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 "0xdljralgwyivdhx2a7kqf3yv4ijl4rdrz2p7p59lj2x5d2qyanf"))))
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 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
860 (build-system r-build-system)
862 `(("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 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
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)))
915 (home-page "http://gforge.se/packages/")
916 (synopsis "Advanced tables for Markdown/HTML")
918 "This package provides functions to build tables with advanced layout
919 elements such as row spanners, column spanners, table spanners, zebra
920 striping, and more. While allowing advanced layout, the underlying
921 CSS-structure is simple in order to maximize compatibility with word
922 processors such as LibreOffice. The package also contains a few text
923 formatting functions that help outputting text compatible with HTML or
925 (license license:gpl3+)))
927 (define-public r-curl
933 (uri (cran-uri "curl" version))
936 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
937 (build-system r-build-system)
940 (modify-phases %standard-phases
941 ;; The environment variable CURL_CA_BUNDLE is only respected when
942 ;; running Windows, so we disable the platform checks.
943 ;; This can be removed once the libcurl has been patched.
944 (add-after 'unpack 'allow-CURL_CA_BUNDLE
946 (substitute* "R/onload.R"
947 (("if \\(!grepl\\(\"mingw\".*")
949 (substitute* "src/handle.c"
952 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
953 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
960 `(("pkg-config" ,pkg-config)))
961 (home-page "https://github.com/jeroenooms/curl")
962 (synopsis "HTTP client for R")
964 "The @code{curl()} and @code{curl_download()} functions provide highly
965 configurable drop-in replacements for base @code{url()} and
966 @code{download.file()} with better performance, support for encryption, gzip
967 compression, authentication, and other @code{libcurl} goodies. The core of
968 the package implements a framework for performing fully customized requests
969 where data can be processed either in memory, on disk, or streaming via the
970 callback or connection interfaces.")
971 (license license:expat)))
973 (define-public r-hwriter
980 (uri (cran-uri "hwriter" version))
983 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
984 (build-system r-build-system)
985 (home-page "https://cran.r-project.org/web/packages/hwriter")
986 (synopsis "Output R objects in HTML format")
988 "This package provides easy-to-use and versatile functions to output R
989 objects in HTML format.")
990 (license license:lgpl2.1+)))
992 (define-public r-rjson
999 (uri (cran-uri "rjson" version))
1002 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1003 (build-system r-build-system)
1004 (home-page "https://cran.r-project.org/web/packages/rjson")
1005 (synopsis "JSON library for R")
1007 "This package provides functions to convert R objects into JSON objects
1009 (license license:gpl2+)))
1011 (define-public r-fastmap
1018 (uri (cran-uri "fastmap" version))
1021 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1022 (properties `((upstream-name . "fastmap")))
1023 (build-system r-build-system)
1024 (home-page "https://r-lib.github.io/fastmap/")
1025 (synopsis "Fast implementation of a key-value store")
1027 "This package provides a fast implementation of a key-value store.
1028 Environments are commonly used as key-value stores, but every time a new key
1029 is used, it is added to R's global symbol table, causing a small amount of
1030 memory leakage. This can be problematic in cases where many different keys
1031 are used. Fastmap avoids this memory leak issue by implementing the map using
1032 data structures in C++.")
1033 (license license:expat)))
1035 (define-public r-shiny
1043 (url "https://github.com/rstudio/shiny.git")
1044 (commit (string-append "v" version))))
1045 (file-name (git-file-name name version))
1048 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1049 (build-system r-build-system)
1051 `(#:modules ((guix build r-build-system)
1052 (guix build minify-build-system)
1055 #:imported-modules (,@%r-build-system-modules
1056 (guix build minify-build-system))
1058 (modify-phases (@ (guix build r-build-system) %standard-phases)
1059 (add-after 'unpack 'replace-bundled-minified-JavaScript
1060 (lambda* (#:key inputs #:allow-other-keys)
1061 (let ((replace-file (lambda (old new)
1062 (format #t "replacing ~a with ~a\n" old new)
1064 (symlink new old))))
1065 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1066 ;; contain just data. They are not minified code, so we don't
1068 (with-directory-excursion "inst/www/shared"
1069 (replace-file "bootstrap/shim/respond.min.js"
1070 (string-append (assoc-ref inputs "js-respond")
1071 "/share/javascript/respond.min.js"))
1072 (replace-file "bootstrap/shim/html5shiv.min.js"
1073 (string-append (assoc-ref inputs "js-html5shiv")
1074 "/share/javascript/html5shiv.min.js"))
1075 (replace-file "json2-min.js"
1076 (string-append (assoc-ref inputs "js-json2")
1077 "/share/javascript/json2-min.js"))
1078 (replace-file "strftime/strftime-min.js"
1079 (string-append (assoc-ref inputs "js-strftime")
1080 "/share/javascript/strftime.min.js"))
1081 (replace-file "highlight/highlight.pack.js"
1082 (string-append (assoc-ref inputs "js-highlight")
1083 "/share/javascript/highlight.min.js"))
1084 (replace-file "datatables/js/jquery.dataTables.min.js"
1085 (string-append (assoc-ref inputs "js-datatables")
1086 "/share/javascript/jquery.dataTables.min.js"))
1087 (replace-file "selectize/js/selectize.min.js"
1088 (string-append (assoc-ref inputs "js-selectize")
1089 "/share/javascript/selectize.min.js"))
1090 (replace-file "selectize/js/es5-shim.min.js"
1091 (string-append (assoc-ref inputs "js-es5-shim")
1092 "/share/javascript/es5-shim.min.js"))
1093 (for-each (match-lambda
1095 (delete-file target)
1096 (minify source #:target target)))
1097 '(("jqueryui/jquery-ui.js" .
1098 "jqueryui/jquery-ui.min.js")
1099 ("datepicker/js/bootstrap-datepicker.js" .
1100 "datepicker/js/bootstrap-datepicker.min.js")
1101 ("ionrangeslider/js/ion.rangeSlider.js" .
1102 "ionrangeslider/js/ion.rangeSlider.min.js")
1103 ("bootstrap/js/bootstrap.js" .
1104 "bootstrap/js/bootstrap.min.js")
1109 ("legacy/jquery.js" .
1110 "legacy/jquery.min.js")
1111 ("showdown/src/showdown.js" .
1112 "showdown/compressed/showdown.js")))))
1115 `(("r-crayon" ,r-crayon)
1116 ("r-digest" ,r-digest)
1117 ("r-fastmap" ,r-fastmap)
1118 ("r-htmltools" ,r-htmltools)
1119 ("r-httpuv" ,r-httpuv)
1120 ("r-jsonlite" ,r-jsonlite)
1121 ("r-later" ,r-later)
1123 ("r-promises" ,r-promises)
1125 ("r-rlang" ,r-rlang)
1126 ("r-sourcetools" ,r-sourcetools)
1127 ("r-withr" ,r-withr)
1128 ("r-xtable" ,r-xtable)))
1130 `(("js-datatables" ,js-datatables)
1131 ("js-html5shiv" ,js-html5shiv)
1132 ("js-json2" ,js-json2)
1133 ("js-respond" ,js-respond)
1134 ("js-selectize" ,js-selectize)
1135 ("js-strftime" ,js-strftime)
1136 ("js-highlight" ,js-highlight)
1137 ("js-es5-shim" ,js-es5-shim)))
1139 `(("uglify-js" ,uglify-js)
1140 ("gfortran" ,gfortran)))
1141 (home-page "http://shiny.rstudio.com")
1142 (synopsis "Easy interactive web applications with R")
1144 "Makes it incredibly easy to build interactive web applications
1145 with R. Automatic \"reactive\" binding between inputs and outputs and
1146 extensive prebuilt widgets make it possible to build beautiful,
1147 responsive, and powerful applications with minimal effort.")
1148 (license license:artistic2.0)))
1150 ;; This package includes minified JavaScript files. When upgrading please
1151 ;; check that there are no new minified JavaScript files.
1152 (define-public r-shinytree
1154 (name "r-shinytree")
1159 (uri (cran-uri "shinyTree" version))
1162 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1163 (modules '((guix build utils)))
1166 ;; Delete minified JavaScript
1167 (for-each delete-file
1168 '("inst/www/jsTree-3.3.7/libs/require.js"
1169 "inst/www/jsTree-3.3.7/libs/jquery.js"
1170 "inst/www/jsTree-3.3.7/jstree.min.js"))
1172 (properties `((upstream-name . "shinyTree")))
1173 (build-system r-build-system)
1175 `(#:modules ((guix build utils)
1176 (guix build r-build-system)
1180 (modify-phases %standard-phases
1181 (add-after 'unpack 'replace-minified-javascript
1182 (lambda* (#:key inputs #:allow-other-keys)
1183 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1184 (symlink (string-append (assoc-ref inputs "js-requirejs")
1185 "/share/javascript/require.min.js")
1190 `((,(assoc-ref inputs "js-jquery")
1194 (lambda (sources targets)
1195 (for-each (lambda (source target)
1196 (format #t "Processing ~a --> ~a~%"
1198 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1199 (call-with-output-file target
1201 (dump-port minified port)))))
1205 `(("r-htmlwidgets" ,r-htmlwidgets)
1206 ("r-jsonlite" ,r-jsonlite)
1207 ("r-promises" ,r-promises)
1208 ("r-shiny" ,r-shiny)
1209 ("r-stringr" ,r-stringr)))
1211 `(("js-requirejs" ,js-requirejs)))
1213 `(("uglify-js" ,uglify-js)
1217 (uri "https://code.jquery.com/jquery-3.3.1.js")
1220 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1221 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1222 (synopsis "jsTree bindings for Shiny")
1224 "This package exposes R bindings to jsTree, a JavaScript library that
1225 supports interactive trees, to enable rich, editable trees in Shiny.")
1226 (license license:expat)))
1228 (define-public r-shinydashboard
1230 (name "r-shinydashboard")
1234 (uri (cran-uri "shinydashboard" version))
1237 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1238 (build-system r-build-system)
1239 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1240 ;; Regenerate it from the included sources.
1242 `(#:modules ((guix build utils)
1243 (guix build r-build-system)
1246 (modify-phases %standard-phases
1247 (add-after 'unpack 'generate-minified-javascript
1249 (with-directory-excursion "inst/AdminLTE"
1250 (delete-file "app.min.js")
1251 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1252 (call-with-output-file "app.min.js"
1254 (dump-port minified port))))))))))
1256 `(("r-htmltools" ,r-htmltools)
1257 ("r-promises" ,r-promises)
1258 ("r-shiny" ,r-shiny)))
1260 `(("uglify-js" ,uglify-js)))
1261 (home-page "https://rstudio.github.io/shinydashboard/")
1262 (synopsis "Create dashboards with shiny")
1263 (description "This package provides an extension to the Shiny web
1264 application framework for R, making it easy to create attractive dashboards.")
1265 ;; This package includes software that was released under the Expat
1266 ;; license, but the whole package is released under GPL version 2 or
1268 (license license:gpl2+)))
1270 (define-public r-shinyfiles
1272 (name "r-shinyfiles")
1277 (uri (cran-uri "shinyFiles" version))
1279 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1280 (properties `((upstream-name . "shinyFiles")))
1281 (build-system r-build-system)
1284 ("r-htmltools" ,r-htmltools)
1285 ("r-jsonlite" ,r-jsonlite)
1286 ("r-shiny" ,r-shiny)
1287 ("r-tibble" ,r-tibble)))
1288 (home-page "https://github.com/thomasp85/shinyFiles")
1289 (synopsis "Server-side file system viewer for Shiny")
1291 "This package provides functionality for client-side navigation of the
1292 server side file system in shiny apps. In case the app is running locally
1293 this gives the user direct access to the file system without the need to
1294 \"download\" files to a temporary location. Both file and folder selection as
1295 well as file saving is available.")
1296 (license license:gpl2+)))
1298 (define-public r-shinythemes
1300 (name "r-shinythemes")
1305 (uri (cran-uri "shinythemes" version))
1308 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1309 (properties `((upstream-name . "shinythemes")))
1310 (build-system r-build-system)
1311 (propagated-inputs `(("r-shiny" ,r-shiny)))
1312 (home-page "https://rstudio.github.io/shinythemes/")
1313 (synopsis "Themes for Shiny")
1315 "This package provides themes for use with Shiny. It includes several
1316 Bootstrap themes, which are packaged for use with Shiny applications.")
1317 ;; The package is released under version 3 of the GPL, but it includes
1318 ;; source files that are covered by the Expat license. It also includes
1319 ;; fonts under SIL or the ASL.
1320 (license (list license:gpl3 license:expat
1321 license:silofl1.1 license:asl2.0))))
1323 ;; The package sources include minified variants of d3.js and non-minified
1324 ;; source code of d3-jetpack.
1325 (define-public r-d3r
1332 (uri (cran-uri "d3r" version))
1335 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1336 (build-system r-build-system)
1338 `(#:modules ((guix build utils)
1339 (guix build r-build-system)
1343 (modify-phases %standard-phases
1344 (add-after 'unpack 'process-javascript
1345 (lambda* (#:key inputs #:allow-other-keys)
1346 (with-directory-excursion "inst/www/d3/"
1350 `((,(assoc-ref inputs "d3.v3.js")
1351 "v3/dist/d3.min.js")
1352 (,(assoc-ref inputs "d3.v4.js")
1353 "v4/dist/d3.min.js")
1354 (,(assoc-ref inputs "d3.v5.js")
1355 "v5/dist/d3.min.js"))))
1356 (lambda (sources targets)
1357 (for-each (lambda (source target)
1358 (format #t "Processing ~a --> ~a~%"
1360 (delete-file target)
1361 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1362 (call-with-output-file target
1364 (dump-port minified port)))))
1368 `(("r-dplyr" ,r-dplyr)
1369 ("r-htmltools" ,r-htmltools)
1370 ("r-rlang" ,r-rlang)
1371 ("r-tidyr" ,r-tidyr)))
1373 `(("uglify-js" ,uglify-js)
1377 (uri "https://d3js.org/d3.v3.js")
1380 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1384 (uri "https://d3js.org/d3.v4.js")
1387 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1391 (uri "https://d3js.org/d3.v5.js")
1394 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1395 (home-page "https://github.com/timelyportfolio/d3r")
1396 (synopsis "d3.js utilities for R")
1398 "This package provides a suite of functions to help ease the use of the
1399 d3.js visualization library in R. These helpers include
1400 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1401 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1402 R objects into the JSON format that the d3.js library expects.")
1403 (license license:bsd-3)))
1405 ;; We use the latest commit here because the last release was in 2016 while
1406 ;; the latest commit was in 2018.
1407 (define-public r-sankeyd3
1408 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1412 (version (git-version "0.3.2" revision commit))
1417 (url "https://github.com/fbreitwieser/sankeyD3.git")
1419 (file-name (git-file-name name version))
1422 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1423 (build-system r-build-system)
1426 ("r-htmlwidgets" ,r-htmlwidgets)
1427 ("r-shiny" ,r-shiny)
1428 ("r-magrittr" ,r-magrittr)))
1429 (home-page "https://github.com/fbreitwieser/sankeyD3")
1430 (synopsis "Sankey network graphs from R")
1432 "This package provides an R library to generate Sankey network graphs
1433 in R and Shiny via the D3 visualization library.")
1434 ;; The R code is licensed under GPLv3+. It includes the non-minified
1435 ;; JavaScript source code of d3-sankey, which is released under the
1436 ;; 3-clause BSD license.
1437 (license (list license:gpl3+ license:bsd-3)))))
1439 (define-public r-crosstalk
1441 (name "r-crosstalk")
1446 (uri (cran-uri "crosstalk" version))
1449 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1450 (build-system r-build-system)
1452 `(("r-htmltools" ,r-htmltools)
1453 ("r-jsonlite" ,r-jsonlite)
1454 ("r-lazyeval" ,r-lazyeval)
1456 (home-page "https://rstudio.github.io/crosstalk/")
1457 (synopsis "Inter-widget interactivity for HTML widgets")
1459 "This package provides building blocks for allowing HTML widgets to
1460 communicate with each other, with Shiny or without (i.e. static @code{.html}
1461 files). It currently supports linked brushing and filtering.")
1462 (license license:expat)))
1464 (define-public r-rook
1471 (uri (cran-uri "Rook" version))
1474 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1475 (properties `((upstream-name . "Rook")))
1476 (build-system r-build-system)
1477 (propagated-inputs `(("r-brew" ,r-brew)))
1478 (home-page "https://cran.r-project.org/web/packages/Rook")
1479 (synopsis "Web server interface for R")
1481 "This package contains the Rook specification and convenience software
1482 for building and running Rook applications. A Rook application is an R
1483 reference class object that implements a @code{call} method or an R closure
1484 that takes exactly one argument, an environment, and returns a list with three
1485 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1486 (license license:gpl2)))
1488 (define-public r-miniui
1495 (uri (cran-uri "miniUI" version))
1498 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1499 (properties `((upstream-name . "miniUI")))
1500 (build-system r-build-system)
1502 `(("r-htmltools" ,r-htmltools)
1503 ("r-shiny" ,r-shiny)))
1504 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1505 (synopsis "Shiny UI widgets for small screens")
1507 "This package provides UI widget and layout functions for writing Shiny apps that
1508 work well on small screens.")
1509 (license license:gpl3)))
1511 (define-public r-feather
1518 (uri (cran-uri "feather" version))
1521 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1522 (build-system r-build-system)
1526 ("r-tibble" ,r-tibble)))
1527 (home-page "https://github.com/wesm/feather")
1528 (synopsis "R Bindings to the Feather API")
1529 (description "Read and write feather files, a lightweight binary columnar
1530 data store designed for maximum speed.")
1531 (license license:asl2.0)))
1533 (define-public r-maps
1540 (uri (cran-uri "maps" version))
1543 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1544 (build-system r-build-system)
1545 (home-page "https://cran.r-project.org/web/packages/maps")
1546 (synopsis "Draw geographical maps")
1547 (description "This package provides an R module for display of maps.
1548 Projection code and larger maps are in separate packages (@code{mapproj} and
1550 (license license:gpl2)))
1552 (define-public r-mapproj
1559 (uri (cran-uri "mapproj" version))
1562 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1563 (build-system r-build-system)
1564 (propagated-inputs `(("r-maps" ,r-maps)))
1565 (home-page "https://cran.r-project.org/web/packages/mapproj")
1566 (synopsis "Map projection in R")
1567 (description "This package converts latitude/longitude into projected
1569 (license (list license:gpl2 ; The R interface
1570 (license:non-copyleft ; The C code
1571 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1572 "Lucent Public License Version 1.02")))))
1574 (define-public r-rgooglemaps
1576 (name "r-rgooglemaps")
1581 (uri (cran-uri "RgoogleMaps" version))
1584 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1585 (properties `((upstream-name . "RgoogleMaps")))
1586 (build-system r-build-system)
1590 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1591 (synopsis "Use Google Maps in R")
1592 (description "This package serves two purposes:
1594 @item Provide a comfortable R interface to query the Google server for static
1596 @item Use the map as a background image to overlay plots within R. This
1597 requires proper coordinate scaling.
1599 (license license:gpl2+)))
1601 (define-public r-geosphere
1603 (name "r-geosphere")
1608 (uri (cran-uri "geosphere" version))
1611 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1612 (build-system r-build-system)
1613 (propagated-inputs `(("r-sp" ,r-sp)))
1614 (home-page "https://cran.r-project.org/web/packages/geosphere")
1615 (synopsis "Spherical trigonometry")
1616 (description "This package computes spherical trigonometry for geographic
1617 applications. That is, compute distances and related measures for angular
1618 (longitude/latitude) locations.")
1619 (license license:gpl3+)))
1621 (define-public r-jpeg
1628 (uri (cran-uri "jpeg" version))
1631 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1632 (build-system r-build-system)
1633 (inputs `(("libjpeg" ,libjpeg-turbo)))
1634 (home-page "https://www.rforge.net/jpeg/")
1635 (synopsis "Read and write JPEG images with R")
1636 (description "This package provides a way to read, write and display
1637 bitmap images stored in the JPEG format with R. It can read and write both
1638 files and in-memory raw vectors.")
1639 (license license:gpl2+)))
1641 (define-public r-ggmap
1648 (uri (cran-uri "ggmap" version))
1651 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1652 (build-system r-build-system)
1654 `(("r-bitops" ,r-bitops)
1655 ("r-digest" ,r-digest)
1656 ("r-dplyr" ,r-dplyr)
1657 ("r-ggplot2" ,r-ggplot2)
1661 ("r-magrittr" ,r-magrittr)
1664 ("r-purrr" ,r-purrr)
1665 ("r-rgooglemaps" ,r-rgooglemaps)
1666 ("r-rjson" ,r-rjson)
1667 ("r-scales" ,r-scales)
1668 ("r-stringr" ,r-stringr)
1669 ("r-tibble" ,r-tibble)
1670 ("r-tidyr" ,r-tidyr)))
1671 (home-page "https://github.com/dkahle/ggmap")
1672 (synopsis "Spatial visualization with ggplot2")
1673 (description "This package provides a collection of functions to visualize
1674 spatial data and models on top of static maps from various online sources (e.g
1675 Google Maps and Stamen Maps). It includes tools common to those tasks,
1676 including functions for geolocation and routing.")
1677 (license license:gpl2)))
1679 (define-public r-haven
1686 (uri (cran-uri "haven" version))
1689 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1690 (build-system r-build-system)
1694 `(("r-knitr" ,r-knitr)))
1696 `(("r-forcats" ,r-forcats)
1699 ("r-rlang" ,r-rlang)
1700 ("r-readr" ,r-readr)
1701 ("r-tibble" ,r-tibble)
1702 ("r-tidyselect" ,r-tidyselect)
1703 ("r-vctrs" ,r-vctrs)))
1704 (home-page "https://haven.tidyverse.org")
1705 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1707 "This package lets you mport foreign statistical formats into R via the
1708 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1709 (license license:expat)))
1711 (define-public r-amap
1717 (uri (cran-uri "amap" version))
1720 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1721 (build-system r-build-system)
1723 `(("gfortran" ,gfortran)))
1724 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1725 (synopsis "Another multidimensional analysis package")
1726 (description "This package provides tools for clustering and principal
1727 component analysis (with robust methods, and parallelized functions).")
1728 (license license:gpl2+)))
1730 (define-public r-ape
1737 (uri (cran-uri "ape" version))
1740 "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
1741 (build-system r-build-system)
1743 `(("r-lattice" ,r-lattice)
1745 ("r-rcpp" ,r-rcpp)))
1746 (home-page "http://ape-package.ird.fr/")
1747 (synopsis "Analyses of phylogenetics and evolution")
1749 "This package provides functions for reading, writing, plotting, and
1750 manipulating phylogenetic trees, analyses of comparative data in a
1751 phylogenetic framework, ancestral character analyses, analyses of
1752 diversification and macroevolution, computing distances from DNA sequences,
1753 and several other tools.")
1754 (license license:gpl2+)))
1756 (define-public r-abbyyr
1763 (uri (cran-uri "abbyyR" version))
1766 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1767 (properties `((upstream-name . "abbyyR")))
1768 (build-system r-build-system)
1770 `(("r-curl" ,r-curl)
1773 ("r-progress" ,r-progress)
1774 ("r-readr" ,r-readr)
1776 (home-page "https://github.com/soodoku/abbyyR")
1777 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1779 "This package provides tools to get text from images of text using Abbyy
1780 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1781 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1782 passports and get the results in a variety of formats including plain text and
1783 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1784 (license license:expat)))
1786 (define-public r-colorspace
1788 (name "r-colorspace")
1793 (uri (cran-uri "colorspace" version))
1795 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1796 (build-system r-build-system)
1797 (home-page "https://cran.r-project.org/web/packages/colorspace")
1798 (synopsis "Color space manipulation")
1800 "This package carries out a mapping between assorted color spaces
1801 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1802 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1803 colors are provided.")
1804 (license license:bsd-3)))
1806 (define-public r-glue
1813 (uri (cran-uri "glue" version))
1816 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1817 (build-system r-build-system)
1818 ;; knitr depends on glue, so we can't add knitr here to build the
1822 `(("r-knitr" ,r-knitr)))
1823 (home-page "https://github.com/tidyverse/glue")
1824 (synopsis "Interpreted string literals")
1826 "This package provides an implementation of interpreted string literals,
1827 inspired by Python's Literal String Interpolation (PEP-0498) and
1828 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1829 (license license:expat)))
1831 (define-public r-pastecs
1837 (uri (cran-uri "pastecs" version))
1840 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1841 (build-system r-build-system)
1843 `(("r-boot" ,r-boot)))
1844 (home-page "http://www.sciviews.org/pastecs")
1845 (synopsis "Analysis of space-time ecological series")
1847 "This package provides functions for regulation, decomposition and analysis
1848 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1849 initiative to bring PASSTEC 2000 functionalities to R.")
1850 (license license:gpl2+)))
1852 (define-public r-plogr
1859 (uri (cran-uri "plogr" version))
1862 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1863 (build-system r-build-system)
1864 (home-page "https://github.com/krlmlr/plogr")
1865 (synopsis "R bindings for the plog C++ logging library")
1867 "This package provides the header files for a stripped-down version of
1868 the plog header-only C++ logging library, and a method to log to R's standard
1870 (license license:expat)))
1872 (define-public r-pls
1879 (uri (cran-uri "pls" version))
1881 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1882 (build-system r-build-system)
1883 (home-page "https://mevik.net/work/software/pls.html")
1884 (synopsis "Partial Least Squares and Principal Component Regression")
1886 "The pls package implements multivariate regression methods: Partial Least
1887 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1888 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1891 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1892 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1893 @item multi-response models (or @dfn{PLS2})
1894 @item flexible cross-validation
1895 @item Jackknife variance estimates of regression coefficients
1896 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1897 (R)MSEP, R², and correlation loadings
1898 @item formula interface, modelled after @code{lm()}, with methods for predict,
1899 print, summary, plot, update, etc.
1900 @item extraction functions for coefficients, scores, and loadings
1901 @item MSEP, RMSEP, and R² estimates
1902 @item multiplicative scatter correction (@dfn{MSC})
1904 (license license:gpl2)))
1913 (uri (cran-uri "ps" version))
1915 (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
1916 (build-system r-build-system)
1917 (home-page "https://ps.r-lib.org")
1918 (synopsis "List, query, and manipulate system processes")
1920 "The ps package implements an API to list, query, and manipulate system
1921 processes. Most of its code is based on the @code{psutil} Python package.")
1922 (license license:bsd-3)))
1924 (define-public r-pkgbuild
1931 (uri (cran-uri "pkgbuild" version))
1933 (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
1934 (build-system r-build-system)
1936 `(("r-callr" ,r-callr)
1938 ("r-crayon" ,r-crayon)
1940 ("r-prettyunits" ,r-prettyunits)
1942 ("r-rprojroot" ,r-rprojroot)
1943 ("r-withr" ,r-withr)))
1944 (home-page "https://github.com/r-pkgs/pkgbuild")
1945 (synopsis "Find tools needed to build R packages")
1947 "This package provides functions used to build R packages. It locates
1948 compilers needed to build R packages on various platforms and ensures the PATH
1949 is configured appropriately so R can use them.")
1950 (license license:gpl3)))
1952 (define-public r-pkgload
1959 (uri (cran-uri "pkgload" version))
1962 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
1963 (build-system r-build-system)
1966 ("r-crayon" ,r-crayon)
1968 ("r-pkgbuild" ,r-pkgbuild)
1969 ("r-rlang" ,r-rlang)
1970 ("r-rprojroot" ,r-rprojroot)
1971 ("r-rstudioapi" ,r-rstudioapi)
1972 ("r-withr" ,r-withr)))
1973 (home-page "https://github.com/r-lib/pkgload")
1974 (synopsis "Simulate package installation and attach")
1976 "This package simulates the process of installing a package and then
1977 attaching it. This is a key part of the @code{devtools} package as it allows
1978 you to rapidly iterate while developing a package.")
1979 (license license:gpl3)))
1981 (define-public r-rcpp
1988 (uri (cran-uri "Rcpp" version))
1990 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1991 (build-system r-build-system)
1992 (home-page "http://www.rcpp.org")
1993 (synopsis "Seamless R and C++ integration")
1995 "The Rcpp package provides R functions as well as C++ classes which offer
1996 a seamless integration of R and C++. Many R data types and objects can be
1997 mapped back and forth to C++ equivalents which facilitates both writing of new
1998 code as well as easier integration of third-party libraries. Documentation
1999 about Rcpp is provided by several vignettes included in this package, via the
2000 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2001 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2002 @code{citation(\"Rcpp\")} for details on these last two.")
2003 (license license:gpl2+)))
2005 (define-public r-bindr
2012 (uri (cran-uri "bindr" version))
2015 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2016 (build-system r-build-system)
2017 (home-page "https://github.com/krlmlr/bindr")
2018 (synopsis "Parametrized active bindings")
2020 "This package provides a simple interface for creating active bindings
2021 where the bound function accepts additional arguments.")
2022 (license license:expat)))
2024 (define-public r-bindrcpp
2031 (uri (cran-uri "bindrcpp" version))
2034 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2035 (build-system r-build-system)
2037 `(("r-bindr" ,r-bindr)
2038 ("r-plogr" ,r-plogr)
2039 ("r-rcpp" ,r-rcpp)))
2040 (home-page "https://github.com/krlmlr/bindrcpp")
2041 (synopsis "Rcpp interface to active bindings")
2043 "This package provides an easy way to fill an environment with active
2044 bindings that call a C++ function.")
2045 (license license:expat)))
2047 (define-public r-auc
2054 (uri (cran-uri "AUC" version))
2057 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2058 (properties `((upstream-name . "AUC")))
2059 (build-system r-build-system)
2060 (home-page "https://cran.r-project.org/web/packages/AUC")
2061 (synopsis "Compute the area under the curve of selected measures")
2063 "This package includes functions to compute the area under the curve of
2064 selected measures: the area under the sensitivity curve (AUSEC), the area
2065 under the specificity curve (AUSPC), the area under the accuracy
2066 curve (AUACC), and the area under the receiver operating characteristic
2067 curve (AUROC). The curves can also be visualized. Support for partial areas
2069 (license license:gpl2+)))
2071 (define-public r-calibrate
2073 (name "r-calibrate")
2078 (uri (cran-uri "calibrate" version))
2080 (base32 "0h91mxf4fy3xk4mavf6cdllglyq5fra8zpz7yvc63n5jigpy2lhd"))))
2081 (build-system r-build-system)
2083 `(("r-mass" ,r-mass)))
2084 (home-page "https://cran.r-project.org/web/packages/calibrate")
2085 (synopsis "Calibration of scatterplot and biplot axes")
2087 "This is a package for drawing calibrated scales with tick marks
2088 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2089 (license license:gpl2)))
2091 (define-public r-shape
2098 (uri (cran-uri "shape" version))
2101 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2102 (build-system r-build-system)
2103 (home-page "https://cran.r-project.org/web/packages/shape")
2104 (synopsis "Functions for plotting graphical shapes")
2106 "This package provides functions for plotting graphical shapes such as
2107 ellipses, circles, cylinders, arrows, ...")
2108 (license license:gpl3+)))
2110 (define-public r-globaloptions
2112 (name "r-globaloptions")
2117 (uri (cran-uri "GlobalOptions" version))
2119 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2120 (properties `((upstream-name . "GlobalOptions")))
2121 (build-system r-build-system)
2123 `(("r-knitr" ,r-knitr)))
2124 (home-page "https://github.com/jokergoo/GlobalOptions")
2125 (synopsis "Generate functions to get or set global options")
2127 "This package provides more controls on the option values such as
2128 validation and filtering on the values, making options invisible or private.")
2129 (license license:gpl2+)))
2131 (define-public r-circlize
2138 (uri (cran-uri "circlize" version))
2141 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2142 (build-system r-build-system)
2144 `(("r-colorspace" ,r-colorspace)
2145 ("r-globaloptions" ,r-globaloptions)
2146 ("r-shape" ,r-shape)))
2148 `(("r-knitr" ,r-knitr)))
2149 (home-page "https://github.com/jokergoo/circlize")
2150 (synopsis "Circular visualization")
2152 "Circular layout is an efficient way to visualise huge amounts of
2153 information. This package provides an implementation of circular layout
2154 generation in R as well as an enhancement of available software. Its
2155 flexibility is based on the usage of low-level graphics functions such that
2156 self-defined high-level graphics can be easily implemented by users for
2157 specific purposes. Together with the seamless connection between the powerful
2158 computational and visual environment in R, it gives users more convenience and
2159 freedom to design figures for better understanding complex patterns behind
2160 multi-dimensional data.")
2161 (license license:gpl2+)))
2163 (define-public r-powerlaw
2170 (uri (cran-uri "poweRlaw" version))
2172 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2173 (properties `((upstream-name . "poweRlaw")))
2174 (build-system r-build-system)
2176 `(("r-pracma" ,r-pracma)))
2178 `(("r-knitr" ,r-knitr)))
2179 (home-page "https://github.com/csgillespie/poweRlaw")
2180 (synopsis "Tools for the analysis of heavy tailed distributions")
2182 "This package provides an implementation of maximum likelihood estimators
2183 for a variety of heavy tailed distributions, including both the discrete and
2184 continuous power law distributions. Additionally, a goodness-of-fit based
2185 approach is used to estimate the lower cut-off for the scaling region.")
2186 ;; Any of these GPL versions.
2187 (license (list license:gpl2 license:gpl3))))
2189 (define-public r-compare
2196 (uri (cran-uri "compare" version))
2199 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2200 (build-system r-build-system)
2201 (home-page "https://cran.r-project.org/web/packages/compare")
2202 (synopsis "Comparing objects for differences")
2204 "This package provides functions to compare a model object to a
2205 comparison object. If the objects are not identical, the functions can be
2206 instructed to explore various modifications of the objects (e.g., sorting
2207 rows, dropping names) to see if the modified versions are identical.")
2208 (license license:gpl2+)))
2210 (define-public r-dendextend
2212 (name "r-dendextend")
2217 (uri (cran-uri "dendextend" version))
2220 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2221 (build-system r-build-system)
2223 `(("r-ggplot2" ,r-ggplot2)
2224 ("r-magrittr" ,r-magrittr)
2225 ("r-viridis" ,r-viridis)))
2226 (home-page "https://cran.r-project.org/web/packages/dendextend")
2227 (synopsis "Extending 'dendrogram' functionality in R")
2229 "This package offers a set of functions for extending @code{dendrogram}
2230 objects in R, letting you visualize and compare trees of hierarchical
2231 clusterings. You can adjust a tree's graphical parameters (the color, size,
2232 type, etc of its branches, nodes and labels) and visually and statistically
2233 compare different dendrograms to one another.")
2234 ;; Any of these versions
2235 (license (list license:gpl2 license:gpl3))))
2237 (define-public r-getoptlong
2239 (name "r-getoptlong")
2244 (uri (cran-uri "GetoptLong" version))
2247 "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
2248 (properties `((upstream-name . "GetoptLong")))
2249 (build-system r-build-system)
2253 `(("r-crayon" ,r-crayon)
2254 ("r-globaloptions" ,r-globaloptions)
2255 ("r-rjson" ,r-rjson)))
2257 `(("r-knitr" ,r-knitr)))
2258 (home-page "https://github.com/jokergoo/GetoptLong")
2259 (synopsis "Parsing command-line arguments and variable interpolation")
2261 "This is yet another command-line argument parser which wraps the
2262 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2263 use in R. It also provides a simple way for variable interpolation in R.")
2264 (license license:gpl2+)))
2266 (define-public r-fastmatch
2268 (name "r-fastmatch")
2273 (uri (cran-uri "fastmatch" version))
2276 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2277 (build-system r-build-system)
2278 (home-page "https://www.rforge.net/fastmatch")
2279 (synopsis "Fast match function")
2281 "This package provides a fast @code{match} replacement for cases that
2282 require repeated look-ups. It is slightly faster that R's built-in
2283 @code{match} function on first match against a table, but extremely fast on
2284 any subsequent lookup as it keeps the hash table in memory.")
2285 (license license:gpl2)))
2290 (version "2.2-14.2")
2294 (uri (cran-uri "ff" version))
2297 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2298 (build-system r-build-system)
2299 (propagated-inputs `(("r-bit" ,r-bit)))
2300 (home-page "http://ff.r-forge.r-project.org/")
2301 (synopsis "Memory-efficient storage of large data on disk and access functions")
2303 "This package provides data structures that are stored on disk but
2304 behave (almost) as if they were in RAM by transparently mapping only a section
2306 ;; error Architecture not supported.
2307 (supported-systems (delete "aarch64-linux" %supported-systems))
2308 (license license:gpl2)))
2310 (define-public r-ffbase
2317 (uri (cran-uri "ffbase" version))
2320 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2321 (build-system r-build-system)
2324 ("r-fastmatch" ,r-fastmatch)
2326 (home-page "http://github.com/edwindj/ffbase")
2327 (synopsis "Basic statistical functions for package 'ff'")
2329 "This package extends the out of memory vectors of @code{ff} with
2330 statistical functions and other utilities to ease their usage.")
2331 (license license:gpl3)))
2333 (define-public r-prettyunits
2335 (name "r-prettyunits")
2340 (uri (cran-uri "prettyunits" version))
2343 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2344 (build-system r-build-system)
2345 (home-page "https://github.com/gaborcsardi/prettyunits")
2346 (synopsis "Pretty, human readable formatting of quantities")
2348 "This package provides tools for pretty, human readable formatting of
2350 (license license:expat)))
2352 (define-public r-reshape
2359 (uri (cran-uri "reshape" version))
2362 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2363 (build-system r-build-system)
2365 `(("r-plyr" ,r-plyr)
2366 ("r-rcpp" ,r-rcpp)))
2367 (home-page "http://had.co.nz/reshape")
2368 (synopsis "Flexibly reshape data")
2370 "Flexibly restructure and aggregate data using just two functions:
2371 @code{melt} and @code{cast}. This package provides them.")
2372 (license license:expat)))
2374 (define-public r-progress
2381 (uri (cran-uri "progress" version))
2384 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2385 (build-system r-build-system)
2387 `(("r-crayon" ,r-crayon)
2389 ("r-prettyunits" ,r-prettyunits)
2391 (home-page "https://github.com/gaborcsardi/progress")
2392 (synopsis "Terminal progress bars")
2394 "This package provides configurable progress bars. They may include
2395 percentage, elapsed time, and/or the estimated completion time. They work in
2396 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2397 package also provides a C++ API, that works with or without Rcpp.")
2398 (license license:expat)))
2400 (define-public r-ggally
2407 (uri (cran-uri "GGally" version))
2410 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2411 (properties `((upstream-name . "GGally")))
2412 (build-system r-build-system)
2414 `(("libressl" ,libressl)))
2416 `(("r-ggplot2" ,r-ggplot2)
2417 ("r-gtable" ,r-gtable)
2418 ("r-lifecycle" ,r-lifecycle)
2420 ("r-progress" ,r-progress)
2421 ("r-rcolorbrewer" ,r-rcolorbrewer)
2422 ("r-reshape" ,r-reshape)
2423 ("r-rlang" ,r-rlang)
2424 ("r-scales" ,r-scales)))
2425 (home-page "https://ggobi.github.io/ggally")
2426 (synopsis "Extension to ggplot2")
2428 "The R package ggplot2 is a plotting system based on the grammar of
2429 graphics. GGally extends ggplot2 by adding several functions to reduce the
2430 complexity of combining geometric objects with transformed data. Some of
2431 these functions include a pairwise plot matrix, a two group pairwise plot
2432 matrix, a parallel coordinates plot, a survival plot, and several functions to
2434 (license license:gpl2+)))
2436 (define-public r-proxy
2443 (uri (cran-uri "proxy" version))
2446 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2447 (build-system r-build-system)
2448 (home-page "https://cran.r-project.org/web/packages/proxy")
2449 (synopsis "Distance and similarity measures")
2451 "This package provides an extensible framework for the efficient
2452 calculation of auto- and cross-proximities, along with implementations of the
2453 most popular ones.")
2454 (license license:gpl2)))
2463 (uri (cran-uri "sp" version))
2465 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2466 (build-system r-build-system)
2468 `(("r-lattice" ,r-lattice)))
2469 (home-page "https://cran.r-project.org/web/packages/sp")
2470 (synopsis "Classes and methods for spatial data")
2472 "This package provides classes and methods for spatial data; the classes
2473 document where the spatial location information resides, for 2D or 3D data.
2474 Utility functions are provided, e.g. for plotting data as maps, spatial
2475 selection, as well as methods for retrieving coordinates, for subsetting,
2476 print, summary, etc.")
2477 (license license:gpl2+)))
2479 (define-public r-rmtstat
2486 (uri (cran-uri "RMTstat" version))
2489 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2490 (properties `((upstream-name . "RMTstat")))
2491 (build-system r-build-system)
2492 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2493 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2495 "This package provides functions for working with the Tracy-Widom laws
2496 and other distributions related to the eigenvalues of large Wishart
2498 (license license:bsd-3)))
2500 (define-public r-rmpi
2506 (uri (cran-uri "Rmpi" version))
2509 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2510 (properties `((upstream-name . "Rmpi")))
2511 (build-system r-build-system)
2513 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2514 #:phases (modify-phases %standard-phases
2515 (add-before 'install 'mpi-setup
2518 `(("openmpi" ,openmpi)))
2520 `(("pkg-config" ,pkg-config)))
2521 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2522 (synopsis "R interface to message-passing interface (MPI)")
2524 "This package provides an interface (wrapper) to MPI APIs. It also
2525 provides an interactive R manager and worker environment.")
2526 (license license:gpl2+)))
2528 (define-public r-lmoments
2535 (uri (cran-uri "Lmoments" version))
2538 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2539 (properties `((upstream-name . "Lmoments")))
2540 (build-system r-build-system)
2542 `(("r-rcpp" ,r-rcpp)
2543 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2544 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2545 (synopsis "L-moments and quantile mixtures")
2547 "This package contains functions to estimate L-moments and trimmed
2548 L-moments from the data. It also contains functions to estimate the
2549 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2550 quantile mixture from L-moments and trimmed L-moments.")
2551 (license license:gpl2)))
2553 (define-public r-distillery
2555 (name "r-distillery")
2560 (uri (cran-uri "distillery" version))
2563 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2564 (build-system r-build-system)
2565 (home-page "https://ral.ucar.edu/staff/ericg/")
2566 (synopsis "Functions for confidence intervals and object information")
2568 "This package provides some very simple method functions for confidence
2569 interval calculation and to distill pertinent information from a potentially
2570 complex object; primarily used in common with the packages extRemes and
2572 (license license:gpl2+)))
2574 (define-public r-extremes
2581 (uri (cran-uri "extRemes" version))
2584 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2585 (properties `((upstream-name . "extRemes")))
2586 (build-system r-build-system)
2588 `(("r-distillery" ,r-distillery)
2589 ("r-lmoments" ,r-lmoments)))
2590 (home-page "https://www.assessment.ucar.edu/toolkit/")
2591 (synopsis "Extreme value analysis")
2593 "ExtRemes is a suite of functions for carrying out analyses on the
2594 extreme values of a process of interest; be they block maxima over long blocks
2595 or excesses over a high threshold.")
2596 (license license:gpl2+)))
2598 (define-public r-lmtest
2605 (uri (cran-uri "lmtest" version))
2608 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2609 (build-system r-build-system)
2611 `(("r-zoo" ,r-zoo)))
2613 `(("gfortran" ,gfortran)))
2614 (home-page "https://cran.r-project.org/web/packages/lmtest")
2615 (synopsis "Testing linear regression models")
2617 "This package provides a collection of tests, data sets, and examples for
2618 diagnostic checking in linear regression models. Furthermore, some generic
2619 tools for inference in parametric models are provided.")
2620 ;; Either version is okay
2621 (license (list license:gpl2 license:gpl3))))
2623 (define-public r-idr
2629 (uri (cran-uri "idr" version))
2632 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2633 (build-system r-build-system)
2634 (home-page "https://cran.r-project.org/web/packages/idr/")
2635 (synopsis "Irreproducible discovery rate")
2637 "This is a package for estimating the copula mixture model and plotting
2638 correspondence curves in \"Measuring reproducibility of high-throughput
2639 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2640 by Li, Brown, Huang, and Bickel")
2641 (license license:gpl2+)))
2643 (define-public r-inline
2649 (uri (cran-uri "inline" version))
2652 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2653 (build-system r-build-system)
2654 (home-page "https://cran.r-project.org/web/packages/inline")
2655 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2657 "This package provides functionality to dynamically define R functions
2658 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2659 @code{.Call} calling conventions.")
2660 ;; Any version of the LGPL.
2661 (license license:lgpl3+)))
2663 (define-public r-inum
2669 (uri (cran-uri "inum" version))
2672 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2673 (build-system r-build-system)
2675 `(("r-libcoin" ,r-libcoin)))
2676 (home-page "https://cran.r-project.org/web/packages/inum/")
2677 (synopsis "Interval and enum-type representation of vectors")
2679 "This package provides an enum-type representation of vectors and
2680 representation of intervals, including a method of coercing variables
2682 (license license:gpl2)))
2684 (define-public r-bdsmatrix
2686 (name "r-bdsmatrix")
2691 (uri (cran-uri "bdsmatrix" version))
2694 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2695 (properties `((upstream-name . "bdsmatrix")))
2696 (build-system r-build-system)
2697 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2698 (synopsis "Routines for block diagonal symmetric matrices")
2700 "This package provides procedures to work with block diagonal symmetric
2701 matrices, a special case of sparse matrices.")
2702 (license license:lgpl2.0)))
2704 (define-public r-bbmle
2707 (version "1.0.23.1")
2711 (uri (cran-uri "bbmle" version))
2714 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2715 (build-system r-build-system)
2717 `(("r-bdsmatrix" ,r-bdsmatrix)
2718 ("r-lattice" ,r-lattice)
2720 ("r-matrix" ,r-matrix)
2721 ("r-mvtnorm" ,r-mvtnorm)
2722 ("r-numderiv" ,r-numderiv)))
2723 (home-page "https://cran.r-project.org/web/packages/bbmle")
2724 (synopsis "Tools for General Maximum Likelihood Estimation")
2726 "This package provides methods and functions for fitting maximum
2727 likelihood models in R. This package modifies and extends the @code{mle}
2728 classes in the @code{stats4} package.")
2729 ;; Any version of the GPL
2730 (license license:gpl2+)))
2732 (define-public r-emdbook
2739 (uri (cran-uri "emdbook" version))
2742 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2743 (build-system r-build-system)
2745 `(("r-bbmle" ,r-bbmle)
2747 ("r-lattice" ,r-lattice)
2749 ("r-plyr" ,r-plyr)))
2750 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2751 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2753 "This package provides auxiliary functions and data sets for \"Ecological
2754 Models and Data\", a book presenting maximum likelihood estimation and related
2755 topics for ecologists (ISBN 978-0-691-12522-0).")
2757 (license (list license:gpl2 license:gpl3))))
2759 (define-public r-lpsolve
2766 (uri (cran-uri "lpSolve" version))
2769 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2770 (properties `((upstream-name . "lpSolve")))
2771 (build-system r-build-system)
2772 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2773 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2775 "Lp_solve is software for solving linear, integer and mixed integer
2776 programs. This implementation supplies a \"wrapper\" function in C and some R
2777 functions that solve general linear/integer problems, assignment problems, and
2778 transportation problems.")
2779 (license license:lgpl2.0)))
2781 (define-public r-limsolve
2788 (uri (cran-uri "limSolve" version))
2791 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2792 (properties `((upstream-name . "limSolve")))
2793 (build-system r-build-system)
2795 `(("r-lpsolve" ,r-lpsolve)
2797 ("r-quadprog" ,r-quadprog)))
2798 (native-inputs `(("gfortran" ,gfortran)))
2799 (home-page "https://cran.r-project.org/web/packages/limSolve")
2800 (synopsis "Solving linear inverse models")
2802 "This package provides functions that:
2805 @item find the minimum/maximum of a linear or quadratic function,
2806 @item sample an underdetermined or overdetermined system,
2807 @item solve a linear system Ax=B for the unknown x.
2810 It includes banded and tridiagonal linear systems. The package calls Fortran
2811 functions from LINPACK.")
2813 (license (list license:gpl2+ license:gpl3+))))
2815 (define-public r-fitdistrplus
2817 (name "r-fitdistrplus")
2822 (uri (cran-uri "fitdistrplus" version))
2825 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2826 (build-system r-build-system)
2828 `(("r-mass" ,r-mass)
2829 ("r-survival" ,r-survival)))
2831 `(("r-knitr" ,r-knitr)))
2832 (home-page "http://riskassessment.r-forge.r-project.org")
2833 (synopsis "Fitting a parametric distribution from data")
2835 "This package extends the @code{fitdistr} function of the MASS package
2836 with several functions to help the fit of a parametric distribution to
2837 non-censored or censored data. Censored data may contain left-censored,
2838 right-censored and interval-censored values, with several lower and upper
2839 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2840 provides moment matching (MME), quantile matching (QME) and maximum
2841 goodness-of-fit estimation (MGE) methods (available only for non-censored
2842 data). Weighted versions of MLE, MME and QME are available.")
2843 (license license:gpl2+)))
2845 (define-public r-energy
2852 (uri (cran-uri "energy" version))
2855 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2856 (build-system r-build-system)
2858 `(("r-boot" ,r-boot)
2859 ("r-rcpp" ,r-rcpp)))
2860 (home-page "https://cran.r-project.org/web/packages/energy")
2861 (synopsis "Multivariate inference via the energy of data")
2863 "This package provides e-statistics (energy) tests and statistics for
2864 multivariate and univariate inference, including distance correlation,
2865 one-sample, two-sample, and multi-sample tests for comparing multivariate
2866 distributions, are implemented. Measuring and testing multivariate
2867 independence based on distance correlation, partial distance correlation,
2868 multivariate goodness-of-fit tests, clustering based on energy distance,
2869 testing for multivariate normality, distance components (disco) for
2870 non-parametric analysis of structured data, and other energy
2871 statistics/methods are implemented.")
2872 (license license:gpl2+)))
2874 (define-public r-suppdists
2876 (name "r-suppdists")
2881 (uri (cran-uri "SuppDists" version))
2884 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2885 (properties `((upstream-name . "SuppDists")))
2886 (build-system r-build-system)
2887 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2888 (synopsis "Supplementary distributions")
2890 "This package provides ten distributions supplementing those built into
2891 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2892 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2893 coefficient, Johnson distributions, normal scores and generalized
2894 hypergeometric distributions. In addition two random number generators of
2895 George Marsaglia are included.")
2896 (license license:gpl2+)))
2898 (define-public r-ksamples
2905 (uri (cran-uri "kSamples" version))
2908 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2909 (properties `((upstream-name . "kSamples")))
2910 (build-system r-build-system)
2912 `(("r-suppdists" ,r-suppdists)))
2913 (home-page "https://cran.r-project.org/web/packages/kSamples")
2914 (synopsis "K-Sample rank tests and their combinations")
2916 "This package provides tools to compares k samples using the
2917 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2918 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2919 test. It computes asymptotic, simulated or (limited) exact P-values, all
2920 valid under randomization, with or without ties, or conditionally under random
2921 sampling from populations, given the observed tie pattern. Except for Steel's
2922 test and the JT test it also combines these tests across several blocks of
2924 (license license:gpl2+)))
2926 (define-public r-cvst
2933 (uri (cran-uri "CVST" version))
2936 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2937 (properties `((upstream-name . "CVST")))
2938 (build-system r-build-system)
2940 `(("r-kernlab" ,r-kernlab)
2941 ("r-matrix" ,r-matrix)))
2942 (home-page "https://cran.r-project.org/web/packages/CVST")
2943 (synopsis "Fast cross-validation via sequential testing")
2945 "This package implements the fast cross-validation via sequential
2946 testing (CVST) procedure. CVST is an improved cross-validation procedure
2947 which uses non-parametric testing coupled with sequential analysis to
2948 determine the best parameter set on linearly increasing subsets of the data.
2949 Additionally to the CVST the package contains an implementation of the
2950 ordinary k-fold cross-validation with a flexible and powerful set of helper
2951 objects and methods to handle the overall model selection process. The
2952 implementations of the Cochran's Q test with permutations and the sequential
2953 testing framework of Wald are generic and can therefore also be used in other
2955 (license license:gpl2+)))
2957 (define-public r-squarem
2964 (uri (cran-uri "SQUAREM" version))
2967 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
2968 (properties `((upstream-name . "SQUAREM")))
2969 (build-system r-build-system)
2970 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2971 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2973 "This package provides algorithms for accelerating the convergence of
2974 slow, monotone sequences from smooth, contraction mapping such as the EM
2975 algorithm. It can be used to accelerate any smooth, linearly convergent
2976 acceleration scheme. A tutorial style introduction to this package is
2977 available in a vignette.")
2978 (license license:gpl2+)))
2980 (define-public r-lava
2987 (uri (cran-uri "lava" version))
2990 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2991 (build-system r-build-system)
2993 `(("r-numderiv" ,r-numderiv)
2994 ("r-squarem" ,r-squarem)
2995 ("r-survival" ,r-survival)))
2996 (home-page "https://github.com/kkholst/lava")
2997 (synopsis "Latent variable models")
2999 "This package provides tools for the estimation and simulation of latent
3001 (license license:gpl3)))
3003 (define-public r-drr
3010 (uri (cran-uri "DRR" version))
3013 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3014 (properties `((upstream-name . "DRR")))
3015 (build-system r-build-system)
3017 `(("r-cvst" ,r-cvst)
3018 ("r-kernlab" ,r-kernlab)
3019 ("r-matrix" ,r-matrix)))
3020 (home-page "https://cran.r-project.org/web/packages/DRR")
3021 (synopsis "Dimensionality reduction via regression")
3023 "This package provides an implementation of dimensionality reduction via
3024 regression using Kernel Ridge Regression.")
3025 (license license:gpl3)))
3027 (define-public r-prodlim
3030 (version "2019.11.13")
3034 (uri (cran-uri "prodlim" version))
3037 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3038 (build-system r-build-system)
3040 `(("r-kernsmooth" ,r-kernsmooth)
3043 ("r-survival" ,r-survival)))
3044 (home-page "https://cran.r-project.org/web/packages/prodlim")
3045 (synopsis "Product-limit estimation for censored event history analysis")
3047 "This package provides a fast and user-friendly implementation of
3048 nonparametric estimators for censored event history (survival) analysis with
3049 the Kaplan-Meier and Aalen-Johansen methods.")
3050 (license license:gpl2+)))
3052 (define-public r-dimred
3059 (uri (cran-uri "dimRed" version))
3062 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3063 (properties `((upstream-name . "dimRed")))
3064 (build-system r-build-system)
3067 ("r-magrittr" ,r-magrittr)))
3068 (home-page "https://github.com/gdkrmr/dimRed")
3069 (synopsis "Framework for dimensionality reduction")
3071 "This package provides a collection of dimensionality reduction
3072 techniques from R packages and provides a common interface for calling the
3074 (license license:gpl3)))
3076 (define-public r-timedate
3079 (version "3043.102")
3083 (uri (cran-uri "timeDate" version))
3086 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3087 (properties `((upstream-name . "timeDate")))
3088 (build-system r-build-system)
3089 (home-page "https://www.rmetrics.org")
3090 (synopsis "Chronological and calendar objects")
3092 "This package provides an environment for teaching \"Financial
3093 Engineering and Computational Finance\" and for managing chronological and
3095 (license license:gpl2+)))
3097 (define-public r-magic
3104 (uri (cran-uri "magic" version))
3107 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3108 (build-system r-build-system)
3110 `(("r-abind" ,r-abind)))
3111 (home-page "https://github.com/RobinHankin/magic.git")
3112 (synopsis "Create and investigate magic squares")
3114 "This package provides a collection of efficient, vectorized algorithms
3115 for the creation and investigation of magic squares and hypercubes, including
3116 a variety of functions for the manipulation and analysis of arbitrarily
3117 dimensioned arrays.")
3118 (license license:gpl2)))
3120 (define-public r-rmysql
3127 (uri (cran-uri "RMySQL" version))
3130 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3131 (properties `((upstream-name . "RMySQL")))
3132 (build-system r-build-system)
3134 `(("mariadb" ,mariadb "lib")
3135 ("mariadb-dev" ,mariadb "dev")
3138 `(("r-dbi" ,r-dbi)))
3139 (home-page "https://github.com/r-dbi/RMySQL")
3140 (synopsis "Database interface and MySQL driver for R")
3142 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3143 package contains an old implementation based on legacy code from S-PLUS which
3144 is being phased out. A modern MySQL client based on Rcpp is available from
3145 the RMariaDB package.")
3146 (license license:gpl2)))
3148 (define-public r-rpostgresql
3150 (name "r-rpostgresql")
3155 (uri (cran-uri "RPostgreSQL" version))
3158 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3159 (properties `((upstream-name . "RPostgreSQL")))
3160 (build-system r-build-system)
3162 `(("postgresql" ,postgresql)))
3164 `(("r-dbi" ,r-dbi)))
3165 (home-page "https://github.com/tomoakin/RPostgreSQL")
3166 (synopsis "R interface to the PostgreSQL database system")
3168 "This package provides a Database Interface (DBI) compliant driver for R
3169 to access PostgreSQL database systems.")
3170 ;; The whole package is released under GPL version 2. It includes code
3171 ;; under the PostgreSQL license.
3172 (license license:gpl2)))
3174 (define-public r-linprog
3181 (uri (cran-uri "linprog" version))
3184 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3185 (build-system r-build-system)
3186 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3187 (home-page "http://linprog.r-forge.r-project.org/")
3188 (synopsis "Linear programming and optimization")
3190 "This package can be used to solve Linear Programming / Linear
3191 Optimization problems by using the simplex algorithm.")
3192 (license license:gpl2+)))
3194 (define-public r-geometry
3201 (uri (cran-uri "geometry" version))
3204 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3205 (build-system r-build-system)
3207 `(("r-magic" ,r-magic)
3208 ("r-linprog" ,r-linprog)
3209 ("r-lpsolve" ,r-lpsolve)
3211 ("r-rcppprogress" ,r-rcppprogress)))
3212 (home-page "http://geometry.r-forge.r-project.org/")
3213 (synopsis "Mesh generation and surface tesselation")
3215 "This package makes the qhull library available in R, in a similar manner
3216 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3217 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3218 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3219 and higher dimensions. It implements the Quickhull algorithm for computing
3220 the convex hull. Qhull does not support constrained Delaunay triangulations,
3221 or mesh generation of non-convex objects, but the package does include some R
3222 functions that allow for this. Currently the package only gives access to
3223 Delaunay triangulation and convex hull computation.")
3224 ;; The Qhull sources are included and are distributed under a custom
3225 ;; non-copyleft license. The R sources are released under GPL version 2.
3226 (license (list license:gpl2
3227 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3229 (define-public r-ddalpha
3236 (uri (cran-uri "ddalpha" version))
3239 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3240 (build-system r-build-system)
3243 ("r-class" ,r-class)
3244 ("r-geometry" ,r-geometry)
3247 ("r-robustbase" ,r-robustbase)
3248 ("r-sfsmisc" ,r-sfsmisc)))
3250 `(("gfortran" ,gfortran)))
3251 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3252 (synopsis "Depth-Based classification and calculation of data depth")
3254 "This package contains procedures for depth-based supervised learning,
3255 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3256 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3257 statistical depth function to a compact low-dimensional space, where the final
3258 classification is done. It also offers an extension to functional data and
3259 routines for calculating certain notions of statistical depth functions. 50
3260 multivariate and 5 functional classification problems are included.")
3261 (license license:gpl2)))
3263 (define-public r-gower
3270 (uri (cran-uri "gower" version))
3273 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
3274 (build-system r-build-system)
3275 (home-page "https://github.com/markvanderloo/gower")
3276 (synopsis "Gower's distance")
3278 "This package provides tools to compute Gower's distance (or similarity)
3279 coefficient between records, and to compute the top-n matches between records.
3280 Core algorithms are executed in parallel on systems supporting OpenMP.")
3281 (license license:gpl3)))
3283 (define-public r-rcpproll
3290 (uri (cran-uri "RcppRoll" version))
3293 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3294 (properties `((upstream-name . "RcppRoll")))
3295 (build-system r-build-system)
3297 `(("r-rcpp" ,r-rcpp)))
3298 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3299 (synopsis "Efficient rolling and windowed operations")
3301 "This package provides fast and efficient routines for common rolling /
3302 windowed operations. Routines for the efficient computation of windowed mean,
3303 median, sum, product, minimum, maximum, standard deviation and variance are
3305 (license license:gpl2+)))
3307 (define-public r-ipred
3314 (uri (cran-uri "ipred" version))
3317 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3318 (build-system r-build-system)
3320 `(("r-class" ,r-class)
3323 ("r-prodlim" ,r-prodlim)
3324 ("r-rpart" ,r-rpart)
3325 ("r-survival" ,r-survival)))
3326 (home-page "https://cran.r-project.org/web/packages/ipred")
3327 (synopsis "Improved predictors")
3329 "This package provides improved predictive models by indirect
3330 classification and bagging for classification, regression and survival
3331 problems as well as resampling based estimators of prediction error.")
3332 (license license:gpl2+)))
3334 (define-public r-psych
3337 (version "1.9.12.31")
3341 (uri (cran-uri "psych" version))
3344 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3345 (build-system r-build-system)
3347 `(("r-lattice" ,r-lattice)
3348 ("r-mnormt" ,r-mnormt)
3349 ("r-nlme" ,r-nlme)))
3350 (home-page "https://cran.r-project.org/web/packages/psych/")
3351 (synopsis "Procedures for psychological, psychometric, and personality research")
3353 "This package provides a general purpose toolbox for personality,
3354 psychometric theory and experimental psychology. Functions are primarily for
3355 multivariate analysis and scale construction using factor analysis, principal
3356 component analysis, cluster analysis and reliability analysis, although others
3357 provide basic descriptive statistics. Item Response Theory is done using
3358 factor analysis of tetrachoric and polychoric correlations. Functions for
3359 analyzing data at multiple levels include within and between group statistics,
3360 including correlations and factor analysis. Functions for simulating and
3361 testing particular item and test structures are included. Several functions
3362 serve as a useful front end for structural equation modeling. Graphical
3363 displays of path diagrams, factor analysis and structural equation models are
3364 created using basic graphics.")
3365 (license license:gpl2+)))
3367 (define-public r-generics
3374 (uri (cran-uri "generics" version))
3377 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3378 (build-system r-build-system)
3379 (home-page "https://github.com/r-lib/generics")
3380 (synopsis "Common S3 generics not provided by base R methods")
3382 "In order to reduce potential package dependencies and conflicts,
3383 generics provides a number of commonly used S3 generics that are not provided
3384 by base R methods related to model fitting.")
3385 (license license:gpl2)))
3387 (define-public r-broom
3394 (uri (cran-uri "broom" version))
3397 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3398 (build-system r-build-system)
3400 `(("r-backports" ,r-backports)
3401 ("r-dplyr" ,r-dplyr)
3402 ("r-generics" ,r-generics)
3404 ("r-purrr" ,r-purrr)
3405 ("r-reshape2" ,r-reshape2)
3406 ("r-stringr" ,r-stringr)
3407 ("r-tibble" ,r-tibble)
3408 ("r-tidyr" ,r-tidyr)))
3410 `(("r-knitr" ,r-knitr)))
3411 (home-page "https://github.com/tidyverse/broom")
3412 (synopsis "Convert statistical analysis objects into tidy data frames")
3414 "This package provides tools to convert statistical analysis objects from
3415 R into tidy data frames, so that they can more easily be combined, reshaped
3416 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3417 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3418 summarizes a model's statistical findings such as coefficients of a
3419 regression; @code{augment}, which adds columns to the original data such as
3420 predictions, residuals and cluster assignments; and @code{glance}, which
3421 provides a one-row summary of model-level statistics.")
3422 (license license:expat)))
3424 (define-public r-recipes
3431 (uri (cran-uri "recipes" version))
3434 "0hbnrqgzazg401nk5fhljif7wnspicki179qf215r34y9wm8g3xj"))))
3435 (build-system r-build-system)
3437 `(("r-dplyr" ,r-dplyr)
3438 ("r-generics" ,r-generics)
3440 ("r-gower" ,r-gower)
3441 ("r-ipred" ,r-ipred)
3442 ("r-lubridate" ,r-lubridate)
3443 ("r-magrittr" ,r-magrittr)
3444 ("r-matrix" ,r-matrix)
3445 ("r-purrr" ,r-purrr)
3446 ("r-rlang" ,r-rlang)
3447 ("r-tibble" ,r-tibble)
3448 ("r-tidyr" ,r-tidyr)
3449 ("r-tidyselect" ,r-tidyselect)
3450 ("r-timedate" ,r-timedate)
3451 ("r-withr" ,r-withr)))
3453 `(("r-knitr" ,r-knitr)))
3454 (home-page "https://github.com/topepo/recipes")
3455 (synopsis "Preprocessing tools to create design matrices")
3457 "Recipes is an extensible framework to create and preprocess design
3458 matrices. Recipes consist of one or more data manipulation and analysis
3459 \"steps\". Statistical parameters for the steps can be estimated from an
3460 initial data set and then applied to other data sets. The resulting design
3461 matrices can then be used as inputs into statistical or machine learning
3463 (license license:gpl2)))
3465 (define-public r-pdist
3472 (uri (cran-uri "pdist" version))
3475 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3476 (build-system r-build-system)
3477 (home-page "https://github.com/jeffwong/pdist")
3478 (synopsis "Partitioned distance function")
3480 "Pdist computes the euclidean distance between rows of a matrix X and
3481 rows of another matrix Y. Previously, this could be done by binding the two
3482 matrices together and calling @code{dist}, but this creates unnecessary
3483 computation by computing the distances between a row of X and another row of
3484 X, and likewise for Y. Pdist strictly computes distances across the two
3485 matrices, not within the same matrix, making computations significantly faster
3486 for certain use cases.")
3487 (license license:gpl3+)))
3489 (define-public r-ggrepel
3496 (uri (cran-uri "ggrepel" version))
3499 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3500 (build-system r-build-system)
3502 `(("r-ggplot2" ,r-ggplot2)
3504 ("r-scales" ,r-scales)))
3506 `(("r-knitr" ,r-knitr))) ; for vignettes
3507 (home-page "http://github.com/slowkow/ggrepel")
3508 (synopsis "Repulsive text and label geometries for ggplot2")
3510 "This package provides text and label geometries for ggplot2 that help to
3511 avoid overlapping text labels. Labels repel away from each other and away
3512 from the data points.")
3513 (license license:gpl3)))
3515 (define-public r-corrplot
3522 (uri (cran-uri "corrplot" version))
3525 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3526 (build-system r-build-system)
3527 (home-page "https://github.com/taiyun/corrplot")
3528 (synopsis "Visualization of a correlation matrix")
3530 "This package provides a graphical display of a correlation matrix or
3531 general matrix. It also contains some algorithms to do matrix reordering. In
3532 addition, corrplot is good at details, including choosing color, text labels,
3533 color labels, layout, etc.")
