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 © 2020 Todor Kondić <tk.code@protonmail.com>
21 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
22 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
23 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; This file is part of GNU Guix.
27 ;;; GNU Guix is free software; you can redistribute it and/or modify it
28 ;;; under the terms of the GNU General Public License as published by
29 ;;; the Free Software Foundation; either version 3 of the License, or (at
30 ;;; your option) any later version.
32 ;;; GNU Guix is distributed in the hope that it will be useful, but
33 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
34 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 ;;; GNU General Public License for more details.
37 ;;; You should have received a copy of the GNU General Public License
38 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
40 (define-module (gnu packages cran)
41 #:use-module ((guix licenses) #:prefix license:)
42 #:use-module (guix packages)
43 #:use-module (guix download)
44 #:use-module (guix git-download)
45 #:use-module (guix utils)
46 #:use-module (guix build-system r)
47 #:use-module (gnu packages algebra)
48 #:use-module (gnu packages autotools)
49 #:use-module (gnu packages base)
50 #:use-module (gnu packages bioinformatics)
51 #:use-module (gnu packages c)
52 #:use-module (gnu packages compression)
53 #:use-module (gnu packages curl)
54 #:use-module (gnu packages databases)
55 #:use-module (gnu packages fontutils)
56 #:use-module (gnu packages gcc)
57 #:use-module (gnu packages geo)
58 #:use-module (gnu packages ghostscript)
59 #:use-module (gnu packages gl)
60 #:use-module (gnu packages gnome)
61 #:use-module (gnu packages graph)
62 #:use-module (gnu packages gtk)
63 #:use-module (gnu packages haskell-xyz)
64 #:use-module (gnu packages icu4c)
65 #:use-module (gnu packages image)
66 #:use-module (gnu packages imagemagick)
67 #:use-module (gnu packages java)
68 #:use-module (gnu packages javascript)
69 #:use-module (gnu packages lisp-xyz)
70 #:use-module (gnu packages machine-learning)
71 #:use-module (gnu packages maths)
72 #:use-module (gnu packages mpi)
73 #:use-module (gnu packages multiprecision)
74 #:use-module (gnu packages networking)
75 #:use-module (gnu packages node)
76 #:use-module (gnu packages pcre)
77 #:use-module (gnu packages perl)
78 #:use-module (gnu packages pkg-config)
79 #:use-module (gnu packages pulseaudio) ;libsndfile
80 #:use-module (gnu packages python)
81 #:use-module (gnu packages python-xyz)
82 #:use-module (gnu packages statistics)
83 #:use-module (gnu packages tcl)
84 #:use-module (gnu packages tls)
85 #:use-module (gnu packages web)
86 #:use-module (gnu packages xorg))
88 (define-public r-bezier
94 (uri (cran-uri "bezier" version))
97 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
98 (build-system r-build-system)
99 (home-page "https://cran.r-project.org/web/packages/bezier/")
100 (synopsis "Bezier curve and spline toolkit")
102 "This package is a toolkit for working with Bezier curves and splines.
103 The package provides functions for point generation, arc length estimation,
104 degree elevation and curve fitting.")
105 (license license:gpl2+)))
114 (uri (cran-uri "V8" version))
117 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
118 (properties `((upstream-name . "V8")))
119 (build-system r-build-system)
122 (modify-phases %standard-phases
123 (add-after 'unpack 'find-v8
124 (lambda* (#:key inputs #:allow-other-keys)
125 (substitute* "configure"
127 (string-append "PKG_LIBS="
128 (assoc-ref inputs "node")
129 "/lib/libnode.so.64\n")))
130 (setenv "INCLUDE_DIR"
132 (assoc-ref inputs "node")
136 (assoc-ref inputs "node") "/lib"))
139 `(("node" ,libnode)))
142 ("r-jsonlite" ,r-jsonlite)
145 `(("r-knitr" ,r-knitr)))
146 (home-page "https://jeroen.cran.dev/V8")
147 (synopsis "Embedded JavaScript and WebAssembly engine for R")
149 "This package provides an R interface to V8: Google's JavaScript and
150 WebAssembly engine.")
151 (license license:expat)))
160 (uri (cran-uri "DOT" version))
163 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
164 (properties `((upstream-name . "DOT")))
165 (build-system r-build-system)
168 (home-page "http://haghish.com/dot")
169 (synopsis "Render and Export DOT Graphs in R")
171 "This package provides tools to render DOT diagram markup language in R
172 and also provides the possibility to export the graphs in PostScript and
173 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
174 programming packages such as @code{knitr} and @code{rmarkdown}.")
175 (license license:expat)))
177 (define-public r-clipr
184 (uri (cran-uri "clipr" version))
187 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
188 (build-system r-build-system)
189 (home-page "https://github.com/mdlincoln/clipr")
190 (synopsis "Read and write from the system clipboard")
192 "This package provides simple utility functions to read from and write to
193 the system clipboards.")
194 (license license:gpl3)))
196 (define-public r-ggpmisc
202 (uri (cran-uri "ggpmisc" version))
205 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
206 (build-system r-build-system)
208 `(("r-broom" ,r-broom)
210 ("r-ggplot2" ,r-ggplot2)
211 ("r-gridextra" ,r-gridextra)
212 ("r-lubridate" ,r-lubridate)
213 ("r-magrittr" ,r-magrittr)
216 ("r-polynom" ,r-polynom)
218 ("r-scales" ,r-scales)
219 ("r-splus2r" ,r-splus2r)
220 ("r-stringr" ,r-stringr)
221 ("r-tibble" ,r-tibble)
225 `(("r-knitr" ,r-knitr)))
226 (home-page "https://www.r4photobiology.info/")
227 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
228 (description "This package provides extensions to @code{ggplot2},
229 respecting the grammar of its graphics paradigm.")
230 (license license:gpl2+)))
232 (define-public r-gprofiler
239 (uri (cran-uri "gProfileR" version))
242 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
243 (properties `((upstream-name . "gProfileR")))
244 (build-system r-build-system)
247 ("r-rcurl" ,r-rcurl)))
248 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
249 (synopsis "Interface to the g:Profiler toolkit")
251 "This package provides tools for functional enrichment analysis,
252 gene identifier conversion and mapping homologous genes across related
253 organisms via the @code{g:Profiler} toolkit.")
254 (license license:gpl2+)))
256 (define-public r-gprofiler2
258 (name "r-gprofiler2")
263 (uri (cran-uri "gprofiler2" version))
266 "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
267 (properties `((upstream-name . "gprofiler2")))
268 (build-system r-build-system)
270 `(("r-crosstalk" ,r-crosstalk)
272 ("r-ggplot2" ,r-ggplot2)
273 ("r-gridextra" ,r-gridextra)
274 ("r-jsonlite" ,r-jsonlite)
275 ("r-plotly" ,r-plotly)
278 ("r-viridislite" ,r-viridislite)))
279 (native-inputs `(("r-knitr" ,r-knitr)))
280 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
281 (synopsis "Interface to the g:Profiler toolset")
283 "This package provides a toolset for functional enrichment analysis and
284 visualization, gene/protein/SNP identifier conversion and mapping orthologous
285 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
289 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
291 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
293 @item @code{g:Orth}, orthology search across species;
294 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
295 genes and variant effects.
298 This package is an R interface corresponding to the 2019 update of
299 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
301 (license license:gpl2+)))
303 (define-public r-oenb
310 (uri (cran-uri "oenb" version))
313 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
314 (properties `((upstream-name . "oenb")))
315 (build-system r-build-system)
317 `(("r-dplyr" ,r-dplyr)
319 (native-inputs `(("r-knitr" ,r-knitr)))
320 (home-page "https://github.com/franzmohr/oenb")
321 (synopsis "Tools for the OeNB Data Web Service")
323 "Tools to access data from the data web service of the
324 @acronym{OeNB, Oesterreichische Nationalbank},
325 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
326 (license license:gpl2+)))
328 (define-public r-scales
335 (uri (cran-uri "scales" version))
337 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
338 (build-system r-build-system)
340 `(("r-farver" ,r-farver)
341 ("r-labeling" ,r-labeling)
342 ("r-lifecycle" ,r-lifecycle)
343 ("r-munsell" ,r-munsell)
344 ("r-rcolorbrewer" ,r-rcolorbrewer)
346 ("r-viridislite" ,r-viridislite)))
347 (home-page "https://github.com/hadley/scales")
348 (synopsis "Scale functions for visualization")
350 "This package provides graphical scales that map data to aesthetics, and
351 provides methods for automatically determining breaks and labels for axes and
353 (license license:expat)))
355 (define-public r-pheatmap
362 (uri (cran-uri "pheatmap" version))
365 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
366 (build-system r-build-system)
368 `(("r-gtable" ,r-gtable)
369 ("r-rcolorbrewer" ,r-rcolorbrewer)
370 ("r-scales" ,r-scales)))
371 (home-page "https://cran.r-project.org/web/packages/pheatmap")
372 (synopsis "Pretty heatmaps")
374 "This package provides an implementation of heatmaps that offers more
375 control over dimensions and appearance.")
376 (license license:gpl2+)))
384 (uri (cran-uri "ecp" version))
387 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
388 (build-system r-build-system)
390 `(("r-rcpp" ,r-rcpp)))
391 (home-page "https://cran.r-project.org/web/packages/ecp/")
392 (synopsis "Multiple change-point analysis of multivariate data")
394 "This package implements various procedures for finding multiple
395 change-points. Two methods make use of dynamic programming and pruning, with
396 no distributional assumptions other than the existence of certain absolute
397 moments in one method. Hierarchical and exact search methods are included.
398 All methods return the set of estimated change-points as well as other summary
400 (license license:gpl2+)))
402 (define-public r-ellipsis
409 (uri (cran-uri "ellipsis" version))
412 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
413 (build-system r-build-system)
415 `(("r-rlang" ,r-rlang)))
416 (home-page "https://github.com/hadley/ellipsis")
417 (synopsis "Tools for working with additional arguments")
419 "In S3 generics, it's useful to take @code{...} so that methods can have
420 additional arguments. But this flexibility comes at a cost: misspelled
421 arguments will be silently ignored. The @code{ellipsis} package is an
422 experiment that allows a generic to warn if any arguments passed in @code{...}
424 (license license:gpl3)))
433 (uri (cran-uri "grr" version))
436 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
437 (build-system r-build-system)
438 (home-page "https://cran.r-project.org/web/packages/grr")
439 (synopsis "Alternative implementations of base R functions")
441 "This package provides alternative implementations of some base R
442 functions, including @code{sort}, @code{order}, and @code{match}. The
443 functions are simplified but can be faster or have other advantages.")
444 (license license:gpl3)))
446 (define-public r-matrix-utils
448 (name "r-matrix-utils")
453 (uri (cran-uri "Matrix.utils" version))
456 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
457 (properties `((upstream-name . "Matrix.utils")))
458 (build-system r-build-system)
461 ("r-matrix" ,r-matrix)))
462 (home-page "https://github.com/cvarrichio/Matrix.utils")
464 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
466 "This package implements data manipulation methods such as @code{cast},
467 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
469 (license license:gpl3)))
478 (uri (cran-uri "sys" version))
481 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
482 (build-system r-build-system)
483 (home-page "https://github.com/jeroen/sys")
484 (synopsis "Powerful and reliable tools for running system commands in R")
486 "This package provides drop-in replacements for the base @code{system2()}
487 function with fine control and consistent behavior across platforms. It
488 supports clean interruption, timeout, background tasks, and streaming STDIN /
489 STDOUT / STDERR over binary or text connections. The package also provides
490 functions for evaluating expressions inside a temporary fork. Such
491 evaluations have no side effects on the main R process, and support reliable
492 interrupts and timeouts. This provides the basis for a sandboxing
494 (license license:expat)))
496 (define-public r-askpass
503 (uri (cran-uri "askpass" version))
506 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
507 (build-system r-build-system)
508 (propagated-inputs `(("r-sys" ,r-sys)))
509 (home-page "https://github.com/jeroen/askpass")
510 (synopsis "Safe password entry for R")
512 "This package provides cross-platform utilities for prompting the user
513 for credentials or a passphrase, for example to authenticate with a server or
514 read a protected key.")
515 (license license:expat)))
517 (define-public r-vegan
524 (uri (cran-uri "vegan" version))
527 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
528 (build-system r-build-system)
530 `(("gfortran" ,gfortran)))
532 `(("r-cluster" ,r-cluster)
533 ("r-knitr" ,r-knitr) ; needed for vignettes
534 ("r-lattice" ,r-lattice)
537 ("r-permute" ,r-permute)))
538 (home-page "https://cran.r-project.org/web/packages/vegan")
539 (synopsis "Functions for community ecology")
541 "The vegan package provides tools for descriptive community ecology. It
542 has most basic functions of diversity analysis, community ordination and
543 dissimilarity analysis. Most of its multivariate tools can be used for other
544 data types as well.")
545 (license license:gpl2+)))
547 (define-public r-tidyverse
554 (uri (cran-uri "tidyverse" version))
557 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
558 (build-system r-build-system)
560 `(("r-broom" ,r-broom)
562 ("r-crayon" ,r-crayon)
563 ("r-dbplyr" ,r-dbplyr)
565 ("r-forcats" ,r-forcats)
566 ("r-ggplot2" ,r-ggplot2)
570 ("r-jsonlite" ,r-jsonlite)
571 ("r-lubridate" ,r-lubridate)
572 ("r-magrittr" ,r-magrittr)
573 ("r-modelr" ,r-modelr)
574 ("r-pillar" ,r-pillar)
577 ("r-readxl" ,r-readxl)
578 ("r-reprex" ,r-reprex)
580 ("r-rstudioapi" ,r-rstudioapi)
582 ("r-stringr" ,r-stringr)
583 ("r-tibble" ,r-tibble)
586 (home-page "https://tidyverse.tidyverse.org")
587 (synopsis "Install and load packages from the \"Tidyverse\"")
589 "The @code{tidyverse} is a set of packages that work in harmony because
590 they share common data representations and API design. This package is
591 designed to make it easy to install and load multiple tidyverse packages in a
593 (license license:gpl3)))
595 (define-public r-rvest
602 (uri (cran-uri "rvest" version))
604 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
605 (build-system r-build-system)
608 ("r-magrittr" ,r-magrittr)
609 ("r-selectr" ,r-selectr)
611 (home-page "https://github.com/hadley/rvest")
612 (synopsis "Simple web scraping for R")
614 "@code{r-rvest} helps you scrape information from web pages. It is
615 designed to work with @code{magrittr} to make it easy to express common web
616 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
617 (license license:gpl3)))
619 (define-public r-selectr
626 (uri (cran-uri "selectr" version))
628 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
629 (build-system r-build-system)
631 `(("r-stringr" ,r-stringr)
633 (home-page "https://sjp.co.nz/projects/selectr/")
634 (synopsis "Translate CSS selectors to XPath expressions")
636 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
637 expression. This allows you to use CSS selectors when working with the XML
638 package as it can only evaluate XPath expressions. Also provided are
639 convenience functions useful for using CSS selectors on XML nodes. This
640 package is a port of the Python package @code{cssselect}.")
641 (license license:bsd-3)))
643 (define-public r-reprex
650 (uri (cran-uri "reprex" version))
653 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
654 (build-system r-build-system)
656 `(("r-callr" ,r-callr)
660 ("r-rmarkdown" ,r-rmarkdown)
661 ("r-whisker" ,r-whisker)
662 ("r-withr" ,r-withr)))
663 (home-page "https://github.com/tidyverse/reprex")
664 (synopsis "Prepare reproducible R code examples for sharing")
666 "This package provides a convenience wrapper that uses the
667 @code{rmarkdown} package to render small snippets of code to target formats
668 that include both code and output. The goal is to encourage the sharing of
669 small, reproducible, and runnable examples on code-oriented websites or email.
670 @code{reprex} also extracts clean, runnable R code from various common formats,
671 such as copy/paste from an R session.")
672 (license license:expat)))
674 (define-public r-reordercluster
676 (name "r-reordercluster")
680 (uri (cran-uri "ReorderCluster" version))
683 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
684 (build-system r-build-system)
686 `(("r-gplots" ,r-gplots)
688 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
689 (synopsis "Reordering the dendrogram according to the class labels")
690 (description "This package provides tools for performing the leaf reordering
691 for the dendrogram that preserves the hierarchical clustering result and at the
692 same time tries to group instances from the same class together.")
693 (license license:gpl3+)))
695 (define-public r-callr
702 (uri (cran-uri "callr" version))
705 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
706 (build-system r-build-system)
709 ("r-processx" ,r-processx)))
710 (home-page "https://github.com/r-lib/callr#readme")
711 (synopsis "Call R from R")
713 "It is sometimes useful to perform a computation in a separate R process,
714 without affecting the current R process at all. This package does exactly
716 (license license:expat)))
718 (define-public r-readxl
725 (uri (cran-uri "readxl" version))
728 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
729 (build-system r-build-system)
731 `(("r-cellranger" ,r-cellranger)
732 ("r-progress" ,r-progress)
734 ("r-tibble" ,r-tibble)))
735 (home-page "https://readxl.tidyverse.org")
736 (synopsis "Read Excel files")
738 "This package lets you import Excel files into R. It supports
739 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
740 the embedded @code{RapidXML} C++ library.")
741 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
742 ;; 'rapidxml' which is Boost.
743 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
745 (define-public r-modelr
752 (uri (cran-uri "modelr" version))
755 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
756 (build-system r-build-system)
758 `(("r-broom" ,r-broom)
759 ("r-magrittr" ,r-magrittr)
762 ("r-tibble" ,r-tibble)
764 ("r-tidyselect" ,r-tidyselect)
765 ("r-vctrs" ,r-vctrs)))
766 (home-page "https://github.com/tidyverse/modelr")
767 (synopsis "Helper functions for modelling in pipelines")
769 "Functions for modelling that help you seamlessly integrate modelling
770 into a pipeline of data manipulation and visualisation.")
771 (license license:gpl3)))
773 (define-public r-httpuv
779 (uri (cran-uri "httpuv" version))
782 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
783 (build-system r-build-system)
787 ("r-promises" ,r-promises)
790 (home-page "https://github.com/rstudio/httpuv")
791 (synopsis "HTTP and WebSocket server library for R")
793 "The httpuv package provides low-level socket and protocol support for
794 handling HTTP and WebSocket requests directly from within R. It is primarily
795 intended as a building block for other packages, rather than making it
796 particularly easy to create complete web applications using httpuv alone.")
797 ;; This package includes third-party code that was originally released
798 ;; under various non-copyleft licenses. Full licensing information can be
799 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
800 (license license:gpl3+)))
802 (define-public r-jsonlite
808 (uri (cran-uri "jsonlite" version))
811 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
812 (build-system r-build-system)
813 (home-page "https://arxiv.org/abs/1403.2805")
814 (synopsis "Robust, high performance JSON parser and generator for R")
816 "The jsonlite package provides a fast JSON parser and generator optimized
817 for statistical data and the web. It offers flexible, robust, high
818 performance tools for working with JSON in R and is particularly powerful for
819 building pipelines and interacting with a web API. In addition to converting
820 JSON data from/to R objects, jsonlite contains functions to stream, validate,
821 and prettify JSON data. The unit tests included with the package verify that
822 all edge cases are encoded and decoded consistently for use with dynamic data
823 in systems and applications.")
824 (license license:expat)))
826 (define-public r-servr
832 (uri (cran-uri "servr" version))
835 "0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7"))))
836 (build-system r-build-system)
838 `(("r-httpuv" ,r-httpuv)
839 ("r-jsonlite" ,r-jsonlite)
842 (home-page "https://github.com/yihui/servr")
843 (synopsis "Simple HTTP server to serve static files or dynamic documents")
845 "Servr provides an HTTP server in R to serve static files, or dynamic
846 documents that can be converted to HTML files (e.g., R Markdown) under a given
848 (license license:expat)))
850 (define-public r-htmltools
856 (uri (cran-uri "htmltools" version))
859 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
860 (build-system r-build-system)
862 `(("r-base64enc" ,r-base64enc)
863 ("r-digest" ,r-digest)
864 ("r-rlang" ,r-rlang)))
865 (home-page "https://cran.r-project.org/web/packages/htmltools")
866 (synopsis "R tools for HTML")
868 "This package provides tools for HTML generation and output in R.")
869 (license license:expat)))
871 (define-public r-htmlwidgets
873 (name "r-htmlwidgets")
877 (uri (cran-uri "htmlwidgets" version))
880 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
881 (build-system r-build-system)
883 `(("r-htmltools" ,r-htmltools)
884 ("r-jsonlite" ,r-jsonlite)
886 (home-page "https://github.com/ramnathv/htmlwidgets")
887 (synopsis "HTML Widgets for R")
889 "HTML widgets is a framework for creating HTML widgets that render in
890 various contexts including the R console, R Markdown documents, and Shiny web
892 (license license:expat)))
894 (define-public r-htmltable
901 (uri (cran-uri "htmlTable" version))
904 "1a1al4kld7lrapc2i086crr78kbgrskahs221iy9v77x0nhin2q3"))))
905 (properties `((upstream-name . "htmlTable")))
906 (build-system r-build-system)
908 `(("r-checkmate" ,r-checkmate)
909 ("r-htmltools" ,r-htmltools)
910 ("r-htmlwidgets" ,r-htmlwidgets)
912 ("r-magrittr" ,r-magrittr)
913 ("r-rstudioapi" ,r-rstudioapi)
914 ("r-stringr" ,r-stringr)))
916 `(("r-knitr" ,r-knitr)))
917 (home-page "http://gforge.se/packages/")
918 (synopsis "Advanced tables for Markdown/HTML")
920 "This package provides functions to build tables with advanced layout
921 elements such as row spanners, column spanners, table spanners, zebra
922 striping, and more. While allowing advanced layout, the underlying
923 CSS-structure is simple in order to maximize compatibility with word
924 processors such as LibreOffice. The package also contains a few text
925 formatting functions that help outputting text compatible with HTML or
927 (license license:gpl3+)))
929 (define-public r-curl
935 (uri (cran-uri "curl" version))
938 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
939 (build-system r-build-system)
942 (modify-phases %standard-phases
943 ;; The environment variable CURL_CA_BUNDLE is only respected when
944 ;; running Windows, so we disable the platform checks.
945 ;; This can be removed once the libcurl has been patched.
946 (add-after 'unpack 'allow-CURL_CA_BUNDLE
948 (substitute* "R/onload.R"
949 (("if \\(!grepl\\(\"mingw\".*")
951 (substitute* "src/handle.c"
954 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
955 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
962 `(("pkg-config" ,pkg-config)))
963 (home-page "https://github.com/jeroenooms/curl")
964 (synopsis "HTTP client for R")
966 "The @code{curl()} and @code{curl_download()} functions provide highly
967 configurable drop-in replacements for base @code{url()} and
968 @code{download.file()} with better performance, support for encryption, gzip
969 compression, authentication, and other @code{libcurl} goodies. The core of
970 the package implements a framework for performing fully customized requests
971 where data can be processed either in memory, on disk, or streaming via the
972 callback or connection interfaces.")
973 (license license:expat)))
975 (define-public r-hwriter
982 (uri (cran-uri "hwriter" version))
985 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
986 (build-system r-build-system)
987 (home-page "https://cran.r-project.org/web/packages/hwriter")
988 (synopsis "Output R objects in HTML format")
990 "This package provides easy-to-use and versatile functions to output R
991 objects in HTML format.")
992 (license license:lgpl2.1+)))
994 (define-public r-rjson
1001 (uri (cran-uri "rjson" version))
1004 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1005 (build-system r-build-system)
1006 (home-page "https://cran.r-project.org/web/packages/rjson")
1007 (synopsis "JSON library for R")
1009 "This package provides functions to convert R objects into JSON objects
1011 (license license:gpl2+)))
1013 (define-public r-fastmap
1020 (uri (cran-uri "fastmap" version))
1023 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1024 (properties `((upstream-name . "fastmap")))
1025 (build-system r-build-system)
1026 (home-page "https://r-lib.github.io/fastmap/")
1027 (synopsis "Fast implementation of a key-value store")
1029 "This package provides a fast implementation of a key-value store.
1030 Environments are commonly used as key-value stores, but every time a new key
1031 is used, it is added to R's global symbol table, causing a small amount of
1032 memory leakage. This can be problematic in cases where many different keys
1033 are used. Fastmap avoids this memory leak issue by implementing the map using
1034 data structures in C++.")
1035 (license license:expat)))
1037 (define-public r-shiny
1045 (url "https://github.com/rstudio/shiny.git")
1046 (commit (string-append "v" version))))
1047 (file-name (git-file-name name version))
1050 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1051 (build-system r-build-system)
1053 `(#:modules ((guix build r-build-system)
1054 (guix build minify-build-system)
1057 #:imported-modules (,@%r-build-system-modules
1058 (guix build minify-build-system))
1060 (modify-phases (@ (guix build r-build-system) %standard-phases)
1061 (add-after 'unpack 'replace-bundled-minified-JavaScript
1062 (lambda* (#:key inputs #:allow-other-keys)
1063 (let ((replace-file (lambda (old new)
1064 (format #t "replacing ~a with ~a\n" old new)
1066 (symlink new old))))
1067 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1068 ;; contain just data. They are not minified code, so we don't
1070 (with-directory-excursion "inst/www/shared"
1071 (replace-file "bootstrap/shim/respond.min.js"
1072 (string-append (assoc-ref inputs "js-respond")
1073 "/share/javascript/respond.min.js"))
1074 (replace-file "bootstrap/shim/html5shiv.min.js"
1075 (string-append (assoc-ref inputs "js-html5shiv")
1076 "/share/javascript/html5shiv.min.js"))
1077 (replace-file "json2-min.js"
1078 (string-append (assoc-ref inputs "js-json2")
1079 "/share/javascript/json2-min.js"))
1080 (replace-file "strftime/strftime-min.js"
1081 (string-append (assoc-ref inputs "js-strftime")
1082 "/share/javascript/strftime.min.js"))
1083 (replace-file "highlight/highlight.pack.js"
1084 (string-append (assoc-ref inputs "js-highlight")
1085 "/share/javascript/highlight.min.js"))
1086 (replace-file "datatables/js/jquery.dataTables.min.js"
1087 (string-append (assoc-ref inputs "js-datatables")
1088 "/share/javascript/jquery.dataTables.min.js"))
1089 (replace-file "selectize/js/selectize.min.js"
1090 (string-append (assoc-ref inputs "js-selectize")
1091 "/share/javascript/selectize.min.js"))
1092 (replace-file "selectize/js/es5-shim.min.js"
1093 (string-append (assoc-ref inputs "js-es5-shim")
1094 "/share/javascript/es5-shim.min.js"))
1095 (for-each (match-lambda
1097 (delete-file target)
1098 (minify source #:target target)))
1099 '(("jqueryui/jquery-ui.js" .
1100 "jqueryui/jquery-ui.min.js")
1101 ("datepicker/js/bootstrap-datepicker.js" .
1102 "datepicker/js/bootstrap-datepicker.min.js")
1103 ("ionrangeslider/js/ion.rangeSlider.js" .
1104 "ionrangeslider/js/ion.rangeSlider.min.js")
1105 ("bootstrap/js/bootstrap.js" .
1106 "bootstrap/js/bootstrap.min.js")
1111 ("legacy/jquery.js" .
1112 "legacy/jquery.min.js")
1113 ("showdown/src/showdown.js" .
1114 "showdown/compressed/showdown.js")))))
1117 `(("r-crayon" ,r-crayon)
1118 ("r-digest" ,r-digest)
1119 ("r-fastmap" ,r-fastmap)
1120 ("r-htmltools" ,r-htmltools)
1121 ("r-httpuv" ,r-httpuv)
1122 ("r-jsonlite" ,r-jsonlite)
1123 ("r-later" ,r-later)
1125 ("r-promises" ,r-promises)
1127 ("r-rlang" ,r-rlang)
1128 ("r-sourcetools" ,r-sourcetools)
1129 ("r-withr" ,r-withr)
1130 ("r-xtable" ,r-xtable)))
1132 `(("js-datatables" ,js-datatables)
1133 ("js-html5shiv" ,js-html5shiv)
1134 ("js-json2" ,js-json2)
1135 ("js-respond" ,js-respond)
1136 ("js-selectize" ,js-selectize)
1137 ("js-strftime" ,js-strftime)
1138 ("js-highlight" ,js-highlight)
1139 ("js-es5-shim" ,js-es5-shim)))
1141 `(("uglify-js" ,uglify-js)
1142 ("gfortran" ,gfortran)))
1143 (home-page "http://shiny.rstudio.com")
1144 (synopsis "Easy interactive web applications with R")
1146 "Makes it incredibly easy to build interactive web applications
1147 with R. Automatic \"reactive\" binding between inputs and outputs and
1148 extensive prebuilt widgets make it possible to build beautiful,
1149 responsive, and powerful applications with minimal effort.")
1150 (license license:artistic2.0)))
1152 ;; This package includes minified JavaScript files. When upgrading please
1153 ;; check that there are no new minified JavaScript files.
1154 (define-public r-shinytree
1156 (name "r-shinytree")
1161 (uri (cran-uri "shinyTree" version))
1164 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1165 (modules '((guix build utils)))
1168 ;; Delete minified JavaScript
1169 (for-each delete-file
1170 '("inst/www/jsTree-3.3.7/libs/require.js"
1171 "inst/www/jsTree-3.3.7/libs/jquery.js"
1172 "inst/www/jsTree-3.3.7/jstree.min.js"))
1174 (properties `((upstream-name . "shinyTree")))
1175 (build-system r-build-system)
1177 `(#:modules ((guix build utils)
1178 (guix build r-build-system)
1182 (modify-phases %standard-phases
1183 (add-after 'unpack 'replace-minified-javascript
1184 (lambda* (#:key inputs #:allow-other-keys)
1185 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1186 (symlink (string-append (assoc-ref inputs "js-requirejs")
1187 "/share/javascript/require.min.js")
1192 `((,(assoc-ref inputs "js-jquery")
1196 (lambda (sources targets)
1197 (for-each (lambda (source target)
1198 (format #t "Processing ~a --> ~a~%"
1200 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1201 (call-with-output-file target
1203 (dump-port minified port)))))
1207 `(("r-htmlwidgets" ,r-htmlwidgets)
1208 ("r-jsonlite" ,r-jsonlite)
1209 ("r-promises" ,r-promises)
1210 ("r-shiny" ,r-shiny)
1211 ("r-stringr" ,r-stringr)))
1213 `(("js-requirejs" ,js-requirejs)))
1215 `(("uglify-js" ,uglify-js)
1219 (uri "https://code.jquery.com/jquery-3.3.1.js")
1222 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1223 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1224 (synopsis "jsTree bindings for Shiny")
1226 "This package exposes R bindings to jsTree, a JavaScript library that
1227 supports interactive trees, to enable rich, editable trees in Shiny.")
1228 (license license:expat)))
1230 (define-public r-shinydashboard
1232 (name "r-shinydashboard")
1236 (uri (cran-uri "shinydashboard" version))
1239 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1240 (build-system r-build-system)
1241 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1242 ;; Regenerate it from the included sources.
1244 `(#:modules ((guix build utils)
1245 (guix build r-build-system)
1248 (modify-phases %standard-phases
1249 (add-after 'unpack 'generate-minified-javascript
1251 (with-directory-excursion "inst/AdminLTE"
1252 (delete-file "app.min.js")
1253 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1254 (call-with-output-file "app.min.js"
1256 (dump-port minified port))))))))))
1258 `(("r-htmltools" ,r-htmltools)
1259 ("r-promises" ,r-promises)
1260 ("r-shiny" ,r-shiny)))
1262 `(("uglify-js" ,uglify-js)))
1263 (home-page "https://rstudio.github.io/shinydashboard/")
1264 (synopsis "Create dashboards with shiny")
1265 (description "This package provides an extension to the Shiny web
1266 application framework for R, making it easy to create attractive dashboards.")
1267 ;; This package includes software that was released under the Expat
1268 ;; license, but the whole package is released under GPL version 2 or
1270 (license license:gpl2+)))
1272 (define-public r-shinyfiles
1274 (name "r-shinyfiles")
1279 (uri (cran-uri "shinyFiles" version))
1281 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1282 (properties `((upstream-name . "shinyFiles")))
1283 (build-system r-build-system)
1286 ("r-htmltools" ,r-htmltools)
1287 ("r-jsonlite" ,r-jsonlite)
1288 ("r-shiny" ,r-shiny)
1289 ("r-tibble" ,r-tibble)))
1290 (home-page "https://github.com/thomasp85/shinyFiles")
1291 (synopsis "Server-side file system viewer for Shiny")
1293 "This package provides functionality for client-side navigation of the
1294 server side file system in shiny apps. In case the app is running locally
1295 this gives the user direct access to the file system without the need to
1296 \"download\" files to a temporary location. Both file and folder selection as
1297 well as file saving is available.")
1298 (license license:gpl2+)))
1300 (define-public r-shinythemes
1302 (name "r-shinythemes")
1307 (uri (cran-uri "shinythemes" version))
1310 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1311 (properties `((upstream-name . "shinythemes")))
1312 (build-system r-build-system)
1313 (propagated-inputs `(("r-shiny" ,r-shiny)))
1314 (home-page "https://rstudio.github.io/shinythemes/")
1315 (synopsis "Themes for Shiny")
1317 "This package provides themes for use with Shiny. It includes several
1318 Bootstrap themes, which are packaged for use with Shiny applications.")
1319 ;; The package is released under version 3 of the GPL, but it includes
1320 ;; source files that are covered by the Expat license. It also includes
1321 ;; fonts under SIL or the ASL.
1322 (license (list license:gpl3 license:expat
1323 license:silofl1.1 license:asl2.0))))
1325 ;; The package sources include minified variants of d3.js and non-minified
1326 ;; source code of d3-jetpack.
1327 (define-public r-d3r
1334 (uri (cran-uri "d3r" version))
1337 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1338 (build-system r-build-system)
1340 `(#:modules ((guix build utils)
1341 (guix build r-build-system)
1345 (modify-phases %standard-phases
1346 (add-after 'unpack 'process-javascript
1347 (lambda* (#:key inputs #:allow-other-keys)
1348 (with-directory-excursion "inst/www/d3/"
1352 `((,(assoc-ref inputs "d3.v3.js")
1353 "v3/dist/d3.min.js")
1354 (,(assoc-ref inputs "d3.v4.js")
1355 "v4/dist/d3.min.js")
1356 (,(assoc-ref inputs "d3.v5.js")
1357 "v5/dist/d3.min.js"))))
1358 (lambda (sources targets)
1359 (for-each (lambda (source target)
1360 (format #t "Processing ~a --> ~a~%"
1362 (delete-file target)
1363 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1364 (call-with-output-file target
1366 (dump-port minified port)))))
1370 `(("r-dplyr" ,r-dplyr)
1371 ("r-htmltools" ,r-htmltools)
1372 ("r-rlang" ,r-rlang)
1373 ("r-tidyr" ,r-tidyr)))
1375 `(("uglify-js" ,uglify-js)
1379 (uri "https://d3js.org/d3.v3.js")
1382 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1386 (uri "https://d3js.org/d3.v4.js")
1389 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1393 (uri "https://d3js.org/d3.v5.js")
1396 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1397 (home-page "https://github.com/timelyportfolio/d3r")
1398 (synopsis "d3.js utilities for R")
1400 "This package provides a suite of functions to help ease the use of the
1401 d3.js visualization library in R. These helpers include
1402 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1403 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1404 R objects into the JSON format that the d3.js library expects.")
1405 (license license:bsd-3)))
1407 ;; We use the latest commit here because the last release was in 2016 while
1408 ;; the latest commit was in 2018.
1409 (define-public r-sankeyd3
1410 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1414 (version (git-version "0.3.2" revision commit))
1419 (url "https://github.com/fbreitwieser/sankeyD3.git")
1421 (file-name (git-file-name name version))
1424 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1425 (build-system r-build-system)
1428 ("r-htmlwidgets" ,r-htmlwidgets)
1429 ("r-shiny" ,r-shiny)
1430 ("r-magrittr" ,r-magrittr)))
1431 (home-page "https://github.com/fbreitwieser/sankeyD3")
1432 (synopsis "Sankey network graphs from R")
1434 "This package provides an R library to generate Sankey network graphs
1435 in R and Shiny via the D3 visualization library.")
1436 ;; The R code is licensed under GPLv3+. It includes the non-minified
1437 ;; JavaScript source code of d3-sankey, which is released under the
1438 ;; 3-clause BSD license.
1439 (license (list license:gpl3+ license:bsd-3)))))
1441 (define-public r-crosstalk
1443 (name "r-crosstalk")
1448 (uri (cran-uri "crosstalk" version))
1451 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1452 (build-system r-build-system)
1454 `(("r-htmltools" ,r-htmltools)
1455 ("r-jsonlite" ,r-jsonlite)
1456 ("r-lazyeval" ,r-lazyeval)
1458 (home-page "https://rstudio.github.io/crosstalk/")
1459 (synopsis "Inter-widget interactivity for HTML widgets")
1461 "This package provides building blocks for allowing HTML widgets to
1462 communicate with each other, with Shiny or without (i.e. static @code{.html}
1463 files). It currently supports linked brushing and filtering.")
1464 (license license:expat)))
1466 (define-public r-rook
1473 (uri (cran-uri "Rook" version))
1476 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1477 (properties `((upstream-name . "Rook")))
1478 (build-system r-build-system)
1479 (propagated-inputs `(("r-brew" ,r-brew)))
1480 (home-page "https://cran.r-project.org/web/packages/Rook")
1481 (synopsis "Web server interface for R")
1483 "This package contains the Rook specification and convenience software
1484 for building and running Rook applications. A Rook application is an R
1485 reference class object that implements a @code{call} method or an R closure
1486 that takes exactly one argument, an environment, and returns a list with three
1487 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1488 (license license:gpl2)))
1490 (define-public r-miniui
1497 (uri (cran-uri "miniUI" version))
1500 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1501 (properties `((upstream-name . "miniUI")))
1502 (build-system r-build-system)
1504 `(("r-htmltools" ,r-htmltools)
1505 ("r-shiny" ,r-shiny)))
1506 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1507 (synopsis "Shiny UI widgets for small screens")
1509 "This package provides UI widget and layout functions for writing Shiny apps that
1510 work well on small screens.")
1511 (license license:gpl3)))
1513 (define-public r-feather
1520 (uri (cran-uri "feather" version))
1523 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1524 (build-system r-build-system)
1528 ("r-tibble" ,r-tibble)))
1529 (home-page "https://github.com/wesm/feather")
1530 (synopsis "R Bindings to the Feather API")
1531 (description "Read and write feather files, a lightweight binary columnar
1532 data store designed for maximum speed.")
1533 (license license:asl2.0)))
1535 (define-public r-maps
1542 (uri (cran-uri "maps" version))
1545 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1546 (build-system r-build-system)
1547 (home-page "https://cran.r-project.org/web/packages/maps")
1548 (synopsis "Draw geographical maps")
1549 (description "This package provides an R module for display of maps.
1550 Projection code and larger maps are in separate packages (@code{mapproj} and
1552 (license license:gpl2)))
1554 (define-public r-mapproj
1561 (uri (cran-uri "mapproj" version))
1564 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1565 (build-system r-build-system)
1566 (propagated-inputs `(("r-maps" ,r-maps)))
1567 (home-page "https://cran.r-project.org/web/packages/mapproj")
1568 (synopsis "Map projection in R")
1569 (description "This package converts latitude/longitude into projected
1571 (license (list license:gpl2 ; The R interface
1572 (license:non-copyleft ; The C code
1573 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1574 "Lucent Public License Version 1.02")))))
1576 (define-public r-rgooglemaps
1578 (name "r-rgooglemaps")
1583 (uri (cran-uri "RgoogleMaps" version))
1586 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1587 (properties `((upstream-name . "RgoogleMaps")))
1588 (build-system r-build-system)
1592 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1593 (synopsis "Use Google Maps in R")
1594 (description "This package serves two purposes:
1596 @item Provide a comfortable R interface to query the Google server for static
1598 @item Use the map as a background image to overlay plots within R. This
1599 requires proper coordinate scaling.
1601 (license license:gpl2+)))
1603 (define-public r-geosphere
1605 (name "r-geosphere")
1610 (uri (cran-uri "geosphere" version))
1613 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1614 (build-system r-build-system)
1615 (propagated-inputs `(("r-sp" ,r-sp)))
1616 (home-page "https://cran.r-project.org/web/packages/geosphere")
1617 (synopsis "Spherical trigonometry")
1618 (description "This package computes spherical trigonometry for geographic
1619 applications. That is, compute distances and related measures for angular
1620 (longitude/latitude) locations.")
1621 (license license:gpl3+)))
1623 (define-public r-jpeg
1630 (uri (cran-uri "jpeg" version))
1633 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1634 (build-system r-build-system)
1635 (inputs `(("libjpeg" ,libjpeg-turbo)))
1636 (home-page "https://www.rforge.net/jpeg/")
1637 (synopsis "Read and write JPEG images with R")
1638 (description "This package provides a way to read, write and display
1639 bitmap images stored in the JPEG format with R. It can read and write both
1640 files and in-memory raw vectors.")
1641 (license license:gpl2+)))
1643 (define-public r-ggmap
1650 (uri (cran-uri "ggmap" version))
1653 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1654 (build-system r-build-system)
1656 `(("r-bitops" ,r-bitops)
1657 ("r-digest" ,r-digest)
1658 ("r-dplyr" ,r-dplyr)
1659 ("r-ggplot2" ,r-ggplot2)
1663 ("r-magrittr" ,r-magrittr)
1666 ("r-purrr" ,r-purrr)
1667 ("r-rgooglemaps" ,r-rgooglemaps)
1668 ("r-rjson" ,r-rjson)
1669 ("r-scales" ,r-scales)
1670 ("r-stringr" ,r-stringr)
1671 ("r-tibble" ,r-tibble)
1672 ("r-tidyr" ,r-tidyr)))
1673 (home-page "https://github.com/dkahle/ggmap")
1674 (synopsis "Spatial visualization with ggplot2")
1675 (description "This package provides a collection of functions to visualize
1676 spatial data and models on top of static maps from various online sources (e.g
1677 Google Maps and Stamen Maps). It includes tools common to those tasks,
1678 including functions for geolocation and routing.")
1679 (license license:gpl2)))
1681 (define-public r-haven
1688 (uri (cran-uri "haven" version))
1691 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1692 (build-system r-build-system)
1696 `(("r-knitr" ,r-knitr)))
1698 `(("r-forcats" ,r-forcats)
1701 ("r-rlang" ,r-rlang)
1702 ("r-readr" ,r-readr)
1703 ("r-tibble" ,r-tibble)
1704 ("r-tidyselect" ,r-tidyselect)
1705 ("r-vctrs" ,r-vctrs)))
1706 (home-page "https://haven.tidyverse.org")
1707 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1709 "This package lets you mport foreign statistical formats into R via the
1710 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1711 (license license:expat)))
1713 (define-public r-amap
1719 (uri (cran-uri "amap" version))
1722 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1723 (build-system r-build-system)
1725 `(("gfortran" ,gfortran)))
1726 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1727 (synopsis "Another multidimensional analysis package")
1728 (description "This package provides tools for clustering and principal
1729 component analysis (with robust methods, and parallelized functions).")
1730 (license license:gpl2+)))
1732 (define-public r-ape
1739 (uri (cran-uri "ape" version))
1742 "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
1743 (build-system r-build-system)
1745 `(("r-lattice" ,r-lattice)
1747 ("r-rcpp" ,r-rcpp)))
1748 (home-page "http://ape-package.ird.fr/")
1749 (synopsis "Analyses of phylogenetics and evolution")
1751 "This package provides functions for reading, writing, plotting, and
1752 manipulating phylogenetic trees, analyses of comparative data in a
1753 phylogenetic framework, ancestral character analyses, analyses of
1754 diversification and macroevolution, computing distances from DNA sequences,
1755 and several other tools.")
1756 (license license:gpl2+)))
1758 (define-public r-abbyyr
1765 (uri (cran-uri "abbyyR" version))
1768 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1769 (properties `((upstream-name . "abbyyR")))
1770 (build-system r-build-system)
1772 `(("r-curl" ,r-curl)
1775 ("r-progress" ,r-progress)
1776 ("r-readr" ,r-readr)
1778 (home-page "https://github.com/soodoku/abbyyR")
1779 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1781 "This package provides tools to get text from images of text using Abbyy
1782 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1783 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1784 passports and get the results in a variety of formats including plain text and
1785 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1786 (license license:expat)))
1788 (define-public r-colorspace
1790 (name "r-colorspace")
1795 (uri (cran-uri "colorspace" version))
1797 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1798 (build-system r-build-system)
1799 (home-page "https://cran.r-project.org/web/packages/colorspace")
1800 (synopsis "Color space manipulation")
1802 "This package carries out a mapping between assorted color spaces
1803 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1804 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1805 colors are provided.")
1806 (license license:bsd-3)))
1808 (define-public r-glue
1815 (uri (cran-uri "glue" version))
1818 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1819 (build-system r-build-system)
1820 ;; knitr depends on glue, so we can't add knitr here to build the
1824 `(("r-knitr" ,r-knitr)))
1825 (home-page "https://github.com/tidyverse/glue")
1826 (synopsis "Interpreted string literals")
1828 "This package provides an implementation of interpreted string literals,
1829 inspired by Python's Literal String Interpolation (PEP-0498) and
1830 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1831 (license license:expat)))
1833 (define-public r-pastecs
1839 (uri (cran-uri "pastecs" version))
1842 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1843 (build-system r-build-system)
1845 `(("r-boot" ,r-boot)))
1846 (home-page "http://www.sciviews.org/pastecs")
1847 (synopsis "Analysis of space-time ecological series")
1849 "This package provides functions for regulation, decomposition and analysis
1850 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1851 initiative to bring PASSTEC 2000 functionalities to R.")
1852 (license license:gpl2+)))
1854 (define-public r-plogr
1861 (uri (cran-uri "plogr" version))
1864 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1865 (build-system r-build-system)
1866 (home-page "https://github.com/krlmlr/plogr")
1867 (synopsis "R bindings for the plog C++ logging library")
1869 "This package provides the header files for a stripped-down version of
1870 the plog header-only C++ logging library, and a method to log to R's standard
1872 (license license:expat)))
1874 (define-public r-pls
1881 (uri (cran-uri "pls" version))
1883 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1884 (build-system r-build-system)
1885 (home-page "https://mevik.net/work/software/pls.html")
1886 (synopsis "Partial Least Squares and Principal Component Regression")
1888 "The pls package implements multivariate regression methods: Partial Least
1889 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1890 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1893 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1894 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1895 @item multi-response models (or @dfn{PLS2})
1896 @item flexible cross-validation
1897 @item Jackknife variance estimates of regression coefficients
1898 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1899 (R)MSEP, R², and correlation loadings
1900 @item formula interface, modelled after @code{lm()}, with methods for predict,
1901 print, summary, plot, update, etc.
1902 @item extraction functions for coefficients, scores, and loadings
1903 @item MSEP, RMSEP, and R² estimates
1904 @item multiplicative scatter correction (@dfn{MSC})
1906 (license license:gpl2)))
1915 (uri (cran-uri "ps" version))
1917 (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
1918 (build-system r-build-system)
1919 (home-page "https://ps.r-lib.org")
1920 (synopsis "List, query, and manipulate system processes")
1922 "The ps package implements an API to list, query, and manipulate system
1923 processes. Most of its code is based on the @code{psutil} Python package.")
1924 (license license:bsd-3)))
1926 (define-public r-pkgbuild
1933 (uri (cran-uri "pkgbuild" version))
1935 (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
1936 (build-system r-build-system)
1938 `(("r-callr" ,r-callr)
1940 ("r-crayon" ,r-crayon)
1942 ("r-prettyunits" ,r-prettyunits)
1944 ("r-rprojroot" ,r-rprojroot)
1945 ("r-withr" ,r-withr)))
1946 (home-page "https://github.com/r-pkgs/pkgbuild")
1947 (synopsis "Find tools needed to build R packages")
1949 "This package provides functions used to build R packages. It locates
1950 compilers needed to build R packages on various platforms and ensures the PATH
1951 is configured appropriately so R can use them.")
1952 (license license:gpl3)))
1954 (define-public r-pkgload
1961 (uri (cran-uri "pkgload" version))
1964 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
1965 (build-system r-build-system)
1968 ("r-crayon" ,r-crayon)
1970 ("r-pkgbuild" ,r-pkgbuild)
1971 ("r-rlang" ,r-rlang)
1972 ("r-rprojroot" ,r-rprojroot)
1973 ("r-rstudioapi" ,r-rstudioapi)
1974 ("r-withr" ,r-withr)))
1975 (home-page "https://github.com/r-lib/pkgload")
1976 (synopsis "Simulate package installation and attach")
1978 "This package simulates the process of installing a package and then
1979 attaching it. This is a key part of the @code{devtools} package as it allows
1980 you to rapidly iterate while developing a package.")
1981 (license license:gpl3)))
1983 (define-public r-rcpp
1990 (uri (cran-uri "Rcpp" version))
1992 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1993 (build-system r-build-system)
1994 (home-page "http://www.rcpp.org")
1995 (synopsis "Seamless R and C++ integration")
1997 "The Rcpp package provides R functions as well as C++ classes which offer
1998 a seamless integration of R and C++. Many R data types and objects can be
1999 mapped back and forth to C++ equivalents which facilitates both writing of new
2000 code as well as easier integration of third-party libraries. Documentation
2001 about Rcpp is provided by several vignettes included in this package, via the
2002 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2003 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2004 @code{citation(\"Rcpp\")} for details on these last two.")
2005 (license license:gpl2+)))
2007 (define-public r-bindr
2014 (uri (cran-uri "bindr" version))
2017 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2018 (build-system r-build-system)
2019 (home-page "https://github.com/krlmlr/bindr")
2020 (synopsis "Parametrized active bindings")
2022 "This package provides a simple interface for creating active bindings
2023 where the bound function accepts additional arguments.")
2024 (license license:expat)))
2026 (define-public r-bindrcpp
2033 (uri (cran-uri "bindrcpp" version))
2036 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2037 (build-system r-build-system)
2039 `(("r-bindr" ,r-bindr)
2040 ("r-plogr" ,r-plogr)
2041 ("r-rcpp" ,r-rcpp)))
2042 (home-page "https://github.com/krlmlr/bindrcpp")
2043 (synopsis "Rcpp interface to active bindings")
2045 "This package provides an easy way to fill an environment with active
2046 bindings that call a C++ function.")
2047 (license license:expat)))
2049 (define-public r-auc
2056 (uri (cran-uri "AUC" version))
2059 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2060 (properties `((upstream-name . "AUC")))
2061 (build-system r-build-system)
2062 (home-page "https://cran.r-project.org/web/packages/AUC")
2063 (synopsis "Compute the area under the curve of selected measures")
2065 "This package includes functions to compute the area under the curve of
2066 selected measures: the area under the sensitivity curve (AUSEC), the area
2067 under the specificity curve (AUSPC), the area under the accuracy
2068 curve (AUACC), and the area under the receiver operating characteristic
2069 curve (AUROC). The curves can also be visualized. Support for partial areas
2071 (license license:gpl2+)))
2073 (define-public r-calibrate
2075 (name "r-calibrate")
2080 (uri (cran-uri "calibrate" version))
2082 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2083 (build-system r-build-system)
2085 `(("r-mass" ,r-mass)))
2086 (home-page "https://cran.r-project.org/web/packages/calibrate")
2087 (synopsis "Calibration of scatterplot and biplot axes")
2089 "This is a package for drawing calibrated scales with tick marks
2090 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2091 (license license:gpl2)))
2093 (define-public r-shape
2100 (uri (cran-uri "shape" version))
2103 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2104 (build-system r-build-system)
2105 (home-page "https://cran.r-project.org/web/packages/shape")
2106 (synopsis "Functions for plotting graphical shapes")
2108 "This package provides functions for plotting graphical shapes such as
2109 ellipses, circles, cylinders, arrows, ...")
2110 (license license:gpl3+)))
2112 (define-public r-globaloptions
2114 (name "r-globaloptions")
2119 (uri (cran-uri "GlobalOptions" version))
2121 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2122 (properties `((upstream-name . "GlobalOptions")))
2123 (build-system r-build-system)
2125 `(("r-knitr" ,r-knitr)))
2126 (home-page "https://github.com/jokergoo/GlobalOptions")
2127 (synopsis "Generate functions to get or set global options")
2129 "This package provides more controls on the option values such as
2130 validation and filtering on the values, making options invisible or private.")
2131 (license license:gpl2+)))
2133 (define-public r-circlize
2140 (uri (cran-uri "circlize" version))
2143 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2144 (build-system r-build-system)
2146 `(("r-colorspace" ,r-colorspace)
2147 ("r-globaloptions" ,r-globaloptions)
2148 ("r-shape" ,r-shape)))
2150 `(("r-knitr" ,r-knitr)))
2151 (home-page "https://github.com/jokergoo/circlize")
2152 (synopsis "Circular visualization")
2154 "Circular layout is an efficient way to visualise huge amounts of
2155 information. This package provides an implementation of circular layout
2156 generation in R as well as an enhancement of available software. Its
2157 flexibility is based on the usage of low-level graphics functions such that
2158 self-defined high-level graphics can be easily implemented by users for
2159 specific purposes. Together with the seamless connection between the powerful
2160 computational and visual environment in R, it gives users more convenience and
2161 freedom to design figures for better understanding complex patterns behind
2162 multi-dimensional data.")
2163 (license license:gpl2+)))
2165 (define-public r-powerlaw
2172 (uri (cran-uri "poweRlaw" version))
2174 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2175 (properties `((upstream-name . "poweRlaw")))
2176 (build-system r-build-system)
2178 `(("r-pracma" ,r-pracma)))
2180 `(("r-knitr" ,r-knitr)))
2181 (home-page "https://github.com/csgillespie/poweRlaw")
2182 (synopsis "Tools for the analysis of heavy tailed distributions")
2184 "This package provides an implementation of maximum likelihood estimators
2185 for a variety of heavy tailed distributions, including both the discrete and
2186 continuous power law distributions. Additionally, a goodness-of-fit based
2187 approach is used to estimate the lower cut-off for the scaling region.")
2188 ;; Any of these GPL versions.
2189 (license (list license:gpl2 license:gpl3))))
2191 (define-public r-compare
2198 (uri (cran-uri "compare" version))
2201 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2202 (build-system r-build-system)
2203 (home-page "https://cran.r-project.org/web/packages/compare")
2204 (synopsis "Comparing objects for differences")
2206 "This package provides functions to compare a model object to a
2207 comparison object. If the objects are not identical, the functions can be
2208 instructed to explore various modifications of the objects (e.g., sorting
2209 rows, dropping names) to see if the modified versions are identical.")
2210 (license license:gpl2+)))
2212 (define-public r-dendextend
2214 (name "r-dendextend")
2219 (uri (cran-uri "dendextend" version))
2222 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2223 (build-system r-build-system)
2225 `(("r-ggplot2" ,r-ggplot2)
2226 ("r-magrittr" ,r-magrittr)
2227 ("r-viridis" ,r-viridis)))
2228 (home-page "https://cran.r-project.org/web/packages/dendextend")
2229 (synopsis "Extending 'dendrogram' functionality in R")
2231 "This package offers a set of functions for extending @code{dendrogram}
2232 objects in R, letting you visualize and compare trees of hierarchical
2233 clusterings. You can adjust a tree's graphical parameters (the color, size,
2234 type, etc of its branches, nodes and labels) and visually and statistically
2235 compare different dendrograms to one another.")
2236 ;; Any of these versions
2237 (license (list license:gpl2 license:gpl3))))
2239 (define-public r-getoptlong
2241 (name "r-getoptlong")
2246 (uri (cran-uri "GetoptLong" version))
2249 "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
2250 (properties `((upstream-name . "GetoptLong")))
2251 (build-system r-build-system)
2255 `(("r-crayon" ,r-crayon)
2256 ("r-globaloptions" ,r-globaloptions)
2257 ("r-rjson" ,r-rjson)))
2259 `(("r-knitr" ,r-knitr)))
2260 (home-page "https://github.com/jokergoo/GetoptLong")
2261 (synopsis "Parsing command-line arguments and variable interpolation")
2263 "This is yet another command-line argument parser which wraps the
2264 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2265 use in R. It also provides a simple way for variable interpolation in R.")
2266 (license license:gpl2+)))
2268 (define-public r-fastmatch
2270 (name "r-fastmatch")
2275 (uri (cran-uri "fastmatch" version))
2278 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2279 (build-system r-build-system)
2280 (home-page "https://www.rforge.net/fastmatch")
2281 (synopsis "Fast match function")
2283 "This package provides a fast @code{match} replacement for cases that
2284 require repeated look-ups. It is slightly faster that R's built-in
2285 @code{match} function on first match against a table, but extremely fast on
2286 any subsequent lookup as it keeps the hash table in memory.")
2287 (license license:gpl2)))
2292 (version "2.2-14.2")
2296 (uri (cran-uri "ff" version))
2299 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2300 (build-system r-build-system)
2301 (propagated-inputs `(("r-bit" ,r-bit)))
2302 (home-page "http://ff.r-forge.r-project.org/")
2303 (synopsis "Memory-efficient storage of large data on disk and access functions")
2305 "This package provides data structures that are stored on disk but
2306 behave (almost) as if they were in RAM by transparently mapping only a section
2308 ;; error Architecture not supported.
2309 (supported-systems (delete "aarch64-linux" %supported-systems))
2310 (license license:gpl2)))
2312 (define-public r-ffbase
2319 (uri (cran-uri "ffbase" version))
2322 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2323 (build-system r-build-system)
2326 ("r-fastmatch" ,r-fastmatch)
2328 (home-page "http://github.com/edwindj/ffbase")
2329 (synopsis "Basic statistical functions for package 'ff'")
2331 "This package extends the out of memory vectors of @code{ff} with
2332 statistical functions and other utilities to ease their usage.")
2333 (license license:gpl3)))
2335 (define-public r-prettyunits
2337 (name "r-prettyunits")
2342 (uri (cran-uri "prettyunits" version))
2345 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2346 (build-system r-build-system)
2347 (home-page "https://github.com/gaborcsardi/prettyunits")
2348 (synopsis "Pretty, human readable formatting of quantities")
2350 "This package provides tools for pretty, human readable formatting of
2352 (license license:expat)))
2354 (define-public r-reshape
2361 (uri (cran-uri "reshape" version))
2364 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2365 (build-system r-build-system)
2367 `(("r-plyr" ,r-plyr)
2368 ("r-rcpp" ,r-rcpp)))
2369 (home-page "http://had.co.nz/reshape")
2370 (synopsis "Flexibly reshape data")
2372 "Flexibly restructure and aggregate data using just two functions:
2373 @code{melt} and @code{cast}. This package provides them.")
2374 (license license:expat)))
2376 (define-public r-progress
2383 (uri (cran-uri "progress" version))
2386 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2387 (build-system r-build-system)
2389 `(("r-crayon" ,r-crayon)
2391 ("r-prettyunits" ,r-prettyunits)
2393 (home-page "https://github.com/gaborcsardi/progress")
2394 (synopsis "Terminal progress bars")
2396 "This package provides configurable progress bars. They may include
2397 percentage, elapsed time, and/or the estimated completion time. They work in
2398 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2399 package also provides a C++ API, that works with or without Rcpp.")
2400 (license license:expat)))
2402 (define-public r-ggally
2409 (uri (cran-uri "GGally" version))
2412 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2413 (properties `((upstream-name . "GGally")))
2414 (build-system r-build-system)
2416 `(("libressl" ,libressl)))
2418 `(("r-ggplot2" ,r-ggplot2)
2419 ("r-gtable" ,r-gtable)
2420 ("r-lifecycle" ,r-lifecycle)
2422 ("r-progress" ,r-progress)
2423 ("r-rcolorbrewer" ,r-rcolorbrewer)
2424 ("r-reshape" ,r-reshape)
2425 ("r-rlang" ,r-rlang)
2426 ("r-scales" ,r-scales)))
2427 (home-page "https://ggobi.github.io/ggally")
2428 (synopsis "Extension to ggplot2")
2430 "The R package ggplot2 is a plotting system based on the grammar of
2431 graphics. GGally extends ggplot2 by adding several functions to reduce the
2432 complexity of combining geometric objects with transformed data. Some of
2433 these functions include a pairwise plot matrix, a two group pairwise plot
2434 matrix, a parallel coordinates plot, a survival plot, and several functions to
2436 (license license:gpl2+)))
2438 (define-public r-proxy
2445 (uri (cran-uri "proxy" version))
2448 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2449 (build-system r-build-system)
2450 (home-page "https://cran.r-project.org/web/packages/proxy")
2451 (synopsis "Distance and similarity measures")
2453 "This package provides an extensible framework for the efficient
2454 calculation of auto- and cross-proximities, along with implementations of the
2455 most popular ones.")
2456 (license license:gpl2)))
2465 (uri (cran-uri "sp" version))
2467 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2468 (build-system r-build-system)
2470 `(("r-lattice" ,r-lattice)))
2471 (home-page "https://cran.r-project.org/web/packages/sp")
2472 (synopsis "Classes and methods for spatial data")
2474 "This package provides classes and methods for spatial data; the classes
2475 document where the spatial location information resides, for 2D or 3D data.
2476 Utility functions are provided, e.g. for plotting data as maps, spatial
2477 selection, as well as methods for retrieving coordinates, for subsetting,
2478 print, summary, etc.")
2479 (license license:gpl2+)))
2481 (define-public r-rmtstat
2488 (uri (cran-uri "RMTstat" version))
2491 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2492 (properties `((upstream-name . "RMTstat")))
2493 (build-system r-build-system)
2494 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2495 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2497 "This package provides functions for working with the Tracy-Widom laws
2498 and other distributions related to the eigenvalues of large Wishart
2500 (license license:bsd-3)))
2502 (define-public r-rmpi
2508 (uri (cran-uri "Rmpi" version))
2511 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2512 (properties `((upstream-name . "Rmpi")))
2513 (build-system r-build-system)
2515 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2516 #:phases (modify-phases %standard-phases
2517 (add-before 'install 'mpi-setup
2520 `(("openmpi" ,openmpi)))
2522 `(("pkg-config" ,pkg-config)))
2523 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2524 (synopsis "R interface to message-passing interface (MPI)")
2526 "This package provides an interface (wrapper) to MPI APIs. It also
2527 provides an interactive R manager and worker environment.")
2528 (license license:gpl2+)))
2530 (define-public r-lmoments
2537 (uri (cran-uri "Lmoments" version))
2540 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2541 (properties `((upstream-name . "Lmoments")))
2542 (build-system r-build-system)
2544 `(("r-rcpp" ,r-rcpp)
2545 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2546 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2547 (synopsis "L-moments and quantile mixtures")
2549 "This package contains functions to estimate L-moments and trimmed
2550 L-moments from the data. It also contains functions to estimate the
2551 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2552 quantile mixture from L-moments and trimmed L-moments.")
2553 (license license:gpl2)))
2555 (define-public r-distillery
2557 (name "r-distillery")
2562 (uri (cran-uri "distillery" version))
2565 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2566 (build-system r-build-system)
2567 (home-page "https://ral.ucar.edu/staff/ericg/")
2568 (synopsis "Functions for confidence intervals and object information")
2570 "This package provides some very simple method functions for confidence
2571 interval calculation and to distill pertinent information from a potentially
2572 complex object; primarily used in common with the packages extRemes and
2574 (license license:gpl2+)))
2576 (define-public r-extremes
2583 (uri (cran-uri "extRemes" version))
2586 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2587 (properties `((upstream-name . "extRemes")))
2588 (build-system r-build-system)
2590 `(("r-distillery" ,r-distillery)
2591 ("r-lmoments" ,r-lmoments)))
2592 (home-page "https://www.assessment.ucar.edu/toolkit/")
2593 (synopsis "Extreme value analysis")
2595 "ExtRemes is a suite of functions for carrying out analyses on the
2596 extreme values of a process of interest; be they block maxima over long blocks
2597 or excesses over a high threshold.")
2598 (license license:gpl2+)))
2600 (define-public r-lmtest
2607 (uri (cran-uri "lmtest" version))
2610 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2611 (build-system r-build-system)
2613 `(("r-zoo" ,r-zoo)))
2615 `(("gfortran" ,gfortran)))
2616 (home-page "https://cran.r-project.org/web/packages/lmtest")
2617 (synopsis "Testing linear regression models")
2619 "This package provides a collection of tests, data sets, and examples for
2620 diagnostic checking in linear regression models. Furthermore, some generic
2621 tools for inference in parametric models are provided.")
2622 ;; Either version is okay
2623 (license (list license:gpl2 license:gpl3))))
2625 (define-public r-idr
2631 (uri (cran-uri "idr" version))
2634 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2635 (build-system r-build-system)
2636 (home-page "https://cran.r-project.org/web/packages/idr/")
2637 (synopsis "Irreproducible discovery rate")
2639 "This is a package for estimating the copula mixture model and plotting
2640 correspondence curves in \"Measuring reproducibility of high-throughput
2641 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2642 by Li, Brown, Huang, and Bickel")
2643 (license license:gpl2+)))
2645 (define-public r-inline
2651 (uri (cran-uri "inline" version))
2654 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2655 (build-system r-build-system)
2656 (home-page "https://cran.r-project.org/web/packages/inline")
2657 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2659 "This package provides functionality to dynamically define R functions
2660 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2661 @code{.Call} calling conventions.")
2662 ;; Any version of the LGPL.
2663 (license license:lgpl3+)))
2665 (define-public r-inum
2671 (uri (cran-uri "inum" version))
2674 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2675 (build-system r-build-system)
2677 `(("r-libcoin" ,r-libcoin)))
2678 (home-page "https://cran.r-project.org/web/packages/inum/")
2679 (synopsis "Interval and enum-type representation of vectors")
2681 "This package provides an enum-type representation of vectors and
2682 representation of intervals, including a method of coercing variables
2684 (license license:gpl2)))
2686 (define-public r-bdsmatrix
2688 (name "r-bdsmatrix")
2693 (uri (cran-uri "bdsmatrix" version))
2696 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2697 (properties `((upstream-name . "bdsmatrix")))
2698 (build-system r-build-system)
2699 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2700 (synopsis "Routines for block diagonal symmetric matrices")
2702 "This package provides procedures to work with block diagonal symmetric
2703 matrices, a special case of sparse matrices.")
2704 (license license:lgpl2.0)))
2706 (define-public r-bbmle
2709 (version "1.0.23.1")
2713 (uri (cran-uri "bbmle" version))
2716 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2717 (build-system r-build-system)
2719 `(("r-bdsmatrix" ,r-bdsmatrix)
2720 ("r-lattice" ,r-lattice)
2722 ("r-matrix" ,r-matrix)
2723 ("r-mvtnorm" ,r-mvtnorm)
2724 ("r-numderiv" ,r-numderiv)))
2725 (home-page "https://cran.r-project.org/web/packages/bbmle")
2726 (synopsis "Tools for General Maximum Likelihood Estimation")
2728 "This package provides methods and functions for fitting maximum
2729 likelihood models in R. This package modifies and extends the @code{mle}
2730 classes in the @code{stats4} package.")
2731 ;; Any version of the GPL
2732 (license license:gpl2+)))
2734 (define-public r-emdbook
2741 (uri (cran-uri "emdbook" version))
2744 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2745 (build-system r-build-system)
2747 `(("r-bbmle" ,r-bbmle)
2749 ("r-lattice" ,r-lattice)
2751 ("r-plyr" ,r-plyr)))
2752 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2753 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2755 "This package provides auxiliary functions and data sets for \"Ecological
2756 Models and Data\", a book presenting maximum likelihood estimation and related
2757 topics for ecologists (ISBN 978-0-691-12522-0).")
2759 (license (list license:gpl2 license:gpl3))))
2761 (define-public r-lpsolve
2768 (uri (cran-uri "lpSolve" version))
2771 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2772 (properties `((upstream-name . "lpSolve")))
2773 (build-system r-build-system)
2774 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2775 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2777 "Lp_solve is software for solving linear, integer and mixed integer
2778 programs. This implementation supplies a \"wrapper\" function in C and some R
2779 functions that solve general linear/integer problems, assignment problems, and
2780 transportation problems.")
2781 (license license:lgpl2.0)))
2783 (define-public r-limsolve
2790 (uri (cran-uri "limSolve" version))
2793 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2794 (properties `((upstream-name . "limSolve")))
2795 (build-system r-build-system)
2797 `(("r-lpsolve" ,r-lpsolve)
2799 ("r-quadprog" ,r-quadprog)))
2800 (native-inputs `(("gfortran" ,gfortran)))
2801 (home-page "https://cran.r-project.org/web/packages/limSolve")
2802 (synopsis "Solving linear inverse models")
2804 "This package provides functions that:
2807 @item find the minimum/maximum of a linear or quadratic function,
2808 @item sample an underdetermined or overdetermined system,
2809 @item solve a linear system Ax=B for the unknown x.
2812 It includes banded and tridiagonal linear systems. The package calls Fortran
2813 functions from LINPACK.")
2815 (license (list license:gpl2+ license:gpl3+))))
2817 (define-public r-fitdistrplus
2819 (name "r-fitdistrplus")
2824 (uri (cran-uri "fitdistrplus" version))
2827 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2828 (build-system r-build-system)
2830 `(("r-mass" ,r-mass)
2831 ("r-survival" ,r-survival)))
2833 `(("r-knitr" ,r-knitr)))
2834 (home-page "http://riskassessment.r-forge.r-project.org")
2835 (synopsis "Fitting a parametric distribution from data")
2837 "This package extends the @code{fitdistr} function of the MASS package
2838 with several functions to help the fit of a parametric distribution to
2839 non-censored or censored data. Censored data may contain left-censored,
2840 right-censored and interval-censored values, with several lower and upper
2841 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2842 provides moment matching (MME), quantile matching (QME) and maximum
2843 goodness-of-fit estimation (MGE) methods (available only for non-censored
2844 data). Weighted versions of MLE, MME and QME are available.")
