply)
22709 ("r-ggplot2" ,r-ggplot2)
22710 ("r-gridextra" ,r-gridextra)
22711 ("r-metrics" ,r-metrics)
22712 ("r-prediction" ,r-prediction)
22714 (native-inputs `(("r-knitr" ,r-knitr)))
22715 (home-page "https://github.com/christophM/iml")
22716 (synopsis "Interpretable machine learning")
22718 "This package provides interpretability methods to analyze the behavior
22719 and predictions of any machine learning model. Implemented methods are:
22722 @item Feature importance described by Fisher et al. (2018),
22723 @item accumulated local effects plots described by Apley (2018),
22724 @item partial dependence plots described by Friedman (2001),
22725 @item individual conditional expectation ('ice') plots described by Goldstein
22726 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
22727 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
22728 @item the Shapley Value described by Strumbelj et. al (2014)
22729 @url{https://doi.org/10.1007/s10115-013-0679-x},
22730 @item feature interactions described by Friedman et. al
22731 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
22734 (license license:expat)))