3534 ;; Any version of the GPL
3535 (license license:gpl2+)))
3537 (define-public r-stringdist
3539 (name "r-stringdist")
3544 (uri (cran-uri "stringdist" version))
3546 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3547 (build-system r-build-system)
3548 (home-page "https://github.com/markvanderloo/stringdist")
3549 (synopsis "Approximate string matching and string distance functions")
3551 "This package implements an approximate string matching version of R's
3552 native @code{match} function. It can calculate various string distances based
3553 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3554 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3555 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3556 can be computed between character vectors while taking proper care of encoding
3557 or between integer vectors representing generic sequences.")
3558 (license license:gpl3+)))
3560 (define-public r-ucminf
3567 (uri (cran-uri "ucminf" version))
3570 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3571 (build-system r-build-system)
3572 (native-inputs `(("gfortran" ,gfortran)))
3573 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3574 (synopsis "General-purpose unconstrained non-linear optimization")
3576 "This package provides an implementation of an algorithm for
3577 general-purpose unconstrained non-linear optimization. The algorithm is of
3578 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3579 search with a trust region type monitoring of the input to the line search
3580 algorithm. The interface of @code{ucminf} is designed for easy interchange
3581 with the package @code{optim}.")
3582 (license license:gpl2+)))
3584 (define-public r-ordinal
3587 (version "2019.12-10")
3591 (uri (cran-uri "ordinal" version))
3594 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3595 (build-system r-build-system)
3597 `(("r-mass" ,r-mass)
3598 ("r-matrix" ,r-matrix)
3599 ("r-numderiv" ,r-numderiv)
3600 ("r-ucminf" ,r-ucminf)))
3601 (home-page "https://github.com/runehaubo/ordinal")
3602 (synopsis "Regression models for ordinal data")
3604 "This package provides an implementation of cumulative link (mixed)
3605 models also known as ordered regression models, proportional odds models,
3606 proportional hazards models for grouped survival times and ordered models.
3607 Estimation is via maximum likelihood and mixed models are fitted with the
3608 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3609 (license license:gpl2+)))
3611 (define-public r-jomo
3618 (uri (cran-uri "jomo" version))
3621 "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w"))))
3622 (build-system r-build-system)
3624 `(("r-lme4" ,r-lme4)
3626 ("r-ordinal" ,r-ordinal)
3627 ("r-survival" ,r-survival)))
3628 (home-page "https://cran.r-project.org/web/packages/jomo/")
3629 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3631 "Similarly to Schafer's package pan, jomo is a package for multilevel
3632 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3633 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3634 possibility of handling binary and categorical data through latent normal
3635 variables, the option to use cluster-specific covariance matrices and to
3636 impute compatibly with the substantive model.")
3637 (license license:gpl2)))
3639 (define-public r-pan
3646 (uri (cran-uri "pan" version))
3649 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3650 (build-system r-build-system)
3651 (native-inputs `(("gfortran" ,gfortran)))
3652 (home-page "https://cran.r-project.org/web/packages/pan/")
3653 (synopsis "Multiple imputation for multivariate panel or clustered data")
3655 "This package implements multiple imputation for multivariate panel or
3657 (license license:gpl3)))
3659 (define-public r-mitml
3666 (uri (cran-uri "mitml" version))
3669 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3670 (build-system r-build-system)
3672 `(("r-haven" ,r-haven)
3675 (home-page "https://cran.r-project.org/web/packages/mitml/")
3676 (synopsis "Tools for multiple imputation in multilevel modeling")
3678 "This package provides tools for multiple imputation of missing data in
3679 multilevel modeling. It includes a user-friendly interface to the packages
3680 pan and jomo, and several functions for visualization, data management and the
3681 analysis of multiply imputed data sets.")
3682 (license license:gpl2+)))
3684 (define-public r-mice
3691 (uri (cran-uri "mice" version))
3694 "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn"))))
3695 (build-system r-build-system)
3697 `(("r-broom" ,r-broom)
3698 ("r-dplyr" ,r-dplyr)
3699 ("r-lattice" ,r-lattice)
3701 ("r-tidyr" ,r-tidyr)))
3702 (home-page "https://cran.r-project.org/web/packages/mice/")
3703 (synopsis "Multivariate imputation by chained equations")
3705 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3706 implemented by the MICE algorithm as described in @url{Van Buuren and
3707 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3708 variable has its own imputation model. Built-in imputation models are
3709 provided for continuous data (predictive mean matching, normal), binary
3710 data (logistic regression), unordered categorical data (polytomous logistic
3711 regression) and ordered categorical data (proportional odds). MICE can also
3712 impute continuous two-level data (normal model, pan, second-level variables).
3713 Passive imputation can be used to maintain consistency between variables.
3714 Various diagnostic plots are available to inspect the quality of the
3716 ;; Any of these two versions.
3717 (license (list license:gpl2 license:gpl3))))
3719 (define-public r-truncnorm
3721 (name "r-truncnorm")
3726 (uri (cran-uri "truncnorm" version))
3729 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3730 (build-system r-build-system)
3731 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3732 (synopsis "Truncated normal distribution")
3733 (description "This package provides functions for the truncated normal
3734 distribution with mean equal to @code{mean} and standard deviation equal to
3735 @code{sd}. It includes density, distribution, quantile, and expected value
3736 functions, as well as a random generation function.")
3737 (license license:gpl2)))
3739 (define-public r-rsolnp
3746 (uri (cran-uri "Rsolnp" version))
3749 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3750 (properties `((upstream-name . "Rsolnp")))
3751 (build-system r-build-system)
3753 `(("r-truncnorm" ,r-truncnorm)))
3754 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3755 (synopsis "General non-linear optimization")
3756 (description "The Rsolnp package implements a general non-linear augmented
3757 Lagrange multiplier method solver, a @dfn{sequential quadratic
3758 programming} (SQP) based solver).")
3759 ;; Any version of the GPL.
3760 (license license:gpl2+)))
3762 (define-public r-hardyweinberg
3764 (name "r-hardyweinberg")
3769 (uri (cran-uri "HardyWeinberg" version))
3772 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3773 (properties `((upstream-name . "HardyWeinberg")))
3774 (build-system r-build-system)
3776 `(("r-mice" ,r-mice)
3778 ("r-rsolnp" ,r-rsolnp)))
3779 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3780 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3782 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3783 diallelic genetic marker data. All classical tests (chi-square, exact,
3784 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3785 included in the package, as well as functions for power computation and for
3786 the simulation of marker data under equilibrium and disequilibrium. Routines
3787 for dealing with markers on the X-chromosome are included. Functions for
3788 testing equilibrium in the presence of missing data by using multiple
3789 imputation are also provided. Implements several graphics for exploring the
3790 equilibrium status of a large set of diallelic markers: ternary plots with
3791 acceptance regions, log-ratio plots and Q-Q plots.")
3792 (license license:gpl2+)))
3801 (uri (cran-uri "sm" version))
3804 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3805 (build-system r-build-system)
3806 (native-inputs `(("gfortran" ,gfortran)))
3807 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3808 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3810 "This is software accompanying the book 'Applied Smoothing Techniques for
3811 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3812 University Press. It provides smoothing methods for nonparametric regression
3813 and density estimation")
3814 (license license:gpl2+)))
3816 (define-public r-venndiagram
3818 (name "r-venndiagram")
3822 (uri (cran-uri "VennDiagram" version))
3825 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3826 (properties `((upstream-name . "VennDiagram")))
3827 (build-system r-build-system)
3829 `(("r-futile-logger" ,r-futile-logger)))
3830 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3831 (synopsis "Generate High-Resolution Venn and Euler Plots")
3833 "This package provides a set of functions to generate high-resolution
3834 Venn and Euler plots. It includes handling for several special cases,
3835 including two-case scaling, and extensive customization of plot shape and
3837 (license license:gpl2+)))
3839 (define-public r-vioplot
3846 (uri (cran-uri "vioplot" version))
3849 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3850 (build-system r-build-system)
3855 `(("r-knitr" ,r-knitr)))
3856 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3857 (synopsis "Violin plot")
3859 "This package provides a violin plot, which is a combination of a box
3860 plot and a kernel density plot.")
3861 (license license:bsd-3)))
3863 (define-public r-rsofia
3869 ;; This package has been removed from CRAN, so we can
3870 ;; only fetch it from the archives.
3871 (uri (string-append "https://cran.r-project.org/src/"
3872 "contrib/Archive/RSofia/RSofia_"
3876 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3877 (properties `((upstream-name . "RSofia")))
3878 (build-system r-build-system)
3880 `(("r-rcpp" ,r-rcpp)))
3881 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3882 (synopsis "Port of sofia-ml to R")
3883 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3884 suite of fast incremental algorithms for machine learning that can be used for
3885 training models for classification or ranking.")
3886 (license license:asl2.0)))
3888 (define-public r-xts
3895 (uri (cran-uri "xts" version))
3898 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3899 (build-system r-build-system)
3900 (propagated-inputs `(("r-zoo" ,r-zoo)))
3901 (home-page "https://github.com/joshuaulrich/xts")
3902 (synopsis "Extensible time series")
3904 "This package provides for uniform handling of R's different time-based
3905 data classes by extending @code{zoo}, maximizing native format information
3906 preservation and allowing for user-level customization and extension, while
3907 simplifying cross-class interoperability.")
3908 (license license:gpl2+)))
3910 (define-public r-performanceanalytics
3912 (name "r-performanceanalytics")
3917 (uri (cran-uri "PerformanceAnalytics" version))
3920 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3922 `((upstream-name . "PerformanceAnalytics")))
3923 (build-system r-build-system)
3925 `(("r-quadprog" ,r-quadprog)
3928 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3929 (synopsis "Econometric tools for performance and risk analysis")
3930 (description "This is a collection of econometric functions for
3931 performance and risk analysis. This package aims to aid practitioners and
3932 researchers in utilizing the latest research in analysis of non-normal return
3933 streams. In general, it is most tested on return (rather than price) data on
3934 a regular scale, but most functions will work with irregular return data as
3935 well, and increasing numbers of functions will work with P&L or price data
3937 ;; Either version may be picked.
3938 (license (list license:gpl2 license:gpl3))))
3940 (define-public r-laeken
3947 (uri (cran-uri "laeken" version))
3950 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3951 (build-system r-build-system)
3953 `(("r-boot" ,r-boot)
3954 ("r-mass" ,r-mass)))
3955 (home-page "https://cran.r-project.org/web/packages/laeken/")
3956 (synopsis "Estimation of indicators on social exclusion and poverty")
3957 (description "This package provides tools for the estimation of indicators
3958 on social exclusion and poverty, as well as an implementation of Pareto tail
3959 modeling for empirical income distributions.")
3960 (license license:gpl2+)))
3962 (define-public r-vcd
3969 (uri (cran-uri "vcd" version))
3972 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3973 (build-system r-build-system)
3975 `(("r-colorspace" ,r-colorspace)
3976 ("r-lmtest" ,r-lmtest)
3977 ("r-mass" ,r-mass)))
3978 (home-page "https://cran.r-project.org/web/packages/vcd/")
3979 (synopsis "Visualizing categorical data")
3980 (description "This package provides visualization techniques, data sets,
3981 summary and inference procedures aimed particularly at categorical data.
3982 Special emphasis is given to highly extensible grid graphics. The package was
3983 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3984 Friendly and is now the main support package for a new book, \"Discrete Data
3985 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3986 (license license:gpl2)))
3988 (define-public r-ica
3995 (uri (cran-uri "ica" version))
3998 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3999 (build-system r-build-system)
4000 (home-page "https://cran.r-project.org/web/packages/ica/")
4001 (synopsis "Independent component analysis")
4002 (description "This package provides tools for @dfn{Independent Component
4003 Analysis} (ICA) using various algorithms: FastICA,
4004 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4005 of Eigenmatrices} (JADE).")
4006 (license license:gpl2+)))
4008 (define-public r-dtw
4015 (uri (cran-uri "dtw" version))
4018 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4019 (build-system r-build-system)
4020 (propagated-inputs `(("r-proxy" ,r-proxy)))
4021 (home-page "http://dtw.r-forge.r-project.org/")
4022 (synopsis "Dynamic Time Warping Algorithms")
4023 (description "This package provides a comprehensive implementation of
4024 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4025 optimal (least cumulative distance) alignment between points of two time
4026 series. Common DTW variants covered include local (slope) and global (window)
4027 constraints, subsequence matches, arbitrary distance definitions,
4028 normalizations, minimum variance matching, and so on.")
4029 (license license:gpl2+)))
4031 (define-public r-sdmtools
4034 (version "1.1-221.2")
4038 (uri (cran-uri "SDMTools" version))
4041 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4042 (properties `((upstream-name . "SDMTools")))
4043 (build-system r-build-system)
4044 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4045 (home-page "https://www.rforge.net/SDMTools/")
4046 (synopsis "Species distribution modelling tools")
4047 (description "This package provides a set of tools for post processing
4048 the outcomes of species distribution modeling exercises. It includes novel
4049 methods for comparing models and tracking changes in distributions through
4050 time. It further includes methods for visualizing outcomes, selecting
4051 thresholds, calculating measures of accuracy and landscape fragmentation
4053 (license license:gpl3+)))
4055 (define-public r-scatterplot3d
4057 (name "r-scatterplot3d")
4062 (uri (cran-uri "scatterplot3d" version))
4065 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4066 (build-system r-build-system)
4067 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4068 (synopsis "3D scatter plot")
4069 (description "This package provides an implementation of scatter plots for
4070 plotting. a three dimensional point cloud.")
4071 (license license:gpl2)))
4073 (define-public r-ggridges
4080 (uri (cran-uri "ggridges" version))
4083 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4084 (build-system r-build-system)
4086 `(("r-ggplot2" ,r-ggplot2)
4088 ("r-scales" ,r-scales)
4089 ("r-withr" ,r-withr)))
4090 (home-page "https://github.com/clauswilke/ggridges")
4091 (synopsis "Ridgeline plots in ggplot2")
4093 "Ridgeline plots provide a convenient way of visualizing changes in
4094 distributions over time or space. This package enables the creation of such
4095 plots in @code{ggplot2}.")
4096 (license license:gpl2)))
4098 (define-public r-ggjoy
4105 (uri (cran-uri "ggjoy" version))
4108 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4109 (build-system r-build-system)
4111 `(("r-ggplot2" ,r-ggplot2)
4112 ("r-ggridges" ,r-ggridges)))
4113 (home-page "https://github.com/clauswilke/ggjoy")
4114 (synopsis "Joyplots in ggplot2")
4115 (description "Joyplots provide a convenient way of visualizing changes in
4116 distributions over time or space. This package enables the creation of such
4117 plots in @code{ggplot2}.")
4118 (license license:gpl2)))
4120 (define-public r-cli
4127 (uri (cran-uri "cli" version))
4130 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4131 (build-system r-build-system)
4133 `(("r-assertthat" ,r-assertthat)
4134 ("r-crayon" ,r-crayon)
4135 ("r-fansi" ,r-fansi)
4136 ("r-glue" ,r-glue)))
4137 (home-page "https://github.com/r-lib/cli#readme")
4138 (synopsis "Helpers for developing command line interfaces")
4139 (description "This package provides a suite of tools designed to build
4140 attractive command line interfaces (CLIs). It includes tools for drawing
4141 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4142 (license license:expat)))
4144 (define-public r-argparser
4146 (name "r-argparser")
4151 (uri (cran-uri "argparser" version))
4154 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4155 (build-system r-build-system)
4156 (home-page "https://bitbucket.org/djhshih/argparser")
4157 (synopsis "Command-line argument parser")
4159 "This package provides a cross-platform command-line argument parser
4160 written purely in R with no external dependencies. It is useful with the
4161 Rscript front-end and facilitates turning an R script into an executable
4163 (license license:gpl3+)))
4165 (define-public r-debugme
4172 (uri (cran-uri "debugme" version))
4175 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4176 (build-system r-build-system)
4177 (propagated-inputs `(("r-crayon" ,r-crayon)))
4178 (home-page "https://github.com/r-lib/debugme#readme")
4179 (synopsis "Debug R packages")
4181 "This package allows the user to specify debug messages as special string
4182 constants, and control debugging of packages via environment variables.")
4183 (license license:expat)))
4185 (define-public r-processx
4192 (uri (cran-uri "processx" version))
4195 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4196 (build-system r-build-system)
4200 (home-page "https://github.com/r-lib/processx3")
4201 (synopsis "Execute and control system processes")
4203 "This package provides portable tools to run system processes in the
4204 background. It can check if a background process is running; wait on a
4205 background process to finish; get the exit status of finished processes; kill
4206 background processes and their children; restart processes. It can read the
4207 standard output and error of the processes, using non-blocking connections.
4208 @code{processx} can poll a process for standard output or error, with a
4209 timeout. It can also poll several processes at once.")
4210 (license license:expat)))
4212 (define-public r-tsp
4219 (uri (cran-uri "TSP" version))
4222 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4223 (properties `((upstream-name . "TSP")))
4224 (build-system r-build-system)
4225 (propagated-inputs `(("r-foreach" ,r-foreach)))
4226 (home-page "https://cran.r-project.org/web/packages/TSP/")
4227 (synopsis "Traveling salesperson problem (TSP)")
4228 (description "This package provides basic infrastructure and some
4229 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4230 traveling salesman problem).")
4231 (license license:gpl3)))
4233 (define-public r-qap
4240 (uri (cran-uri "qap" version))
4243 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4244 (build-system r-build-system)
4245 (native-inputs `(("gfortran" ,gfortran)))
4246 (home-page "https://cran.r-project.org/web/packages/qap/")
4247 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4248 (description "This package implements heuristics for the @dfn{quadratic
4249 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4251 (license license:gpl3)))
4253 (define-public r-gclus
4260 (uri (cran-uri "gclus" version))
4263 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4264 (build-system r-build-system)
4265 (propagated-inputs `(("r-cluster" ,r-cluster)))
4266 (home-page "https://cran.r-project.org/web/packages/gclus/")
4267 (synopsis "Clustering graphics")
4268 (description "This package orders panels in scatterplot matrices and
4269 parallel coordinate displays by some merit index. It contains various indices
4270 of merit, ordering functions, and enhanced versions of @code{pairs} and
4271 @code{parcoord} which color panels according to their merit level.")
4272 (license license:gpl2+)))
4274 (define-public r-webshot
4281 (uri (cran-uri "webshot" version))
4284 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4285 (build-system r-build-system)
4287 `(("r-callr" ,r-callr)
4288 ("r-jsonlite" ,r-jsonlite)
4289 ("r-magrittr" ,r-magrittr)))
4290 (home-page "https://github.com/wch/webshot/")
4291 (synopsis "Take screenshots of web pages")
4293 "Webshot makes it easy to take screenshots of web pages from within R.
4294 It can also run Shiny applications locally and take screenshots of the
4295 application; and it can render and screenshot static as well as interactive R
4296 Markdown documents.")
4297 (license license:gpl2)))
4299 (define-public r-seriation
4301 (name "r-seriation")
4306 (uri (cran-uri "seriation" version))
4309 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4310 (build-system r-build-system)
4312 `(("r-cluster" ,r-cluster)
4313 ("r-colorspace" ,r-colorspace)
4314 ("r-dendextend" ,r-dendextend)
4315 ("r-gclus" ,r-gclus)
4316 ("r-gplots" ,r-gplots)
4319 ("r-registry" ,r-registry)
4321 (native-inputs `(("gfortran" ,gfortran)))
4322 (home-page "https://s2.smu.edu/IDA/seriation/")
4323 (synopsis "Infrastructure for ordering objects using seriation")
4325 "This package provides infrastructure for seriation with an
4326 implementation of several seriation/sequencing techniques to reorder matrices,
4327 dissimilarity matrices, and dendrograms. It also provides (optimally)
4328 reordered heatmaps, color images and clustering visualizations like
4329 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4331 (license license:gpl3)))
4333 (define-public r-xfun
4340 (uri (cran-uri "xfun" version))
4342 (base32 "183f6d7lr116f90j37a8hfr6ni1x9xkqj79s8lnky1jwr6zj3ha9"))))
4343 (build-system r-build-system)
4344 ;; knitr itself depends on xfun
4347 `(("r-knitr" ,r-knitr)))
4348 (home-page "https://github.com/yihui/xfun")
4349 (synopsis "Miscellaneous functions")
4351 "This package provides miscellaneous functions commonly used in other
4352 packages maintained by Yihui Xie.")
4353 (license license:expat)))
4355 (define-public r-utf8
4362 (uri (cran-uri "utf8" version))
4365 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4366 (build-system r-build-system)
4367 (home-page "https://github.com/patperry/r-utf8")
4368 (synopsis "Unicode text processing")
4370 "This package provides tools to process and print UTF-8 encoded
4371 international text (Unicode). Input, validate, normalize, encode, format, and
4373 (license license:asl2.0)))
4375 (define-public r-zeallot
4382 (uri (cran-uri "zeallot" version))
4385 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4386 (build-system r-build-system)
4387 (home-page "https://github.com/nteetor/zeallot")
4388 (synopsis "Multiple, unpacking, and destructuring assignment")
4390 "This package provides a @code{%<-%} operator to perform multiple,
4391 unpacking, and destructuring assignment in R. The operator unpacks the
4392 right-hand side of an assignment into multiple values and assigns these values
4393 to variables on the left-hand side of the assignment.")
4394 (license license:expat)))
4396 (define-public r-vctrs
4403 (uri (cran-uri "vctrs" version))
4406 "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp"))))
4407 (build-system r-build-system)
4409 `(("r-digest" ,r-digest)
4410 ("r-ellipsis" ,r-ellipsis)
4412 ("r-rlang" ,r-rlang)))
4414 `(("r-knitr" ,r-knitr)))
4415 (home-page "https://github.com/r-lib/vctrs")
4416 (synopsis "Vector helpers")
4418 "There are three main goals to the @code{vctrs} package:
4421 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4422 @code{length()} and @code{class()}. These definitions are paired with a
4423 framework for type-coercion and size-recycling.
4424 @item To define type- and size-stability as desirable function properties, use
4425 them to analyse existing base function, and to propose better alternatives.
4426 This work has been particularly motivated by thinking about the ideal
4427 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4428 @item To provide a new @code{vctr} base class that makes it easy to create new
4429 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4430 a few new @code{vctrs} generics, making implementation considerably simpler
4433 (license license:gpl3)))
4435 (define-public r-pillar
4442 (uri (cran-uri "pillar" version))
4445 "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1"))))
4446 (build-system r-build-system)
4449 ("r-crayon" ,r-crayon)
4450 ("r-fansi" ,r-fansi)
4451 ("r-rlang" ,r-rlang)
4453 ("r-vctrs" ,r-vctrs)))
4454 (home-page "https://github.com/r-lib/pillar")
4455 (synopsis "Coloured formatting for columns")
4457 "This package provides a @code{pillar} generic designed for formatting
4458 columns of data using the full range of colours provided by modern
4460 (license license:gpl3)))
4462 (define-public r-uuid
4469 (uri (cran-uri "uuid" version))
4472 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4473 (build-system r-build-system)
4474 (home-page "https://www.rforge.net/uuid")
4475 (synopsis "Tools for generating and handling of UUIDs")
4477 "This package provides tools for generating and handling of
4478 @dfn{Universally Unique Identifiers} (UUIDs).")
4479 (license license:expat)))
4481 (define-public r-tinytex
4488 (uri (cran-uri "tinytex" version))
4491 "084jd1m2i3zyxxlls7skq3jxv3b5cgps3yk60q1yzyy9sxslab7m"))))
4492 (build-system r-build-system)
4494 `(("r-xfun" ,r-xfun)))
4495 (home-page "https://github.com/yihui/tinytex")
4496 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4498 "This package provides helper functions to install and maintain the LaTeX
4499 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4500 easy-to-maintain version of TeX Live. This package also contains helper
4501 functions to compile LaTeX documents, and install missing LaTeX packages
4503 (license license:expat)))
4505 (define-public r-network
4512 (uri (cran-uri "network" version))
4515 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4516 (build-system r-build-system)
4518 `(("r-magrittr" ,r-magrittr)
4519 ("r-tibble" ,r-tibble)))
4520 (home-page "https://statnet.org/")
4521 (synopsis "Classes for relational data")
4523 "This package provides tools to create and modify network objects. The
4524 @code{network} class can represent a range of relational data types, and
4525 supports arbitrary vertex/edge/graph attributes.")
4526 (license license:gpl2+)))
4528 (define-public r-statnet-common
4530 (name "r-statnet-common")
4535 (uri (cran-uri "statnet.common" version))
4538 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4540 `((upstream-name . "statnet.common")))
4541 (build-system r-build-system)
4543 `(("r-coda" ,r-coda)))
4544 (home-page "https://statnet.org")
4545 (synopsis "R scripts and utilities used by the Statnet software")
4546 (description "This package provides non-statistical utilities used by the
4547 software developed by the Statnet Project.")
4548 (license license:gpl3)))
4550 (define-public r-statcheck
4552 (name "r-statcheck")
4557 (uri (cran-uri "statcheck" version))
4560 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4561 (build-system r-build-system)
4563 `(("r-ggplot2" ,r-ggplot2)
4565 ("r-rmarkdown" ,r-rmarkdown)))
4566 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4567 (synopsis "Extract statistics from articles and recompute p-values")
4568 (description "This package can automatically extract statistical
4569 null-hypothesis significant testing (NHST) results from articles and recompute
4570 the p-values based on the reported test statistic and degrees of freedom to
4571 detect possible inconsistencies.")
4572 (license license:gpl2)))
4574 (define-public r-sna
4581 (uri (cran-uri "sna" version))
4584 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4585 (build-system r-build-system)
4587 `(("r-network" ,r-network)
4588 ("r-statnet-common" ,r-statnet-common)))
4589 (home-page "https://statnet.org")
4590 (synopsis "Tools for social network analysis")
4592 "This package provides a range of tools for social network analysis,
4593 including node and graph-level indices, structural distance and covariance
4594 methods, structural equivalence detection, network regression, random graph
4595 generation, and 2D/3D network visualization.")
4596 (license license:gpl2+)))
4598 (define-public r-tfisher
4605 (uri (cran-uri "TFisher" version))
4608 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4609 (properties `((upstream-name . "TFisher")))
4610 (build-system r-build-system)
4612 `(("r-matrix" ,r-matrix)
4613 ("r-mvtnorm" ,r-mvtnorm)
4615 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4616 (synopsis "Optimal thresholding Fisher's p-value combination method")
4618 "This package provides the @dfn{cumulative distribution function} (CDF),
4619 quantile, and statistical power calculator for a collection of thresholding
4620 Fisher's p-value combination methods, including Fisher's p-value combination
4621 method, truncated product method and, in particular, soft-thresholding
4622 Fisher's p-value combination method which is proven to be optimal in some
4623 context of signal detection. The p-value calculator for the omnibus version
4624 of these tests are also included.")
4625 (license license:gpl2)))
4627 (define-public r-ttr
4634 (uri (cran-uri "TTR" version))
4637 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4638 (properties `((upstream-name . "TTR")))
4639 (build-system r-build-system)
4641 `(("r-curl" ,r-curl)
4644 (home-page "https://github.com/joshuaulrich/TTR")
4645 (synopsis "Technical trading rules")
4647 "This package provides functions and data to construct technical trading
4649 (license license:gpl2)))
4651 (define-public r-leaps
4658 (uri (cran-uri "leaps" version))
4661 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4662 (build-system r-build-system)
4663 (native-inputs `(("gfortran" ,gfortran)))
4664 (home-page "https://cran.r-project.org/web/packages/leaps/")
4665 (synopsis "Regression subset selection")
4667 "This package provides tools for regression subset selection, including
4668 exhaustive search.")
4669 (license license:gpl2+)))
4671 (define-public r-splus2r
4678 (uri (cran-uri "splus2R" version))
4681 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4682 (properties `((upstream-name . "splus2R")))
4683 (build-system r-build-system)
4684 (native-inputs `(("gfortran" ,gfortran)))
4685 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4686 (synopsis "Supplemental S-PLUS functionality in R")
4688 "Currently there are many functions in S-PLUS that are missing in R. To
4689 facilitate the conversion of S-PLUS packages to R packages, this package
4690 provides some missing S-PLUS functionality in R.")
4691 (license license:gpl2)))
4693 (define-public r-ifultools
4695 (name "r-ifultools")
4700 (uri (cran-uri "ifultools" version))
4703 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4704 (build-system r-build-system)
4706 `(("r-mass" ,r-mass)
4707 ("r-splus2r" ,r-splus2r)))
4708 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4709 (synopsis "Insightful research tools")
4710 (description "This package provides C code used by the wmtsa, fractal, and
4712 (license license:gpl2)))
4714 (define-public r-sapa
4721 (uri (cran-uri "sapa" version))
4724 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4725 (build-system r-build-system)
4727 `(("r-ifultools" ,r-ifultools)
4728 ("r-splus2r" ,r-splus2r)))
4729 (home-page "https://cran.r-project.org/web/packages/sapa/")
4730 (synopsis "Spectral analysis for physical applications")
4731 (description "This package provides software for the book Spectral
4732 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4733 Cambridge University Press, 1993.")
4734 (license license:gpl2)))
4736 (define-public r-aggregation
4738 (name "r-aggregation")
4743 (uri (cran-uri "aggregation" version))
4746 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4747 (build-system r-build-system)
4748 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4749 (synopsis "Methods for p-value aggregation")
4751 "This package contains functionality for performing the following methods
4752 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4753 Fisher's method), and Sidak correction.")
4754 (license license:gpl3)))
4756 (define-public r-quantmod
4763 (uri (cran-uri "quantmod" version))
4766 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4767 (build-system r-build-system)
4769 `(("r-curl" ,r-curl)
4773 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4774 (synopsis "Quantitative financial modelling framework")
4775 (description "This package provides a quantitative financial modelling
4776 framework to allow users to specify, build, trade, and analyse quantitative
4777 financial trading strategies.")
4778 (license license:gpl3)))
4780 (define-public r-tseries
4787 (uri (cran-uri "tseries" version))
4790 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4791 (build-system r-build-system)
4793 `(("r-quadprog" ,r-quadprog)
4794 ("r-quantmod" ,r-quantmod)
4797 `(("gfortran" ,gfortran)))
4798 (home-page "https://cran.r-project.org/web/packages/tseries/")
4799 (synopsis "Time series analysis and computational finance")
4801 "This package provides functions relating to time series analysis and
4802 computational finance.")
4803 (license license:gpl2)))
4805 (define-public r-wmtsa
4812 (uri (cran-uri "wmtsa" version))
4815 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4816 (build-system r-build-system)
4818 `(("r-ifultools" ,r-ifultools)
4820 ("r-splus2r" ,r-splus2r)))
4821 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4822 (synopsis "Wavelet methods for time series analysis")
4824 "This package provides software to accompany the book \"Wavelet Methods
4825 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4826 University Press, 2000.")
4827 (license license:gpl2)))
4829 (define-public r-tsa
4836 (uri (cran-uri "TSA" version))
4839 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4840 (properties `((upstream-name . "TSA")))
4841 (build-system r-build-system)
4843 `(("r-leaps" ,r-leaps)
4844 ("r-locfit" ,r-locfit)
4845 ("r-mgcv" ,r-mgcv)))
4846 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4847 (synopsis "Time series analysis")
4849 "This package contains R functions and datasets detailed in the book
4850 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4851 Cryer and Kung-Sik Chan.")
4852 (license license:gpl2+)))
4854 (define-public r-extradistr
4856 (name "r-extradistr")
4861 (uri (cran-uri "extraDistr" version))
4864 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4865 (properties `((upstream-name . "extraDistr")))
4866 (build-system r-build-system)
4868 `(("r-rcpp" ,r-rcpp)))
4869 (home-page "https://github.com/twolodzko/extraDistr")
4870 (synopsis "Additional univariate and multivariate distributions")
4872 "This package implements density, distribution functions, quantile
4873 functions and random generation functions for a large number of univariate and
4874 multivariate distributions.")
4875 (license license:gpl2)))
4877 (define-public r-fractal
4884 (uri (cran-uri "fractal" version))
4887 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4888 (build-system r-build-system)
4890 `(("r-ifultools" ,r-ifultools)
4893 ("r-scatterplot3d" ,r-scatterplot3d)
4894 ("r-splus2r" ,r-splus2r)
4895 ("r-wmtsa" ,r-wmtsa)))
4896 (home-page "https://cran.r-project.org/web/packages/fractal/")
4897 (synopsis "Fractal time series modeling and analysis")
4899 "This package provides tools for stochastic fractal and deterministic
4900 chaotic time series analysis.")
4901 (license license:gpl2)))
4903 (define-public r-urca
4910 (uri (cran-uri "urca" version))
4913 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4914 (build-system r-build-system)
4915 (propagated-inputs `(("r-nlme" ,r-nlme)))
4916 (native-inputs `(("gfortran" ,gfortran)))
4917 (home-page "https://cran.r-project.org/web/packages/urca/")
4918 (synopsis "Unit root and cointegration tests for time series data")
4920 "This package provides unit root and cointegration tests encountered in
4921 applied econometric analysis.")
4922 (license license:gpl2+)))
4924 (define-public r-cubature
4931 (uri (cran-uri "cubature" version))
4934 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4935 (build-system r-build-system)
4937 `(("r-rcpp" ,r-rcpp)))
4938 (home-page "https://github.com/bnaras/cubature")
4939 (synopsis "Adaptive multivariate integration over hypercubes")
4941 "This package is an R wrapper around the cubature C library for adaptive
4942 multivariate integration over hypercubes. This version provides both
4943 @code{hcubature} and @code{pcubature} routines in addition to a vector
4945 ;; The included cubature C library is released under GPLv2+, but the
4946 ;; wrapper declares the license to be GPLv3+.
4947 (license (list license:gpl2+ license:gpl3+))))
4949 (define-public r-trend
4956 (uri (cran-uri "trend" version))
4959 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4960 (build-system r-build-system)
4962 `(("r-extradistr" ,r-extradistr)))
4964 `(("gfortran" ,gfortran)))
4965 (home-page "https://cran.r-project.org/web/packages/trend/")
4966 (synopsis "Non-parametric trend tests and change-point detection")
4968 "The analysis of environmental data often requires the detection of
4969 trends and change-points. This package includes tests for trend
4970 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4971 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4972 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4973 correlation trend test), change-point detection (Lanzante's test procedures,
4974 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4975 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4976 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4977 sample Robust Rank-Order Distributional Test.")
4978 (license license:gpl3)))
4980 (define-public r-expm
4987 (uri (cran-uri "expm" version))
4990 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4991 (build-system r-build-system)
4992 (propagated-inputs `(("r-matrix" ,r-matrix)))
4993 (native-inputs `(("gfortran" ,gfortran)))
4994 (home-page "https://r-forge.r-project.org/projects/expm/")
4995 (synopsis "Tools for matrix exponentials and related quantities")
4997 "This package provides tools for the computation of the matrix
4998 exponential, logarithm, square root, and related quantities.")
4999 (license license:gpl2+)))
5001 (define-public r-complexplus
5003 (name "r-complexplus")
5008 (uri (cran-uri "complexplus" version))
5011 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5012 (build-system r-build-system)
5014 `(("r-expm" ,r-expm)
5015 ("r-matrix" ,r-matrix)))
5016 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5017 (synopsis "Functions of complex or real variables")
5019 "This package extends several functions to the complex domain, including
5020 the matrix exponential and logarithm, and the determinant.")
5021 (license license:gpl2)))
5023 (define-public r-phontools
5025 (name "r-phontools")
5030 (uri (cran-uri "phonTools" version))
5033 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5034 (properties `((upstream-name . "phonTools")))
5035 (build-system r-build-system)
5036 (home-page "http://www.santiagobarreda.com/rscripts.html")
5037 (synopsis "Tools for phonetic and acoustic analyses")
5039 "This package contains tools for the organization, display, and analysis
5040 of the sorts of data frequently encountered in phonetics research and
5041 experimentation, including the easy creation of IPA vowel plots, and the
5042 creation and manipulation of WAVE audio files.")
5043 (license license:bsd-2)))
5052 (uri (cran-uri "np" version))
5055 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5056 (build-system r-build-system)
5058 `(("r-boot" ,r-boot)
5059 ("r-cubature" ,r-cubature)
5060 ("r-quadprog" ,r-quadprog)
5061 ("r-quantreg" ,r-quantreg)))
5062 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5063 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5064 (description "This package provides non-parametric (and semi-parametric)
5065 kernel methods that seamlessly handle a mix of continuous, unordered, and
5066 ordered factor data types.")
5067 ;; Any version of the GPL.
5068 (license license:gpl3+)))
5070 (define-public r-powerplus
5072 (name "r-powerplus")
5077 (uri (cran-uri "powerplus" version))
5080 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5081 (build-system r-build-system)
5083 `(("r-complexplus" ,r-complexplus)
5086 ("r-matrix" ,r-matrix)
5087 ("r-phontools" ,r-phontools)))
5088 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5089 (synopsis "Exponentiation operations")
5091 "This package provides tools for the computation of matrix and scalar
5093 (license license:gpl2)))
5095 (define-public r-egg
5102 (uri (cran-uri "egg" version))
5105 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5106 (properties `((upstream-name . "egg")))
5107 (build-system r-build-system)
5109 `(("r-ggplot2" ,r-ggplot2)
5110 ("r-gridextra" ,r-gridextra)
5111 ("r-gtable" ,r-gtable)))
5112 (home-page "https://cran.r-project.org/web/packages/egg")
5113 (synopsis "Extensions for ggplot2")
5115 "This package provides miscellaneous functions to help customize ggplot2
5116 objects. High-level functions are provided to post-process ggplot2 layouts
5117 and allow alignment between plot panels, as well as setting panel sizes to
5118 fixed values. Other functions include a custom @code{geom}, and helper
5119 functions to enforce symmetric scales or add tags to facetted plots.")
5120 (license license:gpl3)))
5122 (define-public r-heatmaply
5124 (name "r-heatmaply")
5129 (uri (cran-uri "heatmaply" version))
5132 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5133 (build-system r-build-system)
5135 `(("r-assertthat" ,r-assertthat)
5136 ("r-colorspace" ,r-colorspace)
5137 ("r-dendextend" ,r-dendextend)
5139 ("r-ggplot2" ,r-ggplot2)
5140 ("r-htmlwidgets" ,r-htmlwidgets)
5141 ("r-magrittr" ,r-magrittr)
5142 ("r-plotly" ,r-plotly)
5143 ("r-rcolorbrewer" ,r-rcolorbrewer)
5144 ("r-reshape2" ,r-reshape2)
5145 ("r-scales" ,r-scales)
5146 ("r-seriation" ,r-seriation)
5147 ("r-viridis" ,r-viridis)
5148 ("r-webshot" ,r-webshot)))
5150 `(("r-knitr" ,r-knitr)))
5151 (home-page "https://cran.r-project.org/package=heatmaply")
5152 (synopsis "Interactive cluster heat maps using plotly")
5154 "This package enables you to create interactive cluster heatmaps that can
5155 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5156 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5157 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5158 a popular graphical method for visualizing high-dimensional data, in which a
5159 table of numbers is encoded as a grid of colored cells. The rows and columns
5160 of the matrix are ordered to highlight patterns and are often accompanied by
5162 ;; Either version of the license.
5163 (license (list license:gpl2 license:gpl3))))
5172 (uri (cran-uri "h5" version))
5175 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5176 (build-system r-build-system)
5181 `(("which" ,which)))
5183 `(("r-rcpp" ,r-rcpp)))
5184 (home-page "https://github.com/mannau/h5")
5185 (synopsis "Interface to the HDF5 Library")
5187 "This package provides an S4 interface to the HDF5 library supporting
5188 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5189 binary files in a language independent format. The HDF5 format can therefore
5190 be used as an alternative to R's save/load mechanism. Since h5 is able to
5191 access only subsets of stored data it can also handle data sets which do not
5193 (license license:bsd-2)))
5195 (define-public r-cgdsr
5202 (uri (cran-uri "cgdsr" version))
5205 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5206 (build-system r-build-system)
5208 `(("r-httr" ,r-httr)
5209 ("r-r-methodss3" ,r-r-methodss3)
5210 ("r-r-oo" ,r-r-oo)))
5211 (home-page "https://github.com/cBioPortal/cgdsr")
5212 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5214 "This package provides a basic set of R functions for querying the Cancer
5215 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5216 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5217 (license license:lgpl3)))
5219 (define-public r-import
5226 (uri (cran-uri "import" version))
5229 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5230 (build-system r-build-system)
5231 (home-page "https://github.com/smbache/import")
5232 (synopsis "Import mechanism for R")
5234 "This is an alternative mechanism for importing objects from packages.
5235 The syntax allows for importing multiple objects from a package with a single
5236 command in an expressive way. The import package bridges some of the gap
5237 between using @code{library} (or @code{require}) and direct (single-object)
5238 imports. Furthermore the imported objects are not placed in the current
5239 environment. It is also possible to import objects from stand-alone @code{.R}
5241 (license license:expat)))
5243 (define-public r-shinyace
5250 (uri (cran-uri "shinyAce" version))
5253 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5254 (properties `((upstream-name . "shinyAce")))
5255 (build-system r-build-system)
5257 `(("r-shiny" ,r-shiny)
5258 ("r-jsonlite" ,r-jsonlite)))
5259 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5260 (synopsis "Ace editor bindings for Shiny")
5262 "This package provides Ace editor bindings to enable a rich text editing
5263 environment within Shiny.")
5264 (license license:expat)))
5266 (define-public r-randomizr
5268 (name "r-randomizr")
5273 (uri (cran-uri "randomizr" version))
5276 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5277 (properties `((upstream-name . "randomizr")))
5278 (build-system r-build-system)
5280 `(("r-knitr" ,r-knitr)))
5281 (home-page "https://declaredesign.org/r/randomizr/")
5282 (synopsis "Tools for common forms of random assignment and sampling")
5284 "This package provides tools for generating random assignments for common
5285 experimental designs and random samples for common sampling designs.")
5286 (license license:expat)))
5288 (define-public r-base64url
5290 (name "r-base64url")
5295 (uri (cran-uri "base64url" version))
5298 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5299 (build-system r-build-system)
5301 `(("r-backports" ,r-backports)))
5302 (home-page "https://github.com/mllg/base64url")
5303 (synopsis "Fast and URL-safe base64 encoder and decoder")
5305 "This package provides a URL-safe base64 encoder and decoder. In
5306 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5307 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5308 encoder does not fill the string with trailing @code{=}. The resulting
5309 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5310 and thus are safe to use in URLs or for file names. The package also comes
5311 with a simple base32 encoder/decoder suited for case insensitive file
5313 (license license:gpl3)))
5315 (define-public r-radiant-data
5317 (name "r-radiant-data")
5322 (uri (cran-uri "radiant.data" version))
5325 "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
5326 (modules '((guix build utils)))
5329 ;; Delete files that are under CC-NC-SA.
5330 (delete-file-recursively "inst/app/tools/help")
5332 (properties `((upstream-name . "radiant.data")))
5333 (build-system r-build-system)
5335 `(("r-base64enc" ,r-base64enc)
5336 ("r-broom" ,r-broom)
5339 ("r-dplyr" ,r-dplyr)
5342 ("r-ggplot2" ,r-ggplot2)
5343 ("r-import" ,r-import)
5344 ("r-jsonlite" ,r-jsonlite)
5345 ("r-knitr" ,r-knitr)
5346 ("r-lubridate" ,r-lubridate)
5347 ("r-magrittr" ,r-magrittr)
5348 ("r-markdown" ,r-markdown)
5350 ("r-patchwork" ,r-patchwork)
5351 ("r-plotly" ,r-plotly)
5352 ("r-psych" ,r-psych)
5353 ("r-randomizr" ,r-randomizr)
5354 ("r-readr" ,r-readr)
5355 ("r-readxl" ,r-readxl)
5356 ("r-rlang" ,r-rlang)
5357 ("r-rmarkdown" ,r-rmarkdown)
5358 ("r-rstudioapi" ,r-rstudioapi)
5359 ("r-scales" ,r-scales)
5360 ("r-shiny" ,r-shiny)
5361 ("r-shinyfiles" ,r-shinyfiles)
5362 ("r-shinyace" ,r-shinyace)
5363 ("r-stringi" ,r-stringi)
5364 ("r-tibble" ,r-tibble)
5365 ("r-tidyr" ,r-tidyr)
5366 ("r-writexl" ,r-writexl)))
5367 (home-page "https://github.com/radiant-rstats/radiant.data")
5368 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5370 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5371 visualizing, summarizing, transforming, and combining data. It also contains
5372 functionality to generate reproducible reports of the analyses conducted in
5374 (license license:agpl3)))
5376 (define-public r-algdesign
5378 (name "r-algdesign")
5383 (uri (cran-uri "AlgDesign" version))
5385 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5386 (properties `((upstream-name . "AlgDesign")))
5387 (build-system r-build-system)
5388 (home-page "https://github.com/jvbraun/AlgDesign")
5389 (synopsis "Algorithmic experimental design")
5391 "This package provides tools to calculate exact and approximate theory
5392 experimental designs for D, A, and I criteria. Very large designs may be
5393 created. Experimental designs may be blocked or blocked designs created from
5394 a candidate list, using several criteria. The blocking can be done when whole
5395 and within plot factors interact.")
5396 (license license:gpl2+)))
5398 (define-public r-signal
5405 (uri (cran-uri "signal" version))
5408 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5409 (build-system r-build-system)
5410 (propagated-inputs `(("r-mass" ,r-mass)))
5411 (native-inputs `(("gfortran" ,gfortran)))
5412 (home-page "https://cran.r-project.org/web/packages/signal/")
5413 (synopsis "Signal processing")
5415 "This package provides a set of signal processing functions originally
5416 written for Matlab and GNU Octave. It includes filter generation utilities,
5417 filtering functions, resampling routines, and visualization of filter models.
5418 It also includes interpolation functions.")
5419 (license license:gpl2)))
5421 (define-public r-gsubfn
5428 (uri (cran-uri "gsubfn" version))
5431 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5432 (build-system r-build-system)
5433 (propagated-inputs `(("r-proto" ,r-proto)))
5434 (home-page "https://code.google.com/archive/p/gsubfn/")
5435 (synopsis "Utilities for strings and function arguments.")
5437 "This package provides @code{gsubfn} which is like @code{gsub} but can
5438 take a replacement function or certain other objects instead of the
5439 replacement string. Matches and back references are input to the replacement
5440 function and replaced by the function output. @code{gsubfn} can be used to
5441 split strings based on content rather than delimiters and for quasi-perl-style
5442 string interpolation. The package also has facilities for translating
5443 formulas to functions and allowing such formulas in function calls instead of
5445 (license license:gpl2+)))
5447 (define-public r-sqldf
5454 (uri (cran-uri "sqldf" version))
5457 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5458 (build-system r-build-system)
5460 `(("r-chron" ,r-chron)
5462 ("r-gsubfn" ,r-gsubfn)
5463 ("r-proto" ,r-proto)
5464 ("r-rsqlite" ,r-rsqlite)))
5465 (home-page "https://github.com/ggrothendieck/sqldf")
5466 (synopsis "Manipulate R data frames using SQL")
5468 "The @code{sqldf} function is typically passed a single argument which is
5469 an SQL select statement where the table names are ordinary R data frame names.
5470 @code{sqldf} transparently sets up a database, imports the data frames into
5471 that database, performs the SQL statement and returns the result using a
5472 heuristic to determine which class to assign to each column of the returned
5473 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5474 used to read filtered files into R even if the original files are larger than
5475 R itself can handle.")
5476 (license license:gpl2)))
5478 (define-public r-abind
5485 (uri (cran-uri "abind" version))
5488 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5489 (build-system r-build-system)
5490 (home-page "https://cran.r-project.org/web/packages/abind/")
5491 (synopsis "Combine multidimensional arrays")
5493 "This package provides tools to combine multidimensional arrays into a
5494 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5495 works with vectors, matrices, and higher-dimensional arrays. It also provides
5496 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5497 extracting and replacing data in arrays.")
5498 (license license:lgpl2.0+)))
5500 (define-public r-prroc
5507 (uri (cran-uri "PRROC" version))
5510 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5511 (properties `((upstream-name . "PRROC")))
5512 (build-system r-build-system)
5513 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5514 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5516 "This package computes the areas under the @dfn{precision-recall} (PR)
5517 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5518 contrast to other implementations, the interpolation between points of the PR
5519 curve is done by a non-linear piecewise function. In addition to the areas
5520 under the curves, the curves themselves can also be computed and plotted by a
5521 specific S3-method.")
5522 (license license:gpl3)))
5524 (define-public r-vim
5531 (uri (cran-uri "VIM" version))
5534 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5535 (properties `((upstream-name . "VIM")))
5536 (build-system r-build-system)
5539 ("r-colorspace" ,r-colorspace)
5540 ("r-data-table" ,r-data-table)
5541 ("r-e1071" ,r-e1071)
5542 ("r-laeken" ,r-laeken)
5543 ("r-magrittr" ,r-magrittr)
5546 ("r-ranger" ,r-ranger)
5548 ("r-robustbase" ,r-robustbase)
5552 `(("r-knitr" ,r-knitr)))
5553 (home-page "https://github.com/alexkowa/VIM")
5554 (synopsis "Visualization and imputation of missing values")
5556 "This package provides tools for the visualization of missing and/or
5557 imputed values are introduced, which can be used for exploring the data and
5558 the structure of the missing and/or imputed values. Depending on this
5559 structure of the missing values, the corresponding methods may help to
5560 identify the mechanism generating the missing values and allows to explore the
5561 data including missing values. In addition, the quality of imputation can be
5562 visually explored using various univariate, bivariate, multiple and
5563 multivariate plot methods.")
5564 (license license:gpl2+)))
5566 (define-public r-fnn
5573 (uri (cran-uri "FNN" version))
5576 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5577 (properties `((upstream-name . "FNN")))
5578 (build-system r-build-system)
5579 (home-page "https://cran.r-project.org/web/packages/FNN")
5580 (synopsis "Fast nearest neighbor search algorithms and applications")
5582 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5583 search algorithms. Related applications including KNN classification,
5584 regression and information measures are implemented.")
5585 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5586 ;; later can be used.
5587 (license license:gpl2+)))
5589 (define-public r-smoother
5596 (uri (cran-uri "smoother" version))
5599 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5600 (build-system r-build-system)
5602 `(("r-ttr" ,r-ttr)))
5603 (home-page "https://cran.r-project.org/web/packages/smoother")
5604 (synopsis "Functions relating to the smoothing of numerical data")
5606 "This package provides a collection of methods for smoothing numerical
5607 data, commencing with a port of the Matlab gaussian window smoothing function.
5608 In addition, several functions typically used in smoothing of financial data
5610 (license license:gpl2)))
5612 (define-public r-riverplot
5614 (name "r-riverplot")
5619 (uri (cran-uri "riverplot" version))
5622 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5623 (build-system r-build-system)
5624 (home-page "https://logfc.wordpress.com")
5625 (synopsis "Sankey or ribbon plots")
5627 "Sankey plots are a type of diagram that is convenient to illustrate how
5628 flow of information, resources etc. separates and joins, much like observing
5629 how rivers split and merge. For example, they can be used to compare
5630 different clusterings. This package provides an implementation of Sankey
5632 (license license:gpl2+)))
5634 (define-public r-dyn
5641 (uri (cran-uri "dyn" version))
5644 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5645 (build-system r-build-system)
5647 `(("r-zoo" ,r-zoo)))
5648 (home-page "https://cran.r-project.org/web/packages/dyn")
5649 (synopsis "Time series regression")
5651 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5652 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5653 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5654 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5655 @code{randomForest::randomForest()} and other regression functions, allowing
5656 those functions to be used with time series including specifications that may
5657 contain lags, diffs and missing values.")
5659 (license license:gpl2+)))
5661 (define-public r-catdap
5668 (uri (cran-uri "catdap" version))
5671 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5672 (build-system r-build-system)
5674 `(("gfortran" ,gfortran)))
5675 (home-page "https://cran.r-project.org/web/packages/catdap/")
5676 (synopsis "Tools for categorical data analysis")
5678 "This package provides functions for analyzing multivariate data.
5679 Dependencies of the distribution of the specified variable (response
5680 variable) to other variables (explanatory variables) are derived and
5681 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5682 (license license:gpl2+)))
5684 (define-public r-arules
5691 (uri (cran-uri "arules" version))
5694 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5695 (build-system r-build-system)
5697 `(("r-matrix" ,r-matrix)))
5698 (home-page "https://github.com/mhahsler/arules")
5699 (synopsis "Mining association rules and frequent itemsets")
5701 "This package provides an infrastructure for representing, manipulating
5702 and analyzing transaction data and patterns (frequent itemsets and association rules).
5703 It also provides C implementations of the association mining algorithms Apriori
5705 (license license:gpl3)))
5707 (define-public r-parsedate
5709 (name "r-parsedate")
5714 (uri (cran-uri "parsedate" version))
5717 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5718 (build-system r-build-system)
5720 `(("r-rematch2" ,r-rematch2)))
5721 (home-page "https://github.com/gaborcsardi/parsedate")
5723 "Recognize and parse dates in various formats")
5725 "This package provides three functions for dealing with dates:
5726 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5727 time formats, @code{parse_date} parses dates in unspecified formats,
5728 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5729 (license license:gpl2)))
5731 (define-public r-abc-data
5738 (uri (cran-uri "abc.data" version))
5741 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5742 (properties `((upstream-name . "abc.data")))
5743 (build-system r-build-system)
5744 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5745 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5747 "This package contains data which are used by functions of the abc
5748 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5749 algorithms for performing parameter estimation, model selection, and
5751 (license license:gpl3+)))
5753 (define-public r-abc
5760 (uri (cran-uri "abc" version))
5763 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5764 (build-system r-build-system)
5766 `(("r-abc-data" ,r-abc-data)
5767 ("r-locfit" ,r-locfit)
5770 ("r-quantreg" ,r-quantreg)))
5771 (home-page "https://cran.r-project.org/web/packages/abc/")
5772 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5774 "This package implements several @dfn{Approximate Bayesian
5775 Computation} (ABC) algorithms for performing parameter estimation, model
5776 selection, and goodness-of-fit. Cross-validation tools are also available for
5777 measuring the accuracy of ABC estimates, and to calculate the
5778 misclassification probabilities of different models.")
5779 (license license:gpl3+)))
5781 (define-public r-zip
5788 (uri (cran-uri "zip" version))
5791 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5792 (build-system r-build-system)
5793 (home-page "https://github.com/gaborcsardi/zip")
5794 (synopsis "Cross-platform Zip compression")
5796 "This package provides a cross-platform Zip compression library for R.
5797 It is a replacement for the @code{zip} function, that does not require any
5798 additional external tools on any platform.")
5799 (license license:cc0)))
5801 (define-public r-openxlsx
5808 (uri (cran-uri "openxlsx" version))
5811 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5812 (build-system r-build-system)
5814 `(("r-rcpp" ,r-rcpp)
5815 ("r-stringi" ,r-stringi)
5818 `(("r-knitr" ,r-knitr)))
5819 (home-page "https://github.com/awalker89/openxlsx")
5820 (synopsis "Read, write and edit XLSX files")
5822 "This package simplifies the creation of Excel @code{.xlsx} files by
5823 providing a high level interface to writing, styling and editing worksheets.
5824 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5825 and @code{XLConnect} packages with the added benefit of removing the
5826 dependency on Java.")
5827 (license license:gpl3)))
5829 (define-public r-rio
5836 (uri (cran-uri "rio" version))
5839 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5840 (build-system r-build-system)
5842 `(("r-curl" ,r-curl)
5843 ("r-data-table" ,r-data-table)
5844 ("r-foreign" ,r-foreign)
5845 ("r-haven" ,r-haven)
5846 ("r-openxlsx" ,r-openxlsx)
5847 ("r-readxl" ,r-readxl)
5848 ("r-tibble" ,r-tibble)))
5849 (home-page "https://github.com/leeper/rio")
5850 (synopsis "Swiss-army knife for data I/O")
5852 "This package provides streamlined data import and export infrastructure
5853 by making assumptions that the user is probably willing to make: @code{import}
5854 and @code{export} determine the data structure from the file extension,
5855 reasonable defaults are used for data import and export (e.g.,
5856 @code{stringsAsFactors=FALSE}), web-based import is natively
5857 supported (including from SSL/HTTPS), compressed files can be read directly
5858 without explicit decompression, and fast import packages are used where
5859 appropriate. An additional convenience function, @code{convert}, provides a
5860 simple method for converting between file types.")
5861 (license license:gpl2)))
5863 (define-public r-maptools
5870 (uri (cran-uri "maptools" version))
5873 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5874 (build-system r-build-system)
5876 `(("r-foreign" ,r-foreign)
5877 ("r-lattice" ,r-lattice)
5879 (home-page "https://r-forge.r-project.org/projects/maptools/")
5880 (synopsis "Tools for reading and handling spatial objects")
5882 "This package provides a set of tools for manipulating and reading
5883 geographic data, in particular ESRI Shapefiles. It includes binary access to
5884 GSHHG shoreline files. The package also provides interface wrappers for
5885 exchanging spatial objects with other R packages.")
5886 ;; The C source files from shapelib are released under the Expat license.
5887 ;; The R code is released under GPL version 2 or later.
5888 (license (list license:gpl2+
5891 (define-public r-later
5898 (uri (cran-uri "later" version))
5901 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5902 (build-system r-build-system)
5906 ("r-rlang" ,r-rlang)))
5908 `(("r-knitr" ,r-knitr)))
5909 (home-page "https://github.com/r-lib/later")
5910 (synopsis "Utilities for delaying function execution")
5912 "This package provides tools to execute arbitrary R or C functions some
5913 time after the current time, after the R execution stack has emptied.")
5914 (license license:gpl2+)))
5916 (define-public r-promises
5923 (uri (cran-uri "promises" version))
5926 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5927 (build-system r-build-system)
5929 `(("r-later" ,r-later)
5930 ("r-magrittr" ,r-magrittr)
5933 ("r-rlang" ,r-rlang)))
5935 `(("r-knitr" ,r-knitr)))
5936 (home-page "https://rstudio.github.io/promises")
5937 (synopsis "Abstractions for promise-based asynchronous programming")
5939 "This package provides fundamental abstractions for doing asynchronous
5940 programming in R using promises. Asynchronous programming is useful for
5941 allowing a single R process to orchestrate multiple tasks in the background
5942 while also attending to something else. Semantics are similar to JavaScript
5943 promises, but with a syntax that is idiomatic R.")
5944 (license license:expat)))
5946 (define-public r-dosnow
5953 (uri (cran-uri "doSNOW" version))
5956 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5957 (properties `((upstream-name . "doSNOW")))
5958 (build-system r-build-system)
5960 `(("r-foreach" ,r-foreach)
5961 ("r-iterators" ,r-iterators)
5962 ("r-snow" ,r-snow)))
5963 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5964 (synopsis "Foreach parallel adaptor for the snow package")
5966 "This package provides a parallel backend for the @code{%dopar%} function
5967 using the @code{snow} package.")
5968 (license license:gpl2)))
5970 (define-public r-snowfall
5973 (version "1.84-6.1")
5976 (uri (cran-uri "snowfall" version))
5978 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5979 (build-system r-build-system)
5981 `(("r-snow" ,r-snow)))
5982 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5983 (synopsis "Easier cluster computing")
5984 (description "This package is a usability wrapper around snow for easier
5985 development of parallel R programs. This package offers e.g. extended error
5986 checks, and additional functions. All functions work in sequential mode, too,
5987 if no cluster is present or wished. The package is also designed as connector
5988 to the cluster management tool @code{sfCluster}, but can also used without
5990 (license license:gpl2+)))
5992 (define-public r-rappdirs
5999 (uri (cran-uri "rappdirs" version))
6002 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6003 (build-system r-build-system)
6004 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6005 (synopsis "Determine where to save data, caches, and logs")
6007 "This package provides an easy way to determine which directories on the
6008 user's computer should be used to save data, caches and logs. It is a port of
6009 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6010 (license license:expat)))
6012 (define-public r-renv
6019 (uri (cran-uri "renv" version))
6022 "0yy24kq60dh9n68my132xhhkbnbs7q91z55b1yd6ymr7rxj32mif"))))
6023 (properties `((upstream-name . "renv")))
6024 (build-system r-build-system)
6026 `(("r-knitr" ,r-knitr)))
6027 (home-page "https://rstudio.github.io/renv")
6028 (synopsis "Project environments")
6030 "This package provides a dependency management toolkit for R. Using
6031 renv, you can create and manage project-local R libraries, save the state of
6032 these libraries to a lockfile, and later restore your library as required.
6033 Together, these tools can help make your projects more isolated, portable, and
6035 (license license:expat)))
6037 (define-public r-learnr
6044 (uri (cran-uri "learnr" version))
6047 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6048 (build-system r-build-system)
6050 `(("r-checkmate" ,r-checkmate)
6051 ("r-ellipsis" ,r-ellipsis)
6052 ("r-evaluate" ,r-evaluate)
6053 ("r-htmltools" ,r-htmltools)
6054 ("r-htmlwidgets" ,r-htmlwidgets)
6055 ("r-jsonlite" ,r-jsonlite)
6056 ("r-knitr" ,r-knitr)
6057 ("r-markdown" ,r-markdown)
6058 ("r-rappdirs" ,r-rappdirs)
6060 ("r-rmarkdown" ,r-rmarkdown)
6061 ("r-rprojroot" ,r-rprojroot)
6062 ("r-shiny" ,r-shiny)
6063 ("r-withr" ,r-withr)))
6064 (home-page "https://rstudio.github.io/learnr/")
6065 (synopsis "Interactive tutorials for R")
6067 "This package provides tools to create interactive tutorials using R
6068 Markdown. Use a combination of narrative, figures, videos, exercises, and
6069 quizzes to create self-paced tutorials for learning about R and R packages.")
6070 (license license:asl2.0)))
6072 (define-public r-analytics
6074 (name "r-analytics")
6079 (uri (cran-uri "analytics" version))
6082 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6083 (build-system r-build-system)
6086 ("r-cluster" ,r-cluster)
6087 ("r-fractal" ,r-fractal)
6088 ("r-lmtest" ,r-lmtest)
6091 ("r-powerplus" ,r-powerplus)
6092 ("r-robust" ,r-robust)
6093 ("r-trend" ,r-trend)
6097 (home-page "https://cran.r-project.org/web/packages/analytics/")
6098 (synopsis "Collection of data analysis tools")
6100 "This package is a collection of data analysis tools. It includes tools
6101 for regression outlier detection in a fitted linear model, stationary
6102 bootstrap using a truncated geometric distribution, a comprehensive test for
6103 weak stationarity, column means by group, weighted biplots, and a heuristic to
6104 obtain a better initial configuration in non-metric MDS.")
6105 (license license:gpl2)))
6107 (define-public r-reticulate
6109 (name "r-reticulate")
6114 (uri (cran-uri "reticulate" version))
6117 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6118 (build-system r-build-system)
6119 (inputs `(("python" ,python)))
6121 `(("r-rappdirs" ,r-rappdirs)
6122 ("r-jsonlite" ,r-jsonlite)
6123 ("r-matrix" ,r-matrix)
6124 ("r-rcpp" ,r-rcpp)))
6126 `(("r-knitr" ,r-knitr)))
6127 (home-page "https://github.com/rstudio/reticulate")
6128 (synopsis "R interface to Python")
6130 "This package provides an interface from R to Python modules, classes,
6131 and functions. When calling into Python, R data types are automatically
6132 converted to their equivalent Python types. When values are returned from
6133 Python to R they are converted back to R types.")
6134 (license license:asl2.0)))
6136 (define-public r-bibtex
6143 (uri (cran-uri "bibtex" version))
6146 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6147 (build-system r-build-system)
6148 (propagated-inputs `(("r-stringr" ,r-stringr)))
6149 (home-page "https://github.com/romainfrancois/bibtex")
6150 (synopsis "Bibtex parser")
6151 (description "This package provides a utility for R to parse a bibtex
6153 (license license:gpl2+)))
6155 (define-public r-ggseqlogo
6157 (name "r-ggseqlogo")
6162 (uri (cran-uri "ggseqlogo" version))
6165 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6166 (build-system r-build-system)
6167 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6168 (home-page "https://github.com/omarwagih/ggseqlogo")
6169 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6171 "The range of functions provided by this package makes it possible to
6172 draw highly versatile genomic sequence logos. Features include, but are not
6173 limited to, modifying colour schemes and fonts used to draw the logo,
6174 generating multiple logo plots, and aiding the visualisation with annotations.
6175 Sequence logos can easily be combined with other ggplot2 plots.")
6176 ;; Unspecified version of the LGPL.
6177 (license license:lgpl3+)))
6179 (define-public r-ggsci
6186 (uri (cran-uri "ggsci" version))
6189 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6190 (build-system r-build-system)
6192 `(("r-ggplot2" ,r-ggplot2)
6193 ("r-scales" ,r-scales)))
6194 (home-page "https://nanx.me/ggsci/")
6195 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6197 "This package provides a collection of ggplot2 color palettes inspired by
6198 plots in scientific journals, data visualization libraries, science fiction
6199 movies, and TV shows.")
6200 (license license:gpl3)))
6202 (define-public r-ggsignif
6209 (uri (cran-uri "ggsignif" version))
6212 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6213 (build-system r-build-system)
6215 `(("r-knitr" ,r-knitr)))
6217 `(("r-ggplot2" ,r-ggplot2)))
6218 (home-page "https://github.com/const-ae/ggsignif")
6219 (synopsis "Significance brackets for ggplot2")
6221 "Enrich your ggplots with group-wise comparisons. This package provides
6222 an easy way to indicate if two groups are significantly different. Commonly
6223 this is shown by a bracket on top connecting the groups of interest which
6224 itself is annotated with the level of significance. The package provides a
6225 single layer that takes the groups for comparison and the test as arguments
6226 and adds the annotation to the plot.")
6227 (license license:gpl3)))
6229 (define-public r-rstatix
6236 (uri (cran-uri "rstatix" version))
6239 "0ikbjmr58ah39rlwyiix50kl3yk9j7jngsvl6hh973392qdvmch6"))))
6240 (properties `((upstream-name . "rstatix")))
6241 (build-system r-build-system)
6243 `(("r-broom" ,r-broom)
6245 ("r-corrplot" ,r-corrplot)
6246 ("r-dplyr" ,r-dplyr)
6247 ("r-magrittr" ,r-magrittr)
6248 ("r-purrr" ,r-purrr)
6249 ("r-rlang" ,r-rlang)
6250 ("r-tibble" ,r-tibble)
6251 ("r-tidyr" ,r-tidyr)
6252 ("r-tidyselect" ,r-tidyselect)))
6253 (home-page "https://rpkgs.datanovia.com/rstatix/")
6254 (synopsis "Pipe-friendly framework for basic statistical tests")
6256 "This package provides a simple and intuitive pipe-friendly framework,
6257 coherent with the @code{tidyverse} design philosophy, for performing basic
6258 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6259 correlation analyses. The output of each test is automatically transformed
6260 into a tidy data frame to facilitate visualization. Additional functions are
6261 available for reshaping, reordering, manipulating and visualizing correlation
6263 (license license:gpl2)))
6265 (define-public r-ggpubr
6272 (uri (cran-uri "ggpubr" version))
6275 "1dly74cnn8iq7vsgmcz0czszdsmg5cgzm4w3s0v30k4psmmzqbxq"))))
6276 (build-system r-build-system)
6278 `(("r-cowplot" ,r-cowplot)
6279 ("r-dplyr" ,r-dplyr)
6280 ("r-ggplot2" ,r-ggplot2)
6281 ("r-ggrepel" ,r-ggrepel)
6282 ("r-ggsci" ,r-ggsci)
6283 ("r-ggsignif" ,r-ggsignif)
6285 ("r-gridextra" ,r-gridextra)
6286 ("r-magrittr" ,r-magrittr)
6287 ("r-polynom" ,r-polynom)
6288 ("r-purrr" ,r-purrr)
6289 ("r-rlang" ,r-rlang)
6290 ("r-scales" ,r-scales)
6291 ("r-rstatix" ,r-rstatix)
6292 ("r-tibble" ,r-tibble)
6293 ("r-tidyr" ,r-tidyr)))
6294 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6295 (synopsis "ggplot2-based publication-ready plots")
6297 "The ggplot2 package is an excellent and flexible package for elegant
6298 data visualization in R. However the default generated plots require some
6299 formatting before we can send them for publication. The ggpubr package
6300 provides some easy-to-use functions for creating and customizing ggplot2-based
6301 publication-ready plots.")