2845 (license license:gpl2+)))
2847 (define-public r-energy
2854 (uri (cran-uri "energy" version))
2857 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2858 (build-system r-build-system)
2860 `(("r-boot" ,r-boot)
2861 ("r-rcpp" ,r-rcpp)))
2862 (home-page "https://cran.r-project.org/web/packages/energy")
2863 (synopsis "Multivariate inference via the energy of data")
2865 "This package provides e-statistics (energy) tests and statistics for
2866 multivariate and univariate inference, including distance correlation,
2867 one-sample, two-sample, and multi-sample tests for comparing multivariate
2868 distributions, are implemented. Measuring and testing multivariate
2869 independence based on distance correlation, partial distance correlation,
2870 multivariate goodness-of-fit tests, clustering based on energy distance,
2871 testing for multivariate normality, distance components (disco) for
2872 non-parametric analysis of structured data, and other energy
2873 statistics/methods are implemented.")
2874 (license license:gpl2+)))
2876 (define-public r-suppdists
2878 (name "r-suppdists")
2883 (uri (cran-uri "SuppDists" version))
2886 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2887 (properties `((upstream-name . "SuppDists")))
2888 (build-system r-build-system)
2889 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2890 (synopsis "Supplementary distributions")
2892 "This package provides ten distributions supplementing those built into
2893 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2894 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2895 coefficient, Johnson distributions, normal scores and generalized
2896 hypergeometric distributions. In addition two random number generators of
2897 George Marsaglia are included.")
2898 (license license:gpl2+)))
2900 (define-public r-ksamples
2907 (uri (cran-uri "kSamples" version))
2910 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2911 (properties `((upstream-name . "kSamples")))
2912 (build-system r-build-system)
2914 `(("r-suppdists" ,r-suppdists)))
2915 (home-page "https://cran.r-project.org/web/packages/kSamples")
2916 (synopsis "K-Sample rank tests and their combinations")
2918 "This package provides tools to compares k samples using the
2919 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2920 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2921 test. It computes asymptotic, simulated or (limited) exact P-values, all
2922 valid under randomization, with or without ties, or conditionally under random
2923 sampling from populations, given the observed tie pattern. Except for Steel's
2924 test and the JT test it also combines these tests across several blocks of
2926 (license license:gpl2+)))
2928 (define-public r-cvst
2935 (uri (cran-uri "CVST" version))
2938 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2939 (properties `((upstream-name . "CVST")))
2940 (build-system r-build-system)
2942 `(("r-kernlab" ,r-kernlab)
2943 ("r-matrix" ,r-matrix)))
2944 (home-page "https://cran.r-project.org/web/packages/CVST")
2945 (synopsis "Fast cross-validation via sequential testing")
2947 "This package implements the fast cross-validation via sequential
2948 testing (CVST) procedure. CVST is an improved cross-validation procedure
2949 which uses non-parametric testing coupled with sequential analysis to
2950 determine the best parameter set on linearly increasing subsets of the data.
2951 Additionally to the CVST the package contains an implementation of the
2952 ordinary k-fold cross-validation with a flexible and powerful set of helper
2953 objects and methods to handle the overall model selection process. The
2954 implementations of the Cochran's Q test with permutations and the sequential
2955 testing framework of Wald are generic and can therefore also be used in other
2957 (license license:gpl2+)))
2959 (define-public r-squarem
2966 (uri (cran-uri "SQUAREM" version))
2969 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
2970 (properties `((upstream-name . "SQUAREM")))
2971 (build-system r-build-system)
2972 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2973 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2975 "This package provides algorithms for accelerating the convergence of
2976 slow, monotone sequences from smooth, contraction mapping such as the EM
2977 algorithm. It can be used to accelerate any smooth, linearly convergent
2978 acceleration scheme. A tutorial style introduction to this package is
2979 available in a vignette.")
2980 (license license:gpl2+)))
2982 (define-public r-lava
2989 (uri (cran-uri "lava" version))
2992 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2993 (build-system r-build-system)
2995 `(("r-numderiv" ,r-numderiv)
2996 ("r-squarem" ,r-squarem)
2997 ("r-survival" ,r-survival)))
2998 (home-page "https://github.com/kkholst/lava")
2999 (synopsis "Latent variable models")
3001 "This package provides tools for the estimation and simulation of latent
3003 (license license:gpl3)))
3005 (define-public r-drr
3012 (uri (cran-uri "DRR" version))
3015 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3016 (properties `((upstream-name . "DRR")))
3017 (build-system r-build-system)
3019 `(("r-cvst" ,r-cvst)
3020 ("r-kernlab" ,r-kernlab)
3021 ("r-matrix" ,r-matrix)))
3022 (home-page "https://cran.r-project.org/web/packages/DRR")
3023 (synopsis "Dimensionality reduction via regression")
3025 "This package provides an implementation of dimensionality reduction via
3026 regression using Kernel Ridge Regression.")
3027 (license license:gpl3)))
3029 (define-public r-prodlim
3032 (version "2019.11.13")
3036 (uri (cran-uri "prodlim" version))
3039 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3040 (build-system r-build-system)
3042 `(("r-kernsmooth" ,r-kernsmooth)
3045 ("r-survival" ,r-survival)))
3046 (home-page "https://cran.r-project.org/web/packages/prodlim")
3047 (synopsis "Product-limit estimation for censored event history analysis")
3049 "This package provides a fast and user-friendly implementation of
3050 nonparametric estimators for censored event history (survival) analysis with
3051 the Kaplan-Meier and Aalen-Johansen methods.")
3052 (license license:gpl2+)))
3054 (define-public r-dimred
3061 (uri (cran-uri "dimRed" version))
3064 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3065 (properties `((upstream-name . "dimRed")))
3066 (build-system r-build-system)
3069 ("r-magrittr" ,r-magrittr)))
3070 (home-page "https://github.com/gdkrmr/dimRed")
3071 (synopsis "Framework for dimensionality reduction")
3073 "This package provides a collection of dimensionality reduction
3074 techniques from R packages and provides a common interface for calling the
3076 (license license:gpl3)))
3078 (define-public r-timedate
3081 (version "3043.102")
3085 (uri (cran-uri "timeDate" version))
3088 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3089 (properties `((upstream-name . "timeDate")))
3090 (build-system r-build-system)
3091 (home-page "https://www.rmetrics.org")
3092 (synopsis "Chronological and calendar objects")
3094 "This package provides an environment for teaching \"Financial
3095 Engineering and Computational Finance\" and for managing chronological and
3097 (license license:gpl2+)))
3099 (define-public r-magic
3106 (uri (cran-uri "magic" version))
3109 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3110 (build-system r-build-system)
3112 `(("r-abind" ,r-abind)))
3113 (home-page "https://github.com/RobinHankin/magic.git")
3114 (synopsis "Create and investigate magic squares")
3116 "This package provides a collection of efficient, vectorized algorithms
3117 for the creation and investigation of magic squares and hypercubes, including
3118 a variety of functions for the manipulation and analysis of arbitrarily
3119 dimensioned arrays.")
3120 (license license:gpl2)))
3122 (define-public r-rmysql
3129 (uri (cran-uri "RMySQL" version))
3132 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3133 (properties `((upstream-name . "RMySQL")))
3134 (build-system r-build-system)
3136 `(("mariadb" ,mariadb "lib")
3137 ("mariadb-dev" ,mariadb "dev")
3140 `(("r-dbi" ,r-dbi)))
3141 (home-page "https://github.com/r-dbi/RMySQL")
3142 (synopsis "Database interface and MySQL driver for R")
3144 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3145 package contains an old implementation based on legacy code from S-PLUS which
3146 is being phased out. A modern MySQL client based on Rcpp is available from
3147 the RMariaDB package.")
3148 (license license:gpl2)))
3150 (define-public r-rpostgresql
3152 (name "r-rpostgresql")
3157 (uri (cran-uri "RPostgreSQL" version))
3160 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3161 (properties `((upstream-name . "RPostgreSQL")))
3162 (build-system r-build-system)
3164 `(("postgresql" ,postgresql)))
3166 `(("r-dbi" ,r-dbi)))
3167 (home-page "https://github.com/tomoakin/RPostgreSQL")
3168 (synopsis "R interface to the PostgreSQL database system")
3170 "This package provides a Database Interface (DBI) compliant driver for R
3171 to access PostgreSQL database systems.")
3172 ;; The whole package is released under GPL version 2. It includes code
3173 ;; under the PostgreSQL license.
3174 (license license:gpl2)))
3176 (define-public r-linprog
3183 (uri (cran-uri "linprog" version))
3186 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3187 (build-system r-build-system)
3188 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3189 (home-page "http://linprog.r-forge.r-project.org/")
3190 (synopsis "Linear programming and optimization")
3192 "This package can be used to solve Linear Programming / Linear
3193 Optimization problems by using the simplex algorithm.")
3194 (license license:gpl2+)))
3196 (define-public r-geometry
3203 (uri (cran-uri "geometry" version))
3206 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3207 (build-system r-build-system)
3209 `(("r-magic" ,r-magic)
3210 ("r-linprog" ,r-linprog)
3211 ("r-lpsolve" ,r-lpsolve)
3213 ("r-rcppprogress" ,r-rcppprogress)))
3214 (home-page "http://geometry.r-forge.r-project.org/")
3215 (synopsis "Mesh generation and surface tesselation")
3217 "This package makes the qhull library available in R, in a similar manner
3218 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3219 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3220 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3221 and higher dimensions. It implements the Quickhull algorithm for computing
3222 the convex hull. Qhull does not support constrained Delaunay triangulations,
3223 or mesh generation of non-convex objects, but the package does include some R
3224 functions that allow for this. Currently the package only gives access to
3225 Delaunay triangulation and convex hull computation.")
3226 ;; The Qhull sources are included and are distributed under a custom
3227 ;; non-copyleft license. The R sources are released under GPL version 2.
3228 (license (list license:gpl2
3229 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3231 (define-public r-ddalpha
3238 (uri (cran-uri "ddalpha" version))
3241 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3242 (build-system r-build-system)
3245 ("r-class" ,r-class)
3246 ("r-geometry" ,r-geometry)
3249 ("r-robustbase" ,r-robustbase)
3250 ("r-sfsmisc" ,r-sfsmisc)))
3252 `(("gfortran" ,gfortran)))
3253 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3254 (synopsis "Depth-Based classification and calculation of data depth")
3256 "This package contains procedures for depth-based supervised learning,
3257 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3258 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3259 statistical depth function to a compact low-dimensional space, where the final
3260 classification is done. It also offers an extension to functional data and
3261 routines for calculating certain notions of statistical depth functions. 50
3262 multivariate and 5 functional classification problems are included.")
3263 (license license:gpl2)))
3265 (define-public r-gower
3272 (uri (cran-uri "gower" version))
3275 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
3276 (build-system r-build-system)
3277 (home-page "https://github.com/markvanderloo/gower")
3278 (synopsis "Gower's distance")
3280 "This package provides tools to compute Gower's distance (or similarity)
3281 coefficient between records, and to compute the top-n matches between records.
3282 Core algorithms are executed in parallel on systems supporting OpenMP.")
3283 (license license:gpl3)))
3285 (define-public r-rcpproll
3292 (uri (cran-uri "RcppRoll" version))
3295 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3296 (properties `((upstream-name . "RcppRoll")))
3297 (build-system r-build-system)
3299 `(("r-rcpp" ,r-rcpp)))
3300 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3301 (synopsis "Efficient rolling and windowed operations")
3303 "This package provides fast and efficient routines for common rolling /
3304 windowed operations. Routines for the efficient computation of windowed mean,
3305 median, sum, product, minimum, maximum, standard deviation and variance are
3307 (license license:gpl2+)))
3309 (define-public r-ipred
3316 (uri (cran-uri "ipred" version))
3319 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3320 (build-system r-build-system)
3322 `(("r-class" ,r-class)
3325 ("r-prodlim" ,r-prodlim)
3326 ("r-rpart" ,r-rpart)
3327 ("r-survival" ,r-survival)))
3328 (home-page "https://cran.r-project.org/web/packages/ipred")
3329 (synopsis "Improved predictors")
3331 "This package provides improved predictive models by indirect
3332 classification and bagging for classification, regression and survival
3333 problems as well as resampling based estimators of prediction error.")
3334 (license license:gpl2+)))
3336 (define-public r-psych
3339 (version "1.9.12.31")
3343 (uri (cran-uri "psych" version))
3346 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3347 (build-system r-build-system)
3349 `(("r-lattice" ,r-lattice)
3350 ("r-mnormt" ,r-mnormt)
3351 ("r-nlme" ,r-nlme)))
3352 (home-page "https://cran.r-project.org/web/packages/psych/")
3353 (synopsis "Procedures for psychological, psychometric, and personality research")
3355 "This package provides a general purpose toolbox for personality,
3356 psychometric theory and experimental psychology. Functions are primarily for
3357 multivariate analysis and scale construction using factor analysis, principal
3358 component analysis, cluster analysis and reliability analysis, although others
3359 provide basic descriptive statistics. Item Response Theory is done using
3360 factor analysis of tetrachoric and polychoric correlations. Functions for
3361 analyzing data at multiple levels include within and between group statistics,
3362 including correlations and factor analysis. Functions for simulating and
3363 testing particular item and test structures are included. Several functions
3364 serve as a useful front end for structural equation modeling. Graphical
3365 displays of path diagrams, factor analysis and structural equation models are
3366 created using basic graphics.")
3367 (license license:gpl2+)))
3369 (define-public r-generics
3376 (uri (cran-uri "generics" version))
3379 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3380 (build-system r-build-system)
3381 (home-page "https://github.com/r-lib/generics")
3382 (synopsis "Common S3 generics not provided by base R methods")
3384 "In order to reduce potential package dependencies and conflicts,
3385 generics provides a number of commonly used S3 generics that are not provided
3386 by base R methods related to model fitting.")
3387 (license license:gpl2)))
3389 (define-public r-broom
3396 (uri (cran-uri "broom" version))
3399 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3400 (build-system r-build-system)
3402 `(("r-backports" ,r-backports)
3403 ("r-dplyr" ,r-dplyr)
3404 ("r-generics" ,r-generics)
3406 ("r-purrr" ,r-purrr)
3407 ("r-reshape2" ,r-reshape2)
3408 ("r-stringr" ,r-stringr)
3409 ("r-tibble" ,r-tibble)
3410 ("r-tidyr" ,r-tidyr)))
3412 `(("r-knitr" ,r-knitr)))
3413 (home-page "https://github.com/tidyverse/broom")
3414 (synopsis "Convert statistical analysis objects into tidy data frames")
3416 "This package provides tools to convert statistical analysis objects from
3417 R into tidy data frames, so that they can more easily be combined, reshaped
3418 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3419 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3420 summarizes a model's statistical findings such as coefficients of a
3421 regression; @code{augment}, which adds columns to the original data such as
3422 predictions, residuals and cluster assignments; and @code{glance}, which
3423 provides a one-row summary of model-level statistics.")
3424 (license license:expat)))
3426 (define-public r-recipes
3433 (uri (cran-uri "recipes" version))
3436 "0hbnrqgzazg401nk5fhljif7wnspicki179qf215r34y9wm8g3xj"))))
3437 (build-system r-build-system)
3439 `(("r-dplyr" ,r-dplyr)
3440 ("r-generics" ,r-generics)
3442 ("r-gower" ,r-gower)
3443 ("r-ipred" ,r-ipred)
3444 ("r-lubridate" ,r-lubridate)
3445 ("r-magrittr" ,r-magrittr)
3446 ("r-matrix" ,r-matrix)
3447 ("r-purrr" ,r-purrr)
3448 ("r-rlang" ,r-rlang)
3449 ("r-tibble" ,r-tibble)
3450 ("r-tidyr" ,r-tidyr)
3451 ("r-tidyselect" ,r-tidyselect)
3452 ("r-timedate" ,r-timedate)
3453 ("r-withr" ,r-withr)))
3455 `(("r-knitr" ,r-knitr)))
3456 (home-page "https://github.com/topepo/recipes")
3457 (synopsis "Preprocessing tools to create design matrices")
3459 "Recipes is an extensible framework to create and preprocess design
3460 matrices. Recipes consist of one or more data manipulation and analysis
3461 \"steps\". Statistical parameters for the steps can be estimated from an
3462 initial data set and then applied to other data sets. The resulting design
3463 matrices can then be used as inputs into statistical or machine learning
3465 (license license:gpl2)))
3467 (define-public r-pdist
3474 (uri (cran-uri "pdist" version))
3477 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3478 (build-system r-build-system)
3479 (home-page "https://github.com/jeffwong/pdist")
3480 (synopsis "Partitioned distance function")
3482 "Pdist computes the euclidean distance between rows of a matrix X and
3483 rows of another matrix Y. Previously, this could be done by binding the two
3484 matrices together and calling @code{dist}, but this creates unnecessary
3485 computation by computing the distances between a row of X and another row of
3486 X, and likewise for Y. Pdist strictly computes distances across the two
3487 matrices, not within the same matrix, making computations significantly faster
3488 for certain use cases.")
3489 (license license:gpl3+)))
3491 (define-public r-ggrepel
3498 (uri (cran-uri "ggrepel" version))
3501 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3502 (build-system r-build-system)
3504 `(("r-ggplot2" ,r-ggplot2)
3506 ("r-scales" ,r-scales)))
3508 `(("r-knitr" ,r-knitr))) ; for vignettes
3509 (home-page "http://github.com/slowkow/ggrepel")
3510 (synopsis "Repulsive text and label geometries for ggplot2")
3512 "This package provides text and label geometries for ggplot2 that help to
3513 avoid overlapping text labels. Labels repel away from each other and away
3514 from the data points.")
3515 (license license:gpl3)))
3517 (define-public r-corrplot
3524 (uri (cran-uri "corrplot" version))
3527 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3528 (build-system r-build-system)
3529 (home-page "https://github.com/taiyun/corrplot")
3530 (synopsis "Visualization of a correlation matrix")
3532 "This package provides a graphical display of a correlation matrix or
3533 general matrix. It also contains some algorithms to do matrix reordering. In
3534 addition, corrplot is good at details, including choosing color, text labels,
3535 color labels, layout, etc.")
3536 ;; Any version of the GPL
3537 (license license:gpl2+)))
3539 (define-public r-stringdist
3541 (name "r-stringdist")
3546 (uri (cran-uri "stringdist" version))
3548 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3549 (build-system r-build-system)
3550 (home-page "https://github.com/markvanderloo/stringdist")
3551 (synopsis "Approximate string matching and string distance functions")
3553 "This package implements an approximate string matching version of R's
3554 native @code{match} function. It can calculate various string distances based
3555 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3556 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3557 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3558 can be computed between character vectors while taking proper care of encoding
3559 or between integer vectors representing generic sequences.")
3560 (license license:gpl3+)))
3562 (define-public r-ucminf
3569 (uri (cran-uri "ucminf" version))
3572 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3573 (build-system r-build-system)
3574 (native-inputs `(("gfortran" ,gfortran)))
3575 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3576 (synopsis "General-purpose unconstrained non-linear optimization")
3578 "This package provides an implementation of an algorithm for
3579 general-purpose unconstrained non-linear optimization. The algorithm is of
3580 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3581 search with a trust region type monitoring of the input to the line search
3582 algorithm. The interface of @code{ucminf} is designed for easy interchange
3583 with the package @code{optim}.")
3584 (license license:gpl2+)))
3586 (define-public r-ordinal
3589 (version "2019.12-10")
3593 (uri (cran-uri "ordinal" version))
3596 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3597 (build-system r-build-system)
3599 `(("r-mass" ,r-mass)
3600 ("r-matrix" ,r-matrix)
3601 ("r-numderiv" ,r-numderiv)
3602 ("r-ucminf" ,r-ucminf)))
3603 (home-page "https://github.com/runehaubo/ordinal")
3604 (synopsis "Regression models for ordinal data")
3606 "This package provides an implementation of cumulative link (mixed)
3607 models also known as ordered regression models, proportional odds models,
3608 proportional hazards models for grouped survival times and ordered models.
3609 Estimation is via maximum likelihood and mixed models are fitted with the
3610 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3611 (license license:gpl2+)))
3613 (define-public r-jomo
3620 (uri (cran-uri "jomo" version))
3623 "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w"))))
3624 (build-system r-build-system)
3626 `(("r-lme4" ,r-lme4)
3628 ("r-ordinal" ,r-ordinal)
3629 ("r-survival" ,r-survival)))
3630 (home-page "https://cran.r-project.org/web/packages/jomo/")
3631 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3633 "Similarly to Schafer's package pan, jomo is a package for multilevel
3634 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3635 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3636 possibility of handling binary and categorical data through latent normal
3637 variables, the option to use cluster-specific covariance matrices and to
3638 impute compatibly with the substantive model.")
3639 (license license:gpl2)))
3641 (define-public r-pan
3648 (uri (cran-uri "pan" version))
3651 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3652 (build-system r-build-system)
3653 (native-inputs `(("gfortran" ,gfortran)))
3654 (home-page "https://cran.r-project.org/web/packages/pan/")
3655 (synopsis "Multiple imputation for multivariate panel or clustered data")
3657 "This package implements multiple imputation for multivariate panel or
3659 (license license:gpl3)))
3661 (define-public r-mitml
3668 (uri (cran-uri "mitml" version))
3671 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3672 (build-system r-build-system)
3674 `(("r-haven" ,r-haven)
3677 (home-page "https://cran.r-project.org/web/packages/mitml/")
3678 (synopsis "Tools for multiple imputation in multilevel modeling")
3680 "This package provides tools for multiple imputation of missing data in
3681 multilevel modeling. It includes a user-friendly interface to the packages
3682 pan and jomo, and several functions for visualization, data management and the
3683 analysis of multiply imputed data sets.")
3684 (license license:gpl2+)))
3686 (define-public r-mice
3693 (uri (cran-uri "mice" version))
3696 "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn"))))
3697 (build-system r-build-system)
3699 `(("r-broom" ,r-broom)
3700 ("r-dplyr" ,r-dplyr)
3701 ("r-lattice" ,r-lattice)
3703 ("r-tidyr" ,r-tidyr)))
3704 (home-page "https://cran.r-project.org/web/packages/mice/")
3705 (synopsis "Multivariate imputation by chained equations")
3707 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3708 implemented by the MICE algorithm as described in @url{Van Buuren and
3709 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3710 variable has its own imputation model. Built-in imputation models are
3711 provided for continuous data (predictive mean matching, normal), binary
3712 data (logistic regression), unordered categorical data (polytomous logistic
3713 regression) and ordered categorical data (proportional odds). MICE can also
3714 impute continuous two-level data (normal model, pan, second-level variables).
3715 Passive imputation can be used to maintain consistency between variables.
3716 Various diagnostic plots are available to inspect the quality of the
3718 ;; Any of these two versions.
3719 (license (list license:gpl2 license:gpl3))))
3721 (define-public r-truncnorm
3723 (name "r-truncnorm")
3728 (uri (cran-uri "truncnorm" version))
3731 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3732 (build-system r-build-system)
3733 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3734 (synopsis "Truncated normal distribution")
3735 (description "This package provides functions for the truncated normal
3736 distribution with mean equal to @code{mean} and standard deviation equal to
3737 @code{sd}. It includes density, distribution, quantile, and expected value
3738 functions, as well as a random generation function.")
3739 (license license:gpl2)))
3741 (define-public r-rsolnp
3748 (uri (cran-uri "Rsolnp" version))
3751 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3752 (properties `((upstream-name . "Rsolnp")))
3753 (build-system r-build-system)
3755 `(("r-truncnorm" ,r-truncnorm)))
3756 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3757 (synopsis "General non-linear optimization")
3758 (description "The Rsolnp package implements a general non-linear augmented
3759 Lagrange multiplier method solver, a @dfn{sequential quadratic
3760 programming} (SQP) based solver).")
3761 ;; Any version of the GPL.
3762 (license license:gpl2+)))
3764 (define-public r-hardyweinberg
3766 (name "r-hardyweinberg")
3771 (uri (cran-uri "HardyWeinberg" version))
3774 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3775 (properties `((upstream-name . "HardyWeinberg")))
3776 (build-system r-build-system)
3778 `(("r-mice" ,r-mice)
3780 ("r-rsolnp" ,r-rsolnp)))
3781 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3782 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3784 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3785 diallelic genetic marker data. All classical tests (chi-square, exact,
3786 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3787 included in the package, as well as functions for power computation and for
3788 the simulation of marker data under equilibrium and disequilibrium. Routines
3789 for dealing with markers on the X-chromosome are included. Functions for
3790 testing equilibrium in the presence of missing data by using multiple
3791 imputation are also provided. Implements several graphics for exploring the
3792 equilibrium status of a large set of diallelic markers: ternary plots with
3793 acceptance regions, log-ratio plots and Q-Q plots.")
3794 (license license:gpl2+)))
3803 (uri (cran-uri "sm" version))
3806 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3807 (build-system r-build-system)
3808 (native-inputs `(("gfortran" ,gfortran)))
3809 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3810 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3812 "This is software accompanying the book 'Applied Smoothing Techniques for
3813 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3814 University Press. It provides smoothing methods for nonparametric regression
3815 and density estimation")
3816 (license license:gpl2+)))
3818 (define-public r-venndiagram
3820 (name "r-venndiagram")
3824 (uri (cran-uri "VennDiagram" version))
3827 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3828 (properties `((upstream-name . "VennDiagram")))
3829 (build-system r-build-system)
3831 `(("r-futile-logger" ,r-futile-logger)))
3832 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3833 (synopsis "Generate High-Resolution Venn and Euler Plots")
3835 "This package provides a set of functions to generate high-resolution
3836 Venn and Euler plots. It includes handling for several special cases,
3837 including two-case scaling, and extensive customization of plot shape and
3839 (license license:gpl2+)))
3841 (define-public r-vioplot
3848 (uri (cran-uri "vioplot" version))
3851 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3852 (build-system r-build-system)
3857 `(("r-knitr" ,r-knitr)))
3858 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3859 (synopsis "Violin plot")
3861 "This package provides a violin plot, which is a combination of a box
3862 plot and a kernel density plot.")
3863 (license license:bsd-3)))
3865 (define-public r-rsofia
3871 ;; This package has been removed from CRAN, so we can
3872 ;; only fetch it from the archives.
3873 (uri (string-append "https://cran.r-project.org/src/"
3874 "contrib/Archive/RSofia/RSofia_"
3878 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3879 (properties `((upstream-name . "RSofia")))
3880 (build-system r-build-system)
3882 `(("r-rcpp" ,r-rcpp)))
3883 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3884 (synopsis "Port of sofia-ml to R")
3885 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3886 suite of fast incremental algorithms for machine learning that can be used for
3887 training models for classification or ranking.")
3888 (license license:asl2.0)))
3890 (define-public r-xts
3897 (uri (cran-uri "xts" version))
3900 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3901 (build-system r-build-system)
3902 (propagated-inputs `(("r-zoo" ,r-zoo)))
3903 (home-page "https://github.com/joshuaulrich/xts")
3904 (synopsis "Extensible time series")
3906 "This package provides for uniform handling of R's different time-based
3907 data classes by extending @code{zoo}, maximizing native format information
3908 preservation and allowing for user-level customization and extension, while
3909 simplifying cross-class interoperability.")
3910 (license license:gpl2+)))
3912 (define-public r-performanceanalytics
3914 (name "r-performanceanalytics")
3919 (uri (cran-uri "PerformanceAnalytics" version))
3922 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3924 `((upstream-name . "PerformanceAnalytics")))
3925 (build-system r-build-system)
3927 `(("r-quadprog" ,r-quadprog)
3930 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3931 (synopsis "Econometric tools for performance and risk analysis")
3932 (description "This is a collection of econometric functions for
3933 performance and risk analysis. This package aims to aid practitioners and
3934 researchers in utilizing the latest research in analysis of non-normal return
3935 streams. In general, it is most tested on return (rather than price) data on
3936 a regular scale, but most functions will work with irregular return data as
3937 well, and increasing numbers of functions will work with P&L or price data
3939 ;; Either version may be picked.
3940 (license (list license:gpl2 license:gpl3))))
3942 (define-public r-laeken
3949 (uri (cran-uri "laeken" version))
3952 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3953 (build-system r-build-system)
3955 `(("r-boot" ,r-boot)
3956 ("r-mass" ,r-mass)))
3957 (home-page "https://cran.r-project.org/web/packages/laeken/")
3958 (synopsis "Estimation of indicators on social exclusion and poverty")
3959 (description "This package provides tools for the estimation of indicators
3960 on social exclusion and poverty, as well as an implementation of Pareto tail
3961 modeling for empirical income distributions.")
3962 (license license:gpl2+)))
3964 (define-public r-vcd
3971 (uri (cran-uri "vcd" version))
3974 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3975 (build-system r-build-system)
3977 `(("r-colorspace" ,r-colorspace)
3978 ("r-lmtest" ,r-lmtest)
3979 ("r-mass" ,r-mass)))
3980 (home-page "https://cran.r-project.org/web/packages/vcd/")
3981 (synopsis "Visualizing categorical data")
3982 (description "This package provides visualization techniques, data sets,
3983 summary and inference procedures aimed particularly at categorical data.
3984 Special emphasis is given to highly extensible grid graphics. The package was
3985 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3986 Friendly and is now the main support package for a new book, \"Discrete Data
3987 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3988 (license license:gpl2)))
3990 (define-public r-ica
3997 (uri (cran-uri "ica" version))
4000 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4001 (build-system r-build-system)
4002 (home-page "https://cran.r-project.org/web/packages/ica/")
4003 (synopsis "Independent component analysis")
4004 (description "This package provides tools for @dfn{Independent Component
4005 Analysis} (ICA) using various algorithms: FastICA,
4006 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4007 of Eigenmatrices} (JADE).")
4008 (license license:gpl2+)))
4010 (define-public r-dtw
4017 (uri (cran-uri "dtw" version))
4020 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4021 (build-system r-build-system)
4022 (propagated-inputs `(("r-proxy" ,r-proxy)))
4023 (home-page "http://dtw.r-forge.r-project.org/")
4024 (synopsis "Dynamic Time Warping Algorithms")
4025 (description "This package provides a comprehensive implementation of
4026 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4027 optimal (least cumulative distance) alignment between points of two time
4028 series. Common DTW variants covered include local (slope) and global (window)
4029 constraints, subsequence matches, arbitrary distance definitions,
4030 normalizations, minimum variance matching, and so on.")
4031 (license license:gpl2+)))
4033 (define-public r-sdmtools
4036 (version "1.1-221.2")
4040 (uri (cran-uri "SDMTools" version))
4043 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4044 (properties `((upstream-name . "SDMTools")))
4045 (build-system r-build-system)
4046 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4047 (home-page "https://www.rforge.net/SDMTools/")
4048 (synopsis "Species distribution modelling tools")
4049 (description "This package provides a set of tools for post processing
4050 the outcomes of species distribution modeling exercises. It includes novel
4051 methods for comparing models and tracking changes in distributions through
4052 time. It further includes methods for visualizing outcomes, selecting
4053 thresholds, calculating measures of accuracy and landscape fragmentation
4055 (license license:gpl3+)))
4057 (define-public r-scatterplot3d
4059 (name "r-scatterplot3d")
4064 (uri (cran-uri "scatterplot3d" version))
4067 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4068 (build-system r-build-system)
4069 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4070 (synopsis "3D scatter plot")
4071 (description "This package provides an implementation of scatter plots for
4072 plotting. a three dimensional point cloud.")
4073 (license license:gpl2)))
4075 (define-public r-ggridges
4082 (uri (cran-uri "ggridges" version))
4085 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4086 (build-system r-build-system)
4088 `(("r-ggplot2" ,r-ggplot2)
4090 ("r-scales" ,r-scales)
4091 ("r-withr" ,r-withr)))
4092 (home-page "https://github.com/clauswilke/ggridges")
4093 (synopsis "Ridgeline plots in ggplot2")
4095 "Ridgeline plots provide a convenient way of visualizing changes in
4096 distributions over time or space. This package enables the creation of such
4097 plots in @code{ggplot2}.")
4098 (license license:gpl2)))
4100 (define-public r-ggjoy
4107 (uri (cran-uri "ggjoy" version))
4110 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4111 (build-system r-build-system)
4113 `(("r-ggplot2" ,r-ggplot2)
4114 ("r-ggridges" ,r-ggridges)))
4115 (home-page "https://github.com/clauswilke/ggjoy")
4116 (synopsis "Joyplots in ggplot2")
4117 (description "Joyplots provide a convenient way of visualizing changes in
4118 distributions over time or space. This package enables the creation of such
4119 plots in @code{ggplot2}.")
4120 (license license:gpl2)))
4122 (define-public r-cli
4129 (uri (cran-uri "cli" version))
4132 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4133 (build-system r-build-system)
4135 `(("r-assertthat" ,r-assertthat)
4136 ("r-crayon" ,r-crayon)
4137 ("r-fansi" ,r-fansi)
4138 ("r-glue" ,r-glue)))
4139 (home-page "https://github.com/r-lib/cli#readme")
4140 (synopsis "Helpers for developing command line interfaces")
4141 (description "This package provides a suite of tools designed to build
4142 attractive command line interfaces (CLIs). It includes tools for drawing
4143 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4144 (license license:expat)))
4146 (define-public r-argparser
4148 (name "r-argparser")
4153 (uri (cran-uri "argparser" version))
4156 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4157 (build-system r-build-system)
4158 (home-page "https://bitbucket.org/djhshih/argparser")
4159 (synopsis "Command-line argument parser")
4161 "This package provides a cross-platform command-line argument parser
4162 written purely in R with no external dependencies. It is useful with the
4163 Rscript front-end and facilitates turning an R script into an executable
4165 (license license:gpl3+)))
4167 (define-public r-debugme
4174 (uri (cran-uri "debugme" version))
4177 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4178 (build-system r-build-system)
4179 (propagated-inputs `(("r-crayon" ,r-crayon)))
4180 (home-page "https://github.com/r-lib/debugme#readme")
4181 (synopsis "Debug R packages")
4183 "This package allows the user to specify debug messages as special string
4184 constants, and control debugging of packages via environment variables.")
4185 (license license:expat)))
4187 (define-public r-processx
4194 (uri (cran-uri "processx" version))
4197 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4198 (build-system r-build-system)
4202 (home-page "https://github.com/r-lib/processx3")
4203 (synopsis "Execute and control system processes")
4205 "This package provides portable tools to run system processes in the
4206 background. It can check if a background process is running; wait on a
4207 background process to finish; get the exit status of finished processes; kill
4208 background processes and their children; restart processes. It can read the
4209 standard output and error of the processes, using non-blocking connections.
4210 @code{processx} can poll a process for standard output or error, with a
4211 timeout. It can also poll several processes at once.")
4212 (license license:expat)))
4214 (define-public r-tsp
4221 (uri (cran-uri "TSP" version))
4224 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4225 (properties `((upstream-name . "TSP")))
4226 (build-system r-build-system)
4227 (propagated-inputs `(("r-foreach" ,r-foreach)))
4228 (home-page "https://cran.r-project.org/web/packages/TSP/")
4229 (synopsis "Traveling salesperson problem (TSP)")
4230 (description "This package provides basic infrastructure and some
4231 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4232 traveling salesman problem).")
4233 (license license:gpl3)))
4235 (define-public r-qap
4242 (uri (cran-uri "qap" version))
4245 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4246 (build-system r-build-system)
4247 (native-inputs `(("gfortran" ,gfortran)))
4248 (home-page "https://cran.r-project.org/web/packages/qap/")
4249 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4250 (description "This package implements heuristics for the @dfn{quadratic
4251 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4253 (license license:gpl3)))
4255 (define-public r-gclus
4262 (uri (cran-uri "gclus" version))
4265 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4266 (build-system r-build-system)
4267 (propagated-inputs `(("r-cluster" ,r-cluster)))
4268 (home-page "https://cran.r-project.org/web/packages/gclus/")
4269 (synopsis "Clustering graphics")
4270 (description "This package orders panels in scatterplot matrices and
4271 parallel coordinate displays by some merit index. It contains various indices
4272 of merit, ordering functions, and enhanced versions of @code{pairs} and
4273 @code{parcoord} which color panels according to their merit level.")
4274 (license license:gpl2+)))
4276 (define-public r-webshot
4283 (uri (cran-uri "webshot" version))
4286 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4287 (build-system r-build-system)
4289 `(("r-callr" ,r-callr)
4290 ("r-jsonlite" ,r-jsonlite)
4291 ("r-magrittr" ,r-magrittr)))
4292 (home-page "https://github.com/wch/webshot/")
4293 (synopsis "Take screenshots of web pages")
4295 "Webshot makes it easy to take screenshots of web pages from within R.
4296 It can also run Shiny applications locally and take screenshots of the
4297 application; and it can render and screenshot static as well as interactive R
4298 Markdown documents.")
4299 (license license:gpl2)))
4301 (define-public r-seriation
4303 (name "r-seriation")
4308 (uri (cran-uri "seriation" version))
4311 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4312 (build-system r-build-system)
4314 `(("r-cluster" ,r-cluster)
4315 ("r-colorspace" ,r-colorspace)
4316 ("r-dendextend" ,r-dendextend)
4317 ("r-gclus" ,r-gclus)
4318 ("r-gplots" ,r-gplots)
4321 ("r-registry" ,r-registry)
4323 (native-inputs `(("gfortran" ,gfortran)))
4324 (home-page "https://s2.smu.edu/IDA/seriation/")
4325 (synopsis "Infrastructure for ordering objects using seriation")
4327 "This package provides infrastructure for seriation with an
4328 implementation of several seriation/sequencing techniques to reorder matrices,
4329 dissimilarity matrices, and dendrograms. It also provides (optimally)
4330 reordered heatmaps, color images and clustering visualizations like
4331 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4333 (license license:gpl3)))
4335 (define-public r-xfun
4342 (uri (cran-uri "xfun" version))
4344 (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj"))))
4345 (build-system r-build-system)
4346 ;; knitr itself depends on xfun
4349 `(("r-knitr" ,r-knitr)))
4350 (home-page "https://github.com/yihui/xfun")
4351 (synopsis "Miscellaneous functions")
4353 "This package provides miscellaneous functions commonly used in other
4354 packages maintained by Yihui Xie.")
4355 (license license:expat)))
4357 (define-public r-utf8
4364 (uri (cran-uri "utf8" version))
4367 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4368 (build-system r-build-system)
4369 (home-page "https://github.com/patperry/r-utf8")
4370 (synopsis "Unicode text processing")
4372 "This package provides tools to process and print UTF-8 encoded
4373 international text (Unicode). Input, validate, normalize, encode, format, and
4375 (license license:asl2.0)))
4377 (define-public r-zeallot
4384 (uri (cran-uri "zeallot" version))
4387 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4388 (build-system r-build-system)
4389 (home-page "https://github.com/nteetor/zeallot")
4390 (synopsis "Multiple, unpacking, and destructuring assignment")
4392 "This package provides a @code{%<-%} operator to perform multiple,
4393 unpacking, and destructuring assignment in R. The operator unpacks the
4394 right-hand side of an assignment into multiple values and assigns these values
4395 to variables on the left-hand side of the assignment.")
4396 (license license:expat)))
4398 (define-public r-vctrs
4405 (uri (cran-uri "vctrs" version))
4408 "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp"))))
4409 (build-system r-build-system)
4411 `(("r-digest" ,r-digest)
4412 ("r-ellipsis" ,r-ellipsis)
4414 ("r-rlang" ,r-rlang)))
4416 `(("r-knitr" ,r-knitr)))
4417 (home-page "https://github.com/r-lib/vctrs")
4418 (synopsis "Vector helpers")
4420 "There are three main goals to the @code{vctrs} package:
4423 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4424 @code{length()} and @code{class()}. These definitions are paired with a
4425 framework for type-coercion and size-recycling.
4426 @item To define type- and size-stability as desirable function properties, use
4427 them to analyse existing base function, and to propose better alternatives.
4428 This work has been particularly motivated by thinking about the ideal
4429 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4430 @item To provide a new @code{vctr} base class that makes it easy to create new
4431 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4432 a few new @code{vctrs} generics, making implementation considerably simpler
4435 (license license:gpl3)))
4437 (define-public r-pillar
4444 (uri (cran-uri "pillar" version))
4447 "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1"))))
4448 (build-system r-build-system)
4451 ("r-crayon" ,r-crayon)
4452 ("r-fansi" ,r-fansi)
4453 ("r-rlang" ,r-rlang)
4455 ("r-vctrs" ,r-vctrs)))
4456 (home-page "https://github.com/r-lib/pillar")
4457 (synopsis "Coloured formatting for columns")
4459 "This package provides a @code{pillar} generic designed for formatting
4460 columns of data using the full range of colours provided by modern
4462 (license license:gpl3)))
4464 (define-public r-uuid
4471 (uri (cran-uri "uuid" version))
4474 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4475 (build-system r-build-system)
4476 (home-page "https://www.rforge.net/uuid")
4477 (synopsis "Tools for generating and handling of UUIDs")
4479 "This package provides tools for generating and handling of
4480 @dfn{Universally Unique Identifiers} (UUIDs).")
4481 (license license:expat)))
4483 (define-public r-tinytex
4490 (uri (cran-uri "tinytex" version))
4493 "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr"))))
4494 (build-system r-build-system)
4496 `(("r-xfun" ,r-xfun)))
4497 (home-page "https://github.com/yihui/tinytex")
4498 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4500 "This package provides helper functions to install and maintain the LaTeX
4501 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4502 easy-to-maintain version of TeX Live. This package also contains helper
4503 functions to compile LaTeX documents, and install missing LaTeX packages
4505 (license license:expat)))
4507 (define-public r-network
4514 (uri (cran-uri "network" version))
4517 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4518 (build-system r-build-system)
4520 `(("r-magrittr" ,r-magrittr)
4521 ("r-tibble" ,r-tibble)))
4522 (home-page "https://statnet.org/")
4523 (synopsis "Classes for relational data")
4525 "This package provides tools to create and modify network objects. The
4526 @code{network} class can represent a range of relational data types, and
4527 supports arbitrary vertex/edge/graph attributes.")
4528 (license license:gpl2+)))
4530 (define-public r-statnet-common
4532 (name "r-statnet-common")
4537 (uri (cran-uri "statnet.common" version))
4540 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4542 `((upstream-name . "statnet.common")))
4543 (build-system r-build-system)
4545 `(("r-coda" ,r-coda)))
4546 (home-page "https://statnet.org")
4547 (synopsis "R scripts and utilities used by the Statnet software")
4548 (description "This package provides non-statistical utilities used by the
4549 software developed by the Statnet Project.")
4550 (license license:gpl3)))
4552 (define-public r-statcheck
4554 (name "r-statcheck")
4559 (uri (cran-uri "statcheck" version))
4562 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4563 (build-system r-build-system)
4565 `(("r-ggplot2" ,r-ggplot2)
4567 ("r-rmarkdown" ,r-rmarkdown)))
4568 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4569 (synopsis "Extract statistics from articles and recompute p-values")
4570 (description "This package can automatically extract statistical
4571 null-hypothesis significant testing (NHST) results from articles and recompute
4572 the p-values based on the reported test statistic and degrees of freedom to
4573 detect possible inconsistencies.")
4574 (license license:gpl2)))
4576 (define-public r-sna
4583 (uri (cran-uri "sna" version))
4586 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4587 (build-system r-build-system)
4589 `(("r-network" ,r-network)
4590 ("r-statnet-common" ,r-statnet-common)))
4591 (home-page "https://statnet.org")
4592 (synopsis "Tools for social network analysis")
4594 "This package provides a range of tools for social network analysis,
4595 including node and graph-level indices, structural distance and covariance
4596 methods, structural equivalence detection, network regression, random graph
4597 generation, and 2D/3D network visualization.")
4598 (license license:gpl2+)))
4600 (define-public r-tfisher
4607 (uri (cran-uri "TFisher" version))
4610 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4611 (properties `((upstream-name . "TFisher")))
4612 (build-system r-build-system)
4614 `(("r-matrix" ,r-matrix)
4615 ("r-mvtnorm" ,r-mvtnorm)
4617 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4618 (synopsis "Optimal thresholding Fisher's p-value combination method")
4620 "This package provides the @dfn{cumulative distribution function} (CDF),
4621 quantile, and statistical power calculator for a collection of thresholding
4622 Fisher's p-value combination methods, including Fisher's p-value combination
4623 method, truncated product method and, in particular, soft-thresholding
4624 Fisher's p-value combination method which is proven to be optimal in some
4625 context of signal detection. The p-value calculator for the omnibus version
4626 of these tests are also included.")
4627 (license license:gpl2)))
4629 (define-public r-ttr
4636 (uri (cran-uri "TTR" version))
4639 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4640 (properties `((upstream-name . "TTR")))
4641 (build-system r-build-system)
4643 `(("r-curl" ,r-curl)
4646 (home-page "https://github.com/joshuaulrich/TTR")
4647 (synopsis "Technical trading rules")
4649 "This package provides functions and data to construct technical trading
4651 (license license:gpl2)))
4653 (define-public r-leaps
4660 (uri (cran-uri "leaps" version))
4663 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4664 (build-system r-build-system)
4665 (native-inputs `(("gfortran" ,gfortran)))
4666 (home-page "https://cran.r-project.org/web/packages/leaps/")
4667 (synopsis "Regression subset selection")
4669 "This package provides tools for regression subset selection, including
4670 exhaustive search.")
4671 (license license:gpl2+)))
4673 (define-public r-splus2r
4680 (uri (cran-uri "splus2R" version))
4683 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4684 (properties `((upstream-name . "splus2R")))
4685 (build-system r-build-system)
4686 (native-inputs `(("gfortran" ,gfortran)))
4687 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4688 (synopsis "Supplemental S-PLUS functionality in R")
4690 "Currently there are many functions in S-PLUS that are missing in R. To
4691 facilitate the conversion of S-PLUS packages to R packages, this package
4692 provides some missing S-PLUS functionality in R.")
4693 (license license:gpl2)))
4695 (define-public r-ifultools
4697 (name "r-ifultools")
4702 (uri (cran-uri "ifultools" version))
4705 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4706 (build-system r-build-system)
4708 `(("r-mass" ,r-mass)
4709 ("r-splus2r" ,r-splus2r)))
4710 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4711 (synopsis "Insightful research tools")
4712 (description "This package provides C code used by the wmtsa, fractal, and
4714 (license license:gpl2)))
4716 (define-public r-sapa
4723 (uri (cran-uri "sapa" version))
4726 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4727 (build-system r-build-system)
4729 `(("r-ifultools" ,r-ifultools)
4730 ("r-splus2r" ,r-splus2r)))
4731 (home-page "https://cran.r-project.org/web/packages/sapa/")
4732 (synopsis "Spectral analysis for physical applications")
4733 (description "This package provides software for the book Spectral
4734 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4735 Cambridge University Press, 1993.")
4736 (license license:gpl2)))
4738 (define-public r-aggregation
4740 (name "r-aggregation")
4745 (uri (cran-uri "aggregation" version))
4748 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4749 (build-system r-build-system)
4750 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4751 (synopsis "Methods for p-value aggregation")
4753 "This package contains functionality for performing the following methods
4754 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4755 Fisher's method), and Sidak correction.")
4756 (license license:gpl3)))
4758 (define-public r-quantmod
4765 (uri (cran-uri "quantmod" version))
4768 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4769 (build-system r-build-system)
4771 `(("r-curl" ,r-curl)
4775 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4776 (synopsis "Quantitative financial modelling framework")
4777 (description "This package provides a quantitative financial modelling
4778 framework to allow users to specify, build, trade, and analyse quantitative
4779 financial trading strategies.")
4780 (license license:gpl3)))
4782 (define-public r-tseries
4789 (uri (cran-uri "tseries" version))
4792 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4793 (build-system r-build-system)
4795 `(("r-quadprog" ,r-quadprog)
4796 ("r-quantmod" ,r-quantmod)
4799 `(("gfortran" ,gfortran)))
4800 (home-page "https://cran.r-project.org/web/packages/tseries/")
4801 (synopsis "Time series analysis and computational finance")
4803 "This package provides functions relating to time series analysis and
4804 computational finance.")
4805 (license license:gpl2)))
4807 (define-public r-wmtsa
4814 (uri (cran-uri "wmtsa" version))
4817 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4818 (build-system r-build-system)
4820 `(("r-ifultools" ,r-ifultools)
4822 ("r-splus2r" ,r-splus2r)))
4823 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4824 (synopsis "Wavelet methods for time series analysis")
4826 "This package provides software to accompany the book \"Wavelet Methods
4827 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4828 University Press, 2000.")
4829 (license license:gpl2)))
4831 (define-public r-tsa
4838 (uri (cran-uri "TSA" version))
4841 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4842 (properties `((upstream-name . "TSA")))
4843 (build-system r-build-system)
4845 `(("r-leaps" ,r-leaps)
4846 ("r-locfit" ,r-locfit)
4847 ("r-mgcv" ,r-mgcv)))
4848 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4849 (synopsis "Time series analysis")
4851 "This package contains R functions and datasets detailed in the book
4852 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4853 Cryer and Kung-Sik Chan.")
4854 (license license:gpl2+)))
4856 (define-public r-extradistr
4858 (name "r-extradistr")
4863 (uri (cran-uri "extraDistr" version))
4866 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4867 (properties `((upstream-name . "extraDistr")))
4868 (build-system r-build-system)
4870 `(("r-rcpp" ,r-rcpp)))
4871 (home-page "https://github.com/twolodzko/extraDistr")
4872 (synopsis "Additional univariate and multivariate distributions")
4874 "This package implements density, distribution functions, quantile
4875 functions and random generation functions for a large number of univariate and
4876 multivariate distributions.")
4877 (license license:gpl2)))
4879 (define-public r-fractal
4886 (uri (cran-uri "fractal" version))
4889 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4890 (build-system r-build-system)
4892 `(("r-ifultools" ,r-ifultools)
4895 ("r-scatterplot3d" ,r-scatterplot3d)
4896 ("r-splus2r" ,r-splus2r)
4897 ("r-wmtsa" ,r-wmtsa)))
4898 (home-page "https://cran.r-project.org/web/packages/fractal/")
4899 (synopsis "Fractal time series modeling and analysis")
4901 "This package provides tools for stochastic fractal and deterministic
4902 chaotic time series analysis.")
4903 (license license:gpl2)))
4905 (define-public r-urca
4912 (uri (cran-uri "urca" version))
4915 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4916 (build-system r-build-system)
4917 (propagated-inputs `(("r-nlme" ,r-nlme)))
4918 (native-inputs `(("gfortran" ,gfortran)))
4919 (home-page "https://cran.r-project.org/web/packages/urca/")
4920 (synopsis "Unit root and cointegration tests for time series data")
4922 "This package provides unit root and cointegration tests encountered in
4923 applied econometric analysis.")
4924 (license license:gpl2+)))
4926 (define-public r-cubature
4933 (uri (cran-uri "cubature" version))
4936 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4937 (build-system r-build-system)
4939 `(("r-rcpp" ,r-rcpp)))
4940 (home-page "https://github.com/bnaras/cubature")
4941 (synopsis "Adaptive multivariate integration over hypercubes")
4943 "This package is an R wrapper around the cubature C library for adaptive
4944 multivariate integration over hypercubes. This version provides both
4945 @code{hcubature} and @code{pcubature} routines in addition to a vector
4947 ;; The included cubature C library is released under GPLv2+, but the
4948 ;; wrapper declares the license to be GPLv3+.
4949 (license (list license:gpl2+ license:gpl3+))))
4951 (define-public r-trend
4958 (uri (cran-uri "trend" version))
4961 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4962 (build-system r-build-system)
4964 `(("r-extradistr" ,r-extradistr)))
4966 `(("gfortran" ,gfortran)))
4967 (home-page "https://cran.r-project.org/web/packages/trend/")
4968 (synopsis "Non-parametric trend tests and change-point detection")
4970 "The analysis of environmental data often requires the detection of
4971 trends and change-points. This package includes tests for trend
4972 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4973 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4974 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4975 correlation trend test), change-point detection (Lanzante's test procedures,
4976 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4977 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4978 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4979 sample Robust Rank-Order Distributional Test.")
4980 (license license:gpl3)))
4982 (define-public r-expm
4989 (uri (cran-uri "expm" version))
4992 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4993 (build-system r-build-system)
4994 (propagated-inputs `(("r-matrix" ,r-matrix)))
4995 (native-inputs `(("gfortran" ,gfortran)))
4996 (home-page "https://r-forge.r-project.org/projects/expm/")
4997 (synopsis "Tools for matrix exponentials and related quantities")
4999 "This package provides tools for the computation of the matrix
5000 exponential, logarithm, square root, and related quantities.")
5001 (license license:gpl2+)))
5003 (define-public r-complexplus
5005 (name "r-complexplus")
5010 (uri (cran-uri "complexplus" version))
5013 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5014 (build-system r-build-system)
5016 `(("r-expm" ,r-expm)
5017 ("r-matrix" ,r-matrix)))
5018 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5019 (synopsis "Functions of complex or real variables")
5021 "This package extends several functions to the complex domain, including
5022 the matrix exponential and logarithm, and the determinant.")
5023 (license license:gpl2)))
5025 (define-public r-phontools
5027 (name "r-phontools")
5032 (uri (cran-uri "phonTools" version))
5035 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5036 (properties `((upstream-name . "phonTools")))
5037 (build-system r-build-system)
5038 (home-page "http://www.santiagobarreda.com/rscripts.html")
5039 (synopsis "Tools for phonetic and acoustic analyses")
5041 "This package contains tools for the organization, display, and analysis
5042 of the sorts of data frequently encountered in phonetics research and
5043 experimentation, including the easy creation of IPA vowel plots, and the
5044 creation and manipulation of WAVE audio files.")
5045 (license license:bsd-2)))
5054 (uri (cran-uri "np" version))
5057 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5058 (build-system r-build-system)
5060 `(("r-boot" ,r-boot)
5061 ("r-cubature" ,r-cubature)
5062 ("r-quadprog" ,r-quadprog)
5063 ("r-quantreg" ,r-quantreg)))
5064 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5065 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5066 (description "This package provides non-parametric (and semi-parametric)
5067 kernel methods that seamlessly handle a mix of continuous, unordered, and
5068 ordered factor data types.")
5069 ;; Any version of the GPL.
5070 (license license:gpl3+)))
5072 (define-public r-powerplus
5074 (name "r-powerplus")
5079 (uri (cran-uri "powerplus" version))
5082 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5083 (build-system r-build-system)
5085 `(("r-complexplus" ,r-complexplus)
5088 ("r-matrix" ,r-matrix)
5089 ("r-phontools" ,r-phontools)))
5090 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5091 (synopsis "Exponentiation operations")
5093 "This package provides tools for the computation of matrix and scalar
5095 (license license:gpl2)))
5097 (define-public r-egg
5104 (uri (cran-uri "egg" version))
5107 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5108 (properties `((upstream-name . "egg")))
5109 (build-system r-build-system)
5111 `(("r-ggplot2" ,r-ggplot2)
5112 ("r-gridextra" ,r-gridextra)
5113 ("r-gtable" ,r-gtable)))
5114 (home-page "https://cran.r-project.org/web/packages/egg")
5115 (synopsis "Extensions for ggplot2")
5117 "This package provides miscellaneous functions to help customize ggplot2
5118 objects. High-level functions are provided to post-process ggplot2 layouts
5119 and allow alignment between plot panels, as well as setting panel sizes to
5120 fixed values. Other functions include a custom @code{geom}, and helper
5121 functions to enforce symmetric scales or add tags to facetted plots.")
5122 (license license:gpl3)))
5124 (define-public r-heatmaply
5126 (name "r-heatmaply")
5131 (uri (cran-uri "heatmaply" version))
5134 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5135 (build-system r-build-system)
5137 `(("r-assertthat" ,r-assertthat)
5138 ("r-colorspace" ,r-colorspace)
5139 ("r-dendextend" ,r-dendextend)
5141 ("r-ggplot2" ,r-ggplot2)
5142 ("r-htmlwidgets" ,r-htmlwidgets)
5143 ("r-magrittr" ,r-magrittr)
5144 ("r-plotly" ,r-plotly)
5145 ("r-rcolorbrewer" ,r-rcolorbrewer)
5146 ("r-reshape2" ,r-reshape2)
5147 ("r-scales" ,r-scales)
5148 ("r-seriation" ,r-seriation)
5149 ("r-viridis" ,r-viridis)
5150 ("r-webshot" ,r-webshot)))
5152 `(("r-knitr" ,r-knitr)))
5153 (home-page "https://cran.r-project.org/package=heatmaply")
5154 (synopsis "Interactive cluster heat maps using plotly")
5156 "This package enables you to create interactive cluster heatmaps that can
5157 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5158 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5159 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5160 a popular graphical method for visualizing high-dimensional data, in which a
5161 table of numbers is encoded as a grid of colored cells. The rows and columns
5162 of the matrix are ordered to highlight patterns and are often accompanied by
5164 ;; Either version of the license.
5165 (license (list license:gpl2 license:gpl3))))
5174 (uri (cran-uri "h5" version))
5177 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5178 (build-system r-build-system)
5183 `(("which" ,which)))
5185 `(("r-rcpp" ,r-rcpp)))
5186 (home-page "https://github.com/mannau/h5")
5187 (synopsis "Interface to the HDF5 Library")
5189 "This package provides an S4 interface to the HDF5 library supporting
5190 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5191 binary files in a language independent format. The HDF5 format can therefore
5192 be used as an alternative to R's save/load mechanism. Since h5 is able to
5193 access only subsets of stored data it can also handle data sets which do not
5195 (license license:bsd-2)))
5197 (define-public r-cgdsr
5204 (uri (cran-uri "cgdsr" version))
5207 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5208 (build-system r-build-system)
5210 `(("r-httr" ,r-httr)
5211 ("r-r-methodss3" ,r-r-methodss3)
5212 ("r-r-oo" ,r-r-oo)))
5213 (home-page "https://github.com/cBioPortal/cgdsr")
5214 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5216 "This package provides a basic set of R functions for querying the Cancer
5217 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5218 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5219 (license license:lgpl3)))
5221 (define-public r-import
5228 (uri (cran-uri "import" version))
5231 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5232 (build-system r-build-system)
5233 (home-page "https://github.com/smbache/import")
5234 (synopsis "Import mechanism for R")
5236 "This is an alternative mechanism for importing objects from packages.
5237 The syntax allows for importing multiple objects from a package with a single
5238 command in an expressive way. The import package bridges some of the gap
5239 between using @code{library} (or @code{require}) and direct (single-object)
5240 imports. Furthermore the imported objects are not placed in the current
5241 environment. It is also possible to import objects from stand-alone @code{.R}
5243 (license license:expat)))
5245 (define-public r-shinyace
5252 (uri (cran-uri "shinyAce" version))
5255 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5256 (properties `((upstream-name . "shinyAce")))
5257 (build-system r-build-system)
5259 `(("r-shiny" ,r-shiny)
5260 ("r-jsonlite" ,r-jsonlite)))
5261 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5262 (synopsis "Ace editor bindings for Shiny")
5264 "This package provides Ace editor bindings to enable a rich text editing
5265 environment within Shiny.")
5266 (license license:expat)))
5268 (define-public r-randomizr
5270 (name "r-randomizr")
5275 (uri (cran-uri "randomizr" version))
5278 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5279 (properties `((upstream-name . "randomizr")))
5280 (build-system r-build-system)
5282 `(("r-knitr" ,r-knitr)))
5283 (home-page "https://declaredesign.org/r/randomizr/")
5284 (synopsis "Tools for common forms of random assignment and sampling")
5286 "This package provides tools for generating random assignments for common
5287 experimental designs and random samples for common sampling designs.")
5288 (license license:expat)))
5290 (define-public r-base64url
5292 (name "r-base64url")
5297 (uri (cran-uri "base64url" version))
5300 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5301 (build-system r-build-system)
5303 `(("r-backports" ,r-backports)))
5304 (home-page "https://github.com/mllg/base64url")
5305 (synopsis "Fast and URL-safe base64 encoder and decoder")
5307 "This package provides a URL-safe base64 encoder and decoder. In
5308 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5309 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5310 encoder does not fill the string with trailing @code{=}. The resulting
5311 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5312 and thus are safe to use in URLs or for file names. The package also comes
5313 with a simple base32 encoder/decoder suited for case insensitive file
5315 (license license:gpl3)))
5317 (define-public r-radiant-data
5319 (name "r-radiant-data")
5324 (uri (cran-uri "radiant.data" version))
5327 "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0"))
5328 (modules '((guix build utils)))
5331 ;; Delete files that are under CC-NC-SA.
5332 (delete-file-recursively "inst/app/tools/help")
5334 (properties `((upstream-name . "radiant.data")))
5335 (build-system r-build-system)
5337 `(("r-base64enc" ,r-base64enc)
5338 ("r-broom" ,r-broom)
5341 ("r-dplyr" ,r-dplyr)
5344 ("r-ggplot2" ,r-ggplot2)
5345 ("r-import" ,r-import)
5346 ("r-jsonlite" ,r-jsonlite)
5347 ("r-knitr" ,r-knitr)
5348 ("r-lubridate" ,r-lubridate)
5349 ("r-magrittr" ,r-magrittr)
5350 ("r-markdown" ,r-markdown)
5352 ("r-patchwork" ,r-patchwork)
5353 ("r-plotly" ,r-plotly)
5354 ("r-psych" ,r-psych)
5355 ("r-randomizr" ,r-randomizr)
5356 ("r-readr" ,r-readr)
5357 ("r-readxl" ,r-readxl)
5358 ("r-rlang" ,r-rlang)
5359 ("r-rmarkdown" ,r-rmarkdown)
5360 ("r-rstudioapi" ,r-rstudioapi)
5361 ("r-scales" ,r-scales)
5362 ("r-shiny" ,r-shiny)
5363 ("r-shinyfiles" ,r-shinyfiles)
5364 ("r-shinyace" ,r-shinyace)
5365 ("r-stringi" ,r-stringi)
5366 ("r-tibble" ,r-tibble)
5367 ("r-tidyr" ,r-tidyr)
5368 ("r-writexl" ,r-writexl)))
5369 (home-page "https://github.com/radiant-rstats/radiant.data")
5370 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5372 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5373 visualizing, summarizing, transforming, and combining data. It also contains
5374 functionality to generate reproducible reports of the analyses conducted in
5376 (license license:agpl3)))
5378 (define-public r-algdesign
5380 (name "r-algdesign")
5385 (uri (cran-uri "AlgDesign" version))
5387 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5388 (properties `((upstream-name . "AlgDesign")))
5389 (build-system r-build-system)
5390 (home-page "https://github.com/jvbraun/AlgDesign")
5391 (synopsis "Algorithmic experimental design")
5393 "This package provides tools to calculate exact and approximate theory
5394 experimental designs for D, A, and I criteria. Very large designs may be
5395 created. Experimental designs may be blocked or blocked designs created from
5396 a candidate list, using several criteria. The blocking can be done when whole
5397 and within plot factors interact.")
5398 (license license:gpl2+)))
5400 (define-public r-signal
5407 (uri (cran-uri "signal" version))
5410 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5411 (build-system r-build-system)
5412 (propagated-inputs `(("r-mass" ,r-mass)))
5413 (native-inputs `(("gfortran" ,gfortran)))
5414 (home-page "https://cran.r-project.org/web/packages/signal/")
5415 (synopsis "Signal processing")
5417 "This package provides a set of signal processing functions originally
5418 written for Matlab and GNU Octave. It includes filter generation utilities,
5419 filtering functions, resampling routines, and visualization of filter models.
5420 It also includes interpolation functions.")
5421 (license license:gpl2)))
5423 (define-public r-gsubfn
5430 (uri (cran-uri "gsubfn" version))
5433 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5434 (build-system r-build-system)
5435 (propagated-inputs `(("r-proto" ,r-proto)))
5436 (home-page "https://code.google.com/archive/p/gsubfn/")
5437 (synopsis "Utilities for strings and function arguments.")
5439 "This package provides @code{gsubfn} which is like @code{gsub} but can
5440 take a replacement function or certain other objects instead of the
5441 replacement string. Matches and back references are input to the replacement
5442 function and replaced by the function output. @code{gsubfn} can be used to
5443 split strings based on content rather than delimiters and for quasi-perl-style
5444 string interpolation. The package also has facilities for translating
5445 formulas to functions and allowing such formulas in function calls instead of
5447 (license license:gpl2+)))
5449 (define-public r-sqldf
5456 (uri (cran-uri "sqldf" version))
5459 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5460 (build-system r-build-system)
5462 `(("r-chron" ,r-chron)
5464 ("r-gsubfn" ,r-gsubfn)
5465 ("r-proto" ,r-proto)
5466 ("r-rsqlite" ,r-rsqlite)))
5467 (home-page "https://github.com/ggrothendieck/sqldf")
5468 (synopsis "Manipulate R data frames using SQL")
5470 "The @code{sqldf} function is typically passed a single argument which is
5471 an SQL select statement where the table names are ordinary R data frame names.
5472 @code{sqldf} transparently sets up a database, imports the data frames into
5473 that database, performs the SQL statement and returns the result using a
5474 heuristic to determine which class to assign to each column of the returned
5475 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5476 used to read filtered files into R even if the original files are larger than
5477 R itself can handle.")
5478 (license license:gpl2)))
5480 (define-public r-abind
5487 (uri (cran-uri "abind" version))
5490 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5491 (build-system r-build-system)
5492 (home-page "https://cran.r-project.org/web/packages/abind/")
5493 (synopsis "Combine multidimensional arrays")
5495 "This package provides tools to combine multidimensional arrays into a
5496 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5497 works with vectors, matrices, and higher-dimensional arrays. It also provides
5498 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5499 extracting and replacing data in arrays.")
5500 (license license:lgpl2.0+)))
5502 (define-public r-prroc
5509 (uri (cran-uri "PRROC" version))
5512 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5513 (properties `((upstream-name . "PRROC")))
5514 (build-system r-build-system)
5515 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5516 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5518 "This package computes the areas under the @dfn{precision-recall} (PR)
5519 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5520 contrast to other implementations, the interpolation between points of the PR
5521 curve is done by a non-linear piecewise function. In addition to the areas
5522 under the curves, the curves themselves can also be computed and plotted by a
5523 specific S3-method.")
5524 (license license:gpl3)))
5526 (define-public r-vim
5533 (uri (cran-uri "VIM" version))
5536 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5537 (properties `((upstream-name . "VIM")))
5538 (build-system r-build-system)
5541 ("r-colorspace" ,r-colorspace)
5542 ("r-data-table" ,r-data-table)
5543 ("r-e1071" ,r-e1071)
5544 ("r-laeken" ,r-laeken)
5545 ("r-magrittr" ,r-magrittr)
5548 ("r-ranger" ,r-ranger)
5550 ("r-robustbase" ,r-robustbase)
5554 `(("r-knitr" ,r-knitr)))
5555 (home-page "https://github.com/alexkowa/VIM")
5556 (synopsis "Visualization and imputation of missing values")
5558 "This package provides tools for the visualization of missing and/or
5559 imputed values are introduced, which can be used for exploring the data and
5560 the structure of the missing and/or imputed values. Depending on this
5561 structure of the missing values, the corresponding methods may help to
5562 identify the mechanism generating the missing values and allows to explore the
5563 data including missing values. In addition, the quality of imputation can be
5564 visually explored using various univariate, bivariate, multiple and
5565 multivariate plot methods.")
5566 (license license:gpl2+)))
5568 (define-public r-fnn
5575 (uri (cran-uri "FNN" version))
5578 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5579 (properties `((upstream-name . "FNN")))
5580 (build-system r-build-system)
5581 (home-page "https://cran.r-project.org/web/packages/FNN")
5582 (synopsis "Fast nearest neighbor search algorithms and applications")
5584 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5585 search algorithms. Related applications including KNN classification,
5586 regression and information measures are implemented.")
5587 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5588 ;; later can be used.
5589 (license license:gpl2+)))
5591 (define-public r-smoother
5598 (uri (cran-uri "smoother" version))
5601 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5602 (build-system r-build-system)
5604 `(("r-ttr" ,r-ttr)))
5605 (home-page "https://cran.r-project.org/web/packages/smoother")
5606 (synopsis "Functions relating to the smoothing of numerical data")
5608 "This package provides a collection of methods for smoothing numerical
5609 data, commencing with a port of the Matlab gaussian window smoothing function.
5610 In addition, several functions typically used in smoothing of financial data
5612 (license license:gpl2)))
5614 (define-public r-riverplot
5616 (name "r-riverplot")
5621 (uri (cran-uri "riverplot" version))
5624 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5625 (build-system r-build-system)
5626 (home-page "https://logfc.wordpress.com")
5627 (synopsis "Sankey or ribbon plots")
5629 "Sankey plots are a type of diagram that is convenient to illustrate how
5630 flow of information, resources etc. separates and joins, much like observing
5631 how rivers split and merge. For example, they can be used to compare
5632 different clusterings. This package provides an implementation of Sankey
5634 (license license:gpl2+)))
5636 (define-public r-dyn
5643 (uri (cran-uri "dyn" version))
5646 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5647 (build-system r-build-system)
5649 `(("r-zoo" ,r-zoo)))
5650 (home-page "https://cran.r-project.org/web/packages/dyn")
5651 (synopsis "Time series regression")
5653 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5654 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5655 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5656 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5657 @code{randomForest::randomForest()} and other regression functions, allowing
5658 those functions to be used with time series including specifications that may
5659 contain lags, diffs and missing values.")
5661 (license license:gpl2+)))
5663 (define-public r-catdap
5670 (uri (cran-uri "catdap" version))
5673 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5674 (build-system r-build-system)
5676 `(("gfortran" ,gfortran)))
5677 (home-page "https://cran.r-project.org/web/packages/catdap/")
5678 (synopsis "Tools for categorical data analysis")
5680 "This package provides functions for analyzing multivariate data.