6302 (license license:gpl2)))
6304 (define-public r-ellipse
6311 (uri (cran-uri "ellipse" version))
6314 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6315 (build-system r-build-system)
6316 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6317 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6319 "This package contains various routines for drawing ellipses and
6320 ellipse-like confidence regions, implementing the plots described in Murdoch
6321 and Chow (1996), A graphical display of large correlation matrices, The
6322 American Statistician 50, 178-180. There are also routines implementing the
6323 profile plots described in Bates and Watts (1988), Nonlinear Regression
6324 Analysis and its Applications.")
6325 (license license:gpl2+)))
6327 (define-public r-flashclust
6329 (name "r-flashclust")
6334 (uri (cran-uri "flashClust" version))
6337 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6338 (properties `((upstream-name . "flashClust")))
6339 (build-system r-build-system)
6340 (native-inputs `(("gfortran" ,gfortran)))
6341 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6342 (synopsis "Implementation of optimal hierarchical clustering")
6344 "This package provides a fast implementation of hierarchical
6346 (license license:gpl2+)))
6348 (define-public r-factominer
6350 (name "r-factominer")
6355 (uri (cran-uri "FactoMineR" version))
6358 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6359 (properties `((upstream-name . "FactoMineR")))
6360 (build-system r-build-system)
6363 ("r-cluster" ,r-cluster)
6364 ("r-ellipse" ,r-ellipse)
6365 ("r-flashclust" ,r-flashclust)
6366 ("r-ggplot2" ,r-ggplot2)
6367 ("r-ggrepel" ,r-ggrepel)
6368 ("r-lattice" ,r-lattice)
6369 ("r-leaps" ,r-leaps)
6371 ("r-scatterplot3d" ,r-scatterplot3d)))
6372 (home-page "http://factominer.free.fr")
6373 (synopsis "Multivariate exploratory data analysis and data mining")
6375 "This package provides exploratory data analysis methods to summarize,
6376 visualize and describe datasets. The main principal component methods are
6377 available, those with the largest potential in terms of applications:
6378 principal component analysis (PCA) when variables are quantitative,
6379 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6380 variables are categorical, Multiple Factor Analysis when variables are
6381 structured in groups, etc. and hierarchical cluster analysis.")
6382 (license license:gpl2+)))
6384 (define-public r-factoextra
6386 (name "r-factoextra")
6391 (uri (cran-uri "factoextra" version))
6394 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6395 (build-system r-build-system)
6397 `(("r-abind" ,r-abind)
6398 ("r-cluster" ,r-cluster)
6399 ("r-dendextend" ,r-dendextend)
6400 ("r-factominer" ,r-factominer)
6401 ("r-ggplot2" ,r-ggplot2)
6402 ("r-ggpubr" ,r-ggpubr)
6403 ("r-ggrepel" ,r-ggrepel)
6404 ("r-reshape2" ,r-reshape2)
6405 ("r-tidyr" ,r-tidyr)))
6406 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6407 (synopsis "Extract and visualize the results of multivariate data analyses")
6409 "This package provides some easy-to-use functions to extract and
6410 visualize the output of multivariate data analyses, including
6411 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6412 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6413 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6414 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6415 packages. It contains also functions for simplifying some clustering analysis
6416 steps and provides ggplot2-based elegant data visualization.")
6417 (license license:gpl2)))
6419 (define-public r-fansi
6426 (uri (cran-uri "fansi" version))
6429 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6430 (build-system r-build-system)
6432 `(("r-knitr" ,r-knitr))) ; for vignettes
6433 (home-page "https://github.com/brodieG/fansi")
6434 (synopsis "ANSI control sequence aware string functions")
6436 "This package provides counterparts to R string manipulation functions
6437 that account for the effects of ANSI text formatting control sequences.")
6438 (license license:gpl2+)))
6440 (define-public r-nbclust
6447 (uri (cran-uri "NbClust" version))
6450 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6451 (properties `((upstream-name . "NbClust")))
6452 (build-system r-build-system)
6453 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6454 (synopsis "Determine the best number of clusters in a data set")
6456 "NbClust provides 30 indexes for determining the optimal number of
6457 clusters in a data set and offers the best clustering scheme from different
6458 results to the user.")
6459 (license license:gpl2)))
6461 (define-public r-hdf5r
6468 (uri (cran-uri "hdf5r" version))
6471 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6472 (build-system r-build-system)
6477 `(("r-bit64" ,r-bit64)
6480 `(("r-knitr" ,r-knitr)))
6481 (home-page "https://hhoeflin.github.io/hdf5r")
6482 (synopsis "Interface to the HDF5 binary data format")
6484 "HDF5 is a data model, library and file format for storing and managing
6485 large amounts of data. This package provides a nearly feature complete,
6486 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6487 functionality is added so that HDF5 objects behave very similar to their
6488 corresponding R counterparts.")
6489 (license license:asl2.0)))
6491 (define-public r-itertools
6493 (name "r-itertools")
6498 (uri (cran-uri "itertools" version))
6501 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6502 (build-system r-build-system)
6504 `(("r-iterators" ,r-iterators)))
6505 (home-page "https://cran.r-project.org/web/packages/itertools/")
6506 (synopsis "Iterator tools")
6508 "This package provides various tools for creating iterators, many
6509 patterned after functions in the Python @code{itertools} module, and others
6510 patterned after functions in the snow package.")
6511 (license license:gpl2)))
6513 (define-public r-polynom
6520 (uri (cran-uri "polynom" version))
6523 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6524 (build-system r-build-system)
6525 (home-page "https://cran.r-project.org/web/packages/polynom/")
6526 (synopsis "Functions for univariate polynomial manipulations")
6528 "This package provides a collection of functions to implement a class for
6529 univariate polynomial manipulations.")
6530 (license license:gpl2)))
6532 (define-public r-gbrd
6539 (uri (cran-uri "gbRd" version))
6542 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6543 (properties `((upstream-name . "gbRd")))
6544 (build-system r-build-system)
6545 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6546 (synopsis "Utilities for processing Rd objects and files")
6548 "This package provides utilities for processing Rd objects and files.
6549 Extract argument descriptions and other parts of the help pages of
6551 (license license:gpl2+)))
6553 (define-public r-rjags
6560 (uri (cran-uri "rjags" version))
6563 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6564 (build-system r-build-system)
6566 `(("r-coda" ,r-coda)))
6570 `(("pkg-config" ,pkg-config)))
6571 (home-page "http://mcmc-jags.sourceforge.net")
6572 (synopsis "Bayesian graphical models using MCMC")
6574 "This package provides an R interface to the JAGS MCMC library. JAGS is
6575 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6576 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6577 (license license:gpl2)))
6579 (define-public r-rdpack
6586 (uri (cran-uri "Rdpack" version))
6589 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6590 (properties `((upstream-name . "Rdpack")))
6591 (build-system r-build-system)
6593 `(("r-bibtex" ,r-bibtex)
6594 ("r-gbrd" ,r-gbrd)))
6595 (home-page "https://github.com/GeoBosh/Rdpack")
6596 (synopsis "Update and manipulate Rd documentation objects")
6598 "This package provides functions for manipulation of R documentation
6599 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6600 updating Rd documentation for functions, methods and classes; it also includes
6601 Rd macros for citations and import of references from bibtex files for use in
6602 Rd files and roxygen2 comments, as well as many functions for manipulation of
6603 references and Rd files.")
6604 (license license:gpl2+)))
6606 (define-public r-officer
6613 (uri (cran-uri "officer" version))
6616 "0nwasra2kb5wplcim7n57kynwhyg4vsk3fz42mbpm0hig1lzl9pp"))))
6617 (build-system r-build-system)
6619 `(("r-magrittr" ,r-magrittr)
6625 `(("r-knitr" ,r-knitr)))
6626 (home-page "https://davidgohel.github.io/officer")
6627 (synopsis "Manipulation of Word and PowerPoint documents")
6629 "This package provides tools to access and manipulate Word and PowerPoint
6630 documents from R. The package focuses on tabular and graphical reporting from
6631 R; it also provides two functions that let users get document content into
6632 data objects. A set of functions lets add and remove images, tables and
6633 paragraphs of text in new or existing documents. When working with PowerPoint
6634 presentations, slides can be added or removed; shapes inside slides can also
6635 be added or removed. When working with Word documents, a cursor can be used
6636 to help insert or delete content at a specific location in the document.")
6637 (license license:gpl3)))
6639 (define-public r-profilemodel
6641 (name "r-profilemodel")
6646 (uri (cran-uri "profileModel" version))
6649 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6650 (properties `((upstream-name . "profileModel")))
6651 (build-system r-build-system)
6652 (home-page "https://github.com/ikosmidis/profileModel")
6653 (synopsis "Profiling inference functions for various model classes")
6655 "This package provides tools that can be used to calculate, evaluate,
6656 plot and use for inference the profiles of *arbitrary* inference functions for
6657 arbitrary @code{glm}-like fitted models with linear predictors. More information
6658 on the methods that are implemented can be found in Kosmidis (2008)
6659 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6660 (license license:gpl2+)))
6662 (define-public r-brglm
6669 (uri (cran-uri "brglm" version))
6672 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6673 (properties `((upstream-name . "brglm")))
6674 (build-system r-build-system)
6676 `(("r-profilemodel" ,r-profilemodel)))
6677 (home-page "https://github.com/ikosmidis/brglm")
6678 (synopsis "Bias reduction in binomial-response generalized linear models")
6680 "Fit generalized linear models with binomial responses using either an
6681 adjusted-score approach to bias reduction or maximum penalized likelihood
6682 where penalization is by Jeffreys invariant prior. These procedures return
6683 estimates with improved frequentist properties (bias, mean squared error) that
6684 are always finite even in cases where the maximum likelihood estimates are
6685 infinite (data separation). Fitting takes place by fitting generalized linear
6686 models on iteratively updated pseudo-data. The interface is essentially the
6687 same as @code{glm}. More flexibility is provided by the fact that custom
6688 pseudo-data representations can be specified and used for model fitting.
6689 Functions are provided for the construction of confidence intervals for the
6690 reduced-bias estimates.")
6691 (license license:gpl2+)))
6693 (define-public r-entropy
6700 (uri (cran-uri "entropy" version))
6703 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6704 (properties `((upstream-name . "entropy")))
6705 (build-system r-build-system)
6706 (home-page "https://www.strimmerlab.org/software/entropy/")
6707 (synopsis "Estimation of entropy, mutual information and related quantities")
6709 "This package implements various estimators of entropy, such as the
6710 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6711 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6712 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6713 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6714 mutual information, and chi-squared statistic of independence. In addition
6715 there are functions for discretizing continuous random variables.")
6716 (license license:gpl3+)))
6718 (define-public r-abn
6725 (uri (cran-uri "abn" version))
6728 "11nbg6dwvbj0ac7qvr203vzjnw5zc1a8cibb9l6rzzr7yfg16xzc"))))
6729 (build-system r-build-system)
6733 `(("r-boot" ,r-boot)
6734 ("r-brglm" ,r-brglm)
6735 ("r-entropy" ,r-entropy)
6738 ("r-moments" ,r-moments)
6741 ("r-rcpparmadillo" ,r-rcpparmadillo)
6742 ("r-rjags" ,r-rjags)))
6743 (home-page "https://r-bayesian-networks.org/")
6744 (synopsis "Modelling multivariate data with additive bayesian networks")
6746 "Bayesian network analysis is a form of probabilistic graphical models
6747 which derives from empirical data a directed acyclic graph, DAG, describing
6748 the dependency structure between random variables. An additive Bayesian
6749 network model consists of a form of a DAG where each node comprises a
6750 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6751 equivalent to Bayesian multivariate regression using graphical modelling, they
6752 generalises the usual multivariable regression, GLM, to multiple dependent
6753 variables. This package provides routines to help determine optimal Bayesian
6754 network models for a given data set, where these models are used to identify
6755 statistical dependencies in messy, complex data.")
6756 (license license:gpl2+)))
6758 (define-public r-acd
6765 (uri (cran-uri "ACD" version))
6768 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6769 (properties `((upstream-name . "ACD")))
6770 (build-system r-build-system)
6771 (home-page "https://cran.r-project.org/web/packages/ACD/")
6772 (synopsis "Categorical data analysis with complete or missing responses")
6774 "This package provides tools for categorical data analysis with complete
6775 or missing responses.")
6776 (license license:gpl2+)))
6778 (define-public r-acdm
6785 (uri (cran-uri "ACDm" version))
6788 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6789 (properties `((upstream-name . "ACDm")))
6790 (build-system r-build-system)
6792 `(("r-dplyr" ,r-dplyr)
6793 ("r-ggplot2" ,r-ggplot2)
6795 ("r-rsolnp" ,r-rsolnp)
6797 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6798 (synopsis "Tools for Autoregressive Conditional Duration Models")
6800 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6801 and Russell, 1998) models. It creates trade, price or volume durations from
6802 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6804 (license license:gpl2+)))
6806 (define-public r-overlap
6813 (uri (cran-uri "overlap" version))
6816 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6817 (build-system r-build-system)
6818 (home-page "https://cran.r-project.org/web/packages/overlap/")
6819 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6821 "This package provides functions to fit kernel density functions to data
6822 on temporal activity patterns of animals; estimate coefficients of overlapping
6823 of densities for two species; and calculate bootstrap estimates of confidence
6825 (license license:gpl3+)))
6827 (define-public r-snakecase
6829 (name "r-snakecase")
6834 (uri (cran-uri "snakecase" version))
6837 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6838 (build-system r-build-system)
6840 `(("r-stringi" ,r-stringi)
6841 ("r-stringr" ,r-stringr)))
6842 (home-page "https://github.com/Tazinho/snakecase")
6843 (synopsis "Convert strings into any case")
6845 "This package provides a consistent, flexible and easy to use tool to
6846 parse and convert strings into cases like snake or camel among others.")
6847 (license license:gpl3)))
6849 (define-public r-prediction
6851 (name "r-prediction")
6856 (uri (cran-uri "prediction" version))
6859 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6860 (build-system r-build-system)
6862 `(("r-data-table" ,r-data-table)))
6863 (home-page "https://github.com/leeper/prediction")
6864 (synopsis "Tidy, type-safe prediction methods")
6866 "This package provides the @code{prediction()} function, a type-safe
6867 alternative to @code{predict()} that always returns a data frame. The package
6868 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6869 from the @code{stats} package, as well as numerous other model classes from
6870 other add-on packages.")
6871 (license license:expat)))
6873 (define-public r-insight
6880 (uri (cran-uri "insight" version))
6883 "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k"))))
6884 (build-system r-build-system)
6886 `(("r-knitr" ,r-knitr)))
6887 (home-page "https://easystats.github.io/insight/")
6888 (synopsis "Easy access to model information for various model objects")
6890 "This package provides a tool to provide an easy, intuitive and
6891 consistent access to information contained in various R models, like model
6892 formulas, model terms, information about random effects, data that was used to
6893 fit the model or data from response variables. The package mainly revolves
6894 around two types of functions: Functions that find (the names of) information,
6895 starting with @code{find_}, and functions that get the underlying data,
6896 starting with @code{get_}. The package has a consistent syntax and works with
6897 many different model objects, where otherwise functions to access these
6898 information are missing.")
6899 (license license:gpl3)))
6901 (define-public r-sjlabelled
6903 (name "r-sjlabelled")
6908 (uri (cran-uri "sjlabelled" version))
6911 "0grskmd7wrw31lkf85z6xz0bv246m6grvqkijvqi4q8zkl6p5vb3"))))
6912 (build-system r-build-system)
6914 `(("r-insight" ,r-insight)))
6916 `(("r-knitr" ,r-knitr)))
6917 (home-page "https://github.com/strengejacke/sjlabelled")
6918 (synopsis "Labelled data utility functions")
6920 "This package provides a collection of functions dealing with labelled
6921 data, like reading and writing data between R and other statistical software
6922 packages. This includes easy ways to get, set or change value and variable
6923 label attributes, to convert labelled vectors into factors or numeric (and
6924 vice versa), or to deal with multiple declared missing values.")
6925 (license license:gpl3)))
6927 (define-public r-sjmisc
6934 (uri (cran-uri "sjmisc" version))
6937 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6938 (build-system r-build-system)
6940 `(("r-dplyr" ,r-dplyr)
6941 ("r-insight" ,r-insight)
6942 ("r-magrittr" ,r-magrittr)
6943 ("r-purrr" ,r-purrr)
6944 ("r-rlang" ,r-rlang)
6945 ("r-sjlabelled" ,r-sjlabelled)
6946 ("r-tidyselect" ,r-tidyselect)))
6948 `(("r-knitr" ,r-knitr)))
6949 (home-page "https://github.com/strengejacke/sjmisc")
6950 (synopsis "Data and variable transformation functions")
6952 "This package is a collection of miscellaneous utility functions,
6953 supporting data transformation tasks like recoding, dichotomizing or grouping
6954 variables, setting and replacing missing values. The data transformation
6955 functions also support labelled data, and all integrate seamlessly into a
6956 tidyverse workflow.")
6957 (license license:gpl3)))
6959 (define-public r-nortest
6966 (uri (cran-uri "nortest" version))
6969 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6970 (build-system r-build-system)
6971 (home-page "https://cran.r-project.org/web/packages/nortest/")
6972 (synopsis "Tests for normality")
6974 "This package provides five omnibus tests for testing the composite
6975 hypothesis of normality.")
6976 (license license:gpl2+)))
6978 (define-public r-moonbook
6985 (uri (cran-uri "moonBook" version))
6988 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6989 (properties `((upstream-name . "moonBook")))
6990 (build-system r-build-system)
6992 `(("r-magrittr" ,r-magrittr)
6993 ("r-nortest" ,r-nortest)
6994 ("r-purrr" ,r-purrr)
6995 ("r-sjmisc" ,r-sjmisc)
6996 ("r-stringr" ,r-stringr)
6997 ("r-survival" ,r-survival)))
6998 (home-page "https://github.com/cardiomoon/moonBook")
6999 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7001 "This package provides several analysis-related functions for the book
7002 entitled \"R statistics and graph for medical articles\" (written in Korean),
7003 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7005 (license license:gpl2)))
7007 (define-public r-flextable
7009 (name "r-flextable")
7014 (uri (cran-uri "flextable" version))
7017 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7018 (build-system r-build-system)
7020 `(("r-base64enc" ,r-base64enc)
7021 ("r-data-table" ,r-data-table)
7022 ("r-gdtools" ,r-gdtools)
7023 ("r-htmltools" ,r-htmltools)
7024 ("r-knitr" ,r-knitr)
7025 ("r-officer" ,r-officer)
7026 ("r-rlang" ,r-rlang)
7027 ("r-rmarkdown" ,r-rmarkdown)
7029 ("r-xml2" ,r-xml2)))
7030 (home-page "https://davidgohel.github.io/flextable")
7031 (synopsis "Functions for tabular reporting")
7033 "This package provides tools to create pretty tables for HTML documents
7034 and other formats. Functions are provided to let users create tables, modify
7035 and format their content. It extends the @code{officer} package and can be
7036 used within R markdown documents when rendering to HTML and to Word
7038 (license license:gpl3)))
7040 (define-public r-writexl
7047 (uri (cran-uri "writexl" version))
7050 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7051 (build-system r-build-system)
7052 (inputs `(("zlib" ,zlib)))
7053 (home-page "https://github.com/ropensci/writexl")
7054 (synopsis "Export data frames to xlsx format")
7056 "This package provides a data frame to xlsx exporter based on
7058 (license license:bsd-2)))
7060 (define-public r-biasedurn
7062 (name "r-biasedurn")
7067 (uri (cran-uri "BiasedUrn" version))
7070 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7071 (properties `((upstream-name . "BiasedUrn")))
7072 (build-system r-build-system)
7073 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7074 (synopsis "Biased Urn model distributions")
7076 "This package provides statistical models of biased sampling in the form
7077 of univariate and multivariate noncentral hypergeometric distributions,
7078 including Wallenius' noncentral hypergeometric distribution and Fisher's
7079 noncentral hypergeometric distribution (also called extended hypergeometric
7081 (license license:gpl3)))
7083 (define-public r-goplot
7090 (uri (cran-uri "GOplot" version))
7093 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7094 (properties `((upstream-name . "GOplot")))
7095 (build-system r-build-system)
7097 `(("r-ggdendro" ,r-ggdendro)
7098 ("r-ggplot2" ,r-ggplot2)
7099 ("r-gridextra" ,r-gridextra)
7100 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7101 (home-page "https://github.com/wencke/wencke.github.io")
7102 (synopsis "Visualization of functional analysis data")
7104 "This package provides an implementation of multilayered visualizations
7105 for enhanced graphical representation of functional analysis data. It
7106 combines and integrates omics data derived from expression and functional
7107 annotation enrichment analyses. Its plotting functions have been developed
7108 with an hierarchical structure in mind: starting from a general overview to
7109 identify the most enriched categories (modified bar plot, bubble plot) to a
7110 more detailed one displaying different types of relevant information for the
7111 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7112 Venn diagram, heatmap).")
7113 (license license:gpl2)))
7115 (define-public r-getopt
7122 (uri (cran-uri "getopt" version))
7125 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7126 (build-system r-build-system)
7127 (home-page "https://github.com/trevorld/getopt")
7128 (synopsis "Command-line option processor for R")
7130 "This package is designed to be used with Rscript to write shebang
7131 scripts that accept short and long options. Many users will prefer to
7132 use the packages @code{optparse} or @code{argparse} which add extra
7133 features like automatically generated help options and usage texts,
7134 support for default values, positional argument support, etc.")
7135 (license license:gpl2+)))
7137 (define-public r-findpython
7139 (name "r-findpython")
7144 (uri (cran-uri "findpython" version))
7147 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7148 (build-system r-build-system)
7149 (home-page "https://github.com/trevorld/findpython")
7150 (synopsis "Functions to find an acceptable Python binary")
7152 "This package was designed to find an acceptable Python binary that
7153 matches version and feature constraints.")
7154 (license license:expat)))
7156 ;; This in not the same as "r-argparser"
7157 (define-public r-argparse
7164 (uri (cran-uri "argparse" version))
7167 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7168 (build-system r-build-system)
7169 (inputs `(("python" ,python)))
7171 `(("r-findpython" ,r-findpython)
7172 ("r-jsonlite" ,r-jsonlite)
7174 (home-page "https://github.com/trevorld/argparse")
7175 (synopsis "Command line optional and positional argument parser")
7177 "This package provides a command line parser to be used with Rscript to
7178 write shebang scripts that gracefully accept positional and optional arguments
7179 and automatically generate usage notices.")
7180 (license license:gpl2+)))
7182 (define-public r-hash
7189 (uri (cran-uri "hash" version))
7192 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7193 (build-system r-build-system)
7194 (home-page "https://cran.r-project.org/web/packages/hash/")
7195 (synopsis "Implementation of hash/associated arrays/dictionaries")
7197 "This package implements a data structure similar to hashes in Perl and
7198 dictionaries in Python but with a purposefully R flavor. For objects of
7199 appreciable size, access using hashes outperforms native named lists and
7201 (license license:gpl2+)))
7203 (define-public r-orddom
7210 (uri (cran-uri "orddom" version))
7213 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7214 (build-system r-build-system)
7215 (propagated-inputs `(("r-psych" ,r-psych)))
7216 (home-page "https://cran.r-project.org/web/packages/orddom/")
7217 (synopsis "Ordinal dominance statistics")
7219 "This package provides tools to compute ordinal, statistics and effect
7220 sizes as an alternative to mean comparison: Cliff's delta or success rate
7221 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7222 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7223 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7224 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7225 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7226 Group (Non-)Overlap considerations.")
7227 (license license:gpl2)))
7229 (define-public r-deriv
7236 (uri (cran-uri "Deriv" version))
7239 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7240 (properties `((upstream-name . "Deriv")))
7241 (build-system r-build-system)
7242 (home-page "https://cran.r-project.org/web/packages/Deriv")
7243 (synopsis "Symbolic differentiation")
7245 "This package provides an R-based solution for symbolic differentiation.
7246 It admits user-defined functions as well as function substitution in arguments
7247 of functions to be differentiated. Some symbolic simplification is part of
7249 (license license:gpl3+)))
7251 (define-public r-doby
7258 (uri (cran-uri "doBy" version))
7261 "0wz1vmsf1545r1m42q88s675ncwvm8figjn7kzbngjn9aqck9qbq"))))
7262 (properties `((upstream-name . "doBy")))
7263 (build-system r-build-system)
7265 `(("r-broom" ,r-broom)
7266 ("r-deriv" ,r-deriv)
7267 ("r-magrittr" ,r-magrittr)
7269 ("r-matrix" ,r-matrix)
7270 ("r-pbkrtest" ,r-pbkrtest)
7271 ("r-tibble" ,r-tibble)))
7273 `(("r-knitr" ,r-knitr)))
7274 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7275 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7277 "This package contains:
7280 @item facilities for working with grouped data: @code{do}
7281 something to data stratified @code{by} some variables.
7282 @item implementations of least-squares means, general linear contrasts, and
7283 @item miscellaneous other utilities.
7285 (license license:gpl2+)))
7287 (define-public r-refgenome
7289 (name "r-refgenome")
7294 (uri (cran-uri "refGenome" version))
7297 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7298 (properties `((upstream-name . "refGenome")))
7299 (build-system r-build-system)
7303 ("r-rsqlite" ,r-rsqlite)))
7304 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7306 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7308 "This package contains functionality for importing and managing of
7309 downloaded genome annotation data from the Ensembl genome browser (European
7310 Bioinformatics Institute) and from the UCSC genome browser (University of
7311 California, Santa Cruz) and annotation routines for genomic positions and
7312 splice site positions.")
7313 (license license:gpl2)))
7315 (define-public r-basix
7322 (uri (cran-uri "BASIX" version))
7325 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7326 (properties `((upstream-name . "BASIX")))
7327 (build-system r-build-system)
7328 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7329 (synopsis "Efficient C/C++ toolset for R")
7331 "BASIX provides some efficient C/C++ implementations of native R
7332 procedures to speed up calculations in R.")
7333 (license license:gpl2)))
7335 (define-public r-blockfest
7337 (name "r-blockfest")
7342 (uri (cran-uri "BlockFeST" version))
7345 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7346 (properties `((upstream-name . "BlockFeST")))
7347 (build-system r-build-system)
7348 (propagated-inputs `(("r-basix" ,r-basix)))
7349 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7350 (synopsis "Bayesian calculation of region-specific fixation index")
7352 "This package provides an R implementation of an extension of the
7353 BayeScan software for codominant markers, adding the option to group
7354 individual SNPs into pre-defined blocks. A typical application of this new
7355 approach is the identification of genomic regions, genes, or gene sets
7356 containing one or more SNPs that evolved under directional selection.")
7357 (license license:gpl2)))
7359 (define-public r-proc
7366 (uri (cran-uri "pROC" version))
7369 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7370 (properties `((upstream-name . "pROC")))
7371 (build-system r-build-system)
7373 `(("r-plyr" ,r-plyr)
7374 ("r-rcpp" ,r-rcpp)))
7375 (home-page "https://web.expasy.org/pROC/")
7376 (synopsis "Display and analyze ROC curves")
7378 "This package provides tools for visualizing, smoothing and comparing
7379 receiver operating characteristic (ROC curves). The area under the
7380 curve (AUC) can be compared with statistical tests based on U-statistics or
7381 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7382 (license license:gpl3+)))
7384 (define-public r-rootsolve
7386 (name "r-rootsolve")
7391 (uri (cran-uri "rootSolve" version))
7394 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7395 (properties `((upstream-name . "rootSolve")))
7396 (build-system r-build-system)
7397 (native-inputs `(("gfortran" ,gfortran)))
7398 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7399 (synopsis "Tools for the analysis of ordinary differential equations")
7401 "This package provides routines to find the root of nonlinear functions,
7402 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7403 differential equations} (ODE). It includes routines that:
7406 @item generate gradient and jacobian matrices (full and banded),
7407 @item find roots of non-linear equations by the Newton-Raphson method,
7408 @item estimate steady-state conditions of a system of (differential) equations
7409 in full, banded or sparse form, using the Newton-Raphson method, or by
7410 dynamically running,
7411 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7412 and 3-D partial differential equations, that have been converted to ordinary
7413 differential equations by numerical differencing (using the method-of-lines
7416 (license license:gpl2+)))
7418 (define-public r-abcanalysis
7420 (name "r-abcanalysis")
7425 (uri (cran-uri "ABCanalysis" version))
7427 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7428 (properties `((upstream-name . "ABCanalysis")))
7429 (build-system r-build-system)
7430 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7431 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7432 (synopsis "Computed ABC Analysis")
7434 "Multivariate data sets often differ in several factors or derived statistical
7435 parameters, which have to be selected for a valid interpretation. Basing this
7436 selection on traditional statistical limits leads occasionally to the perception
7437 of losing information from a data set. This package provides tools to calculate
7438 these limits on the basis of the mathematical properties of the distribution of
7439 the analyzed items.")
7440 (license license:gpl3)))
7442 (define-public r-slam
7449 (uri (cran-uri "slam" version))
7451 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7452 (build-system r-build-system)
7453 (home-page "https://cran.r-project.org/web/packages/slam/")
7454 (synopsis "Sparse lightweight arrays and matrices")
7456 "This package contains data structures and algorithms for sparse arrays and matrices,
7457 based on index arrays and simple triplet representations, respectively.")
7458 (license license:gpl2)))
7460 (define-public r-manipulatewidget
7462 (name "r-manipulatewidget")
7467 (uri (cran-uri "manipulateWidget" version))
7469 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7471 `((upstream-name . "manipulateWidget")))
7472 (build-system r-build-system)
7474 `(("r-base64enc" ,r-base64enc)
7475 ("r-codetools" ,r-codetools)
7476 ("r-htmltools" ,r-htmltools)
7477 ("r-htmlwidgets" ,r-htmlwidgets)
7478 ("r-knitr" ,r-knitr)
7479 ("r-miniui" ,r-miniui)
7480 ("r-shiny" ,r-shiny)
7481 ("r-webshot" ,r-webshot)))
7482 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7483 (synopsis "Add even more interactivity to interactive charts")
7485 "This package lets you create in just a few lines of R code a nice user interface to
7486 modify the data or the graphical parameters of one or multiple interactive
7487 charts. It is useful to quickly explore visually some data or for package
7488 developers to generate user interfaces easy to maintain.")
7489 (license license:gpl2+)))
7498 (uri (cran-uri "A3" version))
7500 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7501 (properties `((upstream-name . "A3")))
7502 (build-system r-build-system)
7504 `(("r-pbapply" ,r-pbapply)
7505 ("r-xtable" ,r-xtable)))
7506 (home-page "https://cran.r-project.org/web/packages/A3/")
7507 (synopsis "Error metrics for predictive models")
7509 "This package supplies tools for tabulating and analyzing the results of predictive
7510 models. The methods employed are applicable to virtually any predictive model
7511 and make comparisons between different methodologies straightforward.")
7512 (license license:gpl2+)))
7514 (define-public r-infotheo
7521 (uri (cran-uri "infotheo" version))
7524 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7525 (build-system r-build-system)
7526 (home-page "http://homepage.meyerp.com/software")
7527 (synopsis "Information-theoretic measures")
7529 "This package implements various measures of information theory based on
7530 several entropy estimators.")
7531 (license license:gpl3+)))
7533 (define-public r-abcoptim
7540 (uri (cran-uri "ABCoptim" version))
7542 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7543 (properties `((upstream-name . "ABCoptim")))
7544 (build-system r-build-system)
7545 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7546 (home-page "https://github.com/gvegayon/ABCoptim/")
7547 (synopsis "Optimization of Artificial Bee Colony algorithm")
7549 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7550 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7551 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7552 algorithms, and uses only common control parameters such as colony size and
7553 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7554 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7555 This version is a work-in-progress and is written in R code.")
7556 (license license:expat)))
7558 (define-public r-abcp2
7565 (uri (cran-uri "ABCp2" version))
7567 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7568 (properties `((upstream-name . "ABCp2")))
7569 (build-system r-build-system)
7570 (propagated-inputs `(("r-mass" ,r-mass)))
7571 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7572 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7574 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7575 Poisson, and Gamma distribution and estimates the proportional paternity of the
7576 second male (P2) based on the best fit distribution.")
7577 (license license:gpl2)))
7579 (define-public r-abcrf
7586 (uri (cran-uri "abcrf" version))
7588 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7589 (build-system r-build-system)
7591 `(("r-doparallel" ,r-doparallel)
7592 ("r-foreach" ,r-foreach)
7594 ("r-matrixstats" ,r-matrixstats)
7595 ("r-ranger" ,r-ranger)
7597 ("r-rcpparmadillo" ,r-rcpparmadillo)
7598 ("r-readr" ,r-readr)
7599 ("r-stringr" ,r-stringr)))
7600 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7601 (synopsis "Approximate bayesian computation via random forests")
7603 "This package performs approximate bayesian computation (ABC) model choice and
7604 parameter inference via random forests. This machine learning tool named random
7605 forests (RF) can conduct selection among the highly complex models covered by
7607 (license license:gpl2+)))
7609 (define-public r-abctools
7616 (uri (cran-uri "abctools" version))
7618 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7619 (build-system r-build-system)
7622 ("r-abind" ,r-abind)
7623 ("r-hmisc" ,r-hmisc)
7624 ("r-plyr" ,r-plyr)))
7625 (home-page "https://github.com/dennisprangle/abctools/")
7626 (synopsis "Tools for ABC analyses")
7628 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7629 including summary statistic selection and assessing coverage. This includes
7630 recent dimension reduction algorithms to tune the choice of summary statistics,
7631 and coverage methods to tune the choice of threshold.")
7632 (license license:gpl2+)))
7634 (define-public r-ggstance
7641 (uri (cran-uri "ggstance" version))
7643 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7644 (build-system r-build-system)
7646 `(("r-ggplot2" ,r-ggplot2)
7648 ("r-rlang" ,r-rlang)
7649 ("r-withr" ,r-withr)))
7650 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7651 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7653 "This package is a @code{r-ggplot2} extension that provides flipped components:
7655 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7656 @item vertical versions of @code{r-ggplot2} positions.
7658 (license license:gpl3)))
7660 (define-public r-mosaiccore
7662 (name "r-mosaiccore")
7667 (uri (cran-uri "mosaicCore" version))
7669 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7670 (properties `((upstream-name . "mosaicCore")))
7671 (build-system r-build-system)
7673 `(("r-dplyr" ,r-dplyr)
7674 ("r-lazyeval" ,r-lazyeval)
7676 ("r-rlang" ,r-rlang)
7677 ("r-tidyr" ,r-tidyr)))
7678 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7679 (synopsis "Common utilities for mosaic family packages")
7681 "Common utilities used in other Mosaic family packages are collected here.")
7682 (license license:gpl2+)))
7684 (define-public r-ggformula
7686 (name "r-ggformula")
7691 (uri (cran-uri "ggformula" version))
7693 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7694 (build-system r-build-system)
7696 `(("r-ggforce" ,r-ggforce)
7697 ("r-ggplot2" ,r-ggplot2)
7698 ("r-ggstance" ,r-ggstance)
7699 ("r-magrittr" ,r-magrittr)
7700 ("r-mosaiccore" ,r-mosaiccore)
7701 ("r-rlang" ,r-rlang)
7702 ("r-stringr" ,r-stringr)
7703 ("r-tibble" ,r-tibble)))
7704 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7705 (synopsis "Formula interface for the @code{r-ggplot2}")
7707 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7708 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7709 and extends the excellent simplicity of the lattice-graphics formula interface,
7710 while providing the intuitive capabilities of @code{r-ggplot2}.")
7711 (license license:expat)))
7713 (define-public r-mosaicdata
7715 (name "r-mosaicdata")
7720 (uri (cran-uri "mosaicData" version))
7722 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7723 (properties `((upstream-name . "mosaicData")))
7724 (build-system r-build-system)
7725 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7726 (synopsis "Data sets for project Mosaic")
7728 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7729 used to teach mathematics, statistics, computation and modeling.")
7730 (license license:gpl2+)))
7732 (define-public r-raster
7739 (uri (cran-uri "raster" version))
7742 "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
7743 (build-system r-build-system)
7745 `(("r-rcpp" ,r-rcpp)
7747 (home-page "https://www.rspatial.org/")
7748 (synopsis "Geographic data analysis and modeling")
7750 "The package implements basic and high-level functions for reading,
7751 writing, manipulating, analyzing and modeling of gridded spatial data.
7752 Processing of very large files is supported.")
7753 (license license:gpl3+)))
7755 (define-public r-mosaic
7762 (uri (cran-uri "mosaic" version))
7764 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7765 (build-system r-build-system)
7767 `(("r-broom" ,r-broom)
7768 ("r-dplyr" ,r-dplyr)
7769 ("r-ggdendro" ,r-ggdendro)
7770 ("r-ggformula" ,r-ggformula)
7771 ("r-ggplot2" ,r-ggplot2)
7772 ("r-ggrepel" ,r-ggrepel)
7774 ("r-gridextra" ,r-gridextra)
7775 ("r-lattice" ,r-lattice)
7776 ("r-latticeextra" ,r-latticeextra)
7777 ("r-lazyeval" ,r-lazyeval)
7779 ("r-matrix" ,r-matrix)
7780 ("r-mosaiccore" ,r-mosaiccore)
7781 ("r-mosaicdata" ,r-mosaicdata)
7782 ("r-readr" ,r-readr)
7783 ("r-tidyr" ,r-tidyr)))
7785 `(("r-knitr" ,r-knitr)))
7786 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7787 (synopsis "Mathematics, statistics, and computation teaching utilities")
7789 "This package contain data sets and utilities from
7790 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7791 statistics, computation and modeling. Project MOSAIC is a community of
7792 educators working to tie together aspects of quantitative work that students
7793 in science, technology, engineering and mathematics will need in their
7794 professional lives, but which are usually taught in isolation, if at all.")
7795 (license license:gpl2+)))
7797 (define-public r-abd
7804 (uri (cran-uri "abd" version))
7806 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7807 (build-system r-build-system)
7809 `(("r-lattice" ,r-lattice)
7810 ("r-mosaic" ,r-mosaic)
7811 ("r-nlme" ,r-nlme)))
7812 (home-page "https://cran.r-project.org/web/packages/abd/")
7813 (synopsis "Analysis of biological data")
7815 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7816 biological data by Michael Whitlock and Dolph Schluter.")
7817 (license license:gpl2)))
7819 (define-public r-svgui
7826 (uri (cran-uri "svGUI" version))
7828 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7829 (properties `((upstream-name . "svGUI")))
7830 (build-system r-build-system)
7831 (home-page "https://github.com/SciViews/svGUI/")
7832 (synopsis "Functions for managing GUI clients in R")
7834 "The SciViews @code{svGUI} package eases the management of Graphical User
7835 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7836 centralizes info about GUI elements currently used, and it dispatches GUI
7837 calls to the particular toolkits in use in function of the context.")
7838 (license license:gpl2)))
7840 (define-public r-svdialogs
7842 (name "r-svdialogs")
7847 (uri (cran-uri "svDialogs" version))
7849 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7850 (properties `((upstream-name . "svDialogs")))
7851 (build-system r-build-system)
7854 ("zenity" ,zenity)))
7856 `(("r-rstudioapi" ,r-rstudioapi)
7857 ("r-svgui" ,r-svgui)))
7858 (home-page "https://github.com/SciViews/svDialogs/")
7859 (synopsis "Portable dialog boxes")
7861 "This package helps to construct standard dialog boxes for your GUI, including
7862 message boxes, input boxes, list, file or directory selection, and others. In
7863 case R cannot display GUI dialog boxes, a simpler command line version of these
7864 interactive elements is also provided as a fallback solution.")
7865 (license license:gpl2)))
7867 (define-public r-abe
7874 (uri (cran-uri "abe" version))
7877 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7878 (build-system r-build-system)
7879 (home-page "https://cran.r-project.org/web/packages/abe/")
7880 (synopsis "Augmented backward elimination")
7882 "This package performs augmented backward elimination and checks the
7883 stability of the obtained model. Augmented backward elimination combines
7884 significance or information based criteria with the change in estimate to
7885 either select the optimal model for prediction purposes or to serve as a tool
7886 to obtain a practically sound, highly interpretable model.")
7887 (license license:gpl2+)))
7889 (define-public r-abf2
7896 (uri (cran-uri "abf2" version))
7898 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7899 (build-system r-build-system)
7900 (home-page "https://cran.r-project.org/web/packages/abf2/")
7901 (synopsis "Load gap-free axon @code{r-abf2} files")
7903 "This package loads electrophysiology data from ABF2 files, as created by
7904 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7905 mode are currently supported.")
7906 (license license:artistic2.0)))
7908 (define-public r-abhgenotyper
7910 (name "r-abhgenotyper")
7915 (uri (cran-uri "ABHgenotypeR" version))
7917 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7918 (properties `((upstream-name . "ABHgenotypeR")))
7919 (build-system r-build-system)
7921 `(("r-ggplot2" ,r-ggplot2)
7922 ("r-reshape2" ,r-reshape2)))
7923 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7924 (synopsis "Visualize and manipulate ABH genotypes")
7926 "The @code{r-abhgenotyper} package provides simple imputation,
7927 error-correction and plotting capacities for genotype data. The package is
7928 supposed to serve as an intermediate but independent analysis tool between the
7929 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7930 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7931 genotypes as \"graphical genotypes\".")
7932 (license license:gpl3)))
7934 (define-public r-furrr
7941 (uri (cran-uri "furrr" version))
7944 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7945 (build-system r-build-system)
7947 `(("r-future" ,r-future)
7948 ("r-globals" ,r-globals)
7949 ("r-purrr" ,r-purrr)
7950 ("r-rlang" ,r-rlang)))
7951 (home-page "https://github.com/DavisVaughan/furrr")
7952 (synopsis "Apply mapping functions in parallel using futures")
7954 "This package provides implementations of the family of @code{map()}
7955 functions from the @code{purrr} package that can be resolved using any
7956 @code{future}-supported backend, e.g. parallel on the local machine or
7957 distributed on a compute cluster.")
7958 (license license:lgpl2.1+)))
7960 (define-public r-abjutils
7967 (uri (cran-uri "abjutils" version))
7969 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7970 (build-system r-build-system)
7972 `(("r-devtools" ,r-devtools)
7973 ("r-dplyr" ,r-dplyr)
7974 ("r-furrr" ,r-furrr)
7975 ("r-future" ,r-future)
7978 ("r-magrittr" ,r-magrittr)
7979 ("r-progress" ,r-progress)
7980 ("r-purrr" ,r-purrr)
7981 ("r-readr" ,r-readr)
7982 ("r-rlang" ,r-rlang)
7983 ("r-rstudioapi" ,r-rstudioapi)
7984 ("r-scales" ,r-scales)
7985 ("r-stringi" ,r-stringi)
7986 ("r-stringr" ,r-stringr)
7987 ("r-tibble" ,r-tibble)
7988 ("r-tidyr" ,r-tidyr)))
7989 (home-page "https://github.com/abjur/abjutils/")
7990 (synopsis "Collection of tools for jurimetrical analysis")
7992 "This package implements general purpose tools, such as functions for
7993 sampling and basic manipulation of Brazilian lawsuits identification number.
7994 It also implements functions for text cleaning, such as accentuation
7996 (license license:expat)))
7998 (define-public r-abnormality
8000 (name "r-abnormality")
8005 (uri (cran-uri "abnormality" version))
8007 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8008 (build-system r-build-system)
8010 `(("r-mass" ,r-mass)
8011 ("r-matrix" ,r-matrix)))
8012 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8013 (synopsis "Measure a subject's abnormality with respect to a reference population")
8015 "This package contains functions to implement the methodology and
8016 considerations laid out by Marks et al. in the article \"Measuring abnormality
8017 in high dimensional spaces: applications in biomechanical gait analysis\".
8018 Using high-dimensional datasets to measure a subject's overall level of
8019 abnormality as compared to a reference population is often needed in outcomes
8021 (license license:expat)))
8023 (define-public r-abodoutlier
8025 (name "r-abodoutlier")
8030 (uri (cran-uri "abodOutlier" version))
8032 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8033 (properties `((upstream-name . "abodOutlier")))
8034 (build-system r-build-system)
8036 `(("r-cluster" ,r-cluster)))
8037 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8038 (synopsis "Angle-based outlier detection")
8040 "This package performs angle-based outlier detection on a given data
8041 frame. It offers three methods to process data:
8043 @item full but slow implementation using all the data that has cubic
8045 @item a fully randomized method;
8046 @item a method using k-nearest neighbours.
8048 These algorithms are well suited for high dimensional data outlier
8050 (license license:expat)))
8052 (define-public r-abps
8059 (uri (cran-uri "ABPS" version))
8061 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8062 (properties `((upstream-name . "ABPS")))
8063 (build-system r-build-system)
8064 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8065 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8066 (synopsis "Abnormal blood profile score to detect blood doping")
8068 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8069 The ABPS is a part of the Athlete biological passport program of the World
8070 anti-doping agency, which combines several blood parameters into a single
8071 score in order to detect blood doping. The package also contains functions to
8072 calculate other scores used in anti-doping programs, such as the ratio of
8073 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8074 (license license:gpl2+)))
8076 (define-public r-parmigene
8078 (name "r-parmigene")
8083 (uri (cran-uri "parmigene" version))
8086 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
8087 (build-system r-build-system)
8088 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8089 (synopsis "Mutual information estimation for gene network reconstruction")
8091 "This package provides a parallel estimation of the mutual information
8092 based on entropy estimates from k-nearest neighbors distances and algorithms
8093 for the reconstruction of gene regulatory networks.")
8094 (license license:agpl3+)))
8096 (define-public r-pscl
8103 (uri (cran-uri "pscl" version))
8105 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8106 (build-system r-build-system)
8108 `(("r-mass" ,r-mass)))
8109 (home-page "https://github.com/atahk/pscl/")
8110 (synopsis "Political science computational laboratory")
8112 "The @code{pscl} is an R package providing classes and methods for:
8114 @item Bayesian analysis of roll call data (item-response models);
8115 @item elementary Bayesian statistics;
8116 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8118 @item utility functions.
8120 (license license:gpl2)))
8122 (define-public r-accelmissing
8124 (name "r-accelmissing")
8129 (uri (cran-uri "accelmissing" version))
8131 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8132 (build-system r-build-system)
8134 `(("r-mice" ,r-mice)
8135 ("r-pscl" ,r-pscl)))
8136 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8137 (synopsis "Missing value imputation for accelerometer data")
8139 "This package provides a statistical method to impute the missing values in
8140 accelerometer data. The methodology includes both parametric and
8141 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8142 model. It also provides multiple functions to preprocess the accelerometer data
8143 previous to the missing data imputation. These include detecting the wearing
8144 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8145 (license license:gpl2+)))
8147 (define-public r-mhsmm
8154 (uri (cran-uri "mhsmm" version))
8156 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8157 (build-system r-build-system)
8158 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8159 (home-page "https://github.com/jaredo/mhsmm/")
8160 (synopsis "Inference for hidden Markov and semi-Markov models")
8162 "The @code{r-mhsmm} package implements estimation and prediction methods for
8163 hidden Markov and semi-Markov models for multiple observation sequences. Such
8164 techniques are of interest when observed data is thought to be dependent on some
8165 unobserved (or hidden) state. Also, this package is suitable for equidistant
8166 time series data, with multivariate and/or missing data. Allows user defined
8167 emission distributions.")
8168 (license license:gpl2+)))
8170 (define-public r-nleqslv
8177 (uri (cran-uri "nleqslv" version))
8179 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8180 (build-system r-build-system)
8181 (native-inputs `(("gfortran" ,gfortran)))
8182 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8183 (synopsis "Solve systems of nonlinear equations")
8185 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8186 Broyden or a Newton method with a choice of global strategies such as line
8187 search and trust region. There are options for using a numerical or user
8188 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8189 singular or ill-conditioned Jacobian.")
8190 (license license:gpl2+)))
8192 (define-public r-physicalactivity
8194 (name "r-physicalactivity")
8199 (uri (cran-uri "PhysicalActivity" version))
8201 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8203 `((upstream-name . "PhysicalActivity")))
8204 (build-system r-build-system)
8205 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8206 (synopsis "Procesing accelerometer data for physical activity measurement")
8208 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8209 for classification of monitor wear and nonwear time intervals in accelerometer
8210 data collected to assess physical activity. The package also contains functions
8211 for making plots of accelerometer data and obtaining the summary of various
8212 information including daily monitor wear time and the mean monitor wear time
8213 during valid days. The revised package version 0.2-1 improved the functions
8214 regarding speed, robustness and add better support for time zones and daylight
8215 saving. In addition, several functions were added:
8217 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8218 @item the @code{markPAI} can categorize physical activity intensity level based
8219 on user-defined cut-points of accelerometer counts.
8221 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8222 @code{queryActigraph} functions.")
8223 (license license:gpl3+)))
8225 (define-public r-acc
8232 (uri (cran-uri "acc" version))
8234 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8235 (build-system r-build-system)
8237 `(("r-circlize" ,r-circlize)
8239 ("r-ggplot2" ,r-ggplot2)
8240 ("r-iterators" ,r-iterators)
8241 ("r-mhsmm" ,r-mhsmm)
8242 ("r-nleqslv" ,r-nleqslv)
8243 ("r-physicalactivity" ,r-physicalactivity)
8245 ("r-r-utils" ,r-r-utils)
8247 ("r-rcpparmadillo" ,r-rcpparmadillo)
8248 ("r-rsqlite" ,r-rsqlite)
8250 (home-page "https://cran.r-project.org/web/packages/acc/")
8251 (synopsis "Exploring accelerometer data")
8253 "This package processes accelerometer data from uni-axial and tri-axial devices
8254 and generates data summaries. Also, includes functions to plot, analyze, and
8255 simulate accelerometer data.")
8256 (license license:gpl2+)))
8258 (define-public r-rbenchmark
8260 (name "r-rbenchmark")
8265 (uri (cran-uri "rbenchmark" version))
8267 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8268 (build-system r-build-system)
8269 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8270 (synopsis "Benchmarking routine for R")
8272 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8273 and is intended to facilitate benchmarking of arbitrary R code. The library
8274 consists of just one function, benchmark, which is a simple wrapper around
8275 system.time. Given a specification of the benchmarking process (counts of
8276 replications, evaluation environment) and an arbitrary number of expressions,
8277 benchmark evaluates each of the expressions in the specified environment,
8278 replicating the evaluation as many times as specified, and returning the results
8279 conveniently wrapped into a data frame.")
8280 (license license:gpl2+)))
8282 (define-public r-mitools
8289 (uri (cran-uri "mitools" version))
8292 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8293 (build-system r-build-system)
8294 (propagated-inputs `(("r-dbi" ,r-dbi)))
8295 (home-page "https://cran.r-project.org/web/packages/mitools/")
8296 (synopsis "Tools for multiple imputation of missing data")
8298 "This package provides tools to perform analyses and combine results from
8299 multiple-imputation datasets.")
8300 (license license:gpl2)))
8302 (define-public r-magick
8309 (uri (cran-uri "magick" version))
8312 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
8313 (build-system r-build-system)
8315 `(("imagemagick" ,imagemagick)
8318 `(("r-curl" ,r-curl)
8319 ("r-magrittr" ,r-magrittr)
8320 ("r-rcpp" ,r-rcpp)))
8322 `(("pkg-config" ,pkg-config)))
8323 (home-page "https://github.com/ropensci/magick")
8324 (synopsis "Advanced graphics and image-processing in R")
8326 "This package provides bindings to ImageMagick, a comprehensive image
8327 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8328 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8329 operations are vectorized via the Magick++ STL meaning they operate either on
8330 a single frame or a series of frames for working with layers, collages, or
8331 animation. In RStudio, images are automatically previewed when printed to the
8332 console, resulting in an interactive editing environment.")
8333 (license license:expat)))
8335 (define-public r-survey
8342 (uri (cran-uri "survey" version))
8345 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8346 (build-system r-build-system)
8348 `(("r-lattice" ,r-lattice)
8349 ("r-matrix" ,r-matrix)
8350 ("r-minqa" ,r-minqa)
8351 ("r-mitools" ,r-mitools)
8352 ("r-numderiv" ,r-numderiv)
8353 ("r-survival" ,r-survival)))
8354 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8355 (synopsis "Analysis of complex survey samples")
8357 "This package provides tools for the analysis of complex survey samples.
8358 The provided features include: summary statistics, two-sample tests, rank
8359 tests, generalised linear models, cumulative link models, Cox models,
8360 loglinear models, and general maximum pseudolikelihood estimation for
8361 multistage stratified, cluster-sampled, unequally weighted survey samples;
8362 variances by Taylor series linearisation or replicate weights;
8363 post-stratification, calibration, and raking; two-phase subsampling designs;
8364 graphics; PPS sampling without replacement; principal components, and factor
8366 ;; Either version of the GPL.
8367 (license (list license:gpl2 license:gpl3))))
8369 (define-public r-gee
8376 (uri (cran-uri "gee" version))
8379 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8380 (properties `((upstream-name . "gee")))
8381 (build-system r-build-system)
8383 `(("gfortran" ,gfortran)))
8384 (home-page "https://cran.r-project.org/web/packages/gee/")
8385 (synopsis "Generalized estimation equation solver")
8387 "This package provides a solver for generalized estimation equations.")
8388 (license license:gpl2)))
8390 (define-public r-tab
8397 (uri (cran-uri "tab" version))
8400 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8401 (properties `((upstream-name . "tab")))
8402 (build-system r-build-system)
8404 `(("r-dplyr" ,r-dplyr)
8406 ("r-knitr" ,r-knitr)
8408 ("r-survey" ,r-survey)
8409 ("r-survival" ,r-survival)
8410 ("r-xtable" ,r-xtable)))
8411 (home-page "https://cran.r-project.org/web/packages/tab/")
8412 (synopsis "Create summary tables for statistical reports")
8414 "This package contains functions for creating various types of summary
8415 tables, e.g. comparing characteristics across levels of a categorical variable
8416 and summarizing fitted generalized linear models, generalized estimating
8417 equations, and Cox proportional hazards models. Functions are available to
8418 handle data from simple random samples as well as complex surveys.")
8419 (license license:gpl3+)))
8421 (define-public r-dvmisc
8428 (uri (cran-uri "dvmisc" version))
8430 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8431 (build-system r-build-system)
8433 `(("r-cubature" ,r-cubature)
8434 ("r-data-table" ,r-data-table)
8435 ("r-dplyr" ,r-dplyr)
8436 ("r-ggplot2" ,r-ggplot2)
8438 ("r-mvtnorm" ,r-mvtnorm)
8439 ("r-pracma" ,r-pracma)
8440 ("r-rbenchmark" ,r-rbenchmark)
8442 ("r-survey" ,r-survey)
8444 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8445 (synopsis "Faster computation of common statistics and miscellaneous functions")
8447 "This package implements faster versions of base R functions (e.g. mean, standard
8448 deviation, covariance, weighted mean), mostly written in C++, along with
8449 miscellaneous functions for various purposes (e.g. create the histogram with
8450 fitted probability density function or probability mass function curve, create
8451 the body mass index groups, assess the linearity assumption in logistic
8453 (license license:gpl2)))
8455 (define-public r-accelerometry
8457 (name "r-accelerometry")
8462 (uri (cran-uri "accelerometry" version))
8464 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8465 (build-system r-build-system)
8467 `(("r-dvmisc" ,r-dvmisc)
8468 ("r-rcpp" ,r-rcpp)))
8469 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8470 (synopsis "Functions for processing accelerometer data")
8472 "This package provides a collection of functions that perform operations on
8473 time-series accelerometer data, such as identify the non-wear time, flag minutes
8474 that are part of an activity bout, and find the maximum 10-minute average count
8475 value. The functions are generally very flexible, allowing for a variety of
8476 algorithms to be implemented.")
8477 (license license:gpl3)))
8479 (define-public r-absim
8486 (uri (cran-uri "AbSim" version))
8488 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8489 (properties `((upstream-name . "AbSim")))
8490 (build-system r-build-system)
8493 ("r-powerlaw" ,r-powerlaw)))
8494 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8495 (synopsis "Time resolved simulations of antibody repertoires")
8497 "This package provides simulation methods for the evolution of antibody repertoires.
8498 The heavy and light chain variable region of both human and C57BL/6 mice can
8499 be simulated in a time-dependent fashion. Both single lineages using one set of
8500 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8501 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8502 Upon completion, the main loop of the algorithm begins, with each iteration
8503 representing one simulated time step. Various mutation events are possible at
8504 each time step, contributing to a diverse final repertoire.")
8505 (license license:gpl2)))
8507 (define-public r-quic
8514 (uri (cran-uri "QUIC" version))
8516 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8517 (properties `((upstream-name . "QUIC")))
8518 (build-system r-build-system)
8519 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8520 (synopsis "Regularized sparse inverse covariance matrix estimation")
8522 "This package implements the regularized Gaussian maximum likelihood
8523 estimation of the inverse of a covariance matrix. It uses Newton's method and
8524 coordinate descent to solve the regularized inverse covariance matrix
8525 estimation problem.")
8526 ;; The project home page states that the release is under GPLv3 or later.
8527 ;; The CRAN page only says GPL-3.
8528 (license license:gpl3+)))
8530 (define-public r-abundant
8537 (uri (cran-uri "abundant" version))
8539 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8540 (build-system r-build-system)
8542 `(("r-quic" ,r-quic)))
8543 (home-page "https://cran.r-project.org/web/packages/abundant/")
8544 (synopsis "Abundant regression and high-dimensional principal fitted components")
8546 "This package provides tools to fit and predict with the high-dimensional
8547 principal fitted components model. This model is described by Cook, Forzani,
8548 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8549 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8550 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8551 (license license:gpl2+)))
8553 (define-public r-ac3net
8560 (uri (cran-uri "Ac3net" version))
8562 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8563 (properties `((upstream-name . "Ac3net")))
8564 (build-system r-build-system)
8566 `(("r-data-table" ,r-data-table)))
8567 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8568 (synopsis "Inferring directional conservative causal core gene networks")
8569 (description "This package infers directional Conservative causal core
8570 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8571 directional network.")
8572 (license license:gpl3+)))
8574 (define-public r-aca
8581 (uri (cran-uri "ACA" version))
8583 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8584 (properties `((upstream-name . "ACA")))
8585 (build-system r-build-system)
8586 (home-page "https://cran.r-project.org/web/packages/ACA/")
8587 (synopsis "Abrupt change-point or aberration detection in point series")
8589 "This package offers an interactive function for the detection of breakpoints in
8591 ;; Any version of the GPL
8592 (license (list license:gpl2+ license:gpl3+))))
8594 (define-public r-acceptancesampling
8596 (name "r-acceptancesampling")
8601 (uri (cran-uri "AcceptanceSampling" version))
8603 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8605 `((upstream-name . "AcceptanceSampling")))
8606 (build-system r-build-system)
8607 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8608 (synopsis "Creation and evaluation of acceptance sampling plans")
8610 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8611 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8612 in quality control and improvement. International standards of acceptance
8613 sampling provide sampling plans for specific circumstances. The aim of this
8614 package is to provide an easy-to-use interface to visualize single, double or
8615 multiple sampling plans. In addition, methods have been provided to enable the
8616 user to assess sampling plans against pre-specified levels of performance, as
8617 measured by the probability of acceptance for a given level of quality in the
8619 (license license:gpl3+)))
8621 (define-public r-acclma
8628 (uri (cran-uri "ACCLMA" version))
8630 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8631 (properties `((upstream-name . "ACCLMA")))
8632 (build-system r-build-system)
8633 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8634 (synopsis "ACC & LMA graph plotting")
8636 "This package contains a function that imports data from a @acronym{CSV,
8637 Comma-Separated Values} file, or uses manually entered data from the format (x,
8638 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8639 Curve} vs @acronym{LOI, Line of Independence} graph and
8640 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8641 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8642 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8643 string) was passed, a manual data entry window is opened. The header parameter
8644 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8645 a header row or not. The dataset should contain only one independent variable
8646 (x) and one dependent variable (y) and can contain a weight for each
8648 (license license:gpl2)))
8650 (define-public r-aspi
8657 (uri (cran-uri "aspi" version))
8659 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8660 (build-system r-build-system)
8662 "https://cran.r-project.org/web/packages/aspi/")
8664 "Analysis of symmetry of parasitic infections")
8666 "This package provides tools for the analysis and visualization of bilateral
8667 asymmetry in parasitic infections.")
8668 (license license:gpl3+)))
8670 (define-public r-sandwich
8677 (uri (cran-uri "sandwich" version))
8680 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8681 (build-system r-build-system)
8683 `(("r-zoo" ,r-zoo)))
8684 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8685 (synopsis "Robust Covariance Matrix Estimators")
8687 "This package provides model-robust standard error estimators for
8688 cross-sectional, time series, clustered, panel, and longitudinal data.")
8689 ;; Either version of the license.
8690 (license (list license:gpl2 license:gpl3))))
8692 (define-public r-th-data
8699 (uri (cran-uri "TH.data" version))
8702 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8703 (properties `((upstream-name . "TH.data")))
8704 (build-system r-build-system)
8706 `(("r-mass" ,r-mass)
8707 ("r-survival" ,r-survival)))
8708 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8709 (synopsis "Shared data sets")
8711 "This package contains supporting data sets that are used in other
8712 packages maintained by Torsten Hothorn.")
8713 (license license:gpl3)))
8715 (define-public r-multcomp
8722 (uri (cran-uri "multcomp" version))
8725 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8726 (build-system r-build-system)
8728 `(("r-codetools" ,r-codetools)
8729 ("r-mvtnorm" ,r-mvtnorm)
8730 ("r-sandwich" ,r-sandwich)
8731 ("r-survival" ,r-survival)
8732 ("r-th-data" ,r-th-data)))
8733 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8734 (synopsis "Simultaneous inference in general parametric models")
8736 "Simultaneous tests and confidence intervals for general linear
8737 hypotheses in parametric models, including linear, generalized linear, linear
8738 mixed effects, and survival models. The package includes demos reproducing
8739 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8740 Hothorn, Westfall, 2010, CRC Press).")
8741 (license license:gpl2)))
8743 (define-public r-emmeans
8750 (uri (cran-uri "emmeans" version))
8753 "0jh7l1rzsb2ihbnh4r4388kwm629z17rcapvdws1hnkklhr8j74k"))))
8754 (build-system r-build-system)
8756 `(("r-estimability" ,r-estimability)
8757 ("r-mvtnorm" ,r-mvtnorm)
8758 ("r-numderiv" ,r-numderiv)
8760 ("r-xtable" ,r-xtable)))
8762 `(("r-knitr" ,r-knitr)))
8763 (home-page "https://github.com/rvlenth/emmeans")
8764 (synopsis "Estimated marginal means, aka least-squares means")
8766 "This package provides tools to obtain @dfn{estimated marginal
8767 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8768 be used to compute contrasts or linear functions of EMMs, trends, and
8769 comparisons of slopes.")
8770 ;; Either version of the license.
8771 (license (list license:gpl2 license:gpl3))))
8773 (define-public r-pwr
8780 (uri (cran-uri "pwr" version))
8783 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8784 (build-system r-build-system)
8786 `(("r-knitr" ,r-knitr)))
8787 (home-page "https://github.com/heliosdrm/pwr")
8788 (synopsis "Basic functions for power analysis")
8790 "This package provides power analysis functions along the lines of
8792 (license license:gpl3+)))
8794 (define-public r-libcoin
8801 (uri (cran-uri "libcoin" version))
8804 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8805 (build-system r-build-system)
8806 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8807 (home-page "https://cran.r-project.org/web/packages/libcoin")
8808 (synopsis "Linear test statistics for permutation inference")
8810 "This package provides basic infrastructure for linear test statistics
8811 and permutation inference in the framework of Strasser and Weber (1999).")
8812 (license license:gpl2)))
8814 (define-public r-coin
8821 (uri (cran-uri "coin" version))
8824 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8825 (build-system r-build-system)
8827 `(("r-libcoin" ,r-libcoin)
8828 ("r-matrixstats" ,r-matrixstats)
8829 ("r-modeltools" ,r-modeltools)
8830 ("r-multcomp" ,r-multcomp)
8831 ("r-mvtnorm" ,r-mvtnorm)
8832 ("r-survival" ,r-survival)))
8833 (home-page "http://coin.r-forge.r-project.org")
8834 (synopsis "Conditional inference procedures in a permutation test framework")
8836 "This package provides conditional inference procedures for the general
8837 independence problem including two-sample, K-sample (non-parametric ANOVA),
8838 correlation, censored, ordered and multivariate problems.")
8839 (license license:gpl2)))
8841 (define-public r-bayesplot
8843 (name "r-bayesplot")
8848 (uri (cran-uri "bayesplot" version))
8851 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8852 (build-system r-build-system)
8854 `(("pandoc" ,ghc-pandoc)
8855 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8857 `(("r-knitr" ,r-knitr)))
8859 `(("r-dplyr" ,r-dplyr)
8860 ("r-ggplot2" ,r-ggplot2)
8861 ("r-ggridges" ,r-ggridges)
8863 ("r-reshape2" ,r-reshape2)
8864 ("r-rlang" ,r-rlang)
8865 ("r-tibble" ,r-tibble)
8866 ("r-tidyselect" ,r-tidyselect)))
8867 (home-page "https://mc-stan.org/bayesplot")
8868 (synopsis "Plotting for Bayesian models")
8870 "This package provides plotting functions for posterior analysis, model
8871 checking, and MCMC diagnostics. The package is designed not only to provide
8872 convenient functionality for users, but also a common set of functions that
8873 can be easily used by developers working on a variety of R packages for
8874 Bayesian modeling.")
8875 (license license:gpl3+)))
8877 (define-public r-tmb
8884 (uri (cran-uri "TMB" version))
8887 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8888 (properties `((upstream-name . "TMB")))
8889 (build-system r-build-system)
8891 `(("r-matrix" ,r-matrix)
8892 ("r-rcppeigen" ,r-rcppeigen)))
8893 (home-page "http://tmb-project.org")
8894 (synopsis "Template model builder: a general random effect tool")
8896 "With this tool, a user should be able to quickly implement complex
8897 random effect models through simple C++ templates. The package combines
8898 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8899 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8900 from R) to obtain an efficient implementation of the applied Laplace
8901 approximation with exact derivatives. Key features are: Automatic sparseness
8902 detection, parallelism through BLAS and parallel user templates.")