5681 Dependencies of the distribution of the specified variable (response
5682 variable) to other variables (explanatory variables) are derived and
5683 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5684 (license license:gpl2+)))
5686 (define-public r-arules
5693 (uri (cran-uri "arules" version))
5696 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5697 (build-system r-build-system)
5699 `(("r-matrix" ,r-matrix)))
5700 (home-page "https://github.com/mhahsler/arules")
5701 (synopsis "Mining association rules and frequent itemsets")
5703 "This package provides an infrastructure for representing, manipulating
5704 and analyzing transaction data and patterns (frequent itemsets and association rules).
5705 It also provides C implementations of the association mining algorithms Apriori
5707 (license license:gpl3)))
5709 (define-public r-parsedate
5711 (name "r-parsedate")
5716 (uri (cran-uri "parsedate" version))
5719 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5720 (build-system r-build-system)
5722 `(("r-rematch2" ,r-rematch2)))
5723 (home-page "https://github.com/gaborcsardi/parsedate")
5725 "Recognize and parse dates in various formats")
5727 "This package provides three functions for dealing with dates:
5728 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5729 time formats, @code{parse_date} parses dates in unspecified formats,
5730 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5731 (license license:gpl2)))
5733 (define-public r-abc-data
5740 (uri (cran-uri "abc.data" version))
5743 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5744 (properties `((upstream-name . "abc.data")))
5745 (build-system r-build-system)
5746 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5747 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5749 "This package contains data which are used by functions of the abc
5750 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5751 algorithms for performing parameter estimation, model selection, and
5753 (license license:gpl3+)))
5755 (define-public r-abc
5762 (uri (cran-uri "abc" version))
5765 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5766 (build-system r-build-system)
5768 `(("r-abc-data" ,r-abc-data)
5769 ("r-locfit" ,r-locfit)
5772 ("r-quantreg" ,r-quantreg)))
5773 (home-page "https://cran.r-project.org/web/packages/abc/")
5774 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5776 "This package implements several @dfn{Approximate Bayesian
5777 Computation} (ABC) algorithms for performing parameter estimation, model
5778 selection, and goodness-of-fit. Cross-validation tools are also available for
5779 measuring the accuracy of ABC estimates, and to calculate the
5780 misclassification probabilities of different models.")
5781 (license license:gpl3+)))
5783 (define-public r-zip
5790 (uri (cran-uri "zip" version))
5793 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5794 (build-system r-build-system)
5795 (home-page "https://github.com/gaborcsardi/zip")
5796 (synopsis "Cross-platform Zip compression")
5798 "This package provides a cross-platform Zip compression library for R.
5799 It is a replacement for the @code{zip} function, that does not require any
5800 additional external tools on any platform.")
5801 (license license:cc0)))
5803 (define-public r-openxlsx
5810 (uri (cran-uri "openxlsx" version))
5813 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5814 (build-system r-build-system)
5816 `(("r-rcpp" ,r-rcpp)
5817 ("r-stringi" ,r-stringi)
5820 `(("r-knitr" ,r-knitr)))
5821 (home-page "https://github.com/awalker89/openxlsx")
5822 (synopsis "Read, write and edit XLSX files")
5824 "This package simplifies the creation of Excel @code{.xlsx} files by
5825 providing a high level interface to writing, styling and editing worksheets.
5826 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5827 and @code{XLConnect} packages with the added benefit of removing the
5828 dependency on Java.")
5829 (license license:gpl3)))
5831 (define-public r-rio
5838 (uri (cran-uri "rio" version))
5841 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5842 (build-system r-build-system)
5844 `(("r-curl" ,r-curl)
5845 ("r-data-table" ,r-data-table)
5846 ("r-foreign" ,r-foreign)
5847 ("r-haven" ,r-haven)
5848 ("r-openxlsx" ,r-openxlsx)
5849 ("r-readxl" ,r-readxl)
5850 ("r-tibble" ,r-tibble)))
5851 (home-page "https://github.com/leeper/rio")
5852 (synopsis "Swiss-army knife for data I/O")
5854 "This package provides streamlined data import and export infrastructure
5855 by making assumptions that the user is probably willing to make: @code{import}
5856 and @code{export} determine the data structure from the file extension,
5857 reasonable defaults are used for data import and export (e.g.,
5858 @code{stringsAsFactors=FALSE}), web-based import is natively
5859 supported (including from SSL/HTTPS), compressed files can be read directly
5860 without explicit decompression, and fast import packages are used where
5861 appropriate. An additional convenience function, @code{convert}, provides a
5862 simple method for converting between file types.")
5863 (license license:gpl2)))
5865 (define-public r-maptools
5872 (uri (cran-uri "maptools" version))
5875 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5876 (build-system r-build-system)
5878 `(("r-foreign" ,r-foreign)
5879 ("r-lattice" ,r-lattice)
5881 (home-page "https://r-forge.r-project.org/projects/maptools/")
5882 (synopsis "Tools for reading and handling spatial objects")
5884 "This package provides a set of tools for manipulating and reading
5885 geographic data, in particular ESRI Shapefiles. It includes binary access to
5886 GSHHG shoreline files. The package also provides interface wrappers for
5887 exchanging spatial objects with other R packages.")
5888 ;; The C source files from shapelib are released under the Expat license.
5889 ;; The R code is released under GPL version 2 or later.
5890 (license (list license:gpl2+
5893 (define-public r-later
5900 (uri (cran-uri "later" version))
5903 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5904 (build-system r-build-system)
5908 ("r-rlang" ,r-rlang)))
5910 `(("r-knitr" ,r-knitr)))
5911 (home-page "https://github.com/r-lib/later")
5912 (synopsis "Utilities for delaying function execution")
5914 "This package provides tools to execute arbitrary R or C functions some
5915 time after the current time, after the R execution stack has emptied.")
5916 (license license:gpl2+)))
5918 (define-public r-promises
5925 (uri (cran-uri "promises" version))
5928 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5929 (build-system r-build-system)
5931 `(("r-later" ,r-later)
5932 ("r-magrittr" ,r-magrittr)
5935 ("r-rlang" ,r-rlang)))
5937 `(("r-knitr" ,r-knitr)))
5938 (home-page "https://rstudio.github.io/promises")
5939 (synopsis "Abstractions for promise-based asynchronous programming")
5941 "This package provides fundamental abstractions for doing asynchronous
5942 programming in R using promises. Asynchronous programming is useful for
5943 allowing a single R process to orchestrate multiple tasks in the background
5944 while also attending to something else. Semantics are similar to JavaScript
5945 promises, but with a syntax that is idiomatic R.")
5946 (license license:expat)))
5948 (define-public r-dosnow
5955 (uri (cran-uri "doSNOW" version))
5958 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5959 (properties `((upstream-name . "doSNOW")))
5960 (build-system r-build-system)
5962 `(("r-foreach" ,r-foreach)
5963 ("r-iterators" ,r-iterators)
5964 ("r-snow" ,r-snow)))
5965 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5966 (synopsis "Foreach parallel adaptor for the snow package")
5968 "This package provides a parallel backend for the @code{%dopar%} function
5969 using the @code{snow} package.")
5970 (license license:gpl2)))
5972 (define-public r-snowfall
5975 (version "1.84-6.1")
5978 (uri (cran-uri "snowfall" version))
5980 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5981 (build-system r-build-system)
5983 `(("r-snow" ,r-snow)))
5984 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5985 (synopsis "Easier cluster computing")
5986 (description "This package is a usability wrapper around snow for easier
5987 development of parallel R programs. This package offers e.g. extended error
5988 checks, and additional functions. All functions work in sequential mode, too,
5989 if no cluster is present or wished. The package is also designed as connector
5990 to the cluster management tool @code{sfCluster}, but can also used without
5992 (license license:gpl2+)))
5994 (define-public r-rappdirs
6001 (uri (cran-uri "rappdirs" version))
6004 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6005 (build-system r-build-system)
6006 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6007 (synopsis "Determine where to save data, caches, and logs")
6009 "This package provides an easy way to determine which directories on the
6010 user's computer should be used to save data, caches and logs. It is a port of
6011 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6012 (license license:expat)))
6014 (define-public r-renv
6021 (uri (cran-uri "renv" version))
6024 "0yy24kq60dh9n68my132xhhkbnbs7q91z55b1yd6ymr7rxj32mif"))))
6025 (properties `((upstream-name . "renv")))
6026 (build-system r-build-system)
6028 `(("r-knitr" ,r-knitr)))
6029 (home-page "https://rstudio.github.io/renv")
6030 (synopsis "Project environments")
6032 "This package provides a dependency management toolkit for R. Using
6033 renv, you can create and manage project-local R libraries, save the state of
6034 these libraries to a lockfile, and later restore your library as required.
6035 Together, these tools can help make your projects more isolated, portable, and
6037 (license license:expat)))
6039 (define-public r-learnr
6046 (uri (cran-uri "learnr" version))
6049 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6050 (build-system r-build-system)
6052 `(("r-checkmate" ,r-checkmate)
6053 ("r-ellipsis" ,r-ellipsis)
6054 ("r-evaluate" ,r-evaluate)
6055 ("r-htmltools" ,r-htmltools)
6056 ("r-htmlwidgets" ,r-htmlwidgets)
6057 ("r-jsonlite" ,r-jsonlite)
6058 ("r-knitr" ,r-knitr)
6059 ("r-markdown" ,r-markdown)
6060 ("r-rappdirs" ,r-rappdirs)
6062 ("r-rmarkdown" ,r-rmarkdown)
6063 ("r-rprojroot" ,r-rprojroot)
6064 ("r-shiny" ,r-shiny)
6065 ("r-withr" ,r-withr)))
6066 (home-page "https://rstudio.github.io/learnr/")
6067 (synopsis "Interactive tutorials for R")
6069 "This package provides tools to create interactive tutorials using R
6070 Markdown. Use a combination of narrative, figures, videos, exercises, and
6071 quizzes to create self-paced tutorials for learning about R and R packages.")
6072 (license license:asl2.0)))
6074 (define-public r-analytics
6076 (name "r-analytics")
6081 (uri (cran-uri "analytics" version))
6084 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6085 (build-system r-build-system)
6088 ("r-cluster" ,r-cluster)
6089 ("r-fractal" ,r-fractal)
6090 ("r-lmtest" ,r-lmtest)
6093 ("r-powerplus" ,r-powerplus)
6094 ("r-robust" ,r-robust)
6095 ("r-trend" ,r-trend)
6099 (home-page "https://cran.r-project.org/web/packages/analytics/")
6100 (synopsis "Collection of data analysis tools")
6102 "This package is a collection of data analysis tools. It includes tools
6103 for regression outlier detection in a fitted linear model, stationary
6104 bootstrap using a truncated geometric distribution, a comprehensive test for
6105 weak stationarity, column means by group, weighted biplots, and a heuristic to
6106 obtain a better initial configuration in non-metric MDS.")
6107 (license license:gpl2)))
6109 (define-public r-reticulate
6111 (name "r-reticulate")
6116 (uri (cran-uri "reticulate" version))
6119 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6120 (build-system r-build-system)
6121 (inputs `(("python" ,python)))
6123 `(("r-rappdirs" ,r-rappdirs)
6124 ("r-jsonlite" ,r-jsonlite)
6125 ("r-matrix" ,r-matrix)
6126 ("r-rcpp" ,r-rcpp)))
6128 `(("r-knitr" ,r-knitr)))
6129 (home-page "https://github.com/rstudio/reticulate")
6130 (synopsis "R interface to Python")
6132 "This package provides an interface from R to Python modules, classes,
6133 and functions. When calling into Python, R data types are automatically
6134 converted to their equivalent Python types. When values are returned from
6135 Python to R they are converted back to R types.")
6136 (license license:asl2.0)))
6138 (define-public r-bibtex
6145 (uri (cran-uri "bibtex" version))
6148 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6149 (build-system r-build-system)
6150 (propagated-inputs `(("r-stringr" ,r-stringr)))
6151 (home-page "https://github.com/romainfrancois/bibtex")
6152 (synopsis "Bibtex parser")
6153 (description "This package provides a utility for R to parse a bibtex
6155 (license license:gpl2+)))
6157 (define-public r-ggseqlogo
6159 (name "r-ggseqlogo")
6164 (uri (cran-uri "ggseqlogo" version))
6167 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6168 (build-system r-build-system)
6169 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6170 (home-page "https://github.com/omarwagih/ggseqlogo")
6171 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6173 "The range of functions provided by this package makes it possible to
6174 draw highly versatile genomic sequence logos. Features include, but are not
6175 limited to, modifying colour schemes and fonts used to draw the logo,
6176 generating multiple logo plots, and aiding the visualisation with annotations.
6177 Sequence logos can easily be combined with other ggplot2 plots.")
6178 ;; Unspecified version of the LGPL.
6179 (license license:lgpl3+)))
6181 (define-public r-ggsci
6188 (uri (cran-uri "ggsci" version))
6191 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6192 (build-system r-build-system)
6194 `(("r-ggplot2" ,r-ggplot2)
6195 ("r-scales" ,r-scales)))
6196 (home-page "https://nanx.me/ggsci/")
6197 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6199 "This package provides a collection of ggplot2 color palettes inspired by
6200 plots in scientific journals, data visualization libraries, science fiction
6201 movies, and TV shows.")
6202 (license license:gpl3)))
6204 (define-public r-ggsignif
6211 (uri (cran-uri "ggsignif" version))
6214 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6215 (build-system r-build-system)
6217 `(("r-knitr" ,r-knitr)))
6219 `(("r-ggplot2" ,r-ggplot2)))
6220 (home-page "https://github.com/const-ae/ggsignif")
6221 (synopsis "Significance brackets for ggplot2")
6223 "Enrich your ggplots with group-wise comparisons. This package provides
6224 an easy way to indicate if two groups are significantly different. Commonly
6225 this is shown by a bracket on top connecting the groups of interest which
6226 itself is annotated with the level of significance. The package provides a
6227 single layer that takes the groups for comparison and the test as arguments
6228 and adds the annotation to the plot.")
6229 (license license:gpl3)))
6231 (define-public r-rstatix
6238 (uri (cran-uri "rstatix" version))
6241 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6242 (properties `((upstream-name . "rstatix")))
6243 (build-system r-build-system)
6245 `(("r-broom" ,r-broom)
6247 ("r-corrplot" ,r-corrplot)
6248 ("r-dplyr" ,r-dplyr)
6249 ("r-generics" ,r-generics)
6250 ("r-magrittr" ,r-magrittr)
6251 ("r-purrr" ,r-purrr)
6252 ("r-rlang" ,r-rlang)
6253 ("r-tibble" ,r-tibble)
6254 ("r-tidyr" ,r-tidyr)
6255 ("r-tidyselect" ,r-tidyselect)))
6256 (home-page "https://rpkgs.datanovia.com/rstatix/")
6257 (synopsis "Pipe-friendly framework for basic statistical tests")
6259 "This package provides a simple and intuitive pipe-friendly framework,
6260 coherent with the @code{tidyverse} design philosophy, for performing basic
6261 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6262 correlation analyses. The output of each test is automatically transformed
6263 into a tidy data frame to facilitate visualization. Additional functions are
6264 available for reshaping, reordering, manipulating and visualizing correlation
6266 (license license:gpl2)))
6268 (define-public r-ggpubr
6275 (uri (cran-uri "ggpubr" version))
6278 "1dly74cnn8iq7vsgmcz0czszdsmg5cgzm4w3s0v30k4psmmzqbxq"))))
6279 (build-system r-build-system)
6281 `(("r-cowplot" ,r-cowplot)
6282 ("r-dplyr" ,r-dplyr)
6283 ("r-ggplot2" ,r-ggplot2)
6284 ("r-ggrepel" ,r-ggrepel)
6285 ("r-ggsci" ,r-ggsci)
6286 ("r-ggsignif" ,r-ggsignif)
6288 ("r-gridextra" ,r-gridextra)
6289 ("r-magrittr" ,r-magrittr)
6290 ("r-polynom" ,r-polynom)
6291 ("r-purrr" ,r-purrr)
6292 ("r-rlang" ,r-rlang)
6293 ("r-scales" ,r-scales)
6294 ("r-rstatix" ,r-rstatix)
6295 ("r-tibble" ,r-tibble)
6296 ("r-tidyr" ,r-tidyr)))
6297 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6298 (synopsis "ggplot2-based publication-ready plots")
6300 "The ggplot2 package is an excellent and flexible package for elegant
6301 data visualization in R. However the default generated plots require some
6302 formatting before we can send them for publication. The ggpubr package
6303 provides some easy-to-use functions for creating and customizing ggplot2-based
6304 publication-ready plots.")
6305 (license license:gpl2)))
6307 (define-public r-ellipse
6314 (uri (cran-uri "ellipse" version))
6317 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6318 (build-system r-build-system)
6319 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6320 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6322 "This package contains various routines for drawing ellipses and
6323 ellipse-like confidence regions, implementing the plots described in Murdoch
6324 and Chow (1996), A graphical display of large correlation matrices, The
6325 American Statistician 50, 178-180. There are also routines implementing the
6326 profile plots described in Bates and Watts (1988), Nonlinear Regression
6327 Analysis and its Applications.")
6328 (license license:gpl2+)))
6330 (define-public r-flashclust
6332 (name "r-flashclust")
6337 (uri (cran-uri "flashClust" version))
6340 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6341 (properties `((upstream-name . "flashClust")))
6342 (build-system r-build-system)
6343 (native-inputs `(("gfortran" ,gfortran)))
6344 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6345 (synopsis "Implementation of optimal hierarchical clustering")
6347 "This package provides a fast implementation of hierarchical
6349 (license license:gpl2+)))
6351 (define-public r-factominer
6353 (name "r-factominer")
6358 (uri (cran-uri "FactoMineR" version))
6361 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6362 (properties `((upstream-name . "FactoMineR")))
6363 (build-system r-build-system)
6366 ("r-cluster" ,r-cluster)
6367 ("r-ellipse" ,r-ellipse)
6368 ("r-flashclust" ,r-flashclust)
6369 ("r-ggplot2" ,r-ggplot2)
6370 ("r-ggrepel" ,r-ggrepel)
6371 ("r-lattice" ,r-lattice)
6372 ("r-leaps" ,r-leaps)
6374 ("r-scatterplot3d" ,r-scatterplot3d)))
6375 (home-page "http://factominer.free.fr")
6376 (synopsis "Multivariate exploratory data analysis and data mining")
6378 "This package provides exploratory data analysis methods to summarize,
6379 visualize and describe datasets. The main principal component methods are
6380 available, those with the largest potential in terms of applications:
6381 principal component analysis (PCA) when variables are quantitative,
6382 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6383 variables are categorical, Multiple Factor Analysis when variables are
6384 structured in groups, etc. and hierarchical cluster analysis.")
6385 (license license:gpl2+)))
6387 (define-public r-factoextra
6389 (name "r-factoextra")
6394 (uri (cran-uri "factoextra" version))
6397 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6398 (build-system r-build-system)
6400 `(("r-abind" ,r-abind)
6401 ("r-cluster" ,r-cluster)
6402 ("r-dendextend" ,r-dendextend)
6403 ("r-factominer" ,r-factominer)
6404 ("r-ggplot2" ,r-ggplot2)
6405 ("r-ggpubr" ,r-ggpubr)
6406 ("r-ggrepel" ,r-ggrepel)
6407 ("r-reshape2" ,r-reshape2)
6408 ("r-tidyr" ,r-tidyr)))
6409 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6410 (synopsis "Extract and visualize the results of multivariate data analyses")
6412 "This package provides some easy-to-use functions to extract and
6413 visualize the output of multivariate data analyses, including
6414 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6415 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6416 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6417 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6418 packages. It contains also functions for simplifying some clustering analysis
6419 steps and provides ggplot2-based elegant data visualization.")
6420 (license license:gpl2)))
6422 (define-public r-fansi
6429 (uri (cran-uri "fansi" version))
6432 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6433 (build-system r-build-system)
6435 `(("r-knitr" ,r-knitr))) ; for vignettes
6436 (home-page "https://github.com/brodieG/fansi")
6437 (synopsis "ANSI control sequence aware string functions")
6439 "This package provides counterparts to R string manipulation functions
6440 that account for the effects of ANSI text formatting control sequences.")
6441 (license license:gpl2+)))
6443 (define-public r-nbclust
6450 (uri (cran-uri "NbClust" version))
6453 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6454 (properties `((upstream-name . "NbClust")))
6455 (build-system r-build-system)
6456 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6457 (synopsis "Determine the best number of clusters in a data set")
6459 "NbClust provides 30 indexes for determining the optimal number of
6460 clusters in a data set and offers the best clustering scheme from different
6461 results to the user.")
6462 (license license:gpl2)))
6464 (define-public r-hdf5r
6471 (uri (cran-uri "hdf5r" version))
6474 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6475 (build-system r-build-system)
6480 `(("r-bit64" ,r-bit64)
6483 `(("r-knitr" ,r-knitr)))
6484 (home-page "https://hhoeflin.github.io/hdf5r")
6485 (synopsis "Interface to the HDF5 binary data format")
6487 "HDF5 is a data model, library and file format for storing and managing
6488 large amounts of data. This package provides a nearly feature complete,
6489 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6490 functionality is added so that HDF5 objects behave very similar to their
6491 corresponding R counterparts.")
6492 (license license:asl2.0)))
6494 (define-public r-itertools
6496 (name "r-itertools")
6501 (uri (cran-uri "itertools" version))
6504 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6505 (build-system r-build-system)
6507 `(("r-iterators" ,r-iterators)))
6508 (home-page "https://cran.r-project.org/web/packages/itertools/")
6509 (synopsis "Iterator tools")
6511 "This package provides various tools for creating iterators, many
6512 patterned after functions in the Python @code{itertools} module, and others
6513 patterned after functions in the snow package.")
6514 (license license:gpl2)))
6516 (define-public r-polynom
6523 (uri (cran-uri "polynom" version))
6526 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6527 (build-system r-build-system)
6528 (home-page "https://cran.r-project.org/web/packages/polynom/")
6529 (synopsis "Functions for univariate polynomial manipulations")
6531 "This package provides a collection of functions to implement a class for
6532 univariate polynomial manipulations.")
6533 (license license:gpl2)))
6535 (define-public r-gbrd
6542 (uri (cran-uri "gbRd" version))
6545 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6546 (properties `((upstream-name . "gbRd")))
6547 (build-system r-build-system)
6548 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6549 (synopsis "Utilities for processing Rd objects and files")
6551 "This package provides utilities for processing Rd objects and files.
6552 Extract argument descriptions and other parts of the help pages of
6554 (license license:gpl2+)))
6556 (define-public r-rjags
6563 (uri (cran-uri "rjags" version))
6566 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6567 (build-system r-build-system)
6569 `(("r-coda" ,r-coda)))
6573 `(("pkg-config" ,pkg-config)))
6574 (home-page "http://mcmc-jags.sourceforge.net")
6575 (synopsis "Bayesian graphical models using MCMC")
6577 "This package provides an R interface to the JAGS MCMC library. JAGS is
6578 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6579 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6580 (license license:gpl2)))
6582 (define-public r-rdpack
6589 (uri (cran-uri "Rdpack" version))
6592 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6593 (properties `((upstream-name . "Rdpack")))
6594 (build-system r-build-system)
6596 `(("r-bibtex" ,r-bibtex)
6597 ("r-gbrd" ,r-gbrd)))
6598 (home-page "https://github.com/GeoBosh/Rdpack")
6599 (synopsis "Update and manipulate Rd documentation objects")
6601 "This package provides functions for manipulation of R documentation
6602 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6603 updating Rd documentation for functions, methods and classes; it also includes
6604 Rd macros for citations and import of references from bibtex files for use in
6605 Rd files and roxygen2 comments, as well as many functions for manipulation of
6606 references and Rd files.")
6607 (license license:gpl2+)))
6609 (define-public r-officer
6616 (uri (cran-uri "officer" version))
6619 "0nwasra2kb5wplcim7n57kynwhyg4vsk3fz42mbpm0hig1lzl9pp"))))
6620 (build-system r-build-system)
6622 `(("r-magrittr" ,r-magrittr)
6628 `(("r-knitr" ,r-knitr)))
6629 (home-page "https://davidgohel.github.io/officer")
6630 (synopsis "Manipulation of Word and PowerPoint documents")
6632 "This package provides tools to access and manipulate Word and PowerPoint
6633 documents from R. The package focuses on tabular and graphical reporting from
6634 R; it also provides two functions that let users get document content into
6635 data objects. A set of functions lets add and remove images, tables and
6636 paragraphs of text in new or existing documents. When working with PowerPoint
6637 presentations, slides can be added or removed; shapes inside slides can also
6638 be added or removed. When working with Word documents, a cursor can be used
6639 to help insert or delete content at a specific location in the document.")
6640 (license license:gpl3)))
6642 (define-public r-profilemodel
6644 (name "r-profilemodel")
6649 (uri (cran-uri "profileModel" version))
6652 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6653 (properties `((upstream-name . "profileModel")))
6654 (build-system r-build-system)
6655 (home-page "https://github.com/ikosmidis/profileModel")
6656 (synopsis "Profiling inference functions for various model classes")
6658 "This package provides tools that can be used to calculate, evaluate,
6659 plot and use for inference the profiles of *arbitrary* inference functions for
6660 arbitrary @code{glm}-like fitted models with linear predictors. More information
6661 on the methods that are implemented can be found in Kosmidis (2008)
6662 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6663 (license license:gpl2+)))
6665 (define-public r-brglm
6672 (uri (cran-uri "brglm" version))
6675 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6676 (properties `((upstream-name . "brglm")))
6677 (build-system r-build-system)
6679 `(("r-profilemodel" ,r-profilemodel)))
6680 (home-page "https://github.com/ikosmidis/brglm")
6681 (synopsis "Bias reduction in binomial-response generalized linear models")
6683 "Fit generalized linear models with binomial responses using either an
6684 adjusted-score approach to bias reduction or maximum penalized likelihood
6685 where penalization is by Jeffreys invariant prior. These procedures return
6686 estimates with improved frequentist properties (bias, mean squared error) that
6687 are always finite even in cases where the maximum likelihood estimates are
6688 infinite (data separation). Fitting takes place by fitting generalized linear
6689 models on iteratively updated pseudo-data. The interface is essentially the
6690 same as @code{glm}. More flexibility is provided by the fact that custom
6691 pseudo-data representations can be specified and used for model fitting.
6692 Functions are provided for the construction of confidence intervals for the
6693 reduced-bias estimates.")
6694 (license license:gpl2+)))
6696 (define-public r-entropy
6703 (uri (cran-uri "entropy" version))
6706 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6707 (properties `((upstream-name . "entropy")))
6708 (build-system r-build-system)
6709 (home-page "https://www.strimmerlab.org/software/entropy/")
6710 (synopsis "Estimation of entropy, mutual information and related quantities")
6712 "This package implements various estimators of entropy, such as the
6713 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6714 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6715 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6716 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6717 mutual information, and chi-squared statistic of independence. In addition
6718 there are functions for discretizing continuous random variables.")
6719 (license license:gpl3+)))
6721 (define-public r-abn
6728 (uri (cran-uri "abn" version))
6731 "11nbg6dwvbj0ac7qvr203vzjnw5zc1a8cibb9l6rzzr7yfg16xzc"))))
6732 (build-system r-build-system)
6736 `(("r-boot" ,r-boot)
6737 ("r-brglm" ,r-brglm)
6738 ("r-entropy" ,r-entropy)
6741 ("r-moments" ,r-moments)
6744 ("r-rcpparmadillo" ,r-rcpparmadillo)
6745 ("r-rjags" ,r-rjags)))
6746 (home-page "https://r-bayesian-networks.org/")
6747 (synopsis "Modelling multivariate data with additive bayesian networks")
6749 "Bayesian network analysis is a form of probabilistic graphical models
6750 which derives from empirical data a directed acyclic graph, DAG, describing
6751 the dependency structure between random variables. An additive Bayesian
6752 network model consists of a form of a DAG where each node comprises a
6753 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6754 equivalent to Bayesian multivariate regression using graphical modelling, they
6755 generalises the usual multivariable regression, GLM, to multiple dependent
6756 variables. This package provides routines to help determine optimal Bayesian
6757 network models for a given data set, where these models are used to identify
6758 statistical dependencies in messy, complex data.")
6759 (license license:gpl2+)))
6761 (define-public r-acd
6768 (uri (cran-uri "ACD" version))
6771 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6772 (properties `((upstream-name . "ACD")))
6773 (build-system r-build-system)
6774 (home-page "https://cran.r-project.org/web/packages/ACD/")
6775 (synopsis "Categorical data analysis with complete or missing responses")
6777 "This package provides tools for categorical data analysis with complete
6778 or missing responses.")
6779 (license license:gpl2+)))
6781 (define-public r-acdm
6788 (uri (cran-uri "ACDm" version))
6791 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6792 (properties `((upstream-name . "ACDm")))
6793 (build-system r-build-system)
6795 `(("r-dplyr" ,r-dplyr)
6796 ("r-ggplot2" ,r-ggplot2)
6798 ("r-rsolnp" ,r-rsolnp)
6800 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6801 (synopsis "Tools for Autoregressive Conditional Duration Models")
6803 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6804 and Russell, 1998) models. It creates trade, price or volume durations from
6805 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6807 (license license:gpl2+)))
6809 (define-public r-overlap
6816 (uri (cran-uri "overlap" version))
6819 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6820 (build-system r-build-system)
6821 (home-page "https://cran.r-project.org/web/packages/overlap/")
6822 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6824 "This package provides functions to fit kernel density functions to data
6825 on temporal activity patterns of animals; estimate coefficients of overlapping
6826 of densities for two species; and calculate bootstrap estimates of confidence
6828 (license license:gpl3+)))
6830 (define-public r-snakecase
6832 (name "r-snakecase")
6837 (uri (cran-uri "snakecase" version))
6840 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6841 (build-system r-build-system)
6843 `(("r-stringi" ,r-stringi)
6844 ("r-stringr" ,r-stringr)))
6845 (home-page "https://github.com/Tazinho/snakecase")
6846 (synopsis "Convert strings into any case")
6848 "This package provides a consistent, flexible and easy to use tool to
6849 parse and convert strings into cases like snake or camel among others.")
6850 (license license:gpl3)))
6852 (define-public r-prediction
6854 (name "r-prediction")
6859 (uri (cran-uri "prediction" version))
6862 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6863 (build-system r-build-system)
6865 `(("r-data-table" ,r-data-table)))
6866 (home-page "https://github.com/leeper/prediction")
6867 (synopsis "Tidy, type-safe prediction methods")
6869 "This package provides the @code{prediction()} function, a type-safe
6870 alternative to @code{predict()} that always returns a data frame. The package
6871 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6872 from the @code{stats} package, as well as numerous other model classes from
6873 other add-on packages.")
6874 (license license:expat)))
6876 (define-public r-insight
6883 (uri (cran-uri "insight" version))
6886 "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k"))))
6887 (build-system r-build-system)
6889 `(("r-knitr" ,r-knitr)))
6890 (home-page "https://easystats.github.io/insight/")
6891 (synopsis "Easy access to model information for various model objects")
6893 "This package provides a tool to provide an easy, intuitive and
6894 consistent access to information contained in various R models, like model
6895 formulas, model terms, information about random effects, data that was used to
6896 fit the model or data from response variables. The package mainly revolves
6897 around two types of functions: Functions that find (the names of) information,
6898 starting with @code{find_}, and functions that get the underlying data,
6899 starting with @code{get_}. The package has a consistent syntax and works with
6900 many different model objects, where otherwise functions to access these
6901 information are missing.")
6902 (license license:gpl3)))
6904 (define-public r-sjlabelled
6906 (name "r-sjlabelled")
6911 (uri (cran-uri "sjlabelled" version))
6914 "0grskmd7wrw31lkf85z6xz0bv246m6grvqkijvqi4q8zkl6p5vb3"))))
6915 (build-system r-build-system)
6917 `(("r-insight" ,r-insight)))
6919 `(("r-knitr" ,r-knitr)))
6920 (home-page "https://github.com/strengejacke/sjlabelled")
6921 (synopsis "Labelled data utility functions")
6923 "This package provides a collection of functions dealing with labelled
6924 data, like reading and writing data between R and other statistical software
6925 packages. This includes easy ways to get, set or change value and variable
6926 label attributes, to convert labelled vectors into factors or numeric (and
6927 vice versa), or to deal with multiple declared missing values.")
6928 (license license:gpl3)))
6930 (define-public r-sjmisc
6937 (uri (cran-uri "sjmisc" version))
6940 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6941 (build-system r-build-system)
6943 `(("r-dplyr" ,r-dplyr)
6944 ("r-insight" ,r-insight)
6945 ("r-magrittr" ,r-magrittr)
6946 ("r-purrr" ,r-purrr)
6947 ("r-rlang" ,r-rlang)
6948 ("r-sjlabelled" ,r-sjlabelled)
6949 ("r-tidyselect" ,r-tidyselect)))
6951 `(("r-knitr" ,r-knitr)))
6952 (home-page "https://github.com/strengejacke/sjmisc")
6953 (synopsis "Data and variable transformation functions")
6955 "This package is a collection of miscellaneous utility functions,
6956 supporting data transformation tasks like recoding, dichotomizing or grouping
6957 variables, setting and replacing missing values. The data transformation
6958 functions also support labelled data, and all integrate seamlessly into a
6959 tidyverse workflow.")
6960 (license license:gpl3)))
6962 (define-public r-nortest
6969 (uri (cran-uri "nortest" version))
6972 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6973 (build-system r-build-system)
6974 (home-page "https://cran.r-project.org/web/packages/nortest/")
6975 (synopsis "Tests for normality")
6977 "This package provides five omnibus tests for testing the composite
6978 hypothesis of normality.")
6979 (license license:gpl2+)))
6981 (define-public r-moonbook
6988 (uri (cran-uri "moonBook" version))
6991 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6992 (properties `((upstream-name . "moonBook")))
6993 (build-system r-build-system)
6995 `(("r-magrittr" ,r-magrittr)
6996 ("r-nortest" ,r-nortest)
6997 ("r-purrr" ,r-purrr)
6998 ("r-sjmisc" ,r-sjmisc)
6999 ("r-stringr" ,r-stringr)
7000 ("r-survival" ,r-survival)))
7001 (home-page "https://github.com/cardiomoon/moonBook")
7002 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7004 "This package provides several analysis-related functions for the book
7005 entitled \"R statistics and graph for medical articles\" (written in Korean),
7006 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7008 (license license:gpl2)))
7010 (define-public r-flextable
7012 (name "r-flextable")
7017 (uri (cran-uri "flextable" version))
7020 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7021 (build-system r-build-system)
7023 `(("r-base64enc" ,r-base64enc)
7024 ("r-data-table" ,r-data-table)
7025 ("r-gdtools" ,r-gdtools)
7026 ("r-htmltools" ,r-htmltools)
7027 ("r-knitr" ,r-knitr)
7028 ("r-officer" ,r-officer)
7029 ("r-rlang" ,r-rlang)
7030 ("r-rmarkdown" ,r-rmarkdown)
7032 ("r-xml2" ,r-xml2)))
7033 (home-page "https://davidgohel.github.io/flextable")
7034 (synopsis "Functions for tabular reporting")
7036 "This package provides tools to create pretty tables for HTML documents
7037 and other formats. Functions are provided to let users create tables, modify
7038 and format their content. It extends the @code{officer} package and can be
7039 used within R markdown documents when rendering to HTML and to Word
7041 (license license:gpl3)))
7043 (define-public r-writexl
7050 (uri (cran-uri "writexl" version))
7053 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7054 (build-system r-build-system)
7055 (inputs `(("zlib" ,zlib)))
7056 (home-page "https://github.com/ropensci/writexl")
7057 (synopsis "Export data frames to xlsx format")
7059 "This package provides a data frame to xlsx exporter based on
7061 (license license:bsd-2)))
7063 (define-public r-biasedurn
7065 (name "r-biasedurn")
7070 (uri (cran-uri "BiasedUrn" version))
7073 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7074 (properties `((upstream-name . "BiasedUrn")))
7075 (build-system r-build-system)
7076 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7077 (synopsis "Biased Urn model distributions")
7079 "This package provides statistical models of biased sampling in the form
7080 of univariate and multivariate noncentral hypergeometric distributions,
7081 including Wallenius' noncentral hypergeometric distribution and Fisher's
7082 noncentral hypergeometric distribution (also called extended hypergeometric
7084 (license license:gpl3)))
7086 (define-public r-goplot
7093 (uri (cran-uri "GOplot" version))
7096 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7097 (properties `((upstream-name . "GOplot")))
7098 (build-system r-build-system)
7100 `(("r-ggdendro" ,r-ggdendro)
7101 ("r-ggplot2" ,r-ggplot2)
7102 ("r-gridextra" ,r-gridextra)
7103 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7104 (home-page "https://github.com/wencke/wencke.github.io")
7105 (synopsis "Visualization of functional analysis data")
7107 "This package provides an implementation of multilayered visualizations
7108 for enhanced graphical representation of functional analysis data. It
7109 combines and integrates omics data derived from expression and functional
7110 annotation enrichment analyses. Its plotting functions have been developed
7111 with an hierarchical structure in mind: starting from a general overview to
7112 identify the most enriched categories (modified bar plot, bubble plot) to a
7113 more detailed one displaying different types of relevant information for the
7114 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7115 Venn diagram, heatmap).")
7116 (license license:gpl2)))
7118 (define-public r-getopt
7125 (uri (cran-uri "getopt" version))
7128 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7129 (build-system r-build-system)
7130 (home-page "https://github.com/trevorld/getopt")
7131 (synopsis "Command-line option processor for R")
7133 "This package is designed to be used with Rscript to write shebang
7134 scripts that accept short and long options. Many users will prefer to
7135 use the packages @code{optparse} or @code{argparse} which add extra
7136 features like automatically generated help options and usage texts,
7137 support for default values, positional argument support, etc.")
7138 (license license:gpl2+)))
7140 (define-public r-findpython
7142 (name "r-findpython")
7147 (uri (cran-uri "findpython" version))
7150 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7151 (build-system r-build-system)
7152 (home-page "https://github.com/trevorld/findpython")
7153 (synopsis "Functions to find an acceptable Python binary")
7155 "This package was designed to find an acceptable Python binary that
7156 matches version and feature constraints.")
7157 (license license:expat)))
7159 ;; This in not the same as "r-argparser"
7160 (define-public r-argparse
7167 (uri (cran-uri "argparse" version))
7170 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7171 (build-system r-build-system)
7172 (inputs `(("python" ,python)))
7174 `(("r-findpython" ,r-findpython)
7175 ("r-jsonlite" ,r-jsonlite)
7177 (home-page "https://github.com/trevorld/argparse")
7178 (synopsis "Command line optional and positional argument parser")
7180 "This package provides a command line parser to be used with Rscript to
7181 write shebang scripts that gracefully accept positional and optional arguments
7182 and automatically generate usage notices.")
7183 (license license:gpl2+)))
7185 (define-public r-hash
7192 (uri (cran-uri "hash" version))
7195 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7196 (build-system r-build-system)
7197 (home-page "https://cran.r-project.org/web/packages/hash/")
7198 (synopsis "Implementation of hash/associated arrays/dictionaries")
7200 "This package implements a data structure similar to hashes in Perl and
7201 dictionaries in Python but with a purposefully R flavor. For objects of
7202 appreciable size, access using hashes outperforms native named lists and
7204 (license license:gpl2+)))
7206 (define-public r-orddom
7213 (uri (cran-uri "orddom" version))
7216 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7217 (build-system r-build-system)
7218 (propagated-inputs `(("r-psych" ,r-psych)))
7219 (home-page "https://cran.r-project.org/web/packages/orddom/")
7220 (synopsis "Ordinal dominance statistics")
7222 "This package provides tools to compute ordinal, statistics and effect
7223 sizes as an alternative to mean comparison: Cliff's delta or success rate
7224 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7225 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7226 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7227 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7228 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7229 Group (Non-)Overlap considerations.")
7230 (license license:gpl2)))
7232 (define-public r-deriv
7239 (uri (cran-uri "Deriv" version))
7242 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7243 (properties `((upstream-name . "Deriv")))
7244 (build-system r-build-system)
7245 (home-page "https://cran.r-project.org/web/packages/Deriv")
7246 (synopsis "Symbolic differentiation")
7248 "This package provides an R-based solution for symbolic differentiation.
7249 It admits user-defined functions as well as function substitution in arguments
7250 of functions to be differentiated. Some symbolic simplification is part of
7252 (license license:gpl3+)))
7254 (define-public r-doby
7261 (uri (cran-uri "doBy" version))
7264 "0wz1vmsf1545r1m42q88s675ncwvm8figjn7kzbngjn9aqck9qbq"))))
7265 (properties `((upstream-name . "doBy")))
7266 (build-system r-build-system)
7268 `(("r-broom" ,r-broom)
7269 ("r-deriv" ,r-deriv)
7270 ("r-magrittr" ,r-magrittr)
7272 ("r-matrix" ,r-matrix)
7273 ("r-pbkrtest" ,r-pbkrtest)
7274 ("r-tibble" ,r-tibble)))
7276 `(("r-knitr" ,r-knitr)))
7277 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7278 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7280 "This package contains:
7283 @item facilities for working with grouped data: @code{do}
7284 something to data stratified @code{by} some variables.
7285 @item implementations of least-squares means, general linear contrasts, and
7286 @item miscellaneous other utilities.
7288 (license license:gpl2+)))
7290 (define-public r-refgenome
7292 (name "r-refgenome")
7297 (uri (cran-uri "refGenome" version))
7300 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7301 (properties `((upstream-name . "refGenome")))
7302 (build-system r-build-system)
7306 ("r-rsqlite" ,r-rsqlite)))
7307 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7309 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7311 "This package contains functionality for importing and managing of
7312 downloaded genome annotation data from the Ensembl genome browser (European
7313 Bioinformatics Institute) and from the UCSC genome browser (University of
7314 California, Santa Cruz) and annotation routines for genomic positions and
7315 splice site positions.")
7316 (license license:gpl2)))
7318 (define-public r-basix
7325 (uri (cran-uri "BASIX" version))
7328 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7329 (properties `((upstream-name . "BASIX")))
7330 (build-system r-build-system)
7331 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7332 (synopsis "Efficient C/C++ toolset for R")
7334 "BASIX provides some efficient C/C++ implementations of native R
7335 procedures to speed up calculations in R.")
7336 (license license:gpl2)))
7338 (define-public r-blockfest
7340 (name "r-blockfest")
7345 (uri (cran-uri "BlockFeST" version))
7348 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7349 (properties `((upstream-name . "BlockFeST")))
7350 (build-system r-build-system)
7351 (propagated-inputs `(("r-basix" ,r-basix)))
7352 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7353 (synopsis "Bayesian calculation of region-specific fixation index")
7355 "This package provides an R implementation of an extension of the
7356 BayeScan software for codominant markers, adding the option to group
7357 individual SNPs into pre-defined blocks. A typical application of this new
7358 approach is the identification of genomic regions, genes, or gene sets
7359 containing one or more SNPs that evolved under directional selection.")
7360 (license license:gpl2)))
7362 (define-public r-proc
7369 (uri (cran-uri "pROC" version))
7372 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7373 (properties `((upstream-name . "pROC")))
7374 (build-system r-build-system)
7376 `(("r-plyr" ,r-plyr)
7377 ("r-rcpp" ,r-rcpp)))
7378 (home-page "https://web.expasy.org/pROC/")
7379 (synopsis "Display and analyze ROC curves")
7381 "This package provides tools for visualizing, smoothing and comparing
7382 receiver operating characteristic (ROC curves). The area under the
7383 curve (AUC) can be compared with statistical tests based on U-statistics or
7384 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7385 (license license:gpl3+)))
7387 (define-public r-rootsolve
7389 (name "r-rootsolve")
7394 (uri (cran-uri "rootSolve" version))
7397 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7398 (properties `((upstream-name . "rootSolve")))
7399 (build-system r-build-system)
7400 (native-inputs `(("gfortran" ,gfortran)))
7401 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7402 (synopsis "Tools for the analysis of ordinary differential equations")
7404 "This package provides routines to find the root of nonlinear functions,
7405 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7406 differential equations} (ODE). It includes routines that:
7409 @item generate gradient and jacobian matrices (full and banded),
7410 @item find roots of non-linear equations by the Newton-Raphson method,
7411 @item estimate steady-state conditions of a system of (differential) equations
7412 in full, banded or sparse form, using the Newton-Raphson method, or by
7413 dynamically running,
7414 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7415 and 3-D partial differential equations, that have been converted to ordinary
7416 differential equations by numerical differencing (using the method-of-lines
7419 (license license:gpl2+)))
7421 (define-public r-abcanalysis
7423 (name "r-abcanalysis")
7428 (uri (cran-uri "ABCanalysis" version))
7430 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7431 (properties `((upstream-name . "ABCanalysis")))
7432 (build-system r-build-system)
7433 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7434 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7435 (synopsis "Computed ABC Analysis")
7437 "Multivariate data sets often differ in several factors or derived statistical
7438 parameters, which have to be selected for a valid interpretation. Basing this
7439 selection on traditional statistical limits leads occasionally to the perception
7440 of losing information from a data set. This package provides tools to calculate
7441 these limits on the basis of the mathematical properties of the distribution of
7442 the analyzed items.")
7443 (license license:gpl3)))
7445 (define-public r-slam
7452 (uri (cran-uri "slam" version))
7454 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7455 (build-system r-build-system)
7456 (home-page "https://cran.r-project.org/web/packages/slam/")
7457 (synopsis "Sparse lightweight arrays and matrices")
7459 "This package contains data structures and algorithms for sparse arrays and matrices,
7460 based on index arrays and simple triplet representations, respectively.")
7461 (license license:gpl2)))
7463 (define-public r-manipulatewidget
7465 (name "r-manipulatewidget")
7470 (uri (cran-uri "manipulateWidget" version))
7472 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7474 `((upstream-name . "manipulateWidget")))
7475 (build-system r-build-system)
7477 `(("r-base64enc" ,r-base64enc)
7478 ("r-codetools" ,r-codetools)
7479 ("r-htmltools" ,r-htmltools)
7480 ("r-htmlwidgets" ,r-htmlwidgets)
7481 ("r-knitr" ,r-knitr)
7482 ("r-miniui" ,r-miniui)
7483 ("r-shiny" ,r-shiny)
7484 ("r-webshot" ,r-webshot)))
7485 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7486 (synopsis "Add even more interactivity to interactive charts")
7488 "This package lets you create in just a few lines of R code a nice user interface to
7489 modify the data or the graphical parameters of one or multiple interactive
7490 charts. It is useful to quickly explore visually some data or for package
7491 developers to generate user interfaces easy to maintain.")
7492 (license license:gpl2+)))
7501 (uri (cran-uri "A3" version))
7503 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7504 (properties `((upstream-name . "A3")))
7505 (build-system r-build-system)
7507 `(("r-pbapply" ,r-pbapply)
7508 ("r-xtable" ,r-xtable)))
7509 (home-page "https://cran.r-project.org/web/packages/A3/")
7510 (synopsis "Error metrics for predictive models")
7512 "This package supplies tools for tabulating and analyzing the results of predictive
7513 models. The methods employed are applicable to virtually any predictive model
7514 and make comparisons between different methodologies straightforward.")
7515 (license license:gpl2+)))
7517 (define-public r-infotheo
7524 (uri (cran-uri "infotheo" version))
7527 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7528 (build-system r-build-system)
7529 (home-page "http://homepage.meyerp.com/software")
7530 (synopsis "Information-theoretic measures")
7532 "This package implements various measures of information theory based on
7533 several entropy estimators.")
7534 (license license:gpl3+)))
7536 (define-public r-abcoptim
7543 (uri (cran-uri "ABCoptim" version))
7545 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7546 (properties `((upstream-name . "ABCoptim")))
7547 (build-system r-build-system)
7548 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7549 (home-page "https://github.com/gvegayon/ABCoptim/")
7550 (synopsis "Optimization of Artificial Bee Colony algorithm")
7552 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7553 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7554 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7555 algorithms, and uses only common control parameters such as colony size and
7556 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7557 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7558 This version is a work-in-progress and is written in R code.")
7559 (license license:expat)))
7561 (define-public r-abcp2
7568 (uri (cran-uri "ABCp2" version))
7570 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7571 (properties `((upstream-name . "ABCp2")))
7572 (build-system r-build-system)
7573 (propagated-inputs `(("r-mass" ,r-mass)))
7574 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7575 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7577 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7578 Poisson, and Gamma distribution and estimates the proportional paternity of the
7579 second male (P2) based on the best fit distribution.")
7580 (license license:gpl2)))
7582 (define-public r-abcrf
7589 (uri (cran-uri "abcrf" version))
7591 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7592 (build-system r-build-system)
7594 `(("r-doparallel" ,r-doparallel)
7595 ("r-foreach" ,r-foreach)
7597 ("r-matrixstats" ,r-matrixstats)
7598 ("r-ranger" ,r-ranger)
7600 ("r-rcpparmadillo" ,r-rcpparmadillo)
7601 ("r-readr" ,r-readr)
7602 ("r-stringr" ,r-stringr)))
7603 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7604 (synopsis "Approximate bayesian computation via random forests")
7606 "This package performs approximate bayesian computation (ABC) model choice and
7607 parameter inference via random forests. This machine learning tool named random
7608 forests (RF) can conduct selection among the highly complex models covered by
7610 (license license:gpl2+)))
7612 (define-public r-abctools
7619 (uri (cran-uri "abctools" version))
7621 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7622 (build-system r-build-system)
7625 ("r-abind" ,r-abind)
7626 ("r-hmisc" ,r-hmisc)
7627 ("r-plyr" ,r-plyr)))
7628 (home-page "https://github.com/dennisprangle/abctools/")
7629 (synopsis "Tools for ABC analyses")
7631 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7632 including summary statistic selection and assessing coverage. This includes
7633 recent dimension reduction algorithms to tune the choice of summary statistics,
7634 and coverage methods to tune the choice of threshold.")
7635 (license license:gpl2+)))
7637 (define-public r-ggstance
7644 (uri (cran-uri "ggstance" version))
7646 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7647 (build-system r-build-system)
7649 `(("r-ggplot2" ,r-ggplot2)
7651 ("r-rlang" ,r-rlang)
7652 ("r-withr" ,r-withr)))
7653 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7654 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7656 "This package is a @code{r-ggplot2} extension that provides flipped components:
7658 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7659 @item vertical versions of @code{r-ggplot2} positions.
7661 (license license:gpl3)))
7663 (define-public r-mosaiccore
7665 (name "r-mosaiccore")
7670 (uri (cran-uri "mosaicCore" version))
7672 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7673 (properties `((upstream-name . "mosaicCore")))
7674 (build-system r-build-system)
7676 `(("r-dplyr" ,r-dplyr)
7677 ("r-lazyeval" ,r-lazyeval)
7679 ("r-rlang" ,r-rlang)
7680 ("r-tidyr" ,r-tidyr)))
7681 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7682 (synopsis "Common utilities for mosaic family packages")
7684 "Common utilities used in other Mosaic family packages are collected here.")
7685 (license license:gpl2+)))
7687 (define-public r-ggformula
7689 (name "r-ggformula")
7694 (uri (cran-uri "ggformula" version))
7696 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7697 (build-system r-build-system)
7699 `(("r-ggforce" ,r-ggforce)
7700 ("r-ggplot2" ,r-ggplot2)
7701 ("r-ggstance" ,r-ggstance)
7702 ("r-magrittr" ,r-magrittr)
7703 ("r-mosaiccore" ,r-mosaiccore)
7704 ("r-rlang" ,r-rlang)
7705 ("r-stringr" ,r-stringr)
7706 ("r-tibble" ,r-tibble)))
7707 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7708 (synopsis "Formula interface for the @code{r-ggplot2}")
7710 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7711 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7712 and extends the excellent simplicity of the lattice-graphics formula interface,
7713 while providing the intuitive capabilities of @code{r-ggplot2}.")
7714 (license license:expat)))
7716 (define-public r-mosaicdata
7718 (name "r-mosaicdata")
7723 (uri (cran-uri "mosaicData" version))
7725 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7726 (properties `((upstream-name . "mosaicData")))
7727 (build-system r-build-system)
7728 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7729 (synopsis "Data sets for project Mosaic")
7731 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7732 used to teach mathematics, statistics, computation and modeling.")
7733 (license license:gpl2+)))
7735 (define-public r-raster
7742 (uri (cran-uri "raster" version))
7745 "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
7746 (build-system r-build-system)
7748 `(("r-rcpp" ,r-rcpp)
7750 (home-page "https://www.rspatial.org/")
7751 (synopsis "Geographic data analysis and modeling")
7753 "The package implements basic and high-level functions for reading,
7754 writing, manipulating, analyzing and modeling of gridded spatial data.
7755 Processing of very large files is supported.")
7756 (license license:gpl3+)))
7758 (define-public r-mosaic
7765 (uri (cran-uri "mosaic" version))
7767 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7768 (build-system r-build-system)
7770 `(("r-broom" ,r-broom)
7771 ("r-dplyr" ,r-dplyr)
7772 ("r-ggdendro" ,r-ggdendro)
7773 ("r-ggformula" ,r-ggformula)
7774 ("r-ggplot2" ,r-ggplot2)
7775 ("r-ggrepel" ,r-ggrepel)
7777 ("r-gridextra" ,r-gridextra)
7778 ("r-lattice" ,r-lattice)
7779 ("r-latticeextra" ,r-latticeextra)
7780 ("r-lazyeval" ,r-lazyeval)
7782 ("r-matrix" ,r-matrix)
7783 ("r-mosaiccore" ,r-mosaiccore)
7784 ("r-mosaicdata" ,r-mosaicdata)
7785 ("r-readr" ,r-readr)
7786 ("r-tidyr" ,r-tidyr)))
7788 `(("r-knitr" ,r-knitr)))
7789 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7790 (synopsis "Mathematics, statistics, and computation teaching utilities")
7792 "This package contain data sets and utilities from
7793 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7794 statistics, computation and modeling. Project MOSAIC is a community of
7795 educators working to tie together aspects of quantitative work that students
7796 in science, technology, engineering and mathematics will need in their
7797 professional lives, but which are usually taught in isolation, if at all.")
7798 (license license:gpl2+)))
7800 (define-public r-abd
7807 (uri (cran-uri "abd" version))
7809 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7810 (build-system r-build-system)
7812 `(("r-lattice" ,r-lattice)
7813 ("r-mosaic" ,r-mosaic)
7814 ("r-nlme" ,r-nlme)))
7815 (home-page "https://cran.r-project.org/web/packages/abd/")
7816 (synopsis "Analysis of biological data")
7818 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7819 biological data by Michael Whitlock and Dolph Schluter.")
7820 (license license:gpl2)))
7822 (define-public r-svgui
7829 (uri (cran-uri "svGUI" version))
7831 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7832 (properties `((upstream-name . "svGUI")))
7833 (build-system r-build-system)
7834 (home-page "https://github.com/SciViews/svGUI/")
7835 (synopsis "Functions for managing GUI clients in R")
7837 "The SciViews @code{svGUI} package eases the management of Graphical User
7838 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7839 centralizes info about GUI elements currently used, and it dispatches GUI
7840 calls to the particular toolkits in use in function of the context.")
7841 (license license:gpl2)))
7843 (define-public r-svdialogs
7845 (name "r-svdialogs")
7850 (uri (cran-uri "svDialogs" version))
7852 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7853 (properties `((upstream-name . "svDialogs")))
7854 (build-system r-build-system)
7857 ("zenity" ,zenity)))
7859 `(("r-rstudioapi" ,r-rstudioapi)
7860 ("r-svgui" ,r-svgui)))
7861 (home-page "https://github.com/SciViews/svDialogs/")
7862 (synopsis "Portable dialog boxes")
7864 "This package helps to construct standard dialog boxes for your GUI, including
7865 message boxes, input boxes, list, file or directory selection, and others. In
7866 case R cannot display GUI dialog boxes, a simpler command line version of these
7867 interactive elements is also provided as a fallback solution.")
7868 (license license:gpl2)))
7870 (define-public r-abe
7877 (uri (cran-uri "abe" version))
7880 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7881 (build-system r-build-system)
7882 (home-page "https://cran.r-project.org/web/packages/abe/")
7883 (synopsis "Augmented backward elimination")
7885 "This package performs augmented backward elimination and checks the
7886 stability of the obtained model. Augmented backward elimination combines
7887 significance or information based criteria with the change in estimate to
7888 either select the optimal model for prediction purposes or to serve as a tool
7889 to obtain a practically sound, highly interpretable model.")
7890 (license license:gpl2+)))
7892 (define-public r-abf2
7899 (uri (cran-uri "abf2" version))
7901 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7902 (build-system r-build-system)
7903 (home-page "https://cran.r-project.org/web/packages/abf2/")
7904 (synopsis "Load gap-free axon @code{r-abf2} files")
7906 "This package loads electrophysiology data from ABF2 files, as created by
7907 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7908 mode are currently supported.")
7909 (license license:artistic2.0)))
7911 (define-public r-abhgenotyper
7913 (name "r-abhgenotyper")
7918 (uri (cran-uri "ABHgenotypeR" version))
7920 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7921 (properties `((upstream-name . "ABHgenotypeR")))
7922 (build-system r-build-system)
7924 `(("r-ggplot2" ,r-ggplot2)
7925 ("r-reshape2" ,r-reshape2)))
7926 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7927 (synopsis "Visualize and manipulate ABH genotypes")
7929 "The @code{r-abhgenotyper} package provides simple imputation,
7930 error-correction and plotting capacities for genotype data. The package is
7931 supposed to serve as an intermediate but independent analysis tool between the
7932 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7933 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7934 genotypes as \"graphical genotypes\".")
7935 (license license:gpl3)))
7937 (define-public r-furrr
7944 (uri (cran-uri "furrr" version))
7947 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7948 (build-system r-build-system)
7950 `(("r-future" ,r-future)
7951 ("r-globals" ,r-globals)
7952 ("r-purrr" ,r-purrr)
7953 ("r-rlang" ,r-rlang)))
7954 (home-page "https://github.com/DavisVaughan/furrr")
7955 (synopsis "Apply mapping functions in parallel using futures")
7957 "This package provides implementations of the family of @code{map()}
7958 functions from the @code{purrr} package that can be resolved using any
7959 @code{future}-supported backend, e.g. parallel on the local machine or
7960 distributed on a compute cluster.")
7961 (license license:lgpl2.1+)))
7963 (define-public r-abjutils
7970 (uri (cran-uri "abjutils" version))
7972 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7973 (build-system r-build-system)
7975 `(("r-devtools" ,r-devtools)
7976 ("r-dplyr" ,r-dplyr)
7977 ("r-furrr" ,r-furrr)
7978 ("r-future" ,r-future)
7981 ("r-magrittr" ,r-magrittr)
7982 ("r-progress" ,r-progress)
7983 ("r-purrr" ,r-purrr)
7984 ("r-readr" ,r-readr)
7985 ("r-rlang" ,r-rlang)
7986 ("r-rstudioapi" ,r-rstudioapi)
7987 ("r-scales" ,r-scales)
7988 ("r-stringi" ,r-stringi)
7989 ("r-stringr" ,r-stringr)
7990 ("r-tibble" ,r-tibble)
7991 ("r-tidyr" ,r-tidyr)))
7992 (home-page "https://github.com/abjur/abjutils/")
7993 (synopsis "Collection of tools for jurimetrical analysis")
7995 "This package implements general purpose tools, such as functions for
7996 sampling and basic manipulation of Brazilian lawsuits identification number.
7997 It also implements functions for text cleaning, such as accentuation
7999 (license license:expat)))
8001 (define-public r-abnormality
8003 (name "r-abnormality")
8008 (uri (cran-uri "abnormality" version))
8010 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8011 (build-system r-build-system)
8013 `(("r-mass" ,r-mass)
8014 ("r-matrix" ,r-matrix)))
8015 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8016 (synopsis "Measure a subject's abnormality with respect to a reference population")
8018 "This package contains functions to implement the methodology and
8019 considerations laid out by Marks et al. in the article \"Measuring abnormality
8020 in high dimensional spaces: applications in biomechanical gait analysis\".
8021 Using high-dimensional datasets to measure a subject's overall level of
8022 abnormality as compared to a reference population is often needed in outcomes
8024 (license license:expat)))
8026 (define-public r-abodoutlier
8028 (name "r-abodoutlier")
8033 (uri (cran-uri "abodOutlier" version))
8035 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8036 (properties `((upstream-name . "abodOutlier")))
8037 (build-system r-build-system)
8039 `(("r-cluster" ,r-cluster)))
8040 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8041 (synopsis "Angle-based outlier detection")
8043 "This package performs angle-based outlier detection on a given data
8044 frame. It offers three methods to process data:
8046 @item full but slow implementation using all the data that has cubic
8048 @item a fully randomized method;
8049 @item a method using k-nearest neighbours.
8051 These algorithms are well suited for high dimensional data outlier
8053 (license license:expat)))
8055 (define-public r-abps
8062 (uri (cran-uri "ABPS" version))
8064 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8065 (properties `((upstream-name . "ABPS")))
8066 (build-system r-build-system)
8067 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8068 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8069 (synopsis "Abnormal blood profile score to detect blood doping")
8071 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8072 The ABPS is a part of the Athlete biological passport program of the World
8073 anti-doping agency, which combines several blood parameters into a single
8074 score in order to detect blood doping. The package also contains functions to
8075 calculate other scores used in anti-doping programs, such as the ratio of
8076 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8077 (license license:gpl2+)))
8079 (define-public r-parmigene
8081 (name "r-parmigene")
8086 (uri (cran-uri "parmigene" version))
8089 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
8090 (build-system r-build-system)
8091 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8092 (synopsis "Mutual information estimation for gene network reconstruction")
8094 "This package provides a parallel estimation of the mutual information
8095 based on entropy estimates from k-nearest neighbors distances and algorithms
8096 for the reconstruction of gene regulatory networks.")
8097 (license license:agpl3+)))
8099 (define-public r-pscl
8106 (uri (cran-uri "pscl" version))
8108 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8109 (build-system r-build-system)
8111 `(("r-mass" ,r-mass)))
8112 (home-page "https://github.com/atahk/pscl/")
8113 (synopsis "Political science computational laboratory")
8115 "The @code{pscl} is an R package providing classes and methods for:
8117 @item Bayesian analysis of roll call data (item-response models);
8118 @item elementary Bayesian statistics;
8119 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8121 @item utility functions.
8123 (license license:gpl2)))
8125 (define-public r-accelmissing
8127 (name "r-accelmissing")
8132 (uri (cran-uri "accelmissing" version))
8134 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8135 (build-system r-build-system)
8137 `(("r-mice" ,r-mice)
8138 ("r-pscl" ,r-pscl)))
8139 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8140 (synopsis "Missing value imputation for accelerometer data")
8142 "This package provides a statistical method to impute the missing values in
8143 accelerometer data. The methodology includes both parametric and
8144 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8145 model. It also provides multiple functions to preprocess the accelerometer data
8146 previous to the missing data imputation. These include detecting the wearing
8147 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8148 (license license:gpl2+)))
8150 (define-public r-mhsmm
8157 (uri (cran-uri "mhsmm" version))
8159 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8160 (build-system r-build-system)
8161 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8162 (home-page "https://github.com/jaredo/mhsmm/")
8163 (synopsis "Inference for hidden Markov and semi-Markov models")
8165 "The @code{r-mhsmm} package implements estimation and prediction methods for
8166 hidden Markov and semi-Markov models for multiple observation sequences. Such
8167 techniques are of interest when observed data is thought to be dependent on some
8168 unobserved (or hidden) state. Also, this package is suitable for equidistant
8169 time series data, with multivariate and/or missing data. Allows user defined
8170 emission distributions.")
8171 (license license:gpl2+)))
8173 (define-public r-nleqslv
8180 (uri (cran-uri "nleqslv" version))
8182 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8183 (build-system r-build-system)
8184 (native-inputs `(("gfortran" ,gfortran)))
8185 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8186 (synopsis "Solve systems of nonlinear equations")
8188 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8189 Broyden or a Newton method with a choice of global strategies such as line
8190 search and trust region. There are options for using a numerical or user
8191 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8192 singular or ill-conditioned Jacobian.")
8193 (license license:gpl2+)))
8195 (define-public r-physicalactivity
8197 (name "r-physicalactivity")
8202 (uri (cran-uri "PhysicalActivity" version))
8204 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8206 `((upstream-name . "PhysicalActivity")))
8207 (build-system r-build-system)
8208 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8209 (synopsis "Procesing accelerometer data for physical activity measurement")
8211 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8212 for classification of monitor wear and nonwear time intervals in accelerometer
8213 data collected to assess physical activity. The package also contains functions
8214 for making plots of accelerometer data and obtaining the summary of various
8215 information including daily monitor wear time and the mean monitor wear time
8216 during valid days. The revised package version 0.2-1 improved the functions
8217 regarding speed, robustness and add better support for time zones and daylight
8218 saving. In addition, several functions were added:
8220 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8221 @item the @code{markPAI} can categorize physical activity intensity level based
8222 on user-defined cut-points of accelerometer counts.
8224 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8225 @code{queryActigraph} functions.")
8226 (license license:gpl3+)))
8228 (define-public r-acc
8235 (uri (cran-uri "acc" version))
8237 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8238 (build-system r-build-system)
8240 `(("r-circlize" ,r-circlize)
8242 ("r-ggplot2" ,r-ggplot2)
8243 ("r-iterators" ,r-iterators)
8244 ("r-mhsmm" ,r-mhsmm)
8245 ("r-nleqslv" ,r-nleqslv)
8246 ("r-physicalactivity" ,r-physicalactivity)
8248 ("r-r-utils" ,r-r-utils)
8250 ("r-rcpparmadillo" ,r-rcpparmadillo)
8251 ("r-rsqlite" ,r-rsqlite)
8253 (home-page "https://cran.r-project.org/web/packages/acc/")
8254 (synopsis "Exploring accelerometer data")
8256 "This package processes accelerometer data from uni-axial and tri-axial devices
8257 and generates data summaries. Also, includes functions to plot, analyze, and
8258 simulate accelerometer data.")
8259 (license license:gpl2+)))
8261 (define-public r-rbenchmark
8263 (name "r-rbenchmark")
8268 (uri (cran-uri "rbenchmark" version))
8270 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8271 (build-system r-build-system)
8272 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8273 (synopsis "Benchmarking routine for R")
8275 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8276 and is intended to facilitate benchmarking of arbitrary R code. The library
8277 consists of just one function, benchmark, which is a simple wrapper around
8278 system.time. Given a specification of the benchmarking process (counts of
8279 replications, evaluation environment) and an arbitrary number of expressions,
8280 benchmark evaluates each of the expressions in the specified environment,
8281 replicating the evaluation as many times as specified, and returning the results
8282 conveniently wrapped into a data frame.")
8283 (license license:gpl2+)))
8285 (define-public r-mitools
8292 (uri (cran-uri "mitools" version))
8295 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8296 (build-system r-build-system)
8297 (propagated-inputs `(("r-dbi" ,r-dbi)))
8298 (home-page "https://cran.r-project.org/web/packages/mitools/")
8299 (synopsis "Tools for multiple imputation of missing data")
8301 "This package provides tools to perform analyses and combine results from
8302 multiple-imputation datasets.")
8303 (license license:gpl2)))
8305 (define-public r-magick
8312 (uri (cran-uri "magick" version))
8315 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
8316 (build-system r-build-system)
8318 `(("imagemagick" ,imagemagick)
8321 `(("r-curl" ,r-curl)
8322 ("r-magrittr" ,r-magrittr)
8323 ("r-rcpp" ,r-rcpp)))
8325 `(("pkg-config" ,pkg-config)))
8326 (home-page "https://github.com/ropensci/magick")
8327 (synopsis "Advanced graphics and image-processing in R")
8329 "This package provides bindings to ImageMagick, a comprehensive image
8330 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8331 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8332 operations are vectorized via the Magick++ STL meaning they operate either on
8333 a single frame or a series of frames for working with layers, collages, or
8334 animation. In RStudio, images are automatically previewed when printed to the
8335 console, resulting in an interactive editing environment.")
8336 (license license:expat)))
8338 (define-public r-survey
8345 (uri (cran-uri "survey" version))
8348 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8349 (build-system r-build-system)
8351 `(("r-lattice" ,r-lattice)
8352 ("r-matrix" ,r-matrix)
8353 ("r-minqa" ,r-minqa)
8354 ("r-mitools" ,r-mitools)
8355 ("r-numderiv" ,r-numderiv)
8356 ("r-survival" ,r-survival)))
8357 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8358 (synopsis "Analysis of complex survey samples")
8360 "This package provides tools for the analysis of complex survey samples.
8361 The provided features include: summary statistics, two-sample tests, rank
8362 tests, generalised linear models, cumulative link models, Cox models,
8363 loglinear models, and general maximum pseudolikelihood estimation for
8364 multistage stratified, cluster-sampled, unequally weighted survey samples;
8365 variances by Taylor series linearisation or replicate weights;
8366 post-stratification, calibration, and raking; two-phase subsampling designs;
8367 graphics; PPS sampling without replacement; principal components, and factor
8369 ;; Either version of the GPL.
8370 (license (list license:gpl2 license:gpl3))))
8372 (define-public r-gee
8379 (uri (cran-uri "gee" version))
8382 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8383 (properties `((upstream-name . "gee")))
8384 (build-system r-build-system)
8386 `(("gfortran" ,gfortran)))
8387 (home-page "https://cran.r-project.org/web/packages/gee/")
8388 (synopsis "Generalized estimation equation solver")
8390 "This package provides a solver for generalized estimation equations.")