8903 (license license:gpl2)))
8905 (define-public r-sjstats
8912 (uri (cran-uri "sjstats" version))
8914 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8915 (build-system r-build-system)
8917 `(("r-bayestestr" ,r-bayestestr)
8918 ("r-broom" ,r-broom)
8919 ("r-dplyr" ,r-dplyr)
8920 ("r-effectsize" ,r-effectsize)
8921 ("r-emmeans" ,r-emmeans)
8922 ("r-insight" ,r-insight)
8924 ("r-magrittr" ,r-magrittr)
8926 ("r-modelr" ,r-modelr)
8927 ("r-parameters" ,r-parameters)
8928 ("r-performance" ,r-performance)
8929 ("r-purrr" ,r-purrr)
8930 ("r-rlang" ,r-rlang)
8931 ("r-sjlabelled" ,r-sjlabelled)
8932 ("r-sjmisc" ,r-sjmisc)
8933 ("r-tidyr" ,r-tidyr)))
8934 (home-page "https://github.com/strengejacke/sjstats")
8935 (synopsis "Functions for common statistical computations")
8937 "This package provides a collection of convenient functions for common
8938 statistical computations, which are not directly provided by R's @code{base}
8939 or @code{stats} packages. This package aims at providing, first, shortcuts
8940 for statistical measures, which otherwise could only be calculated with
8941 additional effort. Second, these shortcut functions are generic, and can be
8942 applied not only to vectors, but also to other objects as well. The focus of
8943 most functions lies on summary statistics or fit measures for regression
8944 models, including generalized linear models, mixed effects models and Bayesian
8946 (license license:gpl3)))
8948 (define-public r-glmmtmb
8955 (uri (cran-uri "glmmTMB" version))
8958 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8959 (properties `((upstream-name . "glmmTMB")))
8960 (build-system r-build-system)
8962 `(("r-lme4" ,r-lme4)
8963 ("r-matrix" ,r-matrix)
8965 ("r-rcppeigen" ,r-rcppeigen)
8968 `(("r-knitr" ,r-knitr))) ; for vignettes
8969 (home-page "https://github.com/glmmTMB")
8970 (synopsis "Generalized linear mixed models")
8972 "Fit linear and generalized linear mixed models with various extensions,
8973 including zero-inflation. The models are fitted using maximum likelihood
8974 estimation via the Template Model Builder. Random effects are assumed to be
8975 Gaussian on the scale of the linear predictor and are integrated out using the
8976 Laplace approximation. Gradients are calculated using automatic
8978 (license license:agpl3+)))
8980 (define-public r-bayestestr
8982 (name "r-bayestestr")
8987 (uri (cran-uri "bayestestR" version))
8990 "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
8991 (properties `((upstream-name . "bayestestR")))
8992 (build-system r-build-system)
8994 `(("r-insight" ,r-insight)))
8996 `(("r-knitr" ,r-knitr)))
8997 (home-page "https://github.com/easystats/bayestestR")
8998 (synopsis "Describe Bayesian models and posterior distributions")
9000 "This package provides utilities to understand and describe posterior
9001 distributions and Bayesian models. It includes point-estimates such as
9002 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9003 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9004 ROPE percentage and pd).")
9005 (license license:gpl3)))
9007 (define-public r-performance
9009 (name "r-performance")
9014 (uri (cran-uri "performance" version))
9017 "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
9018 (build-system r-build-system)
9020 `(("r-bayestestr" ,r-bayestestr)
9021 ("r-insight" ,r-insight)))
9022 (home-page "https://easystats.github.io/performance/")
9023 (synopsis "Assessment of regression models performance")
9025 "This package provides utilities for computing measures to assess model
9026 quality, which are not directly provided by R's @code{base} or @code{stats}
9027 packages. These include e.g. measures like r-squared, intraclass correlation
9028 coefficient, root mean squared error or functions to check models for
9029 overdispersion, singularity or zero-inflation and more. Functions apply to a
9030 large variety of regression models, including generalized linear models, mixed
9031 effects models and Bayesian models.")
9032 (license license:gpl3)))
9034 (define-public r-ggeffects
9036 (name "r-ggeffects")
9041 (uri (cran-uri "ggeffects" version))
9044 "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
9045 (build-system r-build-system)
9047 `(("r-insight" ,r-insight)
9049 ("r-sjlabelled" ,r-sjlabelled)))
9051 `(("r-knitr" ,r-knitr)))
9052 (home-page "https://github.com/strengejacke/ggeffects")
9053 (synopsis "Create tidy data frames of marginal effects for ggplot")
9055 "This package provides tools to compute marginal effects from statistical
9056 models and return the result as tidy data frames. These data frames are ready
9057 to use with the @code{ggplot2} package. Marginal effects can be calculated
9058 for many different models. Interaction terms, splines and polynomial terms
9059 are also supported. The two main functions are @code{ggpredict()} and
9060 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9061 results using @code{ggplot2}.")
9062 (license license:gpl3)))
9064 (define-public r-effectsize
9066 (name "r-effectsize")
9071 (uri (cran-uri "effectsize" version))
9074 "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
9075 (properties `((upstream-name . "effectsize")))
9076 (build-system r-build-system)
9078 `(("r-bayestestr" ,r-bayestestr)
9079 ("r-insight" ,r-insight)
9080 ("r-parameters" ,r-parameters)))
9082 `(("r-knitr" ,r-knitr)))
9083 (home-page "https://github.com/easystats/effectsize")
9084 (synopsis "Indices of effect size and standardized parameters")
9086 "This package provides utilities to work with indices of effect size and
9087 standardized parameters for a wide variety of models, allowing computation and
9088 conversion of indices such as Cohen's d, r, odds, etc.")
9089 (license license:gpl3)))
9091 (define-public r-sjplot
9098 (uri (cran-uri "sjPlot" version))
9100 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9101 (properties `((upstream-name . "sjPlot")))
9102 (build-system r-build-system)
9104 `(("r-bayestestr" ,r-bayestestr)
9105 ("r-dplyr" ,r-dplyr)
9106 ("r-effectsize" ,r-effectsize)
9107 ("r-ggeffects" ,r-ggeffects)
9108 ("r-ggplot2" ,r-ggplot2)
9109 ("r-insight" ,r-insight)
9110 ("r-knitr" ,r-knitr)
9112 ("r-parameters" ,r-parameters)
9113 ("r-performance" ,r-performance)
9114 ("r-purrr" ,r-purrr)
9115 ("r-rlang" ,r-rlang)
9116 ("r-scales" ,r-scales)
9117 ("r-sjlabelled" ,r-sjlabelled)
9118 ("r-sjmisc" ,r-sjmisc)
9119 ("r-sjstats" ,r-sjstats)
9120 ("r-tidyr" ,r-tidyr)))
9122 `(("r-knitr" ,r-knitr)))
9123 (home-page "https://strengejacke.github.io/sjPlot/")
9124 (synopsis "Data visualization for statistics in social science")
9126 "This package represents a collection of plotting and table output
9127 functions for data visualization. Results of various statistical
9128 analyses (that are commonly used in social sciences) can be visualized using
9129 this package, including simple and cross tabulated frequencies, histograms,
9130 box plots, (generalized) linear models, mixed effects models, principal
9131 component analysis and correlation matrices, cluster analyses, scatter plots,
9132 stacked scales, effects plots of regression models (including interaction
9133 terms) and much more. This package supports labelled data.")
9134 (license license:gpl3)))
9136 (define-public r-ini
9143 (uri (cran-uri "ini" version))
9146 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9147 (build-system r-build-system)
9148 (home-page "https://github.com/dvdscripter/ini")
9149 (synopsis "Read and write configuration files")
9151 "This package provides tools to parse simple @code{.ini} configuration
9152 files to an structured list. Users can manipulate this resulting list with
9153 @code{lapply()} functions. This same structured list can be used to write
9154 back to file after modifications.")
9155 (license license:gpl3)))
9164 (uri (cran-uri "gh" version))
9167 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9168 (build-system r-build-system)
9173 ("r-jsonlite" ,r-jsonlite)))
9174 (home-page "https://github.com/r-lib/gh#readme")
9175 (synopsis "Access the GitHub API via R")
9177 "This package provides a minimal R client to access the GitHub API.")
9178 (license license:expat)))
9187 (uri (cran-uri "fs" version))
9190 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
9191 (build-system r-build-system)
9193 `(("pkg-config" ,pkg-config)
9194 ("r-knitr" ,r-knitr)))
9195 (home-page "https://fs.r-lib.org")
9196 (synopsis "Cross-platform file system operations based on libuv")
9198 "This package provides a cross-platform interface to file system
9199 operations, built on top of the libuv C library.")
9200 (license license:gpl3)))
9202 (define-public r-clisymbols
9204 (name "r-clisymbols")
9209 (uri (cran-uri "clisymbols" version))
9212 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9213 (build-system r-build-system)
9214 (home-page "https://github.com/gaborcsardi/clisymbols")
9215 (synopsis "Unicode symbols at the R prompt")
9217 "This package provides a small subset of Unicode symbols, that are useful
9218 when building command line applications. They fall back to alternatives on
9219 terminals that do not support Unicode.")
9220 (license license:expat)))
9222 (define-public r-usethis
9229 (uri (cran-uri "usethis" version))
9232 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9233 (build-system r-build-system)
9236 ("r-clipr" ,r-clipr)
9237 ("r-crayon" ,r-crayon)
9242 ("r-git2r" ,r-git2r)
9244 ("r-purrr" ,r-purrr)
9245 ("r-rematch2" ,r-rematch2)
9246 ("r-rlang" ,r-rlang)
9247 ("r-rprojroot" ,r-rprojroot)
9248 ("r-rstudioapi" ,r-rstudioapi)
9249 ("r-whisker" ,r-whisker)
9250 ("r-withr" ,r-withr)
9251 ("r-yaml" ,r-yaml)))
9252 (home-page "https://github.com/r-lib/usethis")
9253 (synopsis "Automate R package and project setup")
9255 "This package helps you to automate R package and project setup tasks
9256 that are otherwise performed manually. This includes setting up unit testing,
9257 test coverage, continuous integration, Git, GitHub integration, licenses,
9258 Rcpp, RStudio projects, and more.")
9259 (license license:gpl3)))
9261 (define-public r-sessioninfo
9263 (name "r-sessioninfo")
9268 (uri (cran-uri "sessioninfo" version))
9271 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9272 (build-system r-build-system)
9275 ("r-withr" ,r-withr)))
9276 (home-page "https://github.com/r-lib/sessioninfo#readme")
9277 (synopsis "R session information")
9279 "This package provides tools to query and print information about the
9280 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9281 more information about packages, and where they were installed from.")
9282 (license license:gpl2)))
9284 (define-public r-remotes
9291 (uri (cran-uri "remotes" version))
9294 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
9295 (build-system r-build-system)
9296 (home-page "https://github.com/r-lib/remotes#readme")
9297 (synopsis "R package installation from remote repositories")
9299 "Download and install R packages stored in GitHub, BitBucket, or plain
9300 subversion or git repositories. This package is a lightweight replacement of
9301 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9302 the code was copied over from @code{devtools}.")
9303 (license license:gpl2+)))
9305 (define-public r-xopen
9312 (uri (cran-uri "xopen" version))
9315 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9316 (build-system r-build-system)
9318 `(("r-processx" ,r-processx)))
9319 (home-page "https://github.com/r-lib/xopen#readme")
9320 (synopsis "Open system files, URLs, anything")
9322 "This package provides a cross-platform solution to open files,
9323 directories or URLs with their associated programs.")
9324 (license license:expat)))
9326 (define-public r-rcmdcheck
9328 (name "r-rcmdcheck")
9333 (uri (cran-uri "rcmdcheck" version))
9336 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9337 (build-system r-build-system)
9339 `(("r-callr" ,r-callr)
9341 ("r-crayon" ,r-crayon)
9343 ("r-digest" ,r-digest)
9344 ("r-pkgbuild" ,r-pkgbuild)
9345 ("r-prettyunits" ,r-prettyunits)
9347 ("r-rprojroot" ,r-rprojroot)
9348 ("r-sessioninfo" ,r-sessioninfo)
9349 ("r-withr" ,r-withr)
9350 ("r-xopen" ,r-xopen)))
9351 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9352 (synopsis "Run R CMD check from R and capture results")
9354 "Run @code{R CMD check} from R programmatically, and capture the results
9355 of the individual checks.")
9356 (license license:expat)))
9358 (define-public r-rapportools
9360 (name "r-rapportools")
9365 (uri (cran-uri "rapportools" version))
9368 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9369 (build-system r-build-system)
9371 `(("r-pander" ,r-pander)
9373 ("r-reshape" ,r-reshape)))
9374 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9375 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9377 "This package provides helper functions that act as wrappers to more
9378 advanced statistical methods with the advantage of having sane defaults for
9380 (license license:agpl3+)))
9382 (define-public r-pander
9389 (uri (cran-uri "pander" version))
9392 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9393 (build-system r-build-system)
9395 `(("r-digest" ,r-digest)
9396 ("r-rcpp" ,r-rcpp)))
9397 (home-page "https://rapporter.github.io/pander")
9398 (synopsis "Render R objects into Pandoc's markdown")
9400 "The main aim of the pander R package is to provide a minimal and easy
9401 tool for rendering R objects into Pandoc's markdown. The package is also
9402 capable of exporting/converting complex Pandoc documents (reports) in various
9404 ;; This package is licensed under either the AGPLv3+ or the very rarely
9406 (license license:agpl3+)))
9408 (define-public r-summarytools
9410 (name "r-summarytools")
9415 (uri (cran-uri "summarytools" version))
9418 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9419 (build-system r-build-system)
9421 `(("r-base64enc" ,r-base64enc)
9422 ("r-checkmate" ,r-checkmate)
9423 ("r-dplyr" ,r-dplyr)
9424 ("r-htmltools" ,r-htmltools)
9425 ("r-lubridate" ,r-lubridate)
9426 ("r-magick" ,r-magick)
9427 ("r-matrixstats" ,r-matrixstats)
9428 ("r-pander" ,r-pander)
9430 ("r-rapportools" ,r-rapportools)
9431 ("r-tibble" ,r-tibble)
9432 ("r-tidyr" ,r-tidyr)))
9433 (home-page "https://github.com/dcomtois/summarytools")
9434 (synopsis "Tools to quickly and neatly summarize data")
9436 "This package provides tools for data frame summaries, cross-tabulations,
9437 weight-enabled frequency tables and common univariate statistics in concise
9438 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9439 good point-of-entry for exploring data, both for experienced and new R
9441 (license license:gpl2)))
9443 (define-public r-lsei
9450 (uri (cran-uri "lsei" version))
9453 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9454 (build-system r-build-system)
9456 `(("gfortran" ,gfortran)))
9457 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9458 (synopsis "Solve regression problems under equality/inequality constraints")
9460 "It contains functions that solve least squares linear regression
9461 problems under linear equality/inequality constraints. Functions for solving
9462 quadratic programming problems are also available, which transform such
9463 problems into least squares ones first.")
9464 (license license:gpl2+)))
9466 (define-public r-npsurv
9473 (uri (cran-uri "npsurv" version))
9476 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9477 (build-system r-build-system)
9479 `(("r-lsei" ,r-lsei)))
9480 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9481 (synopsis "Nonparametric survival analysis")
9483 "This package contains functions for non-parametric survival analysis of
9484 exact and interval-censored observations.")
9485 (license license:gpl2+)))
9487 (define-public r-clusteval
9489 (name "r-clusteval")
9494 (uri (cran-uri "clusteval" version))
9497 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9498 (build-system r-build-system)
9500 `(("r-mvtnorm" ,r-mvtnorm)
9501 ("r-rcpp" ,r-rcpp)))
9502 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9503 (synopsis "Evaluation of clustering algorithms")
9505 "This R package provides a suite of tools to evaluate clustering
9506 algorithms, clusterings, and individual clusters.")
9507 (license license:expat)))
9509 (define-public r-tweedie
9516 (uri (cran-uri "tweedie" version))
9519 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9520 (build-system r-build-system)
9521 (native-inputs `(("gfortran" ,gfortran)))
9522 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9523 (synopsis "Evaluation of Tweedie exponential family models")
9525 "Maximum likelihood computations for Tweedie families, including the
9526 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9527 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9528 and related methods.")
9529 (license license:gpl2+)))
9531 (define-public r-rcppgsl
9538 (uri (cran-uri "RcppGSL" version))
9540 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9541 (properties `((upstream-name . "RcppGSL")))
9542 (build-system r-build-system)
9544 `(("r-rcpp" ,r-rcpp)
9547 `(("r-knitr" ,r-knitr))) ; for vignettes
9548 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9549 (synopsis "Rcpp integration for GSL vectors and matrices")
9551 "The GNU Scientific Library (or GSL) is a collection of numerical
9552 routines for scientific computing. It is particularly useful for C and C++
9553 programs as it provides a standard C interface to a wide range of mathematical
9554 routines. There are over 1000 functions in total with an extensive test
9555 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9556 structures and R using concepts from Rcpp which is itself a package that eases
9557 the interfaces between R and C++.")
9558 (license license:gpl2+)))
9560 (define-public r-mvabund
9567 (uri (cran-uri "mvabund" version))
9570 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9571 (build-system r-build-system)
9573 `(("r-mass" ,r-mass)
9575 ("r-rcppgsl" ,r-rcppgsl)
9576 ("r-statmod" ,r-statmod)
9577 ("r-tweedie" ,r-tweedie)))
9578 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9579 (synopsis "Statistical methods for analysing multivariate abundance data")
9581 "This package provides a set of tools for displaying, modeling and
9582 analysing multivariate abundance data in community ecology.")
9583 (license license:lgpl2.1+)))
9585 (define-public r-afex
9592 (uri (cran-uri "afex" version))
9595 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9596 (build-system r-build-system)
9600 ("r-lmertest" ,r-lmertest)
9601 ("r-pbkrtest" ,r-pbkrtest)
9602 ("r-reshape2" ,r-reshape2)))
9604 `(("r-knitr" ,r-knitr)))
9605 (home-page "https://afex.singmann.science/")
9606 (synopsis "Analysis of factorial experiments")
9608 "This package provides convenience functions for analyzing factorial
9609 experiments using ANOVA or mixed models.")
9610 (license license:gpl2+)))
9612 (define-public r-lmertest
9619 (uri (cran-uri "lmerTest" version))
9622 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9623 (properties `((upstream-name . "lmerTest")))
9624 (build-system r-build-system)
9626 `(("r-ggplot2" ,r-ggplot2)
9629 ("r-numderiv" ,r-numderiv)))
9630 (home-page "https://github.com/runehaubo/lmerTestR")
9631 (synopsis "Tests in linear mixed effects models")
9633 "This package provides p-values in type I, II or III anova and summary
9634 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9635 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9636 package. Model selection methods include step, drop1 and anova-like tables
9637 for random effects (ranova). Methods for Least-Square means (LS-means) and
9638 tests of linear contrasts of fixed effects are also available.")
9639 (license license:gpl2+)))
9641 (define-public r-r2glmm
9648 (uri (cran-uri "r2glmm" version))
9651 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9652 (build-system r-build-system)
9654 `(("r-afex" ,r-afex)
9655 ("r-data-table" ,r-data-table)
9656 ("r-dplyr" ,r-dplyr)
9657 ("r-ggplot2" ,r-ggplot2)
9658 ("r-gridextra" ,r-gridextra)
9659 ("r-lmertest" ,r-lmertest)
9661 ("r-matrix" ,r-matrix)
9663 ("r-pbkrtest" ,r-pbkrtest)))
9664 (home-page "https://github.com/bcjaeger/r2glmm")
9665 (synopsis "Compute R squared for mixed (multilevel) models")
9667 "This package computes model and semi partial R squared with confidence
9668 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9669 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9670 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9672 (license license:gpl2)))
9674 (define-public r-weights
9681 (uri (cran-uri "weights" version))
9684 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9685 (build-system r-build-system)
9687 `(("r-gdata" ,r-gdata)
9688 ("r-hmisc" ,r-hmisc)
9689 ("r-mice" ,r-mice)))
9691 "https://cran.r-project.org/web/packages/weights/")
9692 (synopsis "Weighting and weighted statistics")
9693 (description "This package Provides a variety of functions for producing
9694 simple weighted statistics, such as weighted Pearson's correlations, partial
9695 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9696 includes some software for quickly recoding survey data and plotting point
9697 estimates from interaction terms in regressions (and multiply imputed
9698 regressions). NOTE: Weighted partial correlation calculations pulled to
9700 (license license:gpl2+)))
9702 (define-public r-rcppannoy
9704 (name "r-rcppannoy")
9709 (uri (cran-uri "RcppAnnoy" version))
9712 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9713 (properties `((upstream-name . "RcppAnnoy")))
9714 (build-system r-build-system)
9716 `(("r-rcpp" ,r-rcpp)))
9717 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9718 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9720 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9721 for efficient memory usage as well an ability to load from and save to disk.
9722 This package provides an R interface.")
9723 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9725 (license (list license:gpl2+ license:asl2.0))))
9727 (define-public r-rcpphnsw
9734 (uri (cran-uri "RcppHNSW" version))
9737 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9738 (properties `((upstream-name . "RcppHNSW")))
9739 (build-system r-build-system)
9740 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9741 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9742 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9744 "Hnswlib is a C++ library for approximate nearest neighbors. This
9745 package provides a minimal R interface by relying on the Rcpp package.")
9746 ;; hnswlib is released under Version 2.0 of the Apache License.
9747 (license (list license:gpl3 license:asl2.0))))
9749 (define-public r-rcppparallel
9751 (name "r-rcppparallel")
9756 (uri (cran-uri "RcppParallel" version))
9759 "029yyjnixggqmddazwxh1wqid1h7xpwpi4sgixyhbb4kmvqlwfkd"))))
9760 (properties `((upstream-name . "RcppParallel")))
9761 (build-system r-build-system)
9762 (home-page "https://rcppcore.github.io/RcppParallel/")
9763 (synopsis "Parallel programming tools for Rcpp")
9765 "This package provides high level functions for parallel programming with
9766 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9767 the work of a standard serial @code{for} loop into a parallel one and the
9768 @code{parallelReduce()} function can be used for accumulating aggregates or
9770 (license license:gpl2)))
9772 (define-public r-ncdf4
9779 (uri (cran-uri "ncdf4" version))
9782 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9783 (build-system r-build-system)
9785 `(("netcdf" ,netcdf)
9787 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9788 (synopsis "R interface to Unidata netCDF format data files")
9790 "This package provides a high-level R interface to data files written
9791 using Unidata's netCDF library (version 4 or earlier), which are binary data
9792 files that are portable across platforms and include metadata information in
9793 addition to the data sets. Using this package, netCDF files can be opened and
9794 data sets read in easily. It is also easy to create new netCDF dimensions,
9795 variables, and files, in either version 3 or 4 format, and manipulate existing
9797 (license license:gpl3+)))
9799 (define-public r-biocmanager
9801 (name "r-biocmanager")
9806 (uri (cran-uri "BiocManager" version))
9808 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9809 (properties `((upstream-name . "BiocManager")))
9810 (build-system r-build-system)
9811 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9812 (synopsis "Access the Bioconductor project package repository")
9814 "This package provides a convenient tool to install and update
9815 Bioconductor packages.")
9816 (license license:artistic2.0)))
9818 (define-public r-rgl
9821 (version "0.100.54")
9825 (uri (cran-uri "rgl" version))
9828 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9829 (build-system r-build-system)
9831 `(("pkg-config" ,pkg-config)))
9833 `(("freetype" ,freetype)
9837 ("ghc-pandoc" ,ghc-pandoc)
9840 `(("r-crosstalk" ,r-crosstalk)
9841 ("r-htmltools" ,r-htmltools)
9842 ("r-htmlwidgets" ,r-htmlwidgets)
9843 ("r-jsonlite" ,r-jsonlite)
9844 ("r-knitr" ,r-knitr)
9845 ("r-magrittr" ,r-magrittr)
9846 ("r-manipulatewidget" ,r-manipulatewidget)
9847 ("r-shiny" ,r-shiny)))
9848 (home-page "https://r-forge.r-project.org/projects/rgl/")
9849 (synopsis "3D visualization using OpenGL")
9851 "This package provides medium to high level functions for 3D interactive graphics,
9852 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9853 as functions for constructing representations of geometric
9854 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9855 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9856 image formats, including PNG, Postscript, SVG, PGF.")
9857 ;; Any version of the GPL.
9858 (license (list license:gpl2+ license:gpl3+))))
9860 (define-public r-multicool
9862 (name "r-multicool")
9867 (uri (cran-uri "multicool" version))
9870 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9871 (build-system r-build-system)
9872 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9873 (home-page "https://cran.r-project.org/web/packages/multicool/")
9874 (synopsis "Permutations of multisets in cool-lex order")
9876 "This package provides a set of tools to permute multisets without loops
9877 or hash tables and to generate integer partitions. Cool-lex order is similar
9878 to colexicographical order.")
9879 (license license:gpl2)))
9881 (define-public r-misc3d
9888 (uri (cran-uri "misc3d" version))
9891 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9892 (build-system r-build-system)
9893 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9894 (synopsis "Miscellaneous 3D Plots")
9896 "This package provides a collection of miscellaneous 3d plots, including
9898 ;; Any version of the GPL.
9899 (license (list license:gpl2+ license:gpl3+))))
9908 (uri (cran-uri "ks" version))
9910 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9911 (build-system r-build-system)
9914 ("r-kernlab" ,r-kernlab)
9915 ("r-kernsmooth" ,r-kernsmooth)
9916 ("r-matrix" ,r-matrix)
9917 ("r-mclust" ,r-mclust)
9919 ("r-multicool" ,r-multicool)
9920 ("r-mvtnorm" ,r-mvtnorm)))
9921 (home-page "http://www.mvstat.net/tduong/")
9922 (synopsis "Kernel smoothing")
9924 "This package provides kernel smoothers for univariate and multivariate
9925 data, including density functions, density derivatives, cumulative
9926 distributions, modal clustering, discriminant analysis, and two-sample
9927 hypothesis testing.")
9928 ;; Either version of the GPL.
9929 (license (list license:gpl2 license:gpl3))))
9931 (define-public r-feature
9938 (uri (cran-uri "feature" version))
9941 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9942 (build-system r-build-system)
9945 ("r-misc3d" ,r-misc3d)
9947 (home-page "http://www.mvstat.net/tduong/")
9948 (synopsis "Inferential feature significance for kernel density estimation")
9950 "The feature package contains functions to display and compute kernel
9951 density estimates, significant gradient and significant curvature regions.
9952 Significant gradient and/or curvature regions often correspond to significant
9953 features (e.g. local modes).")
9954 ;; Either version of the GPL.
9955 (license (list license:gpl2 license:gpl3))))
9957 (define-public r-arm
9964 (uri (cran-uri "arm" version))
9967 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9968 (build-system r-build-system)
9970 `(("r-abind" ,r-abind)
9974 ("r-matrix" ,r-matrix)
9975 ("r-nlme" ,r-nlme)))
9976 (home-page "https://cran.r-project.org/web/packages/arm/")
9977 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9979 "This package provides functions to accompany A. Gelman and J. Hill,
9980 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9981 University Press, 2007.")
9982 (license license:gpl3+)))
9984 (define-public r-circular
9991 (uri (cran-uri "circular" version))
9994 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9995 (build-system r-build-system)
9997 `(("r-boot" ,r-boot)
9998 ("r-mvtnorm" ,r-mvtnorm)))
10000 `(("gfortran" ,gfortran)))
10001 (home-page "https://cran.r-project.org/web/packages/circular/")
10002 (synopsis "Circular statistics")
10004 "This package provides tools for circular statistics, from \"Topics in
10005 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10007 (license license:gpl2+)))
10009 (define-public r-activity
10011 (name "r-activity")
10016 (uri (cran-uri "activity" version))
10019 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10020 (build-system r-build-system)
10022 `(("r-circular" ,r-circular)
10023 ("r-insol" ,r-insol)
10024 ("r-pbapply" ,r-pbapply)))
10025 (home-page "https://cran.r-project.org/web/packages/activity/")
10026 (synopsis "Animal activity statistics")
10028 "This package provides functions to fit kernel density functions to
10029 animal activity time data; plot activity distributions; quantify overall
10030 levels of activity; statistically compare activity metrics through
10031 bootstrapping; and evaluate variation in linear variables with time (or other
10032 circular variables).")
10033 (license license:gpl3)))
10035 (define-public r-ouch
10042 (uri (cran-uri "ouch" version))
10045 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10046 (build-system r-build-system)
10047 (propagated-inputs `(("r-subplex" ,r-subplex)))
10048 (home-page "https://kingaa.github.io/ouch/")
10049 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10051 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10052 for evolution along a phylogenetic tree.")
10053 (license license:gpl2+)))
10055 (define-public r-fmsb
10062 (uri (cran-uri "fmsb" version))
10065 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10066 (build-system r-build-system)
10067 (home-page "http://minato.sip21c.org/msb/")
10068 (synopsis "Functions for medical statistics book with demographic data")
10070 "This package provides several utility functions for the book entitled
10071 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10072 Japan, 2007) with Japanese demographic data and some demographic analysis
10073 related functions.")
10074 (license license:gpl2+)))
10076 (define-public r-stabledist
10078 (name "r-stabledist")
10083 (uri (cran-uri "stabledist" version))
10086 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10087 (build-system r-build-system)
10088 (home-page "https://www.rmetrics.org")
10089 (synopsis "Stable distribution functions")
10091 "This package provides density, probability and quantile functions, and
10092 random number generation for (skew) stable distributions, using the
10093 parametrizations of Nolan.")
10094 (license license:gpl2+)))
10096 (define-public r-gsl
10103 (uri (cran-uri "gsl" version))
10106 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10107 (build-system r-build-system)
10110 (home-page "https://cran.r-project.org/web/packages/gsl")
10111 (synopsis "Wrapper for the GNU Scientific Library")
10113 "This package provides an R wrapper for the special functions and quasi
10114 random number generators of the GNU Scientific Library.")
10115 (license license:gpl2+)))
10117 (define-public r-adgoftest
10119 (name "r-adgoftest")
10124 (uri (cran-uri "ADGofTest" version))
10127 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10128 (properties `((upstream-name . "ADGofTest")))
10129 (build-system r-build-system)
10130 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10131 (synopsis "Anderson-Darling GoF test")
10133 "This package provides an implementation of the Anderson-Darling GoF test
10134 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10135 Anderson-Darling Distribution\".")
10136 ;; Any version of the GPL.
10137 (license license:gpl3+)))
10139 (define-public r-softimpute
10141 (name "r-softimpute")
10146 (uri (cran-uri "softImpute" version))
10149 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10150 (properties `((upstream-name . "softImpute")))
10151 (build-system r-build-system)
10153 `(("r-matrix" ,r-matrix)))
10155 `(("gfortran" ,gfortran)))
10156 (home-page "https://cran.r-project.org/web/packages/softImpute")
10157 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10159 "This package provides iterative methods for matrix completion that use
10160 nuclear-norm regularization. The package includes procedures for centering
10161 and scaling rows, columns or both, and for computing low-rank @dfn{single
10162 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10164 (license license:gpl2)))
10166 (define-public r-fftwtools
10168 (name "r-fftwtools")
10173 (uri (cran-uri "fftwtools" version))
10176 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10177 (build-system r-build-system)
10178 (inputs `(("fftw" ,fftw)))
10179 (home-page "https://github.com/krahim/fftwtools")
10180 (synopsis "Wrapper for FFTW3")
10182 "This package provides a wrapper for several FFTW functions. It provides
10183 access to the two-dimensional FFT, the multivariate FFT, and the
10184 one-dimensional real to complex FFT using the FFTW3 library. The package
10185 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10186 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10187 The FFT functions have a parameter that allows them to not return the
10188 redundant complex conjugate when the input is real data.")
10189 (license license:gpl2+)))
10191 (define-public r-tiff
10198 (uri (cran-uri "tiff" version))
10201 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10202 (build-system r-build-system)
10204 `(("libtiff" ,libtiff)
10205 ("libjpeg" ,libjpeg-turbo)
10207 (home-page "https://www.rforge.net/tiff/")
10208 (synopsis "Read and write TIFF images")
10210 "This package provides an easy and simple way to read, write and display
10211 bitmap images stored in the TIFF format. It can read and write both files and
10212 in-memory raw vectors.")
10213 ;; Either of these two license versions.
10214 (license (list license:gpl2 license:gpl3))))
10216 (define-public r-nlp
10223 (uri (cran-uri "NLP" version))
10226 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10227 (properties `((upstream-name . "NLP")))
10228 (build-system r-build-system)
10229 (home-page "https://cran.r-project.org/web/packages/NLP/")
10230 (synopsis "Natural language processing infrastructure")
10232 "This package provides basic classes and methods for Natural Language
10234 (license license:gpl3)))
10236 (define-public r-tm
10243 (uri (cran-uri "tm" version))
10246 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10247 (properties `((upstream-name . "tm")))
10248 (build-system r-build-system)
10254 ("r-xml2" ,r-xml2)))
10255 (home-page "http://tm.r-forge.r-project.org/")
10256 (synopsis "Text mining package")
10258 "This package provides a framework for text mining applications within R.")
10259 (license license:gpl3)))
10261 (define-public r-waveslim
10263 (name "r-waveslim")
10268 (uri (cran-uri "waveslim" version))
10271 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10272 (build-system r-build-system)
10274 `(("gfortran" ,gfortran)))
10275 (home-page "http://waveslim.blogspot.com")
10276 (synopsis "Basic wavelet routines for signal processing")
10278 "This package provides basic wavelet routines for time series (1D),
10279 image (2D) and array (3D) analysis. The code provided here is based on
10280 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10281 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10282 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10283 pairs (Selesnick 2001, 2002).")
10284 (license license:bsd-3)))
10286 (define-public r-wordcloud
10288 (name "r-wordcloud")
10293 (uri (cran-uri "wordcloud" version))
10296 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10297 (build-system r-build-system)
10299 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10301 ;; The "tm" package is only "suggested" according to CRAN, but the
10302 ;; wordcloud package cannot be loaded without it.
10304 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10305 (synopsis "Word clouds")
10307 "This package provides functionality to create pretty word clouds,
10308 visualize differences and similarity between documents, and avoid
10309 over-plotting in scatter plots with text.")
10310 (license license:lgpl2.1)))
10312 (define-public r-colorramps
10314 (name "r-colorramps")
10319 (uri (cran-uri "colorRamps" version))
10322 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10323 (properties `((upstream-name . "colorRamps")))
10324 (build-system r-build-system)
10325 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10326 (synopsis "Build color tables")
10327 (description "This package provides features to build gradient color
10329 ;; Any version of the GPL
10330 (license license:gpl3+)))
10332 (define-public r-tidytree
10334 (name "r-tidytree")
10339 (uri (cran-uri "tidytree" version))
10341 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10342 (build-system r-build-system)
10345 ("r-dplyr" ,r-dplyr)
10346 ("r-lazyeval" ,r-lazyeval)
10347 ("r-magrittr" ,r-magrittr)
10348 ("r-rlang" ,r-rlang)
10349 ("r-tibble" ,r-tibble)))
10351 `(("r-knitr" ,r-knitr)))
10352 (home-page "https://github.com/GuangchuangYu/tidytree")
10353 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10355 "Phylogenetic trees generally contain multiple components including nodes,
10356 edges, branches and associated data. This package provides an approach to
10357 convert tree objects to tidy data frames. It also provides tidy interfaces to
10358 manipulate tree data.")
10359 (license license:artistic2.0)))
10361 (define-public r-rvcheck
10368 (uri (cran-uri "rvcheck" version))
10370 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10371 (build-system r-build-system)
10373 `(("r-biocmanager" ,r-biocmanager)
10374 ("r-rlang" ,r-rlang)))
10375 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10376 (synopsis "R package version check")
10378 "This package provides tools to check the latest release version of R and
10379 R packages (on CRAN, Bioconductor or Github).")
10380 (license license:artistic2.0)))
10382 (define-public r-docopt
10389 (uri (cran-uri "docopt" version))
10392 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
10393 (build-system r-build-system)
10394 (home-page "https://github.com/docopt/docopt.R")
10395 (synopsis "Command-line interface specification language")
10397 "This package enables you to define a command-line interface by just
10398 giving it a description in the specific format.")
10399 (license license:expat)))
10401 (define-public r-sparsesvd
10403 (name "r-sparsesvd")
10408 (uri (cran-uri "sparsesvd" version))
10411 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10412 (build-system r-build-system)
10413 (propagated-inputs `(("r-matrix" ,r-matrix)))
10414 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10415 (synopsis "Sparse truncated singular value decomposition")
10417 "This package provides a Wrapper around the SVDLIBC library
10418 for (truncated) singular value decomposition of a sparse matrix. Currently,
10419 only sparse real matrices in Matrix package format are supported.")
10420 ;; SVDLIBC is released under BSD-2. The R interface is released under
10422 (license (list license:bsd-3 license:bsd-2))))
10424 (define-public r-speedglm
10426 (name "r-speedglm")
10431 (uri (cran-uri "speedglm" version))
10434 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10435 (build-system r-build-system)
10437 `(("r-mass" ,r-mass)
10438 ("r-matrix" ,r-matrix)))
10439 (home-page "https://cran.r-project.org/web/packages/speedglm")
10440 (synopsis "Fit linear and generalized linear models to large data sets")
10442 "This package provides tools for fitting linear models and generalized
10443 linear models to large data sets by updating algorithms.")
10444 ;; Any version of the GPL
10445 (license license:gpl2+)))
10447 (define-public r-densityclust
10449 (name "r-densityclust")
10454 (uri (cran-uri "densityClust" version))
10457 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10458 (properties `((upstream-name . "densityClust")))
10459 (build-system r-build-system)
10462 ("r-ggplot2" ,r-ggplot2)
10463 ("r-ggrepel" ,r-ggrepel)
10464 ("r-gridextra" ,r-gridextra)
10465 ("r-rcolorbrewer" ,r-rcolorbrewer)
10467 ("r-rtsne" ,r-rtsne)))
10468 (home-page "https://cran.r-project.org/web/packages/densityClust")
10469 (synopsis "Clustering by fast search and find of density peaks")
10471 "This package provides an improved implementation (based on k-nearest
10472 neighbors) of the density peak clustering algorithm, originally described by
10473 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10474 large datasets (> 100,000 samples) very efficiently.")
10475 (license license:gpl2+)))
10477 (define-public r-combinat
10479 (name "r-combinat")
10484 (uri (cran-uri "combinat" version))
10487 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10488 (build-system r-build-system)
10489 (home-page "https://cran.r-project.org/web/packages/combinat")
10490 (synopsis "Combinatorics utilities")
10491 (description "This package provides assorted routines for combinatorics.")
10492 (license license:gpl2)))
10494 (define-public r-qlcmatrix
10496 (name "r-qlcmatrix")
10501 (uri (cran-uri "qlcMatrix" version))
10504 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10505 (properties `((upstream-name . "qlcMatrix")))
10506 (build-system r-build-system)
10508 `(("r-docopt" ,r-docopt)
10509 ("r-matrix" ,r-matrix)
10511 ("r-sparsesvd" ,r-sparsesvd)))
10512 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10513 (synopsis "Sparse matrix functions for quantitative language comparison")
10515 "This package provides an extension of the functionality of the Matrix
10516 package for using sparse matrices. Some of the functions are very general,
10517 while other are highly specific for the special data format used for
10518 @dfn{quantitative language comparison} (QLC).")
10519 (license license:gpl3)))
10521 (define-public r-ddrtree
10528 (uri (cran-uri "DDRTree" version))
10531 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10532 (properties `((upstream-name . "DDRTree")))
10533 (build-system r-build-system)
10536 ("r-irlba" ,r-irlba)
10538 ("r-rcppeigen" ,r-rcppeigen)))
10539 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10540 (synopsis "Learning principal graphs with DDRTree")
10542 "This package provides an implementation of the framework of
10543 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10544 dimensional space while constructs a principal tree which passes through the
10545 middle of the data simultaneously. DDRTree shows superiority to
10546 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10547 intrinsic structure of single cell genomics data. In general, it could be
10548 used to reconstruct the temporal progression as well as the bifurcation
10549 structure of any data type.")
10550 (license license:asl2.0)))
10552 (define-public r-corpcor
10559 (uri (cran-uri "corpcor" version))
10562 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10563 (build-system r-build-system)
10564 (home-page "http://strimmerlab.org/software/corpcor/")
10565 (synopsis "Efficient estimation of covariance and (partial) correlation")
10567 "This package implements a James-Stein-type shrinkage estimator for the
10568 covariance matrix, with separate shrinkage for variances and correlations.
10569 Furthermore, functions are available for fast singular value decomposition,
10570 for computing the pseudoinverse, and for checking the rank and positive
10571 definiteness of a matrix.")
10572 (license license:gpl3+)))
10574 (define-public r-rspectra
10576 (name "r-rspectra")
10581 (uri (cran-uri "RSpectra" version))
10584 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10585 (properties `((upstream-name . "RSpectra")))
10586 (build-system r-build-system)
10588 `(("r-matrix" ,r-matrix)
10590 ("r-rcppeigen" ,r-rcppeigen)))
10591 (home-page "https://github.com/yixuan/RSpectra")
10592 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10594 "This package provides an R interface to the Spectra library for
10595 large-scale eigenvalue and SVD problems. It is typically used to compute a
10596 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10597 which is usually more efficient than @code{eigen()} if k << n.")
10599 (license license:mpl2.0)))
10601 (define-public r-vbsr
10608 (uri (cran-uri "vbsr" version))
10611 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10612 (build-system r-build-system)
10613 (home-page "https://cran.r-project.org/web/packages/vbsr")
10614 (synopsis "Variational Bayes spike regression regularized linear models")
10616 "This package provides an efficient algorithm for solving ultra-sparse
10617 regularized regression models using a variational Bayes algorithm with a spike
10618 prior. The algorithm is solved on a path, with coordinate updates, and is
10619 capable of generating very sparse models. Very general model
10620 diagnostics for controlling type-1 errors are also provided.")
10621 (license license:gpl2)))
10623 (define-public r-flare
10626 (version "1.6.0.2")
10630 (uri (cran-uri "flare" version))
10633 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10634 (build-system r-build-system)
10636 `(("r-igraph" ,r-igraph)
10637 ("r-lattice" ,r-lattice)
10639 ("r-matrix" ,r-matrix)))
10640 (home-page "https://cran.r-project.org/web/packages/flare")
10641 (synopsis "Family of Lasso regression implementations")
10643 "This package provides implementations of a family of Lasso variants
10644 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10645 high dimensional sparse linear models.")
10646 (license license:gpl2)))
10648 (define-public r-lassopv
10655 (uri (cran-uri "lassopv" version))
10658 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10659 (build-system r-build-system)
10660 (propagated-inputs `(("r-lars" ,r-lars)))
10661 (home-page "https://github.com/lingfeiwang/lassopv")
10662 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10664 "This package enables you to estimate the p-values for predictors x
10665 against target variable y in Lasso regression, using the regularization
10666 strength when each predictor enters the active set of regularization path for
10667 the first time as the statistic.")
10668 (license license:gpl3)))
10670 (define-public r-splitstackshape
10672 (name "r-splitstackshape")
10677 (uri (cran-uri "splitstackshape" version))
10680 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10681 (build-system r-build-system)
10683 `(("r-data-table" ,r-data-table)))
10684 (home-page "https://github.com/mrdwab/splitstackshape")
10685 (synopsis "Stack and reshape datasets after splitting concatenated values")
10687 "Online data collection tools like Google Forms often export
10688 multiple-response questions with data concatenated in cells. The
10689 @code{concat.split} (cSplit) family of functions provided by this package
10690 splits such data into separate cells. This package also includes functions to
10691 stack groups of columns and to reshape wide data, even when the data are
10692 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10693 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10695 (license license:gpl3)))
10697 (define-public r-tfmpvalue
10699 (name "r-tfmpvalue")
10704 (uri (cran-uri "TFMPvalue" version))
10707 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10708 (properties `((upstream-name . "TFMPvalue")))
10709 (build-system r-build-system)
10710 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10711 (home-page "https://github.com/ge11232002/TFMPvalue")
10712 (synopsis "P-value computation for position weight matrices")
10714 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10715 identification from sequence/alignments, we are interested in the significance
10716 of certain match scores. TFMPvalue provides the accurate calculation of a
10717 p-value with a score threshold for position weight matrices, or the score with
10718 a given p-value. It is an interface to code originally made available by
10719 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10720 Touzet and Varre (2007).")
10721 (license license:gpl2)))
10723 (define-public r-rnifti
10730 (uri (cran-uri "RNifti" version))
10733 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10734 (properties `((upstream-name . "RNifti")))
10735 (build-system r-build-system)
10736 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10737 (home-page "https://github.com/jonclayden/RNifti")
10738 (synopsis "Fast R and C++ access to NIfTI images")
10740 "This package provides very fast read and write access to images stored
10741 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10742 compiled C and interpreted R code. It also provides a C/C++ API that can be
10743 used by other packages.")
10744 (license license:gpl2)))
10746 (define-public r-shades
10753 (uri (cran-uri "shades" version))
10756 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10757 (build-system r-build-system)
10758 (home-page "https://github.com/jonclayden/shades")
10759 (synopsis "Simple color manipulation")
10761 "This package provides functions for easily manipulating colors,
10762 creating color scales and calculating color distances.")
10763 (license license:bsd-3)))
10765 (define-public r-ore
10772 (uri (cran-uri "ore" version))
10774 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10775 (build-system r-build-system)
10776 (home-page "https://github.com/jonclayden/ore")
10777 (synopsis "R interface to the Onigmo regular expression library")
10779 "This package provides an alternative to R's built-in functionality for
10780 handling regular expressions, based on the Onigmo library. It offers
10781 first-class compiled regex objects, partial matching and function-based
10782 substitutions, amongst other features.")
10783 (license license:bsd-3)))
10785 (define-public r-reportr
10792 (uri (cran-uri "reportr" version))
10795 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10796 (build-system r-build-system)
10797 (propagated-inputs `(("r-ore" ,r-ore)))
10798 (home-page "https://github.com/jonclayden/reportr")
10799 (synopsis "General message and error reporting system")
10801 "This package provides a system for reporting messages, which offers
10802 certain useful features over the standard R system, such as the incorporation
10803 of output consolidation, message filtering, assertions, expression
10804 substitution, automatic generation of stack traces for debugging, and
10805 conditional reporting based on the current \"output level\".")
10806 (license license:gpl2)))
10808 (define-public r-tractor-base
10810 (name "r-tractor-base")
10815 (uri (cran-uri "tractor.base" version))
10818 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10819 (properties `((upstream-name . "tractor.base")))
10820 (build-system r-build-system)
10823 ("r-reportr" ,r-reportr)
10824 ("r-rnifti" ,r-rnifti)
10825 ("r-shades" ,r-shades)))
10826 (home-page "https://www.tractor-mri.org.uk")
10827 (synopsis "Read, manipulate and visualize magnetic resonance images")
10829 "This package provides functions for working with magnetic resonance
10830 images. It supports reading and writing of popular file formats (DICOM,
10831 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10832 visualization; flexible image manipulation; metadata and sparse image
10834 (license license:gpl2)))
10836 (define-public r-grimport
10838 (name "r-grimport")
10843 (uri (cran-uri "grImport" version))
10846 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10847 (properties `((upstream-name . "grImport")))
10848 (build-system r-build-system)
10850 `(("ghostscript" ,ghostscript)))
10852 `(("r-xml" ,r-xml)))
10853 (home-page "https://cran.r-project.org/web/packages/grImport")
10854 (synopsis "Convert, import, and draw PostScript pictures")
10856 "This package provides functions for converting, importing, and drawing
10857 PostScript pictures in R plots.")
10858 (license license:gpl2+)))
10860 (define-public r-grimport2
10862 (name "r-grimport2")
10867 (uri (cran-uri "grImport2" version))
10870 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10871 (properties `((upstream-name . "grImport2")))
10872 (build-system r-build-system)
10874 `(("r-base64enc" ,r-base64enc)
10878 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10879 (synopsis "Import SVG graphics")
10881 "This package provides functions for importing external vector images and
10882 drawing them as part of R plots. This package is different from the
10883 @code{grImport} package because, where that package imports PostScript format
10884 images, this package imports SVG format images. Furthermore, this package
10885 imports a specific subset of SVG, so external images must be preprocessed
10886 using a package like @code{rsvg} to produce SVG that this package can import.
10887 SVG features that are not supported by R graphics, such as gradient fills, can
10888 be imported and then exported via the @code{gridSVG} package.")
10889 (license license:gpl2+)))
10891 (define-public r-kohonen
10898 (uri (cran-uri "kohonen" version))
10901 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10902 (build-system r-build-system)
10904 `(("r-rcpp" ,r-rcpp)))
10905 (home-page "https://cran.r-project.org/web/packages/kohonen")
10906 (synopsis "Supervised and unsupervised self-organising maps")
10908 "This package provides functions to train @dfn{self-organising
10909 maps} (SOMs). Also interrogation of the maps and prediction using trained
10910 maps are supported. The name of the package refers to Teuvo Kohonen, the
10911 inventor of the SOM.")
10912 (license license:gpl2+)))
10914 (define-public r-nnls
10921 (uri (cran-uri "nnls" version))
10924 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10925 (build-system r-build-system)
10926 (native-inputs `(("gfortran" ,gfortran)))
10927 (home-page "https://cran.r-project.org/web/packages/nnls")
10928 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10930 "This package provides an R interface to the Lawson-Hanson implementation
10931 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10932 the combination of non-negative and non-positive constraints.")
10933 (license license:gpl2+)))
10935 (define-public r-iso
10938 (version "0.0-18.1")
10942 (uri (cran-uri "Iso" version))
10945 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
10946 (properties `((upstream-name . "Iso")))
10947 (build-system r-build-system)
10948 (native-inputs `(("gfortran" ,gfortran)))
10949 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10950 (synopsis "Functions to perform isotonic regression")
10952 "This package provides support for linear order and unimodal
10953 order (univariate) isotonic regression and bivariate isotonic regression with
10954 linear order on both variables.")
10955 (license license:gpl2+)))
10957 (define-public r-chemometricswithr
10959 (name "r-chemometricswithr")
10964 (uri (cran-uri "ChemometricsWithR" version))
10967 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10969 `((upstream-name . "ChemometricsWithR")))
10970 (build-system r-build-system)
10972 `(("r-devtools" ,r-devtools)
10973 ("r-kohonen" ,r-kohonen)
10976 (home-page "https://github.com/rwehrens/CWR")
10977 (synopsis "Chemometrics with R")
10979 "This package provides functions and scripts used in the book
10980 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10981 Life Sciences\" by Ron Wehrens, Springer (2011).")
10982 (license license:gpl2+)))
10984 (define-public r-als
10991 (uri (cran-uri "ALS" version))
10994 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10995 (properties `((upstream-name . "ALS")))
10996 (build-system r-build-system)
10999 ("r-nnls" ,r-nnls)))
11000 (home-page "https://cran.r-project.org/web/packages/ALS")
11001 (synopsis "Multivariate curve resolution alternating least squares")
11003 "Alternating least squares is often used to resolve components
11004 contributing to data with a bilinear structure; the basic technique may be
11005 extended to alternating constrained least squares. This package provides an
11006 implementation of @dfn{multivariate curve resolution alternating least
11007 squares} (MCR-ALS).
11009 Commonly applied constraints include unimodality, non-negativity, and
11010 normalization of components. Several data matrices may be decomposed
11011 simultaneously by assuming that one of the two matrices in the bilinear
11012 decomposition is shared between datasets.")
11013 (license license:gpl2+)))
11015 (define-public r-strucchange
11017 (name "r-strucchange")
11022 (uri (cran-uri "strucchange" version))
11025 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11026 (build-system r-build-system)
11028 `(("r-sandwich" ,r-sandwich)
11030 (home-page "https://cran.r-project.org/web/packages/strucchange")
11031 (synopsis "Testing, monitoring, and dating structural changes")
11033 "This package provides tools for testing, monitoring and dating
11034 structural changes in (linear) regression models. It features tests/methods
11035 from the generalized fluctuation test framework as well as from the F
11036 test (Chow test) framework. This includes methods to fit, plot and test
11037 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11038 statistics, respectively. It is possible to monitor incoming data online
11039 using fluctuation processes. Finally, the breakpoints in regression models
11040 with structural changes can be estimated together with confidence intervals.
11041 Emphasis is always given to methods for visualizing the data.")
11042 ;; Either of these two GPL versions
11043 (license (list license:gpl2 license:gpl3))))
11045 (define-public r-pixmap
11052 (uri (cran-uri "pixmap" version))
11055 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11056 (build-system r-build-system)
11057 (home-page "https://cran.r-project.org/web/packages/pixmap")
11058 (synopsis "Tools for bitmap images")
11060 "This package provides functions for importing, exporting, plotting and
11061 other manipulations of bitmapped images.")
11062 (license license:gpl2)))
11064 (define-public r-rapidjsonr
11066 (name "r-rapidjsonr")
11071 (uri (cran-uri "rapidjsonr" version))
11074 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11075 (build-system r-build-system)
11076 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11077 (synopsis "JSON parser")
11079 "This package provides JSON parsing capability through the Rapidjson
11081 (license license:expat)))
11083 (define-public r-ontologyindex
11085 (name "r-ontologyindex")
11090 (uri (cran-uri "ontologyIndex" version))
11093 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11094 (properties `((upstream-name . "ontologyIndex")))
11095 (build-system r-build-system)
11096 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11097 (synopsis "Functions for processing ontologies in R")
11099 "This package provides functions for reading ontologies into R as lists
11100 and manipulating sets of ontological terms.")
11101 (license license:gpl2+)))
11103 (define-public r-gargle
11110 (uri (cran-uri "gargle" version))
11113 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11114 (build-system r-build-system)
11119 ("r-jsonlite" ,r-jsonlite)
11120 ("r-rlang" ,r-rlang)
11121 ("r-withr" ,r-withr)))
11123 `(("r-knitr" ,r-knitr)))
11124 (home-page "https://gargle.r-lib.org")
11125 (synopsis "Utilities for working with Google APIs")
11127 "This package provides utilities for working with Google APIs. This
11128 includes functions and classes for handling common credential types and for
11129 preparing, executing, and processing HTTP requests.")
11130 (license license:expat)))
11132 (define-public r-bigrquery
11134 (name "r-bigrquery")
11139 (uri (cran-uri "bigrquery" version))
11142 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11143 (build-system r-build-system)
11145 `(("r-assertthat" ,r-assertthat)
11146 ("r-bit64" ,r-bit64)
11149 ("r-gargle" ,r-gargle)
11152 ("r-jsonlite" ,r-jsonlite)
11153 ("r-prettyunits" ,r-prettyunits)
11154 ("r-progress" ,r-progress)
11155 ("r-rapidjsonr" ,r-rapidjsonr)
11157 ("r-rlang" ,r-rlang)
11158 ("r-tibble" ,r-tibble)))
11159 (home-page "https://github.com/rstats-db/bigrquery")
11160 (synopsis "R interface to Google's BigQuery API")
11162 "This package provides an R interface to Google's BigQuery database.")
11163 (license license:gpl3)))
11165 (define-public r-gmp
11172 (uri (cran-uri "gmp" version))
11175 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11176 (build-system r-build-system)
11179 (modify-phases %standard-phases
11180 (add-after 'unpack 'set-CC
11181 (lambda _ (setenv "CC" "gcc") #t)))))
11182 (inputs `(("gmp" ,gmp)))
11183 (home-page "https://cran.r-project.org/web/packages/gmp")
11184 (synopsis "Multiple precision arithmetic")
11186 "This package supports multiple precision arithmetic (big integers and
11187 rationals, prime number tests, matrix computation), \"arithmetic without
11188 limitations\" using the GNU Multiple Precision library.")
11189 ;; Any version of the GPL.
11190 (license license:gpl3+)))
11192 (define-public r-rmpfr
11199 (uri (cran-uri "Rmpfr" version))
11202 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11203 (properties `((upstream-name . "Rmpfr")))
11204 (build-system r-build-system)
11209 `(("r-gmp" ,r-gmp)))
11211 `(("pkg-config" ,pkg-config)))
11212 (home-page "http://rmpfr.r-forge.r-project.org/")
11213 (synopsis "R bindings to the MPFR library")
11215 "This package supports arithmetic (via S4 classes and methods) for
11216 arbitrary precision floating point numbers, including transcendental
11217 functions. To this end, the package interfaces with the @dfn{Multiple
11218 Precision Floating-Point Reliable} (MPFR) library.")
11219 (license license:gpl2+)))
11221 (define-public r-assertive-base
11223 (name "r-assertive-base")
11228 (uri (cran-uri "assertive.base" version))
11231 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11233 `((upstream-name . "assertive.base")))
11234 (build-system r-build-system)
11235 (home-page "https://bitbucket.org/richierocks/assertive.base")
11236 (synopsis "Core of the assertive package")
11238 "This package provides a minimal set of predicates and assertions used by
11239 the assertive package. This is mainly for use by other package developers who
11240 want to include run-time testing features in their own packages.")
11241 (license license:gpl3+)))
11243 (define-public r-assertive-properties
11245 (name "r-assertive-properties")
11250 (uri (cran-uri "assertive.properties" version))
11253 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11255 `((upstream-name . "assertive.properties")))
11256 (build-system r-build-system)
11258 `(("r-assertive-base" ,r-assertive-base)))
11259 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11260 (synopsis "Assertions to check properties of variables")
11262 "This package provides a set of predicates and assertions for checking
11263 the properties of variables, such as length, names and attributes. This is
11264 mainly for use by other package developers who want to include run-time
11265 testing features in their own packages.")
11266 (license license:gpl3+)))
11268 (define-public r-assertive-numbers
11270 (name "r-assertive-numbers")
11275 (uri (cran-uri "assertive.numbers" version))
11278 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11280 `((upstream-name . "assertive.numbers")))
11281 (build-system r-build-system)
11283 `(("r-assertive-base" ,r-assertive-base)))
11284 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11285 (synopsis "Assertions to check properties of numbers")
11287 "This package provides a set of predicates and assertions for checking
11288 the properties of numbers. This is mainly for use by other package developers
11289 who want to include run-time testing features in their own packages.")
11290 (license license:gpl3+)))
11292 (define-public r-assertive-sets
11294 (name "r-assertive-sets")
11299 (uri (cran-uri "assertive.sets" version))
11302 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11304 `((upstream-name . "assertive.sets")))
11305 (build-system r-build-system)
11307 `(("r-assertive-base" ,r-assertive-base)))
11308 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11309 (synopsis "Assertions to check properties of sets")
11311 "This package provides a set of predicates and assertions for checking
11312 the properties of sets. This is mainly for use by other package developers
11313 who want to include run-time testing features in their own packages.")
11314 (license license:gpl3+)))
11316 (define-public r-assertive-matrices
11318 (name "r-assertive-matrices")
11323 (uri (cran-uri "assertive.matrices" version))
11326 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11328 `((upstream-name . "assertive.matrices")))
11329 (build-system r-build-system)
11331 `(("r-assertive-base" ,r-assertive-base)))
11332 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11333 (synopsis "Assertions to check properties of matrices")
11335 "This package provides a set of predicates and assertions for checking
11336 the properties of matrices. This is mainly for use by other package
11337 developers who want to include run-time testing features in their own
11339 (license license:gpl3+)))
11341 (define-public r-assertive-models
11343 (name "r-assertive-models")
11348 (uri (cran-uri "assertive.models" version))
11351 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11353 `((upstream-name . "assertive.models")))
11354 (build-system r-build-system)
11356 `(("r-assertive-base" ,r-assertive-base)))
11357 (home-page "https://bitbucket.org/richierocks/assertive.models")
11358 (synopsis "Assertions to check properties of models")
11360 "This package provides a set of predicates and assertions for checking
11361 the properties of models. This is mainly for use by other package developers
11362 who want to include run-time testing features in their own packages.")
11363 (license license:gpl3+)))
11365 (define-public r-assertive-reflection
11367 (name "r-assertive-reflection")
11372 (uri (cran-uri "assertive.reflection" version))
11375 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11377 `((upstream-name . "assertive.reflection")))
11378 (build-system r-build-system)
11380 `(("r-assertive-base" ,r-assertive-base)))
11381 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11382 (synopsis "Assertions for checking the state of R")
11384 "This package provides a set of predicates and assertions for checking
11385 the state and capabilities of R, the operating system it is running on, and
11386 the IDE being used. This is mainly for use by other package developers who
11387 want to include run-time testing features in their own packages.")
11388 (license license:gpl3+)))
11390 (define-public r-assertive-types
11392 (name "r-assertive-types")
11397 (uri (cran-uri "assertive.types" version))
11400 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11402 `((upstream-name . "assertive.types")))
11403 (build-system r-build-system)
11405 `(("r-assertive-base" ,r-assertive-base)
11406 ("r-assertive-properties" ,r-assertive-properties)
11407 ("r-codetools" ,r-codetools)))
11408 (home-page "https://bitbucket.org/richierocks/assertive.types")
11409 (synopsis "Assertions to check types of variables")
11411 "This package provides a set of predicates and assertions for checking
11412 the types of variables. This is mainly for use by other package developers
11413 who want to include run-time testing features in their own packages.")
11414 (license license:gpl3+)))
11416 (define-public r-assertive-files
11418 (name "r-assertive-files")
11423 (uri (cran-uri "assertive.files" version))
11426 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11428 `((upstream-name . "assertive.files")))
11429 (build-system r-build-system)
11431 `(("r-assertive-base" ,r-assertive-base)
11432 ("r-assertive-numbers" ,r-assertive-numbers)))
11433 (home-page "https://bitbucket.org/richierocks/assertive.files")
11434 (synopsis "Assertions to check properties of files")
11436 "This package provides a set of predicates and assertions for checking
11437 the properties of files and connections. This is mainly for use by other
11438 package developers who want to include run-time testing features in their own
11440 (license license:gpl3+)))
11442 (define-public r-assertive-code
11444 (name "r-assertive-code")
11449 (uri (cran-uri "assertive.code" version))
11452 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11454 `((upstream-name . "assertive.code")))
11455 (build-system r-build-system)
11457 `(("r-assertive-base" ,r-assertive-base)
11458 ("r-assertive-properties" ,r-assertive-properties)
11459 ("r-assertive-types" ,r-assertive-types)))
11460 (home-page "https://bitbucket.org/richierocks/assertive.code")
11461 (synopsis "Assertions to check properties of code")
11463 "This package provides a set of predicates and assertions for checking
11464 the properties of code. This is mainly for use by other package developers
11465 who want to include run-time testing features in their own packages.")
11466 (license license:gpl3+)))
11468 (define-public r-assertive-datetimes
11470 (name "r-assertive-datetimes")
11475 (uri (cran-uri "assertive.datetimes" version))
11478 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11480 `((upstream-name . "assertive.datetimes")))
11481 (build-system r-build-system)
11483 `(("r-assertive-base" ,r-assertive-base)
11484 ("r-assertive-types" ,r-assertive-types)))
11485 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11486 (synopsis "Assertions to check properties of dates and times")
11488 "This package provides a set of predicates and assertions for checking
11489 the properties of dates and times. This is mainly for use by other package
11490 developers who want to include run-time testing features in their own
11492 (license license:gpl3+)))
11494 (define-public r-assertive-strings
11496 (name "r-assertive-strings")
11501 (uri (cran-uri "assertive.strings" version))
11504 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11506 `((upstream-name . "assertive.strings")))
11507 (build-system r-build-system)
11509 `(("r-assertive-base" ,r-assertive-base)
11510 ("r-assertive-types" ,r-assertive-types)
11511 ("r-stringi" ,r-stringi)))
11512 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11513 (synopsis "Assertions to check properties of strings")
11515 "This package provides a set of predicates and assertions for checking
11516 the properties of strings. This is mainly for use by other package developers
11517 who want to include run-time testing features in their own packages.")
11518 (license license:gpl3+)))
11520 (define-public r-assertive-data-us
11522 (name "r-assertive-data-us")
11527 (uri (cran-uri "assertive.data.us" version))
11530 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11532 `((upstream-name . "assertive.data.us")))
11533 (build-system r-build-system)
11535 `(("r-assertive-base" ,r-assertive-base)
11536 ("r-assertive-strings" ,r-assertive-strings)))
11537 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11538 (synopsis "Assertions to check properties of strings")
11540 "This package provides a set of predicates and assertions for checking
11541 the properties of US-specific complex data types. This is mainly for use by
11542 other package developers who want to include run-time testing features in
11543 their own packages.")
11544 (license license:gpl3+)))
11546 (define-public r-assertive-data-uk
11548 (name "r-assertive-data-uk")
11553 (uri (cran-uri "assertive.data.uk" version))
11556 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11558 `((upstream-name . "assertive.data.uk")))
11559 (build-system r-build-system)
11561 `(("r-assertive-base" ,r-assertive-base)
11562 ("r-assertive-strings" ,r-assertive-strings)))
11563 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11564 (synopsis "Assertions to check properties of strings")
11566 "This package provides a set of predicates and assertions for checking
11567 the properties of UK-specific complex data types. This is mainly for use by
11568 other package developers who want to include run-time testing features in
11569 their own packages.")
11570 (license license:gpl3+)))
11572 (define-public r-assertive-data
11574 (name "r-assertive-data")
11579 (uri (cran-uri "assertive.data" version))
11582 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11584 `((upstream-name . "assertive.data")))
11585 (build-system r-build-system)
11587 `(("r-assertive-base" ,r-assertive-base)
11588 ("r-assertive-strings" ,r-assertive-strings)))
11589 (home-page "https://bitbucket.org/richierocks/assertive.data")
11590 (synopsis "Assertions to check properties of data")
11592 "This package provides a set of predicates and assertions for checking
11593 the properties of (country independent) complex data types. This is mainly
11594 for use by other package developers who want to include run-time testing
11595 features in their own packages.")
11596 (license license:gpl3+)))
11598 (define-public r-assertive
11600 (name "r-assertive")
11605 (uri (cran-uri "assertive" version))
11608 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11609 (build-system r-build-system)
11611 `(("r-assertive-base" ,r-assertive-base)
11612 ("r-assertive-code" ,r-assertive-code)
11613 ("r-assertive-data" ,r-assertive-data)
11614 ("r-assertive-data-uk" ,r-assertive-data-uk)
11615 ("r-assertive-data-us" ,r-assertive-data-us)
11616 ("r-assertive-datetimes" ,r-assertive-datetimes)
11617 ("r-assertive-files" ,r-assertive-files)
11618 ("r-assertive-matrices" ,r-assertive-matrices)
11619 ("r-assertive-models" ,r-assertive-models)
11620 ("r-assertive-numbers" ,r-assertive-numbers)
11621 ("r-assertive-properties" ,r-assertive-properties)
11622 ("r-assertive-reflection" ,r-assertive-reflection)
11623 ("r-assertive-sets" ,r-assertive-sets)
11624 ("r-assertive-strings" ,r-assertive-strings)
11625 ("r-assertive-types" ,r-assertive-types)
11626 ("r-knitr" ,r-knitr)))
11627 (home-page "https://bitbucket.org/richierocks/assertive")
11628 (synopsis "Readable check functions to ensure code integrity")
11630 "This package provides lots of predicates (@code{is_*} functions) to
11631 check the state of your variables, and assertions (@code{assert_*} functions)
11632 to throw errors if they aren't in the right form.")
11633 (license license:gpl3+)))
11635 (define-public r-dotcall64
11637 (name "r-dotcall64")
11642 (uri (cran-uri "dotCall64" version))
11645 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11646 (properties `((upstream-name . "dotCall64")))
11647 (build-system r-build-system)
11648 (native-inputs `(("gfortran" ,gfortran)))
11649 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11650 (synopsis "Enhanced foreign function interface supporting long vectors")
11652 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11653 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11654 supports long vectors, arguments of type 64-bit integer, and provides a
11655 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11656 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11657 (license license:gpl2+)))
11659 (define-public r-spam
11666 (uri (cran-uri "spam" version))
11668 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11669 (build-system r-build-system)
11671 `(("r-dotcall64" ,r-dotcall64)))
11672 (native-inputs `(("gfortran" ,gfortran)))
11673 (home-page "https://www.math.uzh.ch/pages/spam/")
11674 (synopsis "Sparse matrix algebra")
11676 "This package provides a set of functions for sparse matrix algebra.
11677 Differences with other sparse matrix packages are:
11680 @item it only supports (essentially) one sparse matrix format;
11681 @item it is based on transparent and simple structure(s);
11682 @item it is tailored for MCMC calculations within G(M)RF;
11683 @item and it is fast and scalable (with the extension package @code{spam64}).
11685 ;; Either of these licenses
11686 (license (list license:bsd-3 license:lgpl2.0))))
11688 (define-public r-fields
11695 (uri (cran-uri "fields" version))
11697 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11698 (build-system r-build-system)
11700 `(("r-maps" ,r-maps)
11701 ("r-spam" ,r-spam)))
11703 `(("gfortran" ,gfortran)))
11704 (home-page "https://www.image.ucar.edu/fields")
11705 (synopsis "Tools for spatial data")
11707 "This is a package for curve, surface and function fitting with an
11708 emphasis on splines, spatial data and spatial statistics. The major methods
11709 include cubic, and thin plate splines, Kriging, and compactly supported
11710 covariance functions for large data sets.")
11711 (license license:gpl2+)))
11713 (define-public r-spatialextremes
11715 (name "r-spatialextremes")
11720 (uri (cran-uri "SpatialExtremes" version))
11723 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11725 `((upstream-name . "SpatialExtremes")))
11726 (build-system r-build-system)
11728 `(("r-fields" ,r-fields)
11729 ("r-maps" ,r-maps)))
11730 (home-page "http://spatialextremes.r-forge.r-project.org/")
11731 (synopsis "Modelling spatial extremes")
11733 "This package provides tools for the statistical modelling of spatial
11734 extremes using max-stable processes, copula or Bayesian hierarchical models.
11735 More precisely, this package allows (conditional) simulations from various
11736 parametric max-stable models, analysis of the extremal spatial dependence, the
11737 fitting of such processes using composite likelihoods or least square (simple
11738 max-stable processes only), model checking and selection and prediction.")
11739 (license license:gpl2+)))
11741 (define-public r-drc
11748 (uri (cran-uri "drc" version))
11751 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11752 (build-system r-build-system)
11755 ("r-gtools" ,r-gtools)
11757 ("r-multcomp" ,r-multcomp)
11758 ("r-plotrix" ,r-plotrix)
11759 ("r-scales" ,r-scales)))
11760 (home-page "https://cran.r-project.org/web/packages/drc")
11761 (synopsis "Analysis of dose-response curves")
11763 "This package provides a suite of flexible and versatile model fitting
11764 and after-fitting functions for the analysis of dose-response data.")
11765 (license license:gpl2+)))
11767 (define-public r-rmeta
11774 (uri (cran-uri "rmeta" version))
11777 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11778 (build-system r-build-system)
11779 (home-page "https://cran.r-project.org/web/packages/rmeta")
11780 (synopsis "Tools for meta-analysis")
11782 "This package provides functions for simple fixed and random effects
11783 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11784 draws standard summary plots, funnel plots, and computes summaries and tests
11785 for association and heterogeneity.")
11786 (license license:gpl2)))
11788 (define-public r-bootstrap
11790 (name "r-bootstrap")
11795 (uri (cran-uri "bootstrap" version))
11798 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11799 (build-system r-build-system)
11800 (native-inputs `(("gfortran" ,gfortran)))
11801 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11802 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11804 "This package provides software and data for the book \"An Introduction
11805 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11806 This package is primarily provided for projects already based on it, and for
11807 support of the book. New projects should preferentially use the recommended
11808 package \"boot\".")
11809 (license license:bsd-3)))
11811 (define-public r-survivalroc
11813 (name "r-survivalroc")
11818 (uri (cran-uri "survivalROC" version))
11821 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11822 (properties `((upstream-name . "survivalROC")))
11823 (build-system r-build-system)
11824 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11825 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11827 "Compute time-dependent ROC curve from censored survival data using
11828 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11829 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11830 (license license:gpl2+)))
11832 (define-public r-longitudinal
11834 (name "r-longitudinal")
11839 (uri (cran-uri "longitudinal" version))
11842 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11843 (build-system r-build-system)
11844 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11845 (home-page "http://strimmerlab.org/software/longitudinal/")
11846 (synopsis "Analysis of multiple time course data")
11848 "This package contains general data structures and functions for
11849 longitudinal data with multiple variables, repeated measurements, and
11850 irregularly spaced time points. It also implements a shrinkage estimator of
11851 dynamical correlation and dynamical covariance.")
11852 (license license:gpl3+)))
11854 (define-public r-genenet
11861 (uri (cran-uri "GeneNet" version))
11864 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11865 (properties `((upstream-name . "GeneNet")))
11866 (build-system r-build-system)
11868 `(("r-corpcor" ,r-corpcor)
11869 ("r-fdrtool" ,r-fdrtool)
11870 ("r-longitudinal" ,r-longitudinal)))
11871 (home-page "http://strimmerlab.org/software/genenet/")
11872 (synopsis "Modeling and inferring gene networks")
11874 "This package analyzes gene expression (time series) data with focus on
11875 the inference of gene networks. In particular, GeneNet implements the methods
11876 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11877 for learning large-scale gene association networks (including assignment of
11878 putative directions).")
11879 (license license:gpl3+)))
11881 (define-public r-rbamtools
11883 (name "r-rbamtools")
11884 (version "2.16.17")
11888 (uri (cran-uri "rbamtools" version))
11891 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11892 (build-system r-build-system)
11893 (inputs `(("zlib" ,zlib)))
11895 `(("r-refgenome" ,r-refgenome)))
11896 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11897 (synopsis "Read and write BAM (binary alignment) files")
11899 "This package provides an R interface to functions of the SAMtools
11901 (license license:artistic2.0)))
11903 (define-public r-protviz
11910 (uri (cran-uri "protViz" version))
11913 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11914 (properties `((upstream-name . "protViz")))
11915 (build-system r-build-system)
11916 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11917 (home-page "https://github.com/protViz/protViz/")
11918 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11920 "This package helps with quality checks, visualizations and analysis of
11921 mass spectrometry data, coming from proteomics experiments. The package is
11922 developed, tested and used at the Functional Genomics Center Zurich, where it
11923 is used mainly for prototyping, teaching, and having fun with proteomics data.
11924 But it can also be used to do data analysis for small scale data sets.")
11925 (license license:gpl3)))
11927 (define-public r-cmprsk
11934 (uri (cran-uri "cmprsk" version))
11936 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11937 (build-system r-build-system)
11939 `(("r-survival" ,r-survival)))
11941 `(("gfortran" ,gfortran)))
11942 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11943 (synopsis "Subdistribution analysis of competing risks")
11945 "This package provides tool for estimation, testing and regression
11946 modeling of subdistribution functions in competing risks, as described in
11947 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11948 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11949 A proportional hazards model for the subdistribution of a competing risk,
11950 JASA, 94:496-509.")
11951 (license license:gpl2+)))
11953 (define-public r-etm
11960 (uri (cran-uri "etm" version))
11963 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11964 (build-system r-build-system)
11966 `(("r-data-table" ,r-data-table)
11967 ("r-lattice" ,r-lattice)
11969 ("r-rcpparmadillo" ,r-rcpparmadillo)
11970 ("r-survival" ,r-survival)))
11971 (home-page "https://cran.r-project.org/web/packages/etm")
11972 (synopsis "Empirical transition matrix")
11974 "The @dfn{empirical transition matrix} (etm) package estimates
11975 the matrix of transition probabilities for any time-inhomogeneous multistate
11976 model with finite state space using the Aalen-Johansen estimator.")
11977 (license license:expat)))
11979 (define-public r-epi
11986 (uri (cran-uri "Epi" version))
11989 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11990 (properties `((upstream-name . "Epi")))
11991 (build-system r-build-system)
11993 `(("r-cmprsk" ,r-cmprsk)
11994 ("r-data-table" ,r-data-table)
11997 ("r-matrix" ,r-matrix)
11999 ("r-numderiv" ,r-numderiv)
12001 ("r-survival" ,r-survival)
12003 (home-page "https://BendixCarstensen.com/Epi/")
12004 (synopsis "Statistical analysis in epidemiology")
12006 "This package provides functions for demographic and epidemiological
12007 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12008 particular representation, manipulation and simulation of multistate data -
12009 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12010 @code{etm} and @code{cmprsk} packages. It also contains functions for
12011 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12012 data and some useful functions for tabulation and plotting, as well as a
12013 number of epidemiological data sets.")
12014 (license license:gpl2)))
12016 (define-public r-ppls
12019 (version "1.6-1.1")
12023 (uri (cran-uri "ppls" version))
12026 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12027 (build-system r-build-system)
12028 (propagated-inputs `(("r-mass" ,r-mass)))
12029 (home-page "https://cran.r-project.org/web/packages/ppls")
12030 (synopsis "Penalized partial least squares")
12032 "This package contains linear and nonlinear regression methods based on
12033 partial least squares and penalization techniques. Model parameters are
12034 selected via cross-validation, and confidence intervals ans tests for the
12035 regression coefficients can be conducted via jackknifing.")
12036 (license license:gpl2+)))
12038 (define-public r-huge
12041 (version "1.3.4.1")
12045 (uri (cran-uri "huge" version))
12047 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12048 (build-system r-build-system)
12050 `(("r-igraph" ,r-igraph)
12052 ("r-matrix" ,r-matrix)
12054 ("r-rcppeigen" ,r-rcppeigen)))
12055 (home-page "https://cran.r-project.org/web/packages/huge")
12056 (synopsis "High-dimensional undirected graph estimation")
12058 "This package provides a general framework for high-dimensional
12059 undirected graph estimation. It integrates data preprocessing, neighborhood
12060 screening, graph estimation, and model selection techniques into a pipeline.")
12061 (license license:gpl2)))
12063 (define-public r-parcor
12070 (uri (cran-uri "parcor" version))
12073 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12074 (build-system r-build-system)
12077 ("r-genenet" ,r-genenet)
12078 ("r-glmnet" ,r-glmnet)
12080 ("r-ppls" ,r-ppls)))
12081 (home-page "https://cran.r-project.org/web/packages/parcor")
12082 (synopsis "Regularized estimation of partial correlation matrices")
12084 "This package estimates the matrix of partial correlations based on
12085 different regularized regression methods: lasso, adaptive lasso, PLS, and
12086 Ridge Regression. In addition, the package provides model selection for
12087 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12088 (license license:gpl2+)))
12090 (define-public r-mcmc
12097 (uri (cran-uri "mcmc" version))
12100 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12101 (build-system r-build-system)
12102 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12103 (synopsis "Markov chain Monte Carlo")
12105 "This package simulates continuous distributions of random vectors using
12106 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12107 function that evaluates the log unnormalized density. Algorithms are random
12108 walk Metropolis algorithm (function @code{metrop}), simulated
12109 tempering (function @code{temper}), and morphometric random walk
12110 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12111 by change of variable.")
12112 (license license:expat)))
12114 (define-public r-listenv
12121 (uri (cran-uri "listenv" version))
12124 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12125 (build-system r-build-system)
12127 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12128 (home-page "https://github.com/HenrikBengtsson/listenv")
12129 (synopsis "Environments behaving (almost) as lists")
12131 "This package implements list environments. List environments are
12132 environments that have list-like properties. For instance, the elements of a
12133 list environment are ordered and can be accessed and iterated over using index
12135 (license license:lgpl2.1+)))
12137 (define-public r-globals
12144 (uri (cran-uri "globals" version))
12147 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12148 (build-system r-build-system)
12150 `(("r-codetools" ,r-codetools)))
12151 (home-page "https://github.com/HenrikBengtsson/globals")
12152 (synopsis "Identify global objects in R expressions")
12154 "This package provides tools to identify global (\"unknown\" or \"free\")
12155 objects in R expressions by code inspection using various strategies, e.g.
12156 conservative or liberal. The objective of this package is to make it as
12157 simple as possible to identify global objects for the purpose of exporting
12158 them in distributed compute environments.")
12159 (license license:lgpl2.1+)))
12161 (define-public r-future
12168 (uri (cran-uri "future" version))
12171 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
12172 (build-system r-build-system)
12174 `(("r-digest" ,r-digest)
12175 ("r-globals" ,r-globals)
12176 ("r-listenv" ,r-listenv)))
12178 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12179 (home-page "https://github.com/HenrikBengtsson/future")
12180 (synopsis "Unified parallel and distributed processing in R")
12182 "The purpose of this package is to provide a lightweight and unified
12183 Future API for sequential and parallel processing of R expression via futures.
12184 This package implements sequential, multicore, multisession, and cluster
12185 futures. With these, R expressions can be evaluated on the local machine, in
12186 parallel a set of local machines, or distributed on a mix of local and remote
12187 machines. Extensions to this package implement additional backends for
12188 processing futures via compute cluster schedulers etc. Because of its unified
12189 API, there is no need to modify any code in order to switch from sequential on
12190 the local machine to, say, distributed processing on a remote compute cluster.")
12191 (license license:lgpl2.1+)))
12193 (define-public r-future-apply
12195 (name "r-future-apply")
12200 (uri (cran-uri "future.apply" version))
12203 "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
12204 (properties `((upstream-name . "future.apply")))
12205 (build-system r-build-system)
12207 `(("r-future" ,r-future)
12208 ("r-globals" ,r-globals)))
12210 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12211 (home-page "https://github.com/HenrikBengtsson/future.apply")
12212 (synopsis "Apply function to elements in parallel using futures")
12214 "This package provides implementations of @code{apply()},
12215 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12216 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12217 can be resolved using any future-supported backend, e.g. parallel on the local
12218 machine or distributed on a compute cluster.")
12219 (license license:gpl2+)))
12221 (define-public r-rsvd
12228 (uri (cran-uri "rsvd" version))
12231 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12232 (build-system r-build-system)
12234 `(("r-matrix" ,r-matrix)))
12235 (home-page "https://github.com/erichson/rSVD")
12236 (synopsis "Randomized singular value decomposition")
12238 "Low-rank matrix decompositions are fundamental tools and widely used for
12239 data analysis, dimension reduction, and data compression. Classically, highly
12240 accurate deterministic matrix algorithms are used for this task. However, the
12241 emergence of large-scale data has severely challenged our computational
12242 ability to analyze big data. The concept of randomness has been demonstrated
12243 as an effective strategy to quickly produce approximate answers to familiar
12244 problems such as the @dfn{singular value decomposition} (SVD). This package
12245 provides several randomized matrix algorithms such as the randomized singular
12246 value decomposition (@code{rsvd}), randomized principal component
12247 analysis (@code{rpca}), randomized robust principal component
12248 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12249 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12250 functions are provided.")
12251 (license license:gpl3+)))
12253 (define-public r-sloop
12260 (uri (cran-uri "sloop" version))
12263 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12264 (build-system r-build-system)
12266 `(("r-codetools" ,r-codetools)
12267 ("r-crayon" ,r-crayon)
12268 ("r-purrr" ,r-purrr)
12269 ("r-rlang" ,r-rlang)
12270 ("r-tibble" ,r-tibble)))
12271 (home-page "https://github.com/r-lib/sloop")
12272 (synopsis "Helpers for object-oriented programming in R")
12274 "This package provides a collection of helper functions designed to
12275 help you to better understand object oriented programming in R, particularly
12277 (license license:gpl3)))
12279 (define-public r-capushe
12286 (uri (cran-uri "capushe" version))
12289 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12290 (build-system r-build-system)
12291 (propagated-inputs `(("r-mass" ,r-mass)))
12292 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12293 (synopsis "Calibrating penalties using slope heuristics")
12295 "This package provides tools for the calibration of penalized criteria
12296 for model selection. The calibration methods available are based on the slope
12298 (license license:gpl2+)))
12300 (define-public r-dorng
12307 (uri (cran-uri "doRNG" version))
12310 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12311 (properties `((upstream-name . "doRNG")))
12312 (build-system r-build-system)
12314 `(("r-foreach" ,r-foreach)
12315 ("r-iterators" ,r-iterators)
12316 ("r-rngtools" ,r-rngtools)))
12317 (home-page "https://renozao.github.io/doRNG/")
12318 (synopsis "Generic reproducible parallel backend for foreach loops")
12320 "This package provides functions to perform reproducible parallel
12321 @code{foreach} loops, using independent random streams as generated by
12322 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12323 convert standard @code{%dopar%} loops into fully reproducible loops,
12324 independently of the number of workers, the task scheduling strategy, or the
12325 chosen parallel environment and associated foreach backend.")
12326 (license license:gpl2+)))
12328 (define-public r-blockmodeling
12330 (name "r-blockmodeling")
12335 (uri (cran-uri "blockmodeling" version))
12338 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
12339 (build-system r-build-system)
12341 `(("r-matrix" ,r-matrix)))
12342 (native-inputs `(("gfortran" ,gfortran)))
12343 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12344 (synopsis "Generalized and classical blockmodeling of valued networks")
12346 "This package is primarily meant as an implementation of generalized
12347 blockmodeling for valued networks. In addition, measures of similarity or
12348 dissimilarity based on structural equivalence and regular equivalence (REGE
12349 algorithms) can be computed and partitioned matrices can be plotted.")
12350 (license license:gpl2+)))
12352 (define-public r-upsetr
12359 (uri (cran-uri "UpSetR" version))
12362 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12363 (properties `((upstream-name . "UpSetR")))
12364 (build-system r-build-system)
12366 `(("r-ggplot2" ,r-ggplot2)
12367 ("r-gridextra" ,r-gridextra)
12369 ("r-scales" ,r-scales)))
12370 (home-page "https://github.com/hms-dbmi/UpSetR")
12371 (synopsis "Visualize intersecting sets")
12373 "This package provides a more scalable alternative to Venn and Euler
12374 diagrams for visualizing intersecting sets. Create visualizations of
12375 intersecting sets using a novel matrix design, along with visualizations of
12376 several common set, element and attribute related tasks.")
12377 (license license:expat)))
12379 ;; This package includes a JavaScript file, which is not minified. When
12380 ;; upgrading please check that there are no new minified JavaScript files.
12381 (define-public r-shinybs
12388 (uri (cran-uri "shinyBS" version))
12391 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12392 (properties `((upstream-name . "shinyBS")))
12393 (build-system r-build-system)
12394 ;; The tests spawn Shiny browser apps. They cannot be run
12395 ;; non-interactively.
12396 (arguments '(#:tests? #f))
12398 `(("r-htmltools" ,r-htmltools)
12399 ("r-shiny" ,r-shiny)))
12400 (home-page "https://ebailey78.github.io/shinyBS/")
12401 (synopsis "Twitter Bootstrap components for Shiny")
12403 "This package adds additional Twitter Bootstrap components to Shiny.")
12404 (license license:gpl3)))
12406 (define-public r-outliers
12408 (name "r-outliers")
12413 (uri (cran-uri "outliers" version))
12416 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12417 (build-system r-build-system)
12418 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12419 (synopsis "Tests for outliers")
12421 "This package provides a collection of some tests commonly used for
12422 identifying outliers.")
12423 (license license:gpl2+)))
12425 (define-public r-bayesm
12432 (uri (cran-uri "bayesm" version))
12434 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12435 (build-system r-build-system)
12437 `(("r-rcpp" ,r-rcpp)
12438 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12439 (home-page "http://www.perossi.org/home/bsm-1")
12440 (synopsis "Bayesian inference for marketing/micro-econometrics")
12442 "This package covers many important models used in marketing and
12443 micro-econometrics applications, including Bayes Regression (univariate or
12444 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12445 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12446 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12447 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12448 Estimation with normal base, Hierarchical Linear Models with normal prior and
12449 covariates, Hierarchical Linear Models with a mixture of normals prior and
12450 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12451 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12452 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12453 analysis of choice-based conjoint data, Bayesian treatment of linear
12454 instrumental variables models, Analysis of Multivariate Ordinal survey data
12455 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12456 Coefficient Logit Models.")
12457 (license license:gpl2+)))
12459 (define-public r-tensora
12466 (uri (cran-uri "tensorA" version))
12469 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12470 (properties `((upstream-name . "tensorA")))
12471 (build-system r-build-system)
12472 (home-page "http://www.stat.boogaart.de/tensorA")
12473 (synopsis "Advanced tensor arithmetic with named indices")
12475 "This package provides convenience functions for advanced linear algebra
12476 with tensors and computation with datasets of tensors on a higher level
12477 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12478 co- and contravariate indices, and parallel computations on sequences of
12480 (license license:gpl2+)))
12482 (define-public r-rarpack
12489 (uri (cran-uri "rARPACK" version))
12492 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12493 (properties `((upstream-name . "rARPACK")))
12494 (build-system r-build-system)
12495 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12496 (home-page "https://github.com/yixuan/rARPACK")
12497 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12499 "This package was previously an R wrapper of the ARPACK library, and now
12500 a shell of the R package RSpectra, an R interface to the Spectra library for
12501 solving large scale eigenvalue/vector problems. The current version of
12502 rARPACK simply imports and exports the functions provided by RSpectra. New
12503 users of rARPACK are advised to switch to the RSpectra package.")
12504 (license license:bsd-3)))
12506 (define-public r-compositions
12508 (name "r-compositions")
12513 (uri (cran-uri "compositions" version))
12516 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12517 (build-system r-build-system)
12519 `(("r-bayesm" ,r-bayesm)
12520 ("r-robustbase" ,r-robustbase)
12521 ("r-tensora" ,r-tensora)))
12522 (home-page "http://www.stat.boogaart.de/compositions")
12523 (synopsis "Compositional data analysis")
12525 "This package provides functions for the consistent analysis of
12526 compositional data (e.g. portions of substances) and positive
12527 numbers (e.g. concentrations).")
12528 (license license:gpl2+)))
12530 (define-public r-cobs
12537 (uri (cran-uri "cobs" version))
12540 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12541 (build-system r-build-system)
12543 `(("r-quantreg" ,r-quantreg)
12544 ("r-sparsem" ,r-sparsem)))
12545 (home-page "https://cran.r-project.org/web/packages/cobs")
12546 (synopsis "Constrained B-Splines (sparse matrix based)")
12548 "This package provides qualitatively constrained (regression) smoothing
12549 splines via linear programming and sparse matrices.")
12550 (license license:gpl2+)))
12552 (define-public r-drimpute
12554 (name "r-drimpute")
12559 (uri (cran-uri "DrImpute" version))
12562 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12563 (properties `((upstream-name . "DrImpute")))
12564 (build-system r-build-system)
12566 `(("r-rcpp" ,r-rcpp)
12567 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12568 (home-page "https://github.com/ikwak2/DrImpute")
12569 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12571 "This is an R package for imputing dropout events. Many statistical
12572 methods in cell type identification, visualization and lineage reconstruction
12573 do not account for dropout events. DrImpute can improve the performance of
12574 such software by imputing dropout events.")
12575 (license license:gpl3)))
12577 (define-public r-gamlss-dist
12579 (name "r-gamlss-dist")
12584 (uri (cran-uri "gamlss.dist" version))
12586 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12587 (properties `((upstream-name . "gamlss.dist")))
12588 (build-system r-build-system)
12589 (propagated-inputs `(("r-mass" ,r-mass)))
12590 (home-page "http://www.gamlss.org/")
12591 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12593 "This package provides a set of distributions which can be used for
12594 modelling the response variables in Generalized Additive Models for Location
12595 Scale and Shape. The distributions can be continuous, discrete or mixed
12596 distributions. Extra distributions can be created, by transforming, any
12597 continuous distribution defined on the real line, to a distribution defined on
12598 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12599 transformation, respectively.")
12600 ;; Either version of the GPL.
12601 (license (list license:gpl2 license:gpl3))))
12603 ;; This package includes JavaScript files, which are not minified. When
12604 ;; upgrading please check that there are no new minified JavaScript files.
12605 (define-public r-shinyjs
12612 (uri (cran-uri "shinyjs" version))
12615 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12616 (build-system r-build-system)
12618 `(("r-digest" ,r-digest)
12619 ("r-htmltools" ,r-htmltools)
12620 ("r-jsonlite" ,r-jsonlite)
12621 ("r-shiny" ,r-shiny)))
12622 (home-page "https://deanattali.com/shinyjs")
12623 (synopsis "Improve the user experience of your Shiny apps")
12625 "Perform common useful JavaScript operations in Shiny apps that will
12626 greatly improve your apps without having to know any JavaScript. Examples
12627 include: hiding an element, disabling an input, resetting an input back to its
12628 original value, delaying code execution by a few seconds, and many more useful
12629 functions for both the end user and the developer. Shinyjs can also be used
12630 to easily call your own custom JavaScript functions from R.")
12631 (license license:agpl3+)))
12633 ;; This package includes minified JavaScript files. When upgrading please
12634 ;; check that there are no new minified JavaScript files.
12635 (define-public r-colourpicker
12637 (name "r-colourpicker")
12642 (uri (cran-uri "colourpicker" version))
12645 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12646 (build-system r-build-system)
12648 `(#:modules ((guix build utils)
12649 (guix build r-build-system)
12653 (modify-phases %standard-phases
12654 (add-after 'unpack 'process-javascript
12655 (lambda* (#:key inputs #:allow-other-keys)
12656 (with-directory-excursion "inst"
12660 `((,(assoc-ref inputs "js-salvattore")
12661 "examples/colourInput/www/salvattore.min.js")
12662 (,(assoc-ref inputs "js-jquery")
12663 "htmlwidgets/lib/jquery/jquery.min.js")
12664 ("www/shared/colourpicker/js/colourpicker.js"
12665 "www/shared/colourpicker/js/colourpicker.min.js"))))
12666 (lambda (sources targets)
12667 (for-each (lambda (source target)
12668 (format #t "Processing ~a --> ~a~%"
12670 (delete-file target)
12671 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12672 (call-with-output-file target
12674 (dump-port minified port)))))
12675 sources targets))))
12678 `(("r-ggplot2" ,r-ggplot2)
12679 ("r-htmltools" ,r-htmltools)
12680 ("r-htmlwidgets" ,r-htmlwidgets)
12681 ("r-jsonlite" ,r-jsonlite)
12682 ("r-miniui" ,r-miniui)
12683 ("r-shiny" ,r-shiny)
12684 ("r-shinyjs" ,r-shinyjs)))
12686 `(("uglify-js" ,uglify-js)
12690 (uri "https://code.jquery.com/jquery-3.3.1.js")
12693 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12697 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12700 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12701 (home-page "https://github.com/daattali/colourpicker")
12702 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12704 "This package provides a color picker that can be used as an input in
12705 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12706 custom color palettes, and many more options. A plot color helper tool is
12707 available as an RStudio Addin, which helps you pick colors to use in your
12708 plots. A more generic color picker RStudio Addin is also provided to let you
12709 select colors to use in your R code.")
12710 (license license:expat)))
12712 (define-public r-ggextra
12719 (uri (cran-uri "ggExtra" version))
12722 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12723 (properties `((upstream-name . "ggExtra")))
12724 (build-system r-build-system)
12726 `(("r-colourpicker" ,r-colourpicker)
12727 ("r-ggplot2" ,r-ggplot2)
12728 ("r-gtable" ,r-gtable)
12729 ("r-miniui" ,r-miniui)
12731 ("r-scales" ,r-scales)
12732 ("r-shiny" ,r-shiny)
12733 ("r-shinyjs" ,r-shinyjs)))
12735 `(("r-knitr" ,r-knitr)))
12736 (home-page "https://github.com/daattali/ggExtra")
12737 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12739 "This package is a collection of functions and layers to enhance ggplot2.
12740 The flagship function is @code{ggMarginal()}, which can be used to add
12741 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12742 (license license:expat)))
12744 (define-public r-minpack-lm
12746 (name "r-minpack-lm")
12751 (uri (cran-uri "minpack.lm" version))
12754 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12755 (properties `((upstream-name . "minpack.lm")))
12756 (build-system r-build-system)
12757 (native-inputs `(("gfortran" ,gfortran)))
12758 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12759 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12761 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12762 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12763 problems by a modification of the Levenberg-Marquardt algorithm, with support
12764 for lower and upper parameter bounds. The implementation can be used via
12765 @code{nls}-like calls using the @code{nlsLM} function.")
12766 (license license:gpl3)))
12768 (define-public r-moments
12775 (uri (cran-uri "moments" version))
12778 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12779 (build-system r-build-system)
12780 (home-page "https://cran.r-project.org/web/packages/moments")
12781 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12783 "This package provides functions to calculate: moments, Pearson's
12784 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12785 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12786 (license license:gpl2+)))
12788 (define-public r-msir
12795 (uri (cran-uri "msir" version))
12798 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12799 (build-system r-build-system)
12801 `(("r-mclust" ,r-mclust)))
12802 (home-page "https://cran.r-project.org/web/packages/msir")
12803 (synopsis "Model-based sliced inverse regression")
12805 "This is an R package for dimension reduction based on finite Gaussian
12806 mixture modeling of inverse regression.")
12807 (license license:gpl2+)))
12809 (define-public r-pbivnorm
12811 (name "r-pbivnorm")
12816 (uri (cran-uri "pbivnorm" version))
12819 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12820 (build-system r-build-system)
12821 (native-inputs `(("gfortran" ,gfortran)))
12822 (home-page "https://github.com/brentonk/pbivnorm")
12823 (synopsis "Vectorized bivariate normal CDF")
12825 "This package provides a vectorized R function for calculating
12826 probabilities from a standard bivariate normal CDF.")
12827 (license license:gpl2+)))
12829 (define-public r-lavaan
12836 (uri (cran-uri "lavaan" version))
12839 "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
12840 (build-system r-build-system)
12842 `(("r-mass" ,r-mass)
12843 ("r-mnormt" ,r-mnormt)
12844 ("r-numderiv" ,r-numderiv)
12845 ("r-pbivnorm" ,r-pbivnorm)))
12846 (home-page "http://lavaan.ugent.be")
12847 (synopsis "Latent variable analysis")
12849 "This package provides tools to fit a variety of latent variable models,
12850 including confirmatory factor analysis, structural equation modeling and
12851 latent growth curve models.")
12852 (license license:gpl2+)))
12854 (define-public r-nonnest2
12856 (name "r-nonnest2")
12861 (uri (cran-uri "nonnest2" version))
12864 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12865 (build-system r-build-system)
12867 `(("r-compquadform" ,r-compquadform)
12868 ("r-lavaan" ,r-lavaan)
12869 ("r-mvtnorm" ,r-mvtnorm)
12870 ("r-sandwich" ,r-sandwich)))
12872 `(("r-knitr" ,r-knitr)))
12873 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12874 (synopsis "Tests of non-nested models")
12876 "This package allows for testing of non-nested models. It includes tests
12877 of model distinguishability and of model fit that can be applied to both
12878 nested and non-nested models. The package also includes functionality to
12879 obtain confidence intervals associated with AIC and BIC.")
12880 ;; Either version of the GPL.
12881 (license (list license:gpl2 license:gpl3))))
12883 (define-public r-penalized
12885 (name "r-penalized")
12890 (uri (cran-uri "penalized" version))
12893 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12894 (build-system r-build-system)
12896 `(("r-rcpp" ,r-rcpp)
12897 ("r-rcpparmadillo" ,r-rcpparmadillo)
12898 ("r-survival" ,r-survival)))
12899 (home-page "https://cran.r-project.org/web/packages/penalized/")
12900 (synopsis "Penalized estimation in GLMs and in the Cox model")
12902 "This package provides tools for fitting possibly high dimensional
12903 penalized regression models. The penalty structure can be any combination of
12904 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12905 constraint on the regression coefficients. The supported regression models
12906 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12907 model. Cross-validation routines allow optimization of the tuning
12909 (license license:gpl2+)))
12911 (define-public r-zim
12918 (uri (cran-uri "ZIM" version))
12921 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12922 (properties `((upstream-name . "ZIM")))
12923 (build-system r-build-system)
12924 (propagated-inputs `(("r-mass" ,r-mass)))
12925 (home-page "https://github.com/biostatstudio/ZIM")
12926 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12928 "Analyze count time series with excess zeros. Two types of statistical
12929 models are supported: Markov regression and state-space models. They are also
12930 known as observation-driven and parameter-driven models respectively in the
12931 time series literature. The functions used for Markov regression or
12932 observation-driven models can also be used to fit ordinary regression models
12933 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12934 negative binomial (ZINB) assumption. The package also contains miscellaneous
12935 functions to compute density, distribution, quantile, and generate random
12936 numbers from ZIP and ZINB distributions.")
12937 (license license:gpl3)))
12939 (define-public r-nor1mix
12946 (uri (cran-uri "nor1mix" version))
12949 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12950 (build-system r-build-system)
12951 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12952 (synopsis "Normal (1-d) mixture models")
12954 "This package provides S3 classes and methods for one-dimensional normal
12955 mixture models, for, e.g., density estimation or clustering algorithms
12956 research and teaching; it provides the widely used Marron-Wand densities. It
12957 also provides tools for efficient random number generation and graphics.")
12958 (license license:gpl2+)))
12960 (define-public r-beanplot
12962 (name "r-beanplot")
12967 (uri (cran-uri "beanplot" version))
12970 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12971 (build-system r-build-system)
12972 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12973 (synopsis "Visualization via beanplots")
12975 "This package provides beanplots, an alternative to
12976 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12978 (license license:gpl2)))
12980 (define-public r-pbdzmq
12987 (uri (cran-uri "pbdZMQ" version))
12990 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12991 (properties `((upstream-name . "pbdZMQ")))
12992 (build-system r-build-system)
12994 `(("zeromq" ,zeromq)
12997 `(("pkg-config" ,pkg-config)))
12998 (home-page "https://pbdr.org/")
12999 (synopsis "R interface to ZeroMQ")
13001 "ZeroMQ is a well-known library for high-performance asynchronous
13002 messaging in scalable, distributed applications. This package provides high
13003 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13004 interactive client/server programming frameworks. A few wrapper functions
13005 compatible with @code{rzmq} are also provided.")
13006 (license license:gpl3)))
13008 (define-public r-repr
13015 (uri (cran-uri "repr" version))
13018 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13019 (build-system r-build-system)
13021 `(("r-base64enc" ,r-base64enc)
13022 ("r-htmltools" ,r-htmltools)
13023 ("r-jsonlite" ,r-jsonlite)
13024 ("r-pillar" ,r-pillar)))
13025 (home-page "https://cran.r-project.org/web/packages/repr/")
13026 (synopsis "Serializable representations")
13028 "This package provides string and binary representations of objects for
13029 several formats and MIME types.")
13030 (license license:gpl3)))
13032 (define-public r-irdisplay
13034 (name "r-irdisplay")
13039 (uri (cran-uri "IRdisplay" version))
13042 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13043 (properties `((upstream-name . "IRdisplay")))
13044 (build-system r-build-system)
13046 `(("r-repr" ,r-repr)))
13047 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13048 (synopsis "Jupyter display machinery")
13050 "This package provides an interface to the rich display capabilities of
13051 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13052 running IRkernel session.")
13053 (license license:expat)))
13055 (define-public r-irkernel
13057 (name "r-irkernel")
13062 (uri (cran-uri "IRkernel" version))
13065 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
13066 (properties `((upstream-name . "IRkernel")))
13067 (build-system r-build-system)
13070 (modify-phases %standard-phases
13071 (add-after 'install 'install-kernelspec
13072 (lambda* (#:key outputs #:allow-other-keys)
13073 (let ((out (assoc-ref outputs "out")))
13074 (setenv "HOME" "/tmp")
13075 (invoke "jupyter" "kernelspec" "install"
13078 (string-append out "/site-library/IRkernel/kernelspec"))
13079 ;; Record the absolute file name of the 'R' executable in
13081 (substitute* (string-append out "/share/jupyter"
13082 "/kernels/ir/kernel.json")
13084 (string-append "[\"" (which "R") "\",")))
13087 `(("jupyter" ,jupyter)))
13089 `(("r-crayon" ,r-crayon)
13090 ("r-digest" ,r-digest)
13091 ("r-evaluate" ,r-evaluate)
13092 ("r-irdisplay" ,r-irdisplay)
13093 ("r-jsonlite" ,r-jsonlite)
13094 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13095 ("r-minimal" ,r-minimal)
13096 ("r-pbdzmq" ,r-pbdzmq)
13098 ("r-uuid" ,r-uuid)))
13099 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13100 (synopsis "Native R kernel for Jupyter")
13102 "The R kernel for the Jupyter environment executes R code which the
13103 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13105 (license license:expat)))
13107 (define-public r-gmodels
13114 (uri (cran-uri "gmodels" version))
13117 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13118 (build-system r-build-system)
13120 `(("r-gdata" ,r-gdata)
13121 ("r-mass" ,r-mass)))
13122 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13123 (synopsis "Various R programming tools for model fitting")
13125 "This package provides various R programming tools for model fitting.")
13126 (license license:gpl2)))
13128 (define-public r-apcluster
13130 (name "r-apcluster")
13135 (uri (cran-uri "apcluster" version))
13138 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13139 (build-system r-build-system)
13141 `(("r-matrix" ,r-matrix)
13142 ("r-rcpp" ,r-rcpp)))
13143 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13144 (synopsis "Affinity propagation clustering")
13146 "This package implements affinity propagation clustering introduced by
13147 Frey and Dueck (2007). The package further provides leveraged affinity
13148 propagation and an algorithm for exemplar-based agglomerative clustering that
13149 can also be used to join clusters obtained from affinity propagation. Various
13150 plotting functions are available for analyzing clustering results.")
13151 (license license:gpl2+)))
13153 (define-public r-valr
13160 (uri (cran-uri "valr" version))
13163 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13164 (build-system r-build-system)
13166 `(("r-broom" ,r-broom)
13167 ("r-dplyr" ,r-dplyr)
13168 ("r-ggplot2" ,r-ggplot2)
13170 ("r-readr" ,r-readr)
13171 ("r-rlang" ,r-rlang)
13172 ("r-stringr" ,r-stringr)
13173 ("r-tibble" ,r-tibble)))
13175 `(("r-knitr" ,r-knitr)))
13176 (home-page "http://github.com/rnabioco/valr")
13177 (synopsis "Genome interval arithmetic in R")
13179 "This package enables you to read and manipulate genome intervals and
13180 signals. It provides functionality similar to command-line tool suites within
13181 R, enabling interactive analysis and visualization of genome-scale data.")
13182 (license license:expat)))
13184 (define-public r-rematch2
13186 (name "r-rematch2")
13191 (uri (cran-uri "rematch2" version))
13194 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13195 (build-system r-build-system)
13197 `(("r-tibble" ,r-tibble)))
13198 (home-page "https://github.com/r-lib/rematch2")
13199 (synopsis "Tidy output from regular expression matching")
13201 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13202 return the match results in tidy data frames.")
13203 (license license:expat)))
13205 (define-public r-picante
13212 (uri (cran-uri "picante" version))
13215 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13216 (build-system r-build-system)
13220 ("r-vegan" ,r-vegan)))
13221 (home-page "https://cran.r-project.org/web/packages/picante/")
13222 (synopsis "Integrating phylogenies and ecology")
13224 "This package provides functions for phylocom integration, community
13225 analyses, null-models, traits and evolution. It implements numerous
13226 ecophylogenetic approaches including measures of community phylogenetic and
13227 trait diversity, phylogenetic signal, estimation of trait values for
13228 unobserved taxa, null models for community and phylogeny randomizations, and
13229 utility functions for data input/output and phylogeny plotting. A full
13230 description of package functionality and methods are provided by Kembel et
13232 (license license:gpl2)))
13234 (define-public r-reinforcelearn
13236 (name "r-reinforcelearn")
13241 (uri (cran-uri "reinforcelearn" version))
13244 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13245 (build-system r-build-system)
13247 `(("r-checkmate" ,r-checkmate)
13249 ("r-purrr" ,r-purrr)
13251 (home-page "https://markusdumke.github.io/reinforcelearn")
13252 (synopsis "Reinforcement learning")
13254 "This package implements reinforcement learning environments and
13255 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13256 can be used with function approximation, eligibility traces (Singh & Sutton,
13257 1996) and experience replay (Mnih et al., 2013).")
13258 (license license:expat)))
13260 (define-public r-lemon
13267 (uri (cran-uri "lemon" version))
13270 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13271 (build-system r-build-system)
13273 `(("r-ggplot2" ,r-ggplot2)
13274 ("r-gridextra" ,r-gridextra)
13275 ("r-gtable" ,r-gtable)
13276 ("r-knitr" ,r-knitr)
13277 ("r-lattice" ,r-lattice)
13279 ("r-rlang" ,r-rlang)
13280 ("r-scales" ,r-scales)))
13282 `(("r-knitr" ,r-knitr)))
13283 (home-page "https://github.com/stefanedwards/lemon")
13284 (synopsis "Freshen up your ggplot2 plots")
13286 "This package provides functions for working with legends and axis lines
13287 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13289 (license license:gpl3)))
13291 (define-public r-wgaim
13298 (uri (cran-uri "wgaim" version))
13300 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13301 (build-system r-build-system)
13303 `(("r-ggplot2" ,r-ggplot2)
13305 (home-page "https://cran.r-project.org/web/packages/wgaim")
13306 (synopsis "Whole genome average interval mapping for QTL detection")
13308 "This package integrates sophisticated mixed modelling methods with a
13309 whole genome approach to detecting significant QTL in linkage maps.")
13310 (license license:gpl2+)))
13312 (define-public r-bedr
13319 (uri (cran-uri "bedr" version))
13322 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13323 (build-system r-build-system)
13325 `(("r-data-table" ,r-data-table)
13326 ("r-r-utils" ,r-r-utils)
13327 ("r-testthat" ,r-testthat)
13328 ("r-venndiagram" ,r-venndiagram)
13331 ("bedtools" ,bedtools)
13332 ("htslib" ,htslib))) ; for tabix
13334 `(("r-knitr" ,r-knitr))) ; for vignettes
13335 (home-page "https://cran.r-project.org/web/packages/bedr")
13336 (synopsis "Genomic region processing")
13338 "This package is for genomic regions processing using command line tools
13339 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13340 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13341 The bedr package's API enhances access to these tools as well as offers
13342 additional utilities for genomic regions processing.")
13343 (license license:gpl2)))
13345 (define-public r-sets
13352 (uri (cran-uri "sets" version))
13355 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13356 (properties `((upstream-name . "sets")))
13357 (build-system r-build-system)
13358 (home-page "https://cran.r-project.org/web/packages/sets")
13359 (synopsis "Sets, generalized sets, customizable sets and intervals")
13361 "This package provides data structures and basic operations for ordinary
13362 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13363 customizable sets, and intervals.")
13364 (license license:gpl2)))
13366 (define-public r-partitions
13368 (name "r-partitions")
13373 (uri (cran-uri "partitions" version))
13376 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13377 (build-system r-build-system)
13380 ("r-polynom" ,r-polynom)
13381 ("r-sets" ,r-sets)))
13382 (home-page "https://cran.r-project.org/web/packages/partitions")
13383 (synopsis "Additive partitions of integers")
13385 "This package provides tools to enumerates the partitions, unequal
13386 partitions, and restricted partitions of an integer; the three corresponding
13387 partition functions are also given.")
13388 ;; Any version of the GPL
13389 (license license:gpl2+)))
13391 (define-public r-brobdingnag
13393 (name "r-brobdingnag")
13398 (uri (cran-uri "Brobdingnag" version))
13401 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13402 (properties `((upstream-name . "Brobdingnag")))
13403 (build-system r-build-system)
13404 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13405 (synopsis "Very large numbers in R")
13407 "This package handles very large numbers in R. Real numbers are held
13408 using their natural logarithms, plus a logical flag indicating sign. The
13409 package includes a vignette that gives a step-by-step introduction to using S4
13411 ;; Any version of the GPL
13412 (license license:gpl2+)))
13414 (define-public r-untb
13421 (uri (cran-uri "untb" version))
13424 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13425 (build-system r-build-system)
13427 `(("r-brobdingnag" ,r-brobdingnag)
13428 ("r-partitions" ,r-partitions)
13429 ("r-polynom" ,r-polynom)))
13430 (home-page "https://github.com/RobinHankin/untb.git")
13431 (synopsis "Ecological drift under the UNTB")
13433 "This package provides numerical simulations, and visualizations, of
13434 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13435 (license license:gpl2+)))
13437 (define-public r-stepwise
13439 (name "r-stepwise")
13444 (uri (cran-uri "stepwise" version))
13447 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13448 (build-system r-build-system)
13449 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13450 (synopsis "Stepwise detection of recombination breakpoints")
13452 "This package provides a stepwise approach to identifying recombination
13453 breakpoints in a genomic sequence alignment.")
13454 (license license:gpl2+)))
13456 (define-public r-snpmaxsel
13458 (name "r-snpmaxsel")
13463 (uri (cran-uri "SNPmaxsel" version))
13466 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13467 (properties `((upstream-name . "SNPmaxsel")))
13468 (build-system r-build-system)
13470 `(("r-combinat" ,r-combinat)
13471 ("r-mvtnorm" ,r-mvtnorm)))
13472 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13473 (synopsis "Maximally selected statistics for SNP data")
13475 "This package implements asymptotic methods related to maximally selected
13476 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13478 (license license:gpl2+)))
13480 (define-public r-acsnminer
13482 (name "r-acsnminer")
13483 (version "0.16.8.25")
13486 (uri (cran-uri "ACSNMineR" version))
13489 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13490 (properties `((upstream-name . "ACSNMineR")))
13491 (build-system r-build-system)
13493 `(("r-ggplot2" ,r-ggplot2)
13494 ("r-gridextra" ,r-gridextra)))
13495 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13496 (synopsis "Gene enrichment analysis")
13498 "This package provides tools to compute and represent gene set enrichment
13499 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13500 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13501 enrichment can be run with hypergeometric test or Fisher exact test, and can
13502 use multiple corrections. Visualization of data can be done either by
13503 barplots or heatmaps.")
13504 (license license:gpl2+)))
13506 (define-public r-seqinr
13513 (uri (cran-uri "seqinr" version))
13516 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13517 (build-system r-build-system)
13519 `(("r-ade4" ,r-ade4)
13520 ("r-segmented" ,r-segmented)))
13523 (home-page "http://seqinr.r-forge.r-project.org/")
13524 (synopsis "Biological sequences retrieval and analysis")
13526 "This package provides tools for exploratory data analysis and data
13527 visualization of biological sequence (DNA and protein) data. It also includes
13528 utilities for sequence data management under the ACNUC system.")
13529 (license license:gpl2+)))
13531 (define-public r-units
13538 (uri (cran-uri "units" version))
13541 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13542 (build-system r-build-system)
13544 `(("udunits" ,udunits)))
13546 `(("r-rcpp" ,r-rcpp)))
13548 `(("r-knitr" ,r-knitr)))
13549 (home-page "https://github.com/r-quantities/units/")
13550 (synopsis "Measurement Units for R Vectors")
13552 "This package provides support for measurement units in R vectors,
13553 matrices and arrays: automatic propagation, conversion, derivation and
13554 simplification of units; raising errors in case of unit incompatibility. It
13555 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13557 (license license:gpl2)))
13559 (define-public r-classint
13561 (name "r-classint")
13566 (uri (cran-uri "classInt" version))
13569 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13570 (properties `((upstream-name . "classInt")))
13571 (build-system r-build-system)
13573 `(("r-class" ,r-class)
13574 ("r-e1071" ,r-e1071)
13575 ("r-kernsmooth" ,r-kernsmooth)))
13577 `(("gfortran" ,gfortran)
13578 ("r-knitr" ,r-knitr)))
13579 (home-page "https://github.com/r-spatial/classInt/")
13580 (synopsis "Choose univariate class intervals")
13582 "This package provides selected commonly used methods for choosing
13583 univariate class intervals for mapping or other graphics purposes.")
13584 (license license:gpl2+)))
13586 (define-public r-spdata
13593 (uri (cran-uri "spData" version))
13596 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13597 (properties `((upstream-name . "spData")))
13598 (build-system r-build-system)
13600 `(("r-raster" ,r-raster)
13602 (home-page "https://github.com/Nowosad/spData")
13603 (synopsis "Datasets for spatial analysis")
13605 "This a package containing diverse spatial datasets for demonstrating,
13606 benchmarking and teaching spatial data analysis. It includes R data of class
13607 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13608 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13609 of the datasets are designed to illustrate specific analysis techniques.
13610 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13611 illustrate point pattern analysis techniques.")
13612 (license license:cc0)))
13614 (define-public r-learnbayes
13616 (name "r-learnbayes")
13621 (uri (cran-uri "LearnBayes" version))
13624 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13625 (properties `((upstream-name . "LearnBayes")))
13626 (build-system r-build-system)
13627 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13628 (synopsis "Functions for learning Bayesian inference")
13630 "This package provides a collection of functions helpful in learning the
13631 basic tenets of Bayesian statistical inference. It contains functions for
13632 summarizing basic one and two parameter posterior distributions and predictive
13633 distributions. It contains MCMC algorithms for summarizing posterior
13634 distributions defined by the user. It also contains functions for regression
13635 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13637 (license license:gpl2+)))
13639 (define-public r-deldir
13646 (uri (cran-uri "deldir" version))
13649 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13650 (build-system r-build-system)
13651 (native-inputs `(("gfortran" ,gfortran)))
13652 (home-page "https://cran.r-project.org/web/packages/deldir")
13653 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13655 "This package provides tools for calculating the Delaunay triangulation
13656 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13657 of a planar point set. It plots triangulations and tessellations in various
13658 ways, clips tessellations to sub-windows, calculates perimeters of
13659 tessellations, and summarizes information about the tiles of the
13661 (license license:gpl2+)))
13663 (define-public r-sf
13670 (uri (cran-uri "sf" version))
13673 "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
13674 (build-system r-build-system)
13681 `(("r-classint" ,r-classint)
13683 ("r-magrittr" ,r-magrittr)
13685 ("r-units" ,r-units)))
13687 `(("pkg-config" ,pkg-config)
13688 ("r-knitr" ,r-knitr)))
13689 (home-page "https://github.com/r-spatial/sf/")
13690 (synopsis "Simple features for R")
13692 "This package provides support for simple features, a standardized way to
13693 encode spatial vector data. It binds to GDAL for reading and writing data, to
13694 GEOS for geometrical operations, and to PROJ for projection conversions and
13695 datum transformations.")
13696 ;; Either of these licenses
13697 (license (list license:gpl2 license:expat))))
13699 (define-public r-spdep
13706 (uri (cran-uri "spdep" version))
13709 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13710 (build-system r-build-system)
13712 `(("r-boot" ,r-boot)
13714 ("r-deldir" ,r-deldir)
13716 ("r-gmodels" ,r-gmodels)
13717 ("r-learnbayes" ,r-learnbayes)
13719 ("r-matrix" ,r-matrix)
13723 ("r-spdata" ,r-spdata)))
13724 (home-page "https://github.com/r-spatial/spdep/")
13725 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13727 "This package provides a collection of functions to create spatial
13728 weights matrix objects from polygon contiguities, from point patterns by
13729 distance and tessellations, for summarizing these objects, and for permitting
13730 their use in spatial data analysis, including regional aggregation by minimum
13732 (license license:gpl2+)))
13734 (define-public r-adegenet
13736 (name "r-adegenet")
13741 (uri (cran-uri "adegenet" version))
13744 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13745 (build-system r-build-system)
13747 `(("r-ade4" ,r-ade4)
13750 ("r-dplyr" ,r-dplyr)
13751 ("r-ggplot2" ,r-ggplot2)
13752 ("r-igraph" ,r-igraph)
13754 ("r-reshape2" ,r-reshape2)
13755 ("r-seqinr" ,r-seqinr)
13756 ("r-shiny" ,r-shiny)
13757 ("r-spdep" ,r-spdep)
13758 ("r-vegan" ,r-vegan)))
13759 (home-page "https://github.com/thibautjombart/adegenet")
13760 (synopsis "Exploratory analysis of genetic and genomic data")
13762 "This package provides a toolset for the exploration of genetic and
13763 genomic data. Adegenet provides formal (S4) classes for storing and handling
13764 various genetic data, including genetic markers with varying ploidy and
13765 hierarchical population structure (@code{genind} class), alleles counts by
13766 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13767 also implements original multivariate methods (DAPC, sPCA), graphics,
13768 statistical tests, simulation tools, distance and similarity measures, and
13769 several spatial methods. A range of both empirical and simulated datasets is
13770 also provided to illustrate various methods.")
13771 (license license:gpl2+)))
13773 (define-public r-pegas
13780 (uri (cran-uri "pegas" version))
13782 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13783 (build-system r-build-system)
13785 `(("r-adegenet" ,r-adegenet)
13787 (home-page "http://ape-package.ird.fr/pegas.html")
13788 (synopsis "Population and evolutionary genetics analysis system")
13790 "This package provides functions for reading, writing, plotting,
13791 analysing, and manipulating allelic and haplotypic data, including from VCF
13792 files, and for the analysis of population nucleotide sequences and
13793 micro-satellites including coalescent analyses, linkage disequilibrium,
13794 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13795 minimum spanning tree and network, and median-joining networks.")
13796 (license license:gpl2+)))
13798 (define-public r-rmetasim
13800 (name "r-rmetasim")
13805 (uri (cran-uri "rmetasim" version))
13808 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13809 (build-system r-build-system)
13811 `(("r-ade4" ,r-ade4)
13812 ("r-adegenet" ,r-adegenet)
13813 ("r-gtools" ,r-gtools)
13814 ("r-pegas" ,r-pegas)))
13815 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13816 (synopsis "Individual-based population genetic simulation environment")
13818 "This package provides an interface between R and the metasim simulation
13819 engine. The simulation environment is documented in: Strand, A.(2002),
13820 Metasim 1.0: an individual-based environment for simulating population
13821 genetics of complex population dynamics.")
13823 (license license:gpl2+)))
13825 (define-public r-genetics
13827 (name "r-genetics")
13828 (version "1.3.8.1.2")
13832 (uri (cran-uri "genetics" version))
13835 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13836 (build-system r-build-system)
13838 `(("r-combinat" ,r-combinat)
13839 ("r-gdata" ,r-gdata)
13840 ("r-gtools" ,r-gtools)
13842 ("r-mvtnorm" ,r-mvtnorm)))
13843 (home-page "https://cran.r-project.org/web/packages/genetics/")
13844 (synopsis "Population genetics")
13846 "This package provides classes and methods for handling genetic data.
13847 It includes classes to represent genotypes and haplotypes at single markers up
13848 to multiple markers on multiple chromosomes. Function include allele
13849 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13850 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13851 and testing for linkage disequilibrium, ...")
13852 ;; Any GPL version.
13853 (license license:gpl2+)))
13855 (define-public r-snp-plotter
13857 (name "r-snp-plotter")
13862 (uri (cran-uri "snp.plotter" version))
13865 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13866 (properties `((upstream-name . "snp.plotter")))
13867 (build-system r-build-system)
13868 (propagated-inputs `(("r-genetics" ,r-genetics)))
13869 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13870 (synopsis "Plot p-values using single SNP and/or haplotype data")
13872 "This package helps you create plots of p-values using single SNP and/or
13873 haplotype data. Main features of the package include options to display a
13874 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13875 datasets simultaneously. Plots can be created using global and/or individual
13876 haplotype p-values along with single SNP p-values. Images are created as
13877 either PDF/EPS files.")
13878 (license license:gpl2+)))
13880 (define-public r-polspline
13882 (name "r-polspline")
13887 (uri (cran-uri "polspline" version))
13889 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13890 (build-system r-build-system)
13891 (native-inputs `(("gfortran" ,gfortran)))
13892 (home-page "https://cran.r-project.org/web/packages/polspline/")
13893 (synopsis "Polynomial spline routines")
13895 "This package provides routines for the polynomial spline fitting
13896 routines hazard regression, hazard estimation with flexible tails, logspline,
13897 lspec, polyclass, and polymars.")
13898 (license license:gpl2+)))
13900 (define-public r-rms
13907 (uri (cran-uri "rms" version))
13909 (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
13910 (build-system r-build-system)
13912 `(("r-cluster" ,r-cluster)
13913 ("r-digest" ,r-digest)
13914 ("r-ggplot2" ,r-ggplot2)
13915 ("r-hmisc" ,r-hmisc)
13916 ("r-htmltable" ,r-htmltable)
13917 ("r-htmltools" ,r-htmltools)
13918 ("r-lattice" ,r-lattice)
13920 ("r-multcomp" ,r-multcomp)
13922 ("r-polspline" ,r-polspline)
13923 ("r-quantreg" ,r-quantreg)
13924 ("r-rpart" ,r-rpart)
13925 ("r-sparsem" ,r-sparsem)
13926 ("r-survival" ,r-survival)))
13927 (native-inputs `(("gfortran" ,gfortran)))
13928 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13929 (synopsis "Regression modeling strategies")
13931 "This is a package for regression modeling, testing, estimation,
13932 validation, graphics, prediction, and typesetting by storing enhanced model
13933 design attributes in the fit. The rms package is a collection of functions
13934 that assist with and streamline modeling. It also contains functions for
13935 binary and ordinal logistic regression models, ordinal models for continuous Y
13936 with a variety of distribution families, and the Buckley-James multiple
13937 regression model for right-censored responses, and implements penalized
13938 maximum likelihood estimation for logistic and ordinary linear models. The
13939 package works with almost any regression model, but it was especially written
13940 to work with binary or ordinal regression models, Cox regression, accelerated
13941 failure time models, ordinary linear models, the Buckley-James model,
13942 generalized least squares for serially or spatially correlated observations,
13943 generalized linear models, and quantile regression.")
13944 (license license:gpl2+)))
13946 (define-public r-haplo-stats
13948 (name "r-haplo-stats")
13953 (uri (cran-uri "haplo.stats" version))
13956 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13957 (properties `((upstream-name . "haplo.stats")))
13958 (build-system r-build-system)
13960 `(("r-rms" ,r-rms)))
13962 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13963 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13964 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13966 "This package provides routines for the analysis of indirectly measured
13967 haplotypes. The statistical methods assume that all subjects are unrelated
13968 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13969 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13970 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13971 examples in the vignette.")
13972 (license license:gpl2+)))
13974 (define-public r-bqtl
13981 (uri (cran-uri "bqtl" version))
13984 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13985 (build-system r-build-system)
13986 (native-inputs `(("gfortran" ,gfortran)))
13987 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13988 (synopsis "Bayesian QTL mapping toolkit")
13990 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13991 lines. It includes maximum likelihood and Bayesian tools.")
13992 (license license:gpl2+)))
13994 (define-public r-ibdreg
14001 (uri (cran-uri "ibdreg" version))
14004 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
14005 (build-system r-build-system)
14006 (home-page "https://www.mayo.edu/research/labs/\
14007 statistical-genetics-genetic-epidemiology/software")
14008 (synopsis "Regression methods for IBD linkage with covariates")
14010 "This package provides a method to test genetic linkage with covariates
14011 by regression methods with response IBD sharing for relative pairs. Account
14012 for correlations of IBD statistics and covariates for relative pairs within
14013 the same pedigree.")
14014 (license license:gpl2+)))
14016 (define-public r-dlmap
14023 (uri (cran-uri "dlmap" version))
14026 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14027 (build-system r-build-system)
14029 `(("r-ibdreg" ,r-ibdreg)
14033 ("r-wgaim" ,r-wgaim)))
14034 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14035 (synopsis "Detection localization mapping for QTL")
14037 "This is package for QTL mapping in a mixed model framework with separate
14038 detection and localization stages. The first stage detects the number of QTL
14039 on each chromosome based on the genetic variation due to grouped markers on
14040 the chromosome; the second stage uses this information to determine the most
14041 likely QTL positions. The mixed model can accommodate general fixed and
14042 random effects, including spatial effects in field trials and pedigree
14043 effects. It is applicable to backcrosses, doubled haploids, recombinant
14044 inbred lines, F2 intercrosses, and association mapping populations.")
14045 (license license:gpl2)))
14047 (define-public r-ldheatmap
14049 (name "r-ldheatmap")
14054 (uri (cran-uri "LDheatmap" version))
14057 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
14058 (properties `((upstream-name . "LDheatmap")))
14059 (build-system r-build-system)
14061 `(("r-genetics" ,r-genetics)
14063 ("r-snpstats" ,r-snpstats)))
14064 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14065 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14067 "This package provides tools to produce a graphical display, as a heat
14068 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14069 optionally include the physical locations or genetic map distances of each SNP
14071 (license license:gpl3)))
14073 (define-public r-hwde
14080 (uri (cran-uri "hwde" version))
14083 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14084 (build-system r-build-system)
14085 (home-page "https://cran.r-project.org/web/packages/hwde/")
14086 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14088 "This package fits models for genotypic disequilibria, as described in
14089 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14090 terms are available that account for first order interactions between loci.
14091 It also implements, for a single locus in a single population, a conditional
14092 exact test for Hardy-Weinberg equilibrium.")
14093 (license license:gpl2+)))
14095 (define-public r-tdthap
14102 (uri (cran-uri "tdthap" version))
14105 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14106 (build-system r-build-system)
14107 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14108 (synopsis "TDT tests for extended haplotypes")
14110 "Functions and examples are provided for transmission/disequilibrium
14111 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14112 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14113 (license license:artistic2.0)))
14115 (define-public r-sparql
14121 (uri (cran-uri "SPARQL" version))
14124 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14125 (properties `((upstream-name . "SPARQL")))
14126 (build-system r-build-system)
14128 `(("r-rcurl" ,r-rcurl)
14130 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14131 (synopsis "SPARQL client for R")
14132 (description "This package provides an interface to use SPARQL to pose
14133 SELECT or UPDATE queries to an end-point.")
14134 ;; The only license indication is found in the DESCRIPTION file,
14135 ;; which states GPL-3. So we cannot assume GPLv3+.
14136 (license license:gpl3)))
14138 (define-public r-bookdown
14140 (name "r-bookdown")
14144 (uri (cran-uri "bookdown" version))
14147 "137l0cyzw9ij2l3zyk3mm1k2db9vhbax6c9y4rydvh4i9gka5vlq"))))
14148 (build-system r-build-system)
14150 `(("r-htmltools" ,r-htmltools)
14151 ("r-knitr" ,r-knitr)
14152 ("r-rmarkdown" ,r-rmarkdown)
14153 ("r-tinytex" ,r-tinytex)
14155 ("pandoc" ,ghc-pandoc)))
14156 (home-page "https://github.com/rstudio/bookdown")
14157 (synopsis "Authoring books and technical documents with R markdown")
14158 (description "This package provides output formats and utilities for
14159 authoring books and technical documents with R Markdown.")
14160 (license license:gpl3)))
14162 (define-public r-optparse
14164 (name "r-optparse")
14169 (uri (cran-uri "optparse" version))
14172 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14173 (build-system r-build-system)
14175 `(("r-getopt" ,r-getopt)))
14177 `(("r-knitr" ,r-knitr)))
14178 (home-page "https://github.com/trevorld/optparse")
14179 (synopsis "Command line option parser")
14181 "This package provides a command line parser inspired by Python's
14182 @code{optparse} library to be used with Rscript to write shebang scripts
14183 that accept short and long options.")
14184 (license license:gpl2+)))
14186 (define-public r-wgcna
14193 (uri (cran-uri "WGCNA" version))
14196 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14197 (properties `((upstream-name . "WGCNA")))
14198 (build-system r-build-system)
14200 `(("r-annotationdbi" ,r-annotationdbi)
14201 ("r-doparallel" ,r-doparallel)
14202 ("r-dynamictreecut" ,r-dynamictreecut)
14203 ("r-fastcluster" ,r-fastcluster)
14204 ("r-foreach" ,r-foreach)
14205 ("r-go-db" ,r-go-db)
14206 ("r-hmisc" ,r-hmisc)
14207 ("r-impute" ,r-impute)
14209 ("r-survival" ,r-survival)
14210 ("r-matrixstats" ,r-matrixstats)
14211 ("r-preprocesscore" ,r-preprocesscore)))
14213 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14214 (synopsis "Weighted correlation network analysis")
14216 "This package provides functions necessary to perform Weighted
14217 Correlation Network Analysis on high-dimensional data. It includes functions
14218 for rudimentary data cleaning, construction and summarization of correlation
14219 networks, module identification and functions for relating both variables and
14220 modules to sample traits. It also includes a number of utility functions for
14221 data manipulation and visualization.")
14222 (license license:gpl2+)))
14224 (define-public r-kernlab
14231 (uri (cran-uri "kernlab" version))
14233 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14234 (build-system r-build-system)
14235 (home-page "https://cran.r-project.org/web/packages/kernlab")
14236 (synopsis "Kernel-based machine learning tools")
14238 "This package provides kernel-based machine learning methods for
14239 classification, regression, clustering, novelty detection, quantile regression
14240 and dimensionality reduction. Among other methods @code{kernlab} includes
14241 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14243 (license license:gpl2)))
14245 (define-public r-hierfstat
14247 (name "r-hierfstat")
14248 (version "0.04-22")
14252 (uri (cran-uri "hierfstat" version))
14255 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
14256 (build-system r-build-system)
14258 `(("r-ade4" ,r-ade4)
14259 ("r-adegenet" ,r-adegenet)
14260 ("r-gtools" ,r-gtools)))
14261 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14262 (synopsis "Estimation and tests of hierarchical F-statistics")
14264 "This package allows the estimation of hierarchical F-statistics from
14265 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14266 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14267 are also given to test via randomisations the significance of each F and
14268 variance components, using the likelihood-ratio statistics G.")
14269 (license license:gpl2+)))
14271 (define-public r-hapassoc
14273 (name "r-hapassoc")
14278 (uri (cran-uri "hapassoc" version))
14281 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14282 (build-system r-build-system)
14283 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14284 (synopsis "Inference of trait associations with SNP haplotypes")
14286 "Hapassoc performs likelihood inference of trait associations with
14287 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14288 functions are developed primarily for data collected in cohort or
14289 cross-sectional studies. They can accommodate uncertain haplotype phase and
14290 handle missing genotypes at some SNPs.")
14291 (license license:gpl2)))
14293 (define-public r-sampling
14295 (name "r-sampling")
14300 (uri (cran-uri "sampling" version))
14303 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14304 (build-system r-build-system)
14306 `(("r-lpsolve" ,r-lpsolve)
14307 ("r-mass" ,r-mass)))
14308 (home-page "https://cran.r-project.org/web/packages/sampling/")
14309 (synopsis "Survey sampling")
14311 "This package provides functions for drawing and calibrating samples.")