8391 (license license:gpl2)))
8393 (define-public r-tab
8400 (uri (cran-uri "tab" version))
8403 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8404 (properties `((upstream-name . "tab")))
8405 (build-system r-build-system)
8407 `(("r-dplyr" ,r-dplyr)
8409 ("r-knitr" ,r-knitr)
8411 ("r-survey" ,r-survey)
8412 ("r-survival" ,r-survival)
8413 ("r-xtable" ,r-xtable)))
8414 (home-page "https://cran.r-project.org/web/packages/tab/")
8415 (synopsis "Create summary tables for statistical reports")
8417 "This package contains functions for creating various types of summary
8418 tables, e.g. comparing characteristics across levels of a categorical variable
8419 and summarizing fitted generalized linear models, generalized estimating
8420 equations, and Cox proportional hazards models. Functions are available to
8421 handle data from simple random samples as well as complex surveys.")
8422 (license license:gpl3+)))
8424 (define-public r-dvmisc
8431 (uri (cran-uri "dvmisc" version))
8433 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8434 (build-system r-build-system)
8436 `(("r-cubature" ,r-cubature)
8437 ("r-data-table" ,r-data-table)
8438 ("r-dplyr" ,r-dplyr)
8439 ("r-ggplot2" ,r-ggplot2)
8441 ("r-mvtnorm" ,r-mvtnorm)
8442 ("r-pracma" ,r-pracma)
8443 ("r-rbenchmark" ,r-rbenchmark)
8445 ("r-survey" ,r-survey)
8447 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8448 (synopsis "Faster computation of common statistics and miscellaneous functions")
8450 "This package implements faster versions of base R functions (e.g. mean, standard
8451 deviation, covariance, weighted mean), mostly written in C++, along with
8452 miscellaneous functions for various purposes (e.g. create the histogram with
8453 fitted probability density function or probability mass function curve, create
8454 the body mass index groups, assess the linearity assumption in logistic
8456 (license license:gpl2)))
8458 (define-public r-accelerometry
8460 (name "r-accelerometry")
8465 (uri (cran-uri "accelerometry" version))
8467 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8468 (build-system r-build-system)
8470 `(("r-dvmisc" ,r-dvmisc)
8471 ("r-rcpp" ,r-rcpp)))
8472 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8473 (synopsis "Functions for processing accelerometer data")
8475 "This package provides a collection of functions that perform operations on
8476 time-series accelerometer data, such as identify the non-wear time, flag minutes
8477 that are part of an activity bout, and find the maximum 10-minute average count
8478 value. The functions are generally very flexible, allowing for a variety of
8479 algorithms to be implemented.")
8480 (license license:gpl3)))
8482 (define-public r-absim
8489 (uri (cran-uri "AbSim" version))
8491 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8492 (properties `((upstream-name . "AbSim")))
8493 (build-system r-build-system)
8496 ("r-powerlaw" ,r-powerlaw)))
8497 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8498 (synopsis "Time resolved simulations of antibody repertoires")
8500 "This package provides simulation methods for the evolution of antibody repertoires.
8501 The heavy and light chain variable region of both human and C57BL/6 mice can
8502 be simulated in a time-dependent fashion. Both single lineages using one set of
8503 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8504 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8505 Upon completion, the main loop of the algorithm begins, with each iteration
8506 representing one simulated time step. Various mutation events are possible at
8507 each time step, contributing to a diverse final repertoire.")
8508 (license license:gpl2)))
8510 (define-public r-quic
8517 (uri (cran-uri "QUIC" version))
8519 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8520 (properties `((upstream-name . "QUIC")))
8521 (build-system r-build-system)
8522 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8523 (synopsis "Regularized sparse inverse covariance matrix estimation")
8525 "This package implements the regularized Gaussian maximum likelihood
8526 estimation of the inverse of a covariance matrix. It uses Newton's method and
8527 coordinate descent to solve the regularized inverse covariance matrix
8528 estimation problem.")
8529 ;; The project home page states that the release is under GPLv3 or later.
8530 ;; The CRAN page only says GPL-3.
8531 (license license:gpl3+)))
8533 (define-public r-abundant
8540 (uri (cran-uri "abundant" version))
8542 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8543 (build-system r-build-system)
8545 `(("r-quic" ,r-quic)))
8546 (home-page "https://cran.r-project.org/web/packages/abundant/")
8547 (synopsis "Abundant regression and high-dimensional principal fitted components")
8549 "This package provides tools to fit and predict with the high-dimensional
8550 principal fitted components model. This model is described by Cook, Forzani,
8551 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8552 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8553 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8554 (license license:gpl2+)))
8556 (define-public r-ac3net
8563 (uri (cran-uri "Ac3net" version))
8565 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8566 (properties `((upstream-name . "Ac3net")))
8567 (build-system r-build-system)
8569 `(("r-data-table" ,r-data-table)))
8570 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8571 (synopsis "Inferring directional conservative causal core gene networks")
8572 (description "This package infers directional Conservative causal core
8573 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8574 directional network.")
8575 (license license:gpl3+)))
8577 (define-public r-aca
8584 (uri (cran-uri "ACA" version))
8586 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8587 (properties `((upstream-name . "ACA")))
8588 (build-system r-build-system)
8589 (home-page "https://cran.r-project.org/web/packages/ACA/")
8590 (synopsis "Abrupt change-point or aberration detection in point series")
8592 "This package offers an interactive function for the detection of breakpoints in
8594 ;; Any version of the GPL
8595 (license (list license:gpl2+ license:gpl3+))))
8597 (define-public r-acceptancesampling
8599 (name "r-acceptancesampling")
8604 (uri (cran-uri "AcceptanceSampling" version))
8606 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8608 `((upstream-name . "AcceptanceSampling")))
8609 (build-system r-build-system)
8610 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8611 (synopsis "Creation and evaluation of acceptance sampling plans")
8613 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8614 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8615 in quality control and improvement. International standards of acceptance
8616 sampling provide sampling plans for specific circumstances. The aim of this
8617 package is to provide an easy-to-use interface to visualize single, double or
8618 multiple sampling plans. In addition, methods have been provided to enable the
8619 user to assess sampling plans against pre-specified levels of performance, as
8620 measured by the probability of acceptance for a given level of quality in the
8622 (license license:gpl3+)))
8624 (define-public r-acclma
8631 (uri (cran-uri "ACCLMA" version))
8633 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8634 (properties `((upstream-name . "ACCLMA")))
8635 (build-system r-build-system)
8636 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8637 (synopsis "ACC & LMA graph plotting")
8639 "This package contains a function that imports data from a @acronym{CSV,
8640 Comma-Separated Values} file, or uses manually entered data from the format (x,
8641 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8642 Curve} vs @acronym{LOI, Line of Independence} graph and
8643 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8644 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8645 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8646 string) was passed, a manual data entry window is opened. The header parameter
8647 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8648 a header row or not. The dataset should contain only one independent variable
8649 (x) and one dependent variable (y) and can contain a weight for each
8651 (license license:gpl2)))
8653 (define-public r-aspi
8660 (uri (cran-uri "aspi" version))
8662 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8663 (build-system r-build-system)
8665 "https://cran.r-project.org/web/packages/aspi/")
8667 "Analysis of symmetry of parasitic infections")
8669 "This package provides tools for the analysis and visualization of bilateral
8670 asymmetry in parasitic infections.")
8671 (license license:gpl3+)))
8673 (define-public r-sandwich
8680 (uri (cran-uri "sandwich" version))
8683 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8684 (build-system r-build-system)
8686 `(("r-zoo" ,r-zoo)))
8687 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8688 (synopsis "Robust Covariance Matrix Estimators")
8690 "This package provides model-robust standard error estimators for
8691 cross-sectional, time series, clustered, panel, and longitudinal data.")
8692 ;; Either version of the license.
8693 (license (list license:gpl2 license:gpl3))))
8695 (define-public r-th-data
8702 (uri (cran-uri "TH.data" version))
8705 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8706 (properties `((upstream-name . "TH.data")))
8707 (build-system r-build-system)
8709 `(("r-mass" ,r-mass)
8710 ("r-survival" ,r-survival)))
8711 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8712 (synopsis "Shared data sets")
8714 "This package contains supporting data sets that are used in other
8715 packages maintained by Torsten Hothorn.")
8716 (license license:gpl3)))
8718 (define-public r-multcomp
8725 (uri (cran-uri "multcomp" version))
8728 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8729 (build-system r-build-system)
8731 `(("r-codetools" ,r-codetools)
8732 ("r-mvtnorm" ,r-mvtnorm)
8733 ("r-sandwich" ,r-sandwich)
8734 ("r-survival" ,r-survival)
8735 ("r-th-data" ,r-th-data)))
8736 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8737 (synopsis "Simultaneous inference in general parametric models")
8739 "Simultaneous tests and confidence intervals for general linear
8740 hypotheses in parametric models, including linear, generalized linear, linear
8741 mixed effects, and survival models. The package includes demos reproducing
8742 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8743 Hothorn, Westfall, 2010, CRC Press).")
8744 (license license:gpl2)))
8746 (define-public r-emmeans
8753 (uri (cran-uri "emmeans" version))
8756 "0jh7l1rzsb2ihbnh4r4388kwm629z17rcapvdws1hnkklhr8j74k"))))
8757 (build-system r-build-system)
8759 `(("r-estimability" ,r-estimability)
8760 ("r-mvtnorm" ,r-mvtnorm)
8761 ("r-numderiv" ,r-numderiv)
8763 ("r-xtable" ,r-xtable)))
8765 `(("r-knitr" ,r-knitr)))
8766 (home-page "https://github.com/rvlenth/emmeans")
8767 (synopsis "Estimated marginal means, aka least-squares means")
8769 "This package provides tools to obtain @dfn{estimated marginal
8770 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8771 be used to compute contrasts or linear functions of EMMs, trends, and
8772 comparisons of slopes.")
8773 ;; Either version of the license.
8774 (license (list license:gpl2 license:gpl3))))
8776 (define-public r-pwr
8783 (uri (cran-uri "pwr" version))
8786 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8787 (build-system r-build-system)
8789 `(("r-knitr" ,r-knitr)))
8790 (home-page "https://github.com/heliosdrm/pwr")
8791 (synopsis "Basic functions for power analysis")
8793 "This package provides power analysis functions along the lines of
8795 (license license:gpl3+)))
8797 (define-public r-libcoin
8804 (uri (cran-uri "libcoin" version))
8807 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8808 (build-system r-build-system)
8809 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8810 (home-page "https://cran.r-project.org/web/packages/libcoin")
8811 (synopsis "Linear test statistics for permutation inference")
8813 "This package provides basic infrastructure for linear test statistics
8814 and permutation inference in the framework of Strasser and Weber (1999).")
8815 (license license:gpl2)))
8817 (define-public r-coin
8824 (uri (cran-uri "coin" version))
8827 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8828 (build-system r-build-system)
8830 `(("r-libcoin" ,r-libcoin)
8831 ("r-matrixstats" ,r-matrixstats)
8832 ("r-modeltools" ,r-modeltools)
8833 ("r-multcomp" ,r-multcomp)
8834 ("r-mvtnorm" ,r-mvtnorm)
8835 ("r-survival" ,r-survival)))
8836 (home-page "http://coin.r-forge.r-project.org")
8837 (synopsis "Conditional inference procedures in a permutation test framework")
8839 "This package provides conditional inference procedures for the general
8840 independence problem including two-sample, K-sample (non-parametric ANOVA),
8841 correlation, censored, ordered and multivariate problems.")
8842 (license license:gpl2)))
8844 (define-public r-bayesplot
8846 (name "r-bayesplot")
8851 (uri (cran-uri "bayesplot" version))
8854 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8855 (build-system r-build-system)
8857 `(("pandoc" ,ghc-pandoc)
8858 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8860 `(("r-knitr" ,r-knitr)))
8862 `(("r-dplyr" ,r-dplyr)
8863 ("r-ggplot2" ,r-ggplot2)
8864 ("r-ggridges" ,r-ggridges)
8866 ("r-reshape2" ,r-reshape2)
8867 ("r-rlang" ,r-rlang)
8868 ("r-tibble" ,r-tibble)
8869 ("r-tidyselect" ,r-tidyselect)))
8870 (home-page "https://mc-stan.org/bayesplot")
8871 (synopsis "Plotting for Bayesian models")
8873 "This package provides plotting functions for posterior analysis, model
8874 checking, and MCMC diagnostics. The package is designed not only to provide
8875 convenient functionality for users, but also a common set of functions that
8876 can be easily used by developers working on a variety of R packages for
8877 Bayesian modeling.")
8878 (license license:gpl3+)))
8880 (define-public r-tmb
8887 (uri (cran-uri "TMB" version))
8890 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8891 (properties `((upstream-name . "TMB")))
8892 (build-system r-build-system)
8894 `(("r-matrix" ,r-matrix)
8895 ("r-rcppeigen" ,r-rcppeigen)))
8896 (home-page "http://tmb-project.org")
8897 (synopsis "Template model builder: a general random effect tool")
8899 "With this tool, a user should be able to quickly implement complex
8900 random effect models through simple C++ templates. The package combines
8901 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8902 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8903 from R) to obtain an efficient implementation of the applied Laplace
8904 approximation with exact derivatives. Key features are: Automatic sparseness
8905 detection, parallelism through BLAS and parallel user templates.")
8906 (license license:gpl2)))
8908 (define-public r-sjstats
8915 (uri (cran-uri "sjstats" version))
8917 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8918 (build-system r-build-system)
8920 `(("r-bayestestr" ,r-bayestestr)
8921 ("r-broom" ,r-broom)
8922 ("r-dplyr" ,r-dplyr)
8923 ("r-effectsize" ,r-effectsize)
8924 ("r-emmeans" ,r-emmeans)
8925 ("r-insight" ,r-insight)
8927 ("r-magrittr" ,r-magrittr)
8929 ("r-modelr" ,r-modelr)
8930 ("r-parameters" ,r-parameters)
8931 ("r-performance" ,r-performance)
8932 ("r-purrr" ,r-purrr)
8933 ("r-rlang" ,r-rlang)
8934 ("r-sjlabelled" ,r-sjlabelled)
8935 ("r-sjmisc" ,r-sjmisc)
8936 ("r-tidyr" ,r-tidyr)))
8937 (home-page "https://github.com/strengejacke/sjstats")
8938 (synopsis "Functions for common statistical computations")
8940 "This package provides a collection of convenient functions for common
8941 statistical computations, which are not directly provided by R's @code{base}
8942 or @code{stats} packages. This package aims at providing, first, shortcuts
8943 for statistical measures, which otherwise could only be calculated with
8944 additional effort. Second, these shortcut functions are generic, and can be
8945 applied not only to vectors, but also to other objects as well. The focus of
8946 most functions lies on summary statistics or fit measures for regression
8947 models, including generalized linear models, mixed effects models and Bayesian
8949 (license license:gpl3)))
8951 (define-public r-glmmtmb
8958 (uri (cran-uri "glmmTMB" version))
8961 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8962 (properties `((upstream-name . "glmmTMB")))
8963 (build-system r-build-system)
8965 `(("r-lme4" ,r-lme4)
8966 ("r-matrix" ,r-matrix)
8968 ("r-rcppeigen" ,r-rcppeigen)
8971 `(("r-knitr" ,r-knitr))) ; for vignettes
8972 (home-page "https://github.com/glmmTMB")
8973 (synopsis "Generalized linear mixed models")
8975 "Fit linear and generalized linear mixed models with various extensions,
8976 including zero-inflation. The models are fitted using maximum likelihood
8977 estimation via the Template Model Builder. Random effects are assumed to be
8978 Gaussian on the scale of the linear predictor and are integrated out using the
8979 Laplace approximation. Gradients are calculated using automatic
8981 (license license:agpl3+)))
8983 (define-public r-bayestestr
8985 (name "r-bayestestr")
8990 (uri (cran-uri "bayestestR" version))
8993 "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd"))))
8994 (properties `((upstream-name . "bayestestR")))
8995 (build-system r-build-system)
8997 `(("r-insight" ,r-insight)))
8999 `(("r-knitr" ,r-knitr)))
9000 (home-page "https://github.com/easystats/bayestestR")
9001 (synopsis "Describe Bayesian models and posterior distributions")
9003 "This package provides utilities to understand and describe posterior
9004 distributions and Bayesian models. It includes point-estimates such as
9005 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9006 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9007 ROPE percentage and pd).")
9008 (license license:gpl3)))
9010 (define-public r-performance
9012 (name "r-performance")
9017 (uri (cran-uri "performance" version))
9020 "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
9021 (build-system r-build-system)
9023 `(("r-bayestestr" ,r-bayestestr)
9024 ("r-insight" ,r-insight)))
9025 (home-page "https://easystats.github.io/performance/")
9026 (synopsis "Assessment of regression models performance")
9028 "This package provides utilities for computing measures to assess model
9029 quality, which are not directly provided by R's @code{base} or @code{stats}
9030 packages. These include e.g. measures like r-squared, intraclass correlation
9031 coefficient, root mean squared error or functions to check models for
9032 overdispersion, singularity or zero-inflation and more. Functions apply to a
9033 large variety of regression models, including generalized linear models, mixed
9034 effects models and Bayesian models.")
9035 (license license:gpl3)))
9037 (define-public r-ggeffects
9039 (name "r-ggeffects")
9044 (uri (cran-uri "ggeffects" version))
9047 "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r"))))
9048 (build-system r-build-system)
9050 `(("r-insight" ,r-insight)
9052 ("r-sjlabelled" ,r-sjlabelled)))
9054 `(("r-knitr" ,r-knitr)))
9055 (home-page "https://github.com/strengejacke/ggeffects")
9056 (synopsis "Create tidy data frames of marginal effects for ggplot")
9058 "This package provides tools to compute marginal effects from statistical
9059 models and return the result as tidy data frames. These data frames are ready
9060 to use with the @code{ggplot2} package. Marginal effects can be calculated
9061 for many different models. Interaction terms, splines and polynomial terms
9062 are also supported. The two main functions are @code{ggpredict()} and
9063 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9064 results using @code{ggplot2}.")
9065 (license license:gpl3)))
9067 (define-public r-effectsize
9069 (name "r-effectsize")
9074 (uri (cran-uri "effectsize" version))
9077 "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
9078 (properties `((upstream-name . "effectsize")))
9079 (build-system r-build-system)
9081 `(("r-bayestestr" ,r-bayestestr)
9082 ("r-insight" ,r-insight)
9083 ("r-parameters" ,r-parameters)))
9085 `(("r-knitr" ,r-knitr)))
9086 (home-page "https://github.com/easystats/effectsize")
9087 (synopsis "Indices of effect size and standardized parameters")
9089 "This package provides utilities to work with indices of effect size and
9090 standardized parameters for a wide variety of models, allowing computation and
9091 conversion of indices such as Cohen's d, r, odds, etc.")
9092 (license license:gpl3)))
9094 (define-public r-sjplot
9101 (uri (cran-uri "sjPlot" version))
9103 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9104 (properties `((upstream-name . "sjPlot")))
9105 (build-system r-build-system)
9107 `(("r-bayestestr" ,r-bayestestr)
9108 ("r-dplyr" ,r-dplyr)
9109 ("r-effectsize" ,r-effectsize)
9110 ("r-ggeffects" ,r-ggeffects)
9111 ("r-ggplot2" ,r-ggplot2)
9112 ("r-insight" ,r-insight)
9113 ("r-knitr" ,r-knitr)
9115 ("r-parameters" ,r-parameters)
9116 ("r-performance" ,r-performance)
9117 ("r-purrr" ,r-purrr)
9118 ("r-rlang" ,r-rlang)
9119 ("r-scales" ,r-scales)
9120 ("r-sjlabelled" ,r-sjlabelled)
9121 ("r-sjmisc" ,r-sjmisc)
9122 ("r-sjstats" ,r-sjstats)
9123 ("r-tidyr" ,r-tidyr)))
9125 `(("r-knitr" ,r-knitr)))
9126 (home-page "https://strengejacke.github.io/sjPlot/")
9127 (synopsis "Data visualization for statistics in social science")
9129 "This package represents a collection of plotting and table output
9130 functions for data visualization. Results of various statistical
9131 analyses (that are commonly used in social sciences) can be visualized using
9132 this package, including simple and cross tabulated frequencies, histograms,
9133 box plots, (generalized) linear models, mixed effects models, principal
9134 component analysis and correlation matrices, cluster analyses, scatter plots,
9135 stacked scales, effects plots of regression models (including interaction
9136 terms) and much more. This package supports labelled data.")
9137 (license license:gpl3)))
9139 (define-public r-ini
9146 (uri (cran-uri "ini" version))
9149 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9150 (build-system r-build-system)
9151 (home-page "https://github.com/dvdscripter/ini")
9152 (synopsis "Read and write configuration files")
9154 "This package provides tools to parse simple @code{.ini} configuration
9155 files to an structured list. Users can manipulate this resulting list with
9156 @code{lapply()} functions. This same structured list can be used to write
9157 back to file after modifications.")
9158 (license license:gpl3)))
9167 (uri (cran-uri "gh" version))
9170 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9171 (build-system r-build-system)
9176 ("r-jsonlite" ,r-jsonlite)))
9177 (home-page "https://github.com/r-lib/gh#readme")
9178 (synopsis "Access the GitHub API via R")
9180 "This package provides a minimal R client to access the GitHub API.")
9181 (license license:expat)))
9190 (uri (cran-uri "fs" version))
9193 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
9194 (build-system r-build-system)
9196 `(("pkg-config" ,pkg-config)
9197 ("r-knitr" ,r-knitr)))
9198 (home-page "https://fs.r-lib.org")
9199 (synopsis "Cross-platform file system operations based on libuv")
9201 "This package provides a cross-platform interface to file system
9202 operations, built on top of the libuv C library.")
9203 (license license:gpl3)))
9205 (define-public r-clisymbols
9207 (name "r-clisymbols")
9212 (uri (cran-uri "clisymbols" version))
9215 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9216 (build-system r-build-system)
9217 (home-page "https://github.com/gaborcsardi/clisymbols")
9218 (synopsis "Unicode symbols at the R prompt")
9220 "This package provides a small subset of Unicode symbols, that are useful
9221 when building command line applications. They fall back to alternatives on
9222 terminals that do not support Unicode.")
9223 (license license:expat)))
9225 (define-public r-usethis
9232 (uri (cran-uri "usethis" version))
9235 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9236 (build-system r-build-system)
9239 ("r-clipr" ,r-clipr)
9240 ("r-crayon" ,r-crayon)
9245 ("r-git2r" ,r-git2r)
9247 ("r-purrr" ,r-purrr)
9248 ("r-rematch2" ,r-rematch2)
9249 ("r-rlang" ,r-rlang)
9250 ("r-rprojroot" ,r-rprojroot)
9251 ("r-rstudioapi" ,r-rstudioapi)
9252 ("r-whisker" ,r-whisker)
9253 ("r-withr" ,r-withr)
9254 ("r-yaml" ,r-yaml)))
9255 (home-page "https://github.com/r-lib/usethis")
9256 (synopsis "Automate R package and project setup")
9258 "This package helps you to automate R package and project setup tasks
9259 that are otherwise performed manually. This includes setting up unit testing,
9260 test coverage, continuous integration, Git, GitHub integration, licenses,
9261 Rcpp, RStudio projects, and more.")
9262 (license license:gpl3)))
9264 (define-public r-sessioninfo
9266 (name "r-sessioninfo")
9271 (uri (cran-uri "sessioninfo" version))
9274 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9275 (build-system r-build-system)
9278 ("r-withr" ,r-withr)))
9279 (home-page "https://github.com/r-lib/sessioninfo#readme")
9280 (synopsis "R session information")
9282 "This package provides tools to query and print information about the
9283 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9284 more information about packages, and where they were installed from.")
9285 (license license:gpl2)))
9287 (define-public r-remotes
9294 (uri (cran-uri "remotes" version))
9297 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
9298 (build-system r-build-system)
9299 (home-page "https://github.com/r-lib/remotes#readme")
9300 (synopsis "R package installation from remote repositories")
9302 "Download and install R packages stored in GitHub, BitBucket, or plain
9303 subversion or git repositories. This package is a lightweight replacement of
9304 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9305 the code was copied over from @code{devtools}.")
9306 (license license:gpl2+)))
9308 (define-public r-xopen
9315 (uri (cran-uri "xopen" version))
9318 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9319 (build-system r-build-system)
9321 `(("r-processx" ,r-processx)))
9322 (home-page "https://github.com/r-lib/xopen#readme")
9323 (synopsis "Open system files, URLs, anything")
9325 "This package provides a cross-platform solution to open files,
9326 directories or URLs with their associated programs.")
9327 (license license:expat)))
9329 (define-public r-rcmdcheck
9331 (name "r-rcmdcheck")
9336 (uri (cran-uri "rcmdcheck" version))
9339 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9340 (build-system r-build-system)
9342 `(("r-callr" ,r-callr)
9344 ("r-crayon" ,r-crayon)
9346 ("r-digest" ,r-digest)
9347 ("r-pkgbuild" ,r-pkgbuild)
9348 ("r-prettyunits" ,r-prettyunits)
9350 ("r-rprojroot" ,r-rprojroot)
9351 ("r-sessioninfo" ,r-sessioninfo)
9352 ("r-withr" ,r-withr)
9353 ("r-xopen" ,r-xopen)))
9354 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9355 (synopsis "Run R CMD check from R and capture results")
9357 "Run @code{R CMD check} from R programmatically, and capture the results
9358 of the individual checks.")
9359 (license license:expat)))
9361 (define-public r-rapportools
9363 (name "r-rapportools")
9368 (uri (cran-uri "rapportools" version))
9371 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9372 (build-system r-build-system)
9374 `(("r-pander" ,r-pander)
9376 ("r-reshape" ,r-reshape)))
9377 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9378 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9380 "This package provides helper functions that act as wrappers to more
9381 advanced statistical methods with the advantage of having sane defaults for
9383 (license license:agpl3+)))
9385 (define-public r-pander
9392 (uri (cran-uri "pander" version))
9395 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9396 (build-system r-build-system)
9398 `(("r-digest" ,r-digest)
9399 ("r-rcpp" ,r-rcpp)))
9400 (home-page "https://rapporter.github.io/pander")
9401 (synopsis "Render R objects into Pandoc's markdown")
9403 "The main aim of the pander R package is to provide a minimal and easy
9404 tool for rendering R objects into Pandoc's markdown. The package is also
9405 capable of exporting/converting complex Pandoc documents (reports) in various
9407 ;; This package is licensed under either the AGPLv3+ or the very rarely
9409 (license license:agpl3+)))
9411 (define-public r-summarytools
9413 (name "r-summarytools")
9418 (uri (cran-uri "summarytools" version))
9421 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9422 (build-system r-build-system)
9424 `(("r-base64enc" ,r-base64enc)
9425 ("r-checkmate" ,r-checkmate)
9426 ("r-dplyr" ,r-dplyr)
9427 ("r-htmltools" ,r-htmltools)
9428 ("r-lubridate" ,r-lubridate)
9429 ("r-magick" ,r-magick)
9430 ("r-matrixstats" ,r-matrixstats)
9431 ("r-pander" ,r-pander)
9433 ("r-rapportools" ,r-rapportools)
9434 ("r-tibble" ,r-tibble)
9435 ("r-tidyr" ,r-tidyr)))
9436 (home-page "https://github.com/dcomtois/summarytools")
9437 (synopsis "Tools to quickly and neatly summarize data")
9439 "This package provides tools for data frame summaries, cross-tabulations,
9440 weight-enabled frequency tables and common univariate statistics in concise
9441 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9442 good point-of-entry for exploring data, both for experienced and new R
9444 (license license:gpl2)))
9446 (define-public r-lsei
9453 (uri (cran-uri "lsei" version))
9456 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9457 (build-system r-build-system)
9459 `(("gfortran" ,gfortran)))
9460 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9461 (synopsis "Solve regression problems under equality/inequality constraints")
9463 "It contains functions that solve least squares linear regression
9464 problems under linear equality/inequality constraints. Functions for solving
9465 quadratic programming problems are also available, which transform such
9466 problems into least squares ones first.")
9467 (license license:gpl2+)))
9469 (define-public r-npsurv
9476 (uri (cran-uri "npsurv" version))
9479 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9480 (build-system r-build-system)
9482 `(("r-lsei" ,r-lsei)))
9483 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9484 (synopsis "Nonparametric survival analysis")
9486 "This package contains functions for non-parametric survival analysis of
9487 exact and interval-censored observations.")
9488 (license license:gpl2+)))
9490 (define-public r-clusteval
9492 (name "r-clusteval")
9497 (uri (cran-uri "clusteval" version))
9500 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9501 (build-system r-build-system)
9503 `(("r-mvtnorm" ,r-mvtnorm)
9504 ("r-rcpp" ,r-rcpp)))
9505 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9506 (synopsis "Evaluation of clustering algorithms")
9508 "This R package provides a suite of tools to evaluate clustering
9509 algorithms, clusterings, and individual clusters.")
9510 (license license:expat)))
9512 (define-public r-tweedie
9519 (uri (cran-uri "tweedie" version))
9522 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9523 (build-system r-build-system)
9524 (native-inputs `(("gfortran" ,gfortran)))
9525 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9526 (synopsis "Evaluation of Tweedie exponential family models")
9528 "Maximum likelihood computations for Tweedie families, including the
9529 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9530 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9531 and related methods.")
9532 (license license:gpl2+)))
9534 (define-public r-rcppgsl
9541 (uri (cran-uri "RcppGSL" version))
9543 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9544 (properties `((upstream-name . "RcppGSL")))
9545 (build-system r-build-system)
9547 `(("r-rcpp" ,r-rcpp)
9549 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9550 (synopsis "Rcpp integration for GSL vectors and matrices")
9552 "The GNU Scientific Library (or GSL) is a collection of numerical
9553 routines for scientific computing. It is particularly useful for C and C++
9554 programs as it provides a standard C interface to a wide range of mathematical
9555 routines. There are over 1000 functions in total with an extensive test
9556 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9557 structures and R using concepts from Rcpp which is itself a package that eases
9558 the interfaces between R and C++.")
9559 (license license:gpl2+)))
9561 (define-public r-mvabund
9568 (uri (cran-uri "mvabund" version))
9571 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9572 (build-system r-build-system)
9574 `(("r-mass" ,r-mass)
9576 ("r-rcppgsl" ,r-rcppgsl)
9577 ("r-statmod" ,r-statmod)
9578 ("r-tweedie" ,r-tweedie)))
9579 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9580 (synopsis "Statistical methods for analysing multivariate abundance data")
9582 "This package provides a set of tools for displaying, modeling and
9583 analysing multivariate abundance data in community ecology.")
9584 (license license:lgpl2.1+)))
9586 (define-public r-afex
9593 (uri (cran-uri "afex" version))
9596 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9597 (build-system r-build-system)
9601 ("r-lmertest" ,r-lmertest)
9602 ("r-pbkrtest" ,r-pbkrtest)
9603 ("r-reshape2" ,r-reshape2)))
9605 `(("r-knitr" ,r-knitr)))
9606 (home-page "https://afex.singmann.science/")
9607 (synopsis "Analysis of factorial experiments")
9609 "This package provides convenience functions for analyzing factorial
9610 experiments using ANOVA or mixed models.")
9611 (license license:gpl2+)))
9613 (define-public r-lmertest
9620 (uri (cran-uri "lmerTest" version))
9623 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9624 (properties `((upstream-name . "lmerTest")))
9625 (build-system r-build-system)
9627 `(("r-ggplot2" ,r-ggplot2)
9630 ("r-numderiv" ,r-numderiv)))
9631 (home-page "https://github.com/runehaubo/lmerTestR")
9632 (synopsis "Tests in linear mixed effects models")
9634 "This package provides p-values in type I, II or III anova and summary
9635 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9636 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9637 package. Model selection methods include step, drop1 and anova-like tables
9638 for random effects (ranova). Methods for Least-Square means (LS-means) and
9639 tests of linear contrasts of fixed effects are also available.")
9640 (license license:gpl2+)))
9642 (define-public r-r2glmm
9649 (uri (cran-uri "r2glmm" version))
9652 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9653 (build-system r-build-system)
9655 `(("r-afex" ,r-afex)
9656 ("r-data-table" ,r-data-table)
9657 ("r-dplyr" ,r-dplyr)
9658 ("r-ggplot2" ,r-ggplot2)
9659 ("r-gridextra" ,r-gridextra)
9660 ("r-lmertest" ,r-lmertest)
9662 ("r-matrix" ,r-matrix)
9664 ("r-pbkrtest" ,r-pbkrtest)))
9665 (home-page "https://github.com/bcjaeger/r2glmm")
9666 (synopsis "Compute R squared for mixed (multilevel) models")
9668 "This package computes model and semi partial R squared with confidence
9669 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9670 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9671 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9673 (license license:gpl2)))
9675 (define-public r-weights
9682 (uri (cran-uri "weights" version))
9685 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9686 (build-system r-build-system)
9688 `(("r-gdata" ,r-gdata)
9689 ("r-hmisc" ,r-hmisc)
9690 ("r-mice" ,r-mice)))
9692 "https://cran.r-project.org/web/packages/weights/")
9693 (synopsis "Weighting and weighted statistics")
9694 (description "This package Provides a variety of functions for producing
9695 simple weighted statistics, such as weighted Pearson's correlations, partial
9696 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9697 includes some software for quickly recoding survey data and plotting point
9698 estimates from interaction terms in regressions (and multiply imputed
9699 regressions). NOTE: Weighted partial correlation calculations pulled to
9701 (license license:gpl2+)))
9703 (define-public r-rcppannoy
9705 (name "r-rcppannoy")
9710 (uri (cran-uri "RcppAnnoy" version))
9713 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9714 (properties `((upstream-name . "RcppAnnoy")))
9715 (build-system r-build-system)
9717 `(("r-rcpp" ,r-rcpp)))
9718 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9719 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9721 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9722 for efficient memory usage as well an ability to load from and save to disk.
9723 This package provides an R interface.")
9724 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9726 (license (list license:gpl2+ license:asl2.0))))
9728 (define-public r-rcpphnsw
9735 (uri (cran-uri "RcppHNSW" version))
9738 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9739 (properties `((upstream-name . "RcppHNSW")))
9740 (build-system r-build-system)
9741 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9742 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9743 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9745 "Hnswlib is a C++ library for approximate nearest neighbors. This
9746 package provides a minimal R interface by relying on the Rcpp package.")
9747 ;; hnswlib is released under Version 2.0 of the Apache License.
9748 (license (list license:gpl3 license:asl2.0))))
9750 (define-public r-rcppparallel
9752 (name "r-rcppparallel")
9757 (uri (cran-uri "RcppParallel" version))
9760 "029yyjnixggqmddazwxh1wqid1h7xpwpi4sgixyhbb4kmvqlwfkd"))))
9761 (properties `((upstream-name . "RcppParallel")))
9762 (build-system r-build-system)
9763 (home-page "https://rcppcore.github.io/RcppParallel/")
9764 (synopsis "Parallel programming tools for Rcpp")
9766 "This package provides high level functions for parallel programming with
9767 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9768 the work of a standard serial @code{for} loop into a parallel one and the
9769 @code{parallelReduce()} function can be used for accumulating aggregates or
9771 (license license:gpl2)))
9773 (define-public r-ncdf4
9780 (uri (cran-uri "ncdf4" version))
9783 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9784 (build-system r-build-system)
9786 `(("netcdf" ,netcdf)
9788 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9789 (synopsis "R interface to Unidata netCDF format data files")
9791 "This package provides a high-level R interface to data files written
9792 using Unidata's netCDF library (version 4 or earlier), which are binary data
9793 files that are portable across platforms and include metadata information in
9794 addition to the data sets. Using this package, netCDF files can be opened and
9795 data sets read in easily. It is also easy to create new netCDF dimensions,
9796 variables, and files, in either version 3 or 4 format, and manipulate existing
9798 (license license:gpl3+)))
9800 (define-public r-biocmanager
9802 (name "r-biocmanager")
9807 (uri (cran-uri "BiocManager" version))
9809 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9810 (properties `((upstream-name . "BiocManager")))
9811 (build-system r-build-system)
9812 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9813 (synopsis "Access the Bioconductor project package repository")
9815 "This package provides a convenient tool to install and update
9816 Bioconductor packages.")
9817 (license license:artistic2.0)))
9819 (define-public r-rgl
9822 (version "0.100.54")
9826 (uri (cran-uri "rgl" version))
9829 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9830 (build-system r-build-system)
9832 `(("pkg-config" ,pkg-config)))
9834 `(("freetype" ,freetype)
9838 ("ghc-pandoc" ,ghc-pandoc)
9841 `(("r-crosstalk" ,r-crosstalk)
9842 ("r-htmltools" ,r-htmltools)
9843 ("r-htmlwidgets" ,r-htmlwidgets)
9844 ("r-jsonlite" ,r-jsonlite)
9845 ("r-knitr" ,r-knitr)
9846 ("r-magrittr" ,r-magrittr)
9847 ("r-manipulatewidget" ,r-manipulatewidget)
9848 ("r-shiny" ,r-shiny)))
9849 (home-page "https://r-forge.r-project.org/projects/rgl/")
9850 (synopsis "3D visualization using OpenGL")
9852 "This package provides medium to high level functions for 3D interactive graphics,
9853 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9854 as functions for constructing representations of geometric
9855 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9856 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9857 image formats, including PNG, Postscript, SVG, PGF.")
9858 ;; Any version of the GPL.
9859 (license (list license:gpl2+ license:gpl3+))))
9861 (define-public r-multicool
9863 (name "r-multicool")
9868 (uri (cran-uri "multicool" version))
9871 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9872 (build-system r-build-system)
9873 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9874 (home-page "https://cran.r-project.org/web/packages/multicool/")
9875 (synopsis "Permutations of multisets in cool-lex order")
9877 "This package provides a set of tools to permute multisets without loops
9878 or hash tables and to generate integer partitions. Cool-lex order is similar
9879 to colexicographical order.")
9880 (license license:gpl2)))
9882 (define-public r-misc3d
9889 (uri (cran-uri "misc3d" version))
9892 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9893 (build-system r-build-system)
9894 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9895 (synopsis "Miscellaneous 3D Plots")
9897 "This package provides a collection of miscellaneous 3d plots, including
9899 ;; Any version of the GPL.
9900 (license (list license:gpl2+ license:gpl3+))))
9909 (uri (cran-uri "ks" version))
9911 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9912 (build-system r-build-system)
9915 ("r-kernlab" ,r-kernlab)
9916 ("r-kernsmooth" ,r-kernsmooth)
9917 ("r-matrix" ,r-matrix)
9918 ("r-mclust" ,r-mclust)
9920 ("r-multicool" ,r-multicool)
9921 ("r-mvtnorm" ,r-mvtnorm)))
9922 (home-page "http://www.mvstat.net/tduong/")
9923 (synopsis "Kernel smoothing")
9925 "This package provides kernel smoothers for univariate and multivariate
9926 data, including density functions, density derivatives, cumulative
9927 distributions, modal clustering, discriminant analysis, and two-sample
9928 hypothesis testing.")
9929 ;; Either version of the GPL.
9930 (license (list license:gpl2 license:gpl3))))
9932 (define-public r-feature
9939 (uri (cran-uri "feature" version))
9942 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9943 (build-system r-build-system)
9946 ("r-misc3d" ,r-misc3d)
9948 (home-page "http://www.mvstat.net/tduong/")
9949 (synopsis "Inferential feature significance for kernel density estimation")
9951 "The feature package contains functions to display and compute kernel
9952 density estimates, significant gradient and significant curvature regions.
9953 Significant gradient and/or curvature regions often correspond to significant
9954 features (e.g. local modes).")
9955 ;; Either version of the GPL.
9956 (license (list license:gpl2 license:gpl3))))
9958 (define-public r-arm
9965 (uri (cran-uri "arm" version))
9968 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9969 (build-system r-build-system)
9971 `(("r-abind" ,r-abind)
9975 ("r-matrix" ,r-matrix)
9976 ("r-nlme" ,r-nlme)))
9977 (home-page "https://cran.r-project.org/web/packages/arm/")
9978 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9980 "This package provides functions to accompany A. Gelman and J. Hill,
9981 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9982 University Press, 2007.")
9983 (license license:gpl3+)))
9985 (define-public r-circular
9992 (uri (cran-uri "circular" version))
9995 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9996 (build-system r-build-system)
9998 `(("r-boot" ,r-boot)
9999 ("r-mvtnorm" ,r-mvtnorm)))
10001 `(("gfortran" ,gfortran)))
10002 (home-page "https://cran.r-project.org/web/packages/circular/")
10003 (synopsis "Circular statistics")
10005 "This package provides tools for circular statistics, from \"Topics in
10006 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10008 (license license:gpl2+)))
10010 (define-public r-activity
10012 (name "r-activity")
10017 (uri (cran-uri "activity" version))
10020 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10021 (build-system r-build-system)
10023 `(("r-circular" ,r-circular)
10024 ("r-insol" ,r-insol)
10025 ("r-pbapply" ,r-pbapply)))
10026 (home-page "https://cran.r-project.org/web/packages/activity/")
10027 (synopsis "Animal activity statistics")
10029 "This package provides functions to fit kernel density functions to
10030 animal activity time data; plot activity distributions; quantify overall
10031 levels of activity; statistically compare activity metrics through
10032 bootstrapping; and evaluate variation in linear variables with time (or other
10033 circular variables).")
10034 (license license:gpl3)))
10036 (define-public r-ouch
10043 (uri (cran-uri "ouch" version))
10046 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10047 (build-system r-build-system)
10048 (propagated-inputs `(("r-subplex" ,r-subplex)))
10049 (home-page "https://kingaa.github.io/ouch/")
10050 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10052 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10053 for evolution along a phylogenetic tree.")
10054 (license license:gpl2+)))
10056 (define-public r-fmsb
10063 (uri (cran-uri "fmsb" version))
10066 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10067 (build-system r-build-system)
10068 (home-page "http://minato.sip21c.org/msb/")
10069 (synopsis "Functions for medical statistics book with demographic data")
10071 "This package provides several utility functions for the book entitled
10072 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10073 Japan, 2007) with Japanese demographic data and some demographic analysis
10074 related functions.")
10075 (license license:gpl2+)))
10077 (define-public r-stabledist
10079 (name "r-stabledist")
10084 (uri (cran-uri "stabledist" version))
10087 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10088 (build-system r-build-system)
10089 (home-page "https://www.rmetrics.org")
10090 (synopsis "Stable distribution functions")
10092 "This package provides density, probability and quantile functions, and
10093 random number generation for (skew) stable distributions, using the
10094 parametrizations of Nolan.")
10095 (license license:gpl2+)))
10097 (define-public r-gsl
10104 (uri (cran-uri "gsl" version))
10107 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10108 (build-system r-build-system)
10111 (home-page "https://cran.r-project.org/web/packages/gsl")
10112 (synopsis "Wrapper for the GNU Scientific Library")
10114 "This package provides an R wrapper for the special functions and quasi
10115 random number generators of the GNU Scientific Library.")
10116 (license license:gpl2+)))
10118 (define-public r-adgoftest
10120 (name "r-adgoftest")
10125 (uri (cran-uri "ADGofTest" version))
10128 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10129 (properties `((upstream-name . "ADGofTest")))
10130 (build-system r-build-system)
10131 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10132 (synopsis "Anderson-Darling GoF test")
10134 "This package provides an implementation of the Anderson-Darling GoF test
10135 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10136 Anderson-Darling Distribution\".")
10137 ;; Any version of the GPL.
10138 (license license:gpl3+)))
10140 (define-public r-softimpute
10142 (name "r-softimpute")
10147 (uri (cran-uri "softImpute" version))
10150 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10151 (properties `((upstream-name . "softImpute")))
10152 (build-system r-build-system)
10154 `(("r-matrix" ,r-matrix)))
10156 `(("gfortran" ,gfortran)))
10157 (home-page "https://cran.r-project.org/web/packages/softImpute")
10158 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10160 "This package provides iterative methods for matrix completion that use
10161 nuclear-norm regularization. The package includes procedures for centering
10162 and scaling rows, columns or both, and for computing low-rank @dfn{single
10163 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10165 (license license:gpl2)))
10167 (define-public r-fftwtools
10169 (name "r-fftwtools")
10174 (uri (cran-uri "fftwtools" version))
10177 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10178 (build-system r-build-system)
10179 (inputs `(("fftw" ,fftw)))
10180 (home-page "https://github.com/krahim/fftwtools")
10181 (synopsis "Wrapper for FFTW3")
10183 "This package provides a wrapper for several FFTW functions. It provides
10184 access to the two-dimensional FFT, the multivariate FFT, and the
10185 one-dimensional real to complex FFT using the FFTW3 library. The package
10186 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10187 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10188 The FFT functions have a parameter that allows them to not return the
10189 redundant complex conjugate when the input is real data.")
10190 (license license:gpl2+)))
10192 (define-public r-tiff
10199 (uri (cran-uri "tiff" version))
10202 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10203 (build-system r-build-system)
10205 `(("libtiff" ,libtiff)
10206 ("libjpeg" ,libjpeg-turbo)
10208 (home-page "https://www.rforge.net/tiff/")
10209 (synopsis "Read and write TIFF images")
10211 "This package provides an easy and simple way to read, write and display
10212 bitmap images stored in the TIFF format. It can read and write both files and
10213 in-memory raw vectors.")
10214 ;; Either of these two license versions.
10215 (license (list license:gpl2 license:gpl3))))
10217 (define-public r-nlp
10224 (uri (cran-uri "NLP" version))
10227 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10228 (properties `((upstream-name . "NLP")))
10229 (build-system r-build-system)
10230 (home-page "https://cran.r-project.org/web/packages/NLP/")
10231 (synopsis "Natural language processing infrastructure")
10233 "This package provides basic classes and methods for Natural Language
10235 (license license:gpl3)))
10237 (define-public r-tm
10244 (uri (cran-uri "tm" version))
10247 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10248 (properties `((upstream-name . "tm")))
10249 (build-system r-build-system)
10255 ("r-xml2" ,r-xml2)))
10256 (home-page "http://tm.r-forge.r-project.org/")
10257 (synopsis "Text mining package")
10259 "This package provides a framework for text mining applications within R.")
10260 (license license:gpl3)))
10262 (define-public r-waveslim
10264 (name "r-waveslim")
10269 (uri (cran-uri "waveslim" version))
10272 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10273 (build-system r-build-system)
10275 `(("gfortran" ,gfortran)))
10276 (home-page "http://waveslim.blogspot.com")
10277 (synopsis "Basic wavelet routines for signal processing")
10279 "This package provides basic wavelet routines for time series (1D),
10280 image (2D) and array (3D) analysis. The code provided here is based on
10281 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10282 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10283 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10284 pairs (Selesnick 2001, 2002).")
10285 (license license:bsd-3)))
10287 (define-public r-wordcloud
10289 (name "r-wordcloud")
10294 (uri (cran-uri "wordcloud" version))
10297 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10298 (build-system r-build-system)
10300 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10302 ;; The "tm" package is only "suggested" according to CRAN, but the
10303 ;; wordcloud package cannot be loaded without it.
10305 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10306 (synopsis "Word clouds")
10308 "This package provides functionality to create pretty word clouds,
10309 visualize differences and similarity between documents, and avoid
10310 over-plotting in scatter plots with text.")
10311 (license license:lgpl2.1)))
10313 (define-public r-colorramps
10315 (name "r-colorramps")
10320 (uri (cran-uri "colorRamps" version))
10323 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10324 (properties `((upstream-name . "colorRamps")))
10325 (build-system r-build-system)
10326 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10327 (synopsis "Build color tables")
10328 (description "This package provides features to build gradient color
10330 ;; Any version of the GPL
10331 (license license:gpl3+)))
10333 (define-public r-tidytree
10335 (name "r-tidytree")
10340 (uri (cran-uri "tidytree" version))
10342 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10343 (build-system r-build-system)
10346 ("r-dplyr" ,r-dplyr)
10347 ("r-lazyeval" ,r-lazyeval)
10348 ("r-magrittr" ,r-magrittr)
10349 ("r-rlang" ,r-rlang)
10350 ("r-tibble" ,r-tibble)))
10352 `(("r-knitr" ,r-knitr)))
10353 (home-page "https://github.com/GuangchuangYu/tidytree")
10354 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10356 "Phylogenetic trees generally contain multiple components including nodes,
10357 edges, branches and associated data. This package provides an approach to
10358 convert tree objects to tidy data frames. It also provides tidy interfaces to
10359 manipulate tree data.")
10360 (license license:artistic2.0)))
10362 (define-public r-rvcheck
10369 (uri (cran-uri "rvcheck" version))
10371 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10372 (build-system r-build-system)
10374 `(("r-biocmanager" ,r-biocmanager)
10375 ("r-rlang" ,r-rlang)))
10376 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10377 (synopsis "R package version check")
10379 "This package provides tools to check the latest release version of R and
10380 R packages (on CRAN, Bioconductor or Github).")
10381 (license license:artistic2.0)))
10383 (define-public r-docopt
10390 (uri (cran-uri "docopt" version))
10393 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
10394 (build-system r-build-system)
10395 (home-page "https://github.com/docopt/docopt.R")
10396 (synopsis "Command-line interface specification language")
10398 "This package enables you to define a command-line interface by just
10399 giving it a description in the specific format.")
10400 (license license:expat)))
10402 (define-public r-sparsesvd
10404 (name "r-sparsesvd")
10409 (uri (cran-uri "sparsesvd" version))
10412 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10413 (build-system r-build-system)
10414 (propagated-inputs `(("r-matrix" ,r-matrix)))
10415 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10416 (synopsis "Sparse truncated singular value decomposition")
10418 "This package provides a Wrapper around the SVDLIBC library
10419 for (truncated) singular value decomposition of a sparse matrix. Currently,
10420 only sparse real matrices in Matrix package format are supported.")
10421 ;; SVDLIBC is released under BSD-2. The R interface is released under
10423 (license (list license:bsd-3 license:bsd-2))))
10425 (define-public r-speedglm
10427 (name "r-speedglm")
10432 (uri (cran-uri "speedglm" version))
10435 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10436 (build-system r-build-system)
10438 `(("r-mass" ,r-mass)
10439 ("r-matrix" ,r-matrix)))
10440 (home-page "https://cran.r-project.org/web/packages/speedglm")
10441 (synopsis "Fit linear and generalized linear models to large data sets")
10443 "This package provides tools for fitting linear models and generalized
10444 linear models to large data sets by updating algorithms.")
10445 ;; Any version of the GPL
10446 (license license:gpl2+)))
10448 (define-public r-densityclust
10450 (name "r-densityclust")
10455 (uri (cran-uri "densityClust" version))
10458 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10459 (properties `((upstream-name . "densityClust")))
10460 (build-system r-build-system)
10463 ("r-ggplot2" ,r-ggplot2)
10464 ("r-ggrepel" ,r-ggrepel)
10465 ("r-gridextra" ,r-gridextra)
10466 ("r-rcolorbrewer" ,r-rcolorbrewer)
10468 ("r-rtsne" ,r-rtsne)))
10469 (home-page "https://cran.r-project.org/web/packages/densityClust")
10470 (synopsis "Clustering by fast search and find of density peaks")
10472 "This package provides an improved implementation (based on k-nearest
10473 neighbors) of the density peak clustering algorithm, originally described by
10474 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10475 large datasets (> 100,000 samples) very efficiently.")
10476 (license license:gpl2+)))
10478 (define-public r-combinat
10480 (name "r-combinat")
10485 (uri (cran-uri "combinat" version))
10488 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10489 (build-system r-build-system)
10490 (home-page "https://cran.r-project.org/web/packages/combinat")
10491 (synopsis "Combinatorics utilities")
10492 (description "This package provides assorted routines for combinatorics.")
10493 (license license:gpl2)))
10495 (define-public r-qlcmatrix
10497 (name "r-qlcmatrix")
10502 (uri (cran-uri "qlcMatrix" version))
10505 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10506 (properties `((upstream-name . "qlcMatrix")))
10507 (build-system r-build-system)
10509 `(("r-docopt" ,r-docopt)
10510 ("r-matrix" ,r-matrix)
10512 ("r-sparsesvd" ,r-sparsesvd)))
10513 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10514 (synopsis "Sparse matrix functions for quantitative language comparison")
10516 "This package provides an extension of the functionality of the Matrix
10517 package for using sparse matrices. Some of the functions are very general,
10518 while other are highly specific for the special data format used for
10519 @dfn{quantitative language comparison} (QLC).")
10520 (license license:gpl3)))
10522 (define-public r-ddrtree
10529 (uri (cran-uri "DDRTree" version))
10532 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10533 (properties `((upstream-name . "DDRTree")))
10534 (build-system r-build-system)
10537 ("r-irlba" ,r-irlba)
10539 ("r-rcppeigen" ,r-rcppeigen)))
10540 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10541 (synopsis "Learning principal graphs with DDRTree")
10543 "This package provides an implementation of the framework of
10544 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10545 dimensional space while constructs a principal tree which passes through the
10546 middle of the data simultaneously. DDRTree shows superiority to
10547 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10548 intrinsic structure of single cell genomics data. In general, it could be
10549 used to reconstruct the temporal progression as well as the bifurcation
10550 structure of any data type.")
10551 (license license:asl2.0)))
10553 (define-public r-corpcor
10560 (uri (cran-uri "corpcor" version))
10563 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10564 (build-system r-build-system)
10565 (home-page "http://strimmerlab.org/software/corpcor/")
10566 (synopsis "Efficient estimation of covariance and (partial) correlation")
10568 "This package implements a James-Stein-type shrinkage estimator for the
10569 covariance matrix, with separate shrinkage for variances and correlations.
10570 Furthermore, functions are available for fast singular value decomposition,
10571 for computing the pseudoinverse, and for checking the rank and positive
10572 definiteness of a matrix.")
10573 (license license:gpl3+)))
10575 (define-public r-rspectra
10577 (name "r-rspectra")
10582 (uri (cran-uri "RSpectra" version))
10585 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10586 (properties `((upstream-name . "RSpectra")))
10587 (build-system r-build-system)
10589 `(("r-matrix" ,r-matrix)
10591 ("r-rcppeigen" ,r-rcppeigen)))
10592 (home-page "https://github.com/yixuan/RSpectra")
10593 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10595 "This package provides an R interface to the Spectra library for
10596 large-scale eigenvalue and SVD problems. It is typically used to compute a
10597 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10598 which is usually more efficient than @code{eigen()} if k << n.")
10600 (license license:mpl2.0)))
10602 (define-public r-vbsr
10609 (uri (cran-uri "vbsr" version))
10612 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10613 (build-system r-build-system)
10614 (home-page "https://cran.r-project.org/web/packages/vbsr")
10615 (synopsis "Variational Bayes spike regression regularized linear models")
10617 "This package provides an efficient algorithm for solving ultra-sparse
10618 regularized regression models using a variational Bayes algorithm with a spike
10619 prior. The algorithm is solved on a path, with coordinate updates, and is
10620 capable of generating very sparse models. Very general model
10621 diagnostics for controlling type-1 errors are also provided.")
10622 (license license:gpl2)))
10624 (define-public r-flare
10627 (version "1.6.0.2")
10631 (uri (cran-uri "flare" version))
10634 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10635 (build-system r-build-system)
10637 `(("r-igraph" ,r-igraph)
10638 ("r-lattice" ,r-lattice)
10640 ("r-matrix" ,r-matrix)))
10641 (home-page "https://cran.r-project.org/web/packages/flare")
10642 (synopsis "Family of Lasso regression implementations")
10644 "This package provides implementations of a family of Lasso variants
10645 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10646 high dimensional sparse linear models.")
10647 (license license:gpl2)))
10649 (define-public r-lassopv
10656 (uri (cran-uri "lassopv" version))
10659 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10660 (build-system r-build-system)
10661 (propagated-inputs `(("r-lars" ,r-lars)))
10662 (home-page "https://github.com/lingfeiwang/lassopv")
10663 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10665 "This package enables you to estimate the p-values for predictors x
10666 against target variable y in Lasso regression, using the regularization
10667 strength when each predictor enters the active set of regularization path for
10668 the first time as the statistic.")
10669 (license license:gpl3)))
10671 (define-public r-splitstackshape
10673 (name "r-splitstackshape")
10678 (uri (cran-uri "splitstackshape" version))
10681 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10682 (build-system r-build-system)
10684 `(("r-data-table" ,r-data-table)))
10685 (home-page "https://github.com/mrdwab/splitstackshape")
10686 (synopsis "Stack and reshape datasets after splitting concatenated values")
10688 "Online data collection tools like Google Forms often export
10689 multiple-response questions with data concatenated in cells. The
10690 @code{concat.split} (cSplit) family of functions provided by this package
10691 splits such data into separate cells. This package also includes functions to
10692 stack groups of columns and to reshape wide data, even when the data are
10693 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10694 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10696 (license license:gpl3)))
10698 (define-public r-tfmpvalue
10700 (name "r-tfmpvalue")
10705 (uri (cran-uri "TFMPvalue" version))
10708 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10709 (properties `((upstream-name . "TFMPvalue")))
10710 (build-system r-build-system)
10711 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10712 (home-page "https://github.com/ge11232002/TFMPvalue")
10713 (synopsis "P-value computation for position weight matrices")
10715 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10716 identification from sequence/alignments, we are interested in the significance
10717 of certain match scores. TFMPvalue provides the accurate calculation of a
10718 p-value with a score threshold for position weight matrices, or the score with
10719 a given p-value. It is an interface to code originally made available by
10720 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10721 Touzet and Varre (2007).")
10722 (license license:gpl2)))
10724 (define-public r-rnifti
10731 (uri (cran-uri "RNifti" version))
10734 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10735 (properties `((upstream-name . "RNifti")))
10736 (build-system r-build-system)
10737 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10738 (home-page "https://github.com/jonclayden/RNifti")
10739 (synopsis "Fast R and C++ access to NIfTI images")
10741 "This package provides very fast read and write access to images stored
10742 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10743 compiled C and interpreted R code. It also provides a C/C++ API that can be
10744 used by other packages.")
10745 (license license:gpl2)))
10747 (define-public r-shades
10754 (uri (cran-uri "shades" version))
10757 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10758 (build-system r-build-system)
10759 (home-page "https://github.com/jonclayden/shades")
10760 (synopsis "Simple color manipulation")
10762 "This package provides functions for easily manipulating colors,
10763 creating color scales and calculating color distances.")
10764 (license license:bsd-3)))
10766 (define-public r-ore
10773 (uri (cran-uri "ore" version))
10775 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10776 (build-system r-build-system)
10777 (home-page "https://github.com/jonclayden/ore")
10778 (synopsis "R interface to the Onigmo regular expression library")
10780 "This package provides an alternative to R's built-in functionality for
10781 handling regular expressions, based on the Onigmo library. It offers
10782 first-class compiled regex objects, partial matching and function-based
10783 substitutions, amongst other features.")
10784 (license license:bsd-3)))
10786 (define-public r-reportr
10793 (uri (cran-uri "reportr" version))
10796 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10797 (build-system r-build-system)
10798 (propagated-inputs `(("r-ore" ,r-ore)))
10799 (home-page "https://github.com/jonclayden/reportr")
10800 (synopsis "General message and error reporting system")
10802 "This package provides a system for reporting messages, which offers
10803 certain useful features over the standard R system, such as the incorporation
10804 of output consolidation, message filtering, assertions, expression
10805 substitution, automatic generation of stack traces for debugging, and
10806 conditional reporting based on the current \"output level\".")
10807 (license license:gpl2)))
10809 (define-public r-tractor-base
10811 (name "r-tractor-base")
10816 (uri (cran-uri "tractor.base" version))
10819 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10820 (properties `((upstream-name . "tractor.base")))
10821 (build-system r-build-system)
10824 ("r-reportr" ,r-reportr)
10825 ("r-rnifti" ,r-rnifti)
10826 ("r-shades" ,r-shades)))
10827 (home-page "https://www.tractor-mri.org.uk")
10828 (synopsis "Read, manipulate and visualize magnetic resonance images")
10830 "This package provides functions for working with magnetic resonance
10831 images. It supports reading and writing of popular file formats (DICOM,
10832 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10833 visualization; flexible image manipulation; metadata and sparse image
10835 (license license:gpl2)))
10837 (define-public r-grimport
10839 (name "r-grimport")
10844 (uri (cran-uri "grImport" version))
10847 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10848 (properties `((upstream-name . "grImport")))
10849 (build-system r-build-system)
10851 `(("ghostscript" ,ghostscript)))
10853 `(("r-xml" ,r-xml)))
10854 (home-page "https://cran.r-project.org/web/packages/grImport")
10855 (synopsis "Convert, import, and draw PostScript pictures")
10857 "This package provides functions for converting, importing, and drawing
10858 PostScript pictures in R plots.")
10859 (license license:gpl2+)))
10861 (define-public r-grimport2
10863 (name "r-grimport2")
10868 (uri (cran-uri "grImport2" version))
10871 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10872 (properties `((upstream-name . "grImport2")))
10873 (build-system r-build-system)
10875 `(("r-base64enc" ,r-base64enc)
10879 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10880 (synopsis "Import SVG graphics")
10882 "This package provides functions for importing external vector images and
10883 drawing them as part of R plots. This package is different from the
10884 @code{grImport} package because, where that package imports PostScript format
10885 images, this package imports SVG format images. Furthermore, this package
10886 imports a specific subset of SVG, so external images must be preprocessed
10887 using a package like @code{rsvg} to produce SVG that this package can import.
10888 SVG features that are not supported by R graphics, such as gradient fills, can
10889 be imported and then exported via the @code{gridSVG} package.")
10890 (license license:gpl2+)))
10892 (define-public r-kohonen
10899 (uri (cran-uri "kohonen" version))
10902 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10903 (build-system r-build-system)
10905 `(("r-rcpp" ,r-rcpp)))
10906 (home-page "https://cran.r-project.org/web/packages/kohonen")
10907 (synopsis "Supervised and unsupervised self-organising maps")
10909 "This package provides functions to train @dfn{self-organising
10910 maps} (SOMs). Also interrogation of the maps and prediction using trained
10911 maps are supported. The name of the package refers to Teuvo Kohonen, the
10912 inventor of the SOM.")
10913 (license license:gpl2+)))
10915 (define-public r-nnls
10922 (uri (cran-uri "nnls" version))
10925 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10926 (build-system r-build-system)
10927 (native-inputs `(("gfortran" ,gfortran)))
10928 (home-page "https://cran.r-project.org/web/packages/nnls")
10929 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10931 "This package provides an R interface to the Lawson-Hanson implementation
10932 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10933 the combination of non-negative and non-positive constraints.")
10934 (license license:gpl2+)))
10936 (define-public r-iso
10939 (version "0.0-18.1")
10943 (uri (cran-uri "Iso" version))
10946 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
10947 (properties `((upstream-name . "Iso")))
10948 (build-system r-build-system)
10949 (native-inputs `(("gfortran" ,gfortran)))
10950 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10951 (synopsis "Functions to perform isotonic regression")
10953 "This package provides support for linear order and unimodal
10954 order (univariate) isotonic regression and bivariate isotonic regression with
10955 linear order on both variables.")
10956 (license license:gpl2+)))
10958 (define-public r-chemometricswithr
10960 (name "r-chemometricswithr")
10965 (uri (cran-uri "ChemometricsWithR" version))
10968 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10970 `((upstream-name . "ChemometricsWithR")))
10971 (build-system r-build-system)
10973 `(("r-devtools" ,r-devtools)
10974 ("r-kohonen" ,r-kohonen)
10977 (home-page "https://github.com/rwehrens/CWR")
10978 (synopsis "Chemometrics with R")
10980 "This package provides functions and scripts used in the book
10981 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10982 Life Sciences\" by Ron Wehrens, Springer (2011).")
10983 (license license:gpl2+)))
10985 (define-public r-als
10992 (uri (cran-uri "ALS" version))
10995 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10996 (properties `((upstream-name . "ALS")))
10997 (build-system r-build-system)
11000 ("r-nnls" ,r-nnls)))
11001 (home-page "https://cran.r-project.org/web/packages/ALS")
11002 (synopsis "Multivariate curve resolution alternating least squares")
11004 "Alternating least squares is often used to resolve components
11005 contributing to data with a bilinear structure; the basic technique may be
11006 extended to alternating constrained least squares. This package provides an
11007 implementation of @dfn{multivariate curve resolution alternating least
11008 squares} (MCR-ALS).
11010 Commonly applied constraints include unimodality, non-negativity, and
11011 normalization of components. Several data matrices may be decomposed
11012 simultaneously by assuming that one of the two matrices in the bilinear
11013 decomposition is shared between datasets.")
11014 (license license:gpl2+)))
11016 (define-public r-strucchange
11018 (name "r-strucchange")
11023 (uri (cran-uri "strucchange" version))
11026 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11027 (build-system r-build-system)
11029 `(("r-sandwich" ,r-sandwich)
11031 (home-page "https://cran.r-project.org/web/packages/strucchange")
11032 (synopsis "Testing, monitoring, and dating structural changes")
11034 "This package provides tools for testing, monitoring and dating
11035 structural changes in (linear) regression models. It features tests/methods
11036 from the generalized fluctuation test framework as well as from the F
11037 test (Chow test) framework. This includes methods to fit, plot and test
11038 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11039 statistics, respectively. It is possible to monitor incoming data online
11040 using fluctuation processes. Finally, the breakpoints in regression models
11041 with structural changes can be estimated together with confidence intervals.
11042 Emphasis is always given to methods for visualizing the data.")
11043 ;; Either of these two GPL versions
11044 (license (list license:gpl2 license:gpl3))))
11046 (define-public r-pixmap
11053 (uri (cran-uri "pixmap" version))
11056 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11057 (build-system r-build-system)
11058 (home-page "https://cran.r-project.org/web/packages/pixmap")
11059 (synopsis "Tools for bitmap images")
11061 "This package provides functions for importing, exporting, plotting and
11062 other manipulations of bitmapped images.")
11063 (license license:gpl2)))
11065 (define-public r-rapidjsonr
11067 (name "r-rapidjsonr")
11072 (uri (cran-uri "rapidjsonr" version))
11075 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11076 (build-system r-build-system)
11077 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11078 (synopsis "JSON parser")
11080 "This package provides JSON parsing capability through the Rapidjson
11082 (license license:expat)))
11084 (define-public r-ontologyindex
11086 (name "r-ontologyindex")
11091 (uri (cran-uri "ontologyIndex" version))
11094 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11095 (properties `((upstream-name . "ontologyIndex")))
11096 (build-system r-build-system)
11097 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11098 (synopsis "Functions for processing ontologies in R")
11100 "This package provides functions for reading ontologies into R as lists
11101 and manipulating sets of ontological terms.")
11102 (license license:gpl2+)))
11104 (define-public r-gargle
11111 (uri (cran-uri "gargle" version))
11114 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11115 (build-system r-build-system)
11120 ("r-jsonlite" ,r-jsonlite)
11121 ("r-rlang" ,r-rlang)
11122 ("r-withr" ,r-withr)))
11124 `(("r-knitr" ,r-knitr)))
11125 (home-page "https://gargle.r-lib.org")
11126 (synopsis "Utilities for working with Google APIs")
11128 "This package provides utilities for working with Google APIs. This
11129 includes functions and classes for handling common credential types and for
11130 preparing, executing, and processing HTTP requests.")
11131 (license license:expat)))
11133 (define-public r-bigrquery
11135 (name "r-bigrquery")
11140 (uri (cran-uri "bigrquery" version))
11143 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11144 (build-system r-build-system)
11146 `(("r-assertthat" ,r-assertthat)
11147 ("r-bit64" ,r-bit64)
11150 ("r-gargle" ,r-gargle)
11153 ("r-jsonlite" ,r-jsonlite)
11154 ("r-prettyunits" ,r-prettyunits)
11155 ("r-progress" ,r-progress)
11156 ("r-rapidjsonr" ,r-rapidjsonr)
11158 ("r-rlang" ,r-rlang)
11159 ("r-tibble" ,r-tibble)))
11160 (home-page "https://github.com/rstats-db/bigrquery")
11161 (synopsis "R interface to Google's BigQuery API")
11163 "This package provides an R interface to Google's BigQuery database.")
11164 (license license:gpl3)))
11166 (define-public r-gmp
11173 (uri (cran-uri "gmp" version))
11176 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11177 (build-system r-build-system)
11180 (modify-phases %standard-phases
11181 (add-after 'unpack 'set-CC
11182 (lambda _ (setenv "CC" "gcc") #t)))))
11183 (inputs `(("gmp" ,gmp)))
11184 (home-page "https://cran.r-project.org/web/packages/gmp")
11185 (synopsis "Multiple precision arithmetic")
11187 "This package supports multiple precision arithmetic (big integers and
11188 rationals, prime number tests, matrix computation), \"arithmetic without
11189 limitations\" using the GNU Multiple Precision library.")
11190 ;; Any version of the GPL.
11191 (license license:gpl3+)))
11193 (define-public r-rmpfr
11200 (uri (cran-uri "Rmpfr" version))
11203 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11204 (properties `((upstream-name . "Rmpfr")))
11205 (build-system r-build-system)
11210 `(("r-gmp" ,r-gmp)))
11212 `(("pkg-config" ,pkg-config)))
11213 (home-page "http://rmpfr.r-forge.r-project.org/")
11214 (synopsis "R bindings to the MPFR library")
11216 "This package supports arithmetic (via S4 classes and methods) for
11217 arbitrary precision floating point numbers, including transcendental
11218 functions. To this end, the package interfaces with the @dfn{Multiple
11219 Precision Floating-Point Reliable} (MPFR) library.")
11220 (license license:gpl2+)))
11222 (define-public r-assertive-base
11224 (name "r-assertive-base")
11229 (uri (cran-uri "assertive.base" version))
11232 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11234 `((upstream-name . "assertive.base")))
11235 (build-system r-build-system)
11236 (home-page "https://bitbucket.org/richierocks/assertive.base")
11237 (synopsis "Core of the assertive package")
11239 "This package provides a minimal set of predicates and assertions used by
11240 the assertive package. This is mainly for use by other package developers who
11241 want to include run-time testing features in their own packages.")