14312 (license license:gpl2+)))
14314 (define-public r-r2html
14321 (uri (cran-uri "R2HTML" version))
14324 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14325 (properties `((upstream-name . "R2HTML")))
14326 (build-system r-build-system)
14327 (home-page "https://github.com/nalimilan/R2HTML")
14328 (synopsis "HTML export for R objects")
14330 "This package includes HTML functions and methods to write in an HTML
14331 file. Thus, making HTML reports is easy. It includes a function that allows
14332 redirection on the fly, which appears to be very useful for teaching purposes,
14333 as the student can keep a copy of the produced output to keep all that they
14334 did during the course. The package comes with a vignette describing how to
14335 write HTML reports for statistical analysis. Finally, a driver for Sweave
14336 parses HTML flat files containing R code and to automatically write
14337 the corresponding outputs (tables and graphs).")
14338 (license license:gpl2+)))
14340 (define-public r-rjava
14347 (uri (cran-uri "rJava" version))
14350 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14351 (properties `((upstream-name . "rJava")))
14352 (build-system r-build-system)
14354 `(#:modules ((guix build utils)
14355 (guix build r-build-system)
14358 (modify-phases %standard-phases
14359 (add-after 'unpack 'set-JAVA_HOME
14360 (lambda* (#:key inputs #:allow-other-keys)
14361 (let ((jdk (assoc-ref inputs "jdk")))
14362 (setenv "JAVA_HOME" jdk)
14363 (setenv "JAVA" (which "java"))
14364 (setenv "JAR" (which "jar"))
14365 (setenv "JAVAC" (which "javac"))
14366 (setenv "JAVAH" (which "javah"))
14367 (setenv "JAVA_CPPFLAGS"
14368 (string-append "-I" jdk "/include "
14369 "-I" jdk "/include/linux"))
14370 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14371 ((lib) (setenv "JAVA_LIBS" lib))
14372 (_ (error "Could not find libjvm.so"))))
14376 ("jdk" ,icedtea-8 "jdk")
14379 (home-page "https://www.rforge.net/rJava/")
14380 (synopsis "Low-Level R to Java interface")
14382 "This package provides a low-level interface to the Java VM very much
14383 like .C/.Call and friends. It allows the creation of objects, calling methods
14384 and accessing fields.")
14385 (license license:gpl2)))
14387 (define-public r-svmisc
14394 (uri (cran-uri "svMisc" version))
14397 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14398 (properties `((upstream-name . "svMisc")))
14399 (build-system r-build-system)
14400 (home-page "https://github.com/SciViews/svMisc")
14401 (synopsis "Miscellaneous functions for SciViews")
14403 "This package provides miscellaneous functions for SciViews or general
14404 use, including tools to manage a temporary environment attached to the search
14405 path for temporary variables you do not want to @code{save()} or
14406 @code{load()}; test the current platform; showing progress bars, etc.")
14407 (license license:gpl2)))
14409 (define-public r-xyz
14416 (uri (cran-uri "xyz" version))
14419 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14420 (build-system r-build-system)
14422 `(("r-rcpp" ,r-rcpp)))
14423 (home-page "https://cran.r-project.org/web/packages/xyz/")
14424 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14426 "High dimensional interaction search by brute force requires a quadratic
14427 computational cost in the number of variables. The xyz algorithm provably
14428 finds strong interactions in almost linear time. For details of the algorithm
14429 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14430 interaction search in high-dimensional data.")
14431 ;; Any version of the GPL.
14432 (license license:gpl2+)))
14434 (define-public r-rttf2pt1
14436 (name "r-rttf2pt1")
14441 (uri (cran-uri "Rttf2pt1" version))
14444 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14445 (properties `((upstream-name . "Rttf2pt1")))
14446 (build-system r-build-system)
14447 (home-page "https://github.com/wch/Rttf2pt1")
14448 (synopsis "Font conversion utility")
14450 "This package contains the program @code{ttf2pt1}, for use with the
14451 @code{extrafont} package.")
14452 ;; Most of the files are covered under the Expat license. Some files are
14453 ;; covered under BSD-3. Deviations for individual files are recorded in
14454 ;; the LICENSE file.
14455 (license (list license:bsd-3 license:expat
14456 (license:non-copyleft "file://LICENSE")))))
14458 (define-public r-extrafontdb
14460 (name "r-extrafontdb")
14465 (uri (cran-uri "extrafontdb" version))
14468 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14469 (build-system r-build-system)
14470 (home-page "https://github.com/wch/extrafontdb")
14471 (synopsis "Database for the extrafont package")
14473 "This package holds the database for the @code{extrafont} package.")
14474 (license license:gpl2)))
14476 (define-public r-extrafont
14478 (name "r-extrafont")
14483 (uri (cran-uri "extrafont" version))
14486 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14487 (build-system r-build-system)
14489 `(("r-extrafontdb" ,r-extrafontdb)
14490 ("r-rttf2pt1" ,r-rttf2pt1)))
14491 (home-page "https://github.com/wch/extrafont")
14492 (synopsis "Tools for using fonts in R")
14494 "The extrafont package makes it easier to use fonts other than the basic
14495 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14496 used with PDF or PostScript output files. There are two hurdles for using
14497 fonts in PDF (or Postscript) output files:
14500 @item Making R aware of the font and the dimensions of the characters.
14501 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14502 properly on a device that doesn't have the font. This is usually needed if
14503 you want to print the PDF file or share it with others.
14506 The extrafont package makes both of these things easier.")
14507 (license license:gpl2)))
14509 (define-public r-xkcd
14516 (uri (cran-uri "xkcd" version))
14519 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14520 (build-system r-build-system)
14522 `(("r-extrafont" ,r-extrafont)
14523 ("r-ggplot2" ,r-ggplot2)
14524 ("r-hmisc" ,r-hmisc)))
14525 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14526 (synopsis "Plot ggplot2 graphics in the XKCD style")
14528 "This package provides the means to plot ggplot2 graphs in the style of
14529 the XKCD web comic.")
14530 (license license:gpl3)))
14532 (define-public r-msigdbr
14539 (uri (cran-uri "msigdbr" version))
14542 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14543 (build-system r-build-system)
14545 `(("r-dplyr" ,r-dplyr)
14546 ("r-magrittr" ,r-magrittr)
14547 ("r-rlang" ,r-rlang)
14548 ("r-tibble" ,r-tibble)))
14550 `(("r-knitr" ,r-knitr)))
14551 (home-page "https://github.com/igordot/msigdbr")
14552 (synopsis "MSigDB gene sets for multiple organisms")
14554 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14555 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14556 software in a standard R data frame with key-value pairs. Included are the
14557 original human gene symbols and Entrez IDs as well as the equivalents for
14558 various frequently studied model organisms such as mouse, rat, pig, fly, and
14560 ;; The package is covered under the Expat license, but the upstream MSigDB
14561 ;; files are made available under the Creative Commons Attribution 4.0
14562 ;; International license.
14563 (license (list license:expat license:cc-by4.0))))
14565 (define-public r-gridgraphics
14567 (name "r-gridgraphics")
14572 (uri (cran-uri "gridGraphics" version))
14575 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14576 (properties `((upstream-name . "gridGraphics")))
14577 (build-system r-build-system)
14578 (home-page "https://github.com/pmur002/gridgraphics")
14579 (synopsis "Redraw base graphics using @code{grid} graphics")
14581 "This package provides functions to convert a page of plots drawn with
14582 the @code{graphics} package into identical output drawn with the @code{grid}
14583 package. The result looks like the original @code{graphics}-based plot, but
14584 consists of @code{grid} grobs and viewports that can then be manipulated with
14585 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14586 (license license:gpl2+)))
14588 (define-public r-farver
14595 (uri (cran-uri "farver" version))
14598 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14599 (build-system r-build-system)
14600 (home-page "https://github.com/thomasp85/farver")
14601 (synopsis "Vectorized color conversion and comparison")
14603 "The encoding of color can be handled in many different ways, using
14604 different color spaces. As different color spaces have different uses,
14605 efficient conversion between these representations are important. This
14606 package provides a set of functions that gives access to very fast color space
14607 conversion and comparisons implemented in C++, and offers 100-fold speed
14608 improvements over the @code{convertColor} function in the @code{grDevices}
14610 (license license:expat)))
14612 (define-public r-ggplotify
14614 (name "r-ggplotify")
14619 (uri (cran-uri "ggplotify" version))
14622 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14623 (build-system r-build-system)
14625 `(("r-ggplot2" ,r-ggplot2)
14626 ("r-gridgraphics" ,r-gridgraphics)
14627 ("r-rvcheck" ,r-rvcheck)))
14629 `(("r-knitr" ,r-knitr)))
14630 (home-page "https://github.com/GuangchuangYu/ggplotify")
14631 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14633 "This package provides tools to convert plot function calls (using
14634 expression or formula) to @code{grob} or @code{ggplot} objects that are
14635 compatible with the @code{grid} and @code{ggplot2} environment. With this
14636 package, we are able to e.g. use @code{cowplot} to align plots produced by
14637 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14638 converting them to @code{ggplot} objects.")
14639 (license license:artistic2.0)))
14641 (define-public r-triebeard
14643 (name "r-triebeard")
14648 (uri (cran-uri "triebeard" version))
14651 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14652 (build-system r-build-system)
14653 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14654 (home-page "https://github.com/Ironholds/triebeard/")
14655 (synopsis "Radix trees in Rcpp")
14657 "Radix trees, or tries, are key-value data structures optimized for
14658 efficient lookups, similar in purpose to hash tables. This package provides
14659 an implementation of radix trees for use in R programming and in developing
14660 packages with Rcpp.")
14661 (license license:expat)))
14663 (define-public r-tweenr
14670 (uri (cran-uri "tweenr" version))
14673 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14674 (build-system r-build-system)
14676 `(("r-farver" ,r-farver)
14677 ("r-magrittr" ,r-magrittr)
14679 ("r-rlang" ,r-rlang)))
14680 (home-page "https://github.com/thomasp85/tweenr")
14681 (synopsis "Interpolate data for smooth animations")
14683 "In order to create smooth animation between states of data, tweening is
14684 necessary. This package provides a range of functions for creating tweened
14685 data that can be used as basis for animation. Furthermore it adds a number of
14686 vectorized interpolaters for common R data types such as numeric, date and
14688 (license license:expat)))
14690 (define-public r-polyclip
14692 (name "r-polyclip")
14697 (uri (cran-uri "polyclip" version))
14700 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14701 (build-system r-build-system)
14702 (native-inputs `(("pkg-config" ,pkg-config)))
14703 (home-page "http://www.angusj.com/delphi/clipper.php")
14704 (synopsis "Polygon clipping")
14706 "This package provides an R port of the library Clipper. It performs
14707 polygon clipping operations (intersection, union, set minus, set difference)
14708 for polygonal regions of arbitrary complexity, including holes. It computes
14709 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14710 dilations) for polygonal regions and polygonal lines. It computes the
14711 Minkowski Sum of general polygons. There is a function for removing
14712 self-intersections from polygon data.")
14713 (license license:boost1.0)))
14715 (define-public r-urltools
14717 (name "r-urltools")
14722 (uri (cran-uri "urltools" version))
14725 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14726 (build-system r-build-system)
14728 `(("r-rcpp" ,r-rcpp)
14729 ("r-triebeard" ,r-triebeard)))
14730 (home-page "https://github.com/Ironholds/urltools/")
14731 (synopsis "Vectorized tools for URL handling and parsing")
14733 "This package provides a toolkit for all URL-handling needs, including
14734 encoding and decoding, parsing, parameter extraction and modification. All
14735 functions are designed to be both fast and entirely vectorized. It is
14736 intended to be useful for people dealing with web-related datasets, such as
14737 server-side logs, although may be useful for other situations involving large
14739 (license license:expat)))
14741 (define-public r-ggforce
14748 (uri (cran-uri "ggforce" version))
14751 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14752 (build-system r-build-system)
14754 `(("r-ggplot2" ,r-ggplot2)
14755 ("r-gtable" ,r-gtable)
14757 ("r-polyclip" ,r-polyclip)
14759 ("r-rcppeigen" ,r-rcppeigen)
14760 ("r-rlang" ,r-rlang)
14761 ("r-scales" ,r-scales)
14762 ("r-tidyselect" ,r-tidyselect)
14763 ("r-tweenr" ,r-tweenr)
14764 ("r-withr" ,r-withr)))
14765 (home-page "https://ggforce.data-imaginist.com")
14766 (synopsis "Accelerating ggplot2")
14768 "The aim of the ggplot2 package is to aid in visual data investigations.
14769 This focus has led to a lack of facilities for composing specialized plots.
14770 Thi package aims to be a collection of mainly new statistics and geometries
14771 that fills this gap.")
14772 (license license:expat)))
14774 (define-public r-europepmc
14776 (name "r-europepmc")
14781 (uri (cran-uri "europepmc" version))
14784 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14785 (build-system r-build-system)
14787 `(("r-dplyr" ,r-dplyr)
14789 ("r-jsonlite" ,r-jsonlite)
14791 ("r-progress" ,r-progress)
14792 ("r-purrr" ,r-purrr)
14793 ("r-rlang" ,r-rlang)
14794 ("r-tibble" ,r-tibble)
14795 ("r-tidyr" ,r-tidyr)
14796 ("r-urltools" ,r-urltools)
14797 ("r-xml2" ,r-xml2)))
14799 `(("r-knitr" ,r-knitr)))
14800 (home-page "https://github.com/ropensci/europepmc/")
14801 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14803 "This package provides an R Client for the
14804 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14805 Service}. It gives access to both metadata on life science literature and
14806 open access full texts. Europe PMC indexes all PubMed content and other
14807 literature sources including Agricola, a bibliographic database of citations
14808 to the agricultural literature, or Biological Patents. In addition to
14809 bibliographic metadata, the client allows users to fetch citations and
14810 reference lists. Links between life-science literature and other EBI
14811 databases, including ENA, PDB or ChEMBL are also accessible.")
14812 (license license:gpl3)))
14814 (define-public r-ggraph
14821 (uri (cran-uri "ggraph" version))
14824 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14825 (build-system r-build-system)
14827 `(("r-digest" ,r-digest)
14828 ("r-dplyr" ,r-dplyr)
14829 ("r-ggforce" ,r-ggforce)
14830 ("r-ggplot2" ,r-ggplot2)
14831 ("r-ggrepel" ,r-ggrepel)
14832 ("r-graphlayouts" ,r-graphlayouts)
14833 ("r-gtable" ,r-gtable)
14834 ("r-igraph" ,r-igraph)
14837 ("r-rlang" ,r-rlang)
14838 ("r-scales" ,r-scales)
14839 ("r-tidygraph" ,r-tidygraph)
14840 ("r-viridis" ,r-viridis)))
14842 `(("r-knitr" ,r-knitr)))
14843 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14844 (synopsis "Implementation of grammar of graphics for graphs and networks")
14846 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14847 graph and network visualizations due to its reliance on tabular data input.
14848 The ggraph package is an extension of the ggplot2 API tailored to graph
14849 visualizations and provides the same flexible approach to building up plots
14851 (license license:gpl3)))
14853 (define-public r-varselrf
14855 (name "r-varselrf")
14860 (uri (cran-uri "varSelRF" version))
14863 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14864 (properties `((upstream-name . "varSelRF")))
14865 (build-system r-build-system)
14867 `(("r-randomforest" ,r-randomforest)))
14868 (home-page "https://www.ligarto.org/rdiaz/software/software")
14869 (synopsis "Variable selection using random forests")
14871 "This package provides tools for the variable selection from random
14872 forests using both backwards variable elimination (for the selection of small
14873 sets of non-redundant variables) and selection based on the importance
14874 spectrum (somewhat similar to scree plots; for the selection of large,
14875 potentially highly-correlated variables). The main applications are in
14876 high-dimensional data (e.g., microarray data, and other genomics and
14877 proteomics applications).")
14878 (license license:gpl2+)))
14880 (define-public r-pamr
14887 (uri (cran-uri "pamr" version))
14890 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14891 (build-system r-build-system)
14893 `(("r-cluster" ,r-cluster)
14894 ("r-survival" ,r-survival)))
14895 (native-inputs `(("gfortran" ,gfortran)))
14896 (home-page "https://cran.r-project.org/web/packages/pamr/")
14897 (synopsis "Prediction Analysis for Microarrays")
14899 "This package provides some functions for sample classification in
14901 (license license:gpl2)))
14903 (define-public r-rda
14906 (version "1.0.2-2.1")
14910 (uri (cran-uri "rda" version))
14913 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14914 (build-system r-build-system)
14915 (home-page "https://cran.r-project.org/web/packages/rda/")
14916 (synopsis "Shrunken centroids regularized discriminant analysis")
14918 "This package provides tools for shrunken centroids regularized
14919 discriminant analysis for the purpose of classifying high dimensional data.")
14920 (license license:gpl2+)))
14922 (define-public r-ggvis
14929 (uri (cran-uri "ggvis" version))
14932 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14933 (build-system r-build-system)
14935 `(("r-assertthat" ,r-assertthat)
14936 ("r-dplyr" ,r-dplyr)
14937 ("r-htmltools" ,r-htmltools)
14938 ("r-jsonlite" ,r-jsonlite)
14939 ("r-lazyeval" ,r-lazyeval)
14940 ("r-magrittr" ,r-magrittr)
14941 ("r-shiny" ,r-shiny)))
14942 (home-page "https://ggvis.rstudio.com/")
14943 (synopsis "Interactive grammar of graphics")
14945 "This package is a data visualization package for R providing an
14946 implementation of an interactive grammar of graphics, taking the best parts of
14947 ggplot2, combining them with the reactive framework of Shiny and drawing web
14948 graphics using Vega.")
14949 (license license:gpl2)))
14951 (define-public r-gbm
14958 (uri (cran-uri "gbm" version))
14961 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14962 (build-system r-build-system)
14964 `(("r-gridextra" ,r-gridextra)
14965 ("r-lattice" ,r-lattice)
14966 ("r-survival" ,r-survival)))
14967 (home-page "https://github.com/gbm-developers/gbm")
14968 (synopsis "Generalized boosted regression models")
14970 "This package is an implementation of extensions to Freund and Schapire's
14971 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14972 regression methods for least squares, absolute loss, t-distribution loss,
14973 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14974 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14975 and Learning to Rank measures (LambdaMart).")
14976 (license license:gpl2+)))
14978 (define-public r-threejs
14985 (uri (cran-uri "threejs" version))
14988 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14989 (build-system r-build-system)
14991 `(#:modules ((guix build utils)
14992 (guix build r-build-system)
14996 (modify-phases %standard-phases
14997 (add-after 'unpack 'process-javascript
14998 (lambda* (#:key inputs #:allow-other-keys)
14999 (with-directory-excursion "inst"
15003 `((,(assoc-ref inputs "js-jquery")
15004 "htmlwidgets/lib/jquery/jquery.min.js")
15005 (,(assoc-ref inputs "js-threejs-111")
15006 "htmlwidgets/lib/threejs-111/three.min.js"))))
15007 (lambda (sources targets)
15008 (for-each (lambda (source target)
15009 (format #t "Processing ~a --> ~a~%"
15011 (delete-file target)
15012 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15013 (call-with-output-file target
15015 (dump-port minified port)))))
15016 sources targets))))
15019 `(("r-base64enc" ,r-base64enc)
15020 ("r-crosstalk" ,r-crosstalk)
15021 ("r-htmlwidgets" ,r-htmlwidgets)
15022 ("r-igraph" ,r-igraph)))
15024 `(("uglify-js" ,uglify-js)
15028 (uri "https://code.jquery.com/jquery-1.12.4.js")
15031 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15035 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15038 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15039 (home-page "https://bwlewis.github.io/rthreejs")
15040 (synopsis "Interactive 3D scatter plots, networks and globes")
15042 "Create interactive 3D scatter plots, network plots, and globes in R
15043 using the three.js visualization library.")
15044 (license license:expat)))
15046 (define-public r-mlbench
15053 (uri (cran-uri "mlbench" version))
15056 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15057 (build-system r-build-system)
15058 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15059 (synopsis "Machine learning benchmark problems")
15061 "This package provides a collection of artificial and real-world machine
15062 learning benchmark problems, including, e.g., several data sets from the UCI
15064 (license license:gpl2)))
15066 (define-public r-mpm
15073 (uri (cran-uri "mpm" version))
15076 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15077 (build-system r-build-system)
15079 `(("r-kernsmooth" ,r-kernsmooth)
15080 ("r-mass" ,r-mass)))
15081 (home-page "http://mpm.r-forge.r-project.org")
15082 (synopsis "Multivariate projection methods")
15084 "This is a package for exploratory graphical analysis of multivariate
15085 data, specifically gene expression data with different projection methods:
15086 principal component analysis, correspondence analysis, spectral map
15088 (license license:gpl2+)))
15090 (define-public r-png
15096 (uri (cran-uri "png" version))
15099 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15100 (build-system r-build-system)
15102 `(("libpng" ,libpng)
15104 (home-page "https://www.rforge.net/png/")
15105 (synopsis "Read and write PNG images")
15107 "This package provides an easy and simple way to read, write and display
15108 bitmap images stored in the PNG format. It can read and write both files and
15109 in-memory raw vectors.")
15110 ;; Any of these GPL versions.
15111 (license (list license:gpl2 license:gpl3))))
15113 (define-public r-ggcorrplot
15115 (name "r-ggcorrplot")
15120 (uri (cran-uri "ggcorrplot" version))
15123 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15124 (build-system r-build-system)
15126 `(("r-ggplot2" ,r-ggplot2)
15127 ("r-reshape2" ,r-reshape2)))
15128 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15129 (synopsis "Visualization of a correlation matrix using ggplot2")
15131 "The ggcorrplot package can be used to visualize easily a correlation
15132 matrix using ggplot2. It provides a solution for reordering the correlation
15133 matrix and displays the significance level on the plot. It also includes a
15134 function for computing a matrix of correlation p-values.")
15135 (license license:gpl2)))
15137 (define-public r-flexdashboard
15139 (name "r-flexdashboard")
15140 (version "0.5.1.1")
15144 (uri (cran-uri "flexdashboard" version))
15147 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
15148 (build-system r-build-system)
15150 `(#:modules ((guix build utils)
15151 (guix build r-build-system)
15155 (ice-9 textual-ports))
15157 (modify-phases %standard-phases
15158 (add-after 'unpack 'process-javascript
15159 (lambda* (#:key inputs #:allow-other-keys)
15160 (with-directory-excursion "inst"
15161 ;; Concatenate all components of prism.js
15162 (let ((contents (string-join
15163 (map (lambda (name)
15164 (call-with-input-file
15165 (assoc-ref inputs name)
15169 "js-prism-line-numbers"))
15171 (call-with-output-file "prism-src.js"
15172 (cut display contents <>)))
15176 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15177 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15179 "www/sly/sly.min.js")
15181 "www/prism/prism.js")
15182 (,(assoc-ref inputs "js-raphael")
15183 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15184 (,(assoc-ref inputs "js-featherlight")
15185 "www/featherlight/featherlight.min.js"))))
15186 (lambda (sources targets)
15187 (for-each (lambda (source target)
15188 (format #t "Processing ~a --> ~a~%"
15190 (delete-file target)
15191 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15192 (call-with-output-file target
15194 (dump-port minified port)))))
15195 sources targets))))
15198 `(("r-htmltools" ,r-htmltools)
15199 ("r-htmlwidgets" ,r-htmlwidgets)
15200 ("r-jsonlite" ,r-jsonlite)
15201 ("r-knitr" ,r-knitr)
15202 ("r-rmarkdown" ,r-rmarkdown)
15203 ("r-shiny" ,r-shiny)))
15205 `(("uglify-js" ,uglify-js)
15209 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15212 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15216 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15219 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15223 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15226 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15227 ("js-prism-line-numbers"
15230 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15233 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15237 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15240 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15241 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15242 (synopsis "R Markdown format for flexible dashboards")
15244 "This package provides an R Markdown format for converting an R Markdown
15245 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15246 of its components to the containing web page.")
15247 (license license:expat)))
15249 (define-public r-preseqr
15256 (uri (cran-uri "preseqR" version))
15259 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15260 (properties `((upstream-name . "preseqR")))
15261 (build-system r-build-system)
15263 `(("r-polynom" ,r-polynom)))
15264 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15265 (synopsis "Predicting species accumulation curves")
15267 "This package can be used to predict the r-species accumulation
15268 curve (r-SAC), which is the number of species represented at least r times as
15269 a function of the sampling effort. When r = 1, the curve is known as the
15270 species accumulation curve, or the library complexity curve in high-throughput
15271 genomic sequencing. The package includes both parametric and nonparametric
15272 methods, as described by Deng C, et al. (2018).")
15273 (license license:gpl3)))
15275 (define-public r-mapplots
15277 (name "r-mapplots")
15282 (uri (cran-uri "mapplots" version))
15285 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15286 (build-system r-build-system)
15287 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15288 (synopsis "Data visualization on maps")
15290 "This package helps you create simple maps; add sub-plots like pie plots
15291 to a map or any other plot; format, plot and export gridded data. The package
15292 was developed for displaying fisheries data but most functions can be used for
15293 more generic data visualisation.")
15294 (license license:gpl2+)))
15296 (define-public r-pmcmr
15303 (uri (cran-uri "PMCMR" version))
15306 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15307 (properties `((upstream-name . "PMCMR")))
15308 (build-system r-build-system)
15309 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15310 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15312 "This is a deprecated package for calculating pairwise multiple
15313 comparisons of mean rank sums. This package is superseded by the novel
15314 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15315 compatibility of dependent packages for some time.")
15316 (license license:gpl3+)))
15318 (define-public r-downloader
15320 (name "r-downloader")
15325 (uri (cran-uri "downloader" version))
15328 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15329 (build-system r-build-system)
15331 `(("r-digest" ,r-digest)))
15332 (home-page "https://github.com/wch/downloader")
15333 (synopsis "Download files over HTTP and HTTPS")
15335 "This package provides a wrapper for the @code{download.file} function,
15336 making it possible to download files over HTTPS across platforms. The
15337 @code{RCurl} package provides this functionality (and much more) but has
15338 external dependencies. This package has is implemented purely in R.")
15339 (license license:gpl2)))
15341 (define-public r-rex
15348 (uri (cran-uri "rex" version))
15351 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15352 (build-system r-build-system)
15354 `(("r-lazyeval" ,r-lazyeval)))
15356 `(("r-knitr" ,r-knitr)))
15357 (home-page "https://github.com/kevinushey/rex")
15358 (synopsis "Friendly regular expressions")
15360 "This package provides a friendly interface for the construction of
15361 regular expressions. Regular expressions are a very powerful feature, however
15362 they are often difficult to interpret. Rex allows you to build complex
15363 regular expressions from human readable expressions")
15364 (license license:expat)))
15366 (define-public r-xmlparsedata
15368 (name "r-xmlparsedata")
15373 (uri (cran-uri "xmlparsedata" version))
15376 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15377 (properties `((upstream-name . "xmlparsedata")))
15378 (build-system r-build-system)
15379 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15380 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15382 "This package provides tools to convert the output of
15383 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15384 @code{XPath}, and is easier to manipulate in general.")
15385 (license license:expat)))
15387 (define-public r-cyclocomp
15389 (name "r-cyclocomp")
15394 (uri (cran-uri "cyclocomp" version))
15397 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15398 (properties `((upstream-name . "cyclocomp")))
15399 (build-system r-build-system)
15401 `(("r-callr" ,r-callr)
15402 ("r-crayon" ,r-crayon)
15404 ("r-remotes" ,r-remotes)
15405 ("r-withr" ,r-withr)))
15406 (home-page "https://github.com/MangoTheCat/cyclocomp")
15407 (synopsis "Cyclomatic complexity of R code")
15409 "Cyclomatic complexity is a software metric, used to indicate the
15410 complexity of a program. It is a quantitative measure of the number of
15411 linearly independent paths through a program's source code. This package
15412 provides tools to compute this metric.")
15413 (license license:expat)))
15415 (define-public r-lintr
15422 (uri (cran-uri "lintr" version))
15425 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15426 (properties `((upstream-name . "lintr")))
15427 (build-system r-build-system)
15429 `(("r-codetools" ,r-codetools)
15430 ("r-crayon" ,r-crayon)
15431 ("r-cyclocomp" ,r-cyclocomp)
15432 ("r-digest" ,r-digest)
15434 ("r-jsonlite" ,r-jsonlite)
15435 ("r-knitr" ,r-knitr)
15437 ("r-rstudioapi" ,r-rstudioapi)
15438 ("r-testthat" ,r-testthat)
15440 ("r-xmlparsedata" ,r-xmlparsedata)))
15441 (home-page "https://github.com/jimhester/lintr")
15442 (synopsis "Linter for R code")
15443 (description "This package checks adherence to a given style, syntax
15444 errors and possible semantic issues. It supports on the fly checking of R
15445 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15446 (license license:expat)))
15448 (define-public r-sctransform
15450 (name "r-sctransform")
15455 (uri (cran-uri "sctransform" version))
15458 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15459 (build-system r-build-system)
15461 `(("r-future-apply" ,r-future-apply)
15462 ("r-ggplot2" ,r-ggplot2)
15463 ("r-gridextra" ,r-gridextra)
15465 ("r-matrix" ,r-matrix)
15467 ("r-rcppeigen" ,r-rcppeigen)
15468 ("r-reshape2" ,r-reshape2)))
15469 (home-page "https://github.com/ChristophH/sctransform")
15470 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15472 "This package provides a normalization method for single-cell UMI count
15473 data using a variance stabilizing transformation. The transformation is based
15474 on a negative binomial regression model with regularized parameters. As part
15475 of the same regression framework, this package also provides functions for
15476 batch correction, and data correction.")
15477 (license license:gpl3)))
15479 (define-public r-styler
15486 (uri (cran-uri "styler" version))
15489 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15490 (build-system r-build-system)
15492 `(("r-backports" ,r-backports)
15494 ("r-magrittr" ,r-magrittr)
15495 ("r-purrr" ,r-purrr)
15496 ("r-r-cache" ,r-r-cache)
15497 ("r-rematch2" ,r-rematch2)
15498 ("r-rlang" ,r-rlang)
15499 ("r-rprojroot" ,r-rprojroot)
15500 ("r-tibble" ,r-tibble)
15501 ("r-withr" ,r-withr)
15502 ("r-xfun" ,r-xfun)))
15503 (home-page "https://github.com/r-lib/styler")
15504 (synopsis "Non-invasive pretty printing of R code")
15506 "This is a package for pretty-printing R code without changing the user's
15507 formatting intent.")
15508 (license license:gpl3)))
15510 (define-public r-scrime
15517 (uri (cran-uri "scrime" version))
15520 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15521 (build-system r-build-system)
15522 (home-page "https://cran.r-project.org/web/packages/scrime/")
15523 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15525 "This package provides tools for the analysis of high-dimensional data
15526 developed/implemented at the group \"Statistical Complexity Reduction In
15527 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15528 the functions can also be applied to other types of categorical data.")
15529 (license license:gpl2)))
15531 (define-public r-pbmcapply
15533 (name "r-pbmcapply")
15538 (uri (cran-uri "pbmcapply" version))
15541 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15542 (build-system r-build-system)
15543 (home-page "https://github.com/kvnkuang/pbmcapply")
15544 (synopsis "Track the progress of apply procedures with a progress bar")
15546 "This light-weight package helps you track and visualize the progress of
15547 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15548 (license license:expat)))
15550 (define-public r-blme
15557 (uri (cran-uri "blme" version))
15560 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15561 (build-system r-build-system)
15562 (propagated-inputs `(("r-lme4" ,r-lme4)))
15563 (home-page "https://github.com/vdorie/blme")
15564 (synopsis "Bayesian linear mixed-effects models")
15566 "This package provides tools for maximum a posteriori estimation for
15567 linear and generalized linear mixed-effects models in a Bayesian setting. It
15568 extends the lme4 package.")
15569 (license license:gpl2+)))
15571 (define-public r-batchtools
15573 (name "r-batchtools")
15578 (uri (cran-uri "batchtools" version))
15581 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15582 (build-system r-build-system)
15584 `(("r-backports" ,r-backports)
15585 ("r-base64url" ,r-base64url)
15587 ("r-checkmate" ,r-checkmate)
15588 ("r-data-table" ,r-data-table)
15589 ("r-digest" ,r-digest)
15591 ("r-progress" ,r-progress)
15593 ("r-rappdirs" ,r-rappdirs)
15594 ("r-stringi" ,r-stringi)
15595 ("r-withr" ,r-withr)))
15597 `(("r-knitr" ,r-knitr)))
15598 (home-page "https://github.com/mllg/batchtools")
15599 (synopsis "Tools for computation on batch systems")
15601 "As a successor of the packages BatchJobs and BatchExperiments, this
15602 package provides a parallel implementation of the Map function for high
15603 performance computing systems managed by various schedulers. A multicore and
15604 socket mode allow the parallelization on a local machines, and multiple
15605 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15606 the package provides an abstraction mechanism to define large-scale computer
15607 experiments in a well-organized and reproducible way.")
15608 (license license:lgpl3)))
15610 (define-public r-clue
15617 (uri (cran-uri "clue" version))
15620 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15621 (build-system r-build-system)
15622 (propagated-inputs `(("r-cluster" ,r-cluster)))
15623 (home-page "https://cran.r-project.org/web/packages/clue/")
15624 (synopsis "Tools for analyzing cluster ensembles")
15625 (description "Cluster ensembles are collections of individual solutions to
15626 a given clustering problem which are useful or necessary to consider in a wide
15627 range of applications. This R package provides an extensible computational
15628 environment for creating and analyzing cluster ensembles, with basic data
15629 structures for representing partitions and hierarchies, and facilities for
15630 computing on them, including methods for measuring proximity and obtaining
15631 consensus and secondary clusterings.")
15632 (license license:gpl2)))
15634 (define-public r-sitmo
15641 (uri (cran-uri "sitmo" version))
15644 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15645 (build-system r-build-system)
15646 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15647 (home-page "https://github.com/coatless/sitmo/")
15648 (synopsis "Parallel pseudo random number generator header files")
15650 "This package provides two high quality and fast PPRNGs that may be used
15651 in an OpenMP parallel environment. In addition, there is a generator for one
15652 dimensional low-discrepancy sequence.")
15653 (license license:expat)))
15655 (define-public r-dqrng
15662 (uri (cran-uri "dqrng" version))
15665 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15666 (build-system r-build-system)
15670 ("r-sitmo" ,r-sitmo)))
15671 (home-page "https://www.daqana.org/dqrng")
15672 (synopsis "Fast pseudo random number generators")
15674 "Several fast random number generators are provided as C++ header-only
15675 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15676 Additionally, fast functions for generating random numbers according to a
15677 uniform, normal and exponential distribution are included. The latter two use
15678 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15679 functions are exported to R and as a C++ interface and are enabled for use
15680 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15681 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15682 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15683 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15684 ;; whole is distributed under the terms of the AGPL 3.
15685 (license license:agpl3)))
15687 (define-public r-ingredients
15689 (name "r-ingredients")
15694 (uri (cran-uri "ingredients" version))
15697 "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
15698 (properties `((upstream-name . "ingredients")))
15699 (build-system r-build-system)
15701 `(("r-ggplot2" ,r-ggplot2)
15702 ("r-gridextra" ,r-gridextra)
15703 ("r-scales" ,r-scales)))
15704 (native-inputs `(("r-knitr" ,r-knitr)))
15705 (home-page "https://ModelOriented.github.io/ingredients/")
15706 (synopsis "Effects and importances of model ingredients")
15708 "This is a collection of tools for assessment of feature importance and
15709 feature effects. Key functions are:
15712 @item @code{feature_importance()} for assessment of global level feature
15714 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15715 @item @code{partial_dependence()} for partial dependence plots,
15716 @item @code{conditional_dependence()} for conditional dependence plots,
15717 @item @code{accumulated_dependence()} for accumulated local effects plots,
15718 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15719 aggregation of ceteris paribus profiles,
15720 @item generic @code{print()} and @code{plot()} for better usability of
15721 selected explainers,
15722 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15723 @item generic @code{describe()} for explanations in natural language.
15725 (license license:gpl3)))
15727 (define-public r-ibreakdown
15729 (name "r-ibreakdown")
15734 (uri (cran-uri "iBreakDown" version))
15737 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15738 (properties `((upstream-name . "iBreakDown")))
15739 (build-system r-build-system)
15740 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15741 (native-inputs `(("r-knitr" ,r-knitr)))
15742 (home-page "https://ModelOriented.github.io/iBreakDown/")
15743 (synopsis "Model agnostic instance level variable attributions")
15745 "This package provides a model agnostic tool for decomposition of
15746 predictions from black boxes. It supports additive attributions and
15747 attributions with interactions. The Break Down Table shows contributions of
15748 every variable to a final prediction. The Break Down Plot presents variable
15749 contributions in a concise graphical way. This package works for
15750 classification and regression models.")
15751 (license license:gpl3)))
15753 (define-public r-dalex
15760 (uri (cran-uri "DALEX" version))
15763 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15764 (properties `((upstream-name . "DALEX")))
15765 (build-system r-build-system)
15767 `(("r-ggplot2" ,r-ggplot2)
15768 ("r-ibreakdown" ,r-ibreakdown)
15769 ("r-ingredients" ,r-ingredients)))
15770 (home-page "https://pbiecek.github.io/DALEX/")
15771 (synopsis "Descriptive machine learning explanations")
15773 "Machine Learning models are widely used and have various applications in
15774 classification or regression. Models created with boosting, bagging, stacking
15775 or similar techniques are often used due to their high performance, but such
15776 black-box models usually lack interpretability. The DALEX package contains
15777 various explainers that help to understand the link between input variables
15778 and model output.")
15779 ;; Any version of the GPL
15780 (license license:gpl3+)))
15782 (define-public r-enrichr
15789 (uri (cran-uri "enrichR" version))
15792 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15793 (properties `((upstream-name . "enrichR")))
15794 (build-system r-build-system)
15796 `(("r-httr" ,r-httr)
15797 ("r-rjson" ,r-rjson)))
15798 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15799 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15801 "This package provides an R interface to all Enrichr databases, a
15802 web-based tool for analyzing gene sets and returns any enrichment of common
15803 annotated biological functions.")
15804 (license license:gpl2+)))
15806 (define-public r-plot3d
15813 (uri (cran-uri "plot3D" version))
15816 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15817 (properties `((upstream-name . "plot3D")))
15818 (build-system r-build-system)
15819 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15820 (home-page "https://cran.r-project.org/web/packages/plot3D")
15821 (synopsis "Plot multi-dimensional data")
15823 "This package provides functions for viewing 2D and 3D data, including
15824 perspective plots, slice plots, surface plots, scatter plots, etc. It
15825 includes data sets from oceanography.")
15826 (license license:gpl3+)))
15828 (define-public r-ggfortify
15830 (name "r-ggfortify")
15835 (uri (cran-uri "ggfortify" version))
15838 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15839 (build-system r-build-system)
15841 `(("r-dplyr" ,r-dplyr)
15842 ("r-ggplot2" ,r-ggplot2)
15843 ("r-gridextra" ,r-gridextra)
15844 ("r-scales" ,r-scales)
15845 ("r-stringr" ,r-stringr)
15846 ("r-tibble" ,r-tibble)
15847 ("r-tidyr" ,r-tidyr)))
15849 `(("r-knitr" ,r-knitr)))
15850 (home-page "https://github.com/sinhrks/ggfortify")
15851 (synopsis "Data visualization tools for statistical analysis results")
15853 "This package provides unified plotting tools for statistics commonly
15854 used, such as GLM, time series, PCA families, clustering and survival
15855 analysis. The package offers a single plotting interface for these analysis
15856 results and plots in a unified style using the @code{ggplot2} package.")
15857 (license license:gpl2)))
15859 (define-public r-refmanager
15861 (name "r-refmanager")
15866 (uri (cran-uri "RefManageR" version))
15869 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15870 (properties `((upstream-name . "RefManageR")))
15871 (build-system r-build-system)
15873 `(("r-bibtex" ,r-bibtex)
15875 ("r-jsonlite" ,r-jsonlite)
15876 ("r-lubridate" ,r-lubridate)
15878 ("r-stringr" ,r-stringr)
15879 ("r-xml2" ,r-xml2)))
15880 (home-page "https://github.com/ropensci/RefManageR/")
15881 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15883 "This package provides tools for importing and working with bibliographic
15884 references. It greatly enhances the @code{bibentry} class by providing a
15885 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15886 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15887 by various formats for name lists (author by last names, translator by full
15888 names, etc.). Entries can be updated, combined, sorted, printed in a number
15889 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15890 into R and converted to @code{BibEntry} objects.")
15891 ;; Any of these licenses may be picked.
15892 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15894 (define-public r-citr
15901 (uri (cran-uri "citr" version))
15904 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15905 (build-system r-build-system)
15907 `(("r-assertthat" ,r-assertthat)
15910 ("r-miniui" ,r-miniui)
15911 ("r-refmanager" ,r-refmanager)
15912 ("r-rstudioapi" ,r-rstudioapi)
15913 ("r-shiny" ,r-shiny)
15914 ("r-shinyjs" ,r-shinyjs)
15915 ("r-yaml" ,r-yaml)))
15916 (home-page "https://github.com/crsh/citr")
15917 (synopsis "RStudio add-in to insert Markdown citations")
15919 "This package provides functions and an RStudio add-in that search a
15920 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15921 the current document.")
15922 (license license:expat)))
15924 (define-public r-xgboost
15927 (version "1.1.1.1")
15931 (uri (cran-uri "xgboost" version))
15934 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
15935 (build-system r-build-system)
15937 `(("r-data-table" ,r-data-table)
15938 ("r-magrittr" ,r-magrittr)
15939 ("r-matrix" ,r-matrix)
15940 ("r-stringi" ,r-stringi)))
15942 `(("r-knitr" ,r-knitr)))
15943 (home-page "https://github.com/dmlc/xgboost")
15944 (synopsis "Extreme gradient boosting")
15946 "This package provides an R interface to Extreme Gradient Boosting, which
15947 is an efficient implementation of the gradient boosting framework from Chen
15948 and Guestrin (2016). The package includes efficient linear model solver and
15949 tree learning algorithms. The package can automatically do parallel
15950 computation on a single machine. It supports various objective functions,
15951 including regression, classification and ranking. The package is made to be
15952 extensible, so that users are also allowed to define their own objectives
15954 (license license:asl2.0)))
15956 (define-public r-umap
15959 (version "0.2.5.0")
15963 (uri (cran-uri "umap" version))
15966 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15967 (build-system r-build-system)
15969 `(("r-openssl" ,r-openssl)
15971 ("r-reticulate" ,r-reticulate)
15972 ("r-rspectra" ,r-rspectra)))
15974 `(("r-knitr" ,r-knitr)))
15975 (home-page "https://github.com/tkonopka/umap")
15976 (synopsis "Uniform manifold approximation and projection")
15978 "Uniform manifold approximation and projection is a technique for
15979 dimension reduction. This package provides an interface to the UMAP algorithm
15980 in R, including a translation of the original algorithm into R.")
15981 (license license:expat)))
15983 (define-public r-uwot
15990 (uri (cran-uri "uwot" version))
15993 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15994 (build-system r-build-system)
15996 `(("r-dqrng" ,r-dqrng)
15998 ("r-irlba" ,r-irlba)
15999 ("r-matrix" ,r-matrix)
16001 ("r-rcppannoy" ,r-rcppannoy)
16002 ("r-rcppprogress" ,r-rcppprogress)
16003 ("r-rspectra" ,r-rspectra)))
16004 (home-page "https://github.com/jlmelville/uwot")
16005 (synopsis "Uniform manifold approximation and projection")
16007 "This package provides an implementation of the Uniform Manifold
16008 Approximation and Projection dimensionality reduction by McInnes et
16009 al. (2018). It also provides means to transform new data and to carry out
16010 supervised dimensionality reduction. An implementation of the related
16011 LargeVis method of Tang et al. (2016) is also provided.")
16012 (license license:gpl3)))
16014 (define-public r-kableextra
16016 (name "r-kableextra")
16021 (uri (cran-uri "kableExtra" version))
16024 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16025 (properties `((upstream-name . "kableExtra")))
16026 (build-system r-build-system)
16028 `(("r-digest" ,r-digest)
16030 ("r-htmltools" ,r-htmltools)
16031 ("r-knitr" ,r-knitr)
16032 ("r-magrittr" ,r-magrittr)
16033 ("r-readr" ,r-readr)
16034 ("r-rmarkdown" ,r-rmarkdown)
16035 ("r-rstudioapi" ,r-rstudioapi)
16036 ("r-rvest" ,r-rvest)
16037 ("r-scales" ,r-scales)
16038 ("r-stringr" ,r-stringr)
16039 ("r-viridislite" ,r-viridislite)
16040 ("r-webshot" ,r-webshot)
16041 ("r-xml2" ,r-xml2)))
16042 (home-page "https://haozhu233.github.io/kableExtra/")
16043 (synopsis "Construct complex tables with pipe syntax")
16045 "Build complex HTML or LaTeX tables using @code{kable()} from
16046 @code{knitr} and the piping syntax from @code{magrittr}. The function
16047 @code{kable()} is a light weight table generator coming from @code{knitr}.
16048 This package simplifies the way to manipulate the HTML or LaTeX codes
16049 generated by @code{kable()} and allows users to construct complex tables and
16050 customize styles using a readable syntax.")
16051 (license license:expat)))
16053 (define-public r-glasso
16060 (uri (cran-uri "glasso" version))
16062 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16063 (build-system r-build-system)
16064 (native-inputs `(("gfortran" ,gfortran)))
16065 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16066 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16068 "This is a package for estimation of a sparse inverse covariance matrix
16069 using a lasso (L1) penalty. Facilities are provided for estimates along a
16070 path of values for the regularization parameter.")
16071 (license license:gpl2)))
16073 (define-public r-rhpcblasctl
16075 (name "r-rhpcblasctl")
16076 (version "0.20-137")
16080 (uri (cran-uri "RhpcBLASctl" version))
16083 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16084 (properties `((upstream-name . "RhpcBLASctl")))
16085 (build-system r-build-system)
16086 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16087 (synopsis "Control the number of threads on BLAS")
16089 "This package allows you to control the number of threads the BLAS
16090 library uses. It is also possible to control the number of threads in
16092 (license license:agpl3+)))
16094 (define-public r-lda
16101 (uri (cran-uri "lda" version))
16104 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16105 (build-system r-build-system)
16106 (home-page "https://cran.r-project.org/web/packages/lda/")
16107 (synopsis "Collapsed Gibbs sampling methods for topic models")
16109 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16110 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16111 mixed-membership stochastic blockmodel. Inference for all of these models is
16112 implemented via a fast collapsed Gibbs sampler written in C. Utility
16113 functions for reading/writing data typically used in topic models, as well as
16114 tools for examining posterior distributions are also included.")
16115 ;; Any version of the LGPL
16116 (license license:lgpl3+)))
16118 (define-public r-rann-l1
16125 (uri (cran-uri "RANN.L1" version))
16128 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16129 (properties `((upstream-name . "RANN.L1")))
16130 (build-system r-build-system)
16131 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16132 (synopsis "Fast nearest neighbour search using L1 metric")
16134 "This package provides tools to find the k nearest neighbours for every
16135 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16136 library. There is support for approximate as well as exact searches, fixed
16137 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16138 computed using the L1 (Manhattan, taxicab) metric.")
16139 (license license:gpl3+)))
16141 (define-public r-leiden
16148 (uri (cran-uri "leiden" version))
16151 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16152 (properties `((upstream-name . "leiden")))
16153 (build-system r-build-system)
16155 `(("r-igraph" ,r-igraph)
16156 ("r-matrix" ,r-matrix)
16157 ("r-reticulate" ,r-reticulate)))
16158 (home-page "https://github.com/TomKellyGenetics/leiden")
16159 (synopsis "R implementation of Leiden clustering algorithm")
16161 "This package implements the Python @code{leidenalg} module to be called
16162 in R. It enables clustering using the Leiden algorithm for partitioning a
16163 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16164 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16165 (license license:gpl3)))
16167 (define-public r-patchwork
16169 (name "r-patchwork")
16174 (uri (cran-uri "patchwork" version))
16177 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
16178 (build-system r-build-system)
16180 `(("r-ggplot2" ,r-ggplot2)
16181 ("r-gtable" ,r-gtable)))
16183 `(("r-knitr" ,r-knitr)))
16184 (home-page "https://github.com/thomasp85/patchwork")
16185 (synopsis "Compose ggplot2 plots")
16187 "The @code{ggplot2} package provides a strong API for sequentially
16188 building up a plot, but does not concern itself with composition of multiple
16189 plots. Patchwork is a package that expands the API to allow for arbitrarily
16190 complex composition of plots by providing mathmatical operators for combining
16192 (license license:expat)))
16194 (define-public r-liger
16201 (uri (git-reference
16202 (url "https://github.com/MacoskoLab/liger.git")
16203 (commit (string-append "v" version))))
16204 (file-name (git-file-name name version))
16207 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16208 (modules '((guix build utils)))
16211 (delete-file "inst/java/ModularityOptimizer.jar")
16213 (build-system r-build-system)
16216 (modify-phases %standard-phases
16217 (add-after 'unpack 'build-java-part
16218 (lambda* (#:key inputs #:allow-other-keys)
16219 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16220 (for-each (lambda (file) (invoke "javac" file))
16221 (find-files "." "\\.java$"))
16222 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16223 (find-files "." "\\.class$"))
16226 `(("r-cowplot" ,r-cowplot)
16227 ("r-dosnow" ,r-dosnow)
16228 ("r-dplyr" ,r-dplyr)
16230 ("r-foreach" ,r-foreach)
16231 ("r-ggplot2" ,r-ggplot2)
16232 ("r-ggrepel" ,r-ggrepel)
16233 ("r-hmisc" ,r-hmisc)
16235 ("r-irlba" ,r-irlba)
16236 ("r-matrix" ,r-matrix)
16237 ("r-mclust" ,r-mclust)
16238 ("r-patchwork" ,r-patchwork)
16240 ("r-rann-l1" ,r-rann-l1)
16242 ("r-rcpparmadillo" ,r-rcpparmadillo)
16243 ("r-riverplot" ,r-riverplot)
16244 ("r-rtsne" ,r-rtsne)
16245 ("r-snow" ,r-snow)))
16247 `(("jdk" ,icedtea "jdk")
16248 ;; See https://github.com/MacoskoLab/liger/issues/96
16249 ;; The optimizer is released under the Expat license.
16253 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16256 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16258 ("r-knitr" ,r-knitr))) ; for vignettes
16259 (home-page "https://github.com/MacoskoLab/liger")
16260 (synopsis "Integrate and analyze multiple single-cell datasets")
16262 "LIGER is a package for integrating and analyzing multiple single-cell
16263 datasets, developed and maintained by the Macosko lab. It relies on
16264 integrative non-negative matrix factorization to identify shared and
16265 dataset-specific factors.")
16266 (license license:gpl3)))
16268 (define-public r-harmony
16275 (uri (git-reference
16276 (url "https://github.com/immunogenomics/harmony")
16278 (file-name (git-file-name name version))
16281 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16282 (modules '((guix build utils)))
16285 (for-each delete-file '("config.status" "configure"))
16287 (build-system r-build-system)
16289 `(("r-cowplot" ,r-cowplot)
16290 ("r-dplyr" ,r-dplyr)
16291 ("r-ggplot2" ,r-ggplot2)
16292 ("r-irlba" ,r-irlba)
16293 ("r-matrix" ,r-matrix)
16295 ("r-rcpparmadillo" ,r-rcpparmadillo)
16296 ("r-rcppprogress" ,r-rcppprogress)
16297 ("r-rlang" ,r-rlang)
16298 ("r-tibble" ,r-tibble)
16299 ("r-tidyr" ,r-tidyr)))
16301 `(("autoconf" ,autoconf)))
16302 (home-page "https://github.com/immunogenomics/harmony")
16303 (synopsis "Integration of single cell sequencing data")
16305 "This package provides an implementation of the Harmony algorithm for
16306 single cell integration, described in Korsunsky et al
16307 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16308 function and interfaces to external frameworks.")
16309 (license license:gpl3)))
16311 (define-public r-covr
16318 (uri (cran-uri "covr" version))
16320 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16321 (properties `((upstream-name . "covr")))
16322 (build-system r-build-system)
16324 `(("r-crayon" ,r-crayon)
16325 ("r-digest" ,r-digest)
16327 ("r-jsonlite" ,r-jsonlite)
16329 ("r-withr" ,r-withr)
16330 ("r-yaml" ,r-yaml)))
16332 `(("r-knitr" ,r-knitr))) ; for vignettes
16333 (home-page "https://github.com/r-lib/covr")
16334 (synopsis "Test coverage for R packages")
16336 "Thisp package enables you to track and report code coverage for your
16337 package and (optionally) upload the results to a coverage service. Code
16338 coverage is a measure of the amount of code being exercised by a set of tests.
16339 It is an indirect measure of test quality and completeness. This package is
16340 compatible with any testing methodology or framework and tracks coverage of
16341 both R code and compiled C/C++/FORTRAN code.")
16342 (license license:gpl3)))
16344 (define-public r-systemfonts
16346 (name "r-systemfonts")
16351 (uri (cran-uri "systemfonts" version))
16354 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16355 (properties `((upstream-name . "systemfonts")))
16356 (build-system r-build-system)
16358 `(("fontconfig" ,fontconfig)
16361 `(("pkg-config" ,pkg-config)
16362 ("r-knitr" ,r-knitr)))
16363 (home-page "https://github.com/r-lib/systemfonts")
16364 (synopsis "System native font finding")
16366 "This package provides system native access to the font catalogue. As
16367 font handling varies between systems it is difficult to correctly locate
16368 installed fonts across different operating systems. The 'systemfonts' package
16369 provides bindings to the native libraries for finding font files that can then
16370 be used further by e.g. graphic devices.")
16371 (license license:expat)))
16373 (define-public r-graphlayouts
16375 (name "r-graphlayouts")
16380 (uri (cran-uri "graphlayouts" version))
16383 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16384 (properties `((upstream-name . "graphlayouts")))
16385 (build-system r-build-system)
16387 `(("r-igraph" ,r-igraph)
16389 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16390 (home-page "https://github.com/schochastics/graphlayouts")
16391 (synopsis "Additional layout algorithms for network visualizations")
16393 "This package provides several layout algorithms to visualize networks
16394 which are not part of the igraph library. Most are based on the concept of
16395 stress majorization by Gansner et al. (2004)
16396 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16397 emphasize hidden group structures in networks or focus on specific nodes.")
16398 (license license:expat)))
16400 (define-public r-tidygraph
16402 (name "r-tidygraph")
16407 (uri (cran-uri "tidygraph" version))
16410 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16411 (properties `((upstream-name . "tidygraph")))
16412 (build-system r-build-system)
16414 `(("r-dplyr" ,r-dplyr)
16415 ("r-igraph" ,r-igraph)
16416 ("r-magrittr" ,r-magrittr)
16417 ("r-pillar" ,r-pillar)
16420 ("r-rlang" ,r-rlang)
16421 ("r-tibble" ,r-tibble)
16422 ("r-tidyr" ,r-tidyr)))
16423 (home-page "https://github.com/thomasp85/tidygraph")
16424 (synopsis "Tidy API for graph manipulation")
16426 "This package provides a graph implementation that can be thought of as
16427 two tidy data frames describing node and edge data respectively. It provides
16428 an approach to manipulate these two virtual data frames using the API defined
16429 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16430 common graph algorithms.")
16431 (license license:expat)))
16433 (define-public r-soupx
16434 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16438 (version (git-version "0.3.1" revision commit))
16442 (uri (git-reference
16443 (url "https://github.com/constantAmateur/SoupX")
16445 (file-name (git-file-name name version))
16448 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16449 (properties `((upstream-name . "SoupX")))
16450 (build-system r-build-system)
16452 `(("r-ggplot2" ,r-ggplot2)
16453 ("r-matrix" ,r-matrix)
16454 ("r-seurat" ,r-seurat)))
16455 (home-page "https://github.com/constantAmateur/SoupX")
16456 (synopsis "Single cell mRNA Soup eXterminator")
16458 "This package provides a package for quantifying, profiling and
16459 removing cell free mRNA contamination (the \"soup\") from droplet based single
16460 cell RNA-seq experiments.")
16461 (license license:gpl2))))
16463 (define-public r-assertr
16470 (uri (cran-uri "assertr" version))
16473 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16474 (build-system r-build-system)
16476 `(("r-dplyr" ,r-dplyr)
16478 ("r-rlang" ,r-rlang)))
16480 `(("r-knitr" ,r-knitr))) ; needed for vignette
16481 (home-page "https://github.com/ropensci/assertr")
16482 (synopsis "Assertive programming for R analysis pipelines")
16484 "This package provides functionality to assert conditions that have to be
16485 met so that errors in data used in analysis pipelines can fail quickly. It is
16486 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16488 (license license:expat)))
16490 (define-public r-parameters
16492 (name "r-parameters")
16497 (uri (cran-uri "parameters" version))
16500 "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
16501 (properties `((upstream-name . "parameters")))
16502 (build-system r-build-system)
16504 `(("r-bayestestr" ,r-bayestestr)
16505 ("r-insight" ,r-insight)))
16507 `(("r-knitr" ,r-knitr)))
16508 (home-page "https://cran.r-project.org/web/packages/parameters")
16509 (synopsis "Processing of model parameters")
16511 "This package provides utilities for processing the parameters of various
16512 statistical models. Beyond computing p values, CIs, and other indices for a
16513 wide variety of models, this package implements features like standardization
16514 or bootstrapping of parameters and models, feature reduction (feature
16515 extraction and variable selection) as well as conversion between indices of
16517 (license license:gpl3)))
16519 (define-public r-rgdal
16526 (uri (cran-uri "rgdal" version))
16528 (base32 "02z7rhpizzmymiqpi90nm15bjdz0411bqlavlk0lhwxb42ilhif6"))))
16529 (properties `((upstream-name . "rgdal")))
16530 (build-system r-build-system)
16538 `(("pkg-config" ,pkg-config)
16539 ("r-knitr" ,r-knitr)))
16540 (home-page "http://rgdal.r-forge.r-project.org")
16541 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16543 "This package provides bindings to the Geospatial Data Abstraction
16544 Library (GDAL) and access to projection/transformation operations from the
16546 (license license:gpl2+)))
16548 (define-public r-insol
16555 (uri (cran-uri "insol" version))
16558 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16559 (properties `((upstream-name . "insol")))
16560 (build-system r-build-system)
16562 `(("r-raster" ,r-raster)))
16564 `(("gfortran" ,gfortran)))
16565 (home-page "https://meteoexploration.com/R/insol/index.html")
16566 (synopsis "Tools for calculating solar radiation")
16568 "This package provides functions to compute insolation on tilted
16569 surfaces, computes atmospheric transmittance and related parameters such as:
16570 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16571 time, vector in the direction of the sun, vector normal to surface, and some
16572 atmospheric physics.")
16573 (license license:gpl2+)))
16575 (define-public r-lifecycle
16577 (name "r-lifecycle")
16582 (uri (cran-uri "lifecycle" version))
16585 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16586 (properties `((upstream-name . "lifecycle")))
16587 (build-system r-build-system)
16589 `(("r-glue" ,r-glue)
16590 ("r-rlang" ,r-rlang)))
16592 `(("r-knitr" ,r-knitr))) ; for vignettes
16593 (home-page "https://github.com/r-lib/lifecycle")
16594 (synopsis "Manage the life cycle of your package functions")
16596 "Manage the life cycle of your exported functions with shared
16597 conventions, documentation badges, and non-invasive deprecation warnings. The
16598 lifecycle package defines four development stages (experimental, maturing,
16599 stable, and questioning) and three deprecation stages (soft-deprecated,
16600 deprecated, and defunct). It makes it easy to insert badges corresponding to
16601 these stages in your documentation. Usage of deprecated functions are
16602 signalled with increasing levels of non-invasive verbosity.")
16603 (license license:gpl3)))
16605 (define-public r-assertable
16607 (name "r-assertable")
16612 (uri (cran-uri "assertable" version))
16615 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16616 (build-system r-build-system)
16618 `(("r-data-table" ,r-data-table)))
16619 (home-page "https://cran.r-project.org/web/packages/assertable/")
16620 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16621 (description "This package provides simple, flexible assertions on
16622 data.frame or data.table objects with verbose output for vetting. While other
16623 assertion packages apply towards more general use-cases, @code{assertable} is
16624 tailored towards tabular data. It includes functions to check variable names
16625 and values, whether the dataset contains all combinations of a given set of
16626 unique identifiers, and whether it is a certain length. In addition,
16627 @code{assertable} includes utility functions to check the existence of target
16628 files and to efficiently import multiple tabular data files into one
16630 (license license:gpl3)))
16632 (define-public r-quadprog
16634 (name "r-quadprog")
16639 (uri (cran-uri "quadprog" version))
16641 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16642 (build-system r-build-system)
16644 `(("gfortran" ,gfortran)))
16645 (home-page "https://cran.r-project.org/web/packages/quadprog")
16646 (synopsis "Functions to solve quadratic programming problems")
16648 "This package contains routines and documentation for solving quadratic
16649 programming problems.")
16650 (license license:gpl3+)))
16652 (define-public r-desolve
16659 (uri (cran-uri "deSolve" version))
16661 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16662 (properties `((upstream-name . "deSolve")))
16663 (build-system r-build-system)
16665 `(("gfortran" ,gfortran)))
16666 (home-page "https://desolve.r-forge.r-project.org/")
16667 (synopsis "Solvers for initial value problems of differential equations")
16668 (description "This package provides functions that solve initial value
16669 problems of a system of first-order @dfn{ordinary differential
16670 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16671 @dfn{differential algebraic equations} (DAE), and of delay differential
16672 equations. The functions provide an interface to the FORTRAN functions
16673 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16674 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16675 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16676 time steps. The package contains routines designed for solving ODEs resulting
16677 from 1-D, 2-D and 3-D partial differential equations that have been converted
16678 to ODEs by numerical differencing.")
16679 (license license:gpl2+)))
16681 (define-public r-pracma
16687 (uri (cran-uri "pracma" version))
16689 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16690 (build-system r-build-system)
16691 (home-page "https://cran.r-project.org/web/packages/pracma/")
16692 (synopsis "Practical numerical math functions")
16693 (description "This package provides functions for numerical analysis and
16694 linear algebra, numerical optimization, differential equations, plus some
16695 special functions. It uses Matlab function names where appropriate to simplify
16697 (license license:gpl3+)))
16699 (define-public r-subplex
16706 (uri (cran-uri "subplex" version))
16709 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16710 (build-system r-build-system)
16712 `(("gfortran" ,gfortran)))
16713 (home-page "https://cran.r-project.org/web/packages/subplex")
16714 (synopsis "Unconstrained optimization using the subplex algorithm")
16716 "This package implements the Subplex optimization algorithm.
16717 It solves unconstrained optimization problems using a simplex method on
16718 subspaces. The method is well suited for optimizing objective functions that
16719 are noisy or are discontinuous at the solution.")
16720 (license license:gpl3+)))
16722 (define-public r-txtplot
16729 (uri (cran-uri "txtplot" version))
16732 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16733 (build-system r-build-system)
16734 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16735 (synopsis "Text-based plotting")
16736 (description "This package provides functions to produce rudimentary ASCII
16737 graphics directly in the terminal window. This package provides a basic
16738 plotting function (and equivalents of curve, density, acf and barplot) as well
16739 as a boxplot function.")
16740 (license license:lgpl3+)))
16742 (define-public r-bio3d
16749 (uri (cran-uri "bio3d" version))
16752 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16753 (properties `((upstream-name . "bio3d")))
16754 (build-system r-build-system)
16755 (inputs `(("zlib" ,zlib)))
16756 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16757 (home-page "http://thegrantlab.org/bio3d/")
16758 (synopsis "Biological structure analysis")
16760 "This package provides utilities to process, organize and explore protein
16761 structure, sequence and dynamics data. Features include the ability to read
16762 and write structure, sequence and dynamic trajectory data, perform sequence
16763 and structure database searches, data summaries, atom selection, alignment,
16764 superposition, rigid core identification, clustering, torsion analysis,
16765 distance matrix analysis, structure and sequence conservation analysis, normal
16766 mode analysis, principal component analysis of heterogeneous structure data,
16767 and correlation network analysis from normal mode and molecular dynamics data.
16768 In addition, various utility functions are provided to enable the statistical
16769 and graphical power of the R environment to work with biological sequence and
16771 (license license:gpl2+)))
16773 (define-public r-bios2cor
16775 (name "r-bios2cor")
16780 (uri (cran-uri "Bios2cor" version))
16783 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16784 (properties `((upstream-name . "Bios2cor")))
16785 (build-system r-build-system)
16787 `(("r-bigmemory" ,r-bigmemory)
16788 ("r-bio3d" ,r-bio3d)
16789 ("r-circular" ,r-circular)
16790 ("r-igraph" ,r-igraph)))
16791 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16792 (synopsis "From biological sequences and simulations to correlation analysis")
16794 "This package provides utilities for computation and analysis of
16795 correlation/covariation in multiple sequence alignments and in side chain
16796 motions during molecular dynamics simulations. Features include the
16797 computation of correlation/covariation scores using a variety of scoring
16798 functions between either sequence positions in alignments or side chain
16799 dihedral angles in molecular dynamics simulations and utilities to analyze the
16800 correlation/covariation matrix through a variety of tools including network
16801 representation and principal components analysis. In addition, several
16802 utility functions are based on the R graphical environment to provide friendly
16803 tools for help in data interpretation.")
16804 (license license:gpl2+)))
16806 ;; This package includes minified JavaScript files. When upgrading please
16807 ;; check that there are no new minified JavaScript files.
16808 (define-public r-networkd3
16810 (name "r-networkd3")
16815 (uri (cran-uri "networkD3" version))
16818 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16821 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16823 (properties `((upstream-name . "networkD3")))
16824 (build-system r-build-system)
16826 `(#:modules ((guix build utils)
16827 (guix build r-build-system)
16831 (modify-phases %standard-phases
16832 (add-after 'unpack 'process-javascript
16833 (lambda* (#:key inputs #:allow-other-keys)
16834 (with-directory-excursion "inst/htmlwidgets/lib/"
16838 `((,(assoc-ref inputs "d3.v4.js")
16839 "d3-4.5.0/d3.min.js"))))
16840 (lambda (sources targets)
16841 (for-each (lambda (source target)
16842 (format #t "Processing ~a --> ~a~%"
16844 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16845 (call-with-output-file target
16847 (dump-port minified port)))))
16848 sources targets))))
16851 `(("uglify-js" ,uglify-js)
16852 ;; NOTE: Make sure that this version of d3 is still valid when
16853 ;; upgrading the package.
16857 (uri "https://d3js.org/d3.v4.js")
16860 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16862 `(("r-htmlwidgets" ,r-htmlwidgets)
16863 ("r-igraph" ,r-igraph)
16864 ("r-magrittr" ,r-magrittr)))
16865 (home-page "https://cran.r-project.org/package=networkD3")
16866 (synopsis "D3 JavaScript network graphs from R")
16868 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16870 (license license:gpl3+)))
16872 (define-public r-aasea
16879 (uri (cran-uri "aaSEA" version))
16882 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16883 (properties `((upstream-name . "aaSEA")))
16884 (build-system r-build-system)
16886 `(("r-bios2cor" ,r-bios2cor)
16888 ("r-hmisc" ,r-hmisc)
16889 ("r-magrittr" ,r-magrittr)
16890 ("r-networkd3" ,r-networkd3)
16891 ("r-plotly" ,r-plotly)
16892 ("r-seqinr" ,r-seqinr)
16893 ("r-shiny" ,r-shiny)
16894 ("r-shinydashboard" ,r-shinydashboard)))
16895 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16896 (synopsis "Amino acid substitution effect analyzer")
16898 "Given a protein multiple sequence alignment, it is a daunting task to
16899 assess the effects of substitutions along sequence length. The aaSEA package
16900 is intended to help researchers to rapidly analyze property changes caused by
16901 single, multiple and correlated amino acid substitutions in proteins.")
16902 (license license:gpl3)))
16904 (define-public r-abacus
16911 (uri (cran-uri "ABACUS" version))
16914 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16915 (properties `((upstream-name . "ABACUS")))
16916 (build-system r-build-system)
16918 `(("r-ggplot2" ,r-ggplot2)
16919 ("r-shiny" ,r-shiny)))
16920 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16921 (synopsis "Apps-based activities for communicating and understanding statistics")
16923 "This package provides a set of Shiny apps for effective communication
16924 and understanding in statistics. The current version includes properties of
16925 normal distribution, properties of sampling distribution, one-sample z and t
16926 tests, two samples independent (unpaired) t test and analysis of variance.")
16927 (license license:gpl3)))
16929 (define-public r-abc-rap
16936 (uri (cran-uri "ABC.RAP" version))
16939 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16940 (properties `((upstream-name . "ABC.RAP")))
16941 (build-system r-build-system)
16942 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16943 (synopsis "Array-based CpG region analysis pipeline")
16945 "This package aims to identify candidate genes that are differentially
16946 methylated between cases and controls. It applies Student's t-test and delta
16947 beta analysis to identify candidate genes containing multiple CpG sites.")
16948 (license license:gpl3)))
16950 (define-public r-abcadm
16957 (uri (cran-uri "abcADM" version))
16960 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16961 (properties `((upstream-name . "abcADM")))
16962 (build-system r-build-system)
16965 ("r-rcpp" ,r-rcpp)))
16966 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16967 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16969 "This package provides tools to estimate parameters of accumulated
16970 damage (load duration) models based on failure time data under a Bayesian
16971 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16972 long-term reliability under stochastic load profiles.")
16973 (license license:gpl3)))
16975 (define-public r-rglpk
16982 (uri (cran-uri "Rglpk" version))
16985 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16986 (properties `((upstream-name . "Rglpk")))
16987 (build-system r-build-system)
16989 `(("r-slam" ,r-slam)))
16992 (home-page "https://r-forge.r-project.org/projects/rglp/")
16993 (synopsis "R interface to the GNU Linear Programming Kit")
16995 "This package provides an R interface to the GNU Linear Programming Kit,
16996 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16997 integer linear programming} (MILP) and other related problems.")
16999 (license (list license:gpl2 license:gpl3))))
17001 (define-public r-abcdefba
17003 (name "r-abcdefba")
17008 (uri (cran-uri "abcdeFBA" version))
17011 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17012 (properties `((upstream-name . "abcdeFBA")))
17013 (build-system r-build-system)
17015 `(("r-corrplot" ,r-corrplot)
17016 ("r-lattice" ,r-lattice)
17018 ("r-rglpk" ,r-rglpk)))
17019 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17020 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17022 "This package provides functions for Constraint Based Simulation using
17023 Flux Balance Analysis and informative analysis of the data generated during
17025 (license license:gpl2)))
17027 (define-public r-abcrlda
17034 (uri (cran-uri "abcrlda" version))
17037 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17038 (properties `((upstream-name . "abcrlda")))
17039 (build-system r-build-system)
17040 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17041 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17043 "This package offers methods to perform @dfn{asymptotically
17044 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17045 cost-sensitive binary classification. The bias-correction is an estimate of
17046 the bias term added to regularized discriminant analysis that minimizes the
17048 (license license:gpl3)))
17050 (define-public r-abemus
17057 (uri (cran-uri "abemus" version))
17060 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17061 (properties `((upstream-name . "abemus")))
17062 (build-system r-build-system)
17064 `(("r-data-table" ,r-data-table)))
17065 (home-page "https://cran.r-project.org/web/packages/abemus/")
17066 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17068 "This package provides an implementation of @dfn{Adaptive Base Error
17069 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17070 platform-specific genetic knowledge and empirical signal to readily detect and
17071 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17072 cell free DNA} (cfDNA).")
17073 (license license:gpl3)))
17075 ;; This package includes minified JavaScript files. When upgrading please
17076 ;; check that there are no new minified JavaScript files.
17077 (define-public r-rintrojs
17079 (name "r-rintrojs")
17084 (uri (cran-uri "rintrojs" version))
17087 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17088 (properties `((upstream-name . "rintrojs")))
17089 (build-system r-build-system)
17091 `(#:modules ((guix build utils)
17092 (guix build r-build-system)
17096 (modify-phases %standard-phases
17097 (add-after 'unpack 'process-javascript
17098 (lambda* (#:key inputs #:allow-other-keys)
17099 (with-directory-excursion "inst/javascript/introjs/"
17103 `((,(assoc-ref inputs "intro.js")
17105 (lambda (sources targets)
17106 (for-each (lambda (source target)
17107 (format #t "Processing ~a --> ~a~%"
17109 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17110 (call-with-output-file target
17112 (dump-port minified port)))))
17113 sources targets))))
17116 `(("uglify-js" ,uglify-js)
17120 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17123 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17125 `(("r-jsonlite" ,r-jsonlite)
17126 ("r-shiny" ,r-shiny)))
17127 (home-page "https://github.com/carlganz/rintrojs")
17128 (synopsis "Wrapper for the Intro.js library")
17130 "This package provides a wrapper for the @url{http://www.introjs.com,
17131 Intro.js} library. This package makes it easy to include step-by-step
17132 introductions, and clickable hints in a Shiny application. It supports both
17133 static introductions in the UI, and programmatic introductions from the
17135 (license license:agpl3+)))
17137 (define-public r-sysfonts
17139 (name "r-sysfonts")
17144 (uri (cran-uri "sysfonts" version))
17147 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17148 (properties `((upstream-name . "sysfonts")))
17149 (build-system r-build-system)
17151 `(("freetype" ,freetype)
17155 `(("pkg-config" ,pkg-config)))
17156 (home-page "https://github.com/yixuan/sysfonts")
17157 (synopsis "Loading fonts into R")
17159 "This is a package to simplify loading of system fonts and Google Fonts
17160 into R, in order to support other packages.")
17161 (license license:gpl2)))
17163 (define-public r-showtextdb
17165 (name "r-showtextdb")
17170 (uri (cran-uri "showtextdb" version))
17173 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17174 (properties `((upstream-name . "showtextdb")))
17175 (build-system r-build-system)
17177 `(("r-sysfonts" ,r-sysfonts)))
17178 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17179 (synopsis "Font files for the 'showtext' package")
17181 "This package provides font files that can be used by the @code{showtext}
17183 (license license:asl2.0)))
17185 (define-public r-showtext
17187 (name "r-showtext")
17192 (uri (cran-uri "showtext" version))
17195 "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
17196 (properties `((upstream-name . "showtext")))
17197 (build-system r-build-system)
17199 `(("freetype" ,freetype)
17203 `(("r-showtextdb" ,r-showtextdb)
17204 ("r-sysfonts" ,r-sysfonts)))
17206 `(("pkg-config" ,pkg-config)
17207 ("r-knitr" ,r-knitr)))
17208 (home-page "https://github.com/yixuan/showtext")
17209 (synopsis "Using fonts more easily in R graphs")
17211 "This package aims to make it easy to use various types of
17212 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17213 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17214 will be converted into polygons or raster images, hence after the plot has
17215 been created, it no longer relies on the font files. No external software
17216 such as Ghostscript is needed to use this package.")
17217 (license license:asl2.0)))
17219 (define-public r-emojifont
17221 (name "r-emojifont")
17226 (uri (cran-uri "emojifont" version))
17229 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17230 (properties `((upstream-name . "emojifont")))
17231 (build-system r-build-system)
17233 `(("r-ggplot2" ,r-ggplot2)
17234 ("r-proto" ,r-proto)
17235 ("r-showtext" ,r-showtext)
17236 ("r-sysfonts" ,r-sysfonts)))
17237 (home-page "https://guangchuangyu.github.io/emojifont")
17238 (synopsis "Emoji and Font Awesome in R graphics")
17240 "This package enables the use of emoji and the Font Awesome glyphs in
17241 both base and ggplot2 graphics.")
17242 (license license:artistic2.0)))
17244 (define-public r-abstractr
17246 (name "r-abstractr")
17251 (uri (cran-uri "abstractr" version))
17254 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17255 (properties `((upstream-name . "abstractr")))
17256 (build-system r-build-system)
17258 `(("r-colourpicker" ,r-colourpicker)
17259 ("r-emojifont" ,r-emojifont)
17260 ("r-ggplot2" ,r-ggplot2)
17261 ("r-gridextra" ,r-gridextra)
17262 ("r-rintrojs" ,r-rintrojs)
17263 ("r-shiny" ,r-shiny)
17264 ("r-shinythemes" ,r-shinythemes)))
17265 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17266 (synopsis "R-Shiny application for creating visual abstracts")
17268 "This package provides an R Shiny application to create visual abstracts
17269 for original research. A variety of user defined options and formatting are
17271 (license license:gpl3)))
17273 (define-public r-qgam
17280 (uri (cran-uri "qgam" version))
17283 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17284 (properties `((upstream-name . "qgam")))
17285 (build-system r-build-system)
17287 `(("r-doparallel" ,r-doparallel)
17290 ("r-shiny" ,r-shiny)))
17291 (native-inputs `(("r-knitr" ,r-knitr)))
17292 (home-page "https://cran.r-project.org/web/packages/qgam/")
17293 (synopsis "Smooth additive quantile regression models")
17295 "This package provides smooth additive quantile regression models, fitted
17296 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17297 the smoothing parameters are estimated automatically by marginal loss
17298 minimization, while the regression coefficients are estimated using either
17299 PIRLS or Newton algorithm. The learning rate is determined so that the
17300 Bayesian credible intervals of the estimated effects have approximately the
17301 correct coverage. The main function is @code{qgam()} which is similar to
17302 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17303 regression models.")
17304 (license license:gpl2+)))
17306 (define-public r-abtest
17313 (uri (cran-uri "abtest" version))
17316 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17317 (properties `((upstream-name . "abtest")))
17318 (build-system r-build-system)
17320 `(("r-matrix" ,r-matrix)
17321 ("r-mvtnorm" ,r-mvtnorm)
17322 ("r-plotrix" ,r-plotrix)
17324 ("r-rcolorbrewer" ,r-rcolorbrewer)
17327 ("r-truncnorm" ,r-truncnorm)))
17328 (home-page "https://cran.r-project.org/web/packages/abtest/")
17329 (synopsis "Bayesian A/B testing")
17331 "This package provides functions for Bayesian A/B testing including prior
17332 elicitation options based on Kass and Vaidyanathan (1992)
17333 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17334 (license license:gpl2+)))
17336 (define-public r-accept
17343 (uri (cran-uri "accept" version))
17346 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17347 (properties `((upstream-name . "accept")))
17348 (build-system r-build-system)
17350 `(("r-dplyr" ,r-dplyr)
17351 ("r-extrafont" ,r-extrafont)
17353 ("r-plotly" ,r-plotly)
17354 ("r-stringr" ,r-stringr)
17355 ("r-viridis" ,r-viridis)))
17356 (home-page "https://cran.r-project.org/web/packages/accept/")
17357 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17359 "This package allows clinicians to predict the rate and severity of
17360 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17361 Disease} (COPD) patients, based on the clinical prediction model published in
17362 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17363 (license license:gpl3)))
17365 (define-public r-smpracticals
17367 (name "r-smpracticals")
17372 (uri (cran-uri "SMPracticals" version))
17375 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17376 (properties `((upstream-name . "SMPracticals")))
17377 (build-system r-build-system)
17379 `(("r-ellipse" ,r-ellipse)
17382 ("r-survival" ,r-survival)))
17383 (home-page "http://statwww.epfl.ch/davison/SM/")
17384 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17386 "This package contains the datasets and a few functions for use with the
17387 practicals outlined in Appendix A of the book Statistical Models (Davison,
17388 2003, Cambridge University Press). The practicals themselves can be found at
17389 @url{http://statwww.epfl.ch/davison/SM/}.")
17390 (license license:gpl2+)))
17392 (define-public r-fgui
17399 (uri (cran-uri "fgui" version))
17402 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17403 (properties `((upstream-name . "fgui")))
17404 (build-system r-build-system)
17406 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17407 (synopsis "Create GUI for R functions")
17409 "Rapidly create a GUI for a function you created by automatically
17410 creating widgets for arguments of the function. This package automatically
17411 parses help routines for context-sensitive help to these arguments. The
17412 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17413 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17414 incorporated into the interface for greater customization for the more
17416 ;; Any version of the GPL.
17417 (license (list license:gpl2+ license:gpl3+))))
17419 (define-public r-tcltk2
17426 (uri (cran-uri "tcltk2" version))
17429 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17430 (properties `((upstream-name . "tcltk2")))
17431 (build-system r-build-system)
17435 (home-page "https://www.sciviews.org/SciViews-R")
17436 (synopsis "Tcl/Tk additions")
17438 "This package provides a series of additional Tcl commands and Tk widgets
17439 with style and various functions to supplement the tcltk package")
17440 (license license:lgpl3)))
17442 (define-public r-accrual
17449 (uri (cran-uri "accrual" version))
17452 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17453 (properties `((upstream-name . "accrual")))
17454 (build-system r-build-system)
17456 `(("r-fgui" ,r-fgui)
17457 ("r-smpracticals" ,r-smpracticals)
17458 ("r-tcltk2" ,r-tcltk2)))
17459 (home-page "https://cran.r-project.org/web/packages/accrual/")
17460 (synopsis "Bayesian accrual prediction")
17462 "Subject recruitment for medical research is challenging. Slow patient
17463 accrual leads to delay in research. Accrual monitoring during the process of
17464 recruitment is critical. Researchers need reliable tools to manage the
17465 accrual rate. This package provides an implementation of a Bayesian method
17466 that integrates researcher's experience on previous trials and data from the
17467 current study, providing reliable prediction on accrual rate for clinical
17468 studies. It provides functions for Bayesian accrual prediction which can be
17469 easily used by statisticians and clinical researchers.")
17470 (license license:gpl2)))
17472 (define-public r-accrued
17479 (uri (cran-uri "accrued" version))
17482 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17483 (properties `((upstream-name . "accrued")))
17484 (build-system r-build-system)
17485 (home-page "https://cran.r-project.org/web/packages/accrued/")
17486 (synopsis "Data quality visualization tools for partially accruing data")
17488 "This is a package for visualizing data quality of partially accruing
17490 (license license:gpl3)))
17492 (define-public r-mda
17499 (uri (cran-uri "mda" version))
17502 "01pjrz9xv1rx78ndy0x9dc32ws8brcvwyb500m1f0dqd42375vmx"))))
17503 (properties `((upstream-name . "mda")))
17504 (build-system r-build-system)
17505 (propagated-inputs `(("r-class" ,r-class)))
17506 (native-inputs `(("gfortran" ,gfortran)))
17507 (home-page "https://cran.r-project.org/web/packages/mda/")
17508 (synopsis "Mixture and flexible discriminant analysis")
17510 "This is a package for mixture and flexible discriminant analysis,
17511 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17512 (license license:gpl2)))
17514 (define-public r-elasticnet
17516 (name "r-elasticnet")
17521 (uri (cran-uri "elasticnet" version))
17524 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17525 (properties `((upstream-name . "elasticnet")))
17526 (build-system r-build-system)
17528 `(("r-lars" ,r-lars)))
17529 (home-page "http://users.stat.umn.edu/~zouxx019/")
17530 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17532 "This package provides functions for fitting the entire solution path of
17533 the Elastic-Net and also provides functions for estimating sparse Principal
17534 Components. The Lasso solution paths can be computed by the same function.")
17535 (license license:gpl2+)))
17537 (define-public r-sparselda
17539 (name "r-sparselda")
17544 (uri (cran-uri "sparseLDA" version))
17547 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17548 (properties `((upstream-name . "sparseLDA")))
17549 (build-system r-build-system)
17551 `(("r-elasticnet" ,r-elasticnet)
17554 (home-page "https://www.imm.dtu.dk/~lkhc/")
17555 (synopsis "Sparse discriminant analysis")
17557 "This package performs sparse linear discriminant analysis for Gaussians
17558 and mixture of Gaussian models.")
17559 (license license:gpl2+)))
17561 (define-public r-accsda
17568 (uri (cran-uri "accSDA" version))
17571 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17572 (properties `((upstream-name . "accSDA")))
17573 (build-system r-build-system)
17575 `(("r-ggplot2" ,r-ggplot2)
17576 ("r-ggthemes" ,r-ggthemes)
17577 ("r-gridextra" ,r-gridextra)
17579 ("r-rarpack" ,r-rarpack)
17580 ("r-sparselda" ,r-sparselda)))
17581 (home-page "https://github.com/gumeo/accSDA/wiki")
17582 (synopsis "Accelerated sparse discriminant analysis")
17584 "This package provides an implementation of sparse linear discriminant
17585 analysis, which is a supervised classification method for multiple classes.
17586 Various novel optimization approaches to this problem are implemented
17587 including @dfn{alternating direction method of multipliers} (ADMM),
17588 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17589 Functions for performing cross validation are also supplied along with basic
17590 prediction and plotting functions. @dfn{Sparse zero variance
17591 discriminant} (SZVD) analysis is also included in the package.")
17592 (license license:gpl2+)))
17594 (define-public r-ace2fastq
17596 (name "r-ace2fastq")
17601 (uri (cran-uri "ace2fastq" version))
17604 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17605 (properties `((upstream-name . "ace2fastq")))
17606 (build-system r-build-system)
17608 `(("r-stringr" ,r-stringr)))
17609 (home-page "https://github.com/c5sire/ace2fastq")
17610 (synopsis "ACE file to FASTQ converter")
17612 "The ACE file format is used in genomics to store contigs from sequencing
17613 machines. This tools converts it into FASTQ format. Both formats contain the
17614 sequence characters and their corresponding quality information. Unlike the
17615 FASTQ file, the ACE file stores the quality values numerically. The
17616 conversion algorithm uses the standard Sanger formula. The package
17617 facilitates insertion into pipelines, and content inspection.")
17618 (license license:gpl3)))
17620 (define-public r-rngwell
17627 (uri (cran-uri "rngWELL" version))
17630 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17631 (properties `((upstream-name . "rngWELL")))
17632 (build-system r-build-system)
17633 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17634 (synopsis "Toolbox for WELL random number generators")
17636 "This is a dedicated package to WELL pseudo random generators, which were
17637 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17638 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17639 (license license:bsd-3)))
17641 (define-public r-randtoolbox
17643 (name "r-randtoolbox")
17648 (uri (cran-uri "randtoolbox" version))
17651 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17652 (properties `((upstream-name . "randtoolbox")))
17653 (build-system r-build-system)
17655 `(("r-rngwell" ,r-rngwell)))
17657 `(("gfortran" ,gfortran)))
17658 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17659 (synopsis "Toolbox for pseudo and quasi random number generation")
17661 "This package provides
17664 @item pseudo random generators, such as general linear
17665 congruential generators, multiple recursive generators and generalized
17666 feedback shift register (SF-Mersenne Twister algorithm and WELL
17669 @item quasi random generators, such as the Torus algorithm, the Sobol
17670 sequence, the Halton sequence (including the Van der Corput sequence), and
17672 @item some generator tests: the gap test, the serial test, the poker test.
17675 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17676 (license license:bsd-3)))
17678 (define-public r-lhs
17685 (uri (cran-uri "lhs" version))
17688 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17689 (properties `((upstream-name . "lhs")))
17690 (build-system r-build-system)
17691 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17693 `(("r-knitr" ,r-knitr)))
17694 (home-page "https://github.com/bertcarnell/lhs")
17695 (synopsis "Latin Hypercube Samples")
17697 "This package provides a number of methods for creating and augmenting
17698 Latin Hypercube Samples.")
17699 (license license:gpl3)))
17701 (define-public r-acebayes
17703 (name "r-acebayes")
17708 (uri (cran-uri "acebayes" version))
17711 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17712 (properties `((upstream-name . "acebayes")))
17713 (build-system r-build-system)
17715 `(("r-compare" ,r-compare)
17717 ("r-randtoolbox" ,r-randtoolbox)
17719 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17720 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17721 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17723 "Finding an optimal Bayesian experimental design involves maximizing an
17724 objective function given by the expectation of some appropriately chosen
17725 utility function with respect to the joint distribution of unknown
17726 quantities (including responses). This objective function is usually not
17727 available in closed form and the design space can be continuous and of high
17728 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17729 to maximise an approximation to the expectation of the utility function.")
17730 (license license:gpl2)))
17732 (define-public r-acet
17739 (uri (cran-uri "ACEt" version))
17742 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17743 (properties `((upstream-name . "ACEt")))
17744 (build-system r-build-system)
17749 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17750 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17751 (synopsis "Estimating dynamic heritability and twin model comparison")
17753 "This package supports twin models that are able to estimate the dynamic
17754 behaviour of the variance components in the classical twin models with respect
17755 to age using B-splines and P-splines.")
17756 (license license:gpl2+)))
17758 (define-public r-acfmperiod
17760 (name "r-acfmperiod")
17765 (uri (cran-uri "acfMPeriod" version))
17768 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17769 (properties `((upstream-name . "acfMPeriod")))
17770 (build-system r-build-system)
17772 `(("r-mass" ,r-mass)))
17773 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17774 (synopsis "Estimation of the ACF from the M-periodogram")
17776 "This package support non-robust and robust computations of the sample
17777 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17778 univariate and multivariate processes. The methodology consists in reversing
17779 the diagonalization procedure involving the periodogram or the
17780 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17781 ACOVF or the ACF as discussed in Fuller (1995)
17782 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17783 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17784 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17785 (license license:gpl2+)))
17787 (define-public r-gamlss-data
17789 (name "r-gamlss-data")
17794 (uri (cran-uri "gamlss.data" version))
17797 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17798 (properties `((upstream-name . "gamlss.data")))
17799 (build-system r-build-system)
17800 (home-page "http://www.gamlss.org/")
17801 (synopsis "GAMLSS data")
17803 "This package provides data used as examples to demonstrate GAMLSS
17805 ;; Either version of the license
17806 (license (list license:gpl2 license:gpl3))))
17808 (define-public r-gamlss
17815 (uri (cran-uri "gamlss" version))
17818 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17819 (properties `((upstream-name . "gamlss")))
17820 (build-system r-build-system)
17822 `(("r-gamlss-data" ,r-gamlss-data)
17823 ("r-gamlss-dist" ,r-gamlss-dist)
17826 ("r-survival" ,r-survival)))
17827 (home-page "http://www.gamlss.org/")
17828 (synopsis "Generalized additive models for location scale and shape")
17830 "This package provides functions for fitting the generalized additive
17831 models for location scale and shape introduced by Rigby and
17832 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17833 use a distributional regression approach where all the parameters of the
17834 conditional distribution of the response variable are modelled using
17835 explanatory variables.")
17836 ;; Either version of the license
17837 (license (list license:gpl2 license:gpl3))))
17839 (define-public r-acid
17846 (uri (cran-uri "acid" version))
17849 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17850 (properties `((upstream-name . "acid")))
17851 (build-system r-build-system)
17853 `(("r-gamlss" ,r-gamlss)
17854 ("r-gamlss-dist" ,r-gamlss-dist)
17855 ("r-hmisc" ,r-hmisc)))
17856 (home-page "https://cran.r-project.org/web/packages/acid/")
17857 (synopsis "Analysing conditional income distributions")
17859 "This package provides functions for the analysis of income distributions
17860 for subgroups of the population as defined by a set of variables like age,
17861 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17862 distribution as well as functions for moments, inequality measures, entropy
17863 measures and polarisation measures of income distributions. This package thus
17864 aides the analysis of income inequality by offering tools for the exploratory
17865 analysis of income distributions at the disaggregated level.")
17866 (license license:gpl3)))
17868 (define-public r-acm4r
17875 (uri (cran-uri "acm4r" version))
17878 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17879 (properties `((upstream-name . "acm4r")))
17880 (build-system r-build-system)
17881 (propagated-inputs `(("r-mass" ,r-mass)))
17882 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17883 (synopsis "Align-and-count method comparisons of RFLP data")
17885 "This is a package to compare sequence fragment lengths or molecular
17886 weights from pairs of lanes. The number of matching bands in the
17887 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17888 the align-and-count method.")
17889 ;; Any version of the GPL
17890 (license (list license:gpl2+ license:gpl3+))))
17892 (define-public r-filematrix
17894 (name "r-filematrix")
17899 (uri (cran-uri "filematrix" version))
17902 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17903 (properties `((upstream-name . "filematrix")))
17904 (build-system r-build-system)
17905 ;; These inputs are needed for vignettes
17907 `(("r-knitr" ,r-knitr)
17908 ("r-rmarkdown" ,r-rmarkdown)
17909 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17910 (home-page "https://github.com/andreyshabalin/filematrix")
17911 (synopsis "File-backed matrix class with convenient read and write access")
17913 "This package provides an interface for working with large matrices
17914 stored in files, not in computer memory. It supports multiple non-character
17915 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17916 byte real values). Access to parts of the matrix is done by indexing, exactly
17917 as with usual R matrices. It supports very large matrices; the package has
17918 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17919 columns, ad allows for quick addition of extra columns to a filematrix.")
17920 (license license:lgpl3)))
17922 (define-public r-acmeeqtl
17924 (name "r-acmeeqtl")
17929 (uri (cran-uri "ACMEeqtl" version))
17932 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17933 (properties `((upstream-name . "ACMEeqtl")))
17934 (build-system r-build-system)
17936 `(("r-filematrix" ,r-filematrix)))
17937 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17938 (synopsis "Estimation of interpretable eQTL effect sizes")
17940 "This package provides a non-linear model, termed ACME, that reflects a
17941 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17942 With non-linear least-squares algorithm the maximum likelihood parameters can
17943 be estimated. The ACME model provides interpretable effect size estimates and
17944 p-values with well controlled Type-I error.")
17945 (license license:lgpl3)))
17947 (define-public r-acmer
17954 (uri (cran-uri "acmeR" version))
17957 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17958 (properties `((upstream-name . "acmeR")))
17959 (build-system r-build-system)
17960 (propagated-inputs `(("r-foreign" ,r-foreign)))
17961 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17962 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17964 "This package provides an implementation of the ACME estimator, described
17965 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17966 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17967 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17968 as carcasses age; variable bleed-through at successive searches; and interval
17969 mortality estimates. The package provides, based on search data, functions
17970 for estimating the mortality inflation factor in Frequentist and Bayesian
17972 (license license:expat)))
17974 (define-public r-r-huge
17981 (uri (cran-uri "R.huge" version))
17984 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17985 (properties `((upstream-name . "R.huge")))
17986 (build-system r-build-system)
17988 `(("r-r-methodss3" ,r-r-methodss3)
17990 ("r-r-utils" ,r-r-utils)))
17991 (home-page "https://github.com/HenrikBengtsson/R.huge")
17992 (synopsis "Methods for accessing huge amounts of data")
17994 "This is a deprecated package for accessing huge amounts of data.
17995 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17996 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17997 the @code{aroma.affymetrix} package.")
17998 (license license:lgpl2.1+)))
18000 (define-public r-r-filesets
18002 (name "r-r-filesets")
18007 (uri (cran-uri "R.filesets" version))
18010 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18011 (properties `((upstream-name . "R.filesets")))
18012 (build-system r-build-system)
18014 `(("r-digest" ,r-digest)
18015 ("r-r-cache" ,r-r-cache)
18016 ("r-r-methodss3" ,r-r-methodss3)
18018 ("r-r-utils" ,r-r-utils)))
18019 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18020 (synopsis "Easy handling of and access to files")
18022 "This package provides classes and methods to locate, setup, subset,
18023 navigate and iterate file sets, i.e. sets of files located in one or more
18024 directories on the file system. The API is designed such that these classes
18025 can be extended via inheritance to provide a richer API for special file
18026 formats. Moreover, a specific name format is defined such that filenames and
18027 directories can be considered to have full names which consists of a name
18028 followed by comma-separated tags. This adds additional flexibility to
18029 identify file sets and individual files.")
18030 (license license:lgpl2.1+)))
18032 (define-public r-r-devices
18034 (name "r-r-devices")
18039 (uri (cran-uri "R.devices" version))
18042 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18043 (properties `((upstream-name . "R.devices")))
18044 (build-system r-build-system)
18046 `(("r-base64enc" ,r-base64enc)
18047 ("r-r-methodss3" ,r-r-methodss3)
18049 ("r-r-utils" ,r-r-utils)))
18050 (home-page "https://github.com/HenrikBengtsson/R.devices")
18051 (synopsis "Unified handling of graphics devices")
18053 "This package provides functions for creating plots and image files in a
18054 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18055 Default device options as well as scales and aspect ratios are controlled in a
18056 uniform way across all device types. Switching output format requires minimal
18057 changes in code. This package is ideal for large-scale batch processing,
18058 because it will never leave open graphics devices or incomplete image files
18059 behind, even on errors or user interrupts.")
18060 (license license:lgpl2.1+)))
18062 (define-public r-acnr
18069 (uri (cran-uri "acnr" version))
18072 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18073 (properties `((upstream-name . "acnr")))
18074 (build-system r-build-system)
18075 (home-page "https://github.com/mpierrejean/acnr")
18076 (synopsis "Annotated copy-number regions")
18078 "This package provides SNP array data from different types of copy-number
18079 regions. These regions were identified manually by the authors of the package
18080 and may be used to generate realistic data sets with known truth.")
18081 (license license:lgpl2.1+)))
18083 (define-public r-acopula
18090 (uri (cran-uri "acopula" version))
18093 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18094 (properties `((upstream-name . "acopula")))
18095 (build-system r-build-system)
18096 (home-page "https://cran.r-project.org/web/packages/acopula/")
18097 (synopsis "Modelling dependence with multivariate Archimax copulas")
18099 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18100 package provides definitions of several parametric families of generator and
18101 dependence function, computes CDF and PDF, estimates parameters, tests for
18102 goodness of fit, generates random sample and checks copula properties for
18103 custom constructs. In the 2-dimensional case explicit formulas for density
18104 are used, contrary to higher dimensions when all derivatives are linearly
18105 approximated. Several non-archimax families (normal, FGM, Plackett) are
18106 provided as well.")
18107 (license license:gpl2)))
18109 (define-public r-tuner
18116 (uri (cran-uri "tuneR" version))
18119 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18120 (properties `((upstream-name . "tuneR")))
18121 (build-system r-build-system)
18122 (propagated-inputs `(("r-signal" ,r-signal)))
18123 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18124 (synopsis "Analysis of music and speech")
18126 "This is a package for the analysis of music and speech. Analyze music
18127 and speech, extract features like MFCCs, handle wave files and their
18128 representation in various ways, read MP3, read MIDI, perform steps of a
18129 transcription, ...")
18130 ;; Either of these versions.
18131 (license (list license:gpl2 license:gpl3))))
18133 (define-public r-seewave
18140 (uri (cran-uri "seewave" version))
18143 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18144 (properties `((upstream-name . "seewave")))
18145 (build-system r-build-system)
18147 `(("libsndfile" ,libsndfile)))
18149 `(("r-tuner" ,r-tuner)))
18150 (home-page "http://rug.mnhn.fr/seewave")
18151 (synopsis "Sound analysis and synthesis")
18153 "This package provides functions for analysing, manipulating, displaying,
18154 editing and synthesizing time waves (particularly sound). This package
18155 processes time analysis (oscillograms and envelopes), spectral content,
18156 resonance quality factor, entropy, cross correlation and autocorrelation,
18157 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18158 and 3D spectrograms and many other analyses.")
18159 (license license:gpl2+)))
18161 (define-public r-acousticndlcoder
18163 (name "r-acousticndlcoder")
18168 (uri (cran-uri "AcousticNDLCodeR" version))
18171 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18173 `((upstream-name . "AcousticNDLCodeR")))
18174 (build-system r-build-system)
18176 `(("r-seewave" ,r-seewave)
18177 ("r-tuner" ,r-tuner)
18179 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18180 (synopsis "Coding sound files for use with NDL")
18182 "Make acoustic cues to use with the R package @code{ndl}.
18183 The package implements functions used in the PLoS ONE paper \"Words from
18184 spontaneous conversational speech can be recognized with human-like accuracy
18185 by an error-driven learning algorithm that discriminates between meanings
18186 straight from smart acoustic features, bypassing the phoneme as recognition
18187 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18188 (license license:gpl2+)))
18190 (define-public r-acp
18197 (uri (cran-uri "acp" version))
18200 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18201 (properties `((upstream-name . "acp")))
18202 (build-system r-build-system)
18204 `(("r-quantmod" ,r-quantmod)
18205 ("r-tseries" ,r-tseries)))
18206 (home-page "https://cran.r-project.org/web/packages/acp/")
18207 (synopsis "Autoregressive conditional Poisson")
18209 "This package supports the analysis of count data exhibiting
18210 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18211 model (ACP(p,q)) proposed by Heinen (2003).")
18212 (license license:gpl2)))
18214 (define-public r-ada
18221 (uri (cran-uri "ada" version))
18224 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18225 (properties `((upstream-name . "ada")))
18226 (build-system r-build-system)
18227 (propagated-inputs `(("r-rpart" ,r-rpart)))
18228 (home-page "https://cran.r-project.org/web/packages/ada/")
18229 (synopsis "Stochastic boosting")
18231 "This package provides a straightforward, well-documented, and broad
18232 boosting routine for classification, ideally suited for small to
18233 moderate-sized data sets. It performs discrete, real, and gentle boost under
18234 both exponential and logistic loss on a given data set.")
18235 ;; Any version of the GPL.
18236 (license (list license:gpl2+ license:gpl3+))))
18238 (define-public r-genalg
18245 (uri (cran-uri "genalg" version))
18248 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18249 (properties `((upstream-name . "genalg")))
18250 (build-system r-build-system)
18251 (home-page "https://github.com/egonw/genalg")
18252 (synopsis "R based genetic algorithm")
18254 "This package provides an R based genetic algorithm for binary and
18255 floating point chromosomes.")
18256 (license license:gpl2)))
18258 (define-public r-kernelfactory
18260 (name "r-kernelfactory")
18265 (uri (cran-uri "kernelFactory" version))
18268 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18269 (properties `((upstream-name . "kernelFactory")))
18270 (build-system r-build-system)
18273 ("r-genalg" ,r-genalg)
18274 ("r-kernlab" ,r-kernlab)
18275 ("r-randomforest" ,r-randomforest)))
18276 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18277 (synopsis "Ensemble of kernel machines")
18279 "Kernel factory is an ensemble method where each base classifier (random
18280 forest) is fit on the kernel matrix of a subset of the training data.")
18281 (license license:gpl2+)))
18283 (define-public r-dummies
18290 (uri (cran-uri "dummies" version))
18293 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18294 (properties `((upstream-name . "dummies")))
18295 (build-system r-build-system)
18296 (home-page "https://decisionpatterns.com")
18297 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18299 "This package lets you expand factors, characters and other eligible
18300 classes into dummy/indicator variables.")
18301 (license license:gpl2+)))
18303 (define-public r-acrm
18310 (uri (cran-uri "aCRM" version))
18313 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18314 (properties `((upstream-name . "aCRM")))
18315 (build-system r-build-system)
18318 ("r-dummies" ,r-dummies)
18319 ("r-kernelfactory" ,r-kernelfactory)
18320 ("r-randomforest" ,r-randomforest)))
18321 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18322 (synopsis "Convenience functions for analytical customer relationship management")
18324 "This package provides convenience functions for data preparation and
18325 modeling often used in @dfn{analytical customer relationship
18326 management} (aCRM).")
18327 (license license:gpl2+)))
18329 (define-public r-treeclust
18331 (name "r-treeclust")
18336 (uri (cran-uri "treeClust" version))
18339 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18340 (properties `((upstream-name . "treeClust")))
18341 (build-system r-build-system)
18343 `(("r-cluster" ,r-cluster)
18344 ("r-rpart" ,r-rpart)))
18345 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18346 (synopsis "Cluster distances through trees")
18348 "This package provides tools to create a measure of inter-point
18349 dissimilarity useful for clustering mixed data, and, optionally, perform the
18351 (license license:gpl2+)))
18353 (define-public r-acrosstic
18355 (name "r-acrosstic")
18360 (uri (cran-uri "AcrossTic" version))
18363 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18364 (properties `((upstream-name . "AcrossTic")))
18365 (build-system r-build-system)
18367 `(("r-lpsolve" ,r-lpsolve)
18368 ("r-treeclust" ,r-treeclust)))
18369 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18370 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18372 "This is a package for constructing minimum-cost regular spanning
18373 subgraph as part of a non-parametric two-sample test for equality of
18375 (license license:gpl2+)))
18377 (define-public r-acrt
18384 (uri (cran-uri "acrt" version))
18387 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18388 (properties `((upstream-name . "acrt")))
18389 (build-system r-build-system)
18391 `(("r-rcpp" ,r-rcpp)
18392 ("r-rcppeigen" ,r-rcppeigen)
18393 ("r-sandwich" ,r-sandwich)))
18394 (home-page "https://cran.r-project.org/web/packages/acrt/")
18395 (synopsis "Autocorrelation robust testing")
18397 "This package provides functions for testing affine hypotheses on the
18398 regression coefficient vector in regression models with autocorrelated
18400 (license license:gpl2)))
18402 (define-public r-acs
18409 (uri (cran-uri "acs" version))
18412 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18413 (properties `((upstream-name . "acs")))
18414 (build-system r-build-system)
18416 `(("r-httr" ,r-httr)
18419 ("r-stringr" ,r-stringr)
18421 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18422 (synopsis "Work with data from the US Census")
18424 "This package provides a general toolkit for downloading, managing,
18425 analyzing, and presenting data from the
18426 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18427 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18428 American Community Survey (ACS). Confidence intervals provided with ACS data
18429 are converted to standard errors to be bundled with estimates in complex
18430 @code{acs} objects. The package provides new methods to conduct standard
18431 operations on @code{acs} objects and present/plot data in statistically
18432 appropriate ways.")
18433 (license license:gpl3)))
18435 (define-public r-acss-data
18437 (name "r-acss-data")
18442 (uri (cran-uri "acss.data" version))
18445 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18446 (properties `((upstream-name . "acss.data")))
18447 (build-system r-build-system)
18448 (home-page "http://complexitycalculator.com/methodology.html")
18449 (synopsis "Data for algorithmic complexity of short strings")
18451 "This is a data only package providing the algorithmic complexity of
18452 short strings, computed using the coding theorem method. For a given set of
18453 symbols in a string, all possible or a large number of random samples of
18454 Turing machines with a given number of states (e.g., 5) and number of symbols
18455 corresponding to the number of symbols in the strings were simulated until
18456 they reached a halting state or failed to end. This package contains data on
18457 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18458 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18459 distribution of the halting states.")
18460 (license license:gpl2+)))
18462 (define-public r-acss
18469 (uri (cran-uri "acss" version))
18472 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18473 (properties `((upstream-name . "acss")))
18474 (build-system r-build-system)
18476 `(("r-acss-data" ,r-acss-data)
18478 (home-page "http://complexitycalculator.com/methodology.html")
18479 (synopsis "Algorithmic complexity for short strings")
18481 "The main purpose of this package is to provide the algorithmic
18482 complexity for short strings, an approximation of the Kolmogorov Complexity of
18483 a short string using the coding theorem method. While the database containing
18484 the complexity is provided in the data only package @code{acss.data}, this
18485 package provides functions accessing the data such as @code{prob_random}
18486 returning the posterior probability that a given string was produced by a
18487 random process. In addition, two traditional (but problematic) measures of
18488 complexity are also provided: entropy and change complexity.")
18489 (license license:gpl2+)))
18491 (define-public r-acswr
18498 (uri (cran-uri "ACSWR" version))
18501 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18502 (properties `((upstream-name . "ACSWR")))
18503 (build-system r-build-system)
18505 `(("r-mass" ,r-mass)))
18506 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18507 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18509 "This is a companion package for the book \"A Course in Statistics with
18510 R\" (ISBN 978-1-119-15272-9.)")
18511 (license license:gpl2)))
18513 (define-public r-alabama
18516 (version "2015.3-1")
18520 (uri (cran-uri "alabama" version))
18523 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18524 (properties `((upstream-name . "alabama")))
18525 (build-system r-build-system)
18526 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18527 (home-page "https://cran.r-project.org/web/packages/alabama/")
18528 (synopsis "Constrained nonlinear optimization")
18530 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18531 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18532 constraints. Linear or nonlinear equality and inequality constraints are
18534 (license license:gpl2+)))
18536 (define-public r-gdina
18543 (uri (cran-uri "GDINA" version))
18546 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18547 (properties `((upstream-name . "GDINA")))
18548 (build-system r-build-system)
18550 `(("r-alabama" ,r-alabama)
18551 ("r-ggplot2" ,r-ggplot2)
18553 ("r-nloptr" ,r-nloptr)
18554 ("r-numderiv" ,r-numderiv)
18556 ("r-rcpparmadillo" ,r-rcpparmadillo)
18557 ("r-rsolnp" ,r-rsolnp)
18558 ("r-shiny" ,r-shiny)
18559 ("r-shinydashboard" ,r-shinydashboard)))
18561 `(("r-knitr" ,r-knitr)))
18562 (home-page "https://github.com/Wenchao-Ma/GDINA")
18563 (synopsis "Generalized DINA model framework")
18565 "This package provides a set of psychometric tools for cognitive
18566 diagnosis modeling based on the generalized deterministic inputs, noisy and
18567 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18568 and its extensions, including the sequential G-DINA model by Ma and de la
18569 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18570 polytomous G-DINA model by Chen and de la Torre
18571 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18572 distribution can be independent, saturated, higher-order, loglinear smoothed
18573 or structured. Q-matrix validation, item and model fit statistics, model
18574 comparison at test and item level and differential item functioning can also
18575 be conducted. A graphical user interface is also provided.")
18576 (license license:gpl3)))
18578 (define-public r-actcd
18585 (uri (cran-uri "ACTCD" version))
18588 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18589 (properties `((upstream-name . "ACTCD")))
18590 (build-system r-build-system)
18592 `(("r-gdina" ,r-gdina)
18593 ("r-r-methodss3" ,r-r-methodss3)))
18595 `(("gfortran" ,gfortran)))
18596 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18597 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18599 "This is a package supporting cluster analysis for cognitive diagnosis
18600 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18601 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18602 sum-scores, cluster analysis techniques can be used to classify examinees into
18603 latent classes based on their attribute patterns. In addition to the
18604 algorithms used to classify data, three labeling approaches are proposed to
18605 label clusters so that examinees' attribute profiles can be obtained.")
18606 (license license:gpl2+)))
18608 (define-public r-ineq
18615 (uri (cran-uri "ineq" version))
18618 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18619 (properties `((upstream-name . "ineq")))
18620 (build-system r-build-system)
18621 (home-page "https://cran.r-project.org/web/packages/ineq/")
18622 (synopsis "Measuring inequality, concentration, and poverty")
18624 "This package provides tools for measuring inequality, concentration, and
18625 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18626 ;; Either of these two versions.
18627 (license (list license:gpl2 license:gpl3))))
18629 (define-public r-actfrag
18636 (uri (cran-uri "ActFrag" version))
18639 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18640 (properties `((upstream-name . "ActFrag")))
18641 (build-system r-build-system)
18643 `(("r-accelerometry" ,r-accelerometry)
18644 ("r-dplyr" ,r-dplyr)
18646 ("r-survival" ,r-survival)
18647 ("r-tidyr" ,r-tidyr)))
18648 (home-page "https://github.com/junruidi/ActFrag")
18649 (synopsis "Activity fragmentation metrics extraction")
18651 "This package provides functions to extract commonly used fragmentation
18652 metrics to quantify time accumulation strategies based on minute level
18653 actigraphy-measured activity counts data.")
18654 (license license:gpl3)))
18656 (define-public r-fda
18663 (uri (cran-uri "fda" version))
18666 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18667 (properties `((upstream-name . "fda")))
18668 (build-system r-build-system)
18670 `(("r-matrix" ,r-matrix)))
18671 (home-page "https://www.functionaldata.org")
18672 (synopsis "Functional data analysis")
18674 "These functions were developed to support functional data analysis as
18675 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18676 Analysis. The package includes data sets and script files working many
18678 (license license:gpl2+)))
18680 (define-public r-actigraphy
18682 (name "r-actigraphy")
18687 (uri (cran-uri "Actigraphy" version))
18690 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18691 (properties `((upstream-name . "Actigraphy")))
18692 (build-system r-build-system)
18694 `(("r-fda" ,r-fda)))
18695 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18696 (synopsis "Actigraphy data analysis")
18698 "This package provides tools for functional linear modeling and analysis
18699 of actigraphy data.")
18700 (license license:asl2.0)))
18702 (define-public r-activedriver
18704 (name "r-activedriver")
18709 (uri (cran-uri "ActiveDriver" version))
18712 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18713 (properties `((upstream-name . "ActiveDriver")))
18714 (build-system r-build-system)
18716 `(("r-mass" ,r-mass)))
18717 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18718 (synopsis "Tools for finding cancer driver proteins")
18720 "This package provides a mutation analysis tool that discovers cancer
18721 driver genes with frequent mutations in protein signalling sites such as
18722 post-translational modifications (phosphorylation, ubiquitination, etc). The
18723 Poisson generalized linear regression model identifies genes where cancer
18724 mutations in signalling sites are more frequent than expected from the
18725 sequence of the entire gene. Integration of mutations with signalling
18726 information helps find new driver genes and propose candidate mechanisms to
18728 (license license:gpl2+)))
18730 (define-public r-activitycounts
18732 (name "r-activitycounts")
18737 (uri (cran-uri "activityCounts" version))
18740 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18742 `((upstream-name . "activityCounts")))
18743 (build-system r-build-system)
18745 `(("r-lubridate" ,r-lubridate)
18746 ("r-magrittr" ,r-magrittr)
18747 ("r-seewave" ,r-seewave)
18748 ("r-signal" ,r-signal)
18749 ("r-tibble" ,r-tibble)))
18750 (home-page "https://github.com/walkabillylab/activityCounts")
18751 (synopsis "Generate ActiLife counts")
18753 "ActiLife generates activity counts from data collected by Actigraph
18754 accelerometers. Actigraph is one of the most common research-grade
18755 accelerometers. There is considerable research validating and developing
18756 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18757 counts are proprietary and difficult to implement if researchers use different
18758 accelerometer brands. The code creates ActiLife counts from raw acceleration
18759 data for different accelerometer brands.")
18760 (license license:gpl3)))
18762 (define-public r-activityindex
18764 (name "r-activityindex")
18769 (uri (cran-uri "ActivityIndex" version))
18772 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18773 (properties `((upstream-name . "ActivityIndex")))
18774 (build-system r-build-system)
18776 `(("r-data-table" ,r-data-table)
18777 ("r-matrixstats" ,r-matrixstats)
18778 ("r-r-utils" ,r-r-utils)))
18779 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18780 (synopsis "Activity Index calculation using raw accelerometry data")
18782 "This is a package to read raw accelerometry from GT3X+ accelerometry
18783 data and plain table data to calculate the Activity Index from Bai et
18784 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18785 (license license:gpl3)))
18787 (define-public r-activpal
18789 (name "r-activpal")
18794 (uri (cran-uri "activPAL" version))
18797 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18798 (properties `((upstream-name . "activPAL")))
18799 (build-system r-build-system)
18801 `(("r-devtools" ,r-devtools)
18802 ("r-dplyr" ,r-dplyr)
18803 ("r-ggplot2" ,r-ggplot2)
18804 ("r-lubridate" ,r-lubridate)
18805 ("r-magrittr" ,r-magrittr)
18806 ("r-tidyr" ,r-tidyr)))
18807 (home-page "https://cran.r-project.org/web/packages/activPAL")
18808 (synopsis "Processing and chart generation from activPAL events files")
18810 "This package contains functions to generate pre-defined summary
18811 statistics from activPAL events files. The package also contains functions to
18812 produce informative graphics that visualize physical activity behaviour and
18813 trends. This includes generating graphs that align physical activity
18814 behaviour with additional time based observations described by other data
18815 sets, such as sleep diaries and continuous glucose monitoring data.")
18816 (license license:gpl3)))
18818 (define-public r-activpalprocessing
18820 (name "r-activpalprocessing")
18825 (uri (cran-uri "activpalProcessing" version))
18828 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18830 `((upstream-name . "activpalProcessing")))
18831 (build-system r-build-system)
18833 `(("r-chron" ,r-chron)))
18834 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18835 (synopsis "Process activPAL events files")
18837 "This package performs estimation of physical activity and sedentary
18838 behavior variables from activPAL events files.")
18839 ;; Either version of the GPL.
18840 (license (list license:gpl2 license:gpl3))))
18842 (define-public r-actogrammr
18844 (name "r-actogrammr")
18849 (uri (cran-uri "actogrammr" version))
18852 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18853 (properties `((upstream-name . "actogrammr")))
18854 (build-system r-build-system)
18856 `(("r-dplyr" ,r-dplyr)
18857 ("r-ggplot2" ,r-ggplot2)
18858 ("r-lubridate" ,r-lubridate)
18859 ("r-readr" ,r-readr)
18860 ("r-tidyr" ,r-tidyr)))
18861 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18862 (synopsis "Read in activity data and plot actograms")
18864 "Read in activity measurements from standard file formats used by
18865 circadian rhythm researchers, currently only ClockLab format, and process and
18866 plot the data. The central type of plot is the actogram, as first described
18867 in \"Activity and distribution of certain wild mice in relation to biotic
18868 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18869 (license license:gpl3)))
18871 (define-public r-expint
18878 (uri (cran-uri "expint" version))
18881 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18882 (properties `((upstream-name . "expint")))
18883 (build-system r-build-system)
18884 (home-page "https://gitlab.com/vigou3/expint")
18885 (synopsis "Exponential integral and incomplete Gamma function")
18887 "This package provides the exponential integrals @code{E_1(x)},
18888 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18889 function @code{G(a, x)} defined for negative values of its first argument.
18890 The package also gives easy access to the underlying C routines through an
18891 API; see the package vignette for details.")
18892 (license license:gpl2+)))
18894 (define-public r-actuar
18901 (uri (cran-uri "actuar" version))
18904 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
18905 (properties `((upstream-name . "actuar")))
18906 (build-system r-build-system)
18907 (propagated-inputs `(("r-expint" ,r-expint)))
18908 (home-page "https://gitlab.com/vigou3/actuar")
18909 (synopsis "Actuarial functions and heavy tailed distributions")
18911 "This package provides functions and data sets for actuarial science:
18912 modeling of loss distributions; risk theory and ruin theory; simulation of
18913 compound models, discrete mixtures and compound hierarchical models;
18914 credibility theory. It boasts support for many additional probability
18915 distributions to model insurance loss amounts and loss frequency: 19
18916 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18917 distribution; zero-truncated and zero-modified extensions of the standard
18918 discrete distributions. It also supports phase-type distributions commonly
18919 used to compute ruin probabilities.")
18920 (license license:gpl2+)))
18922 (define-public r-bmp
18929 (uri (cran-uri "bmp" version))
18932 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18933 (properties `((upstream-name . "bmp")))
18934 (build-system r-build-system)
18935 (home-page "https://cran.r-project.org/web/packages/bmp/")
18936 (synopsis "Read Bitmap (BMP) images")
18938 "This package provides pure R tools to read BMP format images. It is
18939 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18940 (license license:gpl2+)))
18942 (define-public r-readbitmap
18944 (name "r-readbitmap")
18949 (uri (cran-uri "readbitmap" version))
18952 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18953 (properties `((upstream-name . "readbitmap")))
18954 (build-system r-build-system)
18956 `(("libjpeg" ,libjpeg-turbo)
18957 ("libpng" ,libpng)))
18962 ("r-tiff" ,r-tiff)))
18963 (home-page "https://github.com/jefferis/readbitmap")
18964 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18966 "This package provides tools to identify and read BMP, JPEG, PNG, and
18967 TIFF format bitmap images. Identification defaults to the use of the magic
18968 number embedded in the file rather than the file extension.")
18969 (license license:gpl2+)))
18971 (define-public r-imager
18978 (uri (cran-uri "imager" version))
18981 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
18982 (properties `((upstream-name . "imager")))
18983 (build-system r-build-system)
18986 ("libtiff" ,libtiff)
18990 `(("r-downloader" ,r-downloader)
18991 ("r-igraph" ,r-igraph)
18993 ("r-magrittr" ,r-magrittr)
18995 ("r-purrr" ,r-purrr)
18997 ("r-readbitmap" ,r-readbitmap)
18998 ("r-stringr" ,r-stringr)))
19000 `(("pkg-config" ,pkg-config)
19001 ("r-knitr" ,r-knitr)))
19002 (home-page "https://dahtah.github.io/imager/")
19003 (synopsis "Image processing library")
19005 "This is a package for fast image processing for images in up to 4
19006 dimensions (two spatial dimensions, one time/depth dimension, one color
19007 dimension). It provides most traditional image processing tools (filtering,
19008 morphology, transformations, etc.) as well as various functions for easily
19009 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19010 simple, modern C++ library for image processing.")
19011 (license license:lgpl3)))
19013 (define-public r-acuityview
19015 (name "r-acuityview")
19020 (uri (cran-uri "AcuityView" version))
19023 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19024 (properties `((upstream-name . "AcuityView")))
19025 (build-system r-build-system)
19027 `(("r-fftwtools" ,r-fftwtools)
19028 ("r-imager" ,r-imager)
19029 ("r-plotrix" ,r-plotrix)))
19030 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19031 (synopsis "Display scenes as seen by an animal with less acute vision")
19033 "This package provides a simple method for representing a visual scene as
19034 it may be seen by an animal with less acute vision.")
19035 (license license:gpl2+)))
19037 (define-public r-caret
19044 (uri (cran-uri "caret" version))
19047 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19048 (build-system r-build-system)
19050 `(("r-foreach" ,r-foreach)
19051 ("r-ggplot2" ,r-ggplot2)
19052 ("r-lattice" ,r-lattice)
19053 ("r-modelmetrics" ,r-modelmetrics)
19057 ("r-recipes" ,r-recipes)
19058 ("r-reshape2" ,r-reshape2)
19059 ("r-withr" ,r-withr)))
19061 `(("r-knitr" ,r-knitr)))
19062 (home-page "https://github.com/topepo/caret")
19063 (synopsis "Classification and regression training")
19065 "This package provides miscellaneous functions for training and plotting
19066 classification and regression models.")
19067 (license license:gpl2+)))
19069 (define-public r-adabag
19076 (uri (cran-uri "adabag" version))
19079 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19080 (properties `((upstream-name . "adabag")))
19081 (build-system r-build-system)
19083 `(("r-caret" ,r-caret)
19084 ("r-doparallel" ,r-doparallel)
19085 ("r-foreach" ,r-foreach)
19086 ("r-rpart" ,r-rpart)))
19087 (home-page "https://cran.r-project.org/web/packages/adabag/")
19088 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19090 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19091 Breiman's Bagging algorithm using classification trees as individual
19092 classifiers. Once these classifiers have been trained, they can be used to
19093 predict on new data. Also, cross validation estimation of the error can be
19095 (license license:gpl2+)))
19097 (define-public r-adagio
19104 (uri (cran-uri "adagio" version))
19107 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19108 (properties `((upstream-name . "adagio")))
19109 (build-system r-build-system)
19110 (native-inputs `(("gfortran" ,gfortran)))
19111 (home-page "https://cran.r-project.org/web/packages/adagio/")
19112 (synopsis "Discrete and global optimization routines")
19114 "This package provides methods and algorithms for discrete optimization,
19115 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19116 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19118 (license license:gpl3+)))
19120 (define-public r-univoutl
19122 (name "r-univoutl")
19127 (uri (cran-uri "univOutl" version))
19130 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19131 (properties `((upstream-name . "univOutl")))
19132 (build-system r-build-system)
19134 `(("r-hmisc" ,r-hmisc)
19135 ("r-robustbase" ,r-robustbase)))
19136 (home-page "https://github.com/marcellodo/univOutl")
19137 (synopsis "Detection of univariate outliers")
19139 "This package provides well-known outlier detection techniques in the
19140 univariate case. Methods to deal with skewed distribution are included too.
19141 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19142 historical data is implemented as well. When available, survey weights can be
19143 used in outliers detection.")
19144 (license license:gpl2+)))
19146 (define-public r-tolerance
19148 (name "r-tolerance")
19153 (uri (cran-uri "tolerance" version))
19156 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19157 (properties `((upstream-name . "tolerance")))
19158 (build-system r-build-system)
19160 `(("r-mass" ,r-mass)
19162 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19163 (synopsis "Statistical tolerance intervals and regions")
19165 "This package provides functions for estimating tolerance
19166 limits (intervals) for various univariate distributions (binomial, Cauchy,
19167 discrete Pareto, exponential, two-parameter exponential, extreme value,
19168 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19169 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19170 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19171 nonparametric tolerance intervals, tolerance bands for regression
19172 settings (linear regression, nonlinear regression, nonparametric regression,
19173 and multivariate regression), and analysis of variance tolerance intervals.
19174 Visualizations are also available for most of these settings.")
19175 (license license:gpl2+)))
19177 (define-public r-additivitytests
19179 (name "r-additivitytests")
19184 (uri (cran-uri "additivityTests" version))
19187 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19189 `((upstream-name . "additivityTests")))
19190 (build-system r-build-system)
19191 (home-page "https://github.com/simecek/additivityTests")
19192 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19194 "This package provides an implementation of the Tukey, Mandel,
19195 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19196 (license license:gpl3)))
19198 (define-public r-flexclust
19200 (name "r-flexclust")
19205 (uri (cran-uri "flexclust" version))
19208 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19209 (properties `((upstream-name . "flexclust")))
19210 (build-system r-build-system)
19212 `(("r-class" ,r-class)
19213 ("r-lattice" ,r-lattice)
19214 ("r-modeltools" ,r-modeltools)))
19215 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19216 (synopsis "Flexible cluster algorithms")
19218 "The main function @code{kcca} implements a general framework for
19219 k-centroids cluster analysis supporting arbitrary distance measures and
19220 centroid computation. Further cluster methods include hard competitive
19221 learning, neural gas, and QT clustering. There are numerous visualization
19222 methods for cluster results (neighborhood graphs, convex cluster hulls,
19223 barcharts of centroids, ...), and bootstrap methods for the analysis of
19224 cluster stability.")
19225 (license license:gpl2)))
19227 (define-public r-biclust
19234 (uri (cran-uri "biclust" version))
19237 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19238 (properties `((upstream-name . "biclust")))
19239 (build-system r-build-system)
19241 `(("r-additivitytests" ,r-additivitytests)
19242 ("r-colorspace" ,r-colorspace)
19243 ("r-flexclust" ,r-flexclust)
19244 ("r-ggplot2" ,r-ggplot2)
19245 ("r-lattice" ,r-lattice)
19247 ("r-tidyr" ,r-tidyr)))
19248 (home-page "https://cran.r-project.org/web/packages/biclust/")
19249 (synopsis "BiCluster algorithms")
19251 "The main function @code{biclust()} provides several algorithms to find
19252 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19253 In addition, the package provides methods for data
19254 preprocessing (normalization and discretization), visualization, and
19255 validation of bicluster solutions.")
19256 (license license:gpl3)))
19258 (define-public r-icge
19265 (uri (cran-uri "ICGE" version))
19268 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19269 (properties `((upstream-name . "ICGE")))
19270 (build-system r-build-system)
19272 `(("r-cluster" ,r-cluster)
19273 ("r-mass" ,r-mass)))
19274 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19275 (synopsis "Cluster estimation and identification of atypical units")
19277 "ICGE is a package that helps to estimate the number of real clusters in
19278 data as well as to identify atypical units. The underlying methods are based
19279 on distances rather than on unit x variables.")
19280 (license license:gpl2+)))
19282 (define-public r-depth
19285 (version "2.1-1.1")
19289 (uri (cran-uri "depth" version))
19292 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19293 (properties `((upstream-name . "depth")))
19294 (build-system r-build-system)
19296 `(("r-abind" ,r-abind)
19297 ("r-circular" ,r-circular)
19300 `(("gfortran" ,gfortran)))
19301 (home-page "https://cran.r-project.org/web/packages/depth/")
19302 (synopsis "Nonparametric depth functions for multivariate analysis")
19304 "This package provides tools for depth functions methodology applied to
19305 multivariate analysis. Besides allowing calculation of depth values and
19306 depth-based location estimators, the package includes functions or drawing
19307 contour plots and perspective plots of depth functions. Euclidian and
19308 spherical depths are supported.")
19309 (license license:gpl2)))
19311 (define-public r-archetypes
19313 (name "r-archetypes")
19314 (version "2.2-0.1")
19318 (uri (cran-uri "archetypes" version))
19321 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19322 (properties `((upstream-name . "archetypes")))
19323 (build-system r-build-system)
19325 `(("r-modeltools" ,r-modeltools)
19326 ("r-nnls" ,r-nnls)))
19327 (home-page "https://cran.r-project.org/web/packages/archetypes")
19328 (synopsis "Archetypal analysis")
19330 "The main function @code{archetypes} implements a framework for
19331 archetypal analysis supporting arbitrary problem solving mechanisms for the
19332 different conceptual parts of the algorithm.")
19333 (license license:gpl2+)))
19335 (define-public r-shapes
19342 (uri (cran-uri "shapes" version))
19345 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19346 (properties `((upstream-name . "shapes")))
19347 (build-system r-build-system)
19349 `(("r-mass" ,r-mass)
19350 ("r-minpack-lm" ,r-minpack-lm)
19352 ("r-scatterplot3d" ,r-scatterplot3d)))
19353 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19354 (synopsis "Statistical shape analysis")
19356 "This package provides routines for the statistical analysis of landmark
19357 shapes, including Procrustes analysis, graphical displays, principal
19358 components analysis, permutation and bootstrap tests, thin-plate spline
19359 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19360 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19361 Edition), John Wiley and Sons.")
19362 (license license:gpl2)))
19364 (define-public r-anthropometry
19366 (name "r-anthropometry")
19371 (uri (cran-uri "Anthropometry" version))
19374 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19375 (properties `((upstream-name . "Anthropometry")))
19376 (build-system r-build-system)
19378 `(("r-archetypes" ,r-archetypes)
19379 ("r-biclust" ,r-biclust)
19380 ("r-cluster" ,r-cluster)
19381 ("r-depth" ,r-depth)
19386 ("r-shapes" ,r-shapes)))
19388 `(("r-knitr" ,r-knitr)))
19389 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19390 (synopsis "Statistical methods for anthropometric data")
19392 "This package provides statistical methods especially developed to
19393 analyze anthropometric data. These methods are aimed at providing effective
19394 solutions to some commons problems related to Ergonomics and Anthropometry.
19395 They are based on clustering, the statistical concept of data depth,
19396 statistical shape analysis and archetypal analysis.")
19397 (license license:gpl2+)))
19399 (define-public r-adamethods
19401 (name "r-adamethods")
19406 (uri (cran-uri "adamethods" version))
19409 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19410 (properties `((upstream-name . "adamethods")))
19411 (build-system r-build-system)
19413 `(("r-anthropometry" ,r-anthropometry)
19414 ("r-archetypes" ,r-archetypes)
19416 ("r-foreach" ,r-foreach)
19418 ("r-tolerance" ,r-tolerance)
19419 ("r-univoutl" ,r-univoutl)))
19420 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19421 (synopsis "Archetypoid algorithms and anomaly detection")
19423 "This package is a collection of several algorithms to obtain
19424 archetypoids with small and large databases and with both classical
19425 multivariate data and functional data (univariate and multivariate). Some of
19426 these algorithms also allow to detect anomalies (outliers).")
19427 (license license:gpl2+)))
19429 (define-public r-idpmisc
19436 (uri (cran-uri "IDPmisc" version))
19439 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19440 (properties `((upstream-name . "IDPmisc")))
19441 (build-system r-build-system)
19443 `(("r-lattice" ,r-lattice)))
19444 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19445 (synopsis "Functions for data analyses and visualization")
19447 "This package provides different high-level graphics functions for
19448 displaying large datasets, displaying circular data in a very flexible way,
19449 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19450 2D-plots, creating figures with differently colored margin and plot region.
19451 In addition, the package contains auxiliary functions for data manipulation
19452 like omitting observations with irregular values or selecting data by logical
19453 vectors, which include NAs. Other functions are especially useful in
19454 spectroscopy and analyses of environmental data: robust baseline fitting,
19455 finding peaks in spectra, converting humidity measures.")
19456 (license license:gpl3+)))
19458 (define-public r-qqman
19465 (uri (cran-uri "qqman" version))
19468 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19469 (properties `((upstream-name . "qqman")))
19470 (build-system r-build-system)
19472 `(("r-calibrate" ,r-calibrate)))
19473 (home-page "https://cran.r-project.org/web/packages/qqman/")
19474 (synopsis "Q-Q and Manhattan plots for GWAS data")
19476 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19477 from PLINK results.")
19478 (license license:gpl3)))
19480 (define-public r-ggplot-multistats
19482 (name "r-ggplot-multistats")
19487 (uri (cran-uri "ggplot.multistats" version))
19490 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19492 `((upstream-name . "ggplot.multistats")))
19493 (build-system r-build-system)
19495 `(("r-ggplot2" ,r-ggplot2)
19496 ("r-hexbin" ,r-hexbin)
19497 ("r-rlang" ,r-rlang)
19498 ("r-scales" ,r-scales)))
19499 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19500 (synopsis "Multiple summary statistics for binned stats/geometries")
19502 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19503 which functions similar to its singular form, but allows the use of multiple
19504 statistics per bin. Those statistics can be mapped to multiple bin
19506 (license license:gpl3)))
19508 (define-public r-knn-covertree
19510 (name "r-knn-covertree")
19515 (uri (cran-uri "knn.covertree" version))
19518 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19519 (properties `((upstream-name . "knn.covertree")))
19520 (build-system r-build-system)
19522 `(("r-matrix" ,r-matrix)
19524 ("r-rcppeigen" ,r-rcppeigen)))
19525 (home-page "https://github.com/flying-sheep/knn.covertree")
19526 (synopsis "Accurate kNN Implementation with multiple distance measures")
19528 "Similarly to the FNN package, this package allows calculation of the k
19529 nearest neighbors (kNN) of a data matrix. The implementation is based on
19530 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19531 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19532 (license license:agpl3+)))
19534 (define-public r-poibin
19541 (uri (cran-uri "poibin" version))
19544 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19545 (properties `((upstream-name . "poibin")))
19546 (build-system r-build-system)
19547 (home-page "https://cran.r-project.org/web/packages/poibin/")
19548 (synopsis "Poisson binomial distribution")
19550 "This package provides an implementation of both the exact and
19551 approximation methods for computing the @dfn{cumulative distribution
19552 function} (CDF) of the Poisson binomial distribution. It also provides the
19553 @dfn{probability mass function} (PMF), quantile function, and random number
19554 generation for the Poisson binomial distribution.")