11242 (license license:gpl3+)))
11244 (define-public r-assertive-properties
11246 (name "r-assertive-properties")
11251 (uri (cran-uri "assertive.properties" version))
11254 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11256 `((upstream-name . "assertive.properties")))
11257 (build-system r-build-system)
11259 `(("r-assertive-base" ,r-assertive-base)))
11260 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11261 (synopsis "Assertions to check properties of variables")
11263 "This package provides a set of predicates and assertions for checking
11264 the properties of variables, such as length, names and attributes. This is
11265 mainly for use by other package developers who want to include run-time
11266 testing features in their own packages.")
11267 (license license:gpl3+)))
11269 (define-public r-assertive-numbers
11271 (name "r-assertive-numbers")
11276 (uri (cran-uri "assertive.numbers" version))
11279 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11281 `((upstream-name . "assertive.numbers")))
11282 (build-system r-build-system)
11284 `(("r-assertive-base" ,r-assertive-base)))
11285 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11286 (synopsis "Assertions to check properties of numbers")
11288 "This package provides a set of predicates and assertions for checking
11289 the properties of numbers. This is mainly for use by other package developers
11290 who want to include run-time testing features in their own packages.")
11291 (license license:gpl3+)))
11293 (define-public r-assertive-sets
11295 (name "r-assertive-sets")
11300 (uri (cran-uri "assertive.sets" version))
11303 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11305 `((upstream-name . "assertive.sets")))
11306 (build-system r-build-system)
11308 `(("r-assertive-base" ,r-assertive-base)))
11309 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11310 (synopsis "Assertions to check properties of sets")
11312 "This package provides a set of predicates and assertions for checking
11313 the properties of sets. This is mainly for use by other package developers
11314 who want to include run-time testing features in their own packages.")
11315 (license license:gpl3+)))
11317 (define-public r-assertive-matrices
11319 (name "r-assertive-matrices")
11324 (uri (cran-uri "assertive.matrices" version))
11327 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11329 `((upstream-name . "assertive.matrices")))
11330 (build-system r-build-system)
11332 `(("r-assertive-base" ,r-assertive-base)))
11333 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11334 (synopsis "Assertions to check properties of matrices")
11336 "This package provides a set of predicates and assertions for checking
11337 the properties of matrices. This is mainly for use by other package
11338 developers who want to include run-time testing features in their own
11340 (license license:gpl3+)))
11342 (define-public r-assertive-models
11344 (name "r-assertive-models")
11349 (uri (cran-uri "assertive.models" version))
11352 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11354 `((upstream-name . "assertive.models")))
11355 (build-system r-build-system)
11357 `(("r-assertive-base" ,r-assertive-base)))
11358 (home-page "https://bitbucket.org/richierocks/assertive.models")
11359 (synopsis "Assertions to check properties of models")
11361 "This package provides a set of predicates and assertions for checking
11362 the properties of models. This is mainly for use by other package developers
11363 who want to include run-time testing features in their own packages.")
11364 (license license:gpl3+)))
11366 (define-public r-assertive-reflection
11368 (name "r-assertive-reflection")
11373 (uri (cran-uri "assertive.reflection" version))
11376 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11378 `((upstream-name . "assertive.reflection")))
11379 (build-system r-build-system)
11381 `(("r-assertive-base" ,r-assertive-base)))
11382 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11383 (synopsis "Assertions for checking the state of R")
11385 "This package provides a set of predicates and assertions for checking
11386 the state and capabilities of R, the operating system it is running on, and
11387 the IDE being used. This is mainly for use by other package developers who
11388 want to include run-time testing features in their own packages.")
11389 (license license:gpl3+)))
11391 (define-public r-assertive-types
11393 (name "r-assertive-types")
11398 (uri (cran-uri "assertive.types" version))
11401 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11403 `((upstream-name . "assertive.types")))
11404 (build-system r-build-system)
11406 `(("r-assertive-base" ,r-assertive-base)
11407 ("r-assertive-properties" ,r-assertive-properties)
11408 ("r-codetools" ,r-codetools)))
11409 (home-page "https://bitbucket.org/richierocks/assertive.types")
11410 (synopsis "Assertions to check types of variables")
11412 "This package provides a set of predicates and assertions for checking
11413 the types of variables. This is mainly for use by other package developers
11414 who want to include run-time testing features in their own packages.")
11415 (license license:gpl3+)))
11417 (define-public r-assertive-files
11419 (name "r-assertive-files")
11424 (uri (cran-uri "assertive.files" version))
11427 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11429 `((upstream-name . "assertive.files")))
11430 (build-system r-build-system)
11432 `(("r-assertive-base" ,r-assertive-base)
11433 ("r-assertive-numbers" ,r-assertive-numbers)))
11434 (home-page "https://bitbucket.org/richierocks/assertive.files")
11435 (synopsis "Assertions to check properties of files")
11437 "This package provides a set of predicates and assertions for checking
11438 the properties of files and connections. This is mainly for use by other
11439 package developers who want to include run-time testing features in their own
11441 (license license:gpl3+)))
11443 (define-public r-assertive-code
11445 (name "r-assertive-code")
11450 (uri (cran-uri "assertive.code" version))
11453 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11455 `((upstream-name . "assertive.code")))
11456 (build-system r-build-system)
11458 `(("r-assertive-base" ,r-assertive-base)
11459 ("r-assertive-properties" ,r-assertive-properties)
11460 ("r-assertive-types" ,r-assertive-types)))
11461 (home-page "https://bitbucket.org/richierocks/assertive.code")
11462 (synopsis "Assertions to check properties of code")
11464 "This package provides a set of predicates and assertions for checking
11465 the properties of code. This is mainly for use by other package developers
11466 who want to include run-time testing features in their own packages.")
11467 (license license:gpl3+)))
11469 (define-public r-assertive-datetimes
11471 (name "r-assertive-datetimes")
11476 (uri (cran-uri "assertive.datetimes" version))
11479 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11481 `((upstream-name . "assertive.datetimes")))
11482 (build-system r-build-system)
11484 `(("r-assertive-base" ,r-assertive-base)
11485 ("r-assertive-types" ,r-assertive-types)))
11486 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11487 (synopsis "Assertions to check properties of dates and times")
11489 "This package provides a set of predicates and assertions for checking
11490 the properties of dates and times. This is mainly for use by other package
11491 developers who want to include run-time testing features in their own
11493 (license license:gpl3+)))
11495 (define-public r-assertive-strings
11497 (name "r-assertive-strings")
11502 (uri (cran-uri "assertive.strings" version))
11505 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11507 `((upstream-name . "assertive.strings")))
11508 (build-system r-build-system)
11510 `(("r-assertive-base" ,r-assertive-base)
11511 ("r-assertive-types" ,r-assertive-types)
11512 ("r-stringi" ,r-stringi)))
11513 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11514 (synopsis "Assertions to check properties of strings")
11516 "This package provides a set of predicates and assertions for checking
11517 the properties of strings. This is mainly for use by other package developers
11518 who want to include run-time testing features in their own packages.")
11519 (license license:gpl3+)))
11521 (define-public r-assertive-data-us
11523 (name "r-assertive-data-us")
11528 (uri (cran-uri "assertive.data.us" version))
11531 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11533 `((upstream-name . "assertive.data.us")))
11534 (build-system r-build-system)
11536 `(("r-assertive-base" ,r-assertive-base)
11537 ("r-assertive-strings" ,r-assertive-strings)))
11538 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11539 (synopsis "Assertions to check properties of strings")
11541 "This package provides a set of predicates and assertions for checking
11542 the properties of US-specific complex data types. This is mainly for use by
11543 other package developers who want to include run-time testing features in
11544 their own packages.")
11545 (license license:gpl3+)))
11547 (define-public r-assertive-data-uk
11549 (name "r-assertive-data-uk")
11554 (uri (cran-uri "assertive.data.uk" version))
11557 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11559 `((upstream-name . "assertive.data.uk")))
11560 (build-system r-build-system)
11562 `(("r-assertive-base" ,r-assertive-base)
11563 ("r-assertive-strings" ,r-assertive-strings)))
11564 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11565 (synopsis "Assertions to check properties of strings")
11567 "This package provides a set of predicates and assertions for checking
11568 the properties of UK-specific complex data types. This is mainly for use by
11569 other package developers who want to include run-time testing features in
11570 their own packages.")
11571 (license license:gpl3+)))
11573 (define-public r-assertive-data
11575 (name "r-assertive-data")
11580 (uri (cran-uri "assertive.data" version))
11583 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11585 `((upstream-name . "assertive.data")))
11586 (build-system r-build-system)
11588 `(("r-assertive-base" ,r-assertive-base)
11589 ("r-assertive-strings" ,r-assertive-strings)))
11590 (home-page "https://bitbucket.org/richierocks/assertive.data")
11591 (synopsis "Assertions to check properties of data")
11593 "This package provides a set of predicates and assertions for checking
11594 the properties of (country independent) complex data types. This is mainly
11595 for use by other package developers who want to include run-time testing
11596 features in their own packages.")
11597 (license license:gpl3+)))
11599 (define-public r-assertive
11601 (name "r-assertive")
11606 (uri (cran-uri "assertive" version))
11609 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11610 (build-system r-build-system)
11612 `(("r-assertive-base" ,r-assertive-base)
11613 ("r-assertive-code" ,r-assertive-code)
11614 ("r-assertive-data" ,r-assertive-data)
11615 ("r-assertive-data-uk" ,r-assertive-data-uk)
11616 ("r-assertive-data-us" ,r-assertive-data-us)
11617 ("r-assertive-datetimes" ,r-assertive-datetimes)
11618 ("r-assertive-files" ,r-assertive-files)
11619 ("r-assertive-matrices" ,r-assertive-matrices)
11620 ("r-assertive-models" ,r-assertive-models)
11621 ("r-assertive-numbers" ,r-assertive-numbers)
11622 ("r-assertive-properties" ,r-assertive-properties)
11623 ("r-assertive-reflection" ,r-assertive-reflection)
11624 ("r-assertive-sets" ,r-assertive-sets)
11625 ("r-assertive-strings" ,r-assertive-strings)
11626 ("r-assertive-types" ,r-assertive-types)
11627 ("r-knitr" ,r-knitr)))
11628 (home-page "https://bitbucket.org/richierocks/assertive")
11629 (synopsis "Readable check functions to ensure code integrity")
11631 "This package provides lots of predicates (@code{is_*} functions) to
11632 check the state of your variables, and assertions (@code{assert_*} functions)
11633 to throw errors if they aren't in the right form.")
11634 (license license:gpl3+)))
11636 (define-public r-dotcall64
11638 (name "r-dotcall64")
11643 (uri (cran-uri "dotCall64" version))
11646 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11647 (properties `((upstream-name . "dotCall64")))
11648 (build-system r-build-system)
11649 (native-inputs `(("gfortran" ,gfortran)))
11650 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11651 (synopsis "Enhanced foreign function interface supporting long vectors")
11653 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11654 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11655 supports long vectors, arguments of type 64-bit integer, and provides a
11656 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11657 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11658 (license license:gpl2+)))
11660 (define-public r-spam
11667 (uri (cran-uri "spam" version))
11669 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11670 (build-system r-build-system)
11672 `(("r-dotcall64" ,r-dotcall64)))
11673 (native-inputs `(("gfortran" ,gfortran)))
11674 (home-page "https://www.math.uzh.ch/pages/spam/")
11675 (synopsis "Sparse matrix algebra")
11677 "This package provides a set of functions for sparse matrix algebra.
11678 Differences with other sparse matrix packages are:
11681 @item it only supports (essentially) one sparse matrix format;
11682 @item it is based on transparent and simple structure(s);
11683 @item it is tailored for MCMC calculations within G(M)RF;
11684 @item and it is fast and scalable (with the extension package @code{spam64}).
11686 ;; Either of these licenses
11687 (license (list license:bsd-3 license:lgpl2.0))))
11689 (define-public r-fields
11696 (uri (cran-uri "fields" version))
11698 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11699 (build-system r-build-system)
11701 `(("r-maps" ,r-maps)
11702 ("r-spam" ,r-spam)))
11704 `(("gfortran" ,gfortran)))
11705 (home-page "https://www.image.ucar.edu/fields")
11706 (synopsis "Tools for spatial data")
11708 "This is a package for curve, surface and function fitting with an
11709 emphasis on splines, spatial data and spatial statistics. The major methods
11710 include cubic, and thin plate splines, Kriging, and compactly supported
11711 covariance functions for large data sets.")
11712 (license license:gpl2+)))
11714 (define-public r-spatialextremes
11716 (name "r-spatialextremes")
11721 (uri (cran-uri "SpatialExtremes" version))
11724 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11726 `((upstream-name . "SpatialExtremes")))
11727 (build-system r-build-system)
11729 `(("r-fields" ,r-fields)
11730 ("r-maps" ,r-maps)))
11731 (home-page "http://spatialextremes.r-forge.r-project.org/")
11732 (synopsis "Modelling spatial extremes")
11734 "This package provides tools for the statistical modelling of spatial
11735 extremes using max-stable processes, copula or Bayesian hierarchical models.
11736 More precisely, this package allows (conditional) simulations from various
11737 parametric max-stable models, analysis of the extremal spatial dependence, the
11738 fitting of such processes using composite likelihoods or least square (simple
11739 max-stable processes only), model checking and selection and prediction.")
11740 (license license:gpl2+)))
11742 (define-public r-drc
11749 (uri (cran-uri "drc" version))
11752 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11753 (build-system r-build-system)
11756 ("r-gtools" ,r-gtools)
11758 ("r-multcomp" ,r-multcomp)
11759 ("r-plotrix" ,r-plotrix)
11760 ("r-scales" ,r-scales)))
11761 (home-page "https://cran.r-project.org/web/packages/drc")
11762 (synopsis "Analysis of dose-response curves")
11764 "This package provides a suite of flexible and versatile model fitting
11765 and after-fitting functions for the analysis of dose-response data.")
11766 (license license:gpl2+)))
11768 (define-public r-rmeta
11775 (uri (cran-uri "rmeta" version))
11778 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11779 (build-system r-build-system)
11780 (home-page "https://cran.r-project.org/web/packages/rmeta")
11781 (synopsis "Tools for meta-analysis")
11783 "This package provides functions for simple fixed and random effects
11784 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11785 draws standard summary plots, funnel plots, and computes summaries and tests
11786 for association and heterogeneity.")
11787 (license license:gpl2)))
11789 (define-public r-bootstrap
11791 (name "r-bootstrap")
11796 (uri (cran-uri "bootstrap" version))
11799 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11800 (build-system r-build-system)
11801 (native-inputs `(("gfortran" ,gfortran)))
11802 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11803 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11805 "This package provides software and data for the book \"An Introduction
11806 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11807 This package is primarily provided for projects already based on it, and for
11808 support of the book. New projects should preferentially use the recommended
11809 package \"boot\".")
11810 (license license:bsd-3)))
11812 (define-public r-survivalroc
11814 (name "r-survivalroc")
11819 (uri (cran-uri "survivalROC" version))
11822 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11823 (properties `((upstream-name . "survivalROC")))
11824 (build-system r-build-system)
11825 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11826 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11828 "Compute time-dependent ROC curve from censored survival data using
11829 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11830 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11831 (license license:gpl2+)))
11833 (define-public r-longitudinal
11835 (name "r-longitudinal")
11840 (uri (cran-uri "longitudinal" version))
11843 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11844 (build-system r-build-system)
11845 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11846 (home-page "http://strimmerlab.org/software/longitudinal/")
11847 (synopsis "Analysis of multiple time course data")
11849 "This package contains general data structures and functions for
11850 longitudinal data with multiple variables, repeated measurements, and
11851 irregularly spaced time points. It also implements a shrinkage estimator of
11852 dynamical correlation and dynamical covariance.")
11853 (license license:gpl3+)))
11855 (define-public r-genenet
11862 (uri (cran-uri "GeneNet" version))
11865 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11866 (properties `((upstream-name . "GeneNet")))
11867 (build-system r-build-system)
11869 `(("r-corpcor" ,r-corpcor)
11870 ("r-fdrtool" ,r-fdrtool)
11871 ("r-longitudinal" ,r-longitudinal)))
11872 (home-page "http://strimmerlab.org/software/genenet/")
11873 (synopsis "Modeling and inferring gene networks")
11875 "This package analyzes gene expression (time series) data with focus on
11876 the inference of gene networks. In particular, GeneNet implements the methods
11877 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11878 for learning large-scale gene association networks (including assignment of
11879 putative directions).")
11880 (license license:gpl3+)))
11882 (define-public r-rbamtools
11884 (name "r-rbamtools")
11885 (version "2.16.17")
11889 (uri (cran-uri "rbamtools" version))
11892 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11893 (build-system r-build-system)
11894 (inputs `(("zlib" ,zlib)))
11896 `(("r-refgenome" ,r-refgenome)))
11897 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11898 (synopsis "Read and write BAM (binary alignment) files")
11900 "This package provides an R interface to functions of the SAMtools
11902 (license license:artistic2.0)))
11904 (define-public r-protviz
11911 (uri (cran-uri "protViz" version))
11914 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11915 (properties `((upstream-name . "protViz")))
11916 (build-system r-build-system)
11917 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11918 (home-page "https://github.com/protViz/protViz/")
11919 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11921 "This package helps with quality checks, visualizations and analysis of
11922 mass spectrometry data, coming from proteomics experiments. The package is
11923 developed, tested and used at the Functional Genomics Center Zurich, where it
11924 is used mainly for prototyping, teaching, and having fun with proteomics data.
11925 But it can also be used to do data analysis for small scale data sets.")
11926 (license license:gpl3)))
11928 (define-public r-cmprsk
11935 (uri (cran-uri "cmprsk" version))
11937 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11938 (build-system r-build-system)
11940 `(("r-survival" ,r-survival)))
11942 `(("gfortran" ,gfortran)))
11943 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11944 (synopsis "Subdistribution analysis of competing risks")
11946 "This package provides tool for estimation, testing and regression
11947 modeling of subdistribution functions in competing risks, as described in
11948 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11949 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11950 A proportional hazards model for the subdistribution of a competing risk,
11951 JASA, 94:496-509.")
11952 (license license:gpl2+)))
11954 (define-public r-etm
11961 (uri (cran-uri "etm" version))
11964 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11965 (build-system r-build-system)
11967 `(("r-data-table" ,r-data-table)
11968 ("r-lattice" ,r-lattice)
11970 ("r-rcpparmadillo" ,r-rcpparmadillo)
11971 ("r-survival" ,r-survival)))
11972 (home-page "https://cran.r-project.org/web/packages/etm")
11973 (synopsis "Empirical transition matrix")
11975 "The @dfn{empirical transition matrix} (etm) package estimates
11976 the matrix of transition probabilities for any time-inhomogeneous multistate
11977 model with finite state space using the Aalen-Johansen estimator.")
11978 (license license:expat)))
11980 (define-public r-epi
11987 (uri (cran-uri "Epi" version))
11990 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11991 (properties `((upstream-name . "Epi")))
11992 (build-system r-build-system)
11994 `(("r-cmprsk" ,r-cmprsk)
11995 ("r-data-table" ,r-data-table)
11998 ("r-matrix" ,r-matrix)
12000 ("r-numderiv" ,r-numderiv)
12002 ("r-survival" ,r-survival)
12004 (home-page "https://BendixCarstensen.com/Epi/")
12005 (synopsis "Statistical analysis in epidemiology")
12007 "This package provides functions for demographic and epidemiological
12008 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12009 particular representation, manipulation and simulation of multistate data -
12010 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12011 @code{etm} and @code{cmprsk} packages. It also contains functions for
12012 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12013 data and some useful functions for tabulation and plotting, as well as a
12014 number of epidemiological data sets.")
12015 (license license:gpl2)))
12017 (define-public r-ppls
12020 (version "1.6-1.1")
12024 (uri (cran-uri "ppls" version))
12027 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12028 (build-system r-build-system)
12029 (propagated-inputs `(("r-mass" ,r-mass)))
12030 (home-page "https://cran.r-project.org/web/packages/ppls")
12031 (synopsis "Penalized partial least squares")
12033 "This package contains linear and nonlinear regression methods based on
12034 partial least squares and penalization techniques. Model parameters are
12035 selected via cross-validation, and confidence intervals ans tests for the
12036 regression coefficients can be conducted via jackknifing.")
12037 (license license:gpl2+)))
12039 (define-public r-huge
12042 (version "1.3.4.1")
12046 (uri (cran-uri "huge" version))
12048 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12049 (build-system r-build-system)
12051 `(("r-igraph" ,r-igraph)
12053 ("r-matrix" ,r-matrix)
12055 ("r-rcppeigen" ,r-rcppeigen)))
12056 (home-page "https://cran.r-project.org/web/packages/huge")
12057 (synopsis "High-dimensional undirected graph estimation")
12059 "This package provides a general framework for high-dimensional
12060 undirected graph estimation. It integrates data preprocessing, neighborhood
12061 screening, graph estimation, and model selection techniques into a pipeline.")
12062 (license license:gpl2)))
12064 (define-public r-parcor
12071 (uri (cran-uri "parcor" version))
12074 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12075 (build-system r-build-system)
12078 ("r-genenet" ,r-genenet)
12079 ("r-glmnet" ,r-glmnet)
12081 ("r-ppls" ,r-ppls)))
12082 (home-page "https://cran.r-project.org/web/packages/parcor")
12083 (synopsis "Regularized estimation of partial correlation matrices")
12085 "This package estimates the matrix of partial correlations based on
12086 different regularized regression methods: lasso, adaptive lasso, PLS, and
12087 Ridge Regression. In addition, the package provides model selection for
12088 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12089 (license license:gpl2+)))
12091 (define-public r-mcmc
12098 (uri (cran-uri "mcmc" version))
12101 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12102 (build-system r-build-system)
12103 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12104 (synopsis "Markov chain Monte Carlo")
12106 "This package simulates continuous distributions of random vectors using
12107 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12108 function that evaluates the log unnormalized density. Algorithms are random
12109 walk Metropolis algorithm (function @code{metrop}), simulated
12110 tempering (function @code{temper}), and morphometric random walk
12111 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12112 by change of variable.")
12113 (license license:expat)))
12115 (define-public r-listenv
12122 (uri (cran-uri "listenv" version))
12125 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12126 (build-system r-build-system)
12128 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12129 (home-page "https://github.com/HenrikBengtsson/listenv")
12130 (synopsis "Environments behaving (almost) as lists")
12132 "This package implements list environments. List environments are
12133 environments that have list-like properties. For instance, the elements of a
12134 list environment are ordered and can be accessed and iterated over using index
12136 (license license:lgpl2.1+)))
12138 (define-public r-globals
12145 (uri (cran-uri "globals" version))
12148 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12149 (build-system r-build-system)
12151 `(("r-codetools" ,r-codetools)))
12152 (home-page "https://github.com/HenrikBengtsson/globals")
12153 (synopsis "Identify global objects in R expressions")
12155 "This package provides tools to identify global (\"unknown\" or \"free\")
12156 objects in R expressions by code inspection using various strategies, e.g.
12157 conservative or liberal. The objective of this package is to make it as
12158 simple as possible to identify global objects for the purpose of exporting
12159 them in distributed compute environments.")
12160 (license license:lgpl2.1+)))
12162 (define-public r-future
12169 (uri (cran-uri "future" version))
12172 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
12173 (build-system r-build-system)
12175 `(("r-digest" ,r-digest)
12176 ("r-globals" ,r-globals)
12177 ("r-listenv" ,r-listenv)))
12179 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12180 (home-page "https://github.com/HenrikBengtsson/future")
12181 (synopsis "Unified parallel and distributed processing in R")
12183 "The purpose of this package is to provide a lightweight and unified
12184 Future API for sequential and parallel processing of R expression via futures.
12185 This package implements sequential, multicore, multisession, and cluster
12186 futures. With these, R expressions can be evaluated on the local machine, in
12187 parallel a set of local machines, or distributed on a mix of local and remote
12188 machines. Extensions to this package implement additional backends for
12189 processing futures via compute cluster schedulers etc. Because of its unified
12190 API, there is no need to modify any code in order to switch from sequential on
12191 the local machine to, say, distributed processing on a remote compute cluster.")
12192 (license license:lgpl2.1+)))
12194 (define-public r-future-apply
12196 (name "r-future-apply")
12201 (uri (cran-uri "future.apply" version))
12204 "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
12205 (properties `((upstream-name . "future.apply")))
12206 (build-system r-build-system)
12208 `(("r-future" ,r-future)
12209 ("r-globals" ,r-globals)))
12211 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12212 (home-page "https://github.com/HenrikBengtsson/future.apply")
12213 (synopsis "Apply function to elements in parallel using futures")
12215 "This package provides implementations of @code{apply()},
12216 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12217 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12218 can be resolved using any future-supported backend, e.g. parallel on the local
12219 machine or distributed on a compute cluster.")
12220 (license license:gpl2+)))
12222 (define-public r-rsvd
12229 (uri (cran-uri "rsvd" version))
12232 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12233 (build-system r-build-system)
12235 `(("r-matrix" ,r-matrix)))
12236 (home-page "https://github.com/erichson/rSVD")
12237 (synopsis "Randomized singular value decomposition")
12239 "Low-rank matrix decompositions are fundamental tools and widely used for
12240 data analysis, dimension reduction, and data compression. Classically, highly
12241 accurate deterministic matrix algorithms are used for this task. However, the
12242 emergence of large-scale data has severely challenged our computational
12243 ability to analyze big data. The concept of randomness has been demonstrated
12244 as an effective strategy to quickly produce approximate answers to familiar
12245 problems such as the @dfn{singular value decomposition} (SVD). This package
12246 provides several randomized matrix algorithms such as the randomized singular
12247 value decomposition (@code{rsvd}), randomized principal component
12248 analysis (@code{rpca}), randomized robust principal component
12249 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12250 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12251 functions are provided.")
12252 (license license:gpl3+)))
12254 (define-public r-sloop
12261 (uri (cran-uri "sloop" version))
12264 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12265 (build-system r-build-system)
12267 `(("r-codetools" ,r-codetools)
12268 ("r-crayon" ,r-crayon)
12269 ("r-purrr" ,r-purrr)
12270 ("r-rlang" ,r-rlang)
12271 ("r-tibble" ,r-tibble)))
12272 (home-page "https://github.com/r-lib/sloop")
12273 (synopsis "Helpers for object-oriented programming in R")
12275 "This package provides a collection of helper functions designed to
12276 help you to better understand object oriented programming in R, particularly
12278 (license license:gpl3)))
12280 (define-public r-capushe
12287 (uri (cran-uri "capushe" version))
12290 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12291 (build-system r-build-system)
12292 (propagated-inputs `(("r-mass" ,r-mass)))
12293 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12294 (synopsis "Calibrating penalties using slope heuristics")
12296 "This package provides tools for the calibration of penalized criteria
12297 for model selection. The calibration methods available are based on the slope
12299 (license license:gpl2+)))
12301 (define-public r-dorng
12308 (uri (cran-uri "doRNG" version))
12311 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12312 (properties `((upstream-name . "doRNG")))
12313 (build-system r-build-system)
12315 `(("r-foreach" ,r-foreach)
12316 ("r-iterators" ,r-iterators)
12317 ("r-rngtools" ,r-rngtools)))
12318 (home-page "https://renozao.github.io/doRNG/")
12319 (synopsis "Generic reproducible parallel backend for foreach loops")
12321 "This package provides functions to perform reproducible parallel
12322 @code{foreach} loops, using independent random streams as generated by
12323 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12324 convert standard @code{%dopar%} loops into fully reproducible loops,
12325 independently of the number of workers, the task scheduling strategy, or the
12326 chosen parallel environment and associated foreach backend.")
12327 (license license:gpl2+)))
12329 (define-public r-blockmodeling
12331 (name "r-blockmodeling")
12336 (uri (cran-uri "blockmodeling" version))
12339 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
12340 (build-system r-build-system)
12342 `(("r-matrix" ,r-matrix)))
12343 (native-inputs `(("gfortran" ,gfortran)))
12344 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12345 (synopsis "Generalized and classical blockmodeling of valued networks")
12347 "This package is primarily meant as an implementation of generalized
12348 blockmodeling for valued networks. In addition, measures of similarity or
12349 dissimilarity based on structural equivalence and regular equivalence (REGE
12350 algorithms) can be computed and partitioned matrices can be plotted.")
12351 (license license:gpl2+)))
12353 (define-public r-upsetr
12360 (uri (cran-uri "UpSetR" version))
12363 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12364 (properties `((upstream-name . "UpSetR")))
12365 (build-system r-build-system)
12367 `(("r-ggplot2" ,r-ggplot2)
12368 ("r-gridextra" ,r-gridextra)
12370 ("r-scales" ,r-scales)))
12371 (home-page "https://github.com/hms-dbmi/UpSetR")
12372 (synopsis "Visualize intersecting sets")
12374 "This package provides a more scalable alternative to Venn and Euler
12375 diagrams for visualizing intersecting sets. Create visualizations of
12376 intersecting sets using a novel matrix design, along with visualizations of
12377 several common set, element and attribute related tasks.")
12378 (license license:expat)))
12380 ;; This package includes a JavaScript file, which is not minified. When
12381 ;; upgrading please check that there are no new minified JavaScript files.
12382 (define-public r-shinybs
12389 (uri (cran-uri "shinyBS" version))
12392 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12393 (properties `((upstream-name . "shinyBS")))
12394 (build-system r-build-system)
12395 ;; The tests spawn Shiny browser apps. They cannot be run
12396 ;; non-interactively.
12397 (arguments '(#:tests? #f))
12399 `(("r-htmltools" ,r-htmltools)
12400 ("r-shiny" ,r-shiny)))
12401 (home-page "https://ebailey78.github.io/shinyBS/")
12402 (synopsis "Twitter Bootstrap components for Shiny")
12404 "This package adds additional Twitter Bootstrap components to Shiny.")
12405 (license license:gpl3)))
12407 (define-public r-outliers
12409 (name "r-outliers")
12414 (uri (cran-uri "outliers" version))
12417 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12418 (build-system r-build-system)
12419 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12420 (synopsis "Tests for outliers")
12422 "This package provides a collection of some tests commonly used for
12423 identifying outliers.")
12424 (license license:gpl2+)))
12426 (define-public r-bayesm
12433 (uri (cran-uri "bayesm" version))
12435 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12436 (build-system r-build-system)
12438 `(("r-rcpp" ,r-rcpp)
12439 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12440 (home-page "http://www.perossi.org/home/bsm-1")
12441 (synopsis "Bayesian inference for marketing/micro-econometrics")
12443 "This package covers many important models used in marketing and
12444 micro-econometrics applications, including Bayes Regression (univariate or
12445 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12446 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12447 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12448 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12449 Estimation with normal base, Hierarchical Linear Models with normal prior and
12450 covariates, Hierarchical Linear Models with a mixture of normals prior and
12451 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12452 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12453 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12454 analysis of choice-based conjoint data, Bayesian treatment of linear
12455 instrumental variables models, Analysis of Multivariate Ordinal survey data
12456 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12457 Coefficient Logit Models.")
12458 (license license:gpl2+)))
12460 (define-public r-tensora
12467 (uri (cran-uri "tensorA" version))
12470 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12471 (properties `((upstream-name . "tensorA")))
12472 (build-system r-build-system)
12473 (home-page "http://www.stat.boogaart.de/tensorA")
12474 (synopsis "Advanced tensor arithmetic with named indices")
12476 "This package provides convenience functions for advanced linear algebra
12477 with tensors and computation with datasets of tensors on a higher level
12478 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12479 co- and contravariate indices, and parallel computations on sequences of
12481 (license license:gpl2+)))
12483 (define-public r-rarpack
12490 (uri (cran-uri "rARPACK" version))
12493 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12494 (properties `((upstream-name . "rARPACK")))
12495 (build-system r-build-system)
12496 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12497 (home-page "https://github.com/yixuan/rARPACK")
12498 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12500 "This package was previously an R wrapper of the ARPACK library, and now
12501 a shell of the R package RSpectra, an R interface to the Spectra library for
12502 solving large scale eigenvalue/vector problems. The current version of
12503 rARPACK simply imports and exports the functions provided by RSpectra. New
12504 users of rARPACK are advised to switch to the RSpectra package.")
12505 (license license:bsd-3)))
12507 (define-public r-compositions
12509 (name "r-compositions")
12514 (uri (cran-uri "compositions" version))
12517 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12518 (build-system r-build-system)
12520 `(("r-bayesm" ,r-bayesm)
12521 ("r-robustbase" ,r-robustbase)
12522 ("r-tensora" ,r-tensora)))
12523 (home-page "http://www.stat.boogaart.de/compositions")
12524 (synopsis "Compositional data analysis")
12526 "This package provides functions for the consistent analysis of
12527 compositional data (e.g. portions of substances) and positive
12528 numbers (e.g. concentrations).")
12529 (license license:gpl2+)))
12531 (define-public r-cobs
12538 (uri (cran-uri "cobs" version))
12541 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12542 (build-system r-build-system)
12544 `(("r-quantreg" ,r-quantreg)
12545 ("r-sparsem" ,r-sparsem)))
12546 (home-page "https://cran.r-project.org/web/packages/cobs")
12547 (synopsis "Constrained B-Splines (sparse matrix based)")
12549 "This package provides qualitatively constrained (regression) smoothing
12550 splines via linear programming and sparse matrices.")
12551 (license license:gpl2+)))
12553 (define-public r-drimpute
12555 (name "r-drimpute")
12560 (uri (cran-uri "DrImpute" version))
12563 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12564 (properties `((upstream-name . "DrImpute")))
12565 (build-system r-build-system)
12567 `(("r-rcpp" ,r-rcpp)
12568 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12569 (home-page "https://github.com/ikwak2/DrImpute")
12570 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12572 "This is an R package for imputing dropout events. Many statistical
12573 methods in cell type identification, visualization and lineage reconstruction
12574 do not account for dropout events. DrImpute can improve the performance of
12575 such software by imputing dropout events.")
12576 (license license:gpl3)))
12578 (define-public r-gamlss-dist
12580 (name "r-gamlss-dist")
12585 (uri (cran-uri "gamlss.dist" version))
12587 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12588 (properties `((upstream-name . "gamlss.dist")))
12589 (build-system r-build-system)
12590 (propagated-inputs `(("r-mass" ,r-mass)))
12591 (home-page "http://www.gamlss.org/")
12592 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12594 "This package provides a set of distributions which can be used for
12595 modelling the response variables in Generalized Additive Models for Location
12596 Scale and Shape. The distributions can be continuous, discrete or mixed
12597 distributions. Extra distributions can be created, by transforming, any
12598 continuous distribution defined on the real line, to a distribution defined on
12599 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12600 transformation, respectively.")
12601 ;; Either version of the GPL.
12602 (license (list license:gpl2 license:gpl3))))
12604 ;; This package includes JavaScript files, which are not minified. When
12605 ;; upgrading please check that there are no new minified JavaScript files.
12606 (define-public r-shinyjs
12613 (uri (cran-uri "shinyjs" version))
12616 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12617 (build-system r-build-system)
12619 `(("r-digest" ,r-digest)
12620 ("r-htmltools" ,r-htmltools)
12621 ("r-jsonlite" ,r-jsonlite)
12622 ("r-shiny" ,r-shiny)))
12623 (home-page "https://deanattali.com/shinyjs")
12624 (synopsis "Improve the user experience of your Shiny apps")
12626 "Perform common useful JavaScript operations in Shiny apps that will
12627 greatly improve your apps without having to know any JavaScript. Examples
12628 include: hiding an element, disabling an input, resetting an input back to its
12629 original value, delaying code execution by a few seconds, and many more useful
12630 functions for both the end user and the developer. Shinyjs can also be used
12631 to easily call your own custom JavaScript functions from R.")
12632 (license license:agpl3+)))
12634 ;; This package includes minified JavaScript files. When upgrading please
12635 ;; check that there are no new minified JavaScript files.
12636 (define-public r-colourpicker
12638 (name "r-colourpicker")
12643 (uri (cran-uri "colourpicker" version))
12646 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12647 (build-system r-build-system)
12649 `(#:modules ((guix build utils)
12650 (guix build r-build-system)
12654 (modify-phases %standard-phases
12655 (add-after 'unpack 'process-javascript
12656 (lambda* (#:key inputs #:allow-other-keys)
12657 (with-directory-excursion "inst"
12661 `((,(assoc-ref inputs "js-salvattore")
12662 "examples/colourInput/www/salvattore.min.js")
12663 (,(assoc-ref inputs "js-jquery")
12664 "htmlwidgets/lib/jquery/jquery.min.js")
12665 ("www/shared/colourpicker/js/colourpicker.js"
12666 "www/shared/colourpicker/js/colourpicker.min.js"))))
12667 (lambda (sources targets)
12668 (for-each (lambda (source target)
12669 (format #t "Processing ~a --> ~a~%"
12671 (delete-file target)
12672 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12673 (call-with-output-file target
12675 (dump-port minified port)))))
12676 sources targets))))
12679 `(("r-ggplot2" ,r-ggplot2)
12680 ("r-htmltools" ,r-htmltools)
12681 ("r-htmlwidgets" ,r-htmlwidgets)
12682 ("r-jsonlite" ,r-jsonlite)
12683 ("r-miniui" ,r-miniui)
12684 ("r-shiny" ,r-shiny)
12685 ("r-shinyjs" ,r-shinyjs)))
12687 `(("uglify-js" ,uglify-js)
12691 (uri "https://code.jquery.com/jquery-3.3.1.js")
12694 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12698 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12701 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12702 (home-page "https://github.com/daattali/colourpicker")
12703 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12705 "This package provides a color picker that can be used as an input in
12706 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12707 custom color palettes, and many more options. A plot color helper tool is
12708 available as an RStudio Addin, which helps you pick colors to use in your
12709 plots. A more generic color picker RStudio Addin is also provided to let you
12710 select colors to use in your R code.")
12711 (license license:expat)))
12713 (define-public r-ggextra
12720 (uri (cran-uri "ggExtra" version))
12723 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12724 (properties `((upstream-name . "ggExtra")))
12725 (build-system r-build-system)
12727 `(("r-colourpicker" ,r-colourpicker)
12728 ("r-ggplot2" ,r-ggplot2)
12729 ("r-gtable" ,r-gtable)
12730 ("r-miniui" ,r-miniui)
12732 ("r-scales" ,r-scales)
12733 ("r-shiny" ,r-shiny)
12734 ("r-shinyjs" ,r-shinyjs)))
12736 `(("r-knitr" ,r-knitr)))
12737 (home-page "https://github.com/daattali/ggExtra")
12738 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12740 "This package is a collection of functions and layers to enhance ggplot2.
12741 The flagship function is @code{ggMarginal()}, which can be used to add
12742 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12743 (license license:expat)))
12745 (define-public r-minpack-lm
12747 (name "r-minpack-lm")
12752 (uri (cran-uri "minpack.lm" version))
12755 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12756 (properties `((upstream-name . "minpack.lm")))
12757 (build-system r-build-system)
12758 (native-inputs `(("gfortran" ,gfortran)))
12759 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12760 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12762 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12763 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12764 problems by a modification of the Levenberg-Marquardt algorithm, with support
12765 for lower and upper parameter bounds. The implementation can be used via
12766 @code{nls}-like calls using the @code{nlsLM} function.")
12767 (license license:gpl3)))
12769 (define-public r-moments
12776 (uri (cran-uri "moments" version))
12779 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12780 (build-system r-build-system)
12781 (home-page "https://cran.r-project.org/web/packages/moments")
12782 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12784 "This package provides functions to calculate: moments, Pearson's
12785 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12786 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12787 (license license:gpl2+)))
12789 (define-public r-msir
12796 (uri (cran-uri "msir" version))
12799 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12800 (build-system r-build-system)
12802 `(("r-mclust" ,r-mclust)))
12803 (home-page "https://cran.r-project.org/web/packages/msir")
12804 (synopsis "Model-based sliced inverse regression")
12806 "This is an R package for dimension reduction based on finite Gaussian
12807 mixture modeling of inverse regression.")
12808 (license license:gpl2+)))
12810 (define-public r-pbivnorm
12812 (name "r-pbivnorm")
12817 (uri (cran-uri "pbivnorm" version))
12820 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12821 (build-system r-build-system)
12822 (native-inputs `(("gfortran" ,gfortran)))
12823 (home-page "https://github.com/brentonk/pbivnorm")
12824 (synopsis "Vectorized bivariate normal CDF")
12826 "This package provides a vectorized R function for calculating
12827 probabilities from a standard bivariate normal CDF.")
12828 (license license:gpl2+)))
12830 (define-public r-lavaan
12837 (uri (cran-uri "lavaan" version))
12840 "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
12841 (build-system r-build-system)
12843 `(("r-mass" ,r-mass)
12844 ("r-mnormt" ,r-mnormt)
12845 ("r-numderiv" ,r-numderiv)
12846 ("r-pbivnorm" ,r-pbivnorm)))
12847 (home-page "http://lavaan.ugent.be")
12848 (synopsis "Latent variable analysis")
12850 "This package provides tools to fit a variety of latent variable models,
12851 including confirmatory factor analysis, structural equation modeling and
12852 latent growth curve models.")
12853 (license license:gpl2+)))
12855 (define-public r-nonnest2
12857 (name "r-nonnest2")
12862 (uri (cran-uri "nonnest2" version))
12865 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12866 (build-system r-build-system)
12868 `(("r-compquadform" ,r-compquadform)
12869 ("r-lavaan" ,r-lavaan)
12870 ("r-mvtnorm" ,r-mvtnorm)
12871 ("r-sandwich" ,r-sandwich)))
12873 `(("r-knitr" ,r-knitr)))
12874 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12875 (synopsis "Tests of non-nested models")
12877 "This package allows for testing of non-nested models. It includes tests
12878 of model distinguishability and of model fit that can be applied to both
12879 nested and non-nested models. The package also includes functionality to
12880 obtain confidence intervals associated with AIC and BIC.")
12881 ;; Either version of the GPL.
12882 (license (list license:gpl2 license:gpl3))))
12884 (define-public r-penalized
12886 (name "r-penalized")
12891 (uri (cran-uri "penalized" version))
12894 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12895 (build-system r-build-system)
12897 `(("r-rcpp" ,r-rcpp)
12898 ("r-rcpparmadillo" ,r-rcpparmadillo)
12899 ("r-survival" ,r-survival)))
12900 (home-page "https://cran.r-project.org/web/packages/penalized/")
12901 (synopsis "Penalized estimation in GLMs and in the Cox model")
12903 "This package provides tools for fitting possibly high dimensional
12904 penalized regression models. The penalty structure can be any combination of
12905 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12906 constraint on the regression coefficients. The supported regression models
12907 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12908 model. Cross-validation routines allow optimization of the tuning
12910 (license license:gpl2+)))
12912 (define-public r-zim
12919 (uri (cran-uri "ZIM" version))
12922 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12923 (properties `((upstream-name . "ZIM")))
12924 (build-system r-build-system)
12925 (propagated-inputs `(("r-mass" ,r-mass)))
12926 (home-page "https://github.com/biostatstudio/ZIM")
12927 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12929 "Analyze count time series with excess zeros. Two types of statistical
12930 models are supported: Markov regression and state-space models. They are also
12931 known as observation-driven and parameter-driven models respectively in the
12932 time series literature. The functions used for Markov regression or
12933 observation-driven models can also be used to fit ordinary regression models
12934 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12935 negative binomial (ZINB) assumption. The package also contains miscellaneous
12936 functions to compute density, distribution, quantile, and generate random
12937 numbers from ZIP and ZINB distributions.")
12938 (license license:gpl3)))
12940 (define-public r-nor1mix
12947 (uri (cran-uri "nor1mix" version))
12950 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12951 (build-system r-build-system)
12952 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12953 (synopsis "Normal (1-d) mixture models")
12955 "This package provides S3 classes and methods for one-dimensional normal
12956 mixture models, for, e.g., density estimation or clustering algorithms
12957 research and teaching; it provides the widely used Marron-Wand densities. It
12958 also provides tools for efficient random number generation and graphics.")
12959 (license license:gpl2+)))
12961 (define-public r-beanplot
12963 (name "r-beanplot")
12968 (uri (cran-uri "beanplot" version))
12971 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12972 (build-system r-build-system)
12973 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12974 (synopsis "Visualization via beanplots")
12976 "This package provides beanplots, an alternative to
12977 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12979 (license license:gpl2)))
12981 (define-public r-pbdzmq
12988 (uri (cran-uri "pbdZMQ" version))
12991 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12992 (properties `((upstream-name . "pbdZMQ")))
12993 (build-system r-build-system)
12995 `(("zeromq" ,zeromq)
12998 `(("pkg-config" ,pkg-config)))
12999 (home-page "https://pbdr.org/")
13000 (synopsis "R interface to ZeroMQ")
13002 "ZeroMQ is a well-known library for high-performance asynchronous
13003 messaging in scalable, distributed applications. This package provides high
13004 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13005 interactive client/server programming frameworks. A few wrapper functions
13006 compatible with @code{rzmq} are also provided.")
13007 (license license:gpl3)))
13009 (define-public r-repr
13016 (uri (cran-uri "repr" version))
13019 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13020 (build-system r-build-system)
13022 `(("r-base64enc" ,r-base64enc)
13023 ("r-htmltools" ,r-htmltools)
13024 ("r-jsonlite" ,r-jsonlite)
13025 ("r-pillar" ,r-pillar)))
13026 (home-page "https://cran.r-project.org/web/packages/repr/")
13027 (synopsis "Serializable representations")
13029 "This package provides string and binary representations of objects for
13030 several formats and MIME types.")
13031 (license license:gpl3)))
13033 (define-public r-irdisplay
13035 (name "r-irdisplay")
13040 (uri (cran-uri "IRdisplay" version))
13043 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13044 (properties `((upstream-name . "IRdisplay")))
13045 (build-system r-build-system)
13047 `(("r-repr" ,r-repr)))
13048 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13049 (synopsis "Jupyter display machinery")
13051 "This package provides an interface to the rich display capabilities of
13052 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13053 running IRkernel session.")
13054 (license license:expat)))
13056 (define-public r-irkernel
13058 (name "r-irkernel")
13063 (uri (cran-uri "IRkernel" version))
13066 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
13067 (properties `((upstream-name . "IRkernel")))
13068 (build-system r-build-system)
13071 (modify-phases %standard-phases
13072 (add-after 'install 'install-kernelspec
13073 (lambda* (#:key outputs #:allow-other-keys)
13074 (let ((out (assoc-ref outputs "out")))
13075 (setenv "HOME" "/tmp")
13076 (invoke "jupyter" "kernelspec" "install"
13079 (string-append out "/site-library/IRkernel/kernelspec"))
13080 ;; Record the absolute file name of the 'R' executable in
13082 (substitute* (string-append out "/share/jupyter"
13083 "/kernels/ir/kernel.json")
13085 (string-append "[\"" (which "R") "\",")))
13088 `(("jupyter" ,jupyter)))
13090 `(("r-crayon" ,r-crayon)
13091 ("r-digest" ,r-digest)
13092 ("r-evaluate" ,r-evaluate)
13093 ("r-irdisplay" ,r-irdisplay)
13094 ("r-jsonlite" ,r-jsonlite)
13095 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13096 ("r-minimal" ,r-minimal)
13097 ("r-pbdzmq" ,r-pbdzmq)
13099 ("r-uuid" ,r-uuid)))
13100 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13101 (synopsis "Native R kernel for Jupyter")
13103 "The R kernel for the Jupyter environment executes R code which the
13104 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13106 (license license:expat)))
13108 (define-public r-gmodels
13115 (uri (cran-uri "gmodels" version))
13118 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13119 (build-system r-build-system)
13121 `(("r-gdata" ,r-gdata)
13122 ("r-mass" ,r-mass)))
13123 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13124 (synopsis "Various R programming tools for model fitting")
13126 "This package provides various R programming tools for model fitting.")
13127 (license license:gpl2)))
13129 (define-public r-apcluster
13131 (name "r-apcluster")
13136 (uri (cran-uri "apcluster" version))
13139 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13140 (build-system r-build-system)
13142 `(("r-matrix" ,r-matrix)
13143 ("r-rcpp" ,r-rcpp)))
13144 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13145 (synopsis "Affinity propagation clustering")
13147 "This package implements affinity propagation clustering introduced by
13148 Frey and Dueck (2007). The package further provides leveraged affinity
13149 propagation and an algorithm for exemplar-based agglomerative clustering that
13150 can also be used to join clusters obtained from affinity propagation. Various
13151 plotting functions are available for analyzing clustering results.")
13152 (license license:gpl2+)))
13154 (define-public r-valr
13161 (uri (cran-uri "valr" version))
13164 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13165 (build-system r-build-system)
13167 `(("r-broom" ,r-broom)
13168 ("r-dplyr" ,r-dplyr)
13169 ("r-ggplot2" ,r-ggplot2)
13171 ("r-readr" ,r-readr)
13172 ("r-rlang" ,r-rlang)
13173 ("r-stringr" ,r-stringr)
13174 ("r-tibble" ,r-tibble)))
13176 `(("r-knitr" ,r-knitr)))
13177 (home-page "http://github.com/rnabioco/valr")
13178 (synopsis "Genome interval arithmetic in R")
13180 "This package enables you to read and manipulate genome intervals and
13181 signals. It provides functionality similar to command-line tool suites within
13182 R, enabling interactive analysis and visualization of genome-scale data.")
13183 (license license:expat)))
13185 (define-public r-rematch2
13187 (name "r-rematch2")
13192 (uri (cran-uri "rematch2" version))
13195 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13196 (build-system r-build-system)
13198 `(("r-tibble" ,r-tibble)))
13199 (home-page "https://github.com/r-lib/rematch2")
13200 (synopsis "Tidy output from regular expression matching")
13202 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13203 return the match results in tidy data frames.")
13204 (license license:expat)))
13206 (define-public r-picante
13213 (uri (cran-uri "picante" version))
13216 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13217 (build-system r-build-system)
13221 ("r-vegan" ,r-vegan)))
13222 (home-page "https://cran.r-project.org/web/packages/picante/")
13223 (synopsis "Integrating phylogenies and ecology")
13225 "This package provides functions for phylocom integration, community
13226 analyses, null-models, traits and evolution. It implements numerous
13227 ecophylogenetic approaches including measures of community phylogenetic and
13228 trait diversity, phylogenetic signal, estimation of trait values for
13229 unobserved taxa, null models for community and phylogeny randomizations, and
13230 utility functions for data input/output and phylogeny plotting. A full
13231 description of package functionality and methods are provided by Kembel et
13233 (license license:gpl2)))
13235 (define-public r-reinforcelearn
13237 (name "r-reinforcelearn")
13242 (uri (cran-uri "reinforcelearn" version))
13245 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13246 (build-system r-build-system)
13248 `(("r-checkmate" ,r-checkmate)
13250 ("r-purrr" ,r-purrr)
13252 (home-page "https://markusdumke.github.io/reinforcelearn")
13253 (synopsis "Reinforcement learning")
13255 "This package implements reinforcement learning environments and
13256 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13257 can be used with function approximation, eligibility traces (Singh & Sutton,
13258 1996) and experience replay (Mnih et al., 2013).")
13259 (license license:expat)))
13261 (define-public r-lemon
13268 (uri (cran-uri "lemon" version))
13271 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13272 (build-system r-build-system)
13274 `(("r-ggplot2" ,r-ggplot2)
13275 ("r-gridextra" ,r-gridextra)
13276 ("r-gtable" ,r-gtable)
13277 ("r-knitr" ,r-knitr)
13278 ("r-lattice" ,r-lattice)
13280 ("r-rlang" ,r-rlang)
13281 ("r-scales" ,r-scales)))
13283 `(("r-knitr" ,r-knitr)))
13284 (home-page "https://github.com/stefanedwards/lemon")
13285 (synopsis "Freshen up your ggplot2 plots")
13287 "This package provides functions for working with legends and axis lines
13288 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13290 (license license:gpl3)))
13292 (define-public r-wgaim
13299 (uri (cran-uri "wgaim" version))
13301 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13302 (build-system r-build-system)
13304 `(("r-ggplot2" ,r-ggplot2)
13306 (home-page "https://cran.r-project.org/web/packages/wgaim")
13307 (synopsis "Whole genome average interval mapping for QTL detection")
13309 "This package integrates sophisticated mixed modelling methods with a
13310 whole genome approach to detecting significant QTL in linkage maps.")
13311 (license license:gpl2+)))
13313 (define-public r-bedr
13320 (uri (cran-uri "bedr" version))
13323 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13324 (build-system r-build-system)
13326 `(("r-data-table" ,r-data-table)
13327 ("r-r-utils" ,r-r-utils)
13328 ("r-testthat" ,r-testthat)
13329 ("r-venndiagram" ,r-venndiagram)
13332 ("bedtools" ,bedtools)
13333 ("htslib" ,htslib))) ; for tabix
13335 `(("r-knitr" ,r-knitr))) ; for vignettes
13336 (home-page "https://cran.r-project.org/web/packages/bedr")
13337 (synopsis "Genomic region processing")
13339 "This package is for genomic regions processing using command line tools
13340 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13341 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13342 The bedr package's API enhances access to these tools as well as offers
13343 additional utilities for genomic regions processing.")
13344 (license license:gpl2)))
13346 (define-public r-sets
13353 (uri (cran-uri "sets" version))
13356 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13357 (properties `((upstream-name . "sets")))
13358 (build-system r-build-system)
13359 (home-page "https://cran.r-project.org/web/packages/sets")
13360 (synopsis "Sets, generalized sets, customizable sets and intervals")
13362 "This package provides data structures and basic operations for ordinary
13363 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13364 customizable sets, and intervals.")
13365 (license license:gpl2)))
13367 (define-public r-partitions
13369 (name "r-partitions")
13374 (uri (cran-uri "partitions" version))
13377 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13378 (build-system r-build-system)
13381 ("r-polynom" ,r-polynom)
13382 ("r-sets" ,r-sets)))
13383 (home-page "https://cran.r-project.org/web/packages/partitions")
13384 (synopsis "Additive partitions of integers")
13386 "This package provides tools to enumerates the partitions, unequal
13387 partitions, and restricted partitions of an integer; the three corresponding
13388 partition functions are also given.")
13389 ;; Any version of the GPL
13390 (license license:gpl2+)))
13392 (define-public r-brobdingnag
13394 (name "r-brobdingnag")
13399 (uri (cran-uri "Brobdingnag" version))
13402 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13403 (properties `((upstream-name . "Brobdingnag")))
13404 (build-system r-build-system)
13405 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13406 (synopsis "Very large numbers in R")
13408 "This package handles very large numbers in R. Real numbers are held
13409 using their natural logarithms, plus a logical flag indicating sign. The
13410 package includes a vignette that gives a step-by-step introduction to using S4
13412 ;; Any version of the GPL
13413 (license license:gpl2+)))
13415 (define-public r-untb
13422 (uri (cran-uri "untb" version))
13425 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13426 (build-system r-build-system)
13428 `(("r-brobdingnag" ,r-brobdingnag)
13429 ("r-partitions" ,r-partitions)
13430 ("r-polynom" ,r-polynom)))
13431 (home-page "https://github.com/RobinHankin/untb.git")
13432 (synopsis "Ecological drift under the UNTB")
13434 "This package provides numerical simulations, and visualizations, of
13435 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13436 (license license:gpl2+)))
13438 (define-public r-stepwise
13440 (name "r-stepwise")
13445 (uri (cran-uri "stepwise" version))
13448 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13449 (build-system r-build-system)
13450 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13451 (synopsis "Stepwise detection of recombination breakpoints")
13453 "This package provides a stepwise approach to identifying recombination
13454 breakpoints in a genomic sequence alignment.")
13455 (license license:gpl2+)))
13457 (define-public r-snpmaxsel
13459 (name "r-snpmaxsel")
13464 (uri (cran-uri "SNPmaxsel" version))
13467 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13468 (properties `((upstream-name . "SNPmaxsel")))
13469 (build-system r-build-system)
13471 `(("r-combinat" ,r-combinat)
13472 ("r-mvtnorm" ,r-mvtnorm)))
13473 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13474 (synopsis "Maximally selected statistics for SNP data")
13476 "This package implements asymptotic methods related to maximally selected
13477 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13479 (license license:gpl2+)))
13481 (define-public r-acsnminer
13483 (name "r-acsnminer")
13484 (version "0.16.8.25")
13487 (uri (cran-uri "ACSNMineR" version))
13490 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13491 (properties `((upstream-name . "ACSNMineR")))
13492 (build-system r-build-system)
13494 `(("r-ggplot2" ,r-ggplot2)
13495 ("r-gridextra" ,r-gridextra)))
13496 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13497 (synopsis "Gene enrichment analysis")
13499 "This package provides tools to compute and represent gene set enrichment
13500 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13501 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13502 enrichment can be run with hypergeometric test or Fisher exact test, and can
13503 use multiple corrections. Visualization of data can be done either by
13504 barplots or heatmaps.")
13505 (license license:gpl2+)))
13507 (define-public r-seqinr
13514 (uri (cran-uri "seqinr" version))
13517 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13518 (build-system r-build-system)
13520 `(("r-ade4" ,r-ade4)
13521 ("r-segmented" ,r-segmented)))
13524 (home-page "http://seqinr.r-forge.r-project.org/")
13525 (synopsis "Biological sequences retrieval and analysis")
13527 "This package provides tools for exploratory data analysis and data
13528 visualization of biological sequence (DNA and protein) data. It also includes
13529 utilities for sequence data management under the ACNUC system.")
13530 (license license:gpl2+)))
13532 (define-public r-units
13539 (uri (cran-uri "units" version))
13542 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13543 (build-system r-build-system)
13545 `(("udunits" ,udunits)))
13547 `(("r-rcpp" ,r-rcpp)))
13549 `(("r-knitr" ,r-knitr)))
13550 (home-page "https://github.com/r-quantities/units/")
13551 (synopsis "Measurement Units for R Vectors")
13553 "This package provides support for measurement units in R vectors,
13554 matrices and arrays: automatic propagation, conversion, derivation and
13555 simplification of units; raising errors in case of unit incompatibility. It
13556 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13558 (license license:gpl2)))
13560 (define-public r-classint
13562 (name "r-classint")
13567 (uri (cran-uri "classInt" version))
13570 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13571 (properties `((upstream-name . "classInt")))
13572 (build-system r-build-system)
13574 `(("r-class" ,r-class)
13575 ("r-e1071" ,r-e1071)
13576 ("r-kernsmooth" ,r-kernsmooth)))
13578 `(("gfortran" ,gfortran)
13579 ("r-knitr" ,r-knitr)))
13580 (home-page "https://github.com/r-spatial/classInt/")
13581 (synopsis "Choose univariate class intervals")
13583 "This package provides selected commonly used methods for choosing
13584 univariate class intervals for mapping or other graphics purposes.")
13585 (license license:gpl2+)))
13587 (define-public r-spdata
13594 (uri (cran-uri "spData" version))
13597 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13598 (properties `((upstream-name . "spData")))
13599 (build-system r-build-system)
13601 `(("r-raster" ,r-raster)
13603 (home-page "https://github.com/Nowosad/spData")
13604 (synopsis "Datasets for spatial analysis")
13606 "This a package containing diverse spatial datasets for demonstrating,
13607 benchmarking and teaching spatial data analysis. It includes R data of class
13608 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13609 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13610 of the datasets are designed to illustrate specific analysis techniques.
13611 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13612 illustrate point pattern analysis techniques.")
13613 (license license:cc0)))
13615 (define-public r-learnbayes
13617 (name "r-learnbayes")
13622 (uri (cran-uri "LearnBayes" version))
13625 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13626 (properties `((upstream-name . "LearnBayes")))
13627 (build-system r-build-system)
13628 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13629 (synopsis "Functions for learning Bayesian inference")
13631 "This package provides a collection of functions helpful in learning the
13632 basic tenets of Bayesian statistical inference. It contains functions for
13633 summarizing basic one and two parameter posterior distributions and predictive
13634 distributions. It contains MCMC algorithms for summarizing posterior
13635 distributions defined by the user. It also contains functions for regression
13636 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13638 (license license:gpl2+)))
13640 (define-public r-deldir
13647 (uri (cran-uri "deldir" version))
13650 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13651 (build-system r-build-system)
13652 (native-inputs `(("gfortran" ,gfortran)))
13653 (home-page "https://cran.r-project.org/web/packages/deldir")
13654 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13656 "This package provides tools for calculating the Delaunay triangulation
13657 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13658 of a planar point set. It plots triangulations and tessellations in various
13659 ways, clips tessellations to sub-windows, calculates perimeters of
13660 tessellations, and summarizes information about the tiles of the
13662 (license license:gpl2+)))
13664 (define-public r-sf
13671 (uri (cran-uri "sf" version))
13674 "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
13675 (build-system r-build-system)
13682 `(("r-classint" ,r-classint)
13684 ("r-magrittr" ,r-magrittr)
13686 ("r-units" ,r-units)))
13688 `(("pkg-config" ,pkg-config)
13689 ("r-knitr" ,r-knitr)))
13690 (home-page "https://github.com/r-spatial/sf/")
13691 (synopsis "Simple features for R")
13693 "This package provides support for simple features, a standardized way to
13694 encode spatial vector data. It binds to GDAL for reading and writing data, to
13695 GEOS for geometrical operations, and to PROJ for projection conversions and
13696 datum transformations.")
13697 ;; Either of these licenses
13698 (license (list license:gpl2 license:expat))))
13700 (define-public r-spdep
13707 (uri (cran-uri "spdep" version))
13710 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13711 (build-system r-build-system)
13713 `(("r-boot" ,r-boot)
13715 ("r-deldir" ,r-deldir)
13717 ("r-gmodels" ,r-gmodels)
13718 ("r-learnbayes" ,r-learnbayes)
13720 ("r-matrix" ,r-matrix)
13724 ("r-spdata" ,r-spdata)))
13725 (home-page "https://github.com/r-spatial/spdep/")
13726 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13728 "This package provides a collection of functions to create spatial
13729 weights matrix objects from polygon contiguities, from point patterns by
13730 distance and tessellations, for summarizing these objects, and for permitting
13731 their use in spatial data analysis, including regional aggregation by minimum
13733 (license license:gpl2+)))
13735 (define-public r-adegenet
13737 (name "r-adegenet")
13742 (uri (cran-uri "adegenet" version))
13745 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13746 (build-system r-build-system)
13748 `(("r-ade4" ,r-ade4)
13751 ("r-dplyr" ,r-dplyr)
13752 ("r-ggplot2" ,r-ggplot2)
13753 ("r-igraph" ,r-igraph)
13755 ("r-reshape2" ,r-reshape2)
13756 ("r-seqinr" ,r-seqinr)
13757 ("r-shiny" ,r-shiny)
13758 ("r-spdep" ,r-spdep)
13759 ("r-vegan" ,r-vegan)))
13760 (home-page "https://github.com/thibautjombart/adegenet")
13761 (synopsis "Exploratory analysis of genetic and genomic data")
13763 "This package provides a toolset for the exploration of genetic and
13764 genomic data. Adegenet provides formal (S4) classes for storing and handling
13765 various genetic data, including genetic markers with varying ploidy and
13766 hierarchical population structure (@code{genind} class), alleles counts by
13767 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13768 also implements original multivariate methods (DAPC, sPCA), graphics,
13769 statistical tests, simulation tools, distance and similarity measures, and
13770 several spatial methods. A range of both empirical and simulated datasets is
13771 also provided to illustrate various methods.")
13772 (license license:gpl2+)))
13774 (define-public r-pegas
13781 (uri (cran-uri "pegas" version))
13783 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13784 (build-system r-build-system)
13786 `(("r-adegenet" ,r-adegenet)
13788 (home-page "http://ape-package.ird.fr/pegas.html")
13789 (synopsis "Population and evolutionary genetics analysis system")
13791 "This package provides functions for reading, writing, plotting,
13792 analysing, and manipulating allelic and haplotypic data, including from VCF
13793 files, and for the analysis of population nucleotide sequences and
13794 micro-satellites including coalescent analyses, linkage disequilibrium,
13795 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13796 minimum spanning tree and network, and median-joining networks.")
13797 (license license:gpl2+)))
13799 (define-public r-rmetasim
13801 (name "r-rmetasim")
13806 (uri (cran-uri "rmetasim" version))
13809 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13810 (build-system r-build-system)
13812 `(("r-ade4" ,r-ade4)
13813 ("r-adegenet" ,r-adegenet)
13814 ("r-gtools" ,r-gtools)
13815 ("r-pegas" ,r-pegas)))
13816 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13817 (synopsis "Individual-based population genetic simulation environment")
13819 "This package provides an interface between R and the metasim simulation
13820 engine. The simulation environment is documented in: Strand, A.(2002),
13821 Metasim 1.0: an individual-based environment for simulating population
13822 genetics of complex population dynamics.")
13824 (license license:gpl2+)))
13826 (define-public r-genetics
13828 (name "r-genetics")
13829 (version "1.3.8.1.2")
13833 (uri (cran-uri "genetics" version))
13836 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13837 (build-system r-build-system)
13839 `(("r-combinat" ,r-combinat)
13840 ("r-gdata" ,r-gdata)
13841 ("r-gtools" ,r-gtools)
13843 ("r-mvtnorm" ,r-mvtnorm)))
13844 (home-page "https://cran.r-project.org/web/packages/genetics/")
13845 (synopsis "Population genetics")
13847 "This package provides classes and methods for handling genetic data.
13848 It includes classes to represent genotypes and haplotypes at single markers up
13849 to multiple markers on multiple chromosomes. Function include allele
13850 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13851 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13852 and testing for linkage disequilibrium, ...")
13853 ;; Any GPL version.
13854 (license license:gpl2+)))
13856 (define-public r-snp-plotter
13858 (name "r-snp-plotter")
13863 (uri (cran-uri "snp.plotter" version))
13866 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13867 (properties `((upstream-name . "snp.plotter")))
13868 (build-system r-build-system)
13869 (propagated-inputs `(("r-genetics" ,r-genetics)))
13870 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13871 (synopsis "Plot p-values using single SNP and/or haplotype data")
13873 "This package helps you create plots of p-values using single SNP and/or
13874 haplotype data. Main features of the package include options to display a
13875 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13876 datasets simultaneously. Plots can be created using global and/or individual
13877 haplotype p-values along with single SNP p-values. Images are created as
13878 either PDF/EPS files.")
13879 (license license:gpl2+)))
13881 (define-public r-polspline
13883 (name "r-polspline")
13888 (uri (cran-uri "polspline" version))
13890 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13891 (build-system r-build-system)
13892 (native-inputs `(("gfortran" ,gfortran)))
13893 (home-page "https://cran.r-project.org/web/packages/polspline/")
13894 (synopsis "Polynomial spline routines")
13896 "This package provides routines for the polynomial spline fitting
13897 routines hazard regression, hazard estimation with flexible tails, logspline,
13898 lspec, polyclass, and polymars.")
13899 (license license:gpl2+)))
13901 (define-public r-rms
13908 (uri (cran-uri "rms" version))
13910 (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
13911 (build-system r-build-system)
13913 `(("r-cluster" ,r-cluster)
13914 ("r-digest" ,r-digest)
13915 ("r-ggplot2" ,r-ggplot2)
13916 ("r-hmisc" ,r-hmisc)
13917 ("r-htmltable" ,r-htmltable)
13918 ("r-htmltools" ,r-htmltools)
13919 ("r-lattice" ,r-lattice)
13921 ("r-multcomp" ,r-multcomp)
13923 ("r-polspline" ,r-polspline)
13924 ("r-quantreg" ,r-quantreg)
13925 ("r-rpart" ,r-rpart)
13926 ("r-sparsem" ,r-sparsem)
13927 ("r-survival" ,r-survival)))
13928 (native-inputs `(("gfortran" ,gfortran)))
13929 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13930 (synopsis "Regression modeling strategies")
13932 "This is a package for regression modeling, testing, estimation,
13933 validation, graphics, prediction, and typesetting by storing enhanced model
13934 design attributes in the fit. The rms package is a collection of functions
13935 that assist with and streamline modeling. It also contains functions for
13936 binary and ordinal logistic regression models, ordinal models for continuous Y
13937 with a variety of distribution families, and the Buckley-James multiple
13938 regression model for right-censored responses, and implements penalized
13939 maximum likelihood estimation for logistic and ordinary linear models. The
13940 package works with almost any regression model, but it was especially written
13941 to work with binary or ordinal regression models, Cox regression, accelerated
13942 failure time models, ordinary linear models, the Buckley-James model,
13943 generalized least squares for serially or spatially correlated observations,
13944 generalized linear models, and quantile regression.")
13945 (license license:gpl2+)))
13947 (define-public r-haplo-stats
13949 (name "r-haplo-stats")
13954 (uri (cran-uri "haplo.stats" version))
13957 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13958 (properties `((upstream-name . "haplo.stats")))
13959 (build-system r-build-system)
13961 `(("r-rms" ,r-rms)))
13963 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13964 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13965 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13967 "This package provides routines for the analysis of indirectly measured
13968 haplotypes. The statistical methods assume that all subjects are unrelated
13969 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13970 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13971 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13972 examples in the vignette.")
13973 (license license:gpl2+)))
13975 (define-public r-bqtl
13982 (uri (cran-uri "bqtl" version))
13985 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13986 (build-system r-build-system)
13987 (native-inputs `(("gfortran" ,gfortran)))
13988 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13989 (synopsis "Bayesian QTL mapping toolkit")
13991 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13992 lines. It includes maximum likelihood and Bayesian tools.")
13993 (license license:gpl2+)))
13995 (define-public r-ibdreg
14002 (uri (cran-uri "ibdreg" version))
14005 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
14006 (build-system r-build-system)
14007 (home-page "https://www.mayo.edu/research/labs/\
14008 statistical-genetics-genetic-epidemiology/software")
14009 (synopsis "Regression methods for IBD linkage with covariates")
14011 "This package provides a method to test genetic linkage with covariates
14012 by regression methods with response IBD sharing for relative pairs. Account
14013 for correlations of IBD statistics and covariates for relative pairs within
14014 the same pedigree.")