19555 (license license:gpl2)))
19557 (define-public r-diagram
19564 (uri (cran-uri "diagram" version))
19567 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19568 (properties `((upstream-name . "diagram")))
19569 (build-system r-build-system)
19571 `(("r-shape" ,r-shape)))
19572 (home-page "https://cran.r-project.org/web/packages/diagram/")
19573 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19575 "This package provides tools to visualize simple graphs (networks) based
19576 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19577 electrical networks, etc. It also includes supporting material for the book
19578 \"A practical guide to ecological modelling - using R as a simulation
19579 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19580 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19581 Francesca Mazzia (2012).")
19582 (license license:gpl2+)))
19584 (define-public r-lim
19591 (uri (cran-uri "LIM" version))
19594 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19595 (properties `((upstream-name . "LIM")))
19596 (build-system r-build-system)
19598 `(("r-diagram" ,r-diagram)
19599 ("r-limsolve" ,r-limsolve)))
19600 (home-page "https://cran.r-project.org/web/packages/LIM/")
19601 (synopsis "Linear inverse model examples and solution methods")
19603 "This package provides functions that read and solve linear inverse
19604 problems (food web problems, linear programming problems).")
19605 (license license:gpl2+)))
19607 (define-public r-shinycssloaders
19609 (name "r-shinycssloaders")
19614 (uri (cran-uri "shinycssloaders" version))
19617 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19619 `((upstream-name . "shinycssloaders")))
19620 (build-system r-build-system)
19622 `(("r-digest" ,r-digest)
19624 ("r-shiny" ,r-shiny)))
19625 (home-page "https://github.com/andrewsali/shinycssloaders")
19626 (synopsis "Add CSS loading animations to Shiny outputs")
19628 "This package provides tools to create a lightweight Shiny wrapper for
19629 the css-loaders created by Luke Hass
19630 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19631 automatically show a loader when the output is (re)calculating.")
19632 (license license:gpl3)))
19634 (define-public r-rsvg
19641 (uri (cran-uri "rsvg" version))
19644 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19645 (properties `((upstream-name . "rsvg")))
19646 (build-system r-build-system)
19648 `(("librsvg" ,librsvg)
19651 `(("pkg-config" ,pkg-config)
19652 ("r-knitr" ,r-knitr)))
19653 (home-page "https://github.com/jeroen/rsvg#readme")
19654 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19656 "This package allows you to render vector-based SVG images into
19657 high-quality custom-size bitmap arrays using the librsvg2 library. The
19658 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19659 addition, the package can convert images directly to various formats such as
19660 PDF or PostScript.")
19661 (license license:expat)))
19663 (define-public r-influencer
19665 (name "r-influencer")
19670 (uri (cran-uri "influenceR" version))
19673 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19674 (properties `((upstream-name . "influenceR")))
19675 (build-system r-build-system)
19677 `(("r-igraph" ,r-igraph)
19678 ("r-matrix" ,r-matrix)))
19679 (home-page "https://github.com/rcc-uchicago/influenceR")
19680 (synopsis "Tools to quantify structural importance of nodes in a network")
19682 "This package provides functionality to compute various node centrality
19683 measures on networks. Included are functions to compute betweenness
19684 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19685 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19686 algorithm to identify key players, and Valente's bridging metric. The
19687 betweenness, Key Players, and bridging implementations are parallelized with
19689 (license license:gpl2)))
19691 (define-public r-emplik
19698 (uri (cran-uri "emplik" version))
19701 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19702 (properties `((upstream-name . "emplik")))
19703 (build-system r-build-system)
19705 `(("r-quantreg" ,r-quantreg)))
19706 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19707 (synopsis "Empirical likelihood ratio for censored/truncated data")
19709 "This package provides empirical likelihood ratio tests for
19710 means/quantiles/hazards from possibly censored and/or truncated data. It also
19712 (license license:gpl2+)))
19714 (define-public r-imputeyn
19716 (name "r-imputeyn")
19721 (uri (cran-uri "imputeYn" version))
19724 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19725 (properties `((upstream-name . "imputeYn")))
19726 (build-system r-build-system)
19728 `(("r-boot" ,r-boot)
19729 ("r-emplik" ,r-emplik)
19730 ("r-mvtnorm" ,r-mvtnorm)
19731 ("r-quadprog" ,r-quadprog)
19732 ("r-survival" ,r-survival)))
19733 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19734 (synopsis "Impute last largest censored observation under weighted least squares")
19736 "This package allows for the imputation of the last largest censored
19737 observantions. This method brings less bias and more efficient estimates for
19739 (license license:gpl2)))
19741 (define-public r-adapenetclass
19743 (name "r-adapenetclass")
19748 (uri (cran-uri "AdapEnetClass" version))
19751 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19752 (properties `((upstream-name . "AdapEnetClass")))
19753 (build-system r-build-system)
19755 `(("r-glmnet" ,r-glmnet)
19756 ("r-imputeyn" ,r-imputeyn)
19758 ("r-quadprog" ,r-quadprog)))
19759 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19760 (synopsis "Class of adaptive elastic net methods for censored data")
19762 "This package provides methods for variable selection for AFT models.")
19763 (license license:gpl2)))
19765 (define-public r-flock
19772 (uri (cran-uri "flock" version))
19775 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19776 (properties `((upstream-name . "flock")))
19777 (build-system r-build-system)
19778 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19779 (home-page "https://cran.r-project.org/web/packages/flock/")
19780 (synopsis "Process synchronization using file locks")
19782 "This package implements synchronization between R processes (spawned by
19783 using the @code{parallel} package for instance) using file locks. It supports
19784 both exclusive and shared locking.")
19785 (license license:asl2.0)))
19787 (define-public r-archivist
19789 (name "r-archivist")
19794 (uri (cran-uri "archivist" version))
19797 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19798 (properties `((upstream-name . "archivist")))
19799 (build-system r-build-system)
19802 ("r-digest" ,r-digest)
19803 ("r-flock" ,r-flock)
19805 ("r-lubridate" ,r-lubridate)
19806 ("r-magrittr" ,r-magrittr)
19807 ("r-rcurl" ,r-rcurl)
19808 ("r-rsqlite" ,r-rsqlite)))
19809 (home-page "https://pbiecek.github.io/archivist/")
19810 (synopsis "Tools for storing, restoring and searching for R objects")
19812 "Data exploration and modelling is a process in which a lot of data
19813 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19814 statistical models, different versions of data sets and different versions of
19815 results. Archivist helps to store and manage artifacts created in R. It
19816 allows you to store selected artifacts as binary files together with their
19817 metadata and relations. Archivist allows sharing artifacts with others. It
19818 can look for already created artifacts by using its class, name, date of the
19819 creation or other properties. It also makes it easy to restore such
19821 (license license:gpl2)))
19823 (define-public r-versions
19825 (name "r-versions")
19830 (uri (cran-uri "versions" version))
19833 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19834 (properties `((upstream-name . "versions")))
19835 (build-system r-build-system)
19836 (home-page "https://cran.r-project.org/web/packages/versions/")
19837 (synopsis "Query and install specific versions of CRAN packages")
19839 "This package allows you to install specified versions of R packages
19840 hosted on CRAN and provides functions to list available versions and the
19841 versions of currently installed packages.")
19842 (license license:bsd-3)))
19844 (define-public r-adapr
19851 (uri (cran-uri "adapr" version))
19854 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19855 (properties `((upstream-name . "adapr")))
19856 (build-system r-build-system)
19858 `(("r-archivist" ,r-archivist)
19859 ("r-devtools" ,r-devtools)
19860 ("r-digest" ,r-digest)
19861 ("r-doparallel" ,r-doparallel)
19862 ("r-gdata" ,r-gdata)
19863 ("r-ggplot2" ,r-ggplot2)
19864 ("r-git2r" ,r-git2r)
19865 ("r-igraph" ,r-igraph)
19866 ("r-knitr" ,r-knitr)
19867 ("r-plotly" ,r-plotly)
19869 ("r-rmarkdown" ,r-rmarkdown)
19870 ("r-shiny" ,r-shiny)
19871 ("r-shinydashboard" ,r-shinydashboard)
19872 ("r-versions" ,r-versions)))
19873 (home-page "https://cran.r-project.org/web/packages/adapr/")
19874 (synopsis "Implementation of an accountable data analysis process")
19876 "This package tracks reading and writing within R scripts that are
19877 organized into a directed acyclic graph. It contains an interactive Shiny
19878 application @code{adaprApp()}. It uses Git and file hashes to track version
19879 histories of inputs and outputs.")
19880 (license license:lgpl2.0)))
19882 (define-public r-adapsamp
19884 (name "r-adapsamp")
19889 (uri (cran-uri "AdapSamp" version))
19892 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19893 (properties `((upstream-name . "AdapSamp")))
19894 (build-system r-build-system)
19895 (propagated-inputs `(("r-pracma" ,r-pracma)))
19896 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19897 (synopsis "Adaptive sampling algorithms")
19899 "For distributions whose probability density functions are log-concave,
19900 the adaptive rejection sampling algorithm can be used to build envelope
19901 functions for sampling. For others, the modified adaptive rejection sampling
19902 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19903 adaptive slice sampling algorithm can be used. This R package mainly includes
19904 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19905 @code{rASS()}. These functions can realize sampling based on the algorithms
19907 (license license:gpl2)))
19909 (define-public r-adaptalint
19911 (name "r-adaptalint")
19916 (uri (cran-uri "adaptalint" version))
19919 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19920 (properties `((upstream-name . "adaptalint")))
19921 (build-system r-build-system)
19923 `(("r-dplyr" ,r-dplyr)
19924 ("r-lintr" ,r-lintr)
19925 ("r-purrr" ,r-purrr)))
19926 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19927 (synopsis "Check R code style")
19929 "This package provides tools to infer the code style (which style rules
19930 are followed and which ones are not) from one package and use it to check
19931 another. This makes it easier to find and correct the most important problems
19933 (license license:gpl3)))
19935 (define-public r-fracdiff
19937 (name "r-fracdiff")
19942 (uri (cran-uri "fracdiff" version))
19945 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19946 (properties `((upstream-name . "fracdiff")))
19947 (build-system r-build-system)
19948 (home-page "https://github.com/mmaechler/fracdiff")
19950 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19952 "This package provides tools for the maximum likelihood estimation of the
19953 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19954 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19955 (license license:gpl2+)))
19957 (define-public r-forecast
19959 (name "r-forecast")
19964 (uri (cran-uri "forecast" version))
19967 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19968 (properties `((upstream-name . "forecast")))
19969 (build-system r-build-system)
19971 `(("r-colorspace" ,r-colorspace)
19972 ("r-fracdiff" ,r-fracdiff)
19973 ("r-ggplot2" ,r-ggplot2)
19974 ("r-lmtest" ,r-lmtest)
19975 ("r-magrittr" ,r-magrittr)
19978 ("r-rcpparmadillo" ,r-rcpparmadillo)
19979 ("r-timedate" ,r-timedate)
19980 ("r-tseries" ,r-tseries)
19984 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19985 (home-page "https://pkg.robjhyndman.com/forecast/")
19986 (synopsis "Forecasting functions for time series and linear models")
19988 "This package provides methods and tools for displaying and analysing
19989 univariate time series forecasts including exponential smoothing via state
19990 space models and automatic ARIMA modelling.")
19991 (license license:gpl3)))
19993 (define-public r-xmisc
20000 (uri (cran-uri "Xmisc" version))
20003 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20004 (properties `((upstream-name . "Xmisc")))
20005 (build-system r-build-system)
20006 (home-page "https://cran.r-project.org/package=Xmisc")
20008 "Xiaobei's miscellaneous classes and functions")
20010 "This package provides Xiaobei's miscellaneous classes and functions,
20011 which are useful when developing R packages for @dfn{object oriented
20012 programming} (OOP) using R Reference Class.")
20013 (license license:gpl2+)))
20015 (define-public r-proxyc
20022 (uri (cran-uri "proxyC" version))
20025 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20026 (properties `((upstream-name . "proxyC")))
20027 (build-system r-build-system)
20029 `(("r-matrix" ,r-matrix)
20031 ("r-rcpparmadillo" ,r-rcpparmadillo)
20032 ("r-rcppparallel" ,r-rcppparallel)))
20033 (home-page "https://cran.r-project.org/package=proxyC")
20034 (synopsis "Compute proximity in large sparse matrices")
20036 "This package provides efficient tools to compute the proximity between
20037 rows or columns of large matrices. Functions are optimised for large sparse
20038 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20039 similarity/distance measures, computation of correlation, cosine similarity
20040 and Euclidean distance is particularly fast.")
20041 (license license:gpl3)))
20043 (define-public r-isocodes
20045 (name "r-isocodes")
20046 (version "2020.03.16")
20050 (uri (cran-uri "ISOcodes" version))
20053 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20054 (properties `((upstream-name . "ISOcodes")))
20055 (build-system r-build-system)
20056 (home-page "https://cran.r-project.org/package=ISOcodes")
20057 (synopsis "Selected ISO codes")
20059 "This package provides ISO language, territory, currency, script and
20060 character codes. It provides ISO 639 language codes, ISO 3166 territory
20061 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20062 character codes as well as the UN M.49 area codes.")
20063 (license license:gpl2)))
20065 (define-public r-stopwords
20067 (name "r-stopwords")
20072 (uri (cran-uri "stopwords" version))
20075 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20076 (properties `((upstream-name . "stopwords")))
20077 (build-system r-build-system)
20079 `(("r-desc" ,r-desc)
20080 ("r-isocodes" ,r-isocodes)
20081 ("r-usethis" ,r-usethis)))
20082 (home-page "https://github.com/quanteda/stopwords")
20083 (synopsis "Multilingual stopword lists")
20085 "This package provides multiple sources of stopwords, for use in text
20086 analysis and natural language processing.")
20087 (license license:expat)))
20089 (define-public r-spacyr
20096 (uri (cran-uri "spacyr" version))
20099 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20100 (properties `((upstream-name . "spacyr")))
20101 (build-system r-build-system)
20103 `(("r-data-table" ,r-data-table)
20104 ("r-reticulate" ,r-reticulate)))
20105 (home-page "https://spacyr.quanteda.io")
20106 (synopsis "R wrapper for the spaCy NLP library")
20108 "This package provides an R wrapper to the Python @dfn{natural language
20109 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20110 (license license:gpl3)))
20112 (define-public r-snowballc
20114 (name "r-snowballc")
20119 (uri (cran-uri "SnowballC" version))
20122 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20123 (properties `((upstream-name . "SnowballC")))
20124 (build-system r-build-system)
20125 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20126 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20128 "This package provides an R interface to the C @code{libstemmer} library
20129 that implements Porter's word stemming algorithm for collapsing words to a
20130 common root to aid comparison of vocabulary. Currently supported languages
20131 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20132 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20133 (license license:bsd-3)))
20135 (define-public r-quanteda
20137 (name "r-quanteda")
20142 (uri (cran-uri "quanteda" version))
20145 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
20146 (properties `((upstream-name . "quanteda")))
20147 (build-system r-build-system)
20149 `(("r-data-table" ,r-data-table)
20150 ("r-extrafont" ,r-extrafont)
20151 ("r-fastmatch" ,r-fastmatch)
20152 ("r-ggplot2" ,r-ggplot2)
20153 ("r-ggrepel" ,r-ggrepel)
20154 ("r-jsonlite" ,r-jsonlite)
20155 ("r-magrittr" ,r-magrittr)
20156 ("r-matrix" ,r-matrix)
20157 ("r-network" ,r-network)
20158 ("r-proxyc" ,r-proxyc)
20160 ("r-rcpparmadillo" ,r-rcpparmadillo)
20161 ("r-rcppparallel" ,r-rcppparallel)
20163 ("r-snowballc" ,r-snowballc)
20164 ("r-stopwords" ,r-stopwords)
20165 ("r-stringi" ,r-stringi)
20167 ("r-yaml" ,r-yaml)))
20169 `(("r-knitr" ,r-knitr)))
20170 (home-page "https://quanteda.io")
20171 (synopsis "Quantitative analysis of textual data")
20173 "This package provides a fast, flexible, and comprehensive framework for
20174 quantitative text analysis in R. It provides functionality for corpus
20175 management, creating and manipulating tokens and ngrams, exploring keywords in
20176 context, forming and manipulating sparse matrices of documents by features and
20177 feature co-occurrences, analyzing keywords, computing feature similarities and
20178 distances, applying content dictionaries, applying supervised and unsupervised
20179 machine learning, visually representing text and text analyses, and more.")
20180 (license license:gpl3)))
20182 (define-public r-topicmodels
20184 (name "r-topicmodels")
20189 (uri (cran-uri "topicmodels" version))
20192 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20193 (properties `((upstream-name . "topicmodels")))
20194 (build-system r-build-system)
20198 `(("r-modeltools" ,r-modeltools)
20201 (home-page "https://cran.r-project.org/package=topicmodels")
20202 (synopsis "Topic models")
20204 "This package provides an interface to the C code for @dfn{Latent
20205 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20206 David M. Blei and co-authors and the C++ code for fitting LDA models using
20207 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20208 (license license:gpl2)))
20210 (define-public r-stm
20217 (uri (cran-uri "stm" version))
20220 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20221 (properties `((upstream-name . "stm")))
20222 (build-system r-build-system)
20224 `(("r-data-table" ,r-data-table)
20225 ("r-glmnet" ,r-glmnet)
20227 ("r-matrix" ,r-matrix)
20228 ("r-matrixstats" ,r-matrixstats)
20229 ("r-quadprog" ,r-quadprog)
20230 ("r-quanteda" ,r-quanteda)
20232 ("r-rcpparmadillo" ,r-rcpparmadillo)
20234 ("r-stringr" ,r-stringr)))
20235 (home-page "http://www.structuraltopicmodel.com/")
20236 (synopsis "Estimation of the Structural Topic Model")
20238 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20239 topic models with document-level covariates. The package also includes tools
20240 for model selection, visualization, and estimation of topic-covariate
20242 (license license:expat)))
20244 (define-public r-polycor
20251 (uri (cran-uri "polycor" version))
20254 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20255 (properties `((upstream-name . "polycor")))
20256 (build-system r-build-system)
20258 `(("r-matrix" ,r-matrix)
20259 ("r-mvtnorm" ,r-mvtnorm)))
20260 (home-page "https://r-forge.r-project.org/projects/polycor/")
20261 (synopsis "Polychoric and polyserial correlations")
20263 "This package provides tools to compute polychoric and polyserial
20264 correlations by quick \"two-step\" methods or ML, optionally with standard
20265 errors; tetrachoric and biserial correlations are special cases.")
20266 (license license:gpl2+)))
20268 (define-public r-msm
20275 (uri (cran-uri "msm" version))
20278 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20279 (properties `((upstream-name . "msm")))
20280 (build-system r-build-system)
20282 `(("r-expm" ,r-expm)
20283 ("r-mvtnorm" ,r-mvtnorm)
20284 ("r-survival" ,r-survival)))
20285 (home-page "https://github.com/chjackson/msm")
20286 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20288 "This package provides functions for fitting continuous-time Markov and
20289 hidden Markov multi-state models to longitudinal data. It was designed for
20290 processes observed at arbitrary times in continuous time (panel data) but some
20291 other observation schemes are supported. Both Markov transition rates and the
20292 hidden Markov output process can be modelled in terms of covariates, which may
20293 be constant or piecewise-constant in time.")
20294 (license license:gpl2+)))
20296 (define-public r-ltm
20303 (uri (cran-uri "ltm" version))
20306 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20307 (properties `((upstream-name . "ltm")))
20308 (build-system r-build-system)
20310 `(("r-mass" ,r-mass)
20312 ("r-polycor" ,r-polycor)))
20313 (home-page "https://github.com/drizopoulos/ltm")
20314 (synopsis "Latent trait models under IRT")
20316 "This is a package supporting the analysis of multivariate dichotomous
20317 and polytomous data using latent trait models under the Item Response Theory
20318 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20319 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20321 (license license:gpl2+)))
20323 (define-public r-mi
20330 (uri (cran-uri "mi" version))
20333 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20334 (properties `((upstream-name . "mi")))
20335 (build-system r-build-system)
20338 ("r-matrix" ,r-matrix)))
20339 (home-page "http://www.stat.columbia.edu/~gelman/")
20340 (synopsis "Missing data imputation and model checking")
20342 "This package provides functions for data manipulation, imputing missing
20343 values in an approximate Bayesian framework, diagnostics of the models used to
20344 generate the imputations, confidence-building mechanisms to validate some of
20345 the assumptions of the imputation algorithm, and functions to analyze multiply
20346 imputed data sets with the appropriate degree of sampling uncertainty.")
20347 (license license:gpl2+)))
20349 (define-public r-matrixcalc
20351 (name "r-matrixcalc")
20356 (uri (cran-uri "matrixcalc" version))
20359 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20360 (properties `((upstream-name . "matrixcalc")))
20361 (build-system r-build-system)
20362 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20363 (synopsis "Collection of functions for matrix calculations")
20365 "This package provides a collection of functions to support matrix
20366 calculations for probability, econometric and numerical analysis. There are
20367 additional functions that are comparable to APL functions which are useful for
20368 actuarial models such as pension mathematics.")
20369 (license license:gpl2+)))
20371 (define-public r-sem
20378 (uri (cran-uri "sem" version))
20381 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20382 (properties `((upstream-name . "sem")))
20383 (build-system r-build-system)
20385 `(("r-boot" ,r-boot)
20387 ("r-matrixcalc" ,r-matrixcalc)
20389 (home-page "https://cran.r-project.org/package=sem")
20390 (synopsis "Structural equation models")
20392 "This package provides functions for fitting general linear structural
20393 equation models (with observed and latent variables) using the RAM approach,
20394 and for fitting structural equations in observed-variable models by two-stage
20396 (license license:gpl2+)))
20398 (define-public r-semtools
20400 (name "r-semtools")
20405 (uri (cran-uri "semTools" version))
20408 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20409 (properties `((upstream-name . "semTools")))
20410 (build-system r-build-system)
20412 `(("r-lavaan" ,r-lavaan)))
20413 (home-page "https://github.com/simsem/semTools/wiki")
20414 (synopsis "Useful tools for structural equation modeling")
20416 "This package provides useful tools for structural equation modeling.")
20417 (license license:gpl2+)))
20419 (define-public r-regsem
20426 (uri (cran-uri "regsem" version))
20429 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20430 (properties `((upstream-name . "regsem")))
20431 (build-system r-build-system)
20433 `(("r-lavaan" ,r-lavaan)
20435 ("r-rcpparmadillo" ,r-rcpparmadillo)
20436 ("r-rsolnp" ,r-rsolnp)))
20437 (home-page "https://cran.r-project.org/package=regsem")
20438 (synopsis "Regularized structural equation modeling")
20440 "This package uses both ridge and lasso penalties (and extensions) to
20441 penalize specific parameters in structural equation models. The package
20442 offers additional cost functions, cross validation, and other extensions
20443 beyond traditional structural equation models. It also contains a function to
20444 perform @dfn{exploratory mediation} (XMed).")
20445 (license license:gpl2+)))
20447 (define-public r-stanheaders
20449 (name "r-stanheaders")
20450 (version "2.21.0-5")
20454 (uri (cran-uri "StanHeaders" version))
20457 "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
20458 (properties `((upstream-name . "StanHeaders")))
20459 (build-system r-build-system)
20460 (inputs `(("pandoc" ,ghc-pandoc)))
20462 `(("r-rcppeigen" ,r-rcppeigen)
20463 ("r-rcppparallel" ,r-rcppparallel)))
20465 `(("gfortran" ,gfortran)
20466 ("r-knitr" ,r-knitr))) ; for vignettes
20467 (home-page "https://mc-stan.org/")
20468 (synopsis "C++ header files for Stan")
20470 "The C++ header files of the Stan project are provided by this package.
20471 There is a shared object containing part of the @code{CVODES} library, but it
20472 is not accessible from R. @code{r-stanheaders} is only useful for developers
20473 who want to utilize the @code{LinkingTo} directive of their package's
20474 DESCRIPTION file to build on the Stan library without incurring unnecessary
20477 The Stan project develops a probabilistic programming language that implements
20478 full or approximate Bayesian statistical inference via Markov Chain Monte
20479 Carlo or variational methods and implements (optionally penalized) maximum
20480 likelihood estimation via optimization. The Stan library includes an advanced
20481 automatic differentiation scheme, templated statistical and linear algebra
20482 functions that can handle the automatically differentiable scalar types (and
20483 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20484 package provides user-facing R functions to parse, compile, test, estimate,
20485 and analyze Stan models.")
20486 (license license:bsd-3)))
20488 (define-public r-rpf
20495 (uri (cran-uri "rpf" version))
20498 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20499 (properties `((upstream-name . "rpf")))
20500 (build-system r-build-system)
20502 `(("r-lifecycle" ,r-lifecycle)
20503 ("r-mvtnorm" ,r-mvtnorm)
20505 ("r-rcppeigen" ,r-rcppeigen)))
20507 `(("r-knitr" ,r-knitr)))
20508 (home-page "https://github.com/jpritikin/rpf")
20509 (synopsis "Response probability functions")
20511 "The purpose of this package is to factor out logic and math common to
20512 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20513 core support code suitable for more specialized IRT packages to build upon.
20514 Complete access to optimized C functions is made available with
20515 @code{R_RegisterCCallable()}.")
20516 (license license:gpl3+)))
20518 (define-public r-openmx
20525 (uri (cran-uri "OpenMx" version))
20528 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20529 (properties `((upstream-name . "OpenMx")))
20530 (build-system r-build-system)
20533 ("r-digest" ,r-digest)
20535 ("r-matrix" ,r-matrix)
20537 ("r-rcppeigen" ,r-rcppeigen)
20539 ("r-stanheaders" ,r-stanheaders)))
20540 (native-inputs `(("gfortran" ,gfortran)))
20541 (home-page "http://openmx.ssri.psu.edu")
20542 (synopsis "Extended structural equation modelling")
20544 "This package allows for the estimation of a wide variety of advanced
20545 multivariate statistical models. It consists of a library of functions and
20546 optimizers that allow you to quickly and flexibly define an SEM model and
20547 estimate parameters given observed data.")
20548 (license license:asl2.0)))
20550 (define-public r-kutils
20557 (uri (cran-uri "kutils" version))
20560 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20561 (properties `((upstream-name . "kutils")))
20562 (build-system r-build-system)
20564 `(("r-foreign" ,r-foreign)
20565 ("r-openxlsx" ,r-openxlsx)
20567 ("r-runit" ,r-runit)
20568 ("r-xtable" ,r-xtable)))
20569 (home-page "https://cran.r-project.org/package=kutils")
20570 (synopsis "Project management tools")
20572 "This package provides tools for data importation, recoding, and
20573 inspection. There are functions to create new project folders, R code
20574 templates, create uniquely named output directories, and to quickly obtain a
20575 visual summary for each variable in a data frame. The main feature here is
20576 the systematic implementation of the \"variable key\" framework for data
20577 importation and recoding.")
20578 (license license:gpl2)))
20580 (define-public r-rockchalk
20582 (name "r-rockchalk")
20583 (version "1.8.144")
20587 (uri (cran-uri "rockchalk" version))
20590 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20591 (properties `((upstream-name . "rockchalk")))
20592 (build-system r-build-system)
20594 `(("r-cardata" ,r-cardata)
20595 ("r-kutils" ,r-kutils)
20597 ("r-mass" ,r-mass)))
20598 (home-page "https://cran.r-project.org/package=rockchalk")
20599 (synopsis "Regression estimation and presentation")
20601 "This package provides a collection of functions for interpretation and
20602 presentation of regression analysis. These functions are used to produce the
20603 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20604 includes regression diagnostics, regression tables, and plots of interactions
20605 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20606 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20607 fairly comprehensive overview.")
20608 (license license:gpl3+)))
20610 (define-public r-lisreltor
20612 (name "r-lisreltor")
20617 (uri (cran-uri "lisrelToR" version))
20620 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20621 (properties `((upstream-name . "lisrelToR")))
20622 (build-system r-build-system)
20623 (home-page "https://cran.r-project.org/package=lisrelToR")
20624 (synopsis "Import output from LISREL into R")
20626 "This is an unofficial package aimed at automating the import of LISREL
20628 (license license:gpl2)))
20630 (define-public r-bdgraph
20637 (uri (cran-uri "BDgraph" version))
20640 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20641 (properties `((upstream-name . "BDgraph")))
20642 (build-system r-build-system)
20644 `(("r-igraph" ,r-igraph)))
20645 (home-page "https://www.uva.nl/profile/a.mohammadi")
20646 (synopsis "Bayesian structure learning in graphical models")
20648 "This package provides statistical tools for Bayesian structure learning
20649 in undirected graphical models for continuous, discrete, and mixed data. It
20650 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20651 on a continuous-time birth-death process.")
20652 (license license:gpl2+)))
20654 (define-public r-d3network
20656 (name "r-d3network")
20657 (version "0.5.2.1")
20661 (uri (cran-uri "d3Network" version))
20664 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20665 (properties `((upstream-name . "d3Network")))
20666 (build-system r-build-system)
20668 `(("r-plyr" ,r-plyr)
20669 ("r-rjson" ,r-rjson)
20670 ("r-whisker" ,r-whisker)))
20671 (home-page "http://christophergandrud.github.io/d3Network/")
20672 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20674 "This package is intended to make it easy to create D3 JavaScript
20675 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20676 (license license:gpl3+)))
20678 (define-public r-qgraph
20685 (uri (cran-uri "qgraph" version))
20688 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20689 (properties `((upstream-name . "qgraph")))
20690 (build-system r-build-system)
20692 `(("r-abind" ,r-abind)
20693 ("r-bdgraph" ,r-bdgraph)
20694 ("r-colorspace" ,r-colorspace)
20695 ("r-corpcor" ,r-corpcor)
20696 ("r-d3network" ,r-d3network)
20697 ("r-dplyr" ,r-dplyr)
20698 ("r-fdrtool" ,r-fdrtool)
20699 ("r-ggplot2" ,r-ggplot2)
20700 ("r-ggraph" ,r-ggraph)
20701 ("r-glasso" ,r-glasso)
20702 ("r-gtools" ,r-gtools)
20703 ("r-hmisc" ,r-hmisc)
20705 ("r-igraph" ,r-igraph)
20707 ("r-lavaan" ,r-lavaan)
20708 ("r-matrix" ,r-matrix)
20709 ("r-pbapply" ,r-pbapply)
20712 ("r-psych" ,r-psych)
20714 ("r-reshape2" ,r-reshape2)
20715 ("r-tidygraph" ,r-tidygraph)))
20716 (home-page "http://sachaepskamp.com/qgraph/")
20717 (synopsis "Weighted network visualization and analysis")
20719 "This package implements tools for weighted network visualization and
20720 analysis, as well as Gaussian graphical model computation. It contains graph
20721 plotting methods, and tools for psychometric data visualization and graphical
20722 model estimation. See Epskamp et al. (2012)
20723 @url{doi:10.18637/jss.v048.i04}.")
20724 (license license:gpl2)))
20726 (define-public r-semplot
20733 (uri (cran-uri "semPlot" version))
20736 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20737 (properties `((upstream-name . "semPlot")))
20738 (build-system r-build-system)
20740 `(("r-colorspace" ,r-colorspace)
20741 ("r-corpcor" ,r-corpcor)
20742 ("r-igraph" ,r-igraph)
20743 ("r-lavaan" ,r-lavaan)
20744 ("r-lisreltor" ,r-lisreltor)
20745 ("r-openmx" ,r-openmx)
20747 ("r-qgraph" ,r-qgraph)
20748 ("r-regsem" ,r-regsem)
20749 ("r-rockchalk" ,r-rockchalk)
20752 (home-page "https://github.com/SachaEpskamp/semPlot")
20753 (synopsis "Unified visualizations of structural equation models")
20755 "Structural equation modeling (SEM) has a long history of representing
20756 models graphically as path diagrams. The semPlot package for R fills the gap
20757 between advanced, but time-consuming, graphical software and the limited
20758 graphics produced automatically by SEM software. In addition, semPlot offers
20759 more functionality than drawing path diagrams: it can act as a common ground
20760 for importing SEM results into R. Any result usable as input to semPlot can
20761 also be represented in any of the three popular SEM frame-works, as well as
20762 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20763 (license license:gpl2)))
20765 (define-public r-cdm
20772 (uri (cran-uri "CDM" version))
20775 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20776 (properties `((upstream-name . "CDM")))
20777 (build-system r-build-system)
20779 `(("r-mvtnorm" ,r-mvtnorm)
20780 ("r-polycor" ,r-polycor)
20782 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20784 "https://github.com/alexanderrobitzsch/CDM")
20785 (synopsis "Cognitive diagnosis modeling")
20787 "This package provides functions for cognitive diagnosis modeling and
20788 multidimensional item response modeling for dichotomous and polytomous item
20789 responses. It enables the estimation of the DINA and DINO model, the multiple
20790 group (polytomous) GDINA model, the multiple choice DINA model, the general
20791 diagnostic model (GDM), the structured latent class model (SLCA), and
20792 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20793 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20794 estimation and the package structure. For tutorials on how to use the CDM
20795 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20796 well as Ravand and Robitzsch (2015).")
20797 (license license:gpl2+)))
20799 (define-public r-tam
20806 (uri (cran-uri "TAM" version))
20809 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20810 (properties `((upstream-name . "TAM")))
20811 (build-system r-build-system)
20815 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20816 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20817 (synopsis "Test analysis modules")
20819 "This package includes tools for marginal maximum likelihood estimation
20820 and joint maximum likelihood estimation for unidimensional and
20821 multidimensional item response models. The package functionality covers the
20822 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20823 multi-faceted Rasch model, nominal item response model, structured latent
20824 class model, mixture distribution IRT models, and located latent class models.
20825 Latent regression models and plausible value imputation are also supported.")
20826 (license license:gpl2+)))
20828 (define-public r-erm
20835 (uri (cran-uri "eRm" version))
20838 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20839 (properties `((upstream-name . "eRm")))
20840 (build-system r-build-system)
20842 `(("r-colorspace" ,r-colorspace)
20843 ("r-lattice" ,r-lattice)
20845 ("r-matrix" ,r-matrix)
20846 ("r-psych" ,r-psych)))
20847 (native-inputs `(("gfortran" ,gfortran)))
20848 (home-page "https://cran.r-project.org/package=eRm")
20849 (synopsis "Extended Rasch modeling")
20851 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20852 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20853 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20854 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20855 data matrix. Additional features are the ML estimation of the person
20856 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20857 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20858 infit and outfit measures, ICC and other plots, automated stepwise item
20859 elimination, and a simulation module for various binary data matrices.")
20860 (license license:gpl3)))
20862 (define-public r-irtoys
20869 (uri (cran-uri "irtoys" version))
20872 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20873 (properties `((upstream-name . "irtoys")))
20874 (build-system r-build-system)
20878 (home-page "https://cran.r-project.org/package=irtoys")
20879 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20881 "This package provides a collection of functions useful in learning and
20882 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20883 programs. It provides basic CTT analysis, a simple common interface to the
20884 estimation of item parameters in IRT models for binary responses with three
20885 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20886 EAP, WLE, plausible values), item and person fit statistics, scaling
20887 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20888 array of parametric and non-parametric (kernel) plots. It estimates and plots
20889 Haberman's interaction model when all items are dichotomously scored.")
20890 (license license:gpl2+)))
20892 (define-public r-iheatmapr
20894 (name "r-iheatmapr")
20899 (uri (cran-uri "iheatmapr" version))
20902 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20903 (properties `((upstream-name . "iheatmapr")))
20904 (build-system r-build-system)
20906 `(("r-fastcluster" ,r-fastcluster)
20907 ("r-ggdendro" ,r-ggdendro)
20908 ("r-htmlwidgets" ,r-htmlwidgets)
20909 ("r-jsonlite" ,r-jsonlite)
20910 ("r-knitr" ,r-knitr)
20911 ("r-magrittr" ,r-magrittr)
20913 ("r-rcolorbrewer" ,r-rcolorbrewer)
20914 ("r-s4vectors" ,r-s4vectors)
20915 ("r-scales" ,r-scales)))
20916 (home-page "https://docs.ropensci.org/iheatmapr")
20917 (synopsis "Interactive, Complex Heatmaps")
20919 "iheatmapr is an R package for building complex, interactive heatmaps
20920 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20921 subplots along the rows or columns of the main heatmap add more information
20922 about each row or column. For example, a one column additional heatmap may
20923 indicate what group a particular row or column belongs to. Complex heatmaps
20924 may also include multiple side by side heatmaps which show different types of
20925 data for the same conditions. Interactivity can improve complex heatmaps by
20926 providing tooltips with information about each cell and enabling zooming into
20927 interesting features. iheatmapr uses the plotly library for interactivity.")
20928 (license license:expat)))
20930 (define-public r-packrat
20937 (uri (cran-uri "packrat" version))
20940 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20941 (properties `((upstream-name . "packrat")))
20942 (build-system r-build-system)
20943 (home-page "https://github.com/rstudio/packrat/")
20944 (synopsis "Dependency management R projects")
20946 "This package provides a dependency manager for R projects that allows
20947 you to manage the R packages your project depends on in an isolated, portable,
20948 and reproducible way.")
20949 (license license:gpl2)))
20951 (define-public r-rsconnect
20953 (name "r-rsconnect")
20958 (uri (cran-uri "rsconnect" version))
20961 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20962 (properties `((upstream-name . "rsconnect")))
20963 (build-system r-build-system)
20965 `(("r-curl" ,r-curl)
20966 ("r-digest" ,r-digest)
20967 ("r-jsonlite" ,r-jsonlite)
20968 ("r-openssl" ,r-openssl)
20969 ("r-packrat" ,r-packrat)
20970 ("r-rstudioapi" ,r-rstudioapi)
20971 ("r-yaml" ,r-yaml)))
20972 (home-page "https://github.com/rstudio/rsconnect")
20973 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20975 "This package provides a programmatic deployment interface for RPubs,
20976 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20977 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20978 (license license:gpl2)))
20980 ;; This package includes minified JavaScript files. When upgrading please
20981 ;; check that there are no new minified JavaScript files.
20982 (define-public r-dygraphs
20984 (name "r-dygraphs")
20985 (version "1.1.1.6")
20989 (uri (cran-uri "dygraphs" version))
20992 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20993 (properties `((upstream-name . "dygraphs")))
20994 (build-system r-build-system)
20996 `(#:modules ((guix build utils)
20997 (guix build r-build-system)
21001 (modify-phases %standard-phases
21002 (add-after 'unpack 'process-javascript
21003 (lambda* (#:key inputs #:allow-other-keys)
21004 (with-directory-excursion "inst/htmlwidgets/lib/"
21008 `(("dygraphs/dygraph-combined-dev.js"
21009 "dygraph-combined.js")
21010 (,(assoc-ref inputs "js-jquery")
21011 "jquery/jquery.min.js")
21012 (,(assoc-ref inputs "js-fquarter")
21013 "fquarter/moment-fquarter.min.js"))))
21014 (lambda (sources targets)
21015 (for-each (lambda (source target)
21016 (format #t "Processing ~a --> ~a~%"
21018 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21019 (call-with-output-file target
21021 (dump-port minified port)))))
21022 sources targets))))
21025 `(("uglify-js" ,uglify-js)
21026 ;; They actually use version 1.11.1, but this more recent version
21027 ;; should be just fine.
21031 (uri "https://code.jquery.com/jquery-1.12.4.js")
21034 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21038 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21039 "moment-fquarter/1.0.1/moment-fquarter.js"))
21042 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21044 `(("r-htmltools" ,r-htmltools)
21045 ("r-htmlwidgets" ,r-htmlwidgets)
21046 ("r-magrittr" ,r-magrittr)
21049 (home-page "https://github.com/rstudio/dygraphs")
21050 (synopsis "Interface to Dygraphs interactive time series charting library")
21052 "This package provides an R interface to the dygraphs JavaScript charting
21053 library (a copy of which is included in the package). It provides rich
21054 facilities for charting time-series data in R, including highly configurable
21055 series- and axis-display and interactive features like zoom/pan and
21056 series/point highlighting.")
21057 (license license:expat)))
21059 (define-public r-shinystan
21061 (name "r-shinystan")
21066 (uri (cran-uri "shinystan" version))
21069 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21070 (properties `((upstream-name . "shinystan")))
21071 (build-system r-build-system)
21073 `(("r-bayesplot" ,r-bayesplot)
21074 ("r-colourpicker" ,r-colourpicker)
21076 ("r-dygraphs" ,r-dygraphs)
21077 ("r-ggplot2" ,r-ggplot2)
21078 ("r-gridextra" ,r-gridextra)
21079 ("r-gtools" ,r-gtools)
21080 ("r-markdown" ,r-markdown)
21081 ("r-reshape2" ,r-reshape2)
21082 ("r-rsconnect" ,r-rsconnect)
21083 ("r-rstan" ,r-rstan)
21084 ("r-shiny" ,r-shiny)
21085 ("r-shinyjs" ,r-shinyjs)
21086 ("r-shinythemes" ,r-shinythemes)
21087 ("r-threejs" ,r-threejs)
21088 ("r-xtable" ,r-xtable)
21090 (home-page "https://mc-stan.org/")
21091 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21093 "This package provides a graphical user interface for interactive
21094 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21095 for analyzing a posterior sample. The interface is powered by the Shiny web
21096 application framework and works with the output of MCMC programs written in
21097 any programming language (and has extended functionality for Stan models fit
21098 using the @code{rstan} and @code{rstanarm} packages).")
21099 (license license:gpl3+)))
21101 (define-public r-rstantools
21103 (name "r-rstantools")
21108 (uri (cran-uri "rstantools" version))
21111 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
21112 (properties `((upstream-name . "rstantools")))
21113 (build-system r-build-system)
21114 (inputs `(("pandoc" ,ghc-pandoc)))
21116 `(("r-desc" ,r-desc)
21117 ("r-rcpp" ,r-rcpp)))
21118 (home-page "https://mc-stan.org/rstantools/")
21119 (synopsis "Tools for developing R packages interfacing with Stan")
21121 "This package provides various tools for developers of R packages
21122 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21123 up the required package structure, S3 generics and default methods to unify
21124 function naming across Stan-based R packages, and vignettes with
21125 recommendations for developers.")
21126 (license license:gpl3+)))
21128 (define-public r-loo
21135 (uri (cran-uri "loo" version))
21138 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
21139 (properties `((upstream-name . "loo")))
21140 (build-system r-build-system)
21142 `(("pandoc" ,ghc-pandoc)
21143 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21145 `(("r-checkmate" ,r-checkmate)
21146 ("r-matrixstats" ,r-matrixstats)))
21147 (home-page "https://mc-stan.org/loo/")
21148 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21150 "This package provides an implementation of efficient approximate
21151 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21152 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21153 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21154 procedure for regularizing importance weights. As a byproduct of the
21155 calculations, we also obtain approximate standard errors for estimated
21156 predictive errors and for the comparison of predictive errors between models.
21157 The package also provides methods for using stacking and other model weighting
21158 techniques to average Bayesian predictive distributions.")
21159 (license license:gpl3+)))
21161 (define-public r-rstan
21168 (uri (cran-uri "rstan" version))
21171 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
21172 (properties `((upstream-name . "rstan")))
21173 (build-system r-build-system)
21176 (modify-phases %standard-phases
21177 (add-before 'install 'set-timezone
21178 ;; This package is picky about timezones.
21179 (lambda* (#:key inputs #:allow-other-keys)
21180 (setenv "TZ" "UTC+1")
21182 (string-append (assoc-ref inputs "tzdata")
21183 "/share/zoneinfo"))
21186 `(("tzdata" ,tzdata-for-tests)
21187 ("pandoc" ,ghc-pandoc)))
21190 ("r-ggplot2" ,r-ggplot2)
21191 ("r-gridextra" ,r-gridextra)
21192 ("r-inline" ,r-inline)
21194 ("r-pkgbuild" ,r-pkgbuild)
21196 ("r-rcppeigen" ,r-rcppeigen)
21197 ("r-stanheaders" ,r-stanheaders)))
21198 (home-page "https://discourse.mc-stan.org/")
21199 (synopsis "R interface to Stan")
21201 "User-facing R functions are provided to parse, compile, test, estimate,
21202 and analyze Stan models by accessing the header-only Stan library provided by
21203 the StanHeaders package. The Stan project develops a probabilistic
21204 programming language that implements full Bayesian statistical inference via
21205 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21206 approximation, and (optionally penalized) maximum likelihood estimation via
21207 optimization. In all three cases, automatic differentiation is used to
21208 quickly and accurately evaluate gradients without burdening the user with the
21209 need to derive the partial derivatives.")
21210 (license license:gpl3+)))
21212 (define-public r-rstanarm
21214 (name "r-rstanarm")
21219 (uri (cran-uri "rstanarm" version))
21222 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
21223 (properties `((upstream-name . "rstanarm")))
21224 (build-system r-build-system)
21226 `(("pandoc" ,ghc-pandoc)
21227 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21229 `(("r-bayesplot" ,r-bayesplot)
21231 ("r-ggplot2" ,r-ggplot2)
21234 ("r-matrix" ,r-matrix)
21237 ("r-rcppeigen" ,r-rcppeigen)
21238 ("r-rcppparallel" ,r-rcppparallel)
21239 ("r-rstan" ,r-rstan)
21240 ("r-rstantools" ,r-rstantools)
21241 ("r-shinystan" ,r-shinystan)
21242 ("r-stanheaders" ,r-stanheaders)
21243 ("r-survival" ,r-survival)))
21244 (home-page "https://mc-stan.org/rstanarm/")
21245 (synopsis "Bayesian applied regression modeling via Stan")
21247 "This package estimates previously compiled regression models using the
21248 @code{rstan} package, which provides the R interface to the Stan C++ library
21249 for Bayesian estimation. Users specify models via the customary R syntax with
21250 a formula and @code{data.frame} plus some additional arguments for priors.")
21251 (license license:gpl3+)))
21253 (define-public r-kendall
21260 (uri (cran-uri "Kendall" version))
21263 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21264 (properties `((upstream-name . "Kendall")))
21265 (build-system r-build-system)
21267 `(("r-boot" ,r-boot)))
21269 `(("gfortran" ,gfortran)))
21270 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21271 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21273 "This package computes the Kendall rank correlation and Mann-Kendall
21275 (license license:gpl2+)))
21277 (define-public r-zyp
21280 (version "0.10-1.1")
21284 (uri (cran-uri "zyp" version))
21287 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21288 (properties `((upstream-name . "zyp")))
21289 (build-system r-build-system)
21291 `(("r-kendall" ,r-kendall)))
21292 (home-page "https://cran.r-project.org/web/packages/zyp/")
21293 (synopsis "Zhang + Yue-Pilon Trends Package")
21295 "This package contains an efficient implementation of Sen's slope
21296 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21297 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21299 (license license:lgpl2.1)))
21301 (define-public r-zvcv
21308 (uri (cran-uri "ZVCV" version))
21311 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
21312 (properties `((upstream-name . "ZVCV")))
21313 (build-system r-build-system)
21315 `(("r-abind" ,r-abind)
21316 ("r-glmnet" ,r-glmnet)
21317 ("r-mvtnorm" ,r-mvtnorm)
21318 ("r-partitions" ,r-partitions)
21320 ("r-rcpparmadillo" ,r-rcpparmadillo)))
21321 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21322 (synopsis "Zero-Variance Control Variates")
21324 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21325 to reduce the variance of Monte Carlo estimators of expectations using the
21326 derivatives of the log target. Once the derivatives are available, the only
21327 additional computational effort is in solving a linear regression problem.
21328 This method has been extended to higher dimensions using regularisation. This
21329 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21330 samples, derivatives and function evaluations are available. Additional
21331 functions for applying ZV-CV to two estimators for the normalising constant of
21332 the posterior distribution in Bayesian statistics are also supplied.")
21333 (license license:gpl2+)))
21335 (define-public r-ztype
21342 (uri (cran-uri "ztype" version))
21345 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21346 (properties `((upstream-name . "ztype")))
21347 (build-system r-build-system)
21349 `(("r-assertthat" ,r-assertthat)
21350 ("r-dplyr" ,r-dplyr)
21351 ("r-ggplot2" ,r-ggplot2)
21352 ("r-lubridate" ,r-lubridate)
21353 ("r-magrittr" ,r-magrittr)
21354 ("r-rvest" ,r-rvest)
21355 ("r-stringr" ,r-stringr)))
21356 (home-page "https://cran.r-project.org/web/packages/ztype/")
21357 (synopsis "Run a Ztype game loaded with R functions")
21359 "How fast can you type R functions on your keyboard? Find out by running
21360 a @code{zty.pe} game: export R functions as instructions to type to destroy
21361 opponents' vessels.")
21362 (license license:gpl3)))
21364 (define-public r-zseq
21371 (uri (cran-uri "Zseq" version))
21374 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21375 (properties `((upstream-name . "Zseq")))
21376 (build-system r-build-system)
21378 `(("r-gmp" ,r-gmp)))
21379 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21380 (synopsis "Integer sequence generator")
21382 "This package generates well-known integer sequences. The @code{gmp}
21383 package is adopted for computing with arbitrarily large numbers. Every
21384 function has a hyperlink to its corresponding item in the @dfn{On-Line
21385 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21386 (license license:gpl3+)))
21388 (define-public r-isoband
21395 (uri (cran-uri "isoband" version))
21398 "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
21399 (properties `((upstream-name . "isoband")))
21400 (build-system r-build-system)
21402 `(("r-rcpp" ,r-rcpp)
21403 ("r-testthat" ,r-testthat)))
21405 `(("r-knitr" ,r-knitr)))
21406 (home-page "https://github.com/wilkelab/isoband")
21407 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21409 "This package provides a fast C++ implementation to generate contour
21410 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21411 containing elevation data.")
21412 (license license:expat)))
21414 (define-public r-ppcor
21421 (uri (cran-uri "ppcor" version))
21424 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21425 (properties `((upstream-name . "ppcor")))
21426 (build-system r-build-system)
21428 `(("r-mass" ,r-mass)))
21429 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21430 (synopsis "Partial and semi-partial correlation")
21432 "This package provides users not only with a function to readily
21433 calculate the higher-order partial and semi-partial correlations but also with
21434 statistics and p-values of the correlation coefficients.")
21435 (license license:gpl2)))
21437 (define-public r-hrbrthemes
21439 (name "r-hrbrthemes")
21444 (uri (cran-uri "hrbrthemes" version))
21446 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21447 (properties `((upstream-name . "hrbrthemes")))
21448 (build-system r-build-system)
21450 `(("r-extrafont" ,r-extrafont)
21451 ("r-gdtools" ,r-gdtools)
21452 ("r-ggplot2" ,r-ggplot2)
21453 ("r-htmltools" ,r-htmltools)
21454 ("r-knitr" ,r-knitr)
21455 ("r-magrittr" ,r-magrittr)
21456 ("r-rmarkdown" ,r-rmarkdown)
21457 ("r-scales" ,r-scales)))
21459 `(("r-knitr" ,r-knitr)))
21460 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21461 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21463 "This package provides a compilation of extra @code{ggplot2} themes,
21464 scales and utilities, including a spell check function for plot label fields
21465 and an overall emphasis on typography.")
21466 (license license:expat)))
21468 (define-public r-crochet
21475 (uri (cran-uri "crochet" version))
21478 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21479 (build-system r-build-system)
21481 `(("r-knitr" ,r-knitr)))
21482 (home-page "https://github.com/agrueneberg/crochet")
21483 (synopsis "Implementation Helper for Matrix-Like Types")
21485 "Functions to help implement the extraction / subsetting / indexing
21486 function @code{[} and replacement function @code{[<-} of custom matrix-like
21487 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21488 as possible (with tests to prove it).")
21489 (license license:expat)))
21491 (define-public r-boa
21494 (version "1.1.8-2")
21498 (uri (cran-uri "boa" version))
21501 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21502 (properties `((upstream-name . "boa")))
21503 (build-system r-build-system)
21504 (home-page "http://www.jstatsoft.org/v21/i11")
21505 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21507 "This package provides a menu-driven program and library of functions for
21508 carrying out convergence diagnostics and statistical and graphical analysis of
21509 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21510 (license license:gpl2+)))
21512 (define-public r-httpcode
21514 (name "r-httpcode")
21518 (uri (cran-uri "httpcode" version))
21521 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21522 (build-system r-build-system)
21523 (home-page "https://github.com/sckott/httpcode")
21524 (synopsis "HTTP status code helper")
21525 (description "@code{httpcode} provides functionality for finding and
21526 explaining the meaning of @code{HTTP} status codes. Functions are included for
21527 searching for codes by full or partial number, by message, and to get
21528 appropriate dog and cat images for many status codes.")
21529 (license license:expat)))
21531 (define-public r-latex2exp
21533 (name "r-latex2exp")
21537 (uri (cran-uri "latex2exp" version))
21540 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21541 (build-system r-build-system)
21543 `(("r-stringr" ,r-stringr)
21544 ("r-magrittr", r-magrittr)))
21545 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21546 (synopsis "Use LaTeX expressions in plots")
21547 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21548 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21549 rendered as text, axis labels, etc. throughout R's plotting system.")
21550 (license license:expat)))
21552 (define-public r-oai
21558 (uri (cran-uri "oai" version))
21561 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21562 (build-system r-build-system)
21564 `(("r-xml2" ,r-xml2)
21567 ("r-stringr" ,r-stringr)
21568 ("r-tibble" ,r-tibble)))
21569 (home-page "https://github.com/ropensci/oai/")
21570 (synopsis "General purpose OAI-PMH services client")
21571 (description "@code{oai} provides a general purpose client to work with
21572 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21573 service. Functions are provided to work with the OAI-PMH verbs:
21574 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21575 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21576 (license license:expat)))
21578 (define-public r-argon2
21585 (uri (cran-uri "argon2" version))
21588 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21589 (properties `((upstream-name . "argon2")))
21590 (build-system r-build-system)
21591 (home-page "https://github.com/wrathematics/argon2")
21592 (synopsis "Secure password hashing based on the argon2 algorithm")
21594 "This package provides utilities for secure password hashing via the
21595 argon2 algorithm.")
21596 (license license:bsd-2)))
21598 (define-public r-getpass
21605 (uri (cran-uri "getPass" version))
21608 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21609 (properties `((upstream-name . "getPass")))
21610 (build-system r-build-system)
21612 `(("r-rstudioapi" ,r-rstudioapi)))
21613 (home-page "https://github.com/wrathematics/getPass")
21614 (synopsis "Masked user input")
21616 "This package provides a micro-package for reading \"passwords\", i.e.
21617 reading user input with masking, so that the input is not displayed as it is
21618 typed. Currently, RStudio, the command line (every OS), and any platform
21619 where tcltk is present are supported.")
21620 (license license:bsd-2)))
21622 (define-public r-remoter
21629 (uri (cran-uri "remoter" version))
21632 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21633 (properties `((upstream-name . "remoter")))
21634 (build-system r-build-system)
21636 `(("r-argon2" ,r-argon2)
21637 ("r-getpass" ,r-getpass)
21638 ("r-pbdzmq" ,r-pbdzmq)
21640 (home-page "https://github.com/RBigData/remoter")
21641 (synopsis "Control a remote R session from a local one")
21643 "This package provides a set of utilities for client/server computing
21644 with R, controlling a remote R session (the server) from a local one (the
21646 (license license:bsd-2)))
21648 (define-public r-asd
21655 (uri (cran-uri "asd" version))
21658 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21659 (properties `((upstream-name . "asd")))
21660 (build-system r-build-system)
21662 `(("r-mvtnorm" ,r-mvtnorm)))
21663 (home-page "https://cran.r-project.org/web/packages/asd")
21664 (synopsis "Simulations for Adaptive Seamless Designs")
21666 "This package provdes means to run simulations for adaptive seamless
21667 designs with and without early outcomes for treatment selection and
21668 subpopulation type designs.")
21669 (license license:gpl3)))
21671 (define-public r-nbconvertr
21673 (name "r-nbconvertr")
21678 (uri (cran-uri "nbconvertR" version))
21681 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21682 (properties `((upstream-name . "nbconvertR")))
21683 (build-system r-build-system)
21685 `(("jupyter" ,python-nbconvert)
21686 ("pandoc" ,ghc-pandoc)))
21687 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21688 (synopsis "Vignette engine wrapping Jupyter notebooks")
21690 "This package calls the Jupyter script @code{nbconvert} to create
21691 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21692 containing rich text, code, and its output. Code cells can be edited and
21693 evaluated interactively.")
21694 (license license:gpl3)))
21696 (define-public r-bridgesampling
21698 (name "r-bridgesampling")
21703 (uri (cran-uri "bridgesampling" version))
21706 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21708 `((upstream-name . "bridgesampling")))
21709 (build-system r-build-system)
21711 `(("r-brobdingnag" ,r-brobdingnag)
21713 ("r-matrix" ,r-matrix)
21714 ("r-mvtnorm" ,r-mvtnorm)
21715 ("r-scales" ,r-scales)
21716 ("r-stringr" ,r-stringr)))
21718 `(("r-knitr" ,r-knitr)))
21719 (home-page "https://github.com/quentingronau/bridgesampling")
21720 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21722 "This package provides functions for estimating marginal likelihoods,
21723 Bayes factors, posterior model probabilities, and normalizing constants in
21724 general, via different versions of bridge sampling.")
21725 (license license:gpl2+)))
21727 (define-public r-tea
21734 (uri (cran-uri "tea" version))
21737 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21739 `((upstream-name . "tea")))
21740 (build-system r-build-system)
21742 `(("r-matrix" ,r-matrix)))
21743 (home-page "https://cran.r-project.org/web/packages/tea/")
21744 (synopsis "Threshold estimation approaches")
21746 "This package provides different approaches for selecting the threshold
21747 in generalized Pareto distributions. Most of them are based on minimizing the
21748 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21749 Others are heuristically motivated by searching for stable sample paths, i.e.
21750 a nearly constant region of the tail index estimator with respect to k, which
21751 is the number of data in the tail. The third class is motivated by graphical
21752 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21753 is also implemented here.")
21754 (license license:gpl3)))
21756 (define-public r-awsmethods
21758 (name "r-awsmethods")
21763 (uri (cran-uri "awsMethods" version))
21766 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21768 `((upstream-name . "awsMethods")))
21769 (build-system r-build-system)
21770 (home-page "http://www.wias-berlin.de/software/imaging/")
21771 (synopsis "Class and methods definitions")
21773 "This package defines the generic method @code{extract} and provides
21774 @code{openMP} support as needed in several packages like
21775 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21776 (license license:gpl2+)))
21778 (define-public r-aws
21785 (uri (cran-uri "aws" version))
21788 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21790 `((upstream-name . "aws")))
21791 (build-system r-build-system)
21793 `(("r-awsmethods" ,r-awsmethods)
21796 `(("gfortran" ,gfortran)))
21797 (home-page "https://cran.r-project.org/web/packages/aws/")
21798 (synopsis "Adaptive weights smoothing")
21800 "This package provides a collection of R-functions implementing adaptive
21801 smoothing procedures in 1D, 2D and 3D. This includes the
21802 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21803 Confidence Intervals} (ICI), variational approaches, and a non-local means
21805 (license license:gpl2+)))
21807 (define-public r-sgloptim
21809 (name "r-sgloptim")
21814 (uri (cran-uri "sglOptim" version))
21817 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21819 `((upstream-name . "sglOptim")))
21820 (build-system r-build-system)
21823 ("r-doparallel" ,r-doparallel)
21824 ("r-foreach" ,r-foreach)
21825 ("r-matrix" ,r-matrix)
21827 ("r-rcpparmadillo" ,r-rcpparmadillo)
21828 ("r-rcppprogress" ,r-rcppprogress)))
21830 `(("r-knitr" ,r-knitr)))
21831 (home-page "https://github.com/nielsrhansen/sglOptim")
21832 (synopsis "Generic sparse group Lasso solver")
21834 "This package provides a fast generic solver for sparse group lasso
21835 optimization problems. The loss (objective) function must be defined in a C++
21836 module. The optimization problem is solved using a coordinate gradient
21837 descent algorithm. Convergence of the algorithm is established and the
21838 algorithm is applicable to a broad class of loss functions. Use of parallel
21839 computing for cross validation and subsampling is supported through the
21840 @code{foreach} and @code{doParallel} packages.")
21841 (license license:gpl2+)))
21843 (define-public r-grouped
21850 (uri (cran-uri "grouped" version))
21853 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21855 `((upstream-name . "grouped")))
21856 (build-system r-build-system)
21858 `(("r-mass" ,r-mass)))
21859 (home-page "https://cran.r-project.org/web/packages/grouped/")
21860 (synopsis "Regression analysis of grouped and coarse data")
21862 "This package provides regression models for grouped and coarse data,
21863 under the coarsened at random assumption.")
21864 (license license:gpl2+)))
21866 (define-public r-stam
21873 (uri (cran-uri "stam" version))
21876 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21878 `((upstream-name . "stam")))
21879 (build-system r-build-system)
21883 (home-page "https://cran.r-project.org/web/packages/stam")
21884 (synopsis "Spatio-temporal analysis and modelling")
21886 "This package provides various methods to conduct Spatio-Temporal
21887 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21888 Inferred Spatio-Temporal Modelling.")
21889 (license license:gpl2+)))
21891 (define-public r-dcv
21898 (uri (cran-uri "dcv" version))
21901 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21903 `((upstream-name . "dcv")))
21904 (build-system r-build-system)
21906 `(("r-lmtest" ,r-lmtest)))
21907 (home-page "https://cran.r-project.org/web/packages/dcv/")
21908 (synopsis "Conventional cross-validation statistics for climate-growth model")
21910 "This package performs several conventional cross-validation statistical
21911 methods for climate-growth model in the climate reconstruction from tree
21912 rings, including Sign Test statistic, Reduction of Error statistic, Product
21913 Mean Test, Durbin-Watson statistic etc.")
21914 (license license:gpl2)))
21916 (define-public r-rcdd
21923 (uri (cran-uri "rcdd" version))
21926 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21928 `((upstream-name . "rcdd")))
21929 (build-system r-build-system)
21932 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
21933 (synopsis "Computational geometry")
21935 "This package converts back and forth between two representations of a
21936 convex polytope: as solution of a set of linear equalities and inequalities
21937 and as convex hull of set of points and rays. Also does linear programming
21938 and redundant generator elimination. All functions can use exact
21939 infinite-precision rational arithmetic.")
21940 (license license:gpl2)))
21942 (define-public r-rxnat
21949 (uri (cran-uri "Rxnat" version))
21952 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
21954 `((upstream-name . "Rxnat")))
21955 (build-system r-build-system)
21957 `(("r-httr" ,r-httr)
21958 ("r-rcurl" ,r-rcurl)))
21960 `(("r-knitr" ,r-knitr)))
21961 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
21962 (synopsis "Queries and extracts images from neuroimaging datasets")
21964 "This package allows communication with the Extensible Neuroimaging
21965 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
21967 (license license:gpl2)))
21969 (define-public r-rserve
21976 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
21977 version ".tar.gz"))
21980 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
21981 (build-system r-build-system)
21983 `(("r-checkmate" ,r-checkmate)
21985 ("r-jsonlite" ,r-jsonlite)
21986 ("r-knitr" ,r-knitr)
21989 ("r-uuid" ,r-uuid)))
21991 `(("openssl" ,openssl)
21993 (home-page "https://github.com/s-u/Rserve")
21995 "Server providing access to R from many languages and systems")
21997 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
21998 binary requests to be sent to R. Every connection has a separate workspace
21999 and working directory. Client-side implementations are available for popular
22000 languages such as C/C++ and Java, allowing any application to use facilities
22001 of R without the need of linking to R code. Rserve supports remote
22002 connection, user authentication and file transfer. A simple R client is
22003 included in this package as well.")
22004 (license license:gpl2)))
22006 (define-public r-brms
22013 (uri (cran-uri "brms" version))
22016 "0vdncdawxawi16f326qrgy9jjjipmqdjxh741y9p7xdzd4fwaxx3"))))
22017 (properties `((upstream-name . "brms")))
22018 (build-system r-build-system)
22020 `(("r-abind" ,r-abind)
22021 ("r-backports" ,r-backports)
22022 ("r-bayesplot" ,r-bayesplot)
22023 ("r-bridgesampling" ,r-bridgesampling)
22025 ("r-future" ,r-future)
22026 ("r-ggplot2" ,r-ggplot2)
22029 ("r-matrix" ,r-matrix)
22030 ("r-matrixstats" ,r-matrixstats)
22032 ("r-nleqslv" ,r-nleqslv)
22035 ("r-rstan" ,r-rstan)
22036 ("r-rstantools" ,r-rstantools)
22037 ("r-shinystan" ,r-shinystan)))
22038 (native-inputs `(("r-knitr" ,r-knitr)))
22040 "https://github.com/paul-buerkner/brms")
22042 "Bayesian Regression Models using 'Stan'")
22044 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22045 using 'Stan' for full Bayesian inference. A wide range of distributions and
22046 link functions are supported, allowing users to fit -- among others -- linear,
22047 robust linear, count data, survival, response times, ordinal, zero-inflated,
22048 hurdle, and even self-defined mixture models all in a multilevel context.
22049 Further modeling options include non-linear and smooth terms, auto-correlation
22050 structures, censored data, meta-analytic standard errors, and quite a few
22051 more. In addition, all parameters of the response distribution can be
22052 predicted in order to perform distributional regression. Prior specifications
22053 are flexible and explicitly encourage users to apply prior distributions that
22054 actually reflect their beliefs. Model fit can easily be assessed and compared
22055 with posterior predictive checks and leave-one-out cross-validation.")
22056 (license license:gpl2)))
22058 (define-public r-mstate
22065 (uri (cran-uri "mstate" version))
22068 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22069 (properties `((upstream-name . "mstate")))
22070 (build-system r-build-system)
22072 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22073 ("r-survival" ,r-survival)))
22075 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22077 "Data Preparation, Estimation and Prediction in Multi-State Models")
22079 "Contains functions for data preparation, descriptives, hazard estimation
22080 and prediction with Aalen-Johansen or simulation in competing risks and
22081 multi-state models.")
22082 (license license:gpl2+)))
22084 (define-public r-scatterpie
22086 (name "r-scatterpie")
22091 (uri (cran-uri "scatterpie" version))
22094 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22095 (properties `((upstream-name . "scatterpie")))
22096 (build-system r-build-system)
22098 `(("r-ggforce" ,r-ggforce)
22099 ("r-ggplot2" ,r-ggplot2)
22100 ("r-rlang" ,r-rlang)
22101 ("r-rvcheck" ,r-rvcheck)
22102 ("r-tidyr" ,r-tidyr)))
22104 `(("r-knitr" ,r-knitr)))
22105 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22106 (synopsis "Scatter pie plot")
22108 "This package creates scatterpie plots, especially useful for plotting
22110 (license license:artistic2.0)))