14015 (license license:gpl2+)))
14017 (define-public r-dlmap
14024 (uri (cran-uri "dlmap" version))
14027 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14028 (build-system r-build-system)
14030 `(("r-ibdreg" ,r-ibdreg)
14034 ("r-wgaim" ,r-wgaim)))
14035 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14036 (synopsis "Detection localization mapping for QTL")
14038 "This is package for QTL mapping in a mixed model framework with separate
14039 detection and localization stages. The first stage detects the number of QTL
14040 on each chromosome based on the genetic variation due to grouped markers on
14041 the chromosome; the second stage uses this information to determine the most
14042 likely QTL positions. The mixed model can accommodate general fixed and
14043 random effects, including spatial effects in field trials and pedigree
14044 effects. It is applicable to backcrosses, doubled haploids, recombinant
14045 inbred lines, F2 intercrosses, and association mapping populations.")
14046 (license license:gpl2)))
14048 (define-public r-ldheatmap
14050 (name "r-ldheatmap")
14055 (uri (cran-uri "LDheatmap" version))
14058 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
14059 (properties `((upstream-name . "LDheatmap")))
14060 (build-system r-build-system)
14062 `(("r-genetics" ,r-genetics)
14064 ("r-snpstats" ,r-snpstats)))
14065 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14066 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14068 "This package provides tools to produce a graphical display, as a heat
14069 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14070 optionally include the physical locations or genetic map distances of each SNP
14072 (license license:gpl3)))
14074 (define-public r-hwde
14081 (uri (cran-uri "hwde" version))
14084 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14085 (build-system r-build-system)
14086 (home-page "https://cran.r-project.org/web/packages/hwde/")
14087 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14089 "This package fits models for genotypic disequilibria, as described in
14090 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14091 terms are available that account for first order interactions between loci.
14092 It also implements, for a single locus in a single population, a conditional
14093 exact test for Hardy-Weinberg equilibrium.")
14094 (license license:gpl2+)))
14096 (define-public r-tdthap
14103 (uri (cran-uri "tdthap" version))
14106 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14107 (build-system r-build-system)
14108 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14109 (synopsis "TDT tests for extended haplotypes")
14111 "Functions and examples are provided for transmission/disequilibrium
14112 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14113 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14114 (license license:artistic2.0)))
14116 (define-public r-sparql
14122 (uri (cran-uri "SPARQL" version))
14125 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14126 (properties `((upstream-name . "SPARQL")))
14127 (build-system r-build-system)
14129 `(("r-rcurl" ,r-rcurl)
14131 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14132 (synopsis "SPARQL client for R")
14133 (description "This package provides an interface to use SPARQL to pose
14134 SELECT or UPDATE queries to an end-point.")
14135 ;; The only license indication is found in the DESCRIPTION file,
14136 ;; which states GPL-3. So we cannot assume GPLv3+.
14137 (license license:gpl3)))
14139 (define-public r-bookdown
14141 (name "r-bookdown")
14145 (uri (cran-uri "bookdown" version))
14148 "137l0cyzw9ij2l3zyk3mm1k2db9vhbax6c9y4rydvh4i9gka5vlq"))))
14149 (build-system r-build-system)
14151 `(("r-htmltools" ,r-htmltools)
14152 ("r-knitr" ,r-knitr)
14153 ("r-rmarkdown" ,r-rmarkdown)
14154 ("r-tinytex" ,r-tinytex)
14156 ("pandoc" ,ghc-pandoc)))
14157 (home-page "https://github.com/rstudio/bookdown")
14158 (synopsis "Authoring books and technical documents with R markdown")
14159 (description "This package provides output formats and utilities for
14160 authoring books and technical documents with R Markdown.")
14161 (license license:gpl3)))
14163 (define-public r-optparse
14165 (name "r-optparse")
14170 (uri (cran-uri "optparse" version))
14173 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14174 (build-system r-build-system)
14176 `(("r-getopt" ,r-getopt)))
14178 `(("r-knitr" ,r-knitr)))
14179 (home-page "https://github.com/trevorld/optparse")
14180 (synopsis "Command line option parser")
14182 "This package provides a command line parser inspired by Python's
14183 @code{optparse} library to be used with Rscript to write shebang scripts
14184 that accept short and long options.")
14185 (license license:gpl2+)))
14187 (define-public r-wgcna
14194 (uri (cran-uri "WGCNA" version))
14197 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14198 (properties `((upstream-name . "WGCNA")))
14199 (build-system r-build-system)
14201 `(("r-annotationdbi" ,r-annotationdbi)
14202 ("r-doparallel" ,r-doparallel)
14203 ("r-dynamictreecut" ,r-dynamictreecut)
14204 ("r-fastcluster" ,r-fastcluster)
14205 ("r-foreach" ,r-foreach)
14206 ("r-go-db" ,r-go-db)
14207 ("r-hmisc" ,r-hmisc)
14208 ("r-impute" ,r-impute)
14210 ("r-survival" ,r-survival)
14211 ("r-matrixstats" ,r-matrixstats)
14212 ("r-preprocesscore" ,r-preprocesscore)))
14214 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14215 (synopsis "Weighted correlation network analysis")
14217 "This package provides functions necessary to perform Weighted
14218 Correlation Network Analysis on high-dimensional data. It includes functions
14219 for rudimentary data cleaning, construction and summarization of correlation
14220 networks, module identification and functions for relating both variables and
14221 modules to sample traits. It also includes a number of utility functions for
14222 data manipulation and visualization.")
14223 (license license:gpl2+)))
14225 (define-public r-kernlab
14232 (uri (cran-uri "kernlab" version))
14234 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14235 (build-system r-build-system)
14236 (home-page "https://cran.r-project.org/web/packages/kernlab")
14237 (synopsis "Kernel-based machine learning tools")
14239 "This package provides kernel-based machine learning methods for
14240 classification, regression, clustering, novelty detection, quantile regression
14241 and dimensionality reduction. Among other methods @code{kernlab} includes
14242 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14244 (license license:gpl2)))
14246 (define-public r-hierfstat
14248 (name "r-hierfstat")
14249 (version "0.04-22")
14253 (uri (cran-uri "hierfstat" version))
14256 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
14257 (build-system r-build-system)
14259 `(("r-ade4" ,r-ade4)
14260 ("r-adegenet" ,r-adegenet)
14261 ("r-gtools" ,r-gtools)))
14262 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14263 (synopsis "Estimation and tests of hierarchical F-statistics")
14265 "This package allows the estimation of hierarchical F-statistics from
14266 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14267 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14268 are also given to test via randomisations the significance of each F and
14269 variance components, using the likelihood-ratio statistics G.")
14270 (license license:gpl2+)))
14272 (define-public r-hapassoc
14274 (name "r-hapassoc")
14279 (uri (cran-uri "hapassoc" version))
14282 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14283 (build-system r-build-system)
14284 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14285 (synopsis "Inference of trait associations with SNP haplotypes")
14287 "Hapassoc performs likelihood inference of trait associations with
14288 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14289 functions are developed primarily for data collected in cohort or
14290 cross-sectional studies. They can accommodate uncertain haplotype phase and
14291 handle missing genotypes at some SNPs.")
14292 (license license:gpl2)))
14294 (define-public r-sampling
14296 (name "r-sampling")
14301 (uri (cran-uri "sampling" version))
14304 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14305 (build-system r-build-system)
14307 `(("r-lpsolve" ,r-lpsolve)
14308 ("r-mass" ,r-mass)))
14309 (home-page "https://cran.r-project.org/web/packages/sampling/")
14310 (synopsis "Survey sampling")
14312 "This package provides functions for drawing and calibrating samples.")
14313 (license license:gpl2+)))
14315 (define-public r-r2html
14322 (uri (cran-uri "R2HTML" version))
14325 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14326 (properties `((upstream-name . "R2HTML")))
14327 (build-system r-build-system)
14328 (home-page "https://github.com/nalimilan/R2HTML")
14329 (synopsis "HTML export for R objects")
14331 "This package includes HTML functions and methods to write in an HTML
14332 file. Thus, making HTML reports is easy. It includes a function that allows
14333 redirection on the fly, which appears to be very useful for teaching purposes,
14334 as the student can keep a copy of the produced output to keep all that they
14335 did during the course. The package comes with a vignette describing how to
14336 write HTML reports for statistical analysis. Finally, a driver for Sweave
14337 parses HTML flat files containing R code and to automatically write
14338 the corresponding outputs (tables and graphs).")
14339 (license license:gpl2+)))
14341 (define-public r-rjava
14348 (uri (cran-uri "rJava" version))
14351 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14352 (properties `((upstream-name . "rJava")))
14353 (build-system r-build-system)
14355 `(#:modules ((guix build utils)
14356 (guix build r-build-system)
14359 (modify-phases %standard-phases
14360 (add-after 'unpack 'set-JAVA_HOME
14361 (lambda* (#:key inputs #:allow-other-keys)
14362 (let ((jdk (assoc-ref inputs "jdk")))
14363 (setenv "JAVA_HOME" jdk)
14364 (setenv "JAVA" (which "java"))
14365 (setenv "JAR" (which "jar"))
14366 (setenv "JAVAC" (which "javac"))
14367 (setenv "JAVAH" (which "javah"))
14368 (setenv "JAVA_CPPFLAGS"
14369 (string-append "-I" jdk "/include "
14370 "-I" jdk "/include/linux"))
14371 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14372 ((lib) (setenv "JAVA_LIBS" lib))
14373 (_ (error "Could not find libjvm.so"))))
14377 ("jdk" ,icedtea-8 "jdk")
14380 (home-page "https://www.rforge.net/rJava/")
14381 (synopsis "Low-Level R to Java interface")
14383 "This package provides a low-level interface to the Java VM very much
14384 like .C/.Call and friends. It allows the creation of objects, calling methods
14385 and accessing fields.")
14386 (license license:gpl2)))
14388 (define-public r-svmisc
14395 (uri (cran-uri "svMisc" version))
14398 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14399 (properties `((upstream-name . "svMisc")))
14400 (build-system r-build-system)
14401 (home-page "https://github.com/SciViews/svMisc")
14402 (synopsis "Miscellaneous functions for SciViews")
14404 "This package provides miscellaneous functions for SciViews or general
14405 use, including tools to manage a temporary environment attached to the search
14406 path for temporary variables you do not want to @code{save()} or
14407 @code{load()}; test the current platform; showing progress bars, etc.")
14408 (license license:gpl2)))
14410 (define-public r-xyz
14417 (uri (cran-uri "xyz" version))
14420 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14421 (build-system r-build-system)
14423 `(("r-rcpp" ,r-rcpp)))
14424 (home-page "https://cran.r-project.org/web/packages/xyz/")
14425 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14427 "High dimensional interaction search by brute force requires a quadratic
14428 computational cost in the number of variables. The xyz algorithm provably
14429 finds strong interactions in almost linear time. For details of the algorithm
14430 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14431 interaction search in high-dimensional data.")
14432 ;; Any version of the GPL.
14433 (license license:gpl2+)))
14435 (define-public r-rttf2pt1
14437 (name "r-rttf2pt1")
14442 (uri (cran-uri "Rttf2pt1" version))
14445 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14446 (properties `((upstream-name . "Rttf2pt1")))
14447 (build-system r-build-system)
14448 (home-page "https://github.com/wch/Rttf2pt1")
14449 (synopsis "Font conversion utility")
14451 "This package contains the program @code{ttf2pt1}, for use with the
14452 @code{extrafont} package.")
14453 ;; Most of the files are covered under the Expat license. Some files are
14454 ;; covered under BSD-3. Deviations for individual files are recorded in
14455 ;; the LICENSE file.
14456 (license (list license:bsd-3 license:expat
14457 (license:non-copyleft "file://LICENSE")))))
14459 (define-public r-extrafontdb
14461 (name "r-extrafontdb")
14466 (uri (cran-uri "extrafontdb" version))
14469 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14470 (build-system r-build-system)
14471 (home-page "https://github.com/wch/extrafontdb")
14472 (synopsis "Database for the extrafont package")
14474 "This package holds the database for the @code{extrafont} package.")
14475 (license license:gpl2)))
14477 (define-public r-extrafont
14479 (name "r-extrafont")
14484 (uri (cran-uri "extrafont" version))
14487 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14488 (build-system r-build-system)
14490 `(("r-extrafontdb" ,r-extrafontdb)
14491 ("r-rttf2pt1" ,r-rttf2pt1)))
14492 (home-page "https://github.com/wch/extrafont")
14493 (synopsis "Tools for using fonts in R")
14495 "The extrafont package makes it easier to use fonts other than the basic
14496 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14497 used with PDF or PostScript output files. There are two hurdles for using
14498 fonts in PDF (or Postscript) output files:
14501 @item Making R aware of the font and the dimensions of the characters.
14502 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14503 properly on a device that doesn't have the font. This is usually needed if
14504 you want to print the PDF file or share it with others.
14507 The extrafont package makes both of these things easier.")
14508 (license license:gpl2)))
14510 (define-public r-xkcd
14517 (uri (cran-uri "xkcd" version))
14520 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14521 (build-system r-build-system)
14523 `(("r-extrafont" ,r-extrafont)
14524 ("r-ggplot2" ,r-ggplot2)
14525 ("r-hmisc" ,r-hmisc)))
14526 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14527 (synopsis "Plot ggplot2 graphics in the XKCD style")
14529 "This package provides the means to plot ggplot2 graphs in the style of
14530 the XKCD web comic.")
14531 (license license:gpl3)))
14533 (define-public r-msigdbr
14540 (uri (cran-uri "msigdbr" version))
14543 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14544 (build-system r-build-system)
14546 `(("r-dplyr" ,r-dplyr)
14547 ("r-magrittr" ,r-magrittr)
14548 ("r-rlang" ,r-rlang)
14549 ("r-tibble" ,r-tibble)))
14551 `(("r-knitr" ,r-knitr)))
14552 (home-page "https://github.com/igordot/msigdbr")
14553 (synopsis "MSigDB gene sets for multiple organisms")
14555 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14556 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14557 software in a standard R data frame with key-value pairs. Included are the
14558 original human gene symbols and Entrez IDs as well as the equivalents for
14559 various frequently studied model organisms such as mouse, rat, pig, fly, and
14561 ;; The package is covered under the Expat license, but the upstream MSigDB
14562 ;; files are made available under the Creative Commons Attribution 4.0
14563 ;; International license.
14564 (license (list license:expat license:cc-by4.0))))
14566 (define-public r-gridgraphics
14568 (name "r-gridgraphics")
14573 (uri (cran-uri "gridGraphics" version))
14576 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14577 (properties `((upstream-name . "gridGraphics")))
14578 (build-system r-build-system)
14579 (home-page "https://github.com/pmur002/gridgraphics")
14580 (synopsis "Redraw base graphics using @code{grid} graphics")
14582 "This package provides functions to convert a page of plots drawn with
14583 the @code{graphics} package into identical output drawn with the @code{grid}
14584 package. The result looks like the original @code{graphics}-based plot, but
14585 consists of @code{grid} grobs and viewports that can then be manipulated with
14586 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14587 (license license:gpl2+)))
14589 (define-public r-farver
14596 (uri (cran-uri "farver" version))
14599 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14600 (build-system r-build-system)
14601 (home-page "https://github.com/thomasp85/farver")
14602 (synopsis "Vectorized color conversion and comparison")
14604 "The encoding of color can be handled in many different ways, using
14605 different color spaces. As different color spaces have different uses,
14606 efficient conversion between these representations are important. This
14607 package provides a set of functions that gives access to very fast color space
14608 conversion and comparisons implemented in C++, and offers 100-fold speed
14609 improvements over the @code{convertColor} function in the @code{grDevices}
14611 (license license:expat)))
14613 (define-public r-ggplotify
14615 (name "r-ggplotify")
14620 (uri (cran-uri "ggplotify" version))
14623 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14624 (build-system r-build-system)
14626 `(("r-ggplot2" ,r-ggplot2)
14627 ("r-gridgraphics" ,r-gridgraphics)
14628 ("r-rvcheck" ,r-rvcheck)))
14630 `(("r-knitr" ,r-knitr)))
14631 (home-page "https://github.com/GuangchuangYu/ggplotify")
14632 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14634 "This package provides tools to convert plot function calls (using
14635 expression or formula) to @code{grob} or @code{ggplot} objects that are
14636 compatible with the @code{grid} and @code{ggplot2} environment. With this
14637 package, we are able to e.g. use @code{cowplot} to align plots produced by
14638 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14639 converting them to @code{ggplot} objects.")
14640 (license license:artistic2.0)))
14642 (define-public r-triebeard
14644 (name "r-triebeard")
14649 (uri (cran-uri "triebeard" version))
14652 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14653 (build-system r-build-system)
14654 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14655 (home-page "https://github.com/Ironholds/triebeard/")
14656 (synopsis "Radix trees in Rcpp")
14658 "Radix trees, or tries, are key-value data structures optimized for
14659 efficient lookups, similar in purpose to hash tables. This package provides
14660 an implementation of radix trees for use in R programming and in developing
14661 packages with Rcpp.")
14662 (license license:expat)))
14664 (define-public r-tweenr
14671 (uri (cran-uri "tweenr" version))
14674 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14675 (build-system r-build-system)
14677 `(("r-farver" ,r-farver)
14678 ("r-magrittr" ,r-magrittr)
14680 ("r-rlang" ,r-rlang)))
14681 (home-page "https://github.com/thomasp85/tweenr")
14682 (synopsis "Interpolate data for smooth animations")
14684 "In order to create smooth animation between states of data, tweening is
14685 necessary. This package provides a range of functions for creating tweened
14686 data that can be used as basis for animation. Furthermore it adds a number of
14687 vectorized interpolaters for common R data types such as numeric, date and
14689 (license license:expat)))
14691 (define-public r-polyclip
14693 (name "r-polyclip")
14698 (uri (cran-uri "polyclip" version))
14701 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14702 (build-system r-build-system)
14703 (native-inputs `(("pkg-config" ,pkg-config)))
14704 (home-page "http://www.angusj.com/delphi/clipper.php")
14705 (synopsis "Polygon clipping")
14707 "This package provides an R port of the library Clipper. It performs
14708 polygon clipping operations (intersection, union, set minus, set difference)
14709 for polygonal regions of arbitrary complexity, including holes. It computes
14710 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14711 dilations) for polygonal regions and polygonal lines. It computes the
14712 Minkowski Sum of general polygons. There is a function for removing
14713 self-intersections from polygon data.")
14714 (license license:boost1.0)))
14716 (define-public r-urltools
14718 (name "r-urltools")
14723 (uri (cran-uri "urltools" version))
14726 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14727 (build-system r-build-system)
14729 `(("r-rcpp" ,r-rcpp)
14730 ("r-triebeard" ,r-triebeard)))
14731 (home-page "https://github.com/Ironholds/urltools/")
14732 (synopsis "Vectorized tools for URL handling and parsing")
14734 "This package provides a toolkit for all URL-handling needs, including
14735 encoding and decoding, parsing, parameter extraction and modification. All
14736 functions are designed to be both fast and entirely vectorized. It is
14737 intended to be useful for people dealing with web-related datasets, such as
14738 server-side logs, although may be useful for other situations involving large
14740 (license license:expat)))
14742 (define-public r-ggforce
14749 (uri (cran-uri "ggforce" version))
14752 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14753 (build-system r-build-system)
14755 `(("r-ggplot2" ,r-ggplot2)
14756 ("r-gtable" ,r-gtable)
14758 ("r-polyclip" ,r-polyclip)
14760 ("r-rcppeigen" ,r-rcppeigen)
14761 ("r-rlang" ,r-rlang)
14762 ("r-scales" ,r-scales)
14763 ("r-tidyselect" ,r-tidyselect)
14764 ("r-tweenr" ,r-tweenr)
14765 ("r-withr" ,r-withr)))
14766 (home-page "https://ggforce.data-imaginist.com")
14767 (synopsis "Accelerating ggplot2")
14769 "The aim of the ggplot2 package is to aid in visual data investigations.
14770 This focus has led to a lack of facilities for composing specialized plots.
14771 Thi package aims to be a collection of mainly new statistics and geometries
14772 that fills this gap.")
14773 (license license:expat)))
14775 (define-public r-europepmc
14777 (name "r-europepmc")
14782 (uri (cran-uri "europepmc" version))
14785 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14786 (build-system r-build-system)
14788 `(("r-dplyr" ,r-dplyr)
14790 ("r-jsonlite" ,r-jsonlite)
14792 ("r-progress" ,r-progress)
14793 ("r-purrr" ,r-purrr)
14794 ("r-rlang" ,r-rlang)
14795 ("r-tibble" ,r-tibble)
14796 ("r-tidyr" ,r-tidyr)
14797 ("r-urltools" ,r-urltools)
14798 ("r-xml2" ,r-xml2)))
14800 `(("r-knitr" ,r-knitr)))
14801 (home-page "https://github.com/ropensci/europepmc/")
14802 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14804 "This package provides an R Client for the
14805 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14806 Service}. It gives access to both metadata on life science literature and
14807 open access full texts. Europe PMC indexes all PubMed content and other
14808 literature sources including Agricola, a bibliographic database of citations
14809 to the agricultural literature, or Biological Patents. In addition to
14810 bibliographic metadata, the client allows users to fetch citations and
14811 reference lists. Links between life-science literature and other EBI
14812 databases, including ENA, PDB or ChEMBL are also accessible.")
14813 (license license:gpl3)))
14815 (define-public r-ggraph
14822 (uri (cran-uri "ggraph" version))
14825 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14826 (build-system r-build-system)
14828 `(("r-digest" ,r-digest)
14829 ("r-dplyr" ,r-dplyr)
14830 ("r-ggforce" ,r-ggforce)
14831 ("r-ggplot2" ,r-ggplot2)
14832 ("r-ggrepel" ,r-ggrepel)
14833 ("r-graphlayouts" ,r-graphlayouts)
14834 ("r-gtable" ,r-gtable)
14835 ("r-igraph" ,r-igraph)
14838 ("r-rlang" ,r-rlang)
14839 ("r-scales" ,r-scales)
14840 ("r-tidygraph" ,r-tidygraph)
14841 ("r-viridis" ,r-viridis)))
14843 `(("r-knitr" ,r-knitr)))
14844 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14845 (synopsis "Implementation of grammar of graphics for graphs and networks")
14847 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14848 graph and network visualizations due to its reliance on tabular data input.
14849 The ggraph package is an extension of the ggplot2 API tailored to graph
14850 visualizations and provides the same flexible approach to building up plots
14852 (license license:gpl3)))
14854 (define-public r-varselrf
14856 (name "r-varselrf")
14861 (uri (cran-uri "varSelRF" version))
14864 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14865 (properties `((upstream-name . "varSelRF")))
14866 (build-system r-build-system)
14868 `(("r-randomforest" ,r-randomforest)))
14869 (home-page "https://www.ligarto.org/rdiaz/software/software")
14870 (synopsis "Variable selection using random forests")
14872 "This package provides tools for the variable selection from random
14873 forests using both backwards variable elimination (for the selection of small
14874 sets of non-redundant variables) and selection based on the importance
14875 spectrum (somewhat similar to scree plots; for the selection of large,
14876 potentially highly-correlated variables). The main applications are in
14877 high-dimensional data (e.g., microarray data, and other genomics and
14878 proteomics applications).")
14879 (license license:gpl2+)))
14881 (define-public r-pamr
14888 (uri (cran-uri "pamr" version))
14891 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14892 (build-system r-build-system)
14894 `(("r-cluster" ,r-cluster)
14895 ("r-survival" ,r-survival)))
14896 (native-inputs `(("gfortran" ,gfortran)))
14897 (home-page "https://cran.r-project.org/web/packages/pamr/")
14898 (synopsis "Prediction Analysis for Microarrays")
14900 "This package provides some functions for sample classification in
14902 (license license:gpl2)))
14904 (define-public r-rda
14907 (version "1.0.2-2.1")
14911 (uri (cran-uri "rda" version))
14914 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14915 (build-system r-build-system)
14916 (home-page "https://cran.r-project.org/web/packages/rda/")
14917 (synopsis "Shrunken centroids regularized discriminant analysis")
14919 "This package provides tools for shrunken centroids regularized
14920 discriminant analysis for the purpose of classifying high dimensional data.")
14921 (license license:gpl2+)))
14923 (define-public r-ggvis
14930 (uri (cran-uri "ggvis" version))
14933 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14934 (build-system r-build-system)
14936 `(("r-assertthat" ,r-assertthat)
14937 ("r-dplyr" ,r-dplyr)
14938 ("r-htmltools" ,r-htmltools)
14939 ("r-jsonlite" ,r-jsonlite)
14940 ("r-lazyeval" ,r-lazyeval)
14941 ("r-magrittr" ,r-magrittr)
14942 ("r-shiny" ,r-shiny)))
14943 (home-page "https://ggvis.rstudio.com/")
14944 (synopsis "Interactive grammar of graphics")
14946 "This package is a data visualization package for R providing an
14947 implementation of an interactive grammar of graphics, taking the best parts of
14948 ggplot2, combining them with the reactive framework of Shiny and drawing web
14949 graphics using Vega.")
14950 (license license:gpl2)))
14952 (define-public r-gbm
14959 (uri (cran-uri "gbm" version))
14962 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14963 (build-system r-build-system)
14965 `(("r-gridextra" ,r-gridextra)
14966 ("r-lattice" ,r-lattice)
14967 ("r-survival" ,r-survival)))
14968 (home-page "https://github.com/gbm-developers/gbm")
14969 (synopsis "Generalized boosted regression models")
14971 "This package is an implementation of extensions to Freund and Schapire's
14972 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14973 regression methods for least squares, absolute loss, t-distribution loss,
14974 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14975 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14976 and Learning to Rank measures (LambdaMart).")
14977 (license license:gpl2+)))
14979 (define-public r-threejs
14986 (uri (cran-uri "threejs" version))
14989 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14990 (build-system r-build-system)
14992 `(#:modules ((guix build utils)
14993 (guix build r-build-system)
14997 (modify-phases %standard-phases
14998 (add-after 'unpack 'process-javascript
14999 (lambda* (#:key inputs #:allow-other-keys)
15000 (with-directory-excursion "inst"
15004 `((,(assoc-ref inputs "js-jquery")
15005 "htmlwidgets/lib/jquery/jquery.min.js")
15006 (,(assoc-ref inputs "js-threejs-111")
15007 "htmlwidgets/lib/threejs-111/three.min.js"))))
15008 (lambda (sources targets)
15009 (for-each (lambda (source target)
15010 (format #t "Processing ~a --> ~a~%"
15012 (delete-file target)
15013 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15014 (call-with-output-file target
15016 (dump-port minified port)))))
15017 sources targets))))
15020 `(("r-base64enc" ,r-base64enc)
15021 ("r-crosstalk" ,r-crosstalk)
15022 ("r-htmlwidgets" ,r-htmlwidgets)
15023 ("r-igraph" ,r-igraph)))
15025 `(("uglify-js" ,uglify-js)
15029 (uri "https://code.jquery.com/jquery-1.12.4.js")
15032 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15036 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15039 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15040 (home-page "https://bwlewis.github.io/rthreejs")
15041 (synopsis "Interactive 3D scatter plots, networks and globes")
15043 "Create interactive 3D scatter plots, network plots, and globes in R
15044 using the three.js visualization library.")
15045 (license license:expat)))
15047 (define-public r-mlbench
15054 (uri (cran-uri "mlbench" version))
15057 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15058 (build-system r-build-system)
15059 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15060 (synopsis "Machine learning benchmark problems")
15062 "This package provides a collection of artificial and real-world machine
15063 learning benchmark problems, including, e.g., several data sets from the UCI
15065 (license license:gpl2)))
15067 (define-public r-mpm
15074 (uri (cran-uri "mpm" version))
15077 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15078 (build-system r-build-system)
15080 `(("r-kernsmooth" ,r-kernsmooth)
15081 ("r-mass" ,r-mass)))
15082 (home-page "http://mpm.r-forge.r-project.org")
15083 (synopsis "Multivariate projection methods")
15085 "This is a package for exploratory graphical analysis of multivariate
15086 data, specifically gene expression data with different projection methods:
15087 principal component analysis, correspondence analysis, spectral map
15089 (license license:gpl2+)))
15091 (define-public r-png
15097 (uri (cran-uri "png" version))
15100 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15101 (build-system r-build-system)
15103 `(("libpng" ,libpng)
15105 (home-page "https://www.rforge.net/png/")
15106 (synopsis "Read and write PNG images")
15108 "This package provides an easy and simple way to read, write and display
15109 bitmap images stored in the PNG format. It can read and write both files and
15110 in-memory raw vectors.")
15111 ;; Any of these GPL versions.
15112 (license (list license:gpl2 license:gpl3))))
15114 (define-public r-ggcorrplot
15116 (name "r-ggcorrplot")
15121 (uri (cran-uri "ggcorrplot" version))
15124 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15125 (build-system r-build-system)
15127 `(("r-ggplot2" ,r-ggplot2)
15128 ("r-reshape2" ,r-reshape2)))
15129 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15130 (synopsis "Visualization of a correlation matrix using ggplot2")
15132 "The ggcorrplot package can be used to visualize easily a correlation
15133 matrix using ggplot2. It provides a solution for reordering the correlation
15134 matrix and displays the significance level on the plot. It also includes a
15135 function for computing a matrix of correlation p-values.")
15136 (license license:gpl2)))
15138 (define-public r-flexdashboard
15140 (name "r-flexdashboard")
15141 (version "0.5.1.1")
15145 (uri (cran-uri "flexdashboard" version))
15148 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
15149 (build-system r-build-system)
15151 `(#:modules ((guix build utils)
15152 (guix build r-build-system)
15156 (ice-9 textual-ports))
15158 (modify-phases %standard-phases
15159 (add-after 'unpack 'process-javascript
15160 (lambda* (#:key inputs #:allow-other-keys)
15161 (with-directory-excursion "inst"
15162 ;; Concatenate all components of prism.js
15163 (let ((contents (string-join
15164 (map (lambda (name)
15165 (call-with-input-file
15166 (assoc-ref inputs name)
15170 "js-prism-line-numbers"))
15172 (call-with-output-file "prism-src.js"
15173 (cut display contents <>)))
15177 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15178 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15180 "www/sly/sly.min.js")
15182 "www/prism/prism.js")
15183 (,(assoc-ref inputs "js-raphael")
15184 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15185 (,(assoc-ref inputs "js-featherlight")
15186 "www/featherlight/featherlight.min.js"))))
15187 (lambda (sources targets)
15188 (for-each (lambda (source target)
15189 (format #t "Processing ~a --> ~a~%"
15191 (delete-file target)
15192 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15193 (call-with-output-file target
15195 (dump-port minified port)))))
15196 sources targets))))
15199 `(("r-htmltools" ,r-htmltools)
15200 ("r-htmlwidgets" ,r-htmlwidgets)
15201 ("r-jsonlite" ,r-jsonlite)
15202 ("r-knitr" ,r-knitr)
15203 ("r-rmarkdown" ,r-rmarkdown)
15204 ("r-shiny" ,r-shiny)))
15206 `(("uglify-js" ,uglify-js)
15210 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15213 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15217 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15220 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15224 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15227 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15228 ("js-prism-line-numbers"
15231 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15234 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15238 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15241 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15242 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15243 (synopsis "R Markdown format for flexible dashboards")
15245 "This package provides an R Markdown format for converting an R Markdown
15246 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15247 of its components to the containing web page.")
15248 (license license:expat)))
15250 (define-public r-preseqr
15257 (uri (cran-uri "preseqR" version))
15260 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15261 (properties `((upstream-name . "preseqR")))
15262 (build-system r-build-system)
15264 `(("r-polynom" ,r-polynom)))
15265 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15266 (synopsis "Predicting species accumulation curves")
15268 "This package can be used to predict the r-species accumulation
15269 curve (r-SAC), which is the number of species represented at least r times as
15270 a function of the sampling effort. When r = 1, the curve is known as the
15271 species accumulation curve, or the library complexity curve in high-throughput
15272 genomic sequencing. The package includes both parametric and nonparametric
15273 methods, as described by Deng C, et al. (2018).")
15274 (license license:gpl3)))
15276 (define-public r-mapplots
15278 (name "r-mapplots")
15283 (uri (cran-uri "mapplots" version))
15286 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15287 (build-system r-build-system)
15288 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15289 (synopsis "Data visualization on maps")
15291 "This package helps you create simple maps; add sub-plots like pie plots
15292 to a map or any other plot; format, plot and export gridded data. The package
15293 was developed for displaying fisheries data but most functions can be used for
15294 more generic data visualisation.")
15295 (license license:gpl2+)))
15297 (define-public r-pmcmr
15304 (uri (cran-uri "PMCMR" version))
15307 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15308 (properties `((upstream-name . "PMCMR")))
15309 (build-system r-build-system)
15310 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15311 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15313 "This is a deprecated package for calculating pairwise multiple
15314 comparisons of mean rank sums. This package is superseded by the novel
15315 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15316 compatibility of dependent packages for some time.")
15317 (license license:gpl3+)))
15319 (define-public r-downloader
15321 (name "r-downloader")
15326 (uri (cran-uri "downloader" version))
15329 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15330 (build-system r-build-system)
15332 `(("r-digest" ,r-digest)))
15333 (home-page "https://github.com/wch/downloader")
15334 (synopsis "Download files over HTTP and HTTPS")
15336 "This package provides a wrapper for the @code{download.file} function,
15337 making it possible to download files over HTTPS across platforms. The
15338 @code{RCurl} package provides this functionality (and much more) but has
15339 external dependencies. This package has is implemented purely in R.")
15340 (license license:gpl2)))
15342 (define-public r-rex
15349 (uri (cran-uri "rex" version))
15352 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15353 (build-system r-build-system)
15355 `(("r-lazyeval" ,r-lazyeval)))
15357 `(("r-knitr" ,r-knitr)))
15358 (home-page "https://github.com/kevinushey/rex")
15359 (synopsis "Friendly regular expressions")
15361 "This package provides a friendly interface for the construction of
15362 regular expressions. Regular expressions are a very powerful feature, however
15363 they are often difficult to interpret. Rex allows you to build complex
15364 regular expressions from human readable expressions")
15365 (license license:expat)))
15367 (define-public r-xmlparsedata
15369 (name "r-xmlparsedata")
15374 (uri (cran-uri "xmlparsedata" version))
15377 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15378 (properties `((upstream-name . "xmlparsedata")))
15379 (build-system r-build-system)
15380 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15381 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15383 "This package provides tools to convert the output of
15384 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15385 @code{XPath}, and is easier to manipulate in general.")
15386 (license license:expat)))
15388 (define-public r-cyclocomp
15390 (name "r-cyclocomp")
15395 (uri (cran-uri "cyclocomp" version))
15398 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15399 (properties `((upstream-name . "cyclocomp")))
15400 (build-system r-build-system)
15402 `(("r-callr" ,r-callr)
15403 ("r-crayon" ,r-crayon)
15405 ("r-remotes" ,r-remotes)
15406 ("r-withr" ,r-withr)))
15407 (home-page "https://github.com/MangoTheCat/cyclocomp")
15408 (synopsis "Cyclomatic complexity of R code")
15410 "Cyclomatic complexity is a software metric, used to indicate the
15411 complexity of a program. It is a quantitative measure of the number of
15412 linearly independent paths through a program's source code. This package
15413 provides tools to compute this metric.")
15414 (license license:expat)))
15416 (define-public r-lintr
15423 (uri (cran-uri "lintr" version))
15426 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15427 (properties `((upstream-name . "lintr")))
15428 (build-system r-build-system)
15430 `(("r-codetools" ,r-codetools)
15431 ("r-crayon" ,r-crayon)
15432 ("r-cyclocomp" ,r-cyclocomp)
15433 ("r-digest" ,r-digest)
15435 ("r-jsonlite" ,r-jsonlite)
15436 ("r-knitr" ,r-knitr)
15438 ("r-rstudioapi" ,r-rstudioapi)
15439 ("r-testthat" ,r-testthat)
15441 ("r-xmlparsedata" ,r-xmlparsedata)))
15442 (home-page "https://github.com/jimhester/lintr")
15443 (synopsis "Linter for R code")
15444 (description "This package checks adherence to a given style, syntax
15445 errors and possible semantic issues. It supports on the fly checking of R
15446 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15447 (license license:expat)))
15449 (define-public r-sctransform
15451 (name "r-sctransform")
15456 (uri (cran-uri "sctransform" version))
15459 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15460 (build-system r-build-system)
15462 `(("r-future-apply" ,r-future-apply)
15463 ("r-ggplot2" ,r-ggplot2)
15464 ("r-gridextra" ,r-gridextra)
15466 ("r-matrix" ,r-matrix)
15468 ("r-rcppeigen" ,r-rcppeigen)
15469 ("r-reshape2" ,r-reshape2)))
15470 (home-page "https://github.com/ChristophH/sctransform")
15471 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15473 "This package provides a normalization method for single-cell UMI count
15474 data using a variance stabilizing transformation. The transformation is based
15475 on a negative binomial regression model with regularized parameters. As part
15476 of the same regression framework, this package also provides functions for
15477 batch correction, and data correction.")
15478 (license license:gpl3)))
15480 (define-public r-styler
15487 (uri (cran-uri "styler" version))
15490 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15491 (build-system r-build-system)
15493 `(("r-backports" ,r-backports)
15495 ("r-magrittr" ,r-magrittr)
15496 ("r-purrr" ,r-purrr)
15497 ("r-r-cache" ,r-r-cache)
15498 ("r-rematch2" ,r-rematch2)
15499 ("r-rlang" ,r-rlang)
15500 ("r-rprojroot" ,r-rprojroot)
15501 ("r-tibble" ,r-tibble)
15502 ("r-withr" ,r-withr)
15503 ("r-xfun" ,r-xfun)))
15504 (home-page "https://github.com/r-lib/styler")
15505 (synopsis "Non-invasive pretty printing of R code")
15507 "This is a package for pretty-printing R code without changing the user's
15508 formatting intent.")
15509 (license license:gpl3)))
15511 (define-public r-scrime
15518 (uri (cran-uri "scrime" version))
15521 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15522 (build-system r-build-system)
15523 (home-page "https://cran.r-project.org/web/packages/scrime/")
15524 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15526 "This package provides tools for the analysis of high-dimensional data
15527 developed/implemented at the group \"Statistical Complexity Reduction In
15528 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15529 the functions can also be applied to other types of categorical data.")
15530 (license license:gpl2)))
15532 (define-public r-pbmcapply
15534 (name "r-pbmcapply")
15539 (uri (cran-uri "pbmcapply" version))
15542 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15543 (build-system r-build-system)
15544 (home-page "https://github.com/kvnkuang/pbmcapply")
15545 (synopsis "Track the progress of apply procedures with a progress bar")
15547 "This light-weight package helps you track and visualize the progress of
15548 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15549 (license license:expat)))
15551 (define-public r-blme
15558 (uri (cran-uri "blme" version))
15561 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15562 (build-system r-build-system)
15563 (propagated-inputs `(("r-lme4" ,r-lme4)))
15564 (home-page "https://github.com/vdorie/blme")
15565 (synopsis "Bayesian linear mixed-effects models")
15567 "This package provides tools for maximum a posteriori estimation for
15568 linear and generalized linear mixed-effects models in a Bayesian setting. It
15569 extends the lme4 package.")
15570 (license license:gpl2+)))
15572 (define-public r-batchtools
15574 (name "r-batchtools")
15579 (uri (cran-uri "batchtools" version))
15582 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15583 (build-system r-build-system)
15585 `(("r-backports" ,r-backports)
15586 ("r-base64url" ,r-base64url)
15588 ("r-checkmate" ,r-checkmate)
15589 ("r-data-table" ,r-data-table)
15590 ("r-digest" ,r-digest)
15592 ("r-progress" ,r-progress)
15594 ("r-rappdirs" ,r-rappdirs)
15595 ("r-stringi" ,r-stringi)
15596 ("r-withr" ,r-withr)))
15598 `(("r-knitr" ,r-knitr)))
15599 (home-page "https://github.com/mllg/batchtools")
15600 (synopsis "Tools for computation on batch systems")
15602 "As a successor of the packages BatchJobs and BatchExperiments, this
15603 package provides a parallel implementation of the Map function for high
15604 performance computing systems managed by various schedulers. A multicore and
15605 socket mode allow the parallelization on a local machines, and multiple
15606 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15607 the package provides an abstraction mechanism to define large-scale computer
15608 experiments in a well-organized and reproducible way.")
15609 (license license:lgpl3)))
15611 (define-public r-clue
15618 (uri (cran-uri "clue" version))
15621 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15622 (build-system r-build-system)
15623 (propagated-inputs `(("r-cluster" ,r-cluster)))
15624 (home-page "https://cran.r-project.org/web/packages/clue/")
15625 (synopsis "Tools for analyzing cluster ensembles")
15626 (description "Cluster ensembles are collections of individual solutions to
15627 a given clustering problem which are useful or necessary to consider in a wide
15628 range of applications. This R package provides an extensible computational
15629 environment for creating and analyzing cluster ensembles, with basic data
15630 structures for representing partitions and hierarchies, and facilities for
15631 computing on them, including methods for measuring proximity and obtaining
15632 consensus and secondary clusterings.")
15633 (license license:gpl2)))
15635 (define-public r-sitmo
15642 (uri (cran-uri "sitmo" version))
15645 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15646 (build-system r-build-system)
15647 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15648 (home-page "https://github.com/coatless/sitmo/")
15649 (synopsis "Parallel pseudo random number generator header files")
15651 "This package provides two high quality and fast PPRNGs that may be used
15652 in an OpenMP parallel environment. In addition, there is a generator for one
15653 dimensional low-discrepancy sequence.")
15654 (license license:expat)))
15656 (define-public r-dqrng
15663 (uri (cran-uri "dqrng" version))
15666 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15667 (build-system r-build-system)
15671 ("r-sitmo" ,r-sitmo)))
15672 (home-page "https://www.daqana.org/dqrng")
15673 (synopsis "Fast pseudo random number generators")
15675 "Several fast random number generators are provided as C++ header-only
15676 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15677 Additionally, fast functions for generating random numbers according to a
15678 uniform, normal and exponential distribution are included. The latter two use
15679 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15680 functions are exported to R and as a C++ interface and are enabled for use
15681 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15682 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15683 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15684 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15685 ;; whole is distributed under the terms of the AGPL 3.
15686 (license license:agpl3)))
15688 (define-public r-ingredients
15690 (name "r-ingredients")
15695 (uri (cran-uri "ingredients" version))
15698 "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
15699 (properties `((upstream-name . "ingredients")))
15700 (build-system r-build-system)
15702 `(("r-ggplot2" ,r-ggplot2)
15703 ("r-gridextra" ,r-gridextra)
15704 ("r-scales" ,r-scales)))
15705 (native-inputs `(("r-knitr" ,r-knitr)))
15706 (home-page "https://ModelOriented.github.io/ingredients/")
15707 (synopsis "Effects and importances of model ingredients")
15709 "This is a collection of tools for assessment of feature importance and
15710 feature effects. Key functions are:
15713 @item @code{feature_importance()} for assessment of global level feature
15715 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15716 @item @code{partial_dependence()} for partial dependence plots,
15717 @item @code{conditional_dependence()} for conditional dependence plots,
15718 @item @code{accumulated_dependence()} for accumulated local effects plots,
15719 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15720 aggregation of ceteris paribus profiles,
15721 @item generic @code{print()} and @code{plot()} for better usability of
15722 selected explainers,
15723 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15724 @item generic @code{describe()} for explanations in natural language.
15726 (license license:gpl3)))
15728 (define-public r-ibreakdown
15730 (name "r-ibreakdown")
15735 (uri (cran-uri "iBreakDown" version))
15738 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15739 (properties `((upstream-name . "iBreakDown")))
15740 (build-system r-build-system)
15741 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15742 (native-inputs `(("r-knitr" ,r-knitr)))
15743 (home-page "https://ModelOriented.github.io/iBreakDown/")
15744 (synopsis "Model agnostic instance level variable attributions")
15746 "This package provides a model agnostic tool for decomposition of
15747 predictions from black boxes. It supports additive attributions and
15748 attributions with interactions. The Break Down Table shows contributions of
15749 every variable to a final prediction. The Break Down Plot presents variable
15750 contributions in a concise graphical way. This package works for
15751 classification and regression models.")
15752 (license license:gpl3)))
15754 (define-public r-dalex
15761 (uri (cran-uri "DALEX" version))
15764 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15765 (properties `((upstream-name . "DALEX")))
15766 (build-system r-build-system)
15768 `(("r-ggplot2" ,r-ggplot2)
15769 ("r-ibreakdown" ,r-ibreakdown)
15770 ("r-ingredients" ,r-ingredients)))
15771 (home-page "https://pbiecek.github.io/DALEX/")
15772 (synopsis "Descriptive machine learning explanations")
15774 "Machine Learning models are widely used and have various applications in
15775 classification or regression. Models created with boosting, bagging, stacking
15776 or similar techniques are often used due to their high performance, but such
15777 black-box models usually lack interpretability. The DALEX package contains
15778 various explainers that help to understand the link between input variables
15779 and model output.")
15780 ;; Any version of the GPL
15781 (license license:gpl3+)))
15783 (define-public r-enrichr
15790 (uri (cran-uri "enrichR" version))
15793 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15794 (properties `((upstream-name . "enrichR")))
15795 (build-system r-build-system)
15797 `(("r-httr" ,r-httr)
15798 ("r-rjson" ,r-rjson)))
15799 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15800 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15802 "This package provides an R interface to all Enrichr databases, a
15803 web-based tool for analyzing gene sets and returns any enrichment of common
15804 annotated biological functions.")
15805 (license license:gpl2+)))
15807 (define-public r-plot3d
15814 (uri (cran-uri "plot3D" version))
15817 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15818 (properties `((upstream-name . "plot3D")))
15819 (build-system r-build-system)
15820 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15821 (home-page "https://cran.r-project.org/web/packages/plot3D")
15822 (synopsis "Plot multi-dimensional data")
15824 "This package provides functions for viewing 2D and 3D data, including
15825 perspective plots, slice plots, surface plots, scatter plots, etc. It
15826 includes data sets from oceanography.")
15827 (license license:gpl3+)))
15829 (define-public r-ggfortify
15831 (name "r-ggfortify")
15836 (uri (cran-uri "ggfortify" version))
15839 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15840 (build-system r-build-system)
15842 `(("r-dplyr" ,r-dplyr)
15843 ("r-ggplot2" ,r-ggplot2)
15844 ("r-gridextra" ,r-gridextra)
15845 ("r-scales" ,r-scales)
15846 ("r-stringr" ,r-stringr)
15847 ("r-tibble" ,r-tibble)
15848 ("r-tidyr" ,r-tidyr)))
15850 `(("r-knitr" ,r-knitr)))
15851 (home-page "https://github.com/sinhrks/ggfortify")
15852 (synopsis "Data visualization tools for statistical analysis results")
15854 "This package provides unified plotting tools for statistics commonly
15855 used, such as GLM, time series, PCA families, clustering and survival
15856 analysis. The package offers a single plotting interface for these analysis
15857 results and plots in a unified style using the @code{ggplot2} package.")
15858 (license license:gpl2)))
15860 (define-public r-refmanager
15862 (name "r-refmanager")
15867 (uri (cran-uri "RefManageR" version))
15870 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15871 (properties `((upstream-name . "RefManageR")))
15872 (build-system r-build-system)
15874 `(("r-bibtex" ,r-bibtex)
15876 ("r-jsonlite" ,r-jsonlite)
15877 ("r-lubridate" ,r-lubridate)
15879 ("r-stringr" ,r-stringr)
15880 ("r-xml2" ,r-xml2)))
15881 (home-page "https://github.com/ropensci/RefManageR/")
15882 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15884 "This package provides tools for importing and working with bibliographic
15885 references. It greatly enhances the @code{bibentry} class by providing a
15886 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15887 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15888 by various formats for name lists (author by last names, translator by full
15889 names, etc.). Entries can be updated, combined, sorted, printed in a number
15890 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15891 into R and converted to @code{BibEntry} objects.")
15892 ;; Any of these licenses may be picked.
15893 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15895 (define-public r-citr
15902 (uri (cran-uri "citr" version))
15905 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15906 (build-system r-build-system)
15908 `(("r-assertthat" ,r-assertthat)
15911 ("r-miniui" ,r-miniui)
15912 ("r-refmanager" ,r-refmanager)
15913 ("r-rstudioapi" ,r-rstudioapi)
15914 ("r-shiny" ,r-shiny)
15915 ("r-shinyjs" ,r-shinyjs)
15916 ("r-yaml" ,r-yaml)))
15917 (home-page "https://github.com/crsh/citr")
15918 (synopsis "RStudio add-in to insert Markdown citations")
15920 "This package provides functions and an RStudio add-in that search a
15921 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15922 the current document.")
15923 (license license:expat)))
15925 (define-public r-xgboost
15928 (version "1.1.1.1")
15932 (uri (cran-uri "xgboost" version))
15935 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
15936 (build-system r-build-system)
15938 `(("r-data-table" ,r-data-table)
15939 ("r-magrittr" ,r-magrittr)
15940 ("r-matrix" ,r-matrix)
15941 ("r-stringi" ,r-stringi)))
15943 `(("r-knitr" ,r-knitr)))
15944 (home-page "https://github.com/dmlc/xgboost")
15945 (synopsis "Extreme gradient boosting")
15947 "This package provides an R interface to Extreme Gradient Boosting, which
15948 is an efficient implementation of the gradient boosting framework from Chen
15949 and Guestrin (2016). The package includes efficient linear model solver and
15950 tree learning algorithms. The package can automatically do parallel
15951 computation on a single machine. It supports various objective functions,
15952 including regression, classification and ranking. The package is made to be
15953 extensible, so that users are also allowed to define their own objectives
15955 (license license:asl2.0)))
15957 (define-public r-umap
15960 (version "0.2.5.0")
15964 (uri (cran-uri "umap" version))
15967 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15968 (build-system r-build-system)
15970 `(("r-openssl" ,r-openssl)
15972 ("r-reticulate" ,r-reticulate)
15973 ("r-rspectra" ,r-rspectra)))
15975 `(("r-knitr" ,r-knitr)))
15976 (home-page "https://github.com/tkonopka/umap")
15977 (synopsis "Uniform manifold approximation and projection")
15979 "Uniform manifold approximation and projection is a technique for
15980 dimension reduction. This package provides an interface to the UMAP algorithm
15981 in R, including a translation of the original algorithm into R.")
15982 (license license:expat)))
15984 (define-public r-uwot
15991 (uri (cran-uri "uwot" version))
15994 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15995 (build-system r-build-system)
15997 `(("r-dqrng" ,r-dqrng)
15999 ("r-irlba" ,r-irlba)
16000 ("r-matrix" ,r-matrix)
16002 ("r-rcppannoy" ,r-rcppannoy)
16003 ("r-rcppprogress" ,r-rcppprogress)
16004 ("r-rspectra" ,r-rspectra)))
16005 (home-page "https://github.com/jlmelville/uwot")
16006 (synopsis "Uniform manifold approximation and projection")
16008 "This package provides an implementation of the Uniform Manifold
16009 Approximation and Projection dimensionality reduction by McInnes et
16010 al. (2018). It also provides means to transform new data and to carry out
16011 supervised dimensionality reduction. An implementation of the related
16012 LargeVis method of Tang et al. (2016) is also provided.")
16013 (license license:gpl3)))
16015 (define-public r-kableextra
16017 (name "r-kableextra")
16022 (uri (cran-uri "kableExtra" version))
16025 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16026 (properties `((upstream-name . "kableExtra")))
16027 (build-system r-build-system)
16029 `(("r-digest" ,r-digest)
16031 ("r-htmltools" ,r-htmltools)
16032 ("r-knitr" ,r-knitr)
16033 ("r-magrittr" ,r-magrittr)
16034 ("r-readr" ,r-readr)
16035 ("r-rmarkdown" ,r-rmarkdown)
16036 ("r-rstudioapi" ,r-rstudioapi)
16037 ("r-rvest" ,r-rvest)
16038 ("r-scales" ,r-scales)
16039 ("r-stringr" ,r-stringr)
16040 ("r-viridislite" ,r-viridislite)
16041 ("r-webshot" ,r-webshot)
16042 ("r-xml2" ,r-xml2)))
16043 (home-page "https://haozhu233.github.io/kableExtra/")
16044 (synopsis "Construct complex tables with pipe syntax")
16046 "Build complex HTML or LaTeX tables using @code{kable()} from
16047 @code{knitr} and the piping syntax from @code{magrittr}. The function
16048 @code{kable()} is a light weight table generator coming from @code{knitr}.
16049 This package simplifies the way to manipulate the HTML or LaTeX codes
16050 generated by @code{kable()} and allows users to construct complex tables and
16051 customize styles using a readable syntax.")
16052 (license license:expat)))
16054 (define-public r-glasso
16061 (uri (cran-uri "glasso" version))
16063 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16064 (build-system r-build-system)
16065 (native-inputs `(("gfortran" ,gfortran)))
16066 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16067 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16069 "This is a package for estimation of a sparse inverse covariance matrix
16070 using a lasso (L1) penalty. Facilities are provided for estimates along a
16071 path of values for the regularization parameter.")
16072 (license license:gpl2)))
16074 (define-public r-rhpcblasctl
16076 (name "r-rhpcblasctl")
16077 (version "0.20-137")
16081 (uri (cran-uri "RhpcBLASctl" version))
16084 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16085 (properties `((upstream-name . "RhpcBLASctl")))
16086 (build-system r-build-system)
16087 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16088 (synopsis "Control the number of threads on BLAS")
16090 "This package allows you to control the number of threads the BLAS
16091 library uses. It is also possible to control the number of threads in
16093 (license license:agpl3+)))
16095 (define-public r-lda
16102 (uri (cran-uri "lda" version))
16105 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16106 (build-system r-build-system)
16107 (home-page "https://cran.r-project.org/web/packages/lda/")
16108 (synopsis "Collapsed Gibbs sampling methods for topic models")
16110 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16111 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16112 mixed-membership stochastic blockmodel. Inference for all of these models is
16113 implemented via a fast collapsed Gibbs sampler written in C. Utility
16114 functions for reading/writing data typically used in topic models, as well as
16115 tools for examining posterior distributions are also included.")
16116 ;; Any version of the LGPL
16117 (license license:lgpl3+)))
16119 (define-public r-rann-l1
16126 (uri (cran-uri "RANN.L1" version))
16129 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16130 (properties `((upstream-name . "RANN.L1")))
16131 (build-system r-build-system)
16132 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16133 (synopsis "Fast nearest neighbour search using L1 metric")
16135 "This package provides tools to find the k nearest neighbours for every
16136 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16137 library. There is support for approximate as well as exact searches, fixed
16138 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16139 computed using the L1 (Manhattan, taxicab) metric.")
16140 (license license:gpl3+)))
16142 (define-public r-leiden
16149 (uri (cran-uri "leiden" version))
16152 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16153 (properties `((upstream-name . "leiden")))
16154 (build-system r-build-system)
16156 `(("r-igraph" ,r-igraph)
16157 ("r-matrix" ,r-matrix)
16158 ("r-reticulate" ,r-reticulate)))
16159 (home-page "https://github.com/TomKellyGenetics/leiden")
16160 (synopsis "R implementation of Leiden clustering algorithm")
16162 "This package implements the Python @code{leidenalg} module to be called
16163 in R. It enables clustering using the Leiden algorithm for partitioning a
16164 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16165 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16166 (license license:gpl3)))
16168 (define-public r-patchwork
16170 (name "r-patchwork")
16175 (uri (cran-uri "patchwork" version))
16178 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
16179 (build-system r-build-system)
16181 `(("r-ggplot2" ,r-ggplot2)
16182 ("r-gtable" ,r-gtable)))
16184 `(("r-knitr" ,r-knitr)))
16185 (home-page "https://github.com/thomasp85/patchwork")
16186 (synopsis "Compose ggplot2 plots")
16188 "The @code{ggplot2} package provides a strong API for sequentially
16189 building up a plot, but does not concern itself with composition of multiple
16190 plots. Patchwork is a package that expands the API to allow for arbitrarily
16191 complex composition of plots by providing mathmatical operators for combining
16193 (license license:expat)))
16195 (define-public r-liger
16202 (uri (git-reference
16203 (url "https://github.com/MacoskoLab/liger.git")
16204 (commit (string-append "v" version))))
16205 (file-name (git-file-name name version))
16208 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16209 (modules '((guix build utils)))
16212 (delete-file "inst/java/ModularityOptimizer.jar")
16214 (build-system r-build-system)
16217 (modify-phases %standard-phases
16218 (add-after 'unpack 'build-java-part
16219 (lambda* (#:key inputs #:allow-other-keys)
16220 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16221 (for-each (lambda (file) (invoke "javac" file))
16222 (find-files "." "\\.java$"))
16223 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16224 (find-files "." "\\.class$"))
16227 `(("r-cowplot" ,r-cowplot)
16228 ("r-dosnow" ,r-dosnow)
16229 ("r-dplyr" ,r-dplyr)
16231 ("r-foreach" ,r-foreach)
16232 ("r-ggplot2" ,r-ggplot2)
16233 ("r-ggrepel" ,r-ggrepel)
16234 ("r-hmisc" ,r-hmisc)
16236 ("r-irlba" ,r-irlba)
16237 ("r-matrix" ,r-matrix)
16238 ("r-mclust" ,r-mclust)
16239 ("r-patchwork" ,r-patchwork)
16241 ("r-rann-l1" ,r-rann-l1)
16243 ("r-rcpparmadillo" ,r-rcpparmadillo)
16244 ("r-riverplot" ,r-riverplot)
16245 ("r-rtsne" ,r-rtsne)
16246 ("r-snow" ,r-snow)))
16248 `(("jdk" ,icedtea "jdk")
16249 ;; See https://github.com/MacoskoLab/liger/issues/96
16250 ;; The optimizer is released under the Expat license.
16254 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16257 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16259 ("r-knitr" ,r-knitr))) ; for vignettes
16260 (home-page "https://github.com/MacoskoLab/liger")
16261 (synopsis "Integrate and analyze multiple single-cell datasets")
16263 "LIGER is a package for integrating and analyzing multiple single-cell
16264 datasets, developed and maintained by the Macosko lab. It relies on
16265 integrative non-negative matrix factorization to identify shared and
16266 dataset-specific factors.")
16267 (license license:gpl3)))
16269 (define-public r-harmony
16276 (uri (git-reference
16277 (url "https://github.com/immunogenomics/harmony")
16279 (file-name (git-file-name name version))
16282 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16283 (modules '((guix build utils)))
16286 (for-each delete-file '("config.status" "configure"))
16288 (build-system r-build-system)
16290 `(("r-cowplot" ,r-cowplot)
16291 ("r-dplyr" ,r-dplyr)
16292 ("r-ggplot2" ,r-ggplot2)
16293 ("r-irlba" ,r-irlba)
16294 ("r-matrix" ,r-matrix)
16296 ("r-rcpparmadillo" ,r-rcpparmadillo)
16297 ("r-rcppprogress" ,r-rcppprogress)
16298 ("r-rlang" ,r-rlang)
16299 ("r-tibble" ,r-tibble)
16300 ("r-tidyr" ,r-tidyr)))
16302 `(("autoconf" ,autoconf)))
16303 (home-page "https://github.com/immunogenomics/harmony")
16304 (synopsis "Integration of single cell sequencing data")
16306 "This package provides an implementation of the Harmony algorithm for
16307 single cell integration, described in Korsunsky et al
16308 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16309 function and interfaces to external frameworks.")
16310 (license license:gpl3)))
16312 (define-public r-covr
16319 (uri (cran-uri "covr" version))
16321 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16322 (properties `((upstream-name . "covr")))
16323 (build-system r-build-system)
16325 `(("r-crayon" ,r-crayon)
16326 ("r-digest" ,r-digest)
16328 ("r-jsonlite" ,r-jsonlite)
16330 ("r-withr" ,r-withr)
16331 ("r-yaml" ,r-yaml)))
16333 `(("r-knitr" ,r-knitr))) ; for vignettes
16334 (home-page "https://github.com/r-lib/covr")
16335 (synopsis "Test coverage for R packages")
16337 "Thisp package enables you to track and report code coverage for your
16338 package and (optionally) upload the results to a coverage service. Code
16339 coverage is a measure of the amount of code being exercised by a set of tests.
16340 It is an indirect measure of test quality and completeness. This package is
16341 compatible with any testing methodology or framework and tracks coverage of
16342 both R code and compiled C/C++/FORTRAN code.")
16343 (license license:gpl3)))
16345 (define-public r-systemfonts
16347 (name "r-systemfonts")
16352 (uri (cran-uri "systemfonts" version))
16355 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16356 (properties `((upstream-name . "systemfonts")))
16357 (build-system r-build-system)
16359 `(("fontconfig" ,fontconfig)
16362 `(("pkg-config" ,pkg-config)
16363 ("r-knitr" ,r-knitr)))
16364 (home-page "https://github.com/r-lib/systemfonts")
16365 (synopsis "System native font finding")
16367 "This package provides system native access to the font catalogue. As
16368 font handling varies between systems it is difficult to correctly locate
16369 installed fonts across different operating systems. The 'systemfonts' package
16370 provides bindings to the native libraries for finding font files that can then
16371 be used further by e.g. graphic devices.")
16372 (license license:expat)))
16374 (define-public r-graphlayouts
16376 (name "r-graphlayouts")
16381 (uri (cran-uri "graphlayouts" version))
16384 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16385 (properties `((upstream-name . "graphlayouts")))
16386 (build-system r-build-system)
16388 `(("r-igraph" ,r-igraph)
16390 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16391 (home-page "https://github.com/schochastics/graphlayouts")
16392 (synopsis "Additional layout algorithms for network visualizations")
16394 "This package provides several layout algorithms to visualize networks
16395 which are not part of the igraph library. Most are based on the concept of
16396 stress majorization by Gansner et al. (2004)
16397 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16398 emphasize hidden group structures in networks or focus on specific nodes.")
16399 (license license:expat)))
16401 (define-public r-tidygraph
16403 (name "r-tidygraph")
16408 (uri (cran-uri "tidygraph" version))
16411 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16412 (properties `((upstream-name . "tidygraph")))
16413 (build-system r-build-system)
16415 `(("r-dplyr" ,r-dplyr)
16416 ("r-igraph" ,r-igraph)
16417 ("r-magrittr" ,r-magrittr)
16418 ("r-pillar" ,r-pillar)
16421 ("r-rlang" ,r-rlang)
16422 ("r-tibble" ,r-tibble)
16423 ("r-tidyr" ,r-tidyr)))
16424 (home-page "https://github.com/thomasp85/tidygraph")
16425 (synopsis "Tidy API for graph manipulation")
16427 "This package provides a graph implementation that can be thought of as
16428 two tidy data frames describing node and edge data respectively. It provides
16429 an approach to manipulate these two virtual data frames using the API defined
16430 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16431 common graph algorithms.")
16432 (license license:expat)))
16434 (define-public r-soupx
16435 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16439 (version (git-version "0.3.1" revision commit))
16443 (uri (git-reference
16444 (url "https://github.com/constantAmateur/SoupX")
16446 (file-name (git-file-name name version))
16449 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16450 (properties `((upstream-name . "SoupX")))
16451 (build-system r-build-system)
16453 `(("r-ggplot2" ,r-ggplot2)
16454 ("r-matrix" ,r-matrix)
16455 ("r-seurat" ,r-seurat)))
16456 (home-page "https://github.com/constantAmateur/SoupX")
16457 (synopsis "Single cell mRNA Soup eXterminator")
16459 "This package provides a package for quantifying, profiling and
16460 removing cell free mRNA contamination (the \"soup\") from droplet based single
16461 cell RNA-seq experiments.")
16462 (license license:gpl2))))
16464 (define-public r-assertr
16471 (uri (cran-uri "assertr" version))
16474 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16475 (build-system r-build-system)
16477 `(("r-dplyr" ,r-dplyr)
16479 ("r-rlang" ,r-rlang)))
16481 `(("r-knitr" ,r-knitr))) ; needed for vignette
16482 (home-page "https://github.com/ropensci/assertr")
16483 (synopsis "Assertive programming for R analysis pipelines")
16485 "This package provides functionality to assert conditions that have to be
16486 met so that errors in data used in analysis pipelines can fail quickly. It is
16487 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16489 (license license:expat)))
16491 (define-public r-parameters
16493 (name "r-parameters")
16498 (uri (cran-uri "parameters" version))
16501 "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
16502 (properties `((upstream-name . "parameters")))
16503 (build-system r-build-system)
16505 `(("r-bayestestr" ,r-bayestestr)
16506 ("r-insight" ,r-insight)))
16508 `(("r-knitr" ,r-knitr)))
16509 (home-page "https://cran.r-project.org/web/packages/parameters")
16510 (synopsis "Processing of model parameters")
16512 "This package provides utilities for processing the parameters of various
16513 statistical models. Beyond computing p values, CIs, and other indices for a
16514 wide variety of models, this package implements features like standardization
16515 or bootstrapping of parameters and models, feature reduction (feature
16516 extraction and variable selection) as well as conversion between indices of
16518 (license license:gpl3)))
16520 (define-public r-rgdal
16527 (uri (cran-uri "rgdal" version))
16529 (base32 "02z7rhpizzmymiqpi90nm15bjdz0411bqlavlk0lhwxb42ilhif6"))))
16530 (properties `((upstream-name . "rgdal")))
16531 (build-system r-build-system)
16539 `(("pkg-config" ,pkg-config)
16540 ("r-knitr" ,r-knitr)))
16541 (home-page "http://rgdal.r-forge.r-project.org")
16542 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16544 "This package provides bindings to the Geospatial Data Abstraction
16545 Library (GDAL) and access to projection/transformation operations from the
16547 (license license:gpl2+)))
16549 (define-public r-insol
16556 (uri (cran-uri "insol" version))
16559 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16560 (properties `((upstream-name . "insol")))
16561 (build-system r-build-system)
16563 `(("r-raster" ,r-raster)))
16565 `(("gfortran" ,gfortran)))
16566 (home-page "https://meteoexploration.com/R/insol/index.html")
16567 (synopsis "Tools for calculating solar radiation")
16569 "This package provides functions to compute insolation on tilted
16570 surfaces, computes atmospheric transmittance and related parameters such as:
16571 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16572 time, vector in the direction of the sun, vector normal to surface, and some
16573 atmospheric physics.")
16574 (license license:gpl2+)))
16576 (define-public r-lifecycle
16578 (name "r-lifecycle")
16583 (uri (cran-uri "lifecycle" version))
16586 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16587 (properties `((upstream-name . "lifecycle")))
16588 (build-system r-build-system)
16590 `(("r-glue" ,r-glue)
16591 ("r-rlang" ,r-rlang)))
16593 `(("r-knitr" ,r-knitr))) ; for vignettes
16594 (home-page "https://github.com/r-lib/lifecycle")
16595 (synopsis "Manage the life cycle of your package functions")
16597 "Manage the life cycle of your exported functions with shared
16598 conventions, documentation badges, and non-invasive deprecation warnings. The
16599 lifecycle package defines four development stages (experimental, maturing,
16600 stable, and questioning) and three deprecation stages (soft-deprecated,
16601 deprecated, and defunct). It makes it easy to insert badges corresponding to
16602 these stages in your documentation. Usage of deprecated functions are
16603 signalled with increasing levels of non-invasive verbosity.")
16604 (license license:gpl3)))
16606 (define-public r-assertable
16608 (name "r-assertable")
16613 (uri (cran-uri "assertable" version))
16616 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16617 (build-system r-build-system)
16619 `(("r-data-table" ,r-data-table)))
16620 (home-page "https://cran.r-project.org/web/packages/assertable/")
16621 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16622 (description "This package provides simple, flexible assertions on
16623 data.frame or data.table objects with verbose output for vetting. While other
16624 assertion packages apply towards more general use-cases, @code{assertable} is
16625 tailored towards tabular data. It includes functions to check variable names
16626 and values, whether the dataset contains all combinations of a given set of
16627 unique identifiers, and whether it is a certain length. In addition,
16628 @code{assertable} includes utility functions to check the existence of target
16629 files and to efficiently import multiple tabular data files into one
16631 (license license:gpl3)))
16633 (define-public r-quadprog
16635 (name "r-quadprog")
16640 (uri (cran-uri "quadprog" version))
16642 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16643 (build-system r-build-system)
16645 `(("gfortran" ,gfortran)))
16646 (home-page "https://cran.r-project.org/web/packages/quadprog")
16647 (synopsis "Functions to solve quadratic programming problems")
16649 "This package contains routines and documentation for solving quadratic
16650 programming problems.")
16651 (license license:gpl3+)))
16653 (define-public r-desolve
16660 (uri (cran-uri "deSolve" version))
16662 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16663 (properties `((upstream-name . "deSolve")))
16664 (build-system r-build-system)
16666 `(("gfortran" ,gfortran)))
16667 (home-page "https://desolve.r-forge.r-project.org/")
16668 (synopsis "Solvers for initial value problems of differential equations")
16669 (description "This package provides functions that solve initial value
16670 problems of a system of first-order @dfn{ordinary differential
16671 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16672 @dfn{differential algebraic equations} (DAE), and of delay differential
16673 equations. The functions provide an interface to the FORTRAN functions
16674 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16675 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16676 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16677 time steps. The package contains routines designed for solving ODEs resulting
16678 from 1-D, 2-D and 3-D partial differential equations that have been converted
16679 to ODEs by numerical differencing.")
16680 (license license:gpl2+)))
16682 (define-public r-pracma
16688 (uri (cran-uri "pracma" version))
16690 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16691 (build-system r-build-system)
16692 (home-page "https://cran.r-project.org/web/packages/pracma/")
16693 (synopsis "Practical numerical math functions")
16694 (description "This package provides functions for numerical analysis and
16695 linear algebra, numerical optimization, differential equations, plus some
16696 special functions. It uses Matlab function names where appropriate to simplify
16698 (license license:gpl3+)))
16700 (define-public r-subplex
16707 (uri (cran-uri "subplex" version))
16710 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16711 (build-system r-build-system)
16713 `(("gfortran" ,gfortran)))
16714 (home-page "https://cran.r-project.org/web/packages/subplex")
16715 (synopsis "Unconstrained optimization using the subplex algorithm")
16717 "This package implements the Subplex optimization algorithm.
16718 It solves unconstrained optimization problems using a simplex method on
16719 subspaces. The method is well suited for optimizing objective functions that
16720 are noisy or are discontinuous at the solution.")
16721 (license license:gpl3+)))
16723 (define-public r-txtplot
16730 (uri (cran-uri "txtplot" version))
16733 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16734 (build-system r-build-system)
16735 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16736 (synopsis "Text-based plotting")
16737 (description "This package provides functions to produce rudimentary ASCII
16738 graphics directly in the terminal window. This package provides a basic
16739 plotting function (and equivalents of curve, density, acf and barplot) as well
16740 as a boxplot function.")
16741 (license license:lgpl3+)))
16743 (define-public r-bio3d
16750 (uri (cran-uri "bio3d" version))
16753 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16754 (properties `((upstream-name . "bio3d")))
16755 (build-system r-build-system)
16756 (inputs `(("zlib" ,zlib)))
16757 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16758 (home-page "http://thegrantlab.org/bio3d/")
16759 (synopsis "Biological structure analysis")
16761 "This package provides utilities to process, organize and explore protein
16762 structure, sequence and dynamics data. Features include the ability to read
16763 and write structure, sequence and dynamic trajectory data, perform sequence
16764 and structure database searches, data summaries, atom selection, alignment,
16765 superposition, rigid core identification, clustering, torsion analysis,
16766 distance matrix analysis, structure and sequence conservation analysis, normal
16767 mode analysis, principal component analysis of heterogeneous structure data,
16768 and correlation network analysis from normal mode and molecular dynamics data.
16769 In addition, various utility functions are provided to enable the statistical
16770 and graphical power of the R environment to work with biological sequence and
16772 (license license:gpl2+)))
16774 (define-public r-bios2cor
16776 (name "r-bios2cor")
16781 (uri (cran-uri "Bios2cor" version))
16784 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16785 (properties `((upstream-name . "Bios2cor")))
16786 (build-system r-build-system)
16788 `(("r-bigmemory" ,r-bigmemory)
16789 ("r-bio3d" ,r-bio3d)
16790 ("r-circular" ,r-circular)
16791 ("r-igraph" ,r-igraph)))
16792 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16793 (synopsis "From biological sequences and simulations to correlation analysis")
16795 "This package provides utilities for computation and analysis of
16796 correlation/covariation in multiple sequence alignments and in side chain
16797 motions during molecular dynamics simulations. Features include the
16798 computation of correlation/covariation scores using a variety of scoring
16799 functions between either sequence positions in alignments or side chain
16800 dihedral angles in molecular dynamics simulations and utilities to analyze the
16801 correlation/covariation matrix through a variety of tools including network
16802 representation and principal components analysis. In addition, several
16803 utility functions are based on the R graphical environment to provide friendly
16804 tools for help in data interpretation.")
16805 (license license:gpl2+)))
16807 ;; This package includes minified JavaScript files. When upgrading please
16808 ;; check that there are no new minified JavaScript files.
16809 (define-public r-networkd3
16811 (name "r-networkd3")
16816 (uri (cran-uri "networkD3" version))
16819 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16822 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16824 (properties `((upstream-name . "networkD3")))
16825 (build-system r-build-system)
16827 `(#:modules ((guix build utils)
16828 (guix build r-build-system)
16832 (modify-phases %standard-phases
16833 (add-after 'unpack 'process-javascript
16834 (lambda* (#:key inputs #:allow-other-keys)
16835 (with-directory-excursion "inst/htmlwidgets/lib/"
16839 `((,(assoc-ref inputs "d3.v4.js")
16840 "d3-4.5.0/d3.min.js"))))
16841 (lambda (sources targets)
16842 (for-each (lambda (source target)
16843 (format #t "Processing ~a --> ~a~%"
16845 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16846 (call-with-output-file target
16848 (dump-port minified port)))))
16849 sources targets))))
16852 `(("uglify-js" ,uglify-js)
16853 ;; NOTE: Make sure that this version of d3 is still valid when
16854 ;; upgrading the package.
16858 (uri "https://d3js.org/d3.v4.js")
16861 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16863 `(("r-htmlwidgets" ,r-htmlwidgets)
16864 ("r-igraph" ,r-igraph)
16865 ("r-magrittr" ,r-magrittr)))
16866 (home-page "https://cran.r-project.org/package=networkD3")
16867 (synopsis "D3 JavaScript network graphs from R")
16869 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16871 (license license:gpl3+)))
16873 (define-public r-aasea
16880 (uri (cran-uri "aaSEA" version))
16883 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16884 (properties `((upstream-name . "aaSEA")))
16885 (build-system r-build-system)
16887 `(("r-bios2cor" ,r-bios2cor)
16889 ("r-hmisc" ,r-hmisc)
16890 ("r-magrittr" ,r-magrittr)
16891 ("r-networkd3" ,r-networkd3)
16892 ("r-plotly" ,r-plotly)
16893 ("r-seqinr" ,r-seqinr)
16894 ("r-shiny" ,r-shiny)
16895 ("r-shinydashboard" ,r-shinydashboard)))
16896 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16897 (synopsis "Amino acid substitution effect analyzer")
16899 "Given a protein multiple sequence alignment, it is a daunting task to
16900 assess the effects of substitutions along sequence length. The aaSEA package
16901 is intended to help researchers to rapidly analyze property changes caused by
16902 single, multiple and correlated amino acid substitutions in proteins.")
16903 (license license:gpl3)))
16905 (define-public r-abacus
16912 (uri (cran-uri "ABACUS" version))
16915 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16916 (properties `((upstream-name . "ABACUS")))
16917 (build-system r-build-system)
16919 `(("r-ggplot2" ,r-ggplot2)
16920 ("r-shiny" ,r-shiny)))
16921 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16922 (synopsis "Apps-based activities for communicating and understanding statistics")
16924 "This package provides a set of Shiny apps for effective communication
16925 and understanding in statistics. The current version includes properties of
16926 normal distribution, properties of sampling distribution, one-sample z and t
16927 tests, two samples independent (unpaired) t test and analysis of variance.")
16928 (license license:gpl3)))
16930 (define-public r-abc-rap
16937 (uri (cran-uri "ABC.RAP" version))
16940 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16941 (properties `((upstream-name . "ABC.RAP")))
16942 (build-system r-build-system)
16943 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16944 (synopsis "Array-based CpG region analysis pipeline")
16946 "This package aims to identify candidate genes that are differentially
16947 methylated between cases and controls. It applies Student's t-test and delta
16948 beta analysis to identify candidate genes containing multiple CpG sites.")
16949 (license license:gpl3)))
16951 (define-public r-abcadm
16958 (uri (cran-uri "abcADM" version))
16961 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16962 (properties `((upstream-name . "abcADM")))
16963 (build-system r-build-system)
16966 ("r-rcpp" ,r-rcpp)))
16967 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16968 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16970 "This package provides tools to estimate parameters of accumulated
16971 damage (load duration) models based on failure time data under a Bayesian
16972 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16973 long-term reliability under stochastic load profiles.")
16974 (license license:gpl3)))
16976 (define-public r-rglpk
16983 (uri (cran-uri "Rglpk" version))
16986 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16987 (properties `((upstream-name . "Rglpk")))
16988 (build-system r-build-system)
16990 `(("r-slam" ,r-slam)))
16993 (home-page "https://r-forge.r-project.org/projects/rglp/")
16994 (synopsis "R interface to the GNU Linear Programming Kit")
16996 "This package provides an R interface to the GNU Linear Programming Kit,
16997 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16998 integer linear programming} (MILP) and other related problems.")
17000 (license (list license:gpl2 license:gpl3))))
17002 (define-public r-abcdefba
17004 (name "r-abcdefba")
17009 (uri (cran-uri "abcdeFBA" version))
17012 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17013 (properties `((upstream-name . "abcdeFBA")))
17014 (build-system r-build-system)
17016 `(("r-corrplot" ,r-corrplot)
17017 ("r-lattice" ,r-lattice)
17019 ("r-rglpk" ,r-rglpk)))
17020 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17021 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17023 "This package provides functions for Constraint Based Simulation using
17024 Flux Balance Analysis and informative analysis of the data generated during
17026 (license license:gpl2)))
17028 (define-public r-abcrlda
17035 (uri (cran-uri "abcrlda" version))
17038 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17039 (properties `((upstream-name . "abcrlda")))
17040 (build-system r-build-system)
17041 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17042 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17044 "This package offers methods to perform @dfn{asymptotically
17045 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17046 cost-sensitive binary classification. The bias-correction is an estimate of
17047 the bias term added to regularized discriminant analysis that minimizes the
17049 (license license:gpl3)))
17051 (define-public r-abemus
17058 (uri (cran-uri "abemus" version))
17061 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17062 (properties `((upstream-name . "abemus")))
17063 (build-system r-build-system)
17065 `(("r-data-table" ,r-data-table)))
17066 (home-page "https://cran.r-project.org/web/packages/abemus/")
17067 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17069 "This package provides an implementation of @dfn{Adaptive Base Error
17070 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17071 platform-specific genetic knowledge and empirical signal to readily detect and
17072 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17073 cell free DNA} (cfDNA).")
17074 (license license:gpl3)))
17076 ;; This package includes minified JavaScript files. When upgrading please
17077 ;; check that there are no new minified JavaScript files.
17078 (define-public r-rintrojs
17080 (name "r-rintrojs")
17085 (uri (cran-uri "rintrojs" version))
17088 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17089 (properties `((upstream-name . "rintrojs")))
17090 (build-system r-build-system)
17092 `(#:modules ((guix build utils)
17093 (guix build r-build-system)
17097 (modify-phases %standard-phases
17098 (add-after 'unpack 'process-javascript
17099 (lambda* (#:key inputs #:allow-other-keys)
17100 (with-directory-excursion "inst/javascript/introjs/"
17104 `((,(assoc-ref inputs "intro.js")
17106 (lambda (sources targets)
17107 (for-each (lambda (source target)
17108 (format #t "Processing ~a --> ~a~%"
17110 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17111 (call-with-output-file target
17113 (dump-port minified port)))))
17114 sources targets))))
17117 `(("uglify-js" ,uglify-js)
17121 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17124 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17126 `(("r-jsonlite" ,r-jsonlite)
17127 ("r-shiny" ,r-shiny)))
17128 (home-page "https://github.com/carlganz/rintrojs")
17129 (synopsis "Wrapper for the Intro.js library")
17131 "This package provides a wrapper for the @url{http://www.introjs.com,
17132 Intro.js} library. This package makes it easy to include step-by-step
17133 introductions, and clickable hints in a Shiny application. It supports both
17134 static introductions in the UI, and programmatic introductions from the
17136 (license license:agpl3+)))
17138 (define-public r-sysfonts
17140 (name "r-sysfonts")
17145 (uri (cran-uri "sysfonts" version))
17148 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17149 (properties `((upstream-name . "sysfonts")))
17150 (build-system r-build-system)
17152 `(("freetype" ,freetype)
17156 `(("pkg-config" ,pkg-config)))
17157 (home-page "https://github.com/yixuan/sysfonts")
17158 (synopsis "Loading fonts into R")
17160 "This is a package to simplify loading of system fonts and Google Fonts
17161 into R, in order to support other packages.")
17162 (license license:gpl2)))
17164 (define-public r-showtextdb
17166 (name "r-showtextdb")
17171 (uri (cran-uri "showtextdb" version))
17174 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17175 (properties `((upstream-name . "showtextdb")))
17176 (build-system r-build-system)
17178 `(("r-sysfonts" ,r-sysfonts)))
17179 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17180 (synopsis "Font files for the 'showtext' package")
17182 "This package provides font files that can be used by the @code{showtext}
17184 (license license:asl2.0)))
17186 (define-public r-showtext
17188 (name "r-showtext")
17193 (uri (cran-uri "showtext" version))
17196 "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
17197 (properties `((upstream-name . "showtext")))
17198 (build-system r-build-system)
17200 `(("freetype" ,freetype)
17204 `(("r-showtextdb" ,r-showtextdb)
17205 ("r-sysfonts" ,r-sysfonts)))
17207 `(("pkg-config" ,pkg-config)
17208 ("r-knitr" ,r-knitr)))
17209 (home-page "https://github.com/yixuan/showtext")
17210 (synopsis "Using fonts more easily in R graphs")
17212 "This package aims to make it easy to use various types of
17213 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17214 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17215 will be converted into polygons or raster images, hence after the plot has
17216 been created, it no longer relies on the font files. No external software
17217 such as Ghostscript is needed to use this package.")
17218 (license license:asl2.0)))
17220 (define-public r-emojifont
17222 (name "r-emojifont")
17227 (uri (cran-uri "emojifont" version))
17230 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17231 (properties `((upstream-name . "emojifont")))
17232 (build-system r-build-system)
17234 `(("r-ggplot2" ,r-ggplot2)
17235 ("r-proto" ,r-proto)
17236 ("r-showtext" ,r-showtext)
17237 ("r-sysfonts" ,r-sysfonts)))
17238 (home-page "https://guangchuangyu.github.io/emojifont")
17239 (synopsis "Emoji and Font Awesome in R graphics")
17241 "This package enables the use of emoji and the Font Awesome glyphs in
17242 both base and ggplot2 graphics.")
17243 (license license:artistic2.0)))
17245 (define-public r-abstractr
17247 (name "r-abstractr")
17252 (uri (cran-uri "abstractr" version))
17255 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17256 (properties `((upstream-name . "abstractr")))
17257 (build-system r-build-system)
17259 `(("r-colourpicker" ,r-colourpicker)
17260 ("r-emojifont" ,r-emojifont)
17261 ("r-ggplot2" ,r-ggplot2)
17262 ("r-gridextra" ,r-gridextra)
17263 ("r-rintrojs" ,r-rintrojs)
17264 ("r-shiny" ,r-shiny)
17265 ("r-shinythemes" ,r-shinythemes)))
17266 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17267 (synopsis "R-Shiny application for creating visual abstracts")
17269 "This package provides an R Shiny application to create visual abstracts
17270 for original research. A variety of user defined options and formatting are
17272 (license license:gpl3)))
17274 (define-public r-qgam
17281 (uri (cran-uri "qgam" version))
17284 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17285 (properties `((upstream-name . "qgam")))
17286 (build-system r-build-system)
17288 `(("r-doparallel" ,r-doparallel)
17291 ("r-shiny" ,r-shiny)))
17292 (native-inputs `(("r-knitr" ,r-knitr)))
17293 (home-page "https://cran.r-project.org/web/packages/qgam/")
17294 (synopsis "Smooth additive quantile regression models")
17296 "This package provides smooth additive quantile regression models, fitted
17297 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17298 the smoothing parameters are estimated automatically by marginal loss
17299 minimization, while the regression coefficients are estimated using either
17300 PIRLS or Newton algorithm. The learning rate is determined so that the
17301 Bayesian credible intervals of the estimated effects have approximately the
17302 correct coverage. The main function is @code{qgam()} which is similar to
17303 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17304 regression models.")
17305 (license license:gpl2+)))
17307 (define-public r-abtest
17314 (uri (cran-uri "abtest" version))
17317 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17318 (properties `((upstream-name . "abtest")))
17319 (build-system r-build-system)
17321 `(("r-matrix" ,r-matrix)
17322 ("r-mvtnorm" ,r-mvtnorm)
17323 ("r-plotrix" ,r-plotrix)
17325 ("r-rcolorbrewer" ,r-rcolorbrewer)
17328 ("r-truncnorm" ,r-truncnorm)))
17329 (home-page "https://cran.r-project.org/web/packages/abtest/")
17330 (synopsis "Bayesian A/B testing")
17332 "This package provides functions for Bayesian A/B testing including prior
17333 elicitation options based on Kass and Vaidyanathan (1992)
17334 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17335 (license license:gpl2+)))
17337 (define-public r-accept
17344 (uri (cran-uri "accept" version))
17347 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17348 (properties `((upstream-name . "accept")))
17349 (build-system r-build-system)
17351 `(("r-dplyr" ,r-dplyr)
17352 ("r-extrafont" ,r-extrafont)
17354 ("r-plotly" ,r-plotly)
17355 ("r-stringr" ,r-stringr)
17356 ("r-viridis" ,r-viridis)))
17357 (home-page "https://cran.r-project.org/web/packages/accept/")
17358 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17360 "This package allows clinicians to predict the rate and severity of
17361 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17362 Disease} (COPD) patients, based on the clinical prediction model published in
17363 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17364 (license license:gpl3)))
17366 (define-public r-smpracticals
17368 (name "r-smpracticals")
17373 (uri (cran-uri "SMPracticals" version))
17376 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17377 (properties `((upstream-name . "SMPracticals")))
17378 (build-system r-build-system)
17380 `(("r-ellipse" ,r-ellipse)
17383 ("r-survival" ,r-survival)))
17384 (home-page "http://statwww.epfl.ch/davison/SM/")
17385 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17387 "This package contains the datasets and a few functions for use with the
17388 practicals outlined in Appendix A of the book Statistical Models (Davison,
17389 2003, Cambridge University Press). The practicals themselves can be found at
17390 @url{http://statwww.epfl.ch/davison/SM/}.")
17391 (license license:gpl2+)))
17393 (define-public r-fgui
17400 (uri (cran-uri "fgui" version))
17403 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17404 (properties `((upstream-name . "fgui")))
17405 (build-system r-build-system)
17407 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17408 (synopsis "Create GUI for R functions")
17410 "Rapidly create a GUI for a function you created by automatically
17411 creating widgets for arguments of the function. This package automatically
17412 parses help routines for context-sensitive help to these arguments. The
17413 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17414 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17415 incorporated into the interface for greater customization for the more
17417 ;; Any version of the GPL.
17418 (license (list license:gpl2+ license:gpl3+))))
17420 (define-public r-tcltk2
17427 (uri (cran-uri "tcltk2" version))
17430 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17431 (properties `((upstream-name . "tcltk2")))
17432 (build-system r-build-system)
17436 (home-page "https://www.sciviews.org/SciViews-R")
17437 (synopsis "Tcl/Tk additions")
17439 "This package provides a series of additional Tcl commands and Tk widgets
17440 with style and various functions to supplement the tcltk package")
17441 (license license:lgpl3)))
17443 (define-public r-accrual
17450 (uri (cran-uri "accrual" version))
17453 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17454 (properties `((upstream-name . "accrual")))
17455 (build-system r-build-system)
17457 `(("r-fgui" ,r-fgui)
17458 ("r-smpracticals" ,r-smpracticals)
17459 ("r-tcltk2" ,r-tcltk2)))
17460 (home-page "https://cran.r-project.org/web/packages/accrual/")
17461 (synopsis "Bayesian accrual prediction")
17463 "Subject recruitment for medical research is challenging. Slow patient
17464 accrual leads to delay in research. Accrual monitoring during the process of
17465 recruitment is critical. Researchers need reliable tools to manage the
17466 accrual rate. This package provides an implementation of a Bayesian method
17467 that integrates researcher's experience on previous trials and data from the
17468 current study, providing reliable prediction on accrual rate for clinical
17469 studies. It provides functions for Bayesian accrual prediction which can be
17470 easily used by statisticians and clinical researchers.")
17471 (license license:gpl2)))
17473 (define-public r-accrued
17480 (uri (cran-uri "accrued" version))
17483 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17484 (properties `((upstream-name . "accrued")))
17485 (build-system r-build-system)
17486 (home-page "https://cran.r-project.org/web/packages/accrued/")
17487 (synopsis "Data quality visualization tools for partially accruing data")
17489 "This is a package for visualizing data quality of partially accruing
17491 (license license:gpl3)))
17493 (define-public r-mda
17500 (uri (cran-uri "mda" version))
17503 "01pjrz9xv1rx78ndy0x9dc32ws8brcvwyb500m1f0dqd42375vmx"))))
17504 (properties `((upstream-name . "mda")))
17505 (build-system r-build-system)
17506 (propagated-inputs `(("r-class" ,r-class)))
17507 (native-inputs `(("gfortran" ,gfortran)))
17508 (home-page "https://cran.r-project.org/web/packages/mda/")
17509 (synopsis "Mixture and flexible discriminant analysis")
17511 "This is a package for mixture and flexible discriminant analysis,
17512 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17513 (license license:gpl2)))
17515 (define-public r-elasticnet
17517 (name "r-elasticnet")
17522 (uri (cran-uri "elasticnet" version))
17525 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17526 (properties `((upstream-name . "elasticnet")))
17527 (build-system r-build-system)
17529 `(("r-lars" ,r-lars)))
17530 (home-page "http://users.stat.umn.edu/~zouxx019/")
17531 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17533 "This package provides functions for fitting the entire solution path of
17534 the Elastic-Net and also provides functions for estimating sparse Principal
17535 Components. The Lasso solution paths can be computed by the same function.")
17536 (license license:gpl2+)))
17538 (define-public r-sparselda
17540 (name "r-sparselda")
17545 (uri (cran-uri "sparseLDA" version))
17548 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17549 (properties `((upstream-name . "sparseLDA")))
17550 (build-system r-build-system)
17552 `(("r-elasticnet" ,r-elasticnet)
17555 (home-page "https://www.imm.dtu.dk/~lkhc/")
17556 (synopsis "Sparse discriminant analysis")
17558 "This package performs sparse linear discriminant analysis for Gaussians
17559 and mixture of Gaussian models.")
17560 (license license:gpl2+)))
17562 (define-public r-accsda
17569 (uri (cran-uri "accSDA" version))
17572 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17573 (properties `((upstream-name . "accSDA")))
17574 (build-system r-build-system)
17576 `(("r-ggplot2" ,r-ggplot2)
17577 ("r-ggthemes" ,r-ggthemes)
17578 ("r-gridextra" ,r-gridextra)
17580 ("r-rarpack" ,r-rarpack)
17581 ("r-sparselda" ,r-sparselda)))
17582 (home-page "https://github.com/gumeo/accSDA/wiki")
17583 (synopsis "Accelerated sparse discriminant analysis")
17585 "This package provides an implementation of sparse linear discriminant
17586 analysis, which is a supervised classification method for multiple classes.
17587 Various novel optimization approaches to this problem are implemented
17588 including @dfn{alternating direction method of multipliers} (ADMM),
17589 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17590 Functions for performing cross validation are also supplied along with basic
17591 prediction and plotting functions. @dfn{Sparse zero variance
17592 discriminant} (SZVD) analysis is also included in the package.")
17593 (license license:gpl2+)))
17595 (define-public r-ace2fastq
17597 (name "r-ace2fastq")
17602 (uri (cran-uri "ace2fastq" version))
17605 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17606 (properties `((upstream-name . "ace2fastq")))
17607 (build-system r-build-system)
17609 `(("r-stringr" ,r-stringr)))
17610 (home-page "https://github.com/c5sire/ace2fastq")
17611 (synopsis "ACE file to FASTQ converter")
17613 "The ACE file format is used in genomics to store contigs from sequencing
17614 machines. This tools converts it into FASTQ format. Both formats contain the
17615 sequence characters and their corresponding quality information. Unlike the
17616 FASTQ file, the ACE file stores the quality values numerically. The
17617 conversion algorithm uses the standard Sanger formula. The package
17618 facilitates insertion into pipelines, and content inspection.")
17619 (license license:gpl3)))
17621 (define-public r-rngwell
17628 (uri (cran-uri "rngWELL" version))
17631 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17632 (properties `((upstream-name . "rngWELL")))
17633 (build-system r-build-system)
17634 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17635 (synopsis "Toolbox for WELL random number generators")
17637 "This is a dedicated package to WELL pseudo random generators, which were
17638 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17639 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17640 (license license:bsd-3)))
17642 (define-public r-randtoolbox
17644 (name "r-randtoolbox")
17649 (uri (cran-uri "randtoolbox" version))
17652 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17653 (properties `((upstream-name . "randtoolbox")))
17654 (build-system r-build-system)
17656 `(("r-rngwell" ,r-rngwell)))
17658 `(("gfortran" ,gfortran)))
17659 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17660 (synopsis "Toolbox for pseudo and quasi random number generation")
17662 "This package provides
17665 @item pseudo random generators, such as general linear
17666 congruential generators, multiple recursive generators and generalized
17667 feedback shift register (SF-Mersenne Twister algorithm and WELL
17670 @item quasi random generators, such as the Torus algorithm, the Sobol
17671 sequence, the Halton sequence (including the Van der Corput sequence), and
17673 @item some generator tests: the gap test, the serial test, the poker test.
17676 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17677 (license license:bsd-3)))
17679 (define-public r-lhs
17686 (uri (cran-uri "lhs" version))
17689 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17690 (properties `((upstream-name . "lhs")))
17691 (build-system r-build-system)
17692 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17694 `(("r-knitr" ,r-knitr)))
17695 (home-page "https://github.com/bertcarnell/lhs")
17696 (synopsis "Latin Hypercube Samples")
17698 "This package provides a number of methods for creating and augmenting
17699 Latin Hypercube Samples.")
17700 (license license:gpl3)))
17702 (define-public r-acebayes
17704 (name "r-acebayes")
17709 (uri (cran-uri "acebayes" version))
17712 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17713 (properties `((upstream-name . "acebayes")))
17714 (build-system r-build-system)
17716 `(("r-compare" ,r-compare)
17718 ("r-randtoolbox" ,r-randtoolbox)
17720 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17721 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17722 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17724 "Finding an optimal Bayesian experimental design involves maximizing an
17725 objective function given by the expectation of some appropriately chosen
17726 utility function with respect to the joint distribution of unknown
17727 quantities (including responses). This objective function is usually not
17728 available in closed form and the design space can be continuous and of high
17729 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17730 to maximise an approximation to the expectation of the utility function.")
17731 (license license:gpl2)))
17733 (define-public r-acet
17740 (uri (cran-uri "ACEt" version))
17743 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17744 (properties `((upstream-name . "ACEt")))
17745 (build-system r-build-system)
17750 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17751 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17752 (synopsis "Estimating dynamic heritability and twin model comparison")
17754 "This package supports twin models that are able to estimate the dynamic
17755 behaviour of the variance components in the classical twin models with respect
17756 to age using B-splines and P-splines.")
17757 (license license:gpl2+)))
17759 (define-public r-acfmperiod
17761 (name "r-acfmperiod")
17766 (uri (cran-uri "acfMPeriod" version))
17769 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17770 (properties `((upstream-name . "acfMPeriod")))
17771 (build-system r-build-system)
17773 `(("r-mass" ,r-mass)))
17774 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17775 (synopsis "Estimation of the ACF from the M-periodogram")
17777 "This package support non-robust and robust computations of the sample
17778 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17779 univariate and multivariate processes. The methodology consists in reversing
17780 the diagonalization procedure involving the periodogram or the
17781 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17782 ACOVF or the ACF as discussed in Fuller (1995)
17783 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17784 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17785 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17786 (license license:gpl2+)))
17788 (define-public r-gamlss-data
17790 (name "r-gamlss-data")
17795 (uri (cran-uri "gamlss.data" version))
17798 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17799 (properties `((upstream-name . "gamlss.data")))
17800 (build-system r-build-system)
17801 (home-page "http://www.gamlss.org/")
17802 (synopsis "GAMLSS data")
17804 "This package provides data used as examples to demonstrate GAMLSS
17806 ;; Either version of the license
17807 (license (list license:gpl2 license:gpl3))))
17809 (define-public r-gamlss
17816 (uri (cran-uri "gamlss" version))
17819 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17820 (properties `((upstream-name . "gamlss")))
17821 (build-system r-build-system)
17823 `(("r-gamlss-data" ,r-gamlss-data)
17824 ("r-gamlss-dist" ,r-gamlss-dist)
17827 ("r-survival" ,r-survival)))
17828 (home-page "http://www.gamlss.org/")
17829 (synopsis "Generalized additive models for location scale and shape")
17831 "This package provides functions for fitting the generalized additive
17832 models for location scale and shape introduced by Rigby and
17833 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17834 use a distributional regression approach where all the parameters of the
17835 conditional distribution of the response variable are modelled using
17836 explanatory variables.")
17837 ;; Either version of the license
17838 (license (list license:gpl2 license:gpl3))))
17840 (define-public r-acid
17847 (uri (cran-uri "acid" version))
17850 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17851 (properties `((upstream-name . "acid")))
17852 (build-system r-build-system)
17854 `(("r-gamlss" ,r-gamlss)
17855 ("r-gamlss-dist" ,r-gamlss-dist)
17856 ("r-hmisc" ,r-hmisc)))
17857 (home-page "https://cran.r-project.org/web/packages/acid/")
17858 (synopsis "Analysing conditional income distributions")
17860 "This package provides functions for the analysis of income distributions
17861 for subgroups of the population as defined by a set of variables like age,
17862 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17863 distribution as well as functions for moments, inequality measures, entropy
17864 measures and polarisation measures of income distributions. This package thus
17865 aides the analysis of income inequality by offering tools for the exploratory
17866 analysis of income distributions at the disaggregated level.")
17867 (license license:gpl3)))
17869 (define-public r-acm4r
17876 (uri (cran-uri "acm4r" version))
17879 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17880 (properties `((upstream-name . "acm4r")))
17881 (build-system r-build-system)
17882 (propagated-inputs `(("r-mass" ,r-mass)))
17883 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17884 (synopsis "Align-and-count method comparisons of RFLP data")
17886 "This is a package to compare sequence fragment lengths or molecular
17887 weights from pairs of lanes. The number of matching bands in the
17888 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17889 the align-and-count method.")
17890 ;; Any version of the GPL
17891 (license (list license:gpl2+ license:gpl3+))))
17893 (define-public r-filematrix
17895 (name "r-filematrix")
17900 (uri (cran-uri "filematrix" version))
17903 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17904 (properties `((upstream-name . "filematrix")))
17905 (build-system r-build-system)
17906 ;; These inputs are needed for vignettes
17908 `(("r-knitr" ,r-knitr)
17909 ("r-rmarkdown" ,r-rmarkdown)
17910 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17911 (home-page "https://github.com/andreyshabalin/filematrix")
17912 (synopsis "File-backed matrix class with convenient read and write access")
17914 "This package provides an interface for working with large matrices
17915 stored in files, not in computer memory. It supports multiple non-character
17916 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17917 byte real values). Access to parts of the matrix is done by indexing, exactly
17918 as with usual R matrices. It supports very large matrices; the package has
17919 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17920 columns, ad allows for quick addition of extra columns to a filematrix.")
17921 (license license:lgpl3)))
17923 (define-public r-acmeeqtl
17925 (name "r-acmeeqtl")
17930 (uri (cran-uri "ACMEeqtl" version))
17933 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17934 (properties `((upstream-name . "ACMEeqtl")))
17935 (build-system r-build-system)
17937 `(("r-filematrix" ,r-filematrix)))
17938 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17939 (synopsis "Estimation of interpretable eQTL effect sizes")
17941 "This package provides a non-linear model, termed ACME, that reflects a
17942 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17943 With non-linear least-squares algorithm the maximum likelihood parameters can
17944 be estimated. The ACME model provides interpretable effect size estimates and
17945 p-values with well controlled Type-I error.")
17946 (license license:lgpl3)))
17948 (define-public r-acmer
17955 (uri (cran-uri "acmeR" version))
17958 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17959 (properties `((upstream-name . "acmeR")))
17960 (build-system r-build-system)
17961 (propagated-inputs `(("r-foreign" ,r-foreign)))
17962 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17963 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17965 "This package provides an implementation of the ACME estimator, described
17966 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17967 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17968 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17969 as carcasses age; variable bleed-through at successive searches; and interval
17970 mortality estimates. The package provides, based on search data, functions
17971 for estimating the mortality inflation factor in Frequentist and Bayesian
17973 (license license:expat)))
17975 (define-public r-r-huge
17982 (uri (cran-uri "R.huge" version))
17985 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17986 (properties `((upstream-name . "R.huge")))
17987 (build-system r-build-system)
17989 `(("r-r-methodss3" ,r-r-methodss3)
17991 ("r-r-utils" ,r-r-utils)))
17992 (home-page "https://github.com/HenrikBengtsson/R.huge")
17993 (synopsis "Methods for accessing huge amounts of data")
17995 "This is a deprecated package for accessing huge amounts of data.
17996 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17997 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17998 the @code{aroma.affymetrix} package.")
17999 (license license:lgpl2.1+)))
18001 (define-public r-r-filesets
18003 (name "r-r-filesets")
18008 (uri (cran-uri "R.filesets" version))
18011 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18012 (properties `((upstream-name . "R.filesets")))
18013 (build-system r-build-system)
18015 `(("r-digest" ,r-digest)
18016 ("r-r-cache" ,r-r-cache)
18017 ("r-r-methodss3" ,r-r-methodss3)
18019 ("r-r-utils" ,r-r-utils)))
18020 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18021 (synopsis "Easy handling of and access to files")
18023 "This package provides classes and methods to locate, setup, subset,
18024 navigate and iterate file sets, i.e. sets of files located in one or more
18025 directories on the file system. The API is designed such that these classes
18026 can be extended via inheritance to provide a richer API for special file
18027 formats. Moreover, a specific name format is defined such that filenames and
18028 directories can be considered to have full names which consists of a name
18029 followed by comma-separated tags. This adds additional flexibility to
18030 identify file sets and individual files.")
18031 (license license:lgpl2.1+)))
18033 (define-public r-r-devices
18035 (name "r-r-devices")
18040 (uri (cran-uri "R.devices" version))
18043 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18044 (properties `((upstream-name . "R.devices")))
18045 (build-system r-build-system)
18047 `(("r-base64enc" ,r-base64enc)
18048 ("r-r-methodss3" ,r-r-methodss3)
18050 ("r-r-utils" ,r-r-utils)))
18051 (home-page "https://github.com/HenrikBengtsson/R.devices")
18052 (synopsis "Unified handling of graphics devices")
18054 "This package provides functions for creating plots and image files in a
18055 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18056 Default device options as well as scales and aspect ratios are controlled in a
18057 uniform way across all device types. Switching output format requires minimal
18058 changes in code. This package is ideal for large-scale batch processing,
18059 because it will never leave open graphics devices or incomplete image files
18060 behind, even on errors or user interrupts.")
18061 (license license:lgpl2.1+)))
18063 (define-public r-acnr
18070 (uri (cran-uri "acnr" version))
18073 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18074 (properties `((upstream-name . "acnr")))
18075 (build-system r-build-system)
18076 (home-page "https://github.com/mpierrejean/acnr")
18077 (synopsis "Annotated copy-number regions")
18079 "This package provides SNP array data from different types of copy-number
18080 regions. These regions were identified manually by the authors of the package
18081 and may be used to generate realistic data sets with known truth.")
18082 (license license:lgpl2.1+)))
18084 (define-public r-acopula
18091 (uri (cran-uri "acopula" version))
18094 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18095 (properties `((upstream-name . "acopula")))
18096 (build-system r-build-system)
18097 (home-page "https://cran.r-project.org/web/packages/acopula/")
18098 (synopsis "Modelling dependence with multivariate Archimax copulas")
18100 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18101 package provides definitions of several parametric families of generator and
18102 dependence function, computes CDF and PDF, estimates parameters, tests for
18103 goodness of fit, generates random sample and checks copula properties for
18104 custom constructs. In the 2-dimensional case explicit formulas for density
18105 are used, contrary to higher dimensions when all derivatives are linearly
18106 approximated. Several non-archimax families (normal, FGM, Plackett) are
18107 provided as well.")
18108 (license license:gpl2)))
18110 (define-public r-tuner
18117 (uri (cran-uri "tuneR" version))
18120 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18121 (properties `((upstream-name . "tuneR")))
18122 (build-system r-build-system)
18123 (propagated-inputs `(("r-signal" ,r-signal)))
18124 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18125 (synopsis "Analysis of music and speech")
18127 "This is a package for the analysis of music and speech. Analyze music
18128 and speech, extract features like MFCCs, handle wave files and their
18129 representation in various ways, read MP3, read MIDI, perform steps of a
18130 transcription, ...")
18131 ;; Either of these versions.
18132 (license (list license:gpl2 license:gpl3))))
18134 (define-public r-seewave
18141 (uri (cran-uri "seewave" version))
18144 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18145 (properties `((upstream-name . "seewave")))
18146 (build-system r-build-system)
18148 `(("libsndfile" ,libsndfile)))
18150 `(("r-tuner" ,r-tuner)))
18151 (home-page "http://rug.mnhn.fr/seewave")
18152 (synopsis "Sound analysis and synthesis")
18154 "This package provides functions for analysing, manipulating, displaying,
18155 editing and synthesizing time waves (particularly sound). This package
18156 processes time analysis (oscillograms and envelopes), spectral content,
18157 resonance quality factor, entropy, cross correlation and autocorrelation,
18158 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18159 and 3D spectrograms and many other analyses.")
18160 (license license:gpl2+)))
18162 (define-public r-acousticndlcoder
18164 (name "r-acousticndlcoder")
18169 (uri (cran-uri "AcousticNDLCodeR" version))
18172 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18174 `((upstream-name . "AcousticNDLCodeR")))
18175 (build-system r-build-system)
18177 `(("r-seewave" ,r-seewave)
18178 ("r-tuner" ,r-tuner)
18180 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18181 (synopsis "Coding sound files for use with NDL")
18183 "Make acoustic cues to use with the R package @code{ndl}.
18184 The package implements functions used in the PLoS ONE paper \"Words from
18185 spontaneous conversational speech can be recognized with human-like accuracy
18186 by an error-driven learning algorithm that discriminates between meanings
18187 straight from smart acoustic features, bypassing the phoneme as recognition
18188 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18189 (license license:gpl2+)))
18191 (define-public r-acp
18198 (uri (cran-uri "acp" version))
18201 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18202 (properties `((upstream-name . "acp")))
18203 (build-system r-build-system)
18205 `(("r-quantmod" ,r-quantmod)
18206 ("r-tseries" ,r-tseries)))
18207 (home-page "https://cran.r-project.org/web/packages/acp/")
18208 (synopsis "Autoregressive conditional Poisson")
18210 "This package supports the analysis of count data exhibiting
18211 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18212 model (ACP(p,q)) proposed by Heinen (2003).")
18213 (license license:gpl2)))
18215 (define-public r-ada
18222 (uri (cran-uri "ada" version))
18225 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18226 (properties `((upstream-name . "ada")))
18227 (build-system r-build-system)
18228 (propagated-inputs `(("r-rpart" ,r-rpart)))
18229 (home-page "https://cran.r-project.org/web/packages/ada/")
18230 (synopsis "Stochastic boosting")
18232 "This package provides a straightforward, well-documented, and broad
18233 boosting routine for classification, ideally suited for small to
18234 moderate-sized data sets. It performs discrete, real, and gentle boost under
18235 both exponential and logistic loss on a given data set.")
18236 ;; Any version of the GPL.
18237 (license (list license:gpl2+ license:gpl3+))))
18239 (define-public r-genalg
18246 (uri (cran-uri "genalg" version))
18249 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18250 (properties `((upstream-name . "genalg")))
18251 (build-system r-build-system)
18252 (home-page "https://github.com/egonw/genalg")
18253 (synopsis "R based genetic algorithm")
18255 "This package provides an R based genetic algorithm for binary and
18256 floating point chromosomes.")
18257 (license license:gpl2)))
18259 (define-public r-kernelfactory
18261 (name "r-kernelfactory")
18266 (uri (cran-uri "kernelFactory" version))
18269 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18270 (properties `((upstream-name . "kernelFactory")))
18271 (build-system r-build-system)
18274 ("r-genalg" ,r-genalg)
18275 ("r-kernlab" ,r-kernlab)
18276 ("r-randomforest" ,r-randomforest)))
18277 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18278 (synopsis "Ensemble of kernel machines")
18280 "Kernel factory is an ensemble method where each base classifier (random
18281 forest) is fit on the kernel matrix of a subset of the training data.")
18282 (license license:gpl2+)))
18284 (define-public r-dummies
18291 (uri (cran-uri "dummies" version))
18294 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18295 (properties `((upstream-name . "dummies")))
18296 (build-system r-build-system)
18297 (home-page "https://decisionpatterns.com")
18298 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18300 "This package lets you expand factors, characters and other eligible
18301 classes into dummy/indicator variables.")
18302 (license license:gpl2+)))
18304 (define-public r-acrm
18311 (uri (cran-uri "aCRM" version))
18314 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18315 (properties `((upstream-name . "aCRM")))
18316 (build-system r-build-system)
18319 ("r-dummies" ,r-dummies)
18320 ("r-kernelfactory" ,r-kernelfactory)
18321 ("r-randomforest" ,r-randomforest)))
18322 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18323 (synopsis "Convenience functions for analytical customer relationship management")
18325 "This package provides convenience functions for data preparation and
18326 modeling often used in @dfn{analytical customer relationship
18327 management} (aCRM).")
18328 (license license:gpl2+)))
18330 (define-public r-treeclust
18332 (name "r-treeclust")
18337 (uri (cran-uri "treeClust" version))
18340 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18341 (properties `((upstream-name . "treeClust")))
18342 (build-system r-build-system)
18344 `(("r-cluster" ,r-cluster)
18345 ("r-rpart" ,r-rpart)))
18346 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18347 (synopsis "Cluster distances through trees")
18349 "This package provides tools to create a measure of inter-point
18350 dissimilarity useful for clustering mixed data, and, optionally, perform the
18352 (license license:gpl2+)))
18354 (define-public r-acrosstic
18356 (name "r-acrosstic")
18361 (uri (cran-uri "AcrossTic" version))
18364 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18365 (properties `((upstream-name . "AcrossTic")))
18366 (build-system r-build-system)
18368 `(("r-lpsolve" ,r-lpsolve)
18369 ("r-treeclust" ,r-treeclust)))
18370 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18371 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18373 "This is a package for constructing minimum-cost regular spanning
18374 subgraph as part of a non-parametric two-sample test for equality of
18376 (license license:gpl2+)))
18378 (define-public r-acrt
18385 (uri (cran-uri "acrt" version))
18388 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18389 (properties `((upstream-name . "acrt")))
18390 (build-system r-build-system)
18392 `(("r-rcpp" ,r-rcpp)
18393 ("r-rcppeigen" ,r-rcppeigen)
18394 ("r-sandwich" ,r-sandwich)))
18395 (home-page "https://cran.r-project.org/web/packages/acrt/")
18396 (synopsis "Autocorrelation robust testing")
18398 "This package provides functions for testing affine hypotheses on the
18399 regression coefficient vector in regression models with autocorrelated
18401 (license license:gpl2)))
18403 (define-public r-acs
18410 (uri (cran-uri "acs" version))
18413 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18414 (properties `((upstream-name . "acs")))
18415 (build-system r-build-system)
18417 `(("r-httr" ,r-httr)
18420 ("r-stringr" ,r-stringr)
18422 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18423 (synopsis "Work with data from the US Census")
18425 "This package provides a general toolkit for downloading, managing,
18426 analyzing, and presenting data from the
18427 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18428 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18429 American Community Survey (ACS). Confidence intervals provided with ACS data
18430 are converted to standard errors to be bundled with estimates in complex
18431 @code{acs} objects. The package provides new methods to conduct standard
18432 operations on @code{acs} objects and present/plot data in statistically
18433 appropriate ways.")
18434 (license license:gpl3)))
18436 (define-public r-acss-data
18438 (name "r-acss-data")
18443 (uri (cran-uri "acss.data" version))
18446 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18447 (properties `((upstream-name . "acss.data")))
18448 (build-system r-build-system)
18449 (home-page "http://complexitycalculator.com/methodology.html")
18450 (synopsis "Data for algorithmic complexity of short strings")
18452 "This is a data only package providing the algorithmic complexity of
18453 short strings, computed using the coding theorem method. For a given set of
18454 symbols in a string, all possible or a large number of random samples of
18455 Turing machines with a given number of states (e.g., 5) and number of symbols
18456 corresponding to the number of symbols in the strings were simulated until
18457 they reached a halting state or failed to end. This package contains data on
18458 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18459 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18460 distribution of the halting states.")
18461 (license license:gpl2+)))
18463 (define-public r-acss
18470 (uri (cran-uri "acss" version))
18473 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18474 (properties `((upstream-name . "acss")))
18475 (build-system r-build-system)
18477 `(("r-acss-data" ,r-acss-data)
18479 (home-page "http://complexitycalculator.com/methodology.html")
18480 (synopsis "Algorithmic complexity for short strings")
18482 "The main purpose of this package is to provide the algorithmic
18483 complexity for short strings, an approximation of the Kolmogorov Complexity of
18484 a short string using the coding theorem method. While the database containing
18485 the complexity is provided in the data only package @code{acss.data}, this
18486 package provides functions accessing the data such as @code{prob_random}
18487 returning the posterior probability that a given string was produced by a
18488 random process. In addition, two traditional (but problematic) measures of
18489 complexity are also provided: entropy and change complexity.")
18490 (license license:gpl2+)))
18492 (define-public r-acswr
18499 (uri (cran-uri "ACSWR" version))
18502 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18503 (properties `((upstream-name . "ACSWR")))
18504 (build-system r-build-system)
18506 `(("r-mass" ,r-mass)))
18507 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18508 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18510 "This is a companion package for the book \"A Course in Statistics with
18511 R\" (ISBN 978-1-119-15272-9.)")
18512 (license license:gpl2)))
18514 (define-public r-alabama
18517 (version "2015.3-1")
18521 (uri (cran-uri "alabama" version))
18524 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18525 (properties `((upstream-name . "alabama")))
18526 (build-system r-build-system)
18527 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18528 (home-page "https://cran.r-project.org/web/packages/alabama/")
18529 (synopsis "Constrained nonlinear optimization")
18531 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18532 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18533 constraints. Linear or nonlinear equality and inequality constraints are
18535 (license license:gpl2+)))
18537 (define-public r-gdina
18544 (uri (cran-uri "GDINA" version))
18547 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18548 (properties `((upstream-name . "GDINA")))
18549 (build-system r-build-system)
18551 `(("r-alabama" ,r-alabama)
18552 ("r-ggplot2" ,r-ggplot2)
18554 ("r-nloptr" ,r-nloptr)
18555 ("r-numderiv" ,r-numderiv)
18557 ("r-rcpparmadillo" ,r-rcpparmadillo)
18558 ("r-rsolnp" ,r-rsolnp)
18559 ("r-shiny" ,r-shiny)
18560 ("r-shinydashboard" ,r-shinydashboard)))
18562 `(("r-knitr" ,r-knitr)))
18563 (home-page "https://github.com/Wenchao-Ma/GDINA")
18564 (synopsis "Generalized DINA model framework")
18566 "This package provides a set of psychometric tools for cognitive
18567 diagnosis modeling based on the generalized deterministic inputs, noisy and
18568 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18569 and its extensions, including the sequential G-DINA model by Ma and de la
18570 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18571 polytomous G-DINA model by Chen and de la Torre
18572 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18573 distribution can be independent, saturated, higher-order, loglinear smoothed
18574 or structured. Q-matrix validation, item and model fit statistics, model
18575 comparison at test and item level and differential item functioning can also
18576 be conducted. A graphical user interface is also provided.")
18577 (license license:gpl3)))
18579 (define-public r-actcd
18586 (uri (cran-uri "ACTCD" version))
18589 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18590 (properties `((upstream-name . "ACTCD")))
18591 (build-system r-build-system)
18593 `(("r-gdina" ,r-gdina)
18594 ("r-r-methodss3" ,r-r-methodss3)))
18596 `(("gfortran" ,gfortran)))
18597 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18598 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18600 "This is a package supporting cluster analysis for cognitive diagnosis
18601 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18602 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18603 sum-scores, cluster analysis techniques can be used to classify examinees into
18604 latent classes based on their attribute patterns. In addition to the
18605 algorithms used to classify data, three labeling approaches are proposed to
18606 label clusters so that examinees' attribute profiles can be obtained.")
18607 (license license:gpl2+)))
18609 (define-public r-ineq
18616 (uri (cran-uri "ineq" version))
18619 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18620 (properties `((upstream-name . "ineq")))
18621 (build-system r-build-system)
18622 (home-page "https://cran.r-project.org/web/packages/ineq/")
18623 (synopsis "Measuring inequality, concentration, and poverty")
18625 "This package provides tools for measuring inequality, concentration, and
18626 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18627 ;; Either of these two versions.
18628 (license (list license:gpl2 license:gpl3))))
18630 (define-public r-actfrag
18637 (uri (cran-uri "ActFrag" version))
18640 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18641 (properties `((upstream-name . "ActFrag")))
18642 (build-system r-build-system)
18644 `(("r-accelerometry" ,r-accelerometry)
18645 ("r-dplyr" ,r-dplyr)
18647 ("r-survival" ,r-survival)
18648 ("r-tidyr" ,r-tidyr)))
18649 (home-page "https://github.com/junruidi/ActFrag")
18650 (synopsis "Activity fragmentation metrics extraction")
18652 "This package provides functions to extract commonly used fragmentation
18653 metrics to quantify time accumulation strategies based on minute level
18654 actigraphy-measured activity counts data.")
18655 (license license:gpl3)))
18657 (define-public r-fda
18664 (uri (cran-uri "fda" version))
18667 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18668 (properties `((upstream-name . "fda")))
18669 (build-system r-build-system)
18671 `(("r-matrix" ,r-matrix)))
18672 (home-page "https://www.functionaldata.org")
18673 (synopsis "Functional data analysis")
18675 "These functions were developed to support functional data analysis as
18676 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18677 Analysis. The package includes data sets and script files working many
18679 (license license:gpl2+)))
18681 (define-public r-actigraphy
18683 (name "r-actigraphy")
18688 (uri (cran-uri "Actigraphy" version))
18691 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18692 (properties `((upstream-name . "Actigraphy")))
18693 (build-system r-build-system)
18695 `(("r-fda" ,r-fda)))
18696 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18697 (synopsis "Actigraphy data analysis")
18699 "This package provides tools for functional linear modeling and analysis
18700 of actigraphy data.")
18701 (license license:asl2.0)))
18703 (define-public r-activedriver
18705 (name "r-activedriver")
18710 (uri (cran-uri "ActiveDriver" version))
18713 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18714 (properties `((upstream-name . "ActiveDriver")))
18715 (build-system r-build-system)
18717 `(("r-mass" ,r-mass)))
18718 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18719 (synopsis "Tools for finding cancer driver proteins")
18721 "This package provides a mutation analysis tool that discovers cancer
18722 driver genes with frequent mutations in protein signalling sites such as
18723 post-translational modifications (phosphorylation, ubiquitination, etc). The
18724 Poisson generalized linear regression model identifies genes where cancer
18725 mutations in signalling sites are more frequent than expected from the
18726 sequence of the entire gene. Integration of mutations with signalling
18727 information helps find new driver genes and propose candidate mechanisms to
18729 (license license:gpl2+)))
18731 (define-public r-activitycounts
18733 (name "r-activitycounts")
18738 (uri (cran-uri "activityCounts" version))
18741 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18743 `((upstream-name . "activityCounts")))
18744 (build-system r-build-system)
18746 `(("r-lubridate" ,r-lubridate)
18747 ("r-magrittr" ,r-magrittr)
18748 ("r-seewave" ,r-seewave)
18749 ("r-signal" ,r-signal)
18750 ("r-tibble" ,r-tibble)))
18751 (home-page "https://github.com/walkabillylab/activityCounts")
18752 (synopsis "Generate ActiLife counts")
18754 "ActiLife generates activity counts from data collected by Actigraph
18755 accelerometers. Actigraph is one of the most common research-grade
18756 accelerometers. There is considerable research validating and developing
18757 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18758 counts are proprietary and difficult to implement if researchers use different
18759 accelerometer brands. The code creates ActiLife counts from raw acceleration
18760 data for different accelerometer brands.")
18761 (license license:gpl3)))
18763 (define-public r-activityindex
18765 (name "r-activityindex")
18770 (uri (cran-uri "ActivityIndex" version))
18773 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18774 (properties `((upstream-name . "ActivityIndex")))
18775 (build-system r-build-system)
18777 `(("r-data-table" ,r-data-table)
18778 ("r-matrixstats" ,r-matrixstats)
18779 ("r-r-utils" ,r-r-utils)))
18780 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18781 (synopsis "Activity Index calculation using raw accelerometry data")
18783 "This is a package to read raw accelerometry from GT3X+ accelerometry
18784 data and plain table data to calculate the Activity Index from Bai et
18785 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18786 (license license:gpl3)))
18788 (define-public r-activpal
18790 (name "r-activpal")
18795 (uri (cran-uri "activPAL" version))
18798 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18799 (properties `((upstream-name . "activPAL")))
18800 (build-system r-build-system)
18802 `(("r-devtools" ,r-devtools)
18803 ("r-dplyr" ,r-dplyr)
18804 ("r-ggplot2" ,r-ggplot2)
18805 ("r-lubridate" ,r-lubridate)
18806 ("r-magrittr" ,r-magrittr)
18807 ("r-tidyr" ,r-tidyr)))
18808 (home-page "https://cran.r-project.org/web/packages/activPAL")
18809 (synopsis "Processing and chart generation from activPAL events files")
18811 "This package contains functions to generate pre-defined summary
18812 statistics from activPAL events files. The package also contains functions to
18813 produce informative graphics that visualize physical activity behaviour and
18814 trends. This includes generating graphs that align physical activity
18815 behaviour with additional time based observations described by other data
18816 sets, such as sleep diaries and continuous glucose monitoring data.")
18817 (license license:gpl3)))
18819 (define-public r-activpalprocessing
18821 (name "r-activpalprocessing")
18826 (uri (cran-uri "activpalProcessing" version))
18829 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18831 `((upstream-name . "activpalProcessing")))
18832 (build-system r-build-system)
18834 `(("r-chron" ,r-chron)))
18835 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18836 (synopsis "Process activPAL events files")
18838 "This package performs estimation of physical activity and sedentary
18839 behavior variables from activPAL events files.")
18840 ;; Either version of the GPL.
18841 (license (list license:gpl2 license:gpl3))))
18843 (define-public r-actogrammr
18845 (name "r-actogrammr")
18850 (uri (cran-uri "actogrammr" version))
18853 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18854 (properties `((upstream-name . "actogrammr")))
18855 (build-system r-build-system)
18857 `(("r-dplyr" ,r-dplyr)
18858 ("r-ggplot2" ,r-ggplot2)
18859 ("r-lubridate" ,r-lubridate)
18860 ("r-readr" ,r-readr)
18861 ("r-tidyr" ,r-tidyr)))
18862 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18863 (synopsis "Read in activity data and plot actograms")
18865 "Read in activity measurements from standard file formats used by
18866 circadian rhythm researchers, currently only ClockLab format, and process and
18867 plot the data. The central type of plot is the actogram, as first described
18868 in \"Activity and distribution of certain wild mice in relation to biotic
18869 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18870 (license license:gpl3)))
18872 (define-public r-expint
18879 (uri (cran-uri "expint" version))
18882 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18883 (properties `((upstream-name . "expint")))
18884 (build-system r-build-system)
18885 (home-page "https://gitlab.com/vigou3/expint")
18886 (synopsis "Exponential integral and incomplete Gamma function")
18888 "This package provides the exponential integrals @code{E_1(x)},
18889 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18890 function @code{G(a, x)} defined for negative values of its first argument.
18891 The package also gives easy access to the underlying C routines through an
18892 API; see the package vignette for details.")
18893 (license license:gpl2+)))
18895 (define-public r-actuar
18902 (uri (cran-uri "actuar" version))
18905 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
18906 (properties `((upstream-name . "actuar")))
18907 (build-system r-build-system)
18908 (propagated-inputs `(("r-expint" ,r-expint)))
18909 (home-page "https://gitlab.com/vigou3/actuar")
18910 (synopsis "Actuarial functions and heavy tailed distributions")
18912 "This package provides functions and data sets for actuarial science:
18913 modeling of loss distributions; risk theory and ruin theory; simulation of
18914 compound models, discrete mixtures and compound hierarchical models;
18915 credibility theory. It boasts support for many additional probability
18916 distributions to model insurance loss amounts and loss frequency: 19
18917 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18918 distribution; zero-truncated and zero-modified extensions of the standard
18919 discrete distributions. It also supports phase-type distributions commonly
18920 used to compute ruin probabilities.")
18921 (license license:gpl2+)))
18923 (define-public r-bmp
18930 (uri (cran-uri "bmp" version))
18933 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18934 (properties `((upstream-name . "bmp")))
18935 (build-system r-build-system)
18936 (home-page "https://cran.r-project.org/web/packages/bmp/")
18937 (synopsis "Read Bitmap (BMP) images")
18939 "This package provides pure R tools to read BMP format images. It is
18940 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18941 (license license:gpl2+)))
18943 (define-public r-readbitmap
18945 (name "r-readbitmap")
18950 (uri (cran-uri "readbitmap" version))
18953 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18954 (properties `((upstream-name . "readbitmap")))
18955 (build-system r-build-system)
18957 `(("libjpeg" ,libjpeg-turbo)
18958 ("libpng" ,libpng)))
18963 ("r-tiff" ,r-tiff)))
18964 (home-page "https://github.com/jefferis/readbitmap")
18965 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18967 "This package provides tools to identify and read BMP, JPEG, PNG, and
18968 TIFF format bitmap images. Identification defaults to the use of the magic
18969 number embedded in the file rather than the file extension.")
18970 (license license:gpl2+)))
18972 (define-public r-imager
18979 (uri (cran-uri "imager" version))
18982 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
18983 (properties `((upstream-name . "imager")))
18984 (build-system r-build-system)
18987 ("libtiff" ,libtiff)
18991 `(("r-downloader" ,r-downloader)
18992 ("r-igraph" ,r-igraph)
18994 ("r-magrittr" ,r-magrittr)
18996 ("r-purrr" ,r-purrr)
18998 ("r-readbitmap" ,r-readbitmap)
18999 ("r-stringr" ,r-stringr)))
19001 `(("pkg-config" ,pkg-config)
19002 ("r-knitr" ,r-knitr)))
19003 (home-page "https://dahtah.github.io/imager/")
19004 (synopsis "Image processing library")
19006 "This is a package for fast image processing for images in up to 4
19007 dimensions (two spatial dimensions, one time/depth dimension, one color
19008 dimension). It provides most traditional image processing tools (filtering,
19009 morphology, transformations, etc.) as well as various functions for easily
19010 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19011 simple, modern C++ library for image processing.")
19012 (license license:lgpl3)))
19014 (define-public r-acuityview
19016 (name "r-acuityview")
19021 (uri (cran-uri "AcuityView" version))
19024 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19025 (properties `((upstream-name . "AcuityView")))
19026 (build-system r-build-system)
19028 `(("r-fftwtools" ,r-fftwtools)
19029 ("r-imager" ,r-imager)
19030 ("r-plotrix" ,r-plotrix)))
19031 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19032 (synopsis "Display scenes as seen by an animal with less acute vision")
19034 "This package provides a simple method for representing a visual scene as
19035 it may be seen by an animal with less acute vision.")
19036 (license license:gpl2+)))
19038 (define-public r-caret
19045 (uri (cran-uri "caret" version))
19048 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19049 (build-system r-build-system)
19051 `(("r-foreach" ,r-foreach)
19052 ("r-ggplot2" ,r-ggplot2)
19053 ("r-lattice" ,r-lattice)
19054 ("r-modelmetrics" ,r-modelmetrics)
19058 ("r-recipes" ,r-recipes)
19059 ("r-reshape2" ,r-reshape2)
19060 ("r-withr" ,r-withr)))
19062 `(("r-knitr" ,r-knitr)))
19063 (home-page "https://github.com/topepo/caret")
19064 (synopsis "Classification and regression training")
19066 "This package provides miscellaneous functions for training and plotting
19067 classification and regression models.")
19068 (license license:gpl2+)))
19070 (define-public r-adabag
19077 (uri (cran-uri "adabag" version))
19080 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19081 (properties `((upstream-name . "adabag")))
19082 (build-system r-build-system)
19084 `(("r-caret" ,r-caret)
19085 ("r-doparallel" ,r-doparallel)
19086 ("r-foreach" ,r-foreach)
19087 ("r-rpart" ,r-rpart)))
19088 (home-page "https://cran.r-project.org/web/packages/adabag/")
19089 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19091 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19092 Breiman's Bagging algorithm using classification trees as individual
19093 classifiers. Once these classifiers have been trained, they can be used to
19094 predict on new data. Also, cross validation estimation of the error can be
19096 (license license:gpl2+)))
19098 (define-public r-adagio
19105 (uri (cran-uri "adagio" version))
19108 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19109 (properties `((upstream-name . "adagio")))
19110 (build-system r-build-system)
19111 (native-inputs `(("gfortran" ,gfortran)))
19112 (home-page "https://cran.r-project.org/web/packages/adagio/")
19113 (synopsis "Discrete and global optimization routines")
19115 "This package provides methods and algorithms for discrete optimization,
19116 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19117 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19119 (license license:gpl3+)))
19121 (define-public r-univoutl
19123 (name "r-univoutl")
19128 (uri (cran-uri "univOutl" version))
19131 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19132 (properties `((upstream-name . "univOutl")))
19133 (build-system r-build-system)
19135 `(("r-hmisc" ,r-hmisc)
19136 ("r-robustbase" ,r-robustbase)))
19137 (home-page "https://github.com/marcellodo/univOutl")
19138 (synopsis "Detection of univariate outliers")
19140 "This package provides well-known outlier detection techniques in the
19141 univariate case. Methods to deal with skewed distribution are included too.
19142 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19143 historical data is implemented as well. When available, survey weights can be
19144 used in outliers detection.")
19145 (license license:gpl2+)))
19147 (define-public r-tolerance
19149 (name "r-tolerance")
19154 (uri (cran-uri "tolerance" version))
19157 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19158 (properties `((upstream-name . "tolerance")))
19159 (build-system r-build-system)
19161 `(("r-mass" ,r-mass)
19163 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19164 (synopsis "Statistical tolerance intervals and regions")
19166 "This package provides functions for estimating tolerance
19167 limits (intervals) for various univariate distributions (binomial, Cauchy,
19168 discrete Pareto, exponential, two-parameter exponential, extreme value,
19169 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19170 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19171 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19172 nonparametric tolerance intervals, tolerance bands for regression
19173 settings (linear regression, nonlinear regression, nonparametric regression,
19174 and multivariate regression), and analysis of variance tolerance intervals.
19175 Visualizations are also available for most of these settings.")
19176 (license license:gpl2+)))
19178 (define-public r-additivitytests
19180 (name "r-additivitytests")
19185 (uri (cran-uri "additivityTests" version))
19188 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19190 `((upstream-name . "additivityTests")))
19191 (build-system r-build-system)
19192 (home-page "https://github.com/simecek/additivityTests")
19193 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19195 "This package provides an implementation of the Tukey, Mandel,
19196 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19197 (license license:gpl3)))
19199 (define-public r-flexclust
19201 (name "r-flexclust")
19206 (uri (cran-uri "flexclust" version))
19209 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19210 (properties `((upstream-name . "flexclust")))
19211 (build-system r-build-system)
19213 `(("r-class" ,r-class)
19214 ("r-lattice" ,r-lattice)
19215 ("r-modeltools" ,r-modeltools)))
19216 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19217 (synopsis "Flexible cluster algorithms")
19219 "The main function @code{kcca} implements a general framework for
19220 k-centroids cluster analysis supporting arbitrary distance measures and
19221 centroid computation. Further cluster methods include hard competitive
19222 learning, neural gas, and QT clustering. There are numerous visualization
19223 methods for cluster results (neighborhood graphs, convex cluster hulls,
19224 barcharts of centroids, ...), and bootstrap methods for the analysis of
19225 cluster stability.")
19226 (license license:gpl2)))
19228 (define-public r-biclust
19235 (uri (cran-uri "biclust" version))
19238 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19239 (properties `((upstream-name . "biclust")))
19240 (build-system r-build-system)
19242 `(("r-additivitytests" ,r-additivitytests)
19243 ("r-colorspace" ,r-colorspace)
19244 ("r-flexclust" ,r-flexclust)
19245 ("r-ggplot2" ,r-ggplot2)
19246 ("r-lattice" ,r-lattice)
19248 ("r-tidyr" ,r-tidyr)))
19249 (home-page "https://cran.r-project.org/web/packages/biclust/")
19250 (synopsis "BiCluster algorithms")
19252 "The main function @code{biclust()} provides several algorithms to find
19253 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19254 In addition, the package provides methods for data
19255 preprocessing (normalization and discretization), visualization, and
19256 validation of bicluster solutions.")
19257 (license license:gpl3)))
19259 (define-public r-icge
19266 (uri (cran-uri "ICGE" version))
19269 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19270 (properties `((upstream-name . "ICGE")))
19271 (build-system r-build-system)
19273 `(("r-cluster" ,r-cluster)
19274 ("r-mass" ,r-mass)))
19275 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19276 (synopsis "Cluster estimation and identification of atypical units")
19278 "ICGE is a package that helps to estimate the number of real clusters in
19279 data as well as to identify atypical units. The underlying methods are based
19280 on distances rather than on unit x variables.")
19281 (license license:gpl2+)))
19283 (define-public r-depth
19286 (version "2.1-1.1")
19290 (uri (cran-uri "depth" version))
19293 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19294 (properties `((upstream-name . "depth")))
19295 (build-system r-build-system)
19297 `(("r-abind" ,r-abind)
19298 ("r-circular" ,r-circular)
19301 `(("gfortran" ,gfortran)))
19302 (home-page "https://cran.r-project.org/web/packages/depth/")
19303 (synopsis "Nonparametric depth functions for multivariate analysis")
19305 "This package provides tools for depth functions methodology applied to
19306 multivariate analysis. Besides allowing calculation of depth values and
19307 depth-based location estimators, the package includes functions or drawing
19308 contour plots and perspective plots of depth functions. Euclidian and
19309 spherical depths are supported.")
19310 (license license:gpl2)))
19312 (define-public r-archetypes
19314 (name "r-archetypes")
19315 (version "2.2-0.1")
19319 (uri (cran-uri "archetypes" version))
19322 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19323 (properties `((upstream-name . "archetypes")))
19324 (build-system r-build-system)
19326 `(("r-modeltools" ,r-modeltools)
19327 ("r-nnls" ,r-nnls)))
19328 (home-page "https://cran.r-project.org/web/packages/archetypes")
19329 (synopsis "Archetypal analysis")
19331 "The main function @code{archetypes} implements a framework for
19332 archetypal analysis supporting arbitrary problem solving mechanisms for the
19333 different conceptual parts of the algorithm.")
19334 (license license:gpl2+)))
19336 (define-public r-shapes
19343 (uri (cran-uri "shapes" version))
19346 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19347 (properties `((upstream-name . "shapes")))
19348 (build-system r-build-system)
19350 `(("r-mass" ,r-mass)
19351 ("r-minpack-lm" ,r-minpack-lm)
19353 ("r-scatterplot3d" ,r-scatterplot3d)))
19354 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19355 (synopsis "Statistical shape analysis")
19357 "This package provides routines for the statistical analysis of landmark
19358 shapes, including Procrustes analysis, graphical displays, principal
19359 components analysis, permutation and bootstrap tests, thin-plate spline
19360 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19361 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19362 Edition), John Wiley and Sons.")
19363 (license license:gpl2)))
19365 (define-public r-anthropometry
19367 (name "r-anthropometry")
19372 (uri (cran-uri "Anthropometry" version))
19375 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19376 (properties `((upstream-name . "Anthropometry")))
19377 (build-system r-build-system)
19379 `(("r-archetypes" ,r-archetypes)
19380 ("r-biclust" ,r-biclust)
19381 ("r-cluster" ,r-cluster)
19382 ("r-depth" ,r-depth)
19387 ("r-shapes" ,r-shapes)))
19389 `(("r-knitr" ,r-knitr)))
19390 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19391 (synopsis "Statistical methods for anthropometric data")
19393 "This package provides statistical methods especially developed to
19394 analyze anthropometric data. These methods are aimed at providing effective
19395 solutions to some commons problems related to Ergonomics and Anthropometry.
19396 They are based on clustering, the statistical concept of data depth,
19397 statistical shape analysis and archetypal analysis.")
19398 (license license:gpl2+)))
19400 (define-public r-adamethods
19402 (name "r-adamethods")
19407 (uri (cran-uri "adamethods" version))
19410 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19411 (properties `((upstream-name . "adamethods")))
19412 (build-system r-build-system)
19414 `(("r-anthropometry" ,r-anthropometry)
19415 ("r-archetypes" ,r-archetypes)
19417 ("r-foreach" ,r-foreach)
19419 ("r-tolerance" ,r-tolerance)
19420 ("r-univoutl" ,r-univoutl)))
19421 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19422 (synopsis "Archetypoid algorithms and anomaly detection")
19424 "This package is a collection of several algorithms to obtain
19425 archetypoids with small and large databases and with both classical
19426 multivariate data and functional data (univariate and multivariate). Some of
19427 these algorithms also allow to detect anomalies (outliers).")
19428 (license license:gpl2+)))
19430 (define-public r-idpmisc
19437 (uri (cran-uri "IDPmisc" version))
19440 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19441 (properties `((upstream-name . "IDPmisc")))
19442 (build-system r-build-system)
19444 `(("r-lattice" ,r-lattice)))
19445 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19446 (synopsis "Functions for data analyses and visualization")
19448 "This package provides different high-level graphics functions for
19449 displaying large datasets, displaying circular data in a very flexible way,
19450 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19451 2D-plots, creating figures with differently colored margin and plot region.
19452 In addition, the package contains auxiliary functions for data manipulation
19453 like omitting observations with irregular values or selecting data by logical
19454 vectors, which include NAs. Other functions are especially useful in
19455 spectroscopy and analyses of environmental data: robust baseline fitting,
19456 finding peaks in spectra, converting humidity measures.")
19457 (license license:gpl3+)))
19459 (define-public r-qqman
19466 (uri (cran-uri "qqman" version))
19469 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19470 (properties `((upstream-name . "qqman")))
19471 (build-system r-build-system)
19473 `(("r-calibrate" ,r-calibrate)))
19474 (home-page "https://cran.r-project.org/web/packages/qqman/")
19475 (synopsis "Q-Q and Manhattan plots for GWAS data")
19477 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19478 from PLINK results.")
19479 (license license:gpl3)))
19481 (define-public r-ggplot-multistats
19483 (name "r-ggplot-multistats")
19488 (uri (cran-uri "ggplot.multistats" version))
19491 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19493 `((upstream-name . "ggplot.multistats")))
19494 (build-system r-build-system)
19496 `(("r-ggplot2" ,r-ggplot2)
19497 ("r-hexbin" ,r-hexbin)
19498 ("r-rlang" ,r-rlang)
19499 ("r-scales" ,r-scales)))
19500 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19501 (synopsis "Multiple summary statistics for binned stats/geometries")
19503 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19504 which functions similar to its singular form, but allows the use of multiple
19505 statistics per bin. Those statistics can be mapped to multiple bin
19507 (license license:gpl3)))
19509 (define-public r-knn-covertree
19511 (name "r-knn-covertree")
19516 (uri (cran-uri "knn.covertree" version))
19519 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19520 (properties `((upstream-name . "knn.covertree")))
19521 (build-system r-build-system)
19523 `(("r-matrix" ,r-matrix)
19525 ("r-rcppeigen" ,r-rcppeigen)))
19526 (home-page "https://github.com/flying-sheep/knn.covertree")
19527 (synopsis "Accurate kNN Implementation with multiple distance measures")
19529 "Similarly to the FNN package, this package allows calculation of the k
19530 nearest neighbors (kNN) of a data matrix. The implementation is based on
19531 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19532 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19533 (license license:agpl3+)))
19535 (define-public r-poibin
19542 (uri (cran-uri "poibin" version))
19545 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19546 (properties `((upstream-name . "poibin")))
19547 (build-system r-build-system)
19548 (home-page "https://cran.r-project.org/web/packages/poibin/")
19549 (synopsis "Poisson binomial distribution")
19551 "This package provides an implementation of both the exact and
19552 approximation methods for computing the @dfn{cumulative distribution
19553 function} (CDF) of the Poisson binomial distribution. It also provides the
19554 @dfn{probability mass function} (PMF), quantile function, and random number
19555 generation for the Poisson binomial distribution.")
19556 (license license:gpl2)))
19558 (define-public r-diagram
19565 (uri (cran-uri "diagram" version))
19568 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19569 (properties `((upstream-name . "diagram")))
19570 (build-system r-build-system)
19572 `(("r-shape" ,r-shape)))
19573 (home-page "https://cran.r-project.org/web/packages/diagram/")
19574 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19576 "This package provides tools to visualize simple graphs (networks) based
19577 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19578 electrical networks, etc. It also includes supporting material for the book
19579 \"A practical guide to ecological modelling - using R as a simulation
19580 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19581 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19582 Francesca Mazzia (2012).")
19583 (license license:gpl2+)))
19585 (define-public r-lim
19592 (uri (cran-uri "LIM" version))
19595 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19596 (properties `((upstream-name . "LIM")))
19597 (build-system r-build-system)
19599 `(("r-diagram" ,r-diagram)
19600 ("r-limsolve" ,r-limsolve)))
19601 (home-page "https://cran.r-project.org/web/packages/LIM/")
19602 (synopsis "Linear inverse model examples and solution methods")
19604 "This package provides functions that read and solve linear inverse
19605 problems (food web problems, linear programming problems).")
19606 (license license:gpl2+)))
19608 (define-public r-shinycssloaders
19610 (name "r-shinycssloaders")
19615 (uri (cran-uri "shinycssloaders" version))
19618 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19620 `((upstream-name . "shinycssloaders")))
19621 (build-system r-build-system)
19623 `(("r-digest" ,r-digest)
19625 ("r-shiny" ,r-shiny)))
19626 (home-page "https://github.com/andrewsali/shinycssloaders")
19627 (synopsis "Add CSS loading animations to Shiny outputs")
19629 "This package provides tools to create a lightweight Shiny wrapper for
19630 the css-loaders created by Luke Hass
19631 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19632 automatically show a loader when the output is (re)calculating.")
19633 (license license:gpl3)))
19635 (define-public r-rsvg
19642 (uri (cran-uri "rsvg" version))
19645 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19646 (properties `((upstream-name . "rsvg")))
19647 (build-system r-build-system)
19649 `(("librsvg" ,librsvg)
19652 `(("pkg-config" ,pkg-config)
19653 ("r-knitr" ,r-knitr)))
19654 (home-page "https://github.com/jeroen/rsvg#readme")
19655 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19657 "This package allows you to render vector-based SVG images into
19658 high-quality custom-size bitmap arrays using the librsvg2 library. The
19659 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19660 addition, the package can convert images directly to various formats such as
19661 PDF or PostScript.")
19662 (license license:expat)))
19664 (define-public r-influencer
19666 (name "r-influencer")
19671 (uri (cran-uri "influenceR" version))
19674 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19675 (properties `((upstream-name . "influenceR")))
19676 (build-system r-build-system)
19678 `(("r-igraph" ,r-igraph)
19679 ("r-matrix" ,r-matrix)))
19680 (home-page "https://github.com/rcc-uchicago/influenceR")
19681 (synopsis "Tools to quantify structural importance of nodes in a network")
19683 "This package provides functionality to compute various node centrality
19684 measures on networks. Included are functions to compute betweenness
19685 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19686 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19687 algorithm to identify key players, and Valente's bridging metric. The
19688 betweenness, Key Players, and bridging implementations are parallelized with
19690 (license license:gpl2)))
19692 (define-public r-emplik
19699 (uri (cran-uri "emplik" version))
19702 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19703 (properties `((upstream-name . "emplik")))
19704 (build-system r-build-system)
19706 `(("r-quantreg" ,r-quantreg)))
19707 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19708 (synopsis "Empirical likelihood ratio for censored/truncated data")
19710 "This package provides empirical likelihood ratio tests for
19711 means/quantiles/hazards from possibly censored and/or truncated data. It also
19713 (license license:gpl2+)))
19715 (define-public r-imputeyn
19717 (name "r-imputeyn")
19722 (uri (cran-uri "imputeYn" version))
19725 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19726 (properties `((upstream-name . "imputeYn")))
19727 (build-system r-build-system)
19729 `(("r-boot" ,r-boot)
19730 ("r-emplik" ,r-emplik)
19731 ("r-mvtnorm" ,r-mvtnorm)
19732 ("r-quadprog" ,r-quadprog)
19733 ("r-survival" ,r-survival)))
19734 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19735 (synopsis "Impute last largest censored observation under weighted least squares")
19737 "This package allows for the imputation of the last largest censored
19738 observantions. This method brings less bias and more efficient estimates for
19740 (license license:gpl2)))
19742 (define-public r-adapenetclass
19744 (name "r-adapenetclass")
19749 (uri (cran-uri "AdapEnetClass" version))
19752 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19753 (properties `((upstream-name . "AdapEnetClass")))
19754 (build-system r-build-system)
19756 `(("r-glmnet" ,r-glmnet)
19757 ("r-imputeyn" ,r-imputeyn)
19759 ("r-quadprog" ,r-quadprog)))
19760 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19761 (synopsis "Class of adaptive elastic net methods for censored data")
19763 "This package provides methods for variable selection for AFT models.")
19764 (license license:gpl2)))
19766 (define-public r-flock
19773 (uri (cran-uri "flock" version))
19776 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19777 (properties `((upstream-name . "flock")))
19778 (build-system r-build-system)
19779 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19780 (home-page "https://cran.r-project.org/web/packages/flock/")
19781 (synopsis "Process synchronization using file locks")
19783 "This package implements synchronization between R processes (spawned by
19784 using the @code{parallel} package for instance) using file locks. It supports
19785 both exclusive and shared locking.")
19786 (license license:asl2.0)))
19788 (define-public r-archivist
19790 (name "r-archivist")
19795 (uri (cran-uri "archivist" version))
19798 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19799 (properties `((upstream-name . "archivist")))
19800 (build-system r-build-system)
19803 ("r-digest" ,r-digest)
19804 ("r-flock" ,r-flock)
19806 ("r-lubridate" ,r-lubridate)
19807 ("r-magrittr" ,r-magrittr)
19808 ("r-rcurl" ,r-rcurl)
19809 ("r-rsqlite" ,r-rsqlite)))
19810 (home-page "https://pbiecek.github.io/archivist/")
19811 (synopsis "Tools for storing, restoring and searching for R objects")
19813 "Data exploration and modelling is a process in which a lot of data
19814 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19815 statistical models, different versions of data sets and different versions of
19816 results. Archivist helps to store and manage artifacts created in R. It
19817 allows you to store selected artifacts as binary files together with their
19818 metadata and relations. Archivist allows sharing artifacts with others. It
19819 can look for already created artifacts by using its class, name, date of the
19820 creation or other properties. It also makes it easy to restore such
19822 (license license:gpl2)))
19824 (define-public r-versions
19826 (name "r-versions")
19831 (uri (cran-uri "versions" version))
19834 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19835 (properties `((upstream-name . "versions")))
19836 (build-system r-build-system)
19837 (home-page "https://cran.r-project.org/web/packages/versions/")
19838 (synopsis "Query and install specific versions of CRAN packages")
19840 "This package allows you to install specified versions of R packages
19841 hosted on CRAN and provides functions to list available versions and the
19842 versions of currently installed packages.")
19843 (license license:bsd-3)))
19845 (define-public r-adapr
19852 (uri (cran-uri "adapr" version))
19855 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19856 (properties `((upstream-name . "adapr")))
19857 (build-system r-build-system)
19859 `(("r-archivist" ,r-archivist)
19860 ("r-devtools" ,r-devtools)
19861 ("r-digest" ,r-digest)
19862 ("r-doparallel" ,r-doparallel)
19863 ("r-gdata" ,r-gdata)
19864 ("r-ggplot2" ,r-ggplot2)
19865 ("r-git2r" ,r-git2r)
19866 ("r-igraph" ,r-igraph)
19867 ("r-knitr" ,r-knitr)
19868 ("r-plotly" ,r-plotly)
19870 ("r-rmarkdown" ,r-rmarkdown)
19871 ("r-shiny" ,r-shiny)
19872 ("r-shinydashboard" ,r-shinydashboard)
19873 ("r-versions" ,r-versions)))
19874 (home-page "https://cran.r-project.org/web/packages/adapr/")
19875 (synopsis "Implementation of an accountable data analysis process")
19877 "This package tracks reading and writing within R scripts that are
19878 organized into a directed acyclic graph. It contains an interactive Shiny
19879 application @code{adaprApp()}. It uses Git and file hashes to track version
19880 histories of inputs and outputs.")
19881 (license license:lgpl2.0)))
19883 (define-public r-adapsamp
19885 (name "r-adapsamp")
19890 (uri (cran-uri "AdapSamp" version))
19893 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19894 (properties `((upstream-name . "AdapSamp")))
19895 (build-system r-build-system)
19896 (propagated-inputs `(("r-pracma" ,r-pracma)))
19897 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19898 (synopsis "Adaptive sampling algorithms")
19900 "For distributions whose probability density functions are log-concave,
19901 the adaptive rejection sampling algorithm can be used to build envelope
19902 functions for sampling. For others, the modified adaptive rejection sampling
19903 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19904 adaptive slice sampling algorithm can be used. This R package mainly includes
19905 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19906 @code{rASS()}. These functions can realize sampling based on the algorithms
19908 (license license:gpl2)))
19910 (define-public r-adaptalint
19912 (name "r-adaptalint")
19917 (uri (cran-uri "adaptalint" version))
19920 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19921 (properties `((upstream-name . "adaptalint")))
19922 (build-system r-build-system)
19924 `(("r-dplyr" ,r-dplyr)
19925 ("r-lintr" ,r-lintr)
19926 ("r-purrr" ,r-purrr)))
19927 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19928 (synopsis "Check R code style")
19930 "This package provides tools to infer the code style (which style rules
19931 are followed and which ones are not) from one package and use it to check
19932 another. This makes it easier to find and correct the most important problems
19934 (license license:gpl3)))
19936 (define-public r-fracdiff
19938 (name "r-fracdiff")
19943 (uri (cran-uri "fracdiff" version))
19946 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19947 (properties `((upstream-name . "fracdiff")))
19948 (build-system r-build-system)
19949 (home-page "https://github.com/mmaechler/fracdiff")
19951 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19953 "This package provides tools for the maximum likelihood estimation of the
19954 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19955 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19956 (license license:gpl2+)))
19958 (define-public r-forecast
19960 (name "r-forecast")
19965 (uri (cran-uri "forecast" version))
19968 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19969 (properties `((upstream-name . "forecast")))
19970 (build-system r-build-system)
19972 `(("r-colorspace" ,r-colorspace)
19973 ("r-fracdiff" ,r-fracdiff)
19974 ("r-ggplot2" ,r-ggplot2)
19975 ("r-lmtest" ,r-lmtest)
19976 ("r-magrittr" ,r-magrittr)
19979 ("r-rcpparmadillo" ,r-rcpparmadillo)
19980 ("r-timedate" ,r-timedate)
19981 ("r-tseries" ,r-tseries)
19985 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19986 (home-page "https://pkg.robjhyndman.com/forecast/")
19987 (synopsis "Forecasting functions for time series and linear models")
19989 "This package provides methods and tools for displaying and analysing
19990 univariate time series forecasts including exponential smoothing via state
19991 space models and automatic ARIMA modelling.")
19992 (license license:gpl3)))
19994 (define-public r-xmisc
20001 (uri (cran-uri "Xmisc" version))
20004 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20005 (properties `((upstream-name . "Xmisc")))
20006 (build-system r-build-system)
20007 (home-page "https://cran.r-project.org/package=Xmisc")
20009 "Xiaobei's miscellaneous classes and functions")
20011 "This package provides Xiaobei's miscellaneous classes and functions,
20012 which are useful when developing R packages for @dfn{object oriented
20013 programming} (OOP) using R Reference Class.")
20014 (license license:gpl2+)))
20016 (define-public r-proxyc
20023 (uri (cran-uri "proxyC" version))
20026 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20027 (properties `((upstream-name . "proxyC")))
20028 (build-system r-build-system)
20030 `(("r-matrix" ,r-matrix)
20032 ("r-rcpparmadillo" ,r-rcpparmadillo)
20033 ("r-rcppparallel" ,r-rcppparallel)))
20034 (home-page "https://cran.r-project.org/package=proxyC")
20035 (synopsis "Compute proximity in large sparse matrices")
20037 "This package provides efficient tools to compute the proximity between
20038 rows or columns of large matrices. Functions are optimised for large sparse
20039 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20040 similarity/distance measures, computation of correlation, cosine similarity
20041 and Euclidean distance is particularly fast.")
20042 (license license:gpl3)))
20044 (define-public r-isocodes
20046 (name "r-isocodes")
20047 (version "2020.03.16")
20051 (uri (cran-uri "ISOcodes" version))
20054 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20055 (properties `((upstream-name . "ISOcodes")))
20056 (build-system r-build-system)
20057 (home-page "https://cran.r-project.org/package=ISOcodes")
20058 (synopsis "Selected ISO codes")
20060 "This package provides ISO language, territory, currency, script and
20061 character codes. It provides ISO 639 language codes, ISO 3166 territory
20062 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20063 character codes as well as the UN M.49 area codes.")
20064 (license license:gpl2)))
20066 (define-public r-stopwords
20068 (name "r-stopwords")
20073 (uri (cran-uri "stopwords" version))
20076 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20077 (properties `((upstream-name . "stopwords")))
20078 (build-system r-build-system)
20080 `(("r-desc" ,r-desc)
20081 ("r-isocodes" ,r-isocodes)
20082 ("r-usethis" ,r-usethis)))
20083 (home-page "https://github.com/quanteda/stopwords")
20084 (synopsis "Multilingual stopword lists")
20086 "This package provides multiple sources of stopwords, for use in text
20087 analysis and natural language processing.")
20088 (license license:expat)))
20090 (define-public r-spacyr
20097 (uri (cran-uri "spacyr" version))
20100 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20101 (properties `((upstream-name . "spacyr")))
20102 (build-system r-build-system)
20104 `(("r-data-table" ,r-data-table)
20105 ("r-reticulate" ,r-reticulate)))
20106 (home-page "https://spacyr.quanteda.io")
20107 (synopsis "R wrapper for the spaCy NLP library")
20109 "This package provides an R wrapper to the Python @dfn{natural language
20110 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20111 (license license:gpl3)))
20113 (define-public r-snowballc
20115 (name "r-snowballc")
20120 (uri (cran-uri "SnowballC" version))
20123 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20124 (properties `((upstream-name . "SnowballC")))
20125 (build-system r-build-system)
20126 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20127 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20129 "This package provides an R interface to the C @code{libstemmer} library
20130 that implements Porter's word stemming algorithm for collapsing words to a
20131 common root to aid comparison of vocabulary. Currently supported languages
20132 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20133 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20134 (license license:bsd-3)))
20136 (define-public r-quanteda
20138 (name "r-quanteda")
20143 (uri (cran-uri "quanteda" version))
20146 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
20147 (properties `((upstream-name . "quanteda")))
20148 (build-system r-build-system)
20150 `(("r-data-table" ,r-data-table)
20151 ("r-extrafont" ,r-extrafont)
20152 ("r-fastmatch" ,r-fastmatch)
20153 ("r-ggplot2" ,r-ggplot2)
20154 ("r-ggrepel" ,r-ggrepel)
20155 ("r-jsonlite" ,r-jsonlite)
20156 ("r-magrittr" ,r-magrittr)
20157 ("r-matrix" ,r-matrix)
20158 ("r-network" ,r-network)
20159 ("r-proxyc" ,r-proxyc)
20161 ("r-rcpparmadillo" ,r-rcpparmadillo)
20162 ("r-rcppparallel" ,r-rcppparallel)
20164 ("r-snowballc" ,r-snowballc)
20165 ("r-stopwords" ,r-stopwords)
20166 ("r-stringi" ,r-stringi)
20168 ("r-yaml" ,r-yaml)))
20170 `(("r-knitr" ,r-knitr)))
20171 (home-page "https://quanteda.io")
20172 (synopsis "Quantitative analysis of textual data")
20174 "This package provides a fast, flexible, and comprehensive framework for
20175 quantitative text analysis in R. It provides functionality for corpus
20176 management, creating and manipulating tokens and ngrams, exploring keywords in
20177 context, forming and manipulating sparse matrices of documents by features and
20178 feature co-occurrences, analyzing keywords, computing feature similarities and
20179 distances, applying content dictionaries, applying supervised and unsupervised
20180 machine learning, visually representing text and text analyses, and more.")
20181 (license license:gpl3)))
20183 (define-public r-topicmodels
20185 (name "r-topicmodels")
20190 (uri (cran-uri "topicmodels" version))
20193 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20194 (properties `((upstream-name . "topicmodels")))
20195 (build-system r-build-system)
20199 `(("r-modeltools" ,r-modeltools)
20202 (home-page "https://cran.r-project.org/package=topicmodels")
20203 (synopsis "Topic models")
20205 "This package provides an interface to the C code for @dfn{Latent
20206 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20207 David M. Blei and co-authors and the C++ code for fitting LDA models using
20208 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20209 (license license:gpl2)))
20211 (define-public r-stm
20218 (uri (cran-uri "stm" version))
20221 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20222 (properties `((upstream-name . "stm")))
20223 (build-system r-build-system)
20225 `(("r-data-table" ,r-data-table)
20226 ("r-glmnet" ,r-glmnet)
20228 ("r-matrix" ,r-matrix)
20229 ("r-matrixstats" ,r-matrixstats)
20230 ("r-quadprog" ,r-quadprog)
20231 ("r-quanteda" ,r-quanteda)
20233 ("r-rcpparmadillo" ,r-rcpparmadillo)
20235 ("r-stringr" ,r-stringr)))
20236 (home-page "http://www.structuraltopicmodel.com/")
20237 (synopsis "Estimation of the Structural Topic Model")
20239 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20240 topic models with document-level covariates. The package also includes tools
20241 for model selection, visualization, and estimation of topic-covariate
20243 (license license:expat)))
20245 (define-public r-polycor
20252 (uri (cran-uri "polycor" version))
20255 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20256 (properties `((upstream-name . "polycor")))
20257 (build-system r-build-system)
20259 `(("r-matrix" ,r-matrix)
20260 ("r-mvtnorm" ,r-mvtnorm)))
20261 (home-page "https://r-forge.r-project.org/projects/polycor/")
20262 (synopsis "Polychoric and polyserial correlations")
20264 "This package provides tools to compute polychoric and polyserial
20265 correlations by quick \"two-step\" methods or ML, optionally with standard
20266 errors; tetrachoric and biserial correlations are special cases.")
20267 (license license:gpl2+)))
20269 (define-public r-msm
20276 (uri (cran-uri "msm" version))
20279 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20280 (properties `((upstream-name . "msm")))
20281 (build-system r-build-system)
20283 `(("r-expm" ,r-expm)
20284 ("r-mvtnorm" ,r-mvtnorm)
20285 ("r-survival" ,r-survival)))
20286 (home-page "https://github.com/chjackson/msm")
20287 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20289 "This package provides functions for fitting continuous-time Markov and
20290 hidden Markov multi-state models to longitudinal data. It was designed for
20291 processes observed at arbitrary times in continuous time (panel data) but some
20292 other observation schemes are supported. Both Markov transition rates and the
20293 hidden Markov output process can be modelled in terms of covariates, which may
20294 be constant or piecewise-constant in time.")
20295 (license license:gpl2+)))
20297 (define-public r-ltm
20304 (uri (cran-uri "ltm" version))
20307 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20308 (properties `((upstream-name . "ltm")))
20309 (build-system r-build-system)
20311 `(("r-mass" ,r-mass)
20313 ("r-polycor" ,r-polycor)))
20314 (home-page "https://github.com/drizopoulos/ltm")
20315 (synopsis "Latent trait models under IRT")
20317 "This is a package supporting the analysis of multivariate dichotomous
20318 and polytomous data using latent trait models under the Item Response Theory
20319 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20320 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20322 (license license:gpl2+)))
20324 (define-public r-mi
20331 (uri (cran-uri "mi" version))
20334 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20335 (properties `((upstream-name . "mi")))
20336 (build-system r-build-system)
20339 ("r-matrix" ,r-matrix)))
20340 (home-page "http://www.stat.columbia.edu/~gelman/")
20341 (synopsis "Missing data imputation and model checking")
20343 "This package provides functions for data manipulation, imputing missing
20344 values in an approximate Bayesian framework, diagnostics of the models used to
20345 generate the imputations, confidence-building mechanisms to validate some of
20346 the assumptions of the imputation algorithm, and functions to analyze multiply
20347 imputed data sets with the appropriate degree of sampling uncertainty.")
20348 (license license:gpl2+)))
20350 (define-public r-matrixcalc
20352 (name "r-matrixcalc")
20357 (uri (cran-uri "matrixcalc" version))
20360 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20361 (properties `((upstream-name . "matrixcalc")))
20362 (build-system r-build-system)
20363 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20364 (synopsis "Collection of functions for matrix calculations")
20366 "This package provides a collection of functions to support matrix
20367 calculations for probability, econometric and numerical analysis. There are
20368 additional functions that are comparable to APL functions which are useful for
20369 actuarial models such as pension mathematics.")
20370 (license license:gpl2+)))
20372 (define-public r-sem
20379 (uri (cran-uri "sem" version))
20382 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20383 (properties `((upstream-name . "sem")))
20384 (build-system r-build-system)
20386 `(("r-boot" ,r-boot)
20388 ("r-matrixcalc" ,r-matrixcalc)
20390 (home-page "https://cran.r-project.org/package=sem")
20391 (synopsis "Structural equation models")
20393 "This package provides functions for fitting general linear structural
20394 equation models (with observed and latent variables) using the RAM approach,
20395 and for fitting structural equations in observed-variable models by two-stage
20397 (license license:gpl2+)))
20399 (define-public r-semtools
20401 (name "r-semtools")
20406 (uri (cran-uri "semTools" version))
20409 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20410 (properties `((upstream-name . "semTools")))
20411 (build-system r-build-system)
20413 `(("r-lavaan" ,r-lavaan)))
20414 (home-page "https://github.com/simsem/semTools/wiki")
20415 (synopsis "Useful tools for structural equation modeling")
20417 "This package provides useful tools for structural equation modeling.")
20418 (license license:gpl2+)))
20420 (define-public r-regsem
20427 (uri (cran-uri "regsem" version))
20430 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20431 (properties `((upstream-name . "regsem")))
20432 (build-system r-build-system)
20434 `(("r-lavaan" ,r-lavaan)
20436 ("r-rcpparmadillo" ,r-rcpparmadillo)
20437 ("r-rsolnp" ,r-rsolnp)))
20438 (home-page "https://cran.r-project.org/package=regsem")
20439 (synopsis "Regularized structural equation modeling")
20441 "This package uses both ridge and lasso penalties (and extensions) to
20442 penalize specific parameters in structural equation models. The package
20443 offers additional cost functions, cross validation, and other extensions
20444 beyond traditional structural equation models. It also contains a function to
20445 perform @dfn{exploratory mediation} (XMed).")
20446 (license license:gpl2+)))
20448 (define-public r-stanheaders
20450 (name "r-stanheaders")
20451 (version "2.21.0-5")
20455 (uri (cran-uri "StanHeaders" version))
20458 "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
20459 (properties `((upstream-name . "StanHeaders")))
20460 (build-system r-build-system)
20461 (inputs `(("pandoc" ,ghc-pandoc)))
20463 `(("r-rcppeigen" ,r-rcppeigen)
20464 ("r-rcppparallel" ,r-rcppparallel)))
20466 `(("gfortran" ,gfortran)
20467 ("r-knitr" ,r-knitr))) ; for vignettes
20468 (home-page "https://mc-stan.org/")
20469 (synopsis "C++ header files for Stan")
20471 "The C++ header files of the Stan project are provided by this package.
20472 There is a shared object containing part of the @code{CVODES} library, but it
20473 is not accessible from R. @code{r-stanheaders} is only useful for developers
20474 who want to utilize the @code{LinkingTo} directive of their package's
20475 DESCRIPTION file to build on the Stan library without incurring unnecessary
20478 The Stan project develops a probabilistic programming language that implements
20479 full or approximate Bayesian statistical inference via Markov Chain Monte
20480 Carlo or variational methods and implements (optionally penalized) maximum
20481 likelihood estimation via optimization. The Stan library includes an advanced
20482 automatic differentiation scheme, templated statistical and linear algebra
20483 functions that can handle the automatically differentiable scalar types (and
20484 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20485 package provides user-facing R functions to parse, compile, test, estimate,
20486 and analyze Stan models.")
20487 (license license:bsd-3)))
20489 (define-public r-rpf
20496 (uri (cran-uri "rpf" version))
20499 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20500 (properties `((upstream-name . "rpf")))
20501 (build-system r-build-system)
20503 `(("r-lifecycle" ,r-lifecycle)
20504 ("r-mvtnorm" ,r-mvtnorm)
20506 ("r-rcppeigen" ,r-rcppeigen)))
20508 `(("r-knitr" ,r-knitr)))
20509 (home-page "https://github.com/jpritikin/rpf")
20510 (synopsis "Response probability functions")
20512 "The purpose of this package is to factor out logic and math common to
20513 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20514 core support code suitable for more specialized IRT packages to build upon.
20515 Complete access to optimized C functions is made available with
20516 @code{R_RegisterCCallable()}.")
20517 (license license:gpl3+)))
20519 (define-public r-openmx
20526 (uri (cran-uri "OpenMx" version))
20529 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20530 (properties `((upstream-name . "OpenMx")))
20531 (build-system r-build-system)
20534 ("r-digest" ,r-digest)
20536 ("r-matrix" ,r-matrix)
20538 ("r-rcppeigen" ,r-rcppeigen)
20540 ("r-stanheaders" ,r-stanheaders)))
20541 (native-inputs `(("gfortran" ,gfortran)))
20542 (home-page "http://openmx.ssri.psu.edu")
20543 (synopsis "Extended structural equation modelling")
20545 "This package allows for the estimation of a wide variety of advanced
20546 multivariate statistical models. It consists of a library of functions and
20547 optimizers that allow you to quickly and flexibly define an SEM model and
20548 estimate parameters given observed data.")
20549 (license license:asl2.0)))
20551 (define-public r-kutils
20558 (uri (cran-uri "kutils" version))
20561 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20562 (properties `((upstream-name . "kutils")))
20563 (build-system r-build-system)
20565 `(("r-foreign" ,r-foreign)
20566 ("r-openxlsx" ,r-openxlsx)
20568 ("r-runit" ,r-runit)
20569 ("r-xtable" ,r-xtable)))
20570 (home-page "https://cran.r-project.org/package=kutils")
20571 (synopsis "Project management tools")
20573 "This package provides tools for data importation, recoding, and
20574 inspection. There are functions to create new project folders, R code
20575 templates, create uniquely named output directories, and to quickly obtain a
20576 visual summary for each variable in a data frame. The main feature here is
20577 the systematic implementation of the \"variable key\" framework for data
20578 importation and recoding.")
20579 (license license:gpl2)))
20581 (define-public r-rockchalk
20583 (name "r-rockchalk")
20584 (version "1.8.144")
20588 (uri (cran-uri "rockchalk" version))
20591 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20592 (properties `((upstream-name . "rockchalk")))
20593 (build-system r-build-system)
20595 `(("r-cardata" ,r-cardata)
20596 ("r-kutils" ,r-kutils)
20598 ("r-mass" ,r-mass)))
20599 (home-page "https://cran.r-project.org/package=rockchalk")
20600 (synopsis "Regression estimation and presentation")
20602 "This package provides a collection of functions for interpretation and
20603 presentation of regression analysis. These functions are used to produce the
20604 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20605 includes regression diagnostics, regression tables, and plots of interactions
20606 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20607 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20608 fairly comprehensive overview.")
20609 (license license:gpl3+)))
20611 (define-public r-lisreltor
20613 (name "r-lisreltor")
20618 (uri (cran-uri "lisrelToR" version))
20621 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20622 (properties `((upstream-name . "lisrelToR")))
20623 (build-system r-build-system)
20624 (home-page "https://cran.r-project.org/package=lisrelToR")
20625 (synopsis "Import output from LISREL into R")
20627 "This is an unofficial package aimed at automating the import of LISREL
20629 (license license:gpl2)))
20631 (define-public r-bdgraph
20638 (uri (cran-uri "BDgraph" version))
20641 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20642 (properties `((upstream-name . "BDgraph")))
20643 (build-system r-build-system)
20645 `(("r-igraph" ,r-igraph)))
20646 (home-page "https://www.uva.nl/profile/a.mohammadi")
20647 (synopsis "Bayesian structure learning in graphical models")
20649 "This package provides statistical tools for Bayesian structure learning
20650 in undirected graphical models for continuous, discrete, and mixed data. It
20651 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20652 on a continuous-time birth-death process.")
20653 (license license:gpl2+)))
20655 (define-public r-d3network
20657 (name "r-d3network")
20658 (version "0.5.2.1")
20662 (uri (cran-uri "d3Network" version))
20665 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20666 (properties `((upstream-name . "d3Network")))
20667 (build-system r-build-system)
20669 `(("r-plyr" ,r-plyr)
20670 ("r-rjson" ,r-rjson)
20671 ("r-whisker" ,r-whisker)))
20672 (home-page "http://christophergandrud.github.io/d3Network/")
20673 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20675 "This package is intended to make it easy to create D3 JavaScript
20676 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20677 (license license:gpl3+)))
20679 (define-public r-qgraph
20686 (uri (cran-uri "qgraph" version))
20689 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20690 (properties `((upstream-name . "qgraph")))
20691 (build-system r-build-system)
20693 `(("r-abind" ,r-abind)
20694 ("r-bdgraph" ,r-bdgraph)
20695 ("r-colorspace" ,r-colorspace)
20696 ("r-corpcor" ,r-corpcor)
20697 ("r-d3network" ,r-d3network)
20698 ("r-dplyr" ,r-dplyr)
20699 ("r-fdrtool" ,r-fdrtool)
20700 ("r-ggplot2" ,r-ggplot2)
20701 ("r-ggraph" ,r-ggraph)
20702 ("r-glasso" ,r-glasso)
20703 ("r-gtools" ,r-gtools)
20704 ("r-hmisc" ,r-hmisc)
20706 ("r-igraph" ,r-igraph)
20708 ("r-lavaan" ,r-lavaan)
20709 ("r-matrix" ,r-matrix)
20710 ("r-pbapply" ,r-pbapply)
20713 ("r-psych" ,r-psych)
20715 ("r-reshape2" ,r-reshape2)
20716 ("r-tidygraph" ,r-tidygraph)))
20717 (home-page "http://sachaepskamp.com/qgraph/")
20718 (synopsis "Weighted network visualization and analysis")
20720 "This package implements tools for weighted network visualization and
20721 analysis, as well as Gaussian graphical model computation. It contains graph
20722 plotting methods, and tools for psychometric data visualization and graphical
20723 model estimation. See Epskamp et al. (2012)
20724 @url{doi:10.18637/jss.v048.i04}.")
20725 (license license:gpl2)))
20727 (define-public r-semplot
20734 (uri (cran-uri "semPlot" version))
20737 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20738 (properties `((upstream-name . "semPlot")))
20739 (build-system r-build-system)
20741 `(("r-colorspace" ,r-colorspace)
20742 ("r-corpcor" ,r-corpcor)
20743 ("r-igraph" ,r-igraph)
20744 ("r-lavaan" ,r-lavaan)
20745 ("r-lisreltor" ,r-lisreltor)
20746 ("r-openmx" ,r-openmx)
20748 ("r-qgraph" ,r-qgraph)
20749 ("r-regsem" ,r-regsem)
20750 ("r-rockchalk" ,r-rockchalk)
20753 (home-page "https://github.com/SachaEpskamp/semPlot")
20754 (synopsis "Unified visualizations of structural equation models")
20756 "Structural equation modeling (SEM) has a long history of representing
20757 models graphically as path diagrams. The semPlot package for R fills the gap
20758 between advanced, but time-consuming, graphical software and the limited
20759 graphics produced automatically by SEM software. In addition, semPlot offers
20760 more functionality than drawing path diagrams: it can act as a common ground
20761 for importing SEM results into R. Any result usable as input to semPlot can
20762 also be represented in any of the three popular SEM frame-works, as well as
20763 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20764 (license license:gpl2)))
20766 (define-public r-cdm
20773 (uri (cran-uri "CDM" version))
20776 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20777 (properties `((upstream-name . "CDM")))
20778 (build-system r-build-system)
20780 `(("r-mvtnorm" ,r-mvtnorm)
20781 ("r-polycor" ,r-polycor)
20783 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20785 "https://github.com/alexanderrobitzsch/CDM")
20786 (synopsis "Cognitive diagnosis modeling")
20788 "This package provides functions for cognitive diagnosis modeling and
20789 multidimensional item response modeling for dichotomous and polytomous item
20790 responses. It enables the estimation of the DINA and DINO model, the multiple
20791 group (polytomous) GDINA model, the multiple choice DINA model, the general
20792 diagnostic model (GDM), the structured latent class model (SLCA), and
20793 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20794 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20795 estimation and the package structure. For tutorials on how to use the CDM
20796 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20797 well as Ravand and Robitzsch (2015).")
20798 (license license:gpl2+)))
20800 (define-public r-tam
20807 (uri (cran-uri "TAM" version))
20810 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20811 (properties `((upstream-name . "TAM")))
20812 (build-system r-build-system)
20816 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20817 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20818 (synopsis "Test analysis modules")
20820 "This package includes tools for marginal maximum likelihood estimation
20821 and joint maximum likelihood estimation for unidimensional and
20822 multidimensional item response models. The package functionality covers the
20823 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20824 multi-faceted Rasch model, nominal item response model, structured latent
20825 class model, mixture distribution IRT models, and located latent class models.
20826 Latent regression models and plausible value imputation are also supported.")
20827 (license license:gpl2+)))
20829 (define-public r-erm
20836 (uri (cran-uri "eRm" version))
20839 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20840 (properties `((upstream-name . "eRm")))
20841 (build-system r-build-system)
20843 `(("r-colorspace" ,r-colorspace)
20844 ("r-lattice" ,r-lattice)
20846 ("r-matrix" ,r-matrix)
20847 ("r-psych" ,r-psych)))
20848 (native-inputs `(("gfortran" ,gfortran)))
20849 (home-page "https://cran.r-project.org/package=eRm")
20850 (synopsis "Extended Rasch modeling")
20852 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20853 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20854 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20855 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20856 data matrix. Additional features are the ML estimation of the person
20857 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20858 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20859 infit and outfit measures, ICC and other plots, automated stepwise item
20860 elimination, and a simulation module for various binary data matrices.")
20861 (license license:gpl3)))
20863 (define-public r-irtoys
20870 (uri (cran-uri "irtoys" version))
20873 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20874 (properties `((upstream-name . "irtoys")))
20875 (build-system r-build-system)
20879 (home-page "https://cran.r-project.org/package=irtoys")
20880 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20882 "This package provides a collection of functions useful in learning and
20883 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20884 programs. It provides basic CTT analysis, a simple common interface to the
20885 estimation of item parameters in IRT models for binary responses with three
20886 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20887 EAP, WLE, plausible values), item and person fit statistics, scaling
20888 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20889 array of parametric and non-parametric (kernel) plots. It estimates and plots
20890 Haberman's interaction model when all items are dichotomously scored.")
20891 (license license:gpl2+)))
20893 (define-public r-iheatmapr
20895 (name "r-iheatmapr")
20900 (uri (cran-uri "iheatmapr" version))
20903 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20904 (properties `((upstream-name . "iheatmapr")))
20905 (build-system r-build-system)
20907 `(("r-fastcluster" ,r-fastcluster)
20908 ("r-ggdendro" ,r-ggdendro)
20909 ("r-htmlwidgets" ,r-htmlwidgets)
20910 ("r-jsonlite" ,r-jsonlite)
20911 ("r-knitr" ,r-knitr)
20912 ("r-magrittr" ,r-magrittr)
20914 ("r-rcolorbrewer" ,r-rcolorbrewer)
20915 ("r-s4vectors" ,r-s4vectors)
20916 ("r-scales" ,r-scales)))
20917 (home-page "https://docs.ropensci.org/iheatmapr")
20918 (synopsis "Interactive, Complex Heatmaps")
20920 "iheatmapr is an R package for building complex, interactive heatmaps
20921 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20922 subplots along the rows or columns of the main heatmap add more information
20923 about each row or column. For example, a one column additional heatmap may
20924 indicate what group a particular row or column belongs to. Complex heatmaps
20925 may also include multiple side by side heatmaps which show different types of
20926 data for the same conditions. Interactivity can improve complex heatmaps by
20927 providing tooltips with information about each cell and enabling zooming into
20928 interesting features. iheatmapr uses the plotly library for interactivity.")
20929 (license license:expat)))
20931 (define-public r-packrat
20938 (uri (cran-uri "packrat" version))
20941 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20942 (properties `((upstream-name . "packrat")))
20943 (build-system r-build-system)
20944 (home-page "https://github.com/rstudio/packrat/")
20945 (synopsis "Dependency management R projects")
20947 "This package provides a dependency manager for R projects that allows
20948 you to manage the R packages your project depends on in an isolated, portable,
20949 and reproducible way.")
20950 (license license:gpl2)))
20952 (define-public r-rsconnect
20954 (name "r-rsconnect")
20959 (uri (cran-uri "rsconnect" version))
20962 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20963 (properties `((upstream-name . "rsconnect")))
20964 (build-system r-build-system)
20966 `(("r-curl" ,r-curl)
20967 ("r-digest" ,r-digest)
20968 ("r-jsonlite" ,r-jsonlite)
20969 ("r-openssl" ,r-openssl)
20970 ("r-packrat" ,r-packrat)
20971 ("r-rstudioapi" ,r-rstudioapi)
20972 ("r-yaml" ,r-yaml)))
20973 (home-page "https://github.com/rstudio/rsconnect")
20974 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20976 "This package provides a programmatic deployment interface for RPubs,
20977 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20978 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20979 (license license:gpl2)))
20981 ;; This package includes minified JavaScript files. When upgrading please
20982 ;; check that there are no new minified JavaScript files.
20983 (define-public r-dygraphs
20985 (name "r-dygraphs")
20986 (version "1.1.1.6")
20990 (uri (cran-uri "dygraphs" version))
20993 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20994 (properties `((upstream-name . "dygraphs")))
20995 (build-system r-build-system)
20997 `(#:modules ((guix build utils)
20998 (guix build r-build-system)
21002 (modify-phases %standard-phases
21003 (add-after 'unpack 'process-javascript
21004 (lambda* (#:key inputs #:allow-other-keys)
21005 (with-directory-excursion "inst/htmlwidgets/lib/"
21009 `(("dygraphs/dygraph-combined-dev.js"
21010 "dygraph-combined.js")
21011 (,(assoc-ref inputs "js-jquery")
21012 "jquery/jquery.min.js")
21013 (,(assoc-ref inputs "js-fquarter")
21014 "fquarter/moment-fquarter.min.js"))))
21015 (lambda (sources targets)
21016 (for-each (lambda (source target)
21017 (format #t "Processing ~a --> ~a~%"
21019 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21020 (call-with-output-file target
21022 (dump-port minified port)))))
21023 sources targets))))
21026 `(("uglify-js" ,uglify-js)
21027 ;; They actually use version 1.11.1, but this more recent version
21028 ;; should be just fine.
21032 (uri "https://code.jquery.com/jquery-1.12.4.js")
21035 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21039 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21040 "moment-fquarter/1.0.1/moment-fquarter.js"))
21043 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21045 `(("r-htmltools" ,r-htmltools)
21046 ("r-htmlwidgets" ,r-htmlwidgets)
21047 ("r-magrittr" ,r-magrittr)
21050 (home-page "https://github.com/rstudio/dygraphs")
21051 (synopsis "Interface to Dygraphs interactive time series charting library")
21053 "This package provides an R interface to the dygraphs JavaScript charting
21054 library (a copy of which is included in the package). It provides rich
21055 facilities for charting time-series data in R, including highly configurable
21056 series- and axis-display and interactive features like zoom/pan and
21057 series/point highlighting.")
21058 (license license:expat)))
21060 (define-public r-shinystan
21062 (name "r-shinystan")
21067 (uri (cran-uri "shinystan" version))
21070 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21071 (properties `((upstream-name . "shinystan")))
21072 (build-system r-build-system)
21074 `(("r-bayesplot" ,r-bayesplot)
21075 ("r-colourpicker" ,r-colourpicker)
21077 ("r-dygraphs" ,r-dygraphs)
21078 ("r-ggplot2" ,r-ggplot2)
21079 ("r-gridextra" ,r-gridextra)
21080 ("r-gtools" ,r-gtools)
21081 ("r-markdown" ,r-markdown)
21082 ("r-reshape2" ,r-reshape2)
21083 ("r-rsconnect" ,r-rsconnect)
21084 ("r-rstan" ,r-rstan)
21085 ("r-shiny" ,r-shiny)
21086 ("r-shinyjs" ,r-shinyjs)
21087 ("r-shinythemes" ,r-shinythemes)
21088 ("r-threejs" ,r-threejs)
21089 ("r-xtable" ,r-xtable)
21091 (home-page "https://mc-stan.org/")
21092 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21094 "This package provides a graphical user interface for interactive
21095 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21096 for analyzing a posterior sample. The interface is powered by the Shiny web
21097 application framework and works with the output of MCMC programs written in
21098 any programming language (and has extended functionality for Stan models fit
21099 using the @code{rstan} and @code{rstanarm} packages).")
21100 (license license:gpl3+)))
21102 (define-public r-rstantools
21104 (name "r-rstantools")
21109 (uri (cran-uri "rstantools" version))
21112 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
21113 (properties `((upstream-name . "rstantools")))
21114 (build-system r-build-system)
21115 (inputs `(("pandoc" ,ghc-pandoc)))
21117 `(("r-desc" ,r-desc)
21118 ("r-rcpp" ,r-rcpp)))
21119 (home-page "https://mc-stan.org/rstantools/")
21120 (synopsis "Tools for developing R packages interfacing with Stan")
21122 "This package provides various tools for developers of R packages
21123 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21124 up the required package structure, S3 generics and default methods to unify
21125 function naming across Stan-based R packages, and vignettes with
21126 recommendations for developers.")
21127 (license license:gpl3+)))
21129 (define-public r-loo
21136 (uri (cran-uri "loo" version))
21139 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
21140 (properties `((upstream-name . "loo")))
21141 (build-system r-build-system)
21143 `(("pandoc" ,ghc-pandoc)
21144 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21146 `(("r-checkmate" ,r-checkmate)
21147 ("r-matrixstats" ,r-matrixstats)))
21148 (home-page "https://mc-stan.org/loo/")
21149 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21151 "This package provides an implementation of efficient approximate
21152 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21153 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21154 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21155 procedure for regularizing importance weights. As a byproduct of the
21156 calculations, we also obtain approximate standard errors for estimated
21157 predictive errors and for the comparison of predictive errors between models.
21158 The package also provides methods for using stacking and other model weighting
21159 techniques to average Bayesian predictive distributions.")
21160 (license license:gpl3+)))
21162 (define-public r-rstan
21169 (uri (cran-uri "rstan" version))
21172 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
21173 (properties `((upstream-name . "rstan")))
21174 (build-system r-build-system)
21177 (modify-phases %standard-phases
21178 (add-before 'install 'set-timezone
21179 ;; This package is picky about timezones.
21180 (lambda* (#:key inputs #:allow-other-keys)
21181 (setenv "TZ" "UTC+1")
21183 (string-append (assoc-ref inputs "tzdata")
21184 "/share/zoneinfo"))
21187 `(("tzdata" ,tzdata-for-tests)
21188 ("pandoc" ,ghc-pandoc)))
21191 ("r-ggplot2" ,r-ggplot2)
21192 ("r-gridextra" ,r-gridextra)
21193 ("r-inline" ,r-inline)
21195 ("r-pkgbuild" ,r-pkgbuild)
21197 ("r-rcppeigen" ,r-rcppeigen)
21198 ("r-stanheaders" ,r-stanheaders)))
21199 (home-page "https://discourse.mc-stan.org/")
21200 (synopsis "R interface to Stan")
21202 "User-facing R functions are provided to parse, compile, test, estimate,
21203 and analyze Stan models by accessing the header-only Stan library provided by
21204 the StanHeaders package. The Stan project develops a probabilistic
21205 programming language that implements full Bayesian statistical inference via
21206 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21207 approximation, and (optionally penalized) maximum likelihood estimation via
21208 optimization. In all three cases, automatic differentiation is used to
21209 quickly and accurately evaluate gradients without burdening the user with the
21210 need to derive the partial derivatives.")
21211 (license license:gpl3+)))
21213 (define-public r-rstanarm
21215 (name "r-rstanarm")
21220 (uri (cran-uri "rstanarm" version))
21223 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
21224 (properties `((upstream-name . "rstanarm")))
21225 (build-system r-build-system)
21227 `(("pandoc" ,ghc-pandoc)
21228 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21230 `(("r-bayesplot" ,r-bayesplot)
21232 ("r-ggplot2" ,r-ggplot2)
21235 ("r-matrix" ,r-matrix)
21238 ("r-rcppeigen" ,r-rcppeigen)
21239 ("r-rcppparallel" ,r-rcppparallel)
21240 ("r-rstan" ,r-rstan)
21241 ("r-rstantools" ,r-rstantools)
21242 ("r-shinystan" ,r-shinystan)
21243 ("r-stanheaders" ,r-stanheaders)
21244 ("r-survival" ,r-survival)))
21245 (home-page "https://mc-stan.org/rstanarm/")
21246 (synopsis "Bayesian applied regression modeling via Stan")
21248 "This package estimates previously compiled regression models using the
21249 @code{rstan} package, which provides the R interface to the Stan C++ library
21250 for Bayesian estimation. Users specify models via the customary R syntax with
21251 a formula and @code{data.frame} plus some additional arguments for priors.")
21252 (license license:gpl3+)))
21254 (define-public r-kendall
21261 (uri (cran-uri "Kendall" version))
21264 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21265 (properties `((upstream-name . "Kendall")))
21266 (build-system r-build-system)
21268 `(("r-boot" ,r-boot)))
21270 `(("gfortran" ,gfortran)))
21271 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21272 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21274 "This package computes the Kendall rank correlation and Mann-Kendall
21276 (license license:gpl2+)))
21278 (define-public r-zyp
21281 (version "0.10-1.1")
21285 (uri (cran-uri "zyp" version))
21288 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21289 (properties `((upstream-name . "zyp")))
21290 (build-system r-build-system)
21292 `(("r-kendall" ,r-kendall)))
21293 (home-page "https://cran.r-project.org/web/packages/zyp/")
21294 (synopsis "Zhang + Yue-Pilon Trends Package")
21296 "This package contains an efficient implementation of Sen's slope
21297 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21298 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21300 (license license:lgpl2.1)))
21302 (define-public r-rlinsolve
21304 (name "r-rlinsolve")
21309 (uri (cran-uri "Rlinsolve" version))
21312 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21313 (properties `((upstream-name . "Rlinsolve")))
21314 (build-system r-build-system)
21316 `(("r-matrix" ,r-matrix)
21318 ("r-rcpparmadillo" ,r-rcpparmadillo)
21319 ("r-rdpack" ,r-rdpack)))
21320 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21321 (synopsis "Iterative solvers for (sparse) linear system of equations")
21323 "Solving a system of linear equations is one of the most fundamental
21324 computational problems for many fields of mathematical studies, such as
21325 regression problems from statistics or numerical partial differential
21326 equations. This package provides basic stationary iterative solvers such as
21327 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21328 Nonstationary, also known as Krylov subspace methods are also provided.
21329 Sparse matrix computation is also supported in that solving large and sparse
21330 linear systems can be manageable using the @code{Matrix} package along with
21331 @code{RcppArmadillo}.")
21332 (license license:gpl3+)))
21334 (define-public r-zvcv
21341 (uri (cran-uri "ZVCV" version))
21344 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
21345 (properties `((upstream-name . "ZVCV")))
21346 (build-system r-build-system)
21348 `(("r-abind" ,r-abind)
21349 ("r-glmnet" ,r-glmnet)
21350 ("r-mvtnorm" ,r-mvtnorm)
21351 ("r-partitions" ,r-partitions)
21353 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21354 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21355 (synopsis "Zero-Variance Control Variates")
21357 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21358 to reduce the variance of Monte Carlo estimators of expectations using the
21359 derivatives of the log target. Once the derivatives are available, the only
21360 additional computational effort is in solving a linear regression problem.
21361 This method has been extended to higher dimensions using regularisation. This
21362 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21363 samples, derivatives and function evaluations are available. Additional
21364 functions for applying ZV-CV to two estimators for the normalising constant of
21365 the posterior distribution in Bayesian statistics are also supplied.")
21366 (license license:gpl2+)))
21368 (define-public r-ztype
21375 (uri (cran-uri "ztype" version))
21378 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21379 (properties `((upstream-name . "ztype")))
21380 (build-system r-build-system)
21382 `(("r-assertthat" ,r-assertthat)
21383 ("r-dplyr" ,r-dplyr)
21384 ("r-ggplot2" ,r-ggplot2)
21385 ("r-lubridate" ,r-lubridate)
21386 ("r-magrittr" ,r-magrittr)
21387 ("r-rvest" ,r-rvest)
21388 ("r-stringr" ,r-stringr)))
21389 (home-page "https://cran.r-project.org/web/packages/ztype/")
21390 (synopsis "Run a Ztype game loaded with R functions")
21392 "How fast can you type R functions on your keyboard? Find out by running
21393 a @code{zty.pe} game: export R functions as instructions to type to destroy
21394 opponents' vessels.")
21395 (license license:gpl3)))
21397 (define-public r-zseq
21404 (uri (cran-uri "Zseq" version))
21407 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21408 (properties `((upstream-name . "Zseq")))
21409 (build-system r-build-system)
21411 `(("r-gmp" ,r-gmp)))
21412 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21413 (synopsis "Integer sequence generator")
21415 "This package generates well-known integer sequences. The @code{gmp}
21416 package is adopted for computing with arbitrarily large numbers. Every
21417 function has a hyperlink to its corresponding item in the @dfn{On-Line
21418 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21419 (license license:gpl3+)))
21421 (define-public r-isoband
21428 (uri (cran-uri "isoband" version))
21431 "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
21432 (properties `((upstream-name . "isoband")))
21433 (build-system r-build-system)
21435 `(("r-rcpp" ,r-rcpp)
21436 ("r-testthat" ,r-testthat)))
21438 `(("r-knitr" ,r-knitr)))
21439 (home-page "https://github.com/wilkelab/isoband")
21440 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21442 "This package provides a fast C++ implementation to generate contour
21443 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21444 containing elevation data.")
21445 (license license:expat)))
21447 (define-public r-ppcor
21454 (uri (cran-uri "ppcor" version))
21457 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21458 (properties `((upstream-name . "ppcor")))
21459 (build-system r-build-system)
21461 `(("r-mass" ,r-mass)))
21462 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21463 (synopsis "Partial and semi-partial correlation")
21465 "This package provides users not only with a function to readily
21466 calculate the higher-order partial and semi-partial correlations but also with
21467 statistics and p-values of the correlation coefficients.")
21468 (license license:gpl2)))
21470 (define-public r-hrbrthemes
21472 (name "r-hrbrthemes")
21477 (uri (cran-uri "hrbrthemes" version))
21479 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21480 (properties `((upstream-name . "hrbrthemes")))
21481 (build-system r-build-system)
21483 `(("r-extrafont" ,r-extrafont)
21484 ("r-gdtools" ,r-gdtools)
21485 ("r-ggplot2" ,r-ggplot2)
21486 ("r-htmltools" ,r-htmltools)
21487 ("r-knitr" ,r-knitr)
21488 ("r-magrittr" ,r-magrittr)
21489 ("r-rmarkdown" ,r-rmarkdown)
21490 ("r-scales" ,r-scales)))
21492 `(("r-knitr" ,r-knitr)))
21493 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21494 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21496 "This package provides a compilation of extra @code{ggplot2} themes,
21497 scales and utilities, including a spell check function for plot label fields
21498 and an overall emphasis on typography.")
21499 (license license:expat)))
21501 (define-public r-crochet
21508 (uri (cran-uri "crochet" version))
21511 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21512 (build-system r-build-system)
21514 `(("r-knitr" ,r-knitr)))
21515 (home-page "https://github.com/agrueneberg/crochet")
21516 (synopsis "Implementation Helper for Matrix-Like Types")
21518 "Functions to help implement the extraction / subsetting / indexing
21519 function @code{[} and replacement function @code{[<-} of custom matrix-like
21520 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21521 as possible (with tests to prove it).")
21522 (license license:expat)))
21524 (define-public r-boa
21527 (version "1.1.8-2")
21531 (uri (cran-uri "boa" version))
21534 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21535 (properties `((upstream-name . "boa")))
21536 (build-system r-build-system)
21537 (home-page "http://www.jstatsoft.org/v21/i11")
21538 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21540 "This package provides a menu-driven program and library of functions for
21541 carrying out convergence diagnostics and statistical and graphical analysis of
21542 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21543 (license license:gpl2+)))
21545 (define-public r-httpcode
21547 (name "r-httpcode")
21551 (uri (cran-uri "httpcode" version))
21554 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21555 (build-system r-build-system)
21556 (home-page "https://github.com/sckott/httpcode")
21557 (synopsis "HTTP status code helper")
21558 (description "@code{httpcode} provides functionality for finding and
21559 explaining the meaning of @code{HTTP} status codes. Functions are included for
21560 searching for codes by full or partial number, by message, and to get
21561 appropriate dog and cat images for many status codes.")
21562 (license license:expat)))
21564 (define-public r-latex2exp
21566 (name "r-latex2exp")
21570 (uri (cran-uri "latex2exp" version))
21573 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21574 (build-system r-build-system)
21576 `(("r-stringr" ,r-stringr)
21577 ("r-magrittr", r-magrittr)))
21578 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21579 (synopsis "Use LaTeX expressions in plots")
21580 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21581 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21582 rendered as text, axis labels, etc. throughout R's plotting system.")
21583 (license license:expat)))
21585 (define-public r-oai
21591 (uri (cran-uri "oai" version))
21594 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21595 (build-system r-build-system)
21597 `(("r-xml2" ,r-xml2)
21600 ("r-stringr" ,r-stringr)
21601 ("r-tibble" ,r-tibble)))
21602 (home-page "https://github.com/ropensci/oai/")
21603 (synopsis "General purpose OAI-PMH services client")
21604 (description "@code{oai} provides a general purpose client to work with
21605 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21606 service. Functions are provided to work with the OAI-PMH verbs:
21607 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21608 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21609 (license license:expat)))
21611 (define-public r-argon2
21618 (uri (cran-uri "argon2" version))
21621 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21622 (properties `((upstream-name . "argon2")))
21623 (build-system r-build-system)
21624 (home-page "https://github.com/wrathematics/argon2")
21625 (synopsis "Secure password hashing based on the argon2 algorithm")
21627 "This package provides utilities for secure password hashing via the
21628 argon2 algorithm.")
21629 (license license:bsd-2)))
21631 (define-public r-getpass
21638 (uri (cran-uri "getPass" version))
21641 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21642 (properties `((upstream-name . "getPass")))
21643 (build-system r-build-system)
21645 `(("r-rstudioapi" ,r-rstudioapi)))
21646 (home-page "https://github.com/wrathematics/getPass")
21647 (synopsis "Masked user input")
21649 "This package provides a micro-package for reading \"passwords\", i.e.
21650 reading user input with masking, so that the input is not displayed as it is
21651 typed. Currently, RStudio, the command line (every OS), and any platform
21652 where tcltk is present are supported.")
21653 (license license:bsd-2)))
21655 (define-public r-remoter
21662 (uri (cran-uri "remoter" version))
21665 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21666 (properties `((upstream-name . "remoter")))
21667 (build-system r-build-system)
21669 `(("r-argon2" ,r-argon2)
21670 ("r-getpass" ,r-getpass)
21671 ("r-pbdzmq" ,r-pbdzmq)
21673 (home-page "https://github.com/RBigData/remoter")
21674 (synopsis "Control a remote R session from a local one")
21676 "This package provides a set of utilities for client/server computing
21677 with R, controlling a remote R session (the server) from a local one (the
21679 (license license:bsd-2)))
21681 (define-public r-asd
21688 (uri (cran-uri "asd" version))
21691 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21692 (properties `((upstream-name . "asd")))
21693 (build-system r-build-system)
21695 `(("r-mvtnorm" ,r-mvtnorm)))
21696 (home-page "https://cran.r-project.org/web/packages/asd")
21697 (synopsis "Simulations for Adaptive Seamless Designs")
21699 "This package provdes means to run simulations for adaptive seamless
21700 designs with and without early outcomes for treatment selection and
21701 subpopulation type designs.")
21702 (license license:gpl3)))
21704 (define-public r-nbconvertr
21706 (name "r-nbconvertr")
21711 (uri (cran-uri "nbconvertR" version))
21714 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21715 (properties `((upstream-name . "nbconvertR")))
21716 (build-system r-build-system)
21718 `(("jupyter" ,python-nbconvert)
21719 ("pandoc" ,ghc-pandoc)))
21720 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21721 (synopsis "Vignette engine wrapping Jupyter notebooks")
21723 "This package calls the Jupyter script @code{nbconvert} to create
21724 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21725 containing rich text, code, and its output. Code cells can be edited and
21726 evaluated interactively.")
21727 (license license:gpl3)))
21729 (define-public r-bridgesampling
21731 (name "r-bridgesampling")
21736 (uri (cran-uri "bridgesampling" version))
21739 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21741 `((upstream-name . "bridgesampling")))
21742 (build-system r-build-system)
21744 `(("r-brobdingnag" ,r-brobdingnag)
21746 ("r-matrix" ,r-matrix)
21747 ("r-mvtnorm" ,r-mvtnorm)
21748 ("r-scales" ,r-scales)
21749 ("r-stringr" ,r-stringr)))
21751 `(("r-knitr" ,r-knitr)))
21752 (home-page "https://github.com/quentingronau/bridgesampling")
21753 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21755 "This package provides functions for estimating marginal likelihoods,
21756 Bayes factors, posterior model probabilities, and normalizing constants in
21757 general, via different versions of bridge sampling.")
21758 (license license:gpl2+)))
21760 (define-public r-tea
21767 (uri (cran-uri "tea" version))
21770 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21772 `((upstream-name . "tea")))
21773 (build-system r-build-system)
21775 `(("r-matrix" ,r-matrix)))
21776 (home-page "https://cran.r-project.org/web/packages/tea/")
21777 (synopsis "Threshold estimation approaches")
21779 "This package provides different approaches for selecting the threshold
21780 in generalized Pareto distributions. Most of them are based on minimizing the
21781 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21782 Others are heuristically motivated by searching for stable sample paths, i.e.
21783 a nearly constant region of the tail index estimator with respect to k, which
21784 is the number of data in the tail. The third class is motivated by graphical
21785 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21786 is also implemented here.")
21787 (license license:gpl3)))
21789 (define-public r-awsmethods
21791 (name "r-awsmethods")
21796 (uri (cran-uri "awsMethods" version))
21799 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21801 `((upstream-name . "awsMethods")))
21802 (build-system r-build-system)
21803 (home-page "http://www.wias-berlin.de/software/imaging/")
21804 (synopsis "Class and methods definitions")
21806 "This package defines the generic method @code{extract} and provides
21807 @code{openMP} support as needed in several packages like
21808 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21809 (license license:gpl2+)))
21811 (define-public r-aws
21818 (uri (cran-uri "aws" version))
21821 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21823 `((upstream-name . "aws")))
21824 (build-system r-build-system)
21826 `(("r-awsmethods" ,r-awsmethods)
21829 `(("gfortran" ,gfortran)))
21830 (home-page "https://cran.r-project.org/web/packages/aws/")
21831 (synopsis "Adaptive weights smoothing")
21833 "This package provides a collection of R-functions implementing adaptive
21834 smoothing procedures in 1D, 2D and 3D. This includes the
21835 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21836 Confidence Intervals} (ICI), variational approaches, and a non-local means
21838 (license license:gpl2+)))
21840 (define-public r-sgloptim
21842 (name "r-sgloptim")
21847 (uri (cran-uri "sglOptim" version))
21850 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21852 `((upstream-name . "sglOptim")))
21853 (build-system r-build-system)
21856 ("r-doparallel" ,r-doparallel)
21857 ("r-foreach" ,r-foreach)
21858 ("r-matrix" ,r-matrix)
21860 ("r-rcpparmadillo" ,r-rcpparmadillo)
21861 ("r-rcppprogress" ,r-rcppprogress)))
21863 `(("r-knitr" ,r-knitr)))
21864 (home-page "https://github.com/nielsrhansen/sglOptim")
21865 (synopsis "Generic sparse group Lasso solver")
21867 "This package provides a fast generic solver for sparse group lasso
21868 optimization problems. The loss (objective) function must be defined in a C++
21869 module. The optimization problem is solved using a coordinate gradient
21870 descent algorithm. Convergence of the algorithm is established and the
21871 algorithm is applicable to a broad class of loss functions. Use of parallel
21872 computing for cross validation and subsampling is supported through the
21873 @code{foreach} and @code{doParallel} packages.")
21874 (license license:gpl2+)))
21876 (define-public r-grouped
21883 (uri (cran-uri "grouped" version))
21886 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21888 `((upstream-name . "grouped")))
21889 (build-system r-build-system)
21891 `(("r-mass" ,r-mass)))
21892 (home-page "https://cran.r-project.org/web/packages/grouped/")
21893 (synopsis "Regression analysis of grouped and coarse data")
21895 "This package provides regression models for grouped and coarse data,
21896 under the coarsened at random assumption.")
21897 (license license:gpl2+)))
21899 (define-public r-stam
21906 (uri (cran-uri "stam" version))
21909 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21911 `((upstream-name . "stam")))
21912 (build-system r-build-system)
21916 (home-page "https://cran.r-project.org/web/packages/stam")
21917 (synopsis "Spatio-temporal analysis and modelling")
21919 "This package provides various methods to conduct Spatio-Temporal
21920 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21921 Inferred Spatio-Temporal Modelling.")
21922 (license license:gpl2+)))
21924 (define-public r-dcv
21931 (uri (cran-uri "dcv" version))
21934 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21936 `((upstream-name . "dcv")))
21937 (build-system r-build-system)
21939 `(("r-lmtest" ,r-lmtest)))
21940 (home-page "https://cran.r-project.org/web/packages/dcv/")
21941 (synopsis "Conventional cross-validation statistics for climate-growth model")
21943 "This package performs several conventional cross-validation statistical
21944 methods for climate-growth model in the climate reconstruction from tree
21945 rings, including Sign Test statistic, Reduction of Error statistic, Product
21946 Mean Test, Durbin-Watson statistic etc.")
21947 (license license:gpl2)))
21949 (define-public r-rcdd
21956 (uri (cran-uri "rcdd" version))
21959 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21961 `((upstream-name . "rcdd")))
21962 (build-system r-build-system)
21965 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
21966 (synopsis "Computational geometry")
21968 "This package converts back and forth between two representations of a
21969 convex polytope: as solution of a set of linear equalities and inequalities
21970 and as convex hull of set of points and rays. Also does linear programming
21971 and redundant generator elimination. All functions can use exact
21972 infinite-precision rational arithmetic.")
21973 (license license:gpl2)))
21975 (define-public r-rxnat
21982 (uri (cran-uri "Rxnat" version))
21985 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
21987 `((upstream-name . "Rxnat")))
21988 (build-system r-build-system)
21990 `(("r-httr" ,r-httr)
21991 ("r-rcurl" ,r-rcurl)))
21993 `(("r-knitr" ,r-knitr)))
21994 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
21995 (synopsis "Queries and extracts images from neuroimaging datasets")
21997 "This package allows communication with the Extensible Neuroimaging
21998 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22000 (license license:gpl2)))
22002 (define-public r-rserve
22009 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22010 version ".tar.gz"))
22013 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22014 (build-system r-build-system)
22016 `(("r-checkmate" ,r-checkmate)
22018 ("r-jsonlite" ,r-jsonlite)
22019 ("r-knitr" ,r-knitr)
22022 ("r-uuid" ,r-uuid)))
22024 `(("openssl" ,openssl)
22026 (home-page "https://github.com/s-u/Rserve")
22028 "Server providing access to R from many languages and systems")
22030 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22031 binary requests to be sent to R. Every connection has a separate workspace
22032 and working directory. Client-side implementations are available for popular
22033 languages such as C/C++ and Java, allowing any application to use facilities
22034 of R without the need of linking to R code. Rserve supports remote
22035 connection, user authentication and file transfer. A simple R client is
22036 included in this package as well.")
22037 (license license:gpl2)))
22039 (define-public r-brms
22046 (uri (cran-uri "brms" version))
22049 "0vdncdawxawi16f326qrgy9jjjipmqdjxh741y9p7xdzd4fwaxx3"))))
22050 (properties `((upstream-name . "brms")))
22051 (build-system r-build-system)
22053 `(("r-abind" ,r-abind)
22054 ("r-backports" ,r-backports)
22055 ("r-bayesplot" ,r-bayesplot)
22056 ("r-bridgesampling" ,r-bridgesampling)
22058 ("r-future" ,r-future)
22059 ("r-ggplot2" ,r-ggplot2)
22062 ("r-matrix" ,r-matrix)
22063 ("r-matrixstats" ,r-matrixstats)
22065 ("r-nleqslv" ,r-nleqslv)
22068 ("r-rstan" ,r-rstan)
22069 ("r-rstantools" ,r-rstantools)
22070 ("r-shinystan" ,r-shinystan)))
22071 (native-inputs `(("r-knitr" ,r-knitr)))
22073 "https://github.com/paul-buerkner/brms")
22075 "Bayesian Regression Models using 'Stan'")
22077 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22078 using 'Stan' for full Bayesian inference. A wide range of distributions and
22079 link functions are supported, allowing users to fit -- among others -- linear,
22080 robust linear, count data, survival, response times, ordinal, zero-inflated,
22081 hurdle, and even self-defined mixture models all in a multilevel context.
22082 Further modeling options include non-linear and smooth terms, auto-correlation
22083 structures, censored data, meta-analytic standard errors, and quite a few
22084 more. In addition, all parameters of the response distribution can be
22085 predicted in order to perform distributional regression. Prior specifications
22086 are flexible and explicitly encourage users to apply prior distributions that
22087 actually reflect their beliefs. Model fit can easily be assessed and compared
22088 with posterior predictive checks and leave-one-out cross-validation.")
22089 (license license:gpl2)))
22091 (define-public r-mstate
22098 (uri (cran-uri "mstate" version))
22101 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22102 (properties `((upstream-name . "mstate")))
22103 (build-system r-build-system)
22105 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22106 ("r-survival" ,r-survival)))
22108 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22110 "Data Preparation, Estimation and Prediction in Multi-State Models")
22112 "Contains functions for data preparation, descriptives, hazard estimation
22113 and prediction with Aalen-Johansen or simulation in competing risks and
22114 multi-state models.")
22115 (license license:gpl2+)))
22117 (define-public r-scatterpie
22119 (name "r-scatterpie")
22124 (uri (cran-uri "scatterpie" version))
22127 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22128 (properties `((upstream-name . "scatterpie")))
22129 (build-system r-build-system)
22131 `(("r-ggforce" ,r-ggforce)
22132 ("r-ggplot2" ,r-ggplot2)
22133 ("r-rlang" ,r-rlang)
22134 ("r-rvcheck" ,r-rvcheck)
22135 ("r-tidyr" ,r-tidyr)))
22137 `(("r-knitr" ,r-knitr)))
22138 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22139 (synopsis "Scatter pie plot")
22141 "This package creates scatterpie plots, especially useful for plotting
22143 (license license:artistic2.0